[med-svn] [crac] 01/02: Imported Upstream version 1.5.0
Andreas Tille
tille at debian.org
Wed Jul 9 08:33:37 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository crac.
commit 0072f2ebf882d7934b890f45f0c579131303c64b
Author: Andreas Tille <tille at debian.org>
Date: Wed Jul 9 10:32:12 2014 +0200
Imported Upstream version 1.5.0
---
AUTHORS | 20 +
COPYING | 1027 +
ChangeLog | 438 +
INSTALL | 365 +
Makefile.am | 202 +
Makefile.in | 930 +
NEWS | 0
README | 134 +
aclocal.m4 | 8917 +++++++++
config/config.guess | 1502 ++
config/config.h.in | 225 +
config/config.sub | 1714 ++
config/depcomp | 630 +
config/install-sh | 520 +
config/ltmain.sh | 8413 ++++++++
config/missing | 376 +
config/texinfo.tex | 9291 +++++++++
configure | 19188 +++++++++++++++++++
configure.ac | 426 +
control.in | 18 +
crac.lsm.in | 21 +
crac.spec.in | 179 +
doc/CeCILL.texi | 571 +
doc/Makefile.am | 131 +
doc/Makefile.in | 767 +
doc/crac.info | 806 +
doc/crac.texi | 218 +
doc/package.texi.in | 2 +
man/Makefile.am | 110 +
man/Makefile.in | 561 +
man/crac.1.in | 477 +
scripts/Makefile.am | 91 +
scripts/Makefile.in | 521 +
scripts/crac-client | 253 +
scripts/crac-client.in | 253 +
src/CandidatBreak.cpp | 322 +
src/CandidatBreak.h | 332 +
src/Classifier.cpp | 1202 ++
src/Classifier.h | 398 +
src/Makefile.am | 154 +
src/Makefile.in | 839 +
src/Parameters.cpp | 195 +
src/Parameters.h | 198 +
src/Support.cpp | 887 +
src/Support.h | 462 +
src/SupportBreak.cpp | 1621 ++
src/SupportBreak.h | 812 +
src/basic.h | 191 +
src/classifyTags.cpp | 542 +
src/classifyTags.h | 232 +
src/const.h | 327 +
src/crac.cpp | 1016 +
src/libGkArrays/AUTHORS | 19 +
src/libGkArrays/COPYING | 1047 +
src/libGkArrays/ChangeLog | 482 +
src/libGkArrays/INSTALL | 365 +
src/libGkArrays/Makefile.am | 191 +
src/libGkArrays/Makefile.in | 977 +
src/libGkArrays/NEWS | 0
src/libGkArrays/README | 143 +
src/libGkArrays/aclocal.m4 | 8917 +++++++++
src/libGkArrays/config/config.guess | 1530 ++
src/libGkArrays/config/config.h.in | 145 +
src/libGkArrays/config/config.sub | 1773 ++
src/libGkArrays/config/depcomp | 630 +
src/libGkArrays/config/install-sh | 520 +
src/libGkArrays/config/ltmain.sh | 8413 ++++++++
src/libGkArrays/config/missing | 376 +
src/libGkArrays/config/texinfo.tex | 9291 +++++++++
src/libGkArrays/configure | 18480 ++++++++++++++++++
src/libGkArrays/configure.ac | 356 +
src/libGkArrays/control.in | 29 +
src/libGkArrays/doc/CeCILL-C.texi | 587 +
src/libGkArrays/doc/Makefile.am | 129 +
src/libGkArrays/doc/Makefile.in | 829 +
src/libGkArrays/doc/libGkArrays.3.in | 184 +
src/libGkArrays/doc/libGkArrays.info | 899 +
src/libGkArrays/doc/libGkArrays.texi | 400 +
src/libGkArrays/doc/package.texi.in | 2 +
src/libGkArrays/doc/texinfo.tex | 9291 +++++++++
src/libGkArrays/libGkArrays.pc.in | 10 +
src/libGkArrays/postinst.in | 108 +
src/libGkArrays/prerm.in | 108 +
src/libGkArrays/src/Makefile.am | 163 +
src/libGkArrays/src/Makefile.in | 951 +
src/libGkArrays/src/basic.h | 64 +
src/libGkArrays/src/binvect.hxx | 119 +
src/libGkArrays/src/bitvector.cxx | 465 +
src/libGkArrays/src/bitvector.hxx | 159 +
src/libGkArrays/src/buildTables.cpp | 269 +
src/libGkArrays/src/const.h | 119 +
src/libGkArrays/src/gkArrays.cpp | 635 +
src/libGkArrays/src/gkArrays.h | 477 +
src/libGkArrays/src/gkArraysBuilder.cpp | 160 +
src/libGkArrays/src/gkArraysBuilder.h | 141 +
src/libGkArrays/src/gkArraysTypes.h | 139 +
src/libGkArrays/src/gkCFPSBuilder.cpp | 180 +
src/libGkArrays/src/gkCFPSBuilder.h | 146 +
src/libGkArrays/src/gkIFABuilder.cpp | 202 +
src/libGkArrays/src/gkIFABuilder.h | 154 +
src/libGkArrays/src/gkSABuilder.cpp | 486 +
src/libGkArrays/src/gkSABuilder.h | 242 +
src/libGkArrays/src/kseq/Makefile.am | 113 +
src/libGkArrays/src/kseq/Makefile.in | 577 +
src/libGkArrays/src/kseq/kseq.h | 229 +
src/libGkArrays/src/largebinvect.cxx | 1259 ++
src/libGkArrays/src/largebinvect.hxx | 242 +
src/libGkArrays/src/libProgressBar-1.2.0/AUTHORS | 2 +
src/libGkArrays/src/libProgressBar-1.2.0/COPYING | 481 +
src/libGkArrays/src/libProgressBar-1.2.0/ChangeLog | 118 +
src/libGkArrays/src/libProgressBar-1.2.0/INSTALL | 365 +
.../src/libProgressBar-1.2.0/Makefile.am | 124 +
.../src/libProgressBar-1.2.0/Makefile.in | 898 +
src/libGkArrays/src/libProgressBar-1.2.0/NEWS | 0
src/libGkArrays/src/libProgressBar-1.2.0/README | 29 +
.../src/libProgressBar-1.2.0/acinclude.m4 | 40 +
.../src/libProgressBar-1.2.0/aclocal.m4 | 8918 +++++++++
.../src/libProgressBar-1.2.0/config.guess | 1517 ++
.../src/libProgressBar-1.2.0/config.sub | 1760 ++
src/libGkArrays/src/libProgressBar-1.2.0/configure | 18361 ++++++++++++++++++
.../src/libProgressBar-1.2.0/configure.in | 101 +
.../src/libProgressBar-1.2.0/control.in | 18 +
src/libGkArrays/src/libProgressBar-1.2.0/depcomp | 630 +
.../src/libProgressBar-1.2.0/doc/Makefile.am | 47 +
.../src/libProgressBar-1.2.0/doc/Makefile.in | 744 +
.../src/libProgressBar-1.2.0/doc/lgpl.texinfo | 190 +
.../src/libProgressBar-1.2.0/doc/libProgressBar.3 | 94 +
.../libProgressBar-1.2.0/doc/libProgressBar.3.in | 94 +
.../libProgressBar-1.2.0/doc/libProgressBar.info | 294 +
.../doc/libProgressBar.texinfo | 165 +
.../src/libProgressBar-1.2.0/doc/texinfo.tex | 9291 +++++++++
.../src/libProgressBar-1.2.0/install-sh | 520 +
.../src/libProgressBar-1.2.0/libProgressBar.lsm.in | 24 +
.../src/libProgressBar-1.2.0/libProgressBar.pc.in | 10 +
.../libProgressBar-1.2.0/libProgressBar.spec.in | 107 +
.../libProgressBar/Makefile.am | 24 +
.../libProgressBar/Makefile.in | 661 +
.../libProgressBar/config.h.in | 126 +
.../libProgressBar/progressBar.cpp | 191 +
.../libProgressBar/progressBar.h | 269 +
.../libProgressBar-1.2.0/libProgressBar/testPB.cpp | 125 +
src/libGkArrays/src/libProgressBar-1.2.0/ltmain.sh | 8413 ++++++++
src/libGkArrays/src/libProgressBar-1.2.0/missing | 376 +
.../src/libProgressBar-1.2.0/mkinstalldirs | 162 +
.../src/libProgressBar-1.2.0/postinst.in | 4 +
src/libGkArrays/src/libProgressBar-1.2.0/prerm.in | 4 +
src/libGkArrays/src/readsReader.cpp | 405 +
src/libGkArrays/src/readsReader.h | 432 +
src/libGkArrays/src/solArray.cpp | 186 +
src/libGkArrays/src/solArray.h | 260 +
src/libGkArrays/src/sux/COPYING.LIB | 504 +
src/libGkArrays/src/sux/Makefile.am | 113 +
src/libGkArrays/src/sux/Makefile.in | 577 +
src/libGkArrays/src/sux/README | 74 +
src/libGkArrays/src/sux/macros.h | 26 +
src/libGkArrays/src/sux/popcount.h | 15 +
src/libGkArrays/src/sux/rank9b.cpp | 236 +
src/libGkArrays/src/sux/rank9b.h | 89 +
src/libGkArrays/src/utils.cpp | 214 +
src/libGkArrays/src/utils.h | 229 +
src/libGkArrays/tests/Makefile.am | 131 +
src/libGkArrays/tests/Makefile.in | 747 +
src/libGkArrays/tests/checkConsistency.cpp | 332 +
src/libGkArrays/tests/checkConsistency.h | 139 +
src/libGkArrays/tests/checkPairedEnd.cpp | 146 +
src/libGkArrays/tests/checkPairedEnd.h | 107 +
src/libGkArrays/tests/compareVariableFixed.cpp | 190 +
src/libGkArrays/tests/compareVariableFixed.h | 121 +
src/libGkArrays/tests/dataset/data1.fa | 7 +
src/libGkArrays/tests/dataset/data2.fa | 7 +
src/libGkArrays/tests/dataset/variable.fa | 10 +
src/libGkArrays/tests/testConsistency.cpp | 141 +
src/libGkArrays/tests/testPairedEnd.cpp | 123 +
src/libGkArrays/tests/testVariable.h | 106 +
src/libGkArrays/tests/testVariableFixed.cpp | 118 +
src/libGkArrays/tests/testing.h | 65 +
src/libGkArrays/tests/variableAndFixedLength.cpp | 131 +
src/libReadsInfo/BioTagIndelInfo.cpp | 105 +
src/libReadsInfo/BioTagIndelInfo.h | 112 +
src/libReadsInfo/BioUndeterminedInfo.cpp | 138 +
src/libReadsInfo/BioUndeterminedInfo.h | 123 +
src/libReadsInfo/Cigar.cpp | 226 +
src/libReadsInfo/Cigar.h | 222 +
src/libReadsInfo/DuplicationInfo.cpp | 116 +
src/libReadsInfo/DuplicationInfo.h | 117 +
src/libReadsInfo/IndelInfo.cpp | 185 +
src/libReadsInfo/IndelInfo.h | 136 +
src/libReadsInfo/Makefile.am | 132 +
src/libReadsInfo/Makefile.in | 900 +
src/libReadsInfo/SNPInfo.cpp | 208 +
src/libReadsInfo/SNPInfo.h | 150 +
src/libReadsInfo/SeqErrInfo.cpp | 222 +
src/libReadsInfo/SeqErrInfo.h | 154 +
src/libReadsInfo/SpliceInfo.cpp | 108 +
src/libReadsInfo/SpliceInfo.h | 111 +
src/libReadsInfo/SpliceInterInfo.cpp | 149 +
src/libReadsInfo/SpliceInterInfo.h | 127 +
src/libReadsInfo/SpliceIntraInfo.cpp | 108 +
src/libReadsInfo/SpliceIntraInfo.h | 111 +
src/libReadsInfo/SpliceNoCoverInfo.cpp | 108 +
src/libReadsInfo/SpliceNoCoverInfo.h | 111 +
src/libReadsInfo/SplicingInfo.cpp | 146 +
src/libReadsInfo/SplicingInfo.h | 127 +
src/libReadsInfo/cigarTypes.cpp | 144 +
src/libReadsInfo/cigarTypes.h | 135 +
src/libReadsInfo/genericInfo.cpp | 156 +
src/libReadsInfo/genericInfo.h | 139 +
src/libReadsInfo/repetitionInfo.cpp | 145 +
src/libReadsInfo/repetitionInfo.h | 121 +
src/libReadsInfo/samLine.cpp | 421 +
src/libReadsInfo/samLine.h | 270 +
src/libReadsInfo/tagInfo.cpp | 1735 ++
src/libReadsInfo/tagInfo.h | 472 +
src/libReadsInfo/undeterminedErrorInfo.cpp | 125 +
src/libReadsInfo/undeterminedErrorInfo.h | 119 +
src/libSSA/GenomeInfo.cpp | 273 +
src/libSSA/GenomeInfo.h | 246 +
src/libSSA/HuffAlphabetRank.cpp | 344 +
src/libSSA/HuffAlphabetRank.h | 134 +
src/libSSA/Huffman_Codes.cpp | 180 +
src/libSSA/Huffman_Codes.h | 233 +
src/libSSA/Makefile.am | 246 +
src/libSSA/Makefile.in | 804 +
src/libSSA/SSA.cpp | 685 +
src/libSSA/SSA.h | 214 +
src/libSSA/basic.h | 243 +
src/libSSA/bitarray.cpp | 461 +
src/libSSA/bitarray.h | 159 +
src/libSSA/bitrankw32int.cpp | 293 +
src/libSSA/bitrankw32int.h | 141 +
src/libSSA/chrPosition.cpp | 165 +
src/libSSA/chrPosition.h | 136 +
src/libSSA/cracIndex.cpp | 418 +
src/libSSA/cracIndex.h | 141 +
src/libSSA/karkkainen_bwt/alphabet.h | 252 +
src/libSSA/karkkainen_bwt/assert_helpers.h | 259 +
src/libSSA/karkkainen_bwt/auto_array.h | 38 +
src/libSSA/karkkainen_bwt/binary_sa_search.h | 76 +
src/libSSA/karkkainen_bwt/blockwise_sa.h | 902 +
src/libSSA/karkkainen_bwt/diff_sample.h | 982 +
src/libSSA/karkkainen_bwt/multikey_qsort.h | 1144 ++
src/libSSA/karkkainen_bwt/random_source.h | 61 +
src/libSSA/karkkainen_bwt/timer.h | 63 +
src/libSSA/karkkainen_bwt/zbox.h | 76 +
src/libSSA/locateOnGenome.cpp | 462 +
src/libSSA/locateOnGenome.h | 237 +
src/libSSA/locateTags.cpp | 402 +
src/libSSA/locateTags.h | 211 +
src/libSSA/seqan/basic.h | 115 +
src/libSSA/seqan/basic/basic_aggregates.h | 689 +
src/libSSA/seqan/basic/basic_allocator_interface.h | 236 +
src/libSSA/seqan/basic/basic_allocator_multipool.h | 230 +
src/libSSA/seqan/basic/basic_allocator_simple.h | 210 +
.../seqan/basic/basic_allocator_singlepool.h | 299 +
src/libSSA/seqan/basic/basic_allocator_to_std.h | 178 +
src/libSSA/seqan/basic/basic_alphabet_interface.h | 917 +
src/libSSA/seqan/basic/basic_alphabet_interface2.h | 178 +
src/libSSA/seqan/basic/basic_alphabet_simple.h | 1296 ++
.../seqan/basic/basic_alphabet_simple_tabs.h | 439 +
.../seqan/basic/basic_alphabet_trait_basic.h | 733 +
src/libSSA/seqan/basic/basic_compare.h | 60 +
src/libSSA/seqan/basic/basic_converter.h | 117 +
src/libSSA/seqan/basic/basic_counted_ptr.h | 116 +
src/libSSA/seqan/basic/basic_debug.h | 385 +
src/libSSA/seqan/basic/basic_definition.h | 405 +
src/libSSA/seqan/basic/basic_forwards.h | 71 +
src/libSSA/seqan/basic/basic_generated_forwards.h | 1941 ++
src/libSSA/seqan/basic/basic_holder.h | 1120 ++
src/libSSA/seqan/basic/basic_host.h | 171 +
src/libSSA/seqan/basic/basic_iterator.h | 732 +
src/libSSA/seqan/basic/basic_iterator_adapt_std.h | 436 +
src/libSSA/seqan/basic/basic_iterator_adaptor.h | 524 +
src/libSSA/seqan/basic/basic_iterator_base.h | 221 +
src/libSSA/seqan/basic/basic_iterator_position.h | 450 +
src/libSSA/seqan/basic/basic_iterator_simple.h | 117 +
src/libSSA/seqan/basic/basic_metaprogramming.h | 293 +
src/libSSA/seqan/basic/basic_operator.h | 32 +
src/libSSA/seqan/basic/basic_pointer.h | 103 +
src/libSSA/seqan/basic/basic_profile.h | 503 +
src/libSSA/seqan/basic/basic_proxy.h | 606 +
src/libSSA/seqan/basic/basic_tag.h | 173 +
src/libSSA/seqan/basic/basic_transport.h | 196 +
src/libSSA/seqan/basic/basic_type.h | 624 +
src/libSSA/seqan/basic/basic_volatile_ptr.h | 159 +
src/libSSA/seqan/file.h | 89 +
src/libSSA/seqan/file/chunk_collector.h | 534 +
src/libSSA/seqan/file/cstream.h | 283 +
src/libSSA/seqan/file/file_array.h | 427 +
src/libSSA/seqan/file/file_base.h | 697 +
src/libSSA/seqan/file/file_format.h | 686 +
src/libSSA/seqan/file/file_format_cgviz.h | 226 +
src/libSSA/seqan/file/file_format_fasta.h | 520 +
src/libSSA/seqan/file/file_format_fasta_align.h | 320 +
src/libSSA/seqan/file/file_format_guess.h | 103 +
src/libSSA/seqan/file/file_format_raw.h | 345 +
src/libSSA/seqan/file/file_forwards.h | 44 +
src/libSSA/seqan/file/file_generated_forwards.h | 1155 ++
src/libSSA/seqan/file/meta.h | 36 +
src/libSSA/seqan/file/stream.h | 430 +
src/libSSA/seqan/file/stream_algorithms.h | 208 +
src/libSSA/seqan/find.h | 78 +
src/libSSA/seqan/find/find_base.h | 806 +
src/libSSA/seqan/find/find_generated_forwards.h | 838 +
src/libSSA/seqan/find/find_horspool.h | 483 +
src/libSSA/seqan/find/find_multi.h | 143 +
src/libSSA/seqan/find/find_multiple_shiftand.h | 418 +
src/libSSA/seqan/find/find_score.h | 451 +
src/libSSA/seqan/find/find_set_horspool.h | 286 +
src/libSSA/seqan/index.h | 113 +
src/libSSA/seqan/index/index_base.h | 954 +
src/libSSA/seqan/index/index_find.h | 268 +
src/libSSA/seqan/index/index_generated_forwards.h | 2648 +++
src/libSSA/seqan/index/index_manual_forwards.h | 55 +
src/libSSA/seqan/index/index_qgram_find.h | 82 +
src/libSSA/seqan/index/index_sa_lss.h | 427 +
src/libSSA/seqan/index/shape_base.h | 607 +
src/libSSA/seqan/index/shape_gapped.h | 593 +
src/libSSA/seqan/index/shape_predefined.h | 114 +
src/libSSA/seqan/platform.h | 27 +
src/libSSA/seqan/sequence.h | 65 +
src/libSSA/seqan/sequence/lexical.h | 787 +
src/libSSA/seqan/sequence/segment_base.h | 1181 ++
src/libSSA/seqan/sequence/segment_infix.h | 794 +
src/libSSA/seqan/sequence/segment_prefix.h | 595 +
src/libSSA/seqan/sequence/segment_suffix.h | 583 +
src/libSSA/seqan/sequence/sequence_forwards.h | 52 +
.../seqan/sequence/sequence_generated_forwards.h | 1557 ++
src/libSSA/seqan/sequence/sequence_interface.h | 1516 ++
src/libSSA/seqan/sequence/sequence_multiple.h | 2286 +++
src/libSSA/seqan/sequence/sequence_shortcuts.h | 197 +
src/libSSA/seqan/sequence/std_string.h | 691 +
src/libSSA/seqan/sequence/string_alloc.h | 467 +
src/libSSA/seqan/sequence/string_array.h | 237 +
src/libSSA/seqan/sequence/string_base.h | 1695 ++
src/libSSA/seqan/sequence/string_cstyle.h | 808 +
src/libSSA/seqan/sequence/string_packed.h | 1262 ++
src/libSSA/seqan/sequence/string_pointer.h | 842 +
src/libSSA/seqan/sequence/string_stack.h | 532 +
src/libSSA/seqan/sequence/string_value_expand.h | 514 +
src/libSSA/utils.cpp | 122 +
src/libSSA/utils.h | 110 +
src/libgzstream/COPYING.LIB | 504 +
src/libgzstream/Makefile.am | 107 +
src/libgzstream/Makefile.in | 593 +
src/libgzstream/README | 6 +
src/libgzstream/gzstream.cpp | 165 +
src/libgzstream/gzstream.h | 121 +
src/locateServer.cpp | 788 +
src/locateServer.h | 142 +
src/types.h | 153 +
src/utils.cpp | 217 +
src/utils.h | 132 +
test_f/Makefile.am | 125 +
test_f/Makefile.in | 783 +
test_f/bug/Makefile.am | 106 +
test_f/bug/Makefile.in | 471 +
test_f/bug/bug-15605-genome.fa | 5 +
test_f/bug/bug-15605-read.fa | 6 +
test_f/bug/bug-15605.should_get | 7 +
test_f/bug/bug-15605_2-genome.fa | 11 +
test_f/bug/bug-15605_2-read.fa | 6 +
test_f/bug/bug-15605_2.should_get | 7 +
test_f/bug/bug-15630-genome.fa | 15 +
test_f/bug/bug-15630-read.fa | 2 +
test_f/bug/bug-15630.should_get | 6 +
test_f/bug/bug-15639-genome.fa | 144 +
test_f/bug/bug-15639-read.fa | 2 +
test_f/bug/bug-15639.should_get | 7 +
test_f/bug/bug-15646-genome.fa | 88 +
test_f/bug/bug-15646-read.fa | 10 +
test_f/bug/bug-15646.should_get | 11 +
test_f/bug/bug-15649-2.should_get | 6 +
test_f/bug/bug-15649-genome-2.fa | 2 +
test_f/bug/bug-15649-genome.fa | 4 +
test_f/bug/bug-15649-read.fa | 2 +
test_f/bug/bug-15649.should_get | 7 +
test_f/bug/bug-15672-genome.fa | 34 +
test_f/bug/bug-15672-read.fa | 6 +
test_f/bug/bug-15672.should_get | 7 +
test_f/bug/bug-15677-genome.fa | 6 +
test_f/bug/bug-15677-read.fa | 2 +
test_f/bug/bug-15677.should_get | 6 +
test_f/bug/bug-15847-genome.fa | 49 +
test_f/bug/bug-15847-read.fa | 6 +
test_f/bug/bug-15847.should_get | 6 +
test_f/bug/bug-16403-genome.fa | 6 +
test_f/bug/bug-16403-read.fa | 4 +
test_f/bug/bug-16403.should_get | 6 +
test_f/bug/bug-16581-genome.fa | 2 +
test_f/bug/bug-16581-read.fq | 8 +
test_f/bug/bug-16581.should_get | 7 +
test_f/bug/bug-16931.should_get | 11 +
test_f/bug/bug-17175-genome.fa | 8 +
test_f/bug/bug-17175-read.fa | 9 +
test_f/bug/bug-17175.should_get | 17 +
test_f/causes/Makefile.am | 104 +
test_f/causes/Makefile.in | 469 +
test_f/causes/genome.fa | 86 +
test_f/causes/snp.fa | 134 +
test_f/causes/snp.fa.should_get | 58 +
test_f/cigar/Makefile.am | 106 +
test_f/cigar/Makefile.in | 471 +
test_f/cigar/consistency.should_get | 34 +
test_f/cigar/consistency2.should_get | 6 +
test_f/cigar/consistency3.should_get | 51 +
test_f/cigar/genome.fasta | 16 +
test_f/cigar/reads.fasta | 36 +
test_f/cigar/reads_k18.fasta | 4 +
test_f/cigar/reads_sam1.fasta | 22 +
test_f/cigar/reads_sam2.fasta | 22 +
test_f/index_genomes.sh | 15 +
test_f/launch_sg.sh | 11 +
test_f/should-get.sh | 193 +
test_f/test_index.sh | 52 +
test_f/toy.fasta | 21 +
test_f/toy.fastq | 72 +
test_f/toy1.fastq | 28 +
test_f/toy2.fastq | 28 +
test_f/valgrind.supp | 6 +
419 files changed, 277810 insertions(+)
diff --git a/AUTHORS b/AUTHORS
new file mode 100644
index 0000000..86914c1
--- /dev/null
+++ b/AUTHORS
@@ -0,0 +1,20 @@
+CRAC is research project and achievement of:
+ Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+ Mikaël SALSON <mikael.salson at lifl.fr>
+ Thérèse COMMES <therese.commes at univ-montp2.fr>
+ Eric RIVALS <eric.rivals at lirmm.fr>
+
+Supervision by:
+ Thérèse COMMES <therese.commes at univ-montp2.fr>
+ Eric RIVALS <eric.rivals at lirmm.fr>
+
+Programming:
+ Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+ Mikaël SALSON <mikael.salson at lifl.fr>
+
+with additional contribution for the packaging of:
+ Alban MANCHERON <alban.mancheron at lirmm.fr>
+
+
+For any bugs, please contact Nicolas PHILIPPE, Mikael SALSON, Alban MANCHERON at <crac-bugs at lists.gforge.inria.fr>
+For any questions about the paper, please contact Nicolas PHILIPPE, Mikael SALSON, Therese COMMES, Eric RIVALS at <crac-article at lists.gforge.inria.fr>
\ No newline at end of file
diff --git a/COPYING b/COPYING
new file mode 100644
index 0000000..2880c89
--- /dev/null
+++ b/COPYING
@@ -0,0 +1,1027 @@
+***********************************************************************
+******* English translation of the french licence is thereafter *******
+***********************************************************************
+
+CONTRAT DE LICENCE DE LOGICIEL LIBRE CeCILL
+
+
+ Avertissement
+
+Ce contrat est une licence de logiciel libre issue d'une concertation
+entre ses auteurs afin que le respect de deux grands principes préside à
+sa rédaction:
+
+ * d'une part, le respect des principes de diffusion des logiciels
+ libres: accès au code source, droits étendus conférés aux
+ utilisateurs,
+ * d'autre part, la désignation d'un droit applicable, le droit
+ français, auquel elle est conforme, tant au regard du droit de la
+ responsabilité civile que du droit de la propriété intellectuelle
+ et de la protection qu'il offre aux auteurs et titulaires des
+ droits patrimoniaux sur un logiciel.
+
+Les auteurs de la licence CeCILL (pour Ce[a] C[nrs] I[nria] L[ogiciel]
+L[ibre]) sont:
+
+Commissariat à l'Energie Atomique - CEA, établissement public de
+recherche à caractère scientifique, technique et industriel, dont le
+siège est situé 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris.
+
+Centre National de la Recherche Scientifique - CNRS, établissement
+public à caractère scientifique et technologique, dont le siège est
+situé 3 rue Michel-Ange, 75794 Paris cedex 16.
+
+Institut National de Recherche en Informatique et en Automatique -
+INRIA, établissement public à caractère scientifique et technologique,
+dont le siège est situé Domaine de Voluceau, Rocquencourt, BP 105, 78153
+Le Chesnay cedex.
+
+
+ Préambule
+
+Ce contrat est une licence de logiciel libre dont l'objectif est de
+conférer aux utilisateurs la liberté de modification et de
+redistribution du logiciel régi par cette licence dans le cadre d'un
+modèle de diffusion en logiciel libre.
+
+L'exercice de ces libertés est assorti de certains devoirs à la charge
+des utilisateurs afin de préserver ce statut au cours des
+redistributions ultérieures.
+
+L'accessibilité au code source et les droits de copie, de modification
+et de redistribution qui en découlent ont pour contrepartie de n'offrir
+aux utilisateurs qu'une garantie limitée et de ne faire peser sur
+l'auteur du logiciel, le titulaire des droits patrimoniaux et les
+concédants successifs qu'une responsabilité restreinte.
+
+A cet égard l'attention de l'utilisateur est attirée sur les risques
+associés au chargement, à l'utilisation, à la modification et/ou au
+développement et à la reproduction du logiciel par l'utilisateur étant
+donné sa spécificité de logiciel libre, qui peut le rendre complexe à
+manipuler et qui le réserve donc à des développeurs ou des
+professionnels avertis possédant des connaissances informatiques
+approfondies. Les utilisateurs sont donc invités à charger et tester
+l'adéquation du logiciel à leurs besoins dans des conditions permettant
+d'assurer la sécurité de leurs systèmes et/ou de leurs données et, plus
+généralement, à l'utiliser et l'exploiter dans les mêmes conditions de
+sécurité. Ce contrat peut être reproduit et diffusé librement, sous
+réserve de le conserver en l'état, sans ajout ni suppression de clauses.
+
+Ce contrat est susceptible de s'appliquer à tout logiciel dont le
+titulaire des droits patrimoniaux décide de soumettre l'exploitation aux
+dispositions qu'il contient.
+
+
+ Article 1 - DEFINITIONS
+
+Dans ce contrat, les termes suivants, lorsqu'ils seront écrits avec une
+lettre capitale, auront la signification suivante:
+
+Contrat: désigne le présent contrat de licence, ses éventuelles versions
+postérieures et annexes.
+
+Logiciel: désigne le logiciel sous sa forme de Code Objet et/ou de Code
+Source et le cas échéant sa documentation, dans leur état au moment de
+l'acceptation du Contrat par le Licencié.
+
+Logiciel Initial: désigne le Logiciel sous sa forme de Code Source et
+éventuellement de Code Objet et le cas échéant sa documentation, dans
+leur état au moment de leur première diffusion sous les termes du Contrat.
+
+Logiciel Modifié: désigne le Logiciel modifié par au moins une
+Contribution.
+
+Code Source: désigne l'ensemble des instructions et des lignes de
+programme du Logiciel et auquel l'accès est nécessaire en vue de
+modifier le Logiciel.
+
+Code Objet: désigne les fichiers binaires issus de la compilation du
+Code Source.
+
+Titulaire: désigne le ou les détenteurs des droits patrimoniaux d'auteur
+sur le Logiciel Initial.
+
+Licencié: désigne le ou les utilisateurs du Logiciel ayant accepté le
+Contrat.
+
+Contributeur: désigne le Licencié auteur d'au moins une Contribution.
+
+Concédant: désigne le Titulaire ou toute personne physique ou morale
+distribuant le Logiciel sous le Contrat.
+
+Contribution: désigne l'ensemble des modifications, corrections,
+traductions, adaptations et/ou nouvelles fonctionnalités intégrées dans
+le Logiciel par tout Contributeur, ainsi que tout Module Interne.
+
+Module: désigne un ensemble de fichiers sources y compris leur
+documentation qui permet de réaliser des fonctionnalités ou services
+supplémentaires à ceux fournis par le Logiciel.
+
+Module Externe: désigne tout Module, non dérivé du Logiciel, tel que ce
+Module et le Logiciel s'exécutent dans des espaces d'adressage
+différents, l'un appelant l'autre au moment de leur exécution.
+
+Module Interne: désigne tout Module lié au Logiciel de telle sorte
+qu'ils s'exécutent dans le même espace d'adressage.
+
+GNU GPL: désigne la GNU General Public License dans sa version 2 ou
+toute version ultérieure, telle que publiée par Free Software Foundation
+Inc.
+
+Parties: désigne collectivement le Licencié et le Concédant.
+
+Ces termes s'entendent au singulier comme au pluriel.
+
+
+ Article 2 - OBJET
+
+Le Contrat a pour objet la concession par le Concédant au Licencié d'une
+licence non exclusive, cessible et mondiale du Logiciel telle que
+définie ci-après à l'article 5 pour toute la durée de protection des droits
+portant sur ce Logiciel.
+
+
+ Article 3 - ACCEPTATION
+
+3.1 L'acceptation par le Licencié des termes du Contrat est réputée
+acquise du fait du premier des faits suivants:
+
+ * (i) le chargement du Logiciel par tout moyen notamment par
+ téléchargement à partir d'un serveur distant ou par chargement à
+ partir d'un support physique;
+ * (ii) le premier exercice par le Licencié de l'un quelconque des
+ droits concédés par le Contrat.
+
+3.2 Un exemplaire du Contrat, contenant notamment un avertissement
+relatif aux spécificités du Logiciel, à la restriction de garantie et à
+la limitation à un usage par des utilisateurs expérimentés a été mis à
+disposition du Licencié préalablement à son acceptation telle que
+définie à l'article 3.1 ci dessus et le Licencié reconnaît en avoir pris
+connaissance.
+
+
+ Article 4 - ENTREE EN VIGUEUR ET DUREE
+
+
+ 4.1 ENTREE EN VIGUEUR
+
+Le Contrat entre en vigueur à la date de son acceptation par le Licencié
+telle que définie en 3.1.
+
+
+ 4.2 DUREE
+
+Le Contrat produira ses effets pendant toute la durée légale de
+protection des droits patrimoniaux portant sur le Logiciel.
+
+
+ Article 5 - ETENDUE DES DROITS CONCEDES
+
+Le Concédant concède au Licencié, qui accepte, les droits suivants sur
+le Logiciel pour toutes destinations et pour la durée du Contrat dans
+les conditions ci-après détaillées.
+
+Par ailleurs, si le Concédant détient ou venait à détenir un ou
+plusieurs brevets d'invention protégeant tout ou partie des
+fonctionnalités du Logiciel ou de ses composants, il s'engage à ne pas
+opposer les éventuels droits conférés par ces brevets aux Licenciés
+successifs qui utiliseraient, exploiteraient ou modifieraient le
+Logiciel. En cas de cession de ces brevets, le Concédant s'engage à
+faire reprendre les obligations du présent alinéa aux cessionnaires.
+
+
+ 5.1 DROIT D'UTILISATION
+
+Le Licencié est autorisé à utiliser le Logiciel, sans restriction quant
+aux domaines d'application, étant ci-après précisé que cela comporte:
+
+ 1. la reproduction permanente ou provisoire du Logiciel en tout ou
+ partie par tout moyen et sous toute forme.
+
+ 2. le chargement, l'affichage, l'exécution, ou le stockage du
+ Logiciel sur tout support.
+
+ 3. la possibilité d'en observer, d'en étudier, ou d'en tester le
+ fonctionnement afin de déterminer les idées et principes qui sont
+ à la base de n'importe quel élément de ce Logiciel; et ceci,
+ lorsque le Licencié effectue toute opération de chargement,
+ d'affichage, d'exécution, de transmission ou de stockage du
+ Logiciel qu'il est en droit d'effectuer en vertu du Contrat.
+
+
+ 5.2 DROIT D'APPORTER DES CONTRIBUTIONS
+
+Le droit d'apporter des Contributions comporte le droit de traduire,
+d'adapter, d'arranger ou d'apporter toute autre modification au Logiciel
+et le droit de reproduire le logiciel en résultant.
+
+Le Licencié est autorisé à apporter toute Contribution au Logiciel sous
+réserve de mentionner, de façon explicite, son nom en tant qu'auteur de
+cette Contribution et la date de création de celle-ci.
+
+
+ 5.3 DROIT DE DISTRIBUTION
+
+Le droit de distribution comporte notamment le droit de diffuser, de
+transmettre et de communiquer le Logiciel au public sur tout support et
+par tout moyen ainsi que le droit de mettre sur le marché à titre
+onéreux ou gratuit, un ou des exemplaires du Logiciel par tout procédé.
+
+Le Licencié est autorisé à distribuer des copies du Logiciel, modifié ou
+non, à des tiers dans les conditions ci-après détaillées.
+
+
+ 5.3.1 DISTRIBUTION DU LOGICIEL SANS MODIFICATION
+
+Le Licencié est autorisé à distribuer des copies conformes du Logiciel,
+sous forme de Code Source ou de Code Objet, à condition que cette
+distribution respecte les dispositions du Contrat dans leur totalité et
+soit accompagnée:
+
+ 1. d'un exemplaire du Contrat,
+
+ 2. d'un avertissement relatif à la restriction de garantie et de
+ responsabilité du Concédant telle que prévue aux articles 8
+ et 9,
+
+et que, dans le cas où seul le Code Objet du Logiciel est redistribué,
+le Licencié permette aux futurs Licenciés d'accéder facilement au Code
+Source complet du Logiciel en indiquant les modalités d'accès, étant
+entendu que le coût additionnel d'acquisition du Code Source ne devra
+pas excéder le simple coût de transfert des données.
+
+
+ 5.3.2 DISTRIBUTION DU LOGICIEL MODIFIE
+
+Lorsque le Licencié apporte une Contribution au Logiciel, les conditions
+de distribution du Logiciel Modifié en résultant sont alors soumises à
+l'intégralité des dispositions du Contrat.
+
+Le Licencié est autorisé à distribuer le Logiciel Modifié, sous forme de
+code source ou de code objet, à condition que cette distribution
+respecte les dispositions du Contrat dans leur totalité et soit
+accompagnée:
+
+ 1. d'un exemplaire du Contrat,
+
+ 2. d'un avertissement relatif à la restriction de garantie et de
+ responsabilité du Concédant telle que prévue aux articles 8
+ et 9,
+
+et que, dans le cas où seul le code objet du Logiciel Modifié est
+redistribué, le Licencié permette aux futurs Licenciés d'accéder
+facilement au code source complet du Logiciel Modifié en indiquant les
+modalités d'accès, étant entendu que le coût additionnel d'acquisition
+du code source ne devra pas excéder le simple coût de transfert des données.
+
+
+ 5.3.3 DISTRIBUTION DES MODULES EXTERNES
+
+Lorsque le Licencié a développé un Module Externe les conditions du
+Contrat ne s'appliquent pas à ce Module Externe, qui peut être distribué
+sous un contrat de licence différent.
+
+
+ 5.3.4 COMPATIBILITE AVEC LA LICENCE GNU GPL
+
+Le Licencié peut inclure un code soumis aux dispositions d'une des
+versions de la licence GNU GPL dans le Logiciel modifié ou non et
+distribuer l'ensemble sous les conditions de la même version de la
+licence GNU GPL.
+
+Le Licencié peut inclure le Logiciel modifié ou non dans un code soumis
+aux dispositions d'une des versions de la licence GNU GPL et distribuer
+l'ensemble sous les conditions de la même version de la licence GNU GPL.
+
+
+ Article 6 - PROPRIETE INTELLECTUELLE
+
+
+ 6.1 SUR LE LOGICIEL INITIAL
+
+Le Titulaire est détenteur des droits patrimoniaux sur le Logiciel
+Initial. Toute utilisation du Logiciel Initial est soumise au respect
+des conditions dans lesquelles le Titulaire a choisi de diffuser son
+oeuvre et nul autre n'a la faculté de modifier les conditions de
+diffusion de ce Logiciel Initial.
+
+Le Titulaire s'engage à ce que le Logiciel Initial reste au moins régi
+par le Contrat et ce, pour la durée visée à l'article 4.2.
+
+
+ 6.2 SUR LES CONTRIBUTIONS
+
+Le Licencié qui a développé une Contribution est titulaire sur celle-ci
+des droits de propriété intellectuelle dans les conditions définies par
+la législation applicable.
+
+
+ 6.3 SUR LES MODULES EXTERNES
+
+Le Licencié qui a développé un Module Externe est titulaire sur celui-ci
+des droits de propriété intellectuelle dans les conditions définies par
+la législation applicable et reste libre du choix du contrat régissant
+sa diffusion.
+
+
+ 6.4 DISPOSITIONS COMMUNES
+
+Le Licencié s'engage expressément:
+
+ 1. à ne pas supprimer ou modifier de quelque manière que ce soit les
+ mentions de propriété intellectuelle apposées sur le Logiciel;
+
+ 2. à reproduire à l'identique lesdites mentions de propriété
+ intellectuelle sur les copies du Logiciel modifié ou non.
+
+Le Licencié s'engage à ne pas porter atteinte, directement ou
+indirectement, aux droits de propriété intellectuelle du Titulaire et/ou
+des Contributeurs sur le Logiciel et à prendre, le cas échéant, à
+l'égard de son personnel toutes les mesures nécessaires pour assurer le
+respect des dits droits de propriété intellectuelle du Titulaire et/ou
+des Contributeurs.
+
+
+ Article 7 - SERVICES ASSOCIES
+
+7.1 Le Contrat n'oblige en aucun cas le Concédant à la réalisation de
+prestations d'assistance technique ou de maintenance du Logiciel.
+
+Cependant le Concédant reste libre de proposer ce type de services. Les
+termes et conditions d'une telle assistance technique et/ou d'une telle
+maintenance seront alors déterminés dans un acte séparé. Ces actes de
+maintenance et/ou assistance technique n'engageront que la seule
+responsabilité du Concédant qui les propose.
+
+7.2 De même, tout Concédant est libre de proposer, sous sa seule
+responsabilité, à ses licenciés une garantie, qui n'engagera que lui,
+lors de la redistribution du Logiciel et/ou du Logiciel Modifié et ce,
+dans les conditions qu'il souhaite. Cette garantie et les modalités
+financières de son application feront l'objet d'un acte séparé entre le
+Concédant et le Licencié.
+
+
+ Article 8 - RESPONSABILITE
+
+8.1 Sous réserve des dispositions de l'article 8.2, le Licencié a la
+faculté, sous réserve de prouver la faute du Concédant concerné, de
+solliciter la réparation du préjudice direct qu'il subirait du fait du
+Logiciel et dont il apportera la preuve.
+
+8.2 La responsabilité du Concédant est limitée aux engagements pris en
+application du Contrat et ne saurait être engagée en raison notamment:
+(i) des dommages dus à l'inexécution, totale ou partielle, de ses
+obligations par le Licencié, (ii) des dommages directs ou indirects
+découlant de l'utilisation ou des performances du Logiciel subis par le
+Licencié et (iii) plus généralement d'un quelconque dommage indirect. En
+particulier, les Parties conviennent expressément que tout préjudice
+financier ou commercial (par exemple perte de données, perte de
+bénéfices, perte d'exploitation, perte de clientèle ou de commandes,
+manque à gagner, trouble commercial quelconque) ou toute action dirigée
+contre le Licencié par un tiers, constitue un dommage indirect et
+n'ouvre pas droit à réparation par le Concédant.
+
+
+ Article 9 - GARANTIE
+
+9.1 Le Licencié reconnaît que l'état actuel des connaissances
+scientifiques et techniques au moment de la mise en circulation du
+Logiciel ne permet pas d'en tester et d'en vérifier toutes les
+utilisations ni de détecter l'existence d'éventuels défauts. L'attention
+du Licencié a été attirée sur ce point sur les risques associés au
+chargement, à l'utilisation, la modification et/ou au développement et à
+la reproduction du Logiciel qui sont réservés à des utilisateurs avertis.
+
+Il relève de la responsabilité du Licencié de contrôler, par tous
+moyens, l'adéquation du produit à ses besoins, son bon fonctionnement et
+de s'assurer qu'il ne causera pas de dommages aux personnes et aux biens.
+
+9.2 Le Concédant déclare de bonne foi être en droit de concéder
+l'ensemble des droits attachés au Logiciel (comprenant notamment les
+droits visés à l'article 5).
+
+9.3 Le Licencié reconnaît que le Logiciel est fourni "en l'état" par le
+Concédant sans autre garantie, expresse ou tacite, que celle prévue à
+l'article 9.2 et notamment sans aucune garantie sur sa valeur commerciale,
+son caractère sécurisé, innovant ou pertinent.
+
+En particulier, le Concédant ne garantit pas que le Logiciel est exempt
+d'erreur, qu'il fonctionnera sans interruption, qu'il sera compatible
+avec l'équipement du Licencié et sa configuration logicielle ni qu'il
+remplira les besoins du Licencié.
+
+9.4 Le Concédant ne garantit pas, de manière expresse ou tacite, que le
+Logiciel ne porte pas atteinte à un quelconque droit de propriété
+intellectuelle d'un tiers portant sur un brevet, un logiciel ou sur tout
+autre droit de propriété. Ainsi, le Concédant exclut toute garantie au
+profit du Licencié contre les actions en contrefaçon qui pourraient être
+diligentées au titre de l'utilisation, de la modification, et de la
+redistribution du Logiciel. Néanmoins, si de telles actions sont
+exercées contre le Licencié, le Concédant lui apportera son aide
+technique et juridique pour sa défense. Cette aide technique et
+juridique est déterminée au cas par cas entre le Concédant concerné et
+le Licencié dans le cadre d'un protocole d'accord. Le Concédant dégage
+toute responsabilité quant à l'utilisation de la dénomination du
+Logiciel par le Licencié. Aucune garantie n'est apportée quant à
+l'existence de droits antérieurs sur le nom du Logiciel et sur
+l'existence d'une marque.
+
+
+ Article 10 - RESILIATION
+
+10.1 En cas de manquement par le Licencié aux obligations mises à sa
+charge par le Contrat, le Concédant pourra résilier de plein droit le
+Contrat trente (30) jours après notification adressée au Licencié et
+restée sans effet.
+
+10.2 Le Licencié dont le Contrat est résilié n'est plus autorisé à
+utiliser, modifier ou distribuer le Logiciel. Cependant, toutes les
+licences qu'il aura concédées antérieurement à la résiliation du Contrat
+resteront valides sous réserve qu'elles aient été effectuées en
+conformité avec le Contrat.
+
+
+ Article 11 - DISPOSITIONS DIVERSES
+
+
+ 11.1 CAUSE EXTERIEURE
+
+Aucune des Parties ne sera responsable d'un retard ou d'une défaillance
+d'exécution du Contrat qui serait dû à un cas de force majeure, un cas
+fortuit ou une cause extérieure, telle que, notamment, le mauvais
+fonctionnement ou les interruptions du réseau électrique ou de
+télécommunication, la paralysie du réseau liée à une attaque
+informatique, l'intervention des autorités gouvernementales, les
+catastrophes naturelles, les dégâts des eaux, les tremblements de terre,
+le feu, les explosions, les grèves et les conflits sociaux, l'état de
+guerre...
+
+11.2 Le fait, par l'une ou l'autre des Parties, d'omettre en une ou
+plusieurs occasions de se prévaloir d'une ou plusieurs dispositions du
+Contrat, ne pourra en aucun cas impliquer renonciation par la Partie
+intéressée à s'en prévaloir ultérieurement.
+
+11.3 Le Contrat annule et remplace toute convention antérieure, écrite
+ou orale, entre les Parties sur le même objet et constitue l'accord
+entier entre les Parties sur cet objet. Aucune addition ou modification
+aux termes du Contrat n'aura d'effet à l'égard des Parties à moins
+d'être faite par écrit et signée par leurs représentants dûment habilités.
+
+11.4 Dans l'hypothèse où une ou plusieurs des dispositions du Contrat
+s'avèrerait contraire à une loi ou à un texte applicable, existants ou
+futurs, cette loi ou ce texte prévaudrait, et les Parties feraient les
+amendements nécessaires pour se conformer à cette loi ou à ce texte.
+Toutes les autres dispositions resteront en vigueur. De même, la
+nullité, pour quelque raison que ce soit, d'une des dispositions du
+Contrat ne saurait entraîner la nullité de l'ensemble du Contrat.
+
+
+ 11.5 LANGUE
+
+Le Contrat est rédigé en langue française et en langue anglaise, ces
+deux versions faisant également foi.
+
+
+ Article 12 - NOUVELLES VERSIONS DU CONTRAT
+
+12.1 Toute personne est autorisée à copier et distribuer des copies de
+ce Contrat.
+
+12.2 Afin d'en préserver la cohérence, le texte du Contrat est protégé
+et ne peut être modifié que par les auteurs de la licence, lesquels se
+réservent le droit de publier périodiquement des mises à jour ou de
+nouvelles versions du Contrat, qui posséderont chacune un numéro
+distinct. Ces versions ultérieures seront susceptibles de prendre en
+compte de nouvelles problématiques rencontrées par les logiciels libres.
+
+12.3 Tout Logiciel diffusé sous une version donnée du Contrat ne pourra
+faire l'objet d'une diffusion ultérieure que sous la même version du
+Contrat ou une version postérieure, sous réserve des dispositions de
+l'article 5.3.4.
+
+
+ Article 13 - LOI APPLICABLE ET COMPETENCE TERRITORIALE
+
+13.1 Le Contrat est régi par la loi française. Les Parties conviennent
+de tenter de régler à l'amiable les différends ou litiges qui
+viendraient à se produire par suite ou à l'occasion du Contrat.
+
+13.2 A défaut d'accord amiable dans un délai de deux (2) mois à compter
+de leur survenance et sauf situation relevant d'une procédure d'urgence,
+les différends ou litiges seront portés par la Partie la plus diligente
+devant les Tribunaux compétents de Paris.
+
+
+Version 2.0 du 2006-09-05.
+
+***********************************************************************
+***********************************************************************
+***********************************************************************
+
+CeCILL FREE SOFTWARE LICENSE AGREEMENT
+
+
+ Notice
+
+This Agreement is a Free Software license agreement that is the result
+of discussions between its authors in order to ensure compliance with
+the two main principles guiding its drafting:
+
+ * firstly, compliance with the principles governing the distribution
+ of Free Software: access to source code, broad rights granted to
+ users,
+ * secondly, the election of a governing law, French law, with which
+ it is conformant, both as regards the law of torts and
+ intellectual property law, and the protection that it offers to
+ both authors and holders of the economic rights over software.
+
+The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
+license are:
+
+Commissariat à l'Energie Atomique - CEA, a public scientific, technical
+and industrial research establishment, having its principal place of
+business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
+
+Centre National de la Recherche Scientifique - CNRS, a public scientific
+and technological establishment, having its principal place of business
+at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
+
+Institut National de Recherche en Informatique et en Automatique -
+INRIA, a public scientific and technological establishment, having its
+principal place of business at Domaine de Voluceau, Rocquencourt, BP
+105, 78153 Le Chesnay cedex, France.
+
+
+ Preamble
+
+The purpose of this Free Software license agreement is to grant users
+the right to modify and redistribute the software governed by this
+license within the framework of an open source distribution model.
+
+The exercising of these rights is conditional upon certain obligations
+for users so as to preserve this status for all subsequent redistributions.
+
+In consideration of access to the source code and the rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors only have limited liability.
+
+In this respect, the risks associated with loading, using, modifying
+and/or developing or reproducing the software by the user are brought to
+the user's attention, given its Free Software status, which may make it
+complicated to use, with the result that its use is reserved for
+developers and experienced professionals having in-depth computer
+knowledge. Users are therefore encouraged to load and test the
+suitability of the software as regards their requirements in conditions
+enabling the security of their systems and/or data to be ensured and,
+more generally, to use and operate it in the same conditions of
+security. This Agreement may be freely reproduced and published,
+provided it is not altered, and that no provisions are either added or
+removed herefrom.
+
+This Agreement may apply to any or all software for which the holder of
+the economic rights decides to submit the use thereof to its provisions.
+
+
+ Article 1 - DEFINITIONS
+
+For the purpose of this Agreement, when the following expressions
+commence with a capital letter, they shall have the following meaning:
+
+Agreement: means this license agreement, and its possible subsequent
+versions and annexes.
+
+Software: means the software in its Object Code and/or Source Code form
+and, where applicable, its documentation, "as is" when the Licensee
+accepts the Agreement.
+
+Initial Software: means the Software in its Source Code and possibly its
+Object Code form and, where applicable, its documentation, "as is" when
+it is first distributed under the terms and conditions of the Agreement.
+
+Modified Software: means the Software modified by at least one
+Contribution.
+
+Source Code: means all the Software's instructions and program lines to
+which access is required so as to modify the Software.
+
+Object Code: means the binary files originating from the compilation of
+the Source Code.
+
+Holder: means the holder(s) of the economic rights over the Initial
+Software.
+
+Licensee: means the Software user(s) having accepted the Agreement.
+
+Contributor: means a Licensee having made at least one Contribution.
+
+Licensor: means the Holder, or any other individual or legal entity, who
+distributes the Software under the Agreement.
+
+Contribution: means any or all modifications, corrections, translations,
+adaptations and/or new functions integrated into the Software by any or
+all Contributors, as well as any or all Internal Modules.
+
+Module: means a set of sources files including their documentation that
+enables supplementary functions or services in addition to those offered
+by the Software.
+
+External Module: means any or all Modules, not derived from the
+Software, so that this Module and the Software run in separate address
+spaces, with one calling the other when they are run.
+
+Internal Module: means any or all Module, connected to the Software so
+that they both execute in the same address space.
+
+GNU GPL: means the GNU General Public License version 2 or any
+subsequent version, as published by the Free Software Foundation Inc.
+
+Parties: mean both the Licensee and the Licensor.
+
+These expressions may be used both in singular and plural form.
+
+
+ Article 2 - PURPOSE
+
+The purpose of the Agreement is the grant by the Licensor to the
+Licensee of a non-exclusive, transferable and worldwide license for the
+Software as set forth in Article 5 hereinafter for the whole term of the
+protection granted by the rights over said Software.
+
+
+ Article 3 - ACCEPTANCE
+
+3.1 The Licensee shall be deemed as having accepted the terms and
+conditions of this Agreement upon the occurrence of the first of the
+following events:
+
+ * (i) loading the Software by any or all means, notably, by
+ downloading from a remote server, or by loading from a physical
+ medium;
+ * (ii) the first time the Licensee exercises any of the rights
+ granted hereunder.
+
+3.2 One copy of the Agreement, containing a notice relating to the
+characteristics of the Software, to the limited warranty, and to the
+fact that its use is restricted to experienced users has been provided
+to the Licensee prior to its acceptance as set forth in Article 3.1
+hereinabove, and the Licensee hereby acknowledges that it has read and
+understood it.
+
+
+ Article 4 - EFFECTIVE DATE AND TERM
+
+
+ 4.1 EFFECTIVE DATE
+
+The Agreement shall become effective on the date when it is accepted by
+the Licensee as set forth in Article 3.1.
+
+
+ 4.2 TERM
+
+The Agreement shall remain in force for the entire legal term of
+protection of the economic rights over the Software.
+
+
+ Article 5 - SCOPE OF RIGHTS GRANTED
+
+The Licensor hereby grants to the Licensee, who accepts, the following
+rights over the Software for any or all use, and for the term of the
+Agreement, on the basis of the terms and conditions set forth hereinafter.
+
+Besides, if the Licensor owns or comes to own one or more patents
+protecting all or part of the functions of the Software or of its
+components, the Licensor undertakes not to enforce the rights granted by
+these patents against successive Licensees using, exploiting or
+modifying the Software. If these patents are transferred, the Licensor
+undertakes to have the transferees subscribe to the obligations set
+forth in this paragraph.
+
+
+ 5.1 RIGHT OF USE
+
+The Licensee is authorized to use the Software, without any limitation
+as to its fields of application, with it being hereinafter specified
+that this comprises:
+
+ 1. permanent or temporary reproduction of all or part of the Software
+ by any or all means and in any or all form.
+
+ 2. loading, displaying, running, or storing the Software on any or
+ all medium.
+
+ 3. entitlement to observe, study or test its operation so as to
+ determine the ideas and principles behind any or all constituent
+ elements of said Software. This shall apply when the Licensee
+ carries out any or all loading, displaying, running, transmission
+ or storage operation as regards the Software, that it is entitled
+ to carry out hereunder.
+
+
+ 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
+
+The right to make Contributions includes the right to translate, adapt,
+arrange, or make any or all modifications to the Software, and the right
+to reproduce the resulting software.
+
+The Licensee is authorized to make any or all Contributions to the
+Software provided that it includes an explicit notice that it is the
+author of said Contribution and indicates the date of the creation thereof.
+
+
+ 5.3 RIGHT OF DISTRIBUTION
+
+In particular, the right of distribution includes the right to publish,
+transmit and communicate the Software to the general public on any or
+all medium, and by any or all means, and the right to market, either in
+consideration of a fee, or free of charge, one or more copies of the
+Software by any means.
+
+The Licensee is further authorized to distribute copies of the modified
+or unmodified Software to third parties according to the terms and
+conditions set forth hereinafter.
+
+
+ 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+
+The Licensee is authorized to distribute true copies of the Software in
+Source Code or Object Code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ 1. a copy of the Agreement,
+
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+
+and that, in the event that only the Object Code of the Software is
+redistributed, the Licensee allows future Licensees unhindered access to
+the full Source Code of the Software by indicating how to access it, it
+being understood that the additional cost of acquiring the Source Code
+shall not exceed the cost of transferring the data.
+
+
+ 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
+
+When the Licensee makes a Contribution to the Software, the terms and
+conditions for the distribution of the resulting Modified Software
+become subject to all the provisions of this Agreement.
+
+The Licensee is authorized to distribute the Modified Software, in
+source code or object code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ 1. a copy of the Agreement,
+
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+
+and that, in the event that only the object code of the Modified
+Software is redistributed, the Licensee allows future Licensees
+unhindered access to the full source code of the Modified Software by
+indicating how to access it, it being understood that the additional
+cost of acquiring the source code shall not exceed the cost of
+transferring the data.
+
+
+ 5.3.3 DISTRIBUTION OF EXTERNAL MODULES
+
+When the Licensee has developed an External Module, the terms and
+conditions of this Agreement do not apply to said External Module, that
+may be distributed under a separate license agreement.
+
+
+ 5.3.4 COMPATIBILITY WITH THE GNU GPL
+
+The Licensee can include a code that is subject to the provisions of one
+of the versions of the GNU GPL in the Modified or unmodified Software,
+and distribute that entire code under the terms of the same version of
+the GNU GPL.
+
+The Licensee can include the Modified or unmodified Software in a code
+that is subject to the provisions of one of the versions of the GNU GPL,
+and distribute that entire code under the terms of the same version of
+the GNU GPL.
+
+
+ Article 6 - INTELLECTUAL PROPERTY
+
+
+ 6.1 OVER THE INITIAL SOFTWARE
+
+The Holder owns the economic rights over the Initial Software. Any or
+all use of the Initial Software is subject to compliance with the terms
+and conditions under which the Holder has elected to distribute its work
+and no one shall be entitled to modify the terms and conditions for the
+distribution of said Initial Software.
+
+The Holder undertakes that the Initial Software will remain ruled at
+least by this Agreement, for the duration set forth in Article 4.2.
+
+
+ 6.2 OVER THE CONTRIBUTIONS
+
+The Licensee who develops a Contribution is the owner of the
+intellectual property rights over this Contribution as defined by
+applicable law.
+
+
+ 6.3 OVER THE EXTERNAL MODULES
+
+The Licensee who develops an External Module is the owner of the
+intellectual property rights over this External Module as defined by
+applicable law and is free to choose the type of agreement that shall
+govern its distribution.
+
+
+ 6.4 JOINT PROVISIONS
+
+The Licensee expressly undertakes:
+
+ 1. not to remove, or modify, in any manner, the intellectual property
+ notices attached to the Software;
+
+ 2. to reproduce said notices, in an identical manner, in the copies
+ of the Software modified or not.
+
+The Licensee undertakes not to directly or indirectly infringe the
+intellectual property rights of the Holder and/or Contributors on the
+Software and to take, where applicable, vis-à-vis its staff, any and all
+measures required to ensure respect of said intellectual property rights
+of the Holder and/or Contributors.
+
+
+ Article 7 - RELATED SERVICES
+
+7.1 Under no circumstances shall the Agreement oblige the Licensor to
+provide technical assistance or maintenance services for the Software.
+
+However, the Licensor is entitled to offer this type of services. The
+terms and conditions of such technical assistance, and/or such
+maintenance, shall be set forth in a separate instrument. Only the
+Licensor offering said maintenance and/or technical assistance services
+shall incur liability therefor.
+
+7.2 Similarly, any Licensor is entitled to offer to its licensees, under
+its sole responsibility, a warranty, that shall only be binding upon
+itself, for the redistribution of the Software and/or the Modified
+Software, under terms and conditions that it is free to decide. Said
+warranty, and the financial terms and conditions of its application,
+shall be subject of a separate instrument executed between the Licensor
+and the Licensee.
+
+
+ Article 8 - LIABILITY
+
+8.1 Subject to the provisions of Article 8.2, the Licensee shall be
+entitled to claim compensation for any direct loss it may have suffered
+from the Software as a result of a fault on the part of the relevant
+Licensor, subject to providing evidence thereof.
+
+8.2 The Licensor's liability is limited to the commitments made under
+this Agreement and shall not be incurred as a result of in particular:
+(i) loss due the Licensee's total or partial failure to fulfill its
+obligations, (ii) direct or consequential loss that is suffered by the
+Licensee due to the use or performance of the Software, and (iii) more
+generally, any consequential loss. In particular the Parties expressly
+agree that any or all pecuniary or business loss (i.e. loss of data,
+loss of profits, operating loss, loss of customers or orders,
+opportunity cost, any disturbance to business activities) or any or all
+legal proceedings instituted against the Licensee by a third party,
+shall constitute consequential loss and shall not provide entitlement to
+any or all compensation from the Licensor.
+
+
+ Article 9 - WARRANTY
+
+9.1 The Licensee acknowledges that the scientific and technical
+state-of-the-art when the Software was distributed did not enable all
+possible uses to be tested and verified, nor for the presence of
+possible defects to be detected. In this respect, the Licensee's
+attention has been drawn to the risks associated with loading, using,
+modifying and/or developing and reproducing the Software which are
+reserved for experienced users.
+
+The Licensee shall be responsible for verifying, by any or all means,
+the suitability of the product for its requirements, its good working
+order, and for ensuring that it shall not cause damage to either persons
+or properties.
+
+9.2 The Licensor hereby represents, in good faith, that it is entitled
+to grant all the rights over the Software (including in particular the
+rights set forth in Article 5).
+
+9.3 The Licensee acknowledges that the Software is supplied "as is" by
+the Licensor without any other express or tacit warranty, other than
+that provided for in Article 9.2 and, in particular, without any warranty
+as to its commercial value, its secured, safe, innovative or relevant
+nature.
+
+Specifically, the Licensor does not warrant that the Software is free
+from any error, that it will operate without interruption, that it will
+be compatible with the Licensee's own equipment and software
+configuration, nor that it will meet the Licensee's requirements.
+
+9.4 The Licensor does not either expressly or tacitly warrant that the
+Software does not infringe any third party intellectual property right
+relating to a patent, software or any other property right. Therefore,
+the Licensor disclaims any and all liability towards the Licensee
+arising out of any or all proceedings for infringement that may be
+instituted in respect of the use, modification and redistribution of the
+Software. Nevertheless, should such proceedings be instituted against
+the Licensee, the Licensor shall provide it with technical and legal
+assistance for its defense. Such technical and legal assistance shall be
+decided on a case-by-case basis between the relevant Licensor and the
+Licensee pursuant to a memorandum of understanding. The Licensor
+disclaims any and all liability as regards the Licensee's use of the
+name of the Software. No warranty is given as regards the existence of
+prior rights over the name of the Software or as regards the existence
+of a trademark.
+
+
+ Article 10 - TERMINATION
+
+10.1 In the event of a breach by the Licensee of its obligations
+hereunder, the Licensor may automatically terminate this Agreement
+thirty (30) days after notice has been sent to the Licensee and has
+remained ineffective.
+
+10.2 A Licensee whose Agreement is terminated shall no longer be
+authorized to use, modify or distribute the Software. However, any
+licenses that it may have granted prior to termination of the Agreement
+shall remain valid subject to their having been granted in compliance
+with the terms and conditions hereof.
+
+
+ Article 11 - MISCELLANEOUS
+
+
+ 11.1 EXCUSABLE EVENTS
+
+Neither Party shall be liable for any or all delay, or failure to
+perform the Agreement, that may be attributable to an event of force
+majeure, an act of God or an outside cause, such as defective
+functioning or interruptions of the electricity or telecommunications
+networks, network paralysis following a virus attack, intervention by
+government authorities, natural disasters, water damage, earthquakes,
+fire, explosions, strikes and labor unrest, war, etc.
+
+11.2 Any failure by either Party, on one or more occasions, to invoke
+one or more of the provisions hereof, shall under no circumstances be
+interpreted as being a waiver by the interested Party of its right to
+invoke said provision(s) subsequently.
+
+11.3 The Agreement cancels and replaces any or all previous agreements,
+whether written or oral, between the Parties and having the same
+purpose, and constitutes the entirety of the agreement between said
+Parties concerning said purpose. No supplement or modification to the
+terms and conditions hereof shall be effective as between the Parties
+unless it is made in writing and signed by their duly authorized
+representatives.
+
+11.4 In the event that one or more of the provisions hereof were to
+conflict with a current or future applicable act or legislative text,
+said act or legislative text shall prevail, and the Parties shall make
+the necessary amendments so as to comply with said act or legislative
+text. All other provisions shall remain effective. Similarly, invalidity
+of a provision of the Agreement, for any reason whatsoever, shall not
+cause the Agreement as a whole to be invalid.
+
+
+ 11.5 LANGUAGE
+
+The Agreement is drafted in both French and English and both versions
+are deemed authentic.
+
+
+ Article 12 - NEW VERSIONS OF THE AGREEMENT
+
+12.1 Any person is authorized to duplicate and distribute copies of this
+Agreement.
+
+12.2 So as to ensure coherence, the wording of this Agreement is
+protected and may only be modified by the authors of the License, who
+reserve the right to periodically publish updates or new versions of the
+Agreement, each with a separate number. These subsequent versions may
+address new issues encountered by Free Software.
+
+12.3 Any Software distributed under a given version of the Agreement may
+only be subsequently distributed under the same version of the Agreement
+or a subsequent version, subject to the provisions of Article 5.3.4.
+
+
+ Article 13 - GOVERNING LAW AND JURISDICTION
+
+13.1 The Agreement is governed by French law. The Parties agree to
+endeavor to seek an amicable solution to any disagreements or disputes
+that may arise during the performance of the Agreement.
+
+13.2 Failing an amicable solution within two (2) months as from their
+occurrence, and unless emergency proceedings are necessary, the
+disagreements or disputes shall be referred to the Paris Courts having
+jurisdiction, by the more diligent Party.
+
+
+Version 2.0 dated 2006-09-05.
+
+***********************************************************************
diff --git a/ChangeLog b/ChangeLog
new file mode 100644
index 0000000..a87089a
--- /dev/null
+++ b/ChangeLog
@@ -0,0 +1,438 @@
+------------------------------------------------------------------------
+r2851 | jaudoux | 2014-04-04 09:40:56 +0200 (ven. 04 avril 2014) | 1 ligne
+
+tlen set at 0 when PE read are completely overlapping. Add tests to consistency3
+------------------------------------------------------------------------
+r2850 | jaudoux | 2014-04-04 09:21:50 +0200 (ven. 04 avril 2014) | 1 ligne
+
+tlen is back to genomic distance
+------------------------------------------------------------------------
+r2849 | nphilippe | 2014-04-04 09:09:35 +0200 (ven. 04 avril 2014) | 1 ligne
+
+some correction in doc
+------------------------------------------------------------------------
+r2848 | nphilippe | 2014-04-04 08:57:45 +0200 (ven. 04 avril 2014) | 1 ligne
+
+some correction in doc
+------------------------------------------------------------------------
+r2847 | nphilippe | 2014-04-04 08:50:21 +0200 (ven. 04 avril 2014) | 1 ligne
+
+some correction in doc
+------------------------------------------------------------------------
+r2846 | jaudoux | 2014-04-03 17:50:03 +0200 (jeu. 03 avril 2014) | 1 ligne
+
+Draft for the new SAM specifications
+------------------------------------------------------------------------
+r2845 | jaudoux | 2014-04-03 17:44:57 +0200 (jeu. 03 avril 2014) | 1 ligne
+
+change tlen computing, we try to estimate the real RNA template length even if a Splice could be present in the space between PE reads
+------------------------------------------------------------------------
+r2844 | nphilippe | 2014-04-03 17:42:15 +0200 (jeu. 03 avril 2014) | 1 ligne
+
+update doc
+------------------------------------------------------------------------
+r2843 | jaudoux | 2014-04-03 17:33:10 +0200 (jeu. 03 avril 2014) | 1 ligne
+
+Remove Repetition field in SAM output of a repetitions since the field XX is dedicated to repetition, that would be redundant
+------------------------------------------------------------------------
+r2842 | jaudoux | 2014-04-03 17:20:58 +0200 (jeu. 03 avril 2014) | 1 ligne
+
+Change first and second read names
+------------------------------------------------------------------------
+r2841 | nphilippe | 2014-04-03 16:23:11 +0200 (jeu. 03 avril 2014) | 1 ligne
+
+fixed a warning
+------------------------------------------------------------------------
+r2840 | jaudoux | 2014-04-03 15:51:46 +0200 (jeu. 03 avril 2014) | 1 ligne
+
+We display multiple alignement in SAM only when support is not single
+------------------------------------------------------------------------
+r2839 | nphilippe | 2014-04-03 15:42:59 +0200 (jeu. 03 avril 2014) | 1 ligne
+
+decrease threshold for repetition
+------------------------------------------------------------------------
+r2838 | nphilippe | 2014-04-03 15:25:38 +0200 (jeu. 03 avril 2014) | 1 ligne
+
+add a function in SUpport to recond the max_nb_locs in nb_locs profile
+------------------------------------------------------------------------
+r2837 | jaudoux | 2014-04-03 14:47:15 +0200 (jeu. 03 avril 2014) | 1 ligne
+
+Add Repetition info to SAM output as 'XX' optional field
+------------------------------------------------------------------------
+r2836 | nphilippe | 2014-04-03 14:44:04 +0200 (jeu. 03 avril 2014) | 1 ligne
+
+remove condition for repetition
+------------------------------------------------------------------------
+r2835 | jaudoux | 2014-04-03 09:52:19 +0200 (jeu. 03 avril 2014) | 1 ligne
+
+Tlen sign depends on positions of the reads on forward strand not on paired-end identifiers
+------------------------------------------------------------------------
+r2834 | nphilippe | 2014-04-03 08:50:06 +0200 (jeu. 03 avril 2014) | 1 ligne
+
+We did not search fastq files in Makefile.am for the make distcheck...
+------------------------------------------------------------------------
+r2833 | nphilippe | 2014-04-03 08:37:45 +0200 (jeu. 03 avril 2014) | 1 ligne
+
+check, again.... fucking should_get
+------------------------------------------------------------------------
+r2832 | nphilippe | 2014-04-03 04:07:32 +0200 (jeu. 03 avril 2014) | 1 ligne
+
+test the should_get like that
+------------------------------------------------------------------------
+r2831 | nphilippe | 2014-04-02 18:47:16 +0200 (mer. 02 avril 2014) | 1 ligne
+
+first and second fragment are inversed
+------------------------------------------------------------------------
+r2830 | jaudoux | 2014-04-02 18:24:42 +0200 (mer. 02 avril 2014) | 1 ligne
+
+We were missing class 2 chimera in PE chimeras. I also shift PE flags 64 and 128
+------------------------------------------------------------------------
+r2829 | nphilippe | 2014-04-02 18:11:03 +0200 (mer. 02 avril 2014) | 1 ligne
+
+just change a regex to check if jenkins is fine
+------------------------------------------------------------------------
+r2828 | nphilippe | 2014-04-02 18:01:25 +0200 (mer. 02 avril 2014) | 1 ligne
+
+just change a regex to check if jenkins is fine
+------------------------------------------------------------------------
+r2827 | jaudoux | 2014-04-02 17:48:16 +0200 (mer. 02 avril 2014) | 1 ligne
+
+Add value TLEN field in SAM when we have paired-end reads
+------------------------------------------------------------------------
+r2826 | nphilippe | 2014-04-02 16:59:45 +0200 (mer. 02 avril 2014) | 1 ligne
+
+just a copy to test jenkins
+------------------------------------------------------------------------
+r2825 | jaudoux | 2014-04-02 15:46:08 +0200 (mer. 02 avril 2014) | 1 ligne
+
+Tests for bug [#16581]
+------------------------------------------------------------------------
+r2824 | jaudoux | 2014-04-02 15:11:48 +0200 (mer. 02 avril 2014) | 1 ligne
+
+Update optional fields and fix invalid read size in SamLine
+------------------------------------------------------------------------
+r2823 | nphilippe | 2014-04-02 15:07:58 +0200 (mer. 02 avril 2014) | 1 ligne
+
+replace antislash s by space in regex
+------------------------------------------------------------------------
+r2822 | nphilippe | 2014-04-02 11:59:27 +0200 (mer. 02 avril 2014) | 1 ligne
+
+exact mapping not only for DGE but for a reads factor of length k
+------------------------------------------------------------------------
+r2821 | nphilippe | 2014-04-02 11:53:14 +0200 (mer. 02 avril 2014) | 1 ligne
+
+upper case conversion for crac-emt
+------------------------------------------------------------------------
+r2820 | jaudoux | 2014-04-02 10:07:28 +0200 (mer. 02 avril 2014) | 1 ligne
+
+[efficiency] Use pointers and heap allocation to carry around SamLine objects instead of using object copy to the stack
+------------------------------------------------------------------------
+r2819 | nphilippe | 2014-04-01 18:10:33 +0200 (mar. 01 avril 2014) | 1 ligne
+
+add tests to check the consistency of new sam version
+------------------------------------------------------------------------
+r2818 | jaudoux | 2014-04-01 16:50:34 +0200 (mar. 01 avril 2014) | 1 ligne
+
+Add a bunch of new optional fields in SAM output for paired-end/mate, edit distance and remove X? fields for chimeric alignement when it's not the primary line
+------------------------------------------------------------------------
+r2817 | nphilippe | 2014-04-01 16:09:26 +0200 (mar. 01 avril 2014) | 1 ligne
+
+--emt with the possibility to map reads with a k-mer as a factor
+------------------------------------------------------------------------
+r2816 | nphilippe | 2014-04-01 14:54:51 +0200 (mar. 01 avril 2014) | 1 ligne
+
+getLocations return a pair<ChrPos **, uint> rather a ChrPos** and add a condition in hasRepeat function to check if the read is single
+------------------------------------------------------------------------
+r2815 | jaudoux | 2014-04-01 14:40:26 +0200 (mar. 01 avril 2014) | 1 ligne
+
+Set cigar once we are done with it
+------------------------------------------------------------------------
+r2814 | nphilippe | 2014-04-01 14:08:48 +0200 (mar. 01 avril 2014) | 1 ligne
+
+modify multiple nbLocations with setNbLocations was not a good idea
+------------------------------------------------------------------------
+r2813 | nphilippe | 2014-03-31 21:12:42 +0200 (lun. 31 mars 2014) | 1 ligne
+
+emt check memory leek
+------------------------------------------------------------------------
+r2812 | nphilippe | 2014-03-31 17:44:13 +0200 (lun. 31 mars 2014) | 1 ligne
+
+add missing files for compilation
+------------------------------------------------------------------------
+r2811 | nphilippe | 2014-03-31 17:43:57 +0200 (lun. 31 mars 2014) | 1 ligne
+
+add missing files for compilation
+------------------------------------------------------------------------
+r2810 | nphilippe | 2014-03-31 17:06:29 +0200 (lun. 31 mars 2014) | 1 ligne
+
+add multiples alignments in emt process
+------------------------------------------------------------------------
+r2809 | jaudoux | 2014-03-31 16:33:58 +0200 (lun. 31 mars 2014) | 1 ligne
+
+Code cleanup
+------------------------------------------------------------------------
+r2808 | nphilippe | 2014-03-31 10:11:18 +0200 (lun. 31 mars 2014) | 1 ligne
+
+fix 2 warnings
+------------------------------------------------------------------------
+r2800 | nphilippe | 2014-03-30 17:34:53 +0200 (dim. 30 mars 2014) | 1 ligne
+
+check leek
+------------------------------------------------------------------------
+r2799 | nphilippe | 2014-03-30 17:10:32 +0200 (dim. 30 mars 2014) | 1 ligne
+
+check leek
+------------------------------------------------------------------------
+r2798 | nphilippe | 2014-03-30 16:34:53 +0200 (dim. 30 mars 2014) | 1 ligne
+
+check leek
+------------------------------------------------------------------------
+r2797 | nphilippe | 2014-03-30 16:30:14 +0200 (dim. 30 mars 2014) | 1 ligne
+
+check leek
+------------------------------------------------------------------------
+r2796 | nphilippe | 2014-03-30 15:15:11 +0200 (dim. 30 mars 2014) | 1 ligne
+
+check leek
+------------------------------------------------------------------------
+r2795 | nphilippe | 2014-03-30 15:00:46 +0200 (dim. 30 mars 2014) | 1 ligne
+
+check leek
+------------------------------------------------------------------------
+r2794 | nphilippe | 2014-03-30 14:36:06 +0200 (dim. 30 mars 2014) | 1 ligne
+
+check leek
+------------------------------------------------------------------------
+r2793 | nphilippe | 2014-03-30 13:32:43 +0200 (dim. 30 mars 2014) | 1 ligne
+
+delete too many files
+------------------------------------------------------------------------
+r2792 | nphilippe | 2014-03-30 13:25:44 +0200 (dim. 30 mars 2014) | 1 ligne
+
+remove useless Makefile.in files
+------------------------------------------------------------------------
+r2788 | nphilippe | 2014-03-29 19:40:48 +0100 (sam. 29 mars 2014) | 1 ligne
+
+upgrade crac version
+------------------------------------------------------------------------
+r2787 | nphilippe | 2014-03-29 15:36:13 +0100 (sam. 29 mars 2014) | 1 ligne
+
+comment line [multiple.writeline(cout)]
+------------------------------------------------------------------------
+r2786 | nphilippe | 2014-03-29 15:05:02 +0100 (sam. 29 mars 2014) | 1 ligne
+
+streams were initialized two times with --all option
+------------------------------------------------------------------------
+r2785 | nphilippe | 2014-03-29 13:10:53 +0100 (sam. 29 mars 2014) | 1 ligne
+
+init sam_filename with --all
+------------------------------------------------------------------------
+r2784 | nphilippe | 2014-03-29 10:26:36 +0100 (sam. 29 mars 2014) | 1 ligne
+
+update a should get because we consider multiple aligments when the read is a duplication
+------------------------------------------------------------------------
+r2783 | nphilippe | 2014-03-29 10:20:11 +0100 (sam. 29 mars 2014) | 1 ligne
+
+consider multiple alignment when it is a duplication
+------------------------------------------------------------------------
+r2782 | nphilippe | 2014-03-28 19:43:00 +0100 (ven. 28 mars 2014) | 1 ligne
+
+update unit test with new SAM norm.
+------------------------------------------------------------------------
+r2781 | nphilippe | 2014-03-28 19:42:42 +0100 (ven. 28 mars 2014) | 1 ligne
+
+update unit test with new SAM norm.
+------------------------------------------------------------------------
+r2780 | nphilippe | 2014-03-28 16:57:59 +0100 (ven. 28 mars 2014) | 1 ligne
+
+last SAM version consistent (almost done)
+------------------------------------------------------------------------
+r2779 | jaudoux | 2014-03-28 11:30:51 +0100 (ven. 28 mars 2014) | 1 ligne
+
+[in progress] Correct paired-end flags, chimeric alignements in progress...
+------------------------------------------------------------------------
+r2778 | nphilippe | 2014-03-28 11:02:22 +0100 (ven. 28 mars 2014) | 1 ligne
+
+choose to display the most occurrences rather the less
+------------------------------------------------------------------------
+r2777 | jaudoux | 2014-03-28 10:39:01 +0100 (ven. 28 mars 2014) | 1 ligne
+
+Quality should not be defined unless we have a value for it
+------------------------------------------------------------------------
+r2776 | jaudoux | 2014-03-27 18:05:37 +0100 (jeu. 27 mars 2014) | 1 ligne
+
+Integration of new the SAM standart for chimeric alignements
+------------------------------------------------------------------------
+r2775 | salson | 2014-03-27 17:55:22 +0100 (jeu. 27 mars 2014) | 2 lignes
+
+Tests: Missing characters for regexp escape in should_get
+
+------------------------------------------------------------------------
+r2774 | salson | 2014-03-27 17:52:55 +0100 (jeu. 27 mars 2014) | 2 lignes
+
+Tests: should_get files now accept a e flag for exact match
+
+------------------------------------------------------------------------
+r2773 | nphilippe | 2014-03-27 16:03:46 +0100 (jeu. 27 mars 2014) | 1 ligne
+
+only getLocations until max-locs if there are more
+------------------------------------------------------------------------
+r2772 | nphilippe | 2014-03-27 13:26:23 +0100 (jeu. 27 mars 2014) | 1 ligne
+
+add getLocations in Support to manage multiple alignments
+------------------------------------------------------------------------
+r2771 | jaudoux | 2014-03-26 15:35:55 +0100 (mer. 26 mars 2014) | 1 ligne
+
+Problem fot bitset of unmapped PE reads corrected
+------------------------------------------------------------------------
+r2770 | jaudoux | 2014-03-26 14:40:28 +0100 (mer. 26 mars 2014) | 1 ligne
+
+isMapped function has been removed from samline, now please use isSegmentUnmapped that is linked to the corresponding flag of the samline
+------------------------------------------------------------------------
+r2769 | nphilippe | 2014-03-25 17:26:13 +0100 (mar. 25 mars 2014) | 1 ligne
+
+update sam standard [in progress]
+------------------------------------------------------------------------
+r2768 | jaudoux | 2014-03-25 17:11:46 +0100 (mar. 25 mars 2014) | 1 ligne
+
+[In progress] Integration of new SAM specifications
+------------------------------------------------------------------------
+r2767 | jaudoux | 2014-03-18 14:17:58 +0100 (mar. 18 mars 2014) | 1 ligne
+
+Correction to commit 2766
+------------------------------------------------------------------------
+r2766 | jaudoux | 2014-03-18 11:16:15 +0100 (mar. 18 mars 2014) | 1 ligne
+
+Add extended PE field to SAM file in order to indicate at the line of the first PE read the location type we have for the second one if it's mapped (uniqu,multi,dupli)
+------------------------------------------------------------------------
+r2765 | jaudoux | 2014-03-18 11:12:30 +0100 (mar. 18 mars 2014) | 1 ligne
+
+We were setting the reverse value for setIsMapped method
+------------------------------------------------------------------------
+r2764 | jaudoux | 2014-03-18 10:54:44 +0100 (mar. 18 mars 2014) | 1 ligne
+
+Update version micro number
+------------------------------------------------------------------------
+r2763 | jaudoux | 2014-03-18 10:37:29 +0100 (mar. 18 mars 2014) | 1 ligne
+
+bad initialisation of read quality in tagInfo.cpp. The char array was too small and an overlapping in the strncpy copy function was occuring. As a result, strange caracters were appearing at the end of the quality field in the SAM file
+------------------------------------------------------------------------
+r2758 | salson | 2014-01-31 17:53:44 +0100 (ven. 31 janv. 2014) | 5 lignes
+
+CRAC: Version 1.4.1
+
+- Small memory leak corrected in crac-index
+- Bug #16931 addressed (XO field was not correct in some condition)
+
+------------------------------------------------------------------------
+r2757 | salson | 2014-01-31 17:48:50 +0100 (ven. 31 janv. 2014) | 4 lignes
+
+CracIndex: Small memory leak in function get()
+
+GenomeInfo was instantiated but never deleted.
+
+------------------------------------------------------------------------
+r2756 | salson | 2014-01-31 17:34:51 +0100 (ven. 31 janv. 2014) | 4 lignes
+
+CRAC: Correction of bug #16931 reported by M. Hebrard
+
+In some conditions, we were having loc and loc_to_display that were identical (when we just have undetermined breaks).
+Modifying loc_to_display to make it start just after the undetermined break was also modifying loc since they were poiting to the same location. This is corrected. In that case before modifying loc_to_display, we make sure to copy the ChrPosition.
+------------------------------------------------------------------------
+r2752 | jaudoux | 2013-12-18 15:09:55 +0100 (mer. 18 déc. 2013) | 1 ligne
+
+Correct bug [#16807] inconsistency between seq length and quality length in sam file using -m argument
+------------------------------------------------------------------------
+r2747 | nphilippe | 2013-12-11 15:32:26 +0100 (mer. 11 déc. 2013) | 1 ligne
+
+bug fixed fake tty caused bad display of progressBar
+------------------------------------------------------------------------
+r2746 | salson | 2013-12-06 16:20:18 +0100 (ven. 06 déc. 2013) | 1 ligne
+
+Crac: Add tests on genome indexing and retrieval
+------------------------------------------------------------------------
+r2745 | salson | 2013-12-06 16:06:46 +0100 (ven. 06 déc. 2013) | 4 lignes
+
+CRAC-index: Use Dna5 string rather than char
+
+Hence characters different from ACGTN are converted to N.
+
+------------------------------------------------------------------------
+r2744 | salson | 2013-12-06 15:07:57 +0100 (ven. 06 déc. 2013) | 5 lignes
+
+Crac-index: Command get was not working properly with multiple sequences.
+
+There was only one counter for taking into account positions (the position inside the sequence).
+However we need to also record the position inside the global sequence (the concatenation of sequences),
+so that we don't always start the extraction from the start of the global sequence.
+------------------------------------------------------------------------
+r2743 | nphilippe | 2013-12-05 19:39:37 +0100 (jeu. 05 déc. 2013) | 1 ligne
+
+progressBar not by default
+------------------------------------------------------------------------
+r2739 | mancheron | 2013-11-29 19:08:37 +0100 (ven. 29 nov. 2013) | 1 ligne
+
+
+------------------------------------------------------------------------
+r2738 | mancheron | 2013-11-29 19:07:04 +0100 (ven. 29 nov. 2013) | 5 lignes
+
+Updating libProgressBar library.
+Enhance display.
+Remove pkg-config usage to detect library since some people dislike it.
+
+
+------------------------------------------------------------------------
+r2733 | mancheron | 2013-11-28 17:55:30 +0100 (jeu. 28 nov. 2013) | 1 ligne
+
+
+------------------------------------------------------------------------
+r2732 | mancheron | 2013-11-28 17:54:44 +0100 (jeu. 28 nov. 2013) | 2 lignes
+
+Adding Progress Bar.
+
+------------------------------------------------------------------------
+r2726 | mancheron | 2013-11-28 16:51:48 +0100 (jeu. 28 nov. 2013) | 2 lignes
+
+Bug Fix: intel compiler already has __int64 type.
+
+------------------------------------------------------------------------
+r2642 | jaudoux | 2013-10-22 17:26:13 +0200 (mar. 22 oct. 2013) | 1 ligne
+
+Update nb_merges const from --strigent-chimera option to be little less stringent
+------------------------------------------------------------------------
+r2633 | jaudoux | 2013-10-17 14:47:27 +0200 (jeu. 17 oct. 2013) | 1 ligne
+
+hasChimera was indeed hasSpliceInterChr, this name should be updataded one day
+------------------------------------------------------------------------
+r2632 | jaudoux | 2013-10-17 13:54:09 +0200 (jeu. 17 oct. 2013) | 1 ligne
+
+Add Paired-end chimeras information to the SAM and correct paired-end chimera detections to avoid PE reads when one of the read span a chimera
+------------------------------------------------------------------------
+r2622 | nphilippe | 2013-10-15 10:15:58 +0200 (mar. 15 oct. 2013) | 1 ligne
+
+formatting summary
+------------------------------------------------------------------------
+r2576 | nphilippe | 2013-10-03 20:07:22 +0200 (jeu. 03 oct. 2013) | 1 ligne
+
+restablish bug-15672-genome.fa and change the regex in should get because the correction about max_extension_length in SupportBreak
+------------------------------------------------------------------------
+r2575 | nphilippe | 2013-10-03 16:37:32 +0200 (jeu. 03 oct. 2013) | 1 ligne
+
+just a probleme in bug-15646-genome.fa
+------------------------------------------------------------------------
+r2572 | nphilippe | 2013-10-02 10:46:09 +0200 (mer. 02 oct. 2013) | 1 ligne
+
+make a fullhelp lite-version, details are described in man page
+------------------------------------------------------------------------
+r2571 | nphilippe | 2013-10-02 08:54:22 +0200 (mer. 02 oct. 2013) | 1 ligne
+
+change condition to allow an extension until max_extension_length instead of max_extension_length-1
+------------------------------------------------------------------------
+r2570 | jaudoux | 2013-10-01 18:52:11 +0200 (mar. 01 oct. 2013) | 1 ligne
+
+Less tests before writing paired-end chimeras, only asked for both paired-end reads to be single
+------------------------------------------------------------------------
+r2567 | nphilippe | 2013-09-30 17:27:49 +0200 (lun. 30 sept. 2013) | 1 ligne
+
+update doc and man page
+------------------------------------------------------------------------
diff --git a/INSTALL b/INSTALL
new file mode 100644
index 0000000..7d1c323
--- /dev/null
+++ b/INSTALL
@@ -0,0 +1,365 @@
+Installation Instructions
+*************************
+
+Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005,
+2006, 2007, 2008, 2009 Free Software Foundation, Inc.
+
+ Copying and distribution of this file, with or without modification,
+are permitted in any medium without royalty provided the copyright
+notice and this notice are preserved. This file is offered as-is,
+without warranty of any kind.
+
+Basic Installation
+==================
+
+ Briefly, the shell commands `./configure; make; make install' should
+configure, build, and install this package. The following
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+in *note Makefile Conventions: (standards)Makefile Conventions.
+
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+Compilers and Options
+=====================
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+
+ ./configure CC=c99 CFLAGS=-g LIBS=-lposix
+
+ *Note Defining Variables::, for more details.
+
+Compiling For Multiple Architectures
+====================================
+
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+
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+==================
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+=================
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+
+Particular systems
+==================
+
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+
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+
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+
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+
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+
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+
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+
+Specifying the System Type
+==========================
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+
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+================
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+
+Defining Variables
+==================
+
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+
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+an Autoconf bug. Until the bug is fixed you can use this workaround:
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+ CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash
+
+`configure' Invocation
+======================
+
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+
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+
+`--config-cache'
+`-C'
+ Alias for `--cache-file=config.cache'.
+
+`--quiet'
+`--silent'
+`-q'
+ Do not print messages saying which checks are being made. To
+ suppress all normal output, redirect it to `/dev/null' (any error
+ messages will still be shown).
+
+`--srcdir=DIR'
+ Look for the package's source code in directory DIR. Usually
+ `configure' can determine that directory automatically.
+
+`--prefix=DIR'
+ Use DIR as the installation prefix. *note Installation Names::
+ for more details, including other options available for fine-tuning
+ the installation locations.
+
+`--no-create'
+`-n'
+ Run the configure checks, but stop before creating any output
+ files.
+
+`configure' also accepts some other, not widely useful, options. Run
+`configure --help' for more details.
+
diff --git a/Makefile.am b/Makefile.am
new file mode 100644
index 0000000..4afad62
--- /dev/null
+++ b/Makefile.am
@@ -0,0 +1,202 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+
+SUBDIRS = src man scripts test_f
+if BUILD_DOC
+ SUBDIRS += doc
+endif
+
+# uncomment the following if crac requires the math library
+#crac_LDADD=-lm
+
+EXTRA_DIST= @PACKAGE at .lsm.in @PACKAGE at .spec.in control.in AUTHORS COPYING ChangeLog INSTALL NEWS README
+# dist-hook:
+# rm -rf `find $(distdir) -type d -name .svn`
+
+valgrindcheck:
+ LAUNCHER='eval valgrind --tool=memcheck --suppressions=$(abs_top_srcdir)/test_f/valgrind.supp --leak-check=full --show-reachable=yes --undef-value-errors=yes --track-origins=yes --xml=yes --xml-file=$$(mktemp --tmpdir=. --suffix=.valgrind)' make check
+
+
+deb: @PACKAGE at _@PACKAGE_VERSION at _@ARCH at .deb
+
+
+
+always-build:
+
+ at PACKAGE@_ at PACKAGE_VERSION@_ at ARCH@.deb: always-build
+ @if [ "@DEB_BUILDER@" == "" ]; then \
+ echo "You need to install a debian package builder and to reconfigure this package.";\
+ exit 1;\
+ fi
+ $(MAKE) dist
+ $(am__remove_distdir)
+ GZIP=$(GZIP_ENV) gunzip -c $(distdir).tar.gz | $(AMTAR) xf -
+ mkdir $(distdir)/_build
+ mkdir -p $(distdir)/_inst/_deb/$(prefix)
+ chmod a-w $(distdir)
+ dc_install_base=`$(am__cd) $(distdir)/_inst/_deb/$(prefix) && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
+ && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
+ && cd $(distdir)/_build \
+ && localedir=$(datadir)/locale \
+ && ../configure --srcdir=.. --prefix="$$dc_install_base" \
+ --enable-static --disable-shared $(DEB_OPT) \
+ $(DISTCHECK_CONFIGURE_FLAGS) \
+ && $(MAKE) $(AM_MAKEFLAGS) localedir=$$localedir \
+ && $(MAKE) $(AM_MAKEFLAGS) dvi \
+ && $(MAKE) $(AM_MAKEFLAGS) check \
+ && $(MAKE) $(AM_MAKEFLAGS) install \
+ && $(MAKE) $(AM_MAKEFLAGS) installcheck \
+ && cd src/libGkArrays \
+ && $(MAKE) $(AM_MAKEFLAGS) uninstall \
+ && cd ../../ \
+ && cd ../_inst/_deb \
+ && find . -depth -type d -empty -exec rmdir {} \; \
+ && find . -type f -exec md5sum {} \; | sed "s,\.\/,,g" > ../md5sums \
+ && mkdir DEBIAN \
+ && mv ../md5sums DEBIAN/ \
+ && sed "s,^\(Installed-Size:.*\)0$$,\1$$(du -sk $$dc_install_base/ | cut -f1)," ../../_build/control > DEBIAN/control \
+ && cd ../ \
+ && dpkg -b _deb $@ \
+ && mv $@ ../../ \
+ && cd ../_build/src/libGkArrays \
+ && $(MAKE) $(AM_MAKEFLAGS) install \
+ && cd ../../ \
+ && cd ../_build \
+ && $(MAKE) $(AM_MAKEFLAGS) uninstall \
+ && $(MAKE) $(AM_MAKEFLAGS) distuninstallcheck_dir="$$dc_install_base" \
+ distuninstallcheck \
+ && chmod -R a-w "$$dc_install_base" \
+ && ({ \
+ (cd ../.. && $(mkinstalldirs) "$$dc_destdir") \
+ && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" install \
+ && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" uninstall \
+ && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" \
+ distuninstallcheck_dir="$$dc_destdir" distuninstallcheck; \
+ } || { rm -rf "$$dc_destdir"; exit 1; }) \
+ && rm -rf "$$dc_destdir" \
+ && $(MAKE) $(AM_MAKEFLAGS) distcleancheck
+ $(am__remove_distdir)
+ @echo "$@ is ready for distribution" | \
+ sed 'h;s/./=/g;p;x;p;x'
+
+rpm: always-build
+ @if [ "@RPM_BUILDER@" == "" ]; then \
+ echo "You need to install a rpm package builder and to reconfigure this package.";\
+ exit 1;\
+ fi
+ $(MAKE) dist
+ $(am__remove_distdir)
+ - rm -rf $(distdir)/_build/rpm/BUILD/
+ - rm -rf $(distdir)/_build/rpm/RPMS/
+ - rm -rf $(distdir)/_build/rpm/SRPMS/
+ - rm -rf $(distdir)/_build/rpm/SOURCES/
+ mkdir -p $(distdir)/_build/rpm/SOURCES
+ cp $(distdir).tar.gz $(distdir)/_build/rpm/SOURCES/
+ @RPM_BUILDER@ --quiet --nodeps --define="_topdir "$$(pwd)"/$(distdir)/_build/rpm" \
+ -bb crac.spec
+ mv $(distdir)/_build/rpm/RPMS/*/*.rpm .
+
+MOSTLYCLEANFILES=*~
+CLEANFILES=*~
+DISTCLEANFILES=*~ control $(distdir).tar.gz
+DISTCLEANFILES+=@PACKAGE at _@PACKAGE_VERSION at _@ARCH at .deb *.rpm
+MAINTAINERCLEANFILES=*~
+
+ACLOCAL_AMFLAGS = -I config/m4
diff --git a/Makefile.in b/Makefile.in
new file mode 100644
index 0000000..3edeb4b
--- /dev/null
+++ b/Makefile.in
@@ -0,0 +1,930 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
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+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
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+ at BUILD_DOC_TRUE@am__append_1 = doc
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+ $(srcdir)/Makefile.in $(srcdir)/control.in \
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+ config/config.guess config/config.sub config/depcomp \
+ config/install-sh config/ltmain.sh config/missing \
+ config/texinfo.tex
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
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+ETAGS = etags
+CTAGS = ctags
+DIST_SUBDIRS = src man scripts test_f doc
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+distdir = $(PACKAGE)-$(VERSION)
+top_distdir = $(distdir)
+am__remove_distdir = \
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+ || { find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \
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+am__relativize = \
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+ *k*) failcom='fail=yes';; \
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+ || exit 1; \
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+ && cd "$$am__cwd" \
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+ && test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \
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+html-am:
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+install-ps: install-ps-recursive
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+ distcheck distclean distclean-generic distclean-hdr \
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+ distuninstallcheck dvi dvi-am html html-am info info-am \
+ install install-am install-data install-data-am install-dvi \
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+
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+ && cd ../../ \
+ && cd ../_inst/_deb \
+ && find . -depth -type d -empty -exec rmdir {} \; \
+ && find . -type f -exec md5sum {} \; | sed "s,\.\/,,g" > ../md5sums \
+ && mkdir DEBIAN \
+ && mv ../md5sums DEBIAN/ \
+ && sed "s,^\(Installed-Size:.*\)0$$,\1$$(du -sk $$dc_install_base/ | cut -f1)," ../../_build/control > DEBIAN/control \
+ && cd ../ \
+ && dpkg -b _deb $@ \
+ && mv $@ ../../ \
+ && cd ../_build/src/libGkArrays \
+ && $(MAKE) $(AM_MAKEFLAGS) install \
+ && cd ../../ \
+ && cd ../_build \
+ && $(MAKE) $(AM_MAKEFLAGS) uninstall \
+ && $(MAKE) $(AM_MAKEFLAGS) distuninstallcheck_dir="$$dc_install_base" \
+ distuninstallcheck \
+ && chmod -R a-w "$$dc_install_base" \
+ && ({ \
+ (cd ../.. && $(mkinstalldirs) "$$dc_destdir") \
+ && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" install \
+ && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" uninstall \
+ && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" \
+ distuninstallcheck_dir="$$dc_destdir" distuninstallcheck; \
+ } || { rm -rf "$$dc_destdir"; exit 1; }) \
+ && rm -rf "$$dc_destdir" \
+ && $(MAKE) $(AM_MAKEFLAGS) distcleancheck
+ $(am__remove_distdir)
+ @echo "$@ is ready for distribution" | \
+ sed 'h;s/./=/g;p;x;p;x'
+
+rpm: always-build
+ @if [ "@RPM_BUILDER@" == "" ]; then \
+ echo "You need to install a rpm package builder and to reconfigure this package.";\
+ exit 1;\
+ fi
+ $(MAKE) dist
+ $(am__remove_distdir)
+ - rm -rf $(distdir)/_build/rpm/BUILD/
+ - rm -rf $(distdir)/_build/rpm/RPMS/
+ - rm -rf $(distdir)/_build/rpm/SRPMS/
+ - rm -rf $(distdir)/_build/rpm/SOURCES/
+ mkdir -p $(distdir)/_build/rpm/SOURCES
+ cp $(distdir).tar.gz $(distdir)/_build/rpm/SOURCES/
+ @RPM_BUILDER@ --quiet --nodeps --define="_topdir "$$(pwd)"/$(distdir)/_build/rpm" \
+ -bb crac.spec
+ mv $(distdir)/_build/rpm/RPMS/*/*.rpm .
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/NEWS b/NEWS
new file mode 100644
index 0000000..e69de29
diff --git a/README b/README
new file mode 100644
index 0000000..9e5ba43
--- /dev/null
+++ b/README
@@ -0,0 +1,134 @@
+crac - Package
+
+CRAC is a tool to analyze High Throughput Sequencing (HTS) data in
+comparison to a reference genome. It is intended for transcriptomic
+and genomic sequencing reads. More precisely, with transcriptomic
+reads as input, it predicts point mutations, indels, splice junction,
+and chimeric RNAs (ie, non colinear splice junctions). CRAC can also
+output positions and nature of sequence error that it detects in the
+reads. CRAC uses a genome index. This index must be computed before
+running the read analysis. For this sake, use the command "crac-index"
+on your genome files. You can then process the reads using the command
+crac. See the man page of CRAC (help file) by typing "man crac". CRAC
+requires large amount of main memory on your computer. For processing
+against the Human genome, say 50 million reads of 100 nucleotide each,
+CRAC requires about 40 gigabytes of main memory. Check whether the
+system of your computing server is equipped with sufficient amount of
+memory before launching an analysis.
+
+crac - Source code
+
+CRAC is freely available under a GPL-compliant CeCILL license. The
+distribution comes as an archive (a gzipped tarball file .tar.gz)
+containing the source code.
+
+crac - Installation
+
+1) Unpack the archive
+2) Enter the directory crac-version-number
+3) Type ./configure
+4) If everything went fine, run make
+5) You may want to check everything is ok by running make check
+6) Finally, you can install the software on your system by running make install
+
+If the configure step failed, that may be due to a missing library. In particular the zlib is needed. On a Debian or Debian-like system, you'll need to install zlib1g, zlib1g-dev.
+
+After the compilation succeded you can find a more complete documentation
+inside the doc directory and a man page is also available.
+
+-------------------------------------------------------------------------
+
+ Copyright © 2010-2013 -- IRB/INSERM
+ (Institut de Recherches en Biothérapie /
+ Institut National de la Santé et de la Recherche
+ Médicale)
+ LIFL/INRIA
+ (Laboratoire d'Informatique Fondamentale de
+ Lille / Institut National de Recherche en
+ Informatique et Automatique)
+ LIRMM/CNRS
+ (Laboratoire d'Informatique, de Robotique et de
+ Microélectronique de Montpellier /
+ Centre National de la Recherche Scientifique)
+ LITIS
+ (Laboratoire d'Informatique, du Traitement de
+ l'Information et des Systèmes).
+
+ Auteurs/Authors:
+ Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+ Mikaël SALSON <mikael.salson at lifl.fr>
+ Thérèse COMMES <commes at univ-montp2.fr>
+ Éric RIVALS <eric.rivals at lirmm.fr>
+
+ Programmeurs
+ /Progammers:
+ Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+ Mikaël SALSON <mikael.salson at lifl.fr>
+ with additional contribution for the packaging of:
+ Alban MANCHERON <alban.mancheron at lirmm.fr>
+
+ Contact: CRAC list <crac-bugs at lists.gforge.inria.fr>
+ -------------------------------------------------------------------------
+
+ Ce fichier fait partie du programme CRAC.
+
+ Ce logiciel est régi par la licence CeCILL soumise au droit français et
+ respectant les principes de diffusion des logiciels libres. Vous pouvez
+ utiliser, modifier et/ou redistribuer ce programme sous les conditions de
+ la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur
+ le site "http://www.cecill.info".
+
+ En contrepartie de l'accessibilité au code source et des droits de copie,
+ de modification et de redistribution accordés par cette licence, il n'est
+ offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons,
+ seule une responsabilité restreinte pèse sur l'auteur du programme, le
+ titulaire des droits patrimoniaux et les concédants successifs.
+
+ À cet égard l'attention de l'utilisateur est attirée sur les risques
+ associés au chargement, à l'utilisation, à la modification et/ou au
+ développement et à la reproduction du logiciel par l'utilisateur étant
+ donné sa spécificité de logiciel libre, qui peut le rendre complexe à
+ manipuler et qui le réserve donc à des développeurs et des professionnels
+ avertis possédant des connaissances informatiques approfondies. Les
+ utilisateurs sont donc invités à charger et tester l'adéquation du
+ logiciel à leurs besoins dans des conditions permettant d'assurer la
+ sécurité de leurs systêmes et ou de leurs données et, plus généralement,
+ à l'utiliser et l'exploiter dans les mêmes conditions de sécurité.
+
+ Le fait que vous puissiez accéder à cet en-tête signifie que vous avez
+ pris connaissance de la licence CeCILL, et que vous en avez accepté les
+ termes.
+
+ -------------------------------------------------------------------------
+
+ This File is part of the CRAC program.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the same
+ conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+
+-------------------------------------------------------------------------
+
+Les commentaires sont les bienvenus/Comments are welcome.
diff --git a/aclocal.m4 b/aclocal.m4
new file mode 100644
index 0000000..c5edfb1
--- /dev/null
+++ b/aclocal.m4
@@ -0,0 +1,8917 @@
+# generated automatically by aclocal 1.11.1 -*- Autoconf -*-
+
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
+# 2005, 2006, 2007, 2008, 2009 Free Software Foundation, Inc.
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+m4_ifndef([AC_AUTOCONF_VERSION],
+ [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
+m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.67],,
+[m4_warning([this file was generated for autoconf 2.67.
+You have another version of autoconf. It may work, but is not guaranteed to.
+If you have problems, you may need to regenerate the build system entirely.
+To do so, use the procedure documented by the package, typically `autoreconf'.])])
+
+# libtool.m4 - Configure libtool for the host system. -*-Autoconf-*-
+#
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
+# 2006, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gordon Matzigkeit, 1996
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+m4_define([_LT_COPYING], [dnl
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
+# 2006, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gordon Matzigkeit, 1996
+#
+# This file is part of GNU Libtool.
+#
+# GNU Libtool is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License as
+# published by the Free Software Foundation; either version 2 of
+# the License, or (at your option) any later version.
+#
+# As a special exception to the GNU General Public License,
+# if you distribute this file as part of a program or library that
+# is built using GNU Libtool, you may include this file under the
+# same distribution terms that you use for the rest of that program.
+#
+# GNU Libtool is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GNU Libtool; see the file COPYING. If not, a copy
+# can be downloaded from http://www.gnu.org/licenses/gpl.html, or
+# obtained by writing to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+])
+
+# serial 56 LT_INIT
+
+
+# LT_PREREQ(VERSION)
+# ------------------
+# Complain and exit if this libtool version is less that VERSION.
+m4_defun([LT_PREREQ],
+[m4_if(m4_version_compare(m4_defn([LT_PACKAGE_VERSION]), [$1]), -1,
+ [m4_default([$3],
+ [m4_fatal([Libtool version $1 or higher is required],
+ 63)])],
+ [$2])])
+
+
+# _LT_CHECK_BUILDDIR
+# ------------------
+# Complain if the absolute build directory name contains unusual characters
+m4_defun([_LT_CHECK_BUILDDIR],
+[case `pwd` in
+ *\ * | *\ *)
+ AC_MSG_WARN([Libtool does not cope well with whitespace in `pwd`]) ;;
+esac
+])
+
+
+# LT_INIT([OPTIONS])
+# ------------------
+AC_DEFUN([LT_INIT],
+[AC_PREREQ([2.58])dnl We use AC_INCLUDES_DEFAULT
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+AC_BEFORE([$0], [LT_OUTPUT])dnl
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+dnl unless we require an AC_DEFUNed macro:
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+AC_REQUIRE([LTSUGAR_VERSION])dnl
+AC_REQUIRE([LTVERSION_VERSION])dnl
+AC_REQUIRE([LTOBSOLETE_VERSION])dnl
+m4_require([_LT_PROG_LTMAIN])dnl
+
+dnl Parse OPTIONS
+_LT_SET_OPTIONS([$0], [$1])
+
+# This can be used to rebuild libtool when needed
+LIBTOOL_DEPS="$ltmain"
+
+# Always use our own libtool.
+LIBTOOL='$(SHELL) $(top_builddir)/libtool'
+AC_SUBST(LIBTOOL)dnl
+
+_LT_SETUP
+
+# Only expand once:
+m4_define([LT_INIT])
+])# LT_INIT
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+# Old names:
+AU_ALIAS([AC_PROG_LIBTOOL], [LT_INIT])
+AU_ALIAS([AM_PROG_LIBTOOL], [LT_INIT])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_PROG_LIBTOOL], [])
+dnl AC_DEFUN([AM_PROG_LIBTOOL], [])
+
+
+# _LT_CC_BASENAME(CC)
+# -------------------
+# Calculate cc_basename. Skip known compiler wrappers and cross-prefix.
+m4_defun([_LT_CC_BASENAME],
+[for cc_temp in $1""; do
+ case $cc_temp in
+ compile | *[[\\/]]compile | ccache | *[[\\/]]ccache ) ;;
+ distcc | *[[\\/]]distcc | purify | *[[\\/]]purify ) ;;
+ \-*) ;;
+ *) break;;
+ esac
+done
+cc_basename=`$ECHO "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+])
+
+
+# _LT_FILEUTILS_DEFAULTS
+# ----------------------
+# It is okay to use these file commands and assume they have been set
+# sensibly after `m4_require([_LT_FILEUTILS_DEFAULTS])'.
+m4_defun([_LT_FILEUTILS_DEFAULTS],
+[: ${CP="cp -f"}
+: ${MV="mv -f"}
+: ${RM="rm -f"}
+])# _LT_FILEUTILS_DEFAULTS
+
+
+# _LT_SETUP
+# ---------
+m4_defun([_LT_SETUP],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+AC_REQUIRE([AC_CANONICAL_BUILD])dnl
+_LT_DECL([], [host_alias], [0], [The host system])dnl
+_LT_DECL([], [host], [0])dnl
+_LT_DECL([], [host_os], [0])dnl
+dnl
+_LT_DECL([], [build_alias], [0], [The build system])dnl
+_LT_DECL([], [build], [0])dnl
+_LT_DECL([], [build_os], [0])dnl
+dnl
+AC_REQUIRE([AC_PROG_CC])dnl
+AC_REQUIRE([LT_PATH_LD])dnl
+AC_REQUIRE([LT_PATH_NM])dnl
+dnl
+AC_REQUIRE([AC_PROG_LN_S])dnl
+test -z "$LN_S" && LN_S="ln -s"
+_LT_DECL([], [LN_S], [1], [Whether we need soft or hard links])dnl
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+AC_REQUIRE([LT_CMD_MAX_LEN])dnl
+_LT_DECL([objext], [ac_objext], [0], [Object file suffix (normally "o")])dnl
+_LT_DECL([], [exeext], [0], [Executable file suffix (normally "")])dnl
+dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_CHECK_SHELL_FEATURES])dnl
+m4_require([_LT_CMD_RELOAD])dnl
+m4_require([_LT_CHECK_MAGIC_METHOD])dnl
+m4_require([_LT_CMD_OLD_ARCHIVE])dnl
+m4_require([_LT_CMD_GLOBAL_SYMBOLS])dnl
+
+_LT_CONFIG_LIBTOOL_INIT([
+# See if we are running on zsh, and set the options which allow our
+# commands through without removal of \ escapes INIT.
+if test -n "\${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+fi
+])
+if test -n "${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+fi
+
+_LT_CHECK_OBJDIR
+
+m4_require([_LT_TAG_COMPILER])dnl
+_LT_PROG_ECHO_BACKSLASH
+
+case $host_os in
+aix3*)
+ # AIX sometimes has problems with the GCC collect2 program. For some
+ # reason, if we set the COLLECT_NAMES environment variable, the problems
+ # vanish in a puff of smoke.
+ if test "X${COLLECT_NAMES+set}" != Xset; then
+ COLLECT_NAMES=
+ export COLLECT_NAMES
+ fi
+ ;;
+esac
+
+# Sed substitution that helps us do robust quoting. It backslashifies
+# metacharacters that are still active within double-quoted strings.
+sed_quote_subst='s/\([["`$\\]]\)/\\\1/g'
+
+# Same as above, but do not quote variable references.
+double_quote_subst='s/\([["`\\]]\)/\\\1/g'
+
+# Sed substitution to delay expansion of an escaped shell variable in a
+# double_quote_subst'ed string.
+delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g'
+
+# Sed substitution to delay expansion of an escaped single quote.
+delay_single_quote_subst='s/'\''/'\'\\\\\\\'\''/g'
+
+# Sed substitution to avoid accidental globbing in evaled expressions
+no_glob_subst='s/\*/\\\*/g'
+
+# Global variables:
+ofile=libtool
+can_build_shared=yes
+
+# All known linkers require a `.a' archive for static linking (except MSVC,
+# which needs '.lib').
+libext=a
+
+with_gnu_ld="$lt_cv_prog_gnu_ld"
+
+old_CC="$CC"
+old_CFLAGS="$CFLAGS"
+
+# Set sane defaults for various variables
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+test -z "$ac_objext" && ac_objext=o
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+_LT_CC_BASENAME([$compiler])
+
+# Only perform the check for file, if the check method requires it
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+file_magic*)
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+ fi
+ ;;
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+
+# Use C for the default configuration in the libtool script
+LT_SUPPORTED_TAG([CC])
+_LT_LANG_C_CONFIG
+_LT_LANG_DEFAULT_CONFIG
+_LT_CONFIG_COMMANDS
+])# _LT_SETUP
+
+
+# _LT_PROG_LTMAIN
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+])# _LT_PROG_LTMAIN
+
+
+
+# So that we can recreate a full libtool script including additional
+# tags, we accumulate the chunks of code to send to AC_CONFIG_COMMANDS
+# in macros and then make a single call at the end using the `libtool'
+# label.
+
+
+# _LT_CONFIG_LIBTOOL_INIT([INIT-COMMANDS])
+# ----------------------------------------
+# Register INIT-COMMANDS to be passed to AC_CONFIG_COMMANDS later.
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+ [m4_append([_LT_OUTPUT_LIBTOOL_INIT],
+ [$1
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+# Initialize.
+m4_define([_LT_OUTPUT_LIBTOOL_INIT])
+
+
+# _LT_CONFIG_LIBTOOL([COMMANDS])
+# ------------------------------
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+m4_define([_LT_OUTPUT_LIBTOOL_COMMANDS])
+
+
+# _LT_CONFIG_SAVE_COMMANDS([COMMANDS], [INIT_COMMANDS])
+# -----------------------------------------------------
+m4_defun([_LT_CONFIG_SAVE_COMMANDS],
+[_LT_CONFIG_LIBTOOL([$1])
+_LT_CONFIG_LIBTOOL_INIT([$2])
+])
+
+
+# _LT_FORMAT_COMMENT([COMMENT])
+# -----------------------------
+# Add leading comment marks to the start of each line, and a trailing
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+m4_bpatsubst([m4_bpatsubst([$1], [^ *], [# ])],
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+)])
+
+
+
+
+
+# _LT_DECL([CONFIGNAME], VARNAME, VALUE, [DESCRIPTION], [IS-TAGGED?])
+# -------------------------------------------------------------------
+# CONFIGNAME is the name given to the value in the libtool script.
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+# VARNAME. Any other value will be used directly.
+m4_define([_LT_DECL],
+[lt_if_append_uniq([lt_decl_varnames], [$2], [, ],
+ [lt_dict_add_subkey([lt_decl_dict], [$2], [libtool_name],
+ [m4_ifval([$1], [$1], [$2])])
+ lt_dict_add_subkey([lt_decl_dict], [$2], [value], [$3])
+ m4_ifval([$4],
+ [lt_dict_add_subkey([lt_decl_dict], [$2], [description], [$4])])
+ lt_dict_add_subkey([lt_decl_dict], [$2],
+ [tagged?], [m4_ifval([$5], [yes], [no])])])
+])
+
+
+# _LT_TAGDECL([CONFIGNAME], VARNAME, VALUE, [DESCRIPTION])
+# --------------------------------------------------------
+m4_define([_LT_TAGDECL], [_LT_DECL([$1], [$2], [$3], [$4], [yes])])
+
+
+# lt_decl_tag_varnames([SEPARATOR], [VARNAME1...])
+# ------------------------------------------------
+m4_define([lt_decl_tag_varnames],
+[_lt_decl_filter([tagged?], [yes], $@)])
+
+
+# _lt_decl_filter(SUBKEY, VALUE, [SEPARATOR], [VARNAME1..])
+# ---------------------------------------------------------
+m4_define([_lt_decl_filter],
+[m4_case([$#],
+ [0], [m4_fatal([$0: too few arguments: $#])],
+ [1], [m4_fatal([$0: too few arguments: $#: $1])],
+ [2], [lt_dict_filter([lt_decl_dict], [$1], [$2], [], lt_decl_varnames)],
+ [3], [lt_dict_filter([lt_decl_dict], [$1], [$2], [$3], lt_decl_varnames)],
+ [lt_dict_filter([lt_decl_dict], $@)])[]dnl
+])
+
+
+# lt_decl_quote_varnames([SEPARATOR], [VARNAME1...])
+# --------------------------------------------------
+m4_define([lt_decl_quote_varnames],
+[_lt_decl_filter([value], [1], $@)])
+
+
+# lt_decl_dquote_varnames([SEPARATOR], [VARNAME1...])
+# ---------------------------------------------------
+m4_define([lt_decl_dquote_varnames],
+[_lt_decl_filter([value], [2], $@)])
+
+
+# lt_decl_varnames_tagged([SEPARATOR], [VARNAME1...])
+# ---------------------------------------------------
+m4_define([lt_decl_varnames_tagged],
+[m4_assert([$# <= 2])dnl
+_$0(m4_quote(m4_default([$1], [[, ]])),
+ m4_ifval([$2], [[$2]], [m4_dquote(lt_decl_tag_varnames)]),
+ m4_split(m4_normalize(m4_quote(_LT_TAGS)), [ ]))])
+m4_define([_lt_decl_varnames_tagged],
+[m4_ifval([$3], [lt_combine([$1], [$2], [_], $3)])])
+
+
+# lt_decl_all_varnames([SEPARATOR], [VARNAME1...])
+# ------------------------------------------------
+m4_define([lt_decl_all_varnames],
+[_$0(m4_quote(m4_default([$1], [[, ]])),
+ m4_if([$2], [],
+ m4_quote(lt_decl_varnames),
+ m4_quote(m4_shift($@))))[]dnl
+])
+m4_define([_lt_decl_all_varnames],
+[lt_join($@, lt_decl_varnames_tagged([$1],
+ lt_decl_tag_varnames([[, ]], m4_shift($@))))dnl
+])
+
+
+# _LT_CONFIG_STATUS_DECLARE([VARNAME])
+# ------------------------------------
+# Quote a variable value, and forward it to `config.status' so that its
+# declaration there will have the same value as in `configure'. VARNAME
+# must have a single quote delimited value for this to work.
+m4_define([_LT_CONFIG_STATUS_DECLARE],
+[$1='`$ECHO "X$][$1" | $Xsed -e "$delay_single_quote_subst"`'])
+
+
+# _LT_CONFIG_STATUS_DECLARATIONS
+# ------------------------------
+# We delimit libtool config variables with single quotes, so when
+# we write them to config.status, we have to be sure to quote all
+# embedded single quotes properly. In configure, this macro expands
+# each variable declared with _LT_DECL (and _LT_TAGDECL) into:
+#
+# <var>='`$ECHO "X$<var>" | $Xsed -e "$delay_single_quote_subst"`'
+m4_defun([_LT_CONFIG_STATUS_DECLARATIONS],
+[m4_foreach([_lt_var], m4_quote(lt_decl_all_varnames),
+ [m4_n([_LT_CONFIG_STATUS_DECLARE(_lt_var)])])])
+
+
+# _LT_LIBTOOL_TAGS
+# ----------------
+# Output comment and list of tags supported by the script
+m4_defun([_LT_LIBTOOL_TAGS],
+[_LT_FORMAT_COMMENT([The names of the tagged configurations supported by this script])dnl
+available_tags="_LT_TAGS"dnl
+])
+
+
+# _LT_LIBTOOL_DECLARE(VARNAME, [TAG])
+# -----------------------------------
+# Extract the dictionary values for VARNAME (optionally with TAG) and
+# expand to a commented shell variable setting:
+#
+# # Some comment about what VAR is for.
+# visible_name=$lt_internal_name
+m4_define([_LT_LIBTOOL_DECLARE],
+[_LT_FORMAT_COMMENT(m4_quote(lt_dict_fetch([lt_decl_dict], [$1],
+ [description])))[]dnl
+m4_pushdef([_libtool_name],
+ m4_quote(lt_dict_fetch([lt_decl_dict], [$1], [libtool_name])))[]dnl
+m4_case(m4_quote(lt_dict_fetch([lt_decl_dict], [$1], [value])),
+ [0], [_libtool_name=[$]$1],
+ [1], [_libtool_name=$lt_[]$1],
+ [2], [_libtool_name=$lt_[]$1],
+ [_libtool_name=lt_dict_fetch([lt_decl_dict], [$1], [value])])[]dnl
+m4_ifval([$2], [_$2])[]m4_popdef([_libtool_name])[]dnl
+])
+
+
+# _LT_LIBTOOL_CONFIG_VARS
+# -----------------------
+# Produce commented declarations of non-tagged libtool config variables
+# suitable for insertion in the LIBTOOL CONFIG section of the `libtool'
+# script. Tagged libtool config variables (even for the LIBTOOL CONFIG
+# section) are produced by _LT_LIBTOOL_TAG_VARS.
+m4_defun([_LT_LIBTOOL_CONFIG_VARS],
+[m4_foreach([_lt_var],
+ m4_quote(_lt_decl_filter([tagged?], [no], [], lt_decl_varnames)),
+ [m4_n([_LT_LIBTOOL_DECLARE(_lt_var)])])])
+
+
+# _LT_LIBTOOL_TAG_VARS(TAG)
+# -------------------------
+m4_define([_LT_LIBTOOL_TAG_VARS],
+[m4_foreach([_lt_var], m4_quote(lt_decl_tag_varnames),
+ [m4_n([_LT_LIBTOOL_DECLARE(_lt_var, [$1])])])])
+
+
+# _LT_TAGVAR(VARNAME, [TAGNAME])
+# ------------------------------
+m4_define([_LT_TAGVAR], [m4_ifval([$2], [$1_$2], [$1])])
+
+
+# _LT_CONFIG_COMMANDS
+# -------------------
+# Send accumulated output to $CONFIG_STATUS. Thanks to the lists of
+# variables for single and double quote escaping we saved from calls
+# to _LT_DECL, we can put quote escaped variables declarations
+# into `config.status', and then the shell code to quote escape them in
+# for loops in `config.status'. Finally, any additional code accumulated
+# from calls to _LT_CONFIG_LIBTOOL_INIT is expanded.
+m4_defun([_LT_CONFIG_COMMANDS],
+[AC_PROVIDE_IFELSE([LT_OUTPUT],
+ dnl If the libtool generation code has been placed in $CONFIG_LT,
+ dnl instead of duplicating it all over again into config.status,
+ dnl then we will have config.status run $CONFIG_LT later, so it
+ dnl needs to know what name is stored there:
+ [AC_CONFIG_COMMANDS([libtool],
+ [$SHELL $CONFIG_LT || AS_EXIT(1)], [CONFIG_LT='$CONFIG_LT'])],
+ dnl If the libtool generation code is destined for config.status,
+ dnl expand the accumulated commands and init code now:
+ [AC_CONFIG_COMMANDS([libtool],
+ [_LT_OUTPUT_LIBTOOL_COMMANDS], [_LT_OUTPUT_LIBTOOL_COMMANDS_INIT])])
+])#_LT_CONFIG_COMMANDS
+
+
+# Initialize.
+m4_define([_LT_OUTPUT_LIBTOOL_COMMANDS_INIT],
+[
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+sed_quote_subst='$sed_quote_subst'
+double_quote_subst='$double_quote_subst'
+delay_variable_subst='$delay_variable_subst'
+_LT_CONFIG_STATUS_DECLARATIONS
+LTCC='$LTCC'
+LTCFLAGS='$LTCFLAGS'
+compiler='$compiler_DEFAULT'
+
+# Quote evaled strings.
+for var in lt_decl_all_varnames([[ \
+]], lt_decl_quote_varnames); do
+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in
+ *[[\\\\\\\`\\"\\\$]]*)
+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$sed_quote_subst\\"\\\`\\\\\\""
+ ;;
+ *)
+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\""
+ ;;
+ esac
+done
+
+# Double-quote double-evaled strings.
+for var in lt_decl_all_varnames([[ \
+]], lt_decl_dquote_varnames); do
+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in
+ *[[\\\\\\\`\\"\\\$]]*)
+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$double_quote_subst\\" -e \\"\\\$sed_quote_subst\\" -e \\"\\\$delay_variable_subst\\"\\\`\\\\\\""
+ ;;
+ *)
+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\""
+ ;;
+ esac
+done
+
+# Fix-up fallback echo if it was mangled by the above quoting rules.
+case \$lt_ECHO in
+*'\\\[$]0 --fallback-echo"')dnl "
+ lt_ECHO=\`\$ECHO "X\$lt_ECHO" | \$Xsed -e 's/\\\\\\\\\\\\\\\[$]0 --fallback-echo"\[$]/\[$]0 --fallback-echo"/'\`
+ ;;
+esac
+
+_LT_OUTPUT_LIBTOOL_INIT
+])
+
+
+# LT_OUTPUT
+# ---------
+# This macro allows early generation of the libtool script (before
+# AC_OUTPUT is called), incase it is used in configure for compilation
+# tests.
+AC_DEFUN([LT_OUTPUT],
+[: ${CONFIG_LT=./config.lt}
+AC_MSG_NOTICE([creating $CONFIG_LT])
+cat >"$CONFIG_LT" <<_LTEOF
+#! $SHELL
+# Generated by $as_me.
+# Run this file to recreate a libtool stub with the current configuration.
+
+lt_cl_silent=false
+SHELL=\${CONFIG_SHELL-$SHELL}
+_LTEOF
+
+cat >>"$CONFIG_LT" <<\_LTEOF
+AS_SHELL_SANITIZE
+_AS_PREPARE
+
+exec AS_MESSAGE_FD>&1
+exec AS_MESSAGE_LOG_FD>>config.log
+{
+ echo
+ AS_BOX([Running $as_me.])
+} >&AS_MESSAGE_LOG_FD
+
+lt_cl_help="\
+\`$as_me' creates a local libtool stub from the current configuration,
+for use in further configure time tests before the real libtool is
+generated.
+
+Usage: $[0] [[OPTIONS]]
+
+ -h, --help print this help, then exit
+ -V, --version print version number, then exit
+ -q, --quiet do not print progress messages
+ -d, --debug don't remove temporary files
+
+Report bugs to <bug-libtool at gnu.org>."
+
+lt_cl_version="\
+m4_ifset([AC_PACKAGE_NAME], [AC_PACKAGE_NAME ])config.lt[]dnl
+m4_ifset([AC_PACKAGE_VERSION], [ AC_PACKAGE_VERSION])
+configured by $[0], generated by m4_PACKAGE_STRING.
+
+Copyright (C) 2008 Free Software Foundation, Inc.
+This config.lt script is free software; the Free Software Foundation
+gives unlimited permision to copy, distribute and modify it."
+
+while test $[#] != 0
+do
+ case $[1] in
+ --version | --v* | -V )
+ echo "$lt_cl_version"; exit 0 ;;
+ --help | --h* | -h )
+ echo "$lt_cl_help"; exit 0 ;;
+ --debug | --d* | -d )
+ debug=: ;;
+ --quiet | --q* | --silent | --s* | -q )
+ lt_cl_silent=: ;;
+
+ -*) AC_MSG_ERROR([unrecognized option: $[1]
+Try \`$[0] --help' for more information.]) ;;
+
+ *) AC_MSG_ERROR([unrecognized argument: $[1]
+Try \`$[0] --help' for more information.]) ;;
+ esac
+ shift
+done
+
+if $lt_cl_silent; then
+ exec AS_MESSAGE_FD>/dev/null
+fi
+_LTEOF
+
+cat >>"$CONFIG_LT" <<_LTEOF
+_LT_OUTPUT_LIBTOOL_COMMANDS_INIT
+_LTEOF
+
+cat >>"$CONFIG_LT" <<\_LTEOF
+AC_MSG_NOTICE([creating $ofile])
+_LT_OUTPUT_LIBTOOL_COMMANDS
+AS_EXIT(0)
+_LTEOF
+chmod +x "$CONFIG_LT"
+
+# configure is writing to config.log, but config.lt does its own redirection,
+# appending to config.log, which fails on DOS, as config.log is still kept
+# open by configure. Here we exec the FD to /dev/null, effectively closing
+# config.log, so it can be properly (re)opened and appended to by config.lt.
+if test "$no_create" != yes; then
+ lt_cl_success=:
+ test "$silent" = yes &&
+ lt_config_lt_args="$lt_config_lt_args --quiet"
+ exec AS_MESSAGE_LOG_FD>/dev/null
+ $SHELL "$CONFIG_LT" $lt_config_lt_args || lt_cl_success=false
+ exec AS_MESSAGE_LOG_FD>>config.log
+ $lt_cl_success || AS_EXIT(1)
+fi
+])# LT_OUTPUT
+
+
+# _LT_CONFIG(TAG)
+# ---------------
+# If TAG is the built-in tag, create an initial libtool script with a
+# default configuration from the untagged config vars. Otherwise add code
+# to config.status for appending the configuration named by TAG from the
+# matching tagged config vars.
+m4_defun([_LT_CONFIG],
+[m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+_LT_CONFIG_SAVE_COMMANDS([
+ m4_define([_LT_TAG], m4_if([$1], [], [C], [$1]))dnl
+ m4_if(_LT_TAG, [C], [
+ # See if we are running on zsh, and set the options which allow our
+ # commands through without removal of \ escapes.
+ if test -n "${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+ fi
+
+ cfgfile="${ofile}T"
+ trap "$RM \"$cfgfile\"; exit 1" 1 2 15
+ $RM "$cfgfile"
+
+ cat <<_LT_EOF >> "$cfgfile"
+#! $SHELL
+
+# `$ECHO "$ofile" | sed 's%^.*/%%'` - Provide generalized library-building support services.
+# Generated automatically by $as_me ($PACKAGE$TIMESTAMP) $VERSION
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+# NOTE: Changes made to this file will be lost: look at ltmain.sh.
+#
+_LT_COPYING
+_LT_LIBTOOL_TAGS
+
+# ### BEGIN LIBTOOL CONFIG
+_LT_LIBTOOL_CONFIG_VARS
+_LT_LIBTOOL_TAG_VARS
+# ### END LIBTOOL CONFIG
+
+_LT_EOF
+
+ case $host_os in
+ aix3*)
+ cat <<\_LT_EOF >> "$cfgfile"
+# AIX sometimes has problems with the GCC collect2 program. For some
+# reason, if we set the COLLECT_NAMES environment variable, the problems
+# vanish in a puff of smoke.
+if test "X${COLLECT_NAMES+set}" != Xset; then
+ COLLECT_NAMES=
+ export COLLECT_NAMES
+fi
+_LT_EOF
+ ;;
+ esac
+
+ _LT_PROG_LTMAIN
+
+ # We use sed instead of cat because bash on DJGPP gets confused if
+ # if finds mixed CR/LF and LF-only lines. Since sed operates in
+ # text mode, it properly converts lines to CR/LF. This bash problem
+ # is reportedly fixed, but why not run on old versions too?
+ sed '/^# Generated shell functions inserted here/q' "$ltmain" >> "$cfgfile" \
+ || (rm -f "$cfgfile"; exit 1)
+
+ _LT_PROG_XSI_SHELLFNS
+
+ sed -n '/^# Generated shell functions inserted here/,$p' "$ltmain" >> "$cfgfile" \
+ || (rm -f "$cfgfile"; exit 1)
+
+ mv -f "$cfgfile" "$ofile" ||
+ (rm -f "$ofile" && cp "$cfgfile" "$ofile" && rm -f "$cfgfile")
+ chmod +x "$ofile"
+],
+[cat <<_LT_EOF >> "$ofile"
+
+dnl Unfortunately we have to use $1 here, since _LT_TAG is not expanded
+dnl in a comment (ie after a #).
+# ### BEGIN LIBTOOL TAG CONFIG: $1
+_LT_LIBTOOL_TAG_VARS(_LT_TAG)
+# ### END LIBTOOL TAG CONFIG: $1
+_LT_EOF
+])dnl /m4_if
+],
+[m4_if([$1], [], [
+ PACKAGE='$PACKAGE'
+ VERSION='$VERSION'
+ TIMESTAMP='$TIMESTAMP'
+ RM='$RM'
+ ofile='$ofile'], [])
+])dnl /_LT_CONFIG_SAVE_COMMANDS
+])# _LT_CONFIG
+
+
+# LT_SUPPORTED_TAG(TAG)
+# ---------------------
+# Trace this macro to discover what tags are supported by the libtool
+# --tag option, using:
+# autoconf --trace 'LT_SUPPORTED_TAG:$1'
+AC_DEFUN([LT_SUPPORTED_TAG], [])
+
+
+# C support is built-in for now
+m4_define([_LT_LANG_C_enabled], [])
+m4_define([_LT_TAGS], [])
+
+
+# LT_LANG(LANG)
+# -------------
+# Enable libtool support for the given language if not already enabled.
+AC_DEFUN([LT_LANG],
+[AC_BEFORE([$0], [LT_OUTPUT])dnl
+m4_case([$1],
+ [C], [_LT_LANG(C)],
+ [C++], [_LT_LANG(CXX)],
+ [Java], [_LT_LANG(GCJ)],
+ [Fortran 77], [_LT_LANG(F77)],
+ [Fortran], [_LT_LANG(FC)],
+ [Windows Resource], [_LT_LANG(RC)],
+ [m4_ifdef([_LT_LANG_]$1[_CONFIG],
+ [_LT_LANG($1)],
+ [m4_fatal([$0: unsupported language: "$1"])])])dnl
+])# LT_LANG
+
+
+# _LT_LANG(LANGNAME)
+# ------------------
+m4_defun([_LT_LANG],
+[m4_ifdef([_LT_LANG_]$1[_enabled], [],
+ [LT_SUPPORTED_TAG([$1])dnl
+ m4_append([_LT_TAGS], [$1 ])dnl
+ m4_define([_LT_LANG_]$1[_enabled], [])dnl
+ _LT_LANG_$1_CONFIG($1)])dnl
+])# _LT_LANG
+
+
+# _LT_LANG_DEFAULT_CONFIG
+# -----------------------
+m4_defun([_LT_LANG_DEFAULT_CONFIG],
+[AC_PROVIDE_IFELSE([AC_PROG_CXX],
+ [LT_LANG(CXX)],
+ [m4_define([AC_PROG_CXX], defn([AC_PROG_CXX])[LT_LANG(CXX)])])
+
+AC_PROVIDE_IFELSE([AC_PROG_F77],
+ [LT_LANG(F77)],
+ [m4_define([AC_PROG_F77], defn([AC_PROG_F77])[LT_LANG(F77)])])
+
+AC_PROVIDE_IFELSE([AC_PROG_FC],
+ [LT_LANG(FC)],
+ [m4_define([AC_PROG_FC], defn([AC_PROG_FC])[LT_LANG(FC)])])
+
+dnl The call to [A][M_PROG_GCJ] is quoted like that to stop aclocal
+dnl pulling things in needlessly.
+AC_PROVIDE_IFELSE([AC_PROG_GCJ],
+ [LT_LANG(GCJ)],
+ [AC_PROVIDE_IFELSE([A][M_PROG_GCJ],
+ [LT_LANG(GCJ)],
+ [AC_PROVIDE_IFELSE([LT_PROG_GCJ],
+ [LT_LANG(GCJ)],
+ [m4_ifdef([AC_PROG_GCJ],
+ [m4_define([AC_PROG_GCJ], defn([AC_PROG_GCJ])[LT_LANG(GCJ)])])
+ m4_ifdef([A][M_PROG_GCJ],
+ [m4_define([A][M_PROG_GCJ], defn([A][M_PROG_GCJ])[LT_LANG(GCJ)])])
+ m4_ifdef([LT_PROG_GCJ],
+ [m4_define([LT_PROG_GCJ], defn([LT_PROG_GCJ])[LT_LANG(GCJ)])])])])])
+
+AC_PROVIDE_IFELSE([LT_PROG_RC],
+ [LT_LANG(RC)],
+ [m4_define([LT_PROG_RC], defn([LT_PROG_RC])[LT_LANG(RC)])])
+])# _LT_LANG_DEFAULT_CONFIG
+
+# Obsolete macros:
+AU_DEFUN([AC_LIBTOOL_CXX], [LT_LANG(C++)])
+AU_DEFUN([AC_LIBTOOL_F77], [LT_LANG(Fortran 77)])
+AU_DEFUN([AC_LIBTOOL_FC], [LT_LANG(Fortran)])
+AU_DEFUN([AC_LIBTOOL_GCJ], [LT_LANG(Java)])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_CXX], [])
+dnl AC_DEFUN([AC_LIBTOOL_F77], [])
+dnl AC_DEFUN([AC_LIBTOOL_FC], [])
+dnl AC_DEFUN([AC_LIBTOOL_GCJ], [])
+
+
+# _LT_TAG_COMPILER
+# ----------------
+m4_defun([_LT_TAG_COMPILER],
+[AC_REQUIRE([AC_PROG_CC])dnl
+
+_LT_DECL([LTCC], [CC], [1], [A C compiler])dnl
+_LT_DECL([LTCFLAGS], [CFLAGS], [1], [LTCC compiler flags])dnl
+_LT_TAGDECL([CC], [compiler], [1], [A language specific compiler])dnl
+_LT_TAGDECL([with_gcc], [GCC], [0], [Is the compiler the GNU compiler?])dnl
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+])# _LT_TAG_COMPILER
+
+
+# _LT_COMPILER_BOILERPLATE
+# ------------------------
+# Check for compiler boilerplate output or warnings with
+# the simple compiler test code.
+m4_defun([_LT_COMPILER_BOILERPLATE],
+[m4_require([_LT_DECL_SED])dnl
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$RM conftest*
+])# _LT_COMPILER_BOILERPLATE
+
+
+# _LT_LINKER_BOILERPLATE
+# ----------------------
+# Check for linker boilerplate output or warnings with
+# the simple link test code.
+m4_defun([_LT_LINKER_BOILERPLATE],
+[m4_require([_LT_DECL_SED])dnl
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$RM -r conftest*
+])# _LT_LINKER_BOILERPLATE
+
+# _LT_REQUIRED_DARWIN_CHECKS
+# -------------------------
+m4_defun_once([_LT_REQUIRED_DARWIN_CHECKS],[
+ case $host_os in
+ rhapsody* | darwin*)
+ AC_CHECK_TOOL([DSYMUTIL], [dsymutil], [:])
+ AC_CHECK_TOOL([NMEDIT], [nmedit], [:])
+ AC_CHECK_TOOL([LIPO], [lipo], [:])
+ AC_CHECK_TOOL([OTOOL], [otool], [:])
+ AC_CHECK_TOOL([OTOOL64], [otool64], [:])
+ _LT_DECL([], [DSYMUTIL], [1],
+ [Tool to manipulate archived DWARF debug symbol files on Mac OS X])
+ _LT_DECL([], [NMEDIT], [1],
+ [Tool to change global to local symbols on Mac OS X])
+ _LT_DECL([], [LIPO], [1],
+ [Tool to manipulate fat objects and archives on Mac OS X])
+ _LT_DECL([], [OTOOL], [1],
+ [ldd/readelf like tool for Mach-O binaries on Mac OS X])
+ _LT_DECL([], [OTOOL64], [1],
+ [ldd/readelf like tool for 64 bit Mach-O binaries on Mac OS X 10.4])
+
+ AC_CACHE_CHECK([for -single_module linker flag],[lt_cv_apple_cc_single_mod],
+ [lt_cv_apple_cc_single_mod=no
+ if test -z "${LT_MULTI_MODULE}"; then
+ # By default we will add the -single_module flag. You can override
+ # by either setting the environment variable LT_MULTI_MODULE
+ # non-empty at configure time, or by adding -multi_module to the
+ # link flags.
+ rm -rf libconftest.dylib*
+ echo "int foo(void){return 1;}" > conftest.c
+ echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+-dynamiclib -Wl,-single_module conftest.c" >&AS_MESSAGE_LOG_FD
+ $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+ -dynamiclib -Wl,-single_module conftest.c 2>conftest.err
+ _lt_result=$?
+ if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then
+ lt_cv_apple_cc_single_mod=yes
+ else
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ fi
+ rm -rf libconftest.dylib*
+ rm -f conftest.*
+ fi])
+ AC_CACHE_CHECK([for -exported_symbols_list linker flag],
+ [lt_cv_ld_exported_symbols_list],
+ [lt_cv_ld_exported_symbols_list=no
+ save_LDFLAGS=$LDFLAGS
+ echo "_main" > conftest.sym
+ LDFLAGS="$LDFLAGS -Wl,-exported_symbols_list,conftest.sym"
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([],[])],
+ [lt_cv_ld_exported_symbols_list=yes],
+ [lt_cv_ld_exported_symbols_list=no])
+ LDFLAGS="$save_LDFLAGS"
+ ])
+ case $host_os in
+ rhapsody* | darwin1.[[012]])
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}suppress' ;;
+ darwin1.*)
+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+ darwin*) # darwin 5.x on
+ # if running on 10.5 or later, the deployment target defaults
+ # to the OS version, if on x86, and 10.4, the deployment
+ # target defaults to 10.4. Don't you love it?
+ case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in
+ 10.0,*86*-darwin8*|10.0,*-darwin[[91]]*)
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+ 10.[[012]]*)
+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+ 10.*)
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+ esac
+ ;;
+ esac
+ if test "$lt_cv_apple_cc_single_mod" = "yes"; then
+ _lt_dar_single_mod='$single_module'
+ fi
+ if test "$lt_cv_ld_exported_symbols_list" = "yes"; then
+ _lt_dar_export_syms=' ${wl}-exported_symbols_list,$output_objdir/${libname}-symbols.expsym'
+ else
+ _lt_dar_export_syms='~$NMEDIT -s $output_objdir/${libname}-symbols.expsym ${lib}'
+ fi
+ if test "$DSYMUTIL" != ":"; then
+ _lt_dsymutil='~$DSYMUTIL $lib || :'
+ else
+ _lt_dsymutil=
+ fi
+ ;;
+ esac
+])
+
+
+# _LT_DARWIN_LINKER_FEATURES
+# --------------------------
+# Checks for linker and compiler features on darwin
+m4_defun([_LT_DARWIN_LINKER_FEATURES],
+[
+ m4_require([_LT_REQUIRED_DARWIN_CHECKS])
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_automatic, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=''
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(allow_undefined_flag, $1)="$_lt_dar_allow_undefined"
+ case $cc_basename in
+ ifort*) _lt_dar_can_shared=yes ;;
+ *) _lt_dar_can_shared=$GCC ;;
+ esac
+ if test "$_lt_dar_can_shared" = "yes"; then
+ output_verbose_link_cmd=echo
+ _LT_TAGVAR(archive_cmds, $1)="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}"
+ _LT_TAGVAR(module_cmds, $1)="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}"
+ _LT_TAGVAR(archive_expsym_cmds, $1)="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}"
+ _LT_TAGVAR(module_expsym_cmds, $1)="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}"
+ m4_if([$1], [CXX],
+[ if test "$lt_cv_apple_cc_single_mod" != "yes"; then
+ _LT_TAGVAR(archive_cmds, $1)="\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dsymutil}"
+ _LT_TAGVAR(archive_expsym_cmds, $1)="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dar_export_syms}${_lt_dsymutil}"
+ fi
+],[])
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+])
+
+# _LT_SYS_MODULE_PATH_AIX
+# -----------------------
+# Links a minimal program and checks the executable
+# for the system default hardcoded library path. In most cases,
+# this is /usr/lib:/lib, but when the MPI compilers are used
+# the location of the communication and MPI libs are included too.
+# If we don't find anything, use the default library path according
+# to the aix ld manual.
+m4_defun([_LT_SYS_MODULE_PATH_AIX],
+[m4_require([_LT_DECL_SED])dnl
+AC_LINK_IFELSE(AC_LANG_PROGRAM,[
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi],[])
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+])# _LT_SYS_MODULE_PATH_AIX
+
+
+# _LT_SHELL_INIT(ARG)
+# -------------------
+m4_define([_LT_SHELL_INIT],
+[ifdef([AC_DIVERSION_NOTICE],
+ [AC_DIVERT_PUSH(AC_DIVERSION_NOTICE)],
+ [AC_DIVERT_PUSH(NOTICE)])
+$1
+AC_DIVERT_POP
+])# _LT_SHELL_INIT
+
+
+# _LT_PROG_ECHO_BACKSLASH
+# -----------------------
+# Add some code to the start of the generated configure script which
+# will find an echo command which doesn't interpret backslashes.
+m4_defun([_LT_PROG_ECHO_BACKSLASH],
+[_LT_SHELL_INIT([
+# Check that we are running under the correct shell.
+SHELL=${CONFIG_SHELL-/bin/sh}
+
+case X$lt_ECHO in
+X*--fallback-echo)
+ # Remove one level of quotation (which was required for Make).
+ ECHO=`echo "$lt_ECHO" | sed 's,\\\\\[$]\\[$]0,'[$]0','`
+ ;;
+esac
+
+ECHO=${lt_ECHO-echo}
+if test "X[$]1" = X--no-reexec; then
+ # Discard the --no-reexec flag, and continue.
+ shift
+elif test "X[$]1" = X--fallback-echo; then
+ # Avoid inline document here, it may be left over
+ :
+elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' ; then
+ # Yippee, $ECHO works!
+ :
+else
+ # Restart under the correct shell.
+ exec $SHELL "[$]0" --no-reexec ${1+"[$]@"}
+fi
+
+if test "X[$]1" = X--fallback-echo; then
+ # used as fallback echo
+ shift
+ cat <<_LT_EOF
+[$]*
+_LT_EOF
+ exit 0
+fi
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test -z "$lt_ECHO"; then
+ if test "X${echo_test_string+set}" != Xset; then
+ # find a string as large as possible, as long as the shell can cope with it
+ for cmd in 'sed 50q "[$]0"' 'sed 20q "[$]0"' 'sed 10q "[$]0"' 'sed 2q "[$]0"' 'echo test'; do
+ # expected sizes: less than 2Kb, 1Kb, 512 bytes, 16 bytes, ...
+ if { echo_test_string=`eval $cmd`; } 2>/dev/null &&
+ { test "X$echo_test_string" = "X$echo_test_string"; } 2>/dev/null
+ then
+ break
+ fi
+ done
+ fi
+
+ if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ :
+ else
+ # The Solaris, AIX, and Digital Unix default echo programs unquote
+ # backslashes. This makes it impossible to quote backslashes using
+ # echo "$something" | sed 's/\\/\\\\/g'
+ #
+ # So, first we look for a working echo in the user's PATH.
+
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for dir in $PATH /usr/ucb; do
+ IFS="$lt_save_ifs"
+ if (test -f $dir/echo || test -f $dir/echo$ac_exeext) &&
+ test "X`($dir/echo '\t') 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`($dir/echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ ECHO="$dir/echo"
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+
+ if test "X$ECHO" = Xecho; then
+ # We didn't find a better echo, so look for alternatives.
+ if test "X`{ print -r '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ print -r "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ # This shell has a builtin print -r that does the trick.
+ ECHO='print -r'
+ elif { test -f /bin/ksh || test -f /bin/ksh$ac_exeext; } &&
+ test "X$CONFIG_SHELL" != X/bin/ksh; then
+ # If we have ksh, try running configure again with it.
+ ORIGINAL_CONFIG_SHELL=${CONFIG_SHELL-/bin/sh}
+ export ORIGINAL_CONFIG_SHELL
+ CONFIG_SHELL=/bin/ksh
+ export CONFIG_SHELL
+ exec $CONFIG_SHELL "[$]0" --no-reexec ${1+"[$]@"}
+ else
+ # Try using printf.
+ ECHO='printf %s\n'
+ if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ # Cool, printf works
+ :
+ elif echo_testing_string=`($ORIGINAL_CONFIG_SHELL "[$]0" --fallback-echo '\t') 2>/dev/null` &&
+ test "X$echo_testing_string" = 'X\t' &&
+ echo_testing_string=`($ORIGINAL_CONFIG_SHELL "[$]0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ CONFIG_SHELL=$ORIGINAL_CONFIG_SHELL
+ export CONFIG_SHELL
+ SHELL="$CONFIG_SHELL"
+ export SHELL
+ ECHO="$CONFIG_SHELL [$]0 --fallback-echo"
+ elif echo_testing_string=`($CONFIG_SHELL "[$]0" --fallback-echo '\t') 2>/dev/null` &&
+ test "X$echo_testing_string" = 'X\t' &&
+ echo_testing_string=`($CONFIG_SHELL "[$]0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ ECHO="$CONFIG_SHELL [$]0 --fallback-echo"
+ else
+ # maybe with a smaller string...
+ prev=:
+
+ for cmd in 'echo test' 'sed 2q "[$]0"' 'sed 10q "[$]0"' 'sed 20q "[$]0"' 'sed 50q "[$]0"'; do
+ if { test "X$echo_test_string" = "X`eval $cmd`"; } 2>/dev/null
+ then
+ break
+ fi
+ prev="$cmd"
+ done
+
+ if test "$prev" != 'sed 50q "[$]0"'; then
+ echo_test_string=`eval $prev`
+ export echo_test_string
+ exec ${ORIGINAL_CONFIG_SHELL-${CONFIG_SHELL-/bin/sh}} "[$]0" ${1+"[$]@"}
+ else
+ # Oops. We lost completely, so just stick with echo.
+ ECHO=echo
+ fi
+ fi
+ fi
+ fi
+ fi
+fi
+
+# Copy echo and quote the copy suitably for passing to libtool from
+# the Makefile, instead of quoting the original, which is used later.
+lt_ECHO=$ECHO
+if test "X$lt_ECHO" = "X$CONFIG_SHELL [$]0 --fallback-echo"; then
+ lt_ECHO="$CONFIG_SHELL \\\$\[$]0 --fallback-echo"
+fi
+
+AC_SUBST(lt_ECHO)
+])
+_LT_DECL([], [SHELL], [1], [Shell to use when invoking shell scripts])
+_LT_DECL([], [ECHO], [1],
+ [An echo program that does not interpret backslashes])
+])# _LT_PROG_ECHO_BACKSLASH
+
+
+# _LT_ENABLE_LOCK
+# ---------------
+m4_defun([_LT_ENABLE_LOCK],
+[AC_ARG_ENABLE([libtool-lock],
+ [AS_HELP_STRING([--disable-libtool-lock],
+ [avoid locking (might break parallel builds)])])
+test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes
+
+# Some flags need to be propagated to the compiler or linker for good
+# libtool support.
+case $host in
+ia64-*-hpux*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *ELF-32*)
+ HPUX_IA64_MODE="32"
+ ;;
+ *ELF-64*)
+ HPUX_IA64_MODE="64"
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+*-*-irix6*)
+ # Find out which ABI we are using.
+ echo '[#]line __oline__ "configure"' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *32-bit*)
+ LD="${LD-ld} -melf32bsmip"
+ ;;
+ *N32*)
+ LD="${LD-ld} -melf32bmipn32"
+ ;;
+ *64-bit*)
+ LD="${LD-ld} -melf64bmip"
+ ;;
+ esac
+ else
+ case `/usr/bin/file conftest.$ac_objext` in
+ *32-bit*)
+ LD="${LD-ld} -32"
+ ;;
+ *N32*)
+ LD="${LD-ld} -n32"
+ ;;
+ *64-bit*)
+ LD="${LD-ld} -64"
+ ;;
+ esac
+ fi
+ fi
+ rm -rf conftest*
+ ;;
+
+x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \
+s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ case `/usr/bin/file conftest.o` in
+ *32-bit*)
+ case $host in
+ x86_64-*kfreebsd*-gnu)
+ LD="${LD-ld} -m elf_i386_fbsd"
+ ;;
+ x86_64-*linux*)
+ LD="${LD-ld} -m elf_i386"
+ ;;
+ ppc64-*linux*|powerpc64-*linux*)
+ LD="${LD-ld} -m elf32ppclinux"
+ ;;
+ s390x-*linux*)
+ LD="${LD-ld} -m elf_s390"
+ ;;
+ sparc64-*linux*)
+ LD="${LD-ld} -m elf32_sparc"
+ ;;
+ esac
+ ;;
+ *64-bit*)
+ case $host in
+ x86_64-*kfreebsd*-gnu)
+ LD="${LD-ld} -m elf_x86_64_fbsd"
+ ;;
+ x86_64-*linux*)
+ LD="${LD-ld} -m elf_x86_64"
+ ;;
+ ppc*-*linux*|powerpc*-*linux*)
+ LD="${LD-ld} -m elf64ppc"
+ ;;
+ s390*-*linux*|s390*-*tpf*)
+ LD="${LD-ld} -m elf64_s390"
+ ;;
+ sparc*-*linux*)
+ LD="${LD-ld} -m elf64_sparc"
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+
+*-*-sco3.2v5*)
+ # On SCO OpenServer 5, we need -belf to get full-featured binaries.
+ SAVE_CFLAGS="$CFLAGS"
+ CFLAGS="$CFLAGS -belf"
+ AC_CACHE_CHECK([whether the C compiler needs -belf], lt_cv_cc_needs_belf,
+ [AC_LANG_PUSH(C)
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[]],[[]])],[lt_cv_cc_needs_belf=yes],[lt_cv_cc_needs_belf=no])
+ AC_LANG_POP])
+ if test x"$lt_cv_cc_needs_belf" != x"yes"; then
+ # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf
+ CFLAGS="$SAVE_CFLAGS"
+ fi
+ ;;
+sparc*-*solaris*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ case `/usr/bin/file conftest.o` in
+ *64-bit*)
+ case $lt_cv_prog_gnu_ld in
+ yes*) LD="${LD-ld} -m elf64_sparc" ;;
+ *)
+ if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then
+ LD="${LD-ld} -64"
+ fi
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+esac
+
+need_locks="$enable_libtool_lock"
+])# _LT_ENABLE_LOCK
+
+
+# _LT_CMD_OLD_ARCHIVE
+# -------------------
+m4_defun([_LT_CMD_OLD_ARCHIVE],
+[AC_CHECK_TOOL(AR, ar, false)
+test -z "$AR" && AR=ar
+test -z "$AR_FLAGS" && AR_FLAGS=cru
+_LT_DECL([], [AR], [1], [The archiver])
+_LT_DECL([], [AR_FLAGS], [1])
+
+AC_CHECK_TOOL(STRIP, strip, :)
+test -z "$STRIP" && STRIP=:
+_LT_DECL([], [STRIP], [1], [A symbol stripping program])
+
+AC_CHECK_TOOL(RANLIB, ranlib, :)
+test -z "$RANLIB" && RANLIB=:
+_LT_DECL([], [RANLIB], [1],
+ [Commands used to install an old-style archive])
+
+# Determine commands to create old-style static archives.
+old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs'
+old_postinstall_cmds='chmod 644 $oldlib'
+old_postuninstall_cmds=
+
+if test -n "$RANLIB"; then
+ case $host_os in
+ openbsd*)
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib"
+ ;;
+ *)
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib"
+ ;;
+ esac
+ old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib"
+fi
+_LT_DECL([], [old_postinstall_cmds], [2])
+_LT_DECL([], [old_postuninstall_cmds], [2])
+_LT_TAGDECL([], [old_archive_cmds], [2],
+ [Commands used to build an old-style archive])
+])# _LT_CMD_OLD_ARCHIVE
+
+
+# _LT_COMPILER_OPTION(MESSAGE, VARIABLE-NAME, FLAGS,
+# [OUTPUT-FILE], [ACTION-SUCCESS], [ACTION-FAILURE])
+# ----------------------------------------------------------------
+# Check whether the given compiler option works
+AC_DEFUN([_LT_COMPILER_OPTION],
+[m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_SED])dnl
+AC_CACHE_CHECK([$1], [$2],
+ [$2=no
+ m4_if([$4], , [ac_outfile=conftest.$ac_objext], [ac_outfile=$4])
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+ lt_compiler_flag="$3"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ # The option is referenced via a variable to avoid confusing sed.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [[^ ]]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:__oline__: $lt_compile\"" >&AS_MESSAGE_LOG_FD)
+ (eval "$lt_compile" 2>conftest.err)
+ ac_status=$?
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ echo "$as_me:__oline__: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
+ if (exit $ac_status) && test -s "$ac_outfile"; then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings other than the usual output.
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+ $2=yes
+ fi
+ fi
+ $RM conftest*
+])
+
+if test x"[$]$2" = xyes; then
+ m4_if([$5], , :, [$5])
+else
+ m4_if([$6], , :, [$6])
+fi
+])# _LT_COMPILER_OPTION
+
+# Old name:
+AU_ALIAS([AC_LIBTOOL_COMPILER_OPTION], [_LT_COMPILER_OPTION])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_COMPILER_OPTION], [])
+
+
+# _LT_LINKER_OPTION(MESSAGE, VARIABLE-NAME, FLAGS,
+# [ACTION-SUCCESS], [ACTION-FAILURE])
+# ----------------------------------------------------
+# Check whether the given linker option works
+AC_DEFUN([_LT_LINKER_OPTION],
+[m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_SED])dnl
+AC_CACHE_CHECK([$1], [$2],
+ [$2=no
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS $3"
+ echo "$lt_simple_link_test_code" > conftest.$ac_ext
+ if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+ # The linker can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ if test -s conftest.err; then
+ # Append any errors to the config.log.
+ cat conftest.err 1>&AS_MESSAGE_LOG_FD
+ $ECHO "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if diff conftest.exp conftest.er2 >/dev/null; then
+ $2=yes
+ fi
+ else
+ $2=yes
+ fi
+ fi
+ $RM -r conftest*
+ LDFLAGS="$save_LDFLAGS"
+])
+
+if test x"[$]$2" = xyes; then
+ m4_if([$4], , :, [$4])
+else
+ m4_if([$5], , :, [$5])
+fi
+])# _LT_LINKER_OPTION
+
+# Old name:
+AU_ALIAS([AC_LIBTOOL_LINKER_OPTION], [_LT_LINKER_OPTION])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_LINKER_OPTION], [])
+
+
+# LT_CMD_MAX_LEN
+#---------------
+AC_DEFUN([LT_CMD_MAX_LEN],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+# find the maximum length of command line arguments
+AC_MSG_CHECKING([the maximum length of command line arguments])
+AC_CACHE_VAL([lt_cv_sys_max_cmd_len], [dnl
+ i=0
+ teststring="ABCD"
+
+ case $build_os in
+ msdosdjgpp*)
+ # On DJGPP, this test can blow up pretty badly due to problems in libc
+ # (any single argument exceeding 2000 bytes causes a buffer overrun
+ # during glob expansion). Even if it were fixed, the result of this
+ # check would be larger than it should be.
+ lt_cv_sys_max_cmd_len=12288; # 12K is about right
+ ;;
+
+ gnu*)
+ # Under GNU Hurd, this test is not required because there is
+ # no limit to the length of command line arguments.
+ # Libtool will interpret -1 as no limit whatsoever
+ lt_cv_sys_max_cmd_len=-1;
+ ;;
+
+ cygwin* | mingw* | cegcc*)
+ # On Win9x/ME, this test blows up -- it succeeds, but takes
+ # about 5 minutes as the teststring grows exponentially.
+ # Worse, since 9x/ME are not pre-emptively multitasking,
+ # you end up with a "frozen" computer, even though with patience
+ # the test eventually succeeds (with a max line length of 256k).
+ # Instead, let's just punt: use the minimum linelength reported by
+ # all of the supported platforms: 8192 (on NT/2K/XP).
+ lt_cv_sys_max_cmd_len=8192;
+ ;;
+
+ amigaos*)
+ # On AmigaOS with pdksh, this test takes hours, literally.
+ # So we just punt and use a minimum line length of 8192.
+ lt_cv_sys_max_cmd_len=8192;
+ ;;
+
+ netbsd* | freebsd* | openbsd* | darwin* | dragonfly*)
+ # This has been around since 386BSD, at least. Likely further.
+ if test -x /sbin/sysctl; then
+ lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax`
+ elif test -x /usr/sbin/sysctl; then
+ lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax`
+ else
+ lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs
+ fi
+ # And add a safety zone
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+ ;;
+
+ interix*)
+ # We know the value 262144 and hardcode it with a safety zone (like BSD)
+ lt_cv_sys_max_cmd_len=196608
+ ;;
+
+ osf*)
+ # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure
+ # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not
+ # nice to cause kernel panics so lets avoid the loop below.
+ # First set a reasonable default.
+ lt_cv_sys_max_cmd_len=16384
+ #
+ if test -x /sbin/sysconfig; then
+ case `/sbin/sysconfig -q proc exec_disable_arg_limit` in
+ *1*) lt_cv_sys_max_cmd_len=-1 ;;
+ esac
+ fi
+ ;;
+ sco3.2v5*)
+ lt_cv_sys_max_cmd_len=102400
+ ;;
+ sysv5* | sco5v6* | sysv4.2uw2*)
+ kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null`
+ if test -n "$kargmax"; then
+ lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[[ ]]//'`
+ else
+ lt_cv_sys_max_cmd_len=32768
+ fi
+ ;;
+ *)
+ lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null`
+ if test -n "$lt_cv_sys_max_cmd_len"; then
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+ else
+ # Make teststring a little bigger before we do anything with it.
+ # a 1K string should be a reasonable start.
+ for i in 1 2 3 4 5 6 7 8 ; do
+ teststring=$teststring$teststring
+ done
+ SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}}
+ # If test is not a shell built-in, we'll probably end up computing a
+ # maximum length that is only half of the actual maximum length, but
+ # we can't tell.
+ while { test "X"`$SHELL [$]0 --fallback-echo "X$teststring$teststring" 2>/dev/null` \
+ = "XX$teststring$teststring"; } >/dev/null 2>&1 &&
+ test $i != 17 # 1/2 MB should be enough
+ do
+ i=`expr $i + 1`
+ teststring=$teststring$teststring
+ done
+ # Only check the string length outside the loop.
+ lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1`
+ teststring=
+ # Add a significant safety factor because C++ compilers can tack on
+ # massive amounts of additional arguments before passing them to the
+ # linker. It appears as though 1/2 is a usable value.
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2`
+ fi
+ ;;
+ esac
+])
+if test -n $lt_cv_sys_max_cmd_len ; then
+ AC_MSG_RESULT($lt_cv_sys_max_cmd_len)
+else
+ AC_MSG_RESULT(none)
+fi
+max_cmd_len=$lt_cv_sys_max_cmd_len
+_LT_DECL([], [max_cmd_len], [0],
+ [What is the maximum length of a command?])
+])# LT_CMD_MAX_LEN
+
+# Old name:
+AU_ALIAS([AC_LIBTOOL_SYS_MAX_CMD_LEN], [LT_CMD_MAX_LEN])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_SYS_MAX_CMD_LEN], [])
+
+
+# _LT_HEADER_DLFCN
+# ----------------
+m4_defun([_LT_HEADER_DLFCN],
+[AC_CHECK_HEADERS([dlfcn.h], [], [], [AC_INCLUDES_DEFAULT])dnl
+])# _LT_HEADER_DLFCN
+
+
+# _LT_TRY_DLOPEN_SELF (ACTION-IF-TRUE, ACTION-IF-TRUE-W-USCORE,
+# ACTION-IF-FALSE, ACTION-IF-CROSS-COMPILING)
+# ----------------------------------------------------------------
+m4_defun([_LT_TRY_DLOPEN_SELF],
+[m4_require([_LT_HEADER_DLFCN])dnl
+if test "$cross_compiling" = yes; then :
+ [$4]
+else
+ lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
+ lt_status=$lt_dlunknown
+ cat > conftest.$ac_ext <<_LT_EOF
+[#line __oline__ "configure"
+#include "confdefs.h"
+
+#if HAVE_DLFCN_H
+#include <dlfcn.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef RTLD_GLOBAL
+# define LT_DLGLOBAL RTLD_GLOBAL
+#else
+# ifdef DL_GLOBAL
+# define LT_DLGLOBAL DL_GLOBAL
+# else
+# define LT_DLGLOBAL 0
+# endif
+#endif
+
+/* We may have to define LT_DLLAZY_OR_NOW in the command line if we
+ find out it does not work in some platform. */
+#ifndef LT_DLLAZY_OR_NOW
+# ifdef RTLD_LAZY
+# define LT_DLLAZY_OR_NOW RTLD_LAZY
+# else
+# ifdef DL_LAZY
+# define LT_DLLAZY_OR_NOW DL_LAZY
+# else
+# ifdef RTLD_NOW
+# define LT_DLLAZY_OR_NOW RTLD_NOW
+# else
+# ifdef DL_NOW
+# define LT_DLLAZY_OR_NOW DL_NOW
+# else
+# define LT_DLLAZY_OR_NOW 0
+# endif
+# endif
+# endif
+# endif
+#endif
+
+void fnord() { int i=42;}
+int main ()
+{
+ void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW);
+ int status = $lt_dlunknown;
+
+ if (self)
+ {
+ if (dlsym (self,"fnord")) status = $lt_dlno_uscore;
+ else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore;
+ /* dlclose (self); */
+ }
+ else
+ puts (dlerror ());
+
+ return status;
+}]
+_LT_EOF
+ if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext} 2>/dev/null; then
+ (./conftest; exit; ) >&AS_MESSAGE_LOG_FD 2>/dev/null
+ lt_status=$?
+ case x$lt_status in
+ x$lt_dlno_uscore) $1 ;;
+ x$lt_dlneed_uscore) $2 ;;
+ x$lt_dlunknown|x*) $3 ;;
+ esac
+ else :
+ # compilation failed
+ $3
+ fi
+fi
+rm -fr conftest*
+])# _LT_TRY_DLOPEN_SELF
+
+
+# LT_SYS_DLOPEN_SELF
+# ------------------
+AC_DEFUN([LT_SYS_DLOPEN_SELF],
+[m4_require([_LT_HEADER_DLFCN])dnl
+if test "x$enable_dlopen" != xyes; then
+ enable_dlopen=unknown
+ enable_dlopen_self=unknown
+ enable_dlopen_self_static=unknown
+else
+ lt_cv_dlopen=no
+ lt_cv_dlopen_libs=
+
+ case $host_os in
+ beos*)
+ lt_cv_dlopen="load_add_on"
+ lt_cv_dlopen_libs=
+ lt_cv_dlopen_self=yes
+ ;;
+
+ mingw* | pw32* | cegcc*)
+ lt_cv_dlopen="LoadLibrary"
+ lt_cv_dlopen_libs=
+ ;;
+
+ cygwin*)
+ lt_cv_dlopen="dlopen"
+ lt_cv_dlopen_libs=
+ ;;
+
+ darwin*)
+ # if libdl is installed we need to link against it
+ AC_CHECK_LIB([dl], [dlopen],
+ [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"],[
+ lt_cv_dlopen="dyld"
+ lt_cv_dlopen_libs=
+ lt_cv_dlopen_self=yes
+ ])
+ ;;
+
+ *)
+ AC_CHECK_FUNC([shl_load],
+ [lt_cv_dlopen="shl_load"],
+ [AC_CHECK_LIB([dld], [shl_load],
+ [lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-ldld"],
+ [AC_CHECK_FUNC([dlopen],
+ [lt_cv_dlopen="dlopen"],
+ [AC_CHECK_LIB([dl], [dlopen],
+ [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"],
+ [AC_CHECK_LIB([svld], [dlopen],
+ [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld"],
+ [AC_CHECK_LIB([dld], [dld_link],
+ [lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-ldld"])
+ ])
+ ])
+ ])
+ ])
+ ])
+ ;;
+ esac
+
+ if test "x$lt_cv_dlopen" != xno; then
+ enable_dlopen=yes
+ else
+ enable_dlopen=no
+ fi
+
+ case $lt_cv_dlopen in
+ dlopen)
+ save_CPPFLAGS="$CPPFLAGS"
+ test "x$ac_cv_header_dlfcn_h" = xyes && CPPFLAGS="$CPPFLAGS -DHAVE_DLFCN_H"
+
+ save_LDFLAGS="$LDFLAGS"
+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\"
+
+ save_LIBS="$LIBS"
+ LIBS="$lt_cv_dlopen_libs $LIBS"
+
+ AC_CACHE_CHECK([whether a program can dlopen itself],
+ lt_cv_dlopen_self, [dnl
+ _LT_TRY_DLOPEN_SELF(
+ lt_cv_dlopen_self=yes, lt_cv_dlopen_self=yes,
+ lt_cv_dlopen_self=no, lt_cv_dlopen_self=cross)
+ ])
+
+ if test "x$lt_cv_dlopen_self" = xyes; then
+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\"
+ AC_CACHE_CHECK([whether a statically linked program can dlopen itself],
+ lt_cv_dlopen_self_static, [dnl
+ _LT_TRY_DLOPEN_SELF(
+ lt_cv_dlopen_self_static=yes, lt_cv_dlopen_self_static=yes,
+ lt_cv_dlopen_self_static=no, lt_cv_dlopen_self_static=cross)
+ ])
+ fi
+
+ CPPFLAGS="$save_CPPFLAGS"
+ LDFLAGS="$save_LDFLAGS"
+ LIBS="$save_LIBS"
+ ;;
+ esac
+
+ case $lt_cv_dlopen_self in
+ yes|no) enable_dlopen_self=$lt_cv_dlopen_self ;;
+ *) enable_dlopen_self=unknown ;;
+ esac
+
+ case $lt_cv_dlopen_self_static in
+ yes|no) enable_dlopen_self_static=$lt_cv_dlopen_self_static ;;
+ *) enable_dlopen_self_static=unknown ;;
+ esac
+fi
+_LT_DECL([dlopen_support], [enable_dlopen], [0],
+ [Whether dlopen is supported])
+_LT_DECL([dlopen_self], [enable_dlopen_self], [0],
+ [Whether dlopen of programs is supported])
+_LT_DECL([dlopen_self_static], [enable_dlopen_self_static], [0],
+ [Whether dlopen of statically linked programs is supported])
+])# LT_SYS_DLOPEN_SELF
+
+# Old name:
+AU_ALIAS([AC_LIBTOOL_DLOPEN_SELF], [LT_SYS_DLOPEN_SELF])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_DLOPEN_SELF], [])
+
+
+# _LT_COMPILER_C_O([TAGNAME])
+# ---------------------------
+# Check to see if options -c and -o are simultaneously supported by compiler.
+# This macro does not hard code the compiler like AC_PROG_CC_C_O.
+m4_defun([_LT_COMPILER_C_O],
+[m4_require([_LT_DECL_SED])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_TAG_COMPILER])dnl
+AC_CACHE_CHECK([if $compiler supports -c -o file.$ac_objext],
+ [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)],
+ [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [[^ ]]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:__oline__: $lt_compile\"" >&AS_MESSAGE_LOG_FD)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&AS_MESSAGE_LOG_FD
+ echo "$as_me:__oline__: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ _LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=yes
+ fi
+ fi
+ chmod u+w . 2>&AS_MESSAGE_LOG_FD
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+])
+_LT_TAGDECL([compiler_c_o], [lt_cv_prog_compiler_c_o], [1],
+ [Does compiler simultaneously support -c and -o options?])
+])# _LT_COMPILER_C_O
+
+
+# _LT_COMPILER_FILE_LOCKS([TAGNAME])
+# ----------------------------------
+# Check to see if we can do hard links to lock some files if needed
+m4_defun([_LT_COMPILER_FILE_LOCKS],
+[m4_require([_LT_ENABLE_LOCK])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+_LT_COMPILER_C_O([$1])
+
+hard_links="nottested"
+if test "$_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)" = no && test "$need_locks" != no; then
+ # do not overwrite the value of need_locks provided by the user
+ AC_MSG_CHECKING([if we can lock with hard links])
+ hard_links=yes
+ $RM conftest*
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ touch conftest.a
+ ln conftest.a conftest.b 2>&5 || hard_links=no
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ AC_MSG_RESULT([$hard_links])
+ if test "$hard_links" = no; then
+ AC_MSG_WARN([`$CC' does not support `-c -o', so `make -j' may be unsafe])
+ need_locks=warn
+ fi
+else
+ need_locks=no
+fi
+_LT_DECL([], [need_locks], [1], [Must we lock files when doing compilation?])
+])# _LT_COMPILER_FILE_LOCKS
+
+
+# _LT_CHECK_OBJDIR
+# ----------------
+m4_defun([_LT_CHECK_OBJDIR],
+[AC_CACHE_CHECK([for objdir], [lt_cv_objdir],
+[rm -f .libs 2>/dev/null
+mkdir .libs 2>/dev/null
+if test -d .libs; then
+ lt_cv_objdir=.libs
+else
+ # MS-DOS does not allow filenames that begin with a dot.
+ lt_cv_objdir=_libs
+fi
+rmdir .libs 2>/dev/null])
+objdir=$lt_cv_objdir
+_LT_DECL([], [objdir], [0],
+ [The name of the directory that contains temporary libtool files])dnl
+m4_pattern_allow([LT_OBJDIR])dnl
+AC_DEFINE_UNQUOTED(LT_OBJDIR, "$lt_cv_objdir/",
+ [Define to the sub-directory in which libtool stores uninstalled libraries.])
+])# _LT_CHECK_OBJDIR
+
+
+# _LT_LINKER_HARDCODE_LIBPATH([TAGNAME])
+# --------------------------------------
+# Check hardcoding attributes.
+m4_defun([_LT_LINKER_HARDCODE_LIBPATH],
+[AC_MSG_CHECKING([how to hardcode library paths into programs])
+_LT_TAGVAR(hardcode_action, $1)=
+if test -n "$_LT_TAGVAR(hardcode_libdir_flag_spec, $1)" ||
+ test -n "$_LT_TAGVAR(runpath_var, $1)" ||
+ test "X$_LT_TAGVAR(hardcode_automatic, $1)" = "Xyes" ; then
+
+ # We can hardcode non-existent directories.
+ if test "$_LT_TAGVAR(hardcode_direct, $1)" != no &&
+ # If the only mechanism to avoid hardcoding is shlibpath_var, we
+ # have to relink, otherwise we might link with an installed library
+ # when we should be linking with a yet-to-be-installed one
+ ## test "$_LT_TAGVAR(hardcode_shlibpath_var, $1)" != no &&
+ test "$_LT_TAGVAR(hardcode_minus_L, $1)" != no; then
+ # Linking always hardcodes the temporary library directory.
+ _LT_TAGVAR(hardcode_action, $1)=relink
+ else
+ # We can link without hardcoding, and we can hardcode nonexisting dirs.
+ _LT_TAGVAR(hardcode_action, $1)=immediate
+ fi
+else
+ # We cannot hardcode anything, or else we can only hardcode existing
+ # directories.
+ _LT_TAGVAR(hardcode_action, $1)=unsupported
+fi
+AC_MSG_RESULT([$_LT_TAGVAR(hardcode_action, $1)])
+
+if test "$_LT_TAGVAR(hardcode_action, $1)" = relink ||
+ test "$_LT_TAGVAR(inherit_rpath, $1)" = yes; then
+ # Fast installation is not supported
+ enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+ test "$enable_shared" = no; then
+ # Fast installation is not necessary
+ enable_fast_install=needless
+fi
+_LT_TAGDECL([], [hardcode_action], [0],
+ [How to hardcode a shared library path into an executable])
+])# _LT_LINKER_HARDCODE_LIBPATH
+
+
+# _LT_CMD_STRIPLIB
+# ----------------
+m4_defun([_LT_CMD_STRIPLIB],
+[m4_require([_LT_DECL_EGREP])
+striplib=
+old_striplib=
+AC_MSG_CHECKING([whether stripping libraries is possible])
+if test -n "$STRIP" && $STRIP -V 2>&1 | $GREP "GNU strip" >/dev/null; then
+ test -z "$old_striplib" && old_striplib="$STRIP --strip-debug"
+ test -z "$striplib" && striplib="$STRIP --strip-unneeded"
+ AC_MSG_RESULT([yes])
+else
+# FIXME - insert some real tests, host_os isn't really good enough
+ case $host_os in
+ darwin*)
+ if test -n "$STRIP" ; then
+ striplib="$STRIP -x"
+ old_striplib="$STRIP -S"
+ AC_MSG_RESULT([yes])
+ else
+ AC_MSG_RESULT([no])
+ fi
+ ;;
+ *)
+ AC_MSG_RESULT([no])
+ ;;
+ esac
+fi
+_LT_DECL([], [old_striplib], [1], [Commands to strip libraries])
+_LT_DECL([], [striplib], [1])
+])# _LT_CMD_STRIPLIB
+
+
+# _LT_SYS_DYNAMIC_LINKER([TAG])
+# -----------------------------
+# PORTME Fill in your ld.so characteristics
+m4_defun([_LT_SYS_DYNAMIC_LINKER],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+m4_require([_LT_DECL_EGREP])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_OBJDUMP])dnl
+m4_require([_LT_DECL_SED])dnl
+AC_MSG_CHECKING([dynamic linker characteristics])
+m4_if([$1],
+ [], [
+if test "$GCC" = yes; then
+ case $host_os in
+ darwin*) lt_awk_arg="/^libraries:/,/LR/" ;;
+ *) lt_awk_arg="/^libraries:/" ;;
+ esac
+ lt_search_path_spec=`$CC -print-search-dirs | awk $lt_awk_arg | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$lt_search_path_spec" | $GREP ';' >/dev/null ; then
+ # if the path contains ";" then we assume it to be the separator
+ # otherwise default to the standard path separator (i.e. ":") - it is
+ # assumed that no part of a normal pathname contains ";" but that should
+ # okay in the real world where ";" in dirpaths is itself problematic.
+ lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ # Ok, now we have the path, separated by spaces, we can step through it
+ # and add multilib dir if necessary.
+ lt_tmp_lt_search_path_spec=
+ lt_multi_os_dir=`$CC $CPPFLAGS $CFLAGS $LDFLAGS -print-multi-os-directory 2>/dev/null`
+ for lt_sys_path in $lt_search_path_spec; do
+ if test -d "$lt_sys_path/$lt_multi_os_dir"; then
+ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path/$lt_multi_os_dir"
+ else
+ test -d "$lt_sys_path" && \
+ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path"
+ fi
+ done
+ lt_search_path_spec=`$ECHO $lt_tmp_lt_search_path_spec | awk '
+BEGIN {RS=" "; FS="/|\n";} {
+ lt_foo="";
+ lt_count=0;
+ for (lt_i = NF; lt_i > 0; lt_i--) {
+ if ($lt_i != "" && $lt_i != ".") {
+ if ($lt_i == "..") {
+ lt_count++;
+ } else {
+ if (lt_count == 0) {
+ lt_foo="/" $lt_i lt_foo;
+ } else {
+ lt_count--;
+ }
+ }
+ }
+ }
+ if (lt_foo != "") { lt_freq[[lt_foo]]++; }
+ if (lt_freq[[lt_foo]] == 1) { print lt_foo; }
+}'`
+ sys_lib_search_path_spec=`$ECHO $lt_search_path_spec`
+else
+ sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib"
+fi])
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+ shlibpath_var=LIBPATH
+
+ # AIX 3 has no versioning support, so we append a major version to the name.
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+
+aix[[4-9]]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ hardcode_into_libs=yes
+ if test "$host_cpu" = ia64; then
+ # AIX 5 supports IA64
+ library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ else
+ # With GCC up to 2.95.x, collect2 would create an import file
+ # for dependence libraries. The import file would start with
+ # the line `#! .'. This would cause the generated library to
+ # depend on `.', always an invalid library. This was fixed in
+ # development snapshots of GCC prior to 3.0.
+ case $host_os in
+ aix4 | aix4.[[01]] | aix4.[[01]].*)
+ if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+ echo ' yes '
+ echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then
+ :
+ else
+ can_build_shared=no
+ fi
+ ;;
+ esac
+ # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+ # soname into executable. Probably we can add versioning support to
+ # collect2, so additional links can be useful in future.
+ if test "$aix_use_runtimelinking" = yes; then
+ # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+ # instead of lib<name>.a to let people know that these are not
+ # typical AIX shared libraries.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ else
+ # We preserve .a as extension for shared libraries through AIX4.2
+ # and later when we are not doing run time linking.
+ library_names_spec='${libname}${release}.a $libname.a'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ fi
+ shlibpath_var=LIBPATH
+ fi
+ ;;
+
+amigaos*)
+ case $host_cpu in
+ powerpc)
+ # Since July 2007 AmigaOS4 officially supports .so libraries.
+ # When compiling the executable, add -use-dynld -Lsobjs: to the compileline.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ ;;
+ m68k)
+ library_names_spec='$libname.ixlibrary $libname.a'
+ # Create ${libname}_ixlibrary.a entries in /sys/libs.
+ finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$ECHO "X$lib" | $Xsed -e '\''s%^.*/\([[^/]]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+ ;;
+ esac
+ ;;
+
+beos*)
+ library_names_spec='${libname}${shared_ext}'
+ dynamic_linker="$host_os ld.so"
+ shlibpath_var=LIBRARY_PATH
+ ;;
+
+bsdi[[45]]*)
+ version_type=linux
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+ sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+ # the default ld.so.conf also contains /usr/contrib/lib and
+ # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+ # libtool to hard-code these into programs
+ ;;
+
+cygwin* | mingw* | pw32* | cegcc*)
+ version_type=windows
+ shrext_cmds=".dll"
+ need_version=no
+ need_lib_prefix=no
+
+ case $GCC,$host_os in
+ yes,cygwin* | yes,mingw* | yes,pw32* | yes,cegcc*)
+ library_names_spec='$libname.dll.a'
+ # DLL is installed to $(libdir)/../bin by postinstall_cmds
+ postinstall_cmds='base_file=`basename \${file}`~
+ dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i; echo \$dlname'\''`~
+ dldir=$destdir/`dirname \$dlpath`~
+ test -d \$dldir || mkdir -p \$dldir~
+ $install_prog $dir/$dlname \$dldir/$dlname~
+ chmod a+x \$dldir/$dlname~
+ if test -n '\''$stripme'\'' && test -n '\''$striplib'\''; then
+ eval '\''$striplib \$dldir/$dlname'\'' || exit \$?;
+ fi'
+ postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+ dlpath=$dir/\$dldll~
+ $RM \$dlpath'
+ shlibpath_overrides_runpath=yes
+
+ case $host_os in
+ cygwin*)
+ # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+ soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+ ;;
+ mingw* | cegcc*)
+ # MinGW DLLs use traditional 'lib' prefix
+ soname_spec='${libname}`echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec=`$CC -print-search-dirs | $GREP "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$sys_lib_search_path_spec" | [$GREP ';[c-zC-Z]:/' >/dev/null]; then
+ # It is most probably a Windows format PATH printed by
+ # mingw gcc, but we are running on Cygwin. Gcc prints its search
+ # path with ; separators, and with drive letters. We can handle the
+ # drive letters (cygwin fileutils understands them), so leave them,
+ # especially as we might pass files found there to a mingw objdump,
+ # which wouldn't understand a cygwinified path. Ahh.
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ ;;
+ pw32*)
+ # pw32 DLLs use 'pw' prefix rather than 'lib'
+ library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}'
+ ;;
+ esac
+ ;;
+
+ *)
+ library_names_spec='${libname}`echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext} $libname.lib'
+ ;;
+ esac
+ dynamic_linker='Win32 ld.exe'
+ # FIXME: first we should search . and the directory the executable is in
+ shlibpath_var=PATH
+ ;;
+
+darwin* | rhapsody*)
+ dynamic_linker="$host_os dyld"
+ version_type=darwin
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+ soname_spec='${libname}${release}${major}$shared_ext'
+ shlibpath_overrides_runpath=yes
+ shlibpath_var=DYLD_LIBRARY_PATH
+ shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+m4_if([$1], [],[
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /usr/local/lib"])
+ sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+ ;;
+
+dgux*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+freebsd1*)
+ dynamic_linker=no
+ ;;
+
+freebsd* | dragonfly*)
+ # DragonFly does not have aout. When/if they implement a new
+ # versioning mechanism, adjust this.
+ if test -x /usr/bin/objformat; then
+ objformat=`/usr/bin/objformat`
+ else
+ case $host_os in
+ freebsd[[123]]*) objformat=aout ;;
+ *) objformat=elf ;;
+ esac
+ fi
+ version_type=freebsd-$objformat
+ case $version_type in
+ freebsd-elf*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ need_version=no
+ need_lib_prefix=no
+ ;;
+ freebsd-*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+ need_version=yes
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_os in
+ freebsd2*)
+ shlibpath_overrides_runpath=yes
+ ;;
+ freebsd3.[[01]]* | freebsdelf3.[[01]]*)
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ freebsd3.[[2-9]]* | freebsdelf3.[[2-9]]* | \
+ freebsd4.[[0-5]] | freebsdelf4.[[0-5]] | freebsd4.1.1 | freebsdelf4.1.1)
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+ *) # from 4.6 on, and DragonFly
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ esac
+ ;;
+
+gnu*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ hardcode_into_libs=yes
+ ;;
+
+hpux9* | hpux10* | hpux11*)
+ # Give a soname corresponding to the major version so that dld.sl refuses to
+ # link against other versions.
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ case $host_cpu in
+ ia64*)
+ shrext_cmds='.so'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.so"
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ if test "X$HPUX_IA64_MODE" = X32; then
+ sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+ else
+ sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+ fi
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ hppa*64*)
+ shrext_cmds='.sl'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ *)
+ shrext_cmds='.sl'
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=SHLIB_PATH
+ shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+ esac
+ # HP-UX runs *really* slowly unless shared libraries are mode 555.
+ postinstall_cmds='chmod 555 $lib'
+ ;;
+
+interix[[3-9]]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $host_os in
+ nonstopux*) version_type=nonstopux ;;
+ *)
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ version_type=linux
+ else
+ version_type=irix
+ fi ;;
+ esac
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+ case $host_os in
+ irix5* | nonstopux*)
+ libsuff= shlibsuff=
+ ;;
+ *)
+ case $LD in # libtool.m4 will add one of these switches to LD
+ *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+ libsuff= shlibsuff= libmagic=32-bit;;
+ *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+ libsuff=32 shlibsuff=N32 libmagic=N32;;
+ *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+ libsuff=64 shlibsuff=64 libmagic=64-bit;;
+ *) libsuff= shlibsuff= libmagic=never-match;;
+ esac
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+ sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+ hardcode_into_libs=yes
+ ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+ dynamic_linker=no
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ # Some binutils ld are patched to set DT_RUNPATH
+ save_LDFLAGS=$LDFLAGS
+ save_libdir=$libdir
+ eval "libdir=/foo; wl=\"$_LT_TAGVAR(lt_prog_compiler_wl, $1)\"; \
+ LDFLAGS=\"\$LDFLAGS $_LT_TAGVAR(hardcode_libdir_flag_spec, $1)\""
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([],[])],
+ [AS_IF([ ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null],
+ [shlibpath_overrides_runpath=yes])])
+ LDFLAGS=$save_LDFLAGS
+ libdir=$save_libdir
+
+ # This implies no fast_install, which is unacceptable.
+ # Some rework will be needed to allow for fast_install
+ # before this can be enabled.
+ hardcode_into_libs=yes
+
+ # Append ld.so.conf contents to the search path
+ if test -f /etc/ld.so.conf; then
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \[$]2)); skip = 1; } { if (!skip) print \[$]0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ fi
+
+ # We used to test for /lib/ld.so.1 and disable shared libraries on
+ # powerpc, because MkLinux only supported shared libraries with the
+ # GNU dynamic linker. Since this was broken with cross compilers,
+ # most powerpc-linux boxes support dynamic linking these days and
+ # people can always --disable-shared, the test was removed, and we
+ # assume the GNU/Linux dynamic linker is in use.
+ dynamic_linker='GNU/Linux ld.so'
+ ;;
+
+netbsdelf*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='NetBSD ld.elf_so'
+ ;;
+
+netbsd*)
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ dynamic_linker='NetBSD (a.out) ld.so'
+ else
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='NetBSD ld.elf_so'
+ fi
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+
+newsos6)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ ;;
+
+*nto* | *qnx*)
+ version_type=qnx
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='ldqnx.so'
+ ;;
+
+openbsd*)
+ version_type=sunos
+ sys_lib_dlsearch_path_spec="/usr/lib"
+ need_lib_prefix=no
+ # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+ case $host_os in
+ openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+ *) need_version=no ;;
+ esac
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ case $host_os in
+ openbsd2.[[89]] | openbsd2.[[89]].*)
+ shlibpath_overrides_runpath=no
+ ;;
+ *)
+ shlibpath_overrides_runpath=yes
+ ;;
+ esac
+ else
+ shlibpath_overrides_runpath=yes
+ fi
+ ;;
+
+os2*)
+ libname_spec='$name'
+ shrext_cmds=".dll"
+ need_lib_prefix=no
+ library_names_spec='$libname${shared_ext} $libname.a'
+ dynamic_linker='OS/2 ld.exe'
+ shlibpath_var=LIBPATH
+ ;;
+
+osf3* | osf4* | osf5*)
+ version_type=osf
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+ sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+ ;;
+
+rdos*)
+ dynamic_linker=no
+ ;;
+
+solaris*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ # ldd complains unless libraries are executable
+ postinstall_cmds='chmod +x $lib'
+ ;;
+
+sunos4*)
+ version_type=sunos
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ if test "$with_gnu_ld" = yes; then
+ need_lib_prefix=no
+ fi
+ need_version=yes
+ ;;
+
+sysv4 | sysv4.3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_vendor in
+ sni)
+ shlibpath_overrides_runpath=no
+ need_lib_prefix=no
+ runpath_var=LD_RUN_PATH
+ ;;
+ siemens)
+ need_lib_prefix=no
+ ;;
+ motorola)
+ need_lib_prefix=no
+ need_version=no
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+ ;;
+ esac
+ ;;
+
+sysv4*MP*)
+ if test -d /usr/nec ;then
+ version_type=linux
+ library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+ soname_spec='$libname${shared_ext}.$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ fi
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ version_type=freebsd-elf
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ if test "$with_gnu_ld" = yes; then
+ sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+ else
+ sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+ case $host_os in
+ sco3.2v5*)
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+ ;;
+ esac
+ fi
+ sys_lib_dlsearch_path_spec='/usr/lib'
+ ;;
+
+tpf*)
+ # TPF is a cross-target only. Preferred cross-host = GNU/Linux.
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+uts4*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+*)
+ dynamic_linker=no
+ ;;
+esac
+AC_MSG_RESULT([$dynamic_linker])
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+ variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+
+if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then
+ sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec"
+fi
+if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then
+ sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec"
+fi
+
+_LT_DECL([], [variables_saved_for_relink], [1],
+ [Variables whose values should be saved in libtool wrapper scripts and
+ restored at link time])
+_LT_DECL([], [need_lib_prefix], [0],
+ [Do we need the "lib" prefix for modules?])
+_LT_DECL([], [need_version], [0], [Do we need a version for libraries?])
+_LT_DECL([], [version_type], [0], [Library versioning type])
+_LT_DECL([], [runpath_var], [0], [Shared library runtime path variable])
+_LT_DECL([], [shlibpath_var], [0],[Shared library path variable])
+_LT_DECL([], [shlibpath_overrides_runpath], [0],
+ [Is shlibpath searched before the hard-coded library search path?])
+_LT_DECL([], [libname_spec], [1], [Format of library name prefix])
+_LT_DECL([], [library_names_spec], [1],
+ [[List of archive names. First name is the real one, the rest are links.
+ The last name is the one that the linker finds with -lNAME]])
+_LT_DECL([], [soname_spec], [1],
+ [[The coded name of the library, if different from the real name]])
+_LT_DECL([], [postinstall_cmds], [2],
+ [Command to use after installation of a shared archive])
+_LT_DECL([], [postuninstall_cmds], [2],
+ [Command to use after uninstallation of a shared archive])
+_LT_DECL([], [finish_cmds], [2],
+ [Commands used to finish a libtool library installation in a directory])
+_LT_DECL([], [finish_eval], [1],
+ [[As "finish_cmds", except a single script fragment to be evaled but
+ not shown]])
+_LT_DECL([], [hardcode_into_libs], [0],
+ [Whether we should hardcode library paths into libraries])
+_LT_DECL([], [sys_lib_search_path_spec], [2],
+ [Compile-time system search path for libraries])
+_LT_DECL([], [sys_lib_dlsearch_path_spec], [2],
+ [Run-time system search path for libraries])
+])# _LT_SYS_DYNAMIC_LINKER
+
+
+# _LT_PATH_TOOL_PREFIX(TOOL)
+# --------------------------
+# find a file program which can recognize shared library
+AC_DEFUN([_LT_PATH_TOOL_PREFIX],
+[m4_require([_LT_DECL_EGREP])dnl
+AC_MSG_CHECKING([for $1])
+AC_CACHE_VAL(lt_cv_path_MAGIC_CMD,
+[case $MAGIC_CMD in
+[[\\/*] | ?:[\\/]*])
+ lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path.
+ ;;
+*)
+ lt_save_MAGIC_CMD="$MAGIC_CMD"
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+dnl $ac_dummy forces splitting on constant user-supplied paths.
+dnl POSIX.2 word splitting is done only on the output of word expansions,
+dnl not every word. This closes a longstanding sh security hole.
+ ac_dummy="m4_if([$2], , $PATH, [$2])"
+ for ac_dir in $ac_dummy; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f $ac_dir/$1; then
+ lt_cv_path_MAGIC_CMD="$ac_dir/$1"
+ if test -n "$file_magic_test_file"; then
+ case $deplibs_check_method in
+ "file_magic "*)
+ file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"`
+ MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+ if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null |
+ $EGREP "$file_magic_regex" > /dev/null; then
+ :
+ else
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the command libtool uses to detect shared libraries,
+*** $file_magic_cmd, produces output that libtool cannot recognize.
+*** The result is that libtool may fail to recognize shared libraries
+*** as such. This will affect the creation of libtool libraries that
+*** depend on shared libraries, but programs linked with such libtool
+*** libraries will work regardless of this problem. Nevertheless, you
+*** may want to report the problem to your system manager and/or to
+*** bug-libtool at gnu.org
+
+_LT_EOF
+ fi ;;
+ esac
+ fi
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+ MAGIC_CMD="$lt_save_MAGIC_CMD"
+ ;;
+esac])
+MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+if test -n "$MAGIC_CMD"; then
+ AC_MSG_RESULT($MAGIC_CMD)
+else
+ AC_MSG_RESULT(no)
+fi
+_LT_DECL([], [MAGIC_CMD], [0],
+ [Used to examine libraries when file_magic_cmd begins with "file"])dnl
+])# _LT_PATH_TOOL_PREFIX
+
+# Old name:
+AU_ALIAS([AC_PATH_TOOL_PREFIX], [_LT_PATH_TOOL_PREFIX])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_PATH_TOOL_PREFIX], [])
+
+
+# _LT_PATH_MAGIC
+# --------------
+# find a file program which can recognize a shared library
+m4_defun([_LT_PATH_MAGIC],
+[_LT_PATH_TOOL_PREFIX(${ac_tool_prefix}file, /usr/bin$PATH_SEPARATOR$PATH)
+if test -z "$lt_cv_path_MAGIC_CMD"; then
+ if test -n "$ac_tool_prefix"; then
+ _LT_PATH_TOOL_PREFIX(file, /usr/bin$PATH_SEPARATOR$PATH)
+ else
+ MAGIC_CMD=:
+ fi
+fi
+])# _LT_PATH_MAGIC
+
+
+# LT_PATH_LD
+# ----------
+# find the pathname to the GNU or non-GNU linker
+AC_DEFUN([LT_PATH_LD],
+[AC_REQUIRE([AC_PROG_CC])dnl
+AC_REQUIRE([AC_CANONICAL_HOST])dnl
+AC_REQUIRE([AC_CANONICAL_BUILD])dnl
+m4_require([_LT_DECL_SED])dnl
+m4_require([_LT_DECL_EGREP])dnl
+
+AC_ARG_WITH([gnu-ld],
+ [AS_HELP_STRING([--with-gnu-ld],
+ [assume the C compiler uses GNU ld @<:@default=no@:>@])],
+ [test "$withval" = no || with_gnu_ld=yes],
+ [with_gnu_ld=no])dnl
+
+ac_prog=ld
+if test "$GCC" = yes; then
+ # Check if gcc -print-prog-name=ld gives a path.
+ AC_MSG_CHECKING([for ld used by $CC])
+ case $host in
+ *-*-mingw*)
+ # gcc leaves a trailing carriage return which upsets mingw
+ ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+ *)
+ ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+ esac
+ case $ac_prog in
+ # Accept absolute paths.
+ [[\\/]]* | ?:[[\\/]]*)
+ re_direlt='/[[^/]][[^/]]*/\.\./'
+ # Canonicalize the pathname of ld
+ ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'`
+ while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do
+ ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"`
+ done
+ test -z "$LD" && LD="$ac_prog"
+ ;;
+ "")
+ # If it fails, then pretend we aren't using GCC.
+ ac_prog=ld
+ ;;
+ *)
+ # If it is relative, then search for the first ld in PATH.
+ with_gnu_ld=unknown
+ ;;
+ esac
+elif test "$with_gnu_ld" = yes; then
+ AC_MSG_CHECKING([for GNU ld])
+else
+ AC_MSG_CHECKING([for non-GNU ld])
+fi
+AC_CACHE_VAL(lt_cv_path_LD,
+[if test -z "$LD"; then
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+ lt_cv_path_LD="$ac_dir/$ac_prog"
+ # Check to see if the program is GNU ld. I'd rather use --version,
+ # but apparently some variants of GNU ld only accept -v.
+ # Break only if it was the GNU/non-GNU ld that we prefer.
+ case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+ *GNU* | *'with BFD'*)
+ test "$with_gnu_ld" != no && break
+ ;;
+ *)
+ test "$with_gnu_ld" != yes && break
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+else
+ lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi])
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+ AC_MSG_RESULT($LD)
+else
+ AC_MSG_RESULT(no)
+fi
+test -z "$LD" && AC_MSG_ERROR([no acceptable ld found in \$PATH])
+_LT_PATH_LD_GNU
+AC_SUBST([LD])
+
+_LT_TAGDECL([], [LD], [1], [The linker used to build libraries])
+])# LT_PATH_LD
+
+# Old names:
+AU_ALIAS([AM_PROG_LD], [LT_PATH_LD])
+AU_ALIAS([AC_PROG_LD], [LT_PATH_LD])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AM_PROG_LD], [])
+dnl AC_DEFUN([AC_PROG_LD], [])
+
+
+# _LT_PATH_LD_GNU
+#- --------------
+m4_defun([_LT_PATH_LD_GNU],
+[AC_CACHE_CHECK([if the linker ($LD) is GNU ld], lt_cv_prog_gnu_ld,
+[# I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+ lt_cv_prog_gnu_ld=yes
+ ;;
+*)
+ lt_cv_prog_gnu_ld=no
+ ;;
+esac])
+with_gnu_ld=$lt_cv_prog_gnu_ld
+])# _LT_PATH_LD_GNU
+
+
+# _LT_CMD_RELOAD
+# --------------
+# find reload flag for linker
+# -- PORTME Some linkers may need a different reload flag.
+m4_defun([_LT_CMD_RELOAD],
+[AC_CACHE_CHECK([for $LD option to reload object files],
+ lt_cv_ld_reload_flag,
+ [lt_cv_ld_reload_flag='-r'])
+reload_flag=$lt_cv_ld_reload_flag
+case $reload_flag in
+"" | " "*) ;;
+*) reload_flag=" $reload_flag" ;;
+esac
+reload_cmds='$LD$reload_flag -o $output$reload_objs'
+case $host_os in
+ darwin*)
+ if test "$GCC" = yes; then
+ reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs'
+ else
+ reload_cmds='$LD$reload_flag -o $output$reload_objs'
+ fi
+ ;;
+esac
+_LT_DECL([], [reload_flag], [1], [How to create reloadable object files])dnl
+_LT_DECL([], [reload_cmds], [2])dnl
+])# _LT_CMD_RELOAD
+
+
+# _LT_CHECK_MAGIC_METHOD
+# ----------------------
+# how to check for library dependencies
+# -- PORTME fill in with the dynamic library characteristics
+m4_defun([_LT_CHECK_MAGIC_METHOD],
+[m4_require([_LT_DECL_EGREP])
+m4_require([_LT_DECL_OBJDUMP])
+AC_CACHE_CHECK([how to recognize dependent libraries],
+lt_cv_deplibs_check_method,
+[lt_cv_file_magic_cmd='$MAGIC_CMD'
+lt_cv_file_magic_test_file=
+lt_cv_deplibs_check_method='unknown'
+# Need to set the preceding variable on all platforms that support
+# interlibrary dependencies.
+# 'none' -- dependencies not supported.
+# `unknown' -- same as none, but documents that we really don't know.
+# 'pass_all' -- all dependencies passed with no checks.
+# 'test_compile' -- check by making test program.
+# 'file_magic [[regex]]' -- check by looking for files in library path
+# which responds to the $file_magic_cmd with a given extended regex.
+# If you have `file' or equivalent on your system and you're not sure
+# whether `pass_all' will *always* work, you probably want this one.
+
+case $host_os in
+aix[[4-9]]*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+beos*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+bsdi[[45]]*)
+ lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (shared object|dynamic lib)'
+ lt_cv_file_magic_cmd='/usr/bin/file -L'
+ lt_cv_file_magic_test_file=/shlib/libc.so
+ ;;
+
+cygwin*)
+ # func_win32_libid is a shell function defined in ltmain.sh
+ lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+ lt_cv_file_magic_cmd='func_win32_libid'
+ ;;
+
+mingw* | pw32*)
+ # Base MSYS/MinGW do not provide the 'file' command needed by
+ # func_win32_libid shell function, so use a weaker test based on 'objdump',
+ # unless we find 'file', for example because we are cross-compiling.
+ if ( file / ) >/dev/null 2>&1; then
+ lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+ lt_cv_file_magic_cmd='func_win32_libid'
+ else
+ lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?'
+ lt_cv_file_magic_cmd='$OBJDUMP -f'
+ fi
+ ;;
+
+cegcc)
+ # use the weaker test based on 'objdump'. See mingw*.
+ lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?'
+ lt_cv_file_magic_cmd='$OBJDUMP -f'
+ ;;
+
+darwin* | rhapsody*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+freebsd* | dragonfly*)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
+ case $host_cpu in
+ i*86 )
+ # Not sure whether the presence of OpenBSD here was a mistake.
+ # Let's accept both of them until this is cleared up.
+ lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[[3-9]]86 (compact )?demand paged shared library'
+ lt_cv_file_magic_cmd=/usr/bin/file
+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*`
+ ;;
+ esac
+ else
+ lt_cv_deplibs_check_method=pass_all
+ fi
+ ;;
+
+gnu*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+hpux10.20* | hpux11*)
+ lt_cv_file_magic_cmd=/usr/bin/file
+ case $host_cpu in
+ ia64*)
+ lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|ELF-[[0-9]][[0-9]]) shared object file - IA64'
+ lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so
+ ;;
+ hppa*64*)
+ [lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]']
+ lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl
+ ;;
+ *)
+ lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|PA-RISC[[0-9]].[[0-9]]) shared library'
+ lt_cv_file_magic_test_file=/usr/lib/libc.sl
+ ;;
+ esac
+ ;;
+
+interix[[3-9]]*)
+ # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|\.a)$'
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $LD in
+ *-32|*"-32 ") libmagic=32-bit;;
+ *-n32|*"-n32 ") libmagic=N32;;
+ *-64|*"-64 ") libmagic=64-bit;;
+ *) libmagic=never-match;;
+ esac
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$'
+ else
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|_pic\.a)$'
+ fi
+ ;;
+
+newos6*)
+ lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (executable|dynamic lib)'
+ lt_cv_file_magic_cmd=/usr/bin/file
+ lt_cv_file_magic_test_file=/usr/lib/libnls.so
+ ;;
+
+*nto* | *qnx*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+openbsd*)
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|\.so|_pic\.a)$'
+ else
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$'
+ fi
+ ;;
+
+osf3* | osf4* | osf5*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+rdos*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+solaris*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+sysv4 | sysv4.3*)
+ case $host_vendor in
+ motorola)
+ lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (shared object|dynamic lib) M[[0-9]][[0-9]]* Version [[0-9]]'
+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*`
+ ;;
+ ncr)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ sequent)
+ lt_cv_file_magic_cmd='/bin/file'
+ lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB (shared object|dynamic lib )'
+ ;;
+ sni)
+ lt_cv_file_magic_cmd='/bin/file'
+ lt_cv_deplibs_check_method="file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB dynamic lib"
+ lt_cv_file_magic_test_file=/lib/libc.so
+ ;;
+ siemens)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ pc)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ esac
+ ;;
+
+tpf*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+esac
+])
+file_magic_cmd=$lt_cv_file_magic_cmd
+deplibs_check_method=$lt_cv_deplibs_check_method
+test -z "$deplibs_check_method" && deplibs_check_method=unknown
+
+_LT_DECL([], [deplibs_check_method], [1],
+ [Method to check whether dependent libraries are shared objects])
+_LT_DECL([], [file_magic_cmd], [1],
+ [Command to use when deplibs_check_method == "file_magic"])
+])# _LT_CHECK_MAGIC_METHOD
+
+
+# LT_PATH_NM
+# ----------
+# find the pathname to a BSD- or MS-compatible name lister
+AC_DEFUN([LT_PATH_NM],
+[AC_REQUIRE([AC_PROG_CC])dnl
+AC_CACHE_CHECK([for BSD- or MS-compatible name lister (nm)], lt_cv_path_NM,
+[if test -n "$NM"; then
+ # Let the user override the test.
+ lt_cv_path_NM="$NM"
+else
+ lt_nm_to_check="${ac_tool_prefix}nm"
+ if test -n "$ac_tool_prefix" && test "$build" = "$host"; then
+ lt_nm_to_check="$lt_nm_to_check nm"
+ fi
+ for lt_tmp_nm in $lt_nm_to_check; do
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ tmp_nm="$ac_dir/$lt_tmp_nm"
+ if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then
+ # Check to see if the nm accepts a BSD-compat flag.
+ # Adding the `sed 1q' prevents false positives on HP-UX, which says:
+ # nm: unknown option "B" ignored
+ # Tru64's nm complains that /dev/null is an invalid object file
+ case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in
+ */dev/null* | *'Invalid file or object type'*)
+ lt_cv_path_NM="$tmp_nm -B"
+ break
+ ;;
+ *)
+ case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in
+ */dev/null*)
+ lt_cv_path_NM="$tmp_nm -p"
+ break
+ ;;
+ *)
+ lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but
+ continue # so that we can try to find one that supports BSD flags
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+ done
+ : ${lt_cv_path_NM=no}
+fi])
+if test "$lt_cv_path_NM" != "no"; then
+ NM="$lt_cv_path_NM"
+else
+ # Didn't find any BSD compatible name lister, look for dumpbin.
+ AC_CHECK_TOOLS(DUMPBIN, ["dumpbin -symbols" "link -dump -symbols"], :)
+ AC_SUBST([DUMPBIN])
+ if test "$DUMPBIN" != ":"; then
+ NM="$DUMPBIN"
+ fi
+fi
+test -z "$NM" && NM=nm
+AC_SUBST([NM])
+_LT_DECL([], [NM], [1], [A BSD- or MS-compatible name lister])dnl
+
+AC_CACHE_CHECK([the name lister ($NM) interface], [lt_cv_nm_interface],
+ [lt_cv_nm_interface="BSD nm"
+ echo "int some_variable = 0;" > conftest.$ac_ext
+ (eval echo "\"\$as_me:__oline__: $ac_compile\"" >&AS_MESSAGE_LOG_FD)
+ (eval "$ac_compile" 2>conftest.err)
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ (eval echo "\"\$as_me:__oline__: $NM \\\"conftest.$ac_objext\\\"\"" >&AS_MESSAGE_LOG_FD)
+ (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out)
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ (eval echo "\"\$as_me:__oline__: output\"" >&AS_MESSAGE_LOG_FD)
+ cat conftest.out >&AS_MESSAGE_LOG_FD
+ if $GREP 'External.*some_variable' conftest.out > /dev/null; then
+ lt_cv_nm_interface="MS dumpbin"
+ fi
+ rm -f conftest*])
+])# LT_PATH_NM
+
+# Old names:
+AU_ALIAS([AM_PROG_NM], [LT_PATH_NM])
+AU_ALIAS([AC_PROG_NM], [LT_PATH_NM])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AM_PROG_NM], [])
+dnl AC_DEFUN([AC_PROG_NM], [])
+
+
+# LT_LIB_M
+# --------
+# check for math library
+AC_DEFUN([LT_LIB_M],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+LIBM=
+case $host in
+*-*-beos* | *-*-cygwin* | *-*-pw32* | *-*-darwin*)
+ # These system don't have libm, or don't need it
+ ;;
+*-ncr-sysv4.3*)
+ AC_CHECK_LIB(mw, _mwvalidcheckl, LIBM="-lmw")
+ AC_CHECK_LIB(m, cos, LIBM="$LIBM -lm")
+ ;;
+*)
+ AC_CHECK_LIB(m, cos, LIBM="-lm")
+ ;;
+esac
+AC_SUBST([LIBM])
+])# LT_LIB_M
+
+# Old name:
+AU_ALIAS([AC_CHECK_LIBM], [LT_LIB_M])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_CHECK_LIBM], [])
+
+
+# _LT_COMPILER_NO_RTTI([TAGNAME])
+# -------------------------------
+m4_defun([_LT_COMPILER_NO_RTTI],
+[m4_require([_LT_TAG_COMPILER])dnl
+
+_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=
+
+if test "$GCC" = yes; then
+ _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin'
+
+ _LT_COMPILER_OPTION([if $compiler supports -fno-rtti -fno-exceptions],
+ lt_cv_prog_compiler_rtti_exceptions,
+ [-fno-rtti -fno-exceptions], [],
+ [_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)="$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1) -fno-rtti -fno-exceptions"])
+fi
+_LT_TAGDECL([no_builtin_flag], [lt_prog_compiler_no_builtin_flag], [1],
+ [Compiler flag to turn off builtin functions])
+])# _LT_COMPILER_NO_RTTI
+
+
+# _LT_CMD_GLOBAL_SYMBOLS
+# ----------------------
+m4_defun([_LT_CMD_GLOBAL_SYMBOLS],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+AC_REQUIRE([AC_PROG_CC])dnl
+AC_REQUIRE([LT_PATH_NM])dnl
+AC_REQUIRE([LT_PATH_LD])dnl
+m4_require([_LT_DECL_SED])dnl
+m4_require([_LT_DECL_EGREP])dnl
+m4_require([_LT_TAG_COMPILER])dnl
+
+# Check for command to grab the raw symbol name followed by C symbol from nm.
+AC_MSG_CHECKING([command to parse $NM output from $compiler object])
+AC_CACHE_VAL([lt_cv_sys_global_symbol_pipe],
+[
+# These are sane defaults that work on at least a few old systems.
+# [They come from Ultrix. What could be older than Ultrix?!! ;)]
+
+# Character class describing NM global symbol codes.
+symcode='[[BCDEGRST]]'
+
+# Regexp to match symbols that can be accessed directly from C.
+sympat='\([[_A-Za-z]][[_A-Za-z0-9]]*\)'
+
+# Define system-specific variables.
+case $host_os in
+aix*)
+ symcode='[[BCDT]]'
+ ;;
+cygwin* | mingw* | pw32* | cegcc*)
+ symcode='[[ABCDGISTW]]'
+ ;;
+hpux*)
+ if test "$host_cpu" = ia64; then
+ symcode='[[ABCDEGRST]]'
+ fi
+ ;;
+irix* | nonstopux*)
+ symcode='[[BCDEGRST]]'
+ ;;
+osf*)
+ symcode='[[BCDEGQRST]]'
+ ;;
+solaris*)
+ symcode='[[BDRT]]'
+ ;;
+sco3.2v5*)
+ symcode='[[DT]]'
+ ;;
+sysv4.2uw2*)
+ symcode='[[DT]]'
+ ;;
+sysv5* | sco5v6* | unixware* | OpenUNIX*)
+ symcode='[[ABDT]]'
+ ;;
+sysv4)
+ symcode='[[DFNSTU]]'
+ ;;
+esac
+
+# If we're using GNU nm, then use its standard symbol codes.
+case `$NM -V 2>&1` in
+*GNU* | *'with BFD'*)
+ symcode='[[ABCDGIRSTW]]' ;;
+esac
+
+# Transform an extracted symbol line into a proper C declaration.
+# Some systems (esp. on ia64) link data and code symbols differently,
+# so use this general approach.
+lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'"
+
+# Transform an extracted symbol line into symbol name and symbol address
+lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p'"
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \(lib[[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"lib\2\", (void *) \&\2},/p'"
+
+# Handle CRLF in mingw tool chain
+opt_cr=
+case $build_os in
+mingw*)
+ opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp
+ ;;
+esac
+
+# Try without a prefix underscore, then with it.
+for ac_symprfx in "" "_"; do
+
+ # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol.
+ symxfrm="\\1 $ac_symprfx\\2 \\2"
+
+ # Write the raw and C identifiers.
+ if test "$lt_cv_nm_interface" = "MS dumpbin"; then
+ # Fake it for dumpbin and say T for any non-static function
+ # and D for any global variable.
+ # Also find C++ and __fastcall symbols from MSVC++,
+ # which start with @ or ?.
+ lt_cv_sys_global_symbol_pipe="$AWK ['"\
+" {last_section=section; section=\$ 3};"\
+" /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\
+" \$ 0!~/External *\|/{next};"\
+" / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\
+" {if(hide[section]) next};"\
+" {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\
+" {split(\$ 0, a, /\||\r/); split(a[2], s)};"\
+" s[1]~/^[@?]/{print s[1], s[1]; next};"\
+" s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\
+" ' prfx=^$ac_symprfx]"
+ else
+ lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[[ ]]\($symcode$symcode*\)[[ ]][[ ]]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'"
+ fi
+
+ # Check to see that the pipe works correctly.
+ pipe_works=no
+
+ rm -f conftest*
+ cat > conftest.$ac_ext <<_LT_EOF
+#ifdef __cplusplus
+extern "C" {
+#endif
+char nm_test_var;
+void nm_test_func(void);
+void nm_test_func(void){}
+#ifdef __cplusplus
+}
+#endif
+int main(){nm_test_var='a';nm_test_func();return(0);}
+_LT_EOF
+
+ if AC_TRY_EVAL(ac_compile); then
+ # Now try to grab the symbols.
+ nlist=conftest.nm
+ if AC_TRY_EVAL(NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) && test -s "$nlist"; then
+ # Try sorting and uniquifying the output.
+ if sort "$nlist" | uniq > "$nlist"T; then
+ mv -f "$nlist"T "$nlist"
+ else
+ rm -f "$nlist"T
+ fi
+
+ # Make sure that we snagged all the symbols we need.
+ if $GREP ' nm_test_var$' "$nlist" >/dev/null; then
+ if $GREP ' nm_test_func$' "$nlist" >/dev/null; then
+ cat <<_LT_EOF > conftest.$ac_ext
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+_LT_EOF
+ # Now generate the symbol file.
+ eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext'
+
+ cat <<_LT_EOF >> conftest.$ac_ext
+
+/* The mapping between symbol names and symbols. */
+const struct {
+ const char *name;
+ void *address;
+}
+lt__PROGRAM__LTX_preloaded_symbols[[]] =
+{
+ { "@PROGRAM@", (void *) 0 },
+_LT_EOF
+ $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext
+ cat <<\_LT_EOF >> conftest.$ac_ext
+ {0, (void *) 0}
+};
+
+/* This works around a problem in FreeBSD linker */
+#ifdef FREEBSD_WORKAROUND
+static const void *lt_preloaded_setup() {
+ return lt__PROGRAM__LTX_preloaded_symbols;
+}
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+_LT_EOF
+ # Now try linking the two files.
+ mv conftest.$ac_objext conftstm.$ac_objext
+ lt_save_LIBS="$LIBS"
+ lt_save_CFLAGS="$CFLAGS"
+ LIBS="conftstm.$ac_objext"
+ CFLAGS="$CFLAGS$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)"
+ if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext}; then
+ pipe_works=yes
+ fi
+ LIBS="$lt_save_LIBS"
+ CFLAGS="$lt_save_CFLAGS"
+ else
+ echo "cannot find nm_test_func in $nlist" >&AS_MESSAGE_LOG_FD
+ fi
+ else
+ echo "cannot find nm_test_var in $nlist" >&AS_MESSAGE_LOG_FD
+ fi
+ else
+ echo "cannot run $lt_cv_sys_global_symbol_pipe" >&AS_MESSAGE_LOG_FD
+ fi
+ else
+ echo "$progname: failed program was:" >&AS_MESSAGE_LOG_FD
+ cat conftest.$ac_ext >&5
+ fi
+ rm -rf conftest* conftst*
+
+ # Do not use the global_symbol_pipe unless it works.
+ if test "$pipe_works" = yes; then
+ break
+ else
+ lt_cv_sys_global_symbol_pipe=
+ fi
+done
+])
+if test -z "$lt_cv_sys_global_symbol_pipe"; then
+ lt_cv_sys_global_symbol_to_cdecl=
+fi
+if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then
+ AC_MSG_RESULT(failed)
+else
+ AC_MSG_RESULT(ok)
+fi
+
+_LT_DECL([global_symbol_pipe], [lt_cv_sys_global_symbol_pipe], [1],
+ [Take the output of nm and produce a listing of raw symbols and C names])
+_LT_DECL([global_symbol_to_cdecl], [lt_cv_sys_global_symbol_to_cdecl], [1],
+ [Transform the output of nm in a proper C declaration])
+_LT_DECL([global_symbol_to_c_name_address],
+ [lt_cv_sys_global_symbol_to_c_name_address], [1],
+ [Transform the output of nm in a C name address pair])
+_LT_DECL([global_symbol_to_c_name_address_lib_prefix],
+ [lt_cv_sys_global_symbol_to_c_name_address_lib_prefix], [1],
+ [Transform the output of nm in a C name address pair when lib prefix is needed])
+]) # _LT_CMD_GLOBAL_SYMBOLS
+
+
+# _LT_COMPILER_PIC([TAGNAME])
+# ---------------------------
+m4_defun([_LT_COMPILER_PIC],
+[m4_require([_LT_TAG_COMPILER])dnl
+_LT_TAGVAR(lt_prog_compiler_wl, $1)=
+_LT_TAGVAR(lt_prog_compiler_pic, $1)=
+_LT_TAGVAR(lt_prog_compiler_static, $1)=
+
+AC_MSG_CHECKING([for $compiler option to produce PIC])
+m4_if([$1], [CXX], [
+ # C++ specific cases for pic, static, wl, etc.
+ if test "$GXX" = yes; then
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+
+ case $host_os in
+ aix*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ m68k)
+ # FIXME: we need at least 68020 code to build shared libraries, but
+ # adding the `-m68020' flag to GCC prevents building anything better,
+ # like `-m68040'.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4'
+ ;;
+ esac
+ ;;
+
+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+ # PIC is the default for these OSes.
+ ;;
+ mingw* | cygwin* | os2* | pw32* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ # Although the cygwin gcc ignores -fPIC, still need this for old-style
+ # (--disable-auto-import) libraries
+ m4_if([$1], [GCJ], [],
+ [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT'])
+ ;;
+ darwin* | rhapsody*)
+ # PIC is the default on this platform
+ # Common symbols not allowed in MH_DYLIB files
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common'
+ ;;
+ *djgpp*)
+ # DJGPP does not support shared libraries at all
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ ;;
+ interix[[3-9]]*)
+ # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+ # Instead, we relocate shared libraries at runtime.
+ ;;
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic
+ fi
+ ;;
+ hpux*)
+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit
+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag
+ # sets the default TLS model and affects inlining.
+ case $host_cpu in
+ hppa*64*)
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ esac
+ ;;
+ *qnx* | *nto*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared'
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ esac
+ else
+ case $host_os in
+ aix[[4-9]]*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ else
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp'
+ fi
+ ;;
+ chorus*)
+ case $cc_basename in
+ cxch68*)
+ # Green Hills C++ Compiler
+ # _LT_TAGVAR(lt_prog_compiler_static, $1)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a"
+ ;;
+ esac
+ ;;
+ dgux*)
+ case $cc_basename in
+ ec++*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ ;;
+ ghcx*)
+ # Green Hills C++ Compiler
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ freebsd* | dragonfly*)
+ # FreeBSD uses GNU C++
+ ;;
+ hpux9* | hpux10* | hpux11*)
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive'
+ if test "$host_cpu" != ia64; then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z'
+ fi
+ ;;
+ aCC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive'
+ case $host_cpu in
+ hppa*64*|ia64*)
+ # +Z the default
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z'
+ ;;
+ esac
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ interix*)
+ # This is c89, which is MS Visual C++ (no shared libs)
+ # Anyone wants to do a port?
+ ;;
+ irix5* | irix6* | nonstopux*)
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ # CC pic flag -KPIC is the default.
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ KCC*)
+ # KAI C++ Compiler
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ ecpc* )
+ # old Intel C++ for x86_64 which still supported -KPIC.
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ icpc* )
+ # Intel C++, used to be incompatible with GCC.
+ # ICC 10 doesn't accept -KPIC any more.
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ pgCC* | pgcpp*)
+ # Portland Group C++ compiler
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+ cxx*)
+ # Compaq C++
+ # Make sure the PIC flag is empty. It appears that all Alpha
+ # Linux and Compaq Tru64 Unix objects are PIC.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+ xlc* | xlC*)
+ # IBM XL 8.0 on PPC
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink'
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld '
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+ lynxos*)
+ ;;
+ m88k*)
+ ;;
+ mvs*)
+ case $cc_basename in
+ cxx*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-W c,exportall'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ netbsd* | netbsdelf*-gnu)
+ ;;
+ *qnx* | *nto*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared'
+ ;;
+ osf3* | osf4* | osf5*)
+ case $cc_basename in
+ KCC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,'
+ ;;
+ RCC*)
+ # Rational C++ 2.4.1
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ ;;
+ cxx*)
+ # Digital/Compaq C++
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # Make sure the PIC flag is empty. It appears that all Alpha
+ # Linux and Compaq Tru64 Unix objects are PIC.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ psos*)
+ ;;
+ solaris*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.2, 5.x and Centerline C++
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld '
+ ;;
+ gcx*)
+ # Green Hills C++ Compiler
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ sunos4*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.x
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+ lcc*)
+ # Lucid
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+ esac
+ ;;
+ tandem*)
+ case $cc_basename in
+ NCC*)
+ # NonStop-UX NCC 3.20
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ vxworks*)
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+ ;;
+ esac
+ fi
+],
+[
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+
+ case $host_os in
+ aix*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ m68k)
+ # FIXME: we need at least 68020 code to build shared libraries, but
+ # adding the `-m68020' flag to GCC prevents building anything better,
+ # like `-m68040'.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4'
+ ;;
+ esac
+ ;;
+
+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+ # PIC is the default for these OSes.
+ ;;
+
+ mingw* | cygwin* | pw32* | os2* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ # Although the cygwin gcc ignores -fPIC, still need this for old-style
+ # (--disable-auto-import) libraries
+ m4_if([$1], [GCJ], [],
+ [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT'])
+ ;;
+
+ darwin* | rhapsody*)
+ # PIC is the default on this platform
+ # Common symbols not allowed in MH_DYLIB files
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common'
+ ;;
+
+ hpux*)
+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit
+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag
+ # sets the default TLS model and affects inlining.
+ case $host_cpu in
+ hppa*64*)
+ # +Z the default
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ esac
+ ;;
+
+ interix[[3-9]]*)
+ # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+ # Instead, we relocate shared libraries at runtime.
+ ;;
+
+ msdosdjgpp*)
+ # Just because we use GCC doesn't mean we suddenly get shared libraries
+ # on systems that don't support them.
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+ enable_shared=no
+ ;;
+
+ *nto* | *qnx*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic
+ fi
+ ;;
+
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ esac
+ else
+ # PORTME Check for flag to pass linker flags through the system compiler.
+ case $host_os in
+ aix*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ else
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp'
+ fi
+ ;;
+
+ mingw* | cygwin* | pw32* | os2* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ m4_if([$1], [GCJ], [],
+ [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT'])
+ ;;
+
+ hpux9* | hpux10* | hpux11*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+ # not for PA HP-UX.
+ case $host_cpu in
+ hppa*64*|ia64*)
+ # +Z the default
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z'
+ ;;
+ esac
+ # Is there a better lt_prog_compiler_static that works with the bundled CC?
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive'
+ ;;
+
+ irix5* | irix6* | nonstopux*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # PIC (with -KPIC) is the default.
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ # old Intel for x86_64 which still supported -KPIC.
+ ecc*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ # icc used to be incompatible with GCC.
+ # ICC 10 doesn't accept -KPIC any more.
+ icc* | ifort*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ # Lahey Fortran 8.1.
+ lf95*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='--shared'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='--static'
+ ;;
+ pgcc* | pgf77* | pgf90* | pgf95*)
+ # Portland Group compilers (*not* the Pentium gcc compiler,
+ # which looks to be a dead project)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+ ccc*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # All Alpha code is PIC.
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+ xl*)
+ # IBM XL C 8.0/Fortran 10.1 on PPC
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink'
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C 5.9
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ ;;
+ *Sun\ F*)
+ # Sun Fortran 8.3 passes all unrecognized flags to the linker
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)=''
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+
+ newsos6)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ *nto* | *qnx*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared'
+ ;;
+
+ osf3* | osf4* | osf5*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # All OSF/1 code is PIC.
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+
+ rdos*)
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+
+ solaris*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ case $cc_basename in
+ f77* | f90* | f95*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ';;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,';;
+ esac
+ ;;
+
+ sunos4*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld '
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ sysv4 | sysv4.2uw2* | sysv4.3*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec ;then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-Kconform_pic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ fi
+ ;;
+
+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ unicos*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+ ;;
+
+ uts4*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ *)
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+ ;;
+ esac
+ fi
+])
+case $host_os in
+ # For platforms which do not support PIC, -DPIC is meaningless:
+ *djgpp*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)="$_LT_TAGVAR(lt_prog_compiler_pic, $1)@&t at m4_if([$1],[],[ -DPIC],[m4_if([$1],[CXX],[ -DPIC],[])])"
+ ;;
+esac
+AC_MSG_RESULT([$_LT_TAGVAR(lt_prog_compiler_pic, $1)])
+_LT_TAGDECL([wl], [lt_prog_compiler_wl], [1],
+ [How to pass a linker flag through the compiler])
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$_LT_TAGVAR(lt_prog_compiler_pic, $1)"; then
+ _LT_COMPILER_OPTION([if $compiler PIC flag $_LT_TAGVAR(lt_prog_compiler_pic, $1) works],
+ [_LT_TAGVAR(lt_cv_prog_compiler_pic_works, $1)],
+ [$_LT_TAGVAR(lt_prog_compiler_pic, $1)@&t at m4_if([$1],[],[ -DPIC],[m4_if([$1],[CXX],[ -DPIC],[])])], [],
+ [case $_LT_TAGVAR(lt_prog_compiler_pic, $1) in
+ "" | " "*) ;;
+ *) _LT_TAGVAR(lt_prog_compiler_pic, $1)=" $_LT_TAGVAR(lt_prog_compiler_pic, $1)" ;;
+ esac],
+ [_LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no])
+fi
+_LT_TAGDECL([pic_flag], [lt_prog_compiler_pic], [1],
+ [Additional compiler flags for building library objects])
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$_LT_TAGVAR(lt_prog_compiler_wl, $1) eval lt_tmp_static_flag=\"$_LT_TAGVAR(lt_prog_compiler_static, $1)\"
+_LT_LINKER_OPTION([if $compiler static flag $lt_tmp_static_flag works],
+ _LT_TAGVAR(lt_cv_prog_compiler_static_works, $1),
+ $lt_tmp_static_flag,
+ [],
+ [_LT_TAGVAR(lt_prog_compiler_static, $1)=])
+_LT_TAGDECL([link_static_flag], [lt_prog_compiler_static], [1],
+ [Compiler flag to prevent dynamic linking])
+])# _LT_COMPILER_PIC
+
+
+# _LT_LINKER_SHLIBS([TAGNAME])
+# ----------------------------
+# See if the linker supports building shared libraries.
+m4_defun([_LT_LINKER_SHLIBS],
+[AC_REQUIRE([LT_PATH_LD])dnl
+AC_REQUIRE([LT_PATH_NM])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_EGREP])dnl
+m4_require([_LT_DECL_SED])dnl
+m4_require([_LT_CMD_GLOBAL_SYMBOLS])dnl
+m4_require([_LT_TAG_COMPILER])dnl
+AC_MSG_CHECKING([whether the $compiler linker ($LD) supports shared libraries])
+m4_if([$1], [CXX], [
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ case $host_os in
+ aix[[4-9]]*)
+ # If we're using GNU nm, then we don't want the "-C" option.
+ # -C means demangle to AIX nm, but means don't demangle with GNU nm
+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ else
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ fi
+ ;;
+ pw32*)
+ _LT_TAGVAR(export_symbols_cmds, $1)="$ltdll_cmds"
+ ;;
+ cygwin* | mingw* | cegcc*)
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]][[ ]]/s/.*[[ ]]\([[^ ]]*\)/\1 DATA/;/^.*[[ ]]__nm__/s/^.*[[ ]]__nm__\([[^ ]]*\)[[ ]][[^ ]]*/\1 DATA/;/^I[[ ]]/d;/^[[AITW]][[ ]]/s/.* //'\'' | sort | uniq > $export_symbols'
+ ;;
+ linux* | k*bsd*-gnu)
+ _LT_TAGVAR(link_all_deplibs, $1)=no
+ ;;
+ *)
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ ;;
+ esac
+ _LT_TAGVAR(exclude_expsyms, $1)=['_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*']
+], [
+ runpath_var=
+ _LT_TAGVAR(allow_undefined_flag, $1)=
+ _LT_TAGVAR(always_export_symbols, $1)=no
+ _LT_TAGVAR(archive_cmds, $1)=
+ _LT_TAGVAR(archive_expsym_cmds, $1)=
+ _LT_TAGVAR(compiler_needs_object, $1)=no
+ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)=
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ _LT_TAGVAR(hardcode_automatic, $1)=no
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+ _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=
+ _LT_TAGVAR(hardcode_minus_L, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
+ _LT_TAGVAR(inherit_rpath, $1)=no
+ _LT_TAGVAR(link_all_deplibs, $1)=unknown
+ _LT_TAGVAR(module_cmds, $1)=
+ _LT_TAGVAR(module_expsym_cmds, $1)=
+ _LT_TAGVAR(old_archive_from_new_cmds, $1)=
+ _LT_TAGVAR(old_archive_from_expsyms_cmds, $1)=
+ _LT_TAGVAR(thread_safe_flag_spec, $1)=
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ # include_expsyms should be a list of space-separated symbols to be *always*
+ # included in the symbol list
+ _LT_TAGVAR(include_expsyms, $1)=
+ # exclude_expsyms can be an extended regexp of symbols to exclude
+ # it will be wrapped by ` (' and `)$', so one must not match beginning or
+ # end of line. Example: `a|bc|.*d.*' will exclude the symbols `a' and `bc',
+ # as well as any symbol that contains `d'.
+ _LT_TAGVAR(exclude_expsyms, $1)=['_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*']
+ # Although _GLOBAL_OFFSET_TABLE_ is a valid symbol C name, most a.out
+ # platforms (ab)use it in PIC code, but their linkers get confused if
+ # the symbol is explicitly referenced. Since portable code cannot
+ # rely on this symbol name, it's probably fine to never include it in
+ # preloaded symbol tables.
+ # Exclude shared library initialization/finalization symbols.
+dnl Note also adjust exclude_expsyms for C++ above.
+ extract_expsyms_cmds=
+
+ case $host_os in
+ cygwin* | mingw* | pw32* | cegcc*)
+ # FIXME: the MSVC++ port hasn't been tested in a loooong time
+ # When not using gcc, we currently assume that we are using
+ # Microsoft Visual C++.
+ if test "$GCC" != yes; then
+ with_gnu_ld=no
+ fi
+ ;;
+ interix*)
+ # we just hope/assume this is gcc and not c89 (= MSVC++)
+ with_gnu_ld=yes
+ ;;
+ openbsd*)
+ with_gnu_ld=no
+ ;;
+ linux* | k*bsd*-gnu)
+ _LT_TAGVAR(link_all_deplibs, $1)=no
+ ;;
+ esac
+
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ if test "$with_gnu_ld" = yes; then
+ # If archive_cmds runs LD, not CC, wlarc should be empty
+ wlarc='${wl}'
+
+ # Set some defaults for GNU ld with shared library support. These
+ # are reset later if shared libraries are not supported. Putting them
+ # here allows them to be overridden if necessary.
+ runpath_var=LD_RUN_PATH
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+ # ancient GNU ld didn't support --whole-archive et. al.
+ if $LD --help 2>&1 | $GREP 'no-whole-archive' > /dev/null; then
+ _LT_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ else
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ fi
+ supports_anon_versioning=no
+ case `$LD -v 2>&1` in
+ *GNU\ gold*) supports_anon_versioning=yes ;;
+ *\ [[01]].* | *\ 2.[[0-9]].* | *\ 2.10.*) ;; # catch versions < 2.11
+ *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ...
+ *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ...
+ *\ 2.11.*) ;; # other 2.11 versions
+ *) supports_anon_versioning=yes ;;
+ esac
+
+ # See if GNU ld supports shared libraries.
+ case $host_os in
+ aix[[3-9]]*)
+ # On AIX/PPC, the GNU linker is very broken
+ if test "$host_cpu" != ia64; then
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the GNU linker, at least up to release 2.9.1, is reported
+*** to be unable to reliably create shared libraries on AIX.
+*** Therefore, libtool is disabling shared libraries support. If you
+*** really care for shared libraries, you may want to modify your PATH
+*** so that a non-GNU linker is found, and then restart.
+
+_LT_EOF
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)=''
+ ;;
+ m68k)
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ ;;
+ esac
+ ;;
+
+ beos*)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ # Joseph Beckenbach <jrb3 at best.com> says some releases of gcc
+ # support --undefined. This deserves some investigation. FIXME
+ _LT_TAGVAR(archive_cmds, $1)='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # _LT_TAGVAR(hardcode_libdir_flag_spec, $1) is actually meaningless,
+ # as there is no search path for DLLs.
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ _LT_TAGVAR(always_export_symbols, $1)=no
+ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]][[ ]]/s/.*[[ ]]\([[^ ]]*\)/\1 DATA/'\'' | $SED -e '\''/^[[AITW]][[ ]]/s/.*[[ ]]//'\'' | sort | uniq > $export_symbols'
+
+ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ # If the export-symbols file already is a .def file (1st line
+ # is EXPORTS), use it as is; otherwise, prepend...
+ _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+ cp $export_symbols $output_objdir/$soname.def;
+ else
+ echo EXPORTS > $output_objdir/$soname.def;
+ cat $export_symbols >> $output_objdir/$soname.def;
+ fi~
+ $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ interix[[3-9]]*)
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+ # Instead, shared libraries are loaded at an image base (0x10000000 by
+ # default) and relocated if they conflict, which is a slow very memory
+ # consuming and fragmenting process. To avoid this, we pick a random,
+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+ # time. Moving up from 0x10000000 also allows more sbrk(2) space.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ ;;
+
+ gnu* | linux* | tpf* | k*bsd*-gnu | kopensolaris*-gnu)
+ tmp_diet=no
+ if test "$host_os" = linux-dietlibc; then
+ case $cc_basename in
+ diet\ *) tmp_diet=yes;; # linux-dietlibc with static linking (!diet-dyn)
+ esac
+ fi
+ if $LD --help 2>&1 | $EGREP ': supported targets:.* elf' > /dev/null \
+ && test "$tmp_diet" = no
+ then
+ tmp_addflag=
+ tmp_sharedflag='-shared'
+ case $cc_basename,$host_cpu in
+ pgcc*) # Portland Group C compiler
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ tmp_addflag=' $pic_flag'
+ ;;
+ pgf77* | pgf90* | pgf95*) # Portland Group f77 and f90 compilers
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ tmp_addflag=' $pic_flag -Mnomain' ;;
+ ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64
+ tmp_addflag=' -i_dynamic' ;;
+ efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64
+ tmp_addflag=' -i_dynamic -nofor_main' ;;
+ ifc* | ifort*) # Intel Fortran compiler
+ tmp_addflag=' -nofor_main' ;;
+ lf95*) # Lahey Fortran 8.1
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ tmp_sharedflag='--shared' ;;
+ xl[[cC]]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ tmp_sharedflag='-qmkshrobj'
+ tmp_addflag= ;;
+ esac
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*) # Sun C 5.9
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ _LT_TAGVAR(compiler_needs_object, $1)=yes
+ tmp_sharedflag='-G' ;;
+ *Sun\ F*) # Sun Fortran 8.3
+ tmp_sharedflag='-G' ;;
+ esac
+ _LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+
+ if test "x$supports_anon_versioning" = xyes; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+ fi
+
+ case $cc_basename in
+ xlf*)
+ # IBM XL Fortran 10.1 on PPC cannot create shared libs itself
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='--whole-archive$convenience --no-whole-archive'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+ _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='-rpath $libdir'
+ _LT_TAGVAR(archive_cmds, $1)='$LD -shared $libobjs $deplibs $compiler_flags -soname $soname -o $lib'
+ if test "x$supports_anon_versioning" = xyes; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $LD -shared $libobjs $deplibs $compiler_flags -soname $soname -version-script $output_objdir/$libname.ver -o $lib'
+ fi
+ ;;
+ esac
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
+ wlarc=
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ fi
+ ;;
+
+ solaris*)
+ if $LD -v 2>&1 | $GREP 'BFD 2\.8' > /dev/null; then
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: The releases 2.8.* of the GNU linker cannot reliably
+*** create shared libraries on Solaris systems. Therefore, libtool
+*** is disabling shared libraries support. We urge you to upgrade GNU
+*** binutils to release 2.9.1 or newer. Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+ elif $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*)
+ case `$LD -v 2>&1` in
+ *\ [[01]].* | *\ 2.[[0-9]].* | *\ 2.1[[0-5]].*)
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not
+*** reliably create shared libraries on SCO systems. Therefore, libtool
+*** is disabling shared libraries support. We urge you to upgrade GNU
+*** binutils to release 2.16.91.0.3 or newer. Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+ ;;
+ *)
+ # For security reasons, it is highly recommended that you always
+ # use absolute paths for naming shared libraries, and exclude the
+ # DT_RUNPATH tag from executables and libraries. But doing so
+ # requires that you compile everything twice, which is a pain.
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+ ;;
+
+ sunos4*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ wlarc=
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ *)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+
+ if test "$_LT_TAGVAR(ld_shlibs, $1)" = no; then
+ runpath_var=
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)=
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ fi
+ else
+ # PORTME fill in a description of your system's linker (not GNU ld)
+ case $host_os in
+ aix3*)
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ _LT_TAGVAR(always_export_symbols, $1)=yes
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname'
+ # Note: this linker hardcodes the directories in LIBPATH if there
+ # are no directories specified by -L.
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then
+ # Neither direct hardcoding nor static linking is supported with a
+ # broken collect2.
+ _LT_TAGVAR(hardcode_direct, $1)=unsupported
+ fi
+ ;;
+
+ aix[[4-9]]*)
+ if test "$host_cpu" = ia64; then
+ # On IA64, the linker does run time linking by default, so we don't
+ # have to do anything special.
+ aix_use_runtimelinking=no
+ exp_sym_flag='-Bexport'
+ no_entry_flag=""
+ else
+ # If we're using GNU nm, then we don't want the "-C" option.
+ # -C means demangle to AIX nm, but means don't demangle with GNU nm
+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ else
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ fi
+ aix_use_runtimelinking=no
+
+ # Test if we are trying to use run time linking or normal
+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+ # need to do runtime linking.
+ case $host_os in aix4.[[23]]|aix4.[[23]].*|aix[[5-9]]*)
+ for ld_flag in $LDFLAGS; do
+ if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then
+ aix_use_runtimelinking=yes
+ break
+ fi
+ done
+ ;;
+ esac
+
+ exp_sym_flag='-bexport'
+ no_entry_flag='-bnoentry'
+ fi
+
+ # When large executables or shared objects are built, AIX ld can
+ # have problems creating the table of contents. If linking a library
+ # or program results in "error TOC overflow" add -mminimal-toc to
+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not
+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+ _LT_TAGVAR(archive_cmds, $1)=''
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=':'
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(file_list_spec, $1)='${wl}-f,'
+
+ if test "$GCC" = yes; then
+ case $host_os in aix4.[[012]]|aix4.[[012]].*)
+ # We only want to do this on AIX 4.2 and lower, the check
+ # below for broken collect2 doesn't work under 4.3+
+ collect2name=`${CC} -print-prog-name=collect2`
+ if test -f "$collect2name" &&
+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null
+ then
+ # We have reworked collect2
+ :
+ else
+ # We have old collect2
+ _LT_TAGVAR(hardcode_direct, $1)=unsupported
+ # It fails to find uninstalled libraries when the uninstalled
+ # path is not listed in the libpath. Setting hardcode_minus_L
+ # to unsupported forces relinking
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=
+ fi
+ ;;
+ esac
+ shared_flag='-shared'
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag="$shared_flag "'${wl}-G'
+ fi
+ _LT_TAGVAR(link_all_deplibs, $1)=no
+ else
+ # not using gcc
+ if test "$host_cpu" = ia64; then
+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+ # chokes on -Wl,-G. The following line is correct:
+ shared_flag='-G'
+ else
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag='${wl}-G'
+ else
+ shared_flag='${wl}-bM:SRE'
+ fi
+ fi
+ fi
+
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-bexpall'
+ # It seems that -bexpall does not export symbols beginning with
+ # underscore (_), so it is better to generate a list of symbols to export.
+ _LT_TAGVAR(always_export_symbols, $1)=yes
+ if test "$aix_use_runtimelinking" = yes; then
+ # Warning - without using the other runtime loading flags (-brtl),
+ # -berok will link without error, but may produce a broken library.
+ _LT_TAGVAR(allow_undefined_flag, $1)='-berok'
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ _LT_SYS_MODULE_PATH_AIX
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+ else
+ if test "$host_cpu" = ia64; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $libdir:/usr/lib:/lib'
+ _LT_TAGVAR(allow_undefined_flag, $1)="-z nodefs"
+ _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+ else
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ _LT_SYS_MODULE_PATH_AIX
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+ # Warning - without using the other run time loading flags,
+ # -berok will link without error, but may produce a broken library.
+ _LT_TAGVAR(no_undefined_flag, $1)=' ${wl}-bernotok'
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-berok'
+ # Exported symbols can be pulled into shared objects from archives
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='$convenience'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=yes
+ # This is similar to how AIX traditionally builds its shared libraries.
+ _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+ fi
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)=''
+ ;;
+ m68k)
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ ;;
+ esac
+ ;;
+
+ bsdi[[45]]*)
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)=-rdynamic
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # When not using gcc, we currently assume that we are using
+ # Microsoft Visual C++.
+ # hardcode_libdir_flag_spec is actually meaningless, as there is
+ # no search path for DLLs.
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=' '
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ # Tell ltmain to make .lib files, not .a files.
+ libext=lib
+ # Tell ltmain to make .dll files, not .so files.
+ shrext_cmds=".dll"
+ # FIXME: Setting linknames here is a bad hack.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -o $lib $libobjs $compiler_flags `$ECHO "X$deplibs" | $Xsed -e '\''s/ -lc$//'\''` -link -dll~linknames='
+ # The linker will automatically build a .lib file if we build a DLL.
+ _LT_TAGVAR(old_archive_from_new_cmds, $1)='true'
+ # FIXME: Should let the user specify the lib program.
+ _LT_TAGVAR(old_archive_cmds, $1)='lib -OUT:$oldlib$oldobjs$old_deplibs'
+ _LT_TAGVAR(fix_srcfile_path, $1)='`cygpath -w "$srcfile"`'
+ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+ ;;
+
+ darwin* | rhapsody*)
+ _LT_DARWIN_LINKER_FEATURES($1)
+ ;;
+
+ dgux*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ freebsd1*)
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor
+ # support. Future versions do this automatically, but an explicit c++rt0.o
+ # does not break anything, and helps significantly (at the cost of a little
+ # extra space).
+ freebsd2.2*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ # Unfortunately, older versions of FreeBSD 2 do not have this feature.
+ freebsd2*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ # FreeBSD 3 and greater uses gcc -shared to do shared libraries.
+ freebsd* | dragonfly*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ hpux9*)
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ fi
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ ;;
+
+ hpux10*)
+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags'
+ fi
+ if test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='+b $libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ fi
+ ;;
+
+ hpux11*)
+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+ case $host_cpu in
+ hppa*64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ ia64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ else
+ case $host_cpu in
+ hppa*64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ ia64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ fi
+ if test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ case $host_cpu in
+ hppa*64*|ia64*)
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+ *)
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ ;;
+ esac
+ fi
+ ;;
+
+ irix5* | irix6* | nonstopux*)
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ # Try to use the -exported_symbol ld option, if it does not
+ # work, assume that -exports_file does not work either and
+ # implicitly export all symbols.
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null"
+ AC_LINK_IFELSE(int foo(void) {},
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib'
+ )
+ LDFLAGS="$save_LDFLAGS"
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib'
+ fi
+ _LT_TAGVAR(archive_cmds_need_lc, $1)='no'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(inherit_rpath, $1)=yes
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ ;;
+
+ netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF
+ fi
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ newsos6)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ *nto* | *qnx*)
+ ;;
+
+ openbsd*)
+ if test -f /usr/libexec/ld.so; then
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ else
+ case $host_os in
+ openbsd[[01]].* | openbsd2.[[0-7]] | openbsd2.[[0-7]].*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ ;;
+ esac
+ fi
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ os2*)
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ _LT_TAGVAR(archive_cmds, $1)='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def'
+ _LT_TAGVAR(old_archive_from_new_cmds, $1)='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def'
+ ;;
+
+ osf3*)
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ else
+ _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ fi
+ _LT_TAGVAR(archive_cmds_need_lc, $1)='no'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ ;;
+
+ osf4* | osf5*) # as osf3* with the addition of -msym flag
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ else
+ _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~
+ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp'
+
+ # Both c and cxx compiler support -rpath directly
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir'
+ fi
+ _LT_TAGVAR(archive_cmds_need_lc, $1)='no'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ ;;
+
+ solaris*)
+ _LT_TAGVAR(no_undefined_flag, $1)=' -z defs'
+ if test "$GCC" = yes; then
+ wlarc='${wl}'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp'
+ else
+ case `$CC -V 2>&1` in
+ *"Compilers 5.0"*)
+ wlarc=''
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp'
+ ;;
+ *)
+ wlarc='${wl}'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp'
+ ;;
+ esac
+ fi
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ case $host_os in
+ solaris2.[[0-5]] | solaris2.[[0-5]].*) ;;
+ *)
+ # The compiler driver will combine and reorder linker options,
+ # but understands `-z linker_flag'. GCC discards it without `$wl',
+ # but is careful enough not to reorder.
+ # Supported since Solaris 2.6 (maybe 2.5.1?)
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract'
+ else
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='-z allextract$convenience -z defaultextract'
+ fi
+ ;;
+ esac
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ ;;
+
+ sunos4*)
+ if test "x$host_vendor" = xsequent; then
+ # Use $CC to link under sequent, because it throws in some extra .o
+ # files that make .init and .fini sections work.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags'
+ fi
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ sysv4)
+ case $host_vendor in
+ sni)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_direct, $1)=yes # is this really true???
+ ;;
+ siemens)
+ ## LD is ld it makes a PLAMLIB
+ ## CC just makes a GrossModule.
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(reload_cmds, $1)='$CC -r -o $output$reload_objs'
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ ;;
+ motorola)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_direct, $1)=no #Motorola manual says yes, but my tests say they lie
+ ;;
+ esac
+ runpath_var='LD_RUN_PATH'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ sysv4.3*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='-Bexport'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ runpath_var=LD_RUN_PATH
+ hardcode_runpath_var=yes
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ fi
+ ;;
+
+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[[01]].[[10]]* | unixware7* | sco3.2v5.0.[[024]]*)
+ _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ runpath_var='LD_RUN_PATH'
+
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ fi
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6*)
+ # Note: We can NOT use -z defs as we might desire, because we do not
+ # link with -lc, and that would cause any symbols used from libc to
+ # always be unresolved, which means just about no library would
+ # ever link correctly. If we're not using GNU ld we use -z text
+ # though, which does catch some bad symbols but isn't as heavy-handed
+ # as -z defs.
+ _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+ _LT_TAGVAR(allow_undefined_flag, $1)='${wl}-z,nodefs'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R,$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=':'
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Bexport'
+ runpath_var='LD_RUN_PATH'
+
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ fi
+ ;;
+
+ uts4*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ *)
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+
+ if test x$host_vendor = xsni; then
+ case $host in
+ sysv4 | sysv4.2uw2* | sysv4.3* | sysv5*)
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Blargedynsym'
+ ;;
+ esac
+ fi
+ fi
+])
+AC_MSG_RESULT([$_LT_TAGVAR(ld_shlibs, $1)])
+test "$_LT_TAGVAR(ld_shlibs, $1)" = no && can_build_shared=no
+
+_LT_TAGVAR(with_gnu_ld, $1)=$with_gnu_ld
+
+_LT_DECL([], [libext], [0], [Old archive suffix (normally "a")])dnl
+_LT_DECL([], [shrext_cmds], [1], [Shared library suffix (normally ".so")])dnl
+_LT_DECL([], [extract_expsyms_cmds], [2],
+ [The commands to extract the exported symbol list from a shared archive])
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$_LT_TAGVAR(archive_cmds_need_lc, $1)" in
+x|xyes)
+ # Assume -lc should be added
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=yes
+
+ if test "$enable_shared" = yes && test "$GCC" = yes; then
+ case $_LT_TAGVAR(archive_cmds, $1) in
+ *'~'*)
+ # FIXME: we may have to deal with multi-command sequences.
+ ;;
+ '$CC '*)
+ # Test whether the compiler implicitly links with -lc since on some
+ # systems, -lgcc has to come before -lc. If gcc already passes -lc
+ # to ld, don't add -lc before -lgcc.
+ AC_MSG_CHECKING([whether -lc should be explicitly linked in])
+ $RM conftest*
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ if AC_TRY_EVAL(ac_compile) 2>conftest.err; then
+ soname=conftest
+ lib=conftest
+ libobjs=conftest.$ac_objext
+ deplibs=
+ wl=$_LT_TAGVAR(lt_prog_compiler_wl, $1)
+ pic_flag=$_LT_TAGVAR(lt_prog_compiler_pic, $1)
+ compiler_flags=-v
+ linker_flags=-v
+ verstring=
+ output_objdir=.
+ libname=conftest
+ lt_save_allow_undefined_flag=$_LT_TAGVAR(allow_undefined_flag, $1)
+ _LT_TAGVAR(allow_undefined_flag, $1)=
+ if AC_TRY_EVAL(_LT_TAGVAR(archive_cmds, $1) 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1)
+ then
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ else
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=yes
+ fi
+ _LT_TAGVAR(allow_undefined_flag, $1)=$lt_save_allow_undefined_flag
+ else
+ cat conftest.err 1>&5
+ fi
+ $RM conftest*
+ AC_MSG_RESULT([$_LT_TAGVAR(archive_cmds_need_lc, $1)])
+ ;;
+ esac
+ fi
+ ;;
+esac
+
+_LT_TAGDECL([build_libtool_need_lc], [archive_cmds_need_lc], [0],
+ [Whether or not to add -lc for building shared libraries])
+_LT_TAGDECL([allow_libtool_libs_with_static_runtimes],
+ [enable_shared_with_static_runtimes], [0],
+ [Whether or not to disallow shared libs when runtime libs are static])
+_LT_TAGDECL([], [export_dynamic_flag_spec], [1],
+ [Compiler flag to allow reflexive dlopens])
+_LT_TAGDECL([], [whole_archive_flag_spec], [1],
+ [Compiler flag to generate shared objects directly from archives])
+_LT_TAGDECL([], [compiler_needs_object], [1],
+ [Whether the compiler copes with passing no objects directly])
+_LT_TAGDECL([], [old_archive_from_new_cmds], [2],
+ [Create an old-style archive from a shared archive])
+_LT_TAGDECL([], [old_archive_from_expsyms_cmds], [2],
+ [Create a temporary old-style archive to link instead of a shared archive])
+_LT_TAGDECL([], [archive_cmds], [2], [Commands used to build a shared archive])
+_LT_TAGDECL([], [archive_expsym_cmds], [2])
+_LT_TAGDECL([], [module_cmds], [2],
+ [Commands used to build a loadable module if different from building
+ a shared archive.])
+_LT_TAGDECL([], [module_expsym_cmds], [2])
+_LT_TAGDECL([], [with_gnu_ld], [1],
+ [Whether we are building with GNU ld or not])
+_LT_TAGDECL([], [allow_undefined_flag], [1],
+ [Flag that allows shared libraries with undefined symbols to be built])
+_LT_TAGDECL([], [no_undefined_flag], [1],
+ [Flag that enforces no undefined symbols])
+_LT_TAGDECL([], [hardcode_libdir_flag_spec], [1],
+ [Flag to hardcode $libdir into a binary during linking.
+ This must work even if $libdir does not exist])
+_LT_TAGDECL([], [hardcode_libdir_flag_spec_ld], [1],
+ [[If ld is used when linking, flag to hardcode $libdir into a binary
+ during linking. This must work even if $libdir does not exist]])
+_LT_TAGDECL([], [hardcode_libdir_separator], [1],
+ [Whether we need a single "-rpath" flag with a separated argument])
+_LT_TAGDECL([], [hardcode_direct], [0],
+ [Set to "yes" if using DIR/libNAME${shared_ext} during linking hardcodes
+ DIR into the resulting binary])
+_LT_TAGDECL([], [hardcode_direct_absolute], [0],
+ [Set to "yes" if using DIR/libNAME${shared_ext} during linking hardcodes
+ DIR into the resulting binary and the resulting library dependency is
+ "absolute", i.e impossible to change by setting ${shlibpath_var} if the
+ library is relocated])
+_LT_TAGDECL([], [hardcode_minus_L], [0],
+ [Set to "yes" if using the -LDIR flag during linking hardcodes DIR
+ into the resulting binary])
+_LT_TAGDECL([], [hardcode_shlibpath_var], [0],
+ [Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR
+ into the resulting binary])
+_LT_TAGDECL([], [hardcode_automatic], [0],
+ [Set to "yes" if building a shared library automatically hardcodes DIR
+ into the library and all subsequent libraries and executables linked
+ against it])
+_LT_TAGDECL([], [inherit_rpath], [0],
+ [Set to yes if linker adds runtime paths of dependent libraries
+ to runtime path list])
+_LT_TAGDECL([], [link_all_deplibs], [0],
+ [Whether libtool must link a program against all its dependency libraries])
+_LT_TAGDECL([], [fix_srcfile_path], [1],
+ [Fix the shell variable $srcfile for the compiler])
+_LT_TAGDECL([], [always_export_symbols], [0],
+ [Set to "yes" if exported symbols are required])
+_LT_TAGDECL([], [export_symbols_cmds], [2],
+ [The commands to list exported symbols])
+_LT_TAGDECL([], [exclude_expsyms], [1],
+ [Symbols that should not be listed in the preloaded symbols])
+_LT_TAGDECL([], [include_expsyms], [1],
+ [Symbols that must always be exported])
+_LT_TAGDECL([], [prelink_cmds], [2],
+ [Commands necessary for linking programs (against libraries) with templates])
+_LT_TAGDECL([], [file_list_spec], [1],
+ [Specify filename containing input files])
+dnl FIXME: Not yet implemented
+dnl _LT_TAGDECL([], [thread_safe_flag_spec], [1],
+dnl [Compiler flag to generate thread safe objects])
+])# _LT_LINKER_SHLIBS
+
+
+# _LT_LANG_C_CONFIG([TAG])
+# ------------------------
+# Ensure that the configuration variables for a C compiler are suitably
+# defined. These variables are subsequently used by _LT_CONFIG to write
+# the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_C_CONFIG],
+[m4_require([_LT_DECL_EGREP])dnl
+lt_save_CC="$CC"
+AC_LANG_PUSH(C)
+
+# Source file extension for C test sources.
+ac_ext=c
+
+# Object file extension for compiled C test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="int some_variable = 0;"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='int main(){return(0);}'
+
+_LT_TAG_COMPILER
+# Save the default compiler, since it gets overwritten when the other
+# tags are being tested, and _LT_TAGVAR(compiler, []) is a NOP.
+compiler_DEFAULT=$CC
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+if test -n "$compiler"; then
+ _LT_COMPILER_NO_RTTI($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_SYS_DYNAMIC_LINKER($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+ LT_SYS_DLOPEN_SELF
+ _LT_CMD_STRIPLIB
+
+ # Report which library types will actually be built
+ AC_MSG_CHECKING([if libtool supports shared libraries])
+ AC_MSG_RESULT([$can_build_shared])
+
+ AC_MSG_CHECKING([whether to build shared libraries])
+ test "$can_build_shared" = "no" && enable_shared=no
+
+ # On AIX, shared libraries and static libraries use the same namespace, and
+ # are all built from PIC.
+ case $host_os in
+ aix3*)
+ test "$enable_shared" = yes && enable_static=no
+ if test -n "$RANLIB"; then
+ archive_cmds="$archive_cmds~\$RANLIB \$lib"
+ postinstall_cmds='$RANLIB $lib'
+ fi
+ ;;
+
+ aix[[4-9]]*)
+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+ test "$enable_shared" = yes && enable_static=no
+ fi
+ ;;
+ esac
+ AC_MSG_RESULT([$enable_shared])
+
+ AC_MSG_CHECKING([whether to build static libraries])
+ # Make sure either enable_shared or enable_static is yes.
+ test "$enable_shared" = yes || enable_static=yes
+ AC_MSG_RESULT([$enable_static])
+
+ _LT_CONFIG($1)
+fi
+AC_LANG_POP
+CC="$lt_save_CC"
+])# _LT_LANG_C_CONFIG
+
+
+# _LT_PROG_CXX
+# ------------
+# Since AC_PROG_CXX is broken, in that it returns g++ if there is no c++
+# compiler, we have our own version here.
+m4_defun([_LT_PROG_CXX],
+[
+pushdef([AC_MSG_ERROR], [_lt_caught_CXX_error=yes])
+AC_PROG_CXX
+if test -n "$CXX" && ( test "X$CXX" != "Xno" &&
+ ( (test "X$CXX" = "Xg++" && `g++ -v >/dev/null 2>&1` ) ||
+ (test "X$CXX" != "Xg++"))) ; then
+ AC_PROG_CXXCPP
+else
+ _lt_caught_CXX_error=yes
+fi
+popdef([AC_MSG_ERROR])
+])# _LT_PROG_CXX
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([_LT_PROG_CXX], [])
+
+
+# _LT_LANG_CXX_CONFIG([TAG])
+# --------------------------
+# Ensure that the configuration variables for a C++ compiler are suitably
+# defined. These variables are subsequently used by _LT_CONFIG to write
+# the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_CXX_CONFIG],
+[AC_REQUIRE([_LT_PROG_CXX])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_EGREP])dnl
+
+AC_LANG_PUSH(C++)
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+_LT_TAGVAR(allow_undefined_flag, $1)=
+_LT_TAGVAR(always_export_symbols, $1)=no
+_LT_TAGVAR(archive_expsym_cmds, $1)=
+_LT_TAGVAR(compiler_needs_object, $1)=no
+_LT_TAGVAR(export_dynamic_flag_spec, $1)=
+_LT_TAGVAR(hardcode_direct, $1)=no
+_LT_TAGVAR(hardcode_direct_absolute, $1)=no
+_LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+_LT_TAGVAR(hardcode_libdir_separator, $1)=
+_LT_TAGVAR(hardcode_minus_L, $1)=no
+_LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
+_LT_TAGVAR(hardcode_automatic, $1)=no
+_LT_TAGVAR(inherit_rpath, $1)=no
+_LT_TAGVAR(module_cmds, $1)=
+_LT_TAGVAR(module_expsym_cmds, $1)=
+_LT_TAGVAR(link_all_deplibs, $1)=unknown
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+_LT_TAGVAR(no_undefined_flag, $1)=
+_LT_TAGVAR(whole_archive_flag_spec, $1)=
+_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+
+# Source file extension for C++ test sources.
+ac_ext=cpp
+
+# Object file extension for compiled C++ test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# No sense in running all these tests if we already determined that
+# the CXX compiler isn't working. Some variables (like enable_shared)
+# are currently assumed to apply to all compilers on this platform,
+# and will be corrupted by setting them based on a non-working compiler.
+if test "$_lt_caught_CXX_error" != yes; then
+ # Code to be used in simple compile tests
+ lt_simple_compile_test_code="int some_variable = 0;"
+
+ # Code to be used in simple link tests
+ lt_simple_link_test_code='int main(int, char *[[]]) { return(0); }'
+
+ # ltmain only uses $CC for tagged configurations so make sure $CC is set.
+ _LT_TAG_COMPILER
+
+ # save warnings/boilerplate of simple test code
+ _LT_COMPILER_BOILERPLATE
+ _LT_LINKER_BOILERPLATE
+
+ # Allow CC to be a program name with arguments.
+ lt_save_CC=$CC
+ lt_save_LD=$LD
+ lt_save_GCC=$GCC
+ GCC=$GXX
+ lt_save_with_gnu_ld=$with_gnu_ld
+ lt_save_path_LD=$lt_cv_path_LD
+ if test -n "${lt_cv_prog_gnu_ldcxx+set}"; then
+ lt_cv_prog_gnu_ld=$lt_cv_prog_gnu_ldcxx
+ else
+ $as_unset lt_cv_prog_gnu_ld
+ fi
+ if test -n "${lt_cv_path_LDCXX+set}"; then
+ lt_cv_path_LD=$lt_cv_path_LDCXX
+ else
+ $as_unset lt_cv_path_LD
+ fi
+ test -z "${LDCXX+set}" || LD=$LDCXX
+ CC=${CXX-"c++"}
+ compiler=$CC
+ _LT_TAGVAR(compiler, $1)=$CC
+ _LT_CC_BASENAME([$compiler])
+
+ if test -n "$compiler"; then
+ # We don't want -fno-exception when compiling C++ code, so set the
+ # no_builtin_flag separately
+ if test "$GXX" = yes; then
+ _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin'
+ else
+ _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=
+ fi
+
+ if test "$GXX" = yes; then
+ # Set up default GNU C++ configuration
+
+ LT_PATH_LD
+
+ # Check if GNU C++ uses GNU ld as the underlying linker, since the
+ # archiving commands below assume that GNU ld is being used.
+ if test "$with_gnu_ld" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+
+ # If archive_cmds runs LD, not CC, wlarc should be empty
+ # XXX I think wlarc can be eliminated in ltcf-cxx, but I need to
+ # investigate it a little bit more. (MM)
+ wlarc='${wl}'
+
+ # ancient GNU ld didn't support --whole-archive et. al.
+ if eval "`$CC -print-prog-name=ld` --help 2>&1" |
+ $GREP 'no-whole-archive' > /dev/null; then
+ _LT_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ else
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ fi
+ else
+ with_gnu_ld=no
+ wlarc=
+
+ # A generic and very simple default shared library creation
+ # command for GNU C++ for the case where it uses the native
+ # linker, instead of GNU ld. If possible, this setting should
+ # overridden to take advantage of the native linker features on
+ # the platform it is being used on.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+ fi
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+
+ else
+ GXX=no
+ with_gnu_ld=no
+ wlarc=
+ fi
+
+ # PORTME: fill in a description of your system's C++ link characteristics
+ AC_MSG_CHECKING([whether the $compiler linker ($LD) supports shared libraries])
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ case $host_os in
+ aix3*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ aix[[4-9]]*)
+ if test "$host_cpu" = ia64; then
+ # On IA64, the linker does run time linking by default, so we don't
+ # have to do anything special.
+ aix_use_runtimelinking=no
+ exp_sym_flag='-Bexport'
+ no_entry_flag=""
+ else
+ aix_use_runtimelinking=no
+
+ # Test if we are trying to use run time linking or normal
+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+ # need to do runtime linking.
+ case $host_os in aix4.[[23]]|aix4.[[23]].*|aix[[5-9]]*)
+ for ld_flag in $LDFLAGS; do
+ case $ld_flag in
+ *-brtl*)
+ aix_use_runtimelinking=yes
+ break
+ ;;
+ esac
+ done
+ ;;
+ esac
+
+ exp_sym_flag='-bexport'
+ no_entry_flag='-bnoentry'
+ fi
+
+ # When large executables or shared objects are built, AIX ld can
+ # have problems creating the table of contents. If linking a library
+ # or program results in "error TOC overflow" add -mminimal-toc to
+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not
+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+ _LT_TAGVAR(archive_cmds, $1)=''
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=':'
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(file_list_spec, $1)='${wl}-f,'
+
+ if test "$GXX" = yes; then
+ case $host_os in aix4.[[012]]|aix4.[[012]].*)
+ # We only want to do this on AIX 4.2 and lower, the check
+ # below for broken collect2 doesn't work under 4.3+
+ collect2name=`${CC} -print-prog-name=collect2`
+ if test -f "$collect2name" &&
+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null
+ then
+ # We have reworked collect2
+ :
+ else
+ # We have old collect2
+ _LT_TAGVAR(hardcode_direct, $1)=unsupported
+ # It fails to find uninstalled libraries when the uninstalled
+ # path is not listed in the libpath. Setting hardcode_minus_L
+ # to unsupported forces relinking
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=
+ fi
+ esac
+ shared_flag='-shared'
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag="$shared_flag "'${wl}-G'
+ fi
+ else
+ # not using gcc
+ if test "$host_cpu" = ia64; then
+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+ # chokes on -Wl,-G. The following line is correct:
+ shared_flag='-G'
+ else
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag='${wl}-G'
+ else
+ shared_flag='${wl}-bM:SRE'
+ fi
+ fi
+ fi
+
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-bexpall'
+ # It seems that -bexpall does not export symbols beginning with
+ # underscore (_), so it is better to generate a list of symbols to
+ # export.
+ _LT_TAGVAR(always_export_symbols, $1)=yes
+ if test "$aix_use_runtimelinking" = yes; then
+ # Warning - without using the other runtime loading flags (-brtl),
+ # -berok will link without error, but may produce a broken library.
+ _LT_TAGVAR(allow_undefined_flag, $1)='-berok'
+ # Determine the default libpath from the value encoded in an empty
+ # executable.
+ _LT_SYS_MODULE_PATH_AIX
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+ else
+ if test "$host_cpu" = ia64; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $libdir:/usr/lib:/lib'
+ _LT_TAGVAR(allow_undefined_flag, $1)="-z nodefs"
+ _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+ else
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ _LT_SYS_MODULE_PATH_AIX
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+ # Warning - without using the other run time loading flags,
+ # -berok will link without error, but may produce a broken library.
+ _LT_TAGVAR(no_undefined_flag, $1)=' ${wl}-bernotok'
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-berok'
+ # Exported symbols can be pulled into shared objects from archives
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='$convenience'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=yes
+ # This is similar to how AIX traditionally builds its shared
+ # libraries.
+ _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+ fi
+ fi
+ ;;
+
+ beos*)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ # Joseph Beckenbach <jrb3 at best.com> says some releases of gcc
+ # support --undefined. This deserves some investigation. FIXME
+ _LT_TAGVAR(archive_cmds, $1)='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ chorus*)
+ case $cc_basename in
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # _LT_TAGVAR(hardcode_libdir_flag_spec, $1) is actually meaningless,
+ # as there is no search path for DLLs.
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ _LT_TAGVAR(always_export_symbols, $1)=no
+ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+
+ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ # If the export-symbols file already is a .def file (1st line
+ # is EXPORTS), use it as is; otherwise, prepend...
+ _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+ cp $export_symbols $output_objdir/$soname.def;
+ else
+ echo EXPORTS > $output_objdir/$soname.def;
+ cat $export_symbols >> $output_objdir/$soname.def;
+ fi~
+ $CC -shared -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ darwin* | rhapsody*)
+ _LT_DARWIN_LINKER_FEATURES($1)
+ ;;
+
+ dgux*)
+ case $cc_basename in
+ ec++*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ ghcx*)
+ # Green Hills C++ Compiler
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ freebsd[[12]]*)
+ # C++ shared libraries reported to be fairly broken before
+ # switch to ELF
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ freebsd-elf*)
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ ;;
+
+ freebsd* | dragonfly*)
+ # FreeBSD 3 and later use GNU C++ and GNU ld with standard ELF
+ # conventions
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ ;;
+
+ gnu*)
+ ;;
+
+ hpux9*)
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes # Not in the search PATH,
+ # but as the default
+ # location of the library.
+
+ case $cc_basename in
+ CC*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ aCC*)
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -b ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $EGREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -shared -nostdlib -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ else
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+ ;;
+
+ hpux10*|hpux11*)
+ if test $with_gnu_ld = no; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ case $host_cpu in
+ hppa*64*|ia64*)
+ ;;
+ *)
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ ;;
+ esac
+ fi
+ case $host_cpu in
+ hppa*64*|ia64*)
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+ *)
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes # Not in the search PATH,
+ # but as the default
+ # location of the library.
+ ;;
+ esac
+
+ case $cc_basename in
+ CC*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ aCC*)
+ case $host_cpu in
+ hppa*64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ ia64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ esac
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $GREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ if test $with_gnu_ld = no; then
+ case $host_cpu in
+ hppa*64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ ia64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ esac
+ fi
+ else
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+ ;;
+
+ interix[[3-9]]*)
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+ # Instead, shared libraries are loaded at an image base (0x10000000 by
+ # default) and relocated if they conflict, which is a slow very memory
+ # consuming and fragmenting process. To avoid this, we pick a random,
+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+ # time. Moving up from 0x10000000 also allows more sbrk(2) space.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ ;;
+ irix5* | irix6*)
+ case $cc_basename in
+ CC*)
+ # SGI C++
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -all -multigot $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+
+ # Archives containing C++ object files must be created using
+ # "CC -ar", where "CC" is the IRIX C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC -ar -WR,-u -o $oldlib $oldobjs'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ if test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` -o $lib'
+ fi
+ fi
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ ;;
+ esac
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(inherit_rpath, $1)=yes
+ ;;
+
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ KCC*)
+ # Kuck and Associates, Inc. (KAI) C++ Compiler
+
+ # KCC will only create a shared library if the output file
+ # ends with ".so" (or ".sl" for HP-UX), so rename the library
+ # to its proper name (with version) after linking.
+ _LT_TAGVAR(archive_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib ${wl}-retain-symbols-file,$export_symbols; mv \$templib $lib'
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 | $GREP "ld"`; rm -f libconftest$shared_ext; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+
+ # Archives containing C++ object files must be created using
+ # "CC -Bstatic", where "CC" is the KAI C++ compiler.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC -Bstatic -o $oldlib $oldobjs'
+ ;;
+ icpc* | ecpc* )
+ # Intel C++
+ with_gnu_ld=yes
+ # version 8.0 and above of icpc choke on multiply defined symbols
+ # if we add $predep_objects and $postdep_objects, however 7.1 and
+ # earlier do not add the objects themselves.
+ case `$CC -V 2>&1` in
+ *"Version 7."*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ ;;
+ *) # Version 8.0 or newer
+ tmp_idyn=
+ case $host_cpu in
+ ia64*) tmp_idyn=' -i_dynamic';;
+ esac
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ ;;
+ esac
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive$convenience ${wl}--no-whole-archive'
+ ;;
+ pgCC* | pgcpp*)
+ # Portland Group C++ compiler
+ case `$CC -V` in
+ *pgCC\ [[1-5]]* | *pgcpp\ [[1-5]]*)
+ _LT_TAGVAR(prelink_cmds, $1)='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $objs $libobjs $compile_deplibs~
+ compile_command="$compile_command `find $tpldir -name \*.o | $NL2SP`"'
+ _LT_TAGVAR(old_archive_cmds, $1)='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $oldobjs$old_deplibs~
+ $AR $AR_FLAGS $oldlib$oldobjs$old_deplibs `find $tpldir -name \*.o | $NL2SP`~
+ $RANLIB $oldlib'
+ _LT_TAGVAR(archive_cmds, $1)='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~
+ $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~
+ $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+ ;;
+ *) # Version 6 will use weak symbols
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+ ;;
+ esac
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}--rpath ${wl}$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ ;;
+ cxx*)
+ # Compaq C++
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib ${wl}-retain-symbols-file $wl$export_symbols'
+
+ runpath_var=LD_RUN_PATH
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld .*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ xl*)
+ # IBM XL 8.0 on PPC, with GNU ld
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ if test "x$supports_anon_versioning" = xyes; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+ fi
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+ _LT_TAGVAR(no_undefined_flag, $1)=' -zdefs'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file ${wl}$export_symbols'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ _LT_TAGVAR(compiler_needs_object, $1)=yes
+
+ # Not sure whether something based on
+ # $CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1
+ # would be better.
+ output_verbose_link_cmd='echo'
+
+ # Archives containing C++ object files must be created using
+ # "CC -xar", where "CC" is the Sun C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC -xar -o $oldlib $oldobjs'
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+
+ lynxos*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ m88k*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ mvs*)
+ case $cc_basename in
+ cxx*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ netbsd*)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $predep_objects $libobjs $deplibs $postdep_objects $linker_flags'
+ wlarc=
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ fi
+ # Workaround some broken pre-1.5 toolchains
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP conftest.$objext | $SED -e "s:-lgcc -lc -lgcc::"'
+ ;;
+
+ *nto* | *qnx*)
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ ;;
+
+ openbsd2*)
+ # C++ shared libraries are fairly broken
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ openbsd*)
+ if test -f /usr/libexec/ld.so; then
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file,$export_symbols -o $lib'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ _LT_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ fi
+ output_verbose_link_cmd=echo
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ osf3* | osf4* | osf5*)
+ case $cc_basename in
+ KCC*)
+ # Kuck and Associates, Inc. (KAI) C++ Compiler
+
+ # KCC will only create a shared library if the output file
+ # ends with ".so" (or ".sl" for HP-UX), so rename the library
+ # to its proper name (with version) after linking.
+ _LT_TAGVAR(archive_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo "$lib" | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ # Archives containing C++ object files must be created using
+ # the KAI C++ compiler.
+ case $host in
+ osf3*) _LT_TAGVAR(old_archive_cmds, $1)='$CC -Bstatic -o $oldlib $oldobjs' ;;
+ *) _LT_TAGVAR(old_archive_cmds, $1)='$CC -o $oldlib $oldobjs' ;;
+ esac
+ ;;
+ RCC*)
+ # Rational C++ 2.4.1
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ cxx*)
+ case $host in
+ osf3*)
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $soname `test -n "$verstring" && $ECHO "X${wl}-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ ;;
+ *)
+ _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done~
+ echo "-hidden">> $lib.exp~
+ $CC -shared$allow_undefined_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname ${wl}-input ${wl}$lib.exp `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~
+ $RM $lib.exp'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir'
+ ;;
+ esac
+
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld" | $GREP -v "ld:"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld.*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+ case $host in
+ osf3*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ ;;
+ esac
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+
+ else
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+ ;;
+
+ psos*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ sunos4*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.x
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ lcc*)
+ # Lucid
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ solaris*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.2, 5.x and Centerline C++
+ _LT_TAGVAR(archive_cmds_need_lc,$1)=yes
+ _LT_TAGVAR(no_undefined_flag, $1)=' -zdefs'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G${allow_undefined_flag} ${wl}-M ${wl}$lib.exp -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ case $host_os in
+ solaris2.[[0-5]] | solaris2.[[0-5]].*) ;;
+ *)
+ # The compiler driver will combine and reorder linker options,
+ # but understands `-z linker_flag'.
+ # Supported since Solaris 2.6 (maybe 2.5.1?)
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='-z allextract$convenience -z defaultextract'
+ ;;
+ esac
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+
+ output_verbose_link_cmd='echo'
+
+ # Archives containing C++ object files must be created using
+ # "CC -xar", where "CC" is the Sun C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC -xar -o $oldlib $oldobjs'
+ ;;
+ gcx*)
+ # Green Hills C++ Compiler
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+
+ # The C++ compiler must be used to create the archive.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC $LDFLAGS -archive -o $oldlib $oldobjs'
+ ;;
+ *)
+ # GNU C++ compiler with Solaris linker
+ if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(no_undefined_flag, $1)=' ${wl}-z ${wl}defs'
+ if $CC --version | $GREP -v '^2\.7' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -shared -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+ else
+ # g++ 2.7 appears to require `-G' NOT `-shared' on this
+ # platform.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -G $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+ fi
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $wl$libdir'
+ case $host_os in
+ solaris2.[[0-5]] | solaris2.[[0-5]].*) ;;
+ *)
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract'
+ ;;
+ esac
+ fi
+ ;;
+ esac
+ ;;
+
+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[[01]].[[10]]* | unixware7* | sco3.2v5.0.[[024]]*)
+ _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ runpath_var='LD_RUN_PATH'
+
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6*)
+ # Note: We can NOT use -z defs as we might desire, because we do not
+ # link with -lc, and that would cause any symbols used from libc to
+ # always be unresolved, which means just about no library would
+ # ever link correctly. If we're not using GNU ld we use -z text
+ # though, which does catch some bad symbols but isn't as heavy-handed
+ # as -z defs.
+ _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+ _LT_TAGVAR(allow_undefined_flag, $1)='${wl}-z,nodefs'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R,$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=':'
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Bexport'
+ runpath_var='LD_RUN_PATH'
+
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ ;;
+
+ tandem*)
+ case $cc_basename in
+ NCC*)
+ # NonStop-UX NCC 3.20
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ vxworks*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+
+ AC_MSG_RESULT([$_LT_TAGVAR(ld_shlibs, $1)])
+ test "$_LT_TAGVAR(ld_shlibs, $1)" = no && can_build_shared=no
+
+ _LT_TAGVAR(GCC, $1)="$GXX"
+ _LT_TAGVAR(LD, $1)="$LD"
+
+ ## CAVEAT EMPTOR:
+ ## There is no encapsulation within the following macros, do not change
+ ## the running order or otherwise move them around unless you know exactly
+ ## what you are doing...
+ _LT_SYS_HIDDEN_LIBDEPS($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_SYS_DYNAMIC_LINKER($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+ fi # test -n "$compiler"
+
+ CC=$lt_save_CC
+ LDCXX=$LD
+ LD=$lt_save_LD
+ GCC=$lt_save_GCC
+ with_gnu_ld=$lt_save_with_gnu_ld
+ lt_cv_path_LDCXX=$lt_cv_path_LD
+ lt_cv_path_LD=$lt_save_path_LD
+ lt_cv_prog_gnu_ldcxx=$lt_cv_prog_gnu_ld
+ lt_cv_prog_gnu_ld=$lt_save_with_gnu_ld
+fi # test "$_lt_caught_CXX_error" != yes
+
+AC_LANG_POP
+])# _LT_LANG_CXX_CONFIG
+
+
+# _LT_SYS_HIDDEN_LIBDEPS([TAGNAME])
+# ---------------------------------
+# Figure out "hidden" library dependencies from verbose
+# compiler output when linking a shared library.
+# Parse the compiler output and extract the necessary
+# objects, libraries and library flags.
+m4_defun([_LT_SYS_HIDDEN_LIBDEPS],
+[m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+# Dependencies to place before and after the object being linked:
+_LT_TAGVAR(predep_objects, $1)=
+_LT_TAGVAR(postdep_objects, $1)=
+_LT_TAGVAR(predeps, $1)=
+_LT_TAGVAR(postdeps, $1)=
+_LT_TAGVAR(compiler_lib_search_path, $1)=
+
+dnl we can't use the lt_simple_compile_test_code here,
+dnl because it contains code intended for an executable,
+dnl not a library. It's possible we should let each
+dnl tag define a new lt_????_link_test_code variable,
+dnl but it's only used here...
+m4_if([$1], [], [cat > conftest.$ac_ext <<_LT_EOF
+int a;
+void foo (void) { a = 0; }
+_LT_EOF
+], [$1], [CXX], [cat > conftest.$ac_ext <<_LT_EOF
+class Foo
+{
+public:
+ Foo (void) { a = 0; }
+private:
+ int a;
+};
+_LT_EOF
+], [$1], [F77], [cat > conftest.$ac_ext <<_LT_EOF
+ subroutine foo
+ implicit none
+ integer*4 a
+ a=0
+ return
+ end
+_LT_EOF
+], [$1], [FC], [cat > conftest.$ac_ext <<_LT_EOF
+ subroutine foo
+ implicit none
+ integer a
+ a=0
+ return
+ end
+_LT_EOF
+], [$1], [GCJ], [cat > conftest.$ac_ext <<_LT_EOF
+public class foo {
+ private int a;
+ public void bar (void) {
+ a = 0;
+ }
+};
+_LT_EOF
+])
+dnl Parse the compiler output and extract the necessary
+dnl objects, libraries and library flags.
+if AC_TRY_EVAL(ac_compile); then
+ # Parse the compiler output and extract the necessary
+ # objects, libraries and library flags.
+
+ # Sentinel used to keep track of whether or not we are before
+ # the conftest object file.
+ pre_test_object_deps_done=no
+
+ for p in `eval "$output_verbose_link_cmd"`; do
+ case $p in
+
+ -L* | -R* | -l*)
+ # Some compilers place space between "-{L,R}" and the path.
+ # Remove the space.
+ if test $p = "-L" ||
+ test $p = "-R"; then
+ prev=$p
+ continue
+ else
+ prev=
+ fi
+
+ if test "$pre_test_object_deps_done" = no; then
+ case $p in
+ -L* | -R*)
+ # Internal compiler library paths should come after those
+ # provided the user. The postdeps already come after the
+ # user supplied libs so there is no need to process them.
+ if test -z "$_LT_TAGVAR(compiler_lib_search_path, $1)"; then
+ _LT_TAGVAR(compiler_lib_search_path, $1)="${prev}${p}"
+ else
+ _LT_TAGVAR(compiler_lib_search_path, $1)="${_LT_TAGVAR(compiler_lib_search_path, $1)} ${prev}${p}"
+ fi
+ ;;
+ # The "-l" case would never come before the object being
+ # linked, so don't bother handling this case.
+ esac
+ else
+ if test -z "$_LT_TAGVAR(postdeps, $1)"; then
+ _LT_TAGVAR(postdeps, $1)="${prev}${p}"
+ else
+ _LT_TAGVAR(postdeps, $1)="${_LT_TAGVAR(postdeps, $1)} ${prev}${p}"
+ fi
+ fi
+ ;;
+
+ *.$objext)
+ # This assumes that the test object file only shows up
+ # once in the compiler output.
+ if test "$p" = "conftest.$objext"; then
+ pre_test_object_deps_done=yes
+ continue
+ fi
+
+ if test "$pre_test_object_deps_done" = no; then
+ if test -z "$_LT_TAGVAR(predep_objects, $1)"; then
+ _LT_TAGVAR(predep_objects, $1)="$p"
+ else
+ _LT_TAGVAR(predep_objects, $1)="$_LT_TAGVAR(predep_objects, $1) $p"
+ fi
+ else
+ if test -z "$_LT_TAGVAR(postdep_objects, $1)"; then
+ _LT_TAGVAR(postdep_objects, $1)="$p"
+ else
+ _LT_TAGVAR(postdep_objects, $1)="$_LT_TAGVAR(postdep_objects, $1) $p"
+ fi
+ fi
+ ;;
+
+ *) ;; # Ignore the rest.
+
+ esac
+ done
+
+ # Clean up.
+ rm -f a.out a.exe
+else
+ echo "libtool.m4: error: problem compiling $1 test program"
+fi
+
+$RM -f confest.$objext
+
+# PORTME: override above test on systems where it is broken
+m4_if([$1], [CXX],
+[case $host_os in
+interix[[3-9]]*)
+ # Interix 3.5 installs completely hosed .la files for C++, so rather than
+ # hack all around it, let's just trust "g++" to DTRT.
+ _LT_TAGVAR(predep_objects,$1)=
+ _LT_TAGVAR(postdep_objects,$1)=
+ _LT_TAGVAR(postdeps,$1)=
+ ;;
+
+linux*)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+
+ # The more standards-conforming stlport4 library is
+ # incompatible with the Cstd library. Avoid specifying
+ # it if it's in CXXFLAGS. Ignore libCrun as
+ # -library=stlport4 depends on it.
+ case " $CXX $CXXFLAGS " in
+ *" -library=stlport4 "*)
+ solaris_use_stlport4=yes
+ ;;
+ esac
+
+ if test "$solaris_use_stlport4" != yes; then
+ _LT_TAGVAR(postdeps,$1)='-library=Cstd -library=Crun'
+ fi
+ ;;
+ esac
+ ;;
+
+solaris*)
+ case $cc_basename in
+ CC*)
+ # The more standards-conforming stlport4 library is
+ # incompatible with the Cstd library. Avoid specifying
+ # it if it's in CXXFLAGS. Ignore libCrun as
+ # -library=stlport4 depends on it.
+ case " $CXX $CXXFLAGS " in
+ *" -library=stlport4 "*)
+ solaris_use_stlport4=yes
+ ;;
+ esac
+
+ # Adding this requires a known-good setup of shared libraries for
+ # Sun compiler versions before 5.6, else PIC objects from an old
+ # archive will be linked into the output, leading to subtle bugs.
+ if test "$solaris_use_stlport4" != yes; then
+ _LT_TAGVAR(postdeps,$1)='-library=Cstd -library=Crun'
+ fi
+ ;;
+ esac
+ ;;
+esac
+])
+
+case " $_LT_TAGVAR(postdeps, $1) " in
+*" -lc "*) _LT_TAGVAR(archive_cmds_need_lc, $1)=no ;;
+esac
+ _LT_TAGVAR(compiler_lib_search_dirs, $1)=
+if test -n "${_LT_TAGVAR(compiler_lib_search_path, $1)}"; then
+ _LT_TAGVAR(compiler_lib_search_dirs, $1)=`echo " ${_LT_TAGVAR(compiler_lib_search_path, $1)}" | ${SED} -e 's! -L! !g' -e 's!^ !!'`
+fi
+_LT_TAGDECL([], [compiler_lib_search_dirs], [1],
+ [The directories searched by this compiler when creating a shared library])
+_LT_TAGDECL([], [predep_objects], [1],
+ [Dependencies to place before and after the objects being linked to
+ create a shared library])
+_LT_TAGDECL([], [postdep_objects], [1])
+_LT_TAGDECL([], [predeps], [1])
+_LT_TAGDECL([], [postdeps], [1])
+_LT_TAGDECL([], [compiler_lib_search_path], [1],
+ [The library search path used internally by the compiler when linking
+ a shared library])
+])# _LT_SYS_HIDDEN_LIBDEPS
+
+
+# _LT_PROG_F77
+# ------------
+# Since AC_PROG_F77 is broken, in that it returns the empty string
+# if there is no fortran compiler, we have our own version here.
+m4_defun([_LT_PROG_F77],
+[
+pushdef([AC_MSG_ERROR], [_lt_disable_F77=yes])
+AC_PROG_F77
+if test -z "$F77" || test "X$F77" = "Xno"; then
+ _lt_disable_F77=yes
+fi
+popdef([AC_MSG_ERROR])
+])# _LT_PROG_F77
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([_LT_PROG_F77], [])
+
+
+# _LT_LANG_F77_CONFIG([TAG])
+# --------------------------
+# Ensure that the configuration variables for a Fortran 77 compiler are
+# suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_F77_CONFIG],
+[AC_REQUIRE([_LT_PROG_F77])dnl
+AC_LANG_PUSH(Fortran 77)
+
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+_LT_TAGVAR(allow_undefined_flag, $1)=
+_LT_TAGVAR(always_export_symbols, $1)=no
+_LT_TAGVAR(archive_expsym_cmds, $1)=
+_LT_TAGVAR(export_dynamic_flag_spec, $1)=
+_LT_TAGVAR(hardcode_direct, $1)=no
+_LT_TAGVAR(hardcode_direct_absolute, $1)=no
+_LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+_LT_TAGVAR(hardcode_libdir_separator, $1)=
+_LT_TAGVAR(hardcode_minus_L, $1)=no
+_LT_TAGVAR(hardcode_automatic, $1)=no
+_LT_TAGVAR(inherit_rpath, $1)=no
+_LT_TAGVAR(module_cmds, $1)=
+_LT_TAGVAR(module_expsym_cmds, $1)=
+_LT_TAGVAR(link_all_deplibs, $1)=unknown
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+_LT_TAGVAR(no_undefined_flag, $1)=
+_LT_TAGVAR(whole_archive_flag_spec, $1)=
+_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+
+# Source file extension for f77 test sources.
+ac_ext=f
+
+# Object file extension for compiled f77 test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# No sense in running all these tests if we already determined that
+# the F77 compiler isn't working. Some variables (like enable_shared)
+# are currently assumed to apply to all compilers on this platform,
+# and will be corrupted by setting them based on a non-working compiler.
+if test "$_lt_disable_F77" != yes; then
+ # Code to be used in simple compile tests
+ lt_simple_compile_test_code="\
+ subroutine t
+ return
+ end
+"
+
+ # Code to be used in simple link tests
+ lt_simple_link_test_code="\
+ program t
+ end
+"
+
+ # ltmain only uses $CC for tagged configurations so make sure $CC is set.
+ _LT_TAG_COMPILER
+
+ # save warnings/boilerplate of simple test code
+ _LT_COMPILER_BOILERPLATE
+ _LT_LINKER_BOILERPLATE
+
+ # Allow CC to be a program name with arguments.
+ lt_save_CC="$CC"
+ lt_save_GCC=$GCC
+ CC=${F77-"f77"}
+ compiler=$CC
+ _LT_TAGVAR(compiler, $1)=$CC
+ _LT_CC_BASENAME([$compiler])
+ GCC=$G77
+ if test -n "$compiler"; then
+ AC_MSG_CHECKING([if libtool supports shared libraries])
+ AC_MSG_RESULT([$can_build_shared])
+
+ AC_MSG_CHECKING([whether to build shared libraries])
+ test "$can_build_shared" = "no" && enable_shared=no
+
+ # On AIX, shared libraries and static libraries use the same namespace, and
+ # are all built from PIC.
+ case $host_os in
+ aix3*)
+ test "$enable_shared" = yes && enable_static=no
+ if test -n "$RANLIB"; then
+ archive_cmds="$archive_cmds~\$RANLIB \$lib"
+ postinstall_cmds='$RANLIB $lib'
+ fi
+ ;;
+ aix[[4-9]]*)
+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+ test "$enable_shared" = yes && enable_static=no
+ fi
+ ;;
+ esac
+ AC_MSG_RESULT([$enable_shared])
+
+ AC_MSG_CHECKING([whether to build static libraries])
+ # Make sure either enable_shared or enable_static is yes.
+ test "$enable_shared" = yes || enable_static=yes
+ AC_MSG_RESULT([$enable_static])
+
+ _LT_TAGVAR(GCC, $1)="$G77"
+ _LT_TAGVAR(LD, $1)="$LD"
+
+ ## CAVEAT EMPTOR:
+ ## There is no encapsulation within the following macros, do not change
+ ## the running order or otherwise move them around unless you know exactly
+ ## what you are doing...
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_SYS_DYNAMIC_LINKER($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+ fi # test -n "$compiler"
+
+ GCC=$lt_save_GCC
+ CC="$lt_save_CC"
+fi # test "$_lt_disable_F77" != yes
+
+AC_LANG_POP
+])# _LT_LANG_F77_CONFIG
+
+
+# _LT_PROG_FC
+# -----------
+# Since AC_PROG_FC is broken, in that it returns the empty string
+# if there is no fortran compiler, we have our own version here.
+m4_defun([_LT_PROG_FC],
+[
+pushdef([AC_MSG_ERROR], [_lt_disable_FC=yes])
+AC_PROG_FC
+if test -z "$FC" || test "X$FC" = "Xno"; then
+ _lt_disable_FC=yes
+fi
+popdef([AC_MSG_ERROR])
+])# _LT_PROG_FC
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([_LT_PROG_FC], [])
+
+
+# _LT_LANG_FC_CONFIG([TAG])
+# -------------------------
+# Ensure that the configuration variables for a Fortran compiler are
+# suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_FC_CONFIG],
+[AC_REQUIRE([_LT_PROG_FC])dnl
+AC_LANG_PUSH(Fortran)
+
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+_LT_TAGVAR(allow_undefined_flag, $1)=
+_LT_TAGVAR(always_export_symbols, $1)=no
+_LT_TAGVAR(archive_expsym_cmds, $1)=
+_LT_TAGVAR(export_dynamic_flag_spec, $1)=
+_LT_TAGVAR(hardcode_direct, $1)=no
+_LT_TAGVAR(hardcode_direct_absolute, $1)=no
+_LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+_LT_TAGVAR(hardcode_libdir_separator, $1)=
+_LT_TAGVAR(hardcode_minus_L, $1)=no
+_LT_TAGVAR(hardcode_automatic, $1)=no
+_LT_TAGVAR(inherit_rpath, $1)=no
+_LT_TAGVAR(module_cmds, $1)=
+_LT_TAGVAR(module_expsym_cmds, $1)=
+_LT_TAGVAR(link_all_deplibs, $1)=unknown
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+_LT_TAGVAR(no_undefined_flag, $1)=
+_LT_TAGVAR(whole_archive_flag_spec, $1)=
+_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+
+# Source file extension for fc test sources.
+ac_ext=${ac_fc_srcext-f}
+
+# Object file extension for compiled fc test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# No sense in running all these tests if we already determined that
+# the FC compiler isn't working. Some variables (like enable_shared)
+# are currently assumed to apply to all compilers on this platform,
+# and will be corrupted by setting them based on a non-working compiler.
+if test "$_lt_disable_FC" != yes; then
+ # Code to be used in simple compile tests
+ lt_simple_compile_test_code="\
+ subroutine t
+ return
+ end
+"
+
+ # Code to be used in simple link tests
+ lt_simple_link_test_code="\
+ program t
+ end
+"
+
+ # ltmain only uses $CC for tagged configurations so make sure $CC is set.
+ _LT_TAG_COMPILER
+
+ # save warnings/boilerplate of simple test code
+ _LT_COMPILER_BOILERPLATE
+ _LT_LINKER_BOILERPLATE
+
+ # Allow CC to be a program name with arguments.
+ lt_save_CC="$CC"
+ lt_save_GCC=$GCC
+ CC=${FC-"f95"}
+ compiler=$CC
+ GCC=$ac_cv_fc_compiler_gnu
+
+ _LT_TAGVAR(compiler, $1)=$CC
+ _LT_CC_BASENAME([$compiler])
+
+ if test -n "$compiler"; then
+ AC_MSG_CHECKING([if libtool supports shared libraries])
+ AC_MSG_RESULT([$can_build_shared])
+
+ AC_MSG_CHECKING([whether to build shared libraries])
+ test "$can_build_shared" = "no" && enable_shared=no
+
+ # On AIX, shared libraries and static libraries use the same namespace, and
+ # are all built from PIC.
+ case $host_os in
+ aix3*)
+ test "$enable_shared" = yes && enable_static=no
+ if test -n "$RANLIB"; then
+ archive_cmds="$archive_cmds~\$RANLIB \$lib"
+ postinstall_cmds='$RANLIB $lib'
+ fi
+ ;;
+ aix[[4-9]]*)
+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+ test "$enable_shared" = yes && enable_static=no
+ fi
+ ;;
+ esac
+ AC_MSG_RESULT([$enable_shared])
+
+ AC_MSG_CHECKING([whether to build static libraries])
+ # Make sure either enable_shared or enable_static is yes.
+ test "$enable_shared" = yes || enable_static=yes
+ AC_MSG_RESULT([$enable_static])
+
+ _LT_TAGVAR(GCC, $1)="$ac_cv_fc_compiler_gnu"
+ _LT_TAGVAR(LD, $1)="$LD"
+
+ ## CAVEAT EMPTOR:
+ ## There is no encapsulation within the following macros, do not change
+ ## the running order or otherwise move them around unless you know exactly
+ ## what you are doing...
+ _LT_SYS_HIDDEN_LIBDEPS($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_SYS_DYNAMIC_LINKER($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+ fi # test -n "$compiler"
+
+ GCC=$lt_save_GCC
+ CC="$lt_save_CC"
+fi # test "$_lt_disable_FC" != yes
+
+AC_LANG_POP
+])# _LT_LANG_FC_CONFIG
+
+
+# _LT_LANG_GCJ_CONFIG([TAG])
+# --------------------------
+# Ensure that the configuration variables for the GNU Java Compiler compiler
+# are suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_GCJ_CONFIG],
+[AC_REQUIRE([LT_PROG_GCJ])dnl
+AC_LANG_SAVE
+
+# Source file extension for Java test sources.
+ac_ext=java
+
+# Object file extension for compiled Java test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="class foo {}"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='public class conftest { public static void main(String[[]] argv) {}; }'
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+_LT_TAG_COMPILER
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+# Allow CC to be a program name with arguments.
+lt_save_CC="$CC"
+lt_save_GCC=$GCC
+GCC=yes
+CC=${GCJ-"gcj"}
+compiler=$CC
+_LT_TAGVAR(compiler, $1)=$CC
+_LT_TAGVAR(LD, $1)="$LD"
+_LT_CC_BASENAME([$compiler])
+
+# GCJ did not exist at the time GCC didn't implicitly link libc in.
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+
+if test -n "$compiler"; then
+ _LT_COMPILER_NO_RTTI($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+fi
+
+AC_LANG_RESTORE
+
+GCC=$lt_save_GCC
+CC="$lt_save_CC"
+])# _LT_LANG_GCJ_CONFIG
+
+
+# _LT_LANG_RC_CONFIG([TAG])
+# -------------------------
+# Ensure that the configuration variables for the Windows resource compiler
+# are suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_RC_CONFIG],
+[AC_REQUIRE([LT_PROG_RC])dnl
+AC_LANG_SAVE
+
+# Source file extension for RC test sources.
+ac_ext=rc
+
+# Object file extension for compiled RC test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code='sample MENU { MENUITEM "&Soup", 100, CHECKED }'
+
+# Code to be used in simple link tests
+lt_simple_link_test_code="$lt_simple_compile_test_code"
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+_LT_TAG_COMPILER
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+# Allow CC to be a program name with arguments.
+lt_save_CC="$CC"
+lt_save_GCC=$GCC
+GCC=
+CC=${RC-"windres"}
+compiler=$CC
+_LT_TAGVAR(compiler, $1)=$CC
+_LT_CC_BASENAME([$compiler])
+_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=yes
+
+if test -n "$compiler"; then
+ :
+ _LT_CONFIG($1)
+fi
+
+GCC=$lt_save_GCC
+AC_LANG_RESTORE
+CC="$lt_save_CC"
+])# _LT_LANG_RC_CONFIG
+
+
+# LT_PROG_GCJ
+# -----------
+AC_DEFUN([LT_PROG_GCJ],
+[m4_ifdef([AC_PROG_GCJ], [AC_PROG_GCJ],
+ [m4_ifdef([A][M_PROG_GCJ], [A][M_PROG_GCJ],
+ [AC_CHECK_TOOL(GCJ, gcj,)
+ test "x${GCJFLAGS+set}" = xset || GCJFLAGS="-g -O2"
+ AC_SUBST(GCJFLAGS)])])[]dnl
+])
+
+# Old name:
+AU_ALIAS([LT_AC_PROG_GCJ], [LT_PROG_GCJ])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([LT_AC_PROG_GCJ], [])
+
+
+# LT_PROG_RC
+# ----------
+AC_DEFUN([LT_PROG_RC],
+[AC_CHECK_TOOL(RC, windres,)
+])
+
+# Old name:
+AU_ALIAS([LT_AC_PROG_RC], [LT_PROG_RC])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([LT_AC_PROG_RC], [])
+
+
+# _LT_DECL_EGREP
+# --------------
+# If we don't have a new enough Autoconf to choose the best grep
+# available, choose the one first in the user's PATH.
+m4_defun([_LT_DECL_EGREP],
+[AC_REQUIRE([AC_PROG_EGREP])dnl
+AC_REQUIRE([AC_PROG_FGREP])dnl
+test -z "$GREP" && GREP=grep
+_LT_DECL([], [GREP], [1], [A grep program that handles long lines])
+_LT_DECL([], [EGREP], [1], [An ERE matcher])
+_LT_DECL([], [FGREP], [1], [A literal string matcher])
+dnl Non-bleeding-edge autoconf doesn't subst GREP, so do it here too
+AC_SUBST([GREP])
+])
+
+
+# _LT_DECL_OBJDUMP
+# --------------
+# If we don't have a new enough Autoconf to choose the best objdump
+# available, choose the one first in the user's PATH.
+m4_defun([_LT_DECL_OBJDUMP],
+[AC_CHECK_TOOL(OBJDUMP, objdump, false)
+test -z "$OBJDUMP" && OBJDUMP=objdump
+_LT_DECL([], [OBJDUMP], [1], [An object symbol dumper])
+AC_SUBST([OBJDUMP])
+])
+
+
+# _LT_DECL_SED
+# ------------
+# Check for a fully-functional sed program, that truncates
+# as few characters as possible. Prefer GNU sed if found.
+m4_defun([_LT_DECL_SED],
+[AC_PROG_SED
+test -z "$SED" && SED=sed
+Xsed="$SED -e 1s/^X//"
+_LT_DECL([], [SED], [1], [A sed program that does not truncate output])
+_LT_DECL([], [Xsed], ["\$SED -e 1s/^X//"],
+ [Sed that helps us avoid accidentally triggering echo(1) options like -n])
+])# _LT_DECL_SED
+
+m4_ifndef([AC_PROG_SED], [
+# NOTE: This macro has been submitted for inclusion into #
+# GNU Autoconf as AC_PROG_SED. When it is available in #
+# a released version of Autoconf we should remove this #
+# macro and use it instead. #
+
+m4_defun([AC_PROG_SED],
+[AC_MSG_CHECKING([for a sed that does not truncate output])
+AC_CACHE_VAL(lt_cv_path_SED,
+[# Loop through the user's path and test for sed and gsed.
+# Then use that list of sed's as ones to test for truncation.
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for lt_ac_prog in sed gsed; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$lt_ac_prog$ac_exec_ext"; then
+ lt_ac_sed_list="$lt_ac_sed_list $as_dir/$lt_ac_prog$ac_exec_ext"
+ fi
+ done
+ done
+done
+IFS=$as_save_IFS
+lt_ac_max=0
+lt_ac_count=0
+# Add /usr/xpg4/bin/sed as it is typically found on Solaris
+# along with /bin/sed that truncates output.
+for lt_ac_sed in $lt_ac_sed_list /usr/xpg4/bin/sed; do
+ test ! -f $lt_ac_sed && continue
+ cat /dev/null > conftest.in
+ lt_ac_count=0
+ echo $ECHO_N "0123456789$ECHO_C" >conftest.in
+ # Check for GNU sed and select it if it is found.
+ if "$lt_ac_sed" --version 2>&1 < /dev/null | grep 'GNU' > /dev/null; then
+ lt_cv_path_SED=$lt_ac_sed
+ break
+ fi
+ while true; do
+ cat conftest.in conftest.in >conftest.tmp
+ mv conftest.tmp conftest.in
+ cp conftest.in conftest.nl
+ echo >>conftest.nl
+ $lt_ac_sed -e 's/a$//' < conftest.nl >conftest.out || break
+ cmp -s conftest.out conftest.nl || break
+ # 10000 chars as input seems more than enough
+ test $lt_ac_count -gt 10 && break
+ lt_ac_count=`expr $lt_ac_count + 1`
+ if test $lt_ac_count -gt $lt_ac_max; then
+ lt_ac_max=$lt_ac_count
+ lt_cv_path_SED=$lt_ac_sed
+ fi
+ done
+done
+])
+SED=$lt_cv_path_SED
+AC_SUBST([SED])
+AC_MSG_RESULT([$SED])
+])#AC_PROG_SED
+])#m4_ifndef
+
+# Old name:
+AU_ALIAS([LT_AC_PROG_SED], [AC_PROG_SED])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([LT_AC_PROG_SED], [])
+
+
+# _LT_CHECK_SHELL_FEATURES
+# ------------------------
+# Find out whether the shell is Bourne or XSI compatible,
+# or has some other useful features.
+m4_defun([_LT_CHECK_SHELL_FEATURES],
+[AC_MSG_CHECKING([whether the shell understands some XSI constructs])
+# Try some XSI features
+xsi_shell=no
+( _lt_dummy="a/b/c"
+ test "${_lt_dummy##*/},${_lt_dummy%/*},"${_lt_dummy%"$_lt_dummy"}, \
+ = c,a/b,, \
+ && eval 'test $(( 1 + 1 )) -eq 2 \
+ && test "${#_lt_dummy}" -eq 5' ) >/dev/null 2>&1 \
+ && xsi_shell=yes
+AC_MSG_RESULT([$xsi_shell])
+_LT_CONFIG_LIBTOOL_INIT([xsi_shell='$xsi_shell'])
+
+AC_MSG_CHECKING([whether the shell understands "+="])
+lt_shell_append=no
+( foo=bar; set foo baz; eval "$[1]+=\$[2]" && test "$foo" = barbaz ) \
+ >/dev/null 2>&1 \
+ && lt_shell_append=yes
+AC_MSG_RESULT([$lt_shell_append])
+_LT_CONFIG_LIBTOOL_INIT([lt_shell_append='$lt_shell_append'])
+
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+ lt_unset=unset
+else
+ lt_unset=false
+fi
+_LT_DECL([], [lt_unset], [0], [whether the shell understands "unset"])dnl
+
+# test EBCDIC or ASCII
+case `echo X|tr X '\101'` in
+ A) # ASCII based system
+ # \n is not interpreted correctly by Solaris 8 /usr/ucb/tr
+ lt_SP2NL='tr \040 \012'
+ lt_NL2SP='tr \015\012 \040\040'
+ ;;
+ *) # EBCDIC based system
+ lt_SP2NL='tr \100 \n'
+ lt_NL2SP='tr \r\n \100\100'
+ ;;
+esac
+_LT_DECL([SP2NL], [lt_SP2NL], [1], [turn spaces into newlines])dnl
+_LT_DECL([NL2SP], [lt_NL2SP], [1], [turn newlines into spaces])dnl
+])# _LT_CHECK_SHELL_FEATURES
+
+
+# _LT_PROG_XSI_SHELLFNS
+# ---------------------
+# Bourne and XSI compatible variants of some useful shell functions.
+m4_defun([_LT_PROG_XSI_SHELLFNS],
+[case $xsi_shell in
+ yes)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_dirname file append nondir_replacement
+# Compute the dirname of FILE. If nonempty, add APPEND to the result,
+# otherwise set result to NONDIR_REPLACEMENT.
+func_dirname ()
+{
+ case ${1} in
+ */*) func_dirname_result="${1%/*}${2}" ;;
+ * ) func_dirname_result="${3}" ;;
+ esac
+}
+
+# func_basename file
+func_basename ()
+{
+ func_basename_result="${1##*/}"
+}
+
+# func_dirname_and_basename file append nondir_replacement
+# perform func_basename and func_dirname in a single function
+# call:
+# dirname: Compute the dirname of FILE. If nonempty,
+# add APPEND to the result, otherwise set result
+# to NONDIR_REPLACEMENT.
+# value returned in "$func_dirname_result"
+# basename: Compute filename of FILE.
+# value retuned in "$func_basename_result"
+# Implementation must be kept synchronized with func_dirname
+# and func_basename. For efficiency, we do not delegate to
+# those functions but instead duplicate the functionality here.
+func_dirname_and_basename ()
+{
+ case ${1} in
+ */*) func_dirname_result="${1%/*}${2}" ;;
+ * ) func_dirname_result="${3}" ;;
+ esac
+ func_basename_result="${1##*/}"
+}
+
+# func_stripname prefix suffix name
+# strip PREFIX and SUFFIX off of NAME.
+# PREFIX and SUFFIX must not contain globbing or regex special
+# characters, hashes, percent signs, but SUFFIX may contain a leading
+# dot (in which case that matches only a dot).
+func_stripname ()
+{
+ # pdksh 5.2.14 does not do ${X%$Y} correctly if both X and Y are
+ # positional parameters, so assign one to ordinary parameter first.
+ func_stripname_result=${3}
+ func_stripname_result=${func_stripname_result#"${1}"}
+ func_stripname_result=${func_stripname_result%"${2}"}
+}
+
+# func_opt_split
+func_opt_split ()
+{
+ func_opt_split_opt=${1%%=*}
+ func_opt_split_arg=${1#*=}
+}
+
+# func_lo2o object
+func_lo2o ()
+{
+ case ${1} in
+ *.lo) func_lo2o_result=${1%.lo}.${objext} ;;
+ *) func_lo2o_result=${1} ;;
+ esac
+}
+
+# func_xform libobj-or-source
+func_xform ()
+{
+ func_xform_result=${1%.*}.lo
+}
+
+# func_arith arithmetic-term...
+func_arith ()
+{
+ func_arith_result=$(( $[*] ))
+}
+
+# func_len string
+# STRING may not start with a hyphen.
+func_len ()
+{
+ func_len_result=${#1}
+}
+
+_LT_EOF
+ ;;
+ *) # Bourne compatible functions.
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_dirname file append nondir_replacement
+# Compute the dirname of FILE. If nonempty, add APPEND to the result,
+# otherwise set result to NONDIR_REPLACEMENT.
+func_dirname ()
+{
+ # Extract subdirectory from the argument.
+ func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"`
+ if test "X$func_dirname_result" = "X${1}"; then
+ func_dirname_result="${3}"
+ else
+ func_dirname_result="$func_dirname_result${2}"
+ fi
+}
+
+# func_basename file
+func_basename ()
+{
+ func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"`
+}
+
+dnl func_dirname_and_basename
+dnl A portable version of this function is already defined in general.m4sh
+dnl so there is no need for it here.
+
+# func_stripname prefix suffix name
+# strip PREFIX and SUFFIX off of NAME.
+# PREFIX and SUFFIX must not contain globbing or regex special
+# characters, hashes, percent signs, but SUFFIX may contain a leading
+# dot (in which case that matches only a dot).
+# func_strip_suffix prefix name
+func_stripname ()
+{
+ case ${2} in
+ .*) func_stripname_result=`$ECHO "X${3}" \
+ | $Xsed -e "s%^${1}%%" -e "s%\\\\${2}\$%%"`;;
+ *) func_stripname_result=`$ECHO "X${3}" \
+ | $Xsed -e "s%^${1}%%" -e "s%${2}\$%%"`;;
+ esac
+}
+
+# sed scripts:
+my_sed_long_opt='1s/^\(-[[^=]]*\)=.*/\1/;q'
+my_sed_long_arg='1s/^-[[^=]]*=//'
+
+# func_opt_split
+func_opt_split ()
+{
+ func_opt_split_opt=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_opt"`
+ func_opt_split_arg=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_arg"`
+}
+
+# func_lo2o object
+func_lo2o ()
+{
+ func_lo2o_result=`$ECHO "X${1}" | $Xsed -e "$lo2o"`
+}
+
+# func_xform libobj-or-source
+func_xform ()
+{
+ func_xform_result=`$ECHO "X${1}" | $Xsed -e 's/\.[[^.]]*$/.lo/'`
+}
+
+# func_arith arithmetic-term...
+func_arith ()
+{
+ func_arith_result=`expr "$[@]"`
+}
+
+# func_len string
+# STRING may not start with a hyphen.
+func_len ()
+{
+ func_len_result=`expr "$[1]" : ".*" 2>/dev/null || echo $max_cmd_len`
+}
+
+_LT_EOF
+esac
+
+case $lt_shell_append in
+ yes)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$[1]+=\$[2]"
+}
+_LT_EOF
+ ;;
+ *)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$[1]=\$$[1]\$[2]"
+}
+
+_LT_EOF
+ ;;
+ esac
+])
+
+# Helper functions for option handling. -*- Autoconf -*-
+#
+# Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gary V. Vaughan, 2004
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+# serial 6 ltoptions.m4
+
+# This is to help aclocal find these macros, as it can't see m4_define.
+AC_DEFUN([LTOPTIONS_VERSION], [m4_if([1])])
+
+
+# _LT_MANGLE_OPTION(MACRO-NAME, OPTION-NAME)
+# ------------------------------------------
+m4_define([_LT_MANGLE_OPTION],
+[[_LT_OPTION_]m4_bpatsubst($1__$2, [[^a-zA-Z0-9_]], [_])])
+
+
+# _LT_SET_OPTION(MACRO-NAME, OPTION-NAME)
+# ---------------------------------------
+# Set option OPTION-NAME for macro MACRO-NAME, and if there is a
+# matching handler defined, dispatch to it. Other OPTION-NAMEs are
+# saved as a flag.
+m4_define([_LT_SET_OPTION],
+[m4_define(_LT_MANGLE_OPTION([$1], [$2]))dnl
+m4_ifdef(_LT_MANGLE_DEFUN([$1], [$2]),
+ _LT_MANGLE_DEFUN([$1], [$2]),
+ [m4_warning([Unknown $1 option `$2'])])[]dnl
+])
+
+
+# _LT_IF_OPTION(MACRO-NAME, OPTION-NAME, IF-SET, [IF-NOT-SET])
+# ------------------------------------------------------------
+# Execute IF-SET if OPTION is set, IF-NOT-SET otherwise.
+m4_define([_LT_IF_OPTION],
+[m4_ifdef(_LT_MANGLE_OPTION([$1], [$2]), [$3], [$4])])
+
+
+# _LT_UNLESS_OPTIONS(MACRO-NAME, OPTION-LIST, IF-NOT-SET)
+# -------------------------------------------------------
+# Execute IF-NOT-SET unless all options in OPTION-LIST for MACRO-NAME
+# are set.
+m4_define([_LT_UNLESS_OPTIONS],
+[m4_foreach([_LT_Option], m4_split(m4_normalize([$2])),
+ [m4_ifdef(_LT_MANGLE_OPTION([$1], _LT_Option),
+ [m4_define([$0_found])])])[]dnl
+m4_ifdef([$0_found], [m4_undefine([$0_found])], [$3
+])[]dnl
+])
+
+
+# _LT_SET_OPTIONS(MACRO-NAME, OPTION-LIST)
+# ----------------------------------------
+# OPTION-LIST is a space-separated list of Libtool options associated
+# with MACRO-NAME. If any OPTION has a matching handler declared with
+# LT_OPTION_DEFINE, dispatch to that macro; otherwise complain about
+# the unknown option and exit.
+m4_defun([_LT_SET_OPTIONS],
+[# Set options
+m4_foreach([_LT_Option], m4_split(m4_normalize([$2])),
+ [_LT_SET_OPTION([$1], _LT_Option)])
+
+m4_if([$1],[LT_INIT],[
+ dnl
+ dnl Simply set some default values (i.e off) if boolean options were not
+ dnl specified:
+ _LT_UNLESS_OPTIONS([LT_INIT], [dlopen], [enable_dlopen=no
+ ])
+ _LT_UNLESS_OPTIONS([LT_INIT], [win32-dll], [enable_win32_dll=no
+ ])
+ dnl
+ dnl If no reference was made to various pairs of opposing options, then
+ dnl we run the default mode handler for the pair. For example, if neither
+ dnl `shared' nor `disable-shared' was passed, we enable building of shared
+ dnl archives by default:
+ _LT_UNLESS_OPTIONS([LT_INIT], [shared disable-shared], [_LT_ENABLE_SHARED])
+ _LT_UNLESS_OPTIONS([LT_INIT], [static disable-static], [_LT_ENABLE_STATIC])
+ _LT_UNLESS_OPTIONS([LT_INIT], [pic-only no-pic], [_LT_WITH_PIC])
+ _LT_UNLESS_OPTIONS([LT_INIT], [fast-install disable-fast-install],
+ [_LT_ENABLE_FAST_INSTALL])
+ ])
+])# _LT_SET_OPTIONS
+
+
+
+# _LT_MANGLE_DEFUN(MACRO-NAME, OPTION-NAME)
+# -----------------------------------------
+m4_define([_LT_MANGLE_DEFUN],
+[[_LT_OPTION_DEFUN_]m4_bpatsubst(m4_toupper([$1__$2]), [[^A-Z0-9_]], [_])])
+
+
+# LT_OPTION_DEFINE(MACRO-NAME, OPTION-NAME, CODE)
+# -----------------------------------------------
+m4_define([LT_OPTION_DEFINE],
+[m4_define(_LT_MANGLE_DEFUN([$1], [$2]), [$3])[]dnl
+])# LT_OPTION_DEFINE
+
+
+# dlopen
+# ------
+LT_OPTION_DEFINE([LT_INIT], [dlopen], [enable_dlopen=yes
+])
+
+AU_DEFUN([AC_LIBTOOL_DLOPEN],
+[_LT_SET_OPTION([LT_INIT], [dlopen])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you
+put the `dlopen' option into LT_INIT's first parameter.])
+])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_DLOPEN], [])
+
+
+# win32-dll
+# ---------
+# Declare package support for building win32 dll's.
+LT_OPTION_DEFINE([LT_INIT], [win32-dll],
+[enable_win32_dll=yes
+
+case $host in
+*-*-cygwin* | *-*-mingw* | *-*-pw32* | *-cegcc*)
+ AC_CHECK_TOOL(AS, as, false)
+ AC_CHECK_TOOL(DLLTOOL, dlltool, false)
+ AC_CHECK_TOOL(OBJDUMP, objdump, false)
+ ;;
+esac
+
+test -z "$AS" && AS=as
+_LT_DECL([], [AS], [0], [Assembler program])dnl
+
+test -z "$DLLTOOL" && DLLTOOL=dlltool
+_LT_DECL([], [DLLTOOL], [0], [DLL creation program])dnl
+
+test -z "$OBJDUMP" && OBJDUMP=objdump
+_LT_DECL([], [OBJDUMP], [0], [Object dumper program])dnl
+])# win32-dll
+
+AU_DEFUN([AC_LIBTOOL_WIN32_DLL],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+_LT_SET_OPTION([LT_INIT], [win32-dll])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you
+put the `win32-dll' option into LT_INIT's first parameter.])
+])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_WIN32_DLL], [])
+
+
+# _LT_ENABLE_SHARED([DEFAULT])
+# ----------------------------
+# implement the --enable-shared flag, and supports the `shared' and
+# `disable-shared' LT_INIT options.
+# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'.
+m4_define([_LT_ENABLE_SHARED],
+[m4_define([_LT_ENABLE_SHARED_DEFAULT], [m4_if($1, no, no, yes)])dnl
+AC_ARG_ENABLE([shared],
+ [AS_HELP_STRING([--enable-shared@<:@=PKGS@:>@],
+ [build shared libraries @<:@default=]_LT_ENABLE_SHARED_DEFAULT[@:>@])],
+ [p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_shared=yes ;;
+ no) enable_shared=no ;;
+ *)
+ enable_shared=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_shared=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac],
+ [enable_shared=]_LT_ENABLE_SHARED_DEFAULT)
+
+ _LT_DECL([build_libtool_libs], [enable_shared], [0],
+ [Whether or not to build shared libraries])
+])# _LT_ENABLE_SHARED
+
+LT_OPTION_DEFINE([LT_INIT], [shared], [_LT_ENABLE_SHARED([yes])])
+LT_OPTION_DEFINE([LT_INIT], [disable-shared], [_LT_ENABLE_SHARED([no])])
+
+# Old names:
+AC_DEFUN([AC_ENABLE_SHARED],
+[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[shared])
+])
+
+AC_DEFUN([AC_DISABLE_SHARED],
+[_LT_SET_OPTION([LT_INIT], [disable-shared])
+])
+
+AU_DEFUN([AM_ENABLE_SHARED], [AC_ENABLE_SHARED($@)])
+AU_DEFUN([AM_DISABLE_SHARED], [AC_DISABLE_SHARED($@)])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AM_ENABLE_SHARED], [])
+dnl AC_DEFUN([AM_DISABLE_SHARED], [])
+
+
+
+# _LT_ENABLE_STATIC([DEFAULT])
+# ----------------------------
+# implement the --enable-static flag, and support the `static' and
+# `disable-static' LT_INIT options.
+# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'.
+m4_define([_LT_ENABLE_STATIC],
+[m4_define([_LT_ENABLE_STATIC_DEFAULT], [m4_if($1, no, no, yes)])dnl
+AC_ARG_ENABLE([static],
+ [AS_HELP_STRING([--enable-static@<:@=PKGS@:>@],
+ [build static libraries @<:@default=]_LT_ENABLE_STATIC_DEFAULT[@:>@])],
+ [p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_static=yes ;;
+ no) enable_static=no ;;
+ *)
+ enable_static=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_static=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac],
+ [enable_static=]_LT_ENABLE_STATIC_DEFAULT)
+
+ _LT_DECL([build_old_libs], [enable_static], [0],
+ [Whether or not to build static libraries])
+])# _LT_ENABLE_STATIC
+
+LT_OPTION_DEFINE([LT_INIT], [static], [_LT_ENABLE_STATIC([yes])])
+LT_OPTION_DEFINE([LT_INIT], [disable-static], [_LT_ENABLE_STATIC([no])])
+
+# Old names:
+AC_DEFUN([AC_ENABLE_STATIC],
+[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[static])
+])
+
+AC_DEFUN([AC_DISABLE_STATIC],
+[_LT_SET_OPTION([LT_INIT], [disable-static])
+])
+
+AU_DEFUN([AM_ENABLE_STATIC], [AC_ENABLE_STATIC($@)])
+AU_DEFUN([AM_DISABLE_STATIC], [AC_DISABLE_STATIC($@)])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AM_ENABLE_STATIC], [])
+dnl AC_DEFUN([AM_DISABLE_STATIC], [])
+
+
+
+# _LT_ENABLE_FAST_INSTALL([DEFAULT])
+# ----------------------------------
+# implement the --enable-fast-install flag, and support the `fast-install'
+# and `disable-fast-install' LT_INIT options.
+# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'.
+m4_define([_LT_ENABLE_FAST_INSTALL],
+[m4_define([_LT_ENABLE_FAST_INSTALL_DEFAULT], [m4_if($1, no, no, yes)])dnl
+AC_ARG_ENABLE([fast-install],
+ [AS_HELP_STRING([--enable-fast-install@<:@=PKGS@:>@],
+ [optimize for fast installation @<:@default=]_LT_ENABLE_FAST_INSTALL_DEFAULT[@:>@])],
+ [p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_fast_install=yes ;;
+ no) enable_fast_install=no ;;
+ *)
+ enable_fast_install=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_fast_install=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac],
+ [enable_fast_install=]_LT_ENABLE_FAST_INSTALL_DEFAULT)
+
+_LT_DECL([fast_install], [enable_fast_install], [0],
+ [Whether or not to optimize for fast installation])dnl
+])# _LT_ENABLE_FAST_INSTALL
+
+LT_OPTION_DEFINE([LT_INIT], [fast-install], [_LT_ENABLE_FAST_INSTALL([yes])])
+LT_OPTION_DEFINE([LT_INIT], [disable-fast-install], [_LT_ENABLE_FAST_INSTALL([no])])
+
+# Old names:
+AU_DEFUN([AC_ENABLE_FAST_INSTALL],
+[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[fast-install])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you put
+the `fast-install' option into LT_INIT's first parameter.])
+])
+
+AU_DEFUN([AC_DISABLE_FAST_INSTALL],
+[_LT_SET_OPTION([LT_INIT], [disable-fast-install])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you put
+the `disable-fast-install' option into LT_INIT's first parameter.])
+])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_ENABLE_FAST_INSTALL], [])
+dnl AC_DEFUN([AM_DISABLE_FAST_INSTALL], [])
+
+
+# _LT_WITH_PIC([MODE])
+# --------------------
+# implement the --with-pic flag, and support the `pic-only' and `no-pic'
+# LT_INIT options.
+# MODE is either `yes' or `no'. If omitted, it defaults to `both'.
+m4_define([_LT_WITH_PIC],
+[AC_ARG_WITH([pic],
+ [AS_HELP_STRING([--with-pic],
+ [try to use only PIC/non-PIC objects @<:@default=use both@:>@])],
+ [pic_mode="$withval"],
+ [pic_mode=default])
+
+test -z "$pic_mode" && pic_mode=m4_default([$1], [default])
+
+_LT_DECL([], [pic_mode], [0], [What type of objects to build])dnl
+])# _LT_WITH_PIC
+
+LT_OPTION_DEFINE([LT_INIT], [pic-only], [_LT_WITH_PIC([yes])])
+LT_OPTION_DEFINE([LT_INIT], [no-pic], [_LT_WITH_PIC([no])])
+
+# Old name:
+AU_DEFUN([AC_LIBTOOL_PICMODE],
+[_LT_SET_OPTION([LT_INIT], [pic-only])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you
+put the `pic-only' option into LT_INIT's first parameter.])
+])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_PICMODE], [])
+
+
+m4_define([_LTDL_MODE], [])
+LT_OPTION_DEFINE([LTDL_INIT], [nonrecursive],
+ [m4_define([_LTDL_MODE], [nonrecursive])])
+LT_OPTION_DEFINE([LTDL_INIT], [recursive],
+ [m4_define([_LTDL_MODE], [recursive])])
+LT_OPTION_DEFINE([LTDL_INIT], [subproject],
+ [m4_define([_LTDL_MODE], [subproject])])
+
+m4_define([_LTDL_TYPE], [])
+LT_OPTION_DEFINE([LTDL_INIT], [installable],
+ [m4_define([_LTDL_TYPE], [installable])])
+LT_OPTION_DEFINE([LTDL_INIT], [convenience],
+ [m4_define([_LTDL_TYPE], [convenience])])
+
+# ltsugar.m4 -- libtool m4 base layer. -*-Autoconf-*-
+#
+# Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gary V. Vaughan, 2004
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+# serial 6 ltsugar.m4
+
+# This is to help aclocal find these macros, as it can't see m4_define.
+AC_DEFUN([LTSUGAR_VERSION], [m4_if([0.1])])
+
+
+# lt_join(SEP, ARG1, [ARG2...])
+# -----------------------------
+# Produce ARG1SEPARG2...SEPARGn, omitting [] arguments and their
+# associated separator.
+# Needed until we can rely on m4_join from Autoconf 2.62, since all earlier
+# versions in m4sugar had bugs.
+m4_define([lt_join],
+[m4_if([$#], [1], [],
+ [$#], [2], [[$2]],
+ [m4_if([$2], [], [], [[$2]_])$0([$1], m4_shift(m4_shift($@)))])])
+m4_define([_lt_join],
+[m4_if([$#$2], [2], [],
+ [m4_if([$2], [], [], [[$1$2]])$0([$1], m4_shift(m4_shift($@)))])])
+
+
+# lt_car(LIST)
+# lt_cdr(LIST)
+# ------------
+# Manipulate m4 lists.
+# These macros are necessary as long as will still need to support
+# Autoconf-2.59 which quotes differently.
+m4_define([lt_car], [[$1]])
+m4_define([lt_cdr],
+[m4_if([$#], 0, [m4_fatal([$0: cannot be called without arguments])],
+ [$#], 1, [],
+ [m4_dquote(m4_shift($@))])])
+m4_define([lt_unquote], $1)
+
+
+# lt_append(MACRO-NAME, STRING, [SEPARATOR])
+# ------------------------------------------
+# Redefine MACRO-NAME to hold its former content plus `SEPARATOR'`STRING'.
+# Note that neither SEPARATOR nor STRING are expanded; they are appended
+# to MACRO-NAME as is (leaving the expansion for when MACRO-NAME is invoked).
+# No SEPARATOR is output if MACRO-NAME was previously undefined (different
+# than defined and empty).
+#
+# This macro is needed until we can rely on Autoconf 2.62, since earlier
+# versions of m4sugar mistakenly expanded SEPARATOR but not STRING.
+m4_define([lt_append],
+[m4_define([$1],
+ m4_ifdef([$1], [m4_defn([$1])[$3]])[$2])])
+
+
+
+# lt_combine(SEP, PREFIX-LIST, INFIX, SUFFIX1, [SUFFIX2...])
+# ----------------------------------------------------------
+# Produce a SEP delimited list of all paired combinations of elements of
+# PREFIX-LIST with SUFFIX1 through SUFFIXn. Each element of the list
+# has the form PREFIXmINFIXSUFFIXn.
+# Needed until we can rely on m4_combine added in Autoconf 2.62.
+m4_define([lt_combine],
+[m4_if(m4_eval([$# > 3]), [1],
+ [m4_pushdef([_Lt_sep], [m4_define([_Lt_sep], m4_defn([lt_car]))])]]dnl
+[[m4_foreach([_Lt_prefix], [$2],
+ [m4_foreach([_Lt_suffix],
+ ]m4_dquote(m4_dquote(m4_shift(m4_shift(m4_shift($@)))))[,
+ [_Lt_sep([$1])[]m4_defn([_Lt_prefix])[$3]m4_defn([_Lt_suffix])])])])])
+
+
+# lt_if_append_uniq(MACRO-NAME, VARNAME, [SEPARATOR], [UNIQ], [NOT-UNIQ])
+# -----------------------------------------------------------------------
+# Iff MACRO-NAME does not yet contain VARNAME, then append it (delimited
+# by SEPARATOR if supplied) and expand UNIQ, else NOT-UNIQ.
+m4_define([lt_if_append_uniq],
+[m4_ifdef([$1],
+ [m4_if(m4_index([$3]m4_defn([$1])[$3], [$3$2$3]), [-1],
+ [lt_append([$1], [$2], [$3])$4],
+ [$5])],
+ [lt_append([$1], [$2], [$3])$4])])
+
+
+# lt_dict_add(DICT, KEY, VALUE)
+# -----------------------------
+m4_define([lt_dict_add],
+[m4_define([$1($2)], [$3])])
+
+
+# lt_dict_add_subkey(DICT, KEY, SUBKEY, VALUE)
+# --------------------------------------------
+m4_define([lt_dict_add_subkey],
+[m4_define([$1($2:$3)], [$4])])
+
+
+# lt_dict_fetch(DICT, KEY, [SUBKEY])
+# ----------------------------------
+m4_define([lt_dict_fetch],
+[m4_ifval([$3],
+ m4_ifdef([$1($2:$3)], [m4_defn([$1($2:$3)])]),
+ m4_ifdef([$1($2)], [m4_defn([$1($2)])]))])
+
+
+# lt_if_dict_fetch(DICT, KEY, [SUBKEY], VALUE, IF-TRUE, [IF-FALSE])
+# -----------------------------------------------------------------
+m4_define([lt_if_dict_fetch],
+[m4_if(lt_dict_fetch([$1], [$2], [$3]), [$4],
+ [$5],
+ [$6])])
+
+
+# lt_dict_filter(DICT, [SUBKEY], VALUE, [SEPARATOR], KEY, [...])
+# --------------------------------------------------------------
+m4_define([lt_dict_filter],
+[m4_if([$5], [], [],
+ [lt_join(m4_quote(m4_default([$4], [[, ]])),
+ lt_unquote(m4_split(m4_normalize(m4_foreach(_Lt_key, lt_car([m4_shiftn(4, $@)]),
+ [lt_if_dict_fetch([$1], _Lt_key, [$2], [$3], [_Lt_key ])])))))])[]dnl
+])
+
+# ltversion.m4 -- version numbers -*- Autoconf -*-
+#
+# Copyright (C) 2004 Free Software Foundation, Inc.
+# Written by Scott James Remnant, 2004
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+# Generated from ltversion.in.
+
+# serial 3017 ltversion.m4
+# This file is part of GNU Libtool
+
+m4_define([LT_PACKAGE_VERSION], [2.2.6b])
+m4_define([LT_PACKAGE_REVISION], [1.3017])
+
+AC_DEFUN([LTVERSION_VERSION],
+[macro_version='2.2.6b'
+macro_revision='1.3017'
+_LT_DECL(, macro_version, 0, [Which release of libtool.m4 was used?])
+_LT_DECL(, macro_revision, 0)
+])
+
+# lt~obsolete.m4 -- aclocal satisfying obsolete definitions. -*-Autoconf-*-
+#
+# Copyright (C) 2004, 2005, 2007 Free Software Foundation, Inc.
+# Written by Scott James Remnant, 2004.
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+# serial 4 lt~obsolete.m4
+
+# These exist entirely to fool aclocal when bootstrapping libtool.
+#
+# In the past libtool.m4 has provided macros via AC_DEFUN (or AU_DEFUN)
+# which have later been changed to m4_define as they aren't part of the
+# exported API, or moved to Autoconf or Automake where they belong.
+#
+# The trouble is, aclocal is a bit thick. It'll see the old AC_DEFUN
+# in /usr/share/aclocal/libtool.m4 and remember it, then when it sees us
+# using a macro with the same name in our local m4/libtool.m4 it'll
+# pull the old libtool.m4 in (it doesn't see our shiny new m4_define
+# and doesn't know about Autoconf macros at all.)
+#
+# So we provide this file, which has a silly filename so it's always
+# included after everything else. This provides aclocal with the
+# AC_DEFUNs it wants, but when m4 processes it, it doesn't do anything
+# because those macros already exist, or will be overwritten later.
+# We use AC_DEFUN over AU_DEFUN for compatibility with aclocal-1.6.
+#
+# Anytime we withdraw an AC_DEFUN or AU_DEFUN, remember to add it here.
+# Yes, that means every name once taken will need to remain here until
+# we give up compatibility with versions before 1.7, at which point
+# we need to keep only those names which we still refer to.
+
+# This is to help aclocal find these macros, as it can't see m4_define.
+AC_DEFUN([LTOBSOLETE_VERSION], [m4_if([1])])
+
+m4_ifndef([AC_LIBTOOL_LINKER_OPTION], [AC_DEFUN([AC_LIBTOOL_LINKER_OPTION])])
+m4_ifndef([AC_PROG_EGREP], [AC_DEFUN([AC_PROG_EGREP])])
+m4_ifndef([_LT_AC_PROG_ECHO_BACKSLASH], [AC_DEFUN([_LT_AC_PROG_ECHO_BACKSLASH])])
+m4_ifndef([_LT_AC_SHELL_INIT], [AC_DEFUN([_LT_AC_SHELL_INIT])])
+m4_ifndef([_LT_AC_SYS_LIBPATH_AIX], [AC_DEFUN([_LT_AC_SYS_LIBPATH_AIX])])
+m4_ifndef([_LT_PROG_LTMAIN], [AC_DEFUN([_LT_PROG_LTMAIN])])
+m4_ifndef([_LT_AC_TAGVAR], [AC_DEFUN([_LT_AC_TAGVAR])])
+m4_ifndef([AC_LTDL_ENABLE_INSTALL], [AC_DEFUN([AC_LTDL_ENABLE_INSTALL])])
+m4_ifndef([AC_LTDL_PREOPEN], [AC_DEFUN([AC_LTDL_PREOPEN])])
+m4_ifndef([_LT_AC_SYS_COMPILER], [AC_DEFUN([_LT_AC_SYS_COMPILER])])
+m4_ifndef([_LT_AC_LOCK], [AC_DEFUN([_LT_AC_LOCK])])
+m4_ifndef([AC_LIBTOOL_SYS_OLD_ARCHIVE], [AC_DEFUN([AC_LIBTOOL_SYS_OLD_ARCHIVE])])
+m4_ifndef([_LT_AC_TRY_DLOPEN_SELF], [AC_DEFUN([_LT_AC_TRY_DLOPEN_SELF])])
+m4_ifndef([AC_LIBTOOL_PROG_CC_C_O], [AC_DEFUN([AC_LIBTOOL_PROG_CC_C_O])])
+m4_ifndef([AC_LIBTOOL_SYS_HARD_LINK_LOCKS], [AC_DEFUN([AC_LIBTOOL_SYS_HARD_LINK_LOCKS])])
+m4_ifndef([AC_LIBTOOL_OBJDIR], [AC_DEFUN([AC_LIBTOOL_OBJDIR])])
+m4_ifndef([AC_LTDL_OBJDIR], [AC_DEFUN([AC_LTDL_OBJDIR])])
+m4_ifndef([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH], [AC_DEFUN([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH])])
+m4_ifndef([AC_LIBTOOL_SYS_LIB_STRIP], [AC_DEFUN([AC_LIBTOOL_SYS_LIB_STRIP])])
+m4_ifndef([AC_PATH_MAGIC], [AC_DEFUN([AC_PATH_MAGIC])])
+m4_ifndef([AC_PROG_LD_GNU], [AC_DEFUN([AC_PROG_LD_GNU])])
+m4_ifndef([AC_PROG_LD_RELOAD_FLAG], [AC_DEFUN([AC_PROG_LD_RELOAD_FLAG])])
+m4_ifndef([AC_DEPLIBS_CHECK_METHOD], [AC_DEFUN([AC_DEPLIBS_CHECK_METHOD])])
+m4_ifndef([AC_LIBTOOL_PROG_COMPILER_NO_RTTI], [AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_NO_RTTI])])
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+ [_AM_DEPENDENCIES(OBJC)],
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+dnl Hook into `_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
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+# When config.status generates a header, we must update the stamp-h file.
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+# Autoconf calls _AC_AM_CONFIG_HEADER_HOOK (when defined) in the
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+
+# Copyright (C) 2001, 2003, 2005, 2008 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_PROG_INSTALL_SH
+# ------------------
+# Define $install_sh.
+AC_DEFUN([AM_PROG_INSTALL_SH],
+[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+if test x"${install_sh}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
+ *)
+ install_sh="\${SHELL} $am_aux_dir/install-sh"
+ esac
+fi
+AC_SUBST(install_sh)])
+
+# Copyright (C) 2003, 2005 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 2
+
+# Check whether the underlying file-system supports filenames
+# with a leading dot. For instance MS-DOS doesn't.
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+fi
+rmdir .tst 2>/dev/null
+AC_SUBST([am__leading_dot])])
+
+# Check to see how 'make' treats includes. -*- Autoconf -*-
+
+# Copyright (C) 2001, 2002, 2003, 2005, 2009 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 4
+
+# AM_MAKE_INCLUDE()
+# -----------------
+# Check to see how make treats includes.
+AC_DEFUN([AM_MAKE_INCLUDE],
+[am_make=${MAKE-make}
+cat > confinc << 'END'
+am__doit:
+ @echo this is the am__doit target
+.PHONY: am__doit
+END
+# If we don't find an include directive, just comment out the code.
+AC_MSG_CHECKING([for style of include used by $am_make])
+am__include="#"
+am__quote=
+_am_result=none
+# First try GNU make style include.
+echo "include confinc" > confmf
+# Ignore all kinds of additional output from `make'.
+case `$am_make -s -f confmf 2> /dev/null` in #(
+*the\ am__doit\ target*)
+ am__include=include
+ am__quote=
+ _am_result=GNU
+ ;;
+esac
+# Now try BSD make style include.
+if test "$am__include" = "#"; then
+ echo '.include "confinc"' > confmf
+ case `$am_make -s -f confmf 2> /dev/null` in #(
+ *the\ am__doit\ target*)
+ am__include=.include
+ am__quote="\""
+ _am_result=BSD
+ ;;
+ esac
+fi
+AC_SUBST([am__include])
+AC_SUBST([am__quote])
+AC_MSG_RESULT([$_am_result])
+rm -f confinc confmf
+])
+
+# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
+
+# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2004, 2005, 2008
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 6
+
+# AM_MISSING_PROG(NAME, PROGRAM)
+# ------------------------------
+AC_DEFUN([AM_MISSING_PROG],
+[AC_REQUIRE([AM_MISSING_HAS_RUN])
+$1=${$1-"${am_missing_run}$2"}
+AC_SUBST($1)])
+
+
+# AM_MISSING_HAS_RUN
+# ------------------
+# Define MISSING if not defined so far and test if it supports --run.
+# If it does, set am_missing_run to use it, otherwise, to nothing.
+AC_DEFUN([AM_MISSING_HAS_RUN],
+[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+AC_REQUIRE_AUX_FILE([missing])dnl
+if test x"${MISSING+set}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;;
+ *)
+ MISSING="\${SHELL} $am_aux_dir/missing" ;;
+ esac
+fi
+# Use eval to expand $SHELL
+if eval "$MISSING --run true"; then
+ am_missing_run="$MISSING --run "
+else
+ am_missing_run=
+ AC_MSG_WARN([`missing' script is too old or missing])
+fi
+])
+
+# Copyright (C) 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_PROG_MKDIR_P
+# ---------------
+# Check for `mkdir -p'.
+AC_DEFUN([AM_PROG_MKDIR_P],
+[AC_PREREQ([2.60])dnl
+AC_REQUIRE([AC_PROG_MKDIR_P])dnl
+dnl Automake 1.8 to 1.9.6 used to define mkdir_p. We now use MKDIR_P,
+dnl while keeping a definition of mkdir_p for backward compatibility.
+dnl @MKDIR_P@ is magic: AC_OUTPUT adjusts its value for each Makefile.
+dnl However we cannot define mkdir_p as $(MKDIR_P) for the sake of
+dnl Makefile.ins that do not define MKDIR_P, so we do our own
+dnl adjustment using top_builddir (which is defined more often than
+dnl MKDIR_P).
+AC_SUBST([mkdir_p], ["$MKDIR_P"])dnl
+case $mkdir_p in
+ [[\\/$]]* | ?:[[\\/]]*) ;;
+ */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
+esac
+])
+
+# Helper functions for option handling. -*- Autoconf -*-
+
+# Copyright (C) 2001, 2002, 2003, 2005, 2008 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 4
+
+# _AM_MANGLE_OPTION(NAME)
+# -----------------------
+AC_DEFUN([_AM_MANGLE_OPTION],
+[[_AM_OPTION_]m4_bpatsubst($1, [[^a-zA-Z0-9_]], [_])])
+
+# _AM_SET_OPTION(NAME)
+# ------------------------------
+# Set option NAME. Presently that only means defining a flag for this option.
+AC_DEFUN([_AM_SET_OPTION],
+[m4_define(_AM_MANGLE_OPTION([$1]), 1)])
+
+# _AM_SET_OPTIONS(OPTIONS)
+# ----------------------------------
+# OPTIONS is a space-separated list of Automake options.
+AC_DEFUN([_AM_SET_OPTIONS],
+[m4_foreach_w([_AM_Option], [$1], [_AM_SET_OPTION(_AM_Option)])])
+
+# _AM_IF_OPTION(OPTION, IF-SET, [IF-NOT-SET])
+# -------------------------------------------
+# Execute IF-SET if OPTION is set, IF-NOT-SET otherwise.
+AC_DEFUN([_AM_IF_OPTION],
+[m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
+
+# Check to make sure that the build environment is sane. -*- Autoconf -*-
+
+# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005, 2008
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 5
+
+# AM_SANITY_CHECK
+# ---------------
+AC_DEFUN([AM_SANITY_CHECK],
+[AC_MSG_CHECKING([whether build environment is sane])
+# Just in case
+sleep 1
+echo timestamp > conftest.file
+# Reject unsafe characters in $srcdir or the absolute working directory
+# name. Accept space and tab only in the latter.
+am_lf='
+'
+case `pwd` in
+ *[[\\\"\#\$\&\'\`$am_lf]]*)
+ AC_MSG_ERROR([unsafe absolute working directory name]);;
+esac
+case $srcdir in
+ *[[\\\"\#\$\&\'\`$am_lf\ \ ]]*)
+ AC_MSG_ERROR([unsafe srcdir value: `$srcdir']);;
+esac
+
+# Do `set' in a subshell so we don't clobber the current shell's
+# arguments. Must try -L first in case configure is actually a
+# symlink; some systems play weird games with the mod time of symlinks
+# (eg FreeBSD returns the mod time of the symlink's containing
+# directory).
+if (
+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
+ if test "$[*]" = "X"; then
+ # -L didn't work.
+ set X `ls -t "$srcdir/configure" conftest.file`
+ fi
+ rm -f conftest.file
+ if test "$[*]" != "X $srcdir/configure conftest.file" \
+ && test "$[*]" != "X conftest.file $srcdir/configure"; then
+
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ AC_MSG_ERROR([ls -t appears to fail. Make sure there is not a broken
+alias in your environment])
+ fi
+
+ test "$[2]" = conftest.file
+ )
+then
+ # Ok.
+ :
+else
+ AC_MSG_ERROR([newly created file is older than distributed files!
+Check your system clock])
+fi
+AC_MSG_RESULT(yes)])
+
+# Copyright (C) 2001, 2003, 2005 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_PROG_INSTALL_STRIP
+# ---------------------
+# One issue with vendor `install' (even GNU) is that you can't
+# specify the program used to strip binaries. This is especially
+# annoying in cross-compiling environments, where the build's strip
+# is unlikely to handle the host's binaries.
+# Fortunately install-sh will honor a STRIPPROG variable, so we
+# always use install-sh in `make install-strip', and initialize
+# STRIPPROG with the value of the STRIP variable (set by the user).
+AC_DEFUN([AM_PROG_INSTALL_STRIP],
+[AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'. However `strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
+# will honor the `STRIP' environment variable to overrule this program.
+dnl Don't test for $cross_compiling = yes, because it might be `maybe'.
+if test "$cross_compiling" != no; then
+ AC_CHECK_TOOL([STRIP], [strip], :)
+fi
+INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
+AC_SUBST([INSTALL_STRIP_PROGRAM])])
+
+# Copyright (C) 2006, 2008 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 2
+
+# _AM_SUBST_NOTMAKE(VARIABLE)
+# ---------------------------
+# Prevent Automake from outputting VARIABLE = @VARIABLE@ in Makefile.in.
+# This macro is traced by Automake.
+AC_DEFUN([_AM_SUBST_NOTMAKE])
+
+# AM_SUBST_NOTMAKE(VARIABLE)
+# ---------------------------
+# Public sister of _AM_SUBST_NOTMAKE.
+AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
+
+# Check how to create a tarball. -*- Autoconf -*-
+
+# Copyright (C) 2004, 2005 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 2
+
+# _AM_PROG_TAR(FORMAT)
+# --------------------
+# Check how to create a tarball in format FORMAT.
+# FORMAT should be one of `v7', `ustar', or `pax'.
+#
+# Substitute a variable $(am__tar) that is a command
+# writing to stdout a FORMAT-tarball containing the directory
+# $tardir.
+# tardir=directory && $(am__tar) > result.tar
+#
+# Substitute a variable $(am__untar) that extract such
+# a tarball read from stdin.
+# $(am__untar) < result.tar
+AC_DEFUN([_AM_PROG_TAR],
+[# Always define AMTAR for backward compatibility.
+AM_MISSING_PROG([AMTAR], [tar])
+m4_if([$1], [v7],
+ [am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'],
+ [m4_case([$1], [ustar],, [pax],,
+ [m4_fatal([Unknown tar format])])
+AC_MSG_CHECKING([how to create a $1 tar archive])
+# Loop over all known methods to create a tar archive until one works.
+_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
+_am_tools=${am_cv_prog_tar_$1-$_am_tools}
+# Do not fold the above two line into one, because Tru64 sh and
+# Solaris sh will not grok spaces in the rhs of `-'.
+for _am_tool in $_am_tools
+do
+ case $_am_tool in
+ gnutar)
+ for _am_tar in tar gnutar gtar;
+ do
+ AM_RUN_LOG([$_am_tar --version]) && break
+ done
+ am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
+ am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
+ am__untar="$_am_tar -xf -"
+ ;;
+ plaintar)
+ # Must skip GNU tar: if it does not support --format= it doesn't create
+ # ustar tarball either.
+ (tar --version) >/dev/null 2>&1 && continue
+ am__tar='tar chf - "$$tardir"'
+ am__tar_='tar chf - "$tardir"'
+ am__untar='tar xf -'
+ ;;
+ pax)
+ am__tar='pax -L -x $1 -w "$$tardir"'
+ am__tar_='pax -L -x $1 -w "$tardir"'
+ am__untar='pax -r'
+ ;;
+ cpio)
+ am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
+ am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
+ am__untar='cpio -i -H $1 -d'
+ ;;
+ none)
+ am__tar=false
+ am__tar_=false
+ am__untar=false
+ ;;
+ esac
+
+ # If the value was cached, stop now. We just wanted to have am__tar
+ # and am__untar set.
+ test -n "${am_cv_prog_tar_$1}" && break
+
+ # tar/untar a dummy directory, and stop if the command works
+ rm -rf conftest.dir
+ mkdir conftest.dir
+ echo GrepMe > conftest.dir/file
+ AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
+ rm -rf conftest.dir
+ if test -s conftest.tar; then
+ AM_RUN_LOG([$am__untar <conftest.tar])
+ grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
+ fi
+done
+rm -rf conftest.dir
+
+AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
+AC_MSG_RESULT([$am_cv_prog_tar_$1])])
+AC_SUBST([am__tar])
+AC_SUBST([am__untar])
+]) # _AM_PROG_TAR
+
diff --git a/config/config.guess b/config/config.guess
new file mode 100755
index 0000000..c2246a4
--- /dev/null
+++ b/config/config.guess
@@ -0,0 +1,1502 @@
+#! /bin/sh
+# Attempt to guess a canonical system name.
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
+# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010
+# Free Software Foundation, Inc.
+
+timestamp='2009-12-30'
+
+# This file is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
+# 02110-1301, USA.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+
+# Originally written by Per Bothner. Please send patches (context
+# diff format) to <config-patches at gnu.org> and include a ChangeLog
+# entry.
+#
+# This script attempts to guess a canonical system name similar to
+# config.sub. If it succeeds, it prints the system name on stdout, and
+# exits with 0. Otherwise, it exits with 1.
+#
+# You can get the latest version of this script from:
+# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
+
+me=`echo "$0" | sed -e 's,.*/,,'`
+
+usage="\
+Usage: $0 [OPTION]
+
+Output the configuration name of the system \`$me' is run on.
+
+Operation modes:
+ -h, --help print this help, then exit
+ -t, --time-stamp print date of last modification, then exit
+ -v, --version print version number, then exit
+
+Report bugs and patches to <config-patches at gnu.org>."
+
+version="\
+GNU config.guess ($timestamp)
+
+Originally written by Per Bothner.
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000,
+2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free
+Software Foundation, Inc.
+
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+
+help="
+Try \`$me --help' for more information."
+
+# Parse command line
+while test $# -gt 0 ; do
+ case $1 in
+ --time-stamp | --time* | -t )
+ echo "$timestamp" ; exit ;;
+ --version | -v )
+ echo "$version" ; exit ;;
+ --help | --h* | -h )
+ echo "$usage"; exit ;;
+ -- ) # Stop option processing
+ shift; break ;;
+ - ) # Use stdin as input.
+ break ;;
+ -* )
+ echo "$me: invalid option $1$help" >&2
+ exit 1 ;;
+ * )
+ break ;;
+ esac
+done
+
+if test $# != 0; then
+ echo "$me: too many arguments$help" >&2
+ exit 1
+fi
+
+trap 'exit 1' 1 2 15
+
+# CC_FOR_BUILD -- compiler used by this script. Note that the use of a
+# compiler to aid in system detection is discouraged as it requires
+# temporary files to be created and, as you can see below, it is a
+# headache to deal with in a portable fashion.
+
+# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still
+# use `HOST_CC' if defined, but it is deprecated.
+
+# Portable tmp directory creation inspired by the Autoconf team.
+
+set_cc_for_build='
+trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ;
+trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ;
+: ${TMPDIR=/tmp} ;
+ { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
+ { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||
+ { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } ||
+ { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ;
+dummy=$tmp/dummy ;
+tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ;
+case $CC_FOR_BUILD,$HOST_CC,$CC in
+ ,,) echo "int x;" > $dummy.c ;
+ for c in cc gcc c89 c99 ; do
+ if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then
+ CC_FOR_BUILD="$c"; break ;
+ fi ;
+ done ;
+ if test x"$CC_FOR_BUILD" = x ; then
+ CC_FOR_BUILD=no_compiler_found ;
+ fi
+ ;;
+ ,,*) CC_FOR_BUILD=$CC ;;
+ ,*,*) CC_FOR_BUILD=$HOST_CC ;;
+esac ; set_cc_for_build= ;'
+
+# This is needed to find uname on a Pyramid OSx when run in the BSD universe.
+# (ghazi at noc.rutgers.edu 1994-08-24)
+if (test -f /.attbin/uname) >/dev/null 2>&1 ; then
+ PATH=$PATH:/.attbin ; export PATH
+fi
+
+UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown
+UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
+UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown
+UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
+
+# Note: order is significant - the case branches are not exclusive.
+
+case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
+ *:NetBSD:*:*)
+ # NetBSD (nbsd) targets should (where applicable) match one or
+ # more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*,
+ # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently
+ # switched to ELF, *-*-netbsd* would select the old
+ # object file format. This provides both forward
+ # compatibility and a consistent mechanism for selecting the
+ # object file format.
+ #
+ # Note: NetBSD doesn't particularly care about the vendor
+ # portion of the name. We always set it to "unknown".
+ sysctl="sysctl -n hw.machine_arch"
+ UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \
+ /usr/sbin/$sysctl 2>/dev/null || echo unknown)`
+ case "${UNAME_MACHINE_ARCH}" in
+ armeb) machine=armeb-unknown ;;
+ arm*) machine=arm-unknown ;;
+ sh3el) machine=shl-unknown ;;
+ sh3eb) machine=sh-unknown ;;
+ sh5el) machine=sh5le-unknown ;;
+ *) machine=${UNAME_MACHINE_ARCH}-unknown ;;
+ esac
+ # The Operating System including object format, if it has switched
+ # to ELF recently, or will in the future.
+ case "${UNAME_MACHINE_ARCH}" in
+ arm*|i386|m68k|ns32k|sh3*|sparc|vax)
+ eval $set_cc_for_build
+ if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep -q __ELF__
+ then
+ # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout).
+ # Return netbsd for either. FIX?
+ os=netbsd
+ else
+ os=netbsdelf
+ fi
+ ;;
+ *)
+ os=netbsd
+ ;;
+ esac
+ # The OS release
+ # Debian GNU/NetBSD machines have a different userland, and
+ # thus, need a distinct triplet. However, they do not need
+ # kernel version information, so it can be replaced with a
+ # suitable tag, in the style of linux-gnu.
+ case "${UNAME_VERSION}" in
+ Debian*)
+ release='-gnu'
+ ;;
+ *)
+ release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'`
+ ;;
+ esac
+ # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM:
+ # contains redundant information, the shorter form:
+ # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used.
+ echo "${machine}-${os}${release}"
+ exit ;;
+ *:OpenBSD:*:*)
+ UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'`
+ echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE}
+ exit ;;
+ *:ekkoBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE}
+ exit ;;
+ *:SolidBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-solidbsd${UNAME_RELEASE}
+ exit ;;
+ macppc:MirBSD:*:*)
+ echo powerpc-unknown-mirbsd${UNAME_RELEASE}
+ exit ;;
+ *:MirBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE}
+ exit ;;
+ alpha:OSF1:*:*)
+ case $UNAME_RELEASE in
+ *4.0)
+ UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
+ ;;
+ *5.*)
+ UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
+ ;;
+ esac
+ # According to Compaq, /usr/sbin/psrinfo has been available on
+ # OSF/1 and Tru64 systems produced since 1995. I hope that
+ # covers most systems running today. This code pipes the CPU
+ # types through head -n 1, so we only detect the type of CPU 0.
+ ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
+ case "$ALPHA_CPU_TYPE" in
+ "EV4 (21064)")
+ UNAME_MACHINE="alpha" ;;
+ "EV4.5 (21064)")
+ UNAME_MACHINE="alpha" ;;
+ "LCA4 (21066/21068)")
+ UNAME_MACHINE="alpha" ;;
+ "EV5 (21164)")
+ UNAME_MACHINE="alphaev5" ;;
+ "EV5.6 (21164A)")
+ UNAME_MACHINE="alphaev56" ;;
+ "EV5.6 (21164PC)")
+ UNAME_MACHINE="alphapca56" ;;
+ "EV5.7 (21164PC)")
+ UNAME_MACHINE="alphapca57" ;;
+ "EV6 (21264)")
+ UNAME_MACHINE="alphaev6" ;;
+ "EV6.7 (21264A)")
+ UNAME_MACHINE="alphaev67" ;;
+ "EV6.8CB (21264C)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.8AL (21264B)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.8CX (21264D)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.9A (21264/EV69A)")
+ UNAME_MACHINE="alphaev69" ;;
+ "EV7 (21364)")
+ UNAME_MACHINE="alphaev7" ;;
+ "EV7.9 (21364A)")
+ UNAME_MACHINE="alphaev79" ;;
+ esac
+ # A Pn.n version is a patched version.
+ # A Vn.n version is a released version.
+ # A Tn.n version is a released field test version.
+ # A Xn.n version is an unreleased experimental baselevel.
+ # 1.2 uses "1.2" for uname -r.
+ echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
+ exit ;;
+ Alpha\ *:Windows_NT*:*)
+ # How do we know it's Interix rather than the generic POSIX subsystem?
+ # Should we change UNAME_MACHINE based on the output of uname instead
+ # of the specific Alpha model?
+ echo alpha-pc-interix
+ exit ;;
+ 21064:Windows_NT:50:3)
+ echo alpha-dec-winnt3.5
+ exit ;;
+ Amiga*:UNIX_System_V:4.0:*)
+ echo m68k-unknown-sysv4
+ exit ;;
+ *:[Aa]miga[Oo][Ss]:*:*)
+ echo ${UNAME_MACHINE}-unknown-amigaos
+ exit ;;
+ *:[Mm]orph[Oo][Ss]:*:*)
+ echo ${UNAME_MACHINE}-unknown-morphos
+ exit ;;
+ *:OS/390:*:*)
+ echo i370-ibm-openedition
+ exit ;;
+ *:z/VM:*:*)
+ echo s390-ibm-zvmoe
+ exit ;;
+ *:OS400:*:*)
+ echo powerpc-ibm-os400
+ exit ;;
+ arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
+ echo arm-acorn-riscix${UNAME_RELEASE}
+ exit ;;
+ arm:riscos:*:*|arm:RISCOS:*:*)
+ echo arm-unknown-riscos
+ exit ;;
+ SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*)
+ echo hppa1.1-hitachi-hiuxmpp
+ exit ;;
+ Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*)
+ # akee at wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE.
+ if test "`(/bin/universe) 2>/dev/null`" = att ; then
+ echo pyramid-pyramid-sysv3
+ else
+ echo pyramid-pyramid-bsd
+ fi
+ exit ;;
+ NILE*:*:*:dcosx)
+ echo pyramid-pyramid-svr4
+ exit ;;
+ DRS?6000:unix:4.0:6*)
+ echo sparc-icl-nx6
+ exit ;;
+ DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*)
+ case `/usr/bin/uname -p` in
+ sparc) echo sparc-icl-nx7; exit ;;
+ esac ;;
+ s390x:SunOS:*:*)
+ echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4H:SunOS:5.*:*)
+ echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
+ echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*)
+ echo i386-pc-auroraux${UNAME_RELEASE}
+ exit ;;
+ i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*)
+ eval $set_cc_for_build
+ SUN_ARCH="i386"
+ # If there is a compiler, see if it is configured for 64-bit objects.
+ # Note that the Sun cc does not turn __LP64__ into 1 like gcc does.
+ # This test works for both compilers.
+ if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
+ if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \
+ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_64BIT_ARCH >/dev/null
+ then
+ SUN_ARCH="x86_64"
+ fi
+ fi
+ echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4*:SunOS:6*:*)
+ # According to config.sub, this is the proper way to canonicalize
+ # SunOS6. Hard to guess exactly what SunOS6 will be like, but
+ # it's likely to be more like Solaris than SunOS4.
+ echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4*:SunOS:*:*)
+ case "`/usr/bin/arch -k`" in
+ Series*|S4*)
+ UNAME_RELEASE=`uname -v`
+ ;;
+ esac
+ # Japanese Language versions have a version number like `4.1.3-JL'.
+ echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'`
+ exit ;;
+ sun3*:SunOS:*:*)
+ echo m68k-sun-sunos${UNAME_RELEASE}
+ exit ;;
+ sun*:*:4.2BSD:*)
+ UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
+ test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3
+ case "`/bin/arch`" in
+ sun3)
+ echo m68k-sun-sunos${UNAME_RELEASE}
+ ;;
+ sun4)
+ echo sparc-sun-sunos${UNAME_RELEASE}
+ ;;
+ esac
+ exit ;;
+ aushp:SunOS:*:*)
+ echo sparc-auspex-sunos${UNAME_RELEASE}
+ exit ;;
+ # The situation for MiNT is a little confusing. The machine name
+ # can be virtually everything (everything which is not
+ # "atarist" or "atariste" at least should have a processor
+ # > m68000). The system name ranges from "MiNT" over "FreeMiNT"
+ # to the lowercase version "mint" (or "freemint"). Finally
+ # the system name "TOS" denotes a system which is actually not
+ # MiNT. But MiNT is downward compatible to TOS, so this should
+ # be no problem.
+ atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit ;;
+ atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit ;;
+ *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit ;;
+ milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
+ echo m68k-milan-mint${UNAME_RELEASE}
+ exit ;;
+ hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
+ echo m68k-hades-mint${UNAME_RELEASE}
+ exit ;;
+ *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
+ echo m68k-unknown-mint${UNAME_RELEASE}
+ exit ;;
+ m68k:machten:*:*)
+ echo m68k-apple-machten${UNAME_RELEASE}
+ exit ;;
+ powerpc:machten:*:*)
+ echo powerpc-apple-machten${UNAME_RELEASE}
+ exit ;;
+ RISC*:Mach:*:*)
+ echo mips-dec-mach_bsd4.3
+ exit ;;
+ RISC*:ULTRIX:*:*)
+ echo mips-dec-ultrix${UNAME_RELEASE}
+ exit ;;
+ VAX*:ULTRIX*:*:*)
+ echo vax-dec-ultrix${UNAME_RELEASE}
+ exit ;;
+ 2020:CLIX:*:* | 2430:CLIX:*:*)
+ echo clipper-intergraph-clix${UNAME_RELEASE}
+ exit ;;
+ mips:*:*:UMIPS | mips:*:*:RISCos)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+#ifdef __cplusplus
+#include <stdio.h> /* for printf() prototype */
+ int main (int argc, char *argv[]) {
+#else
+ int main (argc, argv) int argc; char *argv[]; {
+#endif
+ #if defined (host_mips) && defined (MIPSEB)
+ #if defined (SYSTYPE_SYSV)
+ printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0);
+ #endif
+ #if defined (SYSTYPE_SVR4)
+ printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0);
+ #endif
+ #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD)
+ printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0);
+ #endif
+ #endif
+ exit (-1);
+ }
+EOF
+ $CC_FOR_BUILD -o $dummy $dummy.c &&
+ dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` &&
+ SYSTEM_NAME=`$dummy $dummyarg` &&
+ { echo "$SYSTEM_NAME"; exit; }
+ echo mips-mips-riscos${UNAME_RELEASE}
+ exit ;;
+ Motorola:PowerMAX_OS:*:*)
+ echo powerpc-motorola-powermax
+ exit ;;
+ Motorola:*:4.3:PL8-*)
+ echo powerpc-harris-powermax
+ exit ;;
+ Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*)
+ echo powerpc-harris-powermax
+ exit ;;
+ Night_Hawk:Power_UNIX:*:*)
+ echo powerpc-harris-powerunix
+ exit ;;
+ m88k:CX/UX:7*:*)
+ echo m88k-harris-cxux7
+ exit ;;
+ m88k:*:4*:R4*)
+ echo m88k-motorola-sysv4
+ exit ;;
+ m88k:*:3*:R3*)
+ echo m88k-motorola-sysv3
+ exit ;;
+ AViiON:dgux:*:*)
+ # DG/UX returns AViiON for all architectures
+ UNAME_PROCESSOR=`/usr/bin/uname -p`
+ if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ]
+ then
+ if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \
+ [ ${TARGET_BINARY_INTERFACE}x = x ]
+ then
+ echo m88k-dg-dgux${UNAME_RELEASE}
+ else
+ echo m88k-dg-dguxbcs${UNAME_RELEASE}
+ fi
+ else
+ echo i586-dg-dgux${UNAME_RELEASE}
+ fi
+ exit ;;
+ M88*:DolphinOS:*:*) # DolphinOS (SVR3)
+ echo m88k-dolphin-sysv3
+ exit ;;
+ M88*:*:R3*:*)
+ # Delta 88k system running SVR3
+ echo m88k-motorola-sysv3
+ exit ;;
+ XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3)
+ echo m88k-tektronix-sysv3
+ exit ;;
+ Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD)
+ echo m68k-tektronix-bsd
+ exit ;;
+ *:IRIX*:*:*)
+ echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'`
+ exit ;;
+ ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX.
+ echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id
+ exit ;; # Note that: echo "'`uname -s`'" gives 'AIX '
+ i*86:AIX:*:*)
+ echo i386-ibm-aix
+ exit ;;
+ ia64:AIX:*:*)
+ if [ -x /usr/bin/oslevel ] ; then
+ IBM_REV=`/usr/bin/oslevel`
+ else
+ IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
+ fi
+ echo ${UNAME_MACHINE}-ibm-aix${IBM_REV}
+ exit ;;
+ *:AIX:2:3)
+ if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #include <sys/systemcfg.h>
+
+ main()
+ {
+ if (!__power_pc())
+ exit(1);
+ puts("powerpc-ibm-aix3.2.5");
+ exit(0);
+ }
+EOF
+ if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy`
+ then
+ echo "$SYSTEM_NAME"
+ else
+ echo rs6000-ibm-aix3.2.5
+ fi
+ elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then
+ echo rs6000-ibm-aix3.2.4
+ else
+ echo rs6000-ibm-aix3.2
+ fi
+ exit ;;
+ *:AIX:*:[456])
+ IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
+ if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
+ IBM_ARCH=rs6000
+ else
+ IBM_ARCH=powerpc
+ fi
+ if [ -x /usr/bin/oslevel ] ; then
+ IBM_REV=`/usr/bin/oslevel`
+ else
+ IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
+ fi
+ echo ${IBM_ARCH}-ibm-aix${IBM_REV}
+ exit ;;
+ *:AIX:*:*)
+ echo rs6000-ibm-aix
+ exit ;;
+ ibmrt:4.4BSD:*|romp-ibm:BSD:*)
+ echo romp-ibm-bsd4.4
+ exit ;;
+ ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and
+ echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to
+ exit ;; # report: romp-ibm BSD 4.3
+ *:BOSX:*:*)
+ echo rs6000-bull-bosx
+ exit ;;
+ DPX/2?00:B.O.S.:*:*)
+ echo m68k-bull-sysv3
+ exit ;;
+ 9000/[34]??:4.3bsd:1.*:*)
+ echo m68k-hp-bsd
+ exit ;;
+ hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*)
+ echo m68k-hp-bsd4.4
+ exit ;;
+ 9000/[34678]??:HP-UX:*:*)
+ HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
+ case "${UNAME_MACHINE}" in
+ 9000/31? ) HP_ARCH=m68000 ;;
+ 9000/[34]?? ) HP_ARCH=m68k ;;
+ 9000/[678][0-9][0-9])
+ if [ -x /usr/bin/getconf ]; then
+ sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
+ sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
+ case "${sc_cpu_version}" in
+ 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
+ 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
+ 532) # CPU_PA_RISC2_0
+ case "${sc_kernel_bits}" in
+ 32) HP_ARCH="hppa2.0n" ;;
+ 64) HP_ARCH="hppa2.0w" ;;
+ '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20
+ esac ;;
+ esac
+ fi
+ if [ "${HP_ARCH}" = "" ]; then
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+
+ #define _HPUX_SOURCE
+ #include <stdlib.h>
+ #include <unistd.h>
+
+ int main ()
+ {
+ #if defined(_SC_KERNEL_BITS)
+ long bits = sysconf(_SC_KERNEL_BITS);
+ #endif
+ long cpu = sysconf (_SC_CPU_VERSION);
+
+ switch (cpu)
+ {
+ case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
+ case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
+ case CPU_PA_RISC2_0:
+ #if defined(_SC_KERNEL_BITS)
+ switch (bits)
+ {
+ case 64: puts ("hppa2.0w"); break;
+ case 32: puts ("hppa2.0n"); break;
+ default: puts ("hppa2.0"); break;
+ } break;
+ #else /* !defined(_SC_KERNEL_BITS) */
+ puts ("hppa2.0"); break;
+ #endif
+ default: puts ("hppa1.0"); break;
+ }
+ exit (0);
+ }
+EOF
+ (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
+ test -z "$HP_ARCH" && HP_ARCH=hppa
+ fi ;;
+ esac
+ if [ ${HP_ARCH} = "hppa2.0w" ]
+ then
+ eval $set_cc_for_build
+
+ # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating
+ # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler
+ # generating 64-bit code. GNU and HP use different nomenclature:
+ #
+ # $ CC_FOR_BUILD=cc ./config.guess
+ # => hppa2.0w-hp-hpux11.23
+ # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess
+ # => hppa64-hp-hpux11.23
+
+ if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) |
+ grep -q __LP64__
+ then
+ HP_ARCH="hppa2.0w"
+ else
+ HP_ARCH="hppa64"
+ fi
+ fi
+ echo ${HP_ARCH}-hp-hpux${HPUX_REV}
+ exit ;;
+ ia64:HP-UX:*:*)
+ HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
+ echo ia64-hp-hpux${HPUX_REV}
+ exit ;;
+ 3050*:HI-UX:*:*)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #include <unistd.h>
+ int
+ main ()
+ {
+ long cpu = sysconf (_SC_CPU_VERSION);
+ /* The order matters, because CPU_IS_HP_MC68K erroneously returns
+ true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct
+ results, however. */
+ if (CPU_IS_PA_RISC (cpu))
+ {
+ switch (cpu)
+ {
+ case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break;
+ case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break;
+ case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break;
+ default: puts ("hppa-hitachi-hiuxwe2"); break;
+ }
+ }
+ else if (CPU_IS_HP_MC68K (cpu))
+ puts ("m68k-hitachi-hiuxwe2");
+ else puts ("unknown-hitachi-hiuxwe2");
+ exit (0);
+ }
+EOF
+ $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` &&
+ { echo "$SYSTEM_NAME"; exit; }
+ echo unknown-hitachi-hiuxwe2
+ exit ;;
+ 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* )
+ echo hppa1.1-hp-bsd
+ exit ;;
+ 9000/8??:4.3bsd:*:*)
+ echo hppa1.0-hp-bsd
+ exit ;;
+ *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*)
+ echo hppa1.0-hp-mpeix
+ exit ;;
+ hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* )
+ echo hppa1.1-hp-osf
+ exit ;;
+ hp8??:OSF1:*:*)
+ echo hppa1.0-hp-osf
+ exit ;;
+ i*86:OSF1:*:*)
+ if [ -x /usr/sbin/sysversion ] ; then
+ echo ${UNAME_MACHINE}-unknown-osf1mk
+ else
+ echo ${UNAME_MACHINE}-unknown-osf1
+ fi
+ exit ;;
+ parisc*:Lites*:*:*)
+ echo hppa1.1-hp-lites
+ exit ;;
+ C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*)
+ echo c1-convex-bsd
+ exit ;;
+ C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*)
+ if getsysinfo -f scalar_acc
+ then echo c32-convex-bsd
+ else echo c2-convex-bsd
+ fi
+ exit ;;
+ C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*)
+ echo c34-convex-bsd
+ exit ;;
+ C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*)
+ echo c38-convex-bsd
+ exit ;;
+ C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*)
+ echo c4-convex-bsd
+ exit ;;
+ CRAY*Y-MP:*:*:*)
+ echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*[A-Z]90:*:*:*)
+ echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \
+ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \
+ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \
+ -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*TS:*:*:*)
+ echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*T3E:*:*:*)
+ echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*SV1:*:*:*)
+ echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ *:UNICOS/mp:*:*)
+ echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
+ FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
+ FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
+ echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+ exit ;;
+ 5000:UNIX_System_V:4.*:*)
+ FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
+ echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+ exit ;;
+ i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
+ echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE}
+ exit ;;
+ sparc*:BSD/OS:*:*)
+ echo sparc-unknown-bsdi${UNAME_RELEASE}
+ exit ;;
+ *:BSD/OS:*:*)
+ echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE}
+ exit ;;
+ *:FreeBSD:*:*)
+ case ${UNAME_MACHINE} in
+ pc98)
+ echo i386-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+ amd64)
+ echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+ *)
+ echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+ esac
+ exit ;;
+ i*:CYGWIN*:*)
+ echo ${UNAME_MACHINE}-pc-cygwin
+ exit ;;
+ *:MINGW*:*)
+ echo ${UNAME_MACHINE}-pc-mingw32
+ exit ;;
+ i*:windows32*:*)
+ # uname -m includes "-pc" on this system.
+ echo ${UNAME_MACHINE}-mingw32
+ exit ;;
+ i*:PW*:*)
+ echo ${UNAME_MACHINE}-pc-pw32
+ exit ;;
+ *:Interix*:*)
+ case ${UNAME_MACHINE} in
+ x86)
+ echo i586-pc-interix${UNAME_RELEASE}
+ exit ;;
+ authenticamd | genuineintel | EM64T)
+ echo x86_64-unknown-interix${UNAME_RELEASE}
+ exit ;;
+ IA64)
+ echo ia64-unknown-interix${UNAME_RELEASE}
+ exit ;;
+ esac ;;
+ [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*)
+ echo i${UNAME_MACHINE}-pc-mks
+ exit ;;
+ 8664:Windows_NT:*)
+ echo x86_64-pc-mks
+ exit ;;
+ i*:Windows_NT*:* | Pentium*:Windows_NT*:*)
+ # How do we know it's Interix rather than the generic POSIX subsystem?
+ # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we
+ # UNAME_MACHINE based on the output of uname instead of i386?
+ echo i586-pc-interix
+ exit ;;
+ i*:UWIN*:*)
+ echo ${UNAME_MACHINE}-pc-uwin
+ exit ;;
+ amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*)
+ echo x86_64-unknown-cygwin
+ exit ;;
+ p*:CYGWIN*:*)
+ echo powerpcle-unknown-cygwin
+ exit ;;
+ prep*:SunOS:5.*:*)
+ echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ *:GNU:*:*)
+ # the GNU system
+ echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
+ exit ;;
+ *:GNU/*:*:*)
+ # other systems with GNU libc and userland
+ echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu
+ exit ;;
+ i*86:Minix:*:*)
+ echo ${UNAME_MACHINE}-pc-minix
+ exit ;;
+ alpha:Linux:*:*)
+ case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
+ EV5) UNAME_MACHINE=alphaev5 ;;
+ EV56) UNAME_MACHINE=alphaev56 ;;
+ PCA56) UNAME_MACHINE=alphapca56 ;;
+ PCA57) UNAME_MACHINE=alphapca56 ;;
+ EV6) UNAME_MACHINE=alphaev6 ;;
+ EV67) UNAME_MACHINE=alphaev67 ;;
+ EV68*) UNAME_MACHINE=alphaev68 ;;
+ esac
+ objdump --private-headers /bin/sh | grep -q ld.so.1
+ if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi
+ echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC}
+ exit ;;
+ arm*:Linux:*:*)
+ eval $set_cc_for_build
+ if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep -q __ARM_EABI__
+ then
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ else
+ echo ${UNAME_MACHINE}-unknown-linux-gnueabi
+ fi
+ exit ;;
+ avr32*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ cris:Linux:*:*)
+ echo cris-axis-linux-gnu
+ exit ;;
+ crisv32:Linux:*:*)
+ echo crisv32-axis-linux-gnu
+ exit ;;
+ frv:Linux:*:*)
+ echo frv-unknown-linux-gnu
+ exit ;;
+ i*86:Linux:*:*)
+ LIBC=gnu
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #ifdef __dietlibc__
+ LIBC=dietlibc
+ #endif
+EOF
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'`
+ echo "${UNAME_MACHINE}-pc-linux-${LIBC}"
+ exit ;;
+ ia64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ m32r*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ m68*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ mips:Linux:*:* | mips64:Linux:*:*)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #undef CPU
+ #undef ${UNAME_MACHINE}
+ #undef ${UNAME_MACHINE}el
+ #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
+ CPU=${UNAME_MACHINE}el
+ #else
+ #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
+ CPU=${UNAME_MACHINE}
+ #else
+ CPU=
+ #endif
+ #endif
+EOF
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'`
+ test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
+ ;;
+ or32:Linux:*:*)
+ echo or32-unknown-linux-gnu
+ exit ;;
+ padre:Linux:*:*)
+ echo sparc-unknown-linux-gnu
+ exit ;;
+ parisc64:Linux:*:* | hppa64:Linux:*:*)
+ echo hppa64-unknown-linux-gnu
+ exit ;;
+ parisc:Linux:*:* | hppa:Linux:*:*)
+ # Look for CPU level
+ case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
+ PA7*) echo hppa1.1-unknown-linux-gnu ;;
+ PA8*) echo hppa2.0-unknown-linux-gnu ;;
+ *) echo hppa-unknown-linux-gnu ;;
+ esac
+ exit ;;
+ ppc64:Linux:*:*)
+ echo powerpc64-unknown-linux-gnu
+ exit ;;
+ ppc:Linux:*:*)
+ echo powerpc-unknown-linux-gnu
+ exit ;;
+ s390:Linux:*:* | s390x:Linux:*:*)
+ echo ${UNAME_MACHINE}-ibm-linux
+ exit ;;
+ sh64*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ sh*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ sparc:Linux:*:* | sparc64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ vax:Linux:*:*)
+ echo ${UNAME_MACHINE}-dec-linux-gnu
+ exit ;;
+ x86_64:Linux:*:*)
+ echo x86_64-unknown-linux-gnu
+ exit ;;
+ xtensa*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ i*86:DYNIX/ptx:4*:*)
+ # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
+ # earlier versions are messed up and put the nodename in both
+ # sysname and nodename.
+ echo i386-sequent-sysv4
+ exit ;;
+ i*86:UNIX_SV:4.2MP:2.*)
+ # Unixware is an offshoot of SVR4, but it has its own version
+ # number series starting with 2...
+ # I am not positive that other SVR4 systems won't match this,
+ # I just have to hope. -- rms.
+ # Use sysv4.2uw... so that sysv4* matches it.
+ echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION}
+ exit ;;
+ i*86:OS/2:*:*)
+ # If we were able to find `uname', then EMX Unix compatibility
+ # is probably installed.
+ echo ${UNAME_MACHINE}-pc-os2-emx
+ exit ;;
+ i*86:XTS-300:*:STOP)
+ echo ${UNAME_MACHINE}-unknown-stop
+ exit ;;
+ i*86:atheos:*:*)
+ echo ${UNAME_MACHINE}-unknown-atheos
+ exit ;;
+ i*86:syllable:*:*)
+ echo ${UNAME_MACHINE}-pc-syllable
+ exit ;;
+ i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*)
+ echo i386-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ i*86:*DOS:*:*)
+ echo ${UNAME_MACHINE}-pc-msdosdjgpp
+ exit ;;
+ i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*)
+ UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'`
+ if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
+ echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL}
+ else
+ echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL}
+ fi
+ exit ;;
+ i*86:*:5:[678]*)
+ # UnixWare 7.x, OpenUNIX and OpenServer 6.
+ case `/bin/uname -X | grep "^Machine"` in
+ *486*) UNAME_MACHINE=i486 ;;
+ *Pentium) UNAME_MACHINE=i586 ;;
+ *Pent*|*Celeron) UNAME_MACHINE=i686 ;;
+ esac
+ echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}
+ exit ;;
+ i*86:*:3.2:*)
+ if test -f /usr/options/cb.name; then
+ UNAME_REL=`sed -n 's/.*Version //p' </usr/options/cb.name`
+ echo ${UNAME_MACHINE}-pc-isc$UNAME_REL
+ elif /bin/uname -X 2>/dev/null >/dev/null ; then
+ UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')`
+ (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486
+ (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \
+ && UNAME_MACHINE=i586
+ (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \
+ && UNAME_MACHINE=i686
+ (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \
+ && UNAME_MACHINE=i686
+ echo ${UNAME_MACHINE}-pc-sco$UNAME_REL
+ else
+ echo ${UNAME_MACHINE}-pc-sysv32
+ fi
+ exit ;;
+ pc:*:*:*)
+ # Left here for compatibility:
+ # uname -m prints for DJGPP always 'pc', but it prints nothing about
+ # the processor, so we play safe by assuming i586.
+ # Note: whatever this is, it MUST be the same as what config.sub
+ # prints for the "djgpp" host, or else GDB configury will decide that
+ # this is a cross-build.
+ echo i586-pc-msdosdjgpp
+ exit ;;
+ Intel:Mach:3*:*)
+ echo i386-pc-mach3
+ exit ;;
+ paragon:*:*:*)
+ echo i860-intel-osf1
+ exit ;;
+ i860:*:4.*:*) # i860-SVR4
+ if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then
+ echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4
+ else # Add other i860-SVR4 vendors below as they are discovered.
+ echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4
+ fi
+ exit ;;
+ mini*:CTIX:SYS*5:*)
+ # "miniframe"
+ echo m68010-convergent-sysv
+ exit ;;
+ mc68k:UNIX:SYSTEM5:3.51m)
+ echo m68k-convergent-sysv
+ exit ;;
+ M680?0:D-NIX:5.3:*)
+ echo m68k-diab-dnix
+ exit ;;
+ M68*:*:R3V[5678]*:*)
+ test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;;
+ 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0)
+ OS_REL=''
+ test -r /etc/.relid \
+ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
+ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
+ 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4; exit; } ;;
+ NCR*:*:4.2:* | MPRAS*:*:4.2:*)
+ OS_REL='.3'
+ test -r /etc/.relid \
+ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
+ && { echo i586-ncr-sysv4.3${OS_REL}; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \
+ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
+ m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
+ echo m68k-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ mc68030:UNIX_System_V:4.*:*)
+ echo m68k-atari-sysv4
+ exit ;;
+ TSUNAMI:LynxOS:2.*:*)
+ echo sparc-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ rs6000:LynxOS:2.*:*)
+ echo rs6000-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*)
+ echo powerpc-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ SM[BE]S:UNIX_SV:*:*)
+ echo mips-dde-sysv${UNAME_RELEASE}
+ exit ;;
+ RM*:ReliantUNIX-*:*:*)
+ echo mips-sni-sysv4
+ exit ;;
+ RM*:SINIX-*:*:*)
+ echo mips-sni-sysv4
+ exit ;;
+ *:SINIX-*:*:*)
+ if uname -p 2>/dev/null >/dev/null ; then
+ UNAME_MACHINE=`(uname -p) 2>/dev/null`
+ echo ${UNAME_MACHINE}-sni-sysv4
+ else
+ echo ns32k-sni-sysv
+ fi
+ exit ;;
+ PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
+ # says <Richard.M.Bartel at ccMail.Census.GOV>
+ echo i586-unisys-sysv4
+ exit ;;
+ *:UNIX_System_V:4*:FTX*)
+ # From Gerald Hewes <hewes at openmarket.com>.
+ # How about differentiating between stratus architectures? -djm
+ echo hppa1.1-stratus-sysv4
+ exit ;;
+ *:*:*:FTX*)
+ # From seanf at swdc.stratus.com.
+ echo i860-stratus-sysv4
+ exit ;;
+ i*86:VOS:*:*)
+ # From Paul.Green at stratus.com.
+ echo ${UNAME_MACHINE}-stratus-vos
+ exit ;;
+ *:VOS:*:*)
+ # From Paul.Green at stratus.com.
+ echo hppa1.1-stratus-vos
+ exit ;;
+ mc68*:A/UX:*:*)
+ echo m68k-apple-aux${UNAME_RELEASE}
+ exit ;;
+ news*:NEWS-OS:6*:*)
+ echo mips-sony-newsos6
+ exit ;;
+ R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
+ if [ -d /usr/nec ]; then
+ echo mips-nec-sysv${UNAME_RELEASE}
+ else
+ echo mips-unknown-sysv${UNAME_RELEASE}
+ fi
+ exit ;;
+ BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only.
+ echo powerpc-be-beos
+ exit ;;
+ BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only.
+ echo powerpc-apple-beos
+ exit ;;
+ BePC:BeOS:*:*) # BeOS running on Intel PC compatible.
+ echo i586-pc-beos
+ exit ;;
+ BePC:Haiku:*:*) # Haiku running on Intel PC compatible.
+ echo i586-pc-haiku
+ exit ;;
+ SX-4:SUPER-UX:*:*)
+ echo sx4-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-5:SUPER-UX:*:*)
+ echo sx5-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-6:SUPER-UX:*:*)
+ echo sx6-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-7:SUPER-UX:*:*)
+ echo sx7-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-8:SUPER-UX:*:*)
+ echo sx8-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-8R:SUPER-UX:*:*)
+ echo sx8r-nec-superux${UNAME_RELEASE}
+ exit ;;
+ Power*:Rhapsody:*:*)
+ echo powerpc-apple-rhapsody${UNAME_RELEASE}
+ exit ;;
+ *:Rhapsody:*:*)
+ echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE}
+ exit ;;
+ *:Darwin:*:*)
+ UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown
+ case $UNAME_PROCESSOR in
+ i386)
+ eval $set_cc_for_build
+ if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
+ if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
+ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_64BIT_ARCH >/dev/null
+ then
+ UNAME_PROCESSOR="x86_64"
+ fi
+ fi ;;
+ unknown) UNAME_PROCESSOR=powerpc ;;
+ esac
+ echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
+ exit ;;
+ *:procnto*:*:* | *:QNX:[0123456789]*:*)
+ UNAME_PROCESSOR=`uname -p`
+ if test "$UNAME_PROCESSOR" = "x86"; then
+ UNAME_PROCESSOR=i386
+ UNAME_MACHINE=pc
+ fi
+ echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE}
+ exit ;;
+ *:QNX:*:4*)
+ echo i386-pc-qnx
+ exit ;;
+ NSE-?:NONSTOP_KERNEL:*:*)
+ echo nse-tandem-nsk${UNAME_RELEASE}
+ exit ;;
+ NSR-?:NONSTOP_KERNEL:*:*)
+ echo nsr-tandem-nsk${UNAME_RELEASE}
+ exit ;;
+ *:NonStop-UX:*:*)
+ echo mips-compaq-nonstopux
+ exit ;;
+ BS2000:POSIX*:*:*)
+ echo bs2000-siemens-sysv
+ exit ;;
+ DS/*:UNIX_System_V:*:*)
+ echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE}
+ exit ;;
+ *:Plan9:*:*)
+ # "uname -m" is not consistent, so use $cputype instead. 386
+ # is converted to i386 for consistency with other x86
+ # operating systems.
+ if test "$cputype" = "386"; then
+ UNAME_MACHINE=i386
+ else
+ UNAME_MACHINE="$cputype"
+ fi
+ echo ${UNAME_MACHINE}-unknown-plan9
+ exit ;;
+ *:TOPS-10:*:*)
+ echo pdp10-unknown-tops10
+ exit ;;
+ *:TENEX:*:*)
+ echo pdp10-unknown-tenex
+ exit ;;
+ KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*)
+ echo pdp10-dec-tops20
+ exit ;;
+ XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*)
+ echo pdp10-xkl-tops20
+ exit ;;
+ *:TOPS-20:*:*)
+ echo pdp10-unknown-tops20
+ exit ;;
+ *:ITS:*:*)
+ echo pdp10-unknown-its
+ exit ;;
+ SEI:*:*:SEIUX)
+ echo mips-sei-seiux${UNAME_RELEASE}
+ exit ;;
+ *:DragonFly:*:*)
+ echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
+ exit ;;
+ *:*VMS:*:*)
+ UNAME_MACHINE=`(uname -p) 2>/dev/null`
+ case "${UNAME_MACHINE}" in
+ A*) echo alpha-dec-vms ; exit ;;
+ I*) echo ia64-dec-vms ; exit ;;
+ V*) echo vax-dec-vms ; exit ;;
+ esac ;;
+ *:XENIX:*:SysV)
+ echo i386-pc-xenix
+ exit ;;
+ i*86:skyos:*:*)
+ echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//'
+ exit ;;
+ i*86:rdos:*:*)
+ echo ${UNAME_MACHINE}-pc-rdos
+ exit ;;
+ i*86:AROS:*:*)
+ echo ${UNAME_MACHINE}-pc-aros
+ exit ;;
+esac
+
+#echo '(No uname command or uname output not recognized.)' 1>&2
+#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2
+
+eval $set_cc_for_build
+cat >$dummy.c <<EOF
+#ifdef _SEQUENT_
+# include <sys/types.h>
+# include <sys/utsname.h>
+#endif
+main ()
+{
+#if defined (sony)
+#if defined (MIPSEB)
+ /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed,
+ I don't know.... */
+ printf ("mips-sony-bsd\n"); exit (0);
+#else
+#include <sys/param.h>
+ printf ("m68k-sony-newsos%s\n",
+#ifdef NEWSOS4
+ "4"
+#else
+ ""
+#endif
+ ); exit (0);
+#endif
+#endif
+
+#if defined (__arm) && defined (__acorn) && defined (__unix)
+ printf ("arm-acorn-riscix\n"); exit (0);
+#endif
+
+#if defined (hp300) && !defined (hpux)
+ printf ("m68k-hp-bsd\n"); exit (0);
+#endif
+
+#if defined (NeXT)
+#if !defined (__ARCHITECTURE__)
+#define __ARCHITECTURE__ "m68k"
+#endif
+ int version;
+ version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`;
+ if (version < 4)
+ printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version);
+ else
+ printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version);
+ exit (0);
+#endif
+
+#if defined (MULTIMAX) || defined (n16)
+#if defined (UMAXV)
+ printf ("ns32k-encore-sysv\n"); exit (0);
+#else
+#if defined (CMU)
+ printf ("ns32k-encore-mach\n"); exit (0);
+#else
+ printf ("ns32k-encore-bsd\n"); exit (0);
+#endif
+#endif
+#endif
+
+#if defined (__386BSD__)
+ printf ("i386-pc-bsd\n"); exit (0);
+#endif
+
+#if defined (sequent)
+#if defined (i386)
+ printf ("i386-sequent-dynix\n"); exit (0);
+#endif
+#if defined (ns32000)
+ printf ("ns32k-sequent-dynix\n"); exit (0);
+#endif
+#endif
+
+#if defined (_SEQUENT_)
+ struct utsname un;
+
+ uname(&un);
+
+ if (strncmp(un.version, "V2", 2) == 0) {
+ printf ("i386-sequent-ptx2\n"); exit (0);
+ }
+ if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */
+ printf ("i386-sequent-ptx1\n"); exit (0);
+ }
+ printf ("i386-sequent-ptx\n"); exit (0);
+
+#endif
+
+#if defined (vax)
+# if !defined (ultrix)
+# include <sys/param.h>
+# if defined (BSD)
+# if BSD == 43
+ printf ("vax-dec-bsd4.3\n"); exit (0);
+# else
+# if BSD == 199006
+ printf ("vax-dec-bsd4.3reno\n"); exit (0);
+# else
+ printf ("vax-dec-bsd\n"); exit (0);
+# endif
+# endif
+# else
+ printf ("vax-dec-bsd\n"); exit (0);
+# endif
+# else
+ printf ("vax-dec-ultrix\n"); exit (0);
+# endif
+#endif
+
+#if defined (alliant) && defined (i860)
+ printf ("i860-alliant-bsd\n"); exit (0);
+#endif
+
+ exit (1);
+}
+EOF
+
+$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` &&
+ { echo "$SYSTEM_NAME"; exit; }
+
+# Apollos put the system type in the environment.
+
+test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; }
+
+# Convex versions that predate uname can use getsysinfo(1)
+
+if [ -x /usr/convex/getsysinfo ]
+then
+ case `getsysinfo -f cpu_type` in
+ c1*)
+ echo c1-convex-bsd
+ exit ;;
+ c2*)
+ if getsysinfo -f scalar_acc
+ then echo c32-convex-bsd
+ else echo c2-convex-bsd
+ fi
+ exit ;;
+ c34*)
+ echo c34-convex-bsd
+ exit ;;
+ c38*)
+ echo c38-convex-bsd
+ exit ;;
+ c4*)
+ echo c4-convex-bsd
+ exit ;;
+ esac
+fi
+
+cat >&2 <<EOF
+$0: unable to guess system type
+
+This script, last modified $timestamp, has failed to recognize
+the operating system you are using. It is advised that you
+download the most up to date version of the config scripts from
+
+ http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
+and
+ http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
+
+If the version you run ($0) is already up to date, please
+send the following data and any information you think might be
+pertinent to <config-patches at gnu.org> in order to provide the needed
+information to handle your system.
+
+config.guess timestamp = $timestamp
+
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null`
+
+hostinfo = `(hostinfo) 2>/dev/null`
+/bin/universe = `(/bin/universe) 2>/dev/null`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null`
+/bin/arch = `(/bin/arch) 2>/dev/null`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null`
+
+UNAME_MACHINE = ${UNAME_MACHINE}
+UNAME_RELEASE = ${UNAME_RELEASE}
+UNAME_SYSTEM = ${UNAME_SYSTEM}
+UNAME_VERSION = ${UNAME_VERSION}
+EOF
+
+exit 1
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "timestamp='"
+# time-stamp-format: "%:y-%02m-%02d"
+# time-stamp-end: "'"
+# End:
diff --git a/config/config.h.in b/config/config.h.in
new file mode 100644
index 0000000..957454a
--- /dev/null
+++ b/config/config.h.in
@@ -0,0 +1,225 @@
+/* config/config.h.in. Generated from configure.ac by autoheader. */
+
+/* Define to one of `_getb67', `GETB67', `getb67' for Cray-2 and Cray-YMP
+ systems. This function is required for `alloca.c' support on those systems.
+ */
+#undef CRAY_STACKSEG_END
+
+/* Define to 1 if using `alloca.c'. */
+#undef C_ALLOCA
+
+/* Define to 1 if you have `alloca', as a function or macro. */
+#undef HAVE_ALLOCA
+
+/* Define to 1 if you have <alloca.h> and it should be used (not on Ultrix).
+ */
+#undef HAVE_ALLOCA_H
+
+/* Define to 1 if you have the <dlfcn.h> header file. */
+#undef HAVE_DLFCN_H
+
+/* Define to 1 if you have the <fcntl.h> header file. */
+#undef HAVE_FCNTL_H
+
+/* Define to 1 if you have the `floor' function. */
+#undef HAVE_FLOOR
+
+/* Define to 1 if you have the `gettimeofday' function. */
+#undef HAVE_GETTIMEOFDAY
+
+/* Define to 1 if you have the <inttypes.h> header file. */
+#undef HAVE_INTTYPES_H
+
+/* Define to 1 if you have the <libintl.h> header file. */
+#undef HAVE_LIBINTL_H
+
+/* Define to 1 if you have the `m' library (-lm). */
+#undef HAVE_LIBM
+
+/* Define to 1 in order to Use libProgressBar */
+#undef HAVE_LIBPROGRESSBAR
+
+/* Define to 1 if you have the `pthread' library (-lpthread). */
+#undef HAVE_LIBPTHREAD
+
+/* Define to 1 if you have the `z' library (-lz). */
+#undef HAVE_LIBZ
+
+/* Define to 1 if you have the <limits.h> header file. */
+#undef HAVE_LIMITS_H
+
+/* Define to 1 if you have the <locale.h> header file. */
+#undef HAVE_LOCALE_H
+
+/* Define to 1 if your system has a GNU libc compatible `malloc' function, and
+ to 0 otherwise. */
+#undef HAVE_MALLOC
+
+/* Define to 1 if you have the `memchr' function. */
+#undef HAVE_MEMCHR
+
+/* Define to 1 if you have the `memmove' function. */
+#undef HAVE_MEMMOVE
+
+/* Define to 1 if you have the <memory.h> header file. */
+#undef HAVE_MEMORY_H
+
+/* Define to 1 if you have the `memset' function. */
+#undef HAVE_MEMSET
+
+/* Define to 1 if you have the `mkfifo' function. */
+#undef HAVE_MKFIFO
+
+/* Define to 1 if you have the `pow' function. */
+#undef HAVE_POW
+
+/* Define to 1 if the system has the type `ptrdiff_t'. */
+#undef HAVE_PTRDIFF_T
+
+/* Define to 1 if your system has a GNU libc compatible `realloc' function,
+ and to 0 otherwise. */
+#undef HAVE_REALLOC
+
+/* Define to 1 if you have the `select' function. */
+#undef HAVE_SELECT
+
+/* Define to 1 if you have the `sqrt' function. */
+#undef HAVE_SQRT
+
+/* Define to 1 if stdbool.h conforms to C99. */
+#undef HAVE_STDBOOL_H
+
+/* Define to 1 if you have the <stdint.h> header file. */
+#undef HAVE_STDINT_H
+
+/* Define to 1 if you have the <stdlib.h> header file. */
+#undef HAVE_STDLIB_H
+
+/* Define to 1 if you have the <strings.h> header file. */
+#undef HAVE_STRINGS_H
+
+/* Define to 1 if you have the <string.h> header file. */
+#undef HAVE_STRING_H
+
+/* Define to 1 if you have the `strrchr' function. */
+#undef HAVE_STRRCHR
+
+/* Define to 1 if you have the `strstr' function. */
+#undef HAVE_STRSTR
+
+/* Define to 1 if you have the `strtol' function. */
+#undef HAVE_STRTOL
+
+/* Define to 1 if `st_blksize' is a member of `struct stat'. */
+#undef HAVE_STRUCT_STAT_ST_BLKSIZE
+
+/* Define to 1 if you have the <sys/file.h> header file. */
+#undef HAVE_SYS_FILE_H
+
+/* Define to 1 if you have the <sys/param.h> header file. */
+#undef HAVE_SYS_PARAM_H
+
+/* Define to 1 if you have the <sys/stat.h> header file. */
+#undef HAVE_SYS_STAT_H
+
+/* Define to 1 if you have the <sys/time.h> header file. */
+#undef HAVE_SYS_TIME_H
+
+/* Define to 1 if you have the <sys/types.h> header file. */
+#undef HAVE_SYS_TYPES_H
+
+/* Define to 1 if you have the <unistd.h> header file. */
+#undef HAVE_UNISTD_H
+
+/* Define to 1 if you have the <utime.h> header file. */
+#undef HAVE_UTIME_H
+
+/* Define to 1 if the system has the type `_Bool'. */
+#undef HAVE__BOOL
+
+/* Define to the sub-directory in which libtool stores uninstalled libraries.
+ */
+#undef LT_OBJDIR
+
+/* Define to 1 if `major', `minor', and `makedev' are declared in <mkdev.h>.
+ */
+#undef MAJOR_IN_MKDEV
+
+/* Define to 1 if `major', `minor', and `makedev' are declared in
+ <sysmacros.h>. */
+#undef MAJOR_IN_SYSMACROS
+
+/* Name of package */
+#undef PACKAGE
+
+/* Define to the address where bug reports for this package should be sent. */
+#undef PACKAGE_BUGREPORT
+
+/* Define to the full name of this package. */
+#undef PACKAGE_NAME
+
+/* Define to the full name and version of this package. */
+#undef PACKAGE_STRING
+
+/* Define to the one symbol short name of this package. */
+#undef PACKAGE_TARNAME
+
+/* Define to the home page for this package. */
+#undef PACKAGE_URL
+
+/* Define to the version of this package. */
+#undef PACKAGE_VERSION
+
+/* If using the C implementation of alloca, define if you know the
+ direction of stack growth for your system; otherwise it will be
+ automatically deduced at runtime.
+ STACK_DIRECTION > 0 => grows toward higher addresses
+ STACK_DIRECTION < 0 => grows toward lower addresses
+ STACK_DIRECTION = 0 => direction of growth unknown */
+#undef STACK_DIRECTION
+
+/* Define to 1 if you have the ANSI C header files. */
+#undef STDC_HEADERS
+
+/* Version number of package */
+#undef VERSION
+
+/* Define for Solaris 2.5.1 so the uint32_t typedef from <sys/synch.h>,
+ <pthread.h>, or <semaphore.h> is not used. If the typedef were allowed, the
+ #define below would cause a syntax error. */
+#undef _UINT32_T
+
+/* Define for Solaris 2.5.1 so the uint8_t typedef from <sys/synch.h>,
+ <pthread.h>, or <semaphore.h> is not used. If the typedef were allowed, the
+ #define below would cause a syntax error. */
+#undef _UINT8_T
+
+/* Define to `__inline__' or `__inline' if that's what the C compiler
+ calls it, or to nothing if 'inline' is not supported under any name. */
+#ifndef __cplusplus
+#undef inline
+#endif
+
+/* Define to the type of a signed integer type of width exactly 64 bits if
+ such a type exists and the standard includes do not define it. */
+#undef int64_t
+
+/* Define to rpl_malloc if the replacement function should be used. */
+#undef malloc
+
+/* Define to `long int' if <sys/types.h> does not define. */
+#undef off_t
+
+/* Define to rpl_realloc if the replacement function should be used. */
+#undef realloc
+
+/* Define to `unsigned int' if <sys/types.h> does not define. */
+#undef size_t
+
+/* Define to the type of an unsigned integer type of width exactly 32 bits if
+ such a type exists and the standard includes do not define it. */
+#undef uint32_t
+
+/* Define to the type of an unsigned integer type of width exactly 8 bits if
+ such a type exists and the standard includes do not define it. */
+#undef uint8_t
diff --git a/config/config.sub b/config/config.sub
new file mode 100755
index 0000000..c2d1257
--- /dev/null
+++ b/config/config.sub
@@ -0,0 +1,1714 @@
+#! /bin/sh
+# Configuration validation subroutine script.
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
+# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010
+# Free Software Foundation, Inc.
+
+timestamp='2010-01-22'
+
+# This file is (in principle) common to ALL GNU software.
+# The presence of a machine in this file suggests that SOME GNU software
+# can handle that machine. It does not imply ALL GNU software can.
+#
+# This file is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
+# 02110-1301, USA.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+
+# Please send patches to <config-patches at gnu.org>. Submit a context
+# diff and a properly formatted GNU ChangeLog entry.
+#
+# Configuration subroutine to validate and canonicalize a configuration type.
+# Supply the specified configuration type as an argument.
+# If it is invalid, we print an error message on stderr and exit with code 1.
+# Otherwise, we print the canonical config type on stdout and succeed.
+
+# You can get the latest version of this script from:
+# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
+
+# This file is supposed to be the same for all GNU packages
+# and recognize all the CPU types, system types and aliases
+# that are meaningful with *any* GNU software.
+# Each package is responsible for reporting which valid configurations
+# it does not support. The user should be able to distinguish
+# a failure to support a valid configuration from a meaningless
+# configuration.
+
+# The goal of this file is to map all the various variations of a given
+# machine specification into a single specification in the form:
+# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM
+# or in some cases, the newer four-part form:
+# CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM
+# It is wrong to echo any other type of specification.
+
+me=`echo "$0" | sed -e 's,.*/,,'`
+
+usage="\
+Usage: $0 [OPTION] CPU-MFR-OPSYS
+ $0 [OPTION] ALIAS
+
+Canonicalize a configuration name.
+
+Operation modes:
+ -h, --help print this help, then exit
+ -t, --time-stamp print date of last modification, then exit
+ -v, --version print version number, then exit
+
+Report bugs and patches to <config-patches at gnu.org>."
+
+version="\
+GNU config.sub ($timestamp)
+
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000,
+2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free
+Software Foundation, Inc.
+
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+
+help="
+Try \`$me --help' for more information."
+
+# Parse command line
+while test $# -gt 0 ; do
+ case $1 in
+ --time-stamp | --time* | -t )
+ echo "$timestamp" ; exit ;;
+ --version | -v )
+ echo "$version" ; exit ;;
+ --help | --h* | -h )
+ echo "$usage"; exit ;;
+ -- ) # Stop option processing
+ shift; break ;;
+ - ) # Use stdin as input.
+ break ;;
+ -* )
+ echo "$me: invalid option $1$help"
+ exit 1 ;;
+
+ *local*)
+ # First pass through any local machine types.
+ echo $1
+ exit ;;
+
+ * )
+ break ;;
+ esac
+done
+
+case $# in
+ 0) echo "$me: missing argument$help" >&2
+ exit 1;;
+ 1) ;;
+ *) echo "$me: too many arguments$help" >&2
+ exit 1;;
+esac
+
+# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any).
+# Here we must recognize all the valid KERNEL-OS combinations.
+maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
+case $maybe_os in
+ nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \
+ uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \
+ kopensolaris*-gnu* | \
+ storm-chaos* | os2-emx* | rtmk-nova*)
+ os=-$maybe_os
+ basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
+ ;;
+ *)
+ basic_machine=`echo $1 | sed 's/-[^-]*$//'`
+ if [ $basic_machine != $1 ]
+ then os=`echo $1 | sed 's/.*-/-/'`
+ else os=; fi
+ ;;
+esac
+
+### Let's recognize common machines as not being operating systems so
+### that things like config.sub decstation-3100 work. We also
+### recognize some manufacturers as not being operating systems, so we
+### can provide default operating systems below.
+case $os in
+ -sun*os*)
+ # Prevent following clause from handling this invalid input.
+ ;;
+ -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \
+ -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \
+ -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \
+ -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
+ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
+ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
+ -apple | -axis | -knuth | -cray | -microblaze)
+ os=
+ basic_machine=$1
+ ;;
+ -bluegene*)
+ os=-cnk
+ ;;
+ -sim | -cisco | -oki | -wec | -winbond)
+ os=
+ basic_machine=$1
+ ;;
+ -scout)
+ ;;
+ -wrs)
+ os=-vxworks
+ basic_machine=$1
+ ;;
+ -chorusos*)
+ os=-chorusos
+ basic_machine=$1
+ ;;
+ -chorusrdb)
+ os=-chorusrdb
+ basic_machine=$1
+ ;;
+ -hiux*)
+ os=-hiuxwe2
+ ;;
+ -sco6)
+ os=-sco5v6
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco5)
+ os=-sco3.2v5
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco4)
+ os=-sco3.2v4
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco3.2.[4-9]*)
+ os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco3.2v[4-9]*)
+ # Don't forget version if it is 3.2v4 or newer.
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco5v6*)
+ # Don't forget version if it is 3.2v4 or newer.
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco*)
+ os=-sco3.2v2
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -udk*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -isc)
+ os=-isc2.2
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -clix*)
+ basic_machine=clipper-intergraph
+ ;;
+ -isc*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -lynx*)
+ os=-lynxos
+ ;;
+ -ptx*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'`
+ ;;
+ -windowsnt*)
+ os=`echo $os | sed -e 's/windowsnt/winnt/'`
+ ;;
+ -psos*)
+ os=-psos
+ ;;
+ -mint | -mint[0-9]*)
+ basic_machine=m68k-atari
+ os=-mint
+ ;;
+esac
+
+# Decode aliases for certain CPU-COMPANY combinations.
+case $basic_machine in
+ # Recognize the basic CPU types without company name.
+ # Some are omitted here because they have special meanings below.
+ 1750a | 580 \
+ | a29k \
+ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \
+ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \
+ | am33_2.0 \
+ | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \
+ | bfin \
+ | c4x | clipper \
+ | d10v | d30v | dlx | dsp16xx \
+ | fido | fr30 | frv \
+ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
+ | i370 | i860 | i960 | ia64 \
+ | ip2k | iq2000 \
+ | lm32 \
+ | m32c | m32r | m32rle | m68000 | m68k | m88k \
+ | maxq | mb | microblaze | mcore | mep | metag \
+ | mips | mipsbe | mipseb | mipsel | mipsle \
+ | mips16 \
+ | mips64 | mips64el \
+ | mips64octeon | mips64octeonel \
+ | mips64orion | mips64orionel \
+ | mips64r5900 | mips64r5900el \
+ | mips64vr | mips64vrel \
+ | mips64vr4100 | mips64vr4100el \
+ | mips64vr4300 | mips64vr4300el \
+ | mips64vr5000 | mips64vr5000el \
+ | mips64vr5900 | mips64vr5900el \
+ | mipsisa32 | mipsisa32el \
+ | mipsisa32r2 | mipsisa32r2el \
+ | mipsisa64 | mipsisa64el \
+ | mipsisa64r2 | mipsisa64r2el \
+ | mipsisa64sb1 | mipsisa64sb1el \
+ | mipsisa64sr71k | mipsisa64sr71kel \
+ | mipstx39 | mipstx39el \
+ | mn10200 | mn10300 \
+ | moxie \
+ | mt \
+ | msp430 \
+ | nios | nios2 \
+ | ns16k | ns32k \
+ | or32 \
+ | pdp10 | pdp11 | pj | pjl \
+ | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \
+ | pyramid \
+ | rx \
+ | score \
+ | sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
+ | sh64 | sh64le \
+ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \
+ | sparcv8 | sparcv9 | sparcv9b | sparcv9v \
+ | spu | strongarm \
+ | tahoe | thumb | tic4x | tic80 | tron \
+ | ubicom32 \
+ | v850 | v850e \
+ | we32k \
+ | x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \
+ | z8k | z80)
+ basic_machine=$basic_machine-unknown
+ ;;
+ m6811 | m68hc11 | m6812 | m68hc12 | picochip)
+ # Motorola 68HC11/12.
+ basic_machine=$basic_machine-unknown
+ os=-none
+ ;;
+ m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k)
+ ;;
+ ms1)
+ basic_machine=mt-unknown
+ ;;
+
+ # We use `pc' rather than `unknown'
+ # because (1) that's what they normally are, and
+ # (2) the word "unknown" tends to confuse beginning users.
+ i*86 | x86_64)
+ basic_machine=$basic_machine-pc
+ ;;
+ # Object if more than one company name word.
+ *-*-*)
+ echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
+ exit 1
+ ;;
+ # Recognize the basic CPU types with company name.
+ 580-* \
+ | a29k-* \
+ | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \
+ | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \
+ | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \
+ | arm-* | armbe-* | armle-* | armeb-* | armv*-* \
+ | avr-* | avr32-* \
+ | bfin-* | bs2000-* \
+ | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \
+ | clipper-* | craynv-* | cydra-* \
+ | d10v-* | d30v-* | dlx-* \
+ | elxsi-* \
+ | f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \
+ | h8300-* | h8500-* \
+ | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
+ | i*86-* | i860-* | i960-* | ia64-* \
+ | ip2k-* | iq2000-* \
+ | lm32-* \
+ | m32c-* | m32r-* | m32rle-* \
+ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
+ | m88110-* | m88k-* | maxq-* | mcore-* | metag-* | microblaze-* \
+ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
+ | mips16-* \
+ | mips64-* | mips64el-* \
+ | mips64octeon-* | mips64octeonel-* \
+ | mips64orion-* | mips64orionel-* \
+ | mips64r5900-* | mips64r5900el-* \
+ | mips64vr-* | mips64vrel-* \
+ | mips64vr4100-* | mips64vr4100el-* \
+ | mips64vr4300-* | mips64vr4300el-* \
+ | mips64vr5000-* | mips64vr5000el-* \
+ | mips64vr5900-* | mips64vr5900el-* \
+ | mipsisa32-* | mipsisa32el-* \
+ | mipsisa32r2-* | mipsisa32r2el-* \
+ | mipsisa64-* | mipsisa64el-* \
+ | mipsisa64r2-* | mipsisa64r2el-* \
+ | mipsisa64sb1-* | mipsisa64sb1el-* \
+ | mipsisa64sr71k-* | mipsisa64sr71kel-* \
+ | mipstx39-* | mipstx39el-* \
+ | mmix-* \
+ | mt-* \
+ | msp430-* \
+ | nios-* | nios2-* \
+ | none-* | np1-* | ns16k-* | ns32k-* \
+ | orion-* \
+ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
+ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \
+ | pyramid-* \
+ | romp-* | rs6000-* | rx-* \
+ | sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \
+ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \
+ | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \
+ | sparclite-* \
+ | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \
+ | tahoe-* | thumb-* \
+ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
+ | tile-* | tilegx-* \
+ | tron-* \
+ | ubicom32-* \
+ | v850-* | v850e-* | vax-* \
+ | we32k-* \
+ | x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \
+ | xstormy16-* | xtensa*-* \
+ | ymp-* \
+ | z8k-* | z80-*)
+ ;;
+ # Recognize the basic CPU types without company name, with glob match.
+ xtensa*)
+ basic_machine=$basic_machine-unknown
+ ;;
+ # Recognize the various machine names and aliases which stand
+ # for a CPU type and a company and sometimes even an OS.
+ 386bsd)
+ basic_machine=i386-unknown
+ os=-bsd
+ ;;
+ 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc)
+ basic_machine=m68000-att
+ ;;
+ 3b*)
+ basic_machine=we32k-att
+ ;;
+ a29khif)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ abacus)
+ basic_machine=abacus-unknown
+ ;;
+ adobe68k)
+ basic_machine=m68010-adobe
+ os=-scout
+ ;;
+ alliant | fx80)
+ basic_machine=fx80-alliant
+ ;;
+ altos | altos3068)
+ basic_machine=m68k-altos
+ ;;
+ am29k)
+ basic_machine=a29k-none
+ os=-bsd
+ ;;
+ amd64)
+ basic_machine=x86_64-pc
+ ;;
+ amd64-*)
+ basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ amdahl)
+ basic_machine=580-amdahl
+ os=-sysv
+ ;;
+ amiga | amiga-*)
+ basic_machine=m68k-unknown
+ ;;
+ amigaos | amigados)
+ basic_machine=m68k-unknown
+ os=-amigaos
+ ;;
+ amigaunix | amix)
+ basic_machine=m68k-unknown
+ os=-sysv4
+ ;;
+ apollo68)
+ basic_machine=m68k-apollo
+ os=-sysv
+ ;;
+ apollo68bsd)
+ basic_machine=m68k-apollo
+ os=-bsd
+ ;;
+ aros)
+ basic_machine=i386-pc
+ os=-aros
+ ;;
+ aux)
+ basic_machine=m68k-apple
+ os=-aux
+ ;;
+ balance)
+ basic_machine=ns32k-sequent
+ os=-dynix
+ ;;
+ blackfin)
+ basic_machine=bfin-unknown
+ os=-linux
+ ;;
+ blackfin-*)
+ basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'`
+ os=-linux
+ ;;
+ bluegene*)
+ basic_machine=powerpc-ibm
+ os=-cnk
+ ;;
+ c90)
+ basic_machine=c90-cray
+ os=-unicos
+ ;;
+ cegcc)
+ basic_machine=arm-unknown
+ os=-cegcc
+ ;;
+ convex-c1)
+ basic_machine=c1-convex
+ os=-bsd
+ ;;
+ convex-c2)
+ basic_machine=c2-convex
+ os=-bsd
+ ;;
+ convex-c32)
+ basic_machine=c32-convex
+ os=-bsd
+ ;;
+ convex-c34)
+ basic_machine=c34-convex
+ os=-bsd
+ ;;
+ convex-c38)
+ basic_machine=c38-convex
+ os=-bsd
+ ;;
+ cray | j90)
+ basic_machine=j90-cray
+ os=-unicos
+ ;;
+ craynv)
+ basic_machine=craynv-cray
+ os=-unicosmp
+ ;;
+ cr16)
+ basic_machine=cr16-unknown
+ os=-elf
+ ;;
+ crds | unos)
+ basic_machine=m68k-crds
+ ;;
+ crisv32 | crisv32-* | etraxfs*)
+ basic_machine=crisv32-axis
+ ;;
+ cris | cris-* | etrax*)
+ basic_machine=cris-axis
+ ;;
+ crx)
+ basic_machine=crx-unknown
+ os=-elf
+ ;;
+ da30 | da30-*)
+ basic_machine=m68k-da30
+ ;;
+ decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn)
+ basic_machine=mips-dec
+ ;;
+ decsystem10* | dec10*)
+ basic_machine=pdp10-dec
+ os=-tops10
+ ;;
+ decsystem20* | dec20*)
+ basic_machine=pdp10-dec
+ os=-tops20
+ ;;
+ delta | 3300 | motorola-3300 | motorola-delta \
+ | 3300-motorola | delta-motorola)
+ basic_machine=m68k-motorola
+ ;;
+ delta88)
+ basic_machine=m88k-motorola
+ os=-sysv3
+ ;;
+ dicos)
+ basic_machine=i686-pc
+ os=-dicos
+ ;;
+ djgpp)
+ basic_machine=i586-pc
+ os=-msdosdjgpp
+ ;;
+ dpx20 | dpx20-*)
+ basic_machine=rs6000-bull
+ os=-bosx
+ ;;
+ dpx2* | dpx2*-bull)
+ basic_machine=m68k-bull
+ os=-sysv3
+ ;;
+ ebmon29k)
+ basic_machine=a29k-amd
+ os=-ebmon
+ ;;
+ elxsi)
+ basic_machine=elxsi-elxsi
+ os=-bsd
+ ;;
+ encore | umax | mmax)
+ basic_machine=ns32k-encore
+ ;;
+ es1800 | OSE68k | ose68k | ose | OSE)
+ basic_machine=m68k-ericsson
+ os=-ose
+ ;;
+ fx2800)
+ basic_machine=i860-alliant
+ ;;
+ genix)
+ basic_machine=ns32k-ns
+ ;;
+ gmicro)
+ basic_machine=tron-gmicro
+ os=-sysv
+ ;;
+ go32)
+ basic_machine=i386-pc
+ os=-go32
+ ;;
+ h3050r* | hiux*)
+ basic_machine=hppa1.1-hitachi
+ os=-hiuxwe2
+ ;;
+ h8300hms)
+ basic_machine=h8300-hitachi
+ os=-hms
+ ;;
+ h8300xray)
+ basic_machine=h8300-hitachi
+ os=-xray
+ ;;
+ h8500hms)
+ basic_machine=h8500-hitachi
+ os=-hms
+ ;;
+ harris)
+ basic_machine=m88k-harris
+ os=-sysv3
+ ;;
+ hp300-*)
+ basic_machine=m68k-hp
+ ;;
+ hp300bsd)
+ basic_machine=m68k-hp
+ os=-bsd
+ ;;
+ hp300hpux)
+ basic_machine=m68k-hp
+ os=-hpux
+ ;;
+ hp3k9[0-9][0-9] | hp9[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hp9k2[0-9][0-9] | hp9k31[0-9])
+ basic_machine=m68000-hp
+ ;;
+ hp9k3[2-9][0-9])
+ basic_machine=m68k-hp
+ ;;
+ hp9k6[0-9][0-9] | hp6[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hp9k7[0-79][0-9] | hp7[0-79][0-9])
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k78[0-9] | hp78[0-9])
+ # FIXME: really hppa2.0-hp
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893)
+ # FIXME: really hppa2.0-hp
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[0-9][13679] | hp8[0-9][13679])
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[0-9][0-9] | hp8[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hppa-next)
+ os=-nextstep3
+ ;;
+ hppaosf)
+ basic_machine=hppa1.1-hp
+ os=-osf
+ ;;
+ hppro)
+ basic_machine=hppa1.1-hp
+ os=-proelf
+ ;;
+ i370-ibm* | ibm*)
+ basic_machine=i370-ibm
+ ;;
+# I'm not sure what "Sysv32" means. Should this be sysv3.2?
+ i*86v32)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv32
+ ;;
+ i*86v4*)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv4
+ ;;
+ i*86v)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv
+ ;;
+ i*86sol2)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-solaris2
+ ;;
+ i386mach)
+ basic_machine=i386-mach
+ os=-mach
+ ;;
+ i386-vsta | vsta)
+ basic_machine=i386-unknown
+ os=-vsta
+ ;;
+ iris | iris4d)
+ basic_machine=mips-sgi
+ case $os in
+ -irix*)
+ ;;
+ *)
+ os=-irix4
+ ;;
+ esac
+ ;;
+ isi68 | isi)
+ basic_machine=m68k-isi
+ os=-sysv
+ ;;
+ m68knommu)
+ basic_machine=m68k-unknown
+ os=-linux
+ ;;
+ m68knommu-*)
+ basic_machine=m68k-`echo $basic_machine | sed 's/^[^-]*-//'`
+ os=-linux
+ ;;
+ m88k-omron*)
+ basic_machine=m88k-omron
+ ;;
+ magnum | m3230)
+ basic_machine=mips-mips
+ os=-sysv
+ ;;
+ merlin)
+ basic_machine=ns32k-utek
+ os=-sysv
+ ;;
+ microblaze)
+ basic_machine=microblaze-xilinx
+ ;;
+ mingw32)
+ basic_machine=i386-pc
+ os=-mingw32
+ ;;
+ mingw32ce)
+ basic_machine=arm-unknown
+ os=-mingw32ce
+ ;;
+ miniframe)
+ basic_machine=m68000-convergent
+ ;;
+ *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*)
+ basic_machine=m68k-atari
+ os=-mint
+ ;;
+ mips3*-*)
+ basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`
+ ;;
+ mips3*)
+ basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown
+ ;;
+ monitor)
+ basic_machine=m68k-rom68k
+ os=-coff
+ ;;
+ morphos)
+ basic_machine=powerpc-unknown
+ os=-morphos
+ ;;
+ msdos)
+ basic_machine=i386-pc
+ os=-msdos
+ ;;
+ ms1-*)
+ basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'`
+ ;;
+ mvs)
+ basic_machine=i370-ibm
+ os=-mvs
+ ;;
+ ncr3000)
+ basic_machine=i486-ncr
+ os=-sysv4
+ ;;
+ netbsd386)
+ basic_machine=i386-unknown
+ os=-netbsd
+ ;;
+ netwinder)
+ basic_machine=armv4l-rebel
+ os=-linux
+ ;;
+ news | news700 | news800 | news900)
+ basic_machine=m68k-sony
+ os=-newsos
+ ;;
+ news1000)
+ basic_machine=m68030-sony
+ os=-newsos
+ ;;
+ news-3600 | risc-news)
+ basic_machine=mips-sony
+ os=-newsos
+ ;;
+ necv70)
+ basic_machine=v70-nec
+ os=-sysv
+ ;;
+ next | m*-next )
+ basic_machine=m68k-next
+ case $os in
+ -nextstep* )
+ ;;
+ -ns2*)
+ os=-nextstep2
+ ;;
+ *)
+ os=-nextstep3
+ ;;
+ esac
+ ;;
+ nh3000)
+ basic_machine=m68k-harris
+ os=-cxux
+ ;;
+ nh[45]000)
+ basic_machine=m88k-harris
+ os=-cxux
+ ;;
+ nindy960)
+ basic_machine=i960-intel
+ os=-nindy
+ ;;
+ mon960)
+ basic_machine=i960-intel
+ os=-mon960
+ ;;
+ nonstopux)
+ basic_machine=mips-compaq
+ os=-nonstopux
+ ;;
+ np1)
+ basic_machine=np1-gould
+ ;;
+ nsr-tandem)
+ basic_machine=nsr-tandem
+ ;;
+ op50n-* | op60c-*)
+ basic_machine=hppa1.1-oki
+ os=-proelf
+ ;;
+ openrisc | openrisc-*)
+ basic_machine=or32-unknown
+ ;;
+ os400)
+ basic_machine=powerpc-ibm
+ os=-os400
+ ;;
+ OSE68000 | ose68000)
+ basic_machine=m68000-ericsson
+ os=-ose
+ ;;
+ os68k)
+ basic_machine=m68k-none
+ os=-os68k
+ ;;
+ pa-hitachi)
+ basic_machine=hppa1.1-hitachi
+ os=-hiuxwe2
+ ;;
+ paragon)
+ basic_machine=i860-intel
+ os=-osf
+ ;;
+ parisc)
+ basic_machine=hppa-unknown
+ os=-linux
+ ;;
+ parisc-*)
+ basic_machine=hppa-`echo $basic_machine | sed 's/^[^-]*-//'`
+ os=-linux
+ ;;
+ pbd)
+ basic_machine=sparc-tti
+ ;;
+ pbb)
+ basic_machine=m68k-tti
+ ;;
+ pc532 | pc532-*)
+ basic_machine=ns32k-pc532
+ ;;
+ pc98)
+ basic_machine=i386-pc
+ ;;
+ pc98-*)
+ basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentium | p5 | k5 | k6 | nexgen | viac3)
+ basic_machine=i586-pc
+ ;;
+ pentiumpro | p6 | 6x86 | athlon | athlon_*)
+ basic_machine=i686-pc
+ ;;
+ pentiumii | pentium2 | pentiumiii | pentium3)
+ basic_machine=i686-pc
+ ;;
+ pentium4)
+ basic_machine=i786-pc
+ ;;
+ pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
+ basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentiumpro-* | p6-* | 6x86-* | athlon-*)
+ basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
+ basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentium4-*)
+ basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pn)
+ basic_machine=pn-gould
+ ;;
+ power) basic_machine=power-ibm
+ ;;
+ ppc) basic_machine=powerpc-unknown
+ ;;
+ ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppcle | powerpclittle | ppc-le | powerpc-little)
+ basic_machine=powerpcle-unknown
+ ;;
+ ppcle-* | powerpclittle-*)
+ basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppc64) basic_machine=powerpc64-unknown
+ ;;
+ ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppc64le | powerpc64little | ppc64-le | powerpc64-little)
+ basic_machine=powerpc64le-unknown
+ ;;
+ ppc64le-* | powerpc64little-*)
+ basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ps2)
+ basic_machine=i386-ibm
+ ;;
+ pw32)
+ basic_machine=i586-unknown
+ os=-pw32
+ ;;
+ rdos)
+ basic_machine=i386-pc
+ os=-rdos
+ ;;
+ rom68k)
+ basic_machine=m68k-rom68k
+ os=-coff
+ ;;
+ rm[46]00)
+ basic_machine=mips-siemens
+ ;;
+ rtpc | rtpc-*)
+ basic_machine=romp-ibm
+ ;;
+ s390 | s390-*)
+ basic_machine=s390-ibm
+ ;;
+ s390x | s390x-*)
+ basic_machine=s390x-ibm
+ ;;
+ sa29200)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ sb1)
+ basic_machine=mipsisa64sb1-unknown
+ ;;
+ sb1el)
+ basic_machine=mipsisa64sb1el-unknown
+ ;;
+ sde)
+ basic_machine=mipsisa32-sde
+ os=-elf
+ ;;
+ sei)
+ basic_machine=mips-sei
+ os=-seiux
+ ;;
+ sequent)
+ basic_machine=i386-sequent
+ ;;
+ sh)
+ basic_machine=sh-hitachi
+ os=-hms
+ ;;
+ sh5el)
+ basic_machine=sh5le-unknown
+ ;;
+ sh64)
+ basic_machine=sh64-unknown
+ ;;
+ sparclite-wrs | simso-wrs)
+ basic_machine=sparclite-wrs
+ os=-vxworks
+ ;;
+ sps7)
+ basic_machine=m68k-bull
+ os=-sysv2
+ ;;
+ spur)
+ basic_machine=spur-unknown
+ ;;
+ st2000)
+ basic_machine=m68k-tandem
+ ;;
+ stratus)
+ basic_machine=i860-stratus
+ os=-sysv4
+ ;;
+ sun2)
+ basic_machine=m68000-sun
+ ;;
+ sun2os3)
+ basic_machine=m68000-sun
+ os=-sunos3
+ ;;
+ sun2os4)
+ basic_machine=m68000-sun
+ os=-sunos4
+ ;;
+ sun3os3)
+ basic_machine=m68k-sun
+ os=-sunos3
+ ;;
+ sun3os4)
+ basic_machine=m68k-sun
+ os=-sunos4
+ ;;
+ sun4os3)
+ basic_machine=sparc-sun
+ os=-sunos3
+ ;;
+ sun4os4)
+ basic_machine=sparc-sun
+ os=-sunos4
+ ;;
+ sun4sol2)
+ basic_machine=sparc-sun
+ os=-solaris2
+ ;;
+ sun3 | sun3-*)
+ basic_machine=m68k-sun
+ ;;
+ sun4)
+ basic_machine=sparc-sun
+ ;;
+ sun386 | sun386i | roadrunner)
+ basic_machine=i386-sun
+ ;;
+ sv1)
+ basic_machine=sv1-cray
+ os=-unicos
+ ;;
+ symmetry)
+ basic_machine=i386-sequent
+ os=-dynix
+ ;;
+ t3e)
+ basic_machine=alphaev5-cray
+ os=-unicos
+ ;;
+ t90)
+ basic_machine=t90-cray
+ os=-unicos
+ ;;
+ tic54x | c54x*)
+ basic_machine=tic54x-unknown
+ os=-coff
+ ;;
+ tic55x | c55x*)
+ basic_machine=tic55x-unknown
+ os=-coff
+ ;;
+ tic6x | c6x*)
+ basic_machine=tic6x-unknown
+ os=-coff
+ ;;
+ # This must be matched before tile*.
+ tilegx*)
+ basic_machine=tilegx-unknown
+ os=-linux-gnu
+ ;;
+ tile*)
+ basic_machine=tile-unknown
+ os=-linux-gnu
+ ;;
+ tx39)
+ basic_machine=mipstx39-unknown
+ ;;
+ tx39el)
+ basic_machine=mipstx39el-unknown
+ ;;
+ toad1)
+ basic_machine=pdp10-xkl
+ os=-tops20
+ ;;
+ tower | tower-32)
+ basic_machine=m68k-ncr
+ ;;
+ tpf)
+ basic_machine=s390x-ibm
+ os=-tpf
+ ;;
+ udi29k)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ ultra3)
+ basic_machine=a29k-nyu
+ os=-sym1
+ ;;
+ v810 | necv810)
+ basic_machine=v810-nec
+ os=-none
+ ;;
+ vaxv)
+ basic_machine=vax-dec
+ os=-sysv
+ ;;
+ vms)
+ basic_machine=vax-dec
+ os=-vms
+ ;;
+ vpp*|vx|vx-*)
+ basic_machine=f301-fujitsu
+ ;;
+ vxworks960)
+ basic_machine=i960-wrs
+ os=-vxworks
+ ;;
+ vxworks68)
+ basic_machine=m68k-wrs
+ os=-vxworks
+ ;;
+ vxworks29k)
+ basic_machine=a29k-wrs
+ os=-vxworks
+ ;;
+ w65*)
+ basic_machine=w65-wdc
+ os=-none
+ ;;
+ w89k-*)
+ basic_machine=hppa1.1-winbond
+ os=-proelf
+ ;;
+ xbox)
+ basic_machine=i686-pc
+ os=-mingw32
+ ;;
+ xps | xps100)
+ basic_machine=xps100-honeywell
+ ;;
+ ymp)
+ basic_machine=ymp-cray
+ os=-unicos
+ ;;
+ z8k-*-coff)
+ basic_machine=z8k-unknown
+ os=-sim
+ ;;
+ z80-*-coff)
+ basic_machine=z80-unknown
+ os=-sim
+ ;;
+ none)
+ basic_machine=none-none
+ os=-none
+ ;;
+
+# Here we handle the default manufacturer of certain CPU types. It is in
+# some cases the only manufacturer, in others, it is the most popular.
+ w89k)
+ basic_machine=hppa1.1-winbond
+ ;;
+ op50n)
+ basic_machine=hppa1.1-oki
+ ;;
+ op60c)
+ basic_machine=hppa1.1-oki
+ ;;
+ romp)
+ basic_machine=romp-ibm
+ ;;
+ mmix)
+ basic_machine=mmix-knuth
+ ;;
+ rs6000)
+ basic_machine=rs6000-ibm
+ ;;
+ vax)
+ basic_machine=vax-dec
+ ;;
+ pdp10)
+ # there are many clones, so DEC is not a safe bet
+ basic_machine=pdp10-unknown
+ ;;
+ pdp11)
+ basic_machine=pdp11-dec
+ ;;
+ we32k)
+ basic_machine=we32k-att
+ ;;
+ sh[1234] | sh[24]a | sh[24]aeb | sh[34]eb | sh[1234]le | sh[23]ele)
+ basic_machine=sh-unknown
+ ;;
+ sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v)
+ basic_machine=sparc-sun
+ ;;
+ cydra)
+ basic_machine=cydra-cydrome
+ ;;
+ orion)
+ basic_machine=orion-highlevel
+ ;;
+ orion105)
+ basic_machine=clipper-highlevel
+ ;;
+ mac | mpw | mac-mpw)
+ basic_machine=m68k-apple
+ ;;
+ pmac | pmac-mpw)
+ basic_machine=powerpc-apple
+ ;;
+ *-unknown)
+ # Make sure to match an already-canonicalized machine name.
+ ;;
+ *)
+ echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
+ exit 1
+ ;;
+esac
+
+# Here we canonicalize certain aliases for manufacturers.
+case $basic_machine in
+ *-digital*)
+ basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'`
+ ;;
+ *-commodore*)
+ basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'`
+ ;;
+ *)
+ ;;
+esac
+
+# Decode manufacturer-specific aliases for certain operating systems.
+
+if [ x"$os" != x"" ]
+then
+case $os in
+ # First match some system type aliases
+ # that might get confused with valid system types.
+ # -solaris* is a basic system type, with this one exception.
+ -auroraux)
+ os=-auroraux
+ ;;
+ -solaris1 | -solaris1.*)
+ os=`echo $os | sed -e 's|solaris1|sunos4|'`
+ ;;
+ -solaris)
+ os=-solaris2
+ ;;
+ -svr4*)
+ os=-sysv4
+ ;;
+ -unixware*)
+ os=-sysv4.2uw
+ ;;
+ -gnu/linux*)
+ os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
+ ;;
+ # First accept the basic system types.
+ # The portable systems comes first.
+ # Each alternative MUST END IN A *, to match a version number.
+ # -sysv* is not here because it comes later, after sysvr4.
+ -gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
+ | -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\
+ | -hpux* | -unos* | -osf* | -luna* | -dgux* | -auroraux* | -solaris* \
+ | -sym* | -kopensolaris* \
+ | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
+ | -aos* | -aros* \
+ | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
+ | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
+ | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \
+ | -openbsd* | -solidbsd* \
+ | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \
+ | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
+ | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
+ | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
+ | -chorusos* | -chorusrdb* | -cegcc* \
+ | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
+ | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \
+ | -uxpv* | -beos* | -mpeix* | -udk* \
+ | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \
+ | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \
+ | -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \
+ | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
+ | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
+ | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
+ | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es*)
+ # Remember, each alternative MUST END IN *, to match a version number.
+ ;;
+ -qnx*)
+ case $basic_machine in
+ x86-* | i*86-*)
+ ;;
+ *)
+ os=-nto$os
+ ;;
+ esac
+ ;;
+ -nto-qnx*)
+ ;;
+ -nto*)
+ os=`echo $os | sed -e 's|nto|nto-qnx|'`
+ ;;
+ -sim | -es1800* | -hms* | -xray | -os68k* | -none* | -v88r* \
+ | -windows* | -osx | -abug | -netware* | -os9* | -beos* | -haiku* \
+ | -macos* | -mpw* | -magic* | -mmixware* | -mon960* | -lnews*)
+ ;;
+ -mac*)
+ os=`echo $os | sed -e 's|mac|macos|'`
+ ;;
+ -linux-dietlibc)
+ os=-linux-dietlibc
+ ;;
+ -linux*)
+ os=`echo $os | sed -e 's|linux|linux-gnu|'`
+ ;;
+ -sunos5*)
+ os=`echo $os | sed -e 's|sunos5|solaris2|'`
+ ;;
+ -sunos6*)
+ os=`echo $os | sed -e 's|sunos6|solaris3|'`
+ ;;
+ -opened*)
+ os=-openedition
+ ;;
+ -os400*)
+ os=-os400
+ ;;
+ -wince*)
+ os=-wince
+ ;;
+ -osfrose*)
+ os=-osfrose
+ ;;
+ -osf*)
+ os=-osf
+ ;;
+ -utek*)
+ os=-bsd
+ ;;
+ -dynix*)
+ os=-bsd
+ ;;
+ -acis*)
+ os=-aos
+ ;;
+ -atheos*)
+ os=-atheos
+ ;;
+ -syllable*)
+ os=-syllable
+ ;;
+ -386bsd)
+ os=-bsd
+ ;;
+ -ctix* | -uts*)
+ os=-sysv
+ ;;
+ -nova*)
+ os=-rtmk-nova
+ ;;
+ -ns2 )
+ os=-nextstep2
+ ;;
+ -nsk*)
+ os=-nsk
+ ;;
+ # Preserve the version number of sinix5.
+ -sinix5.*)
+ os=`echo $os | sed -e 's|sinix|sysv|'`
+ ;;
+ -sinix*)
+ os=-sysv4
+ ;;
+ -tpf*)
+ os=-tpf
+ ;;
+ -triton*)
+ os=-sysv3
+ ;;
+ -oss*)
+ os=-sysv3
+ ;;
+ -svr4)
+ os=-sysv4
+ ;;
+ -svr3)
+ os=-sysv3
+ ;;
+ -sysvr4)
+ os=-sysv4
+ ;;
+ # This must come after -sysvr4.
+ -sysv*)
+ ;;
+ -ose*)
+ os=-ose
+ ;;
+ -es1800*)
+ os=-ose
+ ;;
+ -xenix)
+ os=-xenix
+ ;;
+ -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
+ os=-mint
+ ;;
+ -aros*)
+ os=-aros
+ ;;
+ -kaos*)
+ os=-kaos
+ ;;
+ -zvmoe)
+ os=-zvmoe
+ ;;
+ -dicos*)
+ os=-dicos
+ ;;
+ -nacl*)
+ ;;
+ -none)
+ ;;
+ *)
+ # Get rid of the `-' at the beginning of $os.
+ os=`echo $os | sed 's/[^-]*-//'`
+ echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2
+ exit 1
+ ;;
+esac
+else
+
+# Here we handle the default operating systems that come with various machines.
+# The value should be what the vendor currently ships out the door with their
+# machine or put another way, the most popular os provided with the machine.
+
+# Note that if you're going to try to match "-MANUFACTURER" here (say,
+# "-sun"), then you have to tell the case statement up towards the top
+# that MANUFACTURER isn't an operating system. Otherwise, code above
+# will signal an error saying that MANUFACTURER isn't an operating
+# system, and we'll never get to this point.
+
+case $basic_machine in
+ score-*)
+ os=-elf
+ ;;
+ spu-*)
+ os=-elf
+ ;;
+ *-acorn)
+ os=-riscix1.2
+ ;;
+ arm*-rebel)
+ os=-linux
+ ;;
+ arm*-semi)
+ os=-aout
+ ;;
+ c4x-* | tic4x-*)
+ os=-coff
+ ;;
+ # This must come before the *-dec entry.
+ pdp10-*)
+ os=-tops20
+ ;;
+ pdp11-*)
+ os=-none
+ ;;
+ *-dec | vax-*)
+ os=-ultrix4.2
+ ;;
+ m68*-apollo)
+ os=-domain
+ ;;
+ i386-sun)
+ os=-sunos4.0.2
+ ;;
+ m68000-sun)
+ os=-sunos3
+ # This also exists in the configure program, but was not the
+ # default.
+ # os=-sunos4
+ ;;
+ m68*-cisco)
+ os=-aout
+ ;;
+ mep-*)
+ os=-elf
+ ;;
+ mips*-cisco)
+ os=-elf
+ ;;
+ mips*-*)
+ os=-elf
+ ;;
+ or32-*)
+ os=-coff
+ ;;
+ *-tti) # must be before sparc entry or we get the wrong os.
+ os=-sysv3
+ ;;
+ sparc-* | *-sun)
+ os=-sunos4.1.1
+ ;;
+ *-be)
+ os=-beos
+ ;;
+ *-haiku)
+ os=-haiku
+ ;;
+ *-ibm)
+ os=-aix
+ ;;
+ *-knuth)
+ os=-mmixware
+ ;;
+ *-wec)
+ os=-proelf
+ ;;
+ *-winbond)
+ os=-proelf
+ ;;
+ *-oki)
+ os=-proelf
+ ;;
+ *-hp)
+ os=-hpux
+ ;;
+ *-hitachi)
+ os=-hiux
+ ;;
+ i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent)
+ os=-sysv
+ ;;
+ *-cbm)
+ os=-amigaos
+ ;;
+ *-dg)
+ os=-dgux
+ ;;
+ *-dolphin)
+ os=-sysv3
+ ;;
+ m68k-ccur)
+ os=-rtu
+ ;;
+ m88k-omron*)
+ os=-luna
+ ;;
+ *-next )
+ os=-nextstep
+ ;;
+ *-sequent)
+ os=-ptx
+ ;;
+ *-crds)
+ os=-unos
+ ;;
+ *-ns)
+ os=-genix
+ ;;
+ i370-*)
+ os=-mvs
+ ;;
+ *-next)
+ os=-nextstep3
+ ;;
+ *-gould)
+ os=-sysv
+ ;;
+ *-highlevel)
+ os=-bsd
+ ;;
+ *-encore)
+ os=-bsd
+ ;;
+ *-sgi)
+ os=-irix
+ ;;
+ *-siemens)
+ os=-sysv4
+ ;;
+ *-masscomp)
+ os=-rtu
+ ;;
+ f30[01]-fujitsu | f700-fujitsu)
+ os=-uxpv
+ ;;
+ *-rom68k)
+ os=-coff
+ ;;
+ *-*bug)
+ os=-coff
+ ;;
+ *-apple)
+ os=-macos
+ ;;
+ *-atari*)
+ os=-mint
+ ;;
+ *)
+ os=-none
+ ;;
+esac
+fi
+
+# Here we handle the case where we know the os, and the CPU type, but not the
+# manufacturer. We pick the logical manufacturer.
+vendor=unknown
+case $basic_machine in
+ *-unknown)
+ case $os in
+ -riscix*)
+ vendor=acorn
+ ;;
+ -sunos*)
+ vendor=sun
+ ;;
+ -cnk*|-aix*)
+ vendor=ibm
+ ;;
+ -beos*)
+ vendor=be
+ ;;
+ -hpux*)
+ vendor=hp
+ ;;
+ -mpeix*)
+ vendor=hp
+ ;;
+ -hiux*)
+ vendor=hitachi
+ ;;
+ -unos*)
+ vendor=crds
+ ;;
+ -dgux*)
+ vendor=dg
+ ;;
+ -luna*)
+ vendor=omron
+ ;;
+ -genix*)
+ vendor=ns
+ ;;
+ -mvs* | -opened*)
+ vendor=ibm
+ ;;
+ -os400*)
+ vendor=ibm
+ ;;
+ -ptx*)
+ vendor=sequent
+ ;;
+ -tpf*)
+ vendor=ibm
+ ;;
+ -vxsim* | -vxworks* | -windiss*)
+ vendor=wrs
+ ;;
+ -aux*)
+ vendor=apple
+ ;;
+ -hms*)
+ vendor=hitachi
+ ;;
+ -mpw* | -macos*)
+ vendor=apple
+ ;;
+ -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
+ vendor=atari
+ ;;
+ -vos*)
+ vendor=stratus
+ ;;
+ esac
+ basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"`
+ ;;
+esac
+
+echo $basic_machine$os
+exit
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "timestamp='"
+# time-stamp-format: "%:y-%02m-%02d"
+# time-stamp-end: "'"
+# End:
diff --git a/config/depcomp b/config/depcomp
new file mode 100755
index 0000000..df8eea7
--- /dev/null
+++ b/config/depcomp
@@ -0,0 +1,630 @@
+#! /bin/sh
+# depcomp - compile a program generating dependencies as side-effects
+
+scriptversion=2009-04-28.21; # UTC
+
+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free
+# Software Foundation, Inc.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# Originally written by Alexandre Oliva <oliva at dcc.unicamp.br>.
+
+case $1 in
+ '')
+ echo "$0: No command. Try \`$0 --help' for more information." 1>&2
+ exit 1;
+ ;;
+ -h | --h*)
+ cat <<\EOF
+Usage: depcomp [--help] [--version] PROGRAM [ARGS]
+
+Run PROGRAMS ARGS to compile a file, generating dependencies
+as side-effects.
+
+Environment variables:
+ depmode Dependency tracking mode.
+ source Source file read by `PROGRAMS ARGS'.
+ object Object file output by `PROGRAMS ARGS'.
+ DEPDIR directory where to store dependencies.
+ depfile Dependency file to output.
+ tmpdepfile Temporary file to use when outputing dependencies.
+ libtool Whether libtool is used (yes/no).
+
+Report bugs to <bug-automake at gnu.org>.
+EOF
+ exit $?
+ ;;
+ -v | --v*)
+ echo "depcomp $scriptversion"
+ exit $?
+ ;;
+esac
+
+if test -z "$depmode" || test -z "$source" || test -z "$object"; then
+ echo "depcomp: Variables source, object and depmode must be set" 1>&2
+ exit 1
+fi
+
+# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
+depfile=${depfile-`echo "$object" |
+ sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
+tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
+
+rm -f "$tmpdepfile"
+
+# Some modes work just like other modes, but use different flags. We
+# parameterize here, but still list the modes in the big case below,
+# to make depend.m4 easier to write. Note that we *cannot* use a case
+# here, because this file can only contain one case statement.
+if test "$depmode" = hp; then
+ # HP compiler uses -M and no extra arg.
+ gccflag=-M
+ depmode=gcc
+fi
+
+if test "$depmode" = dashXmstdout; then
+ # This is just like dashmstdout with a different argument.
+ dashmflag=-xM
+ depmode=dashmstdout
+fi
+
+cygpath_u="cygpath -u -f -"
+if test "$depmode" = msvcmsys; then
+ # This is just like msvisualcpp but w/o cygpath translation.
+ # Just convert the backslash-escaped backslashes to single forward
+ # slashes to satisfy depend.m4
+ cygpath_u="sed s,\\\\\\\\,/,g"
+ depmode=msvisualcpp
+fi
+
+case "$depmode" in
+gcc3)
+## gcc 3 implements dependency tracking that does exactly what
+## we want. Yay! Note: for some reason libtool 1.4 doesn't like
+## it if -MD -MP comes after the -MF stuff. Hmm.
+## Unfortunately, FreeBSD c89 acceptance of flags depends upon
+## the command line argument order; so add the flags where they
+## appear in depend2.am. Note that the slowdown incurred here
+## affects only configure: in makefiles, %FASTDEP% shortcuts this.
+ for arg
+ do
+ case $arg in
+ -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;;
+ *) set fnord "$@" "$arg" ;;
+ esac
+ shift # fnord
+ shift # $arg
+ done
+ "$@"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ mv "$tmpdepfile" "$depfile"
+ ;;
+
+gcc)
+## There are various ways to get dependency output from gcc. Here's
+## why we pick this rather obscure method:
+## - Don't want to use -MD because we'd like the dependencies to end
+## up in a subdir. Having to rename by hand is ugly.
+## (We might end up doing this anyway to support other compilers.)
+## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
+## -MM, not -M (despite what the docs say).
+## - Using -M directly means running the compiler twice (even worse
+## than renaming).
+ if test -z "$gccflag"; then
+ gccflag=-MD,
+ fi
+ "$@" -Wp,"$gccflag$tmpdepfile"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
+## The second -e expression handles DOS-style file names with drive letters.
+ sed -e 's/^[^:]*: / /' \
+ -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
+## This next piece of magic avoids the `deleted header file' problem.
+## The problem is that when a header file which appears in a .P file
+## is deleted, the dependency causes make to die (because there is
+## typically no way to rebuild the header). We avoid this by adding
+## dummy dependencies for each header file. Too bad gcc doesn't do
+## this for us directly.
+ tr ' ' '
+' < "$tmpdepfile" |
+## Some versions of gcc put a space before the `:'. On the theory
+## that the space means something, we add a space to the output as
+## well.
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+hp)
+ # This case exists only to let depend.m4 do its work. It works by
+ # looking at the text of this script. This case will never be run,
+ # since it is checked for above.
+ exit 1
+ ;;
+
+sgi)
+ if test "$libtool" = yes; then
+ "$@" "-Wp,-MDupdate,$tmpdepfile"
+ else
+ "$@" -MDupdate "$tmpdepfile"
+ fi
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+
+ if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
+ echo "$object : \\" > "$depfile"
+
+ # Clip off the initial element (the dependent). Don't try to be
+ # clever and replace this with sed code, as IRIX sed won't handle
+ # lines with more than a fixed number of characters (4096 in
+ # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
+ # the IRIX cc adds comments like `#:fec' to the end of the
+ # dependency line.
+ tr ' ' '
+' < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
+ tr '
+' ' ' >> "$depfile"
+ echo >> "$depfile"
+
+ # The second pass generates a dummy entry for each header file.
+ tr ' ' '
+' < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
+ >> "$depfile"
+ else
+ # The sourcefile does not contain any dependencies, so just
+ # store a dummy comment line, to avoid errors with the Makefile
+ # "include basename.Plo" scheme.
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+aix)
+ # The C for AIX Compiler uses -M and outputs the dependencies
+ # in a .u file. In older versions, this file always lives in the
+ # current directory. Also, the AIX compiler puts `$object:' at the
+ # start of each line; $object doesn't have directory information.
+ # Version 6 uses the directory in both cases.
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+ if test "$libtool" = yes; then
+ tmpdepfile1=$dir$base.u
+ tmpdepfile2=$base.u
+ tmpdepfile3=$dir.libs/$base.u
+ "$@" -Wc,-M
+ else
+ tmpdepfile1=$dir$base.u
+ tmpdepfile2=$dir$base.u
+ tmpdepfile3=$dir$base.u
+ "$@" -M
+ fi
+ stat=$?
+
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ if test -f "$tmpdepfile"; then
+ # Each line is of the form `foo.o: dependent.h'.
+ # Do two passes, one to just change these to
+ # `$object: dependent.h' and one to simply `dependent.h:'.
+ sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+ # That's a tab and a space in the [].
+ sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
+ else
+ # The sourcefile does not contain any dependencies, so just
+ # store a dummy comment line, to avoid errors with the Makefile
+ # "include basename.Plo" scheme.
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+icc)
+ # Intel's C compiler understands `-MD -MF file'. However on
+ # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
+ # ICC 7.0 will fill foo.d with something like
+ # foo.o: sub/foo.c
+ # foo.o: sub/foo.h
+ # which is wrong. We want:
+ # sub/foo.o: sub/foo.c
+ # sub/foo.o: sub/foo.h
+ # sub/foo.c:
+ # sub/foo.h:
+ # ICC 7.1 will output
+ # foo.o: sub/foo.c sub/foo.h
+ # and will wrap long lines using \ :
+ # foo.o: sub/foo.c ... \
+ # sub/foo.h ... \
+ # ...
+
+ "$@" -MD -MF "$tmpdepfile"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+ # Each line is of the form `foo.o: dependent.h',
+ # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
+ # Do two passes, one to just change these to
+ # `$object: dependent.h' and one to simply `dependent.h:'.
+ sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
+ # Some versions of the HPUX 10.20 sed can't process this invocation
+ # correctly. Breaking it into two sed invocations is a workaround.
+ sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
+ sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+hp2)
+ # The "hp" stanza above does not work with aCC (C++) and HP's ia64
+ # compilers, which have integrated preprocessors. The correct option
+ # to use with these is +Maked; it writes dependencies to a file named
+ # 'foo.d', which lands next to the object file, wherever that
+ # happens to be.
+ # Much of this is similar to the tru64 case; see comments there.
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+ if test "$libtool" = yes; then
+ tmpdepfile1=$dir$base.d
+ tmpdepfile2=$dir.libs/$base.d
+ "$@" -Wc,+Maked
+ else
+ tmpdepfile1=$dir$base.d
+ tmpdepfile2=$dir$base.d
+ "$@" +Maked
+ fi
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ if test -f "$tmpdepfile"; then
+ sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
+ # Add `dependent.h:' lines.
+ sed -ne '2,${
+ s/^ *//
+ s/ \\*$//
+ s/$/:/
+ p
+ }' "$tmpdepfile" >> "$depfile"
+ else
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile" "$tmpdepfile2"
+ ;;
+
+tru64)
+ # The Tru64 compiler uses -MD to generate dependencies as a side
+ # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
+ # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
+ # dependencies in `foo.d' instead, so we check for that too.
+ # Subdirectories are respected.
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+
+ if test "$libtool" = yes; then
+ # With Tru64 cc, shared objects can also be used to make a
+ # static library. This mechanism is used in libtool 1.4 series to
+ # handle both shared and static libraries in a single compilation.
+ # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
+ #
+ # With libtool 1.5 this exception was removed, and libtool now
+ # generates 2 separate objects for the 2 libraries. These two
+ # compilations output dependencies in $dir.libs/$base.o.d and
+ # in $dir$base.o.d. We have to check for both files, because
+ # one of the two compilations can be disabled. We should prefer
+ # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
+ # automatically cleaned when .libs/ is deleted, while ignoring
+ # the former would cause a distcleancheck panic.
+ tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
+ tmpdepfile2=$dir$base.o.d # libtool 1.5
+ tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
+ tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
+ "$@" -Wc,-MD
+ else
+ tmpdepfile1=$dir$base.o.d
+ tmpdepfile2=$dir$base.d
+ tmpdepfile3=$dir$base.d
+ tmpdepfile4=$dir$base.d
+ "$@" -MD
+ fi
+
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ if test -f "$tmpdepfile"; then
+ sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+ # That's a tab and a space in the [].
+ sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
+ else
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+#nosideeffect)
+ # This comment above is used by automake to tell side-effect
+ # dependency tracking mechanisms from slower ones.
+
+dashmstdout)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout, regardless of -o.
+ "$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
+ # Remove `-o $object'.
+ IFS=" "
+ for arg
+ do
+ case $arg in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift # fnord
+ shift # $arg
+ ;;
+ esac
+ done
+
+ test -z "$dashmflag" && dashmflag=-M
+ # Require at least two characters before searching for `:'
+ # in the target name. This is to cope with DOS-style filenames:
+ # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
+ "$@" $dashmflag |
+ sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
+ rm -f "$depfile"
+ cat < "$tmpdepfile" > "$depfile"
+ tr ' ' '
+' < "$tmpdepfile" | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+dashXmstdout)
+ # This case only exists to satisfy depend.m4. It is never actually
+ # run, as this mode is specially recognized in the preamble.
+ exit 1
+ ;;
+
+makedepend)
+ "$@" || exit $?
+ # Remove any Libtool call
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+ # X makedepend
+ shift
+ cleared=no eat=no
+ for arg
+ do
+ case $cleared in
+ no)
+ set ""; shift
+ cleared=yes ;;
+ esac
+ if test $eat = yes; then
+ eat=no
+ continue
+ fi
+ case "$arg" in
+ -D*|-I*)
+ set fnord "$@" "$arg"; shift ;;
+ # Strip any option that makedepend may not understand. Remove
+ # the object too, otherwise makedepend will parse it as a source file.
+ -arch)
+ eat=yes ;;
+ -*|$object)
+ ;;
+ *)
+ set fnord "$@" "$arg"; shift ;;
+ esac
+ done
+ obj_suffix=`echo "$object" | sed 's/^.*\././'`
+ touch "$tmpdepfile"
+ ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
+ rm -f "$depfile"
+ cat < "$tmpdepfile" > "$depfile"
+ sed '1,2d' "$tmpdepfile" | tr ' ' '
+' | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile" "$tmpdepfile".bak
+ ;;
+
+cpp)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout.
+ "$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
+ # Remove `-o $object'.
+ IFS=" "
+ for arg
+ do
+ case $arg in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift # fnord
+ shift # $arg
+ ;;
+ esac
+ done
+
+ "$@" -E |
+ sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
+ -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
+ sed '$ s: \\$::' > "$tmpdepfile"
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ cat < "$tmpdepfile" >> "$depfile"
+ sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+msvisualcpp)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout.
+ "$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
+ IFS=" "
+ for arg
+ do
+ case "$arg" in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
+ "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
+ set fnord "$@"
+ shift
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift
+ shift
+ ;;
+ esac
+ done
+ "$@" -E 2>/dev/null |
+ sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
+ echo " " >> "$depfile"
+ sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+msvcmsys)
+ # This case exists only to let depend.m4 do its work. It works by
+ # looking at the text of this script. This case will never be run,
+ # since it is checked for above.
+ exit 1
+ ;;
+
+none)
+ exec "$@"
+ ;;
+
+*)
+ echo "Unknown depmode $depmode" 1>&2
+ exit 1
+ ;;
+esac
+
+exit 0
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/config/install-sh b/config/install-sh
new file mode 100755
index 0000000..6781b98
--- /dev/null
+++ b/config/install-sh
@@ -0,0 +1,520 @@
+#!/bin/sh
+# install - install a program, script, or datafile
+
+scriptversion=2009-04-28.21; # UTC
+
+# This originates from X11R5 (mit/util/scripts/install.sh), which was
+# later released in X11R6 (xc/config/util/install.sh) with the
+# following copyright and license.
+#
+# Copyright (C) 1994 X Consortium
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to
+# deal in the Software without restriction, including without limitation the
+# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+# sell copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
+# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
+# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Except as contained in this notice, the name of the X Consortium shall not
+# be used in advertising or otherwise to promote the sale, use or other deal-
+# ings in this Software without prior written authorization from the X Consor-
+# tium.
+#
+#
+# FSF changes to this file are in the public domain.
+#
+# Calling this script install-sh is preferred over install.sh, to prevent
+# `make' implicit rules from creating a file called install from it
+# when there is no Makefile.
+#
+# This script is compatible with the BSD install script, but was written
+# from scratch.
+
+nl='
+'
+IFS=" "" $nl"
+
+# set DOITPROG to echo to test this script
+
+# Don't use :- since 4.3BSD and earlier shells don't like it.
+doit=${DOITPROG-}
+if test -z "$doit"; then
+ doit_exec=exec
+else
+ doit_exec=$doit
+fi
+
+# Put in absolute file names if you don't have them in your path;
+# or use environment vars.
+
+chgrpprog=${CHGRPPROG-chgrp}
+chmodprog=${CHMODPROG-chmod}
+chownprog=${CHOWNPROG-chown}
+cmpprog=${CMPPROG-cmp}
+cpprog=${CPPROG-cp}
+mkdirprog=${MKDIRPROG-mkdir}
+mvprog=${MVPROG-mv}
+rmprog=${RMPROG-rm}
+stripprog=${STRIPPROG-strip}
+
+posix_glob='?'
+initialize_posix_glob='
+ test "$posix_glob" != "?" || {
+ if (set -f) 2>/dev/null; then
+ posix_glob=
+ else
+ posix_glob=:
+ fi
+ }
+'
+
+posix_mkdir=
+
+# Desired mode of installed file.
+mode=0755
+
+chgrpcmd=
+chmodcmd=$chmodprog
+chowncmd=
+mvcmd=$mvprog
+rmcmd="$rmprog -f"
+stripcmd=
+
+src=
+dst=
+dir_arg=
+dst_arg=
+
+copy_on_change=false
+no_target_directory=
+
+usage="\
+Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
+ or: $0 [OPTION]... SRCFILES... DIRECTORY
+ or: $0 [OPTION]... -t DIRECTORY SRCFILES...
+ or: $0 [OPTION]... -d DIRECTORIES...
+
+In the 1st form, copy SRCFILE to DSTFILE.
+In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
+In the 4th, create DIRECTORIES.
+
+Options:
+ --help display this help and exit.
+ --version display version info and exit.
+
+ -c (ignored)
+ -C install only if different (preserve the last data modification time)
+ -d create directories instead of installing files.
+ -g GROUP $chgrpprog installed files to GROUP.
+ -m MODE $chmodprog installed files to MODE.
+ -o USER $chownprog installed files to USER.
+ -s $stripprog installed files.
+ -t DIRECTORY install into DIRECTORY.
+ -T report an error if DSTFILE is a directory.
+
+Environment variables override the default commands:
+ CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG
+ RMPROG STRIPPROG
+"
+
+while test $# -ne 0; do
+ case $1 in
+ -c) ;;
+
+ -C) copy_on_change=true;;
+
+ -d) dir_arg=true;;
+
+ -g) chgrpcmd="$chgrpprog $2"
+ shift;;
+
+ --help) echo "$usage"; exit $?;;
+
+ -m) mode=$2
+ case $mode in
+ *' '* | *' '* | *'
+'* | *'*'* | *'?'* | *'['*)
+ echo "$0: invalid mode: $mode" >&2
+ exit 1;;
+ esac
+ shift;;
+
+ -o) chowncmd="$chownprog $2"
+ shift;;
+
+ -s) stripcmd=$stripprog;;
+
+ -t) dst_arg=$2
+ shift;;
+
+ -T) no_target_directory=true;;
+
+ --version) echo "$0 $scriptversion"; exit $?;;
+
+ --) shift
+ break;;
+
+ -*) echo "$0: invalid option: $1" >&2
+ exit 1;;
+
+ *) break;;
+ esac
+ shift
+done
+
+if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
+ # When -d is used, all remaining arguments are directories to create.
+ # When -t is used, the destination is already specified.
+ # Otherwise, the last argument is the destination. Remove it from $@.
+ for arg
+ do
+ if test -n "$dst_arg"; then
+ # $@ is not empty: it contains at least $arg.
+ set fnord "$@" "$dst_arg"
+ shift # fnord
+ fi
+ shift # arg
+ dst_arg=$arg
+ done
+fi
+
+if test $# -eq 0; then
+ if test -z "$dir_arg"; then
+ echo "$0: no input file specified." >&2
+ exit 1
+ fi
+ # It's OK to call `install-sh -d' without argument.
+ # This can happen when creating conditional directories.
+ exit 0
+fi
+
+if test -z "$dir_arg"; then
+ trap '(exit $?); exit' 1 2 13 15
+
+ # Set umask so as not to create temps with too-generous modes.
+ # However, 'strip' requires both read and write access to temps.
+ case $mode in
+ # Optimize common cases.
+ *644) cp_umask=133;;
+ *755) cp_umask=22;;
+
+ *[0-7])
+ if test -z "$stripcmd"; then
+ u_plus_rw=
+ else
+ u_plus_rw='% 200'
+ fi
+ cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
+ *)
+ if test -z "$stripcmd"; then
+ u_plus_rw=
+ else
+ u_plus_rw=,u+rw
+ fi
+ cp_umask=$mode$u_plus_rw;;
+ esac
+fi
+
+for src
+do
+ # Protect names starting with `-'.
+ case $src in
+ -*) src=./$src;;
+ esac
+
+ if test -n "$dir_arg"; then
+ dst=$src
+ dstdir=$dst
+ test -d "$dstdir"
+ dstdir_status=$?
+ else
+
+ # Waiting for this to be detected by the "$cpprog $src $dsttmp" command
+ # might cause directories to be created, which would be especially bad
+ # if $src (and thus $dsttmp) contains '*'.
+ if test ! -f "$src" && test ! -d "$src"; then
+ echo "$0: $src does not exist." >&2
+ exit 1
+ fi
+
+ if test -z "$dst_arg"; then
+ echo "$0: no destination specified." >&2
+ exit 1
+ fi
+
+ dst=$dst_arg
+ # Protect names starting with `-'.
+ case $dst in
+ -*) dst=./$dst;;
+ esac
+
+ # If destination is a directory, append the input filename; won't work
+ # if double slashes aren't ignored.
+ if test -d "$dst"; then
+ if test -n "$no_target_directory"; then
+ echo "$0: $dst_arg: Is a directory" >&2
+ exit 1
+ fi
+ dstdir=$dst
+ dst=$dstdir/`basename "$src"`
+ dstdir_status=0
+ else
+ # Prefer dirname, but fall back on a substitute if dirname fails.
+ dstdir=`
+ (dirname "$dst") 2>/dev/null ||
+ expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$dst" : 'X\(//\)[^/]' \| \
+ X"$dst" : 'X\(//\)$' \| \
+ X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
+ echo X"$dst" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'
+ `
+
+ test -d "$dstdir"
+ dstdir_status=$?
+ fi
+ fi
+
+ obsolete_mkdir_used=false
+
+ if test $dstdir_status != 0; then
+ case $posix_mkdir in
+ '')
+ # Create intermediate dirs using mode 755 as modified by the umask.
+ # This is like FreeBSD 'install' as of 1997-10-28.
+ umask=`umask`
+ case $stripcmd.$umask in
+ # Optimize common cases.
+ *[2367][2367]) mkdir_umask=$umask;;
+ .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
+
+ *[0-7])
+ mkdir_umask=`expr $umask + 22 \
+ - $umask % 100 % 40 + $umask % 20 \
+ - $umask % 10 % 4 + $umask % 2
+ `;;
+ *) mkdir_umask=$umask,go-w;;
+ esac
+
+ # With -d, create the new directory with the user-specified mode.
+ # Otherwise, rely on $mkdir_umask.
+ if test -n "$dir_arg"; then
+ mkdir_mode=-m$mode
+ else
+ mkdir_mode=
+ fi
+
+ posix_mkdir=false
+ case $umask in
+ *[123567][0-7][0-7])
+ # POSIX mkdir -p sets u+wx bits regardless of umask, which
+ # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
+ ;;
+ *)
+ tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
+ trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
+
+ if (umask $mkdir_umask &&
+ exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
+ then
+ if test -z "$dir_arg" || {
+ # Check for POSIX incompatibilities with -m.
+ # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
+ # other-writeable bit of parent directory when it shouldn't.
+ # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
+ ls_ld_tmpdir=`ls -ld "$tmpdir"`
+ case $ls_ld_tmpdir in
+ d????-?r-*) different_mode=700;;
+ d????-?--*) different_mode=755;;
+ *) false;;
+ esac &&
+ $mkdirprog -m$different_mode -p -- "$tmpdir" && {
+ ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
+ test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
+ }
+ }
+ then posix_mkdir=:
+ fi
+ rmdir "$tmpdir/d" "$tmpdir"
+ else
+ # Remove any dirs left behind by ancient mkdir implementations.
+ rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
+ fi
+ trap '' 0;;
+ esac;;
+ esac
+
+ if
+ $posix_mkdir && (
+ umask $mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
+ )
+ then :
+ else
+
+ # The umask is ridiculous, or mkdir does not conform to POSIX,
+ # or it failed possibly due to a race condition. Create the
+ # directory the slow way, step by step, checking for races as we go.
+
+ case $dstdir in
+ /*) prefix='/';;
+ -*) prefix='./';;
+ *) prefix='';;
+ esac
+
+ eval "$initialize_posix_glob"
+
+ oIFS=$IFS
+ IFS=/
+ $posix_glob set -f
+ set fnord $dstdir
+ shift
+ $posix_glob set +f
+ IFS=$oIFS
+
+ prefixes=
+
+ for d
+ do
+ test -z "$d" && continue
+
+ prefix=$prefix$d
+ if test -d "$prefix"; then
+ prefixes=
+ else
+ if $posix_mkdir; then
+ (umask=$mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
+ # Don't fail if two instances are running concurrently.
+ test -d "$prefix" || exit 1
+ else
+ case $prefix in
+ *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
+ *) qprefix=$prefix;;
+ esac
+ prefixes="$prefixes '$qprefix'"
+ fi
+ fi
+ prefix=$prefix/
+ done
+
+ if test -n "$prefixes"; then
+ # Don't fail if two instances are running concurrently.
+ (umask $mkdir_umask &&
+ eval "\$doit_exec \$mkdirprog $prefixes") ||
+ test -d "$dstdir" || exit 1
+ obsolete_mkdir_used=true
+ fi
+ fi
+ fi
+
+ if test -n "$dir_arg"; then
+ { test -z "$chowncmd" || $doit $chowncmd "$dst"; } &&
+ { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } &&
+ { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false ||
+ test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1
+ else
+
+ # Make a couple of temp file names in the proper directory.
+ dsttmp=$dstdir/_inst.$$_
+ rmtmp=$dstdir/_rm.$$_
+
+ # Trap to clean up those temp files at exit.
+ trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
+
+ # Copy the file name to the temp name.
+ (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") &&
+
+ # and set any options; do chmod last to preserve setuid bits.
+ #
+ # If any of these fail, we abort the whole thing. If we want to
+ # ignore errors from any of these, just make sure not to ignore
+ # errors from the above "$doit $cpprog $src $dsttmp" command.
+ #
+ { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&
+ { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&
+ { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&
+ { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
+
+ # If -C, don't bother to copy if it wouldn't change the file.
+ if $copy_on_change &&
+ old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
+ new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
+
+ eval "$initialize_posix_glob" &&
+ $posix_glob set -f &&
+ set X $old && old=:$2:$4:$5:$6 &&
+ set X $new && new=:$2:$4:$5:$6 &&
+ $posix_glob set +f &&
+
+ test "$old" = "$new" &&
+ $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
+ then
+ rm -f "$dsttmp"
+ else
+ # Rename the file to the real destination.
+ $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||
+
+ # The rename failed, perhaps because mv can't rename something else
+ # to itself, or perhaps because mv is so ancient that it does not
+ # support -f.
+ {
+ # Now remove or move aside any old file at destination location.
+ # We try this two ways since rm can't unlink itself on some
+ # systems and the destination file might be busy for other
+ # reasons. In this case, the final cleanup might fail but the new
+ # file should still install successfully.
+ {
+ test ! -f "$dst" ||
+ $doit $rmcmd -f "$dst" 2>/dev/null ||
+ { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
+ { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
+ } ||
+ { echo "$0: cannot unlink or rename $dst" >&2
+ (exit 1); exit 1
+ }
+ } &&
+
+ # Now rename the file to the real destination.
+ $doit $mvcmd "$dsttmp" "$dst"
+ }
+ fi || exit 1
+
+ trap '' 0
+ fi
+done
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/config/ltmain.sh b/config/ltmain.sh
new file mode 100755
index 0000000..d88da2c
--- /dev/null
+++ b/config/ltmain.sh
@@ -0,0 +1,8413 @@
+# Generated from ltmain.m4sh.
+
+# ltmain.sh (GNU libtool) 2.2.6b
+# Written by Gordon Matzigkeit <gord at gnu.ai.mit.edu>, 1996
+
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, 2006, 2007 2008 Free Software Foundation, Inc.
+# This is free software; see the source for copying conditions. There is NO
+# warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+# GNU Libtool is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# As a special exception to the GNU General Public License,
+# if you distribute this file as part of a program or library that
+# is built using GNU Libtool, you may include this file under the
+# same distribution terms that you use for the rest of that program.
+#
+# GNU Libtool is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GNU Libtool; see the file COPYING. If not, a copy
+# can be downloaded from http://www.gnu.org/licenses/gpl.html,
+# or obtained by writing to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# Usage: $progname [OPTION]... [MODE-ARG]...
+#
+# Provide generalized library-building support services.
+#
+# --config show all configuration variables
+# --debug enable verbose shell tracing
+# -n, --dry-run display commands without modifying any files
+# --features display basic configuration information and exit
+# --mode=MODE use operation mode MODE
+# --preserve-dup-deps don't remove duplicate dependency libraries
+# --quiet, --silent don't print informational messages
+# --tag=TAG use configuration variables from tag TAG
+# -v, --verbose print informational messages (default)
+# --version print version information
+# -h, --help print short or long help message
+#
+# MODE must be one of the following:
+#
+# clean remove files from the build directory
+# compile compile a source file into a libtool object
+# execute automatically set library path, then run a program
+# finish complete the installation of libtool libraries
+# install install libraries or executables
+# link create a library or an executable
+# uninstall remove libraries from an installed directory
+#
+# MODE-ARGS vary depending on the MODE.
+# Try `$progname --help --mode=MODE' for a more detailed description of MODE.
+#
+# When reporting a bug, please describe a test case to reproduce it and
+# include the following information:
+#
+# host-triplet: $host
+# shell: $SHELL
+# compiler: $LTCC
+# compiler flags: $LTCFLAGS
+# linker: $LD (gnu? $with_gnu_ld)
+# $progname: (GNU libtool) 2.2.6b Debian-2.2.6b-2
+# automake: $automake_version
+# autoconf: $autoconf_version
+#
+# Report bugs to <bug-libtool at gnu.org>.
+
+PROGRAM=ltmain.sh
+PACKAGE=libtool
+VERSION="2.2.6b Debian-2.2.6b-2"
+TIMESTAMP=""
+package_revision=1.3017
+
+# Be Bourne compatible
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in *posix*) set -o posix;; esac
+fi
+BIN_SH=xpg4; export BIN_SH # for Tru64
+DUALCASE=1; export DUALCASE # for MKS sh
+
+# NLS nuisances: We save the old values to restore during execute mode.
+# Only set LANG and LC_ALL to C if already set.
+# These must not be set unconditionally because not all systems understand
+# e.g. LANG=C (notably SCO).
+lt_user_locale=
+lt_safe_locale=
+for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES
+do
+ eval "if test \"\${$lt_var+set}\" = set; then
+ save_$lt_var=\$$lt_var
+ $lt_var=C
+ export $lt_var
+ lt_user_locale=\"$lt_var=\\\$save_\$lt_var; \$lt_user_locale\"
+ lt_safe_locale=\"$lt_var=C; \$lt_safe_locale\"
+ fi"
+done
+
+$lt_unset CDPATH
+
+
+
+
+
+: ${CP="cp -f"}
+: ${ECHO="echo"}
+: ${EGREP="/bin/grep -E"}
+: ${FGREP="/bin/grep -F"}
+: ${GREP="/bin/grep"}
+: ${LN_S="ln -s"}
+: ${MAKE="make"}
+: ${MKDIR="mkdir"}
+: ${MV="mv -f"}
+: ${RM="rm -f"}
+: ${SED="/bin/sed"}
+: ${SHELL="${CONFIG_SHELL-/bin/sh}"}
+: ${Xsed="$SED -e 1s/^X//"}
+
+# Global variables:
+EXIT_SUCCESS=0
+EXIT_FAILURE=1
+EXIT_MISMATCH=63 # $? = 63 is used to indicate version mismatch to missing.
+EXIT_SKIP=77 # $? = 77 is used to indicate a skipped test to automake.
+
+exit_status=$EXIT_SUCCESS
+
+# Make sure IFS has a sensible default
+lt_nl='
+'
+IFS=" $lt_nl"
+
+dirname="s,/[^/]*$,,"
+basename="s,^.*/,,"
+
+# func_dirname_and_basename file append nondir_replacement
+# perform func_basename and func_dirname in a single function
+# call:
+# dirname: Compute the dirname of FILE. If nonempty,
+# add APPEND to the result, otherwise set result
+# to NONDIR_REPLACEMENT.
+# value returned in "$func_dirname_result"
+# basename: Compute filename of FILE.
+# value retuned in "$func_basename_result"
+# Implementation must be kept synchronized with func_dirname
+# and func_basename. For efficiency, we do not delegate to
+# those functions but instead duplicate the functionality here.
+func_dirname_and_basename ()
+{
+ # Extract subdirectory from the argument.
+ func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"`
+ if test "X$func_dirname_result" = "X${1}"; then
+ func_dirname_result="${3}"
+ else
+ func_dirname_result="$func_dirname_result${2}"
+ fi
+ func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"`
+}
+
+# Generated shell functions inserted here.
+
+# Work around backward compatibility issue on IRIX 6.5. On IRIX 6.4+, sh
+# is ksh but when the shell is invoked as "sh" and the current value of
+# the _XPG environment variable is not equal to 1 (one), the special
+# positional parameter $0, within a function call, is the name of the
+# function.
+progpath="$0"
+
+# The name of this program:
+# In the unlikely event $progname began with a '-', it would play havoc with
+# func_echo (imagine progname=-n), so we prepend ./ in that case:
+func_dirname_and_basename "$progpath"
+progname=$func_basename_result
+case $progname in
+ -*) progname=./$progname ;;
+esac
+
+# Make sure we have an absolute path for reexecution:
+case $progpath in
+ [\\/]*|[A-Za-z]:\\*) ;;
+ *[\\/]*)
+ progdir=$func_dirname_result
+ progdir=`cd "$progdir" && pwd`
+ progpath="$progdir/$progname"
+ ;;
+ *)
+ save_IFS="$IFS"
+ IFS=:
+ for progdir in $PATH; do
+ IFS="$save_IFS"
+ test -x "$progdir/$progname" && break
+ done
+ IFS="$save_IFS"
+ test -n "$progdir" || progdir=`pwd`
+ progpath="$progdir/$progname"
+ ;;
+esac
+
+# Sed substitution that helps us do robust quoting. It backslashifies
+# metacharacters that are still active within double-quoted strings.
+Xsed="${SED}"' -e 1s/^X//'
+sed_quote_subst='s/\([`"$\\]\)/\\\1/g'
+
+# Same as above, but do not quote variable references.
+double_quote_subst='s/\(["`\\]\)/\\\1/g'
+
+# Re-`\' parameter expansions in output of double_quote_subst that were
+# `\'-ed in input to the same. If an odd number of `\' preceded a '$'
+# in input to double_quote_subst, that '$' was protected from expansion.
+# Since each input `\' is now two `\'s, look for any number of runs of
+# four `\'s followed by two `\'s and then a '$'. `\' that '$'.
+bs='\\'
+bs2='\\\\'
+bs4='\\\\\\\\'
+dollar='\$'
+sed_double_backslash="\
+ s/$bs4/&\\
+/g
+ s/^$bs2$dollar/$bs&/
+ s/\\([^$bs]\\)$bs2$dollar/\\1$bs2$bs$dollar/g
+ s/\n//g"
+
+# Standard options:
+opt_dry_run=false
+opt_help=false
+opt_quiet=false
+opt_verbose=false
+opt_warning=:
+
+# func_echo arg...
+# Echo program name prefixed message, along with the current mode
+# name if it has been set yet.
+func_echo ()
+{
+ $ECHO "$progname${mode+: }$mode: $*"
+}
+
+# func_verbose arg...
+# Echo program name prefixed message in verbose mode only.
+func_verbose ()
+{
+ $opt_verbose && func_echo ${1+"$@"}
+
+ # A bug in bash halts the script if the last line of a function
+ # fails when set -e is in force, so we need another command to
+ # work around that:
+ :
+}
+
+# func_error arg...
+# Echo program name prefixed message to standard error.
+func_error ()
+{
+ $ECHO "$progname${mode+: }$mode: "${1+"$@"} 1>&2
+}
+
+# func_warning arg...
+# Echo program name prefixed warning message to standard error.
+func_warning ()
+{
+ $opt_warning && $ECHO "$progname${mode+: }$mode: warning: "${1+"$@"} 1>&2
+
+ # bash bug again:
+ :
+}
+
+# func_fatal_error arg...
+# Echo program name prefixed message to standard error, and exit.
+func_fatal_error ()
+{
+ func_error ${1+"$@"}
+ exit $EXIT_FAILURE
+}
+
+# func_fatal_help arg...
+# Echo program name prefixed message to standard error, followed by
+# a help hint, and exit.
+func_fatal_help ()
+{
+ func_error ${1+"$@"}
+ func_fatal_error "$help"
+}
+help="Try \`$progname --help' for more information." ## default
+
+
+# func_grep expression filename
+# Check whether EXPRESSION matches any line of FILENAME, without output.
+func_grep ()
+{
+ $GREP "$1" "$2" >/dev/null 2>&1
+}
+
+
+# func_mkdir_p directory-path
+# Make sure the entire path to DIRECTORY-PATH is available.
+func_mkdir_p ()
+{
+ my_directory_path="$1"
+ my_dir_list=
+
+ if test -n "$my_directory_path" && test "$opt_dry_run" != ":"; then
+
+ # Protect directory names starting with `-'
+ case $my_directory_path in
+ -*) my_directory_path="./$my_directory_path" ;;
+ esac
+
+ # While some portion of DIR does not yet exist...
+ while test ! -d "$my_directory_path"; do
+ # ...make a list in topmost first order. Use a colon delimited
+ # list incase some portion of path contains whitespace.
+ my_dir_list="$my_directory_path:$my_dir_list"
+
+ # If the last portion added has no slash in it, the list is done
+ case $my_directory_path in */*) ;; *) break ;; esac
+
+ # ...otherwise throw away the child directory and loop
+ my_directory_path=`$ECHO "X$my_directory_path" | $Xsed -e "$dirname"`
+ done
+ my_dir_list=`$ECHO "X$my_dir_list" | $Xsed -e 's,:*$,,'`
+
+ save_mkdir_p_IFS="$IFS"; IFS=':'
+ for my_dir in $my_dir_list; do
+ IFS="$save_mkdir_p_IFS"
+ # mkdir can fail with a `File exist' error if two processes
+ # try to create one of the directories concurrently. Don't
+ # stop in that case!
+ $MKDIR "$my_dir" 2>/dev/null || :
+ done
+ IFS="$save_mkdir_p_IFS"
+
+ # Bail out if we (or some other process) failed to create a directory.
+ test -d "$my_directory_path" || \
+ func_fatal_error "Failed to create \`$1'"
+ fi
+}
+
+
+# func_mktempdir [string]
+# Make a temporary directory that won't clash with other running
+# libtool processes, and avoids race conditions if possible. If
+# given, STRING is the basename for that directory.
+func_mktempdir ()
+{
+ my_template="${TMPDIR-/tmp}/${1-$progname}"
+
+ if test "$opt_dry_run" = ":"; then
+ # Return a directory name, but don't create it in dry-run mode
+ my_tmpdir="${my_template}-$$"
+ else
+
+ # If mktemp works, use that first and foremost
+ my_tmpdir=`mktemp -d "${my_template}-XXXXXXXX" 2>/dev/null`
+
+ if test ! -d "$my_tmpdir"; then
+ # Failing that, at least try and use $RANDOM to avoid a race
+ my_tmpdir="${my_template}-${RANDOM-0}$$"
+
+ save_mktempdir_umask=`umask`
+ umask 0077
+ $MKDIR "$my_tmpdir"
+ umask $save_mktempdir_umask
+ fi
+
+ # If we're not in dry-run mode, bomb out on failure
+ test -d "$my_tmpdir" || \
+ func_fatal_error "cannot create temporary directory \`$my_tmpdir'"
+ fi
+
+ $ECHO "X$my_tmpdir" | $Xsed
+}
+
+
+# func_quote_for_eval arg
+# Aesthetically quote ARG to be evaled later.
+# This function returns two values: FUNC_QUOTE_FOR_EVAL_RESULT
+# is double-quoted, suitable for a subsequent eval, whereas
+# FUNC_QUOTE_FOR_EVAL_UNQUOTED_RESULT has merely all characters
+# which are still active within double quotes backslashified.
+func_quote_for_eval ()
+{
+ case $1 in
+ *[\\\`\"\$]*)
+ func_quote_for_eval_unquoted_result=`$ECHO "X$1" | $Xsed -e "$sed_quote_subst"` ;;
+ *)
+ func_quote_for_eval_unquoted_result="$1" ;;
+ esac
+
+ case $func_quote_for_eval_unquoted_result in
+ # Double-quote args containing shell metacharacters to delay
+ # word splitting, command substitution and and variable
+ # expansion for a subsequent eval.
+ # Many Bourne shells cannot handle close brackets correctly
+ # in scan sets, so we specify it separately.
+ *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"")
+ func_quote_for_eval_result="\"$func_quote_for_eval_unquoted_result\""
+ ;;
+ *)
+ func_quote_for_eval_result="$func_quote_for_eval_unquoted_result"
+ esac
+}
+
+
+# func_quote_for_expand arg
+# Aesthetically quote ARG to be evaled later; same as above,
+# but do not quote variable references.
+func_quote_for_expand ()
+{
+ case $1 in
+ *[\\\`\"]*)
+ my_arg=`$ECHO "X$1" | $Xsed \
+ -e "$double_quote_subst" -e "$sed_double_backslash"` ;;
+ *)
+ my_arg="$1" ;;
+ esac
+
+ case $my_arg in
+ # Double-quote args containing shell metacharacters to delay
+ # word splitting and command substitution for a subsequent eval.
+ # Many Bourne shells cannot handle close brackets correctly
+ # in scan sets, so we specify it separately.
+ *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"")
+ my_arg="\"$my_arg\""
+ ;;
+ esac
+
+ func_quote_for_expand_result="$my_arg"
+}
+
+
+# func_show_eval cmd [fail_exp]
+# Unless opt_silent is true, then output CMD. Then, if opt_dryrun is
+# not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP
+# is given, then evaluate it.
+func_show_eval ()
+{
+ my_cmd="$1"
+ my_fail_exp="${2-:}"
+
+ ${opt_silent-false} || {
+ func_quote_for_expand "$my_cmd"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+
+ if ${opt_dry_run-false}; then :; else
+ eval "$my_cmd"
+ my_status=$?
+ if test "$my_status" -eq 0; then :; else
+ eval "(exit $my_status); $my_fail_exp"
+ fi
+ fi
+}
+
+
+# func_show_eval_locale cmd [fail_exp]
+# Unless opt_silent is true, then output CMD. Then, if opt_dryrun is
+# not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP
+# is given, then evaluate it. Use the saved locale for evaluation.
+func_show_eval_locale ()
+{
+ my_cmd="$1"
+ my_fail_exp="${2-:}"
+
+ ${opt_silent-false} || {
+ func_quote_for_expand "$my_cmd"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+
+ if ${opt_dry_run-false}; then :; else
+ eval "$lt_user_locale
+ $my_cmd"
+ my_status=$?
+ eval "$lt_safe_locale"
+ if test "$my_status" -eq 0; then :; else
+ eval "(exit $my_status); $my_fail_exp"
+ fi
+ fi
+}
+
+
+
+
+
+# func_version
+# Echo version message to standard output and exit.
+func_version ()
+{
+ $SED -n '/^# '$PROGRAM' (GNU /,/# warranty; / {
+ s/^# //
+ s/^# *$//
+ s/\((C)\)[ 0-9,-]*\( [1-9][0-9]*\)/\1\2/
+ p
+ }' < "$progpath"
+ exit $?
+}
+
+# func_usage
+# Echo short help message to standard output and exit.
+func_usage ()
+{
+ $SED -n '/^# Usage:/,/# -h/ {
+ s/^# //
+ s/^# *$//
+ s/\$progname/'$progname'/
+ p
+ }' < "$progpath"
+ $ECHO
+ $ECHO "run \`$progname --help | more' for full usage"
+ exit $?
+}
+
+# func_help
+# Echo long help message to standard output and exit.
+func_help ()
+{
+ $SED -n '/^# Usage:/,/# Report bugs to/ {
+ s/^# //
+ s/^# *$//
+ s*\$progname*'$progname'*
+ s*\$host*'"$host"'*
+ s*\$SHELL*'"$SHELL"'*
+ s*\$LTCC*'"$LTCC"'*
+ s*\$LTCFLAGS*'"$LTCFLAGS"'*
+ s*\$LD*'"$LD"'*
+ s/\$with_gnu_ld/'"$with_gnu_ld"'/
+ s/\$automake_version/'"`(automake --version) 2>/dev/null |$SED 1q`"'/
+ s/\$autoconf_version/'"`(autoconf --version) 2>/dev/null |$SED 1q`"'/
+ p
+ }' < "$progpath"
+ exit $?
+}
+
+# func_missing_arg argname
+# Echo program name prefixed message to standard error and set global
+# exit_cmd.
+func_missing_arg ()
+{
+ func_error "missing argument for $1"
+ exit_cmd=exit
+}
+
+exit_cmd=:
+
+
+
+
+
+# Check that we have a working $ECHO.
+if test "X$1" = X--no-reexec; then
+ # Discard the --no-reexec flag, and continue.
+ shift
+elif test "X$1" = X--fallback-echo; then
+ # Avoid inline document here, it may be left over
+ :
+elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t'; then
+ # Yippee, $ECHO works!
+ :
+else
+ # Restart under the correct shell, and then maybe $ECHO will work.
+ exec $SHELL "$progpath" --no-reexec ${1+"$@"}
+fi
+
+if test "X$1" = X--fallback-echo; then
+ # used as fallback echo
+ shift
+ cat <<EOF
+$*
+EOF
+ exit $EXIT_SUCCESS
+fi
+
+magic="%%%MAGIC variable%%%"
+magic_exe="%%%MAGIC EXE variable%%%"
+
+# Global variables.
+# $mode is unset
+nonopt=
+execute_dlfiles=
+preserve_args=
+lo2o="s/\\.lo\$/.${objext}/"
+o2lo="s/\\.${objext}\$/.lo/"
+extracted_archives=
+extracted_serial=0
+
+opt_dry_run=false
+opt_duplicate_deps=false
+opt_silent=false
+opt_debug=:
+
+# If this variable is set in any of the actions, the command in it
+# will be execed at the end. This prevents here-documents from being
+# left over by shells.
+exec_cmd=
+
+# func_fatal_configuration arg...
+# Echo program name prefixed message to standard error, followed by
+# a configuration failure hint, and exit.
+func_fatal_configuration ()
+{
+ func_error ${1+"$@"}
+ func_error "See the $PACKAGE documentation for more information."
+ func_fatal_error "Fatal configuration error."
+}
+
+
+# func_config
+# Display the configuration for all the tags in this script.
+func_config ()
+{
+ re_begincf='^# ### BEGIN LIBTOOL'
+ re_endcf='^# ### END LIBTOOL'
+
+ # Default configuration.
+ $SED "1,/$re_begincf CONFIG/d;/$re_endcf CONFIG/,\$d" < "$progpath"
+
+ # Now print the configurations for the tags.
+ for tagname in $taglist; do
+ $SED -n "/$re_begincf TAG CONFIG: $tagname\$/,/$re_endcf TAG CONFIG: $tagname\$/p" < "$progpath"
+ done
+
+ exit $?
+}
+
+# func_features
+# Display the features supported by this script.
+func_features ()
+{
+ $ECHO "host: $host"
+ if test "$build_libtool_libs" = yes; then
+ $ECHO "enable shared libraries"
+ else
+ $ECHO "disable shared libraries"
+ fi
+ if test "$build_old_libs" = yes; then
+ $ECHO "enable static libraries"
+ else
+ $ECHO "disable static libraries"
+ fi
+
+ exit $?
+}
+
+# func_enable_tag tagname
+# Verify that TAGNAME is valid, and either flag an error and exit, or
+# enable the TAGNAME tag. We also add TAGNAME to the global $taglist
+# variable here.
+func_enable_tag ()
+{
+ # Global variable:
+ tagname="$1"
+
+ re_begincf="^# ### BEGIN LIBTOOL TAG CONFIG: $tagname\$"
+ re_endcf="^# ### END LIBTOOL TAG CONFIG: $tagname\$"
+ sed_extractcf="/$re_begincf/,/$re_endcf/p"
+
+ # Validate tagname.
+ case $tagname in
+ *[!-_A-Za-z0-9,/]*)
+ func_fatal_error "invalid tag name: $tagname"
+ ;;
+ esac
+
+ # Don't test for the "default" C tag, as we know it's
+ # there but not specially marked.
+ case $tagname in
+ CC) ;;
+ *)
+ if $GREP "$re_begincf" "$progpath" >/dev/null 2>&1; then
+ taglist="$taglist $tagname"
+
+ # Evaluate the configuration. Be careful to quote the path
+ # and the sed script, to avoid splitting on whitespace, but
+ # also don't use non-portable quotes within backquotes within
+ # quotes we have to do it in 2 steps:
+ extractedcf=`$SED -n -e "$sed_extractcf" < "$progpath"`
+ eval "$extractedcf"
+ else
+ func_error "ignoring unknown tag $tagname"
+ fi
+ ;;
+ esac
+}
+
+# Parse options once, thoroughly. This comes as soon as possible in
+# the script to make things like `libtool --version' happen quickly.
+{
+
+ # Shorthand for --mode=foo, only valid as the first argument
+ case $1 in
+ clean|clea|cle|cl)
+ shift; set dummy --mode clean ${1+"$@"}; shift
+ ;;
+ compile|compil|compi|comp|com|co|c)
+ shift; set dummy --mode compile ${1+"$@"}; shift
+ ;;
+ execute|execut|execu|exec|exe|ex|e)
+ shift; set dummy --mode execute ${1+"$@"}; shift
+ ;;
+ finish|finis|fini|fin|fi|f)
+ shift; set dummy --mode finish ${1+"$@"}; shift
+ ;;
+ install|instal|insta|inst|ins|in|i)
+ shift; set dummy --mode install ${1+"$@"}; shift
+ ;;
+ link|lin|li|l)
+ shift; set dummy --mode link ${1+"$@"}; shift
+ ;;
+ uninstall|uninstal|uninsta|uninst|unins|unin|uni|un|u)
+ shift; set dummy --mode uninstall ${1+"$@"}; shift
+ ;;
+ esac
+
+ # Parse non-mode specific arguments:
+ while test "$#" -gt 0; do
+ opt="$1"
+ shift
+
+ case $opt in
+ --config) func_config ;;
+
+ --debug) preserve_args="$preserve_args $opt"
+ func_echo "enabling shell trace mode"
+ opt_debug='set -x'
+ $opt_debug
+ ;;
+
+ -dlopen) test "$#" -eq 0 && func_missing_arg "$opt" && break
+ execute_dlfiles="$execute_dlfiles $1"
+ shift
+ ;;
+
+ --dry-run | -n) opt_dry_run=: ;;
+ --features) func_features ;;
+ --finish) mode="finish" ;;
+
+ --mode) test "$#" -eq 0 && func_missing_arg "$opt" && break
+ case $1 in
+ # Valid mode arguments:
+ clean) ;;
+ compile) ;;
+ execute) ;;
+ finish) ;;
+ install) ;;
+ link) ;;
+ relink) ;;
+ uninstall) ;;
+
+ # Catch anything else as an error
+ *) func_error "invalid argument for $opt"
+ exit_cmd=exit
+ break
+ ;;
+ esac
+
+ mode="$1"
+ shift
+ ;;
+
+ --preserve-dup-deps)
+ opt_duplicate_deps=: ;;
+
+ --quiet|--silent) preserve_args="$preserve_args $opt"
+ opt_silent=:
+ ;;
+
+ --verbose| -v) preserve_args="$preserve_args $opt"
+ opt_silent=false
+ ;;
+
+ --tag) test "$#" -eq 0 && func_missing_arg "$opt" && break
+ preserve_args="$preserve_args $opt $1"
+ func_enable_tag "$1" # tagname is set here
+ shift
+ ;;
+
+ # Separate optargs to long options:
+ -dlopen=*|--mode=*|--tag=*)
+ func_opt_split "$opt"
+ set dummy "$func_opt_split_opt" "$func_opt_split_arg" ${1+"$@"}
+ shift
+ ;;
+
+ -\?|-h) func_usage ;;
+ --help) opt_help=: ;;
+ --version) func_version ;;
+
+ -*) func_fatal_help "unrecognized option \`$opt'" ;;
+
+ *) nonopt="$opt"
+ break
+ ;;
+ esac
+ done
+
+
+ case $host in
+ *cygwin* | *mingw* | *pw32* | *cegcc*)
+ # don't eliminate duplications in $postdeps and $predeps
+ opt_duplicate_compiler_generated_deps=:
+ ;;
+ *)
+ opt_duplicate_compiler_generated_deps=$opt_duplicate_deps
+ ;;
+ esac
+
+ # Having warned about all mis-specified options, bail out if
+ # anything was wrong.
+ $exit_cmd $EXIT_FAILURE
+}
+
+# func_check_version_match
+# Ensure that we are using m4 macros, and libtool script from the same
+# release of libtool.
+func_check_version_match ()
+{
+ if test "$package_revision" != "$macro_revision"; then
+ if test "$VERSION" != "$macro_version"; then
+ if test -z "$macro_version"; then
+ cat >&2 <<_LT_EOF
+$progname: Version mismatch error. This is $PACKAGE $VERSION, but the
+$progname: definition of this LT_INIT comes from an older release.
+$progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION
+$progname: and run autoconf again.
+_LT_EOF
+ else
+ cat >&2 <<_LT_EOF
+$progname: Version mismatch error. This is $PACKAGE $VERSION, but the
+$progname: definition of this LT_INIT comes from $PACKAGE $macro_version.
+$progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION
+$progname: and run autoconf again.
+_LT_EOF
+ fi
+ else
+ cat >&2 <<_LT_EOF
+$progname: Version mismatch error. This is $PACKAGE $VERSION, revision $package_revision,
+$progname: but the definition of this LT_INIT comes from revision $macro_revision.
+$progname: You should recreate aclocal.m4 with macros from revision $package_revision
+$progname: of $PACKAGE $VERSION and run autoconf again.
+_LT_EOF
+ fi
+
+ exit $EXIT_MISMATCH
+ fi
+}
+
+
+## ----------- ##
+## Main. ##
+## ----------- ##
+
+$opt_help || {
+ # Sanity checks first:
+ func_check_version_match
+
+ if test "$build_libtool_libs" != yes && test "$build_old_libs" != yes; then
+ func_fatal_configuration "not configured to build any kind of library"
+ fi
+
+ test -z "$mode" && func_fatal_error "error: you must specify a MODE."
+
+
+ # Darwin sucks
+ eval std_shrext=\"$shrext_cmds\"
+
+
+ # Only execute mode is allowed to have -dlopen flags.
+ if test -n "$execute_dlfiles" && test "$mode" != execute; then
+ func_error "unrecognized option \`-dlopen'"
+ $ECHO "$help" 1>&2
+ exit $EXIT_FAILURE
+ fi
+
+ # Change the help message to a mode-specific one.
+ generic_help="$help"
+ help="Try \`$progname --help --mode=$mode' for more information."
+}
+
+
+# func_lalib_p file
+# True iff FILE is a libtool `.la' library or `.lo' object file.
+# This function is only a basic sanity check; it will hardly flush out
+# determined imposters.
+func_lalib_p ()
+{
+ test -f "$1" &&
+ $SED -e 4q "$1" 2>/dev/null \
+ | $GREP "^# Generated by .*$PACKAGE" > /dev/null 2>&1
+}
+
+# func_lalib_unsafe_p file
+# True iff FILE is a libtool `.la' library or `.lo' object file.
+# This function implements the same check as func_lalib_p without
+# resorting to external programs. To this end, it redirects stdin and
+# closes it afterwards, without saving the original file descriptor.
+# As a safety measure, use it only where a negative result would be
+# fatal anyway. Works if `file' does not exist.
+func_lalib_unsafe_p ()
+{
+ lalib_p=no
+ if test -f "$1" && test -r "$1" && exec 5<&0 <"$1"; then
+ for lalib_p_l in 1 2 3 4
+ do
+ read lalib_p_line
+ case "$lalib_p_line" in
+ \#\ Generated\ by\ *$PACKAGE* ) lalib_p=yes; break;;
+ esac
+ done
+ exec 0<&5 5<&-
+ fi
+ test "$lalib_p" = yes
+}
+
+# func_ltwrapper_script_p file
+# True iff FILE is a libtool wrapper script
+# This function is only a basic sanity check; it will hardly flush out
+# determined imposters.
+func_ltwrapper_script_p ()
+{
+ func_lalib_p "$1"
+}
+
+# func_ltwrapper_executable_p file
+# True iff FILE is a libtool wrapper executable
+# This function is only a basic sanity check; it will hardly flush out
+# determined imposters.
+func_ltwrapper_executable_p ()
+{
+ func_ltwrapper_exec_suffix=
+ case $1 in
+ *.exe) ;;
+ *) func_ltwrapper_exec_suffix=.exe ;;
+ esac
+ $GREP "$magic_exe" "$1$func_ltwrapper_exec_suffix" >/dev/null 2>&1
+}
+
+# func_ltwrapper_scriptname file
+# Assumes file is an ltwrapper_executable
+# uses $file to determine the appropriate filename for a
+# temporary ltwrapper_script.
+func_ltwrapper_scriptname ()
+{
+ func_ltwrapper_scriptname_result=""
+ if func_ltwrapper_executable_p "$1"; then
+ func_dirname_and_basename "$1" "" "."
+ func_stripname '' '.exe' "$func_basename_result"
+ func_ltwrapper_scriptname_result="$func_dirname_result/$objdir/${func_stripname_result}_ltshwrapper"
+ fi
+}
+
+# func_ltwrapper_p file
+# True iff FILE is a libtool wrapper script or wrapper executable
+# This function is only a basic sanity check; it will hardly flush out
+# determined imposters.
+func_ltwrapper_p ()
+{
+ func_ltwrapper_script_p "$1" || func_ltwrapper_executable_p "$1"
+}
+
+
+# func_execute_cmds commands fail_cmd
+# Execute tilde-delimited COMMANDS.
+# If FAIL_CMD is given, eval that upon failure.
+# FAIL_CMD may read-access the current command in variable CMD!
+func_execute_cmds ()
+{
+ $opt_debug
+ save_ifs=$IFS; IFS='~'
+ for cmd in $1; do
+ IFS=$save_ifs
+ eval cmd=\"$cmd\"
+ func_show_eval "$cmd" "${2-:}"
+ done
+ IFS=$save_ifs
+}
+
+
+# func_source file
+# Source FILE, adding directory component if necessary.
+# Note that it is not necessary on cygwin/mingw to append a dot to
+# FILE even if both FILE and FILE.exe exist: automatic-append-.exe
+# behavior happens only for exec(3), not for open(2)! Also, sourcing
+# `FILE.' does not work on cygwin managed mounts.
+func_source ()
+{
+ $opt_debug
+ case $1 in
+ */* | *\\*) . "$1" ;;
+ *) . "./$1" ;;
+ esac
+}
+
+
+# func_infer_tag arg
+# Infer tagged configuration to use if any are available and
+# if one wasn't chosen via the "--tag" command line option.
+# Only attempt this if the compiler in the base compile
+# command doesn't match the default compiler.
+# arg is usually of the form 'gcc ...'
+func_infer_tag ()
+{
+ $opt_debug
+ if test -n "$available_tags" && test -z "$tagname"; then
+ CC_quoted=
+ for arg in $CC; do
+ func_quote_for_eval "$arg"
+ CC_quoted="$CC_quoted $func_quote_for_eval_result"
+ done
+ case $@ in
+ # Blanks in the command may have been stripped by the calling shell,
+ # but not from the CC environment variable when configure was run.
+ " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*) ;;
+ # Blanks at the start of $base_compile will cause this to fail
+ # if we don't check for them as well.
+ *)
+ for z in $available_tags; do
+ if $GREP "^# ### BEGIN LIBTOOL TAG CONFIG: $z$" < "$progpath" > /dev/null; then
+ # Evaluate the configuration.
+ eval "`${SED} -n -e '/^# ### BEGIN LIBTOOL TAG CONFIG: '$z'$/,/^# ### END LIBTOOL TAG CONFIG: '$z'$/p' < $progpath`"
+ CC_quoted=
+ for arg in $CC; do
+ # Double-quote args containing other shell metacharacters.
+ func_quote_for_eval "$arg"
+ CC_quoted="$CC_quoted $func_quote_for_eval_result"
+ done
+ case "$@ " in
+ " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*)
+ # The compiler in the base compile command matches
+ # the one in the tagged configuration.
+ # Assume this is the tagged configuration we want.
+ tagname=$z
+ break
+ ;;
+ esac
+ fi
+ done
+ # If $tagname still isn't set, then no tagged configuration
+ # was found and let the user know that the "--tag" command
+ # line option must be used.
+ if test -z "$tagname"; then
+ func_echo "unable to infer tagged configuration"
+ func_fatal_error "specify a tag with \`--tag'"
+# else
+# func_verbose "using $tagname tagged configuration"
+ fi
+ ;;
+ esac
+ fi
+}
+
+
+
+# func_write_libtool_object output_name pic_name nonpic_name
+# Create a libtool object file (analogous to a ".la" file),
+# but don't create it if we're doing a dry run.
+func_write_libtool_object ()
+{
+ write_libobj=${1}
+ if test "$build_libtool_libs" = yes; then
+ write_lobj=\'${2}\'
+ else
+ write_lobj=none
+ fi
+
+ if test "$build_old_libs" = yes; then
+ write_oldobj=\'${3}\'
+ else
+ write_oldobj=none
+ fi
+
+ $opt_dry_run || {
+ cat >${write_libobj}T <<EOF
+# $write_libobj - a libtool object file
+# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object=$write_lobj
+
+# Name of the non-PIC object
+non_pic_object=$write_oldobj
+
+EOF
+ $MV "${write_libobj}T" "${write_libobj}"
+ }
+}
+
+# func_mode_compile arg...
+func_mode_compile ()
+{
+ $opt_debug
+ # Get the compilation command and the source file.
+ base_compile=
+ srcfile="$nonopt" # always keep a non-empty value in "srcfile"
+ suppress_opt=yes
+ suppress_output=
+ arg_mode=normal
+ libobj=
+ later=
+ pie_flag=
+
+ for arg
+ do
+ case $arg_mode in
+ arg )
+ # do not "continue". Instead, add this to base_compile
+ lastarg="$arg"
+ arg_mode=normal
+ ;;
+
+ target )
+ libobj="$arg"
+ arg_mode=normal
+ continue
+ ;;
+
+ normal )
+ # Accept any command-line options.
+ case $arg in
+ -o)
+ test -n "$libobj" && \
+ func_fatal_error "you cannot specify \`-o' more than once"
+ arg_mode=target
+ continue
+ ;;
+
+ -pie | -fpie | -fPIE)
+ pie_flag="$pie_flag $arg"
+ continue
+ ;;
+
+ -shared | -static | -prefer-pic | -prefer-non-pic)
+ later="$later $arg"
+ continue
+ ;;
+
+ -no-suppress)
+ suppress_opt=no
+ continue
+ ;;
+
+ -Xcompiler)
+ arg_mode=arg # the next one goes into the "base_compile" arg list
+ continue # The current "srcfile" will either be retained or
+ ;; # replaced later. I would guess that would be a bug.
+
+ -Wc,*)
+ func_stripname '-Wc,' '' "$arg"
+ args=$func_stripname_result
+ lastarg=
+ save_ifs="$IFS"; IFS=','
+ for arg in $args; do
+ IFS="$save_ifs"
+ func_quote_for_eval "$arg"
+ lastarg="$lastarg $func_quote_for_eval_result"
+ done
+ IFS="$save_ifs"
+ func_stripname ' ' '' "$lastarg"
+ lastarg=$func_stripname_result
+
+ # Add the arguments to base_compile.
+ base_compile="$base_compile $lastarg"
+ continue
+ ;;
+
+ *)
+ # Accept the current argument as the source file.
+ # The previous "srcfile" becomes the current argument.
+ #
+ lastarg="$srcfile"
+ srcfile="$arg"
+ ;;
+ esac # case $arg
+ ;;
+ esac # case $arg_mode
+
+ # Aesthetically quote the previous argument.
+ func_quote_for_eval "$lastarg"
+ base_compile="$base_compile $func_quote_for_eval_result"
+ done # for arg
+
+ case $arg_mode in
+ arg)
+ func_fatal_error "you must specify an argument for -Xcompile"
+ ;;
+ target)
+ func_fatal_error "you must specify a target with \`-o'"
+ ;;
+ *)
+ # Get the name of the library object.
+ test -z "$libobj" && {
+ func_basename "$srcfile"
+ libobj="$func_basename_result"
+ }
+ ;;
+ esac
+
+ # Recognize several different file suffixes.
+ # If the user specifies -o file.o, it is replaced with file.lo
+ case $libobj in
+ *.[cCFSifmso] | \
+ *.ada | *.adb | *.ads | *.asm | \
+ *.c++ | *.cc | *.ii | *.class | *.cpp | *.cxx | \
+ *.[fF][09]? | *.for | *.java | *.obj | *.sx)
+ func_xform "$libobj"
+ libobj=$func_xform_result
+ ;;
+ esac
+
+ case $libobj in
+ *.lo) func_lo2o "$libobj"; obj=$func_lo2o_result ;;
+ *)
+ func_fatal_error "cannot determine name of library object from \`$libobj'"
+ ;;
+ esac
+
+ func_infer_tag $base_compile
+
+ for arg in $later; do
+ case $arg in
+ -shared)
+ test "$build_libtool_libs" != yes && \
+ func_fatal_configuration "can not build a shared library"
+ build_old_libs=no
+ continue
+ ;;
+
+ -static)
+ build_libtool_libs=no
+ build_old_libs=yes
+ continue
+ ;;
+
+ -prefer-pic)
+ pic_mode=yes
+ continue
+ ;;
+
+ -prefer-non-pic)
+ pic_mode=no
+ continue
+ ;;
+ esac
+ done
+
+ func_quote_for_eval "$libobj"
+ test "X$libobj" != "X$func_quote_for_eval_result" \
+ && $ECHO "X$libobj" | $GREP '[]~#^*{};<>?"'"'"' &()|`$[]' \
+ && func_warning "libobj name \`$libobj' may not contain shell special characters."
+ func_dirname_and_basename "$obj" "/" ""
+ objname="$func_basename_result"
+ xdir="$func_dirname_result"
+ lobj=${xdir}$objdir/$objname
+
+ test -z "$base_compile" && \
+ func_fatal_help "you must specify a compilation command"
+
+ # Delete any leftover library objects.
+ if test "$build_old_libs" = yes; then
+ removelist="$obj $lobj $libobj ${libobj}T"
+ else
+ removelist="$lobj $libobj ${libobj}T"
+ fi
+
+ # On Cygwin there's no "real" PIC flag so we must build both object types
+ case $host_os in
+ cygwin* | mingw* | pw32* | os2* | cegcc*)
+ pic_mode=default
+ ;;
+ esac
+ if test "$pic_mode" = no && test "$deplibs_check_method" != pass_all; then
+ # non-PIC code in shared libraries is not supported
+ pic_mode=default
+ fi
+
+ # Calculate the filename of the output object if compiler does
+ # not support -o with -c
+ if test "$compiler_c_o" = no; then
+ output_obj=`$ECHO "X$srcfile" | $Xsed -e 's%^.*/%%' -e 's%\.[^.]*$%%'`.${objext}
+ lockfile="$output_obj.lock"
+ else
+ output_obj=
+ need_locks=no
+ lockfile=
+ fi
+
+ # Lock this critical section if it is needed
+ # We use this script file to make the link, it avoids creating a new file
+ if test "$need_locks" = yes; then
+ until $opt_dry_run || ln "$progpath" "$lockfile" 2>/dev/null; do
+ func_echo "Waiting for $lockfile to be removed"
+ sleep 2
+ done
+ elif test "$need_locks" = warn; then
+ if test -f "$lockfile"; then
+ $ECHO "\
+*** ERROR, $lockfile exists and contains:
+`cat $lockfile 2>/dev/null`
+
+This indicates that another process is trying to use the same
+temporary object file, and libtool could not work around it because
+your compiler does not support \`-c' and \`-o' together. If you
+repeat this compilation, it may succeed, by chance, but you had better
+avoid parallel builds (make -j) in this platform, or get a better
+compiler."
+
+ $opt_dry_run || $RM $removelist
+ exit $EXIT_FAILURE
+ fi
+ removelist="$removelist $output_obj"
+ $ECHO "$srcfile" > "$lockfile"
+ fi
+
+ $opt_dry_run || $RM $removelist
+ removelist="$removelist $lockfile"
+ trap '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' 1 2 15
+
+ if test -n "$fix_srcfile_path"; then
+ eval srcfile=\"$fix_srcfile_path\"
+ fi
+ func_quote_for_eval "$srcfile"
+ qsrcfile=$func_quote_for_eval_result
+
+ # Only build a PIC object if we are building libtool libraries.
+ if test "$build_libtool_libs" = yes; then
+ # Without this assignment, base_compile gets emptied.
+ fbsd_hideous_sh_bug=$base_compile
+
+ if test "$pic_mode" != no; then
+ command="$base_compile $qsrcfile $pic_flag"
+ else
+ # Don't build PIC code
+ command="$base_compile $qsrcfile"
+ fi
+
+ func_mkdir_p "$xdir$objdir"
+
+ if test -z "$output_obj"; then
+ # Place PIC objects in $objdir
+ command="$command -o $lobj"
+ fi
+
+ func_show_eval_locale "$command" \
+ 'test -n "$output_obj" && $RM $removelist; exit $EXIT_FAILURE'
+
+ if test "$need_locks" = warn &&
+ test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then
+ $ECHO "\
+*** ERROR, $lockfile contains:
+`cat $lockfile 2>/dev/null`
+
+but it should contain:
+$srcfile
+
+This indicates that another process is trying to use the same
+temporary object file, and libtool could not work around it because
+your compiler does not support \`-c' and \`-o' together. If you
+repeat this compilation, it may succeed, by chance, but you had better
+avoid parallel builds (make -j) in this platform, or get a better
+compiler."
+
+ $opt_dry_run || $RM $removelist
+ exit $EXIT_FAILURE
+ fi
+
+ # Just move the object if needed, then go on to compile the next one
+ if test -n "$output_obj" && test "X$output_obj" != "X$lobj"; then
+ func_show_eval '$MV "$output_obj" "$lobj"' \
+ 'error=$?; $opt_dry_run || $RM $removelist; exit $error'
+ fi
+
+ # Allow error messages only from the first compilation.
+ if test "$suppress_opt" = yes; then
+ suppress_output=' >/dev/null 2>&1'
+ fi
+ fi
+
+ # Only build a position-dependent object if we build old libraries.
+ if test "$build_old_libs" = yes; then
+ if test "$pic_mode" != yes; then
+ # Don't build PIC code
+ command="$base_compile $qsrcfile$pie_flag"
+ else
+ command="$base_compile $qsrcfile $pic_flag"
+ fi
+ if test "$compiler_c_o" = yes; then
+ command="$command -o $obj"
+ fi
+
+ # Suppress compiler output if we already did a PIC compilation.
+ command="$command$suppress_output"
+ func_show_eval_locale "$command" \
+ '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE'
+
+ if test "$need_locks" = warn &&
+ test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then
+ $ECHO "\
+*** ERROR, $lockfile contains:
+`cat $lockfile 2>/dev/null`
+
+but it should contain:
+$srcfile
+
+This indicates that another process is trying to use the same
+temporary object file, and libtool could not work around it because
+your compiler does not support \`-c' and \`-o' together. If you
+repeat this compilation, it may succeed, by chance, but you had better
+avoid parallel builds (make -j) in this platform, or get a better
+compiler."
+
+ $opt_dry_run || $RM $removelist
+ exit $EXIT_FAILURE
+ fi
+
+ # Just move the object if needed
+ if test -n "$output_obj" && test "X$output_obj" != "X$obj"; then
+ func_show_eval '$MV "$output_obj" "$obj"' \
+ 'error=$?; $opt_dry_run || $RM $removelist; exit $error'
+ fi
+ fi
+
+ $opt_dry_run || {
+ func_write_libtool_object "$libobj" "$objdir/$objname" "$objname"
+
+ # Unlock the critical section if it was locked
+ if test "$need_locks" != no; then
+ removelist=$lockfile
+ $RM "$lockfile"
+ fi
+ }
+
+ exit $EXIT_SUCCESS
+}
+
+$opt_help || {
+test "$mode" = compile && func_mode_compile ${1+"$@"}
+}
+
+func_mode_help ()
+{
+ # We need to display help for each of the modes.
+ case $mode in
+ "")
+ # Generic help is extracted from the usage comments
+ # at the start of this file.
+ func_help
+ ;;
+
+ clean)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=clean RM [RM-OPTION]... FILE...
+
+Remove files from the build directory.
+
+RM is the name of the program to use to delete files associated with each FILE
+(typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed
+to RM.
+
+If FILE is a libtool library, object or program, all the files associated
+with it are deleted. Otherwise, only FILE itself is deleted using RM."
+ ;;
+
+ compile)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=compile COMPILE-COMMAND... SOURCEFILE
+
+Compile a source file into a libtool library object.
+
+This mode accepts the following additional options:
+
+ -o OUTPUT-FILE set the output file name to OUTPUT-FILE
+ -no-suppress do not suppress compiler output for multiple passes
+ -prefer-pic try to building PIC objects only
+ -prefer-non-pic try to building non-PIC objects only
+ -shared do not build a \`.o' file suitable for static linking
+ -static only build a \`.o' file suitable for static linking
+
+COMPILE-COMMAND is a command to be used in creating a \`standard' object file
+from the given SOURCEFILE.
+
+The output file name is determined by removing the directory component from
+SOURCEFILE, then substituting the C source code suffix \`.c' with the
+library object suffix, \`.lo'."
+ ;;
+
+ execute)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=execute COMMAND [ARGS]...
+
+Automatically set library path, then run a program.
+
+This mode accepts the following additional options:
+
+ -dlopen FILE add the directory containing FILE to the library path
+
+This mode sets the library path environment variable according to \`-dlopen'
+flags.
+
+If any of the ARGS are libtool executable wrappers, then they are translated
+into their corresponding uninstalled binary, and any of their required library
+directories are added to the library path.
+
+Then, COMMAND is executed, with ARGS as arguments."
+ ;;
+
+ finish)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=finish [LIBDIR]...
+
+Complete the installation of libtool libraries.
+
+Each LIBDIR is a directory that contains libtool libraries.
+
+The commands that this mode executes may require superuser privileges. Use
+the \`--dry-run' option if you just want to see what would be executed."
+ ;;
+
+ install)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=install INSTALL-COMMAND...
+
+Install executables or libraries.
+
+INSTALL-COMMAND is the installation command. The first component should be
+either the \`install' or \`cp' program.
+
+The following components of INSTALL-COMMAND are treated specially:
+
+ -inst-prefix PREFIX-DIR Use PREFIX-DIR as a staging area for installation
+
+The rest of the components are interpreted as arguments to that command (only
+BSD-compatible install options are recognized)."
+ ;;
+
+ link)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=link LINK-COMMAND...
+
+Link object files or libraries together to form another library, or to
+create an executable program.
+
+LINK-COMMAND is a command using the C compiler that you would use to create
+a program from several object files.
+
+The following components of LINK-COMMAND are treated specially:
+
+ -all-static do not do any dynamic linking at all
+ -avoid-version do not add a version suffix if possible
+ -dlopen FILE \`-dlpreopen' FILE if it cannot be dlopened at runtime
+ -dlpreopen FILE link in FILE and add its symbols to lt_preloaded_symbols
+ -export-dynamic allow symbols from OUTPUT-FILE to be resolved with dlsym(3)
+ -export-symbols SYMFILE
+ try to export only the symbols listed in SYMFILE
+ -export-symbols-regex REGEX
+ try to export only the symbols matching REGEX
+ -LLIBDIR search LIBDIR for required installed libraries
+ -lNAME OUTPUT-FILE requires the installed library libNAME
+ -module build a library that can dlopened
+ -no-fast-install disable the fast-install mode
+ -no-install link a not-installable executable
+ -no-undefined declare that a library does not refer to external symbols
+ -o OUTPUT-FILE create OUTPUT-FILE from the specified objects
+ -objectlist FILE Use a list of object files found in FILE to specify objects
+ -precious-files-regex REGEX
+ don't remove output files matching REGEX
+ -release RELEASE specify package release information
+ -rpath LIBDIR the created library will eventually be installed in LIBDIR
+ -R[ ]LIBDIR add LIBDIR to the runtime path of programs and libraries
+ -shared only do dynamic linking of libtool libraries
+ -shrext SUFFIX override the standard shared library file extension
+ -static do not do any dynamic linking of uninstalled libtool libraries
+ -static-libtool-libs
+ do not do any dynamic linking of libtool libraries
+ -version-info CURRENT[:REVISION[:AGE]]
+ specify library version info [each variable defaults to 0]
+ -weak LIBNAME declare that the target provides the LIBNAME interface
+
+All other options (arguments beginning with \`-') are ignored.
+
+Every other argument is treated as a filename. Files ending in \`.la' are
+treated as uninstalled libtool libraries, other files are standard or library
+object files.
+
+If the OUTPUT-FILE ends in \`.la', then a libtool library is created,
+only library objects (\`.lo' files) may be specified, and \`-rpath' is
+required, except when creating a convenience library.
+
+If OUTPUT-FILE ends in \`.a' or \`.lib', then a standard library is created
+using \`ar' and \`ranlib', or on Windows using \`lib'.
+
+If OUTPUT-FILE ends in \`.lo' or \`.${objext}', then a reloadable object file
+is created, otherwise an executable program is created."
+ ;;
+
+ uninstall)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=uninstall RM [RM-OPTION]... FILE...
+
+Remove libraries from an installation directory.
+
+RM is the name of the program to use to delete files associated with each FILE
+(typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed
+to RM.
+
+If FILE is a libtool library, all the files associated with it are deleted.
+Otherwise, only FILE itself is deleted using RM."
+ ;;
+
+ *)
+ func_fatal_help "invalid operation mode \`$mode'"
+ ;;
+ esac
+
+ $ECHO
+ $ECHO "Try \`$progname --help' for more information about other modes."
+
+ exit $?
+}
+
+ # Now that we've collected a possible --mode arg, show help if necessary
+ $opt_help && func_mode_help
+
+
+# func_mode_execute arg...
+func_mode_execute ()
+{
+ $opt_debug
+ # The first argument is the command name.
+ cmd="$nonopt"
+ test -z "$cmd" && \
+ func_fatal_help "you must specify a COMMAND"
+
+ # Handle -dlopen flags immediately.
+ for file in $execute_dlfiles; do
+ test -f "$file" \
+ || func_fatal_help "\`$file' is not a file"
+
+ dir=
+ case $file in
+ *.la)
+ # Check to see that this really is a libtool archive.
+ func_lalib_unsafe_p "$file" \
+ || func_fatal_help "\`$lib' is not a valid libtool archive"
+
+ # Read the libtool library.
+ dlname=
+ library_names=
+ func_source "$file"
+
+ # Skip this library if it cannot be dlopened.
+ if test -z "$dlname"; then
+ # Warn if it was a shared library.
+ test -n "$library_names" && \
+ func_warning "\`$file' was not linked with \`-export-dynamic'"
+ continue
+ fi
+
+ func_dirname "$file" "" "."
+ dir="$func_dirname_result"
+
+ if test -f "$dir/$objdir/$dlname"; then
+ dir="$dir/$objdir"
+ else
+ if test ! -f "$dir/$dlname"; then
+ func_fatal_error "cannot find \`$dlname' in \`$dir' or \`$dir/$objdir'"
+ fi
+ fi
+ ;;
+
+ *.lo)
+ # Just add the directory containing the .lo file.
+ func_dirname "$file" "" "."
+ dir="$func_dirname_result"
+ ;;
+
+ *)
+ func_warning "\`-dlopen' is ignored for non-libtool libraries and objects"
+ continue
+ ;;
+ esac
+
+ # Get the absolute pathname.
+ absdir=`cd "$dir" && pwd`
+ test -n "$absdir" && dir="$absdir"
+
+ # Now add the directory to shlibpath_var.
+ if eval "test -z \"\$$shlibpath_var\""; then
+ eval "$shlibpath_var=\"\$dir\""
+ else
+ eval "$shlibpath_var=\"\$dir:\$$shlibpath_var\""
+ fi
+ done
+
+ # This variable tells wrapper scripts just to set shlibpath_var
+ # rather than running their programs.
+ libtool_execute_magic="$magic"
+
+ # Check if any of the arguments is a wrapper script.
+ args=
+ for file
+ do
+ case $file in
+ -*) ;;
+ *)
+ # Do a test to see if this is really a libtool program.
+ if func_ltwrapper_script_p "$file"; then
+ func_source "$file"
+ # Transform arg to wrapped name.
+ file="$progdir/$program"
+ elif func_ltwrapper_executable_p "$file"; then
+ func_ltwrapper_scriptname "$file"
+ func_source "$func_ltwrapper_scriptname_result"
+ # Transform arg to wrapped name.
+ file="$progdir/$program"
+ fi
+ ;;
+ esac
+ # Quote arguments (to preserve shell metacharacters).
+ func_quote_for_eval "$file"
+ args="$args $func_quote_for_eval_result"
+ done
+
+ if test "X$opt_dry_run" = Xfalse; then
+ if test -n "$shlibpath_var"; then
+ # Export the shlibpath_var.
+ eval "export $shlibpath_var"
+ fi
+
+ # Restore saved environment variables
+ for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES
+ do
+ eval "if test \"\${save_$lt_var+set}\" = set; then
+ $lt_var=\$save_$lt_var; export $lt_var
+ else
+ $lt_unset $lt_var
+ fi"
+ done
+
+ # Now prepare to actually exec the command.
+ exec_cmd="\$cmd$args"
+ else
+ # Display what would be done.
+ if test -n "$shlibpath_var"; then
+ eval "\$ECHO \"\$shlibpath_var=\$$shlibpath_var\""
+ $ECHO "export $shlibpath_var"
+ fi
+ $ECHO "$cmd$args"
+ exit $EXIT_SUCCESS
+ fi
+}
+
+test "$mode" = execute && func_mode_execute ${1+"$@"}
+
+
+# func_mode_finish arg...
+func_mode_finish ()
+{
+ $opt_debug
+ libdirs="$nonopt"
+ admincmds=
+
+ if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then
+ for dir
+ do
+ libdirs="$libdirs $dir"
+ done
+
+ for libdir in $libdirs; do
+ if test -n "$finish_cmds"; then
+ # Do each command in the finish commands.
+ func_execute_cmds "$finish_cmds" 'admincmds="$admincmds
+'"$cmd"'"'
+ fi
+ if test -n "$finish_eval"; then
+ # Do the single finish_eval.
+ eval cmds=\"$finish_eval\"
+ $opt_dry_run || eval "$cmds" || admincmds="$admincmds
+ $cmds"
+ fi
+ done
+ fi
+
+ # Exit here if they wanted silent mode.
+ $opt_silent && exit $EXIT_SUCCESS
+
+ $ECHO "X----------------------------------------------------------------------" | $Xsed
+ $ECHO "Libraries have been installed in:"
+ for libdir in $libdirs; do
+ $ECHO " $libdir"
+ done
+ $ECHO
+ $ECHO "If you ever happen to want to link against installed libraries"
+ $ECHO "in a given directory, LIBDIR, you must either use libtool, and"
+ $ECHO "specify the full pathname of the library, or use the \`-LLIBDIR'"
+ $ECHO "flag during linking and do at least one of the following:"
+ if test -n "$shlibpath_var"; then
+ $ECHO " - add LIBDIR to the \`$shlibpath_var' environment variable"
+ $ECHO " during execution"
+ fi
+ if test -n "$runpath_var"; then
+ $ECHO " - add LIBDIR to the \`$runpath_var' environment variable"
+ $ECHO " during linking"
+ fi
+ if test -n "$hardcode_libdir_flag_spec"; then
+ libdir=LIBDIR
+ eval flag=\"$hardcode_libdir_flag_spec\"
+
+ $ECHO " - use the \`$flag' linker flag"
+ fi
+ if test -n "$admincmds"; then
+ $ECHO " - have your system administrator run these commands:$admincmds"
+ fi
+ if test -f /etc/ld.so.conf; then
+ $ECHO " - have your system administrator add LIBDIR to \`/etc/ld.so.conf'"
+ fi
+ $ECHO
+
+ $ECHO "See any operating system documentation about shared libraries for"
+ case $host in
+ solaris2.[6789]|solaris2.1[0-9])
+ $ECHO "more information, such as the ld(1), crle(1) and ld.so(8) manual"
+ $ECHO "pages."
+ ;;
+ *)
+ $ECHO "more information, such as the ld(1) and ld.so(8) manual pages."
+ ;;
+ esac
+ $ECHO "X----------------------------------------------------------------------" | $Xsed
+ exit $EXIT_SUCCESS
+}
+
+test "$mode" = finish && func_mode_finish ${1+"$@"}
+
+
+# func_mode_install arg...
+func_mode_install ()
+{
+ $opt_debug
+ # There may be an optional sh(1) argument at the beginning of
+ # install_prog (especially on Windows NT).
+ if test "$nonopt" = "$SHELL" || test "$nonopt" = /bin/sh ||
+ # Allow the use of GNU shtool's install command.
+ $ECHO "X$nonopt" | $GREP shtool >/dev/null; then
+ # Aesthetically quote it.
+ func_quote_for_eval "$nonopt"
+ install_prog="$func_quote_for_eval_result "
+ arg=$1
+ shift
+ else
+ install_prog=
+ arg=$nonopt
+ fi
+
+ # The real first argument should be the name of the installation program.
+ # Aesthetically quote it.
+ func_quote_for_eval "$arg"
+ install_prog="$install_prog$func_quote_for_eval_result"
+
+ # We need to accept at least all the BSD install flags.
+ dest=
+ files=
+ opts=
+ prev=
+ install_type=
+ isdir=no
+ stripme=
+ for arg
+ do
+ if test -n "$dest"; then
+ files="$files $dest"
+ dest=$arg
+ continue
+ fi
+
+ case $arg in
+ -d) isdir=yes ;;
+ -f)
+ case " $install_prog " in
+ *[\\\ /]cp\ *) ;;
+ *) prev=$arg ;;
+ esac
+ ;;
+ -g | -m | -o)
+ prev=$arg
+ ;;
+ -s)
+ stripme=" -s"
+ continue
+ ;;
+ -*)
+ ;;
+ *)
+ # If the previous option needed an argument, then skip it.
+ if test -n "$prev"; then
+ prev=
+ else
+ dest=$arg
+ continue
+ fi
+ ;;
+ esac
+
+ # Aesthetically quote the argument.
+ func_quote_for_eval "$arg"
+ install_prog="$install_prog $func_quote_for_eval_result"
+ done
+
+ test -z "$install_prog" && \
+ func_fatal_help "you must specify an install program"
+
+ test -n "$prev" && \
+ func_fatal_help "the \`$prev' option requires an argument"
+
+ if test -z "$files"; then
+ if test -z "$dest"; then
+ func_fatal_help "no file or destination specified"
+ else
+ func_fatal_help "you must specify a destination"
+ fi
+ fi
+
+ # Strip any trailing slash from the destination.
+ func_stripname '' '/' "$dest"
+ dest=$func_stripname_result
+
+ # Check to see that the destination is a directory.
+ test -d "$dest" && isdir=yes
+ if test "$isdir" = yes; then
+ destdir="$dest"
+ destname=
+ else
+ func_dirname_and_basename "$dest" "" "."
+ destdir="$func_dirname_result"
+ destname="$func_basename_result"
+
+ # Not a directory, so check to see that there is only one file specified.
+ set dummy $files; shift
+ test "$#" -gt 1 && \
+ func_fatal_help "\`$dest' is not a directory"
+ fi
+ case $destdir in
+ [\\/]* | [A-Za-z]:[\\/]*) ;;
+ *)
+ for file in $files; do
+ case $file in
+ *.lo) ;;
+ *)
+ func_fatal_help "\`$destdir' must be an absolute directory name"
+ ;;
+ esac
+ done
+ ;;
+ esac
+
+ # This variable tells wrapper scripts just to set variables rather
+ # than running their programs.
+ libtool_install_magic="$magic"
+
+ staticlibs=
+ future_libdirs=
+ current_libdirs=
+ for file in $files; do
+
+ # Do each installation.
+ case $file in
+ *.$libext)
+ # Do the static libraries later.
+ staticlibs="$staticlibs $file"
+ ;;
+
+ *.la)
+ # Check to see that this really is a libtool archive.
+ func_lalib_unsafe_p "$file" \
+ || func_fatal_help "\`$file' is not a valid libtool archive"
+
+ library_names=
+ old_library=
+ relink_command=
+ func_source "$file"
+
+ # Add the libdir to current_libdirs if it is the destination.
+ if test "X$destdir" = "X$libdir"; then
+ case "$current_libdirs " in
+ *" $libdir "*) ;;
+ *) current_libdirs="$current_libdirs $libdir" ;;
+ esac
+ else
+ # Note the libdir as a future libdir.
+ case "$future_libdirs " in
+ *" $libdir "*) ;;
+ *) future_libdirs="$future_libdirs $libdir" ;;
+ esac
+ fi
+
+ func_dirname "$file" "/" ""
+ dir="$func_dirname_result"
+ dir="$dir$objdir"
+
+ if test -n "$relink_command"; then
+ # Determine the prefix the user has applied to our future dir.
+ inst_prefix_dir=`$ECHO "X$destdir" | $Xsed -e "s%$libdir\$%%"`
+
+ # Don't allow the user to place us outside of our expected
+ # location b/c this prevents finding dependent libraries that
+ # are installed to the same prefix.
+ # At present, this check doesn't affect windows .dll's that
+ # are installed into $libdir/../bin (currently, that works fine)
+ # but it's something to keep an eye on.
+ test "$inst_prefix_dir" = "$destdir" && \
+ func_fatal_error "error: cannot install \`$file' to a directory not ending in $libdir"
+
+ if test -n "$inst_prefix_dir"; then
+ # Stick the inst_prefix_dir data into the link command.
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%"`
+ else
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%%"`
+ fi
+
+ func_warning "relinking \`$file'"
+ func_show_eval "$relink_command" \
+ 'func_fatal_error "error: relink \`$file'\'' with the above command before installing it"'
+ fi
+
+ # See the names of the shared library.
+ set dummy $library_names; shift
+ if test -n "$1"; then
+ realname="$1"
+ shift
+
+ srcname="$realname"
+ test -n "$relink_command" && srcname="$realname"T
+
+ # Install the shared library and build the symlinks.
+ func_show_eval "$install_prog $dir/$srcname $destdir/$realname" \
+ 'exit $?'
+ tstripme="$stripme"
+ case $host_os in
+ cygwin* | mingw* | pw32* | cegcc*)
+ case $realname in
+ *.dll.a)
+ tstripme=""
+ ;;
+ esac
+ ;;
+ esac
+ if test -n "$tstripme" && test -n "$striplib"; then
+ func_show_eval "$striplib $destdir/$realname" 'exit $?'
+ fi
+
+ if test "$#" -gt 0; then
+ # Delete the old symlinks, and create new ones.
+ # Try `ln -sf' first, because the `ln' binary might depend on
+ # the symlink we replace! Solaris /bin/ln does not understand -f,
+ # so we also need to try rm && ln -s.
+ for linkname
+ do
+ test "$linkname" != "$realname" \
+ && func_show_eval "(cd $destdir && { $LN_S -f $realname $linkname || { $RM $linkname && $LN_S $realname $linkname; }; })"
+ done
+ fi
+
+ # Do each command in the postinstall commands.
+ lib="$destdir/$realname"
+ func_execute_cmds "$postinstall_cmds" 'exit $?'
+ fi
+
+ # Install the pseudo-library for information purposes.
+ func_basename "$file"
+ name="$func_basename_result"
+ instname="$dir/$name"i
+ func_show_eval "$install_prog $instname $destdir/$name" 'exit $?'
+
+ # Maybe install the static library, too.
+ test -n "$old_library" && staticlibs="$staticlibs $dir/$old_library"
+ ;;
+
+ *.lo)
+ # Install (i.e. copy) a libtool object.
+
+ # Figure out destination file name, if it wasn't already specified.
+ if test -n "$destname"; then
+ destfile="$destdir/$destname"
+ else
+ func_basename "$file"
+ destfile="$func_basename_result"
+ destfile="$destdir/$destfile"
+ fi
+
+ # Deduce the name of the destination old-style object file.
+ case $destfile in
+ *.lo)
+ func_lo2o "$destfile"
+ staticdest=$func_lo2o_result
+ ;;
+ *.$objext)
+ staticdest="$destfile"
+ destfile=
+ ;;
+ *)
+ func_fatal_help "cannot copy a libtool object to \`$destfile'"
+ ;;
+ esac
+
+ # Install the libtool object if requested.
+ test -n "$destfile" && \
+ func_show_eval "$install_prog $file $destfile" 'exit $?'
+
+ # Install the old object if enabled.
+ if test "$build_old_libs" = yes; then
+ # Deduce the name of the old-style object file.
+ func_lo2o "$file"
+ staticobj=$func_lo2o_result
+ func_show_eval "$install_prog \$staticobj \$staticdest" 'exit $?'
+ fi
+ exit $EXIT_SUCCESS
+ ;;
+
+ *)
+ # Figure out destination file name, if it wasn't already specified.
+ if test -n "$destname"; then
+ destfile="$destdir/$destname"
+ else
+ func_basename "$file"
+ destfile="$func_basename_result"
+ destfile="$destdir/$destfile"
+ fi
+
+ # If the file is missing, and there is a .exe on the end, strip it
+ # because it is most likely a libtool script we actually want to
+ # install
+ stripped_ext=""
+ case $file in
+ *.exe)
+ if test ! -f "$file"; then
+ func_stripname '' '.exe' "$file"
+ file=$func_stripname_result
+ stripped_ext=".exe"
+ fi
+ ;;
+ esac
+
+ # Do a test to see if this is really a libtool program.
+ case $host in
+ *cygwin* | *mingw*)
+ if func_ltwrapper_executable_p "$file"; then
+ func_ltwrapper_scriptname "$file"
+ wrapper=$func_ltwrapper_scriptname_result
+ else
+ func_stripname '' '.exe' "$file"
+ wrapper=$func_stripname_result
+ fi
+ ;;
+ *)
+ wrapper=$file
+ ;;
+ esac
+ if func_ltwrapper_script_p "$wrapper"; then
+ notinst_deplibs=
+ relink_command=
+
+ func_source "$wrapper"
+
+ # Check the variables that should have been set.
+ test -z "$generated_by_libtool_version" && \
+ func_fatal_error "invalid libtool wrapper script \`$wrapper'"
+
+ finalize=yes
+ for lib in $notinst_deplibs; do
+ # Check to see that each library is installed.
+ libdir=
+ if test -f "$lib"; then
+ func_source "$lib"
+ fi
+ libfile="$libdir/"`$ECHO "X$lib" | $Xsed -e 's%^.*/%%g'` ### testsuite: skip nested quoting test
+ if test -n "$libdir" && test ! -f "$libfile"; then
+ func_warning "\`$lib' has not been installed in \`$libdir'"
+ finalize=no
+ fi
+ done
+
+ relink_command=
+ func_source "$wrapper"
+
+ outputname=
+ if test "$fast_install" = no && test -n "$relink_command"; then
+ $opt_dry_run || {
+ if test "$finalize" = yes; then
+ tmpdir=`func_mktempdir`
+ func_basename "$file$stripped_ext"
+ file="$func_basename_result"
+ outputname="$tmpdir/$file"
+ # Replace the output file specification.
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e 's%@OUTPUT@%'"$outputname"'%g'`
+
+ $opt_silent || {
+ func_quote_for_expand "$relink_command"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+ if eval "$relink_command"; then :
+ else
+ func_error "error: relink \`$file' with the above command before installing it"
+ $opt_dry_run || ${RM}r "$tmpdir"
+ continue
+ fi
+ file="$outputname"
+ else
+ func_warning "cannot relink \`$file'"
+ fi
+ }
+ else
+ # Install the binary that we compiled earlier.
+ file=`$ECHO "X$file$stripped_ext" | $Xsed -e "s%\([^/]*\)$%$objdir/\1%"`
+ fi
+ fi
+
+ # remove .exe since cygwin /usr/bin/install will append another
+ # one anyway
+ case $install_prog,$host in
+ */usr/bin/install*,*cygwin*)
+ case $file:$destfile in
+ *.exe:*.exe)
+ # this is ok
+ ;;
+ *.exe:*)
+ destfile=$destfile.exe
+ ;;
+ *:*.exe)
+ func_stripname '' '.exe' "$destfile"
+ destfile=$func_stripname_result
+ ;;
+ esac
+ ;;
+ esac
+ func_show_eval "$install_prog\$stripme \$file \$destfile" 'exit $?'
+ $opt_dry_run || if test -n "$outputname"; then
+ ${RM}r "$tmpdir"
+ fi
+ ;;
+ esac
+ done
+
+ for file in $staticlibs; do
+ func_basename "$file"
+ name="$func_basename_result"
+
+ # Set up the ranlib parameters.
+ oldlib="$destdir/$name"
+
+ func_show_eval "$install_prog \$file \$oldlib" 'exit $?'
+
+ if test -n "$stripme" && test -n "$old_striplib"; then
+ func_show_eval "$old_striplib $oldlib" 'exit $?'
+ fi
+
+ # Do each command in the postinstall commands.
+ func_execute_cmds "$old_postinstall_cmds" 'exit $?'
+ done
+
+ test -n "$future_libdirs" && \
+ func_warning "remember to run \`$progname --finish$future_libdirs'"
+
+ if test -n "$current_libdirs"; then
+ # Maybe just do a dry run.
+ $opt_dry_run && current_libdirs=" -n$current_libdirs"
+ exec_cmd='$SHELL $progpath $preserve_args --finish$current_libdirs'
+ else
+ exit $EXIT_SUCCESS
+ fi
+}
+
+test "$mode" = install && func_mode_install ${1+"$@"}
+
+
+# func_generate_dlsyms outputname originator pic_p
+# Extract symbols from dlprefiles and create ${outputname}S.o with
+# a dlpreopen symbol table.
+func_generate_dlsyms ()
+{
+ $opt_debug
+ my_outputname="$1"
+ my_originator="$2"
+ my_pic_p="${3-no}"
+ my_prefix=`$ECHO "$my_originator" | sed 's%[^a-zA-Z0-9]%_%g'`
+ my_dlsyms=
+
+ if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
+ if test -n "$NM" && test -n "$global_symbol_pipe"; then
+ my_dlsyms="${my_outputname}S.c"
+ else
+ func_error "not configured to extract global symbols from dlpreopened files"
+ fi
+ fi
+
+ if test -n "$my_dlsyms"; then
+ case $my_dlsyms in
+ "") ;;
+ *.c)
+ # Discover the nlist of each of the dlfiles.
+ nlist="$output_objdir/${my_outputname}.nm"
+
+ func_show_eval "$RM $nlist ${nlist}S ${nlist}T"
+
+ # Parse the name list into a source file.
+ func_verbose "creating $output_objdir/$my_dlsyms"
+
+ $opt_dry_run || $ECHO > "$output_objdir/$my_dlsyms" "\
+/* $my_dlsyms - symbol resolution table for \`$my_outputname' dlsym emulation. */
+/* Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION */
+
+#ifdef __cplusplus
+extern \"C\" {
+#endif
+
+/* External symbol declarations for the compiler. */\
+"
+
+ if test "$dlself" = yes; then
+ func_verbose "generating symbol list for \`$output'"
+
+ $opt_dry_run || echo ': @PROGRAM@ ' > "$nlist"
+
+ # Add our own program objects to the symbol list.
+ progfiles=`$ECHO "X$objs$old_deplibs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+ for progfile in $progfiles; do
+ func_verbose "extracting global C symbols from \`$progfile'"
+ $opt_dry_run || eval "$NM $progfile | $global_symbol_pipe >> '$nlist'"
+ done
+
+ if test -n "$exclude_expsyms"; then
+ $opt_dry_run || {
+ eval '$EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T'
+ eval '$MV "$nlist"T "$nlist"'
+ }
+ fi
+
+ if test -n "$export_symbols_regex"; then
+ $opt_dry_run || {
+ eval '$EGREP -e "$export_symbols_regex" "$nlist" > "$nlist"T'
+ eval '$MV "$nlist"T "$nlist"'
+ }
+ fi
+
+ # Prepare the list of exported symbols
+ if test -z "$export_symbols"; then
+ export_symbols="$output_objdir/$outputname.exp"
+ $opt_dry_run || {
+ $RM $export_symbols
+ eval "${SED} -n -e '/^: @PROGRAM@ $/d' -e 's/^.* \(.*\)$/\1/p' "'< "$nlist" > "$export_symbols"'
+ case $host in
+ *cygwin* | *mingw* | *cegcc* )
+ eval "echo EXPORTS "'> "$output_objdir/$outputname.def"'
+ eval 'cat "$export_symbols" >> "$output_objdir/$outputname.def"'
+ ;;
+ esac
+ }
+ else
+ $opt_dry_run || {
+ eval "${SED} -e 's/\([].[*^$]\)/\\\\\1/g' -e 's/^/ /' -e 's/$/$/'"' < "$export_symbols" > "$output_objdir/$outputname.exp"'
+ eval '$GREP -f "$output_objdir/$outputname.exp" < "$nlist" > "$nlist"T'
+ eval '$MV "$nlist"T "$nlist"'
+ case $host in
+ *cygwin | *mingw* | *cegcc* )
+ eval "echo EXPORTS "'> "$output_objdir/$outputname.def"'
+ eval 'cat "$nlist" >> "$output_objdir/$outputname.def"'
+ ;;
+ esac
+ }
+ fi
+ fi
+
+ for dlprefile in $dlprefiles; do
+ func_verbose "extracting global C symbols from \`$dlprefile'"
+ func_basename "$dlprefile"
+ name="$func_basename_result"
+ $opt_dry_run || {
+ eval '$ECHO ": $name " >> "$nlist"'
+ eval "$NM $dlprefile 2>/dev/null | $global_symbol_pipe >> '$nlist'"
+ }
+ done
+
+ $opt_dry_run || {
+ # Make sure we have at least an empty file.
+ test -f "$nlist" || : > "$nlist"
+
+ if test -n "$exclude_expsyms"; then
+ $EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T
+ $MV "$nlist"T "$nlist"
+ fi
+
+ # Try sorting and uniquifying the output.
+ if $GREP -v "^: " < "$nlist" |
+ if sort -k 3 </dev/null >/dev/null 2>&1; then
+ sort -k 3
+ else
+ sort +2
+ fi |
+ uniq > "$nlist"S; then
+ :
+ else
+ $GREP -v "^: " < "$nlist" > "$nlist"S
+ fi
+
+ if test -f "$nlist"S; then
+ eval "$global_symbol_to_cdecl"' < "$nlist"S >> "$output_objdir/$my_dlsyms"'
+ else
+ $ECHO '/* NONE */' >> "$output_objdir/$my_dlsyms"
+ fi
+
+ $ECHO >> "$output_objdir/$my_dlsyms" "\
+
+/* The mapping between symbol names and symbols. */
+typedef struct {
+ const char *name;
+ void *address;
+} lt_dlsymlist;
+"
+ case $host in
+ *cygwin* | *mingw* | *cegcc* )
+ $ECHO >> "$output_objdir/$my_dlsyms" "\
+/* DATA imports from DLLs on WIN32 con't be const, because
+ runtime relocations are performed -- see ld's documentation
+ on pseudo-relocs. */"
+ lt_dlsym_const= ;;
+ *osf5*)
+ echo >> "$output_objdir/$my_dlsyms" "\
+/* This system does not cope well with relocations in const data */"
+ lt_dlsym_const= ;;
+ *)
+ lt_dlsym_const=const ;;
+ esac
+
+ $ECHO >> "$output_objdir/$my_dlsyms" "\
+extern $lt_dlsym_const lt_dlsymlist
+lt_${my_prefix}_LTX_preloaded_symbols[];
+$lt_dlsym_const lt_dlsymlist
+lt_${my_prefix}_LTX_preloaded_symbols[] =
+{\
+ { \"$my_originator\", (void *) 0 },"
+
+ case $need_lib_prefix in
+ no)
+ eval "$global_symbol_to_c_name_address" < "$nlist" >> "$output_objdir/$my_dlsyms"
+ ;;
+ *)
+ eval "$global_symbol_to_c_name_address_lib_prefix" < "$nlist" >> "$output_objdir/$my_dlsyms"
+ ;;
+ esac
+ $ECHO >> "$output_objdir/$my_dlsyms" "\
+ {0, (void *) 0}
+};
+
+/* This works around a problem in FreeBSD linker */
+#ifdef FREEBSD_WORKAROUND
+static const void *lt_preloaded_setup() {
+ return lt_${my_prefix}_LTX_preloaded_symbols;
+}
+#endif
+
+#ifdef __cplusplus
+}
+#endif\
+"
+ } # !$opt_dry_run
+
+ pic_flag_for_symtable=
+ case "$compile_command " in
+ *" -static "*) ;;
+ *)
+ case $host in
+ # compiling the symbol table file with pic_flag works around
+ # a FreeBSD bug that causes programs to crash when -lm is
+ # linked before any other PIC object. But we must not use
+ # pic_flag when linking with -static. The problem exists in
+ # FreeBSD 2.2.6 and is fixed in FreeBSD 3.1.
+ *-*-freebsd2*|*-*-freebsd3.0*|*-*-freebsdelf3.0*)
+ pic_flag_for_symtable=" $pic_flag -DFREEBSD_WORKAROUND" ;;
+ *-*-hpux*)
+ pic_flag_for_symtable=" $pic_flag" ;;
+ *)
+ if test "X$my_pic_p" != Xno; then
+ pic_flag_for_symtable=" $pic_flag"
+ fi
+ ;;
+ esac
+ ;;
+ esac
+ symtab_cflags=
+ for arg in $LTCFLAGS; do
+ case $arg in
+ -pie | -fpie | -fPIE) ;;
+ *) symtab_cflags="$symtab_cflags $arg" ;;
+ esac
+ done
+
+ # Now compile the dynamic symbol file.
+ func_show_eval '(cd $output_objdir && $LTCC$symtab_cflags -c$no_builtin_flag$pic_flag_for_symtable "$my_dlsyms")' 'exit $?'
+
+ # Clean up the generated files.
+ func_show_eval '$RM "$output_objdir/$my_dlsyms" "$nlist" "${nlist}S" "${nlist}T"'
+
+ # Transform the symbol file into the correct name.
+ symfileobj="$output_objdir/${my_outputname}S.$objext"
+ case $host in
+ *cygwin* | *mingw* | *cegcc* )
+ if test -f "$output_objdir/$my_outputname.def"; then
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"`
+ finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"`
+ else
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"`
+ finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"`
+ fi
+ ;;
+ *)
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"`
+ finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"`
+ ;;
+ esac
+ ;;
+ *)
+ func_fatal_error "unknown suffix for \`$my_dlsyms'"
+ ;;
+ esac
+ else
+ # We keep going just in case the user didn't refer to
+ # lt_preloaded_symbols. The linker will fail if global_symbol_pipe
+ # really was required.
+
+ # Nullify the symbol file.
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e "s% @SYMFILE@%%"`
+ finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s% @SYMFILE@%%"`
+ fi
+}
+
+# func_win32_libid arg
+# return the library type of file 'arg'
+#
+# Need a lot of goo to handle *both* DLLs and import libs
+# Has to be a shell function in order to 'eat' the argument
+# that is supplied when $file_magic_command is called.
+func_win32_libid ()
+{
+ $opt_debug
+ win32_libid_type="unknown"
+ win32_fileres=`file -L $1 2>/dev/null`
+ case $win32_fileres in
+ *ar\ archive\ import\ library*) # definitely import
+ win32_libid_type="x86 archive import"
+ ;;
+ *ar\ archive*) # could be an import, or static
+ if eval $OBJDUMP -f $1 | $SED -e '10q' 2>/dev/null |
+ $EGREP 'file format pe-i386(.*architecture: i386)?' >/dev/null ; then
+ win32_nmres=`eval $NM -f posix -A $1 |
+ $SED -n -e '
+ 1,100{
+ / I /{
+ s,.*,import,
+ p
+ q
+ }
+ }'`
+ case $win32_nmres in
+ import*) win32_libid_type="x86 archive import";;
+ *) win32_libid_type="x86 archive static";;
+ esac
+ fi
+ ;;
+ *DLL*)
+ win32_libid_type="x86 DLL"
+ ;;
+ *executable*) # but shell scripts are "executable" too...
+ case $win32_fileres in
+ *MS\ Windows\ PE\ Intel*)
+ win32_libid_type="x86 DLL"
+ ;;
+ esac
+ ;;
+ esac
+ $ECHO "$win32_libid_type"
+}
+
+
+
+# func_extract_an_archive dir oldlib
+func_extract_an_archive ()
+{
+ $opt_debug
+ f_ex_an_ar_dir="$1"; shift
+ f_ex_an_ar_oldlib="$1"
+ func_show_eval "(cd \$f_ex_an_ar_dir && $AR x \"\$f_ex_an_ar_oldlib\")" 'exit $?'
+ if ($AR t "$f_ex_an_ar_oldlib" | sort | sort -uc >/dev/null 2>&1); then
+ :
+ else
+ func_fatal_error "object name conflicts in archive: $f_ex_an_ar_dir/$f_ex_an_ar_oldlib"
+ fi
+}
+
+
+# func_extract_archives gentop oldlib ...
+func_extract_archives ()
+{
+ $opt_debug
+ my_gentop="$1"; shift
+ my_oldlibs=${1+"$@"}
+ my_oldobjs=""
+ my_xlib=""
+ my_xabs=""
+ my_xdir=""
+
+ for my_xlib in $my_oldlibs; do
+ # Extract the objects.
+ case $my_xlib in
+ [\\/]* | [A-Za-z]:[\\/]*) my_xabs="$my_xlib" ;;
+ *) my_xabs=`pwd`"/$my_xlib" ;;
+ esac
+ func_basename "$my_xlib"
+ my_xlib="$func_basename_result"
+ my_xlib_u=$my_xlib
+ while :; do
+ case " $extracted_archives " in
+ *" $my_xlib_u "*)
+ func_arith $extracted_serial + 1
+ extracted_serial=$func_arith_result
+ my_xlib_u=lt$extracted_serial-$my_xlib ;;
+ *) break ;;
+ esac
+ done
+ extracted_archives="$extracted_archives $my_xlib_u"
+ my_xdir="$my_gentop/$my_xlib_u"
+
+ func_mkdir_p "$my_xdir"
+
+ case $host in
+ *-darwin*)
+ func_verbose "Extracting $my_xabs"
+ # Do not bother doing anything if just a dry run
+ $opt_dry_run || {
+ darwin_orig_dir=`pwd`
+ cd $my_xdir || exit $?
+ darwin_archive=$my_xabs
+ darwin_curdir=`pwd`
+ darwin_base_archive=`basename "$darwin_archive"`
+ darwin_arches=`$LIPO -info "$darwin_archive" 2>/dev/null | $GREP Architectures 2>/dev/null || true`
+ if test -n "$darwin_arches"; then
+ darwin_arches=`$ECHO "$darwin_arches" | $SED -e 's/.*are://'`
+ darwin_arch=
+ func_verbose "$darwin_base_archive has multiple architectures $darwin_arches"
+ for darwin_arch in $darwin_arches ; do
+ func_mkdir_p "unfat-$$/${darwin_base_archive}-${darwin_arch}"
+ $LIPO -thin $darwin_arch -output "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" "${darwin_archive}"
+ cd "unfat-$$/${darwin_base_archive}-${darwin_arch}"
+ func_extract_an_archive "`pwd`" "${darwin_base_archive}"
+ cd "$darwin_curdir"
+ $RM "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}"
+ done # $darwin_arches
+ ## Okay now we've a bunch of thin objects, gotta fatten them up :)
+ darwin_filelist=`find unfat-$$ -type f -name \*.o -print -o -name \*.lo -print | $SED -e "$basename" | sort -u`
+ darwin_file=
+ darwin_files=
+ for darwin_file in $darwin_filelist; do
+ darwin_files=`find unfat-$$ -name $darwin_file -print | $NL2SP`
+ $LIPO -create -output "$darwin_file" $darwin_files
+ done # $darwin_filelist
+ $RM -rf unfat-$$
+ cd "$darwin_orig_dir"
+ else
+ cd $darwin_orig_dir
+ func_extract_an_archive "$my_xdir" "$my_xabs"
+ fi # $darwin_arches
+ } # !$opt_dry_run
+ ;;
+ *)
+ func_extract_an_archive "$my_xdir" "$my_xabs"
+ ;;
+ esac
+ my_oldobjs="$my_oldobjs "`find $my_xdir -name \*.$objext -print -o -name \*.lo -print | $NL2SP`
+ done
+
+ func_extract_archives_result="$my_oldobjs"
+}
+
+
+
+# func_emit_wrapper_part1 [arg=no]
+#
+# Emit the first part of a libtool wrapper script on stdout.
+# For more information, see the description associated with
+# func_emit_wrapper(), below.
+func_emit_wrapper_part1 ()
+{
+ func_emit_wrapper_part1_arg1=no
+ if test -n "$1" ; then
+ func_emit_wrapper_part1_arg1=$1
+ fi
+
+ $ECHO "\
+#! $SHELL
+
+# $output - temporary wrapper script for $objdir/$outputname
+# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
+#
+# The $output program cannot be directly executed until all the libtool
+# libraries that it depends on are installed.
+#
+# This wrapper script should never be moved out of the build directory.
+# If it is, it will not operate correctly.
+
+# Sed substitution that helps us do robust quoting. It backslashifies
+# metacharacters that are still active within double-quoted strings.
+Xsed='${SED} -e 1s/^X//'
+sed_quote_subst='$sed_quote_subst'
+
+# Be Bourne compatible
+if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Zsh 3.x and 4.x performs word splitting on \${1+\"\$@\"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '\${1+\"\$@\"}'='\"\$@\"'
+ setopt NO_GLOB_SUBST
+else
+ case \`(set -o) 2>/dev/null\` in *posix*) set -o posix;; esac
+fi
+BIN_SH=xpg4; export BIN_SH # for Tru64
+DUALCASE=1; export DUALCASE # for MKS sh
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+relink_command=\"$relink_command\"
+
+# This environment variable determines our operation mode.
+if test \"\$libtool_install_magic\" = \"$magic\"; then
+ # install mode needs the following variables:
+ generated_by_libtool_version='$macro_version'
+ notinst_deplibs='$notinst_deplibs'
+else
+ # When we are sourced in execute mode, \$file and \$ECHO are already set.
+ if test \"\$libtool_execute_magic\" != \"$magic\"; then
+ ECHO=\"$qecho\"
+ file=\"\$0\"
+ # Make sure echo works.
+ if test \"X\$1\" = X--no-reexec; then
+ # Discard the --no-reexec flag, and continue.
+ shift
+ elif test \"X\`{ \$ECHO '\t'; } 2>/dev/null\`\" = 'X\t'; then
+ # Yippee, \$ECHO works!
+ :
+ else
+ # Restart under the correct shell, and then maybe \$ECHO will work.
+ exec $SHELL \"\$0\" --no-reexec \${1+\"\$@\"}
+ fi
+ fi\
+"
+ $ECHO "\
+
+ # Find the directory that this script lives in.
+ thisdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*$%%'\`
+ test \"x\$thisdir\" = \"x\$file\" && thisdir=.
+
+ # Follow symbolic links until we get to the real thisdir.
+ file=\`ls -ld \"\$file\" | ${SED} -n 's/.*-> //p'\`
+ while test -n \"\$file\"; do
+ destdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*\$%%'\`
+
+ # If there was a directory component, then change thisdir.
+ if test \"x\$destdir\" != \"x\$file\"; then
+ case \"\$destdir\" in
+ [\\\\/]* | [A-Za-z]:[\\\\/]*) thisdir=\"\$destdir\" ;;
+ *) thisdir=\"\$thisdir/\$destdir\" ;;
+ esac
+ fi
+
+ file=\`\$ECHO \"X\$file\" | \$Xsed -e 's%^.*/%%'\`
+ file=\`ls -ld \"\$thisdir/\$file\" | ${SED} -n 's/.*-> //p'\`
+ done
+"
+}
+# end: func_emit_wrapper_part1
+
+# func_emit_wrapper_part2 [arg=no]
+#
+# Emit the second part of a libtool wrapper script on stdout.
+# For more information, see the description associated with
+# func_emit_wrapper(), below.
+func_emit_wrapper_part2 ()
+{
+ func_emit_wrapper_part2_arg1=no
+ if test -n "$1" ; then
+ func_emit_wrapper_part2_arg1=$1
+ fi
+
+ $ECHO "\
+
+ # Usually 'no', except on cygwin/mingw when embedded into
+ # the cwrapper.
+ WRAPPER_SCRIPT_BELONGS_IN_OBJDIR=$func_emit_wrapper_part2_arg1
+ if test \"\$WRAPPER_SCRIPT_BELONGS_IN_OBJDIR\" = \"yes\"; then
+ # special case for '.'
+ if test \"\$thisdir\" = \".\"; then
+ thisdir=\`pwd\`
+ fi
+ # remove .libs from thisdir
+ case \"\$thisdir\" in
+ *[\\\\/]$objdir ) thisdir=\`\$ECHO \"X\$thisdir\" | \$Xsed -e 's%[\\\\/][^\\\\/]*$%%'\` ;;
+ $objdir ) thisdir=. ;;
+ esac
+ fi
+
+ # Try to get the absolute directory name.
+ absdir=\`cd \"\$thisdir\" && pwd\`
+ test -n \"\$absdir\" && thisdir=\"\$absdir\"
+"
+
+ if test "$fast_install" = yes; then
+ $ECHO "\
+ program=lt-'$outputname'$exeext
+ progdir=\"\$thisdir/$objdir\"
+
+ if test ! -f \"\$progdir/\$program\" ||
+ { file=\`ls -1dt \"\$progdir/\$program\" \"\$progdir/../\$program\" 2>/dev/null | ${SED} 1q\`; \\
+ test \"X\$file\" != \"X\$progdir/\$program\"; }; then
+
+ file=\"\$\$-\$program\"
+
+ if test ! -d \"\$progdir\"; then
+ $MKDIR \"\$progdir\"
+ else
+ $RM \"\$progdir/\$file\"
+ fi"
+
+ $ECHO "\
+
+ # relink executable if necessary
+ if test -n \"\$relink_command\"; then
+ if relink_command_output=\`eval \$relink_command 2>&1\`; then :
+ else
+ $ECHO \"\$relink_command_output\" >&2
+ $RM \"\$progdir/\$file\"
+ exit 1
+ fi
+ fi
+
+ $MV \"\$progdir/\$file\" \"\$progdir/\$program\" 2>/dev/null ||
+ { $RM \"\$progdir/\$program\";
+ $MV \"\$progdir/\$file\" \"\$progdir/\$program\"; }
+ $RM \"\$progdir/\$file\"
+ fi"
+ else
+ $ECHO "\
+ program='$outputname'
+ progdir=\"\$thisdir/$objdir\"
+"
+ fi
+
+ $ECHO "\
+
+ if test -f \"\$progdir/\$program\"; then"
+
+ # Export our shlibpath_var if we have one.
+ if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then
+ $ECHO "\
+ # Add our own library path to $shlibpath_var
+ $shlibpath_var=\"$temp_rpath\$$shlibpath_var\"
+
+ # Some systems cannot cope with colon-terminated $shlibpath_var
+ # The second colon is a workaround for a bug in BeOS R4 sed
+ $shlibpath_var=\`\$ECHO \"X\$$shlibpath_var\" | \$Xsed -e 's/::*\$//'\`
+
+ export $shlibpath_var
+"
+ fi
+
+ # fixup the dll searchpath if we need to.
+ if test -n "$dllsearchpath"; then
+ $ECHO "\
+ # Add the dll search path components to the executable PATH
+ PATH=$dllsearchpath:\$PATH
+"
+ fi
+
+ $ECHO "\
+ if test \"\$libtool_execute_magic\" != \"$magic\"; then
+ # Run the actual program with our arguments.
+"
+ case $host in
+ # Backslashes separate directories on plain windows
+ *-*-mingw | *-*-os2* | *-cegcc*)
+ $ECHO "\
+ exec \"\$progdir\\\\\$program\" \${1+\"\$@\"}
+"
+ ;;
+
+ *)
+ $ECHO "\
+ exec \"\$progdir/\$program\" \${1+\"\$@\"}
+"
+ ;;
+ esac
+ $ECHO "\
+ \$ECHO \"\$0: cannot exec \$program \$*\" 1>&2
+ exit 1
+ fi
+ else
+ # The program doesn't exist.
+ \$ECHO \"\$0: error: \\\`\$progdir/\$program' does not exist\" 1>&2
+ \$ECHO \"This script is just a wrapper for \$program.\" 1>&2
+ $ECHO \"See the $PACKAGE documentation for more information.\" 1>&2
+ exit 1
+ fi
+fi\
+"
+}
+# end: func_emit_wrapper_part2
+
+
+# func_emit_wrapper [arg=no]
+#
+# Emit a libtool wrapper script on stdout.
+# Don't directly open a file because we may want to
+# incorporate the script contents within a cygwin/mingw
+# wrapper executable. Must ONLY be called from within
+# func_mode_link because it depends on a number of variables
+# set therein.
+#
+# ARG is the value that the WRAPPER_SCRIPT_BELONGS_IN_OBJDIR
+# variable will take. If 'yes', then the emitted script
+# will assume that the directory in which it is stored is
+# the $objdir directory. This is a cygwin/mingw-specific
+# behavior.
+func_emit_wrapper ()
+{
+ func_emit_wrapper_arg1=no
+ if test -n "$1" ; then
+ func_emit_wrapper_arg1=$1
+ fi
+
+ # split this up so that func_emit_cwrapperexe_src
+ # can call each part independently.
+ func_emit_wrapper_part1 "${func_emit_wrapper_arg1}"
+ func_emit_wrapper_part2 "${func_emit_wrapper_arg1}"
+}
+
+
+# func_to_host_path arg
+#
+# Convert paths to host format when used with build tools.
+# Intended for use with "native" mingw (where libtool itself
+# is running under the msys shell), or in the following cross-
+# build environments:
+# $build $host
+# mingw (msys) mingw [e.g. native]
+# cygwin mingw
+# *nix + wine mingw
+# where wine is equipped with the `winepath' executable.
+# In the native mingw case, the (msys) shell automatically
+# converts paths for any non-msys applications it launches,
+# but that facility isn't available from inside the cwrapper.
+# Similar accommodations are necessary for $host mingw and
+# $build cygwin. Calling this function does no harm for other
+# $host/$build combinations not listed above.
+#
+# ARG is the path (on $build) that should be converted to
+# the proper representation for $host. The result is stored
+# in $func_to_host_path_result.
+func_to_host_path ()
+{
+ func_to_host_path_result="$1"
+ if test -n "$1" ; then
+ case $host in
+ *mingw* )
+ lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g'
+ case $build in
+ *mingw* ) # actually, msys
+ # awkward: cmd appends spaces to result
+ lt_sed_strip_trailing_spaces="s/[ ]*\$//"
+ func_to_host_path_tmp1=`( cmd //c echo "$1" |\
+ $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""`
+ func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ ;;
+ *cygwin* )
+ func_to_host_path_tmp1=`cygpath -w "$1"`
+ func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ ;;
+ * )
+ # Unfortunately, winepath does not exit with a non-zero
+ # error code, so we are forced to check the contents of
+ # stdout. On the other hand, if the command is not
+ # found, the shell will set an exit code of 127 and print
+ # *an error message* to stdout. So we must check for both
+ # error code of zero AND non-empty stdout, which explains
+ # the odd construction:
+ func_to_host_path_tmp1=`winepath -w "$1" 2>/dev/null`
+ if test "$?" -eq 0 && test -n "${func_to_host_path_tmp1}"; then
+ func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ else
+ # Allow warning below.
+ func_to_host_path_result=""
+ fi
+ ;;
+ esac
+ if test -z "$func_to_host_path_result" ; then
+ func_error "Could not determine host path corresponding to"
+ func_error " '$1'"
+ func_error "Continuing, but uninstalled executables may not work."
+ # Fallback:
+ func_to_host_path_result="$1"
+ fi
+ ;;
+ esac
+ fi
+}
+# end: func_to_host_path
+
+# func_to_host_pathlist arg
+#
+# Convert pathlists to host format when used with build tools.
+# See func_to_host_path(), above. This function supports the
+# following $build/$host combinations (but does no harm for
+# combinations not listed here):
+# $build $host
+# mingw (msys) mingw [e.g. native]
+# cygwin mingw
+# *nix + wine mingw
+#
+# Path separators are also converted from $build format to
+# $host format. If ARG begins or ends with a path separator
+# character, it is preserved (but converted to $host format)
+# on output.
+#
+# ARG is a pathlist (on $build) that should be converted to
+# the proper representation on $host. The result is stored
+# in $func_to_host_pathlist_result.
+func_to_host_pathlist ()
+{
+ func_to_host_pathlist_result="$1"
+ if test -n "$1" ; then
+ case $host in
+ *mingw* )
+ lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g'
+ # Remove leading and trailing path separator characters from
+ # ARG. msys behavior is inconsistent here, cygpath turns them
+ # into '.;' and ';.', and winepath ignores them completely.
+ func_to_host_pathlist_tmp2="$1"
+ # Once set for this call, this variable should not be
+ # reassigned. It is used in tha fallback case.
+ func_to_host_pathlist_tmp1=`echo "$func_to_host_pathlist_tmp2" |\
+ $SED -e 's|^:*||' -e 's|:*$||'`
+ case $build in
+ *mingw* ) # Actually, msys.
+ # Awkward: cmd appends spaces to result.
+ lt_sed_strip_trailing_spaces="s/[ ]*\$//"
+ func_to_host_pathlist_tmp2=`( cmd //c echo "$func_to_host_pathlist_tmp1" |\
+ $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""`
+ func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ ;;
+ *cygwin* )
+ func_to_host_pathlist_tmp2=`cygpath -w -p "$func_to_host_pathlist_tmp1"`
+ func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ ;;
+ * )
+ # unfortunately, winepath doesn't convert pathlists
+ func_to_host_pathlist_result=""
+ func_to_host_pathlist_oldIFS=$IFS
+ IFS=:
+ for func_to_host_pathlist_f in $func_to_host_pathlist_tmp1 ; do
+ IFS=$func_to_host_pathlist_oldIFS
+ if test -n "$func_to_host_pathlist_f" ; then
+ func_to_host_path "$func_to_host_pathlist_f"
+ if test -n "$func_to_host_path_result" ; then
+ if test -z "$func_to_host_pathlist_result" ; then
+ func_to_host_pathlist_result="$func_to_host_path_result"
+ else
+ func_to_host_pathlist_result="$func_to_host_pathlist_result;$func_to_host_path_result"
+ fi
+ fi
+ fi
+ IFS=:
+ done
+ IFS=$func_to_host_pathlist_oldIFS
+ ;;
+ esac
+ if test -z "$func_to_host_pathlist_result" ; then
+ func_error "Could not determine the host path(s) corresponding to"
+ func_error " '$1'"
+ func_error "Continuing, but uninstalled executables may not work."
+ # Fallback. This may break if $1 contains DOS-style drive
+ # specifications. The fix is not to complicate the expression
+ # below, but for the user to provide a working wine installation
+ # with winepath so that path translation in the cross-to-mingw
+ # case works properly.
+ lt_replace_pathsep_nix_to_dos="s|:|;|g"
+ func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp1" |\
+ $SED -e "$lt_replace_pathsep_nix_to_dos"`
+ fi
+ # Now, add the leading and trailing path separators back
+ case "$1" in
+ :* ) func_to_host_pathlist_result=";$func_to_host_pathlist_result"
+ ;;
+ esac
+ case "$1" in
+ *: ) func_to_host_pathlist_result="$func_to_host_pathlist_result;"
+ ;;
+ esac
+ ;;
+ esac
+ fi
+}
+# end: func_to_host_pathlist
+
+# func_emit_cwrapperexe_src
+# emit the source code for a wrapper executable on stdout
+# Must ONLY be called from within func_mode_link because
+# it depends on a number of variable set therein.
+func_emit_cwrapperexe_src ()
+{
+ cat <<EOF
+
+/* $cwrappersource - temporary wrapper executable for $objdir/$outputname
+ Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
+
+ The $output program cannot be directly executed until all the libtool
+ libraries that it depends on are installed.
+
+ This wrapper executable should never be moved out of the build directory.
+ If it is, it will not operate correctly.
+
+ Currently, it simply execs the wrapper *script* "$SHELL $output",
+ but could eventually absorb all of the scripts functionality and
+ exec $objdir/$outputname directly.
+*/
+EOF
+ cat <<"EOF"
+#include <stdio.h>
+#include <stdlib.h>
+#ifdef _MSC_VER
+# include <direct.h>
+# include <process.h>
+# include <io.h>
+# define setmode _setmode
+#else
+# include <unistd.h>
+# include <stdint.h>
+# ifdef __CYGWIN__
+# include <io.h>
+# define HAVE_SETENV
+# ifdef __STRICT_ANSI__
+char *realpath (const char *, char *);
+int putenv (char *);
+int setenv (const char *, const char *, int);
+# endif
+# endif
+#endif
+#include <malloc.h>
+#include <stdarg.h>
+#include <assert.h>
+#include <string.h>
+#include <ctype.h>
+#include <errno.h>
+#include <fcntl.h>
+#include <sys/stat.h>
+
+#if defined(PATH_MAX)
+# define LT_PATHMAX PATH_MAX
+#elif defined(MAXPATHLEN)
+# define LT_PATHMAX MAXPATHLEN
+#else
+# define LT_PATHMAX 1024
+#endif
+
+#ifndef S_IXOTH
+# define S_IXOTH 0
+#endif
+#ifndef S_IXGRP
+# define S_IXGRP 0
+#endif
+
+#ifdef _MSC_VER
+# define S_IXUSR _S_IEXEC
+# define stat _stat
+# ifndef _INTPTR_T_DEFINED
+# define intptr_t int
+# endif
+#endif
+
+#ifndef DIR_SEPARATOR
+# define DIR_SEPARATOR '/'
+# define PATH_SEPARATOR ':'
+#endif
+
+#if defined (_WIN32) || defined (__MSDOS__) || defined (__DJGPP__) || \
+ defined (__OS2__)
+# define HAVE_DOS_BASED_FILE_SYSTEM
+# define FOPEN_WB "wb"
+# ifndef DIR_SEPARATOR_2
+# define DIR_SEPARATOR_2 '\\'
+# endif
+# ifndef PATH_SEPARATOR_2
+# define PATH_SEPARATOR_2 ';'
+# endif
+#endif
+
+#ifndef DIR_SEPARATOR_2
+# define IS_DIR_SEPARATOR(ch) ((ch) == DIR_SEPARATOR)
+#else /* DIR_SEPARATOR_2 */
+# define IS_DIR_SEPARATOR(ch) \
+ (((ch) == DIR_SEPARATOR) || ((ch) == DIR_SEPARATOR_2))
+#endif /* DIR_SEPARATOR_2 */
+
+#ifndef PATH_SEPARATOR_2
+# define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR)
+#else /* PATH_SEPARATOR_2 */
+# define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR_2)
+#endif /* PATH_SEPARATOR_2 */
+
+#ifdef __CYGWIN__
+# define FOPEN_WB "wb"
+#endif
+
+#ifndef FOPEN_WB
+# define FOPEN_WB "w"
+#endif
+#ifndef _O_BINARY
+# define _O_BINARY 0
+#endif
+
+#define XMALLOC(type, num) ((type *) xmalloc ((num) * sizeof(type)))
+#define XFREE(stale) do { \
+ if (stale) { free ((void *) stale); stale = 0; } \
+} while (0)
+
+#undef LTWRAPPER_DEBUGPRINTF
+#if defined DEBUGWRAPPER
+# define LTWRAPPER_DEBUGPRINTF(args) ltwrapper_debugprintf args
+static void
+ltwrapper_debugprintf (const char *fmt, ...)
+{
+ va_list args;
+ va_start (args, fmt);
+ (void) vfprintf (stderr, fmt, args);
+ va_end (args);
+}
+#else
+# define LTWRAPPER_DEBUGPRINTF(args)
+#endif
+
+const char *program_name = NULL;
+
+void *xmalloc (size_t num);
+char *xstrdup (const char *string);
+const char *base_name (const char *name);
+char *find_executable (const char *wrapper);
+char *chase_symlinks (const char *pathspec);
+int make_executable (const char *path);
+int check_executable (const char *path);
+char *strendzap (char *str, const char *pat);
+void lt_fatal (const char *message, ...);
+void lt_setenv (const char *name, const char *value);
+char *lt_extend_str (const char *orig_value, const char *add, int to_end);
+void lt_opt_process_env_set (const char *arg);
+void lt_opt_process_env_prepend (const char *arg);
+void lt_opt_process_env_append (const char *arg);
+int lt_split_name_value (const char *arg, char** name, char** value);
+void lt_update_exe_path (const char *name, const char *value);
+void lt_update_lib_path (const char *name, const char *value);
+
+static const char *script_text_part1 =
+EOF
+
+ func_emit_wrapper_part1 yes |
+ $SED -e 's/\([\\"]\)/\\\1/g' \
+ -e 's/^/ "/' -e 's/$/\\n"/'
+ echo ";"
+ cat <<EOF
+
+static const char *script_text_part2 =
+EOF
+ func_emit_wrapper_part2 yes |
+ $SED -e 's/\([\\"]\)/\\\1/g' \
+ -e 's/^/ "/' -e 's/$/\\n"/'
+ echo ";"
+
+ cat <<EOF
+const char * MAGIC_EXE = "$magic_exe";
+const char * LIB_PATH_VARNAME = "$shlibpath_var";
+EOF
+
+ if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then
+ func_to_host_pathlist "$temp_rpath"
+ cat <<EOF
+const char * LIB_PATH_VALUE = "$func_to_host_pathlist_result";
+EOF
+ else
+ cat <<"EOF"
+const char * LIB_PATH_VALUE = "";
+EOF
+ fi
+
+ if test -n "$dllsearchpath"; then
+ func_to_host_pathlist "$dllsearchpath:"
+ cat <<EOF
+const char * EXE_PATH_VARNAME = "PATH";
+const char * EXE_PATH_VALUE = "$func_to_host_pathlist_result";
+EOF
+ else
+ cat <<"EOF"
+const char * EXE_PATH_VARNAME = "";
+const char * EXE_PATH_VALUE = "";
+EOF
+ fi
+
+ if test "$fast_install" = yes; then
+ cat <<EOF
+const char * TARGET_PROGRAM_NAME = "lt-$outputname"; /* hopefully, no .exe */
+EOF
+ else
+ cat <<EOF
+const char * TARGET_PROGRAM_NAME = "$outputname"; /* hopefully, no .exe */
+EOF
+ fi
+
+
+ cat <<"EOF"
+
+#define LTWRAPPER_OPTION_PREFIX "--lt-"
+#define LTWRAPPER_OPTION_PREFIX_LENGTH 5
+
+static const size_t opt_prefix_len = LTWRAPPER_OPTION_PREFIX_LENGTH;
+static const char *ltwrapper_option_prefix = LTWRAPPER_OPTION_PREFIX;
+
+static const char *dumpscript_opt = LTWRAPPER_OPTION_PREFIX "dump-script";
+
+static const size_t env_set_opt_len = LTWRAPPER_OPTION_PREFIX_LENGTH + 7;
+static const char *env_set_opt = LTWRAPPER_OPTION_PREFIX "env-set";
+ /* argument is putenv-style "foo=bar", value of foo is set to bar */
+
+static const size_t env_prepend_opt_len = LTWRAPPER_OPTION_PREFIX_LENGTH + 11;
+static const char *env_prepend_opt = LTWRAPPER_OPTION_PREFIX "env-prepend";
+ /* argument is putenv-style "foo=bar", new value of foo is bar${foo} */
+
+static const size_t env_append_opt_len = LTWRAPPER_OPTION_PREFIX_LENGTH + 10;
+static const char *env_append_opt = LTWRAPPER_OPTION_PREFIX "env-append";
+ /* argument is putenv-style "foo=bar", new value of foo is ${foo}bar */
+
+int
+main (int argc, char *argv[])
+{
+ char **newargz;
+ int newargc;
+ char *tmp_pathspec;
+ char *actual_cwrapper_path;
+ char *actual_cwrapper_name;
+ char *target_name;
+ char *lt_argv_zero;
+ intptr_t rval = 127;
+
+ int i;
+
+ program_name = (char *) xstrdup (base_name (argv[0]));
+ LTWRAPPER_DEBUGPRINTF (("(main) argv[0] : %s\n", argv[0]));
+ LTWRAPPER_DEBUGPRINTF (("(main) program_name : %s\n", program_name));
+
+ /* very simple arg parsing; don't want to rely on getopt */
+ for (i = 1; i < argc; i++)
+ {
+ if (strcmp (argv[i], dumpscript_opt) == 0)
+ {
+EOF
+ case "$host" in
+ *mingw* | *cygwin* )
+ # make stdout use "unix" line endings
+ echo " setmode(1,_O_BINARY);"
+ ;;
+ esac
+
+ cat <<"EOF"
+ printf ("%s", script_text_part1);
+ printf ("%s", script_text_part2);
+ return 0;
+ }
+ }
+
+ newargz = XMALLOC (char *, argc + 1);
+ tmp_pathspec = find_executable (argv[0]);
+ if (tmp_pathspec == NULL)
+ lt_fatal ("Couldn't find %s", argv[0]);
+ LTWRAPPER_DEBUGPRINTF (("(main) found exe (before symlink chase) at : %s\n",
+ tmp_pathspec));
+
+ actual_cwrapper_path = chase_symlinks (tmp_pathspec);
+ LTWRAPPER_DEBUGPRINTF (("(main) found exe (after symlink chase) at : %s\n",
+ actual_cwrapper_path));
+ XFREE (tmp_pathspec);
+
+ actual_cwrapper_name = xstrdup( base_name (actual_cwrapper_path));
+ strendzap (actual_cwrapper_path, actual_cwrapper_name);
+
+ /* wrapper name transforms */
+ strendzap (actual_cwrapper_name, ".exe");
+ tmp_pathspec = lt_extend_str (actual_cwrapper_name, ".exe", 1);
+ XFREE (actual_cwrapper_name);
+ actual_cwrapper_name = tmp_pathspec;
+ tmp_pathspec = 0;
+
+ /* target_name transforms -- use actual target program name; might have lt- prefix */
+ target_name = xstrdup (base_name (TARGET_PROGRAM_NAME));
+ strendzap (target_name, ".exe");
+ tmp_pathspec = lt_extend_str (target_name, ".exe", 1);
+ XFREE (target_name);
+ target_name = tmp_pathspec;
+ tmp_pathspec = 0;
+
+ LTWRAPPER_DEBUGPRINTF (("(main) libtool target name: %s\n",
+ target_name));
+EOF
+
+ cat <<EOF
+ newargz[0] =
+ XMALLOC (char, (strlen (actual_cwrapper_path) +
+ strlen ("$objdir") + 1 + strlen (actual_cwrapper_name) + 1));
+ strcpy (newargz[0], actual_cwrapper_path);
+ strcat (newargz[0], "$objdir");
+ strcat (newargz[0], "/");
+EOF
+
+ cat <<"EOF"
+ /* stop here, and copy so we don't have to do this twice */
+ tmp_pathspec = xstrdup (newargz[0]);
+
+ /* do NOT want the lt- prefix here, so use actual_cwrapper_name */
+ strcat (newargz[0], actual_cwrapper_name);
+
+ /* DO want the lt- prefix here if it exists, so use target_name */
+ lt_argv_zero = lt_extend_str (tmp_pathspec, target_name, 1);
+ XFREE (tmp_pathspec);
+ tmp_pathspec = NULL;
+EOF
+
+ case $host_os in
+ mingw*)
+ cat <<"EOF"
+ {
+ char* p;
+ while ((p = strchr (newargz[0], '\\')) != NULL)
+ {
+ *p = '/';
+ }
+ while ((p = strchr (lt_argv_zero, '\\')) != NULL)
+ {
+ *p = '/';
+ }
+ }
+EOF
+ ;;
+ esac
+
+ cat <<"EOF"
+ XFREE (target_name);
+ XFREE (actual_cwrapper_path);
+ XFREE (actual_cwrapper_name);
+
+ lt_setenv ("BIN_SH", "xpg4"); /* for Tru64 */
+ lt_setenv ("DUALCASE", "1"); /* for MSK sh */
+ lt_update_lib_path (LIB_PATH_VARNAME, LIB_PATH_VALUE);
+ lt_update_exe_path (EXE_PATH_VARNAME, EXE_PATH_VALUE);
+
+ newargc=0;
+ for (i = 1; i < argc; i++)
+ {
+ if (strncmp (argv[i], env_set_opt, env_set_opt_len) == 0)
+ {
+ if (argv[i][env_set_opt_len] == '=')
+ {
+ const char *p = argv[i] + env_set_opt_len + 1;
+ lt_opt_process_env_set (p);
+ }
+ else if (argv[i][env_set_opt_len] == '\0' && i + 1 < argc)
+ {
+ lt_opt_process_env_set (argv[++i]); /* don't copy */
+ }
+ else
+ lt_fatal ("%s missing required argument", env_set_opt);
+ continue;
+ }
+ if (strncmp (argv[i], env_prepend_opt, env_prepend_opt_len) == 0)
+ {
+ if (argv[i][env_prepend_opt_len] == '=')
+ {
+ const char *p = argv[i] + env_prepend_opt_len + 1;
+ lt_opt_process_env_prepend (p);
+ }
+ else if (argv[i][env_prepend_opt_len] == '\0' && i + 1 < argc)
+ {
+ lt_opt_process_env_prepend (argv[++i]); /* don't copy */
+ }
+ else
+ lt_fatal ("%s missing required argument", env_prepend_opt);
+ continue;
+ }
+ if (strncmp (argv[i], env_append_opt, env_append_opt_len) == 0)
+ {
+ if (argv[i][env_append_opt_len] == '=')
+ {
+ const char *p = argv[i] + env_append_opt_len + 1;
+ lt_opt_process_env_append (p);
+ }
+ else if (argv[i][env_append_opt_len] == '\0' && i + 1 < argc)
+ {
+ lt_opt_process_env_append (argv[++i]); /* don't copy */
+ }
+ else
+ lt_fatal ("%s missing required argument", env_append_opt);
+ continue;
+ }
+ if (strncmp (argv[i], ltwrapper_option_prefix, opt_prefix_len) == 0)
+ {
+ /* however, if there is an option in the LTWRAPPER_OPTION_PREFIX
+ namespace, but it is not one of the ones we know about and
+ have already dealt with, above (inluding dump-script), then
+ report an error. Otherwise, targets might begin to believe
+ they are allowed to use options in the LTWRAPPER_OPTION_PREFIX
+ namespace. The first time any user complains about this, we'll
+ need to make LTWRAPPER_OPTION_PREFIX a configure-time option
+ or a configure.ac-settable value.
+ */
+ lt_fatal ("Unrecognized option in %s namespace: '%s'",
+ ltwrapper_option_prefix, argv[i]);
+ }
+ /* otherwise ... */
+ newargz[++newargc] = xstrdup (argv[i]);
+ }
+ newargz[++newargc] = NULL;
+
+ LTWRAPPER_DEBUGPRINTF (("(main) lt_argv_zero : %s\n", (lt_argv_zero ? lt_argv_zero : "<NULL>")));
+ for (i = 0; i < newargc; i++)
+ {
+ LTWRAPPER_DEBUGPRINTF (("(main) newargz[%d] : %s\n", i, (newargz[i] ? newargz[i] : "<NULL>")));
+ }
+
+EOF
+
+ case $host_os in
+ mingw*)
+ cat <<"EOF"
+ /* execv doesn't actually work on mingw as expected on unix */
+ rval = _spawnv (_P_WAIT, lt_argv_zero, (const char * const *) newargz);
+ if (rval == -1)
+ {
+ /* failed to start process */
+ LTWRAPPER_DEBUGPRINTF (("(main) failed to launch target \"%s\": errno = %d\n", lt_argv_zero, errno));
+ return 127;
+ }
+ return rval;
+EOF
+ ;;
+ *)
+ cat <<"EOF"
+ execv (lt_argv_zero, newargz);
+ return rval; /* =127, but avoids unused variable warning */
+EOF
+ ;;
+ esac
+
+ cat <<"EOF"
+}
+
+void *
+xmalloc (size_t num)
+{
+ void *p = (void *) malloc (num);
+ if (!p)
+ lt_fatal ("Memory exhausted");
+
+ return p;
+}
+
+char *
+xstrdup (const char *string)
+{
+ return string ? strcpy ((char *) xmalloc (strlen (string) + 1),
+ string) : NULL;
+}
+
+const char *
+base_name (const char *name)
+{
+ const char *base;
+
+#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
+ /* Skip over the disk name in MSDOS pathnames. */
+ if (isalpha ((unsigned char) name[0]) && name[1] == ':')
+ name += 2;
+#endif
+
+ for (base = name; *name; name++)
+ if (IS_DIR_SEPARATOR (*name))
+ base = name + 1;
+ return base;
+}
+
+int
+check_executable (const char *path)
+{
+ struct stat st;
+
+ LTWRAPPER_DEBUGPRINTF (("(check_executable) : %s\n",
+ path ? (*path ? path : "EMPTY!") : "NULL!"));
+ if ((!path) || (!*path))
+ return 0;
+
+ if ((stat (path, &st) >= 0)
+ && (st.st_mode & (S_IXUSR | S_IXGRP | S_IXOTH)))
+ return 1;
+ else
+ return 0;
+}
+
+int
+make_executable (const char *path)
+{
+ int rval = 0;
+ struct stat st;
+
+ LTWRAPPER_DEBUGPRINTF (("(make_executable) : %s\n",
+ path ? (*path ? path : "EMPTY!") : "NULL!"));
+ if ((!path) || (!*path))
+ return 0;
+
+ if (stat (path, &st) >= 0)
+ {
+ rval = chmod (path, st.st_mode | S_IXOTH | S_IXGRP | S_IXUSR);
+ }
+ return rval;
+}
+
+/* Searches for the full path of the wrapper. Returns
+ newly allocated full path name if found, NULL otherwise
+ Does not chase symlinks, even on platforms that support them.
+*/
+char *
+find_executable (const char *wrapper)
+{
+ int has_slash = 0;
+ const char *p;
+ const char *p_next;
+ /* static buffer for getcwd */
+ char tmp[LT_PATHMAX + 1];
+ int tmp_len;
+ char *concat_name;
+
+ LTWRAPPER_DEBUGPRINTF (("(find_executable) : %s\n",
+ wrapper ? (*wrapper ? wrapper : "EMPTY!") : "NULL!"));
+
+ if ((wrapper == NULL) || (*wrapper == '\0'))
+ return NULL;
+
+ /* Absolute path? */
+#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
+ if (isalpha ((unsigned char) wrapper[0]) && wrapper[1] == ':')
+ {
+ concat_name = xstrdup (wrapper);
+ if (check_executable (concat_name))
+ return concat_name;
+ XFREE (concat_name);
+ }
+ else
+ {
+#endif
+ if (IS_DIR_SEPARATOR (wrapper[0]))
+ {
+ concat_name = xstrdup (wrapper);
+ if (check_executable (concat_name))
+ return concat_name;
+ XFREE (concat_name);
+ }
+#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
+ }
+#endif
+
+ for (p = wrapper; *p; p++)
+ if (*p == '/')
+ {
+ has_slash = 1;
+ break;
+ }
+ if (!has_slash)
+ {
+ /* no slashes; search PATH */
+ const char *path = getenv ("PATH");
+ if (path != NULL)
+ {
+ for (p = path; *p; p = p_next)
+ {
+ const char *q;
+ size_t p_len;
+ for (q = p; *q; q++)
+ if (IS_PATH_SEPARATOR (*q))
+ break;
+ p_len = q - p;
+ p_next = (*q == '\0' ? q : q + 1);
+ if (p_len == 0)
+ {
+ /* empty path: current directory */
+ if (getcwd (tmp, LT_PATHMAX) == NULL)
+ lt_fatal ("getcwd failed");
+ tmp_len = strlen (tmp);
+ concat_name =
+ XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1);
+ memcpy (concat_name, tmp, tmp_len);
+ concat_name[tmp_len] = '/';
+ strcpy (concat_name + tmp_len + 1, wrapper);
+ }
+ else
+ {
+ concat_name =
+ XMALLOC (char, p_len + 1 + strlen (wrapper) + 1);
+ memcpy (concat_name, p, p_len);
+ concat_name[p_len] = '/';
+ strcpy (concat_name + p_len + 1, wrapper);
+ }
+ if (check_executable (concat_name))
+ return concat_name;
+ XFREE (concat_name);
+ }
+ }
+ /* not found in PATH; assume curdir */
+ }
+ /* Relative path | not found in path: prepend cwd */
+ if (getcwd (tmp, LT_PATHMAX) == NULL)
+ lt_fatal ("getcwd failed");
+ tmp_len = strlen (tmp);
+ concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1);
+ memcpy (concat_name, tmp, tmp_len);
+ concat_name[tmp_len] = '/';
+ strcpy (concat_name + tmp_len + 1, wrapper);
+
+ if (check_executable (concat_name))
+ return concat_name;
+ XFREE (concat_name);
+ return NULL;
+}
+
+char *
+chase_symlinks (const char *pathspec)
+{
+#ifndef S_ISLNK
+ return xstrdup (pathspec);
+#else
+ char buf[LT_PATHMAX];
+ struct stat s;
+ char *tmp_pathspec = xstrdup (pathspec);
+ char *p;
+ int has_symlinks = 0;
+ while (strlen (tmp_pathspec) && !has_symlinks)
+ {
+ LTWRAPPER_DEBUGPRINTF (("checking path component for symlinks: %s\n",
+ tmp_pathspec));
+ if (lstat (tmp_pathspec, &s) == 0)
+ {
+ if (S_ISLNK (s.st_mode) != 0)
+ {
+ has_symlinks = 1;
+ break;
+ }
+
+ /* search backwards for last DIR_SEPARATOR */
+ p = tmp_pathspec + strlen (tmp_pathspec) - 1;
+ while ((p > tmp_pathspec) && (!IS_DIR_SEPARATOR (*p)))
+ p--;
+ if ((p == tmp_pathspec) && (!IS_DIR_SEPARATOR (*p)))
+ {
+ /* no more DIR_SEPARATORS left */
+ break;
+ }
+ *p = '\0';
+ }
+ else
+ {
+ char *errstr = strerror (errno);
+ lt_fatal ("Error accessing file %s (%s)", tmp_pathspec, errstr);
+ }
+ }
+ XFREE (tmp_pathspec);
+
+ if (!has_symlinks)
+ {
+ return xstrdup (pathspec);
+ }
+
+ tmp_pathspec = realpath (pathspec, buf);
+ if (tmp_pathspec == 0)
+ {
+ lt_fatal ("Could not follow symlinks for %s", pathspec);
+ }
+ return xstrdup (tmp_pathspec);
+#endif
+}
+
+char *
+strendzap (char *str, const char *pat)
+{
+ size_t len, patlen;
+
+ assert (str != NULL);
+ assert (pat != NULL);
+
+ len = strlen (str);
+ patlen = strlen (pat);
+
+ if (patlen <= len)
+ {
+ str += len - patlen;
+ if (strcmp (str, pat) == 0)
+ *str = '\0';
+ }
+ return str;
+}
+
+static void
+lt_error_core (int exit_status, const char *mode,
+ const char *message, va_list ap)
+{
+ fprintf (stderr, "%s: %s: ", program_name, mode);
+ vfprintf (stderr, message, ap);
+ fprintf (stderr, ".\n");
+
+ if (exit_status >= 0)
+ exit (exit_status);
+}
+
+void
+lt_fatal (const char *message, ...)
+{
+ va_list ap;
+ va_start (ap, message);
+ lt_error_core (EXIT_FAILURE, "FATAL", message, ap);
+ va_end (ap);
+}
+
+void
+lt_setenv (const char *name, const char *value)
+{
+ LTWRAPPER_DEBUGPRINTF (("(lt_setenv) setting '%s' to '%s'\n",
+ (name ? name : "<NULL>"),
+ (value ? value : "<NULL>")));
+ {
+#ifdef HAVE_SETENV
+ /* always make a copy, for consistency with !HAVE_SETENV */
+ char *str = xstrdup (value);
+ setenv (name, str, 1);
+#else
+ int len = strlen (name) + 1 + strlen (value) + 1;
+ char *str = XMALLOC (char, len);
+ sprintf (str, "%s=%s", name, value);
+ if (putenv (str) != EXIT_SUCCESS)
+ {
+ XFREE (str);
+ }
+#endif
+ }
+}
+
+char *
+lt_extend_str (const char *orig_value, const char *add, int to_end)
+{
+ char *new_value;
+ if (orig_value && *orig_value)
+ {
+ int orig_value_len = strlen (orig_value);
+ int add_len = strlen (add);
+ new_value = XMALLOC (char, add_len + orig_value_len + 1);
+ if (to_end)
+ {
+ strcpy (new_value, orig_value);
+ strcpy (new_value + orig_value_len, add);
+ }
+ else
+ {
+ strcpy (new_value, add);
+ strcpy (new_value + add_len, orig_value);
+ }
+ }
+ else
+ {
+ new_value = xstrdup (add);
+ }
+ return new_value;
+}
+
+int
+lt_split_name_value (const char *arg, char** name, char** value)
+{
+ const char *p;
+ int len;
+ if (!arg || !*arg)
+ return 1;
+
+ p = strchr (arg, (int)'=');
+
+ if (!p)
+ return 1;
+
+ *value = xstrdup (++p);
+
+ len = strlen (arg) - strlen (*value);
+ *name = XMALLOC (char, len);
+ strncpy (*name, arg, len-1);
+ (*name)[len - 1] = '\0';
+
+ return 0;
+}
+
+void
+lt_opt_process_env_set (const char *arg)
+{
+ char *name = NULL;
+ char *value = NULL;
+
+ if (lt_split_name_value (arg, &name, &value) != 0)
+ {
+ XFREE (name);
+ XFREE (value);
+ lt_fatal ("bad argument for %s: '%s'", env_set_opt, arg);
+ }
+
+ lt_setenv (name, value);
+ XFREE (name);
+ XFREE (value);
+}
+
+void
+lt_opt_process_env_prepend (const char *arg)
+{
+ char *name = NULL;
+ char *value = NULL;
+ char *new_value = NULL;
+
+ if (lt_split_name_value (arg, &name, &value) != 0)
+ {
+ XFREE (name);
+ XFREE (value);
+ lt_fatal ("bad argument for %s: '%s'", env_prepend_opt, arg);
+ }
+
+ new_value = lt_extend_str (getenv (name), value, 0);
+ lt_setenv (name, new_value);
+ XFREE (new_value);
+ XFREE (name);
+ XFREE (value);
+}
+
+void
+lt_opt_process_env_append (const char *arg)
+{
+ char *name = NULL;
+ char *value = NULL;
+ char *new_value = NULL;
+
+ if (lt_split_name_value (arg, &name, &value) != 0)
+ {
+ XFREE (name);
+ XFREE (value);
+ lt_fatal ("bad argument for %s: '%s'", env_append_opt, arg);
+ }
+
+ new_value = lt_extend_str (getenv (name), value, 1);
+ lt_setenv (name, new_value);
+ XFREE (new_value);
+ XFREE (name);
+ XFREE (value);
+}
+
+void
+lt_update_exe_path (const char *name, const char *value)
+{
+ LTWRAPPER_DEBUGPRINTF (("(lt_update_exe_path) modifying '%s' by prepending '%s'\n",
+ (name ? name : "<NULL>"),
+ (value ? value : "<NULL>")));
+
+ if (name && *name && value && *value)
+ {
+ char *new_value = lt_extend_str (getenv (name), value, 0);
+ /* some systems can't cope with a ':'-terminated path #' */
+ int len = strlen (new_value);
+ while (((len = strlen (new_value)) > 0) && IS_PATH_SEPARATOR (new_value[len-1]))
+ {
+ new_value[len-1] = '\0';
+ }
+ lt_setenv (name, new_value);
+ XFREE (new_value);
+ }
+}
+
+void
+lt_update_lib_path (const char *name, const char *value)
+{
+ LTWRAPPER_DEBUGPRINTF (("(lt_update_lib_path) modifying '%s' by prepending '%s'\n",
+ (name ? name : "<NULL>"),
+ (value ? value : "<NULL>")));
+
+ if (name && *name && value && *value)
+ {
+ char *new_value = lt_extend_str (getenv (name), value, 0);
+ lt_setenv (name, new_value);
+ XFREE (new_value);
+ }
+}
+
+
+EOF
+}
+# end: func_emit_cwrapperexe_src
+
+# func_mode_link arg...
+func_mode_link ()
+{
+ $opt_debug
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*)
+ # It is impossible to link a dll without this setting, and
+ # we shouldn't force the makefile maintainer to figure out
+ # which system we are compiling for in order to pass an extra
+ # flag for every libtool invocation.
+ # allow_undefined=no
+
+ # FIXME: Unfortunately, there are problems with the above when trying
+ # to make a dll which has undefined symbols, in which case not
+ # even a static library is built. For now, we need to specify
+ # -no-undefined on the libtool link line when we can be certain
+ # that all symbols are satisfied, otherwise we get a static library.
+ allow_undefined=yes
+ ;;
+ *)
+ allow_undefined=yes
+ ;;
+ esac
+ libtool_args=$nonopt
+ base_compile="$nonopt $@"
+ compile_command=$nonopt
+ finalize_command=$nonopt
+
+ compile_rpath=
+ finalize_rpath=
+ compile_shlibpath=
+ finalize_shlibpath=
+ convenience=
+ old_convenience=
+ deplibs=
+ old_deplibs=
+ compiler_flags=
+ linker_flags=
+ dllsearchpath=
+ lib_search_path=`pwd`
+ inst_prefix_dir=
+ new_inherited_linker_flags=
+
+ avoid_version=no
+ dlfiles=
+ dlprefiles=
+ dlself=no
+ export_dynamic=no
+ export_symbols=
+ export_symbols_regex=
+ generated=
+ libobjs=
+ ltlibs=
+ module=no
+ no_install=no
+ objs=
+ non_pic_objects=
+ precious_files_regex=
+ prefer_static_libs=no
+ preload=no
+ prev=
+ prevarg=
+ release=
+ rpath=
+ xrpath=
+ perm_rpath=
+ temp_rpath=
+ thread_safe=no
+ vinfo=
+ vinfo_number=no
+ weak_libs=
+ single_module="${wl}-single_module"
+ func_infer_tag $base_compile
+
+ # We need to know -static, to get the right output filenames.
+ for arg
+ do
+ case $arg in
+ -shared)
+ test "$build_libtool_libs" != yes && \
+ func_fatal_configuration "can not build a shared library"
+ build_old_libs=no
+ break
+ ;;
+ -all-static | -static | -static-libtool-libs)
+ case $arg in
+ -all-static)
+ if test "$build_libtool_libs" = yes && test -z "$link_static_flag"; then
+ func_warning "complete static linking is impossible in this configuration"
+ fi
+ if test -n "$link_static_flag"; then
+ dlopen_self=$dlopen_self_static
+ fi
+ prefer_static_libs=yes
+ ;;
+ -static)
+ if test -z "$pic_flag" && test -n "$link_static_flag"; then
+ dlopen_self=$dlopen_self_static
+ fi
+ prefer_static_libs=built
+ ;;
+ -static-libtool-libs)
+ if test -z "$pic_flag" && test -n "$link_static_flag"; then
+ dlopen_self=$dlopen_self_static
+ fi
+ prefer_static_libs=yes
+ ;;
+ esac
+ build_libtool_libs=no
+ build_old_libs=yes
+ break
+ ;;
+ esac
+ done
+
+ # See if our shared archives depend on static archives.
+ test -n "$old_archive_from_new_cmds" && build_old_libs=yes
+
+ # Go through the arguments, transforming them on the way.
+ while test "$#" -gt 0; do
+ arg="$1"
+ shift
+ func_quote_for_eval "$arg"
+ qarg=$func_quote_for_eval_unquoted_result
+ func_append libtool_args " $func_quote_for_eval_result"
+
+ # If the previous option needs an argument, assign it.
+ if test -n "$prev"; then
+ case $prev in
+ output)
+ func_append compile_command " @OUTPUT@"
+ func_append finalize_command " @OUTPUT@"
+ ;;
+ esac
+
+ case $prev in
+ dlfiles|dlprefiles)
+ if test "$preload" = no; then
+ # Add the symbol object into the linking commands.
+ func_append compile_command " @SYMFILE@"
+ func_append finalize_command " @SYMFILE@"
+ preload=yes
+ fi
+ case $arg in
+ *.la | *.lo) ;; # We handle these cases below.
+ force)
+ if test "$dlself" = no; then
+ dlself=needless
+ export_dynamic=yes
+ fi
+ prev=
+ continue
+ ;;
+ self)
+ if test "$prev" = dlprefiles; then
+ dlself=yes
+ elif test "$prev" = dlfiles && test "$dlopen_self" != yes; then
+ dlself=yes
+ else
+ dlself=needless
+ export_dynamic=yes
+ fi
+ prev=
+ continue
+ ;;
+ *)
+ if test "$prev" = dlfiles; then
+ dlfiles="$dlfiles $arg"
+ else
+ dlprefiles="$dlprefiles $arg"
+ fi
+ prev=
+ continue
+ ;;
+ esac
+ ;;
+ expsyms)
+ export_symbols="$arg"
+ test -f "$arg" \
+ || func_fatal_error "symbol file \`$arg' does not exist"
+ prev=
+ continue
+ ;;
+ expsyms_regex)
+ export_symbols_regex="$arg"
+ prev=
+ continue
+ ;;
+ framework)
+ case $host in
+ *-*-darwin*)
+ case "$deplibs " in
+ *" $qarg.ltframework "*) ;;
+ *) deplibs="$deplibs $qarg.ltframework" # this is fixed later
+ ;;
+ esac
+ ;;
+ esac
+ prev=
+ continue
+ ;;
+ inst_prefix)
+ inst_prefix_dir="$arg"
+ prev=
+ continue
+ ;;
+ objectlist)
+ if test -f "$arg"; then
+ save_arg=$arg
+ moreargs=
+ for fil in `cat "$save_arg"`
+ do
+# moreargs="$moreargs $fil"
+ arg=$fil
+ # A libtool-controlled object.
+
+ # Check to see that this really is a libtool object.
+ if func_lalib_unsafe_p "$arg"; then
+ pic_object=
+ non_pic_object=
+
+ # Read the .lo file
+ func_source "$arg"
+
+ if test -z "$pic_object" ||
+ test -z "$non_pic_object" ||
+ test "$pic_object" = none &&
+ test "$non_pic_object" = none; then
+ func_fatal_error "cannot find name of object for \`$arg'"
+ fi
+
+ # Extract subdirectory from the argument.
+ func_dirname "$arg" "/" ""
+ xdir="$func_dirname_result"
+
+ if test "$pic_object" != none; then
+ # Prepend the subdirectory the object is found in.
+ pic_object="$xdir$pic_object"
+
+ if test "$prev" = dlfiles; then
+ if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then
+ dlfiles="$dlfiles $pic_object"
+ prev=
+ continue
+ else
+ # If libtool objects are unsupported, then we need to preload.
+ prev=dlprefiles
+ fi
+ fi
+
+ # CHECK ME: I think I busted this. -Ossama
+ if test "$prev" = dlprefiles; then
+ # Preload the old-style object.
+ dlprefiles="$dlprefiles $pic_object"
+ prev=
+ fi
+
+ # A PIC object.
+ func_append libobjs " $pic_object"
+ arg="$pic_object"
+ fi
+
+ # Non-PIC object.
+ if test "$non_pic_object" != none; then
+ # Prepend the subdirectory the object is found in.
+ non_pic_object="$xdir$non_pic_object"
+
+ # A standard non-PIC object
+ func_append non_pic_objects " $non_pic_object"
+ if test -z "$pic_object" || test "$pic_object" = none ; then
+ arg="$non_pic_object"
+ fi
+ else
+ # If the PIC object exists, use it instead.
+ # $xdir was prepended to $pic_object above.
+ non_pic_object="$pic_object"
+ func_append non_pic_objects " $non_pic_object"
+ fi
+ else
+ # Only an error if not doing a dry-run.
+ if $opt_dry_run; then
+ # Extract subdirectory from the argument.
+ func_dirname "$arg" "/" ""
+ xdir="$func_dirname_result"
+
+ func_lo2o "$arg"
+ pic_object=$xdir$objdir/$func_lo2o_result
+ non_pic_object=$xdir$func_lo2o_result
+ func_append libobjs " $pic_object"
+ func_append non_pic_objects " $non_pic_object"
+ else
+ func_fatal_error "\`$arg' is not a valid libtool object"
+ fi
+ fi
+ done
+ else
+ func_fatal_error "link input file \`$arg' does not exist"
+ fi
+ arg=$save_arg
+ prev=
+ continue
+ ;;
+ precious_regex)
+ precious_files_regex="$arg"
+ prev=
+ continue
+ ;;
+ release)
+ release="-$arg"
+ prev=
+ continue
+ ;;
+ rpath | xrpath)
+ # We need an absolute path.
+ case $arg in
+ [\\/]* | [A-Za-z]:[\\/]*) ;;
+ *)
+ func_fatal_error "only absolute run-paths are allowed"
+ ;;
+ esac
+ if test "$prev" = rpath; then
+ case "$rpath " in
+ *" $arg "*) ;;
+ *) rpath="$rpath $arg" ;;
+ esac
+ else
+ case "$xrpath " in
+ *" $arg "*) ;;
+ *) xrpath="$xrpath $arg" ;;
+ esac
+ fi
+ prev=
+ continue
+ ;;
+ shrext)
+ shrext_cmds="$arg"
+ prev=
+ continue
+ ;;
+ weak)
+ weak_libs="$weak_libs $arg"
+ prev=
+ continue
+ ;;
+ xcclinker)
+ linker_flags="$linker_flags $qarg"
+ compiler_flags="$compiler_flags $qarg"
+ prev=
+ func_append compile_command " $qarg"
+ func_append finalize_command " $qarg"
+ continue
+ ;;
+ xcompiler)
+ compiler_flags="$compiler_flags $qarg"
+ prev=
+ func_append compile_command " $qarg"
+ func_append finalize_command " $qarg"
+ continue
+ ;;
+ xlinker)
+ linker_flags="$linker_flags $qarg"
+ compiler_flags="$compiler_flags $wl$qarg"
+ prev=
+ func_append compile_command " $wl$qarg"
+ func_append finalize_command " $wl$qarg"
+ continue
+ ;;
+ *)
+ eval "$prev=\"\$arg\""
+ prev=
+ continue
+ ;;
+ esac
+ fi # test -n "$prev"
+
+ prevarg="$arg"
+
+ case $arg in
+ -all-static)
+ if test -n "$link_static_flag"; then
+ # See comment for -static flag below, for more details.
+ func_append compile_command " $link_static_flag"
+ func_append finalize_command " $link_static_flag"
+ fi
+ continue
+ ;;
+
+ -allow-undefined)
+ # FIXME: remove this flag sometime in the future.
+ func_fatal_error "\`-allow-undefined' must not be used because it is the default"
+ ;;
+
+ -avoid-version)
+ avoid_version=yes
+ continue
+ ;;
+
+ -dlopen)
+ prev=dlfiles
+ continue
+ ;;
+
+ -dlpreopen)
+ prev=dlprefiles
+ continue
+ ;;
+
+ -export-dynamic)
+ export_dynamic=yes
+ continue
+ ;;
+
+ -export-symbols | -export-symbols-regex)
+ if test -n "$export_symbols" || test -n "$export_symbols_regex"; then
+ func_fatal_error "more than one -exported-symbols argument is not allowed"
+ fi
+ if test "X$arg" = "X-export-symbols"; then
+ prev=expsyms
+ else
+ prev=expsyms_regex
+ fi
+ continue
+ ;;
+
+ -framework)
+ prev=framework
+ continue
+ ;;
+
+ -inst-prefix-dir)
+ prev=inst_prefix
+ continue
+ ;;
+
+ # The native IRIX linker understands -LANG:*, -LIST:* and -LNO:*
+ # so, if we see these flags be careful not to treat them like -L
+ -L[A-Z][A-Z]*:*)
+ case $with_gcc/$host in
+ no/*-*-irix* | /*-*-irix*)
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ ;;
+ esac
+ continue
+ ;;
+
+ -L*)
+ func_stripname '-L' '' "$arg"
+ dir=$func_stripname_result
+ if test -z "$dir"; then
+ if test "$#" -gt 0; then
+ func_fatal_error "require no space between \`-L' and \`$1'"
+ else
+ func_fatal_error "need path for \`-L' option"
+ fi
+ fi
+ # We need an absolute path.
+ case $dir in
+ [\\/]* | [A-Za-z]:[\\/]*) ;;
+ *)
+ absdir=`cd "$dir" && pwd`
+ test -z "$absdir" && \
+ func_fatal_error "cannot determine absolute directory name of \`$dir'"
+ dir="$absdir"
+ ;;
+ esac
+ case "$deplibs " in
+ *" -L$dir "*) ;;
+ *)
+ deplibs="$deplibs -L$dir"
+ lib_search_path="$lib_search_path $dir"
+ ;;
+ esac
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*)
+ testbindir=`$ECHO "X$dir" | $Xsed -e 's*/lib$*/bin*'`
+ case :$dllsearchpath: in
+ *":$dir:"*) ;;
+ ::) dllsearchpath=$dir;;
+ *) dllsearchpath="$dllsearchpath:$dir";;
+ esac
+ case :$dllsearchpath: in
+ *":$testbindir:"*) ;;
+ ::) dllsearchpath=$testbindir;;
+ *) dllsearchpath="$dllsearchpath:$testbindir";;
+ esac
+ ;;
+ esac
+ continue
+ ;;
+
+ -l*)
+ if test "X$arg" = "X-lc" || test "X$arg" = "X-lm"; then
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-beos* | *-cegcc*)
+ # These systems don't actually have a C or math library (as such)
+ continue
+ ;;
+ *-*-os2*)
+ # These systems don't actually have a C library (as such)
+ test "X$arg" = "X-lc" && continue
+ ;;
+ *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
+ # Do not include libc due to us having libc/libc_r.
+ test "X$arg" = "X-lc" && continue
+ ;;
+ *-*-rhapsody* | *-*-darwin1.[012])
+ # Rhapsody C and math libraries are in the System framework
+ deplibs="$deplibs System.ltframework"
+ continue
+ ;;
+ *-*-sco3.2v5* | *-*-sco5v6*)
+ # Causes problems with __ctype
+ test "X$arg" = "X-lc" && continue
+ ;;
+ *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*)
+ # Compiler inserts libc in the correct place for threads to work
+ test "X$arg" = "X-lc" && continue
+ ;;
+ esac
+ elif test "X$arg" = "X-lc_r"; then
+ case $host in
+ *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
+ # Do not include libc_r directly, use -pthread flag.
+ continue
+ ;;
+ esac
+ fi
+ deplibs="$deplibs $arg"
+ continue
+ ;;
+
+ -module)
+ module=yes
+ continue
+ ;;
+
+ # Tru64 UNIX uses -model [arg] to determine the layout of C++
+ # classes, name mangling, and exception handling.
+ # Darwin uses the -arch flag to determine output architecture.
+ -model|-arch|-isysroot)
+ compiler_flags="$compiler_flags $arg"
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ prev=xcompiler
+ continue
+ ;;
+
+ -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads)
+ compiler_flags="$compiler_flags $arg"
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ case "$new_inherited_linker_flags " in
+ *" $arg "*) ;;
+ * ) new_inherited_linker_flags="$new_inherited_linker_flags $arg" ;;
+ esac
+ continue
+ ;;
+
+ -multi_module)
+ single_module="${wl}-multi_module"
+ continue
+ ;;
+
+ -no-fast-install)
+ fast_install=no
+ continue
+ ;;
+
+ -no-install)
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-darwin* | *-cegcc*)
+ # The PATH hackery in wrapper scripts is required on Windows
+ # and Darwin in order for the loader to find any dlls it needs.
+ func_warning "\`-no-install' is ignored for $host"
+ func_warning "assuming \`-no-fast-install' instead"
+ fast_install=no
+ ;;
+ *) no_install=yes ;;
+ esac
+ continue
+ ;;
+
+ -no-undefined)
+ allow_undefined=no
+ continue
+ ;;
+
+ -objectlist)
+ prev=objectlist
+ continue
+ ;;
+
+ -o) prev=output ;;
+
+ -precious-files-regex)
+ prev=precious_regex
+ continue
+ ;;
+
+ -release)
+ prev=release
+ continue
+ ;;
+
+ -rpath)
+ prev=rpath
+ continue
+ ;;
+
+ -R)
+ prev=xrpath
+ continue
+ ;;
+
+ -R*)
+ func_stripname '-R' '' "$arg"
+ dir=$func_stripname_result
+ # We need an absolute path.
+ case $dir in
+ [\\/]* | [A-Za-z]:[\\/]*) ;;
+ *)
+ func_fatal_error "only absolute run-paths are allowed"
+ ;;
+ esac
+ case "$xrpath " in
+ *" $dir "*) ;;
+ *) xrpath="$xrpath $dir" ;;
+ esac
+ continue
+ ;;
+
+ -shared)
+ # The effects of -shared are defined in a previous loop.
+ continue
+ ;;
+
+ -shrext)
+ prev=shrext
+ continue
+ ;;
+
+ -static | -static-libtool-libs)
+ # The effects of -static are defined in a previous loop.
+ # We used to do the same as -all-static on platforms that
+ # didn't have a PIC flag, but the assumption that the effects
+ # would be equivalent was wrong. It would break on at least
+ # Digital Unix and AIX.
+ continue
+ ;;
+
+ -thread-safe)
+ thread_safe=yes
+ continue
+ ;;
+
+ -version-info)
+ prev=vinfo
+ continue
+ ;;
+
+ -version-number)
+ prev=vinfo
+ vinfo_number=yes
+ continue
+ ;;
+
+ -weak)
+ prev=weak
+ continue
+ ;;
+
+ -Wc,*)
+ func_stripname '-Wc,' '' "$arg"
+ args=$func_stripname_result
+ arg=
+ save_ifs="$IFS"; IFS=','
+ for flag in $args; do
+ IFS="$save_ifs"
+ func_quote_for_eval "$flag"
+ arg="$arg $wl$func_quote_for_eval_result"
+ compiler_flags="$compiler_flags $func_quote_for_eval_result"
+ done
+ IFS="$save_ifs"
+ func_stripname ' ' '' "$arg"
+ arg=$func_stripname_result
+ ;;
+
+ -Wl,*)
+ func_stripname '-Wl,' '' "$arg"
+ args=$func_stripname_result
+ arg=
+ save_ifs="$IFS"; IFS=','
+ for flag in $args; do
+ IFS="$save_ifs"
+ func_quote_for_eval "$flag"
+ arg="$arg $wl$func_quote_for_eval_result"
+ compiler_flags="$compiler_flags $wl$func_quote_for_eval_result"
+ linker_flags="$linker_flags $func_quote_for_eval_result"
+ done
+ IFS="$save_ifs"
+ func_stripname ' ' '' "$arg"
+ arg=$func_stripname_result
+ ;;
+
+ -Xcompiler)
+ prev=xcompiler
+ continue
+ ;;
+
+ -Xlinker)
+ prev=xlinker
+ continue
+ ;;
+
+ -XCClinker)
+ prev=xcclinker
+ continue
+ ;;
+
+ # -msg_* for osf cc
+ -msg_*)
+ func_quote_for_eval "$arg"
+ arg="$func_quote_for_eval_result"
+ ;;
+
+ # -64, -mips[0-9] enable 64-bit mode on the SGI compiler
+ # -r[0-9][0-9]* specifies the processor on the SGI compiler
+ # -xarch=*, -xtarget=* enable 64-bit mode on the Sun compiler
+ # +DA*, +DD* enable 64-bit mode on the HP compiler
+ # -q* pass through compiler args for the IBM compiler
+ # -m*, -t[45]*, -txscale* pass through architecture-specific
+ # compiler args for GCC
+ # -F/path gives path to uninstalled frameworks, gcc on darwin
+ # -p, -pg, --coverage, -fprofile-* pass through profiling flag for GCC
+ # @file GCC response files
+ -64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*| \
+ -t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*)
+ func_quote_for_eval "$arg"
+ arg="$func_quote_for_eval_result"
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ compiler_flags="$compiler_flags $arg"
+ continue
+ ;;
+
+ # Some other compiler flag.
+ -* | +*)
+ func_quote_for_eval "$arg"
+ arg="$func_quote_for_eval_result"
+ ;;
+
+ *.$objext)
+ # A standard object.
+ objs="$objs $arg"
+ ;;
+
+ *.lo)
+ # A libtool-controlled object.
+
+ # Check to see that this really is a libtool object.
+ if func_lalib_unsafe_p "$arg"; then
+ pic_object=
+ non_pic_object=
+
+ # Read the .lo file
+ func_source "$arg"
+
+ if test -z "$pic_object" ||
+ test -z "$non_pic_object" ||
+ test "$pic_object" = none &&
+ test "$non_pic_object" = none; then
+ func_fatal_error "cannot find name of object for \`$arg'"
+ fi
+
+ # Extract subdirectory from the argument.
+ func_dirname "$arg" "/" ""
+ xdir="$func_dirname_result"
+
+ if test "$pic_object" != none; then
+ # Prepend the subdirectory the object is found in.
+ pic_object="$xdir$pic_object"
+
+ if test "$prev" = dlfiles; then
+ if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then
+ dlfiles="$dlfiles $pic_object"
+ prev=
+ continue
+ else
+ # If libtool objects are unsupported, then we need to preload.
+ prev=dlprefiles
+ fi
+ fi
+
+ # CHECK ME: I think I busted this. -Ossama
+ if test "$prev" = dlprefiles; then
+ # Preload the old-style object.
+ dlprefiles="$dlprefiles $pic_object"
+ prev=
+ fi
+
+ # A PIC object.
+ func_append libobjs " $pic_object"
+ arg="$pic_object"
+ fi
+
+ # Non-PIC object.
+ if test "$non_pic_object" != none; then
+ # Prepend the subdirectory the object is found in.
+ non_pic_object="$xdir$non_pic_object"
+
+ # A standard non-PIC object
+ func_append non_pic_objects " $non_pic_object"
+ if test -z "$pic_object" || test "$pic_object" = none ; then
+ arg="$non_pic_object"
+ fi
+ else
+ # If the PIC object exists, use it instead.
+ # $xdir was prepended to $pic_object above.
+ non_pic_object="$pic_object"
+ func_append non_pic_objects " $non_pic_object"
+ fi
+ else
+ # Only an error if not doing a dry-run.
+ if $opt_dry_run; then
+ # Extract subdirectory from the argument.
+ func_dirname "$arg" "/" ""
+ xdir="$func_dirname_result"
+
+ func_lo2o "$arg"
+ pic_object=$xdir$objdir/$func_lo2o_result
+ non_pic_object=$xdir$func_lo2o_result
+ func_append libobjs " $pic_object"
+ func_append non_pic_objects " $non_pic_object"
+ else
+ func_fatal_error "\`$arg' is not a valid libtool object"
+ fi
+ fi
+ ;;
+
+ *.$libext)
+ # An archive.
+ deplibs="$deplibs $arg"
+ old_deplibs="$old_deplibs $arg"
+ continue
+ ;;
+
+ *.la)
+ # A libtool-controlled library.
+
+ if test "$prev" = dlfiles; then
+ # This library was specified with -dlopen.
+ dlfiles="$dlfiles $arg"
+ prev=
+ elif test "$prev" = dlprefiles; then
+ # The library was specified with -dlpreopen.
+ dlprefiles="$dlprefiles $arg"
+ prev=
+ else
+ deplibs="$deplibs $arg"
+ fi
+ continue
+ ;;
+
+ # Some other compiler argument.
+ *)
+ # Unknown arguments in both finalize_command and compile_command need
+ # to be aesthetically quoted because they are evaled later.
+ func_quote_for_eval "$arg"
+ arg="$func_quote_for_eval_result"
+ ;;
+ esac # arg
+
+ # Now actually substitute the argument into the commands.
+ if test -n "$arg"; then
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ fi
+ done # argument parsing loop
+
+ test -n "$prev" && \
+ func_fatal_help "the \`$prevarg' option requires an argument"
+
+ if test "$export_dynamic" = yes && test -n "$export_dynamic_flag_spec"; then
+ eval arg=\"$export_dynamic_flag_spec\"
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ fi
+
+ oldlibs=
+ # calculate the name of the file, without its directory
+ func_basename "$output"
+ outputname="$func_basename_result"
+ libobjs_save="$libobjs"
+
+ if test -n "$shlibpath_var"; then
+ # get the directories listed in $shlibpath_var
+ eval shlib_search_path=\`\$ECHO \"X\${$shlibpath_var}\" \| \$Xsed -e \'s/:/ /g\'\`
+ else
+ shlib_search_path=
+ fi
+ eval sys_lib_search_path=\"$sys_lib_search_path_spec\"
+ eval sys_lib_dlsearch_path=\"$sys_lib_dlsearch_path_spec\"
+
+ func_dirname "$output" "/" ""
+ output_objdir="$func_dirname_result$objdir"
+ # Create the object directory.
+ func_mkdir_p "$output_objdir"
+
+ # Determine the type of output
+ case $output in
+ "")
+ func_fatal_help "you must specify an output file"
+ ;;
+ *.$libext) linkmode=oldlib ;;
+ *.lo | *.$objext) linkmode=obj ;;
+ *.la) linkmode=lib ;;
+ *) linkmode=prog ;; # Anything else should be a program.
+ esac
+
+ specialdeplibs=
+
+ libs=
+ # Find all interdependent deplibs by searching for libraries
+ # that are linked more than once (e.g. -la -lb -la)
+ for deplib in $deplibs; do
+ if $opt_duplicate_deps ; then
+ case "$libs " in
+ *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+ esac
+ fi
+ libs="$libs $deplib"
+ done
+
+ if test "$linkmode" = lib; then
+ libs="$predeps $libs $compiler_lib_search_path $postdeps"
+
+ # Compute libraries that are listed more than once in $predeps
+ # $postdeps and mark them as special (i.e., whose duplicates are
+ # not to be eliminated).
+ pre_post_deps=
+ if $opt_duplicate_compiler_generated_deps; then
+ for pre_post_dep in $predeps $postdeps; do
+ case "$pre_post_deps " in
+ *" $pre_post_dep "*) specialdeplibs="$specialdeplibs $pre_post_deps" ;;
+ esac
+ pre_post_deps="$pre_post_deps $pre_post_dep"
+ done
+ fi
+ pre_post_deps=
+ fi
+
+ deplibs=
+ newdependency_libs=
+ newlib_search_path=
+ need_relink=no # whether we're linking any uninstalled libtool libraries
+ notinst_deplibs= # not-installed libtool libraries
+ notinst_path= # paths that contain not-installed libtool libraries
+
+ case $linkmode in
+ lib)
+ passes="conv dlpreopen link"
+ for file in $dlfiles $dlprefiles; do
+ case $file in
+ *.la) ;;
+ *)
+ func_fatal_help "libraries can \`-dlopen' only libtool libraries: $file"
+ ;;
+ esac
+ done
+ ;;
+ prog)
+ compile_deplibs=
+ finalize_deplibs=
+ alldeplibs=no
+ newdlfiles=
+ newdlprefiles=
+ passes="conv scan dlopen dlpreopen link"
+ ;;
+ *) passes="conv"
+ ;;
+ esac
+
+ for pass in $passes; do
+ # The preopen pass in lib mode reverses $deplibs; put it back here
+ # so that -L comes before libs that need it for instance...
+ if test "$linkmode,$pass" = "lib,link"; then
+ ## FIXME: Find the place where the list is rebuilt in the wrong
+ ## order, and fix it there properly
+ tmp_deplibs=
+ for deplib in $deplibs; do
+ tmp_deplibs="$deplib $tmp_deplibs"
+ done
+ deplibs="$tmp_deplibs"
+ fi
+
+ if test "$linkmode,$pass" = "lib,link" ||
+ test "$linkmode,$pass" = "prog,scan"; then
+ libs="$deplibs"
+ deplibs=
+ fi
+ if test "$linkmode" = prog; then
+ case $pass in
+ dlopen) libs="$dlfiles" ;;
+ dlpreopen) libs="$dlprefiles" ;;
+ link)
+ libs="$deplibs %DEPLIBS%"
+ test "X$link_all_deplibs" != Xno && libs="$libs $dependency_libs"
+ ;;
+ esac
+ fi
+ if test "$linkmode,$pass" = "lib,dlpreopen"; then
+ # Collect and forward deplibs of preopened libtool libs
+ for lib in $dlprefiles; do
+ # Ignore non-libtool-libs
+ dependency_libs=
+ case $lib in
+ *.la) func_source "$lib" ;;
+ esac
+
+ # Collect preopened libtool deplibs, except any this library
+ # has declared as weak libs
+ for deplib in $dependency_libs; do
+ deplib_base=`$ECHO "X$deplib" | $Xsed -e "$basename"`
+ case " $weak_libs " in
+ *" $deplib_base "*) ;;
+ *) deplibs="$deplibs $deplib" ;;
+ esac
+ done
+ done
+ libs="$dlprefiles"
+ fi
+ if test "$pass" = dlopen; then
+ # Collect dlpreopened libraries
+ save_deplibs="$deplibs"
+ deplibs=
+ fi
+
+ for deplib in $libs; do
+ lib=
+ found=no
+ case $deplib in
+ -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads)
+ if test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ compiler_flags="$compiler_flags $deplib"
+ if test "$linkmode" = lib ; then
+ case "$new_inherited_linker_flags " in
+ *" $deplib "*) ;;
+ * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;;
+ esac
+ fi
+ fi
+ continue
+ ;;
+ -l*)
+ if test "$linkmode" != lib && test "$linkmode" != prog; then
+ func_warning "\`-l' is ignored for archives/objects"
+ continue
+ fi
+ func_stripname '-l' '' "$deplib"
+ name=$func_stripname_result
+ if test "$linkmode" = lib; then
+ searchdirs="$newlib_search_path $lib_search_path $compiler_lib_search_dirs $sys_lib_search_path $shlib_search_path"
+ else
+ searchdirs="$newlib_search_path $lib_search_path $sys_lib_search_path $shlib_search_path"
+ fi
+ for searchdir in $searchdirs; do
+ for search_ext in .la $std_shrext .so .a; do
+ # Search the libtool library
+ lib="$searchdir/lib${name}${search_ext}"
+ if test -f "$lib"; then
+ if test "$search_ext" = ".la"; then
+ found=yes
+ else
+ found=no
+ fi
+ break 2
+ fi
+ done
+ done
+ if test "$found" != yes; then
+ # deplib doesn't seem to be a libtool library
+ if test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ deplibs="$deplib $deplibs"
+ test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs"
+ fi
+ continue
+ else # deplib is a libtool library
+ # If $allow_libtool_libs_with_static_runtimes && $deplib is a stdlib,
+ # We need to do some special things here, and not later.
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $deplib "*)
+ if func_lalib_p "$lib"; then
+ library_names=
+ old_library=
+ func_source "$lib"
+ for l in $old_library $library_names; do
+ ll="$l"
+ done
+ if test "X$ll" = "X$old_library" ; then # only static version available
+ found=no
+ func_dirname "$lib" "" "."
+ ladir="$func_dirname_result"
+ lib=$ladir/$old_library
+ if test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ deplibs="$deplib $deplibs"
+ test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs"
+ fi
+ continue
+ fi
+ fi
+ ;;
+ *) ;;
+ esac
+ fi
+ fi
+ ;; # -l
+ *.ltframework)
+ if test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ deplibs="$deplib $deplibs"
+ if test "$linkmode" = lib ; then
+ case "$new_inherited_linker_flags " in
+ *" $deplib "*) ;;
+ * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;;
+ esac
+ fi
+ fi
+ continue
+ ;;
+ -L*)
+ case $linkmode in
+ lib)
+ deplibs="$deplib $deplibs"
+ test "$pass" = conv && continue
+ newdependency_libs="$deplib $newdependency_libs"
+ func_stripname '-L' '' "$deplib"
+ newlib_search_path="$newlib_search_path $func_stripname_result"
+ ;;
+ prog)
+ if test "$pass" = conv; then
+ deplibs="$deplib $deplibs"
+ continue
+ fi
+ if test "$pass" = scan; then
+ deplibs="$deplib $deplibs"
+ else
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ fi
+ func_stripname '-L' '' "$deplib"
+ newlib_search_path="$newlib_search_path $func_stripname_result"
+ ;;
+ *)
+ func_warning "\`-L' is ignored for archives/objects"
+ ;;
+ esac # linkmode
+ continue
+ ;; # -L
+ -R*)
+ if test "$pass" = link; then
+ func_stripname '-R' '' "$deplib"
+ dir=$func_stripname_result
+ # Make sure the xrpath contains only unique directories.
+ case "$xrpath " in
+ *" $dir "*) ;;
+ *) xrpath="$xrpath $dir" ;;
+ esac
+ fi
+ deplibs="$deplib $deplibs"
+ continue
+ ;;
+ *.la) lib="$deplib" ;;
+ *.$libext)
+ if test "$pass" = conv; then
+ deplibs="$deplib $deplibs"
+ continue
+ fi
+ case $linkmode in
+ lib)
+ # Linking convenience modules into shared libraries is allowed,
+ # but linking other static libraries is non-portable.
+ case " $dlpreconveniencelibs " in
+ *" $deplib "*) ;;
+ *)
+ valid_a_lib=no
+ case $deplibs_check_method in
+ match_pattern*)
+ set dummy $deplibs_check_method; shift
+ match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"`
+ if eval "\$ECHO \"X$deplib\"" 2>/dev/null | $Xsed -e 10q \
+ | $EGREP "$match_pattern_regex" > /dev/null; then
+ valid_a_lib=yes
+ fi
+ ;;
+ pass_all)
+ valid_a_lib=yes
+ ;;
+ esac
+ if test "$valid_a_lib" != yes; then
+ $ECHO
+ $ECHO "*** Warning: Trying to link with static lib archive $deplib."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have"
+ $ECHO "*** because the file extensions .$libext of this argument makes me believe"
+ $ECHO "*** that it is just a static archive that I should not use here."
+ else
+ $ECHO
+ $ECHO "*** Warning: Linking the shared library $output against the"
+ $ECHO "*** static library $deplib is not portable!"
+ deplibs="$deplib $deplibs"
+ fi
+ ;;
+ esac
+ continue
+ ;;
+ prog)
+ if test "$pass" != link; then
+ deplibs="$deplib $deplibs"
+ else
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ fi
+ continue
+ ;;
+ esac # linkmode
+ ;; # *.$libext
+ *.lo | *.$objext)
+ if test "$pass" = conv; then
+ deplibs="$deplib $deplibs"
+ elif test "$linkmode" = prog; then
+ if test "$pass" = dlpreopen || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then
+ # If there is no dlopen support or we're linking statically,
+ # we need to preload.
+ newdlprefiles="$newdlprefiles $deplib"
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ newdlfiles="$newdlfiles $deplib"
+ fi
+ fi
+ continue
+ ;;
+ %DEPLIBS%)
+ alldeplibs=yes
+ continue
+ ;;
+ esac # case $deplib
+
+ if test "$found" = yes || test -f "$lib"; then :
+ else
+ func_fatal_error "cannot find the library \`$lib' or unhandled argument \`$deplib'"
+ fi
+
+ # Check to see that this really is a libtool archive.
+ func_lalib_unsafe_p "$lib" \
+ || func_fatal_error "\`$lib' is not a valid libtool archive"
+
+ func_dirname "$lib" "" "."
+ ladir="$func_dirname_result"
+
+ dlname=
+ dlopen=
+ dlpreopen=
+ libdir=
+ library_names=
+ old_library=
+ inherited_linker_flags=
+ # If the library was installed with an old release of libtool,
+ # it will not redefine variables installed, or shouldnotlink
+ installed=yes
+ shouldnotlink=no
+ avoidtemprpath=
+
+
+ # Read the .la file
+ func_source "$lib"
+
+ # Convert "-framework foo" to "foo.ltframework"
+ if test -n "$inherited_linker_flags"; then
+ tmp_inherited_linker_flags=`$ECHO "X$inherited_linker_flags" | $Xsed -e 's/-framework \([^ $]*\)/\1.ltframework/g'`
+ for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
+ case " $new_inherited_linker_flags " in
+ *" $tmp_inherited_linker_flag "*) ;;
+ *) new_inherited_linker_flags="$new_inherited_linker_flags $tmp_inherited_linker_flag";;
+ esac
+ done
+ fi
+ dependency_libs=`$ECHO "X $dependency_libs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ if test "$linkmode,$pass" = "lib,link" ||
+ test "$linkmode,$pass" = "prog,scan" ||
+ { test "$linkmode" != prog && test "$linkmode" != lib; }; then
+ test -n "$dlopen" && dlfiles="$dlfiles $dlopen"
+ test -n "$dlpreopen" && dlprefiles="$dlprefiles $dlpreopen"
+ fi
+
+ if test "$pass" = conv; then
+ # Only check for convenience libraries
+ deplibs="$lib $deplibs"
+ if test -z "$libdir"; then
+ if test -z "$old_library"; then
+ func_fatal_error "cannot find name of link library for \`$lib'"
+ fi
+ # It is a libtool convenience library, so add in its objects.
+ convenience="$convenience $ladir/$objdir/$old_library"
+ old_convenience="$old_convenience $ladir/$objdir/$old_library"
+ tmp_libs=
+ for deplib in $dependency_libs; do
+ deplibs="$deplib $deplibs"
+ if $opt_duplicate_deps ; then
+ case "$tmp_libs " in
+ *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+ esac
+ fi
+ tmp_libs="$tmp_libs $deplib"
+ done
+ elif test "$linkmode" != prog && test "$linkmode" != lib; then
+ func_fatal_error "\`$lib' is not a convenience library"
+ fi
+ continue
+ fi # $pass = conv
+
+
+ # Get the name of the library we link against.
+ linklib=
+ for l in $old_library $library_names; do
+ linklib="$l"
+ done
+ if test -z "$linklib"; then
+ func_fatal_error "cannot find name of link library for \`$lib'"
+ fi
+
+ # This library was specified with -dlopen.
+ if test "$pass" = dlopen; then
+ if test -z "$libdir"; then
+ func_fatal_error "cannot -dlopen a convenience library: \`$lib'"
+ fi
+ if test -z "$dlname" ||
+ test "$dlopen_support" != yes ||
+ test "$build_libtool_libs" = no; then
+ # If there is no dlname, no dlopen support or we're linking
+ # statically, we need to preload. We also need to preload any
+ # dependent libraries so libltdl's deplib preloader doesn't
+ # bomb out in the load deplibs phase.
+ dlprefiles="$dlprefiles $lib $dependency_libs"
+ else
+ newdlfiles="$newdlfiles $lib"
+ fi
+ continue
+ fi # $pass = dlopen
+
+ # We need an absolute path.
+ case $ladir in
+ [\\/]* | [A-Za-z]:[\\/]*) abs_ladir="$ladir" ;;
+ *)
+ abs_ladir=`cd "$ladir" && pwd`
+ if test -z "$abs_ladir"; then
+ func_warning "cannot determine absolute directory name of \`$ladir'"
+ func_warning "passing it literally to the linker, although it might fail"
+ abs_ladir="$ladir"
+ fi
+ ;;
+ esac
+ func_basename "$lib"
+ laname="$func_basename_result"
+
+ # Find the relevant object directory and library name.
+ if test "X$installed" = Xyes; then
+ if test ! -f "$libdir/$linklib" && test -f "$abs_ladir/$linklib"; then
+ func_warning "library \`$lib' was moved."
+ dir="$ladir"
+ absdir="$abs_ladir"
+ libdir="$abs_ladir"
+ else
+ dir="$libdir"
+ absdir="$libdir"
+ fi
+ test "X$hardcode_automatic" = Xyes && avoidtemprpath=yes
+ else
+ if test ! -f "$ladir/$objdir/$linklib" && test -f "$abs_ladir/$linklib"; then
+ dir="$ladir"
+ absdir="$abs_ladir"
+ # Remove this search path later
+ notinst_path="$notinst_path $abs_ladir"
+ else
+ dir="$ladir/$objdir"
+ absdir="$abs_ladir/$objdir"
+ # Remove this search path later
+ notinst_path="$notinst_path $abs_ladir"
+ fi
+ fi # $installed = yes
+ func_stripname 'lib' '.la' "$laname"
+ name=$func_stripname_result
+
+ # This library was specified with -dlpreopen.
+ if test "$pass" = dlpreopen; then
+ if test -z "$libdir" && test "$linkmode" = prog; then
+ func_fatal_error "only libraries may -dlpreopen a convenience library: \`$lib'"
+ fi
+ # Prefer using a static library (so that no silly _DYNAMIC symbols
+ # are required to link).
+ if test -n "$old_library"; then
+ newdlprefiles="$newdlprefiles $dir/$old_library"
+ # Keep a list of preopened convenience libraries to check
+ # that they are being used correctly in the link pass.
+ test -z "$libdir" && \
+ dlpreconveniencelibs="$dlpreconveniencelibs $dir/$old_library"
+ # Otherwise, use the dlname, so that lt_dlopen finds it.
+ elif test -n "$dlname"; then
+ newdlprefiles="$newdlprefiles $dir/$dlname"
+ else
+ newdlprefiles="$newdlprefiles $dir/$linklib"
+ fi
+ fi # $pass = dlpreopen
+
+ if test -z "$libdir"; then
+ # Link the convenience library
+ if test "$linkmode" = lib; then
+ deplibs="$dir/$old_library $deplibs"
+ elif test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$dir/$old_library $compile_deplibs"
+ finalize_deplibs="$dir/$old_library $finalize_deplibs"
+ else
+ deplibs="$lib $deplibs" # used for prog,scan pass
+ fi
+ continue
+ fi
+
+
+ if test "$linkmode" = prog && test "$pass" != link; then
+ newlib_search_path="$newlib_search_path $ladir"
+ deplibs="$lib $deplibs"
+
+ linkalldeplibs=no
+ if test "$link_all_deplibs" != no || test -z "$library_names" ||
+ test "$build_libtool_libs" = no; then
+ linkalldeplibs=yes
+ fi
+
+ tmp_libs=
+ for deplib in $dependency_libs; do
+ case $deplib in
+ -L*) func_stripname '-L' '' "$deplib"
+ newlib_search_path="$newlib_search_path $func_stripname_result"
+ ;;
+ esac
+ # Need to link against all dependency_libs?
+ if test "$linkalldeplibs" = yes; then
+ deplibs="$deplib $deplibs"
+ else
+ # Need to hardcode shared library paths
+ # or/and link against static libraries
+ newdependency_libs="$deplib $newdependency_libs"
+ fi
+ if $opt_duplicate_deps ; then
+ case "$tmp_libs " in
+ *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+ esac
+ fi
+ tmp_libs="$tmp_libs $deplib"
+ done # for deplib
+ continue
+ fi # $linkmode = prog...
+
+ if test "$linkmode,$pass" = "prog,link"; then
+ if test -n "$library_names" &&
+ { { test "$prefer_static_libs" = no ||
+ test "$prefer_static_libs,$installed" = "built,yes"; } ||
+ test -z "$old_library"; }; then
+ # We need to hardcode the library path
+ if test -n "$shlibpath_var" && test -z "$avoidtemprpath" ; then
+ # Make sure the rpath contains only unique directories.
+ case "$temp_rpath:" in
+ *"$absdir:"*) ;;
+ *) temp_rpath="$temp_rpath$absdir:" ;;
+ esac
+ fi
+
+ # Hardcode the library path.
+ # Skip directories that are in the system default run-time
+ # search path.
+ case " $sys_lib_dlsearch_path " in
+ *" $absdir "*) ;;
+ *)
+ case "$compile_rpath " in
+ *" $absdir "*) ;;
+ *) compile_rpath="$compile_rpath $absdir"
+ esac
+ ;;
+ esac
+ case " $sys_lib_dlsearch_path " in
+ *" $libdir "*) ;;
+ *)
+ case "$finalize_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_rpath="$finalize_rpath $libdir"
+ esac
+ ;;
+ esac
+ fi # $linkmode,$pass = prog,link...
+
+ if test "$alldeplibs" = yes &&
+ { test "$deplibs_check_method" = pass_all ||
+ { test "$build_libtool_libs" = yes &&
+ test -n "$library_names"; }; }; then
+ # We only need to search for static libraries
+ continue
+ fi
+ fi
+
+ link_static=no # Whether the deplib will be linked statically
+ use_static_libs=$prefer_static_libs
+ if test "$use_static_libs" = built && test "$installed" = yes; then
+ use_static_libs=no
+ fi
+ if test -n "$library_names" &&
+ { test "$use_static_libs" = no || test -z "$old_library"; }; then
+ case $host in
+ *cygwin* | *mingw* | *cegcc*)
+ # No point in relinking DLLs because paths are not encoded
+ notinst_deplibs="$notinst_deplibs $lib"
+ need_relink=no
+ ;;
+ *)
+ if test "$installed" = no; then
+ notinst_deplibs="$notinst_deplibs $lib"
+ need_relink=yes
+ fi
+ ;;
+ esac
+ # This is a shared library
+
+ # Warn about portability, can't link against -module's on some
+ # systems (darwin). Don't bleat about dlopened modules though!
+ dlopenmodule=""
+ for dlpremoduletest in $dlprefiles; do
+ if test "X$dlpremoduletest" = "X$lib"; then
+ dlopenmodule="$dlpremoduletest"
+ break
+ fi
+ done
+ if test -z "$dlopenmodule" && test "$shouldnotlink" = yes && test "$pass" = link; then
+ $ECHO
+ if test "$linkmode" = prog; then
+ $ECHO "*** Warning: Linking the executable $output against the loadable module"
+ else
+ $ECHO "*** Warning: Linking the shared library $output against the loadable module"
+ fi
+ $ECHO "*** $linklib is not portable!"
+ fi
+ if test "$linkmode" = lib &&
+ test "$hardcode_into_libs" = yes; then
+ # Hardcode the library path.
+ # Skip directories that are in the system default run-time
+ # search path.
+ case " $sys_lib_dlsearch_path " in
+ *" $absdir "*) ;;
+ *)
+ case "$compile_rpath " in
+ *" $absdir "*) ;;
+ *) compile_rpath="$compile_rpath $absdir"
+ esac
+ ;;
+ esac
+ case " $sys_lib_dlsearch_path " in
+ *" $libdir "*) ;;
+ *)
+ case "$finalize_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_rpath="$finalize_rpath $libdir"
+ esac
+ ;;
+ esac
+ fi
+
+ if test -n "$old_archive_from_expsyms_cmds"; then
+ # figure out the soname
+ set dummy $library_names
+ shift
+ realname="$1"
+ shift
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ # use dlname if we got it. it's perfectly good, no?
+ if test -n "$dlname"; then
+ soname="$dlname"
+ elif test -n "$soname_spec"; then
+ # bleh windows
+ case $host in
+ *cygwin* | mingw* | *cegcc*)
+ func_arith $current - $age
+ major=$func_arith_result
+ versuffix="-$major"
+ ;;
+ esac
+ eval soname=\"$soname_spec\"
+ else
+ soname="$realname"
+ fi
+
+ # Make a new name for the extract_expsyms_cmds to use
+ soroot="$soname"
+ func_basename "$soroot"
+ soname="$func_basename_result"
+ func_stripname 'lib' '.dll' "$soname"
+ newlib=libimp-$func_stripname_result.a
+
+ # If the library has no export list, then create one now
+ if test -f "$output_objdir/$soname-def"; then :
+ else
+ func_verbose "extracting exported symbol list from \`$soname'"
+ func_execute_cmds "$extract_expsyms_cmds" 'exit $?'
+ fi
+
+ # Create $newlib
+ if test -f "$output_objdir/$newlib"; then :; else
+ func_verbose "generating import library for \`$soname'"
+ func_execute_cmds "$old_archive_from_expsyms_cmds" 'exit $?'
+ fi
+ # make sure the library variables are pointing to the new library
+ dir=$output_objdir
+ linklib=$newlib
+ fi # test -n "$old_archive_from_expsyms_cmds"
+
+ if test "$linkmode" = prog || test "$mode" != relink; then
+ add_shlibpath=
+ add_dir=
+ add=
+ lib_linked=yes
+ case $hardcode_action in
+ immediate | unsupported)
+ if test "$hardcode_direct" = no; then
+ add="$dir/$linklib"
+ case $host in
+ *-*-sco3.2v5.0.[024]*) add_dir="-L$dir" ;;
+ *-*-sysv4*uw2*) add_dir="-L$dir" ;;
+ *-*-sysv5OpenUNIX* | *-*-sysv5UnixWare7.[01].[10]* | \
+ *-*-unixware7*) add_dir="-L$dir" ;;
+ *-*-darwin* )
+ # if the lib is a (non-dlopened) module then we can not
+ # link against it, someone is ignoring the earlier warnings
+ if /usr/bin/file -L $add 2> /dev/null |
+ $GREP ": [^:]* bundle" >/dev/null ; then
+ if test "X$dlopenmodule" != "X$lib"; then
+ $ECHO "*** Warning: lib $linklib is a module, not a shared library"
+ if test -z "$old_library" ; then
+ $ECHO
+ $ECHO "*** And there doesn't seem to be a static archive available"
+ $ECHO "*** The link will probably fail, sorry"
+ else
+ add="$dir/$old_library"
+ fi
+ elif test -n "$old_library"; then
+ add="$dir/$old_library"
+ fi
+ fi
+ esac
+ elif test "$hardcode_minus_L" = no; then
+ case $host in
+ *-*-sunos*) add_shlibpath="$dir" ;;
+ esac
+ add_dir="-L$dir"
+ add="-l$name"
+ elif test "$hardcode_shlibpath_var" = no; then
+ add_shlibpath="$dir"
+ add="-l$name"
+ else
+ lib_linked=no
+ fi
+ ;;
+ relink)
+ if test "$hardcode_direct" = yes &&
+ test "$hardcode_direct_absolute" = no; then
+ add="$dir/$linklib"
+ elif test "$hardcode_minus_L" = yes; then
+ add_dir="-L$dir"
+ # Try looking first in the location we're being installed to.
+ if test -n "$inst_prefix_dir"; then
+ case $libdir in
+ [\\/]*)
+ add_dir="$add_dir -L$inst_prefix_dir$libdir"
+ ;;
+ esac
+ fi
+ add="-l$name"
+ elif test "$hardcode_shlibpath_var" = yes; then
+ add_shlibpath="$dir"
+ add="-l$name"
+ else
+ lib_linked=no
+ fi
+ ;;
+ *) lib_linked=no ;;
+ esac
+
+ if test "$lib_linked" != yes; then
+ func_fatal_configuration "unsupported hardcode properties"
+ fi
+
+ if test -n "$add_shlibpath"; then
+ case :$compile_shlibpath: in
+ *":$add_shlibpath:"*) ;;
+ *) compile_shlibpath="$compile_shlibpath$add_shlibpath:" ;;
+ esac
+ fi
+ if test "$linkmode" = prog; then
+ test -n "$add_dir" && compile_deplibs="$add_dir $compile_deplibs"
+ test -n "$add" && compile_deplibs="$add $compile_deplibs"
+ else
+ test -n "$add_dir" && deplibs="$add_dir $deplibs"
+ test -n "$add" && deplibs="$add $deplibs"
+ if test "$hardcode_direct" != yes &&
+ test "$hardcode_minus_L" != yes &&
+ test "$hardcode_shlibpath_var" = yes; then
+ case :$finalize_shlibpath: in
+ *":$libdir:"*) ;;
+ *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;;
+ esac
+ fi
+ fi
+ fi
+
+ if test "$linkmode" = prog || test "$mode" = relink; then
+ add_shlibpath=
+ add_dir=
+ add=
+ # Finalize command for both is simple: just hardcode it.
+ if test "$hardcode_direct" = yes &&
+ test "$hardcode_direct_absolute" = no; then
+ add="$libdir/$linklib"
+ elif test "$hardcode_minus_L" = yes; then
+ add_dir="-L$libdir"
+ add="-l$name"
+ elif test "$hardcode_shlibpath_var" = yes; then
+ case :$finalize_shlibpath: in
+ *":$libdir:"*) ;;
+ *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;;
+ esac
+ add="-l$name"
+ elif test "$hardcode_automatic" = yes; then
+ if test -n "$inst_prefix_dir" &&
+ test -f "$inst_prefix_dir$libdir/$linklib" ; then
+ add="$inst_prefix_dir$libdir/$linklib"
+ else
+ add="$libdir/$linklib"
+ fi
+ else
+ # We cannot seem to hardcode it, guess we'll fake it.
+ add_dir="-L$libdir"
+ # Try looking first in the location we're being installed to.
+ if test -n "$inst_prefix_dir"; then
+ case $libdir in
+ [\\/]*)
+ add_dir="$add_dir -L$inst_prefix_dir$libdir"
+ ;;
+ esac
+ fi
+ add="-l$name"
+ fi
+
+ if test "$linkmode" = prog; then
+ test -n "$add_dir" && finalize_deplibs="$add_dir $finalize_deplibs"
+ test -n "$add" && finalize_deplibs="$add $finalize_deplibs"
+ else
+ test -n "$add_dir" && deplibs="$add_dir $deplibs"
+ test -n "$add" && deplibs="$add $deplibs"
+ fi
+ fi
+ elif test "$linkmode" = prog; then
+ # Here we assume that one of hardcode_direct or hardcode_minus_L
+ # is not unsupported. This is valid on all known static and
+ # shared platforms.
+ if test "$hardcode_direct" != unsupported; then
+ test -n "$old_library" && linklib="$old_library"
+ compile_deplibs="$dir/$linklib $compile_deplibs"
+ finalize_deplibs="$dir/$linklib $finalize_deplibs"
+ else
+ compile_deplibs="-l$name -L$dir $compile_deplibs"
+ finalize_deplibs="-l$name -L$dir $finalize_deplibs"
+ fi
+ elif test "$build_libtool_libs" = yes; then
+ # Not a shared library
+ if test "$deplibs_check_method" != pass_all; then
+ # We're trying link a shared library against a static one
+ # but the system doesn't support it.
+
+ # Just print a warning and add the library to dependency_libs so
+ # that the program can be linked against the static library.
+ $ECHO
+ $ECHO "*** Warning: This system can not link to static lib archive $lib."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have."
+ if test "$module" = yes; then
+ $ECHO "*** But as you try to build a module library, libtool will still create "
+ $ECHO "*** a static module, that should work as long as the dlopening application"
+ $ECHO "*** is linked with the -dlopen flag to resolve symbols at runtime."
+ if test -z "$global_symbol_pipe"; then
+ $ECHO
+ $ECHO "*** However, this would only work if libtool was able to extract symbol"
+ $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could"
+ $ECHO "*** not find such a program. So, this module is probably useless."
+ $ECHO "*** \`nm' from GNU binutils and a full rebuild may help."
+ fi
+ if test "$build_old_libs" = no; then
+ build_libtool_libs=module
+ build_old_libs=yes
+ else
+ build_libtool_libs=no
+ fi
+ fi
+ else
+ deplibs="$dir/$old_library $deplibs"
+ link_static=yes
+ fi
+ fi # link shared/static library?
+
+ if test "$linkmode" = lib; then
+ if test -n "$dependency_libs" &&
+ { test "$hardcode_into_libs" != yes ||
+ test "$build_old_libs" = yes ||
+ test "$link_static" = yes; }; then
+ # Extract -R from dependency_libs
+ temp_deplibs=
+ for libdir in $dependency_libs; do
+ case $libdir in
+ -R*) func_stripname '-R' '' "$libdir"
+ temp_xrpath=$func_stripname_result
+ case " $xrpath " in
+ *" $temp_xrpath "*) ;;
+ *) xrpath="$xrpath $temp_xrpath";;
+ esac;;
+ *) temp_deplibs="$temp_deplibs $libdir";;
+ esac
+ done
+ dependency_libs="$temp_deplibs"
+ fi
+
+ newlib_search_path="$newlib_search_path $absdir"
+ # Link against this library
+ test "$link_static" = no && newdependency_libs="$abs_ladir/$laname $newdependency_libs"
+ # ... and its dependency_libs
+ tmp_libs=
+ for deplib in $dependency_libs; do
+ newdependency_libs="$deplib $newdependency_libs"
+ if $opt_duplicate_deps ; then
+ case "$tmp_libs " in
+ *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+ esac
+ fi
+ tmp_libs="$tmp_libs $deplib"
+ done
+
+ if test "$link_all_deplibs" != no; then
+ # Add the search paths of all dependency libraries
+ for deplib in $dependency_libs; do
+ path=
+ case $deplib in
+ -L*) path="$deplib" ;;
+ *.la)
+ func_dirname "$deplib" "" "."
+ dir="$func_dirname_result"
+ # We need an absolute path.
+ case $dir in
+ [\\/]* | [A-Za-z]:[\\/]*) absdir="$dir" ;;
+ *)
+ absdir=`cd "$dir" && pwd`
+ if test -z "$absdir"; then
+ func_warning "cannot determine absolute directory name of \`$dir'"
+ absdir="$dir"
+ fi
+ ;;
+ esac
+ if $GREP "^installed=no" $deplib > /dev/null; then
+ case $host in
+ *-*-darwin*)
+ depdepl=
+ eval deplibrary_names=`${SED} -n -e 's/^library_names=\(.*\)$/\1/p' $deplib`
+ if test -n "$deplibrary_names" ; then
+ for tmp in $deplibrary_names ; do
+ depdepl=$tmp
+ done
+ if test -f "$absdir/$objdir/$depdepl" ; then
+ depdepl="$absdir/$objdir/$depdepl"
+ darwin_install_name=`${OTOOL} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'`
+ if test -z "$darwin_install_name"; then
+ darwin_install_name=`${OTOOL64} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'`
+ fi
+ compiler_flags="$compiler_flags ${wl}-dylib_file ${wl}${darwin_install_name}:${depdepl}"
+ linker_flags="$linker_flags -dylib_file ${darwin_install_name}:${depdepl}"
+ path=
+ fi
+ fi
+ ;;
+ *)
+ path="-L$absdir/$objdir"
+ ;;
+ esac
+ else
+ eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib`
+ test -z "$libdir" && \
+ func_fatal_error "\`$deplib' is not a valid libtool archive"
+ test "$absdir" != "$libdir" && \
+ func_warning "\`$deplib' seems to be moved"
+
+ path="-L$absdir"
+ fi
+ ;;
+ esac
+ case " $deplibs " in
+ *" $path "*) ;;
+ *) deplibs="$path $deplibs" ;;
+ esac
+ done
+ fi # link_all_deplibs != no
+ fi # linkmode = lib
+ done # for deplib in $libs
+ if test "$pass" = link; then
+ if test "$linkmode" = "prog"; then
+ compile_deplibs="$new_inherited_linker_flags $compile_deplibs"
+ finalize_deplibs="$new_inherited_linker_flags $finalize_deplibs"
+ else
+ compiler_flags="$compiler_flags "`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ fi
+ fi
+ dependency_libs="$newdependency_libs"
+ if test "$pass" = dlpreopen; then
+ # Link the dlpreopened libraries before other libraries
+ for deplib in $save_deplibs; do
+ deplibs="$deplib $deplibs"
+ done
+ fi
+ if test "$pass" != dlopen; then
+ if test "$pass" != conv; then
+ # Make sure lib_search_path contains only unique directories.
+ lib_search_path=
+ for dir in $newlib_search_path; do
+ case "$lib_search_path " in
+ *" $dir "*) ;;
+ *) lib_search_path="$lib_search_path $dir" ;;
+ esac
+ done
+ newlib_search_path=
+ fi
+
+ if test "$linkmode,$pass" != "prog,link"; then
+ vars="deplibs"
+ else
+ vars="compile_deplibs finalize_deplibs"
+ fi
+ for var in $vars dependency_libs; do
+ # Add libraries to $var in reverse order
+ eval tmp_libs=\"\$$var\"
+ new_libs=
+ for deplib in $tmp_libs; do
+ # FIXME: Pedantically, this is the right thing to do, so
+ # that some nasty dependency loop isn't accidentally
+ # broken:
+ #new_libs="$deplib $new_libs"
+ # Pragmatically, this seems to cause very few problems in
+ # practice:
+ case $deplib in
+ -L*) new_libs="$deplib $new_libs" ;;
+ -R*) ;;
+ *)
+ # And here is the reason: when a library appears more
+ # than once as an explicit dependence of a library, or
+ # is implicitly linked in more than once by the
+ # compiler, it is considered special, and multiple
+ # occurrences thereof are not removed. Compare this
+ # with having the same library being listed as a
+ # dependency of multiple other libraries: in this case,
+ # we know (pedantically, we assume) the library does not
+ # need to be listed more than once, so we keep only the
+ # last copy. This is not always right, but it is rare
+ # enough that we require users that really mean to play
+ # such unportable linking tricks to link the library
+ # using -Wl,-lname, so that libtool does not consider it
+ # for duplicate removal.
+ case " $specialdeplibs " in
+ *" $deplib "*) new_libs="$deplib $new_libs" ;;
+ *)
+ case " $new_libs " in
+ *" $deplib "*) ;;
+ *) new_libs="$deplib $new_libs" ;;
+ esac
+ ;;
+ esac
+ ;;
+ esac
+ done
+ tmp_libs=
+ for deplib in $new_libs; do
+ case $deplib in
+ -L*)
+ case " $tmp_libs " in
+ *" $deplib "*) ;;
+ *) tmp_libs="$tmp_libs $deplib" ;;
+ esac
+ ;;
+ *) tmp_libs="$tmp_libs $deplib" ;;
+ esac
+ done
+ eval $var=\"$tmp_libs\"
+ done # for var
+ fi
+ # Last step: remove runtime libs from dependency_libs
+ # (they stay in deplibs)
+ tmp_libs=
+ for i in $dependency_libs ; do
+ case " $predeps $postdeps $compiler_lib_search_path " in
+ *" $i "*)
+ i=""
+ ;;
+ esac
+ if test -n "$i" ; then
+ tmp_libs="$tmp_libs $i"
+ fi
+ done
+ dependency_libs=$tmp_libs
+ done # for pass
+ if test "$linkmode" = prog; then
+ dlfiles="$newdlfiles"
+ fi
+ if test "$linkmode" = prog || test "$linkmode" = lib; then
+ dlprefiles="$newdlprefiles"
+ fi
+
+ case $linkmode in
+ oldlib)
+ if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
+ func_warning "\`-dlopen' is ignored for archives"
+ fi
+
+ case " $deplibs" in
+ *\ -l* | *\ -L*)
+ func_warning "\`-l' and \`-L' are ignored for archives" ;;
+ esac
+
+ test -n "$rpath" && \
+ func_warning "\`-rpath' is ignored for archives"
+
+ test -n "$xrpath" && \
+ func_warning "\`-R' is ignored for archives"
+
+ test -n "$vinfo" && \
+ func_warning "\`-version-info/-version-number' is ignored for archives"
+
+ test -n "$release" && \
+ func_warning "\`-release' is ignored for archives"
+
+ test -n "$export_symbols$export_symbols_regex" && \
+ func_warning "\`-export-symbols' is ignored for archives"
+
+ # Now set the variables for building old libraries.
+ build_libtool_libs=no
+ oldlibs="$output"
+ objs="$objs$old_deplibs"
+ ;;
+
+ lib)
+ # Make sure we only generate libraries of the form `libNAME.la'.
+ case $outputname in
+ lib*)
+ func_stripname 'lib' '.la' "$outputname"
+ name=$func_stripname_result
+ eval shared_ext=\"$shrext_cmds\"
+ eval libname=\"$libname_spec\"
+ ;;
+ *)
+ test "$module" = no && \
+ func_fatal_help "libtool library \`$output' must begin with \`lib'"
+
+ if test "$need_lib_prefix" != no; then
+ # Add the "lib" prefix for modules if required
+ func_stripname '' '.la' "$outputname"
+ name=$func_stripname_result
+ eval shared_ext=\"$shrext_cmds\"
+ eval libname=\"$libname_spec\"
+ else
+ func_stripname '' '.la' "$outputname"
+ libname=$func_stripname_result
+ fi
+ ;;
+ esac
+
+ if test -n "$objs"; then
+ if test "$deplibs_check_method" != pass_all; then
+ func_fatal_error "cannot build libtool library \`$output' from non-libtool objects on this host:$objs"
+ else
+ $ECHO
+ $ECHO "*** Warning: Linking the shared library $output against the non-libtool"
+ $ECHO "*** objects $objs is not portable!"
+ libobjs="$libobjs $objs"
+ fi
+ fi
+
+ test "$dlself" != no && \
+ func_warning "\`-dlopen self' is ignored for libtool libraries"
+
+ set dummy $rpath
+ shift
+ test "$#" -gt 1 && \
+ func_warning "ignoring multiple \`-rpath's for a libtool library"
+
+ install_libdir="$1"
+
+ oldlibs=
+ if test -z "$rpath"; then
+ if test "$build_libtool_libs" = yes; then
+ # Building a libtool convenience library.
+ # Some compilers have problems with a `.al' extension so
+ # convenience libraries should have the same extension an
+ # archive normally would.
+ oldlibs="$output_objdir/$libname.$libext $oldlibs"
+ build_libtool_libs=convenience
+ build_old_libs=yes
+ fi
+
+ test -n "$vinfo" && \
+ func_warning "\`-version-info/-version-number' is ignored for convenience libraries"
+
+ test -n "$release" && \
+ func_warning "\`-release' is ignored for convenience libraries"
+ else
+
+ # Parse the version information argument.
+ save_ifs="$IFS"; IFS=':'
+ set dummy $vinfo 0 0 0
+ shift
+ IFS="$save_ifs"
+
+ test -n "$7" && \
+ func_fatal_help "too many parameters to \`-version-info'"
+
+ # convert absolute version numbers to libtool ages
+ # this retains compatibility with .la files and attempts
+ # to make the code below a bit more comprehensible
+
+ case $vinfo_number in
+ yes)
+ number_major="$1"
+ number_minor="$2"
+ number_revision="$3"
+ #
+ # There are really only two kinds -- those that
+ # use the current revision as the major version
+ # and those that subtract age and use age as
+ # a minor version. But, then there is irix
+ # which has an extra 1 added just for fun
+ #
+ case $version_type in
+ darwin|linux|osf|windows|none)
+ func_arith $number_major + $number_minor
+ current=$func_arith_result
+ age="$number_minor"
+ revision="$number_revision"
+ ;;
+ freebsd-aout|freebsd-elf|sunos)
+ current="$number_major"
+ revision="$number_minor"
+ age="0"
+ ;;
+ irix|nonstopux)
+ func_arith $number_major + $number_minor
+ current=$func_arith_result
+ age="$number_minor"
+ revision="$number_minor"
+ lt_irix_increment=no
+ ;;
+ *)
+ func_fatal_configuration "$modename: unknown library version type \`$version_type'"
+ ;;
+ esac
+ ;;
+ no)
+ current="$1"
+ revision="$2"
+ age="$3"
+ ;;
+ esac
+
+ # Check that each of the things are valid numbers.
+ case $current in
+ 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
+ *)
+ func_error "CURRENT \`$current' must be a nonnegative integer"
+ func_fatal_error "\`$vinfo' is not valid version information"
+ ;;
+ esac
+
+ case $revision in
+ 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
+ *)
+ func_error "REVISION \`$revision' must be a nonnegative integer"
+ func_fatal_error "\`$vinfo' is not valid version information"
+ ;;
+ esac
+
+ case $age in
+ 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
+ *)
+ func_error "AGE \`$age' must be a nonnegative integer"
+ func_fatal_error "\`$vinfo' is not valid version information"
+ ;;
+ esac
+
+ if test "$age" -gt "$current"; then
+ func_error "AGE \`$age' is greater than the current interface number \`$current'"
+ func_fatal_error "\`$vinfo' is not valid version information"
+ fi
+
+ # Calculate the version variables.
+ major=
+ versuffix=
+ verstring=
+ case $version_type in
+ none) ;;
+
+ darwin)
+ # Like Linux, but with the current version available in
+ # verstring for coding it into the library header
+ func_arith $current - $age
+ major=.$func_arith_result
+ versuffix="$major.$age.$revision"
+ # Darwin ld doesn't like 0 for these options...
+ func_arith $current + 1
+ minor_current=$func_arith_result
+ xlcverstring="${wl}-compatibility_version ${wl}$minor_current ${wl}-current_version ${wl}$minor_current.$revision"
+ verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
+ ;;
+
+ freebsd-aout)
+ major=".$current"
+ versuffix=".$current.$revision";
+ ;;
+
+ freebsd-elf)
+ major=".$current"
+ versuffix=".$current"
+ ;;
+
+ irix | nonstopux)
+ if test "X$lt_irix_increment" = "Xno"; then
+ func_arith $current - $age
+ else
+ func_arith $current - $age + 1
+ fi
+ major=$func_arith_result
+
+ case $version_type in
+ nonstopux) verstring_prefix=nonstopux ;;
+ *) verstring_prefix=sgi ;;
+ esac
+ verstring="$verstring_prefix$major.$revision"
+
+ # Add in all the interfaces that we are compatible with.
+ loop=$revision
+ while test "$loop" -ne 0; do
+ func_arith $revision - $loop
+ iface=$func_arith_result
+ func_arith $loop - 1
+ loop=$func_arith_result
+ verstring="$verstring_prefix$major.$iface:$verstring"
+ done
+
+ # Before this point, $major must not contain `.'.
+ major=.$major
+ versuffix="$major.$revision"
+ ;;
+
+ linux)
+ func_arith $current - $age
+ major=.$func_arith_result
+ versuffix="$major.$age.$revision"
+ ;;
+
+ osf)
+ func_arith $current - $age
+ major=.$func_arith_result
+ versuffix=".$current.$age.$revision"
+ verstring="$current.$age.$revision"
+
+ # Add in all the interfaces that we are compatible with.
+ loop=$age
+ while test "$loop" -ne 0; do
+ func_arith $current - $loop
+ iface=$func_arith_result
+ func_arith $loop - 1
+ loop=$func_arith_result
+ verstring="$verstring:${iface}.0"
+ done
+
+ # Make executables depend on our current version.
+ verstring="$verstring:${current}.0"
+ ;;
+
+ qnx)
+ major=".$current"
+ versuffix=".$current"
+ ;;
+
+ sunos)
+ major=".$current"
+ versuffix=".$current.$revision"
+ ;;
+
+ windows)
+ # Use '-' rather than '.', since we only want one
+ # extension on DOS 8.3 filesystems.
+ func_arith $current - $age
+ major=$func_arith_result
+ versuffix="-$major"
+ ;;
+
+ *)
+ func_fatal_configuration "unknown library version type \`$version_type'"
+ ;;
+ esac
+
+ # Clear the version info if we defaulted, and they specified a release.
+ if test -z "$vinfo" && test -n "$release"; then
+ major=
+ case $version_type in
+ darwin)
+ # we can't check for "0.0" in archive_cmds due to quoting
+ # problems, so we reset it completely
+ verstring=
+ ;;
+ *)
+ verstring="0.0"
+ ;;
+ esac
+ if test "$need_version" = no; then
+ versuffix=
+ else
+ versuffix=".0.0"
+ fi
+ fi
+
+ # Remove version info from name if versioning should be avoided
+ if test "$avoid_version" = yes && test "$need_version" = no; then
+ major=
+ versuffix=
+ verstring=""
+ fi
+
+ # Check to see if the archive will have undefined symbols.
+ if test "$allow_undefined" = yes; then
+ if test "$allow_undefined_flag" = unsupported; then
+ func_warning "undefined symbols not allowed in $host shared libraries"
+ build_libtool_libs=no
+ build_old_libs=yes
+ fi
+ else
+ # Don't allow undefined symbols.
+ allow_undefined_flag="$no_undefined_flag"
+ fi
+
+ fi
+
+ func_generate_dlsyms "$libname" "$libname" "yes"
+ libobjs="$libobjs $symfileobj"
+ test "X$libobjs" = "X " && libobjs=
+
+ if test "$mode" != relink; then
+ # Remove our outputs, but don't remove object files since they
+ # may have been created when compiling PIC objects.
+ removelist=
+ tempremovelist=`$ECHO "$output_objdir/*"`
+ for p in $tempremovelist; do
+ case $p in
+ *.$objext | *.gcno)
+ ;;
+ $output_objdir/$outputname | $output_objdir/$libname.* | $output_objdir/${libname}${release}.*)
+ if test "X$precious_files_regex" != "X"; then
+ if $ECHO "$p" | $EGREP -e "$precious_files_regex" >/dev/null 2>&1
+ then
+ continue
+ fi
+ fi
+ removelist="$removelist $p"
+ ;;
+ *) ;;
+ esac
+ done
+ test -n "$removelist" && \
+ func_show_eval "${RM}r \$removelist"
+ fi
+
+ # Now set the variables for building old libraries.
+ if test "$build_old_libs" = yes && test "$build_libtool_libs" != convenience ; then
+ oldlibs="$oldlibs $output_objdir/$libname.$libext"
+
+ # Transform .lo files to .o files.
+ oldobjs="$objs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}'$/d' -e "$lo2o" | $NL2SP`
+ fi
+
+ # Eliminate all temporary directories.
+ #for path in $notinst_path; do
+ # lib_search_path=`$ECHO "X$lib_search_path " | $Xsed -e "s% $path % %g"`
+ # deplibs=`$ECHO "X$deplibs " | $Xsed -e "s% -L$path % %g"`
+ # dependency_libs=`$ECHO "X$dependency_libs " | $Xsed -e "s% -L$path % %g"`
+ #done
+
+ if test -n "$xrpath"; then
+ # If the user specified any rpath flags, then add them.
+ temp_xrpath=
+ for libdir in $xrpath; do
+ temp_xrpath="$temp_xrpath -R$libdir"
+ case "$finalize_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_rpath="$finalize_rpath $libdir" ;;
+ esac
+ done
+ if test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes; then
+ dependency_libs="$temp_xrpath $dependency_libs"
+ fi
+ fi
+
+ # Make sure dlfiles contains only unique files that won't be dlpreopened
+ old_dlfiles="$dlfiles"
+ dlfiles=
+ for lib in $old_dlfiles; do
+ case " $dlprefiles $dlfiles " in
+ *" $lib "*) ;;
+ *) dlfiles="$dlfiles $lib" ;;
+ esac
+ done
+
+ # Make sure dlprefiles contains only unique files
+ old_dlprefiles="$dlprefiles"
+ dlprefiles=
+ for lib in $old_dlprefiles; do
+ case "$dlprefiles " in
+ *" $lib "*) ;;
+ *) dlprefiles="$dlprefiles $lib" ;;
+ esac
+ done
+
+ if test "$build_libtool_libs" = yes; then
+ if test -n "$rpath"; then
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-beos* | *-cegcc*)
+ # these systems don't actually have a c library (as such)!
+ ;;
+ *-*-rhapsody* | *-*-darwin1.[012])
+ # Rhapsody C library is in the System framework
+ deplibs="$deplibs System.ltframework"
+ ;;
+ *-*-netbsd*)
+ # Don't link with libc until the a.out ld.so is fixed.
+ ;;
+ *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
+ # Do not include libc due to us having libc/libc_r.
+ ;;
+ *-*-sco3.2v5* | *-*-sco5v6*)
+ # Causes problems with __ctype
+ ;;
+ *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*)
+ # Compiler inserts libc in the correct place for threads to work
+ ;;
+ *)
+ # Add libc to deplibs on all other systems if necessary.
+ if test "$build_libtool_need_lc" = "yes"; then
+ deplibs="$deplibs -lc"
+ fi
+ ;;
+ esac
+ fi
+
+ # Transform deplibs into only deplibs that can be linked in shared.
+ name_save=$name
+ libname_save=$libname
+ release_save=$release
+ versuffix_save=$versuffix
+ major_save=$major
+ # I'm not sure if I'm treating the release correctly. I think
+ # release should show up in the -l (ie -lgmp5) so we don't want to
+ # add it in twice. Is that correct?
+ release=""
+ versuffix=""
+ major=""
+ newdeplibs=
+ droppeddeps=no
+ case $deplibs_check_method in
+ pass_all)
+ # Don't check for shared/static. Everything works.
+ # This might be a little naive. We might want to check
+ # whether the library exists or not. But this is on
+ # osf3 & osf4 and I'm not really sure... Just
+ # implementing what was already the behavior.
+ newdeplibs=$deplibs
+ ;;
+ test_compile)
+ # This code stresses the "libraries are programs" paradigm to its
+ # limits. Maybe even breaks it. We compile a program, linking it
+ # against the deplibs as a proxy for the library. Then we can check
+ # whether they linked in statically or dynamically with ldd.
+ $opt_dry_run || $RM conftest.c
+ cat > conftest.c <<EOF
+ int main() { return 0; }
+EOF
+ $opt_dry_run || $RM conftest
+ if $LTCC $LTCFLAGS -o conftest conftest.c $deplibs; then
+ ldd_output=`ldd conftest`
+ for i in $deplibs; do
+ case $i in
+ -l*)
+ func_stripname -l '' "$i"
+ name=$func_stripname_result
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $i "*)
+ newdeplibs="$newdeplibs $i"
+ i=""
+ ;;
+ esac
+ fi
+ if test -n "$i" ; then
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ deplib_matches=`eval "\\$ECHO \"$library_names_spec\""`
+ set dummy $deplib_matches; shift
+ deplib_match=$1
+ if test `expr "$ldd_output" : ".*$deplib_match"` -ne 0 ; then
+ newdeplibs="$newdeplibs $i"
+ else
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning: dynamic linker does not accept needed library $i."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which I believe you do not have"
+ $ECHO "*** because a test_compile did reveal that the linker did not use it for"
+ $ECHO "*** its dynamic dependency list that programs get resolved with at runtime."
+ fi
+ fi
+ ;;
+ *)
+ newdeplibs="$newdeplibs $i"
+ ;;
+ esac
+ done
+ else
+ # Error occurred in the first compile. Let's try to salvage
+ # the situation: Compile a separate program for each library.
+ for i in $deplibs; do
+ case $i in
+ -l*)
+ func_stripname -l '' "$i"
+ name=$func_stripname_result
+ $opt_dry_run || $RM conftest
+ if $LTCC $LTCFLAGS -o conftest conftest.c $i; then
+ ldd_output=`ldd conftest`
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $i "*)
+ newdeplibs="$newdeplibs $i"
+ i=""
+ ;;
+ esac
+ fi
+ if test -n "$i" ; then
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ deplib_matches=`eval "\\$ECHO \"$library_names_spec\""`
+ set dummy $deplib_matches; shift
+ deplib_match=$1
+ if test `expr "$ldd_output" : ".*$deplib_match"` -ne 0 ; then
+ newdeplibs="$newdeplibs $i"
+ else
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning: dynamic linker does not accept needed library $i."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have"
+ $ECHO "*** because a test_compile did reveal that the linker did not use this one"
+ $ECHO "*** as a dynamic dependency that programs can get resolved with at runtime."
+ fi
+ fi
+ else
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning! Library $i is needed by this library but I was not able to"
+ $ECHO "*** make it link in! You will probably need to install it or some"
+ $ECHO "*** library that it depends on before this library will be fully"
+ $ECHO "*** functional. Installing it before continuing would be even better."
+ fi
+ ;;
+ *)
+ newdeplibs="$newdeplibs $i"
+ ;;
+ esac
+ done
+ fi
+ ;;
+ file_magic*)
+ set dummy $deplibs_check_method; shift
+ file_magic_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"`
+ for a_deplib in $deplibs; do
+ case $a_deplib in
+ -l*)
+ func_stripname -l '' "$a_deplib"
+ name=$func_stripname_result
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $a_deplib "*)
+ newdeplibs="$newdeplibs $a_deplib"
+ a_deplib=""
+ ;;
+ esac
+ fi
+ if test -n "$a_deplib" ; then
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do
+ potential_libs=`ls $i/$libname[.-]* 2>/dev/null`
+ for potent_lib in $potential_libs; do
+ # Follow soft links.
+ if ls -lLd "$potent_lib" 2>/dev/null |
+ $GREP " -> " >/dev/null; then
+ continue
+ fi
+ # The statement above tries to avoid entering an
+ # endless loop below, in case of cyclic links.
+ # We might still enter an endless loop, since a link
+ # loop can be closed while we follow links,
+ # but so what?
+ potlib="$potent_lib"
+ while test -h "$potlib" 2>/dev/null; do
+ potliblink=`ls -ld $potlib | ${SED} 's/.* -> //'`
+ case $potliblink in
+ [\\/]* | [A-Za-z]:[\\/]*) potlib="$potliblink";;
+ *) potlib=`$ECHO "X$potlib" | $Xsed -e 's,[^/]*$,,'`"$potliblink";;
+ esac
+ done
+ if eval $file_magic_cmd \"\$potlib\" 2>/dev/null |
+ $SED -e 10q |
+ $EGREP "$file_magic_regex" > /dev/null; then
+ newdeplibs="$newdeplibs $a_deplib"
+ a_deplib=""
+ break 2
+ fi
+ done
+ done
+ fi
+ if test -n "$a_deplib" ; then
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning: linker path does not have real file for library $a_deplib."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have"
+ $ECHO "*** because I did check the linker path looking for a file starting"
+ if test -z "$potlib" ; then
+ $ECHO "*** with $libname but no candidates were found. (...for file magic test)"
+ else
+ $ECHO "*** with $libname and none of the candidates passed a file format test"
+ $ECHO "*** using a file magic. Last file checked: $potlib"
+ fi
+ fi
+ ;;
+ *)
+ # Add a -L argument.
+ newdeplibs="$newdeplibs $a_deplib"
+ ;;
+ esac
+ done # Gone through all deplibs.
+ ;;
+ match_pattern*)
+ set dummy $deplibs_check_method; shift
+ match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"`
+ for a_deplib in $deplibs; do
+ case $a_deplib in
+ -l*)
+ func_stripname -l '' "$a_deplib"
+ name=$func_stripname_result
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $a_deplib "*)
+ newdeplibs="$newdeplibs $a_deplib"
+ a_deplib=""
+ ;;
+ esac
+ fi
+ if test -n "$a_deplib" ; then
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do
+ potential_libs=`ls $i/$libname[.-]* 2>/dev/null`
+ for potent_lib in $potential_libs; do
+ potlib="$potent_lib" # see symlink-check above in file_magic test
+ if eval "\$ECHO \"X$potent_lib\"" 2>/dev/null | $Xsed -e 10q | \
+ $EGREP "$match_pattern_regex" > /dev/null; then
+ newdeplibs="$newdeplibs $a_deplib"
+ a_deplib=""
+ break 2
+ fi
+ done
+ done
+ fi
+ if test -n "$a_deplib" ; then
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning: linker path does not have real file for library $a_deplib."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have"
+ $ECHO "*** because I did check the linker path looking for a file starting"
+ if test -z "$potlib" ; then
+ $ECHO "*** with $libname but no candidates were found. (...for regex pattern test)"
+ else
+ $ECHO "*** with $libname and none of the candidates passed a file format test"
+ $ECHO "*** using a regex pattern. Last file checked: $potlib"
+ fi
+ fi
+ ;;
+ *)
+ # Add a -L argument.
+ newdeplibs="$newdeplibs $a_deplib"
+ ;;
+ esac
+ done # Gone through all deplibs.
+ ;;
+ none | unknown | *)
+ newdeplibs=""
+ tmp_deplibs=`$ECHO "X $deplibs" | $Xsed \
+ -e 's/ -lc$//' -e 's/ -[LR][^ ]*//g'`
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ for i in $predeps $postdeps ; do
+ # can't use Xsed below, because $i might contain '/'
+ tmp_deplibs=`$ECHO "X $tmp_deplibs" | $Xsed -e "s,$i,,"`
+ done
+ fi
+ if $ECHO "X $tmp_deplibs" | $Xsed -e 's/[ ]//g' |
+ $GREP . >/dev/null; then
+ $ECHO
+ if test "X$deplibs_check_method" = "Xnone"; then
+ $ECHO "*** Warning: inter-library dependencies are not supported in this platform."
+ else
+ $ECHO "*** Warning: inter-library dependencies are not known to be supported."
+ fi
+ $ECHO "*** All declared inter-library dependencies are being dropped."
+ droppeddeps=yes
+ fi
+ ;;
+ esac
+ versuffix=$versuffix_save
+ major=$major_save
+ release=$release_save
+ libname=$libname_save
+ name=$name_save
+
+ case $host in
+ *-*-rhapsody* | *-*-darwin1.[012])
+ # On Rhapsody replace the C library with the System framework
+ newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's/ -lc / System.ltframework /'`
+ ;;
+ esac
+
+ if test "$droppeddeps" = yes; then
+ if test "$module" = yes; then
+ $ECHO
+ $ECHO "*** Warning: libtool could not satisfy all declared inter-library"
+ $ECHO "*** dependencies of module $libname. Therefore, libtool will create"
+ $ECHO "*** a static module, that should work as long as the dlopening"
+ $ECHO "*** application is linked with the -dlopen flag."
+ if test -z "$global_symbol_pipe"; then
+ $ECHO
+ $ECHO "*** However, this would only work if libtool was able to extract symbol"
+ $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could"
+ $ECHO "*** not find such a program. So, this module is probably useless."
+ $ECHO "*** \`nm' from GNU binutils and a full rebuild may help."
+ fi
+ if test "$build_old_libs" = no; then
+ oldlibs="$output_objdir/$libname.$libext"
+ build_libtool_libs=module
+ build_old_libs=yes
+ else
+ build_libtool_libs=no
+ fi
+ else
+ $ECHO "*** The inter-library dependencies that have been dropped here will be"
+ $ECHO "*** automatically added whenever a program is linked with this library"
+ $ECHO "*** or is declared to -dlopen it."
+
+ if test "$allow_undefined" = no; then
+ $ECHO
+ $ECHO "*** Since this library must not contain undefined symbols,"
+ $ECHO "*** because either the platform does not support them or"
+ $ECHO "*** it was explicitly requested with -no-undefined,"
+ $ECHO "*** libtool will only create a static version of it."
+ if test "$build_old_libs" = no; then
+ oldlibs="$output_objdir/$libname.$libext"
+ build_libtool_libs=module
+ build_old_libs=yes
+ else
+ build_libtool_libs=no
+ fi
+ fi
+ fi
+ fi
+ # Done checking deplibs!
+ deplibs=$newdeplibs
+ fi
+ # Time to change all our "foo.ltframework" stuff back to "-framework foo"
+ case $host in
+ *-*-darwin*)
+ newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ new_inherited_linker_flags=`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ deplibs=`$ECHO "X $deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ ;;
+ esac
+
+ # move library search paths that coincide with paths to not yet
+ # installed libraries to the beginning of the library search list
+ new_libs=
+ for path in $notinst_path; do
+ case " $new_libs " in
+ *" -L$path/$objdir "*) ;;
+ *)
+ case " $deplibs " in
+ *" -L$path/$objdir "*)
+ new_libs="$new_libs -L$path/$objdir" ;;
+ esac
+ ;;
+ esac
+ done
+ for deplib in $deplibs; do
+ case $deplib in
+ -L*)
+ case " $new_libs " in
+ *" $deplib "*) ;;
+ *) new_libs="$new_libs $deplib" ;;
+ esac
+ ;;
+ *) new_libs="$new_libs $deplib" ;;
+ esac
+ done
+ deplibs="$new_libs"
+
+ # All the library-specific variables (install_libdir is set above).
+ library_names=
+ old_library=
+ dlname=
+
+ # Test again, we may have decided not to build it any more
+ if test "$build_libtool_libs" = yes; then
+ if test "$hardcode_into_libs" = yes; then
+ # Hardcode the library paths
+ hardcode_libdirs=
+ dep_rpath=
+ rpath="$finalize_rpath"
+ test "$mode" != relink && rpath="$compile_rpath$rpath"
+ for libdir in $rpath; do
+ if test -n "$hardcode_libdir_flag_spec"; then
+ if test -n "$hardcode_libdir_separator"; then
+ if test -z "$hardcode_libdirs"; then
+ hardcode_libdirs="$libdir"
+ else
+ # Just accumulate the unique libdirs.
+ case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
+ *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
+ ;;
+ *)
+ hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir"
+ ;;
+ esac
+ fi
+ else
+ eval flag=\"$hardcode_libdir_flag_spec\"
+ dep_rpath="$dep_rpath $flag"
+ fi
+ elif test -n "$runpath_var"; then
+ case "$perm_rpath " in
+ *" $libdir "*) ;;
+ *) perm_rpath="$perm_rpath $libdir" ;;
+ esac
+ fi
+ done
+ # Substitute the hardcoded libdirs into the rpath.
+ if test -n "$hardcode_libdir_separator" &&
+ test -n "$hardcode_libdirs"; then
+ libdir="$hardcode_libdirs"
+ if test -n "$hardcode_libdir_flag_spec_ld"; then
+ eval dep_rpath=\"$hardcode_libdir_flag_spec_ld\"
+ else
+ eval dep_rpath=\"$hardcode_libdir_flag_spec\"
+ fi
+ fi
+ if test -n "$runpath_var" && test -n "$perm_rpath"; then
+ # We should set the runpath_var.
+ rpath=
+ for dir in $perm_rpath; do
+ rpath="$rpath$dir:"
+ done
+ eval "$runpath_var='$rpath\$$runpath_var'; export $runpath_var"
+ fi
+ test -n "$dep_rpath" && deplibs="$dep_rpath $deplibs"
+ fi
+
+ shlibpath="$finalize_shlibpath"
+ test "$mode" != relink && shlibpath="$compile_shlibpath$shlibpath"
+ if test -n "$shlibpath"; then
+ eval "$shlibpath_var='$shlibpath\$$shlibpath_var'; export $shlibpath_var"
+ fi
+
+ # Get the real and link names of the library.
+ eval shared_ext=\"$shrext_cmds\"
+ eval library_names=\"$library_names_spec\"
+ set dummy $library_names
+ shift
+ realname="$1"
+ shift
+
+ if test -n "$soname_spec"; then
+ eval soname=\"$soname_spec\"
+ else
+ soname="$realname"
+ fi
+ if test -z "$dlname"; then
+ dlname=$soname
+ fi
+
+ lib="$output_objdir/$realname"
+ linknames=
+ for link
+ do
+ linknames="$linknames $link"
+ done
+
+ # Use standard objects if they are pic
+ test -z "$pic_flag" && libobjs=`$ECHO "X$libobjs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+ test "X$libobjs" = "X " && libobjs=
+
+ delfiles=
+ if test -n "$export_symbols" && test -n "$include_expsyms"; then
+ $opt_dry_run || cp "$export_symbols" "$output_objdir/$libname.uexp"
+ export_symbols="$output_objdir/$libname.uexp"
+ delfiles="$delfiles $export_symbols"
+ fi
+
+ orig_export_symbols=
+ case $host_os in
+ cygwin* | mingw* | cegcc*)
+ if test -n "$export_symbols" && test -z "$export_symbols_regex"; then
+ # exporting using user supplied symfile
+ if test "x`$SED 1q $export_symbols`" != xEXPORTS; then
+ # and it's NOT already a .def file. Must figure out
+ # which of the given symbols are data symbols and tag
+ # them as such. So, trigger use of export_symbols_cmds.
+ # export_symbols gets reassigned inside the "prepare
+ # the list of exported symbols" if statement, so the
+ # include_expsyms logic still works.
+ orig_export_symbols="$export_symbols"
+ export_symbols=
+ always_export_symbols=yes
+ fi
+ fi
+ ;;
+ esac
+
+ # Prepare the list of exported symbols
+ if test -z "$export_symbols"; then
+ if test "$always_export_symbols" = yes || test -n "$export_symbols_regex"; then
+ func_verbose "generating symbol list for \`$libname.la'"
+ export_symbols="$output_objdir/$libname.exp"
+ $opt_dry_run || $RM $export_symbols
+ cmds=$export_symbols_cmds
+ save_ifs="$IFS"; IFS='~'
+ for cmd in $cmds; do
+ IFS="$save_ifs"
+ eval cmd=\"$cmd\"
+ func_len " $cmd"
+ len=$func_len_result
+ if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then
+ func_show_eval "$cmd" 'exit $?'
+ skipped_export=false
+ else
+ # The command line is too long to execute in one step.
+ func_verbose "using reloadable object file for export list..."
+ skipped_export=:
+ # Break out early, otherwise skipped_export may be
+ # set to false by a later but shorter cmd.
+ break
+ fi
+ done
+ IFS="$save_ifs"
+ if test -n "$export_symbols_regex" && test "X$skipped_export" != "X:"; then
+ func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"'
+ func_show_eval '$MV "${export_symbols}T" "$export_symbols"'
+ fi
+ fi
+ fi
+
+ if test -n "$export_symbols" && test -n "$include_expsyms"; then
+ tmp_export_symbols="$export_symbols"
+ test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols"
+ $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"'
+ fi
+
+ if test "X$skipped_export" != "X:" && test -n "$orig_export_symbols"; then
+ # The given exports_symbols file has to be filtered, so filter it.
+ func_verbose "filter symbol list for \`$libname.la' to tag DATA exports"
+ # FIXME: $output_objdir/$libname.filter potentially contains lots of
+ # 's' commands which not all seds can handle. GNU sed should be fine
+ # though. Also, the filter scales superlinearly with the number of
+ # global variables. join(1) would be nice here, but unfortunately
+ # isn't a blessed tool.
+ $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter
+ delfiles="$delfiles $export_symbols $output_objdir/$libname.filter"
+ export_symbols=$output_objdir/$libname.def
+ $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols
+ fi
+
+ tmp_deplibs=
+ for test_deplib in $deplibs; do
+ case " $convenience " in
+ *" $test_deplib "*) ;;
+ *)
+ tmp_deplibs="$tmp_deplibs $test_deplib"
+ ;;
+ esac
+ done
+ deplibs="$tmp_deplibs"
+
+ if test -n "$convenience"; then
+ if test -n "$whole_archive_flag_spec" &&
+ test "$compiler_needs_object" = yes &&
+ test -z "$libobjs"; then
+ # extract the archives, so we have objects to list.
+ # TODO: could optimize this to just extract one archive.
+ whole_archive_flag_spec=
+ fi
+ if test -n "$whole_archive_flag_spec"; then
+ save_libobjs=$libobjs
+ eval libobjs=\"\$libobjs $whole_archive_flag_spec\"
+ test "X$libobjs" = "X " && libobjs=
+ else
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $convenience
+ libobjs="$libobjs $func_extract_archives_result"
+ test "X$libobjs" = "X " && libobjs=
+ fi
+ fi
+
+ if test "$thread_safe" = yes && test -n "$thread_safe_flag_spec"; then
+ eval flag=\"$thread_safe_flag_spec\"
+ linker_flags="$linker_flags $flag"
+ fi
+
+ # Make a backup of the uninstalled library when relinking
+ if test "$mode" = relink; then
+ $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}U && $MV $realname ${realname}U)' || exit $?
+ fi
+
+ # Do each of the archive commands.
+ if test "$module" = yes && test -n "$module_cmds" ; then
+ if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then
+ eval test_cmds=\"$module_expsym_cmds\"
+ cmds=$module_expsym_cmds
+ else
+ eval test_cmds=\"$module_cmds\"
+ cmds=$module_cmds
+ fi
+ else
+ if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then
+ eval test_cmds=\"$archive_expsym_cmds\"
+ cmds=$archive_expsym_cmds
+ else
+ eval test_cmds=\"$archive_cmds\"
+ cmds=$archive_cmds
+ fi
+ fi
+
+ if test "X$skipped_export" != "X:" &&
+ func_len " $test_cmds" &&
+ len=$func_len_result &&
+ test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then
+ :
+ else
+ # The command line is too long to link in one step, link piecewise
+ # or, if using GNU ld and skipped_export is not :, use a linker
+ # script.
+
+ # Save the value of $output and $libobjs because we want to
+ # use them later. If we have whole_archive_flag_spec, we
+ # want to use save_libobjs as it was before
+ # whole_archive_flag_spec was expanded, because we can't
+ # assume the linker understands whole_archive_flag_spec.
+ # This may have to be revisited, in case too many
+ # convenience libraries get linked in and end up exceeding
+ # the spec.
+ if test -z "$convenience" || test -z "$whole_archive_flag_spec"; then
+ save_libobjs=$libobjs
+ fi
+ save_output=$output
+ output_la=`$ECHO "X$output" | $Xsed -e "$basename"`
+
+ # Clear the reloadable object creation command queue and
+ # initialize k to one.
+ test_cmds=
+ concat_cmds=
+ objlist=
+ last_robj=
+ k=1
+
+ if test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "$with_gnu_ld" = yes; then
+ output=${output_objdir}/${output_la}.lnkscript
+ func_verbose "creating GNU ld script: $output"
+ $ECHO 'INPUT (' > $output
+ for obj in $save_libobjs
+ do
+ $ECHO "$obj" >> $output
+ done
+ $ECHO ')' >> $output
+ delfiles="$delfiles $output"
+ elif test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "X$file_list_spec" != X; then
+ output=${output_objdir}/${output_la}.lnk
+ func_verbose "creating linker input file list: $output"
+ : > $output
+ set x $save_libobjs
+ shift
+ firstobj=
+ if test "$compiler_needs_object" = yes; then
+ firstobj="$1 "
+ shift
+ fi
+ for obj
+ do
+ $ECHO "$obj" >> $output
+ done
+ delfiles="$delfiles $output"
+ output=$firstobj\"$file_list_spec$output\"
+ else
+ if test -n "$save_libobjs"; then
+ func_verbose "creating reloadable object files..."
+ output=$output_objdir/$output_la-${k}.$objext
+ eval test_cmds=\"$reload_cmds\"
+ func_len " $test_cmds"
+ len0=$func_len_result
+ len=$len0
+
+ # Loop over the list of objects to be linked.
+ for obj in $save_libobjs
+ do
+ func_len " $obj"
+ func_arith $len + $func_len_result
+ len=$func_arith_result
+ if test "X$objlist" = X ||
+ test "$len" -lt "$max_cmd_len"; then
+ func_append objlist " $obj"
+ else
+ # The command $test_cmds is almost too long, add a
+ # command to the queue.
+ if test "$k" -eq 1 ; then
+ # The first file doesn't have a previous command to add.
+ eval concat_cmds=\"$reload_cmds $objlist $last_robj\"
+ else
+ # All subsequent reloadable object files will link in
+ # the last one created.
+ eval concat_cmds=\"\$concat_cmds~$reload_cmds $objlist $last_robj~\$RM $last_robj\"
+ fi
+ last_robj=$output_objdir/$output_la-${k}.$objext
+ func_arith $k + 1
+ k=$func_arith_result
+ output=$output_objdir/$output_la-${k}.$objext
+ objlist=$obj
+ func_len " $last_robj"
+ func_arith $len0 + $func_len_result
+ len=$func_arith_result
+ fi
+ done
+ # Handle the remaining objects by creating one last
+ # reloadable object file. All subsequent reloadable object
+ # files will link in the last one created.
+ test -z "$concat_cmds" || concat_cmds=$concat_cmds~
+ eval concat_cmds=\"\${concat_cmds}$reload_cmds $objlist $last_robj\"
+ if test -n "$last_robj"; then
+ eval concat_cmds=\"\${concat_cmds}~\$RM $last_robj\"
+ fi
+ delfiles="$delfiles $output"
+
+ else
+ output=
+ fi
+
+ if ${skipped_export-false}; then
+ func_verbose "generating symbol list for \`$libname.la'"
+ export_symbols="$output_objdir/$libname.exp"
+ $opt_dry_run || $RM $export_symbols
+ libobjs=$output
+ # Append the command to create the export file.
+ test -z "$concat_cmds" || concat_cmds=$concat_cmds~
+ eval concat_cmds=\"\$concat_cmds$export_symbols_cmds\"
+ if test -n "$last_robj"; then
+ eval concat_cmds=\"\$concat_cmds~\$RM $last_robj\"
+ fi
+ fi
+
+ test -n "$save_libobjs" &&
+ func_verbose "creating a temporary reloadable object file: $output"
+
+ # Loop through the commands generated above and execute them.
+ save_ifs="$IFS"; IFS='~'
+ for cmd in $concat_cmds; do
+ IFS="$save_ifs"
+ $opt_silent || {
+ func_quote_for_expand "$cmd"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+ $opt_dry_run || eval "$cmd" || {
+ lt_exit=$?
+
+ # Restore the uninstalled library and exit
+ if test "$mode" = relink; then
+ ( cd "$output_objdir" && \
+ $RM "${realname}T" && \
+ $MV "${realname}U" "$realname" )
+ fi
+
+ exit $lt_exit
+ }
+ done
+ IFS="$save_ifs"
+
+ if test -n "$export_symbols_regex" && ${skipped_export-false}; then
+ func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"'
+ func_show_eval '$MV "${export_symbols}T" "$export_symbols"'
+ fi
+ fi
+
+ if ${skipped_export-false}; then
+ if test -n "$export_symbols" && test -n "$include_expsyms"; then
+ tmp_export_symbols="$export_symbols"
+ test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols"
+ $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"'
+ fi
+
+ if test -n "$orig_export_symbols"; then
+ # The given exports_symbols file has to be filtered, so filter it.
+ func_verbose "filter symbol list for \`$libname.la' to tag DATA exports"
+ # FIXME: $output_objdir/$libname.filter potentially contains lots of
+ # 's' commands which not all seds can handle. GNU sed should be fine
+ # though. Also, the filter scales superlinearly with the number of
+ # global variables. join(1) would be nice here, but unfortunately
+ # isn't a blessed tool.
+ $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter
+ delfiles="$delfiles $export_symbols $output_objdir/$libname.filter"
+ export_symbols=$output_objdir/$libname.def
+ $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols
+ fi
+ fi
+
+ libobjs=$output
+ # Restore the value of output.
+ output=$save_output
+
+ if test -n "$convenience" && test -n "$whole_archive_flag_spec"; then
+ eval libobjs=\"\$libobjs $whole_archive_flag_spec\"
+ test "X$libobjs" = "X " && libobjs=
+ fi
+ # Expand the library linking commands again to reset the
+ # value of $libobjs for piecewise linking.
+
+ # Do each of the archive commands.
+ if test "$module" = yes && test -n "$module_cmds" ; then
+ if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then
+ cmds=$module_expsym_cmds
+ else
+ cmds=$module_cmds
+ fi
+ else
+ if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then
+ cmds=$archive_expsym_cmds
+ else
+ cmds=$archive_cmds
+ fi
+ fi
+ fi
+
+ if test -n "$delfiles"; then
+ # Append the command to remove temporary files to $cmds.
+ eval cmds=\"\$cmds~\$RM $delfiles\"
+ fi
+
+ # Add any objects from preloaded convenience libraries
+ if test -n "$dlprefiles"; then
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $dlprefiles
+ libobjs="$libobjs $func_extract_archives_result"
+ test "X$libobjs" = "X " && libobjs=
+ fi
+
+ save_ifs="$IFS"; IFS='~'
+ for cmd in $cmds; do
+ IFS="$save_ifs"
+ eval cmd=\"$cmd\"
+ $opt_silent || {
+ func_quote_for_expand "$cmd"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+ $opt_dry_run || eval "$cmd" || {
+ lt_exit=$?
+
+ # Restore the uninstalled library and exit
+ if test "$mode" = relink; then
+ ( cd "$output_objdir" && \
+ $RM "${realname}T" && \
+ $MV "${realname}U" "$realname" )
+ fi
+
+ exit $lt_exit
+ }
+ done
+ IFS="$save_ifs"
+
+ # Restore the uninstalled library and exit
+ if test "$mode" = relink; then
+ $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}T && $MV $realname ${realname}T && $MV ${realname}U $realname)' || exit $?
+
+ if test -n "$convenience"; then
+ if test -z "$whole_archive_flag_spec"; then
+ func_show_eval '${RM}r "$gentop"'
+ fi
+ fi
+
+ exit $EXIT_SUCCESS
+ fi
+
+ # Create links to the real library.
+ for linkname in $linknames; do
+ if test "$realname" != "$linkname"; then
+ func_show_eval '(cd "$output_objdir" && $RM "$linkname" && $LN_S "$realname" "$linkname")' 'exit $?'
+ fi
+ done
+
+ # If -module or -export-dynamic was specified, set the dlname.
+ if test "$module" = yes || test "$export_dynamic" = yes; then
+ # On all known operating systems, these are identical.
+ dlname="$soname"
+ fi
+ fi
+ ;;
+
+ obj)
+ if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
+ func_warning "\`-dlopen' is ignored for objects"
+ fi
+
+ case " $deplibs" in
+ *\ -l* | *\ -L*)
+ func_warning "\`-l' and \`-L' are ignored for objects" ;;
+ esac
+
+ test -n "$rpath" && \
+ func_warning "\`-rpath' is ignored for objects"
+
+ test -n "$xrpath" && \
+ func_warning "\`-R' is ignored for objects"
+
+ test -n "$vinfo" && \
+ func_warning "\`-version-info' is ignored for objects"
+
+ test -n "$release" && \
+ func_warning "\`-release' is ignored for objects"
+
+ case $output in
+ *.lo)
+ test -n "$objs$old_deplibs" && \
+ func_fatal_error "cannot build library object \`$output' from non-libtool objects"
+
+ libobj=$output
+ func_lo2o "$libobj"
+ obj=$func_lo2o_result
+ ;;
+ *)
+ libobj=
+ obj="$output"
+ ;;
+ esac
+
+ # Delete the old objects.
+ $opt_dry_run || $RM $obj $libobj
+
+ # Objects from convenience libraries. This assumes
+ # single-version convenience libraries. Whenever we create
+ # different ones for PIC/non-PIC, this we'll have to duplicate
+ # the extraction.
+ reload_conv_objs=
+ gentop=
+ # reload_cmds runs $LD directly, so let us get rid of
+ # -Wl from whole_archive_flag_spec and hope we can get by with
+ # turning comma into space..
+ wl=
+
+ if test -n "$convenience"; then
+ if test -n "$whole_archive_flag_spec"; then
+ eval tmp_whole_archive_flags=\"$whole_archive_flag_spec\"
+ reload_conv_objs=$reload_objs\ `$ECHO "X$tmp_whole_archive_flags" | $Xsed -e 's|,| |g'`
+ else
+ gentop="$output_objdir/${obj}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $convenience
+ reload_conv_objs="$reload_objs $func_extract_archives_result"
+ fi
+ fi
+
+ # Create the old-style object.
+ reload_objs="$objs$old_deplibs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}$'/d' -e '/\.lib$/d' -e "$lo2o" | $NL2SP`" $reload_conv_objs" ### testsuite: skip nested quoting test
+
+ output="$obj"
+ func_execute_cmds "$reload_cmds" 'exit $?'
+
+ # Exit if we aren't doing a library object file.
+ if test -z "$libobj"; then
+ if test -n "$gentop"; then
+ func_show_eval '${RM}r "$gentop"'
+ fi
+
+ exit $EXIT_SUCCESS
+ fi
+
+ if test "$build_libtool_libs" != yes; then
+ if test -n "$gentop"; then
+ func_show_eval '${RM}r "$gentop"'
+ fi
+
+ # Create an invalid libtool object if no PIC, so that we don't
+ # accidentally link it into a program.
+ # $show "echo timestamp > $libobj"
+ # $opt_dry_run || eval "echo timestamp > $libobj" || exit $?
+ exit $EXIT_SUCCESS
+ fi
+
+ if test -n "$pic_flag" || test "$pic_mode" != default; then
+ # Only do commands if we really have different PIC objects.
+ reload_objs="$libobjs $reload_conv_objs"
+ output="$libobj"
+ func_execute_cmds "$reload_cmds" 'exit $?'
+ fi
+
+ if test -n "$gentop"; then
+ func_show_eval '${RM}r "$gentop"'
+ fi
+
+ exit $EXIT_SUCCESS
+ ;;
+
+ prog)
+ case $host in
+ *cygwin*) func_stripname '' '.exe' "$output"
+ output=$func_stripname_result.exe;;
+ esac
+ test -n "$vinfo" && \
+ func_warning "\`-version-info' is ignored for programs"
+
+ test -n "$release" && \
+ func_warning "\`-release' is ignored for programs"
+
+ test "$preload" = yes \
+ && test "$dlopen_support" = unknown \
+ && test "$dlopen_self" = unknown \
+ && test "$dlopen_self_static" = unknown && \
+ func_warning "\`LT_INIT([dlopen])' not used. Assuming no dlopen support."
+
+ case $host in
+ *-*-rhapsody* | *-*-darwin1.[012])
+ # On Rhapsody replace the C library is the System framework
+ compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'`
+ finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'`
+ ;;
+ esac
+
+ case $host in
+ *-*-darwin*)
+ # Don't allow lazy linking, it breaks C++ global constructors
+ # But is supposedly fixed on 10.4 or later (yay!).
+ if test "$tagname" = CXX ; then
+ case ${MACOSX_DEPLOYMENT_TARGET-10.0} in
+ 10.[0123])
+ compile_command="$compile_command ${wl}-bind_at_load"
+ finalize_command="$finalize_command ${wl}-bind_at_load"
+ ;;
+ esac
+ fi
+ # Time to change all our "foo.ltframework" stuff back to "-framework foo"
+ compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ ;;
+ esac
+
+
+ # move library search paths that coincide with paths to not yet
+ # installed libraries to the beginning of the library search list
+ new_libs=
+ for path in $notinst_path; do
+ case " $new_libs " in
+ *" -L$path/$objdir "*) ;;
+ *)
+ case " $compile_deplibs " in
+ *" -L$path/$objdir "*)
+ new_libs="$new_libs -L$path/$objdir" ;;
+ esac
+ ;;
+ esac
+ done
+ for deplib in $compile_deplibs; do
+ case $deplib in
+ -L*)
+ case " $new_libs " in
+ *" $deplib "*) ;;
+ *) new_libs="$new_libs $deplib" ;;
+ esac
+ ;;
+ *) new_libs="$new_libs $deplib" ;;
+ esac
+ done
+ compile_deplibs="$new_libs"
+
+
+ compile_command="$compile_command $compile_deplibs"
+ finalize_command="$finalize_command $finalize_deplibs"
+
+ if test -n "$rpath$xrpath"; then
+ # If the user specified any rpath flags, then add them.
+ for libdir in $rpath $xrpath; do
+ # This is the magic to use -rpath.
+ case "$finalize_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_rpath="$finalize_rpath $libdir" ;;
+ esac
+ done
+ fi
+
+ # Now hardcode the library paths
+ rpath=
+ hardcode_libdirs=
+ for libdir in $compile_rpath $finalize_rpath; do
+ if test -n "$hardcode_libdir_flag_spec"; then
+ if test -n "$hardcode_libdir_separator"; then
+ if test -z "$hardcode_libdirs"; then
+ hardcode_libdirs="$libdir"
+ else
+ # Just accumulate the unique libdirs.
+ case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
+ *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
+ ;;
+ *)
+ hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir"
+ ;;
+ esac
+ fi
+ else
+ eval flag=\"$hardcode_libdir_flag_spec\"
+ rpath="$rpath $flag"
+ fi
+ elif test -n "$runpath_var"; then
+ case "$perm_rpath " in
+ *" $libdir "*) ;;
+ *) perm_rpath="$perm_rpath $libdir" ;;
+ esac
+ fi
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*)
+ testbindir=`${ECHO} "$libdir" | ${SED} -e 's*/lib$*/bin*'`
+ case :$dllsearchpath: in
+ *":$libdir:"*) ;;
+ ::) dllsearchpath=$libdir;;
+ *) dllsearchpath="$dllsearchpath:$libdir";;
+ esac
+ case :$dllsearchpath: in
+ *":$testbindir:"*) ;;
+ ::) dllsearchpath=$testbindir;;
+ *) dllsearchpath="$dllsearchpath:$testbindir";;
+ esac
+ ;;
+ esac
+ done
+ # Substitute the hardcoded libdirs into the rpath.
+ if test -n "$hardcode_libdir_separator" &&
+ test -n "$hardcode_libdirs"; then
+ libdir="$hardcode_libdirs"
+ eval rpath=\" $hardcode_libdir_flag_spec\"
+ fi
+ compile_rpath="$rpath"
+
+ rpath=
+ hardcode_libdirs=
+ for libdir in $finalize_rpath; do
+ if test -n "$hardcode_libdir_flag_spec"; then
+ if test -n "$hardcode_libdir_separator"; then
+ if test -z "$hardcode_libdirs"; then
+ hardcode_libdirs="$libdir"
+ else
+ # Just accumulate the unique libdirs.
+ case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
+ *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
+ ;;
+ *)
+ hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir"
+ ;;
+ esac
+ fi
+ else
+ eval flag=\"$hardcode_libdir_flag_spec\"
+ rpath="$rpath $flag"
+ fi
+ elif test -n "$runpath_var"; then
+ case "$finalize_perm_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_perm_rpath="$finalize_perm_rpath $libdir" ;;
+ esac
+ fi
+ done
+ # Substitute the hardcoded libdirs into the rpath.
+ if test -n "$hardcode_libdir_separator" &&
+ test -n "$hardcode_libdirs"; then
+ libdir="$hardcode_libdirs"
+ eval rpath=\" $hardcode_libdir_flag_spec\"
+ fi
+ finalize_rpath="$rpath"
+
+ if test -n "$libobjs" && test "$build_old_libs" = yes; then
+ # Transform all the library objects into standard objects.
+ compile_command=`$ECHO "X$compile_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+ finalize_command=`$ECHO "X$finalize_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+ fi
+
+ func_generate_dlsyms "$outputname" "@PROGRAM@" "no"
+
+ # template prelinking step
+ if test -n "$prelink_cmds"; then
+ func_execute_cmds "$prelink_cmds" 'exit $?'
+ fi
+
+ wrappers_required=yes
+ case $host in
+ *cygwin* | *mingw* )
+ if test "$build_libtool_libs" != yes; then
+ wrappers_required=no
+ fi
+ ;;
+ *cegcc)
+ # Disable wrappers for cegcc, we are cross compiling anyway.
+ wrappers_required=no
+ ;;
+ *)
+ if test "$need_relink" = no || test "$build_libtool_libs" != yes; then
+ wrappers_required=no
+ fi
+ ;;
+ esac
+ if test "$wrappers_required" = no; then
+ # Replace the output file specification.
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'`
+ link_command="$compile_command$compile_rpath"
+
+ # We have no uninstalled library dependencies, so finalize right now.
+ exit_status=0
+ func_show_eval "$link_command" 'exit_status=$?'
+
+ # Delete the generated files.
+ if test -f "$output_objdir/${outputname}S.${objext}"; then
+ func_show_eval '$RM "$output_objdir/${outputname}S.${objext}"'
+ fi
+
+ exit $exit_status
+ fi
+
+ if test -n "$compile_shlibpath$finalize_shlibpath"; then
+ compile_command="$shlibpath_var=\"$compile_shlibpath$finalize_shlibpath\$$shlibpath_var\" $compile_command"
+ fi
+ if test -n "$finalize_shlibpath"; then
+ finalize_command="$shlibpath_var=\"$finalize_shlibpath\$$shlibpath_var\" $finalize_command"
+ fi
+
+ compile_var=
+ finalize_var=
+ if test -n "$runpath_var"; then
+ if test -n "$perm_rpath"; then
+ # We should set the runpath_var.
+ rpath=
+ for dir in $perm_rpath; do
+ rpath="$rpath$dir:"
+ done
+ compile_var="$runpath_var=\"$rpath\$$runpath_var\" "
+ fi
+ if test -n "$finalize_perm_rpath"; then
+ # We should set the runpath_var.
+ rpath=
+ for dir in $finalize_perm_rpath; do
+ rpath="$rpath$dir:"
+ done
+ finalize_var="$runpath_var=\"$rpath\$$runpath_var\" "
+ fi
+ fi
+
+ if test "$no_install" = yes; then
+ # We don't need to create a wrapper script.
+ link_command="$compile_var$compile_command$compile_rpath"
+ # Replace the output file specification.
+ link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'`
+ # Delete the old output file.
+ $opt_dry_run || $RM $output
+ # Link the executable and exit
+ func_show_eval "$link_command" 'exit $?'
+ exit $EXIT_SUCCESS
+ fi
+
+ if test "$hardcode_action" = relink; then
+ # Fast installation is not supported
+ link_command="$compile_var$compile_command$compile_rpath"
+ relink_command="$finalize_var$finalize_command$finalize_rpath"
+
+ func_warning "this platform does not like uninstalled shared libraries"
+ func_warning "\`$output' will be relinked during installation"
+ else
+ if test "$fast_install" != no; then
+ link_command="$finalize_var$compile_command$finalize_rpath"
+ if test "$fast_install" = yes; then
+ relink_command=`$ECHO "X$compile_var$compile_command$compile_rpath" | $Xsed -e 's%@OUTPUT@%\$progdir/\$file%g'`
+ else
+ # fast_install is set to needless
+ relink_command=
+ fi
+ else
+ link_command="$compile_var$compile_command$compile_rpath"
+ relink_command="$finalize_var$finalize_command$finalize_rpath"
+ fi
+ fi
+
+ # Replace the output file specification.
+ link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output_objdir/$outputname"'%g'`
+
+ # Delete the old output files.
+ $opt_dry_run || $RM $output $output_objdir/$outputname $output_objdir/lt-$outputname
+
+ func_show_eval "$link_command" 'exit $?'
+
+ # Now create the wrapper script.
+ func_verbose "creating $output"
+
+ # Quote the relink command for shipping.
+ if test -n "$relink_command"; then
+ # Preserve any variables that may affect compiler behavior
+ for var in $variables_saved_for_relink; do
+ if eval test -z \"\${$var+set}\"; then
+ relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command"
+ elif eval var_value=\$$var; test -z "$var_value"; then
+ relink_command="$var=; export $var; $relink_command"
+ else
+ func_quote_for_eval "$var_value"
+ relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command"
+ fi
+ done
+ relink_command="(cd `pwd`; $relink_command)"
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e "$sed_quote_subst"`
+ fi
+
+ # Quote $ECHO for shipping.
+ if test "X$ECHO" = "X$SHELL $progpath --fallback-echo"; then
+ case $progpath in
+ [\\/]* | [A-Za-z]:[\\/]*) qecho="$SHELL $progpath --fallback-echo";;
+ *) qecho="$SHELL `pwd`/$progpath --fallback-echo";;
+ esac
+ qecho=`$ECHO "X$qecho" | $Xsed -e "$sed_quote_subst"`
+ else
+ qecho=`$ECHO "X$ECHO" | $Xsed -e "$sed_quote_subst"`
+ fi
+
+ # Only actually do things if not in dry run mode.
+ $opt_dry_run || {
+ # win32 will think the script is a binary if it has
+ # a .exe suffix, so we strip it off here.
+ case $output in
+ *.exe) func_stripname '' '.exe' "$output"
+ output=$func_stripname_result ;;
+ esac
+ # test for cygwin because mv fails w/o .exe extensions
+ case $host in
+ *cygwin*)
+ exeext=.exe
+ func_stripname '' '.exe' "$outputname"
+ outputname=$func_stripname_result ;;
+ *) exeext= ;;
+ esac
+ case $host in
+ *cygwin* | *mingw* )
+ func_dirname_and_basename "$output" "" "."
+ output_name=$func_basename_result
+ output_path=$func_dirname_result
+ cwrappersource="$output_path/$objdir/lt-$output_name.c"
+ cwrapper="$output_path/$output_name.exe"
+ $RM $cwrappersource $cwrapper
+ trap "$RM $cwrappersource $cwrapper; exit $EXIT_FAILURE" 1 2 15
+
+ func_emit_cwrapperexe_src > $cwrappersource
+
+ # The wrapper executable is built using the $host compiler,
+ # because it contains $host paths and files. If cross-
+ # compiling, it, like the target executable, must be
+ # executed on the $host or under an emulation environment.
+ $opt_dry_run || {
+ $LTCC $LTCFLAGS -o $cwrapper $cwrappersource
+ $STRIP $cwrapper
+ }
+
+ # Now, create the wrapper script for func_source use:
+ func_ltwrapper_scriptname $cwrapper
+ $RM $func_ltwrapper_scriptname_result
+ trap "$RM $func_ltwrapper_scriptname_result; exit $EXIT_FAILURE" 1 2 15
+ $opt_dry_run || {
+ # note: this script will not be executed, so do not chmod.
+ if test "x$build" = "x$host" ; then
+ $cwrapper --lt-dump-script > $func_ltwrapper_scriptname_result
+ else
+ func_emit_wrapper no > $func_ltwrapper_scriptname_result
+ fi
+ }
+ ;;
+ * )
+ $RM $output
+ trap "$RM $output; exit $EXIT_FAILURE" 1 2 15
+
+ func_emit_wrapper no > $output
+ chmod +x $output
+ ;;
+ esac
+ }
+ exit $EXIT_SUCCESS
+ ;;
+ esac
+
+ # See if we need to build an old-fashioned archive.
+ for oldlib in $oldlibs; do
+
+ if test "$build_libtool_libs" = convenience; then
+ oldobjs="$libobjs_save $symfileobj"
+ addlibs="$convenience"
+ build_libtool_libs=no
+ else
+ if test "$build_libtool_libs" = module; then
+ oldobjs="$libobjs_save"
+ build_libtool_libs=no
+ else
+ oldobjs="$old_deplibs $non_pic_objects"
+ if test "$preload" = yes && test -f "$symfileobj"; then
+ oldobjs="$oldobjs $symfileobj"
+ fi
+ fi
+ addlibs="$old_convenience"
+ fi
+
+ if test -n "$addlibs"; then
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $addlibs
+ oldobjs="$oldobjs $func_extract_archives_result"
+ fi
+
+ # Do each command in the archive commands.
+ if test -n "$old_archive_from_new_cmds" && test "$build_libtool_libs" = yes; then
+ cmds=$old_archive_from_new_cmds
+ else
+
+ # Add any objects from preloaded convenience libraries
+ if test -n "$dlprefiles"; then
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $dlprefiles
+ oldobjs="$oldobjs $func_extract_archives_result"
+ fi
+
+ # POSIX demands no paths to be encoded in archives. We have
+ # to avoid creating archives with duplicate basenames if we
+ # might have to extract them afterwards, e.g., when creating a
+ # static archive out of a convenience library, or when linking
+ # the entirety of a libtool archive into another (currently
+ # not supported by libtool).
+ if (for obj in $oldobjs
+ do
+ func_basename "$obj"
+ $ECHO "$func_basename_result"
+ done | sort | sort -uc >/dev/null 2>&1); then
+ :
+ else
+ $ECHO "copying selected object files to avoid basename conflicts..."
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+ func_mkdir_p "$gentop"
+ save_oldobjs=$oldobjs
+ oldobjs=
+ counter=1
+ for obj in $save_oldobjs
+ do
+ func_basename "$obj"
+ objbase="$func_basename_result"
+ case " $oldobjs " in
+ " ") oldobjs=$obj ;;
+ *[\ /]"$objbase "*)
+ while :; do
+ # Make sure we don't pick an alternate name that also
+ # overlaps.
+ newobj=lt$counter-$objbase
+ func_arith $counter + 1
+ counter=$func_arith_result
+ case " $oldobjs " in
+ *[\ /]"$newobj "*) ;;
+ *) if test ! -f "$gentop/$newobj"; then break; fi ;;
+ esac
+ done
+ func_show_eval "ln $obj $gentop/$newobj || cp $obj $gentop/$newobj"
+ oldobjs="$oldobjs $gentop/$newobj"
+ ;;
+ *) oldobjs="$oldobjs $obj" ;;
+ esac
+ done
+ fi
+ eval cmds=\"$old_archive_cmds\"
+
+ func_len " $cmds"
+ len=$func_len_result
+ if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then
+ cmds=$old_archive_cmds
+ else
+ # the command line is too long to link in one step, link in parts
+ func_verbose "using piecewise archive linking..."
+ save_RANLIB=$RANLIB
+ RANLIB=:
+ objlist=
+ concat_cmds=
+ save_oldobjs=$oldobjs
+ oldobjs=
+ # Is there a better way of finding the last object in the list?
+ for obj in $save_oldobjs
+ do
+ last_oldobj=$obj
+ done
+ eval test_cmds=\"$old_archive_cmds\"
+ func_len " $test_cmds"
+ len0=$func_len_result
+ len=$len0
+ for obj in $save_oldobjs
+ do
+ func_len " $obj"
+ func_arith $len + $func_len_result
+ len=$func_arith_result
+ func_append objlist " $obj"
+ if test "$len" -lt "$max_cmd_len"; then
+ :
+ else
+ # the above command should be used before it gets too long
+ oldobjs=$objlist
+ if test "$obj" = "$last_oldobj" ; then
+ RANLIB=$save_RANLIB
+ fi
+ test -z "$concat_cmds" || concat_cmds=$concat_cmds~
+ eval concat_cmds=\"\${concat_cmds}$old_archive_cmds\"
+ objlist=
+ len=$len0
+ fi
+ done
+ RANLIB=$save_RANLIB
+ oldobjs=$objlist
+ if test "X$oldobjs" = "X" ; then
+ eval cmds=\"\$concat_cmds\"
+ else
+ eval cmds=\"\$concat_cmds~\$old_archive_cmds\"
+ fi
+ fi
+ fi
+ func_execute_cmds "$cmds" 'exit $?'
+ done
+
+ test -n "$generated" && \
+ func_show_eval "${RM}r$generated"
+
+ # Now create the libtool archive.
+ case $output in
+ *.la)
+ old_library=
+ test "$build_old_libs" = yes && old_library="$libname.$libext"
+ func_verbose "creating $output"
+
+ # Preserve any variables that may affect compiler behavior
+ for var in $variables_saved_for_relink; do
+ if eval test -z \"\${$var+set}\"; then
+ relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command"
+ elif eval var_value=\$$var; test -z "$var_value"; then
+ relink_command="$var=; export $var; $relink_command"
+ else
+ func_quote_for_eval "$var_value"
+ relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command"
+ fi
+ done
+ # Quote the link command for shipping.
+ relink_command="(cd `pwd`; $SHELL $progpath $preserve_args --mode=relink $libtool_args @inst_prefix_dir@)"
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e "$sed_quote_subst"`
+ if test "$hardcode_automatic" = yes ; then
+ relink_command=
+ fi
+
+ # Only create the output if not a dry run.
+ $opt_dry_run || {
+ for installed in no yes; do
+ if test "$installed" = yes; then
+ if test -z "$install_libdir"; then
+ break
+ fi
+ output="$output_objdir/$outputname"i
+ # Replace all uninstalled libtool libraries with the installed ones
+ newdependency_libs=
+ for deplib in $dependency_libs; do
+ case $deplib in
+ *.la)
+ func_basename "$deplib"
+ name="$func_basename_result"
+ eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib`
+ test -z "$libdir" && \
+ func_fatal_error "\`$deplib' is not a valid libtool archive"
+ newdependency_libs="$newdependency_libs $libdir/$name"
+ ;;
+ *) newdependency_libs="$newdependency_libs $deplib" ;;
+ esac
+ done
+ dependency_libs="$newdependency_libs"
+ newdlfiles=
+
+ for lib in $dlfiles; do
+ case $lib in
+ *.la)
+ func_basename "$lib"
+ name="$func_basename_result"
+ eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib`
+ test -z "$libdir" && \
+ func_fatal_error "\`$lib' is not a valid libtool archive"
+ newdlfiles="$newdlfiles $libdir/$name"
+ ;;
+ *) newdlfiles="$newdlfiles $lib" ;;
+ esac
+ done
+ dlfiles="$newdlfiles"
+ newdlprefiles=
+ for lib in $dlprefiles; do
+ case $lib in
+ *.la)
+ # Only pass preopened files to the pseudo-archive (for
+ # eventual linking with the app. that links it) if we
+ # didn't already link the preopened objects directly into
+ # the library:
+ func_basename "$lib"
+ name="$func_basename_result"
+ eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib`
+ test -z "$libdir" && \
+ func_fatal_error "\`$lib' is not a valid libtool archive"
+ newdlprefiles="$newdlprefiles $libdir/$name"
+ ;;
+ esac
+ done
+ dlprefiles="$newdlprefiles"
+ else
+ newdlfiles=
+ for lib in $dlfiles; do
+ case $lib in
+ [\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;;
+ *) abs=`pwd`"/$lib" ;;
+ esac
+ newdlfiles="$newdlfiles $abs"
+ done
+ dlfiles="$newdlfiles"
+ newdlprefiles=
+ for lib in $dlprefiles; do
+ case $lib in
+ [\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;;
+ *) abs=`pwd`"/$lib" ;;
+ esac
+ newdlprefiles="$newdlprefiles $abs"
+ done
+ dlprefiles="$newdlprefiles"
+ fi
+ $RM $output
+ # place dlname in correct position for cygwin
+ tdlname=$dlname
+ case $host,$output,$installed,$module,$dlname in
+ *cygwin*,*lai,yes,no,*.dll | *mingw*,*lai,yes,no,*.dll | *cegcc*,*lai,yes,no,*.dll) tdlname=../bin/$dlname ;;
+ esac
+ $ECHO > $output "\
+# $outputname - a libtool library file
+# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# The name that we can dlopen(3).
+dlname='$tdlname'
+
+# Names of this library.
+library_names='$library_names'
+
+# The name of the static archive.
+old_library='$old_library'
+
+# Linker flags that can not go in dependency_libs.
+inherited_linker_flags='$new_inherited_linker_flags'
+
+# Libraries that this one depends upon.
+dependency_libs='$dependency_libs'
+
+# Names of additional weak libraries provided by this library
+weak_library_names='$weak_libs'
+
+# Version information for $libname.
+current=$current
+age=$age
+revision=$revision
+
+# Is this an already installed library?
+installed=$installed
+
+# Should we warn about portability when linking against -modules?
+shouldnotlink=$module
+
+# Files to dlopen/dlpreopen
+dlopen='$dlfiles'
+dlpreopen='$dlprefiles'
+
+# Directory that this library needs to be installed in:
+libdir='$install_libdir'"
+ if test "$installed" = no && test "$need_relink" = yes; then
+ $ECHO >> $output "\
+relink_command=\"$relink_command\""
+ fi
+ done
+ }
+
+ # Do a symbolic link so that the libtool archive can be found in
+ # LD_LIBRARY_PATH before the program is installed.
+ func_show_eval '( cd "$output_objdir" && $RM "$outputname" && $LN_S "../$outputname" "$outputname" )' 'exit $?'
+ ;;
+ esac
+ exit $EXIT_SUCCESS
+}
+
+{ test "$mode" = link || test "$mode" = relink; } &&
+ func_mode_link ${1+"$@"}
+
+
+# func_mode_uninstall arg...
+func_mode_uninstall ()
+{
+ $opt_debug
+ RM="$nonopt"
+ files=
+ rmforce=
+ exit_status=0
+
+ # This variable tells wrapper scripts just to set variables rather
+ # than running their programs.
+ libtool_install_magic="$magic"
+
+ for arg
+ do
+ case $arg in
+ -f) RM="$RM $arg"; rmforce=yes ;;
+ -*) RM="$RM $arg" ;;
+ *) files="$files $arg" ;;
+ esac
+ done
+
+ test -z "$RM" && \
+ func_fatal_help "you must specify an RM program"
+
+ rmdirs=
+
+ origobjdir="$objdir"
+ for file in $files; do
+ func_dirname "$file" "" "."
+ dir="$func_dirname_result"
+ if test "X$dir" = X.; then
+ objdir="$origobjdir"
+ else
+ objdir="$dir/$origobjdir"
+ fi
+ func_basename "$file"
+ name="$func_basename_result"
+ test "$mode" = uninstall && objdir="$dir"
+
+ # Remember objdir for removal later, being careful to avoid duplicates
+ if test "$mode" = clean; then
+ case " $rmdirs " in
+ *" $objdir "*) ;;
+ *) rmdirs="$rmdirs $objdir" ;;
+ esac
+ fi
+
+ # Don't error if the file doesn't exist and rm -f was used.
+ if { test -L "$file"; } >/dev/null 2>&1 ||
+ { test -h "$file"; } >/dev/null 2>&1 ||
+ test -f "$file"; then
+ :
+ elif test -d "$file"; then
+ exit_status=1
+ continue
+ elif test "$rmforce" = yes; then
+ continue
+ fi
+
+ rmfiles="$file"
+
+ case $name in
+ *.la)
+ # Possibly a libtool archive, so verify it.
+ if func_lalib_p "$file"; then
+ func_source $dir/$name
+
+ # Delete the libtool libraries and symlinks.
+ for n in $library_names; do
+ rmfiles="$rmfiles $objdir/$n"
+ done
+ test -n "$old_library" && rmfiles="$rmfiles $objdir/$old_library"
+
+ case "$mode" in
+ clean)
+ case " $library_names " in
+ # " " in the beginning catches empty $dlname
+ *" $dlname "*) ;;
+ *) rmfiles="$rmfiles $objdir/$dlname" ;;
+ esac
+ test -n "$libdir" && rmfiles="$rmfiles $objdir/$name $objdir/${name}i"
+ ;;
+ uninstall)
+ if test -n "$library_names"; then
+ # Do each command in the postuninstall commands.
+ func_execute_cmds "$postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1'
+ fi
+
+ if test -n "$old_library"; then
+ # Do each command in the old_postuninstall commands.
+ func_execute_cmds "$old_postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1'
+ fi
+ # FIXME: should reinstall the best remaining shared library.
+ ;;
+ esac
+ fi
+ ;;
+
+ *.lo)
+ # Possibly a libtool object, so verify it.
+ if func_lalib_p "$file"; then
+
+ # Read the .lo file
+ func_source $dir/$name
+
+ # Add PIC object to the list of files to remove.
+ if test -n "$pic_object" &&
+ test "$pic_object" != none; then
+ rmfiles="$rmfiles $dir/$pic_object"
+ fi
+
+ # Add non-PIC object to the list of files to remove.
+ if test -n "$non_pic_object" &&
+ test "$non_pic_object" != none; then
+ rmfiles="$rmfiles $dir/$non_pic_object"
+ fi
+ fi
+ ;;
+
+ *)
+ if test "$mode" = clean ; then
+ noexename=$name
+ case $file in
+ *.exe)
+ func_stripname '' '.exe' "$file"
+ file=$func_stripname_result
+ func_stripname '' '.exe' "$name"
+ noexename=$func_stripname_result
+ # $file with .exe has already been added to rmfiles,
+ # add $file without .exe
+ rmfiles="$rmfiles $file"
+ ;;
+ esac
+ # Do a test to see if this is a libtool program.
+ if func_ltwrapper_p "$file"; then
+ if func_ltwrapper_executable_p "$file"; then
+ func_ltwrapper_scriptname "$file"
+ relink_command=
+ func_source $func_ltwrapper_scriptname_result
+ rmfiles="$rmfiles $func_ltwrapper_scriptname_result"
+ else
+ relink_command=
+ func_source $dir/$noexename
+ fi
+
+ # note $name still contains .exe if it was in $file originally
+ # as does the version of $file that was added into $rmfiles
+ rmfiles="$rmfiles $objdir/$name $objdir/${name}S.${objext}"
+ if test "$fast_install" = yes && test -n "$relink_command"; then
+ rmfiles="$rmfiles $objdir/lt-$name"
+ fi
+ if test "X$noexename" != "X$name" ; then
+ rmfiles="$rmfiles $objdir/lt-${noexename}.c"
+ fi
+ fi
+ fi
+ ;;
+ esac
+ func_show_eval "$RM $rmfiles" 'exit_status=1'
+ done
+ objdir="$origobjdir"
+
+ # Try to remove the ${objdir}s in the directories where we deleted files
+ for dir in $rmdirs; do
+ if test -d "$dir"; then
+ func_show_eval "rmdir $dir >/dev/null 2>&1"
+ fi
+ done
+
+ exit $exit_status
+}
+
+{ test "$mode" = uninstall || test "$mode" = clean; } &&
+ func_mode_uninstall ${1+"$@"}
+
+test -z "$mode" && {
+ help="$generic_help"
+ func_fatal_help "you must specify a MODE"
+}
+
+test -z "$exec_cmd" && \
+ func_fatal_help "invalid operation mode \`$mode'"
+
+if test -n "$exec_cmd"; then
+ eval exec "$exec_cmd"
+ exit $EXIT_FAILURE
+fi
+
+exit $exit_status
+
+
+# The TAGs below are defined such that we never get into a situation
+# in which we disable both kinds of libraries. Given conflicting
+# choices, we go for a static library, that is the most portable,
+# since we can't tell whether shared libraries were disabled because
+# the user asked for that or because the platform doesn't support
+# them. This is particularly important on AIX, because we don't
+# support having both static and shared libraries enabled at the same
+# time on that platform, so we default to a shared-only configuration.
+# If a disable-shared tag is given, we'll fallback to a static-only
+# configuration. But we'll never go from static-only to shared-only.
+
+# ### BEGIN LIBTOOL TAG CONFIG: disable-shared
+build_libtool_libs=no
+build_old_libs=yes
+# ### END LIBTOOL TAG CONFIG: disable-shared
+
+# ### BEGIN LIBTOOL TAG CONFIG: disable-static
+build_old_libs=`case $build_libtool_libs in yes) echo no;; *) echo yes;; esac`
+# ### END LIBTOOL TAG CONFIG: disable-static
+
+# Local Variables:
+# mode:shell-script
+# sh-indentation:2
+# End:
+# vi:sw=2
+
diff --git a/config/missing b/config/missing
new file mode 100755
index 0000000..28055d2
--- /dev/null
+++ b/config/missing
@@ -0,0 +1,376 @@
+#! /bin/sh
+# Common stub for a few missing GNU programs while installing.
+
+scriptversion=2009-04-28.21; # UTC
+
+# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
+# 2008, 2009 Free Software Foundation, Inc.
+# Originally by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+if test $# -eq 0; then
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+fi
+
+run=:
+sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
+sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
+
+# In the cases where this matters, `missing' is being run in the
+# srcdir already.
+if test -f configure.ac; then
+ configure_ac=configure.ac
+else
+ configure_ac=configure.in
+fi
+
+msg="missing on your system"
+
+case $1 in
+--run)
+ # Try to run requested program, and just exit if it succeeds.
+ run=
+ shift
+ "$@" && exit 0
+ # Exit code 63 means version mismatch. This often happens
+ # when the user try to use an ancient version of a tool on
+ # a file that requires a minimum version. In this case we
+ # we should proceed has if the program had been absent, or
+ # if --run hadn't been passed.
+ if test $? = 63; then
+ run=:
+ msg="probably too old"
+ fi
+ ;;
+
+ -h|--h|--he|--hel|--help)
+ echo "\
+$0 [OPTION]... PROGRAM [ARGUMENT]...
+
+Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
+error status if there is no known handling for PROGRAM.
+
+Options:
+ -h, --help display this help and exit
+ -v, --version output version information and exit
+ --run try to run the given command, and emulate it if it fails
+
+Supported PROGRAM values:
+ aclocal touch file \`aclocal.m4'
+ autoconf touch file \`configure'
+ autoheader touch file \`config.h.in'
+ autom4te touch the output file, or create a stub one
+ automake touch all \`Makefile.in' files
+ bison create \`y.tab.[ch]', if possible, from existing .[ch]
+ flex create \`lex.yy.c', if possible, from existing .c
+ help2man touch the output file
+ lex create \`lex.yy.c', if possible, from existing .c
+ makeinfo touch the output file
+ tar try tar, gnutar, gtar, then tar without non-portable flags
+ yacc create \`y.tab.[ch]', if possible, from existing .[ch]
+
+Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
+\`g' are ignored when checking the name.
+
+Send bug reports to <bug-automake at gnu.org>."
+ exit $?
+ ;;
+
+ -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
+ echo "missing $scriptversion (GNU Automake)"
+ exit $?
+ ;;
+
+ -*)
+ echo 1>&2 "$0: Unknown \`$1' option"
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+ ;;
+
+esac
+
+# normalize program name to check for.
+program=`echo "$1" | sed '
+ s/^gnu-//; t
+ s/^gnu//; t
+ s/^g//; t'`
+
+# Now exit if we have it, but it failed. Also exit now if we
+# don't have it and --version was passed (most likely to detect
+# the program). This is about non-GNU programs, so use $1 not
+# $program.
+case $1 in
+ lex*|yacc*)
+ # Not GNU programs, they don't have --version.
+ ;;
+
+ tar*)
+ if test -n "$run"; then
+ echo 1>&2 "ERROR: \`tar' requires --run"
+ exit 1
+ elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+ exit 1
+ fi
+ ;;
+
+ *)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+ # Could not run --version or --help. This is probably someone
+ # running `$TOOL --version' or `$TOOL --help' to check whether
+ # $TOOL exists and not knowing $TOOL uses missing.
+ exit 1
+ fi
+ ;;
+esac
+
+# If it does not exist, or fails to run (possibly an outdated version),
+# try to emulate it.
+case $program in
+ aclocal*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acinclude.m4' or \`${configure_ac}'. You might want
+ to install the \`Automake' and \`Perl' packages. Grab them from
+ any GNU archive site."
+ touch aclocal.m4
+ ;;
+
+ autoconf*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`${configure_ac}'. You might want to install the
+ \`Autoconf' and \`GNU m4' packages. Grab them from any GNU
+ archive site."
+ touch configure
+ ;;
+
+ autoheader*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acconfig.h' or \`${configure_ac}'. You might want
+ to install the \`Autoconf' and \`GNU m4' packages. Grab them
+ from any GNU archive site."
+ files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
+ test -z "$files" && files="config.h"
+ touch_files=
+ for f in $files; do
+ case $f in
+ *:*) touch_files="$touch_files "`echo "$f" |
+ sed -e 's/^[^:]*://' -e 's/:.*//'`;;
+ *) touch_files="$touch_files $f.in";;
+ esac
+ done
+ touch $touch_files
+ ;;
+
+ automake*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
+ You might want to install the \`Automake' and \`Perl' packages.
+ Grab them from any GNU archive site."
+ find . -type f -name Makefile.am -print |
+ sed 's/\.am$/.in/' |
+ while read f; do touch "$f"; done
+ ;;
+
+ autom4te*)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, but is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them.
+ You can get \`$1' as part of \`Autoconf' from any GNU
+ archive site."
+
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo "#! /bin/sh"
+ echo "# Created by GNU Automake missing as a replacement of"
+ echo "# $ $@"
+ echo "exit 0"
+ chmod +x $file
+ exit 1
+ fi
+ ;;
+
+ bison*|yacc*)
+ echo 1>&2 "\
+WARNING: \`$1' $msg. You should only need it if
+ you modified a \`.y' file. You may need the \`Bison' package
+ in order for those modifications to take effect. You can get
+ \`Bison' from any GNU archive site."
+ rm -f y.tab.c y.tab.h
+ if test $# -ne 1; then
+ eval LASTARG="\${$#}"
+ case $LASTARG in
+ *.y)
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" y.tab.c
+ fi
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" y.tab.h
+ fi
+ ;;
+ esac
+ fi
+ if test ! -f y.tab.h; then
+ echo >y.tab.h
+ fi
+ if test ! -f y.tab.c; then
+ echo 'main() { return 0; }' >y.tab.c
+ fi
+ ;;
+
+ lex*|flex*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.l' file. You may need the \`Flex' package
+ in order for those modifications to take effect. You can get
+ \`Flex' from any GNU archive site."
+ rm -f lex.yy.c
+ if test $# -ne 1; then
+ eval LASTARG="\${$#}"
+ case $LASTARG in
+ *.l)
+ SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" lex.yy.c
+ fi
+ ;;
+ esac
+ fi
+ if test ! -f lex.yy.c; then
+ echo 'main() { return 0; }' >lex.yy.c
+ fi
+ ;;
+
+ help2man*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a dependency of a manual page. You may need the
+ \`Help2man' package in order for those modifications to take
+ effect. You can get \`Help2man' from any GNU archive site."
+
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo ".ab help2man is required to generate this page"
+ exit $?
+ fi
+ ;;
+
+ makeinfo*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.texi' or \`.texinfo' file, or any other file
+ indirectly affecting the aspect of the manual. The spurious
+ call might also be the consequence of using a buggy \`make' (AIX,
+ DU, IRIX). You might want to install the \`Texinfo' package or
+ the \`GNU make' package. Grab either from any GNU archive site."
+ # The file to touch is that specified with -o ...
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -z "$file"; then
+ # ... or it is the one specified with @setfilename ...
+ infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
+ file=`sed -n '
+ /^@setfilename/{
+ s/.* \([^ ]*\) *$/\1/
+ p
+ q
+ }' $infile`
+ # ... or it is derived from the source name (dir/f.texi becomes f.info)
+ test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
+ fi
+ # If the file does not exist, the user really needs makeinfo;
+ # let's fail without touching anything.
+ test -f $file || exit 1
+ touch $file
+ ;;
+
+ tar*)
+ shift
+
+ # We have already tried tar in the generic part.
+ # Look for gnutar/gtar before invocation to avoid ugly error
+ # messages.
+ if (gnutar --version > /dev/null 2>&1); then
+ gnutar "$@" && exit 0
+ fi
+ if (gtar --version > /dev/null 2>&1); then
+ gtar "$@" && exit 0
+ fi
+ firstarg="$1"
+ if shift; then
+ case $firstarg in
+ *o*)
+ firstarg=`echo "$firstarg" | sed s/o//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ case $firstarg in
+ *h*)
+ firstarg=`echo "$firstarg" | sed s/h//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ fi
+
+ echo 1>&2 "\
+WARNING: I can't seem to be able to run \`tar' with the given arguments.
+ You may want to install GNU tar or Free paxutils, or check the
+ command line arguments."
+ exit 1
+ ;;
+
+ *)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, and is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them. Check the \`README' file,
+ it often tells you about the needed prerequisites for installing
+ this package. You may also peek at any GNU archive site, in case
+ some other package would contain this missing \`$1' program."
+ exit 1
+ ;;
+esac
+
+exit 0
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/config/texinfo.tex b/config/texinfo.tex
new file mode 100644
index 0000000..9140826
--- /dev/null
+++ b/config/texinfo.tex
@@ -0,0 +1,9291 @@
+% texinfo.tex -- TeX macros to handle Texinfo files.
+%
+% Load plain if necessary, i.e., if running under initex.
+\expandafter\ifx\csname fmtname\endcsname\relax\input plain\fi
+%
+\def\texinfoversion{2009-08-14.15}
+%
+% Copyright 1985, 1986, 1988, 1990, 1991, 1992, 1993, 1994, 1995,
+% 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006,
+% 2007, 2008, 2009 Free Software Foundation, Inc.
+%
+% This texinfo.tex file is free software: you can redistribute it and/or
+% modify it under the terms of the GNU General Public License as
+% published by the Free Software Foundation, either version 3 of the
+% License, or (at your option) any later version.
+%
+% This texinfo.tex file is distributed in the hope that it will be
+% useful, but WITHOUT ANY WARRANTY; without even the implied warranty
+% of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program. If not, see <http://www.gnu.org/licenses/>.
+%
+% As a special exception, when this file is read by TeX when processing
+% a Texinfo source document, you may use the result without
+% restriction. (This has been our intent since Texinfo was invented.)
+%
+% Please try the latest version of texinfo.tex before submitting bug
+% reports; you can get the latest version from:
+% http://www.gnu.org/software/texinfo/ (the Texinfo home page), or
+% ftp://tug.org/tex/texinfo.tex
+% (and all CTAN mirrors, see http://www.ctan.org).
+% The texinfo.tex in any given distribution could well be out
+% of date, so if that's what you're using, please check.
+%
+% Send bug reports to bug-texinfo at gnu.org. Please include including a
+% complete document in each bug report with which we can reproduce the
+% problem. Patches are, of course, greatly appreciated.
+%
+% To process a Texinfo manual with TeX, it's most reliable to use the
+% texi2dvi shell script that comes with the distribution. For a simple
+% manual foo.texi, however, you can get away with this:
+% tex foo.texi
+% texindex foo.??
+% tex foo.texi
+% tex foo.texi
+% dvips foo.dvi -o # or whatever; this makes foo.ps.
+% The extra TeX runs get the cross-reference information correct.
+% Sometimes one run after texindex suffices, and sometimes you need more
+% than two; texi2dvi does it as many times as necessary.
+%
+% It is possible to adapt texinfo.tex for other languages, to some
+% extent. You can get the existing language-specific files from the
+% full Texinfo distribution.
+%
+% The GNU Texinfo home page is http://www.gnu.org/software/texinfo.
+
+
+\message{Loading texinfo [version \texinfoversion]:}
+
+% If in a .fmt file, print the version number
+% and turn on active characters that we couldn't do earlier because
+% they might have appeared in the input file name.
+\everyjob{\message{[Texinfo version \texinfoversion]}%
+ \catcode`+=\active \catcode`\_=\active}
+
+
+\chardef\other=12
+
+% We never want plain's \outer definition of \+ in Texinfo.
+% For @tex, we can use \tabalign.
+\let\+ = \relax
+
+% Save some plain tex macros whose names we will redefine.
+\let\ptexb=\b
+\let\ptexbullet=\bullet
+\let\ptexc=\c
+\let\ptexcomma=\,
+\let\ptexdot=\.
+\let\ptexdots=\dots
+\let\ptexend=\end
+\let\ptexequiv=\equiv
+\let\ptexexclam=\!
+\let\ptexfootnote=\footnote
+\let\ptexgtr=>
+\let\ptexhat=^
+\let\ptexi=\i
+\let\ptexindent=\indent
+\let\ptexinsert=\insert
+\let\ptexlbrace=\{
+\let\ptexless=<
+\let\ptexnewwrite\newwrite
+\let\ptexnoindent=\noindent
+\let\ptexplus=+
+\let\ptexrbrace=\}
+\let\ptexslash=\/
+\let\ptexstar=\*
+\let\ptext=\t
+\let\ptextop=\top
+{\catcode`\'=\active
+\global\let\ptexquoteright'}% Math-mode def from plain.tex.
+\let\ptexraggedright=\raggedright
+
+% If this character appears in an error message or help string, it
+% starts a new line in the output.
+\newlinechar = `^^J
+
+% Use TeX 3.0's \inputlineno to get the line number, for better error
+% messages, but if we're using an old version of TeX, don't do anything.
+%
+\ifx\inputlineno\thisisundefined
+ \let\linenumber = \empty % Pre-3.0.
+\else
+ \def\linenumber{l.\the\inputlineno:\space}
+\fi
+
+% Set up fixed words for English if not already set.
+\ifx\putwordAppendix\undefined \gdef\putwordAppendix{Appendix}\fi
+\ifx\putwordChapter\undefined \gdef\putwordChapter{Chapter}\fi
+\ifx\putwordfile\undefined \gdef\putwordfile{file}\fi
+\ifx\putwordin\undefined \gdef\putwordin{in}\fi
+\ifx\putwordIndexIsEmpty\undefined \gdef\putwordIndexIsEmpty{(Index is empty)}\fi
+\ifx\putwordIndexNonexistent\undefined \gdef\putwordIndexNonexistent{(Index is nonexistent)}\fi
+\ifx\putwordInfo\undefined \gdef\putwordInfo{Info}\fi
+\ifx\putwordInstanceVariableof\undefined \gdef\putwordInstanceVariableof{Instance Variable of}\fi
+\ifx\putwordMethodon\undefined \gdef\putwordMethodon{Method on}\fi
+\ifx\putwordNoTitle\undefined \gdef\putwordNoTitle{No Title}\fi
+\ifx\putwordof\undefined \gdef\putwordof{of}\fi
+\ifx\putwordon\undefined \gdef\putwordon{on}\fi
+\ifx\putwordpage\undefined \gdef\putwordpage{page}\fi
+\ifx\putwordsection\undefined \gdef\putwordsection{section}\fi
+\ifx\putwordSection\undefined \gdef\putwordSection{Section}\fi
+\ifx\putwordsee\undefined \gdef\putwordsee{see}\fi
+\ifx\putwordSee\undefined \gdef\putwordSee{See}\fi
+\ifx\putwordShortTOC\undefined \gdef\putwordShortTOC{Short Contents}\fi
+\ifx\putwordTOC\undefined \gdef\putwordTOC{Table of Contents}\fi
+%
+\ifx\putwordMJan\undefined \gdef\putwordMJan{January}\fi
+\ifx\putwordMFeb\undefined \gdef\putwordMFeb{February}\fi
+\ifx\putwordMMar\undefined \gdef\putwordMMar{March}\fi
+\ifx\putwordMApr\undefined \gdef\putwordMApr{April}\fi
+\ifx\putwordMMay\undefined \gdef\putwordMMay{May}\fi
+\ifx\putwordMJun\undefined \gdef\putwordMJun{June}\fi
+\ifx\putwordMJul\undefined \gdef\putwordMJul{July}\fi
+\ifx\putwordMAug\undefined \gdef\putwordMAug{August}\fi
+\ifx\putwordMSep\undefined \gdef\putwordMSep{September}\fi
+\ifx\putwordMOct\undefined \gdef\putwordMOct{October}\fi
+\ifx\putwordMNov\undefined \gdef\putwordMNov{November}\fi
+\ifx\putwordMDec\undefined \gdef\putwordMDec{December}\fi
+%
+\ifx\putwordDefmac\undefined \gdef\putwordDefmac{Macro}\fi
+\ifx\putwordDefspec\undefined \gdef\putwordDefspec{Special Form}\fi
+\ifx\putwordDefvar\undefined \gdef\putwordDefvar{Variable}\fi
+\ifx\putwordDefopt\undefined \gdef\putwordDefopt{User Option}\fi
+\ifx\putwordDeffunc\undefined \gdef\putwordDeffunc{Function}\fi
+
+% Since the category of space is not known, we have to be careful.
+\chardef\spacecat = 10
+\def\spaceisspace{\catcode`\ =\spacecat}
+
+% sometimes characters are active, so we need control sequences.
+\chardef\colonChar = `\:
+\chardef\commaChar = `\,
+\chardef\dashChar = `\-
+\chardef\dotChar = `\.
+\chardef\exclamChar= `\!
+\chardef\lquoteChar= `\`
+\chardef\questChar = `\?
+\chardef\rquoteChar= `\'
+\chardef\semiChar = `\;
+\chardef\underChar = `\_
+
+% Ignore a token.
+%
+\def\gobble#1{}
+
+% The following is used inside several \edef's.
+\def\makecsname#1{\expandafter\noexpand\csname#1\endcsname}
+
+% Hyphenation fixes.
+\hyphenation{
+ Flor-i-da Ghost-script Ghost-view Mac-OS Post-Script
+ ap-pen-dix bit-map bit-maps
+ data-base data-bases eshell fall-ing half-way long-est man-u-script
+ man-u-scripts mini-buf-fer mini-buf-fers over-view par-a-digm
+ par-a-digms rath-er rec-tan-gu-lar ro-bot-ics se-vere-ly set-up spa-ces
+ spell-ing spell-ings
+ stand-alone strong-est time-stamp time-stamps which-ever white-space
+ wide-spread wrap-around
+}
+
+% Margin to add to right of even pages, to left of odd pages.
+\newdimen\bindingoffset
+\newdimen\normaloffset
+\newdimen\pagewidth \newdimen\pageheight
+
+% For a final copy, take out the rectangles
+% that mark overfull boxes (in case you have decided
+% that the text looks ok even though it passes the margin).
+%
+\def\finalout{\overfullrule=0pt}
+
+% @| inserts a changebar to the left of the current line. It should
+% surround any changed text. This approach does *not* work if the
+% change spans more than two lines of output. To handle that, we would
+% have adopt a much more difficult approach (putting marks into the main
+% vertical list for the beginning and end of each change).
+%
+\def\|{%
+ % \vadjust can only be used in horizontal mode.
+ \leavevmode
+ %
+ % Append this vertical mode material after the current line in the output.
+ \vadjust{%
+ % We want to insert a rule with the height and depth of the current
+ % leading; that is exactly what \strutbox is supposed to record.
+ \vskip-\baselineskip
+ %
+ % \vadjust-items are inserted at the left edge of the type. So
+ % the \llap here moves out into the left-hand margin.
+ \llap{%
+ %
+ % For a thicker or thinner bar, change the `1pt'.
+ \vrule height\baselineskip width1pt
+ %
+ % This is the space between the bar and the text.
+ \hskip 12pt
+ }%
+ }%
+}
+
+% Sometimes it is convenient to have everything in the transcript file
+% and nothing on the terminal. We don't just call \tracingall here,
+% since that produces some useless output on the terminal. We also make
+% some effort to order the tracing commands to reduce output in the log
+% file; cf. trace.sty in LaTeX.
+%
+\def\gloggingall{\begingroup \globaldefs = 1 \loggingall \endgroup}%
+\def\loggingall{%
+ \tracingstats2
+ \tracingpages1
+ \tracinglostchars2 % 2 gives us more in etex
+ \tracingparagraphs1
+ \tracingoutput1
+ \tracingmacros2
+ \tracingrestores1
+ \showboxbreadth\maxdimen \showboxdepth\maxdimen
+ \ifx\eTeXversion\undefined\else % etex gives us more logging
+ \tracingscantokens1
+ \tracingifs1
+ \tracinggroups1
+ \tracingnesting2
+ \tracingassigns1
+ \fi
+ \tracingcommands3 % 3 gives us more in etex
+ \errorcontextlines16
+}%
+
+% add check for \lastpenalty to plain's definitions. If the last thing
+% we did was a \nobreak, we don't want to insert more space.
+%
+\def\smallbreak{\ifnum\lastpenalty<10000\par\ifdim\lastskip<\smallskipamount
+ \removelastskip\penalty-50\smallskip\fi\fi}
+\def\medbreak{\ifnum\lastpenalty<10000\par\ifdim\lastskip<\medskipamount
+ \removelastskip\penalty-100\medskip\fi\fi}
+\def\bigbreak{\ifnum\lastpenalty<10000\par\ifdim\lastskip<\bigskipamount
+ \removelastskip\penalty-200\bigskip\fi\fi}
+
+% For @cropmarks command.
+% Do @cropmarks to get crop marks.
+%
+\newif\ifcropmarks
+\let\cropmarks = \cropmarkstrue
+%
+% Dimensions to add cropmarks at corners.
+% Added by P. A. MacKay, 12 Nov. 1986
+%
+\newdimen\outerhsize \newdimen\outervsize % set by the paper size routines
+\newdimen\cornerlong \cornerlong=1pc
+\newdimen\cornerthick \cornerthick=.3pt
+\newdimen\topandbottommargin \topandbottommargin=.75in
+
+% Output a mark which sets \thischapter, \thissection and \thiscolor.
+% We dump everything together because we only have one kind of mark.
+% This works because we only use \botmark / \topmark, not \firstmark.
+%
+% A mark contains a subexpression of the \ifcase ... \fi construct.
+% \get*marks macros below extract the needed part using \ifcase.
+%
+% Another complication is to let the user choose whether \thischapter
+% (\thissection) refers to the chapter (section) in effect at the top
+% of a page, or that at the bottom of a page. The solution is
+% described on page 260 of The TeXbook. It involves outputting two
+% marks for the sectioning macros, one before the section break, and
+% one after. I won't pretend I can describe this better than DEK...
+\def\domark{%
+ \toks0=\expandafter{\lastchapterdefs}%
+ \toks2=\expandafter{\lastsectiondefs}%
+ \toks4=\expandafter{\prevchapterdefs}%
+ \toks6=\expandafter{\prevsectiondefs}%
+ \toks8=\expandafter{\lastcolordefs}%
+ \mark{%
+ \the\toks0 \the\toks2
+ \noexpand\or \the\toks4 \the\toks6
+ \noexpand\else \the\toks8
+ }%
+}
+% \topmark doesn't work for the very first chapter (after the title
+% page or the contents), so we use \firstmark there -- this gets us
+% the mark with the chapter defs, unless the user sneaks in, e.g.,
+% @setcolor (or @url, or @link, etc.) between @contents and the very
+% first @chapter.
+\def\gettopheadingmarks{%
+ \ifcase0\topmark\fi
+ \ifx\thischapter\empty \ifcase0\firstmark\fi \fi
+}
+\def\getbottomheadingmarks{\ifcase1\botmark\fi}
+\def\getcolormarks{\ifcase2\topmark\fi}
+
+% Avoid "undefined control sequence" errors.
+\def\lastchapterdefs{}
+\def\lastsectiondefs{}
+\def\prevchapterdefs{}
+\def\prevsectiondefs{}
+\def\lastcolordefs{}
+
+% Main output routine.
+\chardef\PAGE = 255
+\output = {\onepageout{\pagecontents\PAGE}}
+
+\newbox\headlinebox
+\newbox\footlinebox
+
+% \onepageout takes a vbox as an argument. Note that \pagecontents
+% does insertions, but you have to call it yourself.
+\def\onepageout#1{%
+ \ifcropmarks \hoffset=0pt \else \hoffset=\normaloffset \fi
+ %
+ \ifodd\pageno \advance\hoffset by \bindingoffset
+ \else \advance\hoffset by -\bindingoffset\fi
+ %
+ % Do this outside of the \shipout so @code etc. will be expanded in
+ % the headline as they should be, not taken literally (outputting ''code).
+ \ifodd\pageno \getoddheadingmarks \else \getevenheadingmarks \fi
+ \setbox\headlinebox = \vbox{\let\hsize=\pagewidth \makeheadline}%
+ \ifodd\pageno \getoddfootingmarks \else \getevenfootingmarks \fi
+ \setbox\footlinebox = \vbox{\let\hsize=\pagewidth \makefootline}%
+ %
+ {%
+ % Have to do this stuff outside the \shipout because we want it to
+ % take effect in \write's, yet the group defined by the \vbox ends
+ % before the \shipout runs.
+ %
+ \indexdummies % don't expand commands in the output.
+ \normalturnoffactive % \ in index entries must not stay \, e.g., if
+ % the page break happens to be in the middle of an example.
+ % We don't want .vr (or whatever) entries like this:
+ % \entry{{\tt \indexbackslash }acronym}{32}{\code {\acronym}}
+ % "\acronym" won't work when it's read back in;
+ % it needs to be
+ % {\code {{\tt \backslashcurfont }acronym}
+ \shipout\vbox{%
+ % Do this early so pdf references go to the beginning of the page.
+ \ifpdfmakepagedest \pdfdest name{\the\pageno} xyz\fi
+ %
+ \ifcropmarks \vbox to \outervsize\bgroup
+ \hsize = \outerhsize
+ \vskip-\topandbottommargin
+ \vtop to0pt{%
+ \line{\ewtop\hfil\ewtop}%
+ \nointerlineskip
+ \line{%
+ \vbox{\moveleft\cornerthick\nstop}%
+ \hfill
+ \vbox{\moveright\cornerthick\nstop}%
+ }%
+ \vss}%
+ \vskip\topandbottommargin
+ \line\bgroup
+ \hfil % center the page within the outer (page) hsize.
+ \ifodd\pageno\hskip\bindingoffset\fi
+ \vbox\bgroup
+ \fi
+ %
+ \unvbox\headlinebox
+ \pagebody{#1}%
+ \ifdim\ht\footlinebox > 0pt
+ % Only leave this space if the footline is nonempty.
+ % (We lessened \vsize for it in \oddfootingyyy.)
+ % The \baselineskip=24pt in plain's \makefootline has no effect.
+ \vskip 24pt
+ \unvbox\footlinebox
+ \fi
+ %
+ \ifcropmarks
+ \egroup % end of \vbox\bgroup
+ \hfil\egroup % end of (centering) \line\bgroup
+ \vskip\topandbottommargin plus1fill minus1fill
+ \boxmaxdepth = \cornerthick
+ \vbox to0pt{\vss
+ \line{%
+ \vbox{\moveleft\cornerthick\nsbot}%
+ \hfill
+ \vbox{\moveright\cornerthick\nsbot}%
+ }%
+ \nointerlineskip
+ \line{\ewbot\hfil\ewbot}%
+ }%
+ \egroup % \vbox from first cropmarks clause
+ \fi
+ }% end of \shipout\vbox
+ }% end of group with \indexdummies
+ \advancepageno
+ \ifnum\outputpenalty>-20000 \else\dosupereject\fi
+}
+
+\newinsert\margin \dimen\margin=\maxdimen
+
+\def\pagebody#1{\vbox to\pageheight{\boxmaxdepth=\maxdepth #1}}
+{\catcode`\@ =11
+\gdef\pagecontents#1{\ifvoid\topins\else\unvbox\topins\fi
+% marginal hacks, juha at viisa.uucp (Juha Takala)
+\ifvoid\margin\else % marginal info is present
+ \rlap{\kern\hsize\vbox to\z@{\kern1pt\box\margin \vss}}\fi
+\dimen@=\dp#1\relax \unvbox#1\relax
+\ifvoid\footins\else\vskip\skip\footins\footnoterule \unvbox\footins\fi
+\ifr at ggedbottom \kern-\dimen@ \vfil \fi}
+}
+
+% Here are the rules for the cropmarks. Note that they are
+% offset so that the space between them is truly \outerhsize or \outervsize
+% (P. A. MacKay, 12 November, 1986)
+%
+\def\ewtop{\vrule height\cornerthick depth0pt width\cornerlong}
+\def\nstop{\vbox
+ {\hrule height\cornerthick depth\cornerlong width\cornerthick}}
+\def\ewbot{\vrule height0pt depth\cornerthick width\cornerlong}
+\def\nsbot{\vbox
+ {\hrule height\cornerlong depth\cornerthick width\cornerthick}}
+
+% Parse an argument, then pass it to #1. The argument is the rest of
+% the input line (except we remove a trailing comment). #1 should be a
+% macro which expects an ordinary undelimited TeX argument.
+%
+\def\parsearg{\parseargusing{}}
+\def\parseargusing#1#2{%
+ \def\argtorun{#2}%
+ \begingroup
+ \obeylines
+ \spaceisspace
+ #1%
+ \parseargline\empty% Insert the \empty token, see \finishparsearg below.
+}
+
+{\obeylines %
+ \gdef\parseargline#1^^M{%
+ \endgroup % End of the group started in \parsearg.
+ \argremovecomment #1\comment\ArgTerm%
+ }%
+}
+
+% First remove any @comment, then any @c comment.
+\def\argremovecomment#1\comment#2\ArgTerm{\argremovec #1\c\ArgTerm}
+\def\argremovec#1\c#2\ArgTerm{\argcheckspaces#1\^^M\ArgTerm}
+
+% Each occurrence of `\^^M' or `<space>\^^M' is replaced by a single space.
+%
+% \argremovec might leave us with trailing space, e.g.,
+% @end itemize @c foo
+% This space token undergoes the same procedure and is eventually removed
+% by \finishparsearg.
+%
+\def\argcheckspaces#1\^^M{\argcheckspacesX#1\^^M \^^M}
+\def\argcheckspacesX#1 \^^M{\argcheckspacesY#1\^^M}
+\def\argcheckspacesY#1\^^M#2\^^M#3\ArgTerm{%
+ \def\temp{#3}%
+ \ifx\temp\empty
+ % Do not use \next, perhaps the caller of \parsearg uses it; reuse \temp:
+ \let\temp\finishparsearg
+ \else
+ \let\temp\argcheckspaces
+ \fi
+ % Put the space token in:
+ \temp#1 #3\ArgTerm
+}
+
+% If a _delimited_ argument is enclosed in braces, they get stripped; so
+% to get _exactly_ the rest of the line, we had to prevent such situation.
+% We prepended an \empty token at the very beginning and we expand it now,
+% just before passing the control to \argtorun.
+% (Similarly, we have to think about #3 of \argcheckspacesY above: it is
+% either the null string, or it ends with \^^M---thus there is no danger
+% that a pair of braces would be stripped.
+%
+% But first, we have to remove the trailing space token.
+%
+\def\finishparsearg#1 \ArgTerm{\expandafter\argtorun\expandafter{#1}}
+
+% \parseargdef\foo{...}
+% is roughly equivalent to
+% \def\foo{\parsearg\Xfoo}
+% \def\Xfoo#1{...}
+%
+% Actually, I use \csname\string\foo\endcsname, ie. \\foo, as it is my
+% favourite TeX trick. --kasal, 16nov03
+
+\def\parseargdef#1{%
+ \expandafter \doparseargdef \csname\string#1\endcsname #1%
+}
+\def\doparseargdef#1#2{%
+ \def#2{\parsearg#1}%
+ \def#1##1%
+}
+
+% Several utility definitions with active space:
+{
+ \obeyspaces
+ \gdef\obeyedspace{ }
+
+ % Make each space character in the input produce a normal interword
+ % space in the output. Don't allow a line break at this space, as this
+ % is used only in environments like @example, where each line of input
+ % should produce a line of output anyway.
+ %
+ \gdef\sepspaces{\obeyspaces\let =\tie}
+
+ % If an index command is used in an @example environment, any spaces
+ % therein should become regular spaces in the raw index file, not the
+ % expansion of \tie (\leavevmode \penalty \@M \ ).
+ \gdef\unsepspaces{\let =\space}
+}
+
+
+\def\flushcr{\ifx\par\lisppar \def\next##1{}\else \let\next=\relax \fi \next}
+
+% Define the framework for environments in texinfo.tex. It's used like this:
+%
+% \envdef\foo{...}
+% \def\Efoo{...}
+%
+% It's the responsibility of \envdef to insert \begingroup before the
+% actual body; @end closes the group after calling \Efoo. \envdef also
+% defines \thisenv, so the current environment is known; @end checks
+% whether the environment name matches. The \checkenv macro can also be
+% used to check whether the current environment is the one expected.
+%
+% Non-false conditionals (@iftex, @ifset) don't fit into this, so they
+% are not treated as environments; they don't open a group. (The
+% implementation of @end takes care not to call \endgroup in this
+% special case.)
+
+
+% At run-time, environments start with this:
+\def\startenvironment#1{\begingroup\def\thisenv{#1}}
+% initialize
+\let\thisenv\empty
+
+% ... but they get defined via ``\envdef\foo{...}'':
+\long\def\envdef#1#2{\def#1{\startenvironment#1#2}}
+\def\envparseargdef#1#2{\parseargdef#1{\startenvironment#1#2}}
+
+% Check whether we're in the right environment:
+\def\checkenv#1{%
+ \def\temp{#1}%
+ \ifx\thisenv\temp
+ \else
+ \badenverr
+ \fi
+}
+
+% Environment mismatch, #1 expected:
+\def\badenverr{%
+ \errhelp = \EMsimple
+ \errmessage{This command can appear only \inenvironment\temp,
+ not \inenvironment\thisenv}%
+}
+\def\inenvironment#1{%
+ \ifx#1\empty
+ out of any environment%
+ \else
+ in environment \expandafter\string#1%
+ \fi
+}
+
+% @end foo executes the definition of \Efoo.
+% But first, it executes a specialized version of \checkenv
+%
+\parseargdef\end{%
+ \if 1\csname iscond.#1\endcsname
+ \else
+ % The general wording of \badenverr may not be ideal, but... --kasal, 06nov03
+ \expandafter\checkenv\csname#1\endcsname
+ \csname E#1\endcsname
+ \endgroup
+ \fi
+}
+
+\newhelp\EMsimple{Press RETURN to continue.}
+
+
+%% Simple single-character @ commands
+
+% @@ prints an @
+% Kludge this until the fonts are right (grr).
+\def\@{{\tt\char64}}
+
+% This is turned off because it was never documented
+% and you can use @w{...} around a quote to suppress ligatures.
+%% Define @` and @' to be the same as ` and '
+%% but suppressing ligatures.
+%\def\`{{`}}
+%\def\'{{'}}
+
+% Used to generate quoted braces.
+\def\mylbrace {{\tt\char123}}
+\def\myrbrace {{\tt\char125}}
+\let\{=\mylbrace
+\let\}=\myrbrace
+\begingroup
+ % Definitions to produce \{ and \} commands for indices,
+ % and @{ and @} for the aux/toc files.
+ \catcode`\{ = \other \catcode`\} = \other
+ \catcode`\[ = 1 \catcode`\] = 2
+ \catcode`\! = 0 \catcode`\\ = \other
+ !gdef!lbracecmd[\{]%
+ !gdef!rbracecmd[\}]%
+ !gdef!lbraceatcmd[@{]%
+ !gdef!rbraceatcmd[@}]%
+!endgroup
+
+% @comma{} to avoid , parsing problems.
+\let\comma = ,
+
+% Accents: @, @dotaccent @ringaccent @ubaraccent @udotaccent
+% Others are defined by plain TeX: @` @' @" @^ @~ @= @u @v @H.
+\let\, = \c
+\let\dotaccent = \.
+\def\ringaccent#1{{\accent23 #1}}
+\let\tieaccent = \t
+\let\ubaraccent = \b
+\let\udotaccent = \d
+
+% Other special characters: @questiondown @exclamdown @ordf @ordm
+% Plain TeX defines: @AA @AE @O @OE @L (plus lowercase versions) @ss.
+\def\questiondown{?`}
+\def\exclamdown{!`}
+\def\ordf{\leavevmode\raise1ex\hbox{\selectfonts\lllsize \underbar{a}}}
+\def\ordm{\leavevmode\raise1ex\hbox{\selectfonts\lllsize \underbar{o}}}
+
+% Dotless i and dotless j, used for accents.
+\def\imacro{i}
+\def\jmacro{j}
+\def\dotless#1{%
+ \def\temp{#1}%
+ \ifx\temp\imacro \ifmmode\imath \else\ptexi \fi
+ \else\ifx\temp\jmacro \ifmmode\jmath \else\j \fi
+ \else \errmessage{@dotless can be used only with i or j}%
+ \fi\fi
+}
+
+% The \TeX{} logo, as in plain, but resetting the spacing so that a
+% period following counts as ending a sentence. (Idea found in latex.)
+%
+\edef\TeX{\TeX \spacefactor=1000 }
+
+% @LaTeX{} logo. Not quite the same results as the definition in
+% latex.ltx, since we use a different font for the raised A; it's most
+% convenient for us to use an explicitly smaller font, rather than using
+% the \scriptstyle font (since we don't reset \scriptstyle and
+% \scriptscriptstyle).
+%
+\def\LaTeX{%
+ L\kern-.36em
+ {\setbox0=\hbox{T}%
+ \vbox to \ht0{\hbox{\selectfonts\lllsize A}\vss}}%
+ \kern-.15em
+ \TeX
+}
+
+% Be sure we're in horizontal mode when doing a tie, since we make space
+% equivalent to this in @example-like environments. Otherwise, a space
+% at the beginning of a line will start with \penalty -- and
+% since \penalty is valid in vertical mode, we'd end up putting the
+% penalty on the vertical list instead of in the new paragraph.
+{\catcode`@ = 11
+ % Avoid using \@M directly, because that causes trouble
+ % if the definition is written into an index file.
+ \global\let\tiepenalty = \@M
+ \gdef\tie{\leavevmode\penalty\tiepenalty\ }
+}
+
+% @: forces normal size whitespace following.
+\def\:{\spacefactor=1000 }
+
+% @* forces a line break.
+\def\*{\hfil\break\hbox{}\ignorespaces}
+
+% @/ allows a line break.
+\let\/=\allowbreak
+
+% @. is an end-of-sentence period.
+\def\.{.\spacefactor=\endofsentencespacefactor\space}
+
+% @! is an end-of-sentence bang.
+\def\!{!\spacefactor=\endofsentencespacefactor\space}
+
+% @? is an end-of-sentence query.
+\def\?{?\spacefactor=\endofsentencespacefactor\space}
+
+% @frenchspacing on|off says whether to put extra space after punctuation.
+%
+\def\onword{on}
+\def\offword{off}
+%
+\parseargdef\frenchspacing{%
+ \def\temp{#1}%
+ \ifx\temp\onword \plainfrenchspacing
+ \else\ifx\temp\offword \plainnonfrenchspacing
+ \else
+ \errhelp = \EMsimple
+ \errmessage{Unknown @frenchspacing option `\temp', must be on/off}%
+ \fi\fi
+}
+
+% @w prevents a word break. Without the \leavevmode, @w at the
+% beginning of a paragraph, when TeX is still in vertical mode, would
+% produce a whole line of output instead of starting the paragraph.
+\def\w#1{\leavevmode\hbox{#1}}
+
+% @group ... @end group forces ... to be all on one page, by enclosing
+% it in a TeX vbox. We use \vtop instead of \vbox to construct the box
+% to keep its height that of a normal line. According to the rules for
+% \topskip (p.114 of the TeXbook), the glue inserted is
+% max (\topskip - \ht (first item), 0). If that height is large,
+% therefore, no glue is inserted, and the space between the headline and
+% the text is small, which looks bad.
+%
+% Another complication is that the group might be very large. This can
+% cause the glue on the previous page to be unduly stretched, because it
+% does not have much material. In this case, it's better to add an
+% explicit \vfill so that the extra space is at the bottom. The
+% threshold for doing this is if the group is more than \vfilllimit
+% percent of a page (\vfilllimit can be changed inside of @tex).
+%
+\newbox\groupbox
+\def\vfilllimit{0.7}
+%
+\envdef\group{%
+ \ifnum\catcode`\^^M=\active \else
+ \errhelp = \groupinvalidhelp
+ \errmessage{@group invalid in context where filling is enabled}%
+ \fi
+ \startsavinginserts
+ %
+ \setbox\groupbox = \vtop\bgroup
+ % Do @comment since we are called inside an environment such as
+ % @example, where each end-of-line in the input causes an
+ % end-of-line in the output. We don't want the end-of-line after
+ % the `@group' to put extra space in the output. Since @group
+ % should appear on a line by itself (according to the Texinfo
+ % manual), we don't worry about eating any user text.
+ \comment
+}
+%
+% The \vtop produces a box with normal height and large depth; thus, TeX puts
+% \baselineskip glue before it, and (when the next line of text is done)
+% \lineskip glue after it. Thus, space below is not quite equal to space
+% above. But it's pretty close.
+\def\Egroup{%
+ % To get correct interline space between the last line of the group
+ % and the first line afterwards, we have to propagate \prevdepth.
+ \endgraf % Not \par, as it may have been set to \lisppar.
+ \global\dimen1 = \prevdepth
+ \egroup % End the \vtop.
+ % \dimen0 is the vertical size of the group's box.
+ \dimen0 = \ht\groupbox \advance\dimen0 by \dp\groupbox
+ % \dimen2 is how much space is left on the page (more or less).
+ \dimen2 = \pageheight \advance\dimen2 by -\pagetotal
+ % if the group doesn't fit on the current page, and it's a big big
+ % group, force a page break.
+ \ifdim \dimen0 > \dimen2
+ \ifdim \pagetotal < \vfilllimit\pageheight
+ \page
+ \fi
+ \fi
+ \box\groupbox
+ \prevdepth = \dimen1
+ \checkinserts
+}
+%
+% TeX puts in an \escapechar (i.e., `@') at the beginning of the help
+% message, so this ends up printing `@group can only ...'.
+%
+\newhelp\groupinvalidhelp{%
+group can only be used in environments such as @example,^^J%
+where each line of input produces a line of output.}
+
+% @need space-in-mils
+% forces a page break if there is not space-in-mils remaining.
+
+\newdimen\mil \mil=0.001in
+
+% Old definition--didn't work.
+%\parseargdef\need{\par %
+%% This method tries to make TeX break the page naturally
+%% if the depth of the box does not fit.
+%{\baselineskip=0pt%
+%\vtop to #1\mil{\vfil}\kern -#1\mil\nobreak
+%\prevdepth=-1000pt
+%}}
+
+\parseargdef\need{%
+ % Ensure vertical mode, so we don't make a big box in the middle of a
+ % paragraph.
+ \par
+ %
+ % If the @need value is less than one line space, it's useless.
+ \dimen0 = #1\mil
+ \dimen2 = \ht\strutbox
+ \advance\dimen2 by \dp\strutbox
+ \ifdim\dimen0 > \dimen2
+ %
+ % Do a \strut just to make the height of this box be normal, so the
+ % normal leading is inserted relative to the preceding line.
+ % And a page break here is fine.
+ \vtop to #1\mil{\strut\vfil}%
+ %
+ % TeX does not even consider page breaks if a penalty added to the
+ % main vertical list is 10000 or more. But in order to see if the
+ % empty box we just added fits on the page, we must make it consider
+ % page breaks. On the other hand, we don't want to actually break the
+ % page after the empty box. So we use a penalty of 9999.
+ %
+ % There is an extremely small chance that TeX will actually break the
+ % page at this \penalty, if there are no other feasible breakpoints in
+ % sight. (If the user is using lots of big @group commands, which
+ % almost-but-not-quite fill up a page, TeX will have a hard time doing
+ % good page breaking, for example.) However, I could not construct an
+ % example where a page broke at this \penalty; if it happens in a real
+ % document, then we can reconsider our strategy.
+ \penalty9999
+ %
+ % Back up by the size of the box, whether we did a page break or not.
+ \kern -#1\mil
+ %
+ % Do not allow a page break right after this kern.
+ \nobreak
+ \fi
+}
+
+% @br forces paragraph break (and is undocumented).
+
+\let\br = \par
+
+% @page forces the start of a new page.
+%
+\def\page{\par\vfill\supereject}
+
+% @exdent text....
+% outputs text on separate line in roman font, starting at standard page margin
+
+% This records the amount of indent in the innermost environment.
+% That's how much \exdent should take out.
+\newskip\exdentamount
+
+% This defn is used inside fill environments such as @defun.
+\parseargdef\exdent{\hfil\break\hbox{\kern -\exdentamount{\rm#1}}\hfil\break}
+
+% This defn is used inside nofill environments such as @example.
+\parseargdef\nofillexdent{{\advance \leftskip by -\exdentamount
+ \leftline{\hskip\leftskip{\rm#1}}}}
+
+% @inmargin{WHICH}{TEXT} puts TEXT in the WHICH margin next to the current
+% paragraph. For more general purposes, use the \margin insertion
+% class. WHICH is `l' or `r'.
+%
+\newskip\inmarginspacing \inmarginspacing=1cm
+\def\strutdepth{\dp\strutbox}
+%
+\def\doinmargin#1#2{\strut\vadjust{%
+ \nobreak
+ \kern-\strutdepth
+ \vtop to \strutdepth{%
+ \baselineskip=\strutdepth
+ \vss
+ % if you have multiple lines of stuff to put here, you'll need to
+ % make the vbox yourself of the appropriate size.
+ \ifx#1l%
+ \llap{\ignorespaces #2\hskip\inmarginspacing}%
+ \else
+ \rlap{\hskip\hsize \hskip\inmarginspacing \ignorespaces #2}%
+ \fi
+ \null
+ }%
+}}
+\def\inleftmargin{\doinmargin l}
+\def\inrightmargin{\doinmargin r}
+%
+% @inmargin{TEXT [, RIGHT-TEXT]}
+% (if RIGHT-TEXT is given, use TEXT for left page, RIGHT-TEXT for right;
+% else use TEXT for both).
+%
+\def\inmargin#1{\parseinmargin #1,,\finish}
+\def\parseinmargin#1,#2,#3\finish{% not perfect, but better than nothing.
+ \setbox0 = \hbox{\ignorespaces #2}%
+ \ifdim\wd0 > 0pt
+ \def\lefttext{#1}% have both texts
+ \def\righttext{#2}%
+ \else
+ \def\lefttext{#1}% have only one text
+ \def\righttext{#1}%
+ \fi
+ %
+ \ifodd\pageno
+ \def\temp{\inrightmargin\righttext}% odd page -> outside is right margin
+ \else
+ \def\temp{\inleftmargin\lefttext}%
+ \fi
+ \temp
+}
+
+% @include FILE -- \input text of FILE.
+%
+\def\include{\parseargusing\filenamecatcodes\includezzz}
+\def\includezzz#1{%
+ \pushthisfilestack
+ \def\thisfile{#1}%
+ {%
+ \makevalueexpandable % we want to expand any @value in FILE.
+ \turnoffactive % and allow special characters in the expansion
+ \indexnofonts % Allow `@@' and other weird things in file names.
+ \edef\temp{\noexpand\input #1 }%
+ %
+ % This trickery is to read FILE outside of a group, in case it makes
+ % definitions, etc.
+ \expandafter
+ }\temp
+ \popthisfilestack
+}
+\def\filenamecatcodes{%
+ \catcode`\\=\other
+ \catcode`~=\other
+ \catcode`^=\other
+ \catcode`_=\other
+ \catcode`|=\other
+ \catcode`<=\other
+ \catcode`>=\other
+ \catcode`+=\other
+ \catcode`-=\other
+ \catcode`\`=\other
+ \catcode`\'=\other
+}
+
+\def\pushthisfilestack{%
+ \expandafter\pushthisfilestackX\popthisfilestack\StackTerm
+}
+\def\pushthisfilestackX{%
+ \expandafter\pushthisfilestackY\thisfile\StackTerm
+}
+\def\pushthisfilestackY #1\StackTerm #2\StackTerm {%
+ \gdef\popthisfilestack{\gdef\thisfile{#1}\gdef\popthisfilestack{#2}}%
+}
+
+\def\popthisfilestack{\errthisfilestackempty}
+\def\errthisfilestackempty{\errmessage{Internal error:
+ the stack of filenames is empty.}}
+
+\def\thisfile{}
+
+% @center line
+% outputs that line, centered.
+%
+\parseargdef\center{%
+ \ifhmode
+ \let\next\centerH
+ \else
+ \let\next\centerV
+ \fi
+ \next{\hfil \ignorespaces#1\unskip \hfil}%
+}
+\def\centerH#1{%
+ {%
+ \hfil\break
+ \advance\hsize by -\leftskip
+ \advance\hsize by -\rightskip
+ \line{#1}%
+ \break
+ }%
+}
+\def\centerV#1{\line{\kern\leftskip #1\kern\rightskip}}
+
+% @sp n outputs n lines of vertical space
+
+\parseargdef\sp{\vskip #1\baselineskip}
+
+% @comment ...line which is ignored...
+% @c is the same as @comment
+% @ignore ... @end ignore is another way to write a comment
+
+\def\comment{\begingroup \catcode`\^^M=\other%
+\catcode`\@=\other \catcode`\{=\other \catcode`\}=\other%
+\commentxxx}
+{\catcode`\^^M=\other \gdef\commentxxx#1^^M{\endgroup}}
+
+\let\c=\comment
+
+% @paragraphindent NCHARS
+% We'll use ems for NCHARS, close enough.
+% NCHARS can also be the word `asis' or `none'.
+% We cannot feasibly implement @paragraphindent asis, though.
+%
+\def\asisword{asis} % no translation, these are keywords
+\def\noneword{none}
+%
+\parseargdef\paragraphindent{%
+ \def\temp{#1}%
+ \ifx\temp\asisword
+ \else
+ \ifx\temp\noneword
+ \defaultparindent = 0pt
+ \else
+ \defaultparindent = #1em
+ \fi
+ \fi
+ \parindent = \defaultparindent
+}
+
+% @exampleindent NCHARS
+% We'll use ems for NCHARS like @paragraphindent.
+% It seems @exampleindent asis isn't necessary, but
+% I preserve it to make it similar to @paragraphindent.
+\parseargdef\exampleindent{%
+ \def\temp{#1}%
+ \ifx\temp\asisword
+ \else
+ \ifx\temp\noneword
+ \lispnarrowing = 0pt
+ \else
+ \lispnarrowing = #1em
+ \fi
+ \fi
+}
+
+% @firstparagraphindent WORD
+% If WORD is `none', then suppress indentation of the first paragraph
+% after a section heading. If WORD is `insert', then do indent at such
+% paragraphs.
+%
+% The paragraph indentation is suppressed or not by calling
+% \suppressfirstparagraphindent, which the sectioning commands do.
+% We switch the definition of this back and forth according to WORD.
+% By default, we suppress indentation.
+%
+\def\suppressfirstparagraphindent{\dosuppressfirstparagraphindent}
+\def\insertword{insert}
+%
+\parseargdef\firstparagraphindent{%
+ \def\temp{#1}%
+ \ifx\temp\noneword
+ \let\suppressfirstparagraphindent = \dosuppressfirstparagraphindent
+ \else\ifx\temp\insertword
+ \let\suppressfirstparagraphindent = \relax
+ \else
+ \errhelp = \EMsimple
+ \errmessage{Unknown @firstparagraphindent option `\temp'}%
+ \fi\fi
+}
+
+% Here is how we actually suppress indentation. Redefine \everypar to
+% \kern backwards by \parindent, and then reset itself to empty.
+%
+% We also make \indent itself not actually do anything until the next
+% paragraph.
+%
+\gdef\dosuppressfirstparagraphindent{%
+ \gdef\indent{%
+ \restorefirstparagraphindent
+ \indent
+ }%
+ \gdef\noindent{%
+ \restorefirstparagraphindent
+ \noindent
+ }%
+ \global\everypar = {%
+ \kern -\parindent
+ \restorefirstparagraphindent
+ }%
+}
+
+\gdef\restorefirstparagraphindent{%
+ \global \let \indent = \ptexindent
+ \global \let \noindent = \ptexnoindent
+ \global \everypar = {}%
+}
+
+
+% @asis just yields its argument. Used with @table, for example.
+%
+\def\asis#1{#1}
+
+% @math outputs its argument in math mode.
+%
+% One complication: _ usually means subscripts, but it could also mean
+% an actual _ character, as in @math{@var{some_variable} + 1}. So make
+% _ active, and distinguish by seeing if the current family is \slfam,
+% which is what @var uses.
+{
+ \catcode`\_ = \active
+ \gdef\mathunderscore{%
+ \catcode`\_=\active
+ \def_{\ifnum\fam=\slfam \_\else\sb\fi}%
+ }
+}
+% Another complication: we want \\ (and @\) to output a \ character.
+% FYI, plain.tex uses \\ as a temporary control sequence (why?), but
+% this is not advertised and we don't care. Texinfo does not
+% otherwise define @\.
+%
+% The \mathchar is class=0=ordinary, family=7=ttfam, position=5C=\.
+\def\mathbackslash{\ifnum\fam=\ttfam \mathchar"075C \else\backslash \fi}
+%
+\def\math{%
+ \tex
+ \mathunderscore
+ \let\\ = \mathbackslash
+ \mathactive
+ % make the texinfo accent commands work in math mode
+ \let\"=\ddot
+ \let\'=\acute
+ \let\==\bar
+ \let\^=\hat
+ \let\`=\grave
+ \let\u=\breve
+ \let\v=\check
+ \let\~=\tilde
+ \let\dotaccent=\dot
+ $\finishmath
+}
+\def\finishmath#1{#1$\endgroup} % Close the group opened by \tex.
+
+% Some active characters (such as <) are spaced differently in math.
+% We have to reset their definitions in case the @math was an argument
+% to a command which sets the catcodes (such as @item or @section).
+%
+{
+ \catcode`^ = \active
+ \catcode`< = \active
+ \catcode`> = \active
+ \catcode`+ = \active
+ \catcode`' = \active
+ \gdef\mathactive{%
+ \let^ = \ptexhat
+ \let< = \ptexless
+ \let> = \ptexgtr
+ \let+ = \ptexplus
+ \let' = \ptexquoteright
+ }
+}
+
+% Some math mode symbols.
+\def\bullet{$\ptexbullet$}
+\def\geq{\ifmmode \ge\else $\ge$\fi}
+\def\leq{\ifmmode \le\else $\le$\fi}
+\def\minus{\ifmmode -\else $-$\fi}
+
+% @dots{} outputs an ellipsis using the current font.
+% We do .5em per period so that it has the same spacing in the cm
+% typewriter fonts as three actual period characters; on the other hand,
+% in other typewriter fonts three periods are wider than 1.5em. So do
+% whichever is larger.
+%
+\def\dots{%
+ \leavevmode
+ \setbox0=\hbox{...}% get width of three periods
+ \ifdim\wd0 > 1.5em
+ \dimen0 = \wd0
+ \else
+ \dimen0 = 1.5em
+ \fi
+ \hbox to \dimen0{%
+ \hskip 0pt plus.25fil
+ .\hskip 0pt plus1fil
+ .\hskip 0pt plus1fil
+ .\hskip 0pt plus.5fil
+ }%
+}
+
+% @enddots{} is an end-of-sentence ellipsis.
+%
+\def\enddots{%
+ \dots
+ \spacefactor=\endofsentencespacefactor
+}
+
+% @comma{} is so commas can be inserted into text without messing up
+% Texinfo's parsing.
+%
+\let\comma = ,
+
+% @refill is a no-op.
+\let\refill=\relax
+
+% If working on a large document in chapters, it is convenient to
+% be able to disable indexing, cross-referencing, and contents, for test runs.
+% This is done with @novalidate (before @setfilename).
+%
+\newif\iflinks \linkstrue % by default we want the aux files.
+\let\novalidate = \linksfalse
+
+% @setfilename is done at the beginning of every texinfo file.
+% So open here the files we need to have open while reading the input.
+% This makes it possible to make a .fmt file for texinfo.
+\def\setfilename{%
+ \fixbackslash % Turn off hack to swallow `\input texinfo'.
+ \iflinks
+ \tryauxfile
+ % Open the new aux file. TeX will close it automatically at exit.
+ \immediate\openout\auxfile=\jobname.aux
+ \fi % \openindices needs to do some work in any case.
+ \openindices
+ \let\setfilename=\comment % Ignore extra @setfilename cmds.
+ %
+ % If texinfo.cnf is present on the system, read it.
+ % Useful for site-wide @afourpaper, etc.
+ \openin 1 texinfo.cnf
+ \ifeof 1 \else \input texinfo.cnf \fi
+ \closein 1
+ %
+ \comment % Ignore the actual filename.
+}
+
+% Called from \setfilename.
+%
+\def\openindices{%
+ \newindex{cp}%
+ \newcodeindex{fn}%
+ \newcodeindex{vr}%
+ \newcodeindex{tp}%
+ \newcodeindex{ky}%
+ \newcodeindex{pg}%
+}
+
+% @bye.
+\outer\def\bye{\pagealignmacro\tracingstats=1\ptexend}
+
+
+\message{pdf,}
+% adobe `portable' document format
+\newcount\tempnum
+\newcount\lnkcount
+\newtoks\filename
+\newcount\filenamelength
+\newcount\pgn
+\newtoks\toksA
+\newtoks\toksB
+\newtoks\toksC
+\newtoks\toksD
+\newbox\boxA
+\newcount\countA
+\newif\ifpdf
+\newif\ifpdfmakepagedest
+
+% when pdftex is run in dvi mode, \pdfoutput is defined (so \pdfoutput=1
+% can be set). So we test for \relax and 0 as well as \undefined,
+% borrowed from ifpdf.sty.
+\ifx\pdfoutput\undefined
+\else
+ \ifx\pdfoutput\relax
+ \else
+ \ifcase\pdfoutput
+ \else
+ \pdftrue
+ \fi
+ \fi
+\fi
+
+% PDF uses PostScript string constants for the names of xref targets,
+% for display in the outlines, and in other places. Thus, we have to
+% double any backslashes. Otherwise, a name like "\node" will be
+% interpreted as a newline (\n), followed by o, d, e. Not good.
+% http://www.ntg.nl/pipermail/ntg-pdftex/2004-July/000654.html
+% (and related messages, the final outcome is that it is up to the TeX
+% user to double the backslashes and otherwise make the string valid, so
+% that's what we do).
+
+% double active backslashes.
+%
+{\catcode`\@=0 \catcode`\\=\active
+ @gdef at activebackslashdouble{%
+ @catcode`@\=@active
+ @let\=@doublebackslash}
+}
+
+% To handle parens, we must adopt a different approach, since parens are
+% not active characters. hyperref.dtx (which has the same problem as
+% us) handles it with this amazing macro to replace tokens, with minor
+% changes for Texinfo. It is included here under the GPL by permission
+% from the author, Heiko Oberdiek.
+%
+% #1 is the tokens to replace.
+% #2 is the replacement.
+% #3 is the control sequence with the string.
+%
+\def\HyPsdSubst#1#2#3{%
+ \def\HyPsdReplace##1#1##2\END{%
+ ##1%
+ \ifx\\##2\\%
+ \else
+ #2%
+ \HyReturnAfterFi{%
+ \HyPsdReplace##2\END
+ }%
+ \fi
+ }%
+ \xdef#3{\expandafter\HyPsdReplace#3#1\END}%
+}
+\long\def\HyReturnAfterFi#1\fi{\fi#1}
+
+% #1 is a control sequence in which to do the replacements.
+\def\backslashparens#1{%
+ \xdef#1{#1}% redefine it as its expansion; the definition is simply
+ % \lastnode when called from \setref -> \pdfmkdest.
+ \HyPsdSubst{(}{\realbackslash(}{#1}%
+ \HyPsdSubst{)}{\realbackslash)}{#1}%
+}
+
+\newhelp\nopdfimagehelp{Texinfo supports .png, .jpg, .jpeg, and .pdf images
+with PDF output, and none of those formats could be found. (.eps cannot
+be supported due to the design of the PDF format; use regular TeX (DVI
+output) for that.)}
+
+\ifpdf
+ %
+ % Color manipulation macros based on pdfcolor.tex,
+ % except using rgb instead of cmyk; the latter is said to render as a
+ % very dark gray on-screen and a very dark halftone in print, instead
+ % of actual black.
+ \def\rgbDarkRed{0.50 0.09 0.12}
+ \def\rgbBlack{0 0 0}
+ %
+ % k sets the color for filling (usual text, etc.);
+ % K sets the color for stroking (thin rules, e.g., normal _'s).
+ \def\pdfsetcolor#1{\pdfliteral{#1 rg #1 RG}}
+ %
+ % Set color, and create a mark which defines \thiscolor accordingly,
+ % so that \makeheadline knows which color to restore.
+ \def\setcolor#1{%
+ \xdef\lastcolordefs{\gdef\noexpand\thiscolor{#1}}%
+ \domark
+ \pdfsetcolor{#1}%
+ }
+ %
+ \def\maincolor{\rgbBlack}
+ \pdfsetcolor{\maincolor}
+ \edef\thiscolor{\maincolor}
+ \def\lastcolordefs{}
+ %
+ \def\makefootline{%
+ \baselineskip24pt
+ \line{\pdfsetcolor{\maincolor}\the\footline}%
+ }
+ %
+ \def\makeheadline{%
+ \vbox to 0pt{%
+ \vskip-22.5pt
+ \line{%
+ \vbox to8.5pt{}%
+ % Extract \thiscolor definition from the marks.
+ \getcolormarks
+ % Typeset the headline with \maincolor, then restore the color.
+ \pdfsetcolor{\maincolor}\the\headline\pdfsetcolor{\thiscolor}%
+ }%
+ \vss
+ }%
+ \nointerlineskip
+ }
+ %
+ %
+ \pdfcatalog{/PageMode /UseOutlines}
+ %
+ % #1 is image name, #2 width (might be empty/whitespace), #3 height (ditto).
+ \def\dopdfimage#1#2#3{%
+ \def\imagewidth{#2}\setbox0 = \hbox{\ignorespaces #2}%
+ \def\imageheight{#3}\setbox2 = \hbox{\ignorespaces #3}%
+ %
+ % pdftex (and the PDF format) support .png, .jpg, .pdf (among
+ % others). Let's try in that order.
+ \let\pdfimgext=\empty
+ \begingroup
+ \openin 1 #1.png \ifeof 1
+ \openin 1 #1.jpg \ifeof 1
+ \openin 1 #1.jpeg \ifeof 1
+ \openin 1 #1.JPG \ifeof 1
+ \openin 1 #1.pdf \ifeof 1
+ \openin 1 #1.PDF \ifeof 1
+ \errhelp = \nopdfimagehelp
+ \errmessage{Could not find image file #1 for pdf}%
+ \else \gdef\pdfimgext{PDF}%
+ \fi
+ \else \gdef\pdfimgext{pdf}%
+ \fi
+ \else \gdef\pdfimgext{JPG}%
+ \fi
+ \else \gdef\pdfimgext{jpeg}%
+ \fi
+ \else \gdef\pdfimgext{jpg}%
+ \fi
+ \else \gdef\pdfimgext{png}%
+ \fi
+ \closein 1
+ \endgroup
+ %
+ % without \immediate, ancient pdftex seg faults when the same image is
+ % included twice. (Version 3.14159-pre-1.0-unofficial-20010704.)
+ \ifnum\pdftexversion < 14
+ \immediate\pdfimage
+ \else
+ \immediate\pdfximage
+ \fi
+ \ifdim \wd0 >0pt width \imagewidth \fi
+ \ifdim \wd2 >0pt height \imageheight \fi
+ \ifnum\pdftexversion<13
+ #1.\pdfimgext
+ \else
+ {#1.\pdfimgext}%
+ \fi
+ \ifnum\pdftexversion < 14 \else
+ \pdfrefximage \pdflastximage
+ \fi}
+ %
+ \def\pdfmkdest#1{{%
+ % We have to set dummies so commands such as @code, and characters
+ % such as \, aren't expanded when present in a section title.
+ \indexnofonts
+ \turnoffactive
+ \activebackslashdouble
+ \makevalueexpandable
+ \def\pdfdestname{#1}%
+ \backslashparens\pdfdestname
+ \safewhatsit{\pdfdest name{\pdfdestname} xyz}%
+ }}
+ %
+ % used to mark target names; must be expandable.
+ \def\pdfmkpgn#1{#1}
+ %
+ % by default, use a color that is dark enough to print on paper as
+ % nearly black, but still distinguishable for online viewing.
+ \def\urlcolor{\rgbDarkRed}
+ \def\linkcolor{\rgbDarkRed}
+ \def\endlink{\setcolor{\maincolor}\pdfendlink}
+ %
+ % Adding outlines to PDF; macros for calculating structure of outlines
+ % come from Petr Olsak
+ \def\expnumber#1{\expandafter\ifx\csname#1\endcsname\relax 0%
+ \else \csname#1\endcsname \fi}
+ \def\advancenumber#1{\tempnum=\expnumber{#1}\relax
+ \advance\tempnum by 1
+ \expandafter\xdef\csname#1\endcsname{\the\tempnum}}
+ %
+ % #1 is the section text, which is what will be displayed in the
+ % outline by the pdf viewer. #2 is the pdf expression for the number
+ % of subentries (or empty, for subsubsections). #3 is the node text,
+ % which might be empty if this toc entry had no corresponding node.
+ % #4 is the page number
+ %
+ \def\dopdfoutline#1#2#3#4{%
+ % Generate a link to the node text if that exists; else, use the
+ % page number. We could generate a destination for the section
+ % text in the case where a section has no node, but it doesn't
+ % seem worth the trouble, since most documents are normally structured.
+ \def\pdfoutlinedest{#3}%
+ \ifx\pdfoutlinedest\empty
+ \def\pdfoutlinedest{#4}%
+ \else
+ % Doubled backslashes in the name.
+ {\activebackslashdouble \xdef\pdfoutlinedest{#3}%
+ \backslashparens\pdfoutlinedest}%
+ \fi
+ %
+ % Also double the backslashes in the display string.
+ {\activebackslashdouble \xdef\pdfoutlinetext{#1}%
+ \backslashparens\pdfoutlinetext}%
+ %
+ \pdfoutline goto name{\pdfmkpgn{\pdfoutlinedest}}#2{\pdfoutlinetext}%
+ }
+ %
+ \def\pdfmakeoutlines{%
+ \begingroup
+ % Thanh's hack / proper braces in bookmarks
+ \edef\mylbrace{\iftrue \string{\else}\fi}\let\{=\mylbrace
+ \edef\myrbrace{\iffalse{\else\string}\fi}\let\}=\myrbrace
+ %
+ % Read toc silently, to get counts of subentries for \pdfoutline.
+ \def\numchapentry##1##2##3##4{%
+ \def\thischapnum{##2}%
+ \def\thissecnum{0}%
+ \def\thissubsecnum{0}%
+ }%
+ \def\numsecentry##1##2##3##4{%
+ \advancenumber{chap\thischapnum}%
+ \def\thissecnum{##2}%
+ \def\thissubsecnum{0}%
+ }%
+ \def\numsubsecentry##1##2##3##4{%
+ \advancenumber{sec\thissecnum}%
+ \def\thissubsecnum{##2}%
+ }%
+ \def\numsubsubsecentry##1##2##3##4{%
+ \advancenumber{subsec\thissubsecnum}%
+ }%
+ \def\thischapnum{0}%
+ \def\thissecnum{0}%
+ \def\thissubsecnum{0}%
+ %
+ % use \def rather than \let here because we redefine \chapentry et
+ % al. a second time, below.
+ \def\appentry{\numchapentry}%
+ \def\appsecentry{\numsecentry}%
+ \def\appsubsecentry{\numsubsecentry}%
+ \def\appsubsubsecentry{\numsubsubsecentry}%
+ \def\unnchapentry{\numchapentry}%
+ \def\unnsecentry{\numsecentry}%
+ \def\unnsubsecentry{\numsubsecentry}%
+ \def\unnsubsubsecentry{\numsubsubsecentry}%
+ \readdatafile{toc}%
+ %
+ % Read toc second time, this time actually producing the outlines.
+ % The `-' means take the \expnumber as the absolute number of
+ % subentries, which we calculated on our first read of the .toc above.
+ %
+ % We use the node names as the destinations.
+ \def\numchapentry##1##2##3##4{%
+ \dopdfoutline{##1}{count-\expnumber{chap##2}}{##3}{##4}}%
+ \def\numsecentry##1##2##3##4{%
+ \dopdfoutline{##1}{count-\expnumber{sec##2}}{##3}{##4}}%
+ \def\numsubsecentry##1##2##3##4{%
+ \dopdfoutline{##1}{count-\expnumber{subsec##2}}{##3}{##4}}%
+ \def\numsubsubsecentry##1##2##3##4{% count is always zero
+ \dopdfoutline{##1}{}{##3}{##4}}%
+ %
+ % PDF outlines are displayed using system fonts, instead of
+ % document fonts. Therefore we cannot use special characters,
+ % since the encoding is unknown. For example, the eogonek from
+ % Latin 2 (0xea) gets translated to a | character. Info from
+ % Staszek Wawrykiewicz, 19 Jan 2004 04:09:24 +0100.
+ %
+ % xx to do this right, we have to translate 8-bit characters to
+ % their "best" equivalent, based on the @documentencoding. Right
+ % now, I guess we'll just let the pdf reader have its way.
+ \indexnofonts
+ \setupdatafile
+ \catcode`\\=\active \otherbackslash
+ \input \tocreadfilename
+ \endgroup
+ }
+ %
+ \def\skipspaces#1{\def\PP{#1}\def\D{|}%
+ \ifx\PP\D\let\nextsp\relax
+ \else\let\nextsp\skipspaces
+ \ifx\p\space\else\addtokens{\filename}{\PP}%
+ \advance\filenamelength by 1
+ \fi
+ \fi
+ \nextsp}
+ \def\getfilename#1{\filenamelength=0\expandafter\skipspaces#1|\relax}
+ \ifnum\pdftexversion < 14
+ \let \startlink \pdfannotlink
+ \else
+ \let \startlink \pdfstartlink
+ \fi
+ % make a live url in pdf output.
+ \def\pdfurl#1{%
+ \begingroup
+ % it seems we really need yet another set of dummies; have not
+ % tried to figure out what each command should do in the context
+ % of @url. for now, just make @/ a no-op, that's the only one
+ % people have actually reported a problem with.
+ %
+ \normalturnoffactive
+ \def\@{@}%
+ \let\/=\empty
+ \makevalueexpandable
+ % do we want to go so far as to use \indexnofonts instead of just
+ % special-casing \var here?
+ \def\var##1{##1}%
+ %
+ \leavevmode\setcolor{\urlcolor}%
+ \startlink attr{/Border [0 0 0]}%
+ user{/Subtype /Link /A << /S /URI /URI (#1) >>}%
+ \endgroup}
+ \def\pdfgettoks#1.{\setbox\boxA=\hbox{\toksA={#1.}\toksB={}\maketoks}}
+ \def\addtokens#1#2{\edef\addtoks{\noexpand#1={\the#1#2}}\addtoks}
+ \def\adn#1{\addtokens{\toksC}{#1}\global\countA=1\let\next=\maketoks}
+ \def\poptoks#1#2|ENDTOKS|{\let\first=#1\toksD={#1}\toksA={#2}}
+ \def\maketoks{%
+ \expandafter\poptoks\the\toksA|ENDTOKS|\relax
+ \ifx\first0\adn0
+ \else\ifx\first1\adn1 \else\ifx\first2\adn2 \else\ifx\first3\adn3
+ \else\ifx\first4\adn4 \else\ifx\first5\adn5 \else\ifx\first6\adn6
+ \else\ifx\first7\adn7 \else\ifx\first8\adn8 \else\ifx\first9\adn9
+ \else
+ \ifnum0=\countA\else\makelink\fi
+ \ifx\first.\let\next=\done\else
+ \let\next=\maketoks
+ \addtokens{\toksB}{\the\toksD}
+ \ifx\first,\addtokens{\toksB}{\space}\fi
+ \fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \next}
+ \def\makelink{\addtokens{\toksB}%
+ {\noexpand\pdflink{\the\toksC}}\toksC={}\global\countA=0}
+ \def\pdflink#1{%
+ \startlink attr{/Border [0 0 0]} goto name{\pdfmkpgn{#1}}
+ \setcolor{\linkcolor}#1\endlink}
+ \def\done{\edef\st{\global\noexpand\toksA={\the\toksB}}\st}
+\else
+ % non-pdf mode
+ \let\pdfmkdest = \gobble
+ \let\pdfurl = \gobble
+ \let\endlink = \relax
+ \let\setcolor = \gobble
+ \let\pdfsetcolor = \gobble
+ \let\pdfmakeoutlines = \relax
+\fi % \ifx\pdfoutput
+
+
+\message{fonts,}
+
+% Change the current font style to #1, remembering it in \curfontstyle.
+% For now, we do not accumulate font styles: @b{@i{foo}} prints foo in
+% italics, not bold italics.
+%
+\def\setfontstyle#1{%
+ \def\curfontstyle{#1}% not as a control sequence, because we are \edef'd.
+ \csname ten#1\endcsname % change the current font
+}
+
+% Select #1 fonts with the current style.
+%
+\def\selectfonts#1{\csname #1fonts\endcsname \csname\curfontstyle\endcsname}
+
+\def\rm{\fam=0 \setfontstyle{rm}}
+\def\it{\fam=\itfam \setfontstyle{it}}
+\def\sl{\fam=\slfam \setfontstyle{sl}}
+\def\bf{\fam=\bffam \setfontstyle{bf}}\def\bfstylename{bf}
+\def\tt{\fam=\ttfam \setfontstyle{tt}}
+
+% Unfortunately, we have to override this for titles and the like, since
+% in those cases "rm" is bold. Sigh.
+\def\rmisbold{\rm\def\curfontstyle{bf}}
+
+% Texinfo sort of supports the sans serif font style, which plain TeX does not.
+% So we set up a \sf.
+\newfam\sffam
+\def\sf{\fam=\sffam \setfontstyle{sf}}
+\let\li = \sf % Sometimes we call it \li, not \sf.
+
+% We don't need math for this font style.
+\def\ttsl{\setfontstyle{ttsl}}
+
+
+% Default leading.
+\newdimen\textleading \textleading = 13.2pt
+
+% Set the baselineskip to #1, and the lineskip and strut size
+% correspondingly. There is no deep meaning behind these magic numbers
+% used as factors; they just match (closely enough) what Knuth defined.
+%
+\def\lineskipfactor{.08333}
+\def\strutheightpercent{.70833}
+\def\strutdepthpercent {.29167}
+%
+% can get a sort of poor man's double spacing by redefining this.
+\def\baselinefactor{1}
+%
+\def\setleading#1{%
+ \dimen0 = #1\relax
+ \normalbaselineskip = \baselinefactor\dimen0
+ \normallineskip = \lineskipfactor\normalbaselineskip
+ \normalbaselines
+ \setbox\strutbox =\hbox{%
+ \vrule width0pt height\strutheightpercent\baselineskip
+ depth \strutdepthpercent \baselineskip
+ }%
+}
+
+% PDF CMaps. See also LaTeX's t1.cmap.
+%
+% do nothing with this by default.
+\expandafter\let\csname cmapOT1\endcsname\gobble
+\expandafter\let\csname cmapOT1IT\endcsname\gobble
+\expandafter\let\csname cmapOT1TT\endcsname\gobble
+
+% if we are producing pdf, and we have \pdffontattr, then define cmaps.
+% (\pdffontattr was introduced many years ago, but people still run
+% older pdftex's; it's easy to conditionalize, so we do.)
+\ifpdf \ifx\pdffontattr\undefined \else
+ \begingroup
+ \catcode`\^^M=\active \def^^M{^^J}% Output line endings as the ^^J char.
+ \catcode`\%=12 \immediate\pdfobj stream {%!PS-Adobe-3.0 Resource-CMap
+%%DocumentNeededResources: ProcSet (CIDInit)
+%%IncludeResource: ProcSet (CIDInit)
+%%BeginResource: CMap (TeX-OT1-0)
+%%Title: (TeX-OT1-0 TeX OT1 0)
+%%Version: 1.000
+%%EndComments
+/CIDInit /ProcSet findresource begin
+12 dict begin
+begincmap
+/CIDSystemInfo
+<< /Registry (TeX)
+/Ordering (OT1)
+/Supplement 0
+>> def
+/CMapName /TeX-OT1-0 def
+/CMapType 2 def
+1 begincodespacerange
+<00> <7F>
+endcodespacerange
+8 beginbfrange
+<00> <01> <0393>
+<09> <0A> <03A8>
+<23> <26> <0023>
+<28> <3B> <0028>
+<3F> <5B> <003F>
+<5D> <5E> <005D>
+<61> <7A> <0061>
+<7B> <7C> <2013>
+endbfrange
+40 beginbfchar
+<02> <0398>
+<03> <039B>
+<04> <039E>
+<05> <03A0>
+<06> <03A3>
+<07> <03D2>
+<08> <03A6>
+<0B> <00660066>
+<0C> <00660069>
+<0D> <0066006C>
+<0E> <006600660069>
+<0F> <00660066006C>
+<10> <0131>
+<11> <0237>
+<12> <0060>
+<13> <00B4>
+<14> <02C7>
+<15> <02D8>
+<16> <00AF>
+<17> <02DA>
+<18> <00B8>
+<19> <00DF>
+<1A> <00E6>
+<1B> <0153>
+<1C> <00F8>
+<1D> <00C6>
+<1E> <0152>
+<1F> <00D8>
+<21> <0021>
+<22> <201D>
+<27> <2019>
+<3C> <00A1>
+<3D> <003D>
+<3E> <00BF>
+<5C> <201C>
+<5F> <02D9>
+<60> <2018>
+<7D> <02DD>
+<7E> <007E>
+<7F> <00A8>
+endbfchar
+endcmap
+CMapName currentdict /CMap defineresource pop
+end
+end
+%%EndResource
+%%EOF
+ }\endgroup
+ \expandafter\edef\csname cmapOT1\endcsname#1{%
+ \pdffontattr#1{/ToUnicode \the\pdflastobj\space 0 R}%
+ }%
+%
+% \cmapOT1IT
+ \begingroup
+ \catcode`\^^M=\active \def^^M{^^J}% Output line endings as the ^^J char.
+ \catcode`\%=12 \immediate\pdfobj stream {%!PS-Adobe-3.0 Resource-CMap
+%%DocumentNeededResources: ProcSet (CIDInit)
+%%IncludeResource: ProcSet (CIDInit)
+%%BeginResource: CMap (TeX-OT1IT-0)
+%%Title: (TeX-OT1IT-0 TeX OT1IT 0)
+%%Version: 1.000
+%%EndComments
+/CIDInit /ProcSet findresource begin
+12 dict begin
+begincmap
+/CIDSystemInfo
+<< /Registry (TeX)
+/Ordering (OT1IT)
+/Supplement 0
+>> def
+/CMapName /TeX-OT1IT-0 def
+/CMapType 2 def
+1 begincodespacerange
+<00> <7F>
+endcodespacerange
+8 beginbfrange
+<00> <01> <0393>
+<09> <0A> <03A8>
+<25> <26> <0025>
+<28> <3B> <0028>
+<3F> <5B> <003F>
+<5D> <5E> <005D>
+<61> <7A> <0061>
+<7B> <7C> <2013>
+endbfrange
+42 beginbfchar
+<02> <0398>
+<03> <039B>
+<04> <039E>
+<05> <03A0>
+<06> <03A3>
+<07> <03D2>
+<08> <03A6>
+<0B> <00660066>
+<0C> <00660069>
+<0D> <0066006C>
+<0E> <006600660069>
+<0F> <00660066006C>
+<10> <0131>
+<11> <0237>
+<12> <0060>
+<13> <00B4>
+<14> <02C7>
+<15> <02D8>
+<16> <00AF>
+<17> <02DA>
+<18> <00B8>
+<19> <00DF>
+<1A> <00E6>
+<1B> <0153>
+<1C> <00F8>
+<1D> <00C6>
+<1E> <0152>
+<1F> <00D8>
+<21> <0021>
+<22> <201D>
+<23> <0023>
+<24> <00A3>
+<27> <2019>
+<3C> <00A1>
+<3D> <003D>
+<3E> <00BF>
+<5C> <201C>
+<5F> <02D9>
+<60> <2018>
+<7D> <02DD>
+<7E> <007E>
+<7F> <00A8>
+endbfchar
+endcmap
+CMapName currentdict /CMap defineresource pop
+end
+end
+%%EndResource
+%%EOF
+ }\endgroup
+ \expandafter\edef\csname cmapOT1IT\endcsname#1{%
+ \pdffontattr#1{/ToUnicode \the\pdflastobj\space 0 R}%
+ }%
+%
+% \cmapOT1TT
+ \begingroup
+ \catcode`\^^M=\active \def^^M{^^J}% Output line endings as the ^^J char.
+ \catcode`\%=12 \immediate\pdfobj stream {%!PS-Adobe-3.0 Resource-CMap
+%%DocumentNeededResources: ProcSet (CIDInit)
+%%IncludeResource: ProcSet (CIDInit)
+%%BeginResource: CMap (TeX-OT1TT-0)
+%%Title: (TeX-OT1TT-0 TeX OT1TT 0)
+%%Version: 1.000
+%%EndComments
+/CIDInit /ProcSet findresource begin
+12 dict begin
+begincmap
+/CIDSystemInfo
+<< /Registry (TeX)
+/Ordering (OT1TT)
+/Supplement 0
+>> def
+/CMapName /TeX-OT1TT-0 def
+/CMapType 2 def
+1 begincodespacerange
+<00> <7F>
+endcodespacerange
+5 beginbfrange
+<00> <01> <0393>
+<09> <0A> <03A8>
+<21> <26> <0021>
+<28> <5F> <0028>
+<61> <7E> <0061>
+endbfrange
+32 beginbfchar
+<02> <0398>
+<03> <039B>
+<04> <039E>
+<05> <03A0>
+<06> <03A3>
+<07> <03D2>
+<08> <03A6>
+<0B> <2191>
+<0C> <2193>
+<0D> <0027>
+<0E> <00A1>
+<0F> <00BF>
+<10> <0131>
+<11> <0237>
+<12> <0060>
+<13> <00B4>
+<14> <02C7>
+<15> <02D8>
+<16> <00AF>
+<17> <02DA>
+<18> <00B8>
+<19> <00DF>
+<1A> <00E6>
+<1B> <0153>
+<1C> <00F8>
+<1D> <00C6>
+<1E> <0152>
+<1F> <00D8>
+<20> <2423>
+<27> <2019>
+<60> <2018>
+<7F> <00A8>
+endbfchar
+endcmap
+CMapName currentdict /CMap defineresource pop
+end
+end
+%%EndResource
+%%EOF
+ }\endgroup
+ \expandafter\edef\csname cmapOT1TT\endcsname#1{%
+ \pdffontattr#1{/ToUnicode \the\pdflastobj\space 0 R}%
+ }%
+\fi\fi
+
+
+% Set the font macro #1 to the font named #2, adding on the
+% specified font prefix (normally `cm').
+% #3 is the font's design size, #4 is a scale factor, #5 is the CMap
+% encoding (currently only OT1, OT1IT and OT1TT are allowed, pass
+% empty to omit).
+\def\setfont#1#2#3#4#5{%
+ \font#1=\fontprefix#2#3 scaled #4
+ \csname cmap#5\endcsname#1%
+}
+% This is what gets called when #5 of \setfont is empty.
+\let\cmap\gobble
+% emacs-page end of cmaps
+
+% Use cm as the default font prefix.
+% To specify the font prefix, you must define \fontprefix
+% before you read in texinfo.tex.
+\ifx\fontprefix\undefined
+\def\fontprefix{cm}
+\fi
+% Support font families that don't use the same naming scheme as CM.
+\def\rmshape{r}
+\def\rmbshape{bx} %where the normal face is bold
+\def\bfshape{b}
+\def\bxshape{bx}
+\def\ttshape{tt}
+\def\ttbshape{tt}
+\def\ttslshape{sltt}
+\def\itshape{ti}
+\def\itbshape{bxti}
+\def\slshape{sl}
+\def\slbshape{bxsl}
+\def\sfshape{ss}
+\def\sfbshape{ss}
+\def\scshape{csc}
+\def\scbshape{csc}
+
+% Definitions for a main text size of 11pt. This is the default in
+% Texinfo.
+%
+\def\definetextfontsizexi{%
+% Text fonts (11.2pt, magstep1).
+\def\textnominalsize{11pt}
+\edef\mainmagstep{\magstephalf}
+\setfont\textrm\rmshape{10}{\mainmagstep}{OT1}
+\setfont\texttt\ttshape{10}{\mainmagstep}{OT1TT}
+\setfont\textbf\bfshape{10}{\mainmagstep}{OT1}
+\setfont\textit\itshape{10}{\mainmagstep}{OT1IT}
+\setfont\textsl\slshape{10}{\mainmagstep}{OT1}
+\setfont\textsf\sfshape{10}{\mainmagstep}{OT1}
+\setfont\textsc\scshape{10}{\mainmagstep}{OT1}
+\setfont\textttsl\ttslshape{10}{\mainmagstep}{OT1TT}
+\font\texti=cmmi10 scaled \mainmagstep
+\font\textsy=cmsy10 scaled \mainmagstep
+\def\textecsize{1095}
+
+% A few fonts for @defun names and args.
+\setfont\defbf\bfshape{10}{\magstep1}{OT1}
+\setfont\deftt\ttshape{10}{\magstep1}{OT1TT}
+\setfont\defttsl\ttslshape{10}{\magstep1}{OT1TT}
+\def\df{\let\tentt=\deftt \let\tenbf = \defbf \let\tenttsl=\defttsl \bf}
+
+% Fonts for indices, footnotes, small examples (9pt).
+\def\smallnominalsize{9pt}
+\setfont\smallrm\rmshape{9}{1000}{OT1}
+\setfont\smalltt\ttshape{9}{1000}{OT1TT}
+\setfont\smallbf\bfshape{10}{900}{OT1}
+\setfont\smallit\itshape{9}{1000}{OT1IT}
+\setfont\smallsl\slshape{9}{1000}{OT1}
+\setfont\smallsf\sfshape{9}{1000}{OT1}
+\setfont\smallsc\scshape{10}{900}{OT1}
+\setfont\smallttsl\ttslshape{10}{900}{OT1TT}
+\font\smalli=cmmi9
+\font\smallsy=cmsy9
+\def\smallecsize{0900}
+
+% Fonts for small examples (8pt).
+\def\smallernominalsize{8pt}
+\setfont\smallerrm\rmshape{8}{1000}{OT1}
+\setfont\smallertt\ttshape{8}{1000}{OT1TT}
+\setfont\smallerbf\bfshape{10}{800}{OT1}
+\setfont\smallerit\itshape{8}{1000}{OT1IT}
+\setfont\smallersl\slshape{8}{1000}{OT1}
+\setfont\smallersf\sfshape{8}{1000}{OT1}
+\setfont\smallersc\scshape{10}{800}{OT1}
+\setfont\smallerttsl\ttslshape{10}{800}{OT1TT}
+\font\smalleri=cmmi8
+\font\smallersy=cmsy8
+\def\smallerecsize{0800}
+
+% Fonts for title page (20.4pt):
+\def\titlenominalsize{20pt}
+\setfont\titlerm\rmbshape{12}{\magstep3}{OT1}
+\setfont\titleit\itbshape{10}{\magstep4}{OT1IT}
+\setfont\titlesl\slbshape{10}{\magstep4}{OT1}
+\setfont\titlett\ttbshape{12}{\magstep3}{OT1TT}
+\setfont\titlettsl\ttslshape{10}{\magstep4}{OT1TT}
+\setfont\titlesf\sfbshape{17}{\magstep1}{OT1}
+\let\titlebf=\titlerm
+\setfont\titlesc\scbshape{10}{\magstep4}{OT1}
+\font\titlei=cmmi12 scaled \magstep3
+\font\titlesy=cmsy10 scaled \magstep4
+\def\titleecsize{2074}
+
+% Chapter (and unnumbered) fonts (17.28pt).
+\def\chapnominalsize{17pt}
+\setfont\chaprm\rmbshape{12}{\magstep2}{OT1}
+\setfont\chapit\itbshape{10}{\magstep3}{OT1IT}
+\setfont\chapsl\slbshape{10}{\magstep3}{OT1}
+\setfont\chaptt\ttbshape{12}{\magstep2}{OT1TT}
+\setfont\chapttsl\ttslshape{10}{\magstep3}{OT1TT}
+\setfont\chapsf\sfbshape{17}{1000}{OT1}
+\let\chapbf=\chaprm
+\setfont\chapsc\scbshape{10}{\magstep3}{OT1}
+\font\chapi=cmmi12 scaled \magstep2
+\font\chapsy=cmsy10 scaled \magstep3
+\def\chapecsize{1728}
+
+% Section fonts (14.4pt).
+\def\secnominalsize{14pt}
+\setfont\secrm\rmbshape{12}{\magstep1}{OT1}
+\setfont\secit\itbshape{10}{\magstep2}{OT1IT}
+\setfont\secsl\slbshape{10}{\magstep2}{OT1}
+\setfont\sectt\ttbshape{12}{\magstep1}{OT1TT}
+\setfont\secttsl\ttslshape{10}{\magstep2}{OT1TT}
+\setfont\secsf\sfbshape{12}{\magstep1}{OT1}
+\let\secbf\secrm
+\setfont\secsc\scbshape{10}{\magstep2}{OT1}
+\font\seci=cmmi12 scaled \magstep1
+\font\secsy=cmsy10 scaled \magstep2
+\def\sececsize{1440}
+
+% Subsection fonts (13.15pt).
+\def\ssecnominalsize{13pt}
+\setfont\ssecrm\rmbshape{12}{\magstephalf}{OT1}
+\setfont\ssecit\itbshape{10}{1315}{OT1IT}
+\setfont\ssecsl\slbshape{10}{1315}{OT1}
+\setfont\ssectt\ttbshape{12}{\magstephalf}{OT1TT}
+\setfont\ssecttsl\ttslshape{10}{1315}{OT1TT}
+\setfont\ssecsf\sfbshape{12}{\magstephalf}{OT1}
+\let\ssecbf\ssecrm
+\setfont\ssecsc\scbshape{10}{1315}{OT1}
+\font\sseci=cmmi12 scaled \magstephalf
+\font\ssecsy=cmsy10 scaled 1315
+\def\ssececsize{1200}
+
+% Reduced fonts for @acro in text (10pt).
+\def\reducednominalsize{10pt}
+\setfont\reducedrm\rmshape{10}{1000}{OT1}
+\setfont\reducedtt\ttshape{10}{1000}{OT1TT}
+\setfont\reducedbf\bfshape{10}{1000}{OT1}
+\setfont\reducedit\itshape{10}{1000}{OT1IT}
+\setfont\reducedsl\slshape{10}{1000}{OT1}
+\setfont\reducedsf\sfshape{10}{1000}{OT1}
+\setfont\reducedsc\scshape{10}{1000}{OT1}
+\setfont\reducedttsl\ttslshape{10}{1000}{OT1TT}
+\font\reducedi=cmmi10
+\font\reducedsy=cmsy10
+\def\reducedecsize{1000}
+
+% reset the current fonts
+\textfonts
+\rm
+} % end of 11pt text font size definitions
+
+
+% Definitions to make the main text be 10pt Computer Modern, with
+% section, chapter, etc., sizes following suit. This is for the GNU
+% Press printing of the Emacs 22 manual. Maybe other manuals in the
+% future. Used with @smallbook, which sets the leading to 12pt.
+%
+\def\definetextfontsizex{%
+% Text fonts (10pt).
+\def\textnominalsize{10pt}
+\edef\mainmagstep{1000}
+\setfont\textrm\rmshape{10}{\mainmagstep}{OT1}
+\setfont\texttt\ttshape{10}{\mainmagstep}{OT1TT}
+\setfont\textbf\bfshape{10}{\mainmagstep}{OT1}
+\setfont\textit\itshape{10}{\mainmagstep}{OT1IT}
+\setfont\textsl\slshape{10}{\mainmagstep}{OT1}
+\setfont\textsf\sfshape{10}{\mainmagstep}{OT1}
+\setfont\textsc\scshape{10}{\mainmagstep}{OT1}
+\setfont\textttsl\ttslshape{10}{\mainmagstep}{OT1TT}
+\font\texti=cmmi10 scaled \mainmagstep
+\font\textsy=cmsy10 scaled \mainmagstep
+\def\textecsize{1000}
+
+% A few fonts for @defun names and args.
+\setfont\defbf\bfshape{10}{\magstephalf}{OT1}
+\setfont\deftt\ttshape{10}{\magstephalf}{OT1TT}
+\setfont\defttsl\ttslshape{10}{\magstephalf}{OT1TT}
+\def\df{\let\tentt=\deftt \let\tenbf = \defbf \let\tenttsl=\defttsl \bf}
+
+% Fonts for indices, footnotes, small examples (9pt).
+\def\smallnominalsize{9pt}
+\setfont\smallrm\rmshape{9}{1000}{OT1}
+\setfont\smalltt\ttshape{9}{1000}{OT1TT}
+\setfont\smallbf\bfshape{10}{900}{OT1}
+\setfont\smallit\itshape{9}{1000}{OT1IT}
+\setfont\smallsl\slshape{9}{1000}{OT1}
+\setfont\smallsf\sfshape{9}{1000}{OT1}
+\setfont\smallsc\scshape{10}{900}{OT1}
+\setfont\smallttsl\ttslshape{10}{900}{OT1TT}
+\font\smalli=cmmi9
+\font\smallsy=cmsy9
+\def\smallecsize{0900}
+
+% Fonts for small examples (8pt).
+\def\smallernominalsize{8pt}
+\setfont\smallerrm\rmshape{8}{1000}{OT1}
+\setfont\smallertt\ttshape{8}{1000}{OT1TT}
+\setfont\smallerbf\bfshape{10}{800}{OT1}
+\setfont\smallerit\itshape{8}{1000}{OT1IT}
+\setfont\smallersl\slshape{8}{1000}{OT1}
+\setfont\smallersf\sfshape{8}{1000}{OT1}
+\setfont\smallersc\scshape{10}{800}{OT1}
+\setfont\smallerttsl\ttslshape{10}{800}{OT1TT}
+\font\smalleri=cmmi8
+\font\smallersy=cmsy8
+\def\smallerecsize{0800}
+
+% Fonts for title page (20.4pt):
+\def\titlenominalsize{20pt}
+\setfont\titlerm\rmbshape{12}{\magstep3}{OT1}
+\setfont\titleit\itbshape{10}{\magstep4}{OT1IT}
+\setfont\titlesl\slbshape{10}{\magstep4}{OT1}
+\setfont\titlett\ttbshape{12}{\magstep3}{OT1TT}
+\setfont\titlettsl\ttslshape{10}{\magstep4}{OT1TT}
+\setfont\titlesf\sfbshape{17}{\magstep1}{OT1}
+\let\titlebf=\titlerm
+\setfont\titlesc\scbshape{10}{\magstep4}{OT1}
+\font\titlei=cmmi12 scaled \magstep3
+\font\titlesy=cmsy10 scaled \magstep4
+\def\titleecsize{2074}
+
+% Chapter fonts (14.4pt).
+\def\chapnominalsize{14pt}
+\setfont\chaprm\rmbshape{12}{\magstep1}{OT1}
+\setfont\chapit\itbshape{10}{\magstep2}{OT1IT}
+\setfont\chapsl\slbshape{10}{\magstep2}{OT1}
+\setfont\chaptt\ttbshape{12}{\magstep1}{OT1TT}
+\setfont\chapttsl\ttslshape{10}{\magstep2}{OT1TT}
+\setfont\chapsf\sfbshape{12}{\magstep1}{OT1}
+\let\chapbf\chaprm
+\setfont\chapsc\scbshape{10}{\magstep2}{OT1}
+\font\chapi=cmmi12 scaled \magstep1
+\font\chapsy=cmsy10 scaled \magstep2
+\def\chapecsize{1440}
+
+% Section fonts (12pt).
+\def\secnominalsize{12pt}
+\setfont\secrm\rmbshape{12}{1000}{OT1}
+\setfont\secit\itbshape{10}{\magstep1}{OT1IT}
+\setfont\secsl\slbshape{10}{\magstep1}{OT1}
+\setfont\sectt\ttbshape{12}{1000}{OT1TT}
+\setfont\secttsl\ttslshape{10}{\magstep1}{OT1TT}
+\setfont\secsf\sfbshape{12}{1000}{OT1}
+\let\secbf\secrm
+\setfont\secsc\scbshape{10}{\magstep1}{OT1}
+\font\seci=cmmi12
+\font\secsy=cmsy10 scaled \magstep1
+\def\sececsize{1200}
+
+% Subsection fonts (10pt).
+\def\ssecnominalsize{10pt}
+\setfont\ssecrm\rmbshape{10}{1000}{OT1}
+\setfont\ssecit\itbshape{10}{1000}{OT1IT}
+\setfont\ssecsl\slbshape{10}{1000}{OT1}
+\setfont\ssectt\ttbshape{10}{1000}{OT1TT}
+\setfont\ssecttsl\ttslshape{10}{1000}{OT1TT}
+\setfont\ssecsf\sfbshape{10}{1000}{OT1}
+\let\ssecbf\ssecrm
+\setfont\ssecsc\scbshape{10}{1000}{OT1}
+\font\sseci=cmmi10
+\font\ssecsy=cmsy10
+\def\ssececsize{1000}
+
+% Reduced fonts for @acro in text (9pt).
+\def\reducednominalsize{9pt}
+\setfont\reducedrm\rmshape{9}{1000}{OT1}
+\setfont\reducedtt\ttshape{9}{1000}{OT1TT}
+\setfont\reducedbf\bfshape{10}{900}{OT1}
+\setfont\reducedit\itshape{9}{1000}{OT1IT}
+\setfont\reducedsl\slshape{9}{1000}{OT1}
+\setfont\reducedsf\sfshape{9}{1000}{OT1}
+\setfont\reducedsc\scshape{10}{900}{OT1}
+\setfont\reducedttsl\ttslshape{10}{900}{OT1TT}
+\font\reducedi=cmmi9
+\font\reducedsy=cmsy9
+\def\reducedecsize{0900}
+
+% reduce space between paragraphs
+\divide\parskip by 2
+
+% reset the current fonts
+\textfonts
+\rm
+} % end of 10pt text font size definitions
+
+
+% We provide the user-level command
+% @fonttextsize 10
+% (or 11) to redefine the text font size. pt is assumed.
+%
+\def\xword{10}
+\def\xiword{11}
+%
+\parseargdef\fonttextsize{%
+ \def\textsizearg{#1}%
+ \wlog{doing @fonttextsize \textsizearg}%
+ %
+ % Set \globaldefs so that documents can use this inside @tex, since
+ % makeinfo 4.8 does not support it, but we need it nonetheless.
+ %
+ \begingroup \globaldefs=1
+ \ifx\textsizearg\xword \definetextfontsizex
+ \else \ifx\textsizearg\xiword \definetextfontsizexi
+ \else
+ \errhelp=\EMsimple
+ \errmessage{@fonttextsize only supports `10' or `11', not `\textsizearg'}
+ \fi\fi
+ \endgroup
+}
+
+
+% In order for the font changes to affect most math symbols and letters,
+% we have to define the \textfont of the standard families. Since
+% texinfo doesn't allow for producing subscripts and superscripts except
+% in the main text, we don't bother to reset \scriptfont and
+% \scriptscriptfont (which would also require loading a lot more fonts).
+%
+\def\resetmathfonts{%
+ \textfont0=\tenrm \textfont1=\teni \textfont2=\tensy
+ \textfont\itfam=\tenit \textfont\slfam=\tensl \textfont\bffam=\tenbf
+ \textfont\ttfam=\tentt \textfont\sffam=\tensf
+}
+
+% The font-changing commands redefine the meanings of \tenSTYLE, instead
+% of just \STYLE. We do this because \STYLE needs to also set the
+% current \fam for math mode. Our \STYLE (e.g., \rm) commands hardwire
+% \tenSTYLE to set the current font.
+%
+% Each font-changing command also sets the names \lsize (one size lower)
+% and \lllsize (three sizes lower). These relative commands are used in
+% the LaTeX logo and acronyms.
+%
+% This all needs generalizing, badly.
+%
+\def\textfonts{%
+ \let\tenrm=\textrm \let\tenit=\textit \let\tensl=\textsl
+ \let\tenbf=\textbf \let\tentt=\texttt \let\smallcaps=\textsc
+ \let\tensf=\textsf \let\teni=\texti \let\tensy=\textsy
+ \let\tenttsl=\textttsl
+ \def\curfontsize{text}%
+ \def\lsize{reduced}\def\lllsize{smaller}%
+ \resetmathfonts \setleading{\textleading}}
+\def\titlefonts{%
+ \let\tenrm=\titlerm \let\tenit=\titleit \let\tensl=\titlesl
+ \let\tenbf=\titlebf \let\tentt=\titlett \let\smallcaps=\titlesc
+ \let\tensf=\titlesf \let\teni=\titlei \let\tensy=\titlesy
+ \let\tenttsl=\titlettsl
+ \def\curfontsize{title}%
+ \def\lsize{chap}\def\lllsize{subsec}%
+ \resetmathfonts \setleading{25pt}}
+\def\titlefont#1{{\titlefonts\rmisbold #1}}
+\def\chapfonts{%
+ \let\tenrm=\chaprm \let\tenit=\chapit \let\tensl=\chapsl
+ \let\tenbf=\chapbf \let\tentt=\chaptt \let\smallcaps=\chapsc
+ \let\tensf=\chapsf \let\teni=\chapi \let\tensy=\chapsy
+ \let\tenttsl=\chapttsl
+ \def\curfontsize{chap}%
+ \def\lsize{sec}\def\lllsize{text}%
+ \resetmathfonts \setleading{19pt}}
+\def\secfonts{%
+ \let\tenrm=\secrm \let\tenit=\secit \let\tensl=\secsl
+ \let\tenbf=\secbf \let\tentt=\sectt \let\smallcaps=\secsc
+ \let\tensf=\secsf \let\teni=\seci \let\tensy=\secsy
+ \let\tenttsl=\secttsl
+ \def\curfontsize{sec}%
+ \def\lsize{subsec}\def\lllsize{reduced}%
+ \resetmathfonts \setleading{16pt}}
+\def\subsecfonts{%
+ \let\tenrm=\ssecrm \let\tenit=\ssecit \let\tensl=\ssecsl
+ \let\tenbf=\ssecbf \let\tentt=\ssectt \let\smallcaps=\ssecsc
+ \let\tensf=\ssecsf \let\teni=\sseci \let\tensy=\ssecsy
+ \let\tenttsl=\ssecttsl
+ \def\curfontsize{ssec}%
+ \def\lsize{text}\def\lllsize{small}%
+ \resetmathfonts \setleading{15pt}}
+\let\subsubsecfonts = \subsecfonts
+\def\reducedfonts{%
+ \let\tenrm=\reducedrm \let\tenit=\reducedit \let\tensl=\reducedsl
+ \let\tenbf=\reducedbf \let\tentt=\reducedtt \let\reducedcaps=\reducedsc
+ \let\tensf=\reducedsf \let\teni=\reducedi \let\tensy=\reducedsy
+ \let\tenttsl=\reducedttsl
+ \def\curfontsize{reduced}%
+ \def\lsize{small}\def\lllsize{smaller}%
+ \resetmathfonts \setleading{10.5pt}}
+\def\smallfonts{%
+ \let\tenrm=\smallrm \let\tenit=\smallit \let\tensl=\smallsl
+ \let\tenbf=\smallbf \let\tentt=\smalltt \let\smallcaps=\smallsc
+ \let\tensf=\smallsf \let\teni=\smalli \let\tensy=\smallsy
+ \let\tenttsl=\smallttsl
+ \def\curfontsize{small}%
+ \def\lsize{smaller}\def\lllsize{smaller}%
+ \resetmathfonts \setleading{10.5pt}}
+\def\smallerfonts{%
+ \let\tenrm=\smallerrm \let\tenit=\smallerit \let\tensl=\smallersl
+ \let\tenbf=\smallerbf \let\tentt=\smallertt \let\smallcaps=\smallersc
+ \let\tensf=\smallersf \let\teni=\smalleri \let\tensy=\smallersy
+ \let\tenttsl=\smallerttsl
+ \def\curfontsize{smaller}%
+ \def\lsize{smaller}\def\lllsize{smaller}%
+ \resetmathfonts \setleading{9.5pt}}
+
+% Fonts for short table of contents.
+\setfont\shortcontrm\rmshape{12}{1000}{OT1}
+\setfont\shortcontbf\bfshape{10}{\magstep1}{OT1} % no cmb12
+\setfont\shortcontsl\slshape{12}{1000}{OT1}
+\setfont\shortconttt\ttshape{12}{1000}{OT1TT}
+
+% Define these just so they can be easily changed for other fonts.
+\def\angleleft{$\langle$}
+\def\angleright{$\rangle$}
+
+% Set the fonts to use with the @small... environments.
+\let\smallexamplefonts = \smallfonts
+
+% About \smallexamplefonts. If we use \smallfonts (9pt), @smallexample
+% can fit this many characters:
+% 8.5x11=86 smallbook=72 a4=90 a5=69
+% If we use \scriptfonts (8pt), then we can fit this many characters:
+% 8.5x11=90+ smallbook=80 a4=90+ a5=77
+% For me, subjectively, the few extra characters that fit aren't worth
+% the additional smallness of 8pt. So I'm making the default 9pt.
+%
+% By the way, for comparison, here's what fits with @example (10pt):
+% 8.5x11=71 smallbook=60 a4=75 a5=58
+% --karl, 24jan03.
+
+% Set up the default fonts, so we can use them for creating boxes.
+%
+\definetextfontsizexi
+
+
+\message{markup,}
+
+% Check if we are currently using a typewriter font. Since all the
+% Computer Modern typewriter fonts have zero interword stretch (and
+% shrink), and it is reasonable to expect all typewriter fonts to have
+% this property, we can check that font parameter.
+%
+\def\ifmonospace{\ifdim\fontdimen3\font=0pt }
+
+% Markup style infrastructure. \defmarkupstylesetup\INITMACRO will
+% define and register \INITMACRO to be called on markup style changes.
+% \INITMACRO can check \currentmarkupstyle for the innermost
+% style and the set of \ifmarkupSTYLE switches for all styles
+% currently in effect.
+\newif\ifmarkupvar
+\newif\ifmarkupsamp
+\newif\ifmarkupkey
+%\newif\ifmarkupfile % @file == @samp.
+%\newif\ifmarkupoption % @option == @samp.
+\newif\ifmarkupcode
+\newif\ifmarkupkbd
+%\newif\ifmarkupenv % @env == @code.
+%\newif\ifmarkupcommand % @command == @code.
+\newif\ifmarkuptex % @tex (and part of @math, for now).
+\newif\ifmarkupexample
+\newif\ifmarkupverb
+\newif\ifmarkupverbatim
+
+\let\currentmarkupstyle\empty
+
+\def\setupmarkupstyle#1{%
+ \csname markup#1true\endcsname
+ \def\currentmarkupstyle{#1}%
+ \markupstylesetup
+}
+
+\let\markupstylesetup\empty
+
+\def\defmarkupstylesetup#1{%
+ \expandafter\def\expandafter\markupstylesetup
+ \expandafter{\markupstylesetup #1}%
+ \def#1%
+}
+
+% Markup style setup for left and right quotes.
+\defmarkupstylesetup\markupsetuplq{%
+ \expandafter\let\expandafter \temp \csname markupsetuplq\currentmarkupstyle\endcsname
+ \ifx\temp\relax \markupsetuplqdefault \else \temp \fi
+}
+
+\defmarkupstylesetup\markupsetuprq{%
+ \expandafter\let\expandafter \temp \csname markupsetuprq\currentmarkupstyle\endcsname
+ \ifx\temp\relax \markupsetuprqdefault \else \temp \fi
+}
+
+{
+\catcode`\'=\active
+\catcode`\`=\active
+
+\gdef\markupsetuplqdefault{\let`\lq}
+\gdef\markupsetuprqdefault{\let'\rq}
+
+\gdef\markupsetcodequoteleft{\let`\codequoteleft}
+\gdef\markupsetcodequoteright{\let'\codequoteright}
+
+\gdef\markupsetnoligaturesquoteleft{\let`\noligaturesquoteleft}
+}
+
+\let\markupsetuplqcode \markupsetcodequoteleft
+\let\markupsetuprqcode \markupsetcodequoteright
+\let\markupsetuplqexample \markupsetcodequoteleft
+\let\markupsetuprqexample \markupsetcodequoteright
+\let\markupsetuplqverb \markupsetcodequoteleft
+\let\markupsetuprqverb \markupsetcodequoteright
+\let\markupsetuplqverbatim \markupsetcodequoteleft
+\let\markupsetuprqverbatim \markupsetcodequoteright
+
+\let\markupsetuplqsamp \markupsetnoligaturesquoteleft
+\let\markupsetuplqkbd \markupsetnoligaturesquoteleft
+
+% Allow an option to not replace quotes with a regular directed right
+% quote/apostrophe (char 0x27), but instead use the undirected quote
+% from cmtt (char 0x0d). The undirected quote is ugly, so don't make it
+% the default, but it works for pasting with more pdf viewers (at least
+% evince), the lilypond developers report. xpdf does work with the
+% regular 0x27.
+%
+\def\codequoteright{%
+ \expandafter\ifx\csname SETtxicodequoteundirected\endcsname\relax
+ \expandafter\ifx\csname SETcodequoteundirected\endcsname\relax
+ '%
+ \else \char'15 \fi
+ \else \char'15 \fi
+}
+%
+% and a similar option for the left quote char vs. a grave accent.
+% Modern fonts display ASCII 0x60 as a grave accent, so some people like
+% the code environments to do likewise.
+%
+\def\codequoteleft{%
+ \expandafter\ifx\csname SETtxicodequotebacktick\endcsname\relax
+ \expandafter\ifx\csname SETcodequotebacktick\endcsname\relax
+ % [Knuth] pp. 380,381,391
+ % \relax disables Spanish ligatures ?` and !` of \tt font.
+ \relax`%
+ \else \char'22 \fi
+ \else \char'22 \fi
+}
+
+% [Knuth] pp. 380,381,391, disable Spanish ligatures ?` and !` of \tt font.
+\def\noligaturesquoteleft{\relax\lq}
+
+% Count depth in font-changes, for error checks
+\newcount\fontdepth \fontdepth=0
+
+%% Add scribe-like font environments, plus @l for inline lisp (usually sans
+%% serif) and @ii for TeX italic
+
+% \smartitalic{ARG} outputs arg in italics, followed by an italic correction
+% unless the following character is such as not to need one.
+\def\smartitalicx{\ifx\next,\else\ifx\next-\else\ifx\next.\else
+ \ptexslash\fi\fi\fi}
+\def\smartslanted#1{{\ifusingtt\ttsl\sl #1}\futurelet\next\smartitalicx}
+\def\smartitalic#1{{\ifusingtt\ttsl\it #1}\futurelet\next\smartitalicx}
+
+% like \smartslanted except unconditionally uses \ttsl.
+% @var is set to this for defun arguments.
+\def\ttslanted#1{{\ttsl #1}\futurelet\next\smartitalicx}
+
+% @cite is like \smartslanted except unconditionally use \sl. We never want
+% ttsl for book titles, do we?
+\def\cite#1{{\sl #1}\futurelet\next\smartitalicx}
+
+\let\i=\smartitalic
+\let\slanted=\smartslanted
+\def\var#1{{\setupmarkupstyle{var}\smartslanted{#1}}}
+\let\dfn=\smartslanted
+\let\emph=\smartitalic
+
+% Explicit font changes: @r, @sc, undocumented @ii.
+\def\r#1{{\rm #1}} % roman font
+\def\sc#1{{\smallcaps#1}} % smallcaps font
+\def\ii#1{{\it #1}} % italic font
+
+% @b, explicit bold. Also @strong.
+\def\b#1{{\bf #1}}
+\let\strong=\b
+
+% @sansserif, explicit sans.
+\def\sansserif#1{{\sf #1}}
+
+% We can't just use \exhyphenpenalty, because that only has effect at
+% the end of a paragraph. Restore normal hyphenation at the end of the
+% group within which \nohyphenation is presumably called.
+%
+\def\nohyphenation{\hyphenchar\font = -1 \aftergroup\restorehyphenation}
+\def\restorehyphenation{\hyphenchar\font = `- }
+
+% Set sfcode to normal for the chars that usually have another value.
+% Can't use plain's \frenchspacing because it uses the `\x notation, and
+% sometimes \x has an active definition that messes things up.
+%
+\catcode`@=11
+ \def\plainfrenchspacing{%
+ \sfcode\dotChar =\@m \sfcode\questChar=\@m \sfcode\exclamChar=\@m
+ \sfcode\colonChar=\@m \sfcode\semiChar =\@m \sfcode\commaChar =\@m
+ \def\endofsentencespacefactor{1000}% for @. and friends
+ }
+ \def\plainnonfrenchspacing{%
+ \sfcode`\.3000\sfcode`\?3000\sfcode`\!3000
+ \sfcode`\:2000\sfcode`\;1500\sfcode`\,1250
+ \def\endofsentencespacefactor{3000}% for @. and friends
+ }
+\catcode`@=\other
+\def\endofsentencespacefactor{3000}% default
+
+% @t, explicit typewriter.
+\def\t#1{%
+ {\tt \rawbackslash \plainfrenchspacing #1}%
+ \null
+}
+
+% @samp.
+\def\samp#1{{\setupmarkupstyle{samp}\lq\tclose{#1}\rq\null}}
+
+% definition of @key that produces a lozenge. Doesn't adjust to text size.
+%\setfont\keyrm\rmshape{8}{1000}{OT1}
+%\font\keysy=cmsy9
+%\def\key#1{{\keyrm\textfont2=\keysy \leavevmode\hbox{%
+% \raise0.4pt\hbox{\angleleft}\kern-.08em\vtop{%
+% \vbox{\hrule\kern-0.4pt
+% \hbox{\raise0.4pt\hbox{\vphantom{\angleleft}}#1}}%
+% \kern-0.4pt\hrule}%
+% \kern-.06em\raise0.4pt\hbox{\angleright}}}}
+
+% definition of @key with no lozenge. If the current font is already
+% monospace, don't change it; that way, we respect @kbdinputstyle. But
+% if it isn't monospace, then use \tt.
+%
+\def\key#1{{\setupmarkupstyle{key}%
+ \nohyphenation
+ \ifmonospace\else\tt\fi
+ #1}\null}
+
+% ctrl is no longer a Texinfo command.
+\def\ctrl #1{{\tt \rawbackslash \hat}#1}
+
+% @file, @option are the same as @samp.
+\let\file=\samp
+\let\option=\samp
+
+% @code is a modification of @t,
+% which makes spaces the same size as normal in the surrounding text.
+\def\tclose#1{%
+ {%
+ % Change normal interword space to be same as for the current font.
+ \spaceskip = \fontdimen2\font
+ %
+ % Switch to typewriter.
+ \tt
+ %
+ % But `\ ' produces the large typewriter interword space.
+ \def\ {{\spaceskip = 0pt{} }}%
+ %
+ % Turn off hyphenation.
+ \nohyphenation
+ %
+ \rawbackslash
+ \plainfrenchspacing
+ #1%
+ }%
+ \null
+}
+
+% We *must* turn on hyphenation at `-' and `_' in @code.
+% Otherwise, it is too hard to avoid overfull hboxes
+% in the Emacs manual, the Library manual, etc.
+
+% Unfortunately, TeX uses one parameter (\hyphenchar) to control
+% both hyphenation at - and hyphenation within words.
+% We must therefore turn them both off (\tclose does that)
+% and arrange explicitly to hyphenate at a dash.
+% -- rms.
+{
+ \catcode`\-=\active \catcode`\_=\active
+ \catcode`\'=\active \catcode`\`=\active
+ \global\let'=\rq \global\let`=\lq % default definitions
+ %
+ \global\def\code{\begingroup
+ \setupmarkupstyle{code}%
+ % The following should really be moved into \setupmarkupstyle handlers.
+ \catcode\dashChar=\active \catcode\underChar=\active
+ \ifallowcodebreaks
+ \let-\codedash
+ \let_\codeunder
+ \else
+ \let-\realdash
+ \let_\realunder
+ \fi
+ \codex
+ }
+}
+
+\def\realdash{-}
+\def\codedash{-\discretionary{}{}{}}
+\def\codeunder{%
+ % this is all so @math{@code{var_name}+1} can work. In math mode, _
+ % is "active" (mathcode"8000) and \normalunderscore (or \char95, etc.)
+ % will therefore expand the active definition of _, which is us
+ % (inside @code that is), therefore an endless loop.
+ \ifusingtt{\ifmmode
+ \mathchar"075F % class 0=ordinary, family 7=ttfam, pos 0x5F=_.
+ \else\normalunderscore \fi
+ \discretionary{}{}{}}%
+ {\_}%
+}
+\def\codex #1{\tclose{#1}\endgroup}
+
+% An additional complication: the above will allow breaks after, e.g.,
+% each of the four underscores in __typeof__. This is undesirable in
+% some manuals, especially if they don't have long identifiers in
+% general. @allowcodebreaks provides a way to control this.
+%
+\newif\ifallowcodebreaks \allowcodebreakstrue
+
+\def\keywordtrue{true}
+\def\keywordfalse{false}
+
+\parseargdef\allowcodebreaks{%
+ \def\txiarg{#1}%
+ \ifx\txiarg\keywordtrue
+ \allowcodebreakstrue
+ \else\ifx\txiarg\keywordfalse
+ \allowcodebreaksfalse
+ \else
+ \errhelp = \EMsimple
+ \errmessage{Unknown @allowcodebreaks option `\txiarg'}%
+ \fi\fi
+}
+
+% @kbd is like @code, except that if the argument is just one @key command,
+% then @kbd has no effect.
+\def\kbd#1{{\setupmarkupstyle{kbd}\def\look{#1}\expandafter\kbdfoo\look??\par}}
+
+% @kbdinputstyle -- arg is `distinct' (@kbd uses slanted tty font always),
+% `example' (@kbd uses ttsl only inside of @example and friends),
+% or `code' (@kbd uses normal tty font always).
+\parseargdef\kbdinputstyle{%
+ \def\txiarg{#1}%
+ \ifx\txiarg\worddistinct
+ \gdef\kbdexamplefont{\ttsl}\gdef\kbdfont{\ttsl}%
+ \else\ifx\txiarg\wordexample
+ \gdef\kbdexamplefont{\ttsl}\gdef\kbdfont{\tt}%
+ \else\ifx\txiarg\wordcode
+ \gdef\kbdexamplefont{\tt}\gdef\kbdfont{\tt}%
+ \else
+ \errhelp = \EMsimple
+ \errmessage{Unknown @kbdinputstyle option `\txiarg'}%
+ \fi\fi\fi
+}
+\def\worddistinct{distinct}
+\def\wordexample{example}
+\def\wordcode{code}
+
+% Default is `distinct'.
+\kbdinputstyle distinct
+
+\def\xkey{\key}
+\def\kbdfoo#1#2#3\par{\def\one{#1}\def\three{#3}\def\threex{??}%
+\ifx\one\xkey\ifx\threex\three \key{#2}%
+\else{\tclose{\kbdfont\setupmarkupstyle{kbd}\look}}\fi
+\else{\tclose{\kbdfont\setupmarkupstyle{kbd}\look}}\fi}
+
+% For @indicateurl, @env, @command quotes seem unnecessary, so use \code.
+\let\indicateurl=\code
+\let\env=\code
+\let\command=\code
+
+% @clicksequence{File @click{} Open ...}
+\def\clicksequence#1{\begingroup #1\endgroup}
+
+% @clickstyle @arrow (by default)
+\parseargdef\clickstyle{\def\click{#1}}
+\def\click{\arrow}
+
+% @uref (abbreviation for `urlref') takes an optional (comma-separated)
+% second argument specifying the text to display and an optional third
+% arg as text to display instead of (rather than in addition to) the url
+% itself. First (mandatory) arg is the url. Perhaps eventually put in
+% a hypertex \special here.
+%
+\def\uref#1{\douref #1,,,\finish}
+\def\douref#1,#2,#3,#4\finish{\begingroup
+ \unsepspaces
+ \pdfurl{#1}%
+ \setbox0 = \hbox{\ignorespaces #3}%
+ \ifdim\wd0 > 0pt
+ \unhbox0 % third arg given, show only that
+ \else
+ \setbox0 = \hbox{\ignorespaces #2}%
+ \ifdim\wd0 > 0pt
+ \ifpdf
+ \unhbox0 % PDF: 2nd arg given, show only it
+ \else
+ \unhbox0\ (\code{#1})% DVI: 2nd arg given, show both it and url
+ \fi
+ \else
+ \code{#1}% only url given, so show it
+ \fi
+ \fi
+ \endlink
+\endgroup}
+
+% @url synonym for @uref, since that's how everyone uses it.
+%
+\let\url=\uref
+
+% rms does not like angle brackets --karl, 17may97.
+% So now @email is just like @uref, unless we are pdf.
+%
+%\def\email#1{\angleleft{\tt #1}\angleright}
+\ifpdf
+ \def\email#1{\doemail#1,,\finish}
+ \def\doemail#1,#2,#3\finish{\begingroup
+ \unsepspaces
+ \pdfurl{mailto:#1}%
+ \setbox0 = \hbox{\ignorespaces #2}%
+ \ifdim\wd0>0pt\unhbox0\else\code{#1}\fi
+ \endlink
+ \endgroup}
+\else
+ \let\email=\uref
+\fi
+
+% Typeset a dimension, e.g., `in' or `pt'. The only reason for the
+% argument is to make the input look right: @dmn{pt} instead of @dmn{}pt.
+%
+\def\dmn#1{\thinspace #1}
+
+% @l was never documented to mean ``switch to the Lisp font'',
+% and it is not used as such in any manual I can find. We need it for
+% Polish suppressed-l. --karl, 22sep96.
+%\def\l#1{{\li #1}\null}
+
+% @acronym for "FBI", "NATO", and the like.
+% We print this one point size smaller, since it's intended for
+% all-uppercase.
+%
+\def\acronym#1{\doacronym #1,,\finish}
+\def\doacronym#1,#2,#3\finish{%
+ {\selectfonts\lsize #1}%
+ \def\temp{#2}%
+ \ifx\temp\empty \else
+ \space ({\unsepspaces \ignorespaces \temp \unskip})%
+ \fi
+}
+
+% @abbr for "Comput. J." and the like.
+% No font change, but don't do end-of-sentence spacing.
+%
+\def\abbr#1{\doabbr #1,,\finish}
+\def\doabbr#1,#2,#3\finish{%
+ {\plainfrenchspacing #1}%
+ \def\temp{#2}%
+ \ifx\temp\empty \else
+ \space ({\unsepspaces \ignorespaces \temp \unskip})%
+ \fi
+}
+
+
+\message{glyphs,}
+
+% @point{}, @result{}, @expansion{}, @print{}, @equiv{}.
+%
+% Since these characters are used in examples, they should be an even number of
+% \tt widths. Each \tt character is 1en, so two makes it 1em.
+%
+\def\point{$\star$}
+\def\arrow{\leavevmode\raise.05ex\hbox to 1em{\hfil$\rightarrow$\hfil}}
+\def\result{\leavevmode\raise.05ex\hbox to 1em{\hfil$\Rightarrow$\hfil}}
+\def\expansion{\leavevmode\hbox to 1em{\hfil$\mapsto$\hfil}}
+\def\print{\leavevmode\lower.1ex\hbox to 1em{\hfil$\dashv$\hfil}}
+\def\equiv{\leavevmode\hbox to 1em{\hfil$\ptexequiv$\hfil}}
+
+% The @error{} command.
+% Adapted from the TeXbook's \boxit.
+%
+\newbox\errorbox
+%
+{\tentt \global\dimen0 = 3em}% Width of the box.
+\dimen2 = .55pt % Thickness of rules
+% The text. (`r' is open on the right, `e' somewhat less so on the left.)
+\setbox0 = \hbox{\kern-.75pt \reducedsf error\kern-1.5pt}
+%
+\setbox\errorbox=\hbox to \dimen0{\hfil
+ \hsize = \dimen0 \advance\hsize by -5.8pt % Space to left+right.
+ \advance\hsize by -2\dimen2 % Rules.
+ \vbox{%
+ \hrule height\dimen2
+ \hbox{\vrule width\dimen2 \kern3pt % Space to left of text.
+ \vtop{\kern2.4pt \box0 \kern2.4pt}% Space above/below.
+ \kern3pt\vrule width\dimen2}% Space to right.
+ \hrule height\dimen2}
+ \hfil}
+%
+\def\error{\leavevmode\lower.7ex\copy\errorbox}
+
+% @pounds{} is a sterling sign, which Knuth put in the CM italic font.
+%
+\def\pounds{{\it\$}}
+
+% @euro{} comes from a separate font, depending on the current style.
+% We use the free feym* fonts from the eurosym package by Henrik
+% Theiling, which support regular, slanted, bold and bold slanted (and
+% "outlined" (blackboard board, sort of) versions, which we don't need).
+% It is available from http://www.ctan.org/tex-archive/fonts/eurosym.
+%
+% Although only regular is the truly official Euro symbol, we ignore
+% that. The Euro is designed to be slightly taller than the regular
+% font height.
+%
+% feymr - regular
+% feymo - slanted
+% feybr - bold
+% feybo - bold slanted
+%
+% There is no good (free) typewriter version, to my knowledge.
+% A feymr10 euro is ~7.3pt wide, while a normal cmtt10 char is ~5.25pt wide.
+% Hmm.
+%
+% Also doesn't work in math. Do we need to do math with euro symbols?
+% Hope not.
+%
+%
+\def\euro{{\eurofont e}}
+\def\eurofont{%
+ % We set the font at each command, rather than predefining it in
+ % \textfonts and the other font-switching commands, so that
+ % installations which never need the symbol don't have to have the
+ % font installed.
+ %
+ % There is only one designed size (nominal 10pt), so we always scale
+ % that to the current nominal size.
+ %
+ % By the way, simply using "at 1em" works for cmr10 and the like, but
+ % does not work for cmbx10 and other extended/shrunken fonts.
+ %
+ \def\eurosize{\csname\curfontsize nominalsize\endcsname}%
+ %
+ \ifx\curfontstyle\bfstylename
+ % bold:
+ \font\thiseurofont = \ifusingit{feybo10}{feybr10} at \eurosize
+ \else
+ % regular:
+ \font\thiseurofont = \ifusingit{feymo10}{feymr10} at \eurosize
+ \fi
+ \thiseurofont
+}
+
+% Glyphs from the EC fonts. We don't use \let for the aliases, because
+% sometimes we redefine the original macro, and the alias should reflect
+% the redefinition.
+%
+% Use LaTeX names for the Icelandic letters.
+\def\DH{{\ecfont \char"D0}} % Eth
+\def\dh{{\ecfont \char"F0}} % eth
+\def\TH{{\ecfont \char"DE}} % Thorn
+\def\th{{\ecfont \char"FE}} % thorn
+%
+\def\guillemetleft{{\ecfont \char"13}}
+\def\guillemotleft{\guillemetleft}
+\def\guillemetright{{\ecfont \char"14}}
+\def\guillemotright{\guillemetright}
+\def\guilsinglleft{{\ecfont \char"0E}}
+\def\guilsinglright{{\ecfont \char"0F}}
+\def\quotedblbase{{\ecfont \char"12}}
+\def\quotesinglbase{{\ecfont \char"0D}}
+%
+% This positioning is not perfect (see the ogonek LaTeX package), but
+% we have the precomposed glyphs for the most common cases. We put the
+% tests to use those glyphs in the single \ogonek macro so we have fewer
+% dummy definitions to worry about for index entries, etc.
+%
+% ogonek is also used with other letters in Lithuanian (IOU), but using
+% the precomposed glyphs for those is not so easy since they aren't in
+% the same EC font.
+\def\ogonek#1{{%
+ \def\temp{#1}%
+ \ifx\temp\macrocharA\Aogonek
+ \else\ifx\temp\macrochara\aogonek
+ \else\ifx\temp\macrocharE\Eogonek
+ \else\ifx\temp\macrochare\eogonek
+ \else
+ \ecfont \setbox0=\hbox{#1}%
+ \ifdim\ht0=1ex\accent"0C #1%
+ \else\ooalign{\unhbox0\crcr\hidewidth\char"0C \hidewidth}%
+ \fi
+ \fi\fi\fi\fi
+ }%
+}
+\def\Aogonek{{\ecfont \char"81}}\def\macrocharA{A}
+\def\aogonek{{\ecfont \char"A1}}\def\macrochara{a}
+\def\Eogonek{{\ecfont \char"86}}\def\macrocharE{E}
+\def\eogonek{{\ecfont \char"A6}}\def\macrochare{e}
+%
+% Use the ec* fonts (cm-super in outline format) for non-CM glyphs.
+\def\ecfont{%
+ % We can't distinguish serif/sans and italic/slanted, but this
+ % is used for crude hacks anyway (like adding French and German
+ % quotes to documents typeset with CM, where we lose kerning), so
+ % hopefully nobody will notice/care.
+ \edef\ecsize{\csname\curfontsize ecsize\endcsname}%
+ \edef\nominalsize{\csname\curfontsize nominalsize\endcsname}%
+ \ifx\curfontstyle\bfstylename
+ % bold:
+ \font\thisecfont = ecb\ifusingit{i}{x}\ecsize \space at \nominalsize
+ \else
+ % regular:
+ \font\thisecfont = ec\ifusingit{ti}{rm}\ecsize \space at \nominalsize
+ \fi
+ \thisecfont
+}
+
+% @registeredsymbol - R in a circle. The font for the R should really
+% be smaller yet, but lllsize is the best we can do for now.
+% Adapted from the plain.tex definition of \copyright.
+%
+\def\registeredsymbol{%
+ $^{{\ooalign{\hfil\raise.07ex\hbox{\selectfonts\lllsize R}%
+ \hfil\crcr\Orb}}%
+ }$%
+}
+
+% @textdegree - the normal degrees sign.
+%
+\def\textdegree{$^\circ$}
+
+% Laurent Siebenmann reports \Orb undefined with:
+% Textures 1.7.7 (preloaded format=plain 93.10.14) (68K) 16 APR 2004 02:38
+% so we'll define it if necessary.
+%
+\ifx\Orb\undefined
+\def\Orb{\mathhexbox20D}
+\fi
+
+% Quotes.
+\chardef\quotedblleft="5C
+\chardef\quotedblright=`\"
+\chardef\quoteleft=`\`
+\chardef\quoteright=`\'
+
+
+\message{page headings,}
+
+\newskip\titlepagetopglue \titlepagetopglue = 1.5in
+\newskip\titlepagebottomglue \titlepagebottomglue = 2pc
+
+% First the title page. Must do @settitle before @titlepage.
+\newif\ifseenauthor
+\newif\iffinishedtitlepage
+
+% Do an implicit @contents or @shortcontents after @end titlepage if the
+% user says @setcontentsaftertitlepage or @setshortcontentsaftertitlepage.
+%
+\newif\ifsetcontentsaftertitlepage
+ \let\setcontentsaftertitlepage = \setcontentsaftertitlepagetrue
+\newif\ifsetshortcontentsaftertitlepage
+ \let\setshortcontentsaftertitlepage = \setshortcontentsaftertitlepagetrue
+
+\parseargdef\shorttitlepage{\begingroup\hbox{}\vskip 1.5in \chaprm \centerline{#1}%
+ \endgroup\page\hbox{}\page}
+
+\envdef\titlepage{%
+ % Open one extra group, as we want to close it in the middle of \Etitlepage.
+ \begingroup
+ \parindent=0pt \textfonts
+ % Leave some space at the very top of the page.
+ \vglue\titlepagetopglue
+ % No rule at page bottom unless we print one at the top with @title.
+ \finishedtitlepagetrue
+ %
+ % Most title ``pages'' are actually two pages long, with space
+ % at the top of the second. We don't want the ragged left on the second.
+ \let\oldpage = \page
+ \def\page{%
+ \iffinishedtitlepage\else
+ \finishtitlepage
+ \fi
+ \let\page = \oldpage
+ \page
+ \null
+ }%
+}
+
+\def\Etitlepage{%
+ \iffinishedtitlepage\else
+ \finishtitlepage
+ \fi
+ % It is important to do the page break before ending the group,
+ % because the headline and footline are only empty inside the group.
+ % If we use the new definition of \page, we always get a blank page
+ % after the title page, which we certainly don't want.
+ \oldpage
+ \endgroup
+ %
+ % Need this before the \...aftertitlepage checks so that if they are
+ % in effect the toc pages will come out with page numbers.
+ \HEADINGSon
+ %
+ % If they want short, they certainly want long too.
+ \ifsetshortcontentsaftertitlepage
+ \shortcontents
+ \contents
+ \global\let\shortcontents = \relax
+ \global\let\contents = \relax
+ \fi
+ %
+ \ifsetcontentsaftertitlepage
+ \contents
+ \global\let\contents = \relax
+ \global\let\shortcontents = \relax
+ \fi
+}
+
+\def\finishtitlepage{%
+ \vskip4pt \hrule height 2pt width \hsize
+ \vskip\titlepagebottomglue
+ \finishedtitlepagetrue
+}
+
+%%% Macros to be used within @titlepage:
+
+\let\subtitlerm=\tenrm
+\def\subtitlefont{\subtitlerm \normalbaselineskip = 13pt \normalbaselines}
+
+\parseargdef\title{%
+ \checkenv\titlepage
+ \leftline{\titlefonts\rmisbold #1}
+ % print a rule at the page bottom also.
+ \finishedtitlepagefalse
+ \vskip4pt \hrule height 4pt width \hsize \vskip4pt
+}
+
+\parseargdef\subtitle{%
+ \checkenv\titlepage
+ {\subtitlefont \rightline{#1}}%
+}
+
+% @author should come last, but may come many times.
+% It can also be used inside @quotation.
+%
+\parseargdef\author{%
+ \def\temp{\quotation}%
+ \ifx\thisenv\temp
+ \def\quotationauthor{#1}% printed in \Equotation.
+ \else
+ \checkenv\titlepage
+ \ifseenauthor\else \vskip 0pt plus 1filll \seenauthortrue \fi
+ {\secfonts\rmisbold \leftline{#1}}%
+ \fi
+}
+
+
+%%% Set up page headings and footings.
+
+\let\thispage=\folio
+
+\newtoks\evenheadline % headline on even pages
+\newtoks\oddheadline % headline on odd pages
+\newtoks\evenfootline % footline on even pages
+\newtoks\oddfootline % footline on odd pages
+
+% Now make TeX use those variables
+\headline={{\textfonts\rm \ifodd\pageno \the\oddheadline
+ \else \the\evenheadline \fi}}
+\footline={{\textfonts\rm \ifodd\pageno \the\oddfootline
+ \else \the\evenfootline \fi}\HEADINGShook}
+\let\HEADINGShook=\relax
+
+% Commands to set those variables.
+% For example, this is what @headings on does
+% @evenheading @thistitle|@thispage|@thischapter
+% @oddheading @thischapter|@thispage|@thistitle
+% @evenfooting @thisfile||
+% @oddfooting ||@thisfile
+
+
+\def\evenheading{\parsearg\evenheadingxxx}
+\def\evenheadingxxx #1{\evenheadingyyy #1\|\|\|\|\finish}
+\def\evenheadingyyy #1\|#2\|#3\|#4\finish{%
+\global\evenheadline={\rlap{\centerline{#2}}\line{#1\hfil#3}}}
+
+\def\oddheading{\parsearg\oddheadingxxx}
+\def\oddheadingxxx #1{\oddheadingyyy #1\|\|\|\|\finish}
+\def\oddheadingyyy #1\|#2\|#3\|#4\finish{%
+\global\oddheadline={\rlap{\centerline{#2}}\line{#1\hfil#3}}}
+
+\parseargdef\everyheading{\oddheadingxxx{#1}\evenheadingxxx{#1}}%
+
+\def\evenfooting{\parsearg\evenfootingxxx}
+\def\evenfootingxxx #1{\evenfootingyyy #1\|\|\|\|\finish}
+\def\evenfootingyyy #1\|#2\|#3\|#4\finish{%
+\global\evenfootline={\rlap{\centerline{#2}}\line{#1\hfil#3}}}
+
+\def\oddfooting{\parsearg\oddfootingxxx}
+\def\oddfootingxxx #1{\oddfootingyyy #1\|\|\|\|\finish}
+\def\oddfootingyyy #1\|#2\|#3\|#4\finish{%
+ \global\oddfootline = {\rlap{\centerline{#2}}\line{#1\hfil#3}}%
+ %
+ % Leave some space for the footline. Hopefully ok to assume
+ % @evenfooting will not be used by itself.
+ \global\advance\pageheight by -12pt
+ \global\advance\vsize by -12pt
+}
+
+\parseargdef\everyfooting{\oddfootingxxx{#1}\evenfootingxxx{#1}}
+
+% @evenheadingmarks top \thischapter <- chapter at the top of a page
+% @evenheadingmarks bottom \thischapter <- chapter at the bottom of a page
+%
+% The same set of arguments for:
+%
+% @oddheadingmarks
+% @evenfootingmarks
+% @oddfootingmarks
+% @everyheadingmarks
+% @everyfootingmarks
+
+\def\evenheadingmarks{\headingmarks{even}{heading}}
+\def\oddheadingmarks{\headingmarks{odd}{heading}}
+\def\evenfootingmarks{\headingmarks{even}{footing}}
+\def\oddfootingmarks{\headingmarks{odd}{footing}}
+\def\everyheadingmarks#1 {\headingmarks{even}{heading}{#1}
+ \headingmarks{odd}{heading}{#1} }
+\def\everyfootingmarks#1 {\headingmarks{even}{footing}{#1}
+ \headingmarks{odd}{footing}{#1} }
+% #1 = even/odd, #2 = heading/footing, #3 = top/bottom.
+\def\headingmarks#1#2#3 {%
+ \expandafter\let\expandafter\temp \csname get#3headingmarks\endcsname
+ \global\expandafter\let\csname get#1#2marks\endcsname \temp
+}
+
+\everyheadingmarks bottom
+\everyfootingmarks bottom
+
+% @headings double turns headings on for double-sided printing.
+% @headings single turns headings on for single-sided printing.
+% @headings off turns them off.
+% @headings on same as @headings double, retained for compatibility.
+% @headings after turns on double-sided headings after this page.
+% @headings doubleafter turns on double-sided headings after this page.
+% @headings singleafter turns on single-sided headings after this page.
+% By default, they are off at the start of a document,
+% and turned `on' after @end titlepage.
+
+\def\headings #1 {\csname HEADINGS#1\endcsname}
+
+\def\HEADINGSoff{%
+\global\evenheadline={\hfil} \global\evenfootline={\hfil}
+\global\oddheadline={\hfil} \global\oddfootline={\hfil}}
+\HEADINGSoff
+% When we turn headings on, set the page number to 1.
+% For double-sided printing, put current file name in lower left corner,
+% chapter name on inside top of right hand pages, document
+% title on inside top of left hand pages, and page numbers on outside top
+% edge of all pages.
+\def\HEADINGSdouble{%
+\global\pageno=1
+\global\evenfootline={\hfil}
+\global\oddfootline={\hfil}
+\global\evenheadline={\line{\folio\hfil\thistitle}}
+\global\oddheadline={\line{\thischapter\hfil\folio}}
+\global\let\contentsalignmacro = \chapoddpage
+}
+\let\contentsalignmacro = \chappager
+
+% For single-sided printing, chapter title goes across top left of page,
+% page number on top right.
+\def\HEADINGSsingle{%
+\global\pageno=1
+\global\evenfootline={\hfil}
+\global\oddfootline={\hfil}
+\global\evenheadline={\line{\thischapter\hfil\folio}}
+\global\oddheadline={\line{\thischapter\hfil\folio}}
+\global\let\contentsalignmacro = \chappager
+}
+\def\HEADINGSon{\HEADINGSdouble}
+
+\def\HEADINGSafter{\let\HEADINGShook=\HEADINGSdoublex}
+\let\HEADINGSdoubleafter=\HEADINGSafter
+\def\HEADINGSdoublex{%
+\global\evenfootline={\hfil}
+\global\oddfootline={\hfil}
+\global\evenheadline={\line{\folio\hfil\thistitle}}
+\global\oddheadline={\line{\thischapter\hfil\folio}}
+\global\let\contentsalignmacro = \chapoddpage
+}
+
+\def\HEADINGSsingleafter{\let\HEADINGShook=\HEADINGSsinglex}
+\def\HEADINGSsinglex{%
+\global\evenfootline={\hfil}
+\global\oddfootline={\hfil}
+\global\evenheadline={\line{\thischapter\hfil\folio}}
+\global\oddheadline={\line{\thischapter\hfil\folio}}
+\global\let\contentsalignmacro = \chappager
+}
+
+% Subroutines used in generating headings
+% This produces Day Month Year style of output.
+% Only define if not already defined, in case a txi-??.tex file has set
+% up a different format (e.g., txi-cs.tex does this).
+\ifx\today\undefined
+\def\today{%
+ \number\day\space
+ \ifcase\month
+ \or\putwordMJan\or\putwordMFeb\or\putwordMMar\or\putwordMApr
+ \or\putwordMMay\or\putwordMJun\or\putwordMJul\or\putwordMAug
+ \or\putwordMSep\or\putwordMOct\or\putwordMNov\or\putwordMDec
+ \fi
+ \space\number\year}
+\fi
+
+% @settitle line... specifies the title of the document, for headings.
+% It generates no output of its own.
+\def\thistitle{\putwordNoTitle}
+\def\settitle{\parsearg{\gdef\thistitle}}
+
+
+\message{tables,}
+% Tables -- @table, @ftable, @vtable, @item(x).
+
+% default indentation of table text
+\newdimen\tableindent \tableindent=.8in
+% default indentation of @itemize and @enumerate text
+\newdimen\itemindent \itemindent=.3in
+% margin between end of table item and start of table text.
+\newdimen\itemmargin \itemmargin=.1in
+
+% used internally for \itemindent minus \itemmargin
+\newdimen\itemmax
+
+% Note @table, @ftable, and @vtable define @item, @itemx, etc., with
+% these defs.
+% They also define \itemindex
+% to index the item name in whatever manner is desired (perhaps none).
+
+\newif\ifitemxneedsnegativevskip
+
+\def\itemxpar{\par\ifitemxneedsnegativevskip\nobreak\vskip-\parskip\nobreak\fi}
+
+\def\internalBitem{\smallbreak \parsearg\itemzzz}
+\def\internalBitemx{\itemxpar \parsearg\itemzzz}
+
+\def\itemzzz #1{\begingroup %
+ \advance\hsize by -\rightskip
+ \advance\hsize by -\tableindent
+ \setbox0=\hbox{\itemindicate{#1}}%
+ \itemindex{#1}%
+ \nobreak % This prevents a break before @itemx.
+ %
+ % If the item text does not fit in the space we have, put it on a line
+ % by itself, and do not allow a page break either before or after that
+ % line. We do not start a paragraph here because then if the next
+ % command is, e.g., @kindex, the whatsit would get put into the
+ % horizontal list on a line by itself, resulting in extra blank space.
+ \ifdim \wd0>\itemmax
+ %
+ % Make this a paragraph so we get the \parskip glue and wrapping,
+ % but leave it ragged-right.
+ \begingroup
+ \advance\leftskip by-\tableindent
+ \advance\hsize by\tableindent
+ \advance\rightskip by0pt plus1fil
+ \leavevmode\unhbox0\par
+ \endgroup
+ %
+ % We're going to be starting a paragraph, but we don't want the
+ % \parskip glue -- logically it's part of the @item we just started.
+ \nobreak \vskip-\parskip
+ %
+ % Stop a page break at the \parskip glue coming up. However, if
+ % what follows is an environment such as @example, there will be no
+ % \parskip glue; then the negative vskip we just inserted would
+ % cause the example and the item to crash together. So we use this
+ % bizarre value of 10001 as a signal to \aboveenvbreak to insert
+ % \parskip glue after all. Section titles are handled this way also.
+ %
+ \penalty 10001
+ \endgroup
+ \itemxneedsnegativevskipfalse
+ \else
+ % The item text fits into the space. Start a paragraph, so that the
+ % following text (if any) will end up on the same line.
+ \noindent
+ % Do this with kerns and \unhbox so that if there is a footnote in
+ % the item text, it can migrate to the main vertical list and
+ % eventually be printed.
+ \nobreak\kern-\tableindent
+ \dimen0 = \itemmax \advance\dimen0 by \itemmargin \advance\dimen0 by -\wd0
+ \unhbox0
+ \nobreak\kern\dimen0
+ \endgroup
+ \itemxneedsnegativevskiptrue
+ \fi
+}
+
+\def\item{\errmessage{@item while not in a list environment}}
+\def\itemx{\errmessage{@itemx while not in a list environment}}
+
+% @table, @ftable, @vtable.
+\envdef\table{%
+ \let\itemindex\gobble
+ \tablecheck{table}%
+}
+\envdef\ftable{%
+ \def\itemindex ##1{\doind {fn}{\code{##1}}}%
+ \tablecheck{ftable}%
+}
+\envdef\vtable{%
+ \def\itemindex ##1{\doind {vr}{\code{##1}}}%
+ \tablecheck{vtable}%
+}
+\def\tablecheck#1{%
+ \ifnum \the\catcode`\^^M=\active
+ \endgroup
+ \errmessage{This command won't work in this context; perhaps the problem is
+ that we are \inenvironment\thisenv}%
+ \def\next{\doignore{#1}}%
+ \else
+ \let\next\tablex
+ \fi
+ \next
+}
+\def\tablex#1{%
+ \def\itemindicate{#1}%
+ \parsearg\tabley
+}
+\def\tabley#1{%
+ {%
+ \makevalueexpandable
+ \edef\temp{\noexpand\tablez #1\space\space\space}%
+ \expandafter
+ }\temp \endtablez
+}
+\def\tablez #1 #2 #3 #4\endtablez{%
+ \aboveenvbreak
+ \ifnum 0#1>0 \advance \leftskip by #1\mil \fi
+ \ifnum 0#2>0 \tableindent=#2\mil \fi
+ \ifnum 0#3>0 \advance \rightskip by #3\mil \fi
+ \itemmax=\tableindent
+ \advance \itemmax by -\itemmargin
+ \advance \leftskip by \tableindent
+ \exdentamount=\tableindent
+ \parindent = 0pt
+ \parskip = \smallskipamount
+ \ifdim \parskip=0pt \parskip=2pt \fi
+ \let\item = \internalBitem
+ \let\itemx = \internalBitemx
+}
+\def\Etable{\endgraf\afterenvbreak}
+\let\Eftable\Etable
+\let\Evtable\Etable
+\let\Eitemize\Etable
+\let\Eenumerate\Etable
+
+% This is the counter used by @enumerate, which is really @itemize
+
+\newcount \itemno
+
+\envdef\itemize{\parsearg\doitemize}
+
+\def\doitemize#1{%
+ \aboveenvbreak
+ \itemmax=\itemindent
+ \advance\itemmax by -\itemmargin
+ \advance\leftskip by \itemindent
+ \exdentamount=\itemindent
+ \parindent=0pt
+ \parskip=\smallskipamount
+ \ifdim\parskip=0pt \parskip=2pt \fi
+ %
+ % Try typesetting the item mark that if the document erroneously says
+ % something like @itemize @samp (intending @table), there's an error
+ % right away at the @itemize. It's not the best error message in the
+ % world, but it's better than leaving it to the @item. This means if
+ % the user wants an empty mark, they have to say @w{} not just @w.
+ \def\itemcontents{#1}%
+ \setbox0 = \hbox{\itemcontents}%
+ %
+ % @itemize with no arg is equivalent to @itemize @bullet.
+ \ifx\itemcontents\empty\def\itemcontents{\bullet}\fi
+ %
+ \let\item=\itemizeitem
+}
+
+% Definition of @item while inside @itemize and @enumerate.
+%
+\def\itemizeitem{%
+ \advance\itemno by 1 % for enumerations
+ {\let\par=\endgraf \smallbreak}% reasonable place to break
+ {%
+ % If the document has an @itemize directly after a section title, a
+ % \nobreak will be last on the list, and \sectionheading will have
+ % done a \vskip-\parskip. In that case, we don't want to zero
+ % parskip, or the item text will crash with the heading. On the
+ % other hand, when there is normal text preceding the item (as there
+ % usually is), we do want to zero parskip, or there would be too much
+ % space. In that case, we won't have a \nobreak before. At least
+ % that's the theory.
+ \ifnum\lastpenalty<10000 \parskip=0in \fi
+ \noindent
+ \hbox to 0pt{\hss \itemcontents \kern\itemmargin}%
+ %
+ \vadjust{\penalty 1200}}% not good to break after first line of item.
+ \flushcr
+}
+
+% \splitoff TOKENS\endmark defines \first to be the first token in
+% TOKENS, and \rest to be the remainder.
+%
+\def\splitoff#1#2\endmark{\def\first{#1}\def\rest{#2}}%
+
+% Allow an optional argument of an uppercase letter, lowercase letter,
+% or number, to specify the first label in the enumerated list. No
+% argument is the same as `1'.
+%
+\envparseargdef\enumerate{\enumeratey #1 \endenumeratey}
+\def\enumeratey #1 #2\endenumeratey{%
+ % If we were given no argument, pretend we were given `1'.
+ \def\thearg{#1}%
+ \ifx\thearg\empty \def\thearg{1}\fi
+ %
+ % Detect if the argument is a single token. If so, it might be a
+ % letter. Otherwise, the only valid thing it can be is a number.
+ % (We will always have one token, because of the test we just made.
+ % This is a good thing, since \splitoff doesn't work given nothing at
+ % all -- the first parameter is undelimited.)
+ \expandafter\splitoff\thearg\endmark
+ \ifx\rest\empty
+ % Only one token in the argument. It could still be anything.
+ % A ``lowercase letter'' is one whose \lccode is nonzero.
+ % An ``uppercase letter'' is one whose \lccode is both nonzero, and
+ % not equal to itself.
+ % Otherwise, we assume it's a number.
+ %
+ % We need the \relax at the end of the \ifnum lines to stop TeX from
+ % continuing to look for a <number>.
+ %
+ \ifnum\lccode\expandafter`\thearg=0\relax
+ \numericenumerate % a number (we hope)
+ \else
+ % It's a letter.
+ \ifnum\lccode\expandafter`\thearg=\expandafter`\thearg\relax
+ \lowercaseenumerate % lowercase letter
+ \else
+ \uppercaseenumerate % uppercase letter
+ \fi
+ \fi
+ \else
+ % Multiple tokens in the argument. We hope it's a number.
+ \numericenumerate
+ \fi
+}
+
+% An @enumerate whose labels are integers. The starting integer is
+% given in \thearg.
+%
+\def\numericenumerate{%
+ \itemno = \thearg
+ \startenumeration{\the\itemno}%
+}
+
+% The starting (lowercase) letter is in \thearg.
+\def\lowercaseenumerate{%
+ \itemno = \expandafter`\thearg
+ \startenumeration{%
+ % Be sure we're not beyond the end of the alphabet.
+ \ifnum\itemno=0
+ \errmessage{No more lowercase letters in @enumerate; get a bigger
+ alphabet}%
+ \fi
+ \char\lccode\itemno
+ }%
+}
+
+% The starting (uppercase) letter is in \thearg.
+\def\uppercaseenumerate{%
+ \itemno = \expandafter`\thearg
+ \startenumeration{%
+ % Be sure we're not beyond the end of the alphabet.
+ \ifnum\itemno=0
+ \errmessage{No more uppercase letters in @enumerate; get a bigger
+ alphabet}
+ \fi
+ \char\uccode\itemno
+ }%
+}
+
+% Call \doitemize, adding a period to the first argument and supplying the
+% common last two arguments. Also subtract one from the initial value in
+% \itemno, since @item increments \itemno.
+%
+\def\startenumeration#1{%
+ \advance\itemno by -1
+ \doitemize{#1.}\flushcr
+}
+
+% @alphaenumerate and @capsenumerate are abbreviations for giving an arg
+% to @enumerate.
+%
+\def\alphaenumerate{\enumerate{a}}
+\def\capsenumerate{\enumerate{A}}
+\def\Ealphaenumerate{\Eenumerate}
+\def\Ecapsenumerate{\Eenumerate}
+
+
+% @multitable macros
+% Amy Hendrickson, 8/18/94, 3/6/96
+%
+% @multitable ... @end multitable will make as many columns as desired.
+% Contents of each column will wrap at width given in preamble. Width
+% can be specified either with sample text given in a template line,
+% or in percent of \hsize, the current width of text on page.
+
+% Table can continue over pages but will only break between lines.
+
+% To make preamble:
+%
+% Either define widths of columns in terms of percent of \hsize:
+% @multitable @columnfractions .25 .3 .45
+% @item ...
+%
+% Numbers following @columnfractions are the percent of the total
+% current hsize to be used for each column. You may use as many
+% columns as desired.
+
+
+% Or use a template:
+% @multitable {Column 1 template} {Column 2 template} {Column 3 template}
+% @item ...
+% using the widest term desired in each column.
+
+% Each new table line starts with @item, each subsequent new column
+% starts with @tab. Empty columns may be produced by supplying @tab's
+% with nothing between them for as many times as empty columns are needed,
+% ie, @tab at tab@tab will produce two empty columns.
+
+% @item, @tab do not need to be on their own lines, but it will not hurt
+% if they are.
+
+% Sample multitable:
+
+% @multitable {Column 1 template} {Column 2 template} {Column 3 template}
+% @item first col stuff @tab second col stuff @tab third col
+% @item
+% first col stuff
+% @tab
+% second col stuff
+% @tab
+% third col
+% @item first col stuff @tab second col stuff
+% @tab Many paragraphs of text may be used in any column.
+%
+% They will wrap at the width determined by the template.
+% @item at tab@tab This will be in third column.
+% @end multitable
+
+% Default dimensions may be reset by user.
+% @multitableparskip is vertical space between paragraphs in table.
+% @multitableparindent is paragraph indent in table.
+% @multitablecolmargin is horizontal space to be left between columns.
+% @multitablelinespace is space to leave between table items, baseline
+% to baseline.
+% 0pt means it depends on current normal line spacing.
+%
+\newskip\multitableparskip
+\newskip\multitableparindent
+\newdimen\multitablecolspace
+\newskip\multitablelinespace
+\multitableparskip=0pt
+\multitableparindent=6pt
+\multitablecolspace=12pt
+\multitablelinespace=0pt
+
+% Macros used to set up halign preamble:
+%
+\let\endsetuptable\relax
+\def\xendsetuptable{\endsetuptable}
+\let\columnfractions\relax
+\def\xcolumnfractions{\columnfractions}
+\newif\ifsetpercent
+
+% #1 is the @columnfraction, usually a decimal number like .5, but might
+% be just 1. We just use it, whatever it is.
+%
+\def\pickupwholefraction#1 {%
+ \global\advance\colcount by 1
+ \expandafter\xdef\csname col\the\colcount\endcsname{#1\hsize}%
+ \setuptable
+}
+
+\newcount\colcount
+\def\setuptable#1{%
+ \def\firstarg{#1}%
+ \ifx\firstarg\xendsetuptable
+ \let\go = \relax
+ \else
+ \ifx\firstarg\xcolumnfractions
+ \global\setpercenttrue
+ \else
+ \ifsetpercent
+ \let\go\pickupwholefraction
+ \else
+ \global\advance\colcount by 1
+ \setbox0=\hbox{#1\unskip\space}% Add a normal word space as a
+ % separator; typically that is always in the input, anyway.
+ \expandafter\xdef\csname col\the\colcount\endcsname{\the\wd0}%
+ \fi
+ \fi
+ \ifx\go\pickupwholefraction
+ % Put the argument back for the \pickupwholefraction call, so
+ % we'll always have a period there to be parsed.
+ \def\go{\pickupwholefraction#1}%
+ \else
+ \let\go = \setuptable
+ \fi%
+ \fi
+ \go
+}
+
+% multitable-only commands.
+%
+% @headitem starts a heading row, which we typeset in bold.
+% Assignments have to be global since we are inside the implicit group
+% of an alignment entry. \everycr resets \everytab so we don't have to
+% undo it ourselves.
+\def\headitemfont{\b}% for people to use in the template row; not changeable
+\def\headitem{%
+ \checkenv\multitable
+ \crcr
+ \global\everytab={\bf}% can't use \headitemfont since the parsing differs
+ \the\everytab % for the first item
+}%
+%
+% A \tab used to include \hskip1sp. But then the space in a template
+% line is not enough. That is bad. So let's go back to just `&' until
+% we again encounter the problem the 1sp was intended to solve.
+% --karl, nathan at acm.org, 20apr99.
+\def\tab{\checkenv\multitable &\the\everytab}%
+
+% @multitable ... @end multitable definitions:
+%
+\newtoks\everytab % insert after every tab.
+%
+\envdef\multitable{%
+ \vskip\parskip
+ \startsavinginserts
+ %
+ % @item within a multitable starts a normal row.
+ % We use \def instead of \let so that if one of the multitable entries
+ % contains an @itemize, we don't choke on the \item (seen as \crcr aka
+ % \endtemplate) expanding \doitemize.
+ \def\item{\crcr}%
+ %
+ \tolerance=9500
+ \hbadness=9500
+ \setmultitablespacing
+ \parskip=\multitableparskip
+ \parindent=\multitableparindent
+ \overfullrule=0pt
+ \global\colcount=0
+ %
+ \everycr = {%
+ \noalign{%
+ \global\everytab={}%
+ \global\colcount=0 % Reset the column counter.
+ % Check for saved footnotes, etc.
+ \checkinserts
+ % Keeps underfull box messages off when table breaks over pages.
+ %\filbreak
+ % Maybe so, but it also creates really weird page breaks when the
+ % table breaks over pages. Wouldn't \vfil be better? Wait until the
+ % problem manifests itself, so it can be fixed for real --karl.
+ }%
+ }%
+ %
+ \parsearg\domultitable
+}
+\def\domultitable#1{%
+ % To parse everything between @multitable and @item:
+ \setuptable#1 \endsetuptable
+ %
+ % This preamble sets up a generic column definition, which will
+ % be used as many times as user calls for columns.
+ % \vtop will set a single line and will also let text wrap and
+ % continue for many paragraphs if desired.
+ \halign\bgroup &%
+ \global\advance\colcount by 1
+ \multistrut
+ \vtop{%
+ % Use the current \colcount to find the correct column width:
+ \hsize=\expandafter\csname col\the\colcount\endcsname
+ %
+ % In order to keep entries from bumping into each other
+ % we will add a \leftskip of \multitablecolspace to all columns after
+ % the first one.
+ %
+ % If a template has been used, we will add \multitablecolspace
+ % to the width of each template entry.
+ %
+ % If the user has set preamble in terms of percent of \hsize we will
+ % use that dimension as the width of the column, and the \leftskip
+ % will keep entries from bumping into each other. Table will start at
+ % left margin and final column will justify at right margin.
+ %
+ % Make sure we don't inherit \rightskip from the outer environment.
+ \rightskip=0pt
+ \ifnum\colcount=1
+ % The first column will be indented with the surrounding text.
+ \advance\hsize by\leftskip
+ \else
+ \ifsetpercent \else
+ % If user has not set preamble in terms of percent of \hsize
+ % we will advance \hsize by \multitablecolspace.
+ \advance\hsize by \multitablecolspace
+ \fi
+ % In either case we will make \leftskip=\multitablecolspace:
+ \leftskip=\multitablecolspace
+ \fi
+ % Ignoring space at the beginning and end avoids an occasional spurious
+ % blank line, when TeX decides to break the line at the space before the
+ % box from the multistrut, so the strut ends up on a line by itself.
+ % For example:
+ % @multitable @columnfractions .11 .89
+ % @item @code{#}
+ % @tab Legal holiday which is valid in major parts of the whole country.
+ % Is automatically provided with highlighting sequences respectively
+ % marking characters.
+ \noindent\ignorespaces##\unskip\multistrut
+ }\cr
+}
+\def\Emultitable{%
+ \crcr
+ \egroup % end the \halign
+ \global\setpercentfalse
+}
+
+\def\setmultitablespacing{%
+ \def\multistrut{\strut}% just use the standard line spacing
+ %
+ % Compute \multitablelinespace (if not defined by user) for use in
+ % \multitableparskip calculation. We used define \multistrut based on
+ % this, but (ironically) that caused the spacing to be off.
+ % See bug-texinfo report from Werner Lemberg, 31 Oct 2004 12:52:20 +0100.
+\ifdim\multitablelinespace=0pt
+\setbox0=\vbox{X}\global\multitablelinespace=\the\baselineskip
+\global\advance\multitablelinespace by-\ht0
+\fi
+%% Test to see if parskip is larger than space between lines of
+%% table. If not, do nothing.
+%% If so, set to same dimension as multitablelinespace.
+\ifdim\multitableparskip>\multitablelinespace
+\global\multitableparskip=\multitablelinespace
+\global\advance\multitableparskip-7pt %% to keep parskip somewhat smaller
+ %% than skip between lines in the table.
+\fi%
+\ifdim\multitableparskip=0pt
+\global\multitableparskip=\multitablelinespace
+\global\advance\multitableparskip-7pt %% to keep parskip somewhat smaller
+ %% than skip between lines in the table.
+\fi}
+
+
+\message{conditionals,}
+
+% @iftex, @ifnotdocbook, @ifnothtml, @ifnotinfo, @ifnotplaintext,
+% @ifnotxml always succeed. They currently do nothing; we don't
+% attempt to check whether the conditionals are properly nested. But we
+% have to remember that they are conditionals, so that @end doesn't
+% attempt to close an environment group.
+%
+\def\makecond#1{%
+ \expandafter\let\csname #1\endcsname = \relax
+ \expandafter\let\csname iscond.#1\endcsname = 1
+}
+\makecond{iftex}
+\makecond{ifnotdocbook}
+\makecond{ifnothtml}
+\makecond{ifnotinfo}
+\makecond{ifnotplaintext}
+\makecond{ifnotxml}
+
+% Ignore @ignore, @ifhtml, @ifinfo, and the like.
+%
+\def\direntry{\doignore{direntry}}
+\def\documentdescription{\doignore{documentdescription}}
+\def\docbook{\doignore{docbook}}
+\def\html{\doignore{html}}
+\def\ifdocbook{\doignore{ifdocbook}}
+\def\ifhtml{\doignore{ifhtml}}
+\def\ifinfo{\doignore{ifinfo}}
+\def\ifnottex{\doignore{ifnottex}}
+\def\ifplaintext{\doignore{ifplaintext}}
+\def\ifxml{\doignore{ifxml}}
+\def\ignore{\doignore{ignore}}
+\def\menu{\doignore{menu}}
+\def\xml{\doignore{xml}}
+
+% Ignore text until a line `@end #1', keeping track of nested conditionals.
+%
+% A count to remember the depth of nesting.
+\newcount\doignorecount
+
+\def\doignore#1{\begingroup
+ % Scan in ``verbatim'' mode:
+ \obeylines
+ \catcode`\@ = \other
+ \catcode`\{ = \other
+ \catcode`\} = \other
+ %
+ % Make sure that spaces turn into tokens that match what \doignoretext wants.
+ \spaceisspace
+ %
+ % Count number of #1's that we've seen.
+ \doignorecount = 0
+ %
+ % Swallow text until we reach the matching `@end #1'.
+ \dodoignore{#1}%
+}
+
+{ \catcode`_=11 % We want to use \_STOP_ which cannot appear in texinfo source.
+ \obeylines %
+ %
+ \gdef\dodoignore#1{%
+ % #1 contains the command name as a string, e.g., `ifinfo'.
+ %
+ % Define a command to find the next `@end #1'.
+ \long\def\doignoretext##1^^M at end #1{%
+ \doignoretextyyy##1^^M@#1\_STOP_}%
+ %
+ % And this command to find another #1 command, at the beginning of a
+ % line. (Otherwise, we would consider a line `@c @ifset', for
+ % example, to count as an @ifset for nesting.)
+ \long\def\doignoretextyyy##1^^M@#1##2\_STOP_{\doignoreyyy{##2}\_STOP_}%
+ %
+ % And now expand that command.
+ \doignoretext ^^M%
+ }%
+}
+
+\def\doignoreyyy#1{%
+ \def\temp{#1}%
+ \ifx\temp\empty % Nothing found.
+ \let\next\doignoretextzzz
+ \else % Found a nested condition, ...
+ \advance\doignorecount by 1
+ \let\next\doignoretextyyy % ..., look for another.
+ % If we're here, #1 ends with ^^M\ifinfo (for example).
+ \fi
+ \next #1% the token \_STOP_ is present just after this macro.
+}
+
+% We have to swallow the remaining "\_STOP_".
+%
+\def\doignoretextzzz#1{%
+ \ifnum\doignorecount = 0 % We have just found the outermost @end.
+ \let\next\enddoignore
+ \else % Still inside a nested condition.
+ \advance\doignorecount by -1
+ \let\next\doignoretext % Look for the next @end.
+ \fi
+ \next
+}
+
+% Finish off ignored text.
+{ \obeylines%
+ % Ignore anything after the last `@end #1'; this matters in verbatim
+ % environments, where otherwise the newline after an ignored conditional
+ % would result in a blank line in the output.
+ \gdef\enddoignore#1^^M{\endgroup\ignorespaces}%
+}
+
+
+% @set VAR sets the variable VAR to an empty value.
+% @set VAR REST-OF-LINE sets VAR to the value REST-OF-LINE.
+%
+% Since we want to separate VAR from REST-OF-LINE (which might be
+% empty), we can't just use \parsearg; we have to insert a space of our
+% own to delimit the rest of the line, and then take it out again if we
+% didn't need it.
+% We rely on the fact that \parsearg sets \catcode`\ =10.
+%
+\parseargdef\set{\setyyy#1 \endsetyyy}
+\def\setyyy#1 #2\endsetyyy{%
+ {%
+ \makevalueexpandable
+ \def\temp{#2}%
+ \edef\next{\gdef\makecsname{SET#1}}%
+ \ifx\temp\empty
+ \next{}%
+ \else
+ \setzzz#2\endsetzzz
+ \fi
+ }%
+}
+% Remove the trailing space \setxxx inserted.
+\def\setzzz#1 \endsetzzz{\next{#1}}
+
+% @clear VAR clears (i.e., unsets) the variable VAR.
+%
+\parseargdef\clear{%
+ {%
+ \makevalueexpandable
+ \global\expandafter\let\csname SET#1\endcsname=\relax
+ }%
+}
+
+% @value{foo} gets the text saved in variable foo.
+\def\value{\begingroup\makevalueexpandable\valuexxx}
+\def\valuexxx#1{\expandablevalue{#1}\endgroup}
+{
+ \catcode`\- = \active \catcode`\_ = \active
+ %
+ \gdef\makevalueexpandable{%
+ \let\value = \expandablevalue
+ % We don't want these characters active, ...
+ \catcode`\-=\other \catcode`\_=\other
+ % ..., but we might end up with active ones in the argument if
+ % we're called from @code, as @code{@value{foo-bar_}}, though.
+ % So \let them to their normal equivalents.
+ \let-\realdash \let_\normalunderscore
+ }
+}
+
+% We have this subroutine so that we can handle at least some @value's
+% properly in indexes (we call \makevalueexpandable in \indexdummies).
+% The command has to be fully expandable (if the variable is set), since
+% the result winds up in the index file. This means that if the
+% variable's value contains other Texinfo commands, it's almost certain
+% it will fail (although perhaps we could fix that with sufficient work
+% to do a one-level expansion on the result, instead of complete).
+%
+\def\expandablevalue#1{%
+ \expandafter\ifx\csname SET#1\endcsname\relax
+ {[No value for ``#1'']}%
+ \message{Variable `#1', used in @value, is not set.}%
+ \else
+ \csname SET#1\endcsname
+ \fi
+}
+
+% @ifset VAR ... @end ifset reads the `...' iff VAR has been defined
+% with @set.
+%
+% To get special treatment of `@end ifset,' call \makeond and the redefine.
+%
+\makecond{ifset}
+\def\ifset{\parsearg{\doifset{\let\next=\ifsetfail}}}
+\def\doifset#1#2{%
+ {%
+ \makevalueexpandable
+ \let\next=\empty
+ \expandafter\ifx\csname SET#2\endcsname\relax
+ #1% If not set, redefine \next.
+ \fi
+ \expandafter
+ }\next
+}
+\def\ifsetfail{\doignore{ifset}}
+
+% @ifclear VAR ... @end ifclear reads the `...' iff VAR has never been
+% defined with @set, or has been undefined with @clear.
+%
+% The `\else' inside the `\doifset' parameter is a trick to reuse the
+% above code: if the variable is not set, do nothing, if it is set,
+% then redefine \next to \ifclearfail.
+%
+\makecond{ifclear}
+\def\ifclear{\parsearg{\doifset{\else \let\next=\ifclearfail}}}
+\def\ifclearfail{\doignore{ifclear}}
+
+% @dircategory CATEGORY -- specify a category of the dir file
+% which this file should belong to. Ignore this in TeX.
+\let\dircategory=\comment
+
+% @defininfoenclose.
+\let\definfoenclose=\comment
+
+
+\message{indexing,}
+% Index generation facilities
+
+% Define \newwrite to be identical to plain tex's \newwrite
+% except not \outer, so it can be used within macros and \if's.
+\edef\newwrite{\makecsname{ptexnewwrite}}
+
+% \newindex {foo} defines an index named foo.
+% It automatically defines \fooindex such that
+% \fooindex ...rest of line... puts an entry in the index foo.
+% It also defines \fooindfile to be the number of the output channel for
+% the file that accumulates this index. The file's extension is foo.
+% The name of an index should be no more than 2 characters long
+% for the sake of vms.
+%
+\def\newindex#1{%
+ \iflinks
+ \expandafter\newwrite \csname#1indfile\endcsname
+ \openout \csname#1indfile\endcsname \jobname.#1 % Open the file
+ \fi
+ \expandafter\xdef\csname#1index\endcsname{% % Define @#1index
+ \noexpand\doindex{#1}}
+}
+
+% @defindex foo == \newindex{foo}
+%
+\def\defindex{\parsearg\newindex}
+
+% Define @defcodeindex, like @defindex except put all entries in @code.
+%
+\def\defcodeindex{\parsearg\newcodeindex}
+%
+\def\newcodeindex#1{%
+ \iflinks
+ \expandafter\newwrite \csname#1indfile\endcsname
+ \openout \csname#1indfile\endcsname \jobname.#1
+ \fi
+ \expandafter\xdef\csname#1index\endcsname{%
+ \noexpand\docodeindex{#1}}%
+}
+
+
+% @synindex foo bar makes index foo feed into index bar.
+% Do this instead of @defindex foo if you don't want it as a separate index.
+%
+% @syncodeindex foo bar similar, but put all entries made for index foo
+% inside @code.
+%
+\def\synindex#1 #2 {\dosynindex\doindex{#1}{#2}}
+\def\syncodeindex#1 #2 {\dosynindex\docodeindex{#1}{#2}}
+
+% #1 is \doindex or \docodeindex, #2 the index getting redefined (foo),
+% #3 the target index (bar).
+\def\dosynindex#1#2#3{%
+ % Only do \closeout if we haven't already done it, else we'll end up
+ % closing the target index.
+ \expandafter \ifx\csname donesynindex#2\endcsname \relax
+ % The \closeout helps reduce unnecessary open files; the limit on the
+ % Acorn RISC OS is a mere 16 files.
+ \expandafter\closeout\csname#2indfile\endcsname
+ \expandafter\let\csname donesynindex#2\endcsname = 1
+ \fi
+ % redefine \fooindfile:
+ \expandafter\let\expandafter\temp\expandafter=\csname#3indfile\endcsname
+ \expandafter\let\csname#2indfile\endcsname=\temp
+ % redefine \fooindex:
+ \expandafter\xdef\csname#2index\endcsname{\noexpand#1{#3}}%
+}
+
+% Define \doindex, the driver for all \fooindex macros.
+% Argument #1 is generated by the calling \fooindex macro,
+% and it is "foo", the name of the index.
+
+% \doindex just uses \parsearg; it calls \doind for the actual work.
+% This is because \doind is more useful to call from other macros.
+
+% There is also \dosubind {index}{topic}{subtopic}
+% which makes an entry in a two-level index such as the operation index.
+
+\def\doindex#1{\edef\indexname{#1}\parsearg\singleindexer}
+\def\singleindexer #1{\doind{\indexname}{#1}}
+
+% like the previous two, but they put @code around the argument.
+\def\docodeindex#1{\edef\indexname{#1}\parsearg\singlecodeindexer}
+\def\singlecodeindexer #1{\doind{\indexname}{\code{#1}}}
+
+% Take care of Texinfo commands that can appear in an index entry.
+% Since there are some commands we want to expand, and others we don't,
+% we have to laboriously prevent expansion for those that we don't.
+%
+\def\indexdummies{%
+ \escapechar = `\\ % use backslash in output files.
+ \def\@{@}% change to @@ when we switch to @ as escape char in index files.
+ \def\ {\realbackslash\space }%
+ %
+ % Need these in case \tex is in effect and \{ is a \delimiter again.
+ % But can't use \lbracecmd and \rbracecmd because texindex assumes
+ % braces and backslashes are used only as delimiters.
+ \let\{ = \mylbrace
+ \let\} = \myrbrace
+ %
+ % I don't entirely understand this, but when an index entry is
+ % generated from a macro call, the \endinput which \scanmacro inserts
+ % causes processing to be prematurely terminated. This is,
+ % apparently, because \indexsorttmp is fully expanded, and \endinput
+ % is an expandable command. The redefinition below makes \endinput
+ % disappear altogether for that purpose -- although logging shows that
+ % processing continues to some further point. On the other hand, it
+ % seems \endinput does not hurt in the printed index arg, since that
+ % is still getting written without apparent harm.
+ %
+ % Sample source (mac-idx3.tex, reported by Graham Percival to
+ % help-texinfo, 22may06):
+ % @macro funindex {WORD}
+ % @findex xyz
+ % @end macro
+ % ...
+ % @funindex commtest
+ %
+ % The above is not enough to reproduce the bug, but it gives the flavor.
+ %
+ % Sample whatsit resulting:
+ % . at write3{\entry{xyz}{@folio }{@code {xyz at endinput }}}
+ %
+ % So:
+ \let\endinput = \empty
+ %
+ % Do the redefinitions.
+ \commondummies
+}
+
+% For the aux and toc files, @ is the escape character. So we want to
+% redefine everything using @ as the escape character (instead of
+% \realbackslash, still used for index files). When everything uses @,
+% this will be simpler.
+%
+\def\atdummies{%
+ \def\@{@@}%
+ \def\ {@ }%
+ \let\{ = \lbraceatcmd
+ \let\} = \rbraceatcmd
+ %
+ % Do the redefinitions.
+ \commondummies
+ \otherbackslash
+}
+
+% Called from \indexdummies and \atdummies.
+%
+\def\commondummies{%
+ %
+ % \definedummyword defines \#1 as \string\#1\space, thus effectively
+ % preventing its expansion. This is used only for control% words,
+ % not control letters, because the \space would be incorrect for
+ % control characters, but is needed to separate the control word
+ % from whatever follows.
+ %
+ % For control letters, we have \definedummyletter, which omits the
+ % space.
+ %
+ % These can be used both for control words that take an argument and
+ % those that do not. If it is followed by {arg} in the input, then
+ % that will dutifully get written to the index (or wherever).
+ %
+ \def\definedummyword ##1{\def##1{\string##1\space}}%
+ \def\definedummyletter##1{\def##1{\string##1}}%
+ \let\definedummyaccent\definedummyletter
+ %
+ \commondummiesnofonts
+ %
+ \definedummyletter\_%
+ %
+ % Non-English letters.
+ \definedummyword\AA
+ \definedummyword\AE
+ \definedummyword\DH
+ \definedummyword\L
+ \definedummyword\O
+ \definedummyword\OE
+ \definedummyword\TH
+ \definedummyword\aa
+ \definedummyword\ae
+ \definedummyword\dh
+ \definedummyword\exclamdown
+ \definedummyword\l
+ \definedummyword\o
+ \definedummyword\oe
+ \definedummyword\ordf
+ \definedummyword\ordm
+ \definedummyword\questiondown
+ \definedummyword\ss
+ \definedummyword\th
+ %
+ % Although these internal commands shouldn't show up, sometimes they do.
+ \definedummyword\bf
+ \definedummyword\gtr
+ \definedummyword\hat
+ \definedummyword\less
+ \definedummyword\sf
+ \definedummyword\sl
+ \definedummyword\tclose
+ \definedummyword\tt
+ %
+ \definedummyword\LaTeX
+ \definedummyword\TeX
+ %
+ % Assorted special characters.
+ \definedummyword\bullet
+ \definedummyword\comma
+ \definedummyword\copyright
+ \definedummyword\registeredsymbol
+ \definedummyword\dots
+ \definedummyword\enddots
+ \definedummyword\equiv
+ \definedummyword\error
+ \definedummyword\euro
+ \definedummyword\guillemetleft
+ \definedummyword\guillemetright
+ \definedummyword\guilsinglleft
+ \definedummyword\guilsinglright
+ \definedummyword\expansion
+ \definedummyword\minus
+ \definedummyword\ogonek
+ \definedummyword\pounds
+ \definedummyword\point
+ \definedummyword\print
+ \definedummyword\quotedblbase
+ \definedummyword\quotedblleft
+ \definedummyword\quotedblright
+ \definedummyword\quoteleft
+ \definedummyword\quoteright
+ \definedummyword\quotesinglbase
+ \definedummyword\result
+ \definedummyword\textdegree
+ %
+ % We want to disable all macros so that they are not expanded by \write.
+ \macrolist
+ %
+ \normalturnoffactive
+ %
+ % Handle some cases of @value -- where it does not contain any
+ % (non-fully-expandable) commands.
+ \makevalueexpandable
+}
+
+% \commondummiesnofonts: common to \commondummies and \indexnofonts.
+%
+\def\commondummiesnofonts{%
+ % Control letters and accents.
+ \definedummyletter\!%
+ \definedummyaccent\"%
+ \definedummyaccent\'%
+ \definedummyletter\*%
+ \definedummyaccent\,%
+ \definedummyletter\.%
+ \definedummyletter\/%
+ \definedummyletter\:%
+ \definedummyaccent\=%
+ \definedummyletter\?%
+ \definedummyaccent\^%
+ \definedummyaccent\`%
+ \definedummyaccent\~%
+ \definedummyword\u
+ \definedummyword\v
+ \definedummyword\H
+ \definedummyword\dotaccent
+ \definedummyword\ogonek
+ \definedummyword\ringaccent
+ \definedummyword\tieaccent
+ \definedummyword\ubaraccent
+ \definedummyword\udotaccent
+ \definedummyword\dotless
+ %
+ % Texinfo font commands.
+ \definedummyword\b
+ \definedummyword\i
+ \definedummyword\r
+ \definedummyword\sc
+ \definedummyword\t
+ %
+ % Commands that take arguments.
+ \definedummyword\acronym
+ \definedummyword\cite
+ \definedummyword\code
+ \definedummyword\command
+ \definedummyword\dfn
+ \definedummyword\email
+ \definedummyword\emph
+ \definedummyword\env
+ \definedummyword\file
+ \definedummyword\kbd
+ \definedummyword\key
+ \definedummyword\math
+ \definedummyword\option
+ \definedummyword\pxref
+ \definedummyword\ref
+ \definedummyword\samp
+ \definedummyword\strong
+ \definedummyword\tie
+ \definedummyword\uref
+ \definedummyword\url
+ \definedummyword\var
+ \definedummyword\verb
+ \definedummyword\w
+ \definedummyword\xref
+}
+
+% \indexnofonts is used when outputting the strings to sort the index
+% by, and when constructing control sequence names. It eliminates all
+% control sequences and just writes whatever the best ASCII sort string
+% would be for a given command (usually its argument).
+%
+\def\indexnofonts{%
+ % Accent commands should become @asis.
+ \def\definedummyaccent##1{\let##1\asis}%
+ % We can just ignore other control letters.
+ \def\definedummyletter##1{\let##1\empty}%
+ % Hopefully, all control words can become @asis.
+ \let\definedummyword\definedummyaccent
+ %
+ \commondummiesnofonts
+ %
+ % Don't no-op \tt, since it isn't a user-level command
+ % and is used in the definitions of the active chars like <, >, |, etc.
+ % Likewise with the other plain tex font commands.
+ %\let\tt=\asis
+ %
+ \def\ { }%
+ \def\@{@}%
+ % how to handle braces?
+ \def\_{\normalunderscore}%
+ %
+ % Non-English letters.
+ \def\AA{AA}%
+ \def\AE{AE}%
+ \def\DH{DZZ}%
+ \def\L{L}%
+ \def\OE{OE}%
+ \def\O{O}%
+ \def\TH{ZZZ}%
+ \def\aa{aa}%
+ \def\ae{ae}%
+ \def\dh{dzz}%
+ \def\exclamdown{!}%
+ \def\l{l}%
+ \def\oe{oe}%
+ \def\ordf{a}%
+ \def\ordm{o}%
+ \def\o{o}%
+ \def\questiondown{?}%
+ \def\ss{ss}%
+ \def\th{zzz}%
+ %
+ \def\LaTeX{LaTeX}%
+ \def\TeX{TeX}%
+ %
+ % Assorted special characters.
+ % (The following {} will end up in the sort string, but that's ok.)
+ \def\bullet{bullet}%
+ \def\comma{,}%
+ \def\copyright{copyright}%
+ \def\dots{...}%
+ \def\enddots{...}%
+ \def\equiv{==}%
+ \def\error{error}%
+ \def\euro{euro}%
+ \def\expansion{==>}%
+ \def\guillemetleft{<<}%
+ \def\guillemetright{>>}%
+ \def\guilsinglleft{<}%
+ \def\guilsinglright{>}%
+ \def\minus{-}%
+ \def\point{.}%
+ \def\pounds{pounds}%
+ \def\print{-|}%
+ \def\quotedblbase{"}%
+ \def\quotedblleft{"}%
+ \def\quotedblright{"}%
+ \def\quoteleft{`}%
+ \def\quoteright{'}%
+ \def\quotesinglbase{,}%
+ \def\registeredsymbol{R}%
+ \def\result{=>}%
+ \def\textdegree{o}%
+ %
+ % We need to get rid of all macros, leaving only the arguments (if present).
+ % Of course this is not nearly correct, but it is the best we can do for now.
+ % makeinfo does not expand macros in the argument to @deffn, which ends up
+ % writing an index entry, and texindex isn't prepared for an index sort entry
+ % that starts with \.
+ %
+ % Since macro invocations are followed by braces, we can just redefine them
+ % to take a single TeX argument. The case of a macro invocation that
+ % goes to end-of-line is not handled.
+ %
+ \macrolist
+}
+
+\let\indexbackslash=0 %overridden during \printindex.
+\let\SETmarginindex=\relax % put index entries in margin (undocumented)?
+
+% Most index entries go through here, but \dosubind is the general case.
+% #1 is the index name, #2 is the entry text.
+\def\doind#1#2{\dosubind{#1}{#2}{}}
+
+% Workhorse for all \fooindexes.
+% #1 is name of index, #2 is stuff to put there, #3 is subentry --
+% empty if called from \doind, as we usually are (the main exception
+% is with most defuns, which call us directly).
+%
+\def\dosubind#1#2#3{%
+ \iflinks
+ {%
+ % Store the main index entry text (including the third arg).
+ \toks0 = {#2}%
+ % If third arg is present, precede it with a space.
+ \def\thirdarg{#3}%
+ \ifx\thirdarg\empty \else
+ \toks0 = \expandafter{\the\toks0 \space #3}%
+ \fi
+ %
+ \edef\writeto{\csname#1indfile\endcsname}%
+ %
+ \safewhatsit\dosubindwrite
+ }%
+ \fi
+}
+
+% Write the entry in \toks0 to the index file:
+%
+\def\dosubindwrite{%
+ % Put the index entry in the margin if desired.
+ \ifx\SETmarginindex\relax\else
+ \insert\margin{\hbox{\vrule height8pt depth3pt width0pt \the\toks0}}%
+ \fi
+ %
+ % Remember, we are within a group.
+ \indexdummies % Must do this here, since \bf, etc expand at this stage
+ \def\backslashcurfont{\indexbackslash}% \indexbackslash isn't defined now
+ % so it will be output as is; and it will print as backslash.
+ %
+ % Process the index entry with all font commands turned off, to
+ % get the string to sort by.
+ {\indexnofonts
+ \edef\temp{\the\toks0}% need full expansion
+ \xdef\indexsorttmp{\temp}%
+ }%
+ %
+ % Set up the complete index entry, with both the sort key and
+ % the original text, including any font commands. We write
+ % three arguments to \entry to the .?? file (four in the
+ % subentry case), texindex reduces to two when writing the .??s
+ % sorted result.
+ \edef\temp{%
+ \write\writeto{%
+ \string\entry{\indexsorttmp}{\noexpand\folio}{\the\toks0}}%
+ }%
+ \temp
+}
+
+% Take care of unwanted page breaks/skips around a whatsit:
+%
+% If a skip is the last thing on the list now, preserve it
+% by backing up by \lastskip, doing the \write, then inserting
+% the skip again. Otherwise, the whatsit generated by the
+% \write or \pdfdest will make \lastskip zero. The result is that
+% sequences like this:
+% @end defun
+% @tindex whatever
+% @defun ...
+% will have extra space inserted, because the \medbreak in the
+% start of the @defun won't see the skip inserted by the @end of
+% the previous defun.
+%
+% But don't do any of this if we're not in vertical mode. We
+% don't want to do a \vskip and prematurely end a paragraph.
+%
+% Avoid page breaks due to these extra skips, too.
+%
+% But wait, there is a catch there:
+% We'll have to check whether \lastskip is zero skip. \ifdim is not
+% sufficient for this purpose, as it ignores stretch and shrink parts
+% of the skip. The only way seems to be to check the textual
+% representation of the skip.
+%
+% The following is almost like \def\zeroskipmacro{0.0pt} except that
+% the ``p'' and ``t'' characters have catcode \other, not 11 (letter).
+%
+\edef\zeroskipmacro{\expandafter\the\csname z at skip\endcsname}
+%
+\newskip\whatsitskip
+\newcount\whatsitpenalty
+%
+% ..., ready, GO:
+%
+\def\safewhatsit#1{%
+\ifhmode
+ #1%
+\else
+ % \lastskip and \lastpenalty cannot both be nonzero simultaneously.
+ \whatsitskip = \lastskip
+ \edef\lastskipmacro{\the\lastskip}%
+ \whatsitpenalty = \lastpenalty
+ %
+ % If \lastskip is nonzero, that means the last item was a
+ % skip. And since a skip is discardable, that means this
+ % -\whatsitskip glue we're inserting is preceded by a
+ % non-discardable item, therefore it is not a potential
+ % breakpoint, therefore no \nobreak needed.
+ \ifx\lastskipmacro\zeroskipmacro
+ \else
+ \vskip-\whatsitskip
+ \fi
+ %
+ #1%
+ %
+ \ifx\lastskipmacro\zeroskipmacro
+ % If \lastskip was zero, perhaps the last item was a penalty, and
+ % perhaps it was >=10000, e.g., a \nobreak. In that case, we want
+ % to re-insert the same penalty (values >10000 are used for various
+ % signals); since we just inserted a non-discardable item, any
+ % following glue (such as a \parskip) would be a breakpoint. For example:
+ %
+ % @deffn deffn-whatever
+ % @vindex index-whatever
+ % Description.
+ % would allow a break between the index-whatever whatsit
+ % and the "Description." paragraph.
+ \ifnum\whatsitpenalty>9999 \penalty\whatsitpenalty \fi
+ \else
+ % On the other hand, if we had a nonzero \lastskip,
+ % this make-up glue would be preceded by a non-discardable item
+ % (the whatsit from the \write), so we must insert a \nobreak.
+ \nobreak\vskip\whatsitskip
+ \fi
+\fi
+}
+
+% The index entry written in the file actually looks like
+% \entry {sortstring}{page}{topic}
+% or
+% \entry {sortstring}{page}{topic}{subtopic}
+% The texindex program reads in these files and writes files
+% containing these kinds of lines:
+% \initial {c}
+% before the first topic whose initial is c
+% \entry {topic}{pagelist}
+% for a topic that is used without subtopics
+% \primary {topic}
+% for the beginning of a topic that is used with subtopics
+% \secondary {subtopic}{pagelist}
+% for each subtopic.
+
+% Define the user-accessible indexing commands
+% @findex, @vindex, @kindex, @cindex.
+
+\def\findex {\fnindex}
+\def\kindex {\kyindex}
+\def\cindex {\cpindex}
+\def\vindex {\vrindex}
+\def\tindex {\tpindex}
+\def\pindex {\pgindex}
+
+\def\cindexsub {\begingroup\obeylines\cindexsub}
+{\obeylines %
+\gdef\cindexsub "#1" #2^^M{\endgroup %
+\dosubind{cp}{#2}{#1}}}
+
+% Define the macros used in formatting output of the sorted index material.
+
+% @printindex causes a particular index (the ??s file) to get printed.
+% It does not print any chapter heading (usually an @unnumbered).
+%
+\parseargdef\printindex{\begingroup
+ \dobreak \chapheadingskip{10000}%
+ %
+ \smallfonts \rm
+ \tolerance = 9500
+ \plainfrenchspacing
+ \everypar = {}% don't want the \kern\-parindent from indentation suppression.
+ %
+ % See if the index file exists and is nonempty.
+ % Change catcode of @ here so that if the index file contains
+ % \initial {@}
+ % as its first line, TeX doesn't complain about mismatched braces
+ % (because it thinks @} is a control sequence).
+ \catcode`\@ = 11
+ \openin 1 \jobname.#1s
+ \ifeof 1
+ % \enddoublecolumns gets confused if there is no text in the index,
+ % and it loses the chapter title and the aux file entries for the
+ % index. The easiest way to prevent this problem is to make sure
+ % there is some text.
+ \putwordIndexNonexistent
+ \else
+ %
+ % If the index file exists but is empty, then \openin leaves \ifeof
+ % false. We have to make TeX try to read something from the file, so
+ % it can discover if there is anything in it.
+ \read 1 to \temp
+ \ifeof 1
+ \putwordIndexIsEmpty
+ \else
+ % Index files are almost Texinfo source, but we use \ as the escape
+ % character. It would be better to use @, but that's too big a change
+ % to make right now.
+ \def\indexbackslash{\backslashcurfont}%
+ \catcode`\\ = 0
+ \escapechar = `\\
+ \begindoublecolumns
+ \input \jobname.#1s
+ \enddoublecolumns
+ \fi
+ \fi
+ \closein 1
+\endgroup}
+
+% These macros are used by the sorted index file itself.
+% Change them to control the appearance of the index.
+
+\def\initial#1{{%
+ % Some minor font changes for the special characters.
+ \let\tentt=\sectt \let\tt=\sectt \let\sf=\sectt
+ %
+ % Remove any glue we may have, we'll be inserting our own.
+ \removelastskip
+ %
+ % We like breaks before the index initials, so insert a bonus.
+ \nobreak
+ \vskip 0pt plus 3\baselineskip
+ \penalty 0
+ \vskip 0pt plus -3\baselineskip
+ %
+ % Typeset the initial. Making this add up to a whole number of
+ % baselineskips increases the chance of the dots lining up from column
+ % to column. It still won't often be perfect, because of the stretch
+ % we need before each entry, but it's better.
+ %
+ % No shrink because it confuses \balancecolumns.
+ \vskip 1.67\baselineskip plus .5\baselineskip
+ \leftline{\secbf #1}%
+ % Do our best not to break after the initial.
+ \nobreak
+ \vskip .33\baselineskip plus .1\baselineskip
+}}
+
+% \entry typesets a paragraph consisting of the text (#1), dot leaders, and
+% then page number (#2) flushed to the right margin. It is used for index
+% and table of contents entries. The paragraph is indented by \leftskip.
+%
+% A straightforward implementation would start like this:
+% \def\entry#1#2{...
+% But this freezes the catcodes in the argument, and can cause problems to
+% @code, which sets - active. This problem was fixed by a kludge---
+% ``-'' was active throughout whole index, but this isn't really right.
+%
+% The right solution is to prevent \entry from swallowing the whole text.
+% --kasal, 21nov03
+\def\entry{%
+ \begingroup
+ %
+ % Start a new paragraph if necessary, so our assignments below can't
+ % affect previous text.
+ \par
+ %
+ % Do not fill out the last line with white space.
+ \parfillskip = 0in
+ %
+ % No extra space above this paragraph.
+ \parskip = 0in
+ %
+ % Do not prefer a separate line ending with a hyphen to fewer lines.
+ \finalhyphendemerits = 0
+ %
+ % \hangindent is only relevant when the entry text and page number
+ % don't both fit on one line. In that case, bob suggests starting the
+ % dots pretty far over on the line. Unfortunately, a large
+ % indentation looks wrong when the entry text itself is broken across
+ % lines. So we use a small indentation and put up with long leaders.
+ %
+ % \hangafter is reset to 1 (which is the value we want) at the start
+ % of each paragraph, so we need not do anything with that.
+ \hangindent = 2em
+ %
+ % When the entry text needs to be broken, just fill out the first line
+ % with blank space.
+ \rightskip = 0pt plus1fil
+ %
+ % A bit of stretch before each entry for the benefit of balancing
+ % columns.
+ \vskip 0pt plus1pt
+ %
+ % Swallow the left brace of the text (first parameter):
+ \afterassignment\doentry
+ \let\temp =
+}
+\def\doentry{%
+ \bgroup % Instead of the swallowed brace.
+ \noindent
+ \aftergroup\finishentry
+ % And now comes the text of the entry.
+}
+\def\finishentry#1{%
+ % #1 is the page number.
+ %
+ % The following is kludged to not output a line of dots in the index if
+ % there are no page numbers. The next person who breaks this will be
+ % cursed by a Unix daemon.
+ \setbox\boxA = \hbox{#1}%
+ \ifdim\wd\boxA = 0pt
+ \ %
+ \else
+ %
+ % If we must, put the page number on a line of its own, and fill out
+ % this line with blank space. (The \hfil is overwhelmed with the
+ % fill leaders glue in \indexdotfill if the page number does fit.)
+ \hfil\penalty50
+ \null\nobreak\indexdotfill % Have leaders before the page number.
+ %
+ % The `\ ' here is removed by the implicit \unskip that TeX does as
+ % part of (the primitive) \par. Without it, a spurious underfull
+ % \hbox ensues.
+ \ifpdf
+ \pdfgettoks#1.%
+ \ \the\toksA
+ \else
+ \ #1%
+ \fi
+ \fi
+ \par
+ \endgroup
+}
+
+% Like plain.tex's \dotfill, except uses up at least 1 em.
+\def\indexdotfill{\cleaders
+ \hbox{$\mathsurround=0pt \mkern1.5mu.\mkern1.5mu$}\hskip 1em plus 1fill}
+
+\def\primary #1{\line{#1\hfil}}
+
+\newskip\secondaryindent \secondaryindent=0.5cm
+\def\secondary#1#2{{%
+ \parfillskip=0in
+ \parskip=0in
+ \hangindent=1in
+ \hangafter=1
+ \noindent\hskip\secondaryindent\hbox{#1}\indexdotfill
+ \ifpdf
+ \pdfgettoks#2.\ \the\toksA % The page number ends the paragraph.
+ \else
+ #2
+ \fi
+ \par
+}}
+
+% Define two-column mode, which we use to typeset indexes.
+% Adapted from the TeXbook, page 416, which is to say,
+% the manmac.tex format used to print the TeXbook itself.
+\catcode`\@=11
+
+\newbox\partialpage
+\newdimen\doublecolumnhsize
+
+\def\begindoublecolumns{\begingroup % ended by \enddoublecolumns
+ % Grab any single-column material above us.
+ \output = {%
+ %
+ % Here is a possibility not foreseen in manmac: if we accumulate a
+ % whole lot of material, we might end up calling this \output
+ % routine twice in a row (see the doublecol-lose test, which is
+ % essentially a couple of indexes with @setchapternewpage off). In
+ % that case we just ship out what is in \partialpage with the normal
+ % output routine. Generally, \partialpage will be empty when this
+ % runs and this will be a no-op. See the indexspread.tex test case.
+ \ifvoid\partialpage \else
+ \onepageout{\pagecontents\partialpage}%
+ \fi
+ %
+ \global\setbox\partialpage = \vbox{%
+ % Unvbox the main output page.
+ \unvbox\PAGE
+ \kern-\topskip \kern\baselineskip
+ }%
+ }%
+ \eject % run that output routine to set \partialpage
+ %
+ % Use the double-column output routine for subsequent pages.
+ \output = {\doublecolumnout}%
+ %
+ % Change the page size parameters. We could do this once outside this
+ % routine, in each of @smallbook, @afourpaper, and the default 8.5x11
+ % format, but then we repeat the same computation. Repeating a couple
+ % of assignments once per index is clearly meaningless for the
+ % execution time, so we may as well do it in one place.
+ %
+ % First we halve the line length, less a little for the gutter between
+ % the columns. We compute the gutter based on the line length, so it
+ % changes automatically with the paper format. The magic constant
+ % below is chosen so that the gutter has the same value (well, +-<1pt)
+ % as it did when we hard-coded it.
+ %
+ % We put the result in a separate register, \doublecolumhsize, so we
+ % can restore it in \pagesofar, after \hsize itself has (potentially)
+ % been clobbered.
+ %
+ \doublecolumnhsize = \hsize
+ \advance\doublecolumnhsize by -.04154\hsize
+ \divide\doublecolumnhsize by 2
+ \hsize = \doublecolumnhsize
+ %
+ % Double the \vsize as well. (We don't need a separate register here,
+ % since nobody clobbers \vsize.)
+ \vsize = 2\vsize
+}
+
+% The double-column output routine for all double-column pages except
+% the last.
+%
+\def\doublecolumnout{%
+ \splittopskip=\topskip \splitmaxdepth=\maxdepth
+ % Get the available space for the double columns -- the normal
+ % (undoubled) page height minus any material left over from the
+ % previous page.
+ \dimen@ = \vsize
+ \divide\dimen@ by 2
+ \advance\dimen@ by -\ht\partialpage
+ %
+ % box0 will be the left-hand column, box2 the right.
+ \setbox0=\vsplit255 to\dimen@ \setbox2=\vsplit255 to\dimen@
+ \onepageout\pagesofar
+ \unvbox255
+ \penalty\outputpenalty
+}
+%
+% Re-output the contents of the output page -- any previous material,
+% followed by the two boxes we just split, in box0 and box2.
+\def\pagesofar{%
+ \unvbox\partialpage
+ %
+ \hsize = \doublecolumnhsize
+ \wd0=\hsize \wd2=\hsize
+ \hbox to\pagewidth{\box0\hfil\box2}%
+}
+%
+% All done with double columns.
+\def\enddoublecolumns{%
+ % The following penalty ensures that the page builder is exercised
+ % _before_ we change the output routine. This is necessary in the
+ % following situation:
+ %
+ % The last section of the index consists only of a single entry.
+ % Before this section, \pagetotal is less than \pagegoal, so no
+ % break occurs before the last section starts. However, the last
+ % section, consisting of \initial and the single \entry, does not
+ % fit on the page and has to be broken off. Without the following
+ % penalty the page builder will not be exercised until \eject
+ % below, and by that time we'll already have changed the output
+ % routine to the \balancecolumns version, so the next-to-last
+ % double-column page will be processed with \balancecolumns, which
+ % is wrong: The two columns will go to the main vertical list, with
+ % the broken-off section in the recent contributions. As soon as
+ % the output routine finishes, TeX starts reconsidering the page
+ % break. The two columns and the broken-off section both fit on the
+ % page, because the two columns now take up only half of the page
+ % goal. When TeX sees \eject from below which follows the final
+ % section, it invokes the new output routine that we've set after
+ % \balancecolumns below; \onepageout will try to fit the two columns
+ % and the final section into the vbox of \pageheight (see
+ % \pagebody), causing an overfull box.
+ %
+ % Note that glue won't work here, because glue does not exercise the
+ % page builder, unlike penalties (see The TeXbook, pp. 280-281).
+ \penalty0
+ %
+ \output = {%
+ % Split the last of the double-column material. Leave it on the
+ % current page, no automatic page break.
+ \balancecolumns
+ %
+ % If we end up splitting too much material for the current page,
+ % though, there will be another page break right after this \output
+ % invocation ends. Having called \balancecolumns once, we do not
+ % want to call it again. Therefore, reset \output to its normal
+ % definition right away. (We hope \balancecolumns will never be
+ % called on to balance too much material, but if it is, this makes
+ % the output somewhat more palatable.)
+ \global\output = {\onepageout{\pagecontents\PAGE}}%
+ }%
+ \eject
+ \endgroup % started in \begindoublecolumns
+ %
+ % \pagegoal was set to the doubled \vsize above, since we restarted
+ % the current page. We're now back to normal single-column
+ % typesetting, so reset \pagegoal to the normal \vsize (after the
+ % \endgroup where \vsize got restored).
+ \pagegoal = \vsize
+}
+%
+% Called at the end of the double column material.
+\def\balancecolumns{%
+ \setbox0 = \vbox{\unvbox255}% like \box255 but more efficient, see p.120.
+ \dimen@ = \ht0
+ \advance\dimen@ by \topskip
+ \advance\dimen@ by-\baselineskip
+ \divide\dimen@ by 2 % target to split to
+ %debug\message{final 2-column material height=\the\ht0, target=\the\dimen at .}%
+ \splittopskip = \topskip
+ % Loop until we get a decent breakpoint.
+ {%
+ \vbadness = 10000
+ \loop
+ \global\setbox3 = \copy0
+ \global\setbox1 = \vsplit3 to \dimen@
+ \ifdim\ht3>\dimen@
+ \global\advance\dimen@ by 1pt
+ \repeat
+ }%
+ %debug\message{split to \the\dimen@, column heights: \the\ht1, \the\ht3.}%
+ \setbox0=\vbox to\dimen@{\unvbox1}%
+ \setbox2=\vbox to\dimen@{\unvbox3}%
+ %
+ \pagesofar
+}
+\catcode`\@ = \other
+
+
+\message{sectioning,}
+% Chapters, sections, etc.
+
+% \unnumberedno is an oxymoron, of course. But we count the unnumbered
+% sections so that we can refer to them unambiguously in the pdf
+% outlines by their "section number". We avoid collisions with chapter
+% numbers by starting them at 10000. (If a document ever has 10000
+% chapters, we're in trouble anyway, I'm sure.)
+\newcount\unnumberedno \unnumberedno = 10000
+\newcount\chapno
+\newcount\secno \secno=0
+\newcount\subsecno \subsecno=0
+\newcount\subsubsecno \subsubsecno=0
+
+% This counter is funny since it counts through charcodes of letters A, B, ...
+\newcount\appendixno \appendixno = `\@
+%
+% \def\appendixletter{\char\the\appendixno}
+% We do the following ugly conditional instead of the above simple
+% construct for the sake of pdftex, which needs the actual
+% letter in the expansion, not just typeset.
+%
+\def\appendixletter{%
+ \ifnum\appendixno=`A A%
+ \else\ifnum\appendixno=`B B%
+ \else\ifnum\appendixno=`C C%
+ \else\ifnum\appendixno=`D D%
+ \else\ifnum\appendixno=`E E%
+ \else\ifnum\appendixno=`F F%
+ \else\ifnum\appendixno=`G G%
+ \else\ifnum\appendixno=`H H%
+ \else\ifnum\appendixno=`I I%
+ \else\ifnum\appendixno=`J J%
+ \else\ifnum\appendixno=`K K%
+ \else\ifnum\appendixno=`L L%
+ \else\ifnum\appendixno=`M M%
+ \else\ifnum\appendixno=`N N%
+ \else\ifnum\appendixno=`O O%
+ \else\ifnum\appendixno=`P P%
+ \else\ifnum\appendixno=`Q Q%
+ \else\ifnum\appendixno=`R R%
+ \else\ifnum\appendixno=`S S%
+ \else\ifnum\appendixno=`T T%
+ \else\ifnum\appendixno=`U U%
+ \else\ifnum\appendixno=`V V%
+ \else\ifnum\appendixno=`W W%
+ \else\ifnum\appendixno=`X X%
+ \else\ifnum\appendixno=`Y Y%
+ \else\ifnum\appendixno=`Z Z%
+ % The \the is necessary, despite appearances, because \appendixletter is
+ % expanded while writing the .toc file. \char\appendixno is not
+ % expandable, thus it is written literally, thus all appendixes come out
+ % with the same letter (or @) in the toc without it.
+ \else\char\the\appendixno
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi}
+
+% Each @chapter defines these (using marks) as the number+name, number
+% and name of the chapter. Page headings and footings can use
+% these. @section does likewise.
+\def\thischapter{}
+\def\thischapternum{}
+\def\thischaptername{}
+\def\thissection{}
+\def\thissectionnum{}
+\def\thissectionname{}
+
+\newcount\absseclevel % used to calculate proper heading level
+\newcount\secbase\secbase=0 % @raisesections/@lowersections modify this count
+
+% @raisesections: treat @section as chapter, @subsection as section, etc.
+\def\raisesections{\global\advance\secbase by -1}
+\let\up=\raisesections % original BFox name
+
+% @lowersections: treat @chapter as section, @section as subsection, etc.
+\def\lowersections{\global\advance\secbase by 1}
+\let\down=\lowersections % original BFox name
+
+% we only have subsub.
+\chardef\maxseclevel = 3
+%
+% A numbered section within an unnumbered changes to unnumbered too.
+% To achive this, remember the "biggest" unnum. sec. we are currently in:
+\chardef\unmlevel = \maxseclevel
+%
+% Trace whether the current chapter is an appendix or not:
+% \chapheadtype is "N" or "A", unnumbered chapters are ignored.
+\def\chapheadtype{N}
+
+% Choose a heading macro
+% #1 is heading type
+% #2 is heading level
+% #3 is text for heading
+\def\genhead#1#2#3{%
+ % Compute the abs. sec. level:
+ \absseclevel=#2
+ \advance\absseclevel by \secbase
+ % Make sure \absseclevel doesn't fall outside the range:
+ \ifnum \absseclevel < 0
+ \absseclevel = 0
+ \else
+ \ifnum \absseclevel > 3
+ \absseclevel = 3
+ \fi
+ \fi
+ % The heading type:
+ \def\headtype{#1}%
+ \if \headtype U%
+ \ifnum \absseclevel < \unmlevel
+ \chardef\unmlevel = \absseclevel
+ \fi
+ \else
+ % Check for appendix sections:
+ \ifnum \absseclevel = 0
+ \edef\chapheadtype{\headtype}%
+ \else
+ \if \headtype A\if \chapheadtype N%
+ \errmessage{@appendix... within a non-appendix chapter}%
+ \fi\fi
+ \fi
+ % Check for numbered within unnumbered:
+ \ifnum \absseclevel > \unmlevel
+ \def\headtype{U}%
+ \else
+ \chardef\unmlevel = 3
+ \fi
+ \fi
+ % Now print the heading:
+ \if \headtype U%
+ \ifcase\absseclevel
+ \unnumberedzzz{#3}%
+ \or \unnumberedseczzz{#3}%
+ \or \unnumberedsubseczzz{#3}%
+ \or \unnumberedsubsubseczzz{#3}%
+ \fi
+ \else
+ \if \headtype A%
+ \ifcase\absseclevel
+ \appendixzzz{#3}%
+ \or \appendixsectionzzz{#3}%
+ \or \appendixsubseczzz{#3}%
+ \or \appendixsubsubseczzz{#3}%
+ \fi
+ \else
+ \ifcase\absseclevel
+ \chapterzzz{#3}%
+ \or \seczzz{#3}%
+ \or \numberedsubseczzz{#3}%
+ \or \numberedsubsubseczzz{#3}%
+ \fi
+ \fi
+ \fi
+ \suppressfirstparagraphindent
+}
+
+% an interface:
+\def\numhead{\genhead N}
+\def\apphead{\genhead A}
+\def\unnmhead{\genhead U}
+
+% @chapter, @appendix, @unnumbered. Increment top-level counter, reset
+% all lower-level sectioning counters to zero.
+%
+% Also set \chaplevelprefix, which we prepend to @float sequence numbers
+% (e.g., figures), q.v. By default (before any chapter), that is empty.
+\let\chaplevelprefix = \empty
+%
+\outer\parseargdef\chapter{\numhead0{#1}} % normally numhead0 calls chapterzzz
+\def\chapterzzz#1{%
+ % section resetting is \global in case the chapter is in a group, such
+ % as an @include file.
+ \global\secno=0 \global\subsecno=0 \global\subsubsecno=0
+ \global\advance\chapno by 1
+ %
+ % Used for \float.
+ \gdef\chaplevelprefix{\the\chapno.}%
+ \resetallfloatnos
+ %
+ % \putwordChapter can contain complex things in translations.
+ \toks0=\expandafter{\putwordChapter}%
+ \message{\the\toks0 \space \the\chapno}%
+ %
+ % Write the actual heading.
+ \chapmacro{#1}{Ynumbered}{\the\chapno}%
+ %
+ % So @section and the like are numbered underneath this chapter.
+ \global\let\section = \numberedsec
+ \global\let\subsection = \numberedsubsec
+ \global\let\subsubsection = \numberedsubsubsec
+}
+
+\outer\parseargdef\appendix{\apphead0{#1}} % normally calls appendixzzz
+%
+\def\appendixzzz#1{%
+ \global\secno=0 \global\subsecno=0 \global\subsubsecno=0
+ \global\advance\appendixno by 1
+ \gdef\chaplevelprefix{\appendixletter.}%
+ \resetallfloatnos
+ %
+ % \putwordAppendix can contain complex things in translations.
+ \toks0=\expandafter{\putwordAppendix}%
+ \message{\the\toks0 \space \appendixletter}%
+ %
+ \chapmacro{#1}{Yappendix}{\appendixletter}%
+ %
+ \global\let\section = \appendixsec
+ \global\let\subsection = \appendixsubsec
+ \global\let\subsubsection = \appendixsubsubsec
+}
+
+\outer\parseargdef\unnumbered{\unnmhead0{#1}} % normally unnmhead0 calls unnumberedzzz
+\def\unnumberedzzz#1{%
+ \global\secno=0 \global\subsecno=0 \global\subsubsecno=0
+ \global\advance\unnumberedno by 1
+ %
+ % Since an unnumbered has no number, no prefix for figures.
+ \global\let\chaplevelprefix = \empty
+ \resetallfloatnos
+ %
+ % This used to be simply \message{#1}, but TeX fully expands the
+ % argument to \message. Therefore, if #1 contained @-commands, TeX
+ % expanded them. For example, in `@unnumbered The @cite{Book}', TeX
+ % expanded @cite (which turns out to cause errors because \cite is meant
+ % to be executed, not expanded).
+ %
+ % Anyway, we don't want the fully-expanded definition of @cite to appear
+ % as a result of the \message, we just want `@cite' itself. We use
+ % \the<toks register> to achieve this: TeX expands \the<toks> only once,
+ % simply yielding the contents of <toks register>. (We also do this for
+ % the toc entries.)
+ \toks0 = {#1}%
+ \message{(\the\toks0)}%
+ %
+ \chapmacro{#1}{Ynothing}{\the\unnumberedno}%
+ %
+ \global\let\section = \unnumberedsec
+ \global\let\subsection = \unnumberedsubsec
+ \global\let\subsubsection = \unnumberedsubsubsec
+}
+
+% @centerchap is like @unnumbered, but the heading is centered.
+\outer\parseargdef\centerchap{%
+ % Well, we could do the following in a group, but that would break
+ % an assumption that \chapmacro is called at the outermost level.
+ % Thus we are safer this way: --kasal, 24feb04
+ \let\centerparametersmaybe = \centerparameters
+ \unnmhead0{#1}%
+ \let\centerparametersmaybe = \relax
+}
+
+% @top is like @unnumbered.
+\let\top\unnumbered
+
+% Sections.
+\outer\parseargdef\numberedsec{\numhead1{#1}} % normally calls seczzz
+\def\seczzz#1{%
+ \global\subsecno=0 \global\subsubsecno=0 \global\advance\secno by 1
+ \sectionheading{#1}{sec}{Ynumbered}{\the\chapno.\the\secno}%
+}
+
+\outer\parseargdef\appendixsection{\apphead1{#1}} % normally calls appendixsectionzzz
+\def\appendixsectionzzz#1{%
+ \global\subsecno=0 \global\subsubsecno=0 \global\advance\secno by 1
+ \sectionheading{#1}{sec}{Yappendix}{\appendixletter.\the\secno}%
+}
+\let\appendixsec\appendixsection
+
+\outer\parseargdef\unnumberedsec{\unnmhead1{#1}} % normally calls unnumberedseczzz
+\def\unnumberedseczzz#1{%
+ \global\subsecno=0 \global\subsubsecno=0 \global\advance\secno by 1
+ \sectionheading{#1}{sec}{Ynothing}{\the\unnumberedno.\the\secno}%
+}
+
+% Subsections.
+\outer\parseargdef\numberedsubsec{\numhead2{#1}} % normally calls numberedsubseczzz
+\def\numberedsubseczzz#1{%
+ \global\subsubsecno=0 \global\advance\subsecno by 1
+ \sectionheading{#1}{subsec}{Ynumbered}{\the\chapno.\the\secno.\the\subsecno}%
+}
+
+\outer\parseargdef\appendixsubsec{\apphead2{#1}} % normally calls appendixsubseczzz
+\def\appendixsubseczzz#1{%
+ \global\subsubsecno=0 \global\advance\subsecno by 1
+ \sectionheading{#1}{subsec}{Yappendix}%
+ {\appendixletter.\the\secno.\the\subsecno}%
+}
+
+\outer\parseargdef\unnumberedsubsec{\unnmhead2{#1}} %normally calls unnumberedsubseczzz
+\def\unnumberedsubseczzz#1{%
+ \global\subsubsecno=0 \global\advance\subsecno by 1
+ \sectionheading{#1}{subsec}{Ynothing}%
+ {\the\unnumberedno.\the\secno.\the\subsecno}%
+}
+
+% Subsubsections.
+\outer\parseargdef\numberedsubsubsec{\numhead3{#1}} % normally numberedsubsubseczzz
+\def\numberedsubsubseczzz#1{%
+ \global\advance\subsubsecno by 1
+ \sectionheading{#1}{subsubsec}{Ynumbered}%
+ {\the\chapno.\the\secno.\the\subsecno.\the\subsubsecno}%
+}
+
+\outer\parseargdef\appendixsubsubsec{\apphead3{#1}} % normally appendixsubsubseczzz
+\def\appendixsubsubseczzz#1{%
+ \global\advance\subsubsecno by 1
+ \sectionheading{#1}{subsubsec}{Yappendix}%
+ {\appendixletter.\the\secno.\the\subsecno.\the\subsubsecno}%
+}
+
+\outer\parseargdef\unnumberedsubsubsec{\unnmhead3{#1}} %normally unnumberedsubsubseczzz
+\def\unnumberedsubsubseczzz#1{%
+ \global\advance\subsubsecno by 1
+ \sectionheading{#1}{subsubsec}{Ynothing}%
+ {\the\unnumberedno.\the\secno.\the\subsecno.\the\subsubsecno}%
+}
+
+% These macros control what the section commands do, according
+% to what kind of chapter we are in (ordinary, appendix, or unnumbered).
+% Define them by default for a numbered chapter.
+\let\section = \numberedsec
+\let\subsection = \numberedsubsec
+\let\subsubsection = \numberedsubsubsec
+
+% Define @majorheading, @heading and @subheading
+
+% NOTE on use of \vbox for chapter headings, section headings, and such:
+% 1) We use \vbox rather than the earlier \line to permit
+% overlong headings to fold.
+% 2) \hyphenpenalty is set to 10000 because hyphenation in a
+% heading is obnoxious; this forbids it.
+% 3) Likewise, headings look best if no \parindent is used, and
+% if justification is not attempted. Hence \raggedright.
+
+\def\majorheading{%
+ {\advance\chapheadingskip by 10pt \chapbreak }%
+ \parsearg\chapheadingzzz
+}
+
+\def\chapheading{\chapbreak \parsearg\chapheadingzzz}
+\def\chapheadingzzz#1{%
+ {\chapfonts \vbox{\hyphenpenalty=10000\tolerance=5000
+ \parindent=0pt\ptexraggedright
+ \rmisbold #1\hfill}}%
+ \bigskip \par\penalty 200\relax
+ \suppressfirstparagraphindent
+}
+
+% @heading, @subheading, @subsubheading.
+\parseargdef\heading{\sectionheading{#1}{sec}{Yomitfromtoc}{}
+ \suppressfirstparagraphindent}
+\parseargdef\subheading{\sectionheading{#1}{subsec}{Yomitfromtoc}{}
+ \suppressfirstparagraphindent}
+\parseargdef\subsubheading{\sectionheading{#1}{subsubsec}{Yomitfromtoc}{}
+ \suppressfirstparagraphindent}
+
+% These macros generate a chapter, section, etc. heading only
+% (including whitespace, linebreaking, etc. around it),
+% given all the information in convenient, parsed form.
+
+%%% Args are the skip and penalty (usually negative)
+\def\dobreak#1#2{\par\ifdim\lastskip<#1\removelastskip\penalty#2\vskip#1\fi}
+
+%%% Define plain chapter starts, and page on/off switching for it
+% Parameter controlling skip before chapter headings (if needed)
+
+\newskip\chapheadingskip
+
+\def\chapbreak{\dobreak \chapheadingskip {-4000}}
+\def\chappager{\par\vfill\supereject}
+% Because \domark is called before \chapoddpage, the filler page will
+% get the headings for the next chapter, which is wrong. But we don't
+% care -- we just disable all headings on the filler page.
+\def\chapoddpage{%
+ \chappager
+ \ifodd\pageno \else
+ \begingroup
+ \evenheadline={\hfil}\evenfootline={\hfil}%
+ \oddheadline={\hfil}\oddfootline={\hfil}%
+ \hbox to 0pt{}%
+ \chappager
+ \endgroup
+ \fi
+}
+
+\def\setchapternewpage #1 {\csname CHAPPAG#1\endcsname}
+
+\def\CHAPPAGoff{%
+\global\let\contentsalignmacro = \chappager
+\global\let\pchapsepmacro=\chapbreak
+\global\let\pagealignmacro=\chappager}
+
+\def\CHAPPAGon{%
+\global\let\contentsalignmacro = \chappager
+\global\let\pchapsepmacro=\chappager
+\global\let\pagealignmacro=\chappager
+\global\def\HEADINGSon{\HEADINGSsingle}}
+
+\def\CHAPPAGodd{%
+\global\let\contentsalignmacro = \chapoddpage
+\global\let\pchapsepmacro=\chapoddpage
+\global\let\pagealignmacro=\chapoddpage
+\global\def\HEADINGSon{\HEADINGSdouble}}
+
+\CHAPPAGon
+
+% Chapter opening.
+%
+% #1 is the text, #2 is the section type (Ynumbered, Ynothing,
+% Yappendix, Yomitfromtoc), #3 the chapter number.
+%
+% To test against our argument.
+\def\Ynothingkeyword{Ynothing}
+\def\Yomitfromtockeyword{Yomitfromtoc}
+\def\Yappendixkeyword{Yappendix}
+%
+\def\chapmacro#1#2#3{%
+ % Insert the first mark before the heading break (see notes for \domark).
+ \let\prevchapterdefs=\lastchapterdefs
+ \let\prevsectiondefs=\lastsectiondefs
+ \gdef\lastsectiondefs{\gdef\thissectionname{}\gdef\thissectionnum{}%
+ \gdef\thissection{}}%
+ %
+ \def\temptype{#2}%
+ \ifx\temptype\Ynothingkeyword
+ \gdef\lastchapterdefs{\gdef\thischaptername{#1}\gdef\thischapternum{}%
+ \gdef\thischapter{\thischaptername}}%
+ \else\ifx\temptype\Yomitfromtockeyword
+ \gdef\lastchapterdefs{\gdef\thischaptername{#1}\gdef\thischapternum{}%
+ \gdef\thischapter{}}%
+ \else\ifx\temptype\Yappendixkeyword
+ \toks0={#1}%
+ \xdef\lastchapterdefs{%
+ \gdef\noexpand\thischaptername{\the\toks0}%
+ \gdef\noexpand\thischapternum{\appendixletter}%
+ % \noexpand\putwordAppendix avoids expanding indigestible
+ % commands in some of the translations.
+ \gdef\noexpand\thischapter{\noexpand\putwordAppendix{}
+ \noexpand\thischapternum:
+ \noexpand\thischaptername}%
+ }%
+ \else
+ \toks0={#1}%
+ \xdef\lastchapterdefs{%
+ \gdef\noexpand\thischaptername{\the\toks0}%
+ \gdef\noexpand\thischapternum{\the\chapno}%
+ % \noexpand\putwordChapter avoids expanding indigestible
+ % commands in some of the translations.
+ \gdef\noexpand\thischapter{\noexpand\putwordChapter{}
+ \noexpand\thischapternum:
+ \noexpand\thischaptername}%
+ }%
+ \fi\fi\fi
+ %
+ % Output the mark. Pass it through \safewhatsit, to take care of
+ % the preceding space.
+ \safewhatsit\domark
+ %
+ % Insert the chapter heading break.
+ \pchapsepmacro
+ %
+ % Now the second mark, after the heading break. No break points
+ % between here and the heading.
+ \let\prevchapterdefs=\lastchapterdefs
+ \let\prevsectiondefs=\lastsectiondefs
+ \domark
+ %
+ {%
+ \chapfonts \rmisbold
+ %
+ % Have to define \lastsection before calling \donoderef, because the
+ % xref code eventually uses it. On the other hand, it has to be called
+ % after \pchapsepmacro, or the headline will change too soon.
+ \gdef\lastsection{#1}%
+ %
+ % Only insert the separating space if we have a chapter/appendix
+ % number, and don't print the unnumbered ``number''.
+ \ifx\temptype\Ynothingkeyword
+ \setbox0 = \hbox{}%
+ \def\toctype{unnchap}%
+ \else\ifx\temptype\Yomitfromtockeyword
+ \setbox0 = \hbox{}% contents like unnumbered, but no toc entry
+ \def\toctype{omit}%
+ \else\ifx\temptype\Yappendixkeyword
+ \setbox0 = \hbox{\putwordAppendix{} #3\enspace}%
+ \def\toctype{app}%
+ \else
+ \setbox0 = \hbox{#3\enspace}%
+ \def\toctype{numchap}%
+ \fi\fi\fi
+ %
+ % Write the toc entry for this chapter. Must come before the
+ % \donoderef, because we include the current node name in the toc
+ % entry, and \donoderef resets it to empty.
+ \writetocentry{\toctype}{#1}{#3}%
+ %
+ % For pdftex, we have to write out the node definition (aka, make
+ % the pdfdest) after any page break, but before the actual text has
+ % been typeset. If the destination for the pdf outline is after the
+ % text, then jumping from the outline may wind up with the text not
+ % being visible, for instance under high magnification.
+ \donoderef{#2}%
+ %
+ % Typeset the actual heading.
+ \nobreak % Avoid page breaks at the interline glue.
+ \vbox{\hyphenpenalty=10000 \tolerance=5000 \parindent=0pt \ptexraggedright
+ \hangindent=\wd0 \centerparametersmaybe
+ \unhbox0 #1\par}%
+ }%
+ \nobreak\bigskip % no page break after a chapter title
+ \nobreak
+}
+
+% @centerchap -- centered and unnumbered.
+\let\centerparametersmaybe = \relax
+\def\centerparameters{%
+ \advance\rightskip by 3\rightskip
+ \leftskip = \rightskip
+ \parfillskip = 0pt
+}
+
+
+% I don't think this chapter style is supported any more, so I'm not
+% updating it with the new noderef stuff. We'll see. --karl, 11aug03.
+%
+\def\setchapterstyle #1 {\csname CHAPF#1\endcsname}
+%
+\def\unnchfopen #1{%
+\chapoddpage {\chapfonts \vbox{\hyphenpenalty=10000\tolerance=5000
+ \parindent=0pt\ptexraggedright
+ \rmisbold #1\hfill}}\bigskip \par\nobreak
+}
+\def\chfopen #1#2{\chapoddpage {\chapfonts
+\vbox to 3in{\vfil \hbox to\hsize{\hfil #2} \hbox to\hsize{\hfil #1} \vfil}}%
+\par\penalty 5000 %
+}
+\def\centerchfopen #1{%
+\chapoddpage {\chapfonts \vbox{\hyphenpenalty=10000\tolerance=5000
+ \parindent=0pt
+ \hfill {\rmisbold #1}\hfill}}\bigskip \par\nobreak
+}
+\def\CHAPFopen{%
+ \global\let\chapmacro=\chfopen
+ \global\let\centerchapmacro=\centerchfopen}
+
+
+% Section titles. These macros combine the section number parts and
+% call the generic \sectionheading to do the printing.
+%
+\newskip\secheadingskip
+\def\secheadingbreak{\dobreak \secheadingskip{-1000}}
+
+% Subsection titles.
+\newskip\subsecheadingskip
+\def\subsecheadingbreak{\dobreak \subsecheadingskip{-500}}
+
+% Subsubsection titles.
+\def\subsubsecheadingskip{\subsecheadingskip}
+\def\subsubsecheadingbreak{\subsecheadingbreak}
+
+
+% Print any size, any type, section title.
+%
+% #1 is the text, #2 is the section level (sec/subsec/subsubsec), #3 is
+% the section type for xrefs (Ynumbered, Ynothing, Yappendix), #4 is the
+% section number.
+%
+\def\seckeyword{sec}
+%
+\def\sectionheading#1#2#3#4{%
+ {%
+ % Switch to the right set of fonts.
+ \csname #2fonts\endcsname \rmisbold
+ %
+ \def\sectionlevel{#2}%
+ \def\temptype{#3}%
+ %
+ % Insert first mark before the heading break (see notes for \domark).
+ \let\prevsectiondefs=\lastsectiondefs
+ \ifx\temptype\Ynothingkeyword
+ \ifx\sectionlevel\seckeyword
+ \gdef\lastsectiondefs{\gdef\thissectionname{#1}\gdef\thissectionnum{}%
+ \gdef\thissection{\thissectionname}}%
+ \fi
+ \else\ifx\temptype\Yomitfromtockeyword
+ % Don't redefine \thissection.
+ \else\ifx\temptype\Yappendixkeyword
+ \ifx\sectionlevel\seckeyword
+ \toks0={#1}%
+ \xdef\lastsectiondefs{%
+ \gdef\noexpand\thissectionname{\the\toks0}%
+ \gdef\noexpand\thissectionnum{#4}%
+ % \noexpand\putwordSection avoids expanding indigestible
+ % commands in some of the translations.
+ \gdef\noexpand\thissection{\noexpand\putwordSection{}
+ \noexpand\thissectionnum:
+ \noexpand\thissectionname}%
+ }%
+ \fi
+ \else
+ \ifx\sectionlevel\seckeyword
+ \toks0={#1}%
+ \xdef\lastsectiondefs{%
+ \gdef\noexpand\thissectionname{\the\toks0}%
+ \gdef\noexpand\thissectionnum{#4}%
+ % \noexpand\putwordSection avoids expanding indigestible
+ % commands in some of the translations.
+ \gdef\noexpand\thissection{\noexpand\putwordSection{}
+ \noexpand\thissectionnum:
+ \noexpand\thissectionname}%
+ }%
+ \fi
+ \fi\fi\fi
+ %
+ % Go into vertical mode. Usually we'll already be there, but we
+ % don't want the following whatsit to end up in a preceding paragraph
+ % if the document didn't happen to have a blank line.
+ \par
+ %
+ % Output the mark. Pass it through \safewhatsit, to take care of
+ % the preceding space.
+ \safewhatsit\domark
+ %
+ % Insert space above the heading.
+ \csname #2headingbreak\endcsname
+ %
+ % Now the second mark, after the heading break. No break points
+ % between here and the heading.
+ \let\prevsectiondefs=\lastsectiondefs
+ \domark
+ %
+ % Only insert the space after the number if we have a section number.
+ \ifx\temptype\Ynothingkeyword
+ \setbox0 = \hbox{}%
+ \def\toctype{unn}%
+ \gdef\lastsection{#1}%
+ \else\ifx\temptype\Yomitfromtockeyword
+ % for @headings -- no section number, don't include in toc,
+ % and don't redefine \lastsection.
+ \setbox0 = \hbox{}%
+ \def\toctype{omit}%
+ \let\sectionlevel=\empty
+ \else\ifx\temptype\Yappendixkeyword
+ \setbox0 = \hbox{#4\enspace}%
+ \def\toctype{app}%
+ \gdef\lastsection{#1}%
+ \else
+ \setbox0 = \hbox{#4\enspace}%
+ \def\toctype{num}%
+ \gdef\lastsection{#1}%
+ \fi\fi\fi
+ %
+ % Write the toc entry (before \donoderef). See comments in \chapmacro.
+ \writetocentry{\toctype\sectionlevel}{#1}{#4}%
+ %
+ % Write the node reference (= pdf destination for pdftex).
+ % Again, see comments in \chapmacro.
+ \donoderef{#3}%
+ %
+ % Interline glue will be inserted when the vbox is completed.
+ % That glue will be a valid breakpoint for the page, since it'll be
+ % preceded by a whatsit (usually from the \donoderef, or from the
+ % \writetocentry if there was no node). We don't want to allow that
+ % break, since then the whatsits could end up on page n while the
+ % section is on page n+1, thus toc/etc. are wrong. Debian bug 276000.
+ \nobreak
+ %
+ % Output the actual section heading.
+ \vbox{\hyphenpenalty=10000 \tolerance=5000 \parindent=0pt \ptexraggedright
+ \hangindent=\wd0 % zero if no section number
+ \unhbox0 #1}%
+ }%
+ % Add extra space after the heading -- half of whatever came above it.
+ % Don't allow stretch, though.
+ \kern .5 \csname #2headingskip\endcsname
+ %
+ % Do not let the kern be a potential breakpoint, as it would be if it
+ % was followed by glue.
+ \nobreak
+ %
+ % We'll almost certainly start a paragraph next, so don't let that
+ % glue accumulate. (Not a breakpoint because it's preceded by a
+ % discardable item.)
+ \vskip-\parskip
+ %
+ % This is purely so the last item on the list is a known \penalty >
+ % 10000. This is so \startdefun can avoid allowing breakpoints after
+ % section headings. Otherwise, it would insert a valid breakpoint between:
+ %
+ % @section sec-whatever
+ % @deffn def-whatever
+ \penalty 10001
+}
+
+
+\message{toc,}
+% Table of contents.
+\newwrite\tocfile
+
+% Write an entry to the toc file, opening it if necessary.
+% Called from @chapter, etc.
+%
+% Example usage: \writetocentry{sec}{Section Name}{\the\chapno.\the\secno}
+% We append the current node name (if any) and page number as additional
+% arguments for the \{chap,sec,...}entry macros which will eventually
+% read this. The node name is used in the pdf outlines as the
+% destination to jump to.
+%
+% We open the .toc file for writing here instead of at @setfilename (or
+% any other fixed time) so that @contents can be anywhere in the document.
+% But if #1 is `omit', then we don't do anything. This is used for the
+% table of contents chapter openings themselves.
+%
+\newif\iftocfileopened
+\def\omitkeyword{omit}%
+%
+\def\writetocentry#1#2#3{%
+ \edef\writetoctype{#1}%
+ \ifx\writetoctype\omitkeyword \else
+ \iftocfileopened\else
+ \immediate\openout\tocfile = \jobname.toc
+ \global\tocfileopenedtrue
+ \fi
+ %
+ \iflinks
+ {\atdummies
+ \edef\temp{%
+ \write\tocfile{@#1entry{#2}{#3}{\lastnode}{\noexpand\folio}}}%
+ \temp
+ }%
+ \fi
+ \fi
+ %
+ % Tell \shipout to create a pdf destination on each page, if we're
+ % writing pdf. These are used in the table of contents. We can't
+ % just write one on every page because the title pages are numbered
+ % 1 and 2 (the page numbers aren't printed), and so are the first
+ % two pages of the document. Thus, we'd have two destinations named
+ % `1', and two named `2'.
+ \ifpdf \global\pdfmakepagedesttrue \fi
+}
+
+
+% These characters do not print properly in the Computer Modern roman
+% fonts, so we must take special care. This is more or less redundant
+% with the Texinfo input format setup at the end of this file.
+%
+\def\activecatcodes{%
+ \catcode`\"=\active
+ \catcode`\$=\active
+ \catcode`\<=\active
+ \catcode`\>=\active
+ \catcode`\\=\active
+ \catcode`\^=\active
+ \catcode`\_=\active
+ \catcode`\|=\active
+ \catcode`\~=\active
+}
+
+
+% Read the toc file, which is essentially Texinfo input.
+\def\readtocfile{%
+ \setupdatafile
+ \activecatcodes
+ \input \tocreadfilename
+}
+
+\newskip\contentsrightmargin \contentsrightmargin=1in
+\newcount\savepageno
+\newcount\lastnegativepageno \lastnegativepageno = -1
+
+% Prepare to read what we've written to \tocfile.
+%
+\def\startcontents#1{%
+ % If @setchapternewpage on, and @headings double, the contents should
+ % start on an odd page, unlike chapters. Thus, we maintain
+ % \contentsalignmacro in parallel with \pagealignmacro.
+ % From: Torbjorn Granlund <tege at matematik.su.se>
+ \contentsalignmacro
+ \immediate\closeout\tocfile
+ %
+ % Don't need to put `Contents' or `Short Contents' in the headline.
+ % It is abundantly clear what they are.
+ \chapmacro{#1}{Yomitfromtoc}{}%
+ %
+ \savepageno = \pageno
+ \begingroup % Set up to handle contents files properly.
+ \raggedbottom % Worry more about breakpoints than the bottom.
+ \advance\hsize by -\contentsrightmargin % Don't use the full line length.
+ %
+ % Roman numerals for page numbers.
+ \ifnum \pageno>0 \global\pageno = \lastnegativepageno \fi
+}
+
+% redefined for the two-volume lispref. We always output on
+% \jobname.toc even if this is redefined.
+%
+\def\tocreadfilename{\jobname.toc}
+
+% Normal (long) toc.
+%
+\def\contents{%
+ \startcontents{\putwordTOC}%
+ \openin 1 \tocreadfilename\space
+ \ifeof 1 \else
+ \readtocfile
+ \fi
+ \vfill \eject
+ \contentsalignmacro % in case @setchapternewpage odd is in effect
+ \ifeof 1 \else
+ \pdfmakeoutlines
+ \fi
+ \closein 1
+ \endgroup
+ \lastnegativepageno = \pageno
+ \global\pageno = \savepageno
+}
+
+% And just the chapters.
+\def\summarycontents{%
+ \startcontents{\putwordShortTOC}%
+ %
+ \let\numchapentry = \shortchapentry
+ \let\appentry = \shortchapentry
+ \let\unnchapentry = \shortunnchapentry
+ % We want a true roman here for the page numbers.
+ \secfonts
+ \let\rm=\shortcontrm \let\bf=\shortcontbf
+ \let\sl=\shortcontsl \let\tt=\shortconttt
+ \rm
+ \hyphenpenalty = 10000
+ \advance\baselineskip by 1pt % Open it up a little.
+ \def\numsecentry##1##2##3##4{}
+ \let\appsecentry = \numsecentry
+ \let\unnsecentry = \numsecentry
+ \let\numsubsecentry = \numsecentry
+ \let\appsubsecentry = \numsecentry
+ \let\unnsubsecentry = \numsecentry
+ \let\numsubsubsecentry = \numsecentry
+ \let\appsubsubsecentry = \numsecentry
+ \let\unnsubsubsecentry = \numsecentry
+ \openin 1 \tocreadfilename\space
+ \ifeof 1 \else
+ \readtocfile
+ \fi
+ \closein 1
+ \vfill \eject
+ \contentsalignmacro % in case @setchapternewpage odd is in effect
+ \endgroup
+ \lastnegativepageno = \pageno
+ \global\pageno = \savepageno
+}
+\let\shortcontents = \summarycontents
+
+% Typeset the label for a chapter or appendix for the short contents.
+% The arg is, e.g., `A' for an appendix, or `3' for a chapter.
+%
+\def\shortchaplabel#1{%
+ % This space should be enough, since a single number is .5em, and the
+ % widest letter (M) is 1em, at least in the Computer Modern fonts.
+ % But use \hss just in case.
+ % (This space doesn't include the extra space that gets added after
+ % the label; that gets put in by \shortchapentry above.)
+ %
+ % We'd like to right-justify chapter numbers, but that looks strange
+ % with appendix letters. And right-justifying numbers and
+ % left-justifying letters looks strange when there is less than 10
+ % chapters. Have to read the whole toc once to know how many chapters
+ % there are before deciding ...
+ \hbox to 1em{#1\hss}%
+}
+
+% These macros generate individual entries in the table of contents.
+% The first argument is the chapter or section name.
+% The last argument is the page number.
+% The arguments in between are the chapter number, section number, ...
+
+% Chapters, in the main contents.
+\def\numchapentry#1#2#3#4{\dochapentry{#2\labelspace#1}{#4}}
+%
+% Chapters, in the short toc.
+% See comments in \dochapentry re vbox and related settings.
+\def\shortchapentry#1#2#3#4{%
+ \tocentry{\shortchaplabel{#2}\labelspace #1}{\doshortpageno\bgroup#4\egroup}%
+}
+
+% Appendices, in the main contents.
+% Need the word Appendix, and a fixed-size box.
+%
+\def\appendixbox#1{%
+ % We use M since it's probably the widest letter.
+ \setbox0 = \hbox{\putwordAppendix{} M}%
+ \hbox to \wd0{\putwordAppendix{} #1\hss}}
+%
+\def\appentry#1#2#3#4{\dochapentry{\appendixbox{#2}\labelspace#1}{#4}}
+
+% Unnumbered chapters.
+\def\unnchapentry#1#2#3#4{\dochapentry{#1}{#4}}
+\def\shortunnchapentry#1#2#3#4{\tocentry{#1}{\doshortpageno\bgroup#4\egroup}}
+
+% Sections.
+\def\numsecentry#1#2#3#4{\dosecentry{#2\labelspace#1}{#4}}
+\let\appsecentry=\numsecentry
+\def\unnsecentry#1#2#3#4{\dosecentry{#1}{#4}}
+
+% Subsections.
+\def\numsubsecentry#1#2#3#4{\dosubsecentry{#2\labelspace#1}{#4}}
+\let\appsubsecentry=\numsubsecentry
+\def\unnsubsecentry#1#2#3#4{\dosubsecentry{#1}{#4}}
+
+% And subsubsections.
+\def\numsubsubsecentry#1#2#3#4{\dosubsubsecentry{#2\labelspace#1}{#4}}
+\let\appsubsubsecentry=\numsubsubsecentry
+\def\unnsubsubsecentry#1#2#3#4{\dosubsubsecentry{#1}{#4}}
+
+% This parameter controls the indentation of the various levels.
+% Same as \defaultparindent.
+\newdimen\tocindent \tocindent = 15pt
+
+% Now for the actual typesetting. In all these, #1 is the text and #2 is the
+% page number.
+%
+% If the toc has to be broken over pages, we want it to be at chapters
+% if at all possible; hence the \penalty.
+\def\dochapentry#1#2{%
+ \penalty-300 \vskip1\baselineskip plus.33\baselineskip minus.25\baselineskip
+ \begingroup
+ \chapentryfonts
+ \tocentry{#1}{\dopageno\bgroup#2\egroup}%
+ \endgroup
+ \nobreak\vskip .25\baselineskip plus.1\baselineskip
+}
+
+\def\dosecentry#1#2{\begingroup
+ \secentryfonts \leftskip=\tocindent
+ \tocentry{#1}{\dopageno\bgroup#2\egroup}%
+\endgroup}
+
+\def\dosubsecentry#1#2{\begingroup
+ \subsecentryfonts \leftskip=2\tocindent
+ \tocentry{#1}{\dopageno\bgroup#2\egroup}%
+\endgroup}
+
+\def\dosubsubsecentry#1#2{\begingroup
+ \subsubsecentryfonts \leftskip=3\tocindent
+ \tocentry{#1}{\dopageno\bgroup#2\egroup}%
+\endgroup}
+
+% We use the same \entry macro as for the index entries.
+\let\tocentry = \entry
+
+% Space between chapter (or whatever) number and the title.
+\def\labelspace{\hskip1em \relax}
+
+\def\dopageno#1{{\rm #1}}
+\def\doshortpageno#1{{\rm #1}}
+
+\def\chapentryfonts{\secfonts \rm}
+\def\secentryfonts{\textfonts}
+\def\subsecentryfonts{\textfonts}
+\def\subsubsecentryfonts{\textfonts}
+
+
+\message{environments,}
+% @foo ... @end foo.
+
+% @tex ... @end tex escapes into raw Tex temporarily.
+% One exception: @ is still an escape character, so that @end tex works.
+% But \@ or @@ will get a plain tex @ character.
+
+\envdef\tex{%
+ \setupmarkupstyle{tex}%
+ \catcode `\\=0 \catcode `\{=1 \catcode `\}=2
+ \catcode `\$=3 \catcode `\&=4 \catcode `\#=6
+ \catcode `\^=7 \catcode `\_=8 \catcode `\~=\active \let~=\tie
+ \catcode `\%=14
+ \catcode `\+=\other
+ \catcode `\"=\other
+ \catcode `\|=\other
+ \catcode `\<=\other
+ \catcode `\>=\other
+ \catcode`\`=\other
+ \catcode`\'=\other
+ \escapechar=`\\
+ %
+ \let\b=\ptexb
+ \let\bullet=\ptexbullet
+ \let\c=\ptexc
+ \let\,=\ptexcomma
+ \let\.=\ptexdot
+ \let\dots=\ptexdots
+ \let\equiv=\ptexequiv
+ \let\!=\ptexexclam
+ \let\i=\ptexi
+ \let\indent=\ptexindent
+ \let\noindent=\ptexnoindent
+ \let\{=\ptexlbrace
+ \let\+=\tabalign
+ \let\}=\ptexrbrace
+ \let\/=\ptexslash
+ \let\*=\ptexstar
+ \let\t=\ptext
+ \expandafter \let\csname top\endcsname=\ptextop % outer
+ \let\frenchspacing=\plainfrenchspacing
+ %
+ \def\endldots{\mathinner{\ldots\ldots\ldots\ldots}}%
+ \def\enddots{\relax\ifmmode\endldots\else$\mathsurround=0pt \endldots\,$\fi}%
+ \def\@{@}%
+}
+% There is no need to define \Etex.
+
+% Define @lisp ... @end lisp.
+% @lisp environment forms a group so it can rebind things,
+% including the definition of @end lisp (which normally is erroneous).
+
+% Amount to narrow the margins by for @lisp.
+\newskip\lispnarrowing \lispnarrowing=0.4in
+
+% This is the definition that ^^M gets inside @lisp, @example, and other
+% such environments. \null is better than a space, since it doesn't
+% have any width.
+\def\lisppar{\null\endgraf}
+
+% This space is always present above and below environments.
+\newskip\envskipamount \envskipamount = 0pt
+
+% Make spacing and below environment symmetrical. We use \parskip here
+% to help in doing that, since in @example-like environments \parskip
+% is reset to zero; thus the \afterenvbreak inserts no space -- but the
+% start of the next paragraph will insert \parskip.
+%
+\def\aboveenvbreak{{%
+ % =10000 instead of <10000 because of a special case in \itemzzz and
+ % \sectionheading, q.v.
+ \ifnum \lastpenalty=10000 \else
+ \advance\envskipamount by \parskip
+ \endgraf
+ \ifdim\lastskip<\envskipamount
+ \removelastskip
+ % it's not a good place to break if the last penalty was \nobreak
+ % or better ...
+ \ifnum\lastpenalty<10000 \penalty-50 \fi
+ \vskip\envskipamount
+ \fi
+ \fi
+}}
+
+\let\afterenvbreak = \aboveenvbreak
+
+% \nonarrowing is a flag. If "set", @lisp etc don't narrow margins; it will
+% also clear it, so that its embedded environments do the narrowing again.
+\let\nonarrowing=\relax
+
+% @cartouche ... @end cartouche: draw rectangle w/rounded corners around
+% environment contents.
+\font\circle=lcircle10
+\newdimen\circthick
+\newdimen\cartouter\newdimen\cartinner
+\newskip\normbskip\newskip\normpskip\newskip\normlskip
+\circthick=\fontdimen8\circle
+%
+\def\ctl{{\circle\char'013\hskip -6pt}}% 6pt from pl file: 1/2charwidth
+\def\ctr{{\hskip 6pt\circle\char'010}}
+\def\cbl{{\circle\char'012\hskip -6pt}}
+\def\cbr{{\hskip 6pt\circle\char'011}}
+\def\carttop{\hbox to \cartouter{\hskip\lskip
+ \ctl\leaders\hrule height\circthick\hfil\ctr
+ \hskip\rskip}}
+\def\cartbot{\hbox to \cartouter{\hskip\lskip
+ \cbl\leaders\hrule height\circthick\hfil\cbr
+ \hskip\rskip}}
+%
+\newskip\lskip\newskip\rskip
+
+\envdef\cartouche{%
+ \ifhmode\par\fi % can't be in the midst of a paragraph.
+ \startsavinginserts
+ \lskip=\leftskip \rskip=\rightskip
+ \leftskip=0pt\rightskip=0pt % we want these *outside*.
+ \cartinner=\hsize \advance\cartinner by-\lskip
+ \advance\cartinner by-\rskip
+ \cartouter=\hsize
+ \advance\cartouter by 18.4pt % allow for 3pt kerns on either
+ % side, and for 6pt waste from
+ % each corner char, and rule thickness
+ \normbskip=\baselineskip \normpskip=\parskip \normlskip=\lineskip
+ % Flag to tell @lisp, etc., not to narrow margin.
+ \let\nonarrowing = t%
+ \vbox\bgroup
+ \baselineskip=0pt\parskip=0pt\lineskip=0pt
+ \carttop
+ \hbox\bgroup
+ \hskip\lskip
+ \vrule\kern3pt
+ \vbox\bgroup
+ \kern3pt
+ \hsize=\cartinner
+ \baselineskip=\normbskip
+ \lineskip=\normlskip
+ \parskip=\normpskip
+ \vskip -\parskip
+ \comment % For explanation, see the end of \def\group.
+}
+\def\Ecartouche{%
+ \ifhmode\par\fi
+ \kern3pt
+ \egroup
+ \kern3pt\vrule
+ \hskip\rskip
+ \egroup
+ \cartbot
+ \egroup
+ \checkinserts
+}
+
+
+% This macro is called at the beginning of all the @example variants,
+% inside a group.
+\newdimen\nonfillparindent
+\def\nonfillstart{%
+ \aboveenvbreak
+ \hfuzz = 12pt % Don't be fussy
+ \sepspaces % Make spaces be word-separators rather than space tokens.
+ \let\par = \lisppar % don't ignore blank lines
+ \obeylines % each line of input is a line of output
+ \parskip = 0pt
+ % Turn off paragraph indentation but redefine \indent to emulate
+ % the normal \indent.
+ \nonfillparindent=\parindent
+ \parindent = 0pt
+ \let\indent\nonfillindent
+ %
+ \emergencystretch = 0pt % don't try to avoid overfull boxes
+ \ifx\nonarrowing\relax
+ \advance \leftskip by \lispnarrowing
+ \exdentamount=\lispnarrowing
+ \else
+ \let\nonarrowing = \relax
+ \fi
+ \let\exdent=\nofillexdent
+}
+
+\begingroup
+\obeyspaces
+% We want to swallow spaces (but not other tokens) after the fake
+% @indent in our nonfill-environments, where spaces are normally
+% active and set to @tie, resulting in them not being ignored after
+% @indent.
+\gdef\nonfillindent{\futurelet\temp\nonfillindentcheck}%
+\gdef\nonfillindentcheck{%
+\ifx\temp %
+\expandafter\nonfillindentgobble%
+\else%
+\leavevmode\nonfillindentbox%
+\fi%
+}%
+\endgroup
+\def\nonfillindentgobble#1{\nonfillindent}
+\def\nonfillindentbox{\hbox to \nonfillparindent{\hss}}
+
+% If you want all examples etc. small: @set dispenvsize small.
+% If you want even small examples the full size: @set dispenvsize nosmall.
+% This affects the following displayed environments:
+% @example, @display, @format, @lisp
+%
+\def\smallword{small}
+\def\nosmallword{nosmall}
+\let\SETdispenvsize\relax
+\def\setnormaldispenv{%
+ \ifx\SETdispenvsize\smallword
+ % end paragraph for sake of leading, in case document has no blank
+ % line. This is redundant with what happens in \aboveenvbreak, but
+ % we need to do it before changing the fonts, and it's inconvenient
+ % to change the fonts afterward.
+ \ifnum \lastpenalty=10000 \else \endgraf \fi
+ \smallexamplefonts \rm
+ \fi
+}
+\def\setsmalldispenv{%
+ \ifx\SETdispenvsize\nosmallword
+ \else
+ \ifnum \lastpenalty=10000 \else \endgraf \fi
+ \smallexamplefonts \rm
+ \fi
+}
+
+% We often define two environments, @foo and @smallfoo.
+% Let's do it by one command:
+\def\makedispenv #1#2{
+ \expandafter\envdef\csname#1\endcsname {\setnormaldispenv #2}
+ \expandafter\envdef\csname small#1\endcsname {\setsmalldispenv #2}
+ \expandafter\let\csname E#1\endcsname \afterenvbreak
+ \expandafter\let\csname Esmall#1\endcsname \afterenvbreak
+}
+
+% Define two synonyms:
+\def\maketwodispenvs #1#2#3{
+ \makedispenv{#1}{#3}
+ \makedispenv{#2}{#3}
+}
+
+% @lisp: indented, narrowed, typewriter font; @example: same as @lisp.
+%
+% @smallexample and @smalllisp: use smaller fonts.
+% Originally contributed by Pavel at xerox.
+%
+\maketwodispenvs {lisp}{example}{%
+ \nonfillstart
+ \tt\setupmarkupstyle{example}%
+ \let\kbdfont = \kbdexamplefont % Allow @kbd to do something special.
+ \gobble % eat return
+}
+% @display/@smalldisplay: same as @lisp except keep current font.
+%
+\makedispenv {display}{%
+ \nonfillstart
+ \gobble
+}
+
+% @format/@smallformat: same as @display except don't narrow margins.
+%
+\makedispenv{format}{%
+ \let\nonarrowing = t%
+ \nonfillstart
+ \gobble
+}
+
+% @flushleft: same as @format, but doesn't obey \SETdispenvsize.
+\envdef\flushleft{%
+ \let\nonarrowing = t%
+ \nonfillstart
+ \gobble
+}
+\let\Eflushleft = \afterenvbreak
+
+% @flushright.
+%
+\envdef\flushright{%
+ \let\nonarrowing = t%
+ \nonfillstart
+ \advance\leftskip by 0pt plus 1fill
+ \gobble
+}
+\let\Eflushright = \afterenvbreak
+
+
+% @raggedright does more-or-less normal line breaking but no right
+% justification. From plain.tex.
+\envdef\raggedright{%
+ \rightskip0pt plus2em \spaceskip.3333em \xspaceskip.5em\relax
+}
+\let\Eraggedright\par
+
+\envdef\raggedleft{%
+ \parindent=0pt \leftskip0pt plus2em
+ \spaceskip.3333em \xspaceskip.5em \parfillskip=0pt
+ \hbadness=10000 % Last line will usually be underfull, so turn off
+ % badness reporting.
+}
+\let\Eraggedleft\par
+
+\envdef\raggedcenter{%
+ \parindent=0pt \rightskip0pt plus1em \leftskip0pt plus1em
+ \spaceskip.3333em \xspaceskip.5em \parfillskip=0pt
+ \hbadness=10000 % Last line will usually be underfull, so turn off
+ % badness reporting.
+}
+\let\Eraggedcenter\par
+
+
+% @quotation does normal linebreaking (hence we can't use \nonfillstart)
+% and narrows the margins. We keep \parskip nonzero in general, since
+% we're doing normal filling. So, when using \aboveenvbreak and
+% \afterenvbreak, temporarily make \parskip 0.
+%
+\def\quotationstart{%
+ {\parskip=0pt \aboveenvbreak}% because \aboveenvbreak inserts \parskip
+ \parindent=0pt
+ %
+ % @cartouche defines \nonarrowing to inhibit narrowing at next level down.
+ \ifx\nonarrowing\relax
+ \advance\leftskip by \lispnarrowing
+ \advance\rightskip by \lispnarrowing
+ \exdentamount = \lispnarrowing
+ \else
+ \let\nonarrowing = \relax
+ \fi
+ \parsearg\quotationlabel
+}
+
+\envdef\quotation{%
+ \setnormaldispenv
+ \quotationstart
+}
+
+\envdef\smallquotation{%
+ \setsmalldispenv
+ \quotationstart
+}
+\let\Esmallquotation = \Equotation
+
+% We have retained a nonzero parskip for the environment, since we're
+% doing normal filling.
+%
+\def\Equotation{%
+ \par
+ \ifx\quotationauthor\undefined\else
+ % indent a bit.
+ \leftline{\kern 2\leftskip \sl ---\quotationauthor}%
+ \fi
+ {\parskip=0pt \afterenvbreak}%
+}
+
+% If we're given an argument, typeset it in bold with a colon after.
+\def\quotationlabel#1{%
+ \def\temp{#1}%
+ \ifx\temp\empty \else
+ {\bf #1: }%
+ \fi
+}
+
+
+% LaTeX-like @verbatim... at end verbatim and @verb{<char>...<char>}
+% If we want to allow any <char> as delimiter,
+% we need the curly braces so that makeinfo sees the @verb command, eg:
+% `@verbx...x' would look like the '@verbx' command. --janneke at gnu.org
+%
+% [Knuth]: Donald Ervin Knuth, 1996. The TeXbook.
+%
+% [Knuth] p.344; only we need to do the other characters Texinfo sets
+% active too. Otherwise, they get lost as the first character on a
+% verbatim line.
+\def\dospecials{%
+ \do\ \do\\\do\{\do\}\do\$\do\&%
+ \do\#\do\^\do\^^K\do\_\do\^^A\do\%\do\~%
+ \do\<\do\>\do\|\do\@\do+\do\"%
+ % Don't do the quotes -- if we do, @set txicodequoteundirected and
+ % @set txicodequotebacktick will not have effect on @verb and
+ % @verbatim, and ?` and !` ligatures won't get disabled.
+ %\do\`\do\'%
+}
+%
+% [Knuth] p. 380
+\def\uncatcodespecials{%
+ \def\do##1{\catcode`##1=\other}\dospecials}
+%
+% Setup for the @verb command.
+%
+% Eight spaces for a tab
+\begingroup
+ \catcode`\^^I=\active
+ \gdef\tabeightspaces{\catcode`\^^I=\active\def^^I{\ \ \ \ \ \ \ \ }}
+\endgroup
+%
+\def\setupverb{%
+ \tt % easiest (and conventionally used) font for verbatim
+ \def\par{\leavevmode\endgraf}%
+ \setupmarkupstyle{verb}%
+ \tabeightspaces
+ % Respect line breaks,
+ % print special symbols as themselves, and
+ % make each space count
+ % must do in this order:
+ \obeylines \uncatcodespecials \sepspaces
+}
+
+% Setup for the @verbatim environment
+%
+% Real tab expansion
+\newdimen\tabw \setbox0=\hbox{\tt\space} \tabw=8\wd0 % tab amount
+%
+\def\starttabbox{\setbox0=\hbox\bgroup}
+%
+\begingroup
+ \catcode`\^^I=\active
+ \gdef\tabexpand{%
+ \catcode`\^^I=\active
+ \def^^I{\leavevmode\egroup
+ \dimen0=\wd0 % the width so far, or since the previous tab
+ \divide\dimen0 by\tabw
+ \multiply\dimen0 by\tabw % compute previous multiple of \tabw
+ \advance\dimen0 by\tabw % advance to next multiple of \tabw
+ \wd0=\dimen0 \box0 \starttabbox
+ }%
+ }
+\endgroup
+
+% start the verbatim environment.
+\def\setupverbatim{%
+ \let\nonarrowing = t%
+ \nonfillstart
+ % Easiest (and conventionally used) font for verbatim
+ \tt
+ \def\par{\leavevmode\egroup\box0\endgraf}%
+ \tabexpand
+ \setupmarkupstyle{verbatim}%
+ % Respect line breaks,
+ % print special symbols as themselves, and
+ % make each space count
+ % must do in this order:
+ \obeylines \uncatcodespecials \sepspaces
+ \everypar{\starttabbox}%
+}
+
+% Do the @verb magic: verbatim text is quoted by unique
+% delimiter characters. Before first delimiter expect a
+% right brace, after last delimiter expect closing brace:
+%
+% \def\doverb'{'<char>#1<char>'}'{#1}
+%
+% [Knuth] p. 382; only eat outer {}
+\begingroup
+ \catcode`[=1\catcode`]=2\catcode`\{=\other\catcode`\}=\other
+ \gdef\doverb{#1[\def\next##1#1}[##1\endgroup]\next]
+\endgroup
+%
+\def\verb{\begingroup\setupverb\doverb}
+%
+%
+% Do the @verbatim magic: define the macro \doverbatim so that
+% the (first) argument ends when '@end verbatim' is reached, ie:
+%
+% \def\doverbatim#1 at end verbatim{#1}
+%
+% For Texinfo it's a lot easier than for LaTeX,
+% because texinfo's \verbatim doesn't stop at '\end{verbatim}':
+% we need not redefine '\', '{' and '}'.
+%
+% Inspired by LaTeX's verbatim command set [latex.ltx]
+%
+\begingroup
+ \catcode`\ =\active
+ \obeylines %
+ % ignore everything up to the first ^^M, that's the newline at the end
+ % of the @verbatim input line itself. Otherwise we get an extra blank
+ % line in the output.
+ \xdef\doverbatim#1^^M#2 at end verbatim{#2\noexpand\end\gobble verbatim}%
+ % We really want {...\end verbatim} in the body of the macro, but
+ % without the active space; thus we have to use \xdef and \gobble.
+\endgroup
+%
+\envdef\verbatim{%
+ \setupverbatim\doverbatim
+}
+\let\Everbatim = \afterenvbreak
+
+
+% @verbatiminclude FILE - insert text of file in verbatim environment.
+%
+\def\verbatiminclude{\parseargusing\filenamecatcodes\doverbatiminclude}
+%
+\def\doverbatiminclude#1{%
+ {%
+ \makevalueexpandable
+ \setupverbatim
+ \indexnofonts % Allow `@@' and other weird things in file names.
+ \input #1
+ \afterenvbreak
+ }%
+}
+
+% @copying ... @end copying.
+% Save the text away for @insertcopying later.
+%
+% We save the uninterpreted tokens, rather than creating a box.
+% Saving the text in a box would be much easier, but then all the
+% typesetting commands (@smallbook, font changes, etc.) have to be done
+% beforehand -- and a) we want @copying to be done first in the source
+% file; b) letting users define the frontmatter in as flexible order as
+% possible is very desirable.
+%
+\def\copying{\checkenv{}\begingroup\scanargctxt\docopying}
+\def\docopying#1 at end copying{\endgroup\def\copyingtext{#1}}
+%
+\def\insertcopying{%
+ \begingroup
+ \parindent = 0pt % paragraph indentation looks wrong on title page
+ \scanexp\copyingtext
+ \endgroup
+}
+
+
+\message{defuns,}
+% @defun etc.
+
+\newskip\defbodyindent \defbodyindent=.4in
+\newskip\defargsindent \defargsindent=50pt
+\newskip\deflastargmargin \deflastargmargin=18pt
+\newcount\defunpenalty
+
+% Start the processing of @deffn:
+\def\startdefun{%
+ \ifnum\lastpenalty<10000
+ \medbreak
+ \defunpenalty=10003 % Will keep this @deffn together with the
+ % following @def command, see below.
+ \else
+ % If there are two @def commands in a row, we'll have a \nobreak,
+ % which is there to keep the function description together with its
+ % header. But if there's nothing but headers, we need to allow a
+ % break somewhere. Check specifically for penalty 10002, inserted
+ % by \printdefunline, instead of 10000, since the sectioning
+ % commands also insert a nobreak penalty, and we don't want to allow
+ % a break between a section heading and a defun.
+ %
+ % As a minor refinement, we avoid "club" headers by signalling
+ % with penalty of 10003 after the very first @deffn in the
+ % sequence (see above), and penalty of 10002 after any following
+ % @def command.
+ \ifnum\lastpenalty=10002 \penalty2000 \else \defunpenalty=10002 \fi
+ %
+ % Similarly, after a section heading, do not allow a break.
+ % But do insert the glue.
+ \medskip % preceded by discardable penalty, so not a breakpoint
+ \fi
+ %
+ \parindent=0in
+ \advance\leftskip by \defbodyindent
+ \exdentamount=\defbodyindent
+}
+
+\def\dodefunx#1{%
+ % First, check whether we are in the right environment:
+ \checkenv#1%
+ %
+ % As above, allow line break if we have multiple x headers in a row.
+ % It's not a great place, though.
+ \ifnum\lastpenalty=10002 \penalty3000 \else \defunpenalty=10002 \fi
+ %
+ % And now, it's time to reuse the body of the original defun:
+ \expandafter\gobbledefun#1%
+}
+\def\gobbledefun#1\startdefun{}
+
+% \printdefunline \deffnheader{text}
+%
+\def\printdefunline#1#2{%
+ \begingroup
+ % call \deffnheader:
+ #1#2 \endheader
+ % common ending:
+ \interlinepenalty = 10000
+ \advance\rightskip by 0pt plus 1fil
+ \endgraf
+ \nobreak\vskip -\parskip
+ \penalty\defunpenalty % signal to \startdefun and \dodefunx
+ % Some of the @defun-type tags do not enable magic parentheses,
+ % rendering the following check redundant. But we don't optimize.
+ \checkparencounts
+ \endgroup
+}
+
+\def\Edefun{\endgraf\medbreak}
+
+% \makedefun{deffn} creates \deffn, \deffnx and \Edeffn;
+% the only thing remaining is to define \deffnheader.
+%
+\def\makedefun#1{%
+ \expandafter\let\csname E#1\endcsname = \Edefun
+ \edef\temp{\noexpand\domakedefun
+ \makecsname{#1}\makecsname{#1x}\makecsname{#1header}}%
+ \temp
+}
+
+% \domakedefun \deffn \deffnx \deffnheader
+%
+% Define \deffn and \deffnx, without parameters.
+% \deffnheader has to be defined explicitly.
+%
+\def\domakedefun#1#2#3{%
+ \envdef#1{%
+ \startdefun
+ \parseargusing\activeparens{\printdefunline#3}%
+ }%
+ \def#2{\dodefunx#1}%
+ \def#3%
+}
+
+%%% Untyped functions:
+
+% @deffn category name args
+\makedefun{deffn}{\deffngeneral{}}
+
+% @deffn category class name args
+\makedefun{defop}#1 {\defopon{#1\ \putwordon}}
+
+% \defopon {category on}class name args
+\def\defopon#1#2 {\deffngeneral{\putwordon\ \code{#2}}{#1\ \code{#2}} }
+
+% \deffngeneral {subind}category name args
+%
+\def\deffngeneral#1#2 #3 #4\endheader{%
+ % Remember that \dosubind{fn}{foo}{} is equivalent to \doind{fn}{foo}.
+ \dosubind{fn}{\code{#3}}{#1}%
+ \defname{#2}{}{#3}\magicamp\defunargs{#4\unskip}%
+}
+
+%%% Typed functions:
+
+% @deftypefn category type name args
+\makedefun{deftypefn}{\deftypefngeneral{}}
+
+% @deftypeop category class type name args
+\makedefun{deftypeop}#1 {\deftypeopon{#1\ \putwordon}}
+
+% \deftypeopon {category on}class type name args
+\def\deftypeopon#1#2 {\deftypefngeneral{\putwordon\ \code{#2}}{#1\ \code{#2}} }
+
+% \deftypefngeneral {subind}category type name args
+%
+\def\deftypefngeneral#1#2 #3 #4 #5\endheader{%
+ \dosubind{fn}{\code{#4}}{#1}%
+ \defname{#2}{#3}{#4}\defunargs{#5\unskip}%
+}
+
+%%% Typed variables:
+
+% @deftypevr category type var args
+\makedefun{deftypevr}{\deftypecvgeneral{}}
+
+% @deftypecv category class type var args
+\makedefun{deftypecv}#1 {\deftypecvof{#1\ \putwordof}}
+
+% \deftypecvof {category of}class type var args
+\def\deftypecvof#1#2 {\deftypecvgeneral{\putwordof\ \code{#2}}{#1\ \code{#2}} }
+
+% \deftypecvgeneral {subind}category type var args
+%
+\def\deftypecvgeneral#1#2 #3 #4 #5\endheader{%
+ \dosubind{vr}{\code{#4}}{#1}%
+ \defname{#2}{#3}{#4}\defunargs{#5\unskip}%
+}
+
+%%% Untyped variables:
+
+% @defvr category var args
+\makedefun{defvr}#1 {\deftypevrheader{#1} {} }
+
+% @defcv category class var args
+\makedefun{defcv}#1 {\defcvof{#1\ \putwordof}}
+
+% \defcvof {category of}class var args
+\def\defcvof#1#2 {\deftypecvof{#1}#2 {} }
+
+%%% Type:
+% @deftp category name args
+\makedefun{deftp}#1 #2 #3\endheader{%
+ \doind{tp}{\code{#2}}%
+ \defname{#1}{}{#2}\defunargs{#3\unskip}%
+}
+
+% Remaining @defun-like shortcuts:
+\makedefun{defun}{\deffnheader{\putwordDeffunc} }
+\makedefun{defmac}{\deffnheader{\putwordDefmac} }
+\makedefun{defspec}{\deffnheader{\putwordDefspec} }
+\makedefun{deftypefun}{\deftypefnheader{\putwordDeffunc} }
+\makedefun{defvar}{\defvrheader{\putwordDefvar} }
+\makedefun{defopt}{\defvrheader{\putwordDefopt} }
+\makedefun{deftypevar}{\deftypevrheader{\putwordDefvar} }
+\makedefun{defmethod}{\defopon\putwordMethodon}
+\makedefun{deftypemethod}{\deftypeopon\putwordMethodon}
+\makedefun{defivar}{\defcvof\putwordInstanceVariableof}
+\makedefun{deftypeivar}{\deftypecvof\putwordInstanceVariableof}
+
+% \defname, which formats the name of the @def (not the args).
+% #1 is the category, such as "Function".
+% #2 is the return type, if any.
+% #3 is the function name.
+%
+% We are followed by (but not passed) the arguments, if any.
+%
+\def\defname#1#2#3{%
+ % Get the values of \leftskip and \rightskip as they were outside the @def...
+ \advance\leftskip by -\defbodyindent
+ %
+ % How we'll format the type name. Putting it in brackets helps
+ % distinguish it from the body text that may end up on the next line
+ % just below it.
+ \def\temp{#1}%
+ \setbox0=\hbox{\kern\deflastargmargin \ifx\temp\empty\else [\rm\temp]\fi}
+ %
+ % Figure out line sizes for the paragraph shape.
+ % The first line needs space for \box0; but if \rightskip is nonzero,
+ % we need only space for the part of \box0 which exceeds it:
+ \dimen0=\hsize \advance\dimen0 by -\wd0 \advance\dimen0 by \rightskip
+ % The continuations:
+ \dimen2=\hsize \advance\dimen2 by -\defargsindent
+ % (plain.tex says that \dimen1 should be used only as global.)
+ \parshape 2 0in \dimen0 \defargsindent \dimen2
+ %
+ % Put the type name to the right margin.
+ \noindent
+ \hbox to 0pt{%
+ \hfil\box0 \kern-\hsize
+ % \hsize has to be shortened this way:
+ \kern\leftskip
+ % Intentionally do not respect \rightskip, since we need the space.
+ }%
+ %
+ % Allow all lines to be underfull without complaint:
+ \tolerance=10000 \hbadness=10000
+ \exdentamount=\defbodyindent
+ {%
+ % defun fonts. We use typewriter by default (used to be bold) because:
+ % . we're printing identifiers, they should be in tt in principle.
+ % . in languages with many accents, such as Czech or French, it's
+ % common to leave accents off identifiers. The result looks ok in
+ % tt, but exceedingly strange in rm.
+ % . we don't want -- and --- to be treated as ligatures.
+ % . this still does not fix the ?` and !` ligatures, but so far no
+ % one has made identifiers using them :).
+ \df \tt
+ \def\temp{#2}% return value type
+ \ifx\temp\empty\else \tclose{\temp} \fi
+ #3% output function name
+ }%
+ {\rm\enskip}% hskip 0.5 em of \tenrm
+ %
+ \boldbrax
+ % arguments will be output next, if any.
+}
+
+% Print arguments in slanted roman (not ttsl), inconsistently with using
+% tt for the name. This is because literal text is sometimes needed in
+% the argument list (groff manual), and ttsl and tt are not very
+% distinguishable. Prevent hyphenation at `-' chars.
+%
+\def\defunargs#1{%
+ % use sl by default (not ttsl),
+ % tt for the names.
+ \df \sl \hyphenchar\font=0
+ %
+ % On the other hand, if an argument has two dashes (for instance), we
+ % want a way to get ttsl. Let's try @var for that.
+ \def\var##1{{\setupmarkupstyle{var}\ttslanted{##1}}}%
+ #1%
+ \sl\hyphenchar\font=45
+}
+
+% We want ()&[] to print specially on the defun line.
+%
+\def\activeparens{%
+ \catcode`\(=\active \catcode`\)=\active
+ \catcode`\[=\active \catcode`\]=\active
+ \catcode`\&=\active
+}
+
+% Make control sequences which act like normal parenthesis chars.
+\let\lparen = ( \let\rparen = )
+
+% Be sure that we always have a definition for `(', etc. For example,
+% if the fn name has parens in it, \boldbrax will not be in effect yet,
+% so TeX would otherwise complain about undefined control sequence.
+{
+ \activeparens
+ \global\let(=\lparen \global\let)=\rparen
+ \global\let[=\lbrack \global\let]=\rbrack
+ \global\let& = \&
+
+ \gdef\boldbrax{\let(=\opnr\let)=\clnr\let[=\lbrb\let]=\rbrb}
+ \gdef\magicamp{\let&=\amprm}
+}
+
+\newcount\parencount
+
+% If we encounter &foo, then turn on ()-hacking afterwards
+\newif\ifampseen
+\def\amprm#1 {\ampseentrue{\bf\ }}
+
+\def\parenfont{%
+ \ifampseen
+ % At the first level, print parens in roman,
+ % otherwise use the default font.
+ \ifnum \parencount=1 \rm \fi
+ \else
+ % The \sf parens (in \boldbrax) actually are a little bolder than
+ % the contained text. This is especially needed for [ and ] .
+ \sf
+ \fi
+}
+\def\infirstlevel#1{%
+ \ifampseen
+ \ifnum\parencount=1
+ #1%
+ \fi
+ \fi
+}
+\def\bfafterword#1 {#1 \bf}
+
+\def\opnr{%
+ \global\advance\parencount by 1
+ {\parenfont(}%
+ \infirstlevel \bfafterword
+}
+\def\clnr{%
+ {\parenfont)}%
+ \infirstlevel \sl
+ \global\advance\parencount by -1
+}
+
+\newcount\brackcount
+\def\lbrb{%
+ \global\advance\brackcount by 1
+ {\bf[}%
+}
+\def\rbrb{%
+ {\bf]}%
+ \global\advance\brackcount by -1
+}
+
+\def\checkparencounts{%
+ \ifnum\parencount=0 \else \badparencount \fi
+ \ifnum\brackcount=0 \else \badbrackcount \fi
+}
+% these should not use \errmessage; the glibc manual, at least, actually
+% has such constructs (when documenting function pointers).
+\def\badparencount{%
+ \message{Warning: unbalanced parentheses in @def...}%
+ \global\parencount=0
+}
+\def\badbrackcount{%
+ \message{Warning: unbalanced square brackets in @def...}%
+ \global\brackcount=0
+}
+
+
+\message{macros,}
+% @macro.
+
+% To do this right we need a feature of e-TeX, \scantokens,
+% which we arrange to emulate with a temporary file in ordinary TeX.
+\ifx\eTeXversion\undefined
+ \newwrite\macscribble
+ \def\scantokens#1{%
+ \toks0={#1}%
+ \immediate\openout\macscribble=\jobname.tmp
+ \immediate\write\macscribble{\the\toks0}%
+ \immediate\closeout\macscribble
+ \input \jobname.tmp
+ }
+\fi
+
+\def\scanmacro#1{%
+ \begingroup
+ \newlinechar`\^^M
+ \let\xeatspaces\eatspaces
+ % Undo catcode changes of \startcontents and \doprintindex
+ % When called from @insertcopying or (short)caption, we need active
+ % backslash to get it printed correctly. Previously, we had
+ % \catcode`\\=\other instead. We'll see whether a problem appears
+ % with macro expansion. --kasal, 19aug04
+ \catcode`\@=0 \catcode`\\=\active \escapechar=`\@
+ % ... and \example
+ \spaceisspace
+ %
+ % Append \endinput to make sure that TeX does not see the ending newline.
+ % I've verified that it is necessary both for e-TeX and for ordinary TeX
+ % --kasal, 29nov03
+ \scantokens{#1\endinput}%
+ \endgroup
+}
+
+\def\scanexp#1{%
+ \edef\temp{\noexpand\scanmacro{#1}}%
+ \temp
+}
+
+\newcount\paramno % Count of parameters
+\newtoks\macname % Macro name
+\newif\ifrecursive % Is it recursive?
+
+% List of all defined macros in the form
+% \definedummyword\macro1\definedummyword\macro2...
+% Currently is also contains all @aliases; the list can be split
+% if there is a need.
+\def\macrolist{}
+
+% Add the macro to \macrolist
+\def\addtomacrolist#1{\expandafter \addtomacrolistxxx \csname#1\endcsname}
+\def\addtomacrolistxxx#1{%
+ \toks0 = \expandafter{\macrolist\definedummyword#1}%
+ \xdef\macrolist{\the\toks0}%
+}
+
+% Utility routines.
+% This does \let #1 = #2, with \csnames; that is,
+% \let \csname#1\endcsname = \csname#2\endcsname
+% (except of course we have to play expansion games).
+%
+\def\cslet#1#2{%
+ \expandafter\let
+ \csname#1\expandafter\endcsname
+ \csname#2\endcsname
+}
+
+% Trim leading and trailing spaces off a string.
+% Concepts from aro-bend problem 15 (see CTAN).
+{\catcode`\@=11
+\gdef\eatspaces #1{\expandafter\trim@\expandafter{#1 }}
+\gdef\trim@ #1{\trim@@ @#1 @ #1 @ @@}
+\gdef\trim@@ #1@ #2@ #3@@{\trim@@@\empty #2 @}
+\def\unbrace#1{#1}
+\unbrace{\gdef\trim@@@ #1 } #2@{#1}
+}
+
+% Trim a single trailing ^^M off a string.
+{\catcode`\^^M=\other \catcode`\Q=3%
+\gdef\eatcr #1{\eatcra #1Q^^MQ}%
+\gdef\eatcra#1^^MQ{\eatcrb#1Q}%
+\gdef\eatcrb#1Q#2Q{#1}%
+}
+
+% Macro bodies are absorbed as an argument in a context where
+% all characters are catcode 10, 11 or 12, except \ which is active
+% (as in normal texinfo). It is necessary to change the definition of \.
+
+% Non-ASCII encodings make 8-bit characters active, so un-activate
+% them to avoid their expansion. Must do this non-globally, to
+% confine the change to the current group.
+
+% It's necessary to have hard CRs when the macro is executed. This is
+% done by making ^^M (\endlinechar) catcode 12 when reading the macro
+% body, and then making it the \newlinechar in \scanmacro.
+
+\def\scanctxt{%
+ \catcode`\"=\other
+ \catcode`\+=\other
+ \catcode`\<=\other
+ \catcode`\>=\other
+ \catcode`\@=\other
+ \catcode`\^=\other
+ \catcode`\_=\other
+ \catcode`\|=\other
+ \catcode`\~=\other
+ \ifx\declaredencoding\ascii \else \setnonasciicharscatcodenonglobal\other \fi
+}
+
+\def\scanargctxt{%
+ \scanctxt
+ \catcode`\\=\other
+ \catcode`\^^M=\other
+}
+
+\def\macrobodyctxt{%
+ \scanctxt
+ \catcode`\{=\other
+ \catcode`\}=\other
+ \catcode`\^^M=\other
+ \usembodybackslash
+}
+
+\def\macroargctxt{%
+ \scanctxt
+ \catcode`\\=\other
+}
+
+% \mbodybackslash is the definition of \ in @macro bodies.
+% It maps \foo\ => \csname macarg.foo\endcsname => #N
+% where N is the macro parameter number.
+% We define \csname macarg.\endcsname to be \realbackslash, so
+% \\ in macro replacement text gets you a backslash.
+
+{\catcode`@=0 @catcode`@\=@active
+ @gdef at usembodybackslash{@let\=@mbodybackslash}
+ @gdef at mbodybackslash#1\{@csname macarg.#1 at endcsname}
+}
+\expandafter\def\csname macarg.\endcsname{\realbackslash}
+
+\def\macro{\recursivefalse\parsearg\macroxxx}
+\def\rmacro{\recursivetrue\parsearg\macroxxx}
+
+\def\macroxxx#1{%
+ \getargs{#1}% now \macname is the macname and \argl the arglist
+ \ifx\argl\empty % no arguments
+ \paramno=0%
+ \else
+ \expandafter\parsemargdef \argl;%
+ \fi
+ \if1\csname ismacro.\the\macname\endcsname
+ \message{Warning: redefining \the\macname}%
+ \else
+ \expandafter\ifx\csname \the\macname\endcsname \relax
+ \else \errmessage{Macro name \the\macname\space already defined}\fi
+ \global\cslet{macsave.\the\macname}{\the\macname}%
+ \global\expandafter\let\csname ismacro.\the\macname\endcsname=1%
+ \addtomacrolist{\the\macname}%
+ \fi
+ \begingroup \macrobodyctxt
+ \ifrecursive \expandafter\parsermacbody
+ \else \expandafter\parsemacbody
+ \fi}
+
+\parseargdef\unmacro{%
+ \if1\csname ismacro.#1\endcsname
+ \global\cslet{#1}{macsave.#1}%
+ \global\expandafter\let \csname ismacro.#1\endcsname=0%
+ % Remove the macro name from \macrolist:
+ \begingroup
+ \expandafter\let\csname#1\endcsname \relax
+ \let\definedummyword\unmacrodo
+ \xdef\macrolist{\macrolist}%
+ \endgroup
+ \else
+ \errmessage{Macro #1 not defined}%
+ \fi
+}
+
+% Called by \do from \dounmacro on each macro. The idea is to omit any
+% macro definitions that have been changed to \relax.
+%
+\def\unmacrodo#1{%
+ \ifx #1\relax
+ % remove this
+ \else
+ \noexpand\definedummyword \noexpand#1%
+ \fi
+}
+
+% This makes use of the obscure feature that if the last token of a
+% <parameter list> is #, then the preceding argument is delimited by
+% an opening brace, and that opening brace is not consumed.
+\def\getargs#1{\getargsxxx#1{}}
+\def\getargsxxx#1#{\getmacname #1 \relax\getmacargs}
+\def\getmacname #1 #2\relax{\macname={#1}}
+\def\getmacargs#1{\def\argl{#1}}
+
+% Parse the optional {params} list. Set up \paramno and \paramlist
+% so \defmacro knows what to do. Define \macarg.blah for each blah
+% in the params list, to be ##N where N is the position in that list.
+% That gets used by \mbodybackslash (above).
+
+% We need to get `macro parameter char #' into several definitions.
+% The technique used is stolen from LaTeX: let \hash be something
+% unexpandable, insert that wherever you need a #, and then redefine
+% it to # just before using the token list produced.
+%
+% The same technique is used to protect \eatspaces till just before
+% the macro is used.
+
+\def\parsemargdef#1;{\paramno=0\def\paramlist{}%
+ \let\hash\relax\let\xeatspaces\relax\parsemargdefxxx#1,;,}
+\def\parsemargdefxxx#1,{%
+ \if#1;\let\next=\relax
+ \else \let\next=\parsemargdefxxx
+ \advance\paramno by 1%
+ \expandafter\edef\csname macarg.\eatspaces{#1}\endcsname
+ {\xeatspaces{\hash\the\paramno}}%
+ \edef\paramlist{\paramlist\hash\the\paramno,}%
+ \fi\next}
+
+% These two commands read recursive and nonrecursive macro bodies.
+% (They're different since rec and nonrec macros end differently.)
+
+\long\def\parsemacbody#1 at end macro%
+{\xdef\temp{\eatcr{#1}}\endgroup\defmacro}%
+\long\def\parsermacbody#1 at end rmacro%
+{\xdef\temp{\eatcr{#1}}\endgroup\defmacro}%
+
+% This defines the macro itself. There are six cases: recursive and
+% nonrecursive macros of zero, one, and many arguments.
+% Much magic with \expandafter here.
+% \xdef is used so that macro definitions will survive the file
+% they're defined in; @include reads the file inside a group.
+\def\defmacro{%
+ \let\hash=##% convert placeholders to macro parameter chars
+ \ifrecursive
+ \ifcase\paramno
+ % 0
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \noexpand\scanmacro{\temp}}%
+ \or % 1
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \bgroup\noexpand\macroargctxt
+ \noexpand\braceorline
+ \expandafter\noexpand\csname\the\macname xxx\endcsname}%
+ \expandafter\xdef\csname\the\macname xxx\endcsname##1{%
+ \egroup\noexpand\scanmacro{\temp}}%
+ \else % many
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \bgroup\noexpand\macroargctxt
+ \noexpand\csname\the\macname xx\endcsname}%
+ \expandafter\xdef\csname\the\macname xx\endcsname##1{%
+ \expandafter\noexpand\csname\the\macname xxx\endcsname ##1,}%
+ \expandafter\expandafter
+ \expandafter\xdef
+ \expandafter\expandafter
+ \csname\the\macname xxx\endcsname
+ \paramlist{\egroup\noexpand\scanmacro{\temp}}%
+ \fi
+ \else
+ \ifcase\paramno
+ % 0
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \noexpand\norecurse{\the\macname}%
+ \noexpand\scanmacro{\temp}\egroup}%
+ \or % 1
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \bgroup\noexpand\macroargctxt
+ \noexpand\braceorline
+ \expandafter\noexpand\csname\the\macname xxx\endcsname}%
+ \expandafter\xdef\csname\the\macname xxx\endcsname##1{%
+ \egroup
+ \noexpand\norecurse{\the\macname}%
+ \noexpand\scanmacro{\temp}\egroup}%
+ \else % many
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \bgroup\noexpand\macroargctxt
+ \expandafter\noexpand\csname\the\macname xx\endcsname}%
+ \expandafter\xdef\csname\the\macname xx\endcsname##1{%
+ \expandafter\noexpand\csname\the\macname xxx\endcsname ##1,}%
+ \expandafter\expandafter
+ \expandafter\xdef
+ \expandafter\expandafter
+ \csname\the\macname xxx\endcsname
+ \paramlist{%
+ \egroup
+ \noexpand\norecurse{\the\macname}%
+ \noexpand\scanmacro{\temp}\egroup}%
+ \fi
+ \fi}
+
+\def\norecurse#1{\bgroup\cslet{#1}{macsave.#1}}
+
+% \braceorline decides whether the next nonwhitespace character is a
+% {. If so it reads up to the closing }, if not, it reads the whole
+% line. Whatever was read is then fed to the next control sequence
+% as an argument (by \parsebrace or \parsearg)
+\def\braceorline#1{\let\macnamexxx=#1\futurelet\nchar\braceorlinexxx}
+\def\braceorlinexxx{%
+ \ifx\nchar\bgroup\else
+ \expandafter\parsearg
+ \fi \macnamexxx}
+
+
+% @alias.
+% We need some trickery to remove the optional spaces around the equal
+% sign. Just make them active and then expand them all to nothing.
+\def\alias{\parseargusing\obeyspaces\aliasxxx}
+\def\aliasxxx #1{\aliasyyy#1\relax}
+\def\aliasyyy #1=#2\relax{%
+ {%
+ \expandafter\let\obeyedspace=\empty
+ \addtomacrolist{#1}%
+ \xdef\next{\global\let\makecsname{#1}=\makecsname{#2}}%
+ }%
+ \next
+}
+
+
+\message{cross references,}
+
+\newwrite\auxfile
+\newif\ifhavexrefs % True if xref values are known.
+\newif\ifwarnedxrefs % True if we warned once that they aren't known.
+
+% @inforef is relatively simple.
+\def\inforef #1{\inforefzzz #1,,,,**}
+\def\inforefzzz #1,#2,#3,#4**{\putwordSee{} \putwordInfo{} \putwordfile{} \file{\ignorespaces #3{}},
+ node \samp{\ignorespaces#1{}}}
+
+% @node's only job in TeX is to define \lastnode, which is used in
+% cross-references. The @node line might or might not have commas, and
+% might or might not have spaces before the first comma, like:
+% @node foo , bar , ...
+% We don't want such trailing spaces in the node name.
+%
+\parseargdef\node{\checkenv{}\donode #1 ,\finishnodeparse}
+%
+% also remove a trailing comma, in case of something like this:
+% @node Help-Cross, , , Cross-refs
+\def\donode#1 ,#2\finishnodeparse{\dodonode #1,\finishnodeparse}
+\def\dodonode#1,#2\finishnodeparse{\gdef\lastnode{#1}}
+
+\let\nwnode=\node
+\let\lastnode=\empty
+
+% Write a cross-reference definition for the current node. #1 is the
+% type (Ynumbered, Yappendix, Ynothing).
+%
+\def\donoderef#1{%
+ \ifx\lastnode\empty\else
+ \setref{\lastnode}{#1}%
+ \global\let\lastnode=\empty
+ \fi
+}
+
+% @anchor{NAME} -- define xref target at arbitrary point.
+%
+\newcount\savesfregister
+%
+\def\savesf{\relax \ifhmode \savesfregister=\spacefactor \fi}
+\def\restoresf{\relax \ifhmode \spacefactor=\savesfregister \fi}
+\def\anchor#1{\savesf \setref{#1}{Ynothing}\restoresf \ignorespaces}
+
+% \setref{NAME}{SNT} defines a cross-reference point NAME (a node or an
+% anchor), which consists of three parts:
+% 1) NAME-title - the current sectioning name taken from \lastsection,
+% or the anchor name.
+% 2) NAME-snt - section number and type, passed as the SNT arg, or
+% empty for anchors.
+% 3) NAME-pg - the page number.
+%
+% This is called from \donoderef, \anchor, and \dofloat. In the case of
+% floats, there is an additional part, which is not written here:
+% 4) NAME-lof - the text as it should appear in a @listoffloats.
+%
+\def\setref#1#2{%
+ \pdfmkdest{#1}%
+ \iflinks
+ {%
+ \atdummies % preserve commands, but don't expand them
+ \edef\writexrdef##1##2{%
+ \write\auxfile{@xrdef{#1-% #1 of \setref, expanded by the \edef
+ ##1}{##2}}% these are parameters of \writexrdef
+ }%
+ \toks0 = \expandafter{\lastsection}%
+ \immediate \writexrdef{title}{\the\toks0 }%
+ \immediate \writexrdef{snt}{\csname #2\endcsname}% \Ynumbered etc.
+ \safewhatsit{\writexrdef{pg}{\folio}}% will be written later, during \shipout
+ }%
+ \fi
+}
+
+% @xref, @pxref, and @ref generate cross-references. For \xrefX, #1 is
+% the node name, #2 the name of the Info cross-reference, #3 the printed
+% node name, #4 the name of the Info file, #5 the name of the printed
+% manual. All but the node name can be omitted.
+%
+\def\pxref#1{\putwordsee{} \xrefX[#1,,,,,,,]}
+\def\xref#1{\putwordSee{} \xrefX[#1,,,,,,,]}
+\def\ref#1{\xrefX[#1,,,,,,,]}
+\def\xrefX[#1,#2,#3,#4,#5,#6]{\begingroup
+ \unsepspaces
+ \def\printedmanual{\ignorespaces #5}%
+ \def\printedrefname{\ignorespaces #3}%
+ \setbox1=\hbox{\printedmanual\unskip}%
+ \setbox0=\hbox{\printedrefname\unskip}%
+ \ifdim \wd0 = 0pt
+ % No printed node name was explicitly given.
+ \expandafter\ifx\csname SETxref-automatic-section-title\endcsname\relax
+ % Use the node name inside the square brackets.
+ \def\printedrefname{\ignorespaces #1}%
+ \else
+ % Use the actual chapter/section title appear inside
+ % the square brackets. Use the real section title if we have it.
+ \ifdim \wd1 > 0pt
+ % It is in another manual, so we don't have it.
+ \def\printedrefname{\ignorespaces #1}%
+ \else
+ \ifhavexrefs
+ % We know the real title if we have the xref values.
+ \def\printedrefname{\refx{#1-title}{}}%
+ \else
+ % Otherwise just copy the Info node name.
+ \def\printedrefname{\ignorespaces #1}%
+ \fi%
+ \fi
+ \fi
+ \fi
+ %
+ % Make link in pdf output.
+ \ifpdf
+ {\indexnofonts
+ \turnoffactive
+ % This expands tokens, so do it after making catcode changes, so _
+ % etc. don't get their TeX definitions.
+ \getfilename{#4}%
+ %
+ % See comments at \activebackslashdouble.
+ {\activebackslashdouble \xdef\pdfxrefdest{#1}%
+ \backslashparens\pdfxrefdest}%
+ %
+ \leavevmode
+ \startlink attr{/Border [0 0 0]}%
+ \ifnum\filenamelength>0
+ goto file{\the\filename.pdf} name{\pdfxrefdest}%
+ \else
+ goto name{\pdfmkpgn{\pdfxrefdest}}%
+ \fi
+ }%
+ \setcolor{\linkcolor}%
+ \fi
+ %
+ % Float references are printed completely differently: "Figure 1.2"
+ % instead of "[somenode], p.3". We distinguish them by the
+ % LABEL-title being set to a magic string.
+ {%
+ % Have to otherify everything special to allow the \csname to
+ % include an _ in the xref name, etc.
+ \indexnofonts
+ \turnoffactive
+ \expandafter\global\expandafter\let\expandafter\Xthisreftitle
+ \csname XR#1-title\endcsname
+ }%
+ \iffloat\Xthisreftitle
+ % If the user specified the print name (third arg) to the ref,
+ % print it instead of our usual "Figure 1.2".
+ \ifdim\wd0 = 0pt
+ \refx{#1-snt}{}%
+ \else
+ \printedrefname
+ \fi
+ %
+ % if the user also gave the printed manual name (fifth arg), append
+ % "in MANUALNAME".
+ \ifdim \wd1 > 0pt
+ \space \putwordin{} \cite{\printedmanual}%
+ \fi
+ \else
+ % node/anchor (non-float) references.
+ %
+ % If we use \unhbox0 and \unhbox1 to print the node names, TeX does not
+ % insert empty discretionaries after hyphens, which means that it will
+ % not find a line break at a hyphen in a node names. Since some manuals
+ % are best written with fairly long node names, containing hyphens, this
+ % is a loss. Therefore, we give the text of the node name again, so it
+ % is as if TeX is seeing it for the first time.
+ \ifdim \wd1 > 0pt
+ \putwordSection{} ``\printedrefname'' \putwordin{} \cite{\printedmanual}%
+ \else
+ % _ (for example) has to be the character _ for the purposes of the
+ % control sequence corresponding to the node, but it has to expand
+ % into the usual \leavevmode...\vrule stuff for purposes of
+ % printing. So we \turnoffactive for the \refx-snt, back on for the
+ % printing, back off for the \refx-pg.
+ {\turnoffactive
+ % Only output a following space if the -snt ref is nonempty; for
+ % @unnumbered and @anchor, it won't be.
+ \setbox2 = \hbox{\ignorespaces \refx{#1-snt}{}}%
+ \ifdim \wd2 > 0pt \refx{#1-snt}\space\fi
+ }%
+ % output the `[mynode]' via a macro so it can be overridden.
+ \xrefprintnodename\printedrefname
+ %
+ % But we always want a comma and a space:
+ ,\space
+ %
+ % output the `page 3'.
+ \turnoffactive \putwordpage\tie\refx{#1-pg}{}%
+ \fi
+ \fi
+ \endlink
+\endgroup}
+
+% This macro is called from \xrefX for the `[nodename]' part of xref
+% output. It's a separate macro only so it can be changed more easily,
+% since square brackets don't work well in some documents. Particularly
+% one that Bob is working on :).
+%
+\def\xrefprintnodename#1{[#1]}
+
+% Things referred to by \setref.
+%
+\def\Ynothing{}
+\def\Yomitfromtoc{}
+\def\Ynumbered{%
+ \ifnum\secno=0
+ \putwordChapter at tie \the\chapno
+ \else \ifnum\subsecno=0
+ \putwordSection at tie \the\chapno.\the\secno
+ \else \ifnum\subsubsecno=0
+ \putwordSection at tie \the\chapno.\the\secno.\the\subsecno
+ \else
+ \putwordSection at tie \the\chapno.\the\secno.\the\subsecno.\the\subsubsecno
+ \fi\fi\fi
+}
+\def\Yappendix{%
+ \ifnum\secno=0
+ \putwordAppendix at tie @char\the\appendixno{}%
+ \else \ifnum\subsecno=0
+ \putwordSection at tie @char\the\appendixno.\the\secno
+ \else \ifnum\subsubsecno=0
+ \putwordSection at tie @char\the\appendixno.\the\secno.\the\subsecno
+ \else
+ \putwordSection at tie
+ @char\the\appendixno.\the\secno.\the\subsecno.\the\subsubsecno
+ \fi\fi\fi
+}
+
+% Define \refx{NAME}{SUFFIX} to reference a cross-reference string named NAME.
+% If its value is nonempty, SUFFIX is output afterward.
+%
+\def\refx#1#2{%
+ {%
+ \indexnofonts
+ \otherbackslash
+ \expandafter\global\expandafter\let\expandafter\thisrefX
+ \csname XR#1\endcsname
+ }%
+ \ifx\thisrefX\relax
+ % If not defined, say something at least.
+ \angleleft un\-de\-fined\angleright
+ \iflinks
+ \ifhavexrefs
+ \message{\linenumber Undefined cross reference `#1'.}%
+ \else
+ \ifwarnedxrefs\else
+ \global\warnedxrefstrue
+ \message{Cross reference values unknown; you must run TeX again.}%
+ \fi
+ \fi
+ \fi
+ \else
+ % It's defined, so just use it.
+ \thisrefX
+ \fi
+ #2% Output the suffix in any case.
+}
+
+% This is the macro invoked by entries in the aux file. Usually it's
+% just a \def (we prepend XR to the control sequence name to avoid
+% collisions). But if this is a float type, we have more work to do.
+%
+\def\xrdef#1#2{%
+ {% The node name might contain 8-bit characters, which in our current
+ % implementation are changed to commands like @'e. Don't let these
+ % mess up the control sequence name.
+ \indexnofonts
+ \turnoffactive
+ \xdef\safexrefname{#1}%
+ }%
+ %
+ \expandafter\gdef\csname XR\safexrefname\endcsname{#2}% remember this xref
+ %
+ % Was that xref control sequence that we just defined for a float?
+ \expandafter\iffloat\csname XR\safexrefname\endcsname
+ % it was a float, and we have the (safe) float type in \iffloattype.
+ \expandafter\let\expandafter\floatlist
+ \csname floatlist\iffloattype\endcsname
+ %
+ % Is this the first time we've seen this float type?
+ \expandafter\ifx\floatlist\relax
+ \toks0 = {\do}% yes, so just \do
+ \else
+ % had it before, so preserve previous elements in list.
+ \toks0 = \expandafter{\floatlist\do}%
+ \fi
+ %
+ % Remember this xref in the control sequence \floatlistFLOATTYPE,
+ % for later use in \listoffloats.
+ \expandafter\xdef\csname floatlist\iffloattype\endcsname{\the\toks0
+ {\safexrefname}}%
+ \fi
+}
+
+% Read the last existing aux file, if any. No error if none exists.
+%
+\def\tryauxfile{%
+ \openin 1 \jobname.aux
+ \ifeof 1 \else
+ \readdatafile{aux}%
+ \global\havexrefstrue
+ \fi
+ \closein 1
+}
+
+\def\setupdatafile{%
+ \catcode`\^^@=\other
+ \catcode`\^^A=\other
+ \catcode`\^^B=\other
+ \catcode`\^^C=\other
+ \catcode`\^^D=\other
+ \catcode`\^^E=\other
+ \catcode`\^^F=\other
+ \catcode`\^^G=\other
+ \catcode`\^^H=\other
+ \catcode`\^^K=\other
+ \catcode`\^^L=\other
+ \catcode`\^^N=\other
+ \catcode`\^^P=\other
+ \catcode`\^^Q=\other
+ \catcode`\^^R=\other
+ \catcode`\^^S=\other
+ \catcode`\^^T=\other
+ \catcode`\^^U=\other
+ \catcode`\^^V=\other
+ \catcode`\^^W=\other
+ \catcode`\^^X=\other
+ \catcode`\^^Z=\other
+ \catcode`\^^[=\other
+ \catcode`\^^\=\other
+ \catcode`\^^]=\other
+ \catcode`\^^^=\other
+ \catcode`\^^_=\other
+ % It was suggested to set the catcode of ^ to 7, which would allow ^^e4 etc.
+ % in xref tags, i.e., node names. But since ^^e4 notation isn't
+ % supported in the main text, it doesn't seem desirable. Furthermore,
+ % that is not enough: for node names that actually contain a ^
+ % character, we would end up writing a line like this: 'xrdef {'hat
+ % b-title}{'hat b} and \xrdef does a \csname...\endcsname on the first
+ % argument, and \hat is not an expandable control sequence. It could
+ % all be worked out, but why? Either we support ^^ or we don't.
+ %
+ % The other change necessary for this was to define \auxhat:
+ % \def\auxhat{\def^{'hat }}% extra space so ok if followed by letter
+ % and then to call \auxhat in \setq.
+ %
+ \catcode`\^=\other
+ %
+ % Special characters. Should be turned off anyway, but...
+ \catcode`\~=\other
+ \catcode`\[=\other
+ \catcode`\]=\other
+ \catcode`\"=\other
+ \catcode`\_=\other
+ \catcode`\|=\other
+ \catcode`\<=\other
+ \catcode`\>=\other
+ \catcode`\$=\other
+ \catcode`\#=\other
+ \catcode`\&=\other
+ \catcode`\%=\other
+ \catcode`+=\other % avoid \+ for paranoia even though we've turned it off
+ %
+ % This is to support \ in node names and titles, since the \
+ % characters end up in a \csname. It's easier than
+ % leaving it active and making its active definition an actual \
+ % character. What I don't understand is why it works in the *value*
+ % of the xrdef. Seems like it should be a catcode12 \, and that
+ % should not typeset properly. But it works, so I'm moving on for
+ % now. --karl, 15jan04.
+ \catcode`\\=\other
+ %
+ % Make the characters 128-255 be printing characters.
+ {%
+ \count1=128
+ \def\loop{%
+ \catcode\count1=\other
+ \advance\count1 by 1
+ \ifnum \count1<256 \loop \fi
+ }%
+ }%
+ %
+ % @ is our escape character in .aux files, and we need braces.
+ \catcode`\{=1
+ \catcode`\}=2
+ \catcode`\@=0
+}
+
+\def\readdatafile#1{%
+\begingroup
+ \setupdatafile
+ \input\jobname.#1
+\endgroup}
+
+
+\message{insertions,}
+% including footnotes.
+
+\newcount \footnoteno
+
+% The trailing space in the following definition for supereject is
+% vital for proper filling; pages come out unaligned when you do a
+% pagealignmacro call if that space before the closing brace is
+% removed. (Generally, numeric constants should always be followed by a
+% space to prevent strange expansion errors.)
+\def\supereject{\par\penalty -20000\footnoteno =0 }
+
+% @footnotestyle is meaningful for info output only.
+\let\footnotestyle=\comment
+
+{\catcode `\@=11
+%
+% Auto-number footnotes. Otherwise like plain.
+\gdef\footnote{%
+ \let\indent=\ptexindent
+ \let\noindent=\ptexnoindent
+ \global\advance\footnoteno by \@ne
+ \edef\thisfootno{$^{\the\footnoteno}$}%
+ %
+ % In case the footnote comes at the end of a sentence, preserve the
+ % extra spacing after we do the footnote number.
+ \let\@sf\empty
+ \ifhmode\edef\@sf{\spacefactor\the\spacefactor}\ptexslash\fi
+ %
+ % Remove inadvertent blank space before typesetting the footnote number.
+ \unskip
+ \thisfootno\@sf
+ \dofootnote
+}%
+
+% Don't bother with the trickery in plain.tex to not require the
+% footnote text as a parameter. Our footnotes don't need to be so general.
+%
+% Oh yes, they do; otherwise, @ifset (and anything else that uses
+% \parseargline) fails inside footnotes because the tokens are fixed when
+% the footnote is read. --karl, 16nov96.
+%
+\gdef\dofootnote{%
+ \insert\footins\bgroup
+ % We want to typeset this text as a normal paragraph, even if the
+ % footnote reference occurs in (for example) a display environment.
+ % So reset some parameters.
+ \hsize=\pagewidth
+ \interlinepenalty\interfootnotelinepenalty
+ \splittopskip\ht\strutbox % top baseline for broken footnotes
+ \splitmaxdepth\dp\strutbox
+ \floatingpenalty\@MM
+ \leftskip\z at skip
+ \rightskip\z at skip
+ \spaceskip\z at skip
+ \xspaceskip\z at skip
+ \parindent\defaultparindent
+ %
+ \smallfonts \rm
+ %
+ % Because we use hanging indentation in footnotes, a @noindent appears
+ % to exdent this text, so make it be a no-op. makeinfo does not use
+ % hanging indentation so @noindent can still be needed within footnote
+ % text after an @example or the like (not that this is good style).
+ \let\noindent = \relax
+ %
+ % Hang the footnote text off the number. Use \everypar in case the
+ % footnote extends for more than one paragraph.
+ \everypar = {\hang}%
+ \textindent{\thisfootno}%
+ %
+ % Don't crash into the line above the footnote text. Since this
+ % expands into a box, it must come within the paragraph, lest it
+ % provide a place where TeX can split the footnote.
+ \footstrut
+ \futurelet\next\fo at t
+}
+}%end \catcode `\@=11
+
+% In case a @footnote appears in a vbox, save the footnote text and create
+% the real \insert just after the vbox finished. Otherwise, the insertion
+% would be lost.
+% Similarly, if a @footnote appears inside an alignment, save the footnote
+% text to a box and make the \insert when a row of the table is finished.
+% And the same can be done for other insert classes. --kasal, 16nov03.
+
+% Replace the \insert primitive by a cheating macro.
+% Deeper inside, just make sure that the saved insertions are not spilled
+% out prematurely.
+%
+\def\startsavinginserts{%
+ \ifx \insert\ptexinsert
+ \let\insert\saveinsert
+ \else
+ \let\checkinserts\relax
+ \fi
+}
+
+% This \insert replacement works for both \insert\footins{foo} and
+% \insert\footins\bgroup foo\egroup, but it doesn't work for \insert27{foo}.
+%
+\def\saveinsert#1{%
+ \edef\next{\noexpand\savetobox \makeSAVEname#1}%
+ \afterassignment\next
+ % swallow the left brace
+ \let\temp =
+}
+\def\makeSAVEname#1{\makecsname{SAVE\expandafter\gobble\string#1}}
+\def\savetobox#1{\global\setbox#1 = \vbox\bgroup \unvbox#1}
+
+\def\checksaveins#1{\ifvoid#1\else \placesaveins#1\fi}
+
+\def\placesaveins#1{%
+ \ptexinsert \csname\expandafter\gobblesave\string#1\endcsname
+ {\box#1}%
+}
+
+% eat @SAVE -- beware, all of them have catcode \other:
+{
+ \def\dospecials{\do S\do A\do V\do E} \uncatcodespecials % ;-)
+ \gdef\gobblesave @SAVE{}
+}
+
+% initialization:
+\def\newsaveins #1{%
+ \edef\next{\noexpand\newsaveinsX \makeSAVEname#1}%
+ \next
+}
+\def\newsaveinsX #1{%
+ \csname newbox\endcsname #1%
+ \expandafter\def\expandafter\checkinserts\expandafter{\checkinserts
+ \checksaveins #1}%
+}
+
+% initialize:
+\let\checkinserts\empty
+\newsaveins\footins
+\newsaveins\margin
+
+
+% @image. We use the macros from epsf.tex to support this.
+% If epsf.tex is not installed and @image is used, we complain.
+%
+% Check for and read epsf.tex up front. If we read it only at @image
+% time, we might be inside a group, and then its definitions would get
+% undone and the next image would fail.
+\openin 1 = epsf.tex
+\ifeof 1 \else
+ % Do not bother showing banner with epsf.tex v2.7k (available in
+ % doc/epsf.tex and on ctan).
+ \def\epsfannounce{\toks0 = }%
+ \input epsf.tex
+\fi
+\closein 1
+%
+% We will only complain once about lack of epsf.tex.
+\newif\ifwarnednoepsf
+\newhelp\noepsfhelp{epsf.tex must be installed for images to
+ work. It is also included in the Texinfo distribution, or you can get
+ it from ftp://tug.org/tex/epsf.tex.}
+%
+\def\image#1{%
+ \ifx\epsfbox\undefined
+ \ifwarnednoepsf \else
+ \errhelp = \noepsfhelp
+ \errmessage{epsf.tex not found, images will be ignored}%
+ \global\warnednoepsftrue
+ \fi
+ \else
+ \imagexxx #1,,,,,\finish
+ \fi
+}
+%
+% Arguments to @image:
+% #1 is (mandatory) image filename; we tack on .eps extension.
+% #2 is (optional) width, #3 is (optional) height.
+% #4 is (ignored optional) html alt text.
+% #5 is (ignored optional) extension.
+% #6 is just the usual extra ignored arg for parsing this stuff.
+\newif\ifimagevmode
+\def\imagexxx#1,#2,#3,#4,#5,#6\finish{\begingroup
+ \catcode`\^^M = 5 % in case we're inside an example
+ \normalturnoffactive % allow _ et al. in names
+ % If the image is by itself, center it.
+ \ifvmode
+ \imagevmodetrue
+ \nobreak\medskip
+ % Usually we'll have text after the image which will insert
+ % \parskip glue, so insert it here too to equalize the space
+ % above and below.
+ \nobreak\vskip\parskip
+ \nobreak
+ \fi
+ %
+ % Leave vertical mode so that indentation from an enclosing
+ % environment such as @quotation is respected. On the other hand, if
+ % it's at the top level, we don't want the normal paragraph indentation.
+ \noindent
+ %
+ % Output the image.
+ \ifpdf
+ \dopdfimage{#1}{#2}{#3}%
+ \else
+ % \epsfbox itself resets \epsf?size at each figure.
+ \setbox0 = \hbox{\ignorespaces #2}\ifdim\wd0 > 0pt \epsfxsize=#2\relax \fi
+ \setbox0 = \hbox{\ignorespaces #3}\ifdim\wd0 > 0pt \epsfysize=#3\relax \fi
+ \epsfbox{#1.eps}%
+ \fi
+ %
+ \ifimagevmode \medskip \fi % space after the standalone image
+\endgroup}
+
+
+% @float FLOATTYPE,LABEL,LOC ... @end float for displayed figures, tables,
+% etc. We don't actually implement floating yet, we always include the
+% float "here". But it seemed the best name for the future.
+%
+\envparseargdef\float{\eatcommaspace\eatcommaspace\dofloat#1, , ,\finish}
+
+% There may be a space before second and/or third parameter; delete it.
+\def\eatcommaspace#1, {#1,}
+
+% #1 is the optional FLOATTYPE, the text label for this float, typically
+% "Figure", "Table", "Example", etc. Can't contain commas. If omitted,
+% this float will not be numbered and cannot be referred to.
+%
+% #2 is the optional xref label. Also must be present for the float to
+% be referable.
+%
+% #3 is the optional positioning argument; for now, it is ignored. It
+% will somehow specify the positions allowed to float to (here, top, bottom).
+%
+% We keep a separate counter for each FLOATTYPE, which we reset at each
+% chapter-level command.
+\let\resetallfloatnos=\empty
+%
+\def\dofloat#1,#2,#3,#4\finish{%
+ \let\thiscaption=\empty
+ \let\thisshortcaption=\empty
+ %
+ % don't lose footnotes inside @float.
+ %
+ % BEWARE: when the floats start float, we have to issue warning whenever an
+ % insert appears inside a float which could possibly float. --kasal, 26may04
+ %
+ \startsavinginserts
+ %
+ % We can't be used inside a paragraph.
+ \par
+ %
+ \vtop\bgroup
+ \def\floattype{#1}%
+ \def\floatlabel{#2}%
+ \def\floatloc{#3}% we do nothing with this yet.
+ %
+ \ifx\floattype\empty
+ \let\safefloattype=\empty
+ \else
+ {%
+ % the floattype might have accents or other special characters,
+ % but we need to use it in a control sequence name.
+ \indexnofonts
+ \turnoffactive
+ \xdef\safefloattype{\floattype}%
+ }%
+ \fi
+ %
+ % If label is given but no type, we handle that as the empty type.
+ \ifx\floatlabel\empty \else
+ % We want each FLOATTYPE to be numbered separately (Figure 1,
+ % Table 1, Figure 2, ...). (And if no label, no number.)
+ %
+ \expandafter\getfloatno\csname\safefloattype floatno\endcsname
+ \global\advance\floatno by 1
+ %
+ {%
+ % This magic value for \lastsection is output by \setref as the
+ % XREFLABEL-title value. \xrefX uses it to distinguish float
+ % labels (which have a completely different output format) from
+ % node and anchor labels. And \xrdef uses it to construct the
+ % lists of floats.
+ %
+ \edef\lastsection{\floatmagic=\safefloattype}%
+ \setref{\floatlabel}{Yfloat}%
+ }%
+ \fi
+ %
+ % start with \parskip glue, I guess.
+ \vskip\parskip
+ %
+ % Don't suppress indentation if a float happens to start a section.
+ \restorefirstparagraphindent
+}
+
+% we have these possibilities:
+% @float Foo,lbl & @caption{Cap}: Foo 1.1: Cap
+% @float Foo,lbl & no caption: Foo 1.1
+% @float Foo & @caption{Cap}: Foo: Cap
+% @float Foo & no caption: Foo
+% @float ,lbl & Caption{Cap}: 1.1: Cap
+% @float ,lbl & no caption: 1.1
+% @float & @caption{Cap}: Cap
+% @float & no caption:
+%
+\def\Efloat{%
+ \let\floatident = \empty
+ %
+ % In all cases, if we have a float type, it comes first.
+ \ifx\floattype\empty \else \def\floatident{\floattype}\fi
+ %
+ % If we have an xref label, the number comes next.
+ \ifx\floatlabel\empty \else
+ \ifx\floattype\empty \else % if also had float type, need tie first.
+ \appendtomacro\floatident{\tie}%
+ \fi
+ % the number.
+ \appendtomacro\floatident{\chaplevelprefix\the\floatno}%
+ \fi
+ %
+ % Start the printed caption with what we've constructed in
+ % \floatident, but keep it separate; we need \floatident again.
+ \let\captionline = \floatident
+ %
+ \ifx\thiscaption\empty \else
+ \ifx\floatident\empty \else
+ \appendtomacro\captionline{: }% had ident, so need a colon between
+ \fi
+ %
+ % caption text.
+ \appendtomacro\captionline{\scanexp\thiscaption}%
+ \fi
+ %
+ % If we have anything to print, print it, with space before.
+ % Eventually this needs to become an \insert.
+ \ifx\captionline\empty \else
+ \vskip.5\parskip
+ \captionline
+ %
+ % Space below caption.
+ \vskip\parskip
+ \fi
+ %
+ % If have an xref label, write the list of floats info. Do this
+ % after the caption, to avoid chance of it being a breakpoint.
+ \ifx\floatlabel\empty \else
+ % Write the text that goes in the lof to the aux file as
+ % \floatlabel-lof. Besides \floatident, we include the short
+ % caption if specified, else the full caption if specified, else nothing.
+ {%
+ \atdummies
+ %
+ % since we read the caption text in the macro world, where ^^M
+ % is turned into a normal character, we have to scan it back, so
+ % we don't write the literal three characters "^^M" into the aux file.
+ \scanexp{%
+ \xdef\noexpand\gtemp{%
+ \ifx\thisshortcaption\empty
+ \thiscaption
+ \else
+ \thisshortcaption
+ \fi
+ }%
+ }%
+ \immediate\write\auxfile{@xrdef{\floatlabel-lof}{\floatident
+ \ifx\gtemp\empty \else : \gtemp \fi}}%
+ }%
+ \fi
+ \egroup % end of \vtop
+ %
+ % place the captured inserts
+ %
+ % BEWARE: when the floats start floating, we have to issue warning
+ % whenever an insert appears inside a float which could possibly
+ % float. --kasal, 26may04
+ %
+ \checkinserts
+}
+
+% Append the tokens #2 to the definition of macro #1, not expanding either.
+%
+\def\appendtomacro#1#2{%
+ \expandafter\def\expandafter#1\expandafter{#1#2}%
+}
+
+% @caption, @shortcaption
+%
+\def\caption{\docaption\thiscaption}
+\def\shortcaption{\docaption\thisshortcaption}
+\def\docaption{\checkenv\float \bgroup\scanargctxt\defcaption}
+\def\defcaption#1#2{\egroup \def#1{#2}}
+
+% The parameter is the control sequence identifying the counter we are
+% going to use. Create it if it doesn't exist and assign it to \floatno.
+\def\getfloatno#1{%
+ \ifx#1\relax
+ % Haven't seen this figure type before.
+ \csname newcount\endcsname #1%
+ %
+ % Remember to reset this floatno at the next chap.
+ \expandafter\gdef\expandafter\resetallfloatnos
+ \expandafter{\resetallfloatnos #1=0 }%
+ \fi
+ \let\floatno#1%
+}
+
+% \setref calls this to get the XREFLABEL-snt value. We want an @xref
+% to the FLOATLABEL to expand to "Figure 3.1". We call \setref when we
+% first read the @float command.
+%
+\def\Yfloat{\floattype at tie \chaplevelprefix\the\floatno}%
+
+% Magic string used for the XREFLABEL-title value, so \xrefX can
+% distinguish floats from other xref types.
+\def\floatmagic{!!float!!}
+
+% #1 is the control sequence we are passed; we expand into a conditional
+% which is true if #1 represents a float ref. That is, the magic
+% \lastsection value which we \setref above.
+%
+\def\iffloat#1{\expandafter\doiffloat#1==\finish}
+%
+% #1 is (maybe) the \floatmagic string. If so, #2 will be the
+% (safe) float type for this float. We set \iffloattype to #2.
+%
+\def\doiffloat#1=#2=#3\finish{%
+ \def\temp{#1}%
+ \def\iffloattype{#2}%
+ \ifx\temp\floatmagic
+}
+
+% @listoffloats FLOATTYPE - print a list of floats like a table of contents.
+%
+\parseargdef\listoffloats{%
+ \def\floattype{#1}% floattype
+ {%
+ % the floattype might have accents or other special characters,
+ % but we need to use it in a control sequence name.
+ \indexnofonts
+ \turnoffactive
+ \xdef\safefloattype{\floattype}%
+ }%
+ %
+ % \xrdef saves the floats as a \do-list in \floatlistSAFEFLOATTYPE.
+ \expandafter\ifx\csname floatlist\safefloattype\endcsname \relax
+ \ifhavexrefs
+ % if the user said @listoffloats foo but never @float foo.
+ \message{\linenumber No `\safefloattype' floats to list.}%
+ \fi
+ \else
+ \begingroup
+ \leftskip=\tocindent % indent these entries like a toc
+ \let\do=\listoffloatsdo
+ \csname floatlist\safefloattype\endcsname
+ \endgroup
+ \fi
+}
+
+% This is called on each entry in a list of floats. We're passed the
+% xref label, in the form LABEL-title, which is how we save it in the
+% aux file. We strip off the -title and look up \XRLABEL-lof, which
+% has the text we're supposed to typeset here.
+%
+% Figures without xref labels will not be included in the list (since
+% they won't appear in the aux file).
+%
+\def\listoffloatsdo#1{\listoffloatsdoentry#1\finish}
+\def\listoffloatsdoentry#1-title\finish{{%
+ % Can't fully expand XR#1-lof because it can contain anything. Just
+ % pass the control sequence. On the other hand, XR#1-pg is just the
+ % page number, and we want to fully expand that so we can get a link
+ % in pdf output.
+ \toksA = \expandafter{\csname XR#1-lof\endcsname}%
+ %
+ % use the same \entry macro we use to generate the TOC and index.
+ \edef\writeentry{\noexpand\entry{\the\toksA}{\csname XR#1-pg\endcsname}}%
+ \writeentry
+}}
+
+
+\message{localization,}
+
+% For single-language documents, @documentlanguage is usually given very
+% early, just after @documentencoding. Single argument is the language
+% (de) or locale (de_DE) abbreviation.
+%
+{
+ \catcode`\_ = \active
+ \globaldefs=1
+\parseargdef\documentlanguage{\begingroup
+ \let_=\normalunderscore % normal _ character for filenames
+ \tex % read txi-??.tex file in plain TeX.
+ % Read the file by the name they passed if it exists.
+ \openin 1 txi-#1.tex
+ \ifeof 1
+ \documentlanguagetrywithoutunderscore{#1_\finish}%
+ \else
+ \globaldefs = 1 % everything in the txi-LL files needs to persist
+ \input txi-#1.tex
+ \fi
+ \closein 1
+ \endgroup % end raw TeX
+\endgroup}
+%
+% If they passed de_DE, and txi-de_DE.tex doesn't exist,
+% try txi-de.tex.
+%
+\gdef\documentlanguagetrywithoutunderscore#1_#2\finish{%
+ \openin 1 txi-#1.tex
+ \ifeof 1
+ \errhelp = \nolanghelp
+ \errmessage{Cannot read language file txi-#1.tex}%
+ \else
+ \globaldefs = 1 % everything in the txi-LL files needs to persist
+ \input txi-#1.tex
+ \fi
+ \closein 1
+}
+}% end of special _ catcode
+%
+\newhelp\nolanghelp{The given language definition file cannot be found or
+is empty. Maybe you need to install it? Putting it in the current
+directory should work if nowhere else does.}
+
+% This macro is called from txi-??.tex files; the first argument is the
+% \language name to set (without the "\lang@" prefix), the second and
+% third args are \{left,right}hyphenmin.
+%
+% The language names to pass are determined when the format is built.
+% See the etex.log file created at that time, e.g.,
+% /usr/local/texlive/2008/texmf-var/web2c/pdftex/etex.log.
+%
+% With TeX Live 2008, etex now includes hyphenation patterns for all
+% available languages. This means we can support hyphenation in
+% Texinfo, at least to some extent. (This still doesn't solve the
+% accented characters problem.)
+%
+\catcode`@=11
+\def\txisetlanguage#1#2#3{%
+ % do not set the language if the name is undefined in the current TeX.
+ \expandafter\ifx\csname lang@#1\endcsname \relax
+ \message{no patterns for #1}%
+ \else
+ \global\language = \csname lang@#1\endcsname
+ \fi
+ % but there is no harm in adjusting the hyphenmin values regardless.
+ \global\lefthyphenmin = #2\relax
+ \global\righthyphenmin = #3\relax
+}
+
+% Helpers for encodings.
+% Set the catcode of characters 128 through 255 to the specified number.
+%
+\def\setnonasciicharscatcode#1{%
+ \count255=128
+ \loop\ifnum\count255<256
+ \global\catcode\count255=#1\relax
+ \advance\count255 by 1
+ \repeat
+}
+
+\def\setnonasciicharscatcodenonglobal#1{%
+ \count255=128
+ \loop\ifnum\count255<256
+ \catcode\count255=#1\relax
+ \advance\count255 by 1
+ \repeat
+}
+
+% @documentencoding sets the definition of non-ASCII characters
+% according to the specified encoding.
+%
+\parseargdef\documentencoding{%
+ % Encoding being declared for the document.
+ \def\declaredencoding{\csname #1.enc\endcsname}%
+ %
+ % Supported encodings: names converted to tokens in order to be able
+ % to compare them with \ifx.
+ \def\ascii{\csname US-ASCII.enc\endcsname}%
+ \def\latnine{\csname ISO-8859-15.enc\endcsname}%
+ \def\latone{\csname ISO-8859-1.enc\endcsname}%
+ \def\lattwo{\csname ISO-8859-2.enc\endcsname}%
+ \def\utfeight{\csname UTF-8.enc\endcsname}%
+ %
+ \ifx \declaredencoding \ascii
+ \asciichardefs
+ %
+ \else \ifx \declaredencoding \lattwo
+ \setnonasciicharscatcode\active
+ \lattwochardefs
+ %
+ \else \ifx \declaredencoding \latone
+ \setnonasciicharscatcode\active
+ \latonechardefs
+ %
+ \else \ifx \declaredencoding \latnine
+ \setnonasciicharscatcode\active
+ \latninechardefs
+ %
+ \else \ifx \declaredencoding \utfeight
+ \setnonasciicharscatcode\active
+ \utfeightchardefs
+ %
+ \else
+ \message{Unknown document encoding #1, ignoring.}%
+ %
+ \fi % utfeight
+ \fi % latnine
+ \fi % latone
+ \fi % lattwo
+ \fi % ascii
+}
+
+% A message to be logged when using a character that isn't available
+% the default font encoding (OT1).
+%
+\def\missingcharmsg#1{\message{Character missing in OT1 encoding: #1.}}
+
+% Take account of \c (plain) vs. \, (Texinfo) difference.
+\def\cedilla#1{\ifx\c\ptexc\c{#1}\else\,{#1}\fi}
+
+% First, make active non-ASCII characters in order for them to be
+% correctly categorized when TeX reads the replacement text of
+% macros containing the character definitions.
+\setnonasciicharscatcode\active
+%
+% Latin1 (ISO-8859-1) character definitions.
+\def\latonechardefs{%
+ \gdef^^a0{~}
+ \gdef^^a1{\exclamdown}
+ \gdef^^a2{\missingcharmsg{CENT SIGN}}
+ \gdef^^a3{{\pounds}}
+ \gdef^^a4{\missingcharmsg{CURRENCY SIGN}}
+ \gdef^^a5{\missingcharmsg{YEN SIGN}}
+ \gdef^^a6{\missingcharmsg{BROKEN BAR}}
+ \gdef^^a7{\S}
+ \gdef^^a8{\"{}}
+ \gdef^^a9{\copyright}
+ \gdef^^aa{\ordf}
+ \gdef^^ab{\guillemetleft}
+ \gdef^^ac{$\lnot$}
+ \gdef^^ad{\-}
+ \gdef^^ae{\registeredsymbol}
+ \gdef^^af{\={}}
+ %
+ \gdef^^b0{\textdegree}
+ \gdef^^b1{$\pm$}
+ \gdef^^b2{$^2$}
+ \gdef^^b3{$^3$}
+ \gdef^^b4{\'{}}
+ \gdef^^b5{$\mu$}
+ \gdef^^b6{\P}
+ %
+ \gdef^^b7{$^.$}
+ \gdef^^b8{\cedilla\ }
+ \gdef^^b9{$^1$}
+ \gdef^^ba{\ordm}
+ %
+ \gdef^^bb{\guilletright}
+ \gdef^^bc{$1\over4$}
+ \gdef^^bd{$1\over2$}
+ \gdef^^be{$3\over4$}
+ \gdef^^bf{\questiondown}
+ %
+ \gdef^^c0{\`A}
+ \gdef^^c1{\'A}
+ \gdef^^c2{\^A}
+ \gdef^^c3{\~A}
+ \gdef^^c4{\"A}
+ \gdef^^c5{\ringaccent A}
+ \gdef^^c6{\AE}
+ \gdef^^c7{\cedilla C}
+ \gdef^^c8{\`E}
+ \gdef^^c9{\'E}
+ \gdef^^ca{\^E}
+ \gdef^^cb{\"E}
+ \gdef^^cc{\`I}
+ \gdef^^cd{\'I}
+ \gdef^^ce{\^I}
+ \gdef^^cf{\"I}
+ %
+ \gdef^^d0{\DH}
+ \gdef^^d1{\~N}
+ \gdef^^d2{\`O}
+ \gdef^^d3{\'O}
+ \gdef^^d4{\^O}
+ \gdef^^d5{\~O}
+ \gdef^^d6{\"O}
+ \gdef^^d7{$\times$}
+ \gdef^^d8{\O}
+ \gdef^^d9{\`U}
+ \gdef^^da{\'U}
+ \gdef^^db{\^U}
+ \gdef^^dc{\"U}
+ \gdef^^dd{\'Y}
+ \gdef^^de{\TH}
+ \gdef^^df{\ss}
+ %
+ \gdef^^e0{\`a}
+ \gdef^^e1{\'a}
+ \gdef^^e2{\^a}
+ \gdef^^e3{\~a}
+ \gdef^^e4{\"a}
+ \gdef^^e5{\ringaccent a}
+ \gdef^^e6{\ae}
+ \gdef^^e7{\cedilla c}
+ \gdef^^e8{\`e}
+ \gdef^^e9{\'e}
+ \gdef^^ea{\^e}
+ \gdef^^eb{\"e}
+ \gdef^^ec{\`{\dotless i}}
+ \gdef^^ed{\'{\dotless i}}
+ \gdef^^ee{\^{\dotless i}}
+ \gdef^^ef{\"{\dotless i}}
+ %
+ \gdef^^f0{\dh}
+ \gdef^^f1{\~n}
+ \gdef^^f2{\`o}
+ \gdef^^f3{\'o}
+ \gdef^^f4{\^o}
+ \gdef^^f5{\~o}
+ \gdef^^f6{\"o}
+ \gdef^^f7{$\div$}
+ \gdef^^f8{\o}
+ \gdef^^f9{\`u}
+ \gdef^^fa{\'u}
+ \gdef^^fb{\^u}
+ \gdef^^fc{\"u}
+ \gdef^^fd{\'y}
+ \gdef^^fe{\th}
+ \gdef^^ff{\"y}
+}
+
+% Latin9 (ISO-8859-15) encoding character definitions.
+\def\latninechardefs{%
+ % Encoding is almost identical to Latin1.
+ \latonechardefs
+ %
+ \gdef^^a4{\euro}
+ \gdef^^a6{\v S}
+ \gdef^^a8{\v s}
+ \gdef^^b4{\v Z}
+ \gdef^^b8{\v z}
+ \gdef^^bc{\OE}
+ \gdef^^bd{\oe}
+ \gdef^^be{\"Y}
+}
+
+% Latin2 (ISO-8859-2) character definitions.
+\def\lattwochardefs{%
+ \gdef^^a0{~}
+ \gdef^^a1{\ogonek{A}}
+ \gdef^^a2{\u{}}
+ \gdef^^a3{\L}
+ \gdef^^a4{\missingcharmsg{CURRENCY SIGN}}
+ \gdef^^a5{\v L}
+ \gdef^^a6{\'S}
+ \gdef^^a7{\S}
+ \gdef^^a8{\"{}}
+ \gdef^^a9{\v S}
+ \gdef^^aa{\cedilla S}
+ \gdef^^ab{\v T}
+ \gdef^^ac{\'Z}
+ \gdef^^ad{\-}
+ \gdef^^ae{\v Z}
+ \gdef^^af{\dotaccent Z}
+ %
+ \gdef^^b0{\textdegree}
+ \gdef^^b1{\ogonek{a}}
+ \gdef^^b2{\ogonek{ }}
+ \gdef^^b3{\l}
+ \gdef^^b4{\'{}}
+ \gdef^^b5{\v l}
+ \gdef^^b6{\'s}
+ \gdef^^b7{\v{}}
+ \gdef^^b8{\cedilla\ }
+ \gdef^^b9{\v s}
+ \gdef^^ba{\cedilla s}
+ \gdef^^bb{\v t}
+ \gdef^^bc{\'z}
+ \gdef^^bd{\H{}}
+ \gdef^^be{\v z}
+ \gdef^^bf{\dotaccent z}
+ %
+ \gdef^^c0{\'R}
+ \gdef^^c1{\'A}
+ \gdef^^c2{\^A}
+ \gdef^^c3{\u A}
+ \gdef^^c4{\"A}
+ \gdef^^c5{\'L}
+ \gdef^^c6{\'C}
+ \gdef^^c7{\cedilla C}
+ \gdef^^c8{\v C}
+ \gdef^^c9{\'E}
+ \gdef^^ca{\ogonek{E}}
+ \gdef^^cb{\"E}
+ \gdef^^cc{\v E}
+ \gdef^^cd{\'I}
+ \gdef^^ce{\^I}
+ \gdef^^cf{\v D}
+ %
+ \gdef^^d0{\DH}
+ \gdef^^d1{\'N}
+ \gdef^^d2{\v N}
+ \gdef^^d3{\'O}
+ \gdef^^d4{\^O}
+ \gdef^^d5{\H O}
+ \gdef^^d6{\"O}
+ \gdef^^d7{$\times$}
+ \gdef^^d8{\v R}
+ \gdef^^d9{\ringaccent U}
+ \gdef^^da{\'U}
+ \gdef^^db{\H U}
+ \gdef^^dc{\"U}
+ \gdef^^dd{\'Y}
+ \gdef^^de{\cedilla T}
+ \gdef^^df{\ss}
+ %
+ \gdef^^e0{\'r}
+ \gdef^^e1{\'a}
+ \gdef^^e2{\^a}
+ \gdef^^e3{\u a}
+ \gdef^^e4{\"a}
+ \gdef^^e5{\'l}
+ \gdef^^e6{\'c}
+ \gdef^^e7{\cedilla c}
+ \gdef^^e8{\v c}
+ \gdef^^e9{\'e}
+ \gdef^^ea{\ogonek{e}}
+ \gdef^^eb{\"e}
+ \gdef^^ec{\v e}
+ \gdef^^ed{\'\i}
+ \gdef^^ee{\^\i}
+ \gdef^^ef{\v d}
+ %
+ \gdef^^f0{\dh}
+ \gdef^^f1{\'n}
+ \gdef^^f2{\v n}
+ \gdef^^f3{\'o}
+ \gdef^^f4{\^o}
+ \gdef^^f5{\H o}
+ \gdef^^f6{\"o}
+ \gdef^^f7{$\div$}
+ \gdef^^f8{\v r}
+ \gdef^^f9{\ringaccent u}
+ \gdef^^fa{\'u}
+ \gdef^^fb{\H u}
+ \gdef^^fc{\"u}
+ \gdef^^fd{\'y}
+ \gdef^^fe{\cedilla t}
+ \gdef^^ff{\dotaccent{}}
+}
+
+% UTF-8 character definitions.
+%
+% This code to support UTF-8 is based on LaTeX's utf8.def, with some
+% changes for Texinfo conventions. It is included here under the GPL by
+% permission from Frank Mittelbach and the LaTeX team.
+%
+\newcount\countUTFx
+\newcount\countUTFy
+\newcount\countUTFz
+
+\gdef\UTFviiiTwoOctets#1#2{\expandafter
+ \UTFviiiDefined\csname u8:#1\string #2\endcsname}
+%
+\gdef\UTFviiiThreeOctets#1#2#3{\expandafter
+ \UTFviiiDefined\csname u8:#1\string #2\string #3\endcsname}
+%
+\gdef\UTFviiiFourOctets#1#2#3#4{\expandafter
+ \UTFviiiDefined\csname u8:#1\string #2\string #3\string #4\endcsname}
+
+\gdef\UTFviiiDefined#1{%
+ \ifx #1\relax
+ \message{\linenumber Unicode char \string #1 not defined for Texinfo}%
+ \else
+ \expandafter #1%
+ \fi
+}
+
+\begingroup
+ \catcode`\~13
+ \catcode`\"12
+
+ \def\UTFviiiLoop{%
+ \global\catcode\countUTFx\active
+ \uccode`\~\countUTFx
+ \uppercase\expandafter{\UTFviiiTmp}%
+ \advance\countUTFx by 1
+ \ifnum\countUTFx < \countUTFy
+ \expandafter\UTFviiiLoop
+ \fi}
+
+ \countUTFx = "C2
+ \countUTFy = "E0
+ \def\UTFviiiTmp{%
+ \xdef~{\noexpand\UTFviiiTwoOctets\string~}}
+ \UTFviiiLoop
+
+ \countUTFx = "E0
+ \countUTFy = "F0
+ \def\UTFviiiTmp{%
+ \xdef~{\noexpand\UTFviiiThreeOctets\string~}}
+ \UTFviiiLoop
+
+ \countUTFx = "F0
+ \countUTFy = "F4
+ \def\UTFviiiTmp{%
+ \xdef~{\noexpand\UTFviiiFourOctets\string~}}
+ \UTFviiiLoop
+\endgroup
+
+\begingroup
+ \catcode`\"=12
+ \catcode`\<=12
+ \catcode`\.=12
+ \catcode`\,=12
+ \catcode`\;=12
+ \catcode`\!=12
+ \catcode`\~=13
+
+ \gdef\DeclareUnicodeCharacter#1#2{%
+ \countUTFz = "#1\relax
+ \wlog{\space\space defining Unicode char U+#1 (decimal \the\countUTFz)}%
+ \begingroup
+ \parseXMLCharref
+ \def\UTFviiiTwoOctets##1##2{%
+ \csname u8:##1\string ##2\endcsname}%
+ \def\UTFviiiThreeOctets##1##2##3{%
+ \csname u8:##1\string ##2\string ##3\endcsname}%
+ \def\UTFviiiFourOctets##1##2##3##4{%
+ \csname u8:##1\string ##2\string ##3\string ##4\endcsname}%
+ \expandafter\expandafter\expandafter\expandafter
+ \expandafter\expandafter\expandafter
+ \gdef\UTFviiiTmp{#2}%
+ \endgroup}
+
+ \gdef\parseXMLCharref{%
+ \ifnum\countUTFz < "A0\relax
+ \errhelp = \EMsimple
+ \errmessage{Cannot define Unicode char value < 00A0}%
+ \else\ifnum\countUTFz < "800\relax
+ \parseUTFviiiA,%
+ \parseUTFviiiB C\UTFviiiTwoOctets.,%
+ \else\ifnum\countUTFz < "10000\relax
+ \parseUTFviiiA;%
+ \parseUTFviiiA,%
+ \parseUTFviiiB E\UTFviiiThreeOctets.{,;}%
+ \else
+ \parseUTFviiiA;%
+ \parseUTFviiiA,%
+ \parseUTFviiiA!%
+ \parseUTFviiiB F\UTFviiiFourOctets.{!,;}%
+ \fi\fi\fi
+ }
+
+ \gdef\parseUTFviiiA#1{%
+ \countUTFx = \countUTFz
+ \divide\countUTFz by 64
+ \countUTFy = \countUTFz
+ \multiply\countUTFz by 64
+ \advance\countUTFx by -\countUTFz
+ \advance\countUTFx by 128
+ \uccode `#1\countUTFx
+ \countUTFz = \countUTFy}
+
+ \gdef\parseUTFviiiB#1#2#3#4{%
+ \advance\countUTFz by "#10\relax
+ \uccode `#3\countUTFz
+ \uppercase{\gdef\UTFviiiTmp{#2#3#4}}}
+\endgroup
+
+\def\utfeightchardefs{%
+ \DeclareUnicodeCharacter{00A0}{\tie}
+ \DeclareUnicodeCharacter{00A1}{\exclamdown}
+ \DeclareUnicodeCharacter{00A3}{\pounds}
+ \DeclareUnicodeCharacter{00A8}{\"{ }}
+ \DeclareUnicodeCharacter{00A9}{\copyright}
+ \DeclareUnicodeCharacter{00AA}{\ordf}
+ \DeclareUnicodeCharacter{00AB}{\guillemetleft}
+ \DeclareUnicodeCharacter{00AD}{\-}
+ \DeclareUnicodeCharacter{00AE}{\registeredsymbol}
+ \DeclareUnicodeCharacter{00AF}{\={ }}
+
+ \DeclareUnicodeCharacter{00B0}{\ringaccent{ }}
+ \DeclareUnicodeCharacter{00B4}{\'{ }}
+ \DeclareUnicodeCharacter{00B8}{\cedilla{ }}
+ \DeclareUnicodeCharacter{00BA}{\ordm}
+ \DeclareUnicodeCharacter{00BB}{\guillemetright}
+ \DeclareUnicodeCharacter{00BF}{\questiondown}
+
+ \DeclareUnicodeCharacter{00C0}{\`A}
+ \DeclareUnicodeCharacter{00C1}{\'A}
+ \DeclareUnicodeCharacter{00C2}{\^A}
+ \DeclareUnicodeCharacter{00C3}{\~A}
+ \DeclareUnicodeCharacter{00C4}{\"A}
+ \DeclareUnicodeCharacter{00C5}{\AA}
+ \DeclareUnicodeCharacter{00C6}{\AE}
+ \DeclareUnicodeCharacter{00C7}{\cedilla{C}}
+ \DeclareUnicodeCharacter{00C8}{\`E}
+ \DeclareUnicodeCharacter{00C9}{\'E}
+ \DeclareUnicodeCharacter{00CA}{\^E}
+ \DeclareUnicodeCharacter{00CB}{\"E}
+ \DeclareUnicodeCharacter{00CC}{\`I}
+ \DeclareUnicodeCharacter{00CD}{\'I}
+ \DeclareUnicodeCharacter{00CE}{\^I}
+ \DeclareUnicodeCharacter{00CF}{\"I}
+
+ \DeclareUnicodeCharacter{00D0}{\DH}
+ \DeclareUnicodeCharacter{00D1}{\~N}
+ \DeclareUnicodeCharacter{00D2}{\`O}
+ \DeclareUnicodeCharacter{00D3}{\'O}
+ \DeclareUnicodeCharacter{00D4}{\^O}
+ \DeclareUnicodeCharacter{00D5}{\~O}
+ \DeclareUnicodeCharacter{00D6}{\"O}
+ \DeclareUnicodeCharacter{00D8}{\O}
+ \DeclareUnicodeCharacter{00D9}{\`U}
+ \DeclareUnicodeCharacter{00DA}{\'U}
+ \DeclareUnicodeCharacter{00DB}{\^U}
+ \DeclareUnicodeCharacter{00DC}{\"U}
+ \DeclareUnicodeCharacter{00DD}{\'Y}
+ \DeclareUnicodeCharacter{00DE}{\TH}
+ \DeclareUnicodeCharacter{00DF}{\ss}
+
+ \DeclareUnicodeCharacter{00E0}{\`a}
+ \DeclareUnicodeCharacter{00E1}{\'a}
+ \DeclareUnicodeCharacter{00E2}{\^a}
+ \DeclareUnicodeCharacter{00E3}{\~a}
+ \DeclareUnicodeCharacter{00E4}{\"a}
+ \DeclareUnicodeCharacter{00E5}{\aa}
+ \DeclareUnicodeCharacter{00E6}{\ae}
+ \DeclareUnicodeCharacter{00E7}{\cedilla{c}}
+ \DeclareUnicodeCharacter{00E8}{\`e}
+ \DeclareUnicodeCharacter{00E9}{\'e}
+ \DeclareUnicodeCharacter{00EA}{\^e}
+ \DeclareUnicodeCharacter{00EB}{\"e}
+ \DeclareUnicodeCharacter{00EC}{\`{\dotless{i}}}
+ \DeclareUnicodeCharacter{00ED}{\'{\dotless{i}}}
+ \DeclareUnicodeCharacter{00EE}{\^{\dotless{i}}}
+ \DeclareUnicodeCharacter{00EF}{\"{\dotless{i}}}
+
+ \DeclareUnicodeCharacter{00F0}{\dh}
+ \DeclareUnicodeCharacter{00F1}{\~n}
+ \DeclareUnicodeCharacter{00F2}{\`o}
+ \DeclareUnicodeCharacter{00F3}{\'o}
+ \DeclareUnicodeCharacter{00F4}{\^o}
+ \DeclareUnicodeCharacter{00F5}{\~o}
+ \DeclareUnicodeCharacter{00F6}{\"o}
+ \DeclareUnicodeCharacter{00F8}{\o}
+ \DeclareUnicodeCharacter{00F9}{\`u}
+ \DeclareUnicodeCharacter{00FA}{\'u}
+ \DeclareUnicodeCharacter{00FB}{\^u}
+ \DeclareUnicodeCharacter{00FC}{\"u}
+ \DeclareUnicodeCharacter{00FD}{\'y}
+ \DeclareUnicodeCharacter{00FE}{\th}
+ \DeclareUnicodeCharacter{00FF}{\"y}
+
+ \DeclareUnicodeCharacter{0100}{\=A}
+ \DeclareUnicodeCharacter{0101}{\=a}
+ \DeclareUnicodeCharacter{0102}{\u{A}}
+ \DeclareUnicodeCharacter{0103}{\u{a}}
+ \DeclareUnicodeCharacter{0104}{\ogonek{A}}
+ \DeclareUnicodeCharacter{0105}{\ogonek{a}}
+ \DeclareUnicodeCharacter{0106}{\'C}
+ \DeclareUnicodeCharacter{0107}{\'c}
+ \DeclareUnicodeCharacter{0108}{\^C}
+ \DeclareUnicodeCharacter{0109}{\^c}
+ \DeclareUnicodeCharacter{0118}{\ogonek{E}}
+ \DeclareUnicodeCharacter{0119}{\ogonek{e}}
+ \DeclareUnicodeCharacter{010A}{\dotaccent{C}}
+ \DeclareUnicodeCharacter{010B}{\dotaccent{c}}
+ \DeclareUnicodeCharacter{010C}{\v{C}}
+ \DeclareUnicodeCharacter{010D}{\v{c}}
+ \DeclareUnicodeCharacter{010E}{\v{D}}
+
+ \DeclareUnicodeCharacter{0112}{\=E}
+ \DeclareUnicodeCharacter{0113}{\=e}
+ \DeclareUnicodeCharacter{0114}{\u{E}}
+ \DeclareUnicodeCharacter{0115}{\u{e}}
+ \DeclareUnicodeCharacter{0116}{\dotaccent{E}}
+ \DeclareUnicodeCharacter{0117}{\dotaccent{e}}
+ \DeclareUnicodeCharacter{011A}{\v{E}}
+ \DeclareUnicodeCharacter{011B}{\v{e}}
+ \DeclareUnicodeCharacter{011C}{\^G}
+ \DeclareUnicodeCharacter{011D}{\^g}
+ \DeclareUnicodeCharacter{011E}{\u{G}}
+ \DeclareUnicodeCharacter{011F}{\u{g}}
+
+ \DeclareUnicodeCharacter{0120}{\dotaccent{G}}
+ \DeclareUnicodeCharacter{0121}{\dotaccent{g}}
+ \DeclareUnicodeCharacter{0124}{\^H}
+ \DeclareUnicodeCharacter{0125}{\^h}
+ \DeclareUnicodeCharacter{0128}{\~I}
+ \DeclareUnicodeCharacter{0129}{\~{\dotless{i}}}
+ \DeclareUnicodeCharacter{012A}{\=I}
+ \DeclareUnicodeCharacter{012B}{\={\dotless{i}}}
+ \DeclareUnicodeCharacter{012C}{\u{I}}
+ \DeclareUnicodeCharacter{012D}{\u{\dotless{i}}}
+
+ \DeclareUnicodeCharacter{0130}{\dotaccent{I}}
+ \DeclareUnicodeCharacter{0131}{\dotless{i}}
+ \DeclareUnicodeCharacter{0132}{IJ}
+ \DeclareUnicodeCharacter{0133}{ij}
+ \DeclareUnicodeCharacter{0134}{\^J}
+ \DeclareUnicodeCharacter{0135}{\^{\dotless{j}}}
+ \DeclareUnicodeCharacter{0139}{\'L}
+ \DeclareUnicodeCharacter{013A}{\'l}
+
+ \DeclareUnicodeCharacter{0141}{\L}
+ \DeclareUnicodeCharacter{0142}{\l}
+ \DeclareUnicodeCharacter{0143}{\'N}
+ \DeclareUnicodeCharacter{0144}{\'n}
+ \DeclareUnicodeCharacter{0147}{\v{N}}
+ \DeclareUnicodeCharacter{0148}{\v{n}}
+ \DeclareUnicodeCharacter{014C}{\=O}
+ \DeclareUnicodeCharacter{014D}{\=o}
+ \DeclareUnicodeCharacter{014E}{\u{O}}
+ \DeclareUnicodeCharacter{014F}{\u{o}}
+
+ \DeclareUnicodeCharacter{0150}{\H{O}}
+ \DeclareUnicodeCharacter{0151}{\H{o}}
+ \DeclareUnicodeCharacter{0152}{\OE}
+ \DeclareUnicodeCharacter{0153}{\oe}
+ \DeclareUnicodeCharacter{0154}{\'R}
+ \DeclareUnicodeCharacter{0155}{\'r}
+ \DeclareUnicodeCharacter{0158}{\v{R}}
+ \DeclareUnicodeCharacter{0159}{\v{r}}
+ \DeclareUnicodeCharacter{015A}{\'S}
+ \DeclareUnicodeCharacter{015B}{\'s}
+ \DeclareUnicodeCharacter{015C}{\^S}
+ \DeclareUnicodeCharacter{015D}{\^s}
+ \DeclareUnicodeCharacter{015E}{\cedilla{S}}
+ \DeclareUnicodeCharacter{015F}{\cedilla{s}}
+
+ \DeclareUnicodeCharacter{0160}{\v{S}}
+ \DeclareUnicodeCharacter{0161}{\v{s}}
+ \DeclareUnicodeCharacter{0162}{\cedilla{t}}
+ \DeclareUnicodeCharacter{0163}{\cedilla{T}}
+ \DeclareUnicodeCharacter{0164}{\v{T}}
+
+ \DeclareUnicodeCharacter{0168}{\~U}
+ \DeclareUnicodeCharacter{0169}{\~u}
+ \DeclareUnicodeCharacter{016A}{\=U}
+ \DeclareUnicodeCharacter{016B}{\=u}
+ \DeclareUnicodeCharacter{016C}{\u{U}}
+ \DeclareUnicodeCharacter{016D}{\u{u}}
+ \DeclareUnicodeCharacter{016E}{\ringaccent{U}}
+ \DeclareUnicodeCharacter{016F}{\ringaccent{u}}
+
+ \DeclareUnicodeCharacter{0170}{\H{U}}
+ \DeclareUnicodeCharacter{0171}{\H{u}}
+ \DeclareUnicodeCharacter{0174}{\^W}
+ \DeclareUnicodeCharacter{0175}{\^w}
+ \DeclareUnicodeCharacter{0176}{\^Y}
+ \DeclareUnicodeCharacter{0177}{\^y}
+ \DeclareUnicodeCharacter{0178}{\"Y}
+ \DeclareUnicodeCharacter{0179}{\'Z}
+ \DeclareUnicodeCharacter{017A}{\'z}
+ \DeclareUnicodeCharacter{017B}{\dotaccent{Z}}
+ \DeclareUnicodeCharacter{017C}{\dotaccent{z}}
+ \DeclareUnicodeCharacter{017D}{\v{Z}}
+ \DeclareUnicodeCharacter{017E}{\v{z}}
+
+ \DeclareUnicodeCharacter{01C4}{D\v{Z}}
+ \DeclareUnicodeCharacter{01C5}{D\v{z}}
+ \DeclareUnicodeCharacter{01C6}{d\v{z}}
+ \DeclareUnicodeCharacter{01C7}{LJ}
+ \DeclareUnicodeCharacter{01C8}{Lj}
+ \DeclareUnicodeCharacter{01C9}{lj}
+ \DeclareUnicodeCharacter{01CA}{NJ}
+ \DeclareUnicodeCharacter{01CB}{Nj}
+ \DeclareUnicodeCharacter{01CC}{nj}
+ \DeclareUnicodeCharacter{01CD}{\v{A}}
+ \DeclareUnicodeCharacter{01CE}{\v{a}}
+ \DeclareUnicodeCharacter{01CF}{\v{I}}
+
+ \DeclareUnicodeCharacter{01D0}{\v{\dotless{i}}}
+ \DeclareUnicodeCharacter{01D1}{\v{O}}
+ \DeclareUnicodeCharacter{01D2}{\v{o}}
+ \DeclareUnicodeCharacter{01D3}{\v{U}}
+ \DeclareUnicodeCharacter{01D4}{\v{u}}
+
+ \DeclareUnicodeCharacter{01E2}{\={\AE}}
+ \DeclareUnicodeCharacter{01E3}{\={\ae}}
+ \DeclareUnicodeCharacter{01E6}{\v{G}}
+ \DeclareUnicodeCharacter{01E7}{\v{g}}
+ \DeclareUnicodeCharacter{01E8}{\v{K}}
+ \DeclareUnicodeCharacter{01E9}{\v{k}}
+
+ \DeclareUnicodeCharacter{01F0}{\v{\dotless{j}}}
+ \DeclareUnicodeCharacter{01F1}{DZ}
+ \DeclareUnicodeCharacter{01F2}{Dz}
+ \DeclareUnicodeCharacter{01F3}{dz}
+ \DeclareUnicodeCharacter{01F4}{\'G}
+ \DeclareUnicodeCharacter{01F5}{\'g}
+ \DeclareUnicodeCharacter{01F8}{\`N}
+ \DeclareUnicodeCharacter{01F9}{\`n}
+ \DeclareUnicodeCharacter{01FC}{\'{\AE}}
+ \DeclareUnicodeCharacter{01FD}{\'{\ae}}
+ \DeclareUnicodeCharacter{01FE}{\'{\O}}
+ \DeclareUnicodeCharacter{01FF}{\'{\o}}
+
+ \DeclareUnicodeCharacter{021E}{\v{H}}
+ \DeclareUnicodeCharacter{021F}{\v{h}}
+
+ \DeclareUnicodeCharacter{0226}{\dotaccent{A}}
+ \DeclareUnicodeCharacter{0227}{\dotaccent{a}}
+ \DeclareUnicodeCharacter{0228}{\cedilla{E}}
+ \DeclareUnicodeCharacter{0229}{\cedilla{e}}
+ \DeclareUnicodeCharacter{022E}{\dotaccent{O}}
+ \DeclareUnicodeCharacter{022F}{\dotaccent{o}}
+
+ \DeclareUnicodeCharacter{0232}{\=Y}
+ \DeclareUnicodeCharacter{0233}{\=y}
+ \DeclareUnicodeCharacter{0237}{\dotless{j}}
+
+ \DeclareUnicodeCharacter{02DB}{\ogonek{ }}
+
+ \DeclareUnicodeCharacter{1E02}{\dotaccent{B}}
+ \DeclareUnicodeCharacter{1E03}{\dotaccent{b}}
+ \DeclareUnicodeCharacter{1E04}{\udotaccent{B}}
+ \DeclareUnicodeCharacter{1E05}{\udotaccent{b}}
+ \DeclareUnicodeCharacter{1E06}{\ubaraccent{B}}
+ \DeclareUnicodeCharacter{1E07}{\ubaraccent{b}}
+ \DeclareUnicodeCharacter{1E0A}{\dotaccent{D}}
+ \DeclareUnicodeCharacter{1E0B}{\dotaccent{d}}
+ \DeclareUnicodeCharacter{1E0C}{\udotaccent{D}}
+ \DeclareUnicodeCharacter{1E0D}{\udotaccent{d}}
+ \DeclareUnicodeCharacter{1E0E}{\ubaraccent{D}}
+ \DeclareUnicodeCharacter{1E0F}{\ubaraccent{d}}
+
+ \DeclareUnicodeCharacter{1E1E}{\dotaccent{F}}
+ \DeclareUnicodeCharacter{1E1F}{\dotaccent{f}}
+
+ \DeclareUnicodeCharacter{1E20}{\=G}
+ \DeclareUnicodeCharacter{1E21}{\=g}
+ \DeclareUnicodeCharacter{1E22}{\dotaccent{H}}
+ \DeclareUnicodeCharacter{1E23}{\dotaccent{h}}
+ \DeclareUnicodeCharacter{1E24}{\udotaccent{H}}
+ \DeclareUnicodeCharacter{1E25}{\udotaccent{h}}
+ \DeclareUnicodeCharacter{1E26}{\"H}
+ \DeclareUnicodeCharacter{1E27}{\"h}
+
+ \DeclareUnicodeCharacter{1E30}{\'K}
+ \DeclareUnicodeCharacter{1E31}{\'k}
+ \DeclareUnicodeCharacter{1E32}{\udotaccent{K}}
+ \DeclareUnicodeCharacter{1E33}{\udotaccent{k}}
+ \DeclareUnicodeCharacter{1E34}{\ubaraccent{K}}
+ \DeclareUnicodeCharacter{1E35}{\ubaraccent{k}}
+ \DeclareUnicodeCharacter{1E36}{\udotaccent{L}}
+ \DeclareUnicodeCharacter{1E37}{\udotaccent{l}}
+ \DeclareUnicodeCharacter{1E3A}{\ubaraccent{L}}
+ \DeclareUnicodeCharacter{1E3B}{\ubaraccent{l}}
+ \DeclareUnicodeCharacter{1E3E}{\'M}
+ \DeclareUnicodeCharacter{1E3F}{\'m}
+
+ \DeclareUnicodeCharacter{1E40}{\dotaccent{M}}
+ \DeclareUnicodeCharacter{1E41}{\dotaccent{m}}
+ \DeclareUnicodeCharacter{1E42}{\udotaccent{M}}
+ \DeclareUnicodeCharacter{1E43}{\udotaccent{m}}
+ \DeclareUnicodeCharacter{1E44}{\dotaccent{N}}
+ \DeclareUnicodeCharacter{1E45}{\dotaccent{n}}
+ \DeclareUnicodeCharacter{1E46}{\udotaccent{N}}
+ \DeclareUnicodeCharacter{1E47}{\udotaccent{n}}
+ \DeclareUnicodeCharacter{1E48}{\ubaraccent{N}}
+ \DeclareUnicodeCharacter{1E49}{\ubaraccent{n}}
+
+ \DeclareUnicodeCharacter{1E54}{\'P}
+ \DeclareUnicodeCharacter{1E55}{\'p}
+ \DeclareUnicodeCharacter{1E56}{\dotaccent{P}}
+ \DeclareUnicodeCharacter{1E57}{\dotaccent{p}}
+ \DeclareUnicodeCharacter{1E58}{\dotaccent{R}}
+ \DeclareUnicodeCharacter{1E59}{\dotaccent{r}}
+ \DeclareUnicodeCharacter{1E5A}{\udotaccent{R}}
+ \DeclareUnicodeCharacter{1E5B}{\udotaccent{r}}
+ \DeclareUnicodeCharacter{1E5E}{\ubaraccent{R}}
+ \DeclareUnicodeCharacter{1E5F}{\ubaraccent{r}}
+
+ \DeclareUnicodeCharacter{1E60}{\dotaccent{S}}
+ \DeclareUnicodeCharacter{1E61}{\dotaccent{s}}
+ \DeclareUnicodeCharacter{1E62}{\udotaccent{S}}
+ \DeclareUnicodeCharacter{1E63}{\udotaccent{s}}
+ \DeclareUnicodeCharacter{1E6A}{\dotaccent{T}}
+ \DeclareUnicodeCharacter{1E6B}{\dotaccent{t}}
+ \DeclareUnicodeCharacter{1E6C}{\udotaccent{T}}
+ \DeclareUnicodeCharacter{1E6D}{\udotaccent{t}}
+ \DeclareUnicodeCharacter{1E6E}{\ubaraccent{T}}
+ \DeclareUnicodeCharacter{1E6F}{\ubaraccent{t}}
+
+ \DeclareUnicodeCharacter{1E7C}{\~V}
+ \DeclareUnicodeCharacter{1E7D}{\~v}
+ \DeclareUnicodeCharacter{1E7E}{\udotaccent{V}}
+ \DeclareUnicodeCharacter{1E7F}{\udotaccent{v}}
+
+ \DeclareUnicodeCharacter{1E80}{\`W}
+ \DeclareUnicodeCharacter{1E81}{\`w}
+ \DeclareUnicodeCharacter{1E82}{\'W}
+ \DeclareUnicodeCharacter{1E83}{\'w}
+ \DeclareUnicodeCharacter{1E84}{\"W}
+ \DeclareUnicodeCharacter{1E85}{\"w}
+ \DeclareUnicodeCharacter{1E86}{\dotaccent{W}}
+ \DeclareUnicodeCharacter{1E87}{\dotaccent{w}}
+ \DeclareUnicodeCharacter{1E88}{\udotaccent{W}}
+ \DeclareUnicodeCharacter{1E89}{\udotaccent{w}}
+ \DeclareUnicodeCharacter{1E8A}{\dotaccent{X}}
+ \DeclareUnicodeCharacter{1E8B}{\dotaccent{x}}
+ \DeclareUnicodeCharacter{1E8C}{\"X}
+ \DeclareUnicodeCharacter{1E8D}{\"x}
+ \DeclareUnicodeCharacter{1E8E}{\dotaccent{Y}}
+ \DeclareUnicodeCharacter{1E8F}{\dotaccent{y}}
+
+ \DeclareUnicodeCharacter{1E90}{\^Z}
+ \DeclareUnicodeCharacter{1E91}{\^z}
+ \DeclareUnicodeCharacter{1E92}{\udotaccent{Z}}
+ \DeclareUnicodeCharacter{1E93}{\udotaccent{z}}
+ \DeclareUnicodeCharacter{1E94}{\ubaraccent{Z}}
+ \DeclareUnicodeCharacter{1E95}{\ubaraccent{z}}
+ \DeclareUnicodeCharacter{1E96}{\ubaraccent{h}}
+ \DeclareUnicodeCharacter{1E97}{\"t}
+ \DeclareUnicodeCharacter{1E98}{\ringaccent{w}}
+ \DeclareUnicodeCharacter{1E99}{\ringaccent{y}}
+
+ \DeclareUnicodeCharacter{1EA0}{\udotaccent{A}}
+ \DeclareUnicodeCharacter{1EA1}{\udotaccent{a}}
+
+ \DeclareUnicodeCharacter{1EB8}{\udotaccent{E}}
+ \DeclareUnicodeCharacter{1EB9}{\udotaccent{e}}
+ \DeclareUnicodeCharacter{1EBC}{\~E}
+ \DeclareUnicodeCharacter{1EBD}{\~e}
+
+ \DeclareUnicodeCharacter{1ECA}{\udotaccent{I}}
+ \DeclareUnicodeCharacter{1ECB}{\udotaccent{i}}
+ \DeclareUnicodeCharacter{1ECC}{\udotaccent{O}}
+ \DeclareUnicodeCharacter{1ECD}{\udotaccent{o}}
+
+ \DeclareUnicodeCharacter{1EE4}{\udotaccent{U}}
+ \DeclareUnicodeCharacter{1EE5}{\udotaccent{u}}
+
+ \DeclareUnicodeCharacter{1EF2}{\`Y}
+ \DeclareUnicodeCharacter{1EF3}{\`y}
+ \DeclareUnicodeCharacter{1EF4}{\udotaccent{Y}}
+
+ \DeclareUnicodeCharacter{1EF8}{\~Y}
+ \DeclareUnicodeCharacter{1EF9}{\~y}
+
+ \DeclareUnicodeCharacter{2013}{--}
+ \DeclareUnicodeCharacter{2014}{---}
+ \DeclareUnicodeCharacter{2018}{\quoteleft}
+ \DeclareUnicodeCharacter{2019}{\quoteright}
+ \DeclareUnicodeCharacter{201A}{\quotesinglbase}
+ \DeclareUnicodeCharacter{201C}{\quotedblleft}
+ \DeclareUnicodeCharacter{201D}{\quotedblright}
+ \DeclareUnicodeCharacter{201E}{\quotedblbase}
+ \DeclareUnicodeCharacter{2022}{\bullet}
+ \DeclareUnicodeCharacter{2026}{\dots}
+ \DeclareUnicodeCharacter{2039}{\guilsinglleft}
+ \DeclareUnicodeCharacter{203A}{\guilsinglright}
+ \DeclareUnicodeCharacter{20AC}{\euro}
+
+ \DeclareUnicodeCharacter{2192}{\expansion}
+ \DeclareUnicodeCharacter{21D2}{\result}
+
+ \DeclareUnicodeCharacter{2212}{\minus}
+ \DeclareUnicodeCharacter{2217}{\point}
+ \DeclareUnicodeCharacter{2261}{\equiv}
+}% end of \utfeightchardefs
+
+
+% US-ASCII character definitions.
+\def\asciichardefs{% nothing need be done
+ \relax
+}
+
+% Make non-ASCII characters printable again for compatibility with
+% existing Texinfo documents that may use them, even without declaring a
+% document encoding.
+%
+\setnonasciicharscatcode \other
+
+
+\message{formatting,}
+
+\newdimen\defaultparindent \defaultparindent = 15pt
+
+\chapheadingskip = 15pt plus 4pt minus 2pt
+\secheadingskip = 12pt plus 3pt minus 2pt
+\subsecheadingskip = 9pt plus 2pt minus 2pt
+
+% Prevent underfull vbox error messages.
+\vbadness = 10000
+
+% Don't be so finicky about underfull hboxes, either.
+\hbadness = 2000
+
+% Following George Bush, get rid of widows and orphans.
+\widowpenalty=10000
+\clubpenalty=10000
+
+% Use TeX 3.0's \emergencystretch to help line breaking, but if we're
+% using an old version of TeX, don't do anything. We want the amount of
+% stretch added to depend on the line length, hence the dependence on
+% \hsize. We call this whenever the paper size is set.
+%
+\def\setemergencystretch{%
+ \ifx\emergencystretch\thisisundefined
+ % Allow us to assign to \emergencystretch anyway.
+ \def\emergencystretch{\dimen0}%
+ \else
+ \emergencystretch = .15\hsize
+ \fi
+}
+
+% Parameters in order: 1) textheight; 2) textwidth;
+% 3) voffset; 4) hoffset; 5) binding offset; 6) topskip;
+% 7) physical page height; 8) physical page width.
+%
+% We also call \setleading{\textleading}, so the caller should define
+% \textleading. The caller should also set \parskip.
+%
+\def\internalpagesizes#1#2#3#4#5#6#7#8{%
+ \voffset = #3\relax
+ \topskip = #6\relax
+ \splittopskip = \topskip
+ %
+ \vsize = #1\relax
+ \advance\vsize by \topskip
+ \outervsize = \vsize
+ \advance\outervsize by 2\topandbottommargin
+ \pageheight = \vsize
+ %
+ \hsize = #2\relax
+ \outerhsize = \hsize
+ \advance\outerhsize by 0.5in
+ \pagewidth = \hsize
+ %
+ \normaloffset = #4\relax
+ \bindingoffset = #5\relax
+ %
+ \ifpdf
+ \pdfpageheight #7\relax
+ \pdfpagewidth #8\relax
+ % if we don't reset these, they will remain at "1 true in" of
+ % whatever layout pdftex was dumped with.
+ \pdfhorigin = 1 true in
+ \pdfvorigin = 1 true in
+ \fi
+ %
+ \setleading{\textleading}
+ %
+ \parindent = \defaultparindent
+ \setemergencystretch
+}
+
+% @letterpaper (the default).
+\def\letterpaper{{\globaldefs = 1
+ \parskip = 3pt plus 2pt minus 1pt
+ \textleading = 13.2pt
+ %
+ % If page is nothing but text, make it come out even.
+ \internalpagesizes{607.2pt}{6in}% that's 46 lines
+ {\voffset}{.25in}%
+ {\bindingoffset}{36pt}%
+ {11in}{8.5in}%
+}}
+
+% Use @smallbook to reset parameters for 7x9.25 trim size.
+\def\smallbook{{\globaldefs = 1
+ \parskip = 2pt plus 1pt
+ \textleading = 12pt
+ %
+ \internalpagesizes{7.5in}{5in}%
+ {-.2in}{0in}%
+ {\bindingoffset}{16pt}%
+ {9.25in}{7in}%
+ %
+ \lispnarrowing = 0.3in
+ \tolerance = 700
+ \hfuzz = 1pt
+ \contentsrightmargin = 0pt
+ \defbodyindent = .5cm
+}}
+
+% Use @smallerbook to reset parameters for 6x9 trim size.
+% (Just testing, parameters still in flux.)
+\def\smallerbook{{\globaldefs = 1
+ \parskip = 1.5pt plus 1pt
+ \textleading = 12pt
+ %
+ \internalpagesizes{7.4in}{4.8in}%
+ {-.2in}{-.4in}%
+ {0pt}{14pt}%
+ {9in}{6in}%
+ %
+ \lispnarrowing = 0.25in
+ \tolerance = 700
+ \hfuzz = 1pt
+ \contentsrightmargin = 0pt
+ \defbodyindent = .4cm
+}}
+
+% Use @afourpaper to print on European A4 paper.
+\def\afourpaper{{\globaldefs = 1
+ \parskip = 3pt plus 2pt minus 1pt
+ \textleading = 13.2pt
+ %
+ % Double-side printing via postscript on Laserjet 4050
+ % prints double-sided nicely when \bindingoffset=10mm and \hoffset=-6mm.
+ % To change the settings for a different printer or situation, adjust
+ % \normaloffset until the front-side and back-side texts align. Then
+ % do the same for \bindingoffset. You can set these for testing in
+ % your texinfo source file like this:
+ % @tex
+ % \global\normaloffset = -6mm
+ % \global\bindingoffset = 10mm
+ % @end tex
+ \internalpagesizes{673.2pt}{160mm}% that's 51 lines
+ {\voffset}{\hoffset}%
+ {\bindingoffset}{44pt}%
+ {297mm}{210mm}%
+ %
+ \tolerance = 700
+ \hfuzz = 1pt
+ \contentsrightmargin = 0pt
+ \defbodyindent = 5mm
+}}
+
+% Use @afivepaper to print on European A5 paper.
+% From romildo at urano.iceb.ufop.br, 2 July 2000.
+% He also recommends making @example and @lisp be small.
+\def\afivepaper{{\globaldefs = 1
+ \parskip = 2pt plus 1pt minus 0.1pt
+ \textleading = 12.5pt
+ %
+ \internalpagesizes{160mm}{120mm}%
+ {\voffset}{\hoffset}%
+ {\bindingoffset}{8pt}%
+ {210mm}{148mm}%
+ %
+ \lispnarrowing = 0.2in
+ \tolerance = 800
+ \hfuzz = 1.2pt
+ \contentsrightmargin = 0pt
+ \defbodyindent = 2mm
+ \tableindent = 12mm
+}}
+
+% A specific text layout, 24x15cm overall, intended for A4 paper.
+\def\afourlatex{{\globaldefs = 1
+ \afourpaper
+ \internalpagesizes{237mm}{150mm}%
+ {\voffset}{4.6mm}%
+ {\bindingoffset}{7mm}%
+ {297mm}{210mm}%
+ %
+ % Must explicitly reset to 0 because we call \afourpaper.
+ \globaldefs = 0
+}}
+
+% Use @afourwide to print on A4 paper in landscape format.
+\def\afourwide{{\globaldefs = 1
+ \afourpaper
+ \internalpagesizes{241mm}{165mm}%
+ {\voffset}{-2.95mm}%
+ {\bindingoffset}{7mm}%
+ {297mm}{210mm}%
+ \globaldefs = 0
+}}
+
+% @pagesizes TEXTHEIGHT[,TEXTWIDTH]
+% Perhaps we should allow setting the margins, \topskip, \parskip,
+% and/or leading, also. Or perhaps we should compute them somehow.
+%
+\parseargdef\pagesizes{\pagesizesyyy #1,,\finish}
+\def\pagesizesyyy#1,#2,#3\finish{{%
+ \setbox0 = \hbox{\ignorespaces #2}\ifdim\wd0 > 0pt \hsize=#2\relax \fi
+ \globaldefs = 1
+ %
+ \parskip = 3pt plus 2pt minus 1pt
+ \setleading{\textleading}%
+ %
+ \dimen0 = #1\relax
+ \advance\dimen0 by \voffset
+ %
+ \dimen2 = \hsize
+ \advance\dimen2 by \normaloffset
+ %
+ \internalpagesizes{#1}{\hsize}%
+ {\voffset}{\normaloffset}%
+ {\bindingoffset}{44pt}%
+ {\dimen0}{\dimen2}%
+}}
+
+% Set default to letter.
+%
+\letterpaper
+
+
+\message{and turning on texinfo input format.}
+
+% DEL is a comment character, in case @c does not suffice.
+\catcode`\^^? = 14
+
+% Define macros to output various characters with catcode for normal text.
+\catcode`\"=\other
+\catcode`\~=\other
+\catcode`\^=\other
+\catcode`\_=\other
+\catcode`\|=\other
+\catcode`\<=\other
+\catcode`\>=\other
+\catcode`\+=\other
+\catcode`\$=\other
+\def\normaldoublequote{"}
+\def\normaltilde{~}
+\def\normalcaret{^}
+\def\normalunderscore{_}
+\def\normalverticalbar{|}
+\def\normalless{<}
+\def\normalgreater{>}
+\def\normalplus{+}
+\def\normaldollar{$}%$ font-lock fix
+
+% This macro is used to make a character print one way in \tt
+% (where it can probably be output as-is), and another way in other fonts,
+% where something hairier probably needs to be done.
+%
+% #1 is what to print if we are indeed using \tt; #2 is what to print
+% otherwise. Since all the Computer Modern typewriter fonts have zero
+% interword stretch (and shrink), and it is reasonable to expect all
+% typewriter fonts to have this, we can check that font parameter.
+%
+\def\ifusingtt#1#2{\ifdim \fontdimen3\font=0pt #1\else #2\fi}
+
+% Same as above, but check for italic font. Actually this also catches
+% non-italic slanted fonts since it is impossible to distinguish them from
+% italic fonts. But since this is only used by $ and it uses \sl anyway
+% this is not a problem.
+\def\ifusingit#1#2{\ifdim \fontdimen1\font>0pt #1\else #2\fi}
+
+% Turn off all special characters except @
+% (and those which the user can use as if they were ordinary).
+% Most of these we simply print from the \tt font, but for some, we can
+% use math or other variants that look better in normal text.
+
+\catcode`\"=\active
+\def\activedoublequote{{\tt\char34}}
+\let"=\activedoublequote
+\catcode`\~=\active
+\def~{{\tt\char126}}
+\chardef\hat=`\^
+\catcode`\^=\active
+\def^{{\tt \hat}}
+
+\catcode`\_=\active
+\def_{\ifusingtt\normalunderscore\_}
+\let\realunder=_
+% Subroutine for the previous macro.
+\def\_{\leavevmode \kern.07em \vbox{\hrule width.3em height.1ex}\kern .07em }
+
+\catcode`\|=\active
+\def|{{\tt\char124}}
+\chardef \less=`\<
+\catcode`\<=\active
+\def<{{\tt \less}}
+\chardef \gtr=`\>
+\catcode`\>=\active
+\def>{{\tt \gtr}}
+\catcode`\+=\active
+\def+{{\tt \char 43}}
+\catcode`\$=\active
+\def${\ifusingit{{\sl\$}}\normaldollar}%$ font-lock fix
+
+% If a .fmt file is being used, characters that might appear in a file
+% name cannot be active until we have parsed the command line.
+% So turn them off again, and have \everyjob (or @setfilename) turn them on.
+% \otherifyactive is called near the end of this file.
+\def\otherifyactive{\catcode`+=\other \catcode`\_=\other}
+
+% Used sometimes to turn off (effectively) the active characters even after
+% parsing them.
+\def\turnoffactive{%
+ \normalturnoffactive
+ \otherbackslash
+}
+
+\catcode`\@=0
+
+% \backslashcurfont outputs one backslash character in current font,
+% as in \char`\\.
+\global\chardef\backslashcurfont=`\\
+\global\let\rawbackslashxx=\backslashcurfont % let existing .??s files work
+
+% \realbackslash is an actual character `\' with catcode other, and
+% \doublebackslash is two of them (for the pdf outlines).
+{\catcode`\\=\other @gdef at realbackslash{\} @gdef at doublebackslash{\\}}
+
+% In texinfo, backslash is an active character; it prints the backslash
+% in fixed width font.
+\catcode`\\=\active
+ at def@normalbackslash{{@tt at backslashcurfont}}
+% On startup, @fixbackslash assigns:
+% @let \ = @normalbackslash
+
+% \rawbackslash defines an active \ to do \backslashcurfont.
+% \otherbackslash defines an active \ to be a literal `\' character with
+% catcode other.
+ at gdef@rawbackslash{@let\=@backslashcurfont}
+ at gdef@otherbackslash{@let\=@realbackslash}
+
+% Same as @turnoffactive except outputs \ as {\tt\char`\\} instead of
+% the literal character `\'.
+%
+ at def@normalturnoffactive{%
+ @let\=@normalbackslash
+ @let"=@normaldoublequote
+ @let~=@normaltilde
+ @let^=@normalcaret
+ @let_=@normalunderscore
+ @let|=@normalverticalbar
+ @let<=@normalless
+ @let>=@normalgreater
+ @let+=@normalplus
+ @let$=@normaldollar %$ font-lock fix
+ @markupsetuplqdefault
+ @markupsetuprqdefault
+ @unsepspaces
+}
+
+% Make _ and + \other characters, temporarily.
+% This is canceled by @fixbackslash.
+ at otherifyactive
+
+% If a .fmt file is being used, we don't want the `\input texinfo' to show up.
+% That is what \eatinput is for; after that, the `\' should revert to printing
+% a backslash.
+%
+ at gdef@eatinput input texinfo{@fixbackslash}
+ at global@let\ = @eatinput
+
+% On the other hand, perhaps the file did not have a `\input texinfo'. Then
+% the first `\' in the file would cause an error. This macro tries to fix
+% that, assuming it is called before the first `\' could plausibly occur.
+% Also turn back on active characters that might appear in the input
+% file name, in case not using a pre-dumped format.
+%
+ at gdef@fixbackslash{%
+ @ifx\@eatinput @let\ = @normalbackslash @fi
+ @catcode`+=@active
+ @catcode`@_=@active
+}
+
+% Say @foo, not \foo, in error messages.
+ at escapechar = `@@
+
+% These look ok in all fonts, so just make them not special.
+ at catcode`@& = @other
+ at catcode`@# = @other
+ at catcode`@% = @other
+
+ at c Finally, make ` and ' active, so that txicodequoteundirected and
+ at c txicodequotebacktick work right in, e.g., @w{@code{`foo'}}. If we
+ at c don't make ` and ' active, @code will not get them as active chars.
+ at c Do this last of all since we use ` in the previous @catcode assignments.
+ at catcode`@'=@active
+ at catcode`@`=@active
+ at markupsetuplqdefault
+ at markupsetuprqdefault
+
+ at c Local variables:
+ at c eval: (add-hook 'write-file-hooks 'time-stamp)
+ at c page-delimiter: "^\\\\message"
+ at c time-stamp-start: "def\\\\texinfoversion{"
+ at c time-stamp-format: "%:y-%02m-%02d.%02H"
+ at c time-stamp-end: "}"
+ at c End:
+
+ at c vim:sw=2:
+
+ at ignore
+ arch-tag: e1b36e32-c96e-4135-a41a-0b2efa2ea115
+ at end ignore
diff --git a/configure b/configure
new file mode 100755
index 0000000..85fb700
--- /dev/null
+++ b/configure
@@ -0,0 +1,19188 @@
+#! /bin/sh
+# From configure.ac Revision.
+# Guess values for system-dependent variables and create Makefiles.
+# Generated by GNU Autoconf 2.67 for crac 1.5.0.
+#
+# Report bugs to <crac-bugs at lists.gforge.inria.fr>.
+#
+#
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
+# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
+# Foundation, Inc.
+#
+#
+# This configure script is free software; the Free Software Foundation
+# gives unlimited permission to copy, distribute and modify it.
+#
+#
+# *******************************************************************************
+# * *
+# * Copyright © 2010-2013 -- IRB/INSERM *
+# * (Institut de Recherches en Biothérapie / *
+# * Institut National de la Santé et de la Recherche *
+# * Médicale) *
+# * LIFL/INRIA *
+# * (Laboratoire d'Informatique Fondamentale de *
+# * Lille / Institut National de Recherche en *
+# * Informatique et Automatique) *
+# * LIRMM/CNRS *
+# * (Laboratoire d'Informatique, de Robotique et de *
+# * Microélectronique de Montpellier / *
+# * Centre National de la Recherche Scientifique) *
+# * LITIS *
+# * (Laboratoire d'Informatique, du Traitement de *
+# * l'Information et des Systèmes). *
+# * *
+# * *
+# * Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+# * Mikaël SALSON <mikael.salson at lifl.fr> *
+# * Thérèse COMMES <commesd at univ-montp2.fr> *
+# * Éric RIVALS <eric.rivals at lirmm.fr> *
+# * *
+# * Programmeurs *
+# * /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+# * Mikaël SALSON <mikael.salson at lifl.fr> *
+# * with additional contribution of: *
+# * Alban MANCHERON <alban.mancheron at lirmm.fr> *
+# * *
+# * Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+# * *
+# * ------------------------------------------------------------------------- *
+# * *
+# * Ce fichier fait partie du programme CRAC. *
+# * *
+# * Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+# * *
+# * Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+# * respectant les principes de diffusion des logiciels libres. Vous pouvez *
+# * utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+# * la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+# * le site "http://www.cecill.info". *
+# * *
+# * En contrepartie de l'accessibilité au code source et des droits de copie, *
+# * de modification et de redistribution accordés par cette licence, il n'est *
+# * offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+# * seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+# * titulaire des droits patrimoniaux et les concédants successifs. *
+# * *
+# * À cet égard l'attention de l'utilisateur est attirée sur les risques *
+# * associés au chargement, à l'utilisation, à la modification et/ou au *
+# * développement et à la reproduction du logiciel par l'utilisateur étant *
+# * donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+# * manipuler et qui le réserve donc à des développeurs et des professionnels *
+# * avertis possédant des connaissances informatiques approfondies. Les *
+# * utilisateurs sont donc invités à charger et tester l'adéquation du *
+# * logiciel à leurs besoins dans des conditions permettant d'assurer la *
+# * sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+# * à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+# * *
+# * Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+# * pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+# * termes. *
+# * *
+# * ------------------------------------------------------------------------- *
+# * *
+# * This File is part of the CRAC program. *
+# * *
+# * Crac is a tool to analyse RNA-Seq data provided by NGS. *
+# * *
+# * This software is governed by the CeCILL license under French law and *
+# * abiding by the rules of distribution of free software. You can use, *
+# * modify and/ or redistribute the software under the terms of the CeCILL *
+# * license as circulated by CEA, CNRS and INRIA at the following URL *
+# * "http://www.cecill.info". *
+# * *
+# * As a counterpart to the access to the source code and rights to copy, *
+# * modify and redistribute granted by the license, users are provided only *
+# * with a limited warranty and the software's author, the holder of the *
+# * economic rights, and the successive licensors have only limited *
+# * liability. *
+# * *
+# * In this respect, the user's attention is drawn to the risks associated *
+# * with loading, using, modifying and/or developing or reproducing the *
+# * software by the user in light of its specific status of free software, *
+# * that may mean that it is complicated to manipulate, and that also *
+# * therefore means that it is reserved for developers and experienced *
+# * professionals having in-depth computer knowledge. Users are therefore *
+# * encouraged to load and test the software's suitability as regards their *
+# * requirements in conditions enabling the security of their systems and/or *
+# * data to be ensured and, more generally, to use and operate it in the same *
+# * conditions as regards security. *
+# * *
+# * The fact that you are presently reading this means that you have had *
+# * knowledge of the CeCILL license and that you accept its terms. *
+# * *
+# *******************************************************************************
+#
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in #(
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+case $0 in #((
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test "x$CONFIG_SHELL" = x; then
+ as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '\${1+\"\$@\"}'='\"\$@\"'
+ setopt NO_GLOB_SUBST
+else
+ case \`(set -o) 2>/dev/null\` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+"
+ as_required="as_fn_return () { (exit \$1); }
+as_fn_success () { as_fn_return 0; }
+as_fn_failure () { as_fn_return 1; }
+as_fn_ret_success () { return 0; }
+as_fn_ret_failure () { return 1; }
+
+exitcode=0
+as_fn_success || { exitcode=1; echo as_fn_success failed.; }
+as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; }
+as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; }
+as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; }
+if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then :
+
+else
+ exitcode=1; echo positional parameters were not saved.
+fi
+test x\$exitcode = x0 || exit 1"
+ as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
+ as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
+ eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
+ test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1
+test \$(( 1 + 1 )) = 2 || exit 1"
+ if (eval "$as_required") 2>/dev/null; then :
+ as_have_required=yes
+else
+ as_have_required=no
+fi
+ if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then :
+
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+as_found=false
+for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ as_found=:
+ case $as_dir in #(
+ /*)
+ for as_base in sh bash ksh sh5; do
+ # Try only shells that exist, to save several forks.
+ as_shell=$as_dir/$as_base
+ if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ CONFIG_SHELL=$as_shell as_have_required=yes
+ if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ break 2
+fi
+fi
+ done;;
+ esac
+ as_found=false
+done
+$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then :
+ CONFIG_SHELL=$SHELL as_have_required=yes
+fi; }
+IFS=$as_save_IFS
+
+
+ if test "x$CONFIG_SHELL" != x; then :
+ # We cannot yet assume a decent shell, so we have to provide a
+ # neutralization value for shells without unset; and this also
+ # works around shells that cannot unset nonexistent variables.
+ BASH_ENV=/dev/null
+ ENV=/dev/null
+ (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
+ export CONFIG_SHELL
+ exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"}
+fi
+
+ if test x$as_have_required = xno; then :
+ $as_echo "$0: This script requires a shell more modern than all"
+ $as_echo "$0: the shells that I found on your system."
+ if test x${ZSH_VERSION+set} = xset ; then
+ $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should"
+ $as_echo "$0: be upgraded to zsh 4.3.4 or later."
+ else
+ $as_echo "$0: Please tell bug-autoconf at gnu.org and
+$0: crac-bugs at lists.gforge.inria.fr about your system,
+$0: including any error possibly output before this
+$0: message. Then install a modern shell, or manually run
+$0: the script under such a shell if you do have one."
+ fi
+ exit 1
+fi
+fi
+fi
+SHELL=${CONFIG_SHELL-/bin/sh}
+export SHELL
+# Unset more variables known to interfere with behavior of common tools.
+CLICOLOR_FORCE= GREP_OPTIONS=
+unset CLICOLOR_FORCE GREP_OPTIONS
+
+## --------------------- ##
+## M4sh Shell Functions. ##
+## --------------------- ##
+# as_fn_unset VAR
+# ---------------
+# Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+
+# as_fn_set_status STATUS
+# -----------------------
+# Set $? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} # as_fn_set_status
+
+# as_fn_exit STATUS
+# -----------------
+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} # as_fn_exit
+
+# as_fn_mkdir_p
+# -------------
+# Create "$as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
+
+
+} # as_fn_mkdir_p
+# as_fn_append VAR VALUE
+# ----------------------
+# Append the text in VALUE to the end of the definition contained in VAR. Take
+# advantage of any shell optimizations that allow amortized linear growth over
+# repeated appends, instead of the typical quadratic growth present in naive
+# implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+# as_fn_arith ARG...
+# ------------------
+# Perform arithmetic evaluation on the ARGs, and store the result in the
+# global $as_val. Take advantage of shells that can avoid forks. The arguments
+# must be portable across $(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
+# ----------------------------------------
+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+# script with STATUS, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ $as_echo "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} # as_fn_error
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+
+ as_lineno_1=$LINENO as_lineno_1a=$LINENO
+ as_lineno_2=$LINENO as_lineno_2a=$LINENO
+ eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" &&
+ test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || {
+ # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-)
+ sed -n '
+ p
+ /[$]LINENO/=
+ ' <$as_myself |
+ sed '
+ s/[$]LINENO.*/&-/
+ t lineno
+ b
+ :lineno
+ N
+ :loop
+ s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
+ t loop
+ s/-\n.*//
+ ' >$as_me.lineno &&
+ chmod +x "$as_me.lineno" ||
+ { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
+
+ # Don't try to exec as it changes $[0], causing all sort of problems
+ # (the dirname of $[0] is not the place where we might find the
+ # original and so on. Autoconf is especially sensitive to this).
+ . "./$as_me.lineno"
+ # Exit status is that of the last command.
+ exit
+}
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in #(((((
+-n*)
+ case `echo 'xy\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -p'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -p'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -p'
+ fi
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p='mkdir -p "$as_dir"'
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+if test -x / >/dev/null 2>&1; then
+ as_test_x='test -x'
+else
+ if ls -dL / >/dev/null 2>&1; then
+ as_ls_L_option=L
+ else
+ as_ls_L_option=
+ fi
+ as_test_x='
+ eval sh -c '\''
+ if test -d "$1"; then
+ test -d "$1/.";
+ else
+ case $1 in #(
+ -*)set "./$1";;
+ esac;
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
+ ???[sx]*):;;*)false;;esac;fi
+ '\'' sh
+ '
+fi
+as_executable_p=$as_test_x
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+
+# Check that we are running under the correct shell.
+SHELL=${CONFIG_SHELL-/bin/sh}
+
+case X$lt_ECHO in
+X*--fallback-echo)
+ # Remove one level of quotation (which was required for Make).
+ ECHO=`echo "$lt_ECHO" | sed 's,\\\\\$\\$0,'$0','`
+ ;;
+esac
+
+ECHO=${lt_ECHO-echo}
+if test "X$1" = X--no-reexec; then
+ # Discard the --no-reexec flag, and continue.
+ shift
+elif test "X$1" = X--fallback-echo; then
+ # Avoid inline document here, it may be left over
+ :
+elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' ; then
+ # Yippee, $ECHO works!
+ :
+else
+ # Restart under the correct shell.
+ exec $SHELL "$0" --no-reexec ${1+"$@"}
+fi
+
+if test "X$1" = X--fallback-echo; then
+ # used as fallback echo
+ shift
+ cat <<_LT_EOF
+$*
+_LT_EOF
+ exit 0
+fi
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test -z "$lt_ECHO"; then
+ if test "X${echo_test_string+set}" != Xset; then
+ # find a string as large as possible, as long as the shell can cope with it
+ for cmd in 'sed 50q "$0"' 'sed 20q "$0"' 'sed 10q "$0"' 'sed 2q "$0"' 'echo test'; do
+ # expected sizes: less than 2Kb, 1Kb, 512 bytes, 16 bytes, ...
+ if { echo_test_string=`eval $cmd`; } 2>/dev/null &&
+ { test "X$echo_test_string" = "X$echo_test_string"; } 2>/dev/null
+ then
+ break
+ fi
+ done
+ fi
+
+ if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ :
+ else
+ # The Solaris, AIX, and Digital Unix default echo programs unquote
+ # backslashes. This makes it impossible to quote backslashes using
+ # echo "$something" | sed 's/\\/\\\\/g'
+ #
+ # So, first we look for a working echo in the user's PATH.
+
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for dir in $PATH /usr/ucb; do
+ IFS="$lt_save_ifs"
+ if (test -f $dir/echo || test -f $dir/echo$ac_exeext) &&
+ test "X`($dir/echo '\t') 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`($dir/echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ ECHO="$dir/echo"
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+
+ if test "X$ECHO" = Xecho; then
+ # We didn't find a better echo, so look for alternatives.
+ if test "X`{ print -r '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ print -r "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ # This shell has a builtin print -r that does the trick.
+ ECHO='print -r'
+ elif { test -f /bin/ksh || test -f /bin/ksh$ac_exeext; } &&
+ test "X$CONFIG_SHELL" != X/bin/ksh; then
+ # If we have ksh, try running configure again with it.
+ ORIGINAL_CONFIG_SHELL=${CONFIG_SHELL-/bin/sh}
+ export ORIGINAL_CONFIG_SHELL
+ CONFIG_SHELL=/bin/ksh
+ export CONFIG_SHELL
+ exec $CONFIG_SHELL "$0" --no-reexec ${1+"$@"}
+ else
+ # Try using printf.
+ ECHO='printf %s\n'
+ if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ # Cool, printf works
+ :
+ elif echo_testing_string=`($ORIGINAL_CONFIG_SHELL "$0" --fallback-echo '\t') 2>/dev/null` &&
+ test "X$echo_testing_string" = 'X\t' &&
+ echo_testing_string=`($ORIGINAL_CONFIG_SHELL "$0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ CONFIG_SHELL=$ORIGINAL_CONFIG_SHELL
+ export CONFIG_SHELL
+ SHELL="$CONFIG_SHELL"
+ export SHELL
+ ECHO="$CONFIG_SHELL $0 --fallback-echo"
+ elif echo_testing_string=`($CONFIG_SHELL "$0" --fallback-echo '\t') 2>/dev/null` &&
+ test "X$echo_testing_string" = 'X\t' &&
+ echo_testing_string=`($CONFIG_SHELL "$0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ ECHO="$CONFIG_SHELL $0 --fallback-echo"
+ else
+ # maybe with a smaller string...
+ prev=:
+
+ for cmd in 'echo test' 'sed 2q "$0"' 'sed 10q "$0"' 'sed 20q "$0"' 'sed 50q "$0"'; do
+ if { test "X$echo_test_string" = "X`eval $cmd`"; } 2>/dev/null
+ then
+ break
+ fi
+ prev="$cmd"
+ done
+
+ if test "$prev" != 'sed 50q "$0"'; then
+ echo_test_string=`eval $prev`
+ export echo_test_string
+ exec ${ORIGINAL_CONFIG_SHELL-${CONFIG_SHELL-/bin/sh}} "$0" ${1+"$@"}
+ else
+ # Oops. We lost completely, so just stick with echo.
+ ECHO=echo
+ fi
+ fi
+ fi
+ fi
+ fi
+fi
+
+# Copy echo and quote the copy suitably for passing to libtool from
+# the Makefile, instead of quoting the original, which is used later.
+lt_ECHO=$ECHO
+if test "X$lt_ECHO" = "X$CONFIG_SHELL $0 --fallback-echo"; then
+ lt_ECHO="$CONFIG_SHELL \\\$\$0 --fallback-echo"
+fi
+
+
+
+
+test -n "$DJDIR" || exec 7<&0 </dev/null
+exec 6>&1
+
+# Name of the host.
+# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status,
+# so uname gets run too.
+ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
+
+#
+# Initializations.
+#
+ac_default_prefix=/usr/local
+ac_clean_files=
+ac_config_libobj_dir=.
+LIBOBJS=
+cross_compiling=no
+subdirs=
+MFLAGS=
+MAKEFLAGS=
+
+# Identity of this package.
+PACKAGE_NAME='crac'
+PACKAGE_TARNAME='crac'
+PACKAGE_VERSION='1.5.0'
+PACKAGE_STRING='crac 1.5.0'
+PACKAGE_BUGREPORT='crac-bugs at lists.gforge.inria.fr'
+PACKAGE_URL='http://crac.gforge.inria.fr/'
+
+ac_unique_file="src/crac.cpp"
+# Factoring default headers for most tests.
+ac_includes_default="\
+#include <stdio.h>
+#ifdef HAVE_SYS_TYPES_H
+# include <sys/types.h>
+#endif
+#ifdef HAVE_SYS_STAT_H
+# include <sys/stat.h>
+#endif
+#ifdef STDC_HEADERS
+# include <stdlib.h>
+# include <stddef.h>
+#else
+# ifdef HAVE_STDLIB_H
+# include <stdlib.h>
+# endif
+#endif
+#ifdef HAVE_STRING_H
+# if !defined STDC_HEADERS && defined HAVE_MEMORY_H
+# include <memory.h>
+# endif
+# include <string.h>
+#endif
+#ifdef HAVE_STRINGS_H
+# include <strings.h>
+#endif
+#ifdef HAVE_INTTYPES_H
+# include <inttypes.h>
+#endif
+#ifdef HAVE_STDINT_H
+# include <stdint.h>
+#endif
+#ifdef HAVE_UNISTD_H
+# include <unistd.h>
+#endif"
+
+enable_option_checking=no
+ac_subst_vars='am__EXEEXT_FALSE
+am__EXEEXT_TRUE
+LTLIBOBJS
+INCLUDED_GKARRAYS_FALSE
+INCLUDED_GKARRAYS_TRUE
+subdirs
+INCLUDED_PROGRESSBAR_FALSE
+INCLUDED_PROGRESSBAR_TRUE
+LIBOBJS
+ALLOCA
+RPM_BUILDER
+DEB_BUILDER
+ARCH
+ISODATE
+CXXCPP
+OTOOL64
+OTOOL
+LIPO
+NMEDIT
+DSYMUTIL
+lt_ECHO
+RANLIB
+AR
+OBJDUMP
+NM
+ac_ct_DUMPBIN
+DUMPBIN
+LD
+FGREP
+EGREP
+GREP
+SED
+LIBTOOL
+BUILD_DOC_FALSE
+BUILD_DOC_TRUE
+KPSEWHICH
+PDFTEX
+TEXI2DVI
+LN_S
+CPP
+am__fastdepCXX_FALSE
+am__fastdepCXX_TRUE
+CXXDEPMODE
+ac_ct_CXX
+CXXFLAGS
+CXX
+am__fastdepCC_FALSE
+am__fastdepCC_TRUE
+CCDEPMODE
+AMDEPBACKSLASH
+AMDEP_FALSE
+AMDEP_TRUE
+am__quote
+am__include
+DEPDIR
+OBJEXT
+EXEEXT
+ac_ct_CC
+CPPFLAGS
+LDFLAGS
+CFLAGS
+CC
+host_os
+host_vendor
+host_cpu
+host
+build_os
+build_vendor
+build_cpu
+build
+am__untar
+am__tar
+AMTAR
+am__leading_dot
+SET_MAKE
+AWK
+mkdir_p
+MKDIR_P
+INSTALL_STRIP_PROGRAM
+STRIP
+install_sh
+MAKEINFO
+AUTOHEADER
+AUTOMAKE
+AUTOCONF
+ACLOCAL
+VERSION
+PACKAGE
+CYGPATH_W
+am__isrc
+INSTALL_DATA
+INSTALL_SCRIPT
+INSTALL_PROGRAM
+PACKAGE_DESCRIPTION
+target_alias
+host_alias
+build_alias
+LIBS
+ECHO_T
+ECHO_N
+ECHO_C
+DEFS
+mandir
+localedir
+libdir
+psdir
+pdfdir
+dvidir
+htmldir
+infodir
+docdir
+oldincludedir
+includedir
+localstatedir
+sharedstatedir
+sysconfdir
+datadir
+datarootdir
+libexecdir
+sbindir
+bindir
+program_transform_name
+prefix
+exec_prefix
+PACKAGE_URL
+PACKAGE_BUGREPORT
+PACKAGE_STRING
+PACKAGE_VERSION
+PACKAGE_TARNAME
+PACKAGE_NAME
+PATH_SEPARATOR
+SHELL'
+ac_subst_files=''
+ac_user_opts='
+enable_option_checking
+enable_dependency_tracking
+enable_shared
+enable_static
+with_pic
+enable_fast_install
+with_gnu_ld
+enable_libtool_lock
+enable_debug
+with_included_GkArrays
+with_libGkArrays_prefix
+with_included_ProgressBar
+with_libProgressBar_prefix
+'
+ ac_precious_vars='build_alias
+host_alias
+target_alias
+CC
+CFLAGS
+LDFLAGS
+LIBS
+CPPFLAGS
+CXX
+CXXFLAGS
+CCC
+CPP
+CXXCPP'
+ac_subdirs_all='src/libGkArrays'
+
+# Initialize some variables set by options.
+ac_init_help=
+ac_init_version=false
+ac_unrecognized_opts=
+ac_unrecognized_sep=
+# The variables have the same names as the options, with
+# dashes changed to underlines.
+cache_file=/dev/null
+exec_prefix=NONE
+no_create=
+no_recursion=
+prefix=NONE
+program_prefix=NONE
+program_suffix=NONE
+program_transform_name=s,x,x,
+silent=
+site=
+srcdir=
+verbose=
+x_includes=NONE
+x_libraries=NONE
+
+# Installation directory options.
+# These are left unexpanded so users can "make install exec_prefix=/foo"
+# and all the variables that are supposed to be based on exec_prefix
+# by default will actually change.
+# Use braces instead of parens because sh, perl, etc. also accept them.
+# (The list follows the same order as the GNU Coding Standards.)
+bindir='${exec_prefix}/bin'
+sbindir='${exec_prefix}/sbin'
+libexecdir='${exec_prefix}/libexec'
+datarootdir='${prefix}/share'
+datadir='${datarootdir}'
+sysconfdir='${prefix}/etc'
+sharedstatedir='${prefix}/com'
+localstatedir='${prefix}/var'
+includedir='${prefix}/include'
+oldincludedir='/usr/include'
+docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
+infodir='${datarootdir}/info'
+htmldir='${docdir}'
+dvidir='${docdir}'
+pdfdir='${docdir}'
+psdir='${docdir}'
+libdir='${exec_prefix}/lib'
+localedir='${datarootdir}/locale'
+mandir='${datarootdir}/man'
+
+ac_prev=
+ac_dashdash=
+for ac_option
+do
+ # If the previous option needs an argument, assign it.
+ if test -n "$ac_prev"; then
+ eval $ac_prev=\$ac_option
+ ac_prev=
+ continue
+ fi
+
+ case $ac_option in
+ *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
+ *=) ac_optarg= ;;
+ *) ac_optarg=yes ;;
+ esac
+
+ # Accept the important Cygnus configure options, so we can diagnose typos.
+
+ case $ac_dashdash$ac_option in
+ --)
+ ac_dashdash=yes ;;
+
+ -bindir | --bindir | --bindi | --bind | --bin | --bi)
+ ac_prev=bindir ;;
+ -bindir=* | --bindir=* | --bindi=* | --bind=* | --bin=* | --bi=*)
+ bindir=$ac_optarg ;;
+
+ -build | --build | --buil | --bui | --bu)
+ ac_prev=build_alias ;;
+ -build=* | --build=* | --buil=* | --bui=* | --bu=*)
+ build_alias=$ac_optarg ;;
+
+ -cache-file | --cache-file | --cache-fil | --cache-fi \
+ | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)
+ ac_prev=cache_file ;;
+ -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \
+ | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* | --c=*)
+ cache_file=$ac_optarg ;;
+
+ --config-cache | -C)
+ cache_file=config.cache ;;
+
+ -datadir | --datadir | --datadi | --datad)
+ ac_prev=datadir ;;
+ -datadir=* | --datadir=* | --datadi=* | --datad=*)
+ datadir=$ac_optarg ;;
+
+ -datarootdir | --datarootdir | --datarootdi | --datarootd | --dataroot \
+ | --dataroo | --dataro | --datar)
+ ac_prev=datarootdir ;;
+ -datarootdir=* | --datarootdir=* | --datarootdi=* | --datarootd=* \
+ | --dataroot=* | --dataroo=* | --dataro=* | --datar=*)
+ datarootdir=$ac_optarg ;;
+
+ -disable-* | --disable-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid feature name: $ac_useropt"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"enable_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--disable-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval enable_$ac_useropt=no ;;
+
+ -docdir | --docdir | --docdi | --doc | --do)
+ ac_prev=docdir ;;
+ -docdir=* | --docdir=* | --docdi=* | --doc=* | --do=*)
+ docdir=$ac_optarg ;;
+
+ -dvidir | --dvidir | --dvidi | --dvid | --dvi | --dv)
+ ac_prev=dvidir ;;
+ -dvidir=* | --dvidir=* | --dvidi=* | --dvid=* | --dvi=* | --dv=*)
+ dvidir=$ac_optarg ;;
+
+ -enable-* | --enable-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid feature name: $ac_useropt"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"enable_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--enable-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval enable_$ac_useropt=\$ac_optarg ;;
+
+ -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \
+ | --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \
+ | --exec | --exe | --ex)
+ ac_prev=exec_prefix ;;
+ -exec-prefix=* | --exec_prefix=* | --exec-prefix=* | --exec-prefi=* \
+ | --exec-pref=* | --exec-pre=* | --exec-pr=* | --exec-p=* | --exec-=* \
+ | --exec=* | --exe=* | --ex=*)
+ exec_prefix=$ac_optarg ;;
+
+ -gas | --gas | --ga | --g)
+ # Obsolete; use --with-gas.
+ with_gas=yes ;;
+
+ -help | --help | --hel | --he | -h)
+ ac_init_help=long ;;
+ -help=r* | --help=r* | --hel=r* | --he=r* | -hr*)
+ ac_init_help=recursive ;;
+ -help=s* | --help=s* | --hel=s* | --he=s* | -hs*)
+ ac_init_help=short ;;
+
+ -host | --host | --hos | --ho)
+ ac_prev=host_alias ;;
+ -host=* | --host=* | --hos=* | --ho=*)
+ host_alias=$ac_optarg ;;
+
+ -htmldir | --htmldir | --htmldi | --htmld | --html | --htm | --ht)
+ ac_prev=htmldir ;;
+ -htmldir=* | --htmldir=* | --htmldi=* | --htmld=* | --html=* | --htm=* \
+ | --ht=*)
+ htmldir=$ac_optarg ;;
+
+ -includedir | --includedir | --includedi | --included | --include \
+ | --includ | --inclu | --incl | --inc)
+ ac_prev=includedir ;;
+ -includedir=* | --includedir=* | --includedi=* | --included=* | --include=* \
+ | --includ=* | --inclu=* | --incl=* | --inc=*)
+ includedir=$ac_optarg ;;
+
+ -infodir | --infodir | --infodi | --infod | --info | --inf)
+ ac_prev=infodir ;;
+ -infodir=* | --infodir=* | --infodi=* | --infod=* | --info=* | --inf=*)
+ infodir=$ac_optarg ;;
+
+ -libdir | --libdir | --libdi | --libd)
+ ac_prev=libdir ;;
+ -libdir=* | --libdir=* | --libdi=* | --libd=*)
+ libdir=$ac_optarg ;;
+
+ -libexecdir | --libexecdir | --libexecdi | --libexecd | --libexec \
+ | --libexe | --libex | --libe)
+ ac_prev=libexecdir ;;
+ -libexecdir=* | --libexecdir=* | --libexecdi=* | --libexecd=* | --libexec=* \
+ | --libexe=* | --libex=* | --libe=*)
+ libexecdir=$ac_optarg ;;
+
+ -localedir | --localedir | --localedi | --localed | --locale)
+ ac_prev=localedir ;;
+ -localedir=* | --localedir=* | --localedi=* | --localed=* | --locale=*)
+ localedir=$ac_optarg ;;
+
+ -localstatedir | --localstatedir | --localstatedi | --localstated \
+ | --localstate | --localstat | --localsta | --localst | --locals)
+ ac_prev=localstatedir ;;
+ -localstatedir=* | --localstatedir=* | --localstatedi=* | --localstated=* \
+ | --localstate=* | --localstat=* | --localsta=* | --localst=* | --locals=*)
+ localstatedir=$ac_optarg ;;
+
+ -mandir | --mandir | --mandi | --mand | --man | --ma | --m)
+ ac_prev=mandir ;;
+ -mandir=* | --mandir=* | --mandi=* | --mand=* | --man=* | --ma=* | --m=*)
+ mandir=$ac_optarg ;;
+
+ -nfp | --nfp | --nf)
+ # Obsolete; use --without-fp.
+ with_fp=no ;;
+
+ -no-create | --no-create | --no-creat | --no-crea | --no-cre \
+ | --no-cr | --no-c | -n)
+ no_create=yes ;;
+
+ -no-recursion | --no-recursion | --no-recursio | --no-recursi \
+ | --no-recurs | --no-recur | --no-recu | --no-rec | --no-re | --no-r)
+ no_recursion=yes ;;
+
+ -oldincludedir | --oldincludedir | --oldincludedi | --oldincluded \
+ | --oldinclude | --oldinclud | --oldinclu | --oldincl | --oldinc \
+ | --oldin | --oldi | --old | --ol | --o)
+ ac_prev=oldincludedir ;;
+ -oldincludedir=* | --oldincludedir=* | --oldincludedi=* | --oldincluded=* \
+ | --oldinclude=* | --oldinclud=* | --oldinclu=* | --oldincl=* | --oldinc=* \
+ | --oldin=* | --oldi=* | --old=* | --ol=* | --o=*)
+ oldincludedir=$ac_optarg ;;
+
+ -prefix | --prefix | --prefi | --pref | --pre | --pr | --p)
+ ac_prev=prefix ;;
+ -prefix=* | --prefix=* | --prefi=* | --pref=* | --pre=* | --pr=* | --p=*)
+ prefix=$ac_optarg ;;
+
+ -program-prefix | --program-prefix | --program-prefi | --program-pref \
+ | --program-pre | --program-pr | --program-p)
+ ac_prev=program_prefix ;;
+ -program-prefix=* | --program-prefix=* | --program-prefi=* \
+ | --program-pref=* | --program-pre=* | --program-pr=* | --program-p=*)
+ program_prefix=$ac_optarg ;;
+
+ -program-suffix | --program-suffix | --program-suffi | --program-suff \
+ | --program-suf | --program-su | --program-s)
+ ac_prev=program_suffix ;;
+ -program-suffix=* | --program-suffix=* | --program-suffi=* \
+ | --program-suff=* | --program-suf=* | --program-su=* | --program-s=*)
+ program_suffix=$ac_optarg ;;
+
+ -program-transform-name | --program-transform-name \
+ | --program-transform-nam | --program-transform-na \
+ | --program-transform-n | --program-transform- \
+ | --program-transform | --program-transfor \
+ | --program-transfo | --program-transf \
+ | --program-trans | --program-tran \
+ | --progr-tra | --program-tr | --program-t)
+ ac_prev=program_transform_name ;;
+ -program-transform-name=* | --program-transform-name=* \
+ | --program-transform-nam=* | --program-transform-na=* \
+ | --program-transform-n=* | --program-transform-=* \
+ | --program-transform=* | --program-transfor=* \
+ | --program-transfo=* | --program-transf=* \
+ | --program-trans=* | --program-tran=* \
+ | --progr-tra=* | --program-tr=* | --program-t=*)
+ program_transform_name=$ac_optarg ;;
+
+ -pdfdir | --pdfdir | --pdfdi | --pdfd | --pdf | --pd)
+ ac_prev=pdfdir ;;
+ -pdfdir=* | --pdfdir=* | --pdfdi=* | --pdfd=* | --pdf=* | --pd=*)
+ pdfdir=$ac_optarg ;;
+
+ -psdir | --psdir | --psdi | --psd | --ps)
+ ac_prev=psdir ;;
+ -psdir=* | --psdir=* | --psdi=* | --psd=* | --ps=*)
+ psdir=$ac_optarg ;;
+
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil)
+ silent=yes ;;
+
+ -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
+ ac_prev=sbindir ;;
+ -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
+ | --sbi=* | --sb=*)
+ sbindir=$ac_optarg ;;
+
+ -sharedstatedir | --sharedstatedir | --sharedstatedi \
+ | --sharedstated | --sharedstate | --sharedstat | --sharedsta \
+ | --sharedst | --shareds | --shared | --share | --shar \
+ | --sha | --sh)
+ ac_prev=sharedstatedir ;;
+ -sharedstatedir=* | --sharedstatedir=* | --sharedstatedi=* \
+ | --sharedstated=* | --sharedstate=* | --sharedstat=* | --sharedsta=* \
+ | --sharedst=* | --shareds=* | --shared=* | --share=* | --shar=* \
+ | --sha=* | --sh=*)
+ sharedstatedir=$ac_optarg ;;
+
+ -site | --site | --sit)
+ ac_prev=site ;;
+ -site=* | --site=* | --sit=*)
+ site=$ac_optarg ;;
+
+ -srcdir | --srcdir | --srcdi | --srcd | --src | --sr)
+ ac_prev=srcdir ;;
+ -srcdir=* | --srcdir=* | --srcdi=* | --srcd=* | --src=* | --sr=*)
+ srcdir=$ac_optarg ;;
+
+ -sysconfdir | --sysconfdir | --sysconfdi | --sysconfd | --sysconf \
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+ ac_prev=sysconfdir ;;
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+
+Usage: $0 [OPTION]... [VAR=VALUE]...
+
+To assign environment variables (e.g., CC, CFLAGS...), specify them as
+VAR=VALUE. See below for descriptions of some of the useful variables.
+
+Defaults for the options are specified in brackets.
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+ --datadir=DIR read-only architecture-independent data [DATAROOTDIR]
+ --infodir=DIR info documentation [DATAROOTDIR/info]
+ --localedir=DIR locale-dependent data [DATAROOTDIR/locale]
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+ --pdfdir=DIR pdf documentation [DOCDIR]
+ --psdir=DIR ps documentation [DOCDIR]
+_ACEOF
+
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+Program names:
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+_ACEOF
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+
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+ case $ac_init_help in
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+ cat <<\_ACEOF
+
+Optional Features:
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+ --disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
+ --enable-FEATURE[=ARG] include FEATURE [ARG=yes]
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+ --enable-shared[=PKGS] build shared libraries [default=no]
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+ --enable-fast-install[=PKGS]
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+ --enable-debug enable debugging informations
+
+Optional Packages:
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+ --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no)
+ --with-pic try to use only PIC/non-PIC objects [default=use
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+ --with-gnu-ld assume the C compiler uses GNU ld [default=no]
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+ LIBS libraries to pass to the linker, e.g. -l<library>
+ CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
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+ CXX C++ compiler command
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+ CXXCPP C++ preprocessor
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+Use these variables to override the choices made by `configure' or to help
+it to find libraries and programs with nonstandard names/locations.
+
+Report bugs to <crac-bugs at lists.gforge.inria.fr>.
+crac home page: <http://crac.gforge.inria.fr/>.
+_ACEOF
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+fi
+
+if test "$ac_init_help" = "recursive"; then
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+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
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+test -n "$ac_init_help" && exit $ac_status
+if $ac_init_version; then
+ cat <<\_ACEOF
+crac configure 1.5.0
+generated by GNU Autoconf 2.67
+
+Copyright (C) 2010 Free Software Foundation, Inc.
+This configure script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it.
+
+
+*******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+*******************************************************************************
+
+_ACEOF
+ exit
+fi
+
+## ------------------------ ##
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+ac_fn_cxx_try_compile ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext
+ if { { ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compile") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_cxx_try_compile
+
+# ac_fn_c_try_cpp LINENO
+# ----------------------
+# Try to preprocess conftest.$ac_ext, and return whether this succeeded.
+ac_fn_c_try_cpp ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if { { ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } > conftest.i && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_cpp
+
+# ac_fn_c_try_link LINENO
+# -----------------------
+# Try to link conftest.$ac_ext, and return whether this succeeded.
+ac_fn_c_try_link ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext conftest$ac_exeext
+ if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ # Delete the IPA/IPO (Inter Procedural Analysis/Optimization) information
+ # created by the PGI compiler (conftest_ipa8_conftest.oo), as it would
+ # interfere with the next link command; also delete a directory that is
+ # left behind by Apple's compiler. We do this before executing the actions.
+ rm -rf conftest.dSYM conftest_ipa8_conftest.oo
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_link
+
+# ac_fn_c_check_header_compile LINENO HEADER VAR INCLUDES
+# -------------------------------------------------------
+# Tests whether HEADER exists and can be compiled using the include files in
+# INCLUDES, setting the cache variable VAR accordingly.
+ac_fn_c_check_header_compile ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+#include <$2>
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ eval "$3=yes"
+else
+ eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_c_check_header_compile
+
+# ac_fn_c_try_run LINENO
+# ----------------------
+# Try to link conftest.$ac_ext, and return whether this succeeded. Assumes
+# that executables *can* be run.
+ac_fn_c_try_run ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && { ac_try='./conftest$ac_exeext'
+ { { case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=$ac_status
+fi
+ rm -rf conftest.dSYM conftest_ipa8_conftest.oo
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_run
+
+# ac_fn_c_check_func LINENO FUNC VAR
+# ----------------------------------
+# Tests whether FUNC exists, setting the cache variable VAR accordingly
+ac_fn_c_check_func ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+/* Define $2 to an innocuous variant, in case <limits.h> declares $2.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define $2 innocuous_$2
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $2 (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $2
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $2 ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_$2 || defined __stub___$2
+choke me
+#endif
+
+int
+main ()
+{
+return $2 ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ eval "$3=yes"
+else
+ eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_c_check_func
+
+# ac_fn_cxx_try_cpp LINENO
+# ------------------------
+# Try to preprocess conftest.$ac_ext, and return whether this succeeded.
+ac_fn_cxx_try_cpp ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if { { ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } > conftest.i && {
+ test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_cxx_try_cpp
+
+# ac_fn_cxx_try_link LINENO
+# -------------------------
+# Try to link conftest.$ac_ext, and return whether this succeeded.
+ac_fn_cxx_try_link ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext conftest$ac_exeext
+ if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ # Delete the IPA/IPO (Inter Procedural Analysis/Optimization) information
+ # created by the PGI compiler (conftest_ipa8_conftest.oo), as it would
+ # interfere with the next link command; also delete a directory that is
+ # left behind by Apple's compiler. We do this before executing the actions.
+ rm -rf conftest.dSYM conftest_ipa8_conftest.oo
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_cxx_try_link
+
+# ac_fn_cxx_check_func LINENO FUNC VAR
+# ------------------------------------
+# Tests whether FUNC exists, setting the cache variable VAR accordingly
+ac_fn_cxx_check_func ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+/* Define $2 to an innocuous variant, in case <limits.h> declares $2.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define $2 innocuous_$2
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $2 (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $2
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $2 ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_$2 || defined __stub___$2
+choke me
+#endif
+
+int
+main ()
+{
+return $2 ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+ eval "$3=yes"
+else
+ eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_cxx_check_func
+
+# ac_fn_cxx_try_run LINENO
+# ------------------------
+# Try to link conftest.$ac_ext, and return whether this succeeded. Assumes
+# that executables *can* be run.
+ac_fn_cxx_try_run ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && { ac_try='./conftest$ac_exeext'
+ { { case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=$ac_status
+fi
+ rm -rf conftest.dSYM conftest_ipa8_conftest.oo
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_cxx_try_run
+
+# ac_fn_cxx_check_header_mongrel LINENO HEADER VAR INCLUDES
+# ---------------------------------------------------------
+# Tests whether HEADER exists, giving a warning if it cannot be compiled using
+# the include files in INCLUDES and setting the cache variable VAR
+# accordingly.
+ac_fn_cxx_check_header_mongrel ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if eval "test \"\${$3+set}\"" = set; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+else
+ # Is the header compilable?
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 usability" >&5
+$as_echo_n "checking $2 usability... " >&6; }
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+#include <$2>
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_header_compiler=yes
+else
+ ac_header_compiler=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_compiler" >&5
+$as_echo "$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 presence" >&5
+$as_echo_n "checking $2 presence... " >&6; }
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <$2>
+_ACEOF
+if ac_fn_cxx_try_cpp "$LINENO"; then :
+ ac_header_preproc=yes
+else
+ ac_header_preproc=no
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_preproc" >&5
+$as_echo "$ac_header_preproc" >&6; }
+
+# So? What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_cxx_preproc_warn_flag in #((
+ yes:no: )
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&5
+$as_echo "$as_me: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
+ ;;
+ no:yes:* )
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: present but cannot be compiled" >&5
+$as_echo "$as_me: WARNING: $2: present but cannot be compiled" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: check for missing prerequisite headers?" >&5
+$as_echo "$as_me: WARNING: $2: check for missing prerequisite headers?" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: see the Autoconf documentation" >&5
+$as_echo "$as_me: WARNING: $2: see the Autoconf documentation" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&5
+$as_echo "$as_me: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
+( $as_echo "## ---------------------------------------------- ##
+## Report this to crac-bugs at lists.gforge.inria.fr ##
+## ---------------------------------------------- ##"
+ ) | sed "s/^/$as_me: WARNING: /" >&2
+ ;;
+esac
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ eval "$3=\$ac_header_compiler"
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+fi
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_cxx_check_header_mongrel
+
+# ac_fn_cxx_check_type LINENO TYPE VAR INCLUDES
+# ---------------------------------------------
+# Tests whether TYPE exists after having included INCLUDES, setting cache
+# variable VAR accordingly.
+ac_fn_cxx_check_type ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ eval "$3=no"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+int
+main ()
+{
+if (sizeof ($2))
+ return 0;
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+int
+main ()
+{
+if (sizeof (($2)))
+ return 0;
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+
+else
+ eval "$3=yes"
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_cxx_check_type
+
+# ac_fn_c_find_intX_t LINENO BITS VAR
+# -----------------------------------
+# Finds a signed integer type with width BITS, setting cache variable VAR
+# accordingly.
+ac_fn_c_find_intX_t ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for int$2_t" >&5
+$as_echo_n "checking for int$2_t... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ eval "$3=no"
+ # Order is important - never check a type that is potentially smaller
+ # than half of the expected target width.
+ for ac_type in int$2_t 'int' 'long int' \
+ 'long long int' 'short int' 'signed char'; do
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$ac_includes_default
+ enum { N = $2 / 2 - 1 };
+int
+main ()
+{
+static int test_array [1 - 2 * !(0 < ($ac_type) ((((($ac_type) 1 << N) << N) - 1) * 2 + 1))];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$ac_includes_default
+ enum { N = $2 / 2 - 1 };
+int
+main ()
+{
+static int test_array [1 - 2 * !(($ac_type) ((((($ac_type) 1 << N) << N) - 1) * 2 + 1)
+ < ($ac_type) ((((($ac_type) 1 << N) << N) - 1) * 2 + 2))];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+
+else
+ case $ac_type in #(
+ int$2_t) :
+ eval "$3=yes" ;; #(
+ *) :
+ eval "$3=\$ac_type" ;;
+esac
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ if eval test \"x\$"$3"\" = x"no"; then :
+
+else
+ break
+fi
+ done
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_c_find_intX_t
+
+# ac_fn_cxx_check_member LINENO AGGR MEMBER VAR INCLUDES
+# ------------------------------------------------------
+# Tries to find if the field MEMBER exists in type AGGR, after including
+# INCLUDES, setting cache variable VAR accordingly.
+ac_fn_cxx_check_member ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2.$3" >&5
+$as_echo_n "checking for $2.$3... " >&6; }
+if eval "test \"\${$4+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$5
+int
+main ()
+{
+static $2 ac_aggr;
+if (ac_aggr.$3)
+return 0;
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ eval "$4=yes"
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$5
+int
+main ()
+{
+static $2 ac_aggr;
+if (sizeof ac_aggr.$3)
+return 0;
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ eval "$4=yes"
+else
+ eval "$4=no"
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+eval ac_res=\$$4
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_cxx_check_member
+
+# ac_fn_c_find_uintX_t LINENO BITS VAR
+# ------------------------------------
+# Finds an unsigned integer type with width BITS, setting cache variable VAR
+# accordingly.
+ac_fn_c_find_uintX_t ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for uint$2_t" >&5
+$as_echo_n "checking for uint$2_t... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ eval "$3=no"
+ # Order is important - never check a type that is potentially smaller
+ # than half of the expected target width.
+ for ac_type in uint$2_t 'unsigned int' 'unsigned long int' \
+ 'unsigned long long int' 'unsigned short int' 'unsigned char'; do
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !((($ac_type) -1 >> ($2 / 2 - 1)) >> ($2 / 2 - 1) == 3)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ case $ac_type in #(
+ uint$2_t) :
+ eval "$3=yes" ;; #(
+ *) :
+ eval "$3=\$ac_type" ;;
+esac
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ if eval test \"x\$"$3"\" = x"no"; then :
+
+else
+ break
+fi
+ done
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_c_find_uintX_t
+cat >config.log <<_ACEOF
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by crac $as_me 1.5.0, which was
+generated by GNU Autoconf 2.67. Invocation command line was
+
+ $ $0 $@
+
+_ACEOF
+exec 5>>config.log
+{
+cat <<_ASUNAME
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = `(hostname || uname -n) 2>/dev/null | sed 1q`
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null || echo unknown`
+
+/bin/arch = `(/bin/arch) 2>/dev/null || echo unknown`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null || echo unknown`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown`
+/usr/bin/hostinfo = `(/usr/bin/hostinfo) 2>/dev/null || echo unknown`
+/bin/machine = `(/bin/machine) 2>/dev/null || echo unknown`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null || echo unknown`
+/bin/universe = `(/bin/universe) 2>/dev/null || echo unknown`
+
+_ASUNAME
+
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ $as_echo "PATH: $as_dir"
+ done
+IFS=$as_save_IFS
+
+} >&5
+
+cat >&5 <<_ACEOF
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+_ACEOF
+
+
+# Keep a trace of the command line.
+# Strip out --no-create and --no-recursion so they do not pile up.
+# Strip out --silent because we don't want to record it for future runs.
+# Also quote any args containing shell meta-characters.
+# Make two passes to allow for proper duplicate-argument suppression.
+ac_configure_args=
+ac_configure_args0=
+ac_configure_args1=
+ac_must_keep_next=false
+for ac_pass in 1 2
+do
+ for ac_arg
+ do
+ case $ac_arg in
+ -no-create | --no-c* | -n | -no-recursion | --no-r*) continue ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil)
+ continue ;;
+ *\'*)
+ ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ case $ac_pass in
+ 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;;
+ 2)
+ as_fn_append ac_configure_args1 " '$ac_arg'"
+ if test $ac_must_keep_next = true; then
+ ac_must_keep_next=false # Got value, back to normal.
+ else
+ case $ac_arg in
+ *=* | --config-cache | -C | -disable-* | --disable-* \
+ | -enable-* | --enable-* | -gas | --g* | -nfp | --nf* \
+ | -q | -quiet | --q* | -silent | --sil* | -v | -verb* \
+ | -with-* | --with-* | -without-* | --without-* | --x)
+ case "$ac_configure_args0 " in
+ "$ac_configure_args1"*" '$ac_arg' "* ) continue ;;
+ esac
+ ;;
+ -* ) ac_must_keep_next=true ;;
+ esac
+ fi
+ as_fn_append ac_configure_args " '$ac_arg'"
+ ;;
+ esac
+ done
+done
+{ ac_configure_args0=; unset ac_configure_args0;}
+{ ac_configure_args1=; unset ac_configure_args1;}
+
+# When interrupted or exit'd, cleanup temporary files, and complete
+# config.log. We remove comments because anyway the quotes in there
+# would cause problems or look ugly.
+# WARNING: Use '\'' to represent an apostrophe within the trap.
+# WARNING: Do not start the trap code with a newline, due to a FreeBSD 4.0 bug.
+trap 'exit_status=$?
+ # Save into config.log some information that might help in debugging.
+ {
+ echo
+
+ $as_echo "## ---------------- ##
+## Cache variables. ##
+## ---------------- ##"
+ echo
+ # The following way of writing the cache mishandles newlines in values,
+(
+ for ac_var in `(set) 2>&1 | sed -n '\''s/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'\''`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) { eval $ac_var=; unset $ac_var;} ;;
+ esac ;;
+ esac
+ done
+ (set) 2>&1 |
+ case $as_nl`(ac_space='\'' '\''; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ sed -n \
+ "s/'\''/'\''\\\\'\'''\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\''\\2'\''/p"
+ ;; #(
+ *)
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+)
+ echo
+
+ $as_echo "## ----------------- ##
+## Output variables. ##
+## ----------------- ##"
+ echo
+ for ac_var in $ac_subst_vars
+ do
+ eval ac_val=\$$ac_var
+ case $ac_val in
+ *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+ esac
+ $as_echo "$ac_var='\''$ac_val'\''"
+ done | sort
+ echo
+
+ if test -n "$ac_subst_files"; then
+ $as_echo "## ------------------- ##
+## File substitutions. ##
+## ------------------- ##"
+ echo
+ for ac_var in $ac_subst_files
+ do
+ eval ac_val=\$$ac_var
+ case $ac_val in
+ *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+ esac
+ $as_echo "$ac_var='\''$ac_val'\''"
+ done | sort
+ echo
+ fi
+
+ if test -s confdefs.h; then
+ $as_echo "## ----------- ##
+## confdefs.h. ##
+## ----------- ##"
+ echo
+ cat confdefs.h
+ echo
+ fi
+ test "$ac_signal" != 0 &&
+ $as_echo "$as_me: caught signal $ac_signal"
+ $as_echo "$as_me: exit $exit_status"
+ } >&5
+ rm -f core *.core core.conftest.* &&
+ rm -f -r conftest* confdefs* conf$$* $ac_clean_files &&
+ exit $exit_status
+' 0
+for ac_signal in 1 2 13 15; do
+ trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal
+done
+ac_signal=0
+
+# confdefs.h avoids OS command line length limits that DEFS can exceed.
+rm -f -r conftest* confdefs.h
+
+$as_echo "/* confdefs.h */" > confdefs.h
+
+# Predefined preprocessor variables.
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_NAME "$PACKAGE_NAME"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_TARNAME "$PACKAGE_TARNAME"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_VERSION "$PACKAGE_VERSION"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_STRING "$PACKAGE_STRING"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_URL "$PACKAGE_URL"
+_ACEOF
+
+
+# Let the site file select an alternate cache file if it wants to.
+# Prefer an explicitly selected file to automatically selected ones.
+ac_site_file1=NONE
+ac_site_file2=NONE
+if test -n "$CONFIG_SITE"; then
+ # We do not want a PATH search for config.site.
+ case $CONFIG_SITE in #((
+ -*) ac_site_file1=./$CONFIG_SITE;;
+ */*) ac_site_file1=$CONFIG_SITE;;
+ *) ac_site_file1=./$CONFIG_SITE;;
+ esac
+elif test "x$prefix" != xNONE; then
+ ac_site_file1=$prefix/share/config.site
+ ac_site_file2=$prefix/etc/config.site
+else
+ ac_site_file1=$ac_default_prefix/share/config.site
+ ac_site_file2=$ac_default_prefix/etc/config.site
+fi
+for ac_site_file in "$ac_site_file1" "$ac_site_file2"
+do
+ test "x$ac_site_file" = xNONE && continue
+ if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5
+$as_echo "$as_me: loading site script $ac_site_file" >&6;}
+ sed 's/^/| /' "$ac_site_file" >&5
+ . "$ac_site_file" \
+ || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "failed to load site script $ac_site_file
+See \`config.log' for more details" "$LINENO" 5 ; }
+ fi
+done
+
+if test -r "$cache_file"; then
+ # Some versions of bash will fail to source /dev/null (special files
+ # actually), so we avoid doing that. DJGPP emulates it as a regular file.
+ if test /dev/null != "$cache_file" && test -f "$cache_file"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5
+$as_echo "$as_me: loading cache $cache_file" >&6;}
+ case $cache_file in
+ [\\/]* | ?:[\\/]* ) . "$cache_file";;
+ *) . "./$cache_file";;
+ esac
+ fi
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5
+$as_echo "$as_me: creating cache $cache_file" >&6;}
+ >$cache_file
+fi
+
+# Check that the precious variables saved in the cache have kept the same
+# value.
+ac_cache_corrupted=false
+for ac_var in $ac_precious_vars; do
+ eval ac_old_set=\$ac_cv_env_${ac_var}_set
+ eval ac_new_set=\$ac_env_${ac_var}_set
+ eval ac_old_val=\$ac_cv_env_${ac_var}_value
+ eval ac_new_val=\$ac_env_${ac_var}_value
+ case $ac_old_set,$ac_new_set in
+ set,)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
+$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,set)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5
+$as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,);;
+ *)
+ if test "x$ac_old_val" != "x$ac_new_val"; then
+ # differences in whitespace do not lead to failure.
+ ac_old_val_w=`echo x $ac_old_val`
+ ac_new_val_w=`echo x $ac_new_val`
+ if test "$ac_old_val_w" != "$ac_new_val_w"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5
+$as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
+ ac_cache_corrupted=:
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5
+$as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;}
+ eval $ac_var=\$ac_old_val
+ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5
+$as_echo "$as_me: former value: \`$ac_old_val'" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5
+$as_echo "$as_me: current value: \`$ac_new_val'" >&2;}
+ fi;;
+ esac
+ # Pass precious variables to config.status.
+ if test "$ac_new_set" = set; then
+ case $ac_new_val in
+ *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
+ *) ac_arg=$ac_var=$ac_new_val ;;
+ esac
+ case " $ac_configure_args " in
+ *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy.
+ *) as_fn_append ac_configure_args " '$ac_arg'" ;;
+ esac
+ fi
+done
+if $ac_cache_corrupted; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
+$as_echo "$as_me: error: changes in the environment can compromise the build" >&2;}
+ as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
+fi
+## -------------------- ##
+## Main body of script. ##
+## -------------------- ##
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+
+PACKAGE_DESCRIPTION="Crac is a tool to analyse RNA-Seq data provided by NGS"
+
+
+
+
+
+
+if test x"$CFLAGS" == "x"; then :
+ CFLAGS=""
+fi
+if test x"$CPPFLAGS" == "x"; then :
+ CPPFLAGS=""
+fi
+if test x"$CXXFLAGS" == "x"; then :
+ CXXFLAGS=""
+fi
+if test x"$LDFLAGS" == "x"; then :
+ LDFLAGS=""
+fi
+
+ac_aux_dir=
+for ac_dir in config "$srcdir"/config; do
+ if test -f "$ac_dir/install-sh"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install-sh -c"
+ break
+ elif test -f "$ac_dir/install.sh"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install.sh -c"
+ break
+ elif test -f "$ac_dir/shtool"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/shtool install -c"
+ break
+ fi
+done
+if test -z "$ac_aux_dir"; then
+ as_fn_error $? "cannot find install-sh, install.sh, or shtool in config \"$srcdir\"/config" "$LINENO" 5
+fi
+
+# These three variables are undocumented and unsupported,
+# and are intended to be withdrawn in a future Autoconf release.
+# They can cause serious problems if a builder's source tree is in a directory
+# whose full name contains unusual characters.
+ac_config_guess="$SHELL $ac_aux_dir/config.guess" # Please don't use this var.
+ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var.
+ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var.
+
+
+
+ac_config_headers="$ac_config_headers config/config.h"
+
+
+am__api_version='1.11'
+
+# Find a good install program. We prefer a C program (faster),
+# so one script is as good as another. But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AmigaOS /C/install, which installs bootblocks on floppy discs
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# OS/2's system install, which has a completely different semantic
+# ./install, which can be erroneously created by make from ./install.sh.
+# Reject install programs that cannot install multiple files.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5
+$as_echo_n "checking for a BSD-compatible install... " >&6; }
+if test -z "$INSTALL"; then
+if test "${ac_cv_path_install+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ # Account for people who put trailing slashes in PATH elements.
+case $as_dir/ in #((
+ ./ | .// | /[cC]/* | \
+ /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
+ ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \
+ /usr/ucb/* ) ;;
+ *)
+ # OSF1 and SCO ODT 3.0 have their own names for install.
+ # Don't use installbsd from OSF since it installs stuff as root
+ # by default.
+ for ac_prog in ginstall scoinst install; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
+ if test $ac_prog = install &&
+ grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # AIX install. It has an incompatible calling convention.
+ :
+ elif test $ac_prog = install &&
+ grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # program-specific install script used by HP pwplus--don't use.
+ :
+ else
+ rm -rf conftest.one conftest.two conftest.dir
+ echo one > conftest.one
+ echo two > conftest.two
+ mkdir conftest.dir
+ if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" &&
+ test -s conftest.one && test -s conftest.two &&
+ test -s conftest.dir/conftest.one &&
+ test -s conftest.dir/conftest.two
+ then
+ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
+ break 3
+ fi
+ fi
+ fi
+ done
+ done
+ ;;
+esac
+
+ done
+IFS=$as_save_IFS
+
+rm -rf conftest.one conftest.two conftest.dir
+
+fi
+ if test "${ac_cv_path_install+set}" = set; then
+ INSTALL=$ac_cv_path_install
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for INSTALL within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ INSTALL=$ac_install_sh
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5
+$as_echo "$INSTALL" >&6; }
+
+# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
+# It thinks the first close brace ends the variable substitution.
+test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5
+$as_echo_n "checking whether build environment is sane... " >&6; }
+# Just in case
+sleep 1
+echo timestamp > conftest.file
+# Reject unsafe characters in $srcdir or the absolute working directory
+# name. Accept space and tab only in the latter.
+am_lf='
+'
+case `pwd` in
+ *[\\\"\#\$\&\'\`$am_lf]*)
+ as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5 ;;
+esac
+case $srcdir in
+ *[\\\"\#\$\&\'\`$am_lf\ \ ]*)
+ as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5 ;;
+esac
+
+# Do `set' in a subshell so we don't clobber the current shell's
+# arguments. Must try -L first in case configure is actually a
+# symlink; some systems play weird games with the mod time of symlinks
+# (eg FreeBSD returns the mod time of the symlink's containing
+# directory).
+if (
+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
+ if test "$*" = "X"; then
+ # -L didn't work.
+ set X `ls -t "$srcdir/configure" conftest.file`
+ fi
+ rm -f conftest.file
+ if test "$*" != "X $srcdir/configure conftest.file" \
+ && test "$*" != "X conftest.file $srcdir/configure"; then
+
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ as_fn_error $? "ls -t appears to fail. Make sure there is not a broken
+alias in your environment" "$LINENO" 5
+ fi
+
+ test "$2" = conftest.file
+ )
+then
+ # Ok.
+ :
+else
+ as_fn_error $? "newly created file is older than distributed files!
+Check your system clock" "$LINENO" 5
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+test "$program_prefix" != NONE &&
+ program_transform_name="s&^&$program_prefix&;$program_transform_name"
+# Use a double $ so make ignores it.
+test "$program_suffix" != NONE &&
+ program_transform_name="s&\$&$program_suffix&;$program_transform_name"
+# Double any \ or $.
+# By default was `s,x,x', remove it if useless.
+ac_script='s/[\\$]/&&/g;s/;s,x,x,$//'
+program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`
+
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
+
+if test x"${MISSING+set}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;;
+ *)
+ MISSING="\${SHELL} $am_aux_dir/missing" ;;
+ esac
+fi
+# Use eval to expand $SHELL
+if eval "$MISSING --run true"; then
+ am_missing_run="$MISSING --run "
+else
+ am_missing_run=
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`missing' script is too old or missing" >&5
+$as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
+fi
+
+if test x"${install_sh}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
+ *)
+ install_sh="\${SHELL} $am_aux_dir/install-sh"
+ esac
+fi
+
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'. However `strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
+# will honor the `STRIP' environment variable to overrule this program.
+if test "$cross_compiling" != no; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
+set dummy ${ac_tool_prefix}strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_STRIP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$STRIP"; then
+ ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_STRIP="${ac_tool_prefix}strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+STRIP=$ac_cv_prog_STRIP
+if test -n "$STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5
+$as_echo "$STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_STRIP"; then
+ ac_ct_STRIP=$STRIP
+ # Extract the first word of "strip", so it can be a program name with args.
+set dummy strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_STRIP"; then
+ ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_STRIP="strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
+if test -n "$ac_ct_STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5
+$as_echo "$ac_ct_STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_STRIP" = x; then
+ STRIP=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ STRIP=$ac_ct_STRIP
+ fi
+else
+ STRIP="$ac_cv_prog_STRIP"
+fi
+
+fi
+INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5
+$as_echo_n "checking for a thread-safe mkdir -p... " >&6; }
+if test -z "$MKDIR_P"; then
+ if test "${ac_cv_path_mkdir+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/opt/sfw/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in mkdir gmkdir; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue
+ case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #(
+ 'mkdir (GNU coreutils) '* | \
+ 'mkdir (coreutils) '* | \
+ 'mkdir (fileutils) '4.1*)
+ ac_cv_path_mkdir=$as_dir/$ac_prog$ac_exec_ext
+ break 3;;
+ esac
+ done
+ done
+ done
+IFS=$as_save_IFS
+
+fi
+
+ test -d ./--version && rmdir ./--version
+ if test "${ac_cv_path_mkdir+set}" = set; then
+ MKDIR_P="$ac_cv_path_mkdir -p"
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for MKDIR_P within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ MKDIR_P="$ac_install_sh -d"
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
+$as_echo "$MKDIR_P" >&6; }
+
+mkdir_p="$MKDIR_P"
+case $mkdir_p in
+ [\\/$]* | ?:[\\/]*) ;;
+ */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
+esac
+
+for ac_prog in gawk mawk nawk awk
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_AWK+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$AWK"; then
+ ac_cv_prog_AWK="$AWK" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_AWK="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+AWK=$ac_cv_prog_AWK
+if test -n "$AWK"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5
+$as_echo "$AWK" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$AWK" && break
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
+set x ${MAKE-make}
+ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
+if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.make <<\_ACEOF
+SHELL = /bin/sh
+all:
+ @echo '@@@%%%=$(MAKE)=@@@%%%'
+_ACEOF
+# GNU make sometimes prints "make[1]: Entering ...", which would confuse us.
+case `${MAKE-make} -f conftest.make 2>/dev/null` in
+ *@@@%%%=?*=@@@%%%*)
+ eval ac_cv_prog_make_${ac_make}_set=yes;;
+ *)
+ eval ac_cv_prog_make_${ac_make}_set=no;;
+esac
+rm -f conftest.make
+fi
+if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ SET_MAKE=
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ SET_MAKE="MAKE=${MAKE-make}"
+fi
+
+rm -rf .tst 2>/dev/null
+mkdir .tst 2>/dev/null
+if test -d .tst; then
+ am__leading_dot=.
+else
+ am__leading_dot=_
+fi
+rmdir .tst 2>/dev/null
+
+if test "`cd $srcdir && pwd`" != "`pwd`"; then
+ # Use -I$(srcdir) only when $(srcdir) != ., so that make's output
+ # is not polluted with repeated "-I."
+ am__isrc=' -I$(srcdir)'
+ # test to see if srcdir already configured
+ if test -f $srcdir/config.status; then
+ as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5
+ fi
+fi
+
+# test whether we have cygpath
+if test -z "$CYGPATH_W"; then
+ if (cygpath --version) >/dev/null 2>/dev/null; then
+ CYGPATH_W='cygpath -w'
+ else
+ CYGPATH_W=echo
+ fi
+fi
+
+
+# Define the identity of the package.
+ PACKAGE='crac'
+ VERSION='1.5.0'
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE "$PACKAGE"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define VERSION "$VERSION"
+_ACEOF
+
+# Some tools Automake needs.
+
+ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"}
+
+
+AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"}
+
+
+AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"}
+
+
+AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"}
+
+
+MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
+
+# We need awk for the "check" target. The system "awk" is bad on
+# some platforms.
+# Always define AMTAR for backward compatibility.
+
+AMTAR=${AMTAR-"${am_missing_run}tar"}
+
+am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'
+
+
+
+
+
+
+# Make sure we can run config.sub.
+$SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 ||
+ as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5
+$as_echo_n "checking build system type... " >&6; }
+if test "${ac_cv_build+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_build_alias=$build_alias
+test "x$ac_build_alias" = x &&
+ ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"`
+test "x$ac_build_alias" = x &&
+ as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5
+ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` ||
+ as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5
+$as_echo "$ac_cv_build" >&6; }
+case $ac_cv_build in
+*-*-*) ;;
+*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5 ;;
+esac
+build=$ac_cv_build
+ac_save_IFS=$IFS; IFS='-'
+set x $ac_cv_build
+shift
+build_cpu=$1
+build_vendor=$2
+shift; shift
+# Remember, the first character of IFS is used to create $*,
+# except with old shells:
+build_os=$*
+IFS=$ac_save_IFS
+case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5
+$as_echo_n "checking host system type... " >&6; }
+if test "${ac_cv_host+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "x$host_alias" = x; then
+ ac_cv_host=$ac_cv_build
+else
+ ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` ||
+ as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_host" >&5
+$as_echo "$ac_cv_host" >&6; }
+case $ac_cv_host in
+*-*-*) ;;
+*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5 ;;
+esac
+host=$ac_cv_host
+ac_save_IFS=$IFS; IFS='-'
+set x $ac_cv_host
+shift
+host_cpu=$1
+host_vendor=$2
+shift; shift
+# Remember, the first character of IFS is used to create $*,
+# except with old shells:
+host_os=$*
+IFS=$ac_save_IFS
+case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac
+
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+
+
+
+for ac_prog in gawk mawk nawk awk
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_AWK+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$AWK"; then
+ ac_cv_prog_AWK="$AWK" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_AWK="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+AWK=$ac_cv_prog_AWK
+if test -n "$AWK"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5
+$as_echo "$AWK" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$AWK" && break
+done
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}gcc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="${ac_tool_prefix}gcc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_CC"; then
+ ac_ct_CC=$CC
+ # Extract the first word of "gcc", so it can be a program name with args.
+set dummy gcc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CC="gcc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+else
+ CC="$ac_cv_prog_CC"
+fi
+
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}cc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="${ac_tool_prefix}cc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ fi
+fi
+if test -z "$CC"; then
+ # Extract the first word of "cc", so it can be a program name with args.
+set dummy cc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+ ac_prog_rejected=no
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
+ ac_prog_rejected=yes
+ continue
+ fi
+ ac_cv_prog_CC="cc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+if test $ac_prog_rejected = yes; then
+ # We found a bogon in the path, so make sure we never use it.
+ set dummy $ac_cv_prog_CC
+ shift
+ if test $# != 0; then
+ # We chose a different compiler from the bogus one.
+ # However, it has the same basename, so the bogon will be chosen
+ # first if we set CC to just the basename; use the full file name.
+ shift
+ ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@"
+ fi
+fi
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in cl.exe
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CC" && break
+ done
+fi
+if test -z "$CC"; then
+ ac_ct_CC=$CC
+ for ac_prog in cl.exe
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CC="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CC" && break
+done
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+fi
+
+fi
+
+
+test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "no acceptable C compiler found in \$PATH
+See \`config.log' for more details" "$LINENO" 5 ; }
+
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+ { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ sed '10a\
+... rest of stderr output deleted ...
+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
+
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out"
+# Try to create an executable without -o first, disregard a.out.
+# It will help us diagnose broken compilers, and finding out an intuition
+# of exeext.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler works" >&5
+$as_echo_n "checking whether the C compiler works... " >&6; }
+ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
+
+# The possible output files:
+ac_files="a.out conftest.exe conftest a.exe a_out.exe b.out conftest.*"
+
+ac_rmfiles=
+for ac_file in $ac_files
+do
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
+ * ) ac_rmfiles="$ac_rmfiles $ac_file";;
+ esac
+done
+rm -f $ac_rmfiles
+
+if { { ac_try="$ac_link_default"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link_default") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ # Autoconf-2.13 could set the ac_cv_exeext variable to `no'.
+# So ignore a value of `no', otherwise this would lead to `EXEEXT = no'
+# in a Makefile. We should not override ac_cv_exeext if it was cached,
+# so that the user can short-circuit this test for compilers unknown to
+# Autoconf.
+for ac_file in $ac_files ''
+do
+ test -f "$ac_file" || continue
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj )
+ ;;
+ [ab].out )
+ # We found the default executable, but exeext='' is most
+ # certainly right.
+ break;;
+ *.* )
+ if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
+ then :; else
+ ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ fi
+ # We set ac_cv_exeext here because the later test for it is not
+ # safe: cross compilers may not add the suffix if given an `-o'
+ # argument, so we may need to know it at that point already.
+ # Even if this section looks crufty: it has the advantage of
+ # actually working.
+ break;;
+ * )
+ break;;
+ esac
+done
+test "$ac_cv_exeext" = no && ac_cv_exeext=
+
+else
+ ac_file=''
+fi
+if test -z "$ac_file"; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error 77 "C compiler cannot create executables
+See \`config.log' for more details" "$LINENO" 5 ; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler default output file name" >&5
+$as_echo_n "checking for C compiler default output file name... " >&6; }
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5
+$as_echo "$ac_file" >&6; }
+ac_exeext=$ac_cv_exeext
+
+rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out
+ac_clean_files=$ac_clean_files_save
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5
+$as_echo_n "checking for suffix of executables... " >&6; }
+if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ # If both `conftest.exe' and `conftest' are `present' (well, observable)
+# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will
+# work properly (i.e., refer to `conftest.exe'), while it won't with
+# `rm'.
+for ac_file in conftest.exe conftest conftest.*; do
+ test -f "$ac_file" || continue
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
+ *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ break;;
+ * ) break;;
+ esac
+done
+else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details" "$LINENO" 5 ; }
+fi
+rm -f conftest conftest$ac_cv_exeext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5
+$as_echo "$ac_cv_exeext" >&6; }
+
+rm -f conftest.$ac_ext
+EXEEXT=$ac_cv_exeext
+ac_exeext=$EXEEXT
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdio.h>
+int
+main ()
+{
+FILE *f = fopen ("conftest.out", "w");
+ return ferror (f) || fclose (f) != 0;
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files="$ac_clean_files conftest.out"
+# Check that the compiler produces executables we can run. If not, either
+# the compiler is broken, or we cross compile.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5
+$as_echo_n "checking whether we are cross compiling... " >&6; }
+if test "$cross_compiling" != yes; then
+ { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+ if { ac_try='./conftest$ac_cv_exeext'
+ { { case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; }; then
+ cross_compiling=no
+ else
+ if test "$cross_compiling" = maybe; then
+ cross_compiling=yes
+ else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot run C compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details" "$LINENO" 5 ; }
+ fi
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5
+$as_echo "$cross_compiling" >&6; }
+
+rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out
+ac_clean_files=$ac_clean_files_save
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5
+$as_echo_n "checking for suffix of object files... " >&6; }
+if test "${ac_cv_objext+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.o conftest.obj
+if { { ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compile") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ for ac_file in conftest.o conftest.obj conftest.*; do
+ test -f "$ac_file" || continue;
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;;
+ *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'`
+ break;;
+ esac
+done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot compute suffix of object files: cannot compile
+See \`config.log' for more details" "$LINENO" 5 ; }
+fi
+rm -f conftest.$ac_cv_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5
+$as_echo "$ac_cv_objext" >&6; }
+OBJEXT=$ac_cv_objext
+ac_objext=$OBJEXT
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5
+$as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
+if test "${ac_cv_c_compiler_gnu+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_compiler_gnu=yes
+else
+ ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_c_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5
+$as_echo "$ac_cv_c_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GCC=yes
+else
+ GCC=
+fi
+ac_test_CFLAGS=${CFLAGS+set}
+ac_save_CFLAGS=$CFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5
+$as_echo_n "checking whether $CC accepts -g... " >&6; }
+if test "${ac_cv_prog_cc_g+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_c_werror_flag=$ac_c_werror_flag
+ ac_c_werror_flag=yes
+ ac_cv_prog_cc_g=no
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
+else
+ CFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+
+else
+ ac_c_werror_flag=$ac_save_c_werror_flag
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_c_werror_flag=$ac_save_c_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5
+$as_echo "$ac_cv_prog_cc_g" >&6; }
+if test "$ac_test_CFLAGS" = set; then
+ CFLAGS=$ac_save_CFLAGS
+elif test $ac_cv_prog_cc_g = yes; then
+ if test "$GCC" = yes; then
+ CFLAGS="-g -O2"
+ else
+ CFLAGS="-g"
+ fi
+else
+ if test "$GCC" = yes; then
+ CFLAGS="-O2"
+ else
+ CFLAGS=
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5
+$as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
+if test "${ac_cv_prog_cc_c89+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_prog_cc_c89=no
+ac_save_CC=$CC
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdarg.h>
+#include <stdio.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */
+struct buf { int x; };
+FILE * (*rcsopen) (struct buf *, struct stat *, int);
+static char *e (p, i)
+ char **p;
+ int i;
+{
+ return p[i];
+}
+static char *f (char * (*g) (char **, int), char **p, ...)
+{
+ char *s;
+ va_list v;
+ va_start (v,p);
+ s = g (p, va_arg (v,int));
+ va_end (v);
+ return s;
+}
+
+/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has
+ function prototypes and stuff, but not '\xHH' hex character constants.
+ These don't provoke an error unfortunately, instead are silently treated
+ as 'x'. The following induces an error, until -std is added to get
+ proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an
+ array size at least. It's necessary to write '\x00'==0 to get something
+ that's true only with -std. */
+int osf4_cc_array ['\x00' == 0 ? 1 : -1];
+
+/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters
+ inside strings and character constants. */
+#define FOO(x) 'x'
+int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1];
+
+int test (int i, double x);
+struct s1 {int (*f) (int a);};
+struct s2 {int (*f) (double a);};
+int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
+int argc;
+char **argv;
+int
+main ()
+{
+return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1];
+ ;
+ return 0;
+}
+_ACEOF
+for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \
+ -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
+do
+ CC="$ac_save_CC $ac_arg"
+ if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_c89=$ac_arg
+fi
+rm -f core conftest.err conftest.$ac_objext
+ test "x$ac_cv_prog_cc_c89" != "xno" && break
+done
+rm -f conftest.$ac_ext
+CC=$ac_save_CC
+
+fi
+# AC_CACHE_VAL
+case "x$ac_cv_prog_cc_c89" in
+ x)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
+$as_echo "none needed" >&6; } ;;
+ xno)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
+$as_echo "unsupported" >&6; } ;;
+ *)
+ CC="$CC $ac_cv_prog_cc_c89"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5
+$as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
+esac
+if test "x$ac_cv_prog_cc_c89" != xno; then :
+
+fi
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+DEPDIR="${am__leading_dot}deps"
+
+ac_config_commands="$ac_config_commands depfiles"
+
+
+am_make=${MAKE-make}
+cat > confinc << 'END'
+am__doit:
+ @echo this is the am__doit target
+.PHONY: am__doit
+END
+# If we don't find an include directive, just comment out the code.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5
+$as_echo_n "checking for style of include used by $am_make... " >&6; }
+am__include="#"
+am__quote=
+_am_result=none
+# First try GNU make style include.
+echo "include confinc" > confmf
+# Ignore all kinds of additional output from `make'.
+case `$am_make -s -f confmf 2> /dev/null` in #(
+*the\ am__doit\ target*)
+ am__include=include
+ am__quote=
+ _am_result=GNU
+ ;;
+esac
+# Now try BSD make style include.
+if test "$am__include" = "#"; then
+ echo '.include "confinc"' > confmf
+ case `$am_make -s -f confmf 2> /dev/null` in #(
+ *the\ am__doit\ target*)
+ am__include=.include
+ am__quote="\""
+ _am_result=BSD
+ ;;
+ esac
+fi
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5
+$as_echo "$_am_result" >&6; }
+rm -f confinc confmf
+
+# Check whether --enable-dependency-tracking was given.
+if test "${enable_dependency_tracking+set}" = set; then :
+ enableval=$enable_dependency_tracking;
+fi
+
+if test "x$enable_dependency_tracking" != xno; then
+ am_depcomp="$ac_aux_dir/depcomp"
+ AMDEPBACKSLASH='\'
+fi
+ if test "x$enable_dependency_tracking" != xno; then
+ AMDEP_TRUE=
+ AMDEP_FALSE='#'
+else
+ AMDEP_TRUE='#'
+ AMDEP_FALSE=
+fi
+
+
+
+depcc="$CC" am_compiler_list=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CC_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
+ case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CC_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CC_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CC_dependencies_compiler_type" >&6; }
+CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
+ am__fastdepCC_TRUE=
+ am__fastdepCC_FALSE='#'
+else
+ am__fastdepCC_TRUE='#'
+ am__fastdepCC_FALSE=
+fi
+
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+if test -z "$CXX"; then
+ if test -n "$CCC"; then
+ CXX=$CCC
+ else
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CXX"; then
+ ac_cv_prog_CXX="$CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CXX=$ac_cv_prog_CXX
+if test -n "$CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5
+$as_echo "$CXX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CXX" && break
+ done
+fi
+if test -z "$CXX"; then
+ ac_ct_CXX=$CXX
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CXX"; then
+ ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CXX="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
+if test -n "$ac_ct_CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5
+$as_echo "$ac_ct_CXX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CXX" && break
+done
+
+ if test "x$ac_ct_CXX" = x; then
+ CXX="g++"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CXX=$ac_ct_CXX
+ fi
+fi
+
+ fi
+fi
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+ { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ sed '10a\
+... rest of stderr output deleted ...
+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5
+$as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; }
+if test "${ac_cv_cxx_compiler_gnu+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_compiler_gnu=yes
+else
+ ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_cxx_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5
+$as_echo "$ac_cv_cxx_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GXX=yes
+else
+ GXX=
+fi
+ac_test_CXXFLAGS=${CXXFLAGS+set}
+ac_save_CXXFLAGS=$CXXFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5
+$as_echo_n "checking whether $CXX accepts -g... " >&6; }
+if test "${ac_cv_prog_cxx_g+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_cxx_werror_flag=$ac_cxx_werror_flag
+ ac_cxx_werror_flag=yes
+ ac_cv_prog_cxx_g=no
+ CXXFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_prog_cxx_g=yes
+else
+ CXXFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+
+else
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+ CXXFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_prog_cxx_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5
+$as_echo "$ac_cv_prog_cxx_g" >&6; }
+if test "$ac_test_CXXFLAGS" = set; then
+ CXXFLAGS=$ac_save_CXXFLAGS
+elif test $ac_cv_prog_cxx_g = yes; then
+ if test "$GXX" = yes; then
+ CXXFLAGS="-g -O2"
+ else
+ CXXFLAGS="-g"
+ fi
+else
+ if test "$GXX" = yes; then
+ CXXFLAGS="-O2"
+ else
+ CXXFLAGS=
+ fi
+fi
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+depcc="$CXX" am_compiler_list=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CXX_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
+ case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CXX_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CXX_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CXX_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CXX_dependencies_compiler_type" >&6; }
+CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CXX_dependencies_compiler_type" = gcc3; then
+ am__fastdepCXX_TRUE=
+ am__fastdepCXX_FALSE='#'
+else
+ am__fastdepCXX_TRUE='#'
+ am__fastdepCXX_FALSE=
+fi
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C preprocessor" >&5
+$as_echo_n "checking how to run the C preprocessor... " >&6; }
+# On Suns, sometimes $CPP names a directory.
+if test -n "$CPP" && test -d "$CPP"; then
+ CPP=
+fi
+if test -z "$CPP"; then
+ if test "${ac_cv_prog_CPP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ # Double quotes because CPP needs to be expanded
+ for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp"
+ do
+ ac_preproc_ok=false
+for ac_c_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+
+else
+ # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+ # Broken: success on invalid input.
+continue
+else
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.i conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then :
+ break
+fi
+
+ done
+ ac_cv_prog_CPP=$CPP
+
+fi
+ CPP=$ac_cv_prog_CPP
+else
+ ac_cv_prog_CPP=$CPP
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPP" >&5
+$as_echo "$CPP" >&6; }
+ac_preproc_ok=false
+for ac_c_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+
+else
+ # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+ # Broken: success on invalid input.
+continue
+else
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.i conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then :
+
+else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details" "$LINENO" 5 ; }
+fi
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
+set x ${MAKE-make}
+ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
+if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.make <<\_ACEOF
+SHELL = /bin/sh
+all:
+ @echo '@@@%%%=$(MAKE)=@@@%%%'
+_ACEOF
+# GNU make sometimes prints "make[1]: Entering ...", which would confuse us.
+case `${MAKE-make} -f conftest.make 2>/dev/null` in
+ *@@@%%%=?*=@@@%%%*)
+ eval ac_cv_prog_make_${ac_make}_set=yes;;
+ *)
+ eval ac_cv_prog_make_${ac_make}_set=no;;
+esac
+rm -f conftest.make
+fi
+if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ SET_MAKE=
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ SET_MAKE="MAKE=${MAKE-make}"
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ln -s works" >&5
+$as_echo_n "checking whether ln -s works... " >&6; }
+LN_S=$as_ln_s
+if test "$LN_S" = "ln -s"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no, using $LN_S" >&5
+$as_echo "no, using $LN_S" >&6; }
+fi
+
+
+# Extract the first word of "texi2dvi", so it can be a program name with args.
+set dummy texi2dvi; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_TEXI2DVI+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$TEXI2DVI"; then
+ ac_cv_prog_TEXI2DVI="$TEXI2DVI" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_TEXI2DVI="texi2dvi"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+TEXI2DVI=$ac_cv_prog_TEXI2DVI
+if test -n "$TEXI2DVI"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $TEXI2DVI" >&5
+$as_echo "$TEXI2DVI" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+# Extract the first word of "pdftex", so it can be a program name with args.
+set dummy pdftex; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_PDFTEX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$PDFTEX"; then
+ ac_cv_prog_PDFTEX="$PDFTEX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_PDFTEX="pdftex"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+PDFTEX=$ac_cv_prog_PDFTEX
+if test -n "$PDFTEX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PDFTEX" >&5
+$as_echo "$PDFTEX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+# Extract the first word of "kpsewhich", so it can be a program name with args.
+set dummy kpsewhich; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_KPSEWHICH+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$KPSEWHICH"; then
+ ac_cv_prog_KPSEWHICH="$KPSEWHICH" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_KPSEWHICH="kpsewhich"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+KPSEWHICH=$ac_cv_prog_KPSEWHICH
+if test -n "$KPSEWHICH"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $KPSEWHICH" >&5
+$as_echo "$KPSEWHICH" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+BUILD_DOC=false
+if test "x$TEXI2DVI" != "xtexi2dvi" || test "x$PDFTEX" != "xpdftex"; then :
+ BUILD_DOC=false
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: The 'texi2dvi' or 'pdftex' program could not be found. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases." >&5
+$as_echo "$as_me: WARNING: The 'texi2dvi' or 'pdftex' program could not be found. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases." >&2;}
+fi
+
+if test "x$KPSEWHICH" != "xkpsewhich" || test "$(kpsewhich -show-path=fmt)" == "/nonesuch"; then :
+ BUILD_DOC=false
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: The 'texi2dvi' or 'pdftex' is missing a correct latex installation. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases." >&5
+$as_echo "$as_me: WARNING: The 'texi2dvi' or 'pdftex' is missing a correct latex installation. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases." >&2;}
+fi
+ if $BUILD_DOC; then
+ BUILD_DOC_TRUE=
+ BUILD_DOC_FALSE='#'
+else
+ BUILD_DOC_TRUE='#'
+ BUILD_DOC_FALSE=
+fi
+
+
+
+
+# Check whether --enable-shared was given.
+if test "${enable_shared+set}" = set; then :
+ enableval=$enable_shared; p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_shared=yes ;;
+ no) enable_shared=no ;;
+ *)
+ enable_shared=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_shared=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac
+else
+ enable_shared=no
+fi
+
+
+
+
+
+
+
+
+
+
+case `pwd` in
+ *\ * | *\ *)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Libtool does not cope well with whitespace in \`pwd\`" >&5
+$as_echo "$as_me: WARNING: Libtool does not cope well with whitespace in \`pwd\`" >&2;} ;;
+esac
+
+
+
+macro_version='2.2.6b'
+macro_revision='1.3017'
+
+
+
+
+
+
+
+
+
+
+
+
+
+ltmain="$ac_aux_dir/ltmain.sh"
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a sed that does not truncate output" >&5
+$as_echo_n "checking for a sed that does not truncate output... " >&6; }
+if test "${ac_cv_path_SED+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_script=s/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb/
+ for ac_i in 1 2 3 4 5 6 7; do
+ ac_script="$ac_script$as_nl$ac_script"
+ done
+ echo "$ac_script" 2>/dev/null | sed 99q >conftest.sed
+ { ac_script=; unset ac_script;}
+ if test -z "$SED"; then
+ ac_path_SED_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in sed gsed; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_SED="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_SED" && $as_test_x "$ac_path_SED"; } || continue
+# Check for GNU ac_path_SED and select it if it is found.
+ # Check for GNU $ac_path_SED
+case `"$ac_path_SED" --version 2>&1` in
+*GNU*)
+ ac_cv_path_SED="$ac_path_SED" ac_path_SED_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo '' >> "conftest.nl"
+ "$ac_path_SED" -f conftest.sed < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
+ if test $ac_count -gt ${ac_path_SED_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_SED="$ac_path_SED"
+ ac_path_SED_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_SED_found && break 3
+ done
+ done
+ done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_SED"; then
+ as_fn_error $? "no acceptable sed could be found in \$PATH" "$LINENO" 5
+ fi
+else
+ ac_cv_path_SED=$SED
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_SED" >&5
+$as_echo "$ac_cv_path_SED" >&6; }
+ SED="$ac_cv_path_SED"
+ rm -f conftest.sed
+
+test -z "$SED" && SED=sed
+Xsed="$SED -e 1s/^X//"
+
+
+
+
+
+
+
+
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5
+$as_echo_n "checking for grep that handles long lines and -e... " >&6; }
+if test "${ac_cv_path_GREP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$GREP"; then
+ ac_path_GREP_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in grep ggrep; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue
+# Check for GNU ac_path_GREP and select it if it is found.
+ # Check for GNU $ac_path_GREP
+case `"$ac_path_GREP" --version 2>&1` in
+*GNU*)
+ ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo 'GREP' >> "conftest.nl"
+ "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
+ if test $ac_count -gt ${ac_path_GREP_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_GREP="$ac_path_GREP"
+ ac_path_GREP_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_GREP_found && break 3
+ done
+ done
+ done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_GREP"; then
+ as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+ fi
+else
+ ac_cv_path_GREP=$GREP
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5
+$as_echo "$ac_cv_path_GREP" >&6; }
+ GREP="$ac_cv_path_GREP"
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5
+$as_echo_n "checking for egrep... " >&6; }
+if test "${ac_cv_path_EGREP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if echo a | $GREP -E '(a|b)' >/dev/null 2>&1
+ then ac_cv_path_EGREP="$GREP -E"
+ else
+ if test -z "$EGREP"; then
+ ac_path_EGREP_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in egrep; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue
+# Check for GNU ac_path_EGREP and select it if it is found.
+ # Check for GNU $ac_path_EGREP
+case `"$ac_path_EGREP" --version 2>&1` in
+*GNU*)
+ ac_cv_path_EGREP="$ac_path_EGREP" ac_path_EGREP_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo 'EGREP' >> "conftest.nl"
+ "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
+ if test $ac_count -gt ${ac_path_EGREP_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_EGREP="$ac_path_EGREP"
+ ac_path_EGREP_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_EGREP_found && break 3
+ done
+ done
+ done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_EGREP"; then
+ as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+ fi
+else
+ ac_cv_path_EGREP=$EGREP
+fi
+
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5
+$as_echo "$ac_cv_path_EGREP" >&6; }
+ EGREP="$ac_cv_path_EGREP"
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for fgrep" >&5
+$as_echo_n "checking for fgrep... " >&6; }
+if test "${ac_cv_path_FGREP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if echo 'ab*c' | $GREP -F 'ab*c' >/dev/null 2>&1
+ then ac_cv_path_FGREP="$GREP -F"
+ else
+ if test -z "$FGREP"; then
+ ac_path_FGREP_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in fgrep; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_FGREP="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_FGREP" && $as_test_x "$ac_path_FGREP"; } || continue
+# Check for GNU ac_path_FGREP and select it if it is found.
+ # Check for GNU $ac_path_FGREP
+case `"$ac_path_FGREP" --version 2>&1` in
+*GNU*)
+ ac_cv_path_FGREP="$ac_path_FGREP" ac_path_FGREP_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo 'FGREP' >> "conftest.nl"
+ "$ac_path_FGREP" FGREP < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
+ if test $ac_count -gt ${ac_path_FGREP_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_FGREP="$ac_path_FGREP"
+ ac_path_FGREP_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_FGREP_found && break 3
+ done
+ done
+ done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_FGREP"; then
+ as_fn_error $? "no acceptable fgrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+ fi
+else
+ ac_cv_path_FGREP=$FGREP
+fi
+
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_FGREP" >&5
+$as_echo "$ac_cv_path_FGREP" >&6; }
+ FGREP="$ac_cv_path_FGREP"
+
+
+test -z "$GREP" && GREP=grep
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# Check whether --with-gnu-ld was given.
+if test "${with_gnu_ld+set}" = set; then :
+ withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes
+else
+ with_gnu_ld=no
+fi
+
+ac_prog=ld
+if test "$GCC" = yes; then
+ # Check if gcc -print-prog-name=ld gives a path.
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ld used by $CC" >&5
+$as_echo_n "checking for ld used by $CC... " >&6; }
+ case $host in
+ *-*-mingw*)
+ # gcc leaves a trailing carriage return which upsets mingw
+ ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+ *)
+ ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+ esac
+ case $ac_prog in
+ # Accept absolute paths.
+ [\\/]* | ?:[\\/]*)
+ re_direlt='/[^/][^/]*/\.\./'
+ # Canonicalize the pathname of ld
+ ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'`
+ while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do
+ ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"`
+ done
+ test -z "$LD" && LD="$ac_prog"
+ ;;
+ "")
+ # If it fails, then pretend we aren't using GCC.
+ ac_prog=ld
+ ;;
+ *)
+ # If it is relative, then search for the first ld in PATH.
+ with_gnu_ld=unknown
+ ;;
+ esac
+elif test "$with_gnu_ld" = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU ld" >&5
+$as_echo_n "checking for GNU ld... " >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for non-GNU ld" >&5
+$as_echo_n "checking for non-GNU ld... " >&6; }
+fi
+if test "${lt_cv_path_LD+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$LD"; then
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+ lt_cv_path_LD="$ac_dir/$ac_prog"
+ # Check to see if the program is GNU ld. I'd rather use --version,
+ # but apparently some variants of GNU ld only accept -v.
+ # Break only if it was the GNU/non-GNU ld that we prefer.
+ case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+ *GNU* | *'with BFD'*)
+ test "$with_gnu_ld" != no && break
+ ;;
+ *)
+ test "$with_gnu_ld" != yes && break
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+else
+ lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi
+fi
+
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LD" >&5
+$as_echo "$LD" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+test -z "$LD" && as_fn_error $? "no acceptable ld found in \$PATH" "$LINENO" 5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if the linker ($LD) is GNU ld" >&5
+$as_echo_n "checking if the linker ($LD) is GNU ld... " >&6; }
+if test "${lt_cv_prog_gnu_ld+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ # I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+ lt_cv_prog_gnu_ld=yes
+ ;;
+*)
+ lt_cv_prog_gnu_ld=no
+ ;;
+esac
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_gnu_ld" >&5
+$as_echo "$lt_cv_prog_gnu_ld" >&6; }
+with_gnu_ld=$lt_cv_prog_gnu_ld
+
+
+
+
+
+
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for BSD- or MS-compatible name lister (nm)" >&5
+$as_echo_n "checking for BSD- or MS-compatible name lister (nm)... " >&6; }
+if test "${lt_cv_path_NM+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$NM"; then
+ # Let the user override the test.
+ lt_cv_path_NM="$NM"
+else
+ lt_nm_to_check="${ac_tool_prefix}nm"
+ if test -n "$ac_tool_prefix" && test "$build" = "$host"; then
+ lt_nm_to_check="$lt_nm_to_check nm"
+ fi
+ for lt_tmp_nm in $lt_nm_to_check; do
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ tmp_nm="$ac_dir/$lt_tmp_nm"
+ if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then
+ # Check to see if the nm accepts a BSD-compat flag.
+ # Adding the `sed 1q' prevents false positives on HP-UX, which says:
+ # nm: unknown option "B" ignored
+ # Tru64's nm complains that /dev/null is an invalid object file
+ case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in
+ */dev/null* | *'Invalid file or object type'*)
+ lt_cv_path_NM="$tmp_nm -B"
+ break
+ ;;
+ *)
+ case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in
+ */dev/null*)
+ lt_cv_path_NM="$tmp_nm -p"
+ break
+ ;;
+ *)
+ lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but
+ continue # so that we can try to find one that supports BSD flags
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+ done
+ : ${lt_cv_path_NM=no}
+fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_path_NM" >&5
+$as_echo "$lt_cv_path_NM" >&6; }
+if test "$lt_cv_path_NM" != "no"; then
+ NM="$lt_cv_path_NM"
+else
+ # Didn't find any BSD compatible name lister, look for dumpbin.
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in "dumpbin -symbols" "link -dump -symbols"
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_DUMPBIN+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$DUMPBIN"; then
+ ac_cv_prog_DUMPBIN="$DUMPBIN" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_DUMPBIN="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+DUMPBIN=$ac_cv_prog_DUMPBIN
+if test -n "$DUMPBIN"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DUMPBIN" >&5
+$as_echo "$DUMPBIN" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$DUMPBIN" && break
+ done
+fi
+if test -z "$DUMPBIN"; then
+ ac_ct_DUMPBIN=$DUMPBIN
+ for ac_prog in "dumpbin -symbols" "link -dump -symbols"
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_DUMPBIN+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_DUMPBIN"; then
+ ac_cv_prog_ac_ct_DUMPBIN="$ac_ct_DUMPBIN" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_DUMPBIN="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_DUMPBIN=$ac_cv_prog_ac_ct_DUMPBIN
+if test -n "$ac_ct_DUMPBIN"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DUMPBIN" >&5
+$as_echo "$ac_ct_DUMPBIN" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_DUMPBIN" && break
+done
+
+ if test "x$ac_ct_DUMPBIN" = x; then
+ DUMPBIN=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ DUMPBIN=$ac_ct_DUMPBIN
+ fi
+fi
+
+
+ if test "$DUMPBIN" != ":"; then
+ NM="$DUMPBIN"
+ fi
+fi
+test -z "$NM" && NM=nm
+
+
+
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking the name lister ($NM) interface" >&5
+$as_echo_n "checking the name lister ($NM) interface... " >&6; }
+if test "${lt_cv_nm_interface+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_nm_interface="BSD nm"
+ echo "int some_variable = 0;" > conftest.$ac_ext
+ (eval echo "\"\$as_me:5996: $ac_compile\"" >&5)
+ (eval "$ac_compile" 2>conftest.err)
+ cat conftest.err >&5
+ (eval echo "\"\$as_me:5999: $NM \\\"conftest.$ac_objext\\\"\"" >&5)
+ (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out)
+ cat conftest.err >&5
+ (eval echo "\"\$as_me:6002: output\"" >&5)
+ cat conftest.out >&5
+ if $GREP 'External.*some_variable' conftest.out > /dev/null; then
+ lt_cv_nm_interface="MS dumpbin"
+ fi
+ rm -f conftest*
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_nm_interface" >&5
+$as_echo "$lt_cv_nm_interface" >&6; }
+
+# find the maximum length of command line arguments
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking the maximum length of command line arguments" >&5
+$as_echo_n "checking the maximum length of command line arguments... " >&6; }
+if test "${lt_cv_sys_max_cmd_len+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ i=0
+ teststring="ABCD"
+
+ case $build_os in
+ msdosdjgpp*)
+ # On DJGPP, this test can blow up pretty badly due to problems in libc
+ # (any single argument exceeding 2000 bytes causes a buffer overrun
+ # during glob expansion). Even if it were fixed, the result of this
+ # check would be larger than it should be.
+ lt_cv_sys_max_cmd_len=12288; # 12K is about right
+ ;;
+
+ gnu*)
+ # Under GNU Hurd, this test is not required because there is
+ # no limit to the length of command line arguments.
+ # Libtool will interpret -1 as no limit whatsoever
+ lt_cv_sys_max_cmd_len=-1;
+ ;;
+
+ cygwin* | mingw* | cegcc*)
+ # On Win9x/ME, this test blows up -- it succeeds, but takes
+ # about 5 minutes as the teststring grows exponentially.
+ # Worse, since 9x/ME are not pre-emptively multitasking,
+ # you end up with a "frozen" computer, even though with patience
+ # the test eventually succeeds (with a max line length of 256k).
+ # Instead, let's just punt: use the minimum linelength reported by
+ # all of the supported platforms: 8192 (on NT/2K/XP).
+ lt_cv_sys_max_cmd_len=8192;
+ ;;
+
+ amigaos*)
+ # On AmigaOS with pdksh, this test takes hours, literally.
+ # So we just punt and use a minimum line length of 8192.
+ lt_cv_sys_max_cmd_len=8192;
+ ;;
+
+ netbsd* | freebsd* | openbsd* | darwin* | dragonfly*)
+ # This has been around since 386BSD, at least. Likely further.
+ if test -x /sbin/sysctl; then
+ lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax`
+ elif test -x /usr/sbin/sysctl; then
+ lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax`
+ else
+ lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs
+ fi
+ # And add a safety zone
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+ ;;
+
+ interix*)
+ # We know the value 262144 and hardcode it with a safety zone (like BSD)
+ lt_cv_sys_max_cmd_len=196608
+ ;;
+
+ osf*)
+ # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure
+ # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not
+ # nice to cause kernel panics so lets avoid the loop below.
+ # First set a reasonable default.
+ lt_cv_sys_max_cmd_len=16384
+ #
+ if test -x /sbin/sysconfig; then
+ case `/sbin/sysconfig -q proc exec_disable_arg_limit` in
+ *1*) lt_cv_sys_max_cmd_len=-1 ;;
+ esac
+ fi
+ ;;
+ sco3.2v5*)
+ lt_cv_sys_max_cmd_len=102400
+ ;;
+ sysv5* | sco5v6* | sysv4.2uw2*)
+ kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null`
+ if test -n "$kargmax"; then
+ lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[ ]//'`
+ else
+ lt_cv_sys_max_cmd_len=32768
+ fi
+ ;;
+ *)
+ lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null`
+ if test -n "$lt_cv_sys_max_cmd_len"; then
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+ else
+ # Make teststring a little bigger before we do anything with it.
+ # a 1K string should be a reasonable start.
+ for i in 1 2 3 4 5 6 7 8 ; do
+ teststring=$teststring$teststring
+ done
+ SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}}
+ # If test is not a shell built-in, we'll probably end up computing a
+ # maximum length that is only half of the actual maximum length, but
+ # we can't tell.
+ while { test "X"`$SHELL $0 --fallback-echo "X$teststring$teststring" 2>/dev/null` \
+ = "XX$teststring$teststring"; } >/dev/null 2>&1 &&
+ test $i != 17 # 1/2 MB should be enough
+ do
+ i=`expr $i + 1`
+ teststring=$teststring$teststring
+ done
+ # Only check the string length outside the loop.
+ lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1`
+ teststring=
+ # Add a significant safety factor because C++ compilers can tack on
+ # massive amounts of additional arguments before passing them to the
+ # linker. It appears as though 1/2 is a usable value.
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2`
+ fi
+ ;;
+ esac
+
+fi
+
+if test -n $lt_cv_sys_max_cmd_len ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_sys_max_cmd_len" >&5
+$as_echo "$lt_cv_sys_max_cmd_len" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: none" >&5
+$as_echo "none" >&6; }
+fi
+max_cmd_len=$lt_cv_sys_max_cmd_len
+
+
+
+
+
+
+: ${CP="cp -f"}
+: ${MV="mv -f"}
+: ${RM="rm -f"}
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the shell understands some XSI constructs" >&5
+$as_echo_n "checking whether the shell understands some XSI constructs... " >&6; }
+# Try some XSI features
+xsi_shell=no
+( _lt_dummy="a/b/c"
+ test "${_lt_dummy##*/},${_lt_dummy%/*},"${_lt_dummy%"$_lt_dummy"}, \
+ = c,a/b,, \
+ && eval 'test $(( 1 + 1 )) -eq 2 \
+ && test "${#_lt_dummy}" -eq 5' ) >/dev/null 2>&1 \
+ && xsi_shell=yes
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $xsi_shell" >&5
+$as_echo "$xsi_shell" >&6; }
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the shell understands \"+=\"" >&5
+$as_echo_n "checking whether the shell understands \"+=\"... " >&6; }
+lt_shell_append=no
+( foo=bar; set foo baz; eval "$1+=\$2" && test "$foo" = barbaz ) \
+ >/dev/null 2>&1 \
+ && lt_shell_append=yes
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_shell_append" >&5
+$as_echo "$lt_shell_append" >&6; }
+
+
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+ lt_unset=unset
+else
+ lt_unset=false
+fi
+
+
+
+
+
+# test EBCDIC or ASCII
+case `echo X|tr X '\101'` in
+ A) # ASCII based system
+ # \n is not interpreted correctly by Solaris 8 /usr/ucb/tr
+ lt_SP2NL='tr \040 \012'
+ lt_NL2SP='tr \015\012 \040\040'
+ ;;
+ *) # EBCDIC based system
+ lt_SP2NL='tr \100 \n'
+ lt_NL2SP='tr \r\n \100\100'
+ ;;
+esac
+
+
+
+
+
+
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $LD option to reload object files" >&5
+$as_echo_n "checking for $LD option to reload object files... " >&6; }
+if test "${lt_cv_ld_reload_flag+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_ld_reload_flag='-r'
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_reload_flag" >&5
+$as_echo "$lt_cv_ld_reload_flag" >&6; }
+reload_flag=$lt_cv_ld_reload_flag
+case $reload_flag in
+"" | " "*) ;;
+*) reload_flag=" $reload_flag" ;;
+esac
+reload_cmds='$LD$reload_flag -o $output$reload_objs'
+case $host_os in
+ darwin*)
+ if test "$GCC" = yes; then
+ reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs'
+ else
+ reload_cmds='$LD$reload_flag -o $output$reload_objs'
+ fi
+ ;;
+esac
+
+
+
+
+
+
+
+
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}objdump", so it can be a program name with args.
+set dummy ${ac_tool_prefix}objdump; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_OBJDUMP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$OBJDUMP"; then
+ ac_cv_prog_OBJDUMP="$OBJDUMP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_OBJDUMP="${ac_tool_prefix}objdump"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+OBJDUMP=$ac_cv_prog_OBJDUMP
+if test -n "$OBJDUMP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OBJDUMP" >&5
+$as_echo "$OBJDUMP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_OBJDUMP"; then
+ ac_ct_OBJDUMP=$OBJDUMP
+ # Extract the first word of "objdump", so it can be a program name with args.
+set dummy objdump; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_OBJDUMP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_OBJDUMP"; then
+ ac_cv_prog_ac_ct_OBJDUMP="$ac_ct_OBJDUMP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_OBJDUMP="objdump"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_OBJDUMP=$ac_cv_prog_ac_ct_OBJDUMP
+if test -n "$ac_ct_OBJDUMP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OBJDUMP" >&5
+$as_echo "$ac_ct_OBJDUMP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_OBJDUMP" = x; then
+ OBJDUMP="false"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ OBJDUMP=$ac_ct_OBJDUMP
+ fi
+else
+ OBJDUMP="$ac_cv_prog_OBJDUMP"
+fi
+
+test -z "$OBJDUMP" && OBJDUMP=objdump
+
+
+
+
+
+
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to recognize dependent libraries" >&5
+$as_echo_n "checking how to recognize dependent libraries... " >&6; }
+if test "${lt_cv_deplibs_check_method+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_file_magic_cmd='$MAGIC_CMD'
+lt_cv_file_magic_test_file=
+lt_cv_deplibs_check_method='unknown'
+# Need to set the preceding variable on all platforms that support
+# interlibrary dependencies.
+# 'none' -- dependencies not supported.
+# `unknown' -- same as none, but documents that we really don't know.
+# 'pass_all' -- all dependencies passed with no checks.
+# 'test_compile' -- check by making test program.
+# 'file_magic [[regex]]' -- check by looking for files in library path
+# which responds to the $file_magic_cmd with a given extended regex.
+# If you have `file' or equivalent on your system and you're not sure
+# whether `pass_all' will *always* work, you probably want this one.
+
+case $host_os in
+aix[4-9]*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+beos*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+bsdi[45]*)
+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib)'
+ lt_cv_file_magic_cmd='/usr/bin/file -L'
+ lt_cv_file_magic_test_file=/shlib/libc.so
+ ;;
+
+cygwin*)
+ # func_win32_libid is a shell function defined in ltmain.sh
+ lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+ lt_cv_file_magic_cmd='func_win32_libid'
+ ;;
+
+mingw* | pw32*)
+ # Base MSYS/MinGW do not provide the 'file' command needed by
+ # func_win32_libid shell function, so use a weaker test based on 'objdump',
+ # unless we find 'file', for example because we are cross-compiling.
+ if ( file / ) >/dev/null 2>&1; then
+ lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+ lt_cv_file_magic_cmd='func_win32_libid'
+ else
+ lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?'
+ lt_cv_file_magic_cmd='$OBJDUMP -f'
+ fi
+ ;;
+
+cegcc)
+ # use the weaker test based on 'objdump'. See mingw*.
+ lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?'
+ lt_cv_file_magic_cmd='$OBJDUMP -f'
+ ;;
+
+darwin* | rhapsody*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+freebsd* | dragonfly*)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
+ case $host_cpu in
+ i*86 )
+ # Not sure whether the presence of OpenBSD here was a mistake.
+ # Let's accept both of them until this is cleared up.
+ lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[3-9]86 (compact )?demand paged shared library'
+ lt_cv_file_magic_cmd=/usr/bin/file
+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*`
+ ;;
+ esac
+ else
+ lt_cv_deplibs_check_method=pass_all
+ fi
+ ;;
+
+gnu*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+hpux10.20* | hpux11*)
+ lt_cv_file_magic_cmd=/usr/bin/file
+ case $host_cpu in
+ ia64*)
+ lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - IA64'
+ lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so
+ ;;
+ hppa*64*)
+ lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]'
+ lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl
+ ;;
+ *)
+ lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|PA-RISC[0-9].[0-9]) shared library'
+ lt_cv_file_magic_test_file=/usr/lib/libc.sl
+ ;;
+ esac
+ ;;
+
+interix[3-9]*)
+ # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|\.a)$'
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $LD in
+ *-32|*"-32 ") libmagic=32-bit;;
+ *-n32|*"-n32 ") libmagic=N32;;
+ *-64|*"-64 ") libmagic=64-bit;;
+ *) libmagic=never-match;;
+ esac
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$'
+ else
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|_pic\.a)$'
+ fi
+ ;;
+
+newos6*)
+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (executable|dynamic lib)'
+ lt_cv_file_magic_cmd=/usr/bin/file
+ lt_cv_file_magic_test_file=/usr/lib/libnls.so
+ ;;
+
+*nto* | *qnx*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+openbsd*)
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|\.so|_pic\.a)$'
+ else
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$'
+ fi
+ ;;
+
+osf3* | osf4* | osf5*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+rdos*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+solaris*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+sysv4 | sysv4.3*)
+ case $host_vendor in
+ motorola)
+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib) M[0-9][0-9]* Version [0-9]'
+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*`
+ ;;
+ ncr)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ sequent)
+ lt_cv_file_magic_cmd='/bin/file'
+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [LM]SB (shared object|dynamic lib )'
+ ;;
+ sni)
+ lt_cv_file_magic_cmd='/bin/file'
+ lt_cv_deplibs_check_method="file_magic ELF [0-9][0-9]*-bit [LM]SB dynamic lib"
+ lt_cv_file_magic_test_file=/lib/libc.so
+ ;;
+ siemens)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ pc)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ esac
+ ;;
+
+tpf*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+esac
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_deplibs_check_method" >&5
+$as_echo "$lt_cv_deplibs_check_method" >&6; }
+file_magic_cmd=$lt_cv_file_magic_cmd
+deplibs_check_method=$lt_cv_deplibs_check_method
+test -z "$deplibs_check_method" && deplibs_check_method=unknown
+
+
+
+
+
+
+
+
+
+
+
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}ar", so it can be a program name with args.
+set dummy ${ac_tool_prefix}ar; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_AR+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$AR"; then
+ ac_cv_prog_AR="$AR" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_AR="${ac_tool_prefix}ar"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+AR=$ac_cv_prog_AR
+if test -n "$AR"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AR" >&5
+$as_echo "$AR" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_AR"; then
+ ac_ct_AR=$AR
+ # Extract the first word of "ar", so it can be a program name with args.
+set dummy ar; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_AR+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_AR"; then
+ ac_cv_prog_ac_ct_AR="$ac_ct_AR" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_AR="ar"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_AR=$ac_cv_prog_ac_ct_AR
+if test -n "$ac_ct_AR"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_AR" >&5
+$as_echo "$ac_ct_AR" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_AR" = x; then
+ AR="false"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ AR=$ac_ct_AR
+ fi
+else
+ AR="$ac_cv_prog_AR"
+fi
+
+test -z "$AR" && AR=ar
+test -z "$AR_FLAGS" && AR_FLAGS=cru
+
+
+
+
+
+
+
+
+
+
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
+set dummy ${ac_tool_prefix}strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_STRIP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$STRIP"; then
+ ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_STRIP="${ac_tool_prefix}strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+STRIP=$ac_cv_prog_STRIP
+if test -n "$STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5
+$as_echo "$STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_STRIP"; then
+ ac_ct_STRIP=$STRIP
+ # Extract the first word of "strip", so it can be a program name with args.
+set dummy strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_STRIP"; then
+ ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_STRIP="strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
+if test -n "$ac_ct_STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5
+$as_echo "$ac_ct_STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_STRIP" = x; then
+ STRIP=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ STRIP=$ac_ct_STRIP
+ fi
+else
+ STRIP="$ac_cv_prog_STRIP"
+fi
+
+test -z "$STRIP" && STRIP=:
+
+
+
+
+
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args.
+set dummy ${ac_tool_prefix}ranlib; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_RANLIB+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$RANLIB"; then
+ ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+RANLIB=$ac_cv_prog_RANLIB
+if test -n "$RANLIB"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $RANLIB" >&5
+$as_echo "$RANLIB" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_RANLIB"; then
+ ac_ct_RANLIB=$RANLIB
+ # Extract the first word of "ranlib", so it can be a program name with args.
+set dummy ranlib; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_RANLIB"; then
+ ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_RANLIB="ranlib"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB
+if test -n "$ac_ct_RANLIB"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_RANLIB" >&5
+$as_echo "$ac_ct_RANLIB" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_RANLIB" = x; then
+ RANLIB=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ RANLIB=$ac_ct_RANLIB
+ fi
+else
+ RANLIB="$ac_cv_prog_RANLIB"
+fi
+
+test -z "$RANLIB" && RANLIB=:
+
+
+
+
+
+
+# Determine commands to create old-style static archives.
+old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs'
+old_postinstall_cmds='chmod 644 $oldlib'
+old_postuninstall_cmds=
+
+if test -n "$RANLIB"; then
+ case $host_os in
+ openbsd*)
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib"
+ ;;
+ *)
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib"
+ ;;
+ esac
+ old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib"
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+
+# Check for command to grab the raw symbol name followed by C symbol from nm.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking command to parse $NM output from $compiler object" >&5
+$as_echo_n "checking command to parse $NM output from $compiler object... " >&6; }
+if test "${lt_cv_sys_global_symbol_pipe+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+
+# These are sane defaults that work on at least a few old systems.
+# [They come from Ultrix. What could be older than Ultrix?!! ;)]
+
+# Character class describing NM global symbol codes.
+symcode='[BCDEGRST]'
+
+# Regexp to match symbols that can be accessed directly from C.
+sympat='\([_A-Za-z][_A-Za-z0-9]*\)'
+
+# Define system-specific variables.
+case $host_os in
+aix*)
+ symcode='[BCDT]'
+ ;;
+cygwin* | mingw* | pw32* | cegcc*)
+ symcode='[ABCDGISTW]'
+ ;;
+hpux*)
+ if test "$host_cpu" = ia64; then
+ symcode='[ABCDEGRST]'
+ fi
+ ;;
+irix* | nonstopux*)
+ symcode='[BCDEGRST]'
+ ;;
+osf*)
+ symcode='[BCDEGQRST]'
+ ;;
+solaris*)
+ symcode='[BDRT]'
+ ;;
+sco3.2v5*)
+ symcode='[DT]'
+ ;;
+sysv4.2uw2*)
+ symcode='[DT]'
+ ;;
+sysv5* | sco5v6* | unixware* | OpenUNIX*)
+ symcode='[ABDT]'
+ ;;
+sysv4)
+ symcode='[DFNSTU]'
+ ;;
+esac
+
+# If we're using GNU nm, then use its standard symbol codes.
+case `$NM -V 2>&1` in
+*GNU* | *'with BFD'*)
+ symcode='[ABCDGIRSTW]' ;;
+esac
+
+# Transform an extracted symbol line into a proper C declaration.
+# Some systems (esp. on ia64) link data and code symbols differently,
+# so use this general approach.
+lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'"
+
+# Transform an extracted symbol line into symbol name and symbol address
+lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"\2\", (void *) \&\2},/p'"
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \(lib[^ ]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"lib\2\", (void *) \&\2},/p'"
+
+# Handle CRLF in mingw tool chain
+opt_cr=
+case $build_os in
+mingw*)
+ opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp
+ ;;
+esac
+
+# Try without a prefix underscore, then with it.
+for ac_symprfx in "" "_"; do
+
+ # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol.
+ symxfrm="\\1 $ac_symprfx\\2 \\2"
+
+ # Write the raw and C identifiers.
+ if test "$lt_cv_nm_interface" = "MS dumpbin"; then
+ # Fake it for dumpbin and say T for any non-static function
+ # and D for any global variable.
+ # Also find C++ and __fastcall symbols from MSVC++,
+ # which start with @ or ?.
+ lt_cv_sys_global_symbol_pipe="$AWK '"\
+" {last_section=section; section=\$ 3};"\
+" /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\
+" \$ 0!~/External *\|/{next};"\
+" / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\
+" {if(hide[section]) next};"\
+" {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\
+" {split(\$ 0, a, /\||\r/); split(a[2], s)};"\
+" s[1]~/^[@?]/{print s[1], s[1]; next};"\
+" s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\
+" ' prfx=^$ac_symprfx"
+ else
+ lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[ ]\($symcode$symcode*\)[ ][ ]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'"
+ fi
+
+ # Check to see that the pipe works correctly.
+ pipe_works=no
+
+ rm -f conftest*
+ cat > conftest.$ac_ext <<_LT_EOF
+#ifdef __cplusplus
+extern "C" {
+#endif
+char nm_test_var;
+void nm_test_func(void);
+void nm_test_func(void){}
+#ifdef __cplusplus
+}
+#endif
+int main(){nm_test_var='a';nm_test_func();return(0);}
+_LT_EOF
+
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ # Now try to grab the symbols.
+ nlist=conftest.nm
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist\""; } >&5
+ (eval $NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && test -s "$nlist"; then
+ # Try sorting and uniquifying the output.
+ if sort "$nlist" | uniq > "$nlist"T; then
+ mv -f "$nlist"T "$nlist"
+ else
+ rm -f "$nlist"T
+ fi
+
+ # Make sure that we snagged all the symbols we need.
+ if $GREP ' nm_test_var$' "$nlist" >/dev/null; then
+ if $GREP ' nm_test_func$' "$nlist" >/dev/null; then
+ cat <<_LT_EOF > conftest.$ac_ext
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+_LT_EOF
+ # Now generate the symbol file.
+ eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext'
+
+ cat <<_LT_EOF >> conftest.$ac_ext
+
+/* The mapping between symbol names and symbols. */
+const struct {
+ const char *name;
+ void *address;
+}
+lt__PROGRAM__LTX_preloaded_symbols[] =
+{
+ { "@PROGRAM@", (void *) 0 },
+_LT_EOF
+ $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext
+ cat <<\_LT_EOF >> conftest.$ac_ext
+ {0, (void *) 0}
+};
+
+/* This works around a problem in FreeBSD linker */
+#ifdef FREEBSD_WORKAROUND
+static const void *lt_preloaded_setup() {
+ return lt__PROGRAM__LTX_preloaded_symbols;
+}
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+_LT_EOF
+ # Now try linking the two files.
+ mv conftest.$ac_objext conftstm.$ac_objext
+ lt_save_LIBS="$LIBS"
+ lt_save_CFLAGS="$CFLAGS"
+ LIBS="conftstm.$ac_objext"
+ CFLAGS="$CFLAGS$lt_prog_compiler_no_builtin_flag"
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5
+ (eval $ac_link) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && test -s conftest${ac_exeext}; then
+ pipe_works=yes
+ fi
+ LIBS="$lt_save_LIBS"
+ CFLAGS="$lt_save_CFLAGS"
+ else
+ echo "cannot find nm_test_func in $nlist" >&5
+ fi
+ else
+ echo "cannot find nm_test_var in $nlist" >&5
+ fi
+ else
+ echo "cannot run $lt_cv_sys_global_symbol_pipe" >&5
+ fi
+ else
+ echo "$progname: failed program was:" >&5
+ cat conftest.$ac_ext >&5
+ fi
+ rm -rf conftest* conftst*
+
+ # Do not use the global_symbol_pipe unless it works.
+ if test "$pipe_works" = yes; then
+ break
+ else
+ lt_cv_sys_global_symbol_pipe=
+ fi
+done
+
+fi
+
+if test -z "$lt_cv_sys_global_symbol_pipe"; then
+ lt_cv_sys_global_symbol_to_cdecl=
+fi
+if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: failed" >&5
+$as_echo "failed" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: ok" >&5
+$as_echo "ok" >&6; }
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# Check whether --enable-libtool-lock was given.
+if test "${enable_libtool_lock+set}" = set; then :
+ enableval=$enable_libtool_lock;
+fi
+
+test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes
+
+# Some flags need to be propagated to the compiler or linker for good
+# libtool support.
+case $host in
+ia64-*-hpux*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *ELF-32*)
+ HPUX_IA64_MODE="32"
+ ;;
+ *ELF-64*)
+ HPUX_IA64_MODE="64"
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+*-*-irix6*)
+ # Find out which ABI we are using.
+ echo '#line 7197 "configure"' > conftest.$ac_ext
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *32-bit*)
+ LD="${LD-ld} -melf32bsmip"
+ ;;
+ *N32*)
+ LD="${LD-ld} -melf32bmipn32"
+ ;;
+ *64-bit*)
+ LD="${LD-ld} -melf64bmip"
+ ;;
+ esac
+ else
+ case `/usr/bin/file conftest.$ac_objext` in
+ *32-bit*)
+ LD="${LD-ld} -32"
+ ;;
+ *N32*)
+ LD="${LD-ld} -n32"
+ ;;
+ *64-bit*)
+ LD="${LD-ld} -64"
+ ;;
+ esac
+ fi
+ fi
+ rm -rf conftest*
+ ;;
+
+x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \
+s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ case `/usr/bin/file conftest.o` in
+ *32-bit*)
+ case $host in
+ x86_64-*kfreebsd*-gnu)
+ LD="${LD-ld} -m elf_i386_fbsd"
+ ;;
+ x86_64-*linux*)
+ LD="${LD-ld} -m elf_i386"
+ ;;
+ ppc64-*linux*|powerpc64-*linux*)
+ LD="${LD-ld} -m elf32ppclinux"
+ ;;
+ s390x-*linux*)
+ LD="${LD-ld} -m elf_s390"
+ ;;
+ sparc64-*linux*)
+ LD="${LD-ld} -m elf32_sparc"
+ ;;
+ esac
+ ;;
+ *64-bit*)
+ case $host in
+ x86_64-*kfreebsd*-gnu)
+ LD="${LD-ld} -m elf_x86_64_fbsd"
+ ;;
+ x86_64-*linux*)
+ LD="${LD-ld} -m elf_x86_64"
+ ;;
+ ppc*-*linux*|powerpc*-*linux*)
+ LD="${LD-ld} -m elf64ppc"
+ ;;
+ s390*-*linux*|s390*-*tpf*)
+ LD="${LD-ld} -m elf64_s390"
+ ;;
+ sparc*-*linux*)
+ LD="${LD-ld} -m elf64_sparc"
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+
+*-*-sco3.2v5*)
+ # On SCO OpenServer 5, we need -belf to get full-featured binaries.
+ SAVE_CFLAGS="$CFLAGS"
+ CFLAGS="$CFLAGS -belf"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler needs -belf" >&5
+$as_echo_n "checking whether the C compiler needs -belf... " >&6; }
+if test "${lt_cv_cc_needs_belf+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ lt_cv_cc_needs_belf=yes
+else
+ lt_cv_cc_needs_belf=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+ ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_cc_needs_belf" >&5
+$as_echo "$lt_cv_cc_needs_belf" >&6; }
+ if test x"$lt_cv_cc_needs_belf" != x"yes"; then
+ # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf
+ CFLAGS="$SAVE_CFLAGS"
+ fi
+ ;;
+sparc*-*solaris*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ case `/usr/bin/file conftest.o` in
+ *64-bit*)
+ case $lt_cv_prog_gnu_ld in
+ yes*) LD="${LD-ld} -m elf64_sparc" ;;
+ *)
+ if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then
+ LD="${LD-ld} -64"
+ fi
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+esac
+
+need_locks="$enable_libtool_lock"
+
+
+ case $host_os in
+ rhapsody* | darwin*)
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}dsymutil", so it can be a program name with args.
+set dummy ${ac_tool_prefix}dsymutil; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_DSYMUTIL+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$DSYMUTIL"; then
+ ac_cv_prog_DSYMUTIL="$DSYMUTIL" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_DSYMUTIL="${ac_tool_prefix}dsymutil"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+DSYMUTIL=$ac_cv_prog_DSYMUTIL
+if test -n "$DSYMUTIL"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DSYMUTIL" >&5
+$as_echo "$DSYMUTIL" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_DSYMUTIL"; then
+ ac_ct_DSYMUTIL=$DSYMUTIL
+ # Extract the first word of "dsymutil", so it can be a program name with args.
+set dummy dsymutil; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_DSYMUTIL+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_DSYMUTIL"; then
+ ac_cv_prog_ac_ct_DSYMUTIL="$ac_ct_DSYMUTIL" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_DSYMUTIL="dsymutil"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_DSYMUTIL=$ac_cv_prog_ac_ct_DSYMUTIL
+if test -n "$ac_ct_DSYMUTIL"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DSYMUTIL" >&5
+$as_echo "$ac_ct_DSYMUTIL" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_DSYMUTIL" = x; then
+ DSYMUTIL=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ DSYMUTIL=$ac_ct_DSYMUTIL
+ fi
+else
+ DSYMUTIL="$ac_cv_prog_DSYMUTIL"
+fi
+
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}nmedit", so it can be a program name with args.
+set dummy ${ac_tool_prefix}nmedit; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_NMEDIT+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$NMEDIT"; then
+ ac_cv_prog_NMEDIT="$NMEDIT" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_NMEDIT="${ac_tool_prefix}nmedit"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+NMEDIT=$ac_cv_prog_NMEDIT
+if test -n "$NMEDIT"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $NMEDIT" >&5
+$as_echo "$NMEDIT" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_NMEDIT"; then
+ ac_ct_NMEDIT=$NMEDIT
+ # Extract the first word of "nmedit", so it can be a program name with args.
+set dummy nmedit; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_NMEDIT+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_NMEDIT"; then
+ ac_cv_prog_ac_ct_NMEDIT="$ac_ct_NMEDIT" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_NMEDIT="nmedit"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_NMEDIT=$ac_cv_prog_ac_ct_NMEDIT
+if test -n "$ac_ct_NMEDIT"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_NMEDIT" >&5
+$as_echo "$ac_ct_NMEDIT" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_NMEDIT" = x; then
+ NMEDIT=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ NMEDIT=$ac_ct_NMEDIT
+ fi
+else
+ NMEDIT="$ac_cv_prog_NMEDIT"
+fi
+
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}lipo", so it can be a program name with args.
+set dummy ${ac_tool_prefix}lipo; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_LIPO+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$LIPO"; then
+ ac_cv_prog_LIPO="$LIPO" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_LIPO="${ac_tool_prefix}lipo"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+LIPO=$ac_cv_prog_LIPO
+if test -n "$LIPO"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LIPO" >&5
+$as_echo "$LIPO" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_LIPO"; then
+ ac_ct_LIPO=$LIPO
+ # Extract the first word of "lipo", so it can be a program name with args.
+set dummy lipo; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_LIPO+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_LIPO"; then
+ ac_cv_prog_ac_ct_LIPO="$ac_ct_LIPO" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_LIPO="lipo"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_LIPO=$ac_cv_prog_ac_ct_LIPO
+if test -n "$ac_ct_LIPO"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_LIPO" >&5
+$as_echo "$ac_ct_LIPO" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_LIPO" = x; then
+ LIPO=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ LIPO=$ac_ct_LIPO
+ fi
+else
+ LIPO="$ac_cv_prog_LIPO"
+fi
+
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}otool", so it can be a program name with args.
+set dummy ${ac_tool_prefix}otool; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_OTOOL+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$OTOOL"; then
+ ac_cv_prog_OTOOL="$OTOOL" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_OTOOL="${ac_tool_prefix}otool"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+OTOOL=$ac_cv_prog_OTOOL
+if test -n "$OTOOL"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL" >&5
+$as_echo "$OTOOL" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_OTOOL"; then
+ ac_ct_OTOOL=$OTOOL
+ # Extract the first word of "otool", so it can be a program name with args.
+set dummy otool; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_OTOOL+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_OTOOL"; then
+ ac_cv_prog_ac_ct_OTOOL="$ac_ct_OTOOL" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_OTOOL="otool"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_OTOOL=$ac_cv_prog_ac_ct_OTOOL
+if test -n "$ac_ct_OTOOL"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL" >&5
+$as_echo "$ac_ct_OTOOL" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_OTOOL" = x; then
+ OTOOL=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ OTOOL=$ac_ct_OTOOL
+ fi
+else
+ OTOOL="$ac_cv_prog_OTOOL"
+fi
+
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}otool64", so it can be a program name with args.
+set dummy ${ac_tool_prefix}otool64; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_OTOOL64+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$OTOOL64"; then
+ ac_cv_prog_OTOOL64="$OTOOL64" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_OTOOL64="${ac_tool_prefix}otool64"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+OTOOL64=$ac_cv_prog_OTOOL64
+if test -n "$OTOOL64"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL64" >&5
+$as_echo "$OTOOL64" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_OTOOL64"; then
+ ac_ct_OTOOL64=$OTOOL64
+ # Extract the first word of "otool64", so it can be a program name with args.
+set dummy otool64; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_OTOOL64+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_OTOOL64"; then
+ ac_cv_prog_ac_ct_OTOOL64="$ac_ct_OTOOL64" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_OTOOL64="otool64"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_OTOOL64=$ac_cv_prog_ac_ct_OTOOL64
+if test -n "$ac_ct_OTOOL64"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL64" >&5
+$as_echo "$ac_ct_OTOOL64" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_OTOOL64" = x; then
+ OTOOL64=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ OTOOL64=$ac_ct_OTOOL64
+ fi
+else
+ OTOOL64="$ac_cv_prog_OTOOL64"
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -single_module linker flag" >&5
+$as_echo_n "checking for -single_module linker flag... " >&6; }
+if test "${lt_cv_apple_cc_single_mod+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_apple_cc_single_mod=no
+ if test -z "${LT_MULTI_MODULE}"; then
+ # By default we will add the -single_module flag. You can override
+ # by either setting the environment variable LT_MULTI_MODULE
+ # non-empty at configure time, or by adding -multi_module to the
+ # link flags.
+ rm -rf libconftest.dylib*
+ echo "int foo(void){return 1;}" > conftest.c
+ echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+-dynamiclib -Wl,-single_module conftest.c" >&5
+ $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+ -dynamiclib -Wl,-single_module conftest.c 2>conftest.err
+ _lt_result=$?
+ if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then
+ lt_cv_apple_cc_single_mod=yes
+ else
+ cat conftest.err >&5
+ fi
+ rm -rf libconftest.dylib*
+ rm -f conftest.*
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_apple_cc_single_mod" >&5
+$as_echo "$lt_cv_apple_cc_single_mod" >&6; }
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -exported_symbols_list linker flag" >&5
+$as_echo_n "checking for -exported_symbols_list linker flag... " >&6; }
+if test "${lt_cv_ld_exported_symbols_list+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_ld_exported_symbols_list=no
+ save_LDFLAGS=$LDFLAGS
+ echo "_main" > conftest.sym
+ LDFLAGS="$LDFLAGS -Wl,-exported_symbols_list,conftest.sym"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ lt_cv_ld_exported_symbols_list=yes
+else
+ lt_cv_ld_exported_symbols_list=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+ LDFLAGS="$save_LDFLAGS"
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_exported_symbols_list" >&5
+$as_echo "$lt_cv_ld_exported_symbols_list" >&6; }
+ case $host_os in
+ rhapsody* | darwin1.[012])
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}suppress' ;;
+ darwin1.*)
+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+ darwin*) # darwin 5.x on
+ # if running on 10.5 or later, the deployment target defaults
+ # to the OS version, if on x86, and 10.4, the deployment
+ # target defaults to 10.4. Don't you love it?
+ case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in
+ 10.0,*86*-darwin8*|10.0,*-darwin[91]*)
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+ 10.[012]*)
+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+ 10.*)
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+ esac
+ ;;
+ esac
+ if test "$lt_cv_apple_cc_single_mod" = "yes"; then
+ _lt_dar_single_mod='$single_module'
+ fi
+ if test "$lt_cv_ld_exported_symbols_list" = "yes"; then
+ _lt_dar_export_syms=' ${wl}-exported_symbols_list,$output_objdir/${libname}-symbols.expsym'
+ else
+ _lt_dar_export_syms='~$NMEDIT -s $output_objdir/${libname}-symbols.expsym ${lib}'
+ fi
+ if test "$DSYMUTIL" != ":"; then
+ _lt_dsymutil='~$DSYMUTIL $lib || :'
+ else
+ _lt_dsymutil=
+ fi
+ ;;
+ esac
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5
+$as_echo_n "checking for ANSI C header files... " >&6; }
+if test "${ac_cv_header_stdc+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdlib.h>
+#include <stdarg.h>
+#include <string.h>
+#include <float.h>
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_header_stdc=yes
+else
+ ac_cv_header_stdc=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+
+if test $ac_cv_header_stdc = yes; then
+ # SunOS 4.x string.h does not declare mem*, contrary to ANSI.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <string.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "memchr" >/dev/null 2>&1; then :
+
+else
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdlib.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "free" >/dev/null 2>&1; then :
+
+else
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi.
+ if test "$cross_compiling" = yes; then :
+ :
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ctype.h>
+#include <stdlib.h>
+#if ((' ' & 0x0FF) == 0x020)
+# define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
+# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
+#else
+# define ISLOWER(c) \
+ (('a' <= (c) && (c) <= 'i') \
+ || ('j' <= (c) && (c) <= 'r') \
+ || ('s' <= (c) && (c) <= 'z'))
+# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c))
+#endif
+
+#define XOR(e, f) (((e) && !(f)) || (!(e) && (f)))
+int
+main ()
+{
+ int i;
+ for (i = 0; i < 256; i++)
+ if (XOR (islower (i), ISLOWER (i))
+ || toupper (i) != TOUPPER (i))
+ return 2;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_run "$LINENO"; then :
+
+else
+ ac_cv_header_stdc=no
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
+ conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+
+fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5
+$as_echo "$ac_cv_header_stdc" >&6; }
+if test $ac_cv_header_stdc = yes; then
+
+$as_echo "#define STDC_HEADERS 1" >>confdefs.h
+
+fi
+
+# On IRIX 5.3, sys/types and inttypes.h are conflicting.
+for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \
+ inttypes.h stdint.h unistd.h
+do :
+ as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default
+"
+if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+
+for ac_header in dlfcn.h
+do :
+ ac_fn_c_check_header_compile "$LINENO" "dlfcn.h" "ac_cv_header_dlfcn_h" "$ac_includes_default
+"
+if test "x$ac_cv_header_dlfcn_h" = x""yes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_DLFCN_H 1
+_ACEOF
+
+fi
+
+done
+
+
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+if test -z "$CXX"; then
+ if test -n "$CCC"; then
+ CXX=$CCC
+ else
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CXX"; then
+ ac_cv_prog_CXX="$CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CXX=$ac_cv_prog_CXX
+if test -n "$CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5
+$as_echo "$CXX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CXX" && break
+ done
+fi
+if test -z "$CXX"; then
+ ac_ct_CXX=$CXX
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CXX"; then
+ ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CXX="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
+if test -n "$ac_ct_CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5
+$as_echo "$ac_ct_CXX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CXX" && break
+done
+
+ if test "x$ac_ct_CXX" = x; then
+ CXX="g++"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CXX=$ac_ct_CXX
+ fi
+fi
+
+ fi
+fi
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+ { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ sed '10a\
+... rest of stderr output deleted ...
+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5
+$as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; }
+if test "${ac_cv_cxx_compiler_gnu+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_compiler_gnu=yes
+else
+ ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_cxx_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5
+$as_echo "$ac_cv_cxx_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GXX=yes
+else
+ GXX=
+fi
+ac_test_CXXFLAGS=${CXXFLAGS+set}
+ac_save_CXXFLAGS=$CXXFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5
+$as_echo_n "checking whether $CXX accepts -g... " >&6; }
+if test "${ac_cv_prog_cxx_g+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_cxx_werror_flag=$ac_cxx_werror_flag
+ ac_cxx_werror_flag=yes
+ ac_cv_prog_cxx_g=no
+ CXXFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_prog_cxx_g=yes
+else
+ CXXFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+
+else
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+ CXXFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_prog_cxx_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5
+$as_echo "$ac_cv_prog_cxx_g" >&6; }
+if test "$ac_test_CXXFLAGS" = set; then
+ CXXFLAGS=$ac_save_CXXFLAGS
+elif test $ac_cv_prog_cxx_g = yes; then
+ if test "$GXX" = yes; then
+ CXXFLAGS="-g -O2"
+ else
+ CXXFLAGS="-g"
+ fi
+else
+ if test "$GXX" = yes; then
+ CXXFLAGS="-O2"
+ else
+ CXXFLAGS=
+ fi
+fi
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+depcc="$CXX" am_compiler_list=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CXX_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
+ case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CXX_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CXX_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CXX_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CXX_dependencies_compiler_type" >&6; }
+CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CXX_dependencies_compiler_type" = gcc3; then
+ am__fastdepCXX_TRUE=
+ am__fastdepCXX_FALSE='#'
+else
+ am__fastdepCXX_TRUE='#'
+ am__fastdepCXX_FALSE=
+fi
+
+
+if test -n "$CXX" && ( test "X$CXX" != "Xno" &&
+ ( (test "X$CXX" = "Xg++" && `g++ -v >/dev/null 2>&1` ) ||
+ (test "X$CXX" != "Xg++"))) ; then
+ ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C++ preprocessor" >&5
+$as_echo_n "checking how to run the C++ preprocessor... " >&6; }
+if test -z "$CXXCPP"; then
+ if test "${ac_cv_prog_CXXCPP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ # Double quotes because CXXCPP needs to be expanded
+ for CXXCPP in "$CXX -E" "/lib/cpp"
+ do
+ ac_preproc_ok=false
+for ac_cxx_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if ac_fn_cxx_try_cpp "$LINENO"; then :
+
+else
+ # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if ac_fn_cxx_try_cpp "$LINENO"; then :
+ # Broken: success on invalid input.
+continue
+else
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.i conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then :
+ break
+fi
+
+ done
+ ac_cv_prog_CXXCPP=$CXXCPP
+
+fi
+ CXXCPP=$ac_cv_prog_CXXCPP
+else
+ ac_cv_prog_CXXCPP=$CXXCPP
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXXCPP" >&5
+$as_echo "$CXXCPP" >&6; }
+ac_preproc_ok=false
+for ac_cxx_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if ac_fn_cxx_try_cpp "$LINENO"; then :
+
+else
+ # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if ac_fn_cxx_try_cpp "$LINENO"; then :
+ # Broken: success on invalid input.
+continue
+else
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.i conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then :
+
+else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+_lt_caught_CXX_error=yes; }
+fi
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+else
+ _lt_caught_CXX_error=yes
+fi
+
+
+
+
+
+# Set options
+
+
+
+ enable_dlopen=no
+
+
+ enable_win32_dll=no
+
+
+
+ # Check whether --enable-static was given.
+if test "${enable_static+set}" = set; then :
+ enableval=$enable_static; p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_static=yes ;;
+ no) enable_static=no ;;
+ *)
+ enable_static=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_static=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac
+else
+ enable_static=yes
+fi
+
+
+
+
+
+
+
+
+
+
+# Check whether --with-pic was given.
+if test "${with_pic+set}" = set; then :
+ withval=$with_pic; pic_mode="$withval"
+else
+ pic_mode=default
+fi
+
+
+test -z "$pic_mode" && pic_mode=default
+
+
+
+
+
+
+
+ # Check whether --enable-fast-install was given.
+if test "${enable_fast_install+set}" = set; then :
+ enableval=$enable_fast_install; p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_fast_install=yes ;;
+ no) enable_fast_install=no ;;
+ *)
+ enable_fast_install=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_fast_install=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac
+else
+ enable_fast_install=yes
+fi
+
+
+
+
+
+
+
+
+
+
+
+# This can be used to rebuild libtool when needed
+LIBTOOL_DEPS="$ltmain"
+
+# Always use our own libtool.
+LIBTOOL='$(SHELL) $(top_builddir)/libtool'
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+test -z "$LN_S" && LN_S="ln -s"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+if test -n "${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for objdir" >&5
+$as_echo_n "checking for objdir... " >&6; }
+if test "${lt_cv_objdir+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ rm -f .libs 2>/dev/null
+mkdir .libs 2>/dev/null
+if test -d .libs; then
+ lt_cv_objdir=.libs
+else
+ # MS-DOS does not allow filenames that begin with a dot.
+ lt_cv_objdir=_libs
+fi
+rmdir .libs 2>/dev/null
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_objdir" >&5
+$as_echo "$lt_cv_objdir" >&6; }
+objdir=$lt_cv_objdir
+
+
+
+
+
+cat >>confdefs.h <<_ACEOF
+#define LT_OBJDIR "$lt_cv_objdir/"
+_ACEOF
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+case $host_os in
+aix3*)
+ # AIX sometimes has problems with the GCC collect2 program. For some
+ # reason, if we set the COLLECT_NAMES environment variable, the problems
+ # vanish in a puff of smoke.
+ if test "X${COLLECT_NAMES+set}" != Xset; then
+ COLLECT_NAMES=
+ export COLLECT_NAMES
+ fi
+ ;;
+esac
+
+# Sed substitution that helps us do robust quoting. It backslashifies
+# metacharacters that are still active within double-quoted strings.
+sed_quote_subst='s/\(["`$\\]\)/\\\1/g'
+
+# Same as above, but do not quote variable references.
+double_quote_subst='s/\(["`\\]\)/\\\1/g'
+
+# Sed substitution to delay expansion of an escaped shell variable in a
+# double_quote_subst'ed string.
+delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g'
+
+# Sed substitution to delay expansion of an escaped single quote.
+delay_single_quote_subst='s/'\''/'\'\\\\\\\'\''/g'
+
+# Sed substitution to avoid accidental globbing in evaled expressions
+no_glob_subst='s/\*/\\\*/g'
+
+# Global variables:
+ofile=libtool
+can_build_shared=yes
+
+# All known linkers require a `.a' archive for static linking (except MSVC,
+# which needs '.lib').
+libext=a
+
+with_gnu_ld="$lt_cv_prog_gnu_ld"
+
+old_CC="$CC"
+old_CFLAGS="$CFLAGS"
+
+# Set sane defaults for various variables
+test -z "$CC" && CC=cc
+test -z "$LTCC" && LTCC=$CC
+test -z "$LTCFLAGS" && LTCFLAGS=$CFLAGS
+test -z "$LD" && LD=ld
+test -z "$ac_objext" && ac_objext=o
+
+for cc_temp in $compiler""; do
+ case $cc_temp in
+ compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+ distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+ \-*) ;;
+ *) break;;
+ esac
+done
+cc_basename=`$ECHO "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+
+
+# Only perform the check for file, if the check method requires it
+test -z "$MAGIC_CMD" && MAGIC_CMD=file
+case $deplibs_check_method in
+file_magic*)
+ if test "$file_magic_cmd" = '$MAGIC_CMD'; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ${ac_tool_prefix}file" >&5
+$as_echo_n "checking for ${ac_tool_prefix}file... " >&6; }
+if test "${lt_cv_path_MAGIC_CMD+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ case $MAGIC_CMD in
+[\\/*] | ?:[\\/]*)
+ lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path.
+ ;;
+*)
+ lt_save_MAGIC_CMD="$MAGIC_CMD"
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ ac_dummy="/usr/bin$PATH_SEPARATOR$PATH"
+ for ac_dir in $ac_dummy; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f $ac_dir/${ac_tool_prefix}file; then
+ lt_cv_path_MAGIC_CMD="$ac_dir/${ac_tool_prefix}file"
+ if test -n "$file_magic_test_file"; then
+ case $deplibs_check_method in
+ "file_magic "*)
+ file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"`
+ MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+ if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null |
+ $EGREP "$file_magic_regex" > /dev/null; then
+ :
+ else
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the command libtool uses to detect shared libraries,
+*** $file_magic_cmd, produces output that libtool cannot recognize.
+*** The result is that libtool may fail to recognize shared libraries
+*** as such. This will affect the creation of libtool libraries that
+*** depend on shared libraries, but programs linked with such libtool
+*** libraries will work regardless of this problem. Nevertheless, you
+*** may want to report the problem to your system manager and/or to
+*** bug-libtool at gnu.org
+
+_LT_EOF
+ fi ;;
+ esac
+ fi
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+ MAGIC_CMD="$lt_save_MAGIC_CMD"
+ ;;
+esac
+fi
+
+MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+if test -n "$MAGIC_CMD"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MAGIC_CMD" >&5
+$as_echo "$MAGIC_CMD" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+
+
+
+if test -z "$lt_cv_path_MAGIC_CMD"; then
+ if test -n "$ac_tool_prefix"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for file" >&5
+$as_echo_n "checking for file... " >&6; }
+if test "${lt_cv_path_MAGIC_CMD+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ case $MAGIC_CMD in
+[\\/*] | ?:[\\/]*)
+ lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path.
+ ;;
+*)
+ lt_save_MAGIC_CMD="$MAGIC_CMD"
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ ac_dummy="/usr/bin$PATH_SEPARATOR$PATH"
+ for ac_dir in $ac_dummy; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f $ac_dir/file; then
+ lt_cv_path_MAGIC_CMD="$ac_dir/file"
+ if test -n "$file_magic_test_file"; then
+ case $deplibs_check_method in
+ "file_magic "*)
+ file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"`
+ MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+ if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null |
+ $EGREP "$file_magic_regex" > /dev/null; then
+ :
+ else
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the command libtool uses to detect shared libraries,
+*** $file_magic_cmd, produces output that libtool cannot recognize.
+*** The result is that libtool may fail to recognize shared libraries
+*** as such. This will affect the creation of libtool libraries that
+*** depend on shared libraries, but programs linked with such libtool
+*** libraries will work regardless of this problem. Nevertheless, you
+*** may want to report the problem to your system manager and/or to
+*** bug-libtool at gnu.org
+
+_LT_EOF
+ fi ;;
+ esac
+ fi
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+ MAGIC_CMD="$lt_save_MAGIC_CMD"
+ ;;
+esac
+fi
+
+MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+if test -n "$MAGIC_CMD"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MAGIC_CMD" >&5
+$as_echo "$MAGIC_CMD" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ else
+ MAGIC_CMD=:
+ fi
+fi
+
+ fi
+ ;;
+esac
+
+# Use C for the default configuration in the libtool script
+
+lt_save_CC="$CC"
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+# Source file extension for C test sources.
+ac_ext=c
+
+# Object file extension for compiled C test sources.
+objext=o
+objext=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="int some_variable = 0;"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='int main(){return(0);}'
+
+
+
+
+
+
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+# Save the default compiler, since it gets overwritten when the other
+# tags are being tested, and _LT_TAGVAR(compiler, []) is a NOP.
+compiler_DEFAULT=$CC
+
+# save warnings/boilerplate of simple test code
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$RM conftest*
+
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$RM -r conftest*
+
+
+if test -n "$compiler"; then
+
+lt_prog_compiler_no_builtin_flag=
+
+if test "$GCC" = yes; then
+ lt_prog_compiler_no_builtin_flag=' -fno-builtin'
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler supports -fno-rtti -fno-exceptions" >&5
+$as_echo_n "checking if $compiler supports -fno-rtti -fno-exceptions... " >&6; }
+if test "${lt_cv_prog_compiler_rtti_exceptions+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_rtti_exceptions=no
+ ac_outfile=conftest.$ac_objext
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+ lt_compiler_flag="-fno-rtti -fno-exceptions"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ # The option is referenced via a variable to avoid confusing sed.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:9082: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>conftest.err)
+ ac_status=$?
+ cat conftest.err >&5
+ echo "$as_me:9086: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s "$ac_outfile"; then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings other than the usual output.
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_rtti_exceptions=yes
+ fi
+ fi
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_rtti_exceptions" >&5
+$as_echo "$lt_cv_prog_compiler_rtti_exceptions" >&6; }
+
+if test x"$lt_cv_prog_compiler_rtti_exceptions" = xyes; then
+ lt_prog_compiler_no_builtin_flag="$lt_prog_compiler_no_builtin_flag -fno-rtti -fno-exceptions"
+else
+ :
+fi
+
+fi
+
+
+
+
+
+
+ lt_prog_compiler_wl=
+lt_prog_compiler_pic=
+lt_prog_compiler_static=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $compiler option to produce PIC" >&5
+$as_echo_n "checking for $compiler option to produce PIC... " >&6; }
+
+ if test "$GCC" = yes; then
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_static='-static'
+
+ case $host_os in
+ aix*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ lt_prog_compiler_static='-Bstatic'
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ lt_prog_compiler_pic='-fPIC'
+ ;;
+ m68k)
+ # FIXME: we need at least 68020 code to build shared libraries, but
+ # adding the `-m68020' flag to GCC prevents building anything better,
+ # like `-m68040'.
+ lt_prog_compiler_pic='-m68020 -resident32 -malways-restore-a4'
+ ;;
+ esac
+ ;;
+
+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+ # PIC is the default for these OSes.
+ ;;
+
+ mingw* | cygwin* | pw32* | os2* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ # Although the cygwin gcc ignores -fPIC, still need this for old-style
+ # (--disable-auto-import) libraries
+ lt_prog_compiler_pic='-DDLL_EXPORT'
+ ;;
+
+ darwin* | rhapsody*)
+ # PIC is the default on this platform
+ # Common symbols not allowed in MH_DYLIB files
+ lt_prog_compiler_pic='-fno-common'
+ ;;
+
+ hpux*)
+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit
+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag
+ # sets the default TLS model and affects inlining.
+ case $host_cpu in
+ hppa*64*)
+ # +Z the default
+ ;;
+ *)
+ lt_prog_compiler_pic='-fPIC'
+ ;;
+ esac
+ ;;
+
+ interix[3-9]*)
+ # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+ # Instead, we relocate shared libraries at runtime.
+ ;;
+
+ msdosdjgpp*)
+ # Just because we use GCC doesn't mean we suddenly get shared libraries
+ # on systems that don't support them.
+ lt_prog_compiler_can_build_shared=no
+ enable_shared=no
+ ;;
+
+ *nto* | *qnx*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ lt_prog_compiler_pic='-fPIC -shared'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ lt_prog_compiler_pic=-Kconform_pic
+ fi
+ ;;
+
+ *)
+ lt_prog_compiler_pic='-fPIC'
+ ;;
+ esac
+ else
+ # PORTME Check for flag to pass linker flags through the system compiler.
+ case $host_os in
+ aix*)
+ lt_prog_compiler_wl='-Wl,'
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ lt_prog_compiler_static='-Bstatic'
+ else
+ lt_prog_compiler_static='-bnso -bI:/lib/syscalls.exp'
+ fi
+ ;;
+
+ mingw* | cygwin* | pw32* | os2* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ lt_prog_compiler_pic='-DDLL_EXPORT'
+ ;;
+
+ hpux9* | hpux10* | hpux11*)
+ lt_prog_compiler_wl='-Wl,'
+ # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+ # not for PA HP-UX.
+ case $host_cpu in
+ hppa*64*|ia64*)
+ # +Z the default
+ ;;
+ *)
+ lt_prog_compiler_pic='+Z'
+ ;;
+ esac
+ # Is there a better lt_prog_compiler_static that works with the bundled CC?
+ lt_prog_compiler_static='${wl}-a ${wl}archive'
+ ;;
+
+ irix5* | irix6* | nonstopux*)
+ lt_prog_compiler_wl='-Wl,'
+ # PIC (with -KPIC) is the default.
+ lt_prog_compiler_static='-non_shared'
+ ;;
+
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ # old Intel for x86_64 which still supported -KPIC.
+ ecc*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-static'
+ ;;
+ # icc used to be incompatible with GCC.
+ # ICC 10 doesn't accept -KPIC any more.
+ icc* | ifort*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-fPIC'
+ lt_prog_compiler_static='-static'
+ ;;
+ # Lahey Fortran 8.1.
+ lf95*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='--shared'
+ lt_prog_compiler_static='--static'
+ ;;
+ pgcc* | pgf77* | pgf90* | pgf95*)
+ # Portland Group compilers (*not* the Pentium gcc compiler,
+ # which looks to be a dead project)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-fpic'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+ ccc*)
+ lt_prog_compiler_wl='-Wl,'
+ # All Alpha code is PIC.
+ lt_prog_compiler_static='-non_shared'
+ ;;
+ xl*)
+ # IBM XL C 8.0/Fortran 10.1 on PPC
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-qpic'
+ lt_prog_compiler_static='-qstaticlink'
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C 5.9
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ lt_prog_compiler_wl='-Wl,'
+ ;;
+ *Sun\ F*)
+ # Sun Fortran 8.3 passes all unrecognized flags to the linker
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ lt_prog_compiler_wl=''
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+
+ newsos6)
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ *nto* | *qnx*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ lt_prog_compiler_pic='-fPIC -shared'
+ ;;
+
+ osf3* | osf4* | osf5*)
+ lt_prog_compiler_wl='-Wl,'
+ # All OSF/1 code is PIC.
+ lt_prog_compiler_static='-non_shared'
+ ;;
+
+ rdos*)
+ lt_prog_compiler_static='-non_shared'
+ ;;
+
+ solaris*)
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ case $cc_basename in
+ f77* | f90* | f95*)
+ lt_prog_compiler_wl='-Qoption ld ';;
+ *)
+ lt_prog_compiler_wl='-Wl,';;
+ esac
+ ;;
+
+ sunos4*)
+ lt_prog_compiler_wl='-Qoption ld '
+ lt_prog_compiler_pic='-PIC'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ sysv4 | sysv4.2uw2* | sysv4.3*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec ;then
+ lt_prog_compiler_pic='-Kconform_pic'
+ lt_prog_compiler_static='-Bstatic'
+ fi
+ ;;
+
+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ unicos*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_can_build_shared=no
+ ;;
+
+ uts4*)
+ lt_prog_compiler_pic='-pic'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ *)
+ lt_prog_compiler_can_build_shared=no
+ ;;
+ esac
+ fi
+
+case $host_os in
+ # For platforms which do not support PIC, -DPIC is meaningless:
+ *djgpp*)
+ lt_prog_compiler_pic=
+ ;;
+ *)
+ lt_prog_compiler_pic="$lt_prog_compiler_pic -DPIC"
+ ;;
+esac
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_prog_compiler_pic" >&5
+$as_echo "$lt_prog_compiler_pic" >&6; }
+
+
+
+
+
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$lt_prog_compiler_pic"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler PIC flag $lt_prog_compiler_pic works" >&5
+$as_echo_n "checking if $compiler PIC flag $lt_prog_compiler_pic works... " >&6; }
+if test "${lt_cv_prog_compiler_pic_works+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_pic_works=no
+ ac_outfile=conftest.$ac_objext
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+ lt_compiler_flag="$lt_prog_compiler_pic -DPIC"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ # The option is referenced via a variable to avoid confusing sed.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:9421: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>conftest.err)
+ ac_status=$?
+ cat conftest.err >&5
+ echo "$as_me:9425: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s "$ac_outfile"; then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings other than the usual output.
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_pic_works=yes
+ fi
+ fi
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_pic_works" >&5
+$as_echo "$lt_cv_prog_compiler_pic_works" >&6; }
+
+if test x"$lt_cv_prog_compiler_pic_works" = xyes; then
+ case $lt_prog_compiler_pic in
+ "" | " "*) ;;
+ *) lt_prog_compiler_pic=" $lt_prog_compiler_pic" ;;
+ esac
+else
+ lt_prog_compiler_pic=
+ lt_prog_compiler_can_build_shared=no
+fi
+
+fi
+
+
+
+
+
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$lt_prog_compiler_wl eval lt_tmp_static_flag=\"$lt_prog_compiler_static\"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler static flag $lt_tmp_static_flag works" >&5
+$as_echo_n "checking if $compiler static flag $lt_tmp_static_flag works... " >&6; }
+if test "${lt_cv_prog_compiler_static_works+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_static_works=no
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS $lt_tmp_static_flag"
+ echo "$lt_simple_link_test_code" > conftest.$ac_ext
+ if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+ # The linker can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ if test -s conftest.err; then
+ # Append any errors to the config.log.
+ cat conftest.err 1>&5
+ $ECHO "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_static_works=yes
+ fi
+ else
+ lt_cv_prog_compiler_static_works=yes
+ fi
+ fi
+ $RM -r conftest*
+ LDFLAGS="$save_LDFLAGS"
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_static_works" >&5
+$as_echo "$lt_cv_prog_compiler_static_works" >&6; }
+
+if test x"$lt_cv_prog_compiler_static_works" = xyes; then
+ :
+else
+ lt_prog_compiler_static=
+fi
+
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler supports -c -o file.$ac_objext" >&5
+$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; }
+if test "${lt_cv_prog_compiler_c_o+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_c_o=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:9526: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&5
+ echo "$as_me:9530: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_c_o=yes
+ fi
+ fi
+ chmod u+w . 2>&5
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_c_o" >&5
+$as_echo "$lt_cv_prog_compiler_c_o" >&6; }
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler supports -c -o file.$ac_objext" >&5
+$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; }
+if test "${lt_cv_prog_compiler_c_o+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_c_o=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:9581: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&5
+ echo "$as_me:9585: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_c_o=yes
+ fi
+ fi
+ chmod u+w . 2>&5
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_c_o" >&5
+$as_echo "$lt_cv_prog_compiler_c_o" >&6; }
+
+
+
+
+hard_links="nottested"
+if test "$lt_cv_prog_compiler_c_o" = no && test "$need_locks" != no; then
+ # do not overwrite the value of need_locks provided by the user
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if we can lock with hard links" >&5
+$as_echo_n "checking if we can lock with hard links... " >&6; }
+ hard_links=yes
+ $RM conftest*
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ touch conftest.a
+ ln conftest.a conftest.b 2>&5 || hard_links=no
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $hard_links" >&5
+$as_echo "$hard_links" >&6; }
+ if test "$hard_links" = no; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&5
+$as_echo "$as_me: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&2;}
+ need_locks=warn
+ fi
+else
+ need_locks=no
+fi
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+$as_echo_n "checking whether the $compiler linker ($LD) supports shared libraries... " >&6; }
+
+ runpath_var=
+ allow_undefined_flag=
+ always_export_symbols=no
+ archive_cmds=
+ archive_expsym_cmds=
+ compiler_needs_object=no
+ enable_shared_with_static_runtimes=no
+ export_dynamic_flag_spec=
+ export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ hardcode_automatic=no
+ hardcode_direct=no
+ hardcode_direct_absolute=no
+ hardcode_libdir_flag_spec=
+ hardcode_libdir_flag_spec_ld=
+ hardcode_libdir_separator=
+ hardcode_minus_L=no
+ hardcode_shlibpath_var=unsupported
+ inherit_rpath=no
+ link_all_deplibs=unknown
+ module_cmds=
+ module_expsym_cmds=
+ old_archive_from_new_cmds=
+ old_archive_from_expsyms_cmds=
+ thread_safe_flag_spec=
+ whole_archive_flag_spec=
+ # include_expsyms should be a list of space-separated symbols to be *always*
+ # included in the symbol list
+ include_expsyms=
+ # exclude_expsyms can be an extended regexp of symbols to exclude
+ # it will be wrapped by ` (' and `)$', so one must not match beginning or
+ # end of line. Example: `a|bc|.*d.*' will exclude the symbols `a' and `bc',
+ # as well as any symbol that contains `d'.
+ exclude_expsyms='_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*'
+ # Although _GLOBAL_OFFSET_TABLE_ is a valid symbol C name, most a.out
+ # platforms (ab)use it in PIC code, but their linkers get confused if
+ # the symbol is explicitly referenced. Since portable code cannot
+ # rely on this symbol name, it's probably fine to never include it in
+ # preloaded symbol tables.
+ # Exclude shared library initialization/finalization symbols.
+ extract_expsyms_cmds=
+
+ case $host_os in
+ cygwin* | mingw* | pw32* | cegcc*)
+ # FIXME: the MSVC++ port hasn't been tested in a loooong time
+ # When not using gcc, we currently assume that we are using
+ # Microsoft Visual C++.
+ if test "$GCC" != yes; then
+ with_gnu_ld=no
+ fi
+ ;;
+ interix*)
+ # we just hope/assume this is gcc and not c89 (= MSVC++)
+ with_gnu_ld=yes
+ ;;
+ openbsd*)
+ with_gnu_ld=no
+ ;;
+ linux* | k*bsd*-gnu)
+ link_all_deplibs=no
+ ;;
+ esac
+
+ ld_shlibs=yes
+ if test "$with_gnu_ld" = yes; then
+ # If archive_cmds runs LD, not CC, wlarc should be empty
+ wlarc='${wl}'
+
+ # Set some defaults for GNU ld with shared library support. These
+ # are reset later if shared libraries are not supported. Putting them
+ # here allows them to be overridden if necessary.
+ runpath_var=LD_RUN_PATH
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ export_dynamic_flag_spec='${wl}--export-dynamic'
+ # ancient GNU ld didn't support --whole-archive et. al.
+ if $LD --help 2>&1 | $GREP 'no-whole-archive' > /dev/null; then
+ whole_archive_flag_spec="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ else
+ whole_archive_flag_spec=
+ fi
+ supports_anon_versioning=no
+ case `$LD -v 2>&1` in
+ *GNU\ gold*) supports_anon_versioning=yes ;;
+ *\ [01].* | *\ 2.[0-9].* | *\ 2.10.*) ;; # catch versions < 2.11
+ *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ...
+ *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ...
+ *\ 2.11.*) ;; # other 2.11 versions
+ *) supports_anon_versioning=yes ;;
+ esac
+
+ # See if GNU ld supports shared libraries.
+ case $host_os in
+ aix[3-9]*)
+ # On AIX/PPC, the GNU linker is very broken
+ if test "$host_cpu" != ia64; then
+ ld_shlibs=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the GNU linker, at least up to release 2.9.1, is reported
+*** to be unable to reliably create shared libraries on AIX.
+*** Therefore, libtool is disabling shared libraries support. If you
+*** really care for shared libraries, you may want to modify your PATH
+*** so that a non-GNU linker is found, and then restart.
+
+_LT_EOF
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds=''
+ ;;
+ m68k)
+ archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_minus_L=yes
+ ;;
+ esac
+ ;;
+
+ beos*)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ allow_undefined_flag=unsupported
+ # Joseph Beckenbach <jrb3 at best.com> says some releases of gcc
+ # support --undefined. This deserves some investigation. FIXME
+ archive_cmds='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # _LT_TAGVAR(hardcode_libdir_flag_spec, ) is actually meaningless,
+ # as there is no search path for DLLs.
+ hardcode_libdir_flag_spec='-L$libdir'
+ allow_undefined_flag=unsupported
+ always_export_symbols=no
+ enable_shared_with_static_runtimes=yes
+ export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1 DATA/'\'' | $SED -e '\''/^[AITW][ ]/s/.*[ ]//'\'' | sort | uniq > $export_symbols'
+
+ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ # If the export-symbols file already is a .def file (1st line
+ # is EXPORTS), use it as is; otherwise, prepend...
+ archive_expsym_cmds='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+ cp $export_symbols $output_objdir/$soname.def;
+ else
+ echo EXPORTS > $output_objdir/$soname.def;
+ cat $export_symbols >> $output_objdir/$soname.def;
+ fi~
+ $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ interix[3-9]*)
+ hardcode_direct=no
+ hardcode_shlibpath_var=no
+ hardcode_libdir_flag_spec='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec='${wl}-E'
+ # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+ # Instead, shared libraries are loaded at an image base (0x10000000 by
+ # default) and relocated if they conflict, which is a slow very memory
+ # consuming and fragmenting process. To avoid this, we pick a random,
+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+ # time. Moving up from 0x10000000 also allows more sbrk(2) space.
+ archive_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ archive_expsym_cmds='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ ;;
+
+ gnu* | linux* | tpf* | k*bsd*-gnu | kopensolaris*-gnu)
+ tmp_diet=no
+ if test "$host_os" = linux-dietlibc; then
+ case $cc_basename in
+ diet\ *) tmp_diet=yes;; # linux-dietlibc with static linking (!diet-dyn)
+ esac
+ fi
+ if $LD --help 2>&1 | $EGREP ': supported targets:.* elf' > /dev/null \
+ && test "$tmp_diet" = no
+ then
+ tmp_addflag=
+ tmp_sharedflag='-shared'
+ case $cc_basename,$host_cpu in
+ pgcc*) # Portland Group C compiler
+ whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ tmp_addflag=' $pic_flag'
+ ;;
+ pgf77* | pgf90* | pgf95*) # Portland Group f77 and f90 compilers
+ whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ tmp_addflag=' $pic_flag -Mnomain' ;;
+ ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64
+ tmp_addflag=' -i_dynamic' ;;
+ efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64
+ tmp_addflag=' -i_dynamic -nofor_main' ;;
+ ifc* | ifort*) # Intel Fortran compiler
+ tmp_addflag=' -nofor_main' ;;
+ lf95*) # Lahey Fortran 8.1
+ whole_archive_flag_spec=
+ tmp_sharedflag='--shared' ;;
+ xl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ tmp_sharedflag='-qmkshrobj'
+ tmp_addflag= ;;
+ esac
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*) # Sun C 5.9
+ whole_archive_flag_spec='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ compiler_needs_object=yes
+ tmp_sharedflag='-G' ;;
+ *Sun\ F*) # Sun Fortran 8.3
+ tmp_sharedflag='-G' ;;
+ esac
+ archive_cmds='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+
+ if test "x$supports_anon_versioning" = xyes; then
+ archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+ fi
+
+ case $cc_basename in
+ xlf*)
+ # IBM XL Fortran 10.1 on PPC cannot create shared libs itself
+ whole_archive_flag_spec='--whole-archive$convenience --no-whole-archive'
+ hardcode_libdir_flag_spec=
+ hardcode_libdir_flag_spec_ld='-rpath $libdir'
+ archive_cmds='$LD -shared $libobjs $deplibs $compiler_flags -soname $soname -o $lib'
+ if test "x$supports_anon_versioning" = xyes; then
+ archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $LD -shared $libobjs $deplibs $compiler_flags -soname $soname -version-script $output_objdir/$libname.ver -o $lib'
+ fi
+ ;;
+ esac
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ archive_cmds='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
+ wlarc=
+ else
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ fi
+ ;;
+
+ solaris*)
+ if $LD -v 2>&1 | $GREP 'BFD 2\.8' > /dev/null; then
+ ld_shlibs=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: The releases 2.8.* of the GNU linker cannot reliably
+*** create shared libraries on Solaris systems. Therefore, libtool
+*** is disabling shared libraries support. We urge you to upgrade GNU
+*** binutils to release 2.9.1 or newer. Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+ elif $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*)
+ case `$LD -v 2>&1` in
+ *\ [01].* | *\ 2.[0-9].* | *\ 2.1[0-5].*)
+ ld_shlibs=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not
+*** reliably create shared libraries on SCO systems. Therefore, libtool
+*** is disabling shared libraries support. We urge you to upgrade GNU
+*** binutils to release 2.16.91.0.3 or newer. Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+ ;;
+ *)
+ # For security reasons, it is highly recommended that you always
+ # use absolute paths for naming shared libraries, and exclude the
+ # DT_RUNPATH tag from executables and libraries. But doing so
+ # requires that you compile everything twice, which is a pain.
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+ esac
+ ;;
+
+ sunos4*)
+ archive_cmds='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ wlarc=
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ *)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+ esac
+
+ if test "$ld_shlibs" = no; then
+ runpath_var=
+ hardcode_libdir_flag_spec=
+ export_dynamic_flag_spec=
+ whole_archive_flag_spec=
+ fi
+ else
+ # PORTME fill in a description of your system's linker (not GNU ld)
+ case $host_os in
+ aix3*)
+ allow_undefined_flag=unsupported
+ always_export_symbols=yes
+ archive_expsym_cmds='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname'
+ # Note: this linker hardcodes the directories in LIBPATH if there
+ # are no directories specified by -L.
+ hardcode_minus_L=yes
+ if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then
+ # Neither direct hardcoding nor static linking is supported with a
+ # broken collect2.
+ hardcode_direct=unsupported
+ fi
+ ;;
+
+ aix[4-9]*)
+ if test "$host_cpu" = ia64; then
+ # On IA64, the linker does run time linking by default, so we don't
+ # have to do anything special.
+ aix_use_runtimelinking=no
+ exp_sym_flag='-Bexport'
+ no_entry_flag=""
+ else
+ # If we're using GNU nm, then we don't want the "-C" option.
+ # -C means demangle to AIX nm, but means don't demangle with GNU nm
+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then
+ export_symbols_cmds='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ else
+ export_symbols_cmds='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ fi
+ aix_use_runtimelinking=no
+
+ # Test if we are trying to use run time linking or normal
+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+ # need to do runtime linking.
+ case $host_os in aix4.[23]|aix4.[23].*|aix[5-9]*)
+ for ld_flag in $LDFLAGS; do
+ if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then
+ aix_use_runtimelinking=yes
+ break
+ fi
+ done
+ ;;
+ esac
+
+ exp_sym_flag='-bexport'
+ no_entry_flag='-bnoentry'
+ fi
+
+ # When large executables or shared objects are built, AIX ld can
+ # have problems creating the table of contents. If linking a library
+ # or program results in "error TOC overflow" add -mminimal-toc to
+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not
+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+ archive_cmds=''
+ hardcode_direct=yes
+ hardcode_direct_absolute=yes
+ hardcode_libdir_separator=':'
+ link_all_deplibs=yes
+ file_list_spec='${wl}-f,'
+
+ if test "$GCC" = yes; then
+ case $host_os in aix4.[012]|aix4.[012].*)
+ # We only want to do this on AIX 4.2 and lower, the check
+ # below for broken collect2 doesn't work under 4.3+
+ collect2name=`${CC} -print-prog-name=collect2`
+ if test -f "$collect2name" &&
+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null
+ then
+ # We have reworked collect2
+ :
+ else
+ # We have old collect2
+ hardcode_direct=unsupported
+ # It fails to find uninstalled libraries when the uninstalled
+ # path is not listed in the libpath. Setting hardcode_minus_L
+ # to unsupported forces relinking
+ hardcode_minus_L=yes
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_libdir_separator=
+ fi
+ ;;
+ esac
+ shared_flag='-shared'
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag="$shared_flag "'${wl}-G'
+ fi
+ link_all_deplibs=no
+ else
+ # not using gcc
+ if test "$host_cpu" = ia64; then
+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+ # chokes on -Wl,-G. The following line is correct:
+ shared_flag='-G'
+ else
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag='${wl}-G'
+ else
+ shared_flag='${wl}-bM:SRE'
+ fi
+ fi
+ fi
+
+ export_dynamic_flag_spec='${wl}-bexpall'
+ # It seems that -bexpall does not export symbols beginning with
+ # underscore (_), so it is better to generate a list of symbols to export.
+ always_export_symbols=yes
+ if test "$aix_use_runtimelinking" = yes; then
+ # Warning - without using the other runtime loading flags (-brtl),
+ # -berok will link without error, but may produce a broken library.
+ allow_undefined_flag='-berok'
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+ hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath"
+ archive_expsym_cmds='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+ else
+ if test "$host_cpu" = ia64; then
+ hardcode_libdir_flag_spec='${wl}-R $libdir:/usr/lib:/lib'
+ allow_undefined_flag="-z nodefs"
+ archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+ else
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+ hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath"
+ # Warning - without using the other run time loading flags,
+ # -berok will link without error, but may produce a broken library.
+ no_undefined_flag=' ${wl}-bernotok'
+ allow_undefined_flag=' ${wl}-berok'
+ # Exported symbols can be pulled into shared objects from archives
+ whole_archive_flag_spec='$convenience'
+ archive_cmds_need_lc=yes
+ # This is similar to how AIX traditionally builds its shared libraries.
+ archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+ fi
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds=''
+ ;;
+ m68k)
+ archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_minus_L=yes
+ ;;
+ esac
+ ;;
+
+ bsdi[45]*)
+ export_dynamic_flag_spec=-rdynamic
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # When not using gcc, we currently assume that we are using
+ # Microsoft Visual C++.
+ # hardcode_libdir_flag_spec is actually meaningless, as there is
+ # no search path for DLLs.
+ hardcode_libdir_flag_spec=' '
+ allow_undefined_flag=unsupported
+ # Tell ltmain to make .lib files, not .a files.
+ libext=lib
+ # Tell ltmain to make .dll files, not .so files.
+ shrext_cmds=".dll"
+ # FIXME: Setting linknames here is a bad hack.
+ archive_cmds='$CC -o $lib $libobjs $compiler_flags `$ECHO "X$deplibs" | $Xsed -e '\''s/ -lc$//'\''` -link -dll~linknames='
+ # The linker will automatically build a .lib file if we build a DLL.
+ old_archive_from_new_cmds='true'
+ # FIXME: Should let the user specify the lib program.
+ old_archive_cmds='lib -OUT:$oldlib$oldobjs$old_deplibs'
+ fix_srcfile_path='`cygpath -w "$srcfile"`'
+ enable_shared_with_static_runtimes=yes
+ ;;
+
+ darwin* | rhapsody*)
+
+
+ archive_cmds_need_lc=no
+ hardcode_direct=no
+ hardcode_automatic=yes
+ hardcode_shlibpath_var=unsupported
+ whole_archive_flag_spec=''
+ link_all_deplibs=yes
+ allow_undefined_flag="$_lt_dar_allow_undefined"
+ case $cc_basename in
+ ifort*) _lt_dar_can_shared=yes ;;
+ *) _lt_dar_can_shared=$GCC ;;
+ esac
+ if test "$_lt_dar_can_shared" = "yes"; then
+ output_verbose_link_cmd=echo
+ archive_cmds="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}"
+ module_cmds="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}"
+ archive_expsym_cmds="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}"
+ module_expsym_cmds="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}"
+
+ else
+ ld_shlibs=no
+ fi
+
+ ;;
+
+ dgux*)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_shlibpath_var=no
+ ;;
+
+ freebsd1*)
+ ld_shlibs=no
+ ;;
+
+ # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor
+ # support. Future versions do this automatically, but an explicit c++rt0.o
+ # does not break anything, and helps significantly (at the cost of a little
+ # extra space).
+ freebsd2.2*)
+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o'
+ hardcode_libdir_flag_spec='-R$libdir'
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ # Unfortunately, older versions of FreeBSD 2 do not have this feature.
+ freebsd2*)
+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_direct=yes
+ hardcode_minus_L=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ # FreeBSD 3 and greater uses gcc -shared to do shared libraries.
+ freebsd* | dragonfly*)
+ archive_cmds='$CC -shared -o $lib $libobjs $deplibs $compiler_flags'
+ hardcode_libdir_flag_spec='-R$libdir'
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ hpux9*)
+ if test "$GCC" = yes; then
+ archive_cmds='$RM $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ else
+ archive_cmds='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ fi
+ hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
+ hardcode_libdir_separator=:
+ hardcode_direct=yes
+
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ hardcode_minus_L=yes
+ export_dynamic_flag_spec='${wl}-E'
+ ;;
+
+ hpux10*)
+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+ archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags'
+ fi
+ if test "$with_gnu_ld" = no; then
+ hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
+ hardcode_libdir_flag_spec_ld='+b $libdir'
+ hardcode_libdir_separator=:
+ hardcode_direct=yes
+ hardcode_direct_absolute=yes
+ export_dynamic_flag_spec='${wl}-E'
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ hardcode_minus_L=yes
+ fi
+ ;;
+
+ hpux11*)
+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+ case $host_cpu in
+ hppa*64*)
+ archive_cmds='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ ia64*)
+ archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ else
+ case $host_cpu in
+ hppa*64*)
+ archive_cmds='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ ia64*)
+ archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ fi
+ if test "$with_gnu_ld" = no; then
+ hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
+ hardcode_libdir_separator=:
+
+ case $host_cpu in
+ hppa*64*|ia64*)
+ hardcode_direct=no
+ hardcode_shlibpath_var=no
+ ;;
+ *)
+ hardcode_direct=yes
+ hardcode_direct_absolute=yes
+ export_dynamic_flag_spec='${wl}-E'
+
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ hardcode_minus_L=yes
+ ;;
+ esac
+ fi
+ ;;
+
+ irix5* | irix6* | nonstopux*)
+ if test "$GCC" = yes; then
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ # Try to use the -exported_symbol ld option, if it does not
+ # work, assume that -exports_file does not work either and
+ # implicitly export all symbols.
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+int foo(void) {}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib'
+
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+ LDFLAGS="$save_LDFLAGS"
+ else
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib'
+ fi
+ archive_cmds_need_lc='no'
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator=:
+ inherit_rpath=yes
+ link_all_deplibs=yes
+ ;;
+
+ netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out
+ else
+ archive_cmds='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF
+ fi
+ hardcode_libdir_flag_spec='-R$libdir'
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ newsos6)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_direct=yes
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator=:
+ hardcode_shlibpath_var=no
+ ;;
+
+ *nto* | *qnx*)
+ ;;
+
+ openbsd*)
+ if test -f /usr/libexec/ld.so; then
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ hardcode_direct_absolute=yes
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols'
+ hardcode_libdir_flag_spec='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec='${wl}-E'
+ else
+ case $host_os in
+ openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*)
+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_libdir_flag_spec='-R$libdir'
+ ;;
+ *)
+ archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+ hardcode_libdir_flag_spec='${wl}-rpath,$libdir'
+ ;;
+ esac
+ fi
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ os2*)
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_minus_L=yes
+ allow_undefined_flag=unsupported
+ archive_cmds='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def'
+ old_archive_from_new_cmds='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def'
+ ;;
+
+ osf3*)
+ if test "$GCC" = yes; then
+ allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*'
+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ else
+ allow_undefined_flag=' -expect_unresolved \*'
+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ fi
+ archive_cmds_need_lc='no'
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator=:
+ ;;
+
+ osf4* | osf5*) # as osf3* with the addition of -msym flag
+ if test "$GCC" = yes; then
+ allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*'
+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ else
+ allow_undefined_flag=' -expect_unresolved \*'
+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ archive_expsym_cmds='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~
+ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp'
+
+ # Both c and cxx compiler support -rpath directly
+ hardcode_libdir_flag_spec='-rpath $libdir'
+ fi
+ archive_cmds_need_lc='no'
+ hardcode_libdir_separator=:
+ ;;
+
+ solaris*)
+ no_undefined_flag=' -z defs'
+ if test "$GCC" = yes; then
+ wlarc='${wl}'
+ archive_cmds='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp'
+ else
+ case `$CC -V 2>&1` in
+ *"Compilers 5.0"*)
+ wlarc=''
+ archive_cmds='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp'
+ ;;
+ *)
+ wlarc='${wl}'
+ archive_cmds='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp'
+ ;;
+ esac
+ fi
+ hardcode_libdir_flag_spec='-R$libdir'
+ hardcode_shlibpath_var=no
+ case $host_os in
+ solaris2.[0-5] | solaris2.[0-5].*) ;;
+ *)
+ # The compiler driver will combine and reorder linker options,
+ # but understands `-z linker_flag'. GCC discards it without `$wl',
+ # but is careful enough not to reorder.
+ # Supported since Solaris 2.6 (maybe 2.5.1?)
+ if test "$GCC" = yes; then
+ whole_archive_flag_spec='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract'
+ else
+ whole_archive_flag_spec='-z allextract$convenience -z defaultextract'
+ fi
+ ;;
+ esac
+ link_all_deplibs=yes
+ ;;
+
+ sunos4*)
+ if test "x$host_vendor" = xsequent; then
+ # Use $CC to link under sequent, because it throws in some extra .o
+ # files that make .init and .fini sections work.
+ archive_cmds='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ archive_cmds='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags'
+ fi
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_direct=yes
+ hardcode_minus_L=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ sysv4)
+ case $host_vendor in
+ sni)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_direct=yes # is this really true???
+ ;;
+ siemens)
+ ## LD is ld it makes a PLAMLIB
+ ## CC just makes a GrossModule.
+ archive_cmds='$LD -G -o $lib $libobjs $deplibs $linker_flags'
+ reload_cmds='$CC -r -o $output$reload_objs'
+ hardcode_direct=no
+ ;;
+ motorola)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_direct=no #Motorola manual says yes, but my tests say they lie
+ ;;
+ esac
+ runpath_var='LD_RUN_PATH'
+ hardcode_shlibpath_var=no
+ ;;
+
+ sysv4.3*)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_shlibpath_var=no
+ export_dynamic_flag_spec='-Bexport'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_shlibpath_var=no
+ runpath_var=LD_RUN_PATH
+ hardcode_runpath_var=yes
+ ld_shlibs=yes
+ fi
+ ;;
+
+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*)
+ no_undefined_flag='${wl}-z,text'
+ archive_cmds_need_lc=no
+ hardcode_shlibpath_var=no
+ runpath_var='LD_RUN_PATH'
+
+ if test "$GCC" = yes; then
+ archive_cmds='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ archive_cmds='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ fi
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6*)
+ # Note: We can NOT use -z defs as we might desire, because we do not
+ # link with -lc, and that would cause any symbols used from libc to
+ # always be unresolved, which means just about no library would
+ # ever link correctly. If we're not using GNU ld we use -z text
+ # though, which does catch some bad symbols but isn't as heavy-handed
+ # as -z defs.
+ no_undefined_flag='${wl}-z,text'
+ allow_undefined_flag='${wl}-z,nodefs'
+ archive_cmds_need_lc=no
+ hardcode_shlibpath_var=no
+ hardcode_libdir_flag_spec='${wl}-R,$libdir'
+ hardcode_libdir_separator=':'
+ link_all_deplibs=yes
+ export_dynamic_flag_spec='${wl}-Bexport'
+ runpath_var='LD_RUN_PATH'
+
+ if test "$GCC" = yes; then
+ archive_cmds='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ archive_cmds='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ fi
+ ;;
+
+ uts4*)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_shlibpath_var=no
+ ;;
+
+ *)
+ ld_shlibs=no
+ ;;
+ esac
+
+ if test x$host_vendor = xsni; then
+ case $host in
+ sysv4 | sysv4.2uw2* | sysv4.3* | sysv5*)
+ export_dynamic_flag_spec='${wl}-Blargedynsym'
+ ;;
+ esac
+ fi
+ fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ld_shlibs" >&5
+$as_echo "$ld_shlibs" >&6; }
+test "$ld_shlibs" = no && can_build_shared=no
+
+with_gnu_ld=$with_gnu_ld
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$archive_cmds_need_lc" in
+x|xyes)
+ # Assume -lc should be added
+ archive_cmds_need_lc=yes
+
+ if test "$enable_shared" = yes && test "$GCC" = yes; then
+ case $archive_cmds in
+ *'~'*)
+ # FIXME: we may have to deal with multi-command sequences.
+ ;;
+ '$CC '*)
+ # Test whether the compiler implicitly links with -lc since on some
+ # systems, -lgcc has to come before -lc. If gcc already passes -lc
+ # to ld, don't add -lc before -lgcc.
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether -lc should be explicitly linked in" >&5
+$as_echo_n "checking whether -lc should be explicitly linked in... " >&6; }
+ $RM conftest*
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } 2>conftest.err; then
+ soname=conftest
+ lib=conftest
+ libobjs=conftest.$ac_objext
+ deplibs=
+ wl=$lt_prog_compiler_wl
+ pic_flag=$lt_prog_compiler_pic
+ compiler_flags=-v
+ linker_flags=-v
+ verstring=
+ output_objdir=.
+ libname=conftest
+ lt_save_allow_undefined_flag=$allow_undefined_flag
+ allow_undefined_flag=
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$archive_cmds 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1\""; } >&5
+ (eval $archive_cmds 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+ then
+ archive_cmds_need_lc=no
+ else
+ archive_cmds_need_lc=yes
+ fi
+ allow_undefined_flag=$lt_save_allow_undefined_flag
+ else
+ cat conftest.err 1>&5
+ fi
+ $RM conftest*
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $archive_cmds_need_lc" >&5
+$as_echo "$archive_cmds_need_lc" >&6; }
+ ;;
+ esac
+ fi
+ ;;
+esac
+
+
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+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking dynamic linker characteristics" >&5
+$as_echo_n "checking dynamic linker characteristics... " >&6; }
+
+if test "$GCC" = yes; then
+ case $host_os in
+ darwin*) lt_awk_arg="/^libraries:/,/LR/" ;;
+ *) lt_awk_arg="/^libraries:/" ;;
+ esac
+ lt_search_path_spec=`$CC -print-search-dirs | awk $lt_awk_arg | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$lt_search_path_spec" | $GREP ';' >/dev/null ; then
+ # if the path contains ";" then we assume it to be the separator
+ # otherwise default to the standard path separator (i.e. ":") - it is
+ # assumed that no part of a normal pathname contains ";" but that should
+ # okay in the real world where ";" in dirpaths is itself problematic.
+ lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ # Ok, now we have the path, separated by spaces, we can step through it
+ # and add multilib dir if necessary.
+ lt_tmp_lt_search_path_spec=
+ lt_multi_os_dir=`$CC $CPPFLAGS $CFLAGS $LDFLAGS -print-multi-os-directory 2>/dev/null`
+ for lt_sys_path in $lt_search_path_spec; do
+ if test -d "$lt_sys_path/$lt_multi_os_dir"; then
+ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path/$lt_multi_os_dir"
+ else
+ test -d "$lt_sys_path" && \
+ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path"
+ fi
+ done
+ lt_search_path_spec=`$ECHO $lt_tmp_lt_search_path_spec | awk '
+BEGIN {RS=" "; FS="/|\n";} {
+ lt_foo="";
+ lt_count=0;
+ for (lt_i = NF; lt_i > 0; lt_i--) {
+ if ($lt_i != "" && $lt_i != ".") {
+ if ($lt_i == "..") {
+ lt_count++;
+ } else {
+ if (lt_count == 0) {
+ lt_foo="/" $lt_i lt_foo;
+ } else {
+ lt_count--;
+ }
+ }
+ }
+ }
+ if (lt_foo != "") { lt_freq[lt_foo]++; }
+ if (lt_freq[lt_foo] == 1) { print lt_foo; }
+}'`
+ sys_lib_search_path_spec=`$ECHO $lt_search_path_spec`
+else
+ sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib"
+fi
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+ shlibpath_var=LIBPATH
+
+ # AIX 3 has no versioning support, so we append a major version to the name.
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+
+aix[4-9]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ hardcode_into_libs=yes
+ if test "$host_cpu" = ia64; then
+ # AIX 5 supports IA64
+ library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ else
+ # With GCC up to 2.95.x, collect2 would create an import file
+ # for dependence libraries. The import file would start with
+ # the line `#! .'. This would cause the generated library to
+ # depend on `.', always an invalid library. This was fixed in
+ # development snapshots of GCC prior to 3.0.
+ case $host_os in
+ aix4 | aix4.[01] | aix4.[01].*)
+ if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+ echo ' yes '
+ echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then
+ :
+ else
+ can_build_shared=no
+ fi
+ ;;
+ esac
+ # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+ # soname into executable. Probably we can add versioning support to
+ # collect2, so additional links can be useful in future.
+ if test "$aix_use_runtimelinking" = yes; then
+ # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+ # instead of lib<name>.a to let people know that these are not
+ # typical AIX shared libraries.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ else
+ # We preserve .a as extension for shared libraries through AIX4.2
+ # and later when we are not doing run time linking.
+ library_names_spec='${libname}${release}.a $libname.a'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ fi
+ shlibpath_var=LIBPATH
+ fi
+ ;;
+
+amigaos*)
+ case $host_cpu in
+ powerpc)
+ # Since July 2007 AmigaOS4 officially supports .so libraries.
+ # When compiling the executable, add -use-dynld -Lsobjs: to the compileline.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ ;;
+ m68k)
+ library_names_spec='$libname.ixlibrary $libname.a'
+ # Create ${libname}_ixlibrary.a entries in /sys/libs.
+ finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$ECHO "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+ ;;
+ esac
+ ;;
+
+beos*)
+ library_names_spec='${libname}${shared_ext}'
+ dynamic_linker="$host_os ld.so"
+ shlibpath_var=LIBRARY_PATH
+ ;;
+
+bsdi[45]*)
+ version_type=linux
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+ sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+ # the default ld.so.conf also contains /usr/contrib/lib and
+ # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+ # libtool to hard-code these into programs
+ ;;
+
+cygwin* | mingw* | pw32* | cegcc*)
+ version_type=windows
+ shrext_cmds=".dll"
+ need_version=no
+ need_lib_prefix=no
+
+ case $GCC,$host_os in
+ yes,cygwin* | yes,mingw* | yes,pw32* | yes,cegcc*)
+ library_names_spec='$libname.dll.a'
+ # DLL is installed to $(libdir)/../bin by postinstall_cmds
+ postinstall_cmds='base_file=`basename \${file}`~
+ dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i; echo \$dlname'\''`~
+ dldir=$destdir/`dirname \$dlpath`~
+ test -d \$dldir || mkdir -p \$dldir~
+ $install_prog $dir/$dlname \$dldir/$dlname~
+ chmod a+x \$dldir/$dlname~
+ if test -n '\''$stripme'\'' && test -n '\''$striplib'\''; then
+ eval '\''$striplib \$dldir/$dlname'\'' || exit \$?;
+ fi'
+ postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+ dlpath=$dir/\$dldll~
+ $RM \$dlpath'
+ shlibpath_overrides_runpath=yes
+
+ case $host_os in
+ cygwin*)
+ # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+ soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+ ;;
+ mingw* | cegcc*)
+ # MinGW DLLs use traditional 'lib' prefix
+ soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec=`$CC -print-search-dirs | $GREP "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$sys_lib_search_path_spec" | $GREP ';[c-zC-Z]:/' >/dev/null; then
+ # It is most probably a Windows format PATH printed by
+ # mingw gcc, but we are running on Cygwin. Gcc prints its search
+ # path with ; separators, and with drive letters. We can handle the
+ # drive letters (cygwin fileutils understands them), so leave them,
+ # especially as we might pass files found there to a mingw objdump,
+ # which wouldn't understand a cygwinified path. Ahh.
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ ;;
+ pw32*)
+ # pw32 DLLs use 'pw' prefix rather than 'lib'
+ library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ ;;
+ esac
+ ;;
+
+ *)
+ library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib'
+ ;;
+ esac
+ dynamic_linker='Win32 ld.exe'
+ # FIXME: first we should search . and the directory the executable is in
+ shlibpath_var=PATH
+ ;;
+
+darwin* | rhapsody*)
+ dynamic_linker="$host_os dyld"
+ version_type=darwin
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+ soname_spec='${libname}${release}${major}$shared_ext'
+ shlibpath_overrides_runpath=yes
+ shlibpath_var=DYLD_LIBRARY_PATH
+ shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /usr/local/lib"
+ sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+ ;;
+
+dgux*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+freebsd1*)
+ dynamic_linker=no
+ ;;
+
+freebsd* | dragonfly*)
+ # DragonFly does not have aout. When/if they implement a new
+ # versioning mechanism, adjust this.
+ if test -x /usr/bin/objformat; then
+ objformat=`/usr/bin/objformat`
+ else
+ case $host_os in
+ freebsd[123]*) objformat=aout ;;
+ *) objformat=elf ;;
+ esac
+ fi
+ version_type=freebsd-$objformat
+ case $version_type in
+ freebsd-elf*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ need_version=no
+ need_lib_prefix=no
+ ;;
+ freebsd-*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+ need_version=yes
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_os in
+ freebsd2*)
+ shlibpath_overrides_runpath=yes
+ ;;
+ freebsd3.[01]* | freebsdelf3.[01]*)
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ freebsd3.[2-9]* | freebsdelf3.[2-9]* | \
+ freebsd4.[0-5] | freebsdelf4.[0-5] | freebsd4.1.1 | freebsdelf4.1.1)
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+ *) # from 4.6 on, and DragonFly
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ esac
+ ;;
+
+gnu*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ hardcode_into_libs=yes
+ ;;
+
+hpux9* | hpux10* | hpux11*)
+ # Give a soname corresponding to the major version so that dld.sl refuses to
+ # link against other versions.
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ case $host_cpu in
+ ia64*)
+ shrext_cmds='.so'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.so"
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ if test "X$HPUX_IA64_MODE" = X32; then
+ sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+ else
+ sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+ fi
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ hppa*64*)
+ shrext_cmds='.sl'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ *)
+ shrext_cmds='.sl'
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=SHLIB_PATH
+ shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+ esac
+ # HP-UX runs *really* slowly unless shared libraries are mode 555.
+ postinstall_cmds='chmod 555 $lib'
+ ;;
+
+interix[3-9]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $host_os in
+ nonstopux*) version_type=nonstopux ;;
+ *)
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ version_type=linux
+ else
+ version_type=irix
+ fi ;;
+ esac
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+ case $host_os in
+ irix5* | nonstopux*)
+ libsuff= shlibsuff=
+ ;;
+ *)
+ case $LD in # libtool.m4 will add one of these switches to LD
+ *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+ libsuff= shlibsuff= libmagic=32-bit;;
+ *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+ libsuff=32 shlibsuff=N32 libmagic=N32;;
+ *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+ libsuff=64 shlibsuff=64 libmagic=64-bit;;
+ *) libsuff= shlibsuff= libmagic=never-match;;
+ esac
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+ sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+ hardcode_into_libs=yes
+ ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+ dynamic_linker=no
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ # Some binutils ld are patched to set DT_RUNPATH
+ save_LDFLAGS=$LDFLAGS
+ save_libdir=$libdir
+ eval "libdir=/foo; wl=\"$lt_prog_compiler_wl\"; \
+ LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec\""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then :
+ shlibpath_overrides_runpath=yes
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+ LDFLAGS=$save_LDFLAGS
+ libdir=$save_libdir
+
+ # This implies no fast_install, which is unacceptable.
+ # Some rework will be needed to allow for fast_install
+ # before this can be enabled.
+ hardcode_into_libs=yes
+
+ # Append ld.so.conf contents to the search path
+ if test -f /etc/ld.so.conf; then
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ fi
+
+ # We used to test for /lib/ld.so.1 and disable shared libraries on
+ # powerpc, because MkLinux only supported shared libraries with the
+ # GNU dynamic linker. Since this was broken with cross compilers,
+ # most powerpc-linux boxes support dynamic linking these days and
+ # people can always --disable-shared, the test was removed, and we
+ # assume the GNU/Linux dynamic linker is in use.
+ dynamic_linker='GNU/Linux ld.so'
+ ;;
+
+netbsdelf*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='NetBSD ld.elf_so'
+ ;;
+
+netbsd*)
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ dynamic_linker='NetBSD (a.out) ld.so'
+ else
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='NetBSD ld.elf_so'
+ fi
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+
+newsos6)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ ;;
+
+*nto* | *qnx*)
+ version_type=qnx
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='ldqnx.so'
+ ;;
+
+openbsd*)
+ version_type=sunos
+ sys_lib_dlsearch_path_spec="/usr/lib"
+ need_lib_prefix=no
+ # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+ case $host_os in
+ openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+ *) need_version=no ;;
+ esac
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ case $host_os in
+ openbsd2.[89] | openbsd2.[89].*)
+ shlibpath_overrides_runpath=no
+ ;;
+ *)
+ shlibpath_overrides_runpath=yes
+ ;;
+ esac
+ else
+ shlibpath_overrides_runpath=yes
+ fi
+ ;;
+
+os2*)
+ libname_spec='$name'
+ shrext_cmds=".dll"
+ need_lib_prefix=no
+ library_names_spec='$libname${shared_ext} $libname.a'
+ dynamic_linker='OS/2 ld.exe'
+ shlibpath_var=LIBPATH
+ ;;
+
+osf3* | osf4* | osf5*)
+ version_type=osf
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+ sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+ ;;
+
+rdos*)
+ dynamic_linker=no
+ ;;
+
+solaris*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ # ldd complains unless libraries are executable
+ postinstall_cmds='chmod +x $lib'
+ ;;
+
+sunos4*)
+ version_type=sunos
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ if test "$with_gnu_ld" = yes; then
+ need_lib_prefix=no
+ fi
+ need_version=yes
+ ;;
+
+sysv4 | sysv4.3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_vendor in
+ sni)
+ shlibpath_overrides_runpath=no
+ need_lib_prefix=no
+ runpath_var=LD_RUN_PATH
+ ;;
+ siemens)
+ need_lib_prefix=no
+ ;;
+ motorola)
+ need_lib_prefix=no
+ need_version=no
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+ ;;
+ esac
+ ;;
+
+sysv4*MP*)
+ if test -d /usr/nec ;then
+ version_type=linux
+ library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+ soname_spec='$libname${shared_ext}.$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ fi
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ version_type=freebsd-elf
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ if test "$with_gnu_ld" = yes; then
+ sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+ else
+ sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+ case $host_os in
+ sco3.2v5*)
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+ ;;
+ esac
+ fi
+ sys_lib_dlsearch_path_spec='/usr/lib'
+ ;;
+
+tpf*)
+ # TPF is a cross-target only. Preferred cross-host = GNU/Linux.
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+uts4*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+*)
+ dynamic_linker=no
+ ;;
+esac
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $dynamic_linker" >&5
+$as_echo "$dynamic_linker" >&6; }
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+ variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+
+if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then
+ sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec"
+fi
+if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then
+ sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec"
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to hardcode library paths into programs" >&5
+$as_echo_n "checking how to hardcode library paths into programs... " >&6; }
+hardcode_action=
+if test -n "$hardcode_libdir_flag_spec" ||
+ test -n "$runpath_var" ||
+ test "X$hardcode_automatic" = "Xyes" ; then
+
+ # We can hardcode non-existent directories.
+ if test "$hardcode_direct" != no &&
+ # If the only mechanism to avoid hardcoding is shlibpath_var, we
+ # have to relink, otherwise we might link with an installed library
+ # when we should be linking with a yet-to-be-installed one
+ ## test "$_LT_TAGVAR(hardcode_shlibpath_var, )" != no &&
+ test "$hardcode_minus_L" != no; then
+ # Linking always hardcodes the temporary library directory.
+ hardcode_action=relink
+ else
+ # We can link without hardcoding, and we can hardcode nonexisting dirs.
+ hardcode_action=immediate
+ fi
+else
+ # We cannot hardcode anything, or else we can only hardcode existing
+ # directories.
+ hardcode_action=unsupported
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $hardcode_action" >&5
+$as_echo "$hardcode_action" >&6; }
+
+if test "$hardcode_action" = relink ||
+ test "$inherit_rpath" = yes; then
+ # Fast installation is not supported
+ enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+ test "$enable_shared" = no; then
+ # Fast installation is not necessary
+ enable_fast_install=needless
+fi
+
+
+
+
+
+
+ if test "x$enable_dlopen" != xyes; then
+ enable_dlopen=unknown
+ enable_dlopen_self=unknown
+ enable_dlopen_self_static=unknown
+else
+ lt_cv_dlopen=no
+ lt_cv_dlopen_libs=
+
+ case $host_os in
+ beos*)
+ lt_cv_dlopen="load_add_on"
+ lt_cv_dlopen_libs=
+ lt_cv_dlopen_self=yes
+ ;;
+
+ mingw* | pw32* | cegcc*)
+ lt_cv_dlopen="LoadLibrary"
+ lt_cv_dlopen_libs=
+ ;;
+
+ cygwin*)
+ lt_cv_dlopen="dlopen"
+ lt_cv_dlopen_libs=
+ ;;
+
+ darwin*)
+ # if libdl is installed we need to link against it
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -ldl" >&5
+$as_echo_n "checking for dlopen in -ldl... " >&6; }
+if test "${ac_cv_lib_dl_dlopen+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldl $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+int
+main ()
+{
+return dlopen ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_dl_dlopen=yes
+else
+ ac_cv_lib_dl_dlopen=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dl_dlopen" >&5
+$as_echo "$ac_cv_lib_dl_dlopen" >&6; }
+if test "x$ac_cv_lib_dl_dlopen" = x""yes; then :
+ lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"
+else
+
+ lt_cv_dlopen="dyld"
+ lt_cv_dlopen_libs=
+ lt_cv_dlopen_self=yes
+
+fi
+
+ ;;
+
+ *)
+ ac_fn_c_check_func "$LINENO" "shl_load" "ac_cv_func_shl_load"
+if test "x$ac_cv_func_shl_load" = x""yes; then :
+ lt_cv_dlopen="shl_load"
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for shl_load in -ldld" >&5
+$as_echo_n "checking for shl_load in -ldld... " >&6; }
+if test "${ac_cv_lib_dld_shl_load+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldld $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char shl_load ();
+int
+main ()
+{
+return shl_load ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_dld_shl_load=yes
+else
+ ac_cv_lib_dld_shl_load=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dld_shl_load" >&5
+$as_echo "$ac_cv_lib_dld_shl_load" >&6; }
+if test "x$ac_cv_lib_dld_shl_load" = x""yes; then :
+ lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-ldld"
+else
+ ac_fn_c_check_func "$LINENO" "dlopen" "ac_cv_func_dlopen"
+if test "x$ac_cv_func_dlopen" = x""yes; then :
+ lt_cv_dlopen="dlopen"
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -ldl" >&5
+$as_echo_n "checking for dlopen in -ldl... " >&6; }
+if test "${ac_cv_lib_dl_dlopen+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldl $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+int
+main ()
+{
+return dlopen ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_dl_dlopen=yes
+else
+ ac_cv_lib_dl_dlopen=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dl_dlopen" >&5
+$as_echo "$ac_cv_lib_dl_dlopen" >&6; }
+if test "x$ac_cv_lib_dl_dlopen" = x""yes; then :
+ lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -lsvld" >&5
+$as_echo_n "checking for dlopen in -lsvld... " >&6; }
+if test "${ac_cv_lib_svld_dlopen+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lsvld $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+int
+main ()
+{
+return dlopen ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_svld_dlopen=yes
+else
+ ac_cv_lib_svld_dlopen=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_svld_dlopen" >&5
+$as_echo "$ac_cv_lib_svld_dlopen" >&6; }
+if test "x$ac_cv_lib_svld_dlopen" = x""yes; then :
+ lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld"
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dld_link in -ldld" >&5
+$as_echo_n "checking for dld_link in -ldld... " >&6; }
+if test "${ac_cv_lib_dld_dld_link+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldld $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dld_link ();
+int
+main ()
+{
+return dld_link ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_dld_dld_link=yes
+else
+ ac_cv_lib_dld_dld_link=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dld_dld_link" >&5
+$as_echo "$ac_cv_lib_dld_dld_link" >&6; }
+if test "x$ac_cv_lib_dld_dld_link" = x""yes; then :
+ lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-ldld"
+fi
+
+
+fi
+
+
+fi
+
+
+fi
+
+
+fi
+
+
+fi
+
+ ;;
+ esac
+
+ if test "x$lt_cv_dlopen" != xno; then
+ enable_dlopen=yes
+ else
+ enable_dlopen=no
+ fi
+
+ case $lt_cv_dlopen in
+ dlopen)
+ save_CPPFLAGS="$CPPFLAGS"
+ test "x$ac_cv_header_dlfcn_h" = xyes && CPPFLAGS="$CPPFLAGS -DHAVE_DLFCN_H"
+
+ save_LDFLAGS="$LDFLAGS"
+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\"
+
+ save_LIBS="$LIBS"
+ LIBS="$lt_cv_dlopen_libs $LIBS"
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether a program can dlopen itself" >&5
+$as_echo_n "checking whether a program can dlopen itself... " >&6; }
+if test "${lt_cv_dlopen_self+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then :
+ lt_cv_dlopen_self=cross
+else
+ lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
+ lt_status=$lt_dlunknown
+ cat > conftest.$ac_ext <<_LT_EOF
+#line 11965 "configure"
+#include "confdefs.h"
+
+#if HAVE_DLFCN_H
+#include <dlfcn.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef RTLD_GLOBAL
+# define LT_DLGLOBAL RTLD_GLOBAL
+#else
+# ifdef DL_GLOBAL
+# define LT_DLGLOBAL DL_GLOBAL
+# else
+# define LT_DLGLOBAL 0
+# endif
+#endif
+
+/* We may have to define LT_DLLAZY_OR_NOW in the command line if we
+ find out it does not work in some platform. */
+#ifndef LT_DLLAZY_OR_NOW
+# ifdef RTLD_LAZY
+# define LT_DLLAZY_OR_NOW RTLD_LAZY
+# else
+# ifdef DL_LAZY
+# define LT_DLLAZY_OR_NOW DL_LAZY
+# else
+# ifdef RTLD_NOW
+# define LT_DLLAZY_OR_NOW RTLD_NOW
+# else
+# ifdef DL_NOW
+# define LT_DLLAZY_OR_NOW DL_NOW
+# else
+# define LT_DLLAZY_OR_NOW 0
+# endif
+# endif
+# endif
+# endif
+#endif
+
+void fnord() { int i=42;}
+int main ()
+{
+ void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW);
+ int status = $lt_dlunknown;
+
+ if (self)
+ {
+ if (dlsym (self,"fnord")) status = $lt_dlno_uscore;
+ else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore;
+ /* dlclose (self); */
+ }
+ else
+ puts (dlerror ());
+
+ return status;
+}
+_LT_EOF
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5
+ (eval $ac_link) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && test -s conftest${ac_exeext} 2>/dev/null; then
+ (./conftest; exit; ) >&5 2>/dev/null
+ lt_status=$?
+ case x$lt_status in
+ x$lt_dlno_uscore) lt_cv_dlopen_self=yes ;;
+ x$lt_dlneed_uscore) lt_cv_dlopen_self=yes ;;
+ x$lt_dlunknown|x*) lt_cv_dlopen_self=no ;;
+ esac
+ else :
+ # compilation failed
+ lt_cv_dlopen_self=no
+ fi
+fi
+rm -fr conftest*
+
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_dlopen_self" >&5
+$as_echo "$lt_cv_dlopen_self" >&6; }
+
+ if test "x$lt_cv_dlopen_self" = xyes; then
+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether a statically linked program can dlopen itself" >&5
+$as_echo_n "checking whether a statically linked program can dlopen itself... " >&6; }
+if test "${lt_cv_dlopen_self_static+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then :
+ lt_cv_dlopen_self_static=cross
+else
+ lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
+ lt_status=$lt_dlunknown
+ cat > conftest.$ac_ext <<_LT_EOF
+#line 12061 "configure"
+#include "confdefs.h"
+
+#if HAVE_DLFCN_H
+#include <dlfcn.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef RTLD_GLOBAL
+# define LT_DLGLOBAL RTLD_GLOBAL
+#else
+# ifdef DL_GLOBAL
+# define LT_DLGLOBAL DL_GLOBAL
+# else
+# define LT_DLGLOBAL 0
+# endif
+#endif
+
+/* We may have to define LT_DLLAZY_OR_NOW in the command line if we
+ find out it does not work in some platform. */
+#ifndef LT_DLLAZY_OR_NOW
+# ifdef RTLD_LAZY
+# define LT_DLLAZY_OR_NOW RTLD_LAZY
+# else
+# ifdef DL_LAZY
+# define LT_DLLAZY_OR_NOW DL_LAZY
+# else
+# ifdef RTLD_NOW
+# define LT_DLLAZY_OR_NOW RTLD_NOW
+# else
+# ifdef DL_NOW
+# define LT_DLLAZY_OR_NOW DL_NOW
+# else
+# define LT_DLLAZY_OR_NOW 0
+# endif
+# endif
+# endif
+# endif
+#endif
+
+void fnord() { int i=42;}
+int main ()
+{
+ void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW);
+ int status = $lt_dlunknown;
+
+ if (self)
+ {
+ if (dlsym (self,"fnord")) status = $lt_dlno_uscore;
+ else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore;
+ /* dlclose (self); */
+ }
+ else
+ puts (dlerror ());
+
+ return status;
+}
+_LT_EOF
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5
+ (eval $ac_link) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && test -s conftest${ac_exeext} 2>/dev/null; then
+ (./conftest; exit; ) >&5 2>/dev/null
+ lt_status=$?
+ case x$lt_status in
+ x$lt_dlno_uscore) lt_cv_dlopen_self_static=yes ;;
+ x$lt_dlneed_uscore) lt_cv_dlopen_self_static=yes ;;
+ x$lt_dlunknown|x*) lt_cv_dlopen_self_static=no ;;
+ esac
+ else :
+ # compilation failed
+ lt_cv_dlopen_self_static=no
+ fi
+fi
+rm -fr conftest*
+
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_dlopen_self_static" >&5
+$as_echo "$lt_cv_dlopen_self_static" >&6; }
+ fi
+
+ CPPFLAGS="$save_CPPFLAGS"
+ LDFLAGS="$save_LDFLAGS"
+ LIBS="$save_LIBS"
+ ;;
+ esac
+
+ case $lt_cv_dlopen_self in
+ yes|no) enable_dlopen_self=$lt_cv_dlopen_self ;;
+ *) enable_dlopen_self=unknown ;;
+ esac
+
+ case $lt_cv_dlopen_self_static in
+ yes|no) enable_dlopen_self_static=$lt_cv_dlopen_self_static ;;
+ *) enable_dlopen_self_static=unknown ;;
+ esac
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+striplib=
+old_striplib=
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether stripping libraries is possible" >&5
+$as_echo_n "checking whether stripping libraries is possible... " >&6; }
+if test -n "$STRIP" && $STRIP -V 2>&1 | $GREP "GNU strip" >/dev/null; then
+ test -z "$old_striplib" && old_striplib="$STRIP --strip-debug"
+ test -z "$striplib" && striplib="$STRIP --strip-unneeded"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+else
+# FIXME - insert some real tests, host_os isn't really good enough
+ case $host_os in
+ darwin*)
+ if test -n "$STRIP" ; then
+ striplib="$STRIP -x"
+ old_striplib="$STRIP -S"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ fi
+ ;;
+ *)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ ;;
+ esac
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+ # Report which library types will actually be built
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if libtool supports shared libraries" >&5
+$as_echo_n "checking if libtool supports shared libraries... " >&6; }
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $can_build_shared" >&5
+$as_echo "$can_build_shared" >&6; }
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to build shared libraries" >&5
+$as_echo_n "checking whether to build shared libraries... " >&6; }
+ test "$can_build_shared" = "no" && enable_shared=no
+
+ # On AIX, shared libraries and static libraries use the same namespace, and
+ # are all built from PIC.
+ case $host_os in
+ aix3*)
+ test "$enable_shared" = yes && enable_static=no
+ if test -n "$RANLIB"; then
+ archive_cmds="$archive_cmds~\$RANLIB \$lib"
+ postinstall_cmds='$RANLIB $lib'
+ fi
+ ;;
+
+ aix[4-9]*)
+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+ test "$enable_shared" = yes && enable_static=no
+ fi
+ ;;
+ esac
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $enable_shared" >&5
+$as_echo "$enable_shared" >&6; }
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to build static libraries" >&5
+$as_echo_n "checking whether to build static libraries... " >&6; }
+ # Make sure either enable_shared or enable_static is yes.
+ test "$enable_shared" = yes || enable_static=yes
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $enable_static" >&5
+$as_echo "$enable_static" >&6; }
+
+
+
+
+fi
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+CC="$lt_save_CC"
+
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+archive_cmds_need_lc_CXX=no
+allow_undefined_flag_CXX=
+always_export_symbols_CXX=no
+archive_expsym_cmds_CXX=
+compiler_needs_object_CXX=no
+export_dynamic_flag_spec_CXX=
+hardcode_direct_CXX=no
+hardcode_direct_absolute_CXX=no
+hardcode_libdir_flag_spec_CXX=
+hardcode_libdir_flag_spec_ld_CXX=
+hardcode_libdir_separator_CXX=
+hardcode_minus_L_CXX=no
+hardcode_shlibpath_var_CXX=unsupported
+hardcode_automatic_CXX=no
+inherit_rpath_CXX=no
+module_cmds_CXX=
+module_expsym_cmds_CXX=
+link_all_deplibs_CXX=unknown
+old_archive_cmds_CXX=$old_archive_cmds
+no_undefined_flag_CXX=
+whole_archive_flag_spec_CXX=
+enable_shared_with_static_runtimes_CXX=no
+
+# Source file extension for C++ test sources.
+ac_ext=cpp
+
+# Object file extension for compiled C++ test sources.
+objext=o
+objext_CXX=$objext
+
+# No sense in running all these tests if we already determined that
+# the CXX compiler isn't working. Some variables (like enable_shared)
+# are currently assumed to apply to all compilers on this platform,
+# and will be corrupted by setting them based on a non-working compiler.
+if test "$_lt_caught_CXX_error" != yes; then
+ # Code to be used in simple compile tests
+ lt_simple_compile_test_code="int some_variable = 0;"
+
+ # Code to be used in simple link tests
+ lt_simple_link_test_code='int main(int, char *[]) { return(0); }'
+
+ # ltmain only uses $CC for tagged configurations so make sure $CC is set.
+
+
+
+
+
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+
+ # save warnings/boilerplate of simple test code
+ ac_outfile=conftest.$ac_objext
+echo "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$RM conftest*
+
+ ac_outfile=conftest.$ac_objext
+echo "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$RM -r conftest*
+
+
+ # Allow CC to be a program name with arguments.
+ lt_save_CC=$CC
+ lt_save_LD=$LD
+ lt_save_GCC=$GCC
+ GCC=$GXX
+ lt_save_with_gnu_ld=$with_gnu_ld
+ lt_save_path_LD=$lt_cv_path_LD
+ if test -n "${lt_cv_prog_gnu_ldcxx+set}"; then
+ lt_cv_prog_gnu_ld=$lt_cv_prog_gnu_ldcxx
+ else
+ $as_unset lt_cv_prog_gnu_ld
+ fi
+ if test -n "${lt_cv_path_LDCXX+set}"; then
+ lt_cv_path_LD=$lt_cv_path_LDCXX
+ else
+ $as_unset lt_cv_path_LD
+ fi
+ test -z "${LDCXX+set}" || LD=$LDCXX
+ CC=${CXX-"c++"}
+ compiler=$CC
+ compiler_CXX=$CC
+ for cc_temp in $compiler""; do
+ case $cc_temp in
+ compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+ distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+ \-*) ;;
+ *) break;;
+ esac
+done
+cc_basename=`$ECHO "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+
+
+ if test -n "$compiler"; then
+ # We don't want -fno-exception when compiling C++ code, so set the
+ # no_builtin_flag separately
+ if test "$GXX" = yes; then
+ lt_prog_compiler_no_builtin_flag_CXX=' -fno-builtin'
+ else
+ lt_prog_compiler_no_builtin_flag_CXX=
+ fi
+
+ if test "$GXX" = yes; then
+ # Set up default GNU C++ configuration
+
+
+
+# Check whether --with-gnu-ld was given.
+if test "${with_gnu_ld+set}" = set; then :
+ withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes
+else
+ with_gnu_ld=no
+fi
+
+ac_prog=ld
+if test "$GCC" = yes; then
+ # Check if gcc -print-prog-name=ld gives a path.
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ld used by $CC" >&5
+$as_echo_n "checking for ld used by $CC... " >&6; }
+ case $host in
+ *-*-mingw*)
+ # gcc leaves a trailing carriage return which upsets mingw
+ ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+ *)
+ ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+ esac
+ case $ac_prog in
+ # Accept absolute paths.
+ [\\/]* | ?:[\\/]*)
+ re_direlt='/[^/][^/]*/\.\./'
+ # Canonicalize the pathname of ld
+ ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'`
+ while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do
+ ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"`
+ done
+ test -z "$LD" && LD="$ac_prog"
+ ;;
+ "")
+ # If it fails, then pretend we aren't using GCC.
+ ac_prog=ld
+ ;;
+ *)
+ # If it is relative, then search for the first ld in PATH.
+ with_gnu_ld=unknown
+ ;;
+ esac
+elif test "$with_gnu_ld" = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU ld" >&5
+$as_echo_n "checking for GNU ld... " >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for non-GNU ld" >&5
+$as_echo_n "checking for non-GNU ld... " >&6; }
+fi
+if test "${lt_cv_path_LD+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$LD"; then
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+ lt_cv_path_LD="$ac_dir/$ac_prog"
+ # Check to see if the program is GNU ld. I'd rather use --version,
+ # but apparently some variants of GNU ld only accept -v.
+ # Break only if it was the GNU/non-GNU ld that we prefer.
+ case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+ *GNU* | *'with BFD'*)
+ test "$with_gnu_ld" != no && break
+ ;;
+ *)
+ test "$with_gnu_ld" != yes && break
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+else
+ lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi
+fi
+
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LD" >&5
+$as_echo "$LD" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+test -z "$LD" && as_fn_error $? "no acceptable ld found in \$PATH" "$LINENO" 5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if the linker ($LD) is GNU ld" >&5
+$as_echo_n "checking if the linker ($LD) is GNU ld... " >&6; }
+if test "${lt_cv_prog_gnu_ld+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ # I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+ lt_cv_prog_gnu_ld=yes
+ ;;
+*)
+ lt_cv_prog_gnu_ld=no
+ ;;
+esac
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_gnu_ld" >&5
+$as_echo "$lt_cv_prog_gnu_ld" >&6; }
+with_gnu_ld=$lt_cv_prog_gnu_ld
+
+
+
+
+
+
+
+ # Check if GNU C++ uses GNU ld as the underlying linker, since the
+ # archiving commands below assume that GNU ld is being used.
+ if test "$with_gnu_ld" = yes; then
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+
+ # If archive_cmds runs LD, not CC, wlarc should be empty
+ # XXX I think wlarc can be eliminated in ltcf-cxx, but I need to
+ # investigate it a little bit more. (MM)
+ wlarc='${wl}'
+
+ # ancient GNU ld didn't support --whole-archive et. al.
+ if eval "`$CC -print-prog-name=ld` --help 2>&1" |
+ $GREP 'no-whole-archive' > /dev/null; then
+ whole_archive_flag_spec_CXX="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ else
+ whole_archive_flag_spec_CXX=
+ fi
+ else
+ with_gnu_ld=no
+ wlarc=
+
+ # A generic and very simple default shared library creation
+ # command for GNU C++ for the case where it uses the native
+ # linker, instead of GNU ld. If possible, this setting should
+ # overridden to take advantage of the native linker features on
+ # the platform it is being used on.
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+ fi
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+
+ else
+ GXX=no
+ with_gnu_ld=no
+ wlarc=
+ fi
+
+ # PORTME: fill in a description of your system's C++ link characteristics
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+$as_echo_n "checking whether the $compiler linker ($LD) supports shared libraries... " >&6; }
+ ld_shlibs_CXX=yes
+ case $host_os in
+ aix3*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ aix[4-9]*)
+ if test "$host_cpu" = ia64; then
+ # On IA64, the linker does run time linking by default, so we don't
+ # have to do anything special.
+ aix_use_runtimelinking=no
+ exp_sym_flag='-Bexport'
+ no_entry_flag=""
+ else
+ aix_use_runtimelinking=no
+
+ # Test if we are trying to use run time linking or normal
+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+ # need to do runtime linking.
+ case $host_os in aix4.[23]|aix4.[23].*|aix[5-9]*)
+ for ld_flag in $LDFLAGS; do
+ case $ld_flag in
+ *-brtl*)
+ aix_use_runtimelinking=yes
+ break
+ ;;
+ esac
+ done
+ ;;
+ esac
+
+ exp_sym_flag='-bexport'
+ no_entry_flag='-bnoentry'
+ fi
+
+ # When large executables or shared objects are built, AIX ld can
+ # have problems creating the table of contents. If linking a library
+ # or program results in "error TOC overflow" add -mminimal-toc to
+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not
+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+ archive_cmds_CXX=''
+ hardcode_direct_CXX=yes
+ hardcode_direct_absolute_CXX=yes
+ hardcode_libdir_separator_CXX=':'
+ link_all_deplibs_CXX=yes
+ file_list_spec_CXX='${wl}-f,'
+
+ if test "$GXX" = yes; then
+ case $host_os in aix4.[012]|aix4.[012].*)
+ # We only want to do this on AIX 4.2 and lower, the check
+ # below for broken collect2 doesn't work under 4.3+
+ collect2name=`${CC} -print-prog-name=collect2`
+ if test -f "$collect2name" &&
+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null
+ then
+ # We have reworked collect2
+ :
+ else
+ # We have old collect2
+ hardcode_direct_CXX=unsupported
+ # It fails to find uninstalled libraries when the uninstalled
+ # path is not listed in the libpath. Setting hardcode_minus_L
+ # to unsupported forces relinking
+ hardcode_minus_L_CXX=yes
+ hardcode_libdir_flag_spec_CXX='-L$libdir'
+ hardcode_libdir_separator_CXX=
+ fi
+ esac
+ shared_flag='-shared'
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag="$shared_flag "'${wl}-G'
+ fi
+ else
+ # not using gcc
+ if test "$host_cpu" = ia64; then
+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+ # chokes on -Wl,-G. The following line is correct:
+ shared_flag='-G'
+ else
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag='${wl}-G'
+ else
+ shared_flag='${wl}-bM:SRE'
+ fi
+ fi
+ fi
+
+ export_dynamic_flag_spec_CXX='${wl}-bexpall'
+ # It seems that -bexpall does not export symbols beginning with
+ # underscore (_), so it is better to generate a list of symbols to
+ # export.
+ always_export_symbols_CXX=yes
+ if test "$aix_use_runtimelinking" = yes; then
+ # Warning - without using the other runtime loading flags (-brtl),
+ # -berok will link without error, but may produce a broken library.
+ allow_undefined_flag_CXX='-berok'
+ # Determine the default libpath from the value encoded in an empty
+ # executable.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+ hardcode_libdir_flag_spec_CXX='${wl}-blibpath:$libdir:'"$aix_libpath"
+
+ archive_expsym_cmds_CXX='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+ else
+ if test "$host_cpu" = ia64; then
+ hardcode_libdir_flag_spec_CXX='${wl}-R $libdir:/usr/lib:/lib'
+ allow_undefined_flag_CXX="-z nodefs"
+ archive_expsym_cmds_CXX="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+ else
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+ hardcode_libdir_flag_spec_CXX='${wl}-blibpath:$libdir:'"$aix_libpath"
+ # Warning - without using the other run time loading flags,
+ # -berok will link without error, but may produce a broken library.
+ no_undefined_flag_CXX=' ${wl}-bernotok'
+ allow_undefined_flag_CXX=' ${wl}-berok'
+ # Exported symbols can be pulled into shared objects from archives
+ whole_archive_flag_spec_CXX='$convenience'
+ archive_cmds_need_lc_CXX=yes
+ # This is similar to how AIX traditionally builds its shared
+ # libraries.
+ archive_expsym_cmds_CXX="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+ fi
+ fi
+ ;;
+
+ beos*)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ allow_undefined_flag_CXX=unsupported
+ # Joseph Beckenbach <jrb3 at best.com> says some releases of gcc
+ # support --undefined. This deserves some investigation. FIXME
+ archive_cmds_CXX='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ else
+ ld_shlibs_CXX=no
+ fi
+ ;;
+
+ chorus*)
+ case $cc_basename in
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # _LT_TAGVAR(hardcode_libdir_flag_spec, CXX) is actually meaningless,
+ # as there is no search path for DLLs.
+ hardcode_libdir_flag_spec_CXX='-L$libdir'
+ allow_undefined_flag_CXX=unsupported
+ always_export_symbols_CXX=no
+ enable_shared_with_static_runtimes_CXX=yes
+
+ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ # If the export-symbols file already is a .def file (1st line
+ # is EXPORTS), use it as is; otherwise, prepend...
+ archive_expsym_cmds_CXX='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+ cp $export_symbols $output_objdir/$soname.def;
+ else
+ echo EXPORTS > $output_objdir/$soname.def;
+ cat $export_symbols >> $output_objdir/$soname.def;
+ fi~
+ $CC -shared -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ else
+ ld_shlibs_CXX=no
+ fi
+ ;;
+ darwin* | rhapsody*)
+
+
+ archive_cmds_need_lc_CXX=no
+ hardcode_direct_CXX=no
+ hardcode_automatic_CXX=yes
+ hardcode_shlibpath_var_CXX=unsupported
+ whole_archive_flag_spec_CXX=''
+ link_all_deplibs_CXX=yes
+ allow_undefined_flag_CXX="$_lt_dar_allow_undefined"
+ case $cc_basename in
+ ifort*) _lt_dar_can_shared=yes ;;
+ *) _lt_dar_can_shared=$GCC ;;
+ esac
+ if test "$_lt_dar_can_shared" = "yes"; then
+ output_verbose_link_cmd=echo
+ archive_cmds_CXX="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}"
+ module_cmds_CXX="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}"
+ archive_expsym_cmds_CXX="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}"
+ module_expsym_cmds_CXX="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}"
+ if test "$lt_cv_apple_cc_single_mod" != "yes"; then
+ archive_cmds_CXX="\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dsymutil}"
+ archive_expsym_cmds_CXX="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dar_export_syms}${_lt_dsymutil}"
+ fi
+
+ else
+ ld_shlibs_CXX=no
+ fi
+
+ ;;
+
+ dgux*)
+ case $cc_basename in
+ ec++*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ ghcx*)
+ # Green Hills C++ Compiler
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ freebsd[12]*)
+ # C++ shared libraries reported to be fairly broken before
+ # switch to ELF
+ ld_shlibs_CXX=no
+ ;;
+
+ freebsd-elf*)
+ archive_cmds_need_lc_CXX=no
+ ;;
+
+ freebsd* | dragonfly*)
+ # FreeBSD 3 and later use GNU C++ and GNU ld with standard ELF
+ # conventions
+ ld_shlibs_CXX=yes
+ ;;
+
+ gnu*)
+ ;;
+
+ hpux9*)
+ hardcode_libdir_flag_spec_CXX='${wl}+b ${wl}$libdir'
+ hardcode_libdir_separator_CXX=:
+ export_dynamic_flag_spec_CXX='${wl}-E'
+ hardcode_direct_CXX=yes
+ hardcode_minus_L_CXX=yes # Not in the search PATH,
+ # but as the default
+ # location of the library.
+
+ case $cc_basename in
+ CC*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ aCC*)
+ archive_cmds_CXX='$RM $output_objdir/$soname~$CC -b ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $EGREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ archive_cmds_CXX='$RM $output_objdir/$soname~$CC -shared -nostdlib -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ else
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ fi
+ ;;
+ esac
+ ;;
+
+ hpux10*|hpux11*)
+ if test $with_gnu_ld = no; then
+ hardcode_libdir_flag_spec_CXX='${wl}+b ${wl}$libdir'
+ hardcode_libdir_separator_CXX=:
+
+ case $host_cpu in
+ hppa*64*|ia64*)
+ ;;
+ *)
+ export_dynamic_flag_spec_CXX='${wl}-E'
+ ;;
+ esac
+ fi
+ case $host_cpu in
+ hppa*64*|ia64*)
+ hardcode_direct_CXX=no
+ hardcode_shlibpath_var_CXX=no
+ ;;
+ *)
+ hardcode_direct_CXX=yes
+ hardcode_direct_absolute_CXX=yes
+ hardcode_minus_L_CXX=yes # Not in the search PATH,
+ # but as the default
+ # location of the library.
+ ;;
+ esac
+
+ case $cc_basename in
+ CC*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ aCC*)
+ case $host_cpu in
+ hppa*64*)
+ archive_cmds_CXX='$CC -b ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ ia64*)
+ archive_cmds_CXX='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ esac
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $GREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ if test $with_gnu_ld = no; then
+ case $host_cpu in
+ hppa*64*)
+ archive_cmds_CXX='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ ia64*)
+ archive_cmds_CXX='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ esac
+ fi
+ else
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ fi
+ ;;
+ esac
+ ;;
+
+ interix[3-9]*)
+ hardcode_direct_CXX=no
+ hardcode_shlibpath_var_CXX=no
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec_CXX='${wl}-E'
+ # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+ # Instead, shared libraries are loaded at an image base (0x10000000 by
+ # default) and relocated if they conflict, which is a slow very memory
+ # consuming and fragmenting process. To avoid this, we pick a random,
+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+ # time. Moving up from 0x10000000 also allows more sbrk(2) space.
+ archive_cmds_CXX='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ archive_expsym_cmds_CXX='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ ;;
+ irix5* | irix6*)
+ case $cc_basename in
+ CC*)
+ # SGI C++
+ archive_cmds_CXX='$CC -shared -all -multigot $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+
+ # Archives containing C++ object files must be created using
+ # "CC -ar", where "CC" is the IRIX C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ old_archive_cmds_CXX='$CC -ar -WR,-u -o $oldlib $oldobjs'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ if test "$with_gnu_ld" = no; then
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ else
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` -o $lib'
+ fi
+ fi
+ link_all_deplibs_CXX=yes
+ ;;
+ esac
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator_CXX=:
+ inherit_rpath_CXX=yes
+ ;;
+
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ KCC*)
+ # Kuck and Associates, Inc. (KAI) C++ Compiler
+
+ # KCC will only create a shared library if the output file
+ # ends with ".so" (or ".sl" for HP-UX), so rename the library
+ # to its proper name (with version) after linking.
+ archive_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+ archive_expsym_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib ${wl}-retain-symbols-file,$export_symbols; mv \$templib $lib'
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 | $GREP "ld"`; rm -f libconftest$shared_ext; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+
+ # Archives containing C++ object files must be created using
+ # "CC -Bstatic", where "CC" is the KAI C++ compiler.
+ old_archive_cmds_CXX='$CC -Bstatic -o $oldlib $oldobjs'
+ ;;
+ icpc* | ecpc* )
+ # Intel C++
+ with_gnu_ld=yes
+ # version 8.0 and above of icpc choke on multiply defined symbols
+ # if we add $predep_objects and $postdep_objects, however 7.1 and
+ # earlier do not add the objects themselves.
+ case `$CC -V 2>&1` in
+ *"Version 7."*)
+ archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ ;;
+ *) # Version 8.0 or newer
+ tmp_idyn=
+ case $host_cpu in
+ ia64*) tmp_idyn=' -i_dynamic';;
+ esac
+ archive_cmds_CXX='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ ;;
+ esac
+ archive_cmds_need_lc_CXX=no
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+ whole_archive_flag_spec_CXX='${wl}--whole-archive$convenience ${wl}--no-whole-archive'
+ ;;
+ pgCC* | pgcpp*)
+ # Portland Group C++ compiler
+ case `$CC -V` in
+ *pgCC\ [1-5]* | *pgcpp\ [1-5]*)
+ prelink_cmds_CXX='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $objs $libobjs $compile_deplibs~
+ compile_command="$compile_command `find $tpldir -name \*.o | $NL2SP`"'
+ old_archive_cmds_CXX='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $oldobjs$old_deplibs~
+ $AR $AR_FLAGS $oldlib$oldobjs$old_deplibs `find $tpldir -name \*.o | $NL2SP`~
+ $RANLIB $oldlib'
+ archive_cmds_CXX='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~
+ $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+ archive_expsym_cmds_CXX='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~
+ $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+ ;;
+ *) # Version 6 will use weak symbols
+ archive_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+ ;;
+ esac
+
+ hardcode_libdir_flag_spec_CXX='${wl}--rpath ${wl}$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+ whole_archive_flag_spec_CXX='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ ;;
+ cxx*)
+ # Compaq C++
+ archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib ${wl}-retain-symbols-file $wl$export_symbols'
+
+ runpath_var=LD_RUN_PATH
+ hardcode_libdir_flag_spec_CXX='-rpath $libdir'
+ hardcode_libdir_separator_CXX=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld .*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ xl*)
+ # IBM XL 8.0 on PPC, with GNU ld
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+ archive_cmds_CXX='$CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ if test "x$supports_anon_versioning" = xyes; then
+ archive_expsym_cmds_CXX='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+ fi
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+ no_undefined_flag_CXX=' -zdefs'
+ archive_cmds_CXX='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file ${wl}$export_symbols'
+ hardcode_libdir_flag_spec_CXX='-R$libdir'
+ whole_archive_flag_spec_CXX='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ compiler_needs_object_CXX=yes
+
+ # Not sure whether something based on
+ # $CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1
+ # would be better.
+ output_verbose_link_cmd='echo'
+
+ # Archives containing C++ object files must be created using
+ # "CC -xar", where "CC" is the Sun C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ old_archive_cmds_CXX='$CC -xar -o $oldlib $oldobjs'
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+
+ lynxos*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+
+ m88k*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+
+ mvs*)
+ case $cc_basename in
+ cxx*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ netbsd*)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ archive_cmds_CXX='$LD -Bshareable -o $lib $predep_objects $libobjs $deplibs $postdep_objects $linker_flags'
+ wlarc=
+ hardcode_libdir_flag_spec_CXX='-R$libdir'
+ hardcode_direct_CXX=yes
+ hardcode_shlibpath_var_CXX=no
+ fi
+ # Workaround some broken pre-1.5 toolchains
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP conftest.$objext | $SED -e "s:-lgcc -lc -lgcc::"'
+ ;;
+
+ *nto* | *qnx*)
+ ld_shlibs_CXX=yes
+ ;;
+
+ openbsd2*)
+ # C++ shared libraries are fairly broken
+ ld_shlibs_CXX=no
+ ;;
+
+ openbsd*)
+ if test -f /usr/libexec/ld.so; then
+ hardcode_direct_CXX=yes
+ hardcode_shlibpath_var_CXX=no
+ hardcode_direct_absolute_CXX=yes
+ archive_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ archive_expsym_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file,$export_symbols -o $lib'
+ export_dynamic_flag_spec_CXX='${wl}-E'
+ whole_archive_flag_spec_CXX="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ fi
+ output_verbose_link_cmd=echo
+ else
+ ld_shlibs_CXX=no
+ fi
+ ;;
+
+ osf3* | osf4* | osf5*)
+ case $cc_basename in
+ KCC*)
+ # Kuck and Associates, Inc. (KAI) C++ Compiler
+
+ # KCC will only create a shared library if the output file
+ # ends with ".so" (or ".sl" for HP-UX), so rename the library
+ # to its proper name (with version) after linking.
+ archive_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo "$lib" | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ hardcode_libdir_separator_CXX=:
+
+ # Archives containing C++ object files must be created using
+ # the KAI C++ compiler.
+ case $host in
+ osf3*) old_archive_cmds_CXX='$CC -Bstatic -o $oldlib $oldobjs' ;;
+ *) old_archive_cmds_CXX='$CC -o $oldlib $oldobjs' ;;
+ esac
+ ;;
+ RCC*)
+ # Rational C++ 2.4.1
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ cxx*)
+ case $host in
+ osf3*)
+ allow_undefined_flag_CXX=' ${wl}-expect_unresolved ${wl}\*'
+ archive_cmds_CXX='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $soname `test -n "$verstring" && $ECHO "X${wl}-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ ;;
+ *)
+ allow_undefined_flag_CXX=' -expect_unresolved \*'
+ archive_cmds_CXX='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ archive_expsym_cmds_CXX='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done~
+ echo "-hidden">> $lib.exp~
+ $CC -shared$allow_undefined_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname ${wl}-input ${wl}$lib.exp `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~
+ $RM $lib.exp'
+ hardcode_libdir_flag_spec_CXX='-rpath $libdir'
+ ;;
+ esac
+
+ hardcode_libdir_separator_CXX=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld" | $GREP -v "ld:"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld.*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+ allow_undefined_flag_CXX=' ${wl}-expect_unresolved ${wl}\*'
+ case $host in
+ osf3*)
+ archive_cmds_CXX='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ ;;
+ esac
+
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator_CXX=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+
+ else
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ fi
+ ;;
+ esac
+ ;;
+
+ psos*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+
+ sunos4*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.x
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ lcc*)
+ # Lucid
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ solaris*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.2, 5.x and Centerline C++
+ archive_cmds_need_lc_CXX=yes
+ no_undefined_flag_CXX=' -zdefs'
+ archive_cmds_CXX='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ archive_expsym_cmds_CXX='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G${allow_undefined_flag} ${wl}-M ${wl}$lib.exp -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ hardcode_libdir_flag_spec_CXX='-R$libdir'
+ hardcode_shlibpath_var_CXX=no
+ case $host_os in
+ solaris2.[0-5] | solaris2.[0-5].*) ;;
+ *)
+ # The compiler driver will combine and reorder linker options,
+ # but understands `-z linker_flag'.
+ # Supported since Solaris 2.6 (maybe 2.5.1?)
+ whole_archive_flag_spec_CXX='-z allextract$convenience -z defaultextract'
+ ;;
+ esac
+ link_all_deplibs_CXX=yes
+
+ output_verbose_link_cmd='echo'
+
+ # Archives containing C++ object files must be created using
+ # "CC -xar", where "CC" is the Sun C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ old_archive_cmds_CXX='$CC -xar -o $oldlib $oldobjs'
+ ;;
+ gcx*)
+ # Green Hills C++ Compiler
+ archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+
+ # The C++ compiler must be used to create the archive.
+ old_archive_cmds_CXX='$CC $LDFLAGS -archive -o $oldlib $oldobjs'
+ ;;
+ *)
+ # GNU C++ compiler with Solaris linker
+ if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+ no_undefined_flag_CXX=' ${wl}-z ${wl}defs'
+ if $CC --version | $GREP -v '^2\.7' > /dev/null; then
+ archive_cmds_CXX='$CC -shared -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -shared -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+ else
+ # g++ 2.7 appears to require `-G' NOT `-shared' on this
+ # platform.
+ archive_cmds_CXX='$CC -G -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -G $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+ fi
+
+ hardcode_libdir_flag_spec_CXX='${wl}-R $wl$libdir'
+ case $host_os in
+ solaris2.[0-5] | solaris2.[0-5].*) ;;
+ *)
+ whole_archive_flag_spec_CXX='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract'
+ ;;
+ esac
+ fi
+ ;;
+ esac
+ ;;
+
+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*)
+ no_undefined_flag_CXX='${wl}-z,text'
+ archive_cmds_need_lc_CXX=no
+ hardcode_shlibpath_var_CXX=no
+ runpath_var='LD_RUN_PATH'
+
+ case $cc_basename in
+ CC*)
+ archive_cmds_CXX='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6*)
+ # Note: We can NOT use -z defs as we might desire, because we do not
+ # link with -lc, and that would cause any symbols used from libc to
+ # always be unresolved, which means just about no library would
+ # ever link correctly. If we're not using GNU ld we use -z text
+ # though, which does catch some bad symbols but isn't as heavy-handed
+ # as -z defs.
+ no_undefined_flag_CXX='${wl}-z,text'
+ allow_undefined_flag_CXX='${wl}-z,nodefs'
+ archive_cmds_need_lc_CXX=no
+ hardcode_shlibpath_var_CXX=no
+ hardcode_libdir_flag_spec_CXX='${wl}-R,$libdir'
+ hardcode_libdir_separator_CXX=':'
+ link_all_deplibs_CXX=yes
+ export_dynamic_flag_spec_CXX='${wl}-Bexport'
+ runpath_var='LD_RUN_PATH'
+
+ case $cc_basename in
+ CC*)
+ archive_cmds_CXX='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ ;;
+
+ tandem*)
+ case $cc_basename in
+ NCC*)
+ # NonStop-UX NCC 3.20
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ vxworks*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ld_shlibs_CXX" >&5
+$as_echo "$ld_shlibs_CXX" >&6; }
+ test "$ld_shlibs_CXX" = no && can_build_shared=no
+
+ GCC_CXX="$GXX"
+ LD_CXX="$LD"
+
+ ## CAVEAT EMPTOR:
+ ## There is no encapsulation within the following macros, do not change
+ ## the running order or otherwise move them around unless you know exactly
+ ## what you are doing...
+ # Dependencies to place before and after the object being linked:
+predep_objects_CXX=
+postdep_objects_CXX=
+predeps_CXX=
+postdeps_CXX=
+compiler_lib_search_path_CXX=
+
+cat > conftest.$ac_ext <<_LT_EOF
+class Foo
+{
+public:
+ Foo (void) { a = 0; }
+private:
+ int a;
+};
+_LT_EOF
+
+if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ # Parse the compiler output and extract the necessary
+ # objects, libraries and library flags.
+
+ # Sentinel used to keep track of whether or not we are before
+ # the conftest object file.
+ pre_test_object_deps_done=no
+
+ for p in `eval "$output_verbose_link_cmd"`; do
+ case $p in
+
+ -L* | -R* | -l*)
+ # Some compilers place space between "-{L,R}" and the path.
+ # Remove the space.
+ if test $p = "-L" ||
+ test $p = "-R"; then
+ prev=$p
+ continue
+ else
+ prev=
+ fi
+
+ if test "$pre_test_object_deps_done" = no; then
+ case $p in
+ -L* | -R*)
+ # Internal compiler library paths should come after those
+ # provided the user. The postdeps already come after the
+ # user supplied libs so there is no need to process them.
+ if test -z "$compiler_lib_search_path_CXX"; then
+ compiler_lib_search_path_CXX="${prev}${p}"
+ else
+ compiler_lib_search_path_CXX="${compiler_lib_search_path_CXX} ${prev}${p}"
+ fi
+ ;;
+ # The "-l" case would never come before the object being
+ # linked, so don't bother handling this case.
+ esac
+ else
+ if test -z "$postdeps_CXX"; then
+ postdeps_CXX="${prev}${p}"
+ else
+ postdeps_CXX="${postdeps_CXX} ${prev}${p}"
+ fi
+ fi
+ ;;
+
+ *.$objext)
+ # This assumes that the test object file only shows up
+ # once in the compiler output.
+ if test "$p" = "conftest.$objext"; then
+ pre_test_object_deps_done=yes
+ continue
+ fi
+
+ if test "$pre_test_object_deps_done" = no; then
+ if test -z "$predep_objects_CXX"; then
+ predep_objects_CXX="$p"
+ else
+ predep_objects_CXX="$predep_objects_CXX $p"
+ fi
+ else
+ if test -z "$postdep_objects_CXX"; then
+ postdep_objects_CXX="$p"
+ else
+ postdep_objects_CXX="$postdep_objects_CXX $p"
+ fi
+ fi
+ ;;
+
+ *) ;; # Ignore the rest.
+
+ esac
+ done
+
+ # Clean up.
+ rm -f a.out a.exe
+else
+ echo "libtool.m4: error: problem compiling CXX test program"
+fi
+
+$RM -f confest.$objext
+
+# PORTME: override above test on systems where it is broken
+case $host_os in
+interix[3-9]*)
+ # Interix 3.5 installs completely hosed .la files for C++, so rather than
+ # hack all around it, let's just trust "g++" to DTRT.
+ predep_objects_CXX=
+ postdep_objects_CXX=
+ postdeps_CXX=
+ ;;
+
+linux*)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+
+ # The more standards-conforming stlport4 library is
+ # incompatible with the Cstd library. Avoid specifying
+ # it if it's in CXXFLAGS. Ignore libCrun as
+ # -library=stlport4 depends on it.
+ case " $CXX $CXXFLAGS " in
+ *" -library=stlport4 "*)
+ solaris_use_stlport4=yes
+ ;;
+ esac
+
+ if test "$solaris_use_stlport4" != yes; then
+ postdeps_CXX='-library=Cstd -library=Crun'
+ fi
+ ;;
+ esac
+ ;;
+
+solaris*)
+ case $cc_basename in
+ CC*)
+ # The more standards-conforming stlport4 library is
+ # incompatible with the Cstd library. Avoid specifying
+ # it if it's in CXXFLAGS. Ignore libCrun as
+ # -library=stlport4 depends on it.
+ case " $CXX $CXXFLAGS " in
+ *" -library=stlport4 "*)
+ solaris_use_stlport4=yes
+ ;;
+ esac
+
+ # Adding this requires a known-good setup of shared libraries for
+ # Sun compiler versions before 5.6, else PIC objects from an old
+ # archive will be linked into the output, leading to subtle bugs.
+ if test "$solaris_use_stlport4" != yes; then
+ postdeps_CXX='-library=Cstd -library=Crun'
+ fi
+ ;;
+ esac
+ ;;
+esac
+
+
+case " $postdeps_CXX " in
+*" -lc "*) archive_cmds_need_lc_CXX=no ;;
+esac
+ compiler_lib_search_dirs_CXX=
+if test -n "${compiler_lib_search_path_CXX}"; then
+ compiler_lib_search_dirs_CXX=`echo " ${compiler_lib_search_path_CXX}" | ${SED} -e 's! -L! !g' -e 's!^ !!'`
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ lt_prog_compiler_wl_CXX=
+lt_prog_compiler_pic_CXX=
+lt_prog_compiler_static_CXX=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $compiler option to produce PIC" >&5
+$as_echo_n "checking for $compiler option to produce PIC... " >&6; }
+
+ # C++ specific cases for pic, static, wl, etc.
+ if test "$GXX" = yes; then
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_static_CXX='-static'
+
+ case $host_os in
+ aix*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ lt_prog_compiler_static_CXX='-Bstatic'
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ lt_prog_compiler_pic_CXX='-fPIC'
+ ;;
+ m68k)
+ # FIXME: we need at least 68020 code to build shared libraries, but
+ # adding the `-m68020' flag to GCC prevents building anything better,
+ # like `-m68040'.
+ lt_prog_compiler_pic_CXX='-m68020 -resident32 -malways-restore-a4'
+ ;;
+ esac
+ ;;
+
+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+ # PIC is the default for these OSes.
+ ;;
+ mingw* | cygwin* | os2* | pw32* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ # Although the cygwin gcc ignores -fPIC, still need this for old-style
+ # (--disable-auto-import) libraries
+ lt_prog_compiler_pic_CXX='-DDLL_EXPORT'
+ ;;
+ darwin* | rhapsody*)
+ # PIC is the default on this platform
+ # Common symbols not allowed in MH_DYLIB files
+ lt_prog_compiler_pic_CXX='-fno-common'
+ ;;
+ *djgpp*)
+ # DJGPP does not support shared libraries at all
+ lt_prog_compiler_pic_CXX=
+ ;;
+ interix[3-9]*)
+ # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+ # Instead, we relocate shared libraries at runtime.
+ ;;
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ lt_prog_compiler_pic_CXX=-Kconform_pic
+ fi
+ ;;
+ hpux*)
+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit
+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag
+ # sets the default TLS model and affects inlining.
+ case $host_cpu in
+ hppa*64*)
+ ;;
+ *)
+ lt_prog_compiler_pic_CXX='-fPIC'
+ ;;
+ esac
+ ;;
+ *qnx* | *nto*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ lt_prog_compiler_pic_CXX='-fPIC -shared'
+ ;;
+ *)
+ lt_prog_compiler_pic_CXX='-fPIC'
+ ;;
+ esac
+ else
+ case $host_os in
+ aix[4-9]*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ lt_prog_compiler_static_CXX='-Bstatic'
+ else
+ lt_prog_compiler_static_CXX='-bnso -bI:/lib/syscalls.exp'
+ fi
+ ;;
+ chorus*)
+ case $cc_basename in
+ cxch68*)
+ # Green Hills C++ Compiler
+ # _LT_TAGVAR(lt_prog_compiler_static, CXX)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a"
+ ;;
+ esac
+ ;;
+ dgux*)
+ case $cc_basename in
+ ec++*)
+ lt_prog_compiler_pic_CXX='-KPIC'
+ ;;
+ ghcx*)
+ # Green Hills C++ Compiler
+ lt_prog_compiler_pic_CXX='-pic'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ freebsd* | dragonfly*)
+ # FreeBSD uses GNU C++
+ ;;
+ hpux9* | hpux10* | hpux11*)
+ case $cc_basename in
+ CC*)
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_static_CXX='${wl}-a ${wl}archive'
+ if test "$host_cpu" != ia64; then
+ lt_prog_compiler_pic_CXX='+Z'
+ fi
+ ;;
+ aCC*)
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_static_CXX='${wl}-a ${wl}archive'
+ case $host_cpu in
+ hppa*64*|ia64*)
+ # +Z the default
+ ;;
+ *)
+ lt_prog_compiler_pic_CXX='+Z'
+ ;;
+ esac
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ interix*)
+ # This is c89, which is MS Visual C++ (no shared libs)
+ # Anyone wants to do a port?
+ ;;
+ irix5* | irix6* | nonstopux*)
+ case $cc_basename in
+ CC*)
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_static_CXX='-non_shared'
+ # CC pic flag -KPIC is the default.
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ KCC*)
+ # KAI C++ Compiler
+ lt_prog_compiler_wl_CXX='--backend -Wl,'
+ lt_prog_compiler_pic_CXX='-fPIC'
+ ;;
+ ecpc* )
+ # old Intel C++ for x86_64 which still supported -KPIC.
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-KPIC'
+ lt_prog_compiler_static_CXX='-static'
+ ;;
+ icpc* )
+ # Intel C++, used to be incompatible with GCC.
+ # ICC 10 doesn't accept -KPIC any more.
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-fPIC'
+ lt_prog_compiler_static_CXX='-static'
+ ;;
+ pgCC* | pgcpp*)
+ # Portland Group C++ compiler
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-fpic'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ ;;
+ cxx*)
+ # Compaq C++
+ # Make sure the PIC flag is empty. It appears that all Alpha
+ # Linux and Compaq Tru64 Unix objects are PIC.
+ lt_prog_compiler_pic_CXX=
+ lt_prog_compiler_static_CXX='-non_shared'
+ ;;
+ xlc* | xlC*)
+ # IBM XL 8.0 on PPC
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-qpic'
+ lt_prog_compiler_static_CXX='-qstaticlink'
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+ lt_prog_compiler_pic_CXX='-KPIC'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ lt_prog_compiler_wl_CXX='-Qoption ld '
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+ lynxos*)
+ ;;
+ m88k*)
+ ;;
+ mvs*)
+ case $cc_basename in
+ cxx*)
+ lt_prog_compiler_pic_CXX='-W c,exportall'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ netbsd* | netbsdelf*-gnu)
+ ;;
+ *qnx* | *nto*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ lt_prog_compiler_pic_CXX='-fPIC -shared'
+ ;;
+ osf3* | osf4* | osf5*)
+ case $cc_basename in
+ KCC*)
+ lt_prog_compiler_wl_CXX='--backend -Wl,'
+ ;;
+ RCC*)
+ # Rational C++ 2.4.1
+ lt_prog_compiler_pic_CXX='-pic'
+ ;;
+ cxx*)
+ # Digital/Compaq C++
+ lt_prog_compiler_wl_CXX='-Wl,'
+ # Make sure the PIC flag is empty. It appears that all Alpha
+ # Linux and Compaq Tru64 Unix objects are PIC.
+ lt_prog_compiler_pic_CXX=
+ lt_prog_compiler_static_CXX='-non_shared'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ psos*)
+ ;;
+ solaris*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.2, 5.x and Centerline C++
+ lt_prog_compiler_pic_CXX='-KPIC'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ lt_prog_compiler_wl_CXX='-Qoption ld '
+ ;;
+ gcx*)
+ # Green Hills C++ Compiler
+ lt_prog_compiler_pic_CXX='-PIC'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ sunos4*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.x
+ lt_prog_compiler_pic_CXX='-pic'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ ;;
+ lcc*)
+ # Lucid
+ lt_prog_compiler_pic_CXX='-pic'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+ case $cc_basename in
+ CC*)
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-KPIC'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ ;;
+ esac
+ ;;
+ tandem*)
+ case $cc_basename in
+ NCC*)
+ # NonStop-UX NCC 3.20
+ lt_prog_compiler_pic_CXX='-KPIC'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ vxworks*)
+ ;;
+ *)
+ lt_prog_compiler_can_build_shared_CXX=no
+ ;;
+ esac
+ fi
+
+case $host_os in
+ # For platforms which do not support PIC, -DPIC is meaningless:
+ *djgpp*)
+ lt_prog_compiler_pic_CXX=
+ ;;
+ *)
+ lt_prog_compiler_pic_CXX="$lt_prog_compiler_pic_CXX -DPIC"
+ ;;
+esac
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_prog_compiler_pic_CXX" >&5
+$as_echo "$lt_prog_compiler_pic_CXX" >&6; }
+
+
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$lt_prog_compiler_pic_CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler PIC flag $lt_prog_compiler_pic_CXX works" >&5
+$as_echo_n "checking if $compiler PIC flag $lt_prog_compiler_pic_CXX works... " >&6; }
+if test "${lt_cv_prog_compiler_pic_works_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_pic_works_CXX=no
+ ac_outfile=conftest.$ac_objext
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+ lt_compiler_flag="$lt_prog_compiler_pic_CXX -DPIC"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ # The option is referenced via a variable to avoid confusing sed.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:14017: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>conftest.err)
+ ac_status=$?
+ cat conftest.err >&5
+ echo "$as_me:14021: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s "$ac_outfile"; then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings other than the usual output.
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_pic_works_CXX=yes
+ fi
+ fi
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_pic_works_CXX" >&5
+$as_echo "$lt_cv_prog_compiler_pic_works_CXX" >&6; }
+
+if test x"$lt_cv_prog_compiler_pic_works_CXX" = xyes; then
+ case $lt_prog_compiler_pic_CXX in
+ "" | " "*) ;;
+ *) lt_prog_compiler_pic_CXX=" $lt_prog_compiler_pic_CXX" ;;
+ esac
+else
+ lt_prog_compiler_pic_CXX=
+ lt_prog_compiler_can_build_shared_CXX=no
+fi
+
+fi
+
+
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$lt_prog_compiler_wl_CXX eval lt_tmp_static_flag=\"$lt_prog_compiler_static_CXX\"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler static flag $lt_tmp_static_flag works" >&5
+$as_echo_n "checking if $compiler static flag $lt_tmp_static_flag works... " >&6; }
+if test "${lt_cv_prog_compiler_static_works_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_static_works_CXX=no
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS $lt_tmp_static_flag"
+ echo "$lt_simple_link_test_code" > conftest.$ac_ext
+ if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+ # The linker can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ if test -s conftest.err; then
+ # Append any errors to the config.log.
+ cat conftest.err 1>&5
+ $ECHO "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_static_works_CXX=yes
+ fi
+ else
+ lt_cv_prog_compiler_static_works_CXX=yes
+ fi
+ fi
+ $RM -r conftest*
+ LDFLAGS="$save_LDFLAGS"
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_static_works_CXX" >&5
+$as_echo "$lt_cv_prog_compiler_static_works_CXX" >&6; }
+
+if test x"$lt_cv_prog_compiler_static_works_CXX" = xyes; then
+ :
+else
+ lt_prog_compiler_static_CXX=
+fi
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler supports -c -o file.$ac_objext" >&5
+$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; }
+if test "${lt_cv_prog_compiler_c_o_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_c_o_CXX=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:14116: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&5
+ echo "$as_me:14120: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_c_o_CXX=yes
+ fi
+ fi
+ chmod u+w . 2>&5
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_c_o_CXX" >&5
+$as_echo "$lt_cv_prog_compiler_c_o_CXX" >&6; }
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler supports -c -o file.$ac_objext" >&5
+$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; }
+if test "${lt_cv_prog_compiler_c_o_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_c_o_CXX=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:14168: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&5
+ echo "$as_me:14172: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_c_o_CXX=yes
+ fi
+ fi
+ chmod u+w . 2>&5
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_c_o_CXX" >&5
+$as_echo "$lt_cv_prog_compiler_c_o_CXX" >&6; }
+
+
+
+
+hard_links="nottested"
+if test "$lt_cv_prog_compiler_c_o_CXX" = no && test "$need_locks" != no; then
+ # do not overwrite the value of need_locks provided by the user
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if we can lock with hard links" >&5
+$as_echo_n "checking if we can lock with hard links... " >&6; }
+ hard_links=yes
+ $RM conftest*
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ touch conftest.a
+ ln conftest.a conftest.b 2>&5 || hard_links=no
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $hard_links" >&5
+$as_echo "$hard_links" >&6; }
+ if test "$hard_links" = no; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&5
+$as_echo "$as_me: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&2;}
+ need_locks=warn
+ fi
+else
+ need_locks=no
+fi
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+$as_echo_n "checking whether the $compiler linker ($LD) supports shared libraries... " >&6; }
+
+ export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ case $host_os in
+ aix[4-9]*)
+ # If we're using GNU nm, then we don't want the "-C" option.
+ # -C means demangle to AIX nm, but means don't demangle with GNU nm
+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then
+ export_symbols_cmds_CXX='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ else
+ export_symbols_cmds_CXX='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ fi
+ ;;
+ pw32*)
+ export_symbols_cmds_CXX="$ltdll_cmds"
+ ;;
+ cygwin* | mingw* | cegcc*)
+ export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1 DATA/;/^.*[ ]__nm__/s/^.*[ ]__nm__\([^ ]*\)[ ][^ ]*/\1 DATA/;/^I[ ]/d;/^[AITW][ ]/s/.* //'\'' | sort | uniq > $export_symbols'
+ ;;
+ linux* | k*bsd*-gnu)
+ link_all_deplibs_CXX=no
+ ;;
+ *)
+ export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ ;;
+ esac
+ exclude_expsyms_CXX='_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*'
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ld_shlibs_CXX" >&5
+$as_echo "$ld_shlibs_CXX" >&6; }
+test "$ld_shlibs_CXX" = no && can_build_shared=no
+
+with_gnu_ld_CXX=$with_gnu_ld
+
+
+
+
+
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$archive_cmds_need_lc_CXX" in
+x|xyes)
+ # Assume -lc should be added
+ archive_cmds_need_lc_CXX=yes
+
+ if test "$enable_shared" = yes && test "$GCC" = yes; then
+ case $archive_cmds_CXX in
+ *'~'*)
+ # FIXME: we may have to deal with multi-command sequences.
+ ;;
+ '$CC '*)
+ # Test whether the compiler implicitly links with -lc since on some
+ # systems, -lgcc has to come before -lc. If gcc already passes -lc
+ # to ld, don't add -lc before -lgcc.
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether -lc should be explicitly linked in" >&5
+$as_echo_n "checking whether -lc should be explicitly linked in... " >&6; }
+ $RM conftest*
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } 2>conftest.err; then
+ soname=conftest
+ lib=conftest
+ libobjs=conftest.$ac_objext
+ deplibs=
+ wl=$lt_prog_compiler_wl_CXX
+ pic_flag=$lt_prog_compiler_pic_CXX
+ compiler_flags=-v
+ linker_flags=-v
+ verstring=
+ output_objdir=.
+ libname=conftest
+ lt_save_allow_undefined_flag=$allow_undefined_flag_CXX
+ allow_undefined_flag_CXX=
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$archive_cmds_CXX 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1\""; } >&5
+ (eval $archive_cmds_CXX 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+ then
+ archive_cmds_need_lc_CXX=no
+ else
+ archive_cmds_need_lc_CXX=yes
+ fi
+ allow_undefined_flag_CXX=$lt_save_allow_undefined_flag
+ else
+ cat conftest.err 1>&5
+ fi
+ $RM conftest*
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $archive_cmds_need_lc_CXX" >&5
+$as_echo "$archive_cmds_need_lc_CXX" >&6; }
+ ;;
+ esac
+ fi
+ ;;
+esac
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking dynamic linker characteristics" >&5
+$as_echo_n "checking dynamic linker characteristics... " >&6; }
+
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+ shlibpath_var=LIBPATH
+
+ # AIX 3 has no versioning support, so we append a major version to the name.
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+
+aix[4-9]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ hardcode_into_libs=yes
+ if test "$host_cpu" = ia64; then
+ # AIX 5 supports IA64
+ library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ else
+ # With GCC up to 2.95.x, collect2 would create an import file
+ # for dependence libraries. The import file would start with
+ # the line `#! .'. This would cause the generated library to
+ # depend on `.', always an invalid library. This was fixed in
+ # development snapshots of GCC prior to 3.0.
+ case $host_os in
+ aix4 | aix4.[01] | aix4.[01].*)
+ if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+ echo ' yes '
+ echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then
+ :
+ else
+ can_build_shared=no
+ fi
+ ;;
+ esac
+ # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+ # soname into executable. Probably we can add versioning support to
+ # collect2, so additional links can be useful in future.
+ if test "$aix_use_runtimelinking" = yes; then
+ # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+ # instead of lib<name>.a to let people know that these are not
+ # typical AIX shared libraries.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ else
+ # We preserve .a as extension for shared libraries through AIX4.2
+ # and later when we are not doing run time linking.
+ library_names_spec='${libname}${release}.a $libname.a'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ fi
+ shlibpath_var=LIBPATH
+ fi
+ ;;
+
+amigaos*)
+ case $host_cpu in
+ powerpc)
+ # Since July 2007 AmigaOS4 officially supports .so libraries.
+ # When compiling the executable, add -use-dynld -Lsobjs: to the compileline.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ ;;
+ m68k)
+ library_names_spec='$libname.ixlibrary $libname.a'
+ # Create ${libname}_ixlibrary.a entries in /sys/libs.
+ finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$ECHO "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+ ;;
+ esac
+ ;;
+
+beos*)
+ library_names_spec='${libname}${shared_ext}'
+ dynamic_linker="$host_os ld.so"
+ shlibpath_var=LIBRARY_PATH
+ ;;
+
+bsdi[45]*)
+ version_type=linux
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+ sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+ # the default ld.so.conf also contains /usr/contrib/lib and
+ # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+ # libtool to hard-code these into programs
+ ;;
+
+cygwin* | mingw* | pw32* | cegcc*)
+ version_type=windows
+ shrext_cmds=".dll"
+ need_version=no
+ need_lib_prefix=no
+
+ case $GCC,$host_os in
+ yes,cygwin* | yes,mingw* | yes,pw32* | yes,cegcc*)
+ library_names_spec='$libname.dll.a'
+ # DLL is installed to $(libdir)/../bin by postinstall_cmds
+ postinstall_cmds='base_file=`basename \${file}`~
+ dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i; echo \$dlname'\''`~
+ dldir=$destdir/`dirname \$dlpath`~
+ test -d \$dldir || mkdir -p \$dldir~
+ $install_prog $dir/$dlname \$dldir/$dlname~
+ chmod a+x \$dldir/$dlname~
+ if test -n '\''$stripme'\'' && test -n '\''$striplib'\''; then
+ eval '\''$striplib \$dldir/$dlname'\'' || exit \$?;
+ fi'
+ postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+ dlpath=$dir/\$dldll~
+ $RM \$dlpath'
+ shlibpath_overrides_runpath=yes
+
+ case $host_os in
+ cygwin*)
+ # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+ soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+ ;;
+ mingw* | cegcc*)
+ # MinGW DLLs use traditional 'lib' prefix
+ soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec=`$CC -print-search-dirs | $GREP "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$sys_lib_search_path_spec" | $GREP ';[c-zC-Z]:/' >/dev/null; then
+ # It is most probably a Windows format PATH printed by
+ # mingw gcc, but we are running on Cygwin. Gcc prints its search
+ # path with ; separators, and with drive letters. We can handle the
+ # drive letters (cygwin fileutils understands them), so leave them,
+ # especially as we might pass files found there to a mingw objdump,
+ # which wouldn't understand a cygwinified path. Ahh.
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ ;;
+ pw32*)
+ # pw32 DLLs use 'pw' prefix rather than 'lib'
+ library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ ;;
+ esac
+ ;;
+
+ *)
+ library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib'
+ ;;
+ esac
+ dynamic_linker='Win32 ld.exe'
+ # FIXME: first we should search . and the directory the executable is in
+ shlibpath_var=PATH
+ ;;
+
+darwin* | rhapsody*)
+ dynamic_linker="$host_os dyld"
+ version_type=darwin
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+ soname_spec='${libname}${release}${major}$shared_ext'
+ shlibpath_overrides_runpath=yes
+ shlibpath_var=DYLD_LIBRARY_PATH
+ shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+
+ sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+ ;;
+
+dgux*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+freebsd1*)
+ dynamic_linker=no
+ ;;
+
+freebsd* | dragonfly*)
+ # DragonFly does not have aout. When/if they implement a new
+ # versioning mechanism, adjust this.
+ if test -x /usr/bin/objformat; then
+ objformat=`/usr/bin/objformat`
+ else
+ case $host_os in
+ freebsd[123]*) objformat=aout ;;
+ *) objformat=elf ;;
+ esac
+ fi
+ version_type=freebsd-$objformat
+ case $version_type in
+ freebsd-elf*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ need_version=no
+ need_lib_prefix=no
+ ;;
+ freebsd-*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+ need_version=yes
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_os in
+ freebsd2*)
+ shlibpath_overrides_runpath=yes
+ ;;
+ freebsd3.[01]* | freebsdelf3.[01]*)
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ freebsd3.[2-9]* | freebsdelf3.[2-9]* | \
+ freebsd4.[0-5] | freebsdelf4.[0-5] | freebsd4.1.1 | freebsdelf4.1.1)
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+ *) # from 4.6 on, and DragonFly
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ esac
+ ;;
+
+gnu*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ hardcode_into_libs=yes
+ ;;
+
+hpux9* | hpux10* | hpux11*)
+ # Give a soname corresponding to the major version so that dld.sl refuses to
+ # link against other versions.
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ case $host_cpu in
+ ia64*)
+ shrext_cmds='.so'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.so"
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ if test "X$HPUX_IA64_MODE" = X32; then
+ sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+ else
+ sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+ fi
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ hppa*64*)
+ shrext_cmds='.sl'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ *)
+ shrext_cmds='.sl'
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=SHLIB_PATH
+ shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+ esac
+ # HP-UX runs *really* slowly unless shared libraries are mode 555.
+ postinstall_cmds='chmod 555 $lib'
+ ;;
+
+interix[3-9]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $host_os in
+ nonstopux*) version_type=nonstopux ;;
+ *)
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ version_type=linux
+ else
+ version_type=irix
+ fi ;;
+ esac
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+ case $host_os in
+ irix5* | nonstopux*)
+ libsuff= shlibsuff=
+ ;;
+ *)
+ case $LD in # libtool.m4 will add one of these switches to LD
+ *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+ libsuff= shlibsuff= libmagic=32-bit;;
+ *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+ libsuff=32 shlibsuff=N32 libmagic=N32;;
+ *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+ libsuff=64 shlibsuff=64 libmagic=64-bit;;
+ *) libsuff= shlibsuff= libmagic=never-match;;
+ esac
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+ sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+ hardcode_into_libs=yes
+ ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+ dynamic_linker=no
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ # Some binutils ld are patched to set DT_RUNPATH
+ save_LDFLAGS=$LDFLAGS
+ save_libdir=$libdir
+ eval "libdir=/foo; wl=\"$lt_prog_compiler_wl_CXX\"; \
+ LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec_CXX\""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+ if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then :
+ shlibpath_overrides_runpath=yes
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+ LDFLAGS=$save_LDFLAGS
+ libdir=$save_libdir
+
+ # This implies no fast_install, which is unacceptable.
+ # Some rework will be needed to allow for fast_install
+ # before this can be enabled.
+ hardcode_into_libs=yes
+
+ # Append ld.so.conf contents to the search path
+ if test -f /etc/ld.so.conf; then
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ fi
+
+ # We used to test for /lib/ld.so.1 and disable shared libraries on
+ # powerpc, because MkLinux only supported shared libraries with the
+ # GNU dynamic linker. Since this was broken with cross compilers,
+ # most powerpc-linux boxes support dynamic linking these days and
+ # people can always --disable-shared, the test was removed, and we
+ # assume the GNU/Linux dynamic linker is in use.
+ dynamic_linker='GNU/Linux ld.so'
+ ;;
+
+netbsdelf*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='NetBSD ld.elf_so'
+ ;;
+
+netbsd*)
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ dynamic_linker='NetBSD (a.out) ld.so'
+ else
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='NetBSD ld.elf_so'
+ fi
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+
+newsos6)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ ;;
+
+*nto* | *qnx*)
+ version_type=qnx
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='ldqnx.so'
+ ;;
+
+openbsd*)
+ version_type=sunos
+ sys_lib_dlsearch_path_spec="/usr/lib"
+ need_lib_prefix=no
+ # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+ case $host_os in
+ openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+ *) need_version=no ;;
+ esac
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ case $host_os in
+ openbsd2.[89] | openbsd2.[89].*)
+ shlibpath_overrides_runpath=no
+ ;;
+ *)
+ shlibpath_overrides_runpath=yes
+ ;;
+ esac
+ else
+ shlibpath_overrides_runpath=yes
+ fi
+ ;;
+
+os2*)
+ libname_spec='$name'
+ shrext_cmds=".dll"
+ need_lib_prefix=no
+ library_names_spec='$libname${shared_ext} $libname.a'
+ dynamic_linker='OS/2 ld.exe'
+ shlibpath_var=LIBPATH
+ ;;
+
+osf3* | osf4* | osf5*)
+ version_type=osf
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+ sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+ ;;
+
+rdos*)
+ dynamic_linker=no
+ ;;
+
+solaris*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ # ldd complains unless libraries are executable
+ postinstall_cmds='chmod +x $lib'
+ ;;
+
+sunos4*)
+ version_type=sunos
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ if test "$with_gnu_ld" = yes; then
+ need_lib_prefix=no
+ fi
+ need_version=yes
+ ;;
+
+sysv4 | sysv4.3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_vendor in
+ sni)
+ shlibpath_overrides_runpath=no
+ need_lib_prefix=no
+ runpath_var=LD_RUN_PATH
+ ;;
+ siemens)
+ need_lib_prefix=no
+ ;;
+ motorola)
+ need_lib_prefix=no
+ need_version=no
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+ ;;
+ esac
+ ;;
+
+sysv4*MP*)
+ if test -d /usr/nec ;then
+ version_type=linux
+ library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+ soname_spec='$libname${shared_ext}.$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ fi
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ version_type=freebsd-elf
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ if test "$with_gnu_ld" = yes; then
+ sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+ else
+ sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+ case $host_os in
+ sco3.2v5*)
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+ ;;
+ esac
+ fi
+ sys_lib_dlsearch_path_spec='/usr/lib'
+ ;;
+
+tpf*)
+ # TPF is a cross-target only. Preferred cross-host = GNU/Linux.
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+uts4*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+*)
+ dynamic_linker=no
+ ;;
+esac
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $dynamic_linker" >&5
+$as_echo "$dynamic_linker" >&6; }
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+ variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+
+if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then
+ sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec"
+fi
+if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then
+ sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec"
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to hardcode library paths into programs" >&5
+$as_echo_n "checking how to hardcode library paths into programs... " >&6; }
+hardcode_action_CXX=
+if test -n "$hardcode_libdir_flag_spec_CXX" ||
+ test -n "$runpath_var_CXX" ||
+ test "X$hardcode_automatic_CXX" = "Xyes" ; then
+
+ # We can hardcode non-existent directories.
+ if test "$hardcode_direct_CXX" != no &&
+ # If the only mechanism to avoid hardcoding is shlibpath_var, we
+ # have to relink, otherwise we might link with an installed library
+ # when we should be linking with a yet-to-be-installed one
+ ## test "$_LT_TAGVAR(hardcode_shlibpath_var, CXX)" != no &&
+ test "$hardcode_minus_L_CXX" != no; then
+ # Linking always hardcodes the temporary library directory.
+ hardcode_action_CXX=relink
+ else
+ # We can link without hardcoding, and we can hardcode nonexisting dirs.
+ hardcode_action_CXX=immediate
+ fi
+else
+ # We cannot hardcode anything, or else we can only hardcode existing
+ # directories.
+ hardcode_action_CXX=unsupported
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $hardcode_action_CXX" >&5
+$as_echo "$hardcode_action_CXX" >&6; }
+
+if test "$hardcode_action_CXX" = relink ||
+ test "$inherit_rpath_CXX" = yes; then
+ # Fast installation is not supported
+ enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+ test "$enable_shared" = no; then
+ # Fast installation is not necessary
+ enable_fast_install=needless
+fi
+
+
+
+
+
+
+
+ fi # test -n "$compiler"
+
+ CC=$lt_save_CC
+ LDCXX=$LD
+ LD=$lt_save_LD
+ GCC=$lt_save_GCC
+ with_gnu_ld=$lt_save_with_gnu_ld
+ lt_cv_path_LDCXX=$lt_cv_path_LD
+ lt_cv_path_LD=$lt_save_path_LD
+ lt_cv_prog_gnu_ldcxx=$lt_cv_prog_gnu_ld
+ lt_cv_prog_gnu_ld=$lt_save_with_gnu_ld
+fi # test "$_lt_caught_CXX_error" != yes
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ac_config_commands="$ac_config_commands libtool"
+
+
+
+
+# Only expand once:
+
+
+
+
+# Check whether --with-gnu-ld was given.
+if test "${with_gnu_ld+set}" = set; then :
+ withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes
+else
+ with_gnu_ld=no
+fi
+
+ac_prog=ld
+if test "$GCC" = yes; then
+ # Check if gcc -print-prog-name=ld gives a path.
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ld used by $CC" >&5
+$as_echo_n "checking for ld used by $CC... " >&6; }
+ case $host in
+ *-*-mingw*)
+ # gcc leaves a trailing carriage return which upsets mingw
+ ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+ *)
+ ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+ esac
+ case $ac_prog in
+ # Accept absolute paths.
+ [\\/]* | ?:[\\/]*)
+ re_direlt='/[^/][^/]*/\.\./'
+ # Canonicalize the pathname of ld
+ ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'`
+ while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do
+ ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"`
+ done
+ test -z "$LD" && LD="$ac_prog"
+ ;;
+ "")
+ # If it fails, then pretend we aren't using GCC.
+ ac_prog=ld
+ ;;
+ *)
+ # If it is relative, then search for the first ld in PATH.
+ with_gnu_ld=unknown
+ ;;
+ esac
+elif test "$with_gnu_ld" = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU ld" >&5
+$as_echo_n "checking for GNU ld... " >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for non-GNU ld" >&5
+$as_echo_n "checking for non-GNU ld... " >&6; }
+fi
+if test "${lt_cv_path_LD+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$LD"; then
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+ lt_cv_path_LD="$ac_dir/$ac_prog"
+ # Check to see if the program is GNU ld. I'd rather use --version,
+ # but apparently some variants of GNU ld only accept -v.
+ # Break only if it was the GNU/non-GNU ld that we prefer.
+ case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+ *GNU* | *'with BFD'*)
+ test "$with_gnu_ld" != no && break
+ ;;
+ *)
+ test "$with_gnu_ld" != yes && break
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+else
+ lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi
+fi
+
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LD" >&5
+$as_echo "$LD" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+test -z "$LD" && as_fn_error $? "no acceptable ld found in \$PATH" "$LINENO" 5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if the linker ($LD) is GNU ld" >&5
+$as_echo_n "checking if the linker ($LD) is GNU ld... " >&6; }
+if test "${lt_cv_prog_gnu_ld+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ # I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+ lt_cv_prog_gnu_ld=yes
+ ;;
+*)
+ lt_cv_prog_gnu_ld=no
+ ;;
+esac
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_gnu_ld" >&5
+$as_echo "$lt_cv_prog_gnu_ld" >&6; }
+with_gnu_ld=$lt_cv_prog_gnu_ld
+
+
+
+
+
+
+
+ISODATE=`date +%Y-%m-%d`
+
+
+ARCH=`uname -m | sed s/i.86/i386/ | sed s/x86_64/amd64/`
+
+
+# Extract the first word of "dpkg", so it can be a program name with args.
+set dummy dpkg; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_path_DEB_BUILDER+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ case $DEB_BUILDER in
+ [\\/]* | ?:[\\/]*)
+ ac_cv_path_DEB_BUILDER="$DEB_BUILDER" # Let the user override the test with a path.
+ ;;
+ *)
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_path_DEB_BUILDER="$as_dir/$ac_word$ac_exec_ext"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+fi
+DEB_BUILDER=$ac_cv_path_DEB_BUILDER
+if test -n "$DEB_BUILDER"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DEB_BUILDER" >&5
+$as_echo "$DEB_BUILDER" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+# Extract the first word of "rpmbuild", so it can be a program name with args.
+set dummy rpmbuild; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_path_RPM_BUILDER+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ case $RPM_BUILDER in
+ [\\/]* | ?:[\\/]*)
+ ac_cv_path_RPM_BUILDER="$RPM_BUILDER" # Let the user override the test with a path.
+ ;;
+ *)
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_path_RPM_BUILDER="$as_dir/$ac_word$ac_exec_ext"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+fi
+RPM_BUILDER=$ac_cv_path_RPM_BUILDER
+if test -n "$RPM_BUILDER"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $RPM_BUILDER" >&5
+$as_echo "$RPM_BUILDER" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+
+# Checks for libraries.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for sqrt in -lm" >&5
+$as_echo_n "checking for sqrt in -lm... " >&6; }
+if test "${ac_cv_lib_m_sqrt+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lm $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char sqrt ();
+int
+main ()
+{
+return sqrt ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+ ac_cv_lib_m_sqrt=yes
+else
+ ac_cv_lib_m_sqrt=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_sqrt" >&5
+$as_echo "$ac_cv_lib_m_sqrt" >&6; }
+if test "x$ac_cv_lib_m_sqrt" = x""yes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBM 1
+_ACEOF
+
+ LIBS="-lm $LIBS"
+
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for pthread_join in -lpthread" >&5
+$as_echo_n "checking for pthread_join in -lpthread... " >&6; }
+if test "${ac_cv_lib_pthread_pthread_join+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lpthread $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char pthread_join ();
+int
+main ()
+{
+return pthread_join ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+ ac_cv_lib_pthread_pthread_join=yes
+else
+ ac_cv_lib_pthread_pthread_join=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_pthread_pthread_join" >&5
+$as_echo "$ac_cv_lib_pthread_pthread_join" >&6; }
+if test "x$ac_cv_lib_pthread_pthread_join" = x""yes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBPTHREAD 1
+_ACEOF
+
+ LIBS="-lpthread $LIBS"
+
+fi
+
+
+# Checks for header files.
+
+# The Ultrix 4.2 mips builtin alloca declared by alloca.h only works
+# for constant arguments. Useless!
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for working alloca.h" >&5
+$as_echo_n "checking for working alloca.h... " >&6; }
+if test "${ac_cv_working_alloca_h+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <alloca.h>
+int
+main ()
+{
+char *p = (char *) alloca (2 * sizeof (int));
+ if (p) return 0;
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+ ac_cv_working_alloca_h=yes
+else
+ ac_cv_working_alloca_h=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_working_alloca_h" >&5
+$as_echo "$ac_cv_working_alloca_h" >&6; }
+if test $ac_cv_working_alloca_h = yes; then
+
+$as_echo "#define HAVE_ALLOCA_H 1" >>confdefs.h
+
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for alloca" >&5
+$as_echo_n "checking for alloca... " >&6; }
+if test "${ac_cv_func_alloca_works+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifdef __GNUC__
+# define alloca __builtin_alloca
+#else
+# ifdef _MSC_VER
+# include <malloc.h>
+# define alloca _alloca
+# else
+# ifdef HAVE_ALLOCA_H
+# include <alloca.h>
+# else
+# ifdef _AIX
+ #pragma alloca
+# else
+# ifndef alloca /* predefined by HP cc +Olibcalls */
+char *alloca ();
+# endif
+# endif
+# endif
+# endif
+#endif
+
+int
+main ()
+{
+char *p = (char *) alloca (1);
+ if (p) return 0;
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+ ac_cv_func_alloca_works=yes
+else
+ ac_cv_func_alloca_works=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_alloca_works" >&5
+$as_echo "$ac_cv_func_alloca_works" >&6; }
+
+if test $ac_cv_func_alloca_works = yes; then
+
+$as_echo "#define HAVE_ALLOCA 1" >>confdefs.h
+
+else
+ # The SVR3 libPW and SVR4 libucb both contain incompatible functions
+# that cause trouble. Some versions do not even contain alloca or
+# contain a buggy version. If you still want to use their alloca,
+# use ar to extract alloca.o from them instead of compiling alloca.c.
+
+ALLOCA=\${LIBOBJDIR}alloca.$ac_objext
+
+$as_echo "#define C_ALLOCA 1" >>confdefs.h
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether \`alloca.c' needs Cray hooks" >&5
+$as_echo_n "checking whether \`alloca.c' needs Cray hooks... " >&6; }
+if test "${ac_cv_os_cray+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#if defined CRAY && ! defined CRAY2
+webecray
+#else
+wenotbecray
+#endif
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "webecray" >/dev/null 2>&1; then :
+ ac_cv_os_cray=yes
+else
+ ac_cv_os_cray=no
+fi
+rm -f conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_os_cray" >&5
+$as_echo "$ac_cv_os_cray" >&6; }
+if test $ac_cv_os_cray = yes; then
+ for ac_func in _getb67 GETB67 getb67; do
+ as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+ac_fn_cxx_check_func "$LINENO" "$ac_func" "$as_ac_var"
+if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
+
+cat >>confdefs.h <<_ACEOF
+#define CRAY_STACKSEG_END $ac_func
+_ACEOF
+
+ break
+fi
+
+ done
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking stack direction for C alloca" >&5
+$as_echo_n "checking stack direction for C alloca... " >&6; }
+if test "${ac_cv_c_stack_direction+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then :
+ ac_cv_c_stack_direction=0
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$ac_includes_default
+int
+find_stack_direction ()
+{
+ static char *addr = 0;
+ auto char dummy;
+ if (addr == 0)
+ {
+ addr = &dummy;
+ return find_stack_direction ();
+ }
+ else
+ return (&dummy > addr) ? 1 : -1;
+}
+
+int
+main ()
+{
+ return find_stack_direction () < 0;
+}
+_ACEOF
+if ac_fn_cxx_try_run "$LINENO"; then :
+ ac_cv_c_stack_direction=1
+else
+ ac_cv_c_stack_direction=-1
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
+ conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_stack_direction" >&5
+$as_echo "$ac_cv_c_stack_direction" >&6; }
+cat >>confdefs.h <<_ACEOF
+#define STACK_DIRECTION $ac_cv_c_stack_direction
+_ACEOF
+
+
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether sys/types.h defines makedev" >&5
+$as_echo_n "checking whether sys/types.h defines makedev... " >&6; }
+if test "${ac_cv_header_sys_types_h_makedev+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <sys/types.h>
+int
+main ()
+{
+return makedev(0, 0);
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+ ac_cv_header_sys_types_h_makedev=yes
+else
+ ac_cv_header_sys_types_h_makedev=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_sys_types_h_makedev" >&5
+$as_echo "$ac_cv_header_sys_types_h_makedev" >&6; }
+
+if test $ac_cv_header_sys_types_h_makedev = no; then
+ac_fn_cxx_check_header_mongrel "$LINENO" "sys/mkdev.h" "ac_cv_header_sys_mkdev_h" "$ac_includes_default"
+if test "x$ac_cv_header_sys_mkdev_h" = x""yes; then :
+
+$as_echo "#define MAJOR_IN_MKDEV 1" >>confdefs.h
+
+fi
+
+
+
+ if test $ac_cv_header_sys_mkdev_h = no; then
+ ac_fn_cxx_check_header_mongrel "$LINENO" "sys/sysmacros.h" "ac_cv_header_sys_sysmacros_h" "$ac_includes_default"
+if test "x$ac_cv_header_sys_sysmacros_h" = x""yes; then :
+
+$as_echo "#define MAJOR_IN_SYSMACROS 1" >>confdefs.h
+
+fi
+
+
+ fi
+fi
+
+for ac_header in \
+ fcntl.h inttypes.h libintl.h limits.h locale.h \
+ memory.h stdint.h stdlib.h string.h strings.h \
+ sys/file.h sys/param.h sys/time.h unistd.h utime.h \
+
+do :
+ as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+ac_fn_cxx_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default"
+if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+
+# Checks for typedefs, structures, and compiler characteristics.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for stdbool.h that conforms to C99" >&5
+$as_echo_n "checking for stdbool.h that conforms to C99... " >&6; }
+if test "${ac_cv_header_stdbool_h+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+#include <stdbool.h>
+#ifndef bool
+ "error: bool is not defined"
+#endif
+#ifndef false
+ "error: false is not defined"
+#endif
+#if false
+ "error: false is not 0"
+#endif
+#ifndef true
+ "error: true is not defined"
+#endif
+#if true != 1
+ "error: true is not 1"
+#endif
+#ifndef __bool_true_false_are_defined
+ "error: __bool_true_false_are_defined is not defined"
+#endif
+
+ struct s { _Bool s: 1; _Bool t; } s;
+
+ char a[true == 1 ? 1 : -1];
+ char b[false == 0 ? 1 : -1];
+ char c[__bool_true_false_are_defined == 1 ? 1 : -1];
+ char d[(bool) 0.5 == true ? 1 : -1];
+ bool e = &s;
+ char f[(_Bool) 0.0 == false ? 1 : -1];
+ char g[true];
+ char h[sizeof (_Bool)];
+ char i[sizeof s.t];
+ enum { j = false, k = true, l = false * true, m = true * 256 };
+ /* The following fails for
+ HP aC++/ANSI C B3910B A.05.55 [Dec 04 2003]. */
+ _Bool n[m];
+ char o[sizeof n == m * sizeof n[0] ? 1 : -1];
+ char p[-1 - (_Bool) 0 < 0 && -1 - (bool) 0 < 0 ? 1 : -1];
+# if defined __xlc__ || defined __GNUC__
+ /* Catch a bug in IBM AIX xlc compiler version 6.0.0.0
+ reported by James Lemley on 2005-10-05; see
+ http://lists.gnu.org/archive/html/bug-coreutils/2005-10/msg00086.html
+ This test is not quite right, since xlc is allowed to
+ reject this program, as the initializer for xlcbug is
+ not one of the forms that C requires support for.
+ However, doing the test right would require a runtime
+ test, and that would make cross-compilation harder.
+ Let us hope that IBM fixes the xlc bug, and also adds
+ support for this kind of constant expression. In the
+ meantime, this test will reject xlc, which is OK, since
+ our stdbool.h substitute should suffice. We also test
+ this with GCC, where it should work, to detect more
+ quickly whether someone messes up the test in the
+ future. */
+ char digs[] = "0123456789";
+ int xlcbug = 1 / (&(digs + 5)[-2 + (bool) 1] == &digs[4] ? 1 : -1);
+# endif
+ /* Catch a bug in an HP-UX C compiler. See
+ http://gcc.gnu.org/ml/gcc-patches/2003-12/msg02303.html
+ http://lists.gnu.org/archive/html/bug-coreutils/2005-11/msg00161.html
+ */
+ _Bool q = true;
+ _Bool *pq = &q;
+
+int
+main ()
+{
+
+ *pq |= q;
+ *pq |= ! q;
+ /* Refer to every declared value, to avoid compiler optimizations. */
+ return (!a + !b + !c + !d + !e + !f + !g + !h + !i + !!j + !k + !!l
+ + !m + !n + !o + !p + !q + !pq);
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_header_stdbool_h=yes
+else
+ ac_cv_header_stdbool_h=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdbool_h" >&5
+$as_echo "$ac_cv_header_stdbool_h" >&6; }
+ac_fn_cxx_check_type "$LINENO" "_Bool" "ac_cv_type__Bool" "$ac_includes_default"
+if test "x$ac_cv_type__Bool" = x""yes; then :
+
+cat >>confdefs.h <<_ACEOF
+#define HAVE__BOOL 1
+_ACEOF
+
+
+fi
+
+if test $ac_cv_header_stdbool_h = yes; then
+
+$as_echo "#define HAVE_STDBOOL_H 1" >>confdefs.h
+
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for inline" >&5
+$as_echo_n "checking for inline... " >&6; }
+if test "${ac_cv_c_inline+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_c_inline=no
+for ac_kw in inline __inline__ __inline; do
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifndef __cplusplus
+typedef int foo_t;
+static $ac_kw foo_t static_foo () {return 0; }
+$ac_kw foo_t foo () {return 0; }
+#endif
+
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_c_inline=$ac_kw
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ test "$ac_cv_c_inline" != no && break
+done
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_inline" >&5
+$as_echo "$ac_cv_c_inline" >&6; }
+
+case $ac_cv_c_inline in
+ inline | yes) ;;
+ *)
+ case $ac_cv_c_inline in
+ no) ac_val=;;
+ *) ac_val=$ac_cv_c_inline;;
+ esac
+ cat >>confdefs.h <<_ACEOF
+#ifndef __cplusplus
+#define inline $ac_val
+#endif
+_ACEOF
+ ;;
+esac
+
+ac_fn_c_find_intX_t "$LINENO" "64" "ac_cv_c_int64_t"
+case $ac_cv_c_int64_t in #(
+ no|yes) ;; #(
+ *)
+
+cat >>confdefs.h <<_ACEOF
+#define int64_t $ac_cv_c_int64_t
+_ACEOF
+;;
+esac
+
+ac_fn_cxx_check_type "$LINENO" "off_t" "ac_cv_type_off_t" "$ac_includes_default"
+if test "x$ac_cv_type_off_t" = x""yes; then :
+
+else
+
+cat >>confdefs.h <<_ACEOF
+#define off_t long int
+_ACEOF
+
+fi
+
+ac_fn_cxx_check_type "$LINENO" "size_t" "ac_cv_type_size_t" "$ac_includes_default"
+if test "x$ac_cv_type_size_t" = x""yes; then :
+
+else
+
+cat >>confdefs.h <<_ACEOF
+#define size_t unsigned int
+_ACEOF
+
+fi
+
+ac_fn_cxx_check_member "$LINENO" "struct stat" "st_blksize" "ac_cv_member_struct_stat_st_blksize" "$ac_includes_default"
+if test "x$ac_cv_member_struct_stat_st_blksize" = x""yes; then :
+
+cat >>confdefs.h <<_ACEOF
+#define HAVE_STRUCT_STAT_ST_BLKSIZE 1
+_ACEOF
+
+
+fi
+
+ac_fn_c_find_uintX_t "$LINENO" "32" "ac_cv_c_uint32_t"
+case $ac_cv_c_uint32_t in #(
+ no|yes) ;; #(
+ *)
+
+$as_echo "#define _UINT32_T 1" >>confdefs.h
+
+
+cat >>confdefs.h <<_ACEOF
+#define uint32_t $ac_cv_c_uint32_t
+_ACEOF
+;;
+ esac
+
+ac_fn_c_find_uintX_t "$LINENO" "8" "ac_cv_c_uint8_t"
+case $ac_cv_c_uint8_t in #(
+ no|yes) ;; #(
+ *)
+
+$as_echo "#define _UINT8_T 1" >>confdefs.h
+
+
+cat >>confdefs.h <<_ACEOF
+#define uint8_t $ac_cv_c_uint8_t
+_ACEOF
+;;
+ esac
+
+ac_fn_cxx_check_type "$LINENO" "ptrdiff_t" "ac_cv_type_ptrdiff_t" "$ac_includes_default"
+if test "x$ac_cv_type_ptrdiff_t" = x""yes; then :
+
+cat >>confdefs.h <<_ACEOF
+#define HAVE_PTRDIFF_T 1
+_ACEOF
+
+
+fi
+
+
+# Checks for library functions.
+for ac_header in stdlib.h
+do :
+ ac_fn_cxx_check_header_mongrel "$LINENO" "stdlib.h" "ac_cv_header_stdlib_h" "$ac_includes_default"
+if test "x$ac_cv_header_stdlib_h" = x""yes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_STDLIB_H 1
+_ACEOF
+
+fi
+
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU libc compatible malloc" >&5
+$as_echo_n "checking for GNU libc compatible malloc... " >&6; }
+if test "${ac_cv_func_malloc_0_nonnull+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then :
+ ac_cv_func_malloc_0_nonnull=no
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#if defined STDC_HEADERS || defined HAVE_STDLIB_H
+# include <stdlib.h>
+#else
+char *malloc ();
+#endif
+
+int
+main ()
+{
+return ! malloc (0);
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_run "$LINENO"; then :
+ ac_cv_func_malloc_0_nonnull=yes
+else
+ ac_cv_func_malloc_0_nonnull=no
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
+ conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_malloc_0_nonnull" >&5
+$as_echo "$ac_cv_func_malloc_0_nonnull" >&6; }
+if test $ac_cv_func_malloc_0_nonnull = yes; then :
+
+$as_echo "#define HAVE_MALLOC 1" >>confdefs.h
+
+else
+ $as_echo "#define HAVE_MALLOC 0" >>confdefs.h
+
+ case " $LIBOBJS " in
+ *" malloc.$ac_objext "* ) ;;
+ *) LIBOBJS="$LIBOBJS malloc.$ac_objext"
+ ;;
+esac
+
+
+$as_echo "#define malloc rpl_malloc" >>confdefs.h
+
+fi
+
+
+for ac_header in stdlib.h
+do :
+ ac_fn_cxx_check_header_mongrel "$LINENO" "stdlib.h" "ac_cv_header_stdlib_h" "$ac_includes_default"
+if test "x$ac_cv_header_stdlib_h" = x""yes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_STDLIB_H 1
+_ACEOF
+
+fi
+
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU libc compatible realloc" >&5
+$as_echo_n "checking for GNU libc compatible realloc... " >&6; }
+if test "${ac_cv_func_realloc_0_nonnull+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then :
+ ac_cv_func_realloc_0_nonnull=no
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#if defined STDC_HEADERS || defined HAVE_STDLIB_H
+# include <stdlib.h>
+#else
+char *realloc ();
+#endif
+
+int
+main ()
+{
+return ! realloc (0, 0);
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_run "$LINENO"; then :
+ ac_cv_func_realloc_0_nonnull=yes
+else
+ ac_cv_func_realloc_0_nonnull=no
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
+ conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_realloc_0_nonnull" >&5
+$as_echo "$ac_cv_func_realloc_0_nonnull" >&6; }
+if test $ac_cv_func_realloc_0_nonnull = yes; then :
+
+$as_echo "#define HAVE_REALLOC 1" >>confdefs.h
+
+else
+ $as_echo "#define HAVE_REALLOC 0" >>confdefs.h
+
+ case " $LIBOBJS " in
+ *" realloc.$ac_objext "* ) ;;
+ *) LIBOBJS="$LIBOBJS realloc.$ac_objext"
+ ;;
+esac
+
+
+$as_echo "#define realloc rpl_realloc" >>confdefs.h
+
+fi
+
+
+for ac_func in \
+ floor gettimeofday memchr memmove memset \
+ mkfifo pow select sqrt strrchr strstr strtol \
+
+do :
+ as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+ac_fn_cxx_check_func "$LINENO" "$ac_func" "$as_ac_var"
+if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+done
+
+
+
+CPPFLAGS="$CPPFLAGS -Wall -ansi -funroll-loops"
+
+# Check whether --enable-debug was given.
+if test "${enable_debug+set}" = set; then :
+ enableval=$enable_debug; CPPFLAGS="$CPPFLAGS -g -O0"
+else
+ CPPFLAGS="$CPPFLAGS -O4 -DNDEBUG"
+fi
+
+
+
+# Check whether --with-included-GkArrays was given.
+if test "${with_included_GkArrays+set}" = set; then :
+ withval=$with_included_GkArrays;
+else
+ with_included_GkArrays="check"
+fi
+
+
+
+# Check whether --with-libGkArrays-prefix was given.
+if test "${with_libGkArrays_prefix+set}" = set; then :
+ withval=$with_libGkArrays_prefix; LDFLAGS="$LDFLAGS -L$with_libGkArrays_prefix/lib"
+ CPPFLAGS="$CPPFLAGS -I$with_libGkArrays_prefix/include/libGkArrays"
+else
+ with_libGkArrays_prefix=""
+fi
+
+
+if test "x$with_included_GkArrays" == "xcheck"; then :
+ if test "x$with_libGkArrays_prefix" != "x"; then :
+ with_included_GkArrays="no"
+else
+ with_included_GkArrays="yes"
+fi
+fi
+
+if test "x$with_included_GkArrays" == "xyes"; then :
+ if test "x$with_libGkArrays_prefix" != "x"; then :
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "You can't use both --with-included-GkArrays and --with-libGkArrays-prefix options
+See \`config.log' for more details" "$LINENO" 5 ; }
+fi
+fi
+
+
+# Check whether --with-included-ProgressBar was given.
+if test "${with_included_ProgressBar+set}" = set; then :
+ withval=$with_included_ProgressBar;
+else
+ with_included_ProgressBar="check"
+fi
+
+
+
+# Check whether --with-libProgressBar-prefix was given.
+if test "${with_libProgressBar_prefix+set}" = set; then :
+ withval=$with_libProgressBar_prefix; LDFLAGS="$LDFLAGS -L$with_libProgressBar_prefix/lib"
+ CPPFLAGS="$CPPFLAGS -I$with_libProgressBar_prefix/include/libProgressBar"
+else
+ with_libProgressBar_prefix=""
+fi
+
+
+PB_OK=0
+if test "x$with_included_ProgressBar" == "xcheck"; then :
+ if test "x$with_libProgressBar_prefix" != "x"; then :
+ with_included_ProgressBar="no"
+else
+ with_included_ProgressBar="$with_included_GkArrays"
+fi
+fi
+
+if test "x$with_included_ProgressBar" == "xyes"; then :
+ if test "x$with_libProgressBar_prefix" != "x"; then :
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "You can't use both --with-included-ProgressBar and --with-libProgressBar-prefix options
+See \`config.log' for more details" "$LINENO" 5 ; }
+else
+ if test "x$with_included_GkArrays" != "xyes"; then :
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "You can't use both --with-included-ProgressBar and --without-included-GkArrays options
+See \`config.log' for more details" "$LINENO" 5 ; }
+else
+ PB_OK=1
+fi
+
+fi
+else
+ if test "x$with_libProgressBar_prefix" != "x"; then :
+ PB_OK=1
+ LDFLAGS="$LDFLAGS -L$with_libProgressBar_prefix -L$with_libProgressBar_prefix/lib"
+ CPPFLAGS="$CPPFLAGS -I$with_libProgressBar_prefix -I$with_libProgressBar_prefix/include"
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for libProgressBarVersion in -lProgressBar" >&5
+$as_echo_n "checking for libProgressBarVersion in -lProgressBar... " >&6; }
+if test "${ac_cv_lib_ProgressBar_libProgressBarVersion+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lProgressBar $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char libProgressBarVersion ();
+int
+main ()
+{
+return libProgressBarVersion ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+ ac_cv_lib_ProgressBar_libProgressBarVersion=yes
+else
+ ac_cv_lib_ProgressBar_libProgressBarVersion=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_ProgressBar_libProgressBarVersion" >&5
+$as_echo "$ac_cv_lib_ProgressBar_libProgressBarVersion" >&6; }
+if test "x$ac_cv_lib_ProgressBar_libProgressBarVersion" = x""yes; then :
+ PB_OK=1
+ ProgressBar_LIBS=-lProgressBar
+fi
+
+fi
+fi
+if test "$PB_OK" == "1"; then :
+
+$as_echo "#define HAVE_LIBPROGRESSBAR 1" >>confdefs.h
+
+fi
+
+ if test "x$with_included_ProgressBar" == "xyes"; then
+ INCLUDED_PROGRESSBAR_TRUE=
+ INCLUDED_PROGRESSBAR_FALSE='#'
+else
+ INCLUDED_PROGRESSBAR_TRUE='#'
+ INCLUDED_PROGRESSBAR_FALSE=
+fi
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for gzread in -lz" >&5
+$as_echo_n "checking for gzread in -lz... " >&6; }
+if test "${ac_cv_lib_z_gzread+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lz $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char gzread ();
+int
+main ()
+{
+return gzread ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+ ac_cv_lib_z_gzread=yes
+else
+ ac_cv_lib_z_gzread=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_z_gzread" >&5
+$as_echo "$ac_cv_lib_z_gzread" >&6; }
+if test "x$ac_cv_lib_z_gzread" = x""yes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBZ 1
+_ACEOF
+
+ LIBS="-lz $LIBS"
+
+else
+ as_fn_error $? "zlib not found, see http://www.zlib.net" "$LINENO" 5
+fi
+
+
+
+
+if test "x$with_included_GkArrays" != "xyes"; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for libGkArraysVersion in -lGkArrays" >&5
+$as_echo_n "checking for libGkArraysVersion in -lGkArrays... " >&6; }
+if test "${ac_cv_lib_GkArrays_libGkArraysVersion+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lGkArrays $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char libGkArraysVersion ();
+int
+main ()
+{
+return libGkArraysVersion ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+ ac_cv_lib_GkArrays_libGkArraysVersion=yes
+else
+ ac_cv_lib_GkArrays_libGkArraysVersion=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_GkArrays_libGkArraysVersion" >&5
+$as_echo "$ac_cv_lib_GkArrays_libGkArraysVersion" >&6; }
+if test "x$ac_cv_lib_GkArrays_libGkArraysVersion" = x""yes; then :
+ :
+else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "--without-included-GkArrays was given, but test for libGkArrays failed
+See \`config.log' for more details" "$LINENO" 5 ; }
+fi
+
+else
+ subdirs="$subdirs src/libGkArrays"
+
+fi
+
+ if test "x$with_included_GkArrays" == xyes; then
+ INCLUDED_GKARRAYS_TRUE=
+ INCLUDED_GKARRAYS_FALSE='#'
+else
+ INCLUDED_GKARRAYS_TRUE='#'
+ INCLUDED_GKARRAYS_FALSE=
+fi
+
+
+if test "x$enable_shared" == "xyes" ; then :
+ as_fn_append ac_configure_args " --enable-shared"
+else
+ as_fn_append ac_configure_args " --disable-shared"
+fi
+if test "x$enable_static" == "xyes" ; then :
+ as_fn_append ac_configure_args " --enable-static"
+else
+ as_fn_append ac_configure_args " --disable-static"
+fi
+
+as_fn_append ac_configure_args " CPPFLAGS=\"$CPPFLAGS\""
+as_fn_append ac_configure_args " CFLAGS=\"$CFLAGS\""
+as_fn_append ac_configure_args " CXXFLAGS=\"$CXXFLAGS\""
+
+LDFLAGS="$LDFLAGS $ProgressBar_LIBS"
+CPPFLAGS="$CPPFLAGS $ProgressBar_CFLAGS"
+
+ac_config_files="$ac_config_files control crac.spec Makefile src/Makefile scripts/Makefile src/libReadsInfo/Makefile src/libSSA/Makefile src/libgzstream/Makefile doc/Makefile doc/package.texi man/Makefile man/crac.1 scripts/crac-client test_f/Makefile test_f/bug/Makefile test_f/causes/Makefile test_f/cigar/Makefile"
+
+
+cat >confcache <<\_ACEOF
+# This file is a shell script that caches the results of configure
+# tests run on this system so they can be shared between configure
+# scripts and configure runs, see configure's option --config-cache.
+# It is not useful on other systems. If it contains results you don't
+# want to keep, you may remove or edit it.
+#
+# config.status only pays attention to the cache file if you give it
+# the --recheck option to rerun configure.
+#
+# `ac_cv_env_foo' variables (set or unset) will be overridden when
+# loading this file, other *unset* `ac_cv_foo' will be assigned the
+# following values.
+
+_ACEOF
+
+# The following way of writing the cache mishandles newlines in values,
+# but we know of no workaround that is simple, portable, and efficient.
+# So, we kill variables containing newlines.
+# Ultrix sh set writes to stderr and can't be redirected directly,
+# and sets the high bit in the cache file unless we assign to the vars.
+(
+ for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) { eval $ac_var=; unset $ac_var;} ;;
+ esac ;;
+ esac
+ done
+
+ (set) 2>&1 |
+ case $as_nl`(ac_space=' '; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ # `set' does not quote correctly, so add quotes: double-quote
+ # substitution turns \\\\ into \\, and sed turns \\ into \.
+ sed -n \
+ "s/'/'\\\\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
+ ;; #(
+ *)
+ # `set' quotes correctly as required by POSIX, so do not add quotes.
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+) |
+ sed '
+ /^ac_cv_env_/b end
+ t clear
+ :clear
+ s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/
+ t end
+ s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/
+ :end' >>confcache
+if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
+ if test -w "$cache_file"; then
+ test "x$cache_file" != "x/dev/null" &&
+ { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
+$as_echo "$as_me: updating cache $cache_file" >&6;}
+ cat confcache >$cache_file
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
+$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
+ fi
+fi
+rm -f confcache
+
+test "x$prefix" = xNONE && prefix=$ac_default_prefix
+# Let make expand exec_prefix.
+test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
+
+DEFS=-DHAVE_CONFIG_H
+
+ac_libobjs=
+ac_ltlibobjs=
+U=
+for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
+ # 1. Remove the extension, and $U if already installed.
+ ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
+ ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
+ # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
+ # will be set to the directory where LIBOBJS objects are built.
+ as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext"
+ as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo'
+done
+LIBOBJS=$ac_libobjs
+
+LTLIBOBJS=$ac_ltlibobjs
+
+
+ if test -n "$EXEEXT"; then
+ am__EXEEXT_TRUE=
+ am__EXEEXT_FALSE='#'
+else
+ am__EXEEXT_TRUE='#'
+ am__EXEEXT_FALSE=
+fi
+
+if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
+ as_fn_error $? "conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
+ as_fn_error $? "conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
+ as_fn_error $? "conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${BUILD_DOC_TRUE}" && test -z "${BUILD_DOC_FALSE}"; then
+ as_fn_error $? "conditional \"BUILD_DOC\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
+ as_fn_error $? "conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${INCLUDED_PROGRESSBAR_TRUE}" && test -z "${INCLUDED_PROGRESSBAR_FALSE}"; then
+ as_fn_error $? "conditional \"INCLUDED_PROGRESSBAR\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${INCLUDED_GKARRAYS_TRUE}" && test -z "${INCLUDED_GKARRAYS_FALSE}"; then
+ as_fn_error $? "conditional \"INCLUDED_GKARRAYS\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+
+: ${CONFIG_STATUS=./config.status}
+ac_write_fail=0
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files $CONFIG_STATUS"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5
+$as_echo "$as_me: creating $CONFIG_STATUS" >&6;}
+as_write_fail=0
+cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
+#! $SHELL
+# Generated by $as_me.
+# Run this file to recreate the current configuration.
+# Compiler output produced by configure, useful for debugging
+# configure, is in config.log if it exists.
+
+debug=false
+ac_cs_recheck=false
+ac_cs_silent=false
+
+SHELL=\${CONFIG_SHELL-$SHELL}
+export SHELL
+_ASEOF
+cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in #(
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+case $0 in #((
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
+# ----------------------------------------
+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+# script with STATUS, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ $as_echo "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} # as_fn_error
+
+
+# as_fn_set_status STATUS
+# -----------------------
+# Set $? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} # as_fn_set_status
+
+# as_fn_exit STATUS
+# -----------------
+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} # as_fn_exit
+
+# as_fn_unset VAR
+# ---------------
+# Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+# as_fn_append VAR VALUE
+# ----------------------
+# Append the text in VALUE to the end of the definition contained in VAR. Take
+# advantage of any shell optimizations that allow amortized linear growth over
+# repeated appends, instead of the typical quadratic growth present in naive
+# implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+# as_fn_arith ARG...
+# ------------------
+# Perform arithmetic evaluation on the ARGs, and store the result in the
+# global $as_val. Take advantage of shells that can avoid forks. The arguments
+# must be portable across $(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in #(((((
+-n*)
+ case `echo 'xy\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -p'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -p'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -p'
+ fi
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+
+# as_fn_mkdir_p
+# -------------
+# Create "$as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
+
+
+} # as_fn_mkdir_p
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p='mkdir -p "$as_dir"'
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+if test -x / >/dev/null 2>&1; then
+ as_test_x='test -x'
+else
+ if ls -dL / >/dev/null 2>&1; then
+ as_ls_L_option=L
+ else
+ as_ls_L_option=
+ fi
+ as_test_x='
+ eval sh -c '\''
+ if test -d "$1"; then
+ test -d "$1/.";
+ else
+ case $1 in #(
+ -*)set "./$1";;
+ esac;
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
+ ???[sx]*):;;*)false;;esac;fi
+ '\'' sh
+ '
+fi
+as_executable_p=$as_test_x
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+exec 6>&1
+## ----------------------------------- ##
+## Main body of $CONFIG_STATUS script. ##
+## ----------------------------------- ##
+_ASEOF
+test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# Save the log message, to keep $0 and so on meaningful, and to
+# report actual input values of CONFIG_FILES etc. instead of their
+# values after options handling.
+ac_log="
+This file was extended by crac $as_me 1.5.0, which was
+generated by GNU Autoconf 2.67. Invocation command line was
+
+ CONFIG_FILES = $CONFIG_FILES
+ CONFIG_HEADERS = $CONFIG_HEADERS
+ CONFIG_LINKS = $CONFIG_LINKS
+ CONFIG_COMMANDS = $CONFIG_COMMANDS
+ $ $0 $@
+
+on `(hostname || uname -n) 2>/dev/null | sed 1q`
+"
+
+_ACEOF
+
+case $ac_config_files in *"
+"*) set x $ac_config_files; shift; ac_config_files=$*;;
+esac
+
+case $ac_config_headers in *"
+"*) set x $ac_config_headers; shift; ac_config_headers=$*;;
+esac
+
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+# Files that config.status was made for.
+config_files="$ac_config_files"
+config_headers="$ac_config_headers"
+config_commands="$ac_config_commands"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+ac_cs_usage="\
+\`$as_me' instantiates files and other configuration actions
+from templates according to the current configuration. Unless the files
+and actions are specified as TAGs, all are instantiated by default.
+
+Usage: $0 [OPTION]... [TAG]...
+
+ -h, --help print this help, then exit
+ -V, --version print version number and configuration settings, then exit
+ --config print configuration, then exit
+ -q, --quiet, --silent
+ do not print progress messages
+ -d, --debug don't remove temporary files
+ --recheck update $as_me by reconfiguring in the same conditions
+ --file=FILE[:TEMPLATE]
+ instantiate the configuration file FILE
+ --header=FILE[:TEMPLATE]
+ instantiate the configuration header FILE
+
+Configuration files:
+$config_files
+
+Configuration headers:
+$config_headers
+
+Configuration commands:
+$config_commands
+
+Report bugs to <crac-bugs at lists.gforge.inria.fr>.
+crac home page: <http://crac.gforge.inria.fr/>."
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
+ac_cs_version="\\
+crac config.status 1.5.0
+configured by $0, generated by GNU Autoconf 2.67,
+ with options \\"\$ac_cs_config\\"
+
+Copyright (C) 2010 Free Software Foundation, Inc.
+This config.status script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it."
+
+ac_pwd='$ac_pwd'
+srcdir='$srcdir'
+INSTALL='$INSTALL'
+MKDIR_P='$MKDIR_P'
+AWK='$AWK'
+test -n "\$AWK" || AWK=awk
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# The default lists apply if the user does not specify any file.
+ac_need_defaults=:
+while test $# != 0
+do
+ case $1 in
+ --*=?*)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
+ ac_shift=:
+ ;;
+ --*=)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=
+ ac_shift=:
+ ;;
+ *)
+ ac_option=$1
+ ac_optarg=$2
+ ac_shift=shift
+ ;;
+ esac
+
+ case $ac_option in
+ # Handling of the options.
+ -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
+ ac_cs_recheck=: ;;
+ --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
+ $as_echo "$ac_cs_version"; exit ;;
+ --config | --confi | --conf | --con | --co | --c )
+ $as_echo "$ac_cs_config"; exit ;;
+ --debug | --debu | --deb | --de | --d | -d )
+ debug=: ;;
+ --file | --fil | --fi | --f )
+ $ac_shift
+ case $ac_optarg in
+ *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ '') as_fn_error $? "missing file argument" ;;
+ esac
+ as_fn_append CONFIG_FILES " '$ac_optarg'"
+ ac_need_defaults=false;;
+ --header | --heade | --head | --hea )
+ $ac_shift
+ case $ac_optarg in
+ *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ as_fn_append CONFIG_HEADERS " '$ac_optarg'"
+ ac_need_defaults=false;;
+ --he | --h)
+ # Conflict between --help and --header
+ as_fn_error $? "ambiguous option: \`$1'
+Try \`$0 --help' for more information.";;
+ --help | --hel | -h )
+ $as_echo "$ac_cs_usage"; exit ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil | --si | --s)
+ ac_cs_silent=: ;;
+
+ # This is an error.
+ -*) as_fn_error $? "unrecognized option: \`$1'
+Try \`$0 --help' for more information." ;;
+
+ *) as_fn_append ac_config_targets " $1"
+ ac_need_defaults=false ;;
+
+ esac
+ shift
+done
+
+ac_configure_extra_args=
+
+if $ac_cs_silent; then
+ exec 6>/dev/null
+ ac_configure_extra_args="$ac_configure_extra_args --silent"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+if \$ac_cs_recheck; then
+ set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
+ shift
+ \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6
+ CONFIG_SHELL='$SHELL'
+ export CONFIG_SHELL
+ exec "\$@"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+exec 5>>config.log
+{
+ echo
+ sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX
+## Running $as_me. ##
+_ASBOX
+ $as_echo "$ac_log"
+} >&5
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+#
+# INIT-COMMANDS
+#
+AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"
+
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+sed_quote_subst='$sed_quote_subst'
+double_quote_subst='$double_quote_subst'
+delay_variable_subst='$delay_variable_subst'
+enable_shared='`$ECHO "X$enable_shared" | $Xsed -e "$delay_single_quote_subst"`'
+macro_version='`$ECHO "X$macro_version" | $Xsed -e "$delay_single_quote_subst"`'
+macro_revision='`$ECHO "X$macro_revision" | $Xsed -e "$delay_single_quote_subst"`'
+enable_static='`$ECHO "X$enable_static" | $Xsed -e "$delay_single_quote_subst"`'
+pic_mode='`$ECHO "X$pic_mode" | $Xsed -e "$delay_single_quote_subst"`'
+enable_fast_install='`$ECHO "X$enable_fast_install" | $Xsed -e "$delay_single_quote_subst"`'
+host_alias='`$ECHO "X$host_alias" | $Xsed -e "$delay_single_quote_subst"`'
+host='`$ECHO "X$host" | $Xsed -e "$delay_single_quote_subst"`'
+host_os='`$ECHO "X$host_os" | $Xsed -e "$delay_single_quote_subst"`'
+build_alias='`$ECHO "X$build_alias" | $Xsed -e "$delay_single_quote_subst"`'
+build='`$ECHO "X$build" | $Xsed -e "$delay_single_quote_subst"`'
+build_os='`$ECHO "X$build_os" | $Xsed -e "$delay_single_quote_subst"`'
+SED='`$ECHO "X$SED" | $Xsed -e "$delay_single_quote_subst"`'
+Xsed='`$ECHO "X$Xsed" | $Xsed -e "$delay_single_quote_subst"`'
+GREP='`$ECHO "X$GREP" | $Xsed -e "$delay_single_quote_subst"`'
+EGREP='`$ECHO "X$EGREP" | $Xsed -e "$delay_single_quote_subst"`'
+FGREP='`$ECHO "X$FGREP" | $Xsed -e "$delay_single_quote_subst"`'
+LD='`$ECHO "X$LD" | $Xsed -e "$delay_single_quote_subst"`'
+NM='`$ECHO "X$NM" | $Xsed -e "$delay_single_quote_subst"`'
+LN_S='`$ECHO "X$LN_S" | $Xsed -e "$delay_single_quote_subst"`'
+max_cmd_len='`$ECHO "X$max_cmd_len" | $Xsed -e "$delay_single_quote_subst"`'
+ac_objext='`$ECHO "X$ac_objext" | $Xsed -e "$delay_single_quote_subst"`'
+exeext='`$ECHO "X$exeext" | $Xsed -e "$delay_single_quote_subst"`'
+lt_unset='`$ECHO "X$lt_unset" | $Xsed -e "$delay_single_quote_subst"`'
+lt_SP2NL='`$ECHO "X$lt_SP2NL" | $Xsed -e "$delay_single_quote_subst"`'
+lt_NL2SP='`$ECHO "X$lt_NL2SP" | $Xsed -e "$delay_single_quote_subst"`'
+reload_flag='`$ECHO "X$reload_flag" | $Xsed -e "$delay_single_quote_subst"`'
+reload_cmds='`$ECHO "X$reload_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+OBJDUMP='`$ECHO "X$OBJDUMP" | $Xsed -e "$delay_single_quote_subst"`'
+deplibs_check_method='`$ECHO "X$deplibs_check_method" | $Xsed -e "$delay_single_quote_subst"`'
+file_magic_cmd='`$ECHO "X$file_magic_cmd" | $Xsed -e "$delay_single_quote_subst"`'
+AR='`$ECHO "X$AR" | $Xsed -e "$delay_single_quote_subst"`'
+AR_FLAGS='`$ECHO "X$AR_FLAGS" | $Xsed -e "$delay_single_quote_subst"`'
+STRIP='`$ECHO "X$STRIP" | $Xsed -e "$delay_single_quote_subst"`'
+RANLIB='`$ECHO "X$RANLIB" | $Xsed -e "$delay_single_quote_subst"`'
+old_postinstall_cmds='`$ECHO "X$old_postinstall_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+old_postuninstall_cmds='`$ECHO "X$old_postuninstall_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_cmds='`$ECHO "X$old_archive_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+CC='`$ECHO "X$CC" | $Xsed -e "$delay_single_quote_subst"`'
+CFLAGS='`$ECHO "X$CFLAGS" | $Xsed -e "$delay_single_quote_subst"`'
+compiler='`$ECHO "X$compiler" | $Xsed -e "$delay_single_quote_subst"`'
+GCC='`$ECHO "X$GCC" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_pipe='`$ECHO "X$lt_cv_sys_global_symbol_pipe" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_to_cdecl='`$ECHO "X$lt_cv_sys_global_symbol_to_cdecl" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_to_c_name_address='`$ECHO "X$lt_cv_sys_global_symbol_to_c_name_address" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='`$ECHO "X$lt_cv_sys_global_symbol_to_c_name_address_lib_prefix" | $Xsed -e "$delay_single_quote_subst"`'
+objdir='`$ECHO "X$objdir" | $Xsed -e "$delay_single_quote_subst"`'
+SHELL='`$ECHO "X$SHELL" | $Xsed -e "$delay_single_quote_subst"`'
+ECHO='`$ECHO "X$ECHO" | $Xsed -e "$delay_single_quote_subst"`'
+MAGIC_CMD='`$ECHO "X$MAGIC_CMD" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_no_builtin_flag='`$ECHO "X$lt_prog_compiler_no_builtin_flag" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_wl='`$ECHO "X$lt_prog_compiler_wl" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_pic='`$ECHO "X$lt_prog_compiler_pic" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_static='`$ECHO "X$lt_prog_compiler_static" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_prog_compiler_c_o='`$ECHO "X$lt_cv_prog_compiler_c_o" | $Xsed -e "$delay_single_quote_subst"`'
+need_locks='`$ECHO "X$need_locks" | $Xsed -e "$delay_single_quote_subst"`'
+DSYMUTIL='`$ECHO "X$DSYMUTIL" | $Xsed -e "$delay_single_quote_subst"`'
+NMEDIT='`$ECHO "X$NMEDIT" | $Xsed -e "$delay_single_quote_subst"`'
+LIPO='`$ECHO "X$LIPO" | $Xsed -e "$delay_single_quote_subst"`'
+OTOOL='`$ECHO "X$OTOOL" | $Xsed -e "$delay_single_quote_subst"`'
+OTOOL64='`$ECHO "X$OTOOL64" | $Xsed -e "$delay_single_quote_subst"`'
+libext='`$ECHO "X$libext" | $Xsed -e "$delay_single_quote_subst"`'
+shrext_cmds='`$ECHO "X$shrext_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+extract_expsyms_cmds='`$ECHO "X$extract_expsyms_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+archive_cmds_need_lc='`$ECHO "X$archive_cmds_need_lc" | $Xsed -e "$delay_single_quote_subst"`'
+enable_shared_with_static_runtimes='`$ECHO "X$enable_shared_with_static_runtimes" | $Xsed -e "$delay_single_quote_subst"`'
+export_dynamic_flag_spec='`$ECHO "X$export_dynamic_flag_spec" | $Xsed -e "$delay_single_quote_subst"`'
+whole_archive_flag_spec='`$ECHO "X$whole_archive_flag_spec" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_needs_object='`$ECHO "X$compiler_needs_object" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_from_new_cmds='`$ECHO "X$old_archive_from_new_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_from_expsyms_cmds='`$ECHO "X$old_archive_from_expsyms_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+archive_cmds='`$ECHO "X$archive_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+archive_expsym_cmds='`$ECHO "X$archive_expsym_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+module_cmds='`$ECHO "X$module_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+module_expsym_cmds='`$ECHO "X$module_expsym_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+with_gnu_ld='`$ECHO "X$with_gnu_ld" | $Xsed -e "$delay_single_quote_subst"`'
+allow_undefined_flag='`$ECHO "X$allow_undefined_flag" | $Xsed -e "$delay_single_quote_subst"`'
+no_undefined_flag='`$ECHO "X$no_undefined_flag" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_flag_spec='`$ECHO "X$hardcode_libdir_flag_spec" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_flag_spec_ld='`$ECHO "X$hardcode_libdir_flag_spec_ld" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_separator='`$ECHO "X$hardcode_libdir_separator" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_direct='`$ECHO "X$hardcode_direct" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_direct_absolute='`$ECHO "X$hardcode_direct_absolute" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_minus_L='`$ECHO "X$hardcode_minus_L" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_shlibpath_var='`$ECHO "X$hardcode_shlibpath_var" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_automatic='`$ECHO "X$hardcode_automatic" | $Xsed -e "$delay_single_quote_subst"`'
+inherit_rpath='`$ECHO "X$inherit_rpath" | $Xsed -e "$delay_single_quote_subst"`'
+link_all_deplibs='`$ECHO "X$link_all_deplibs" | $Xsed -e "$delay_single_quote_subst"`'
+fix_srcfile_path='`$ECHO "X$fix_srcfile_path" | $Xsed -e "$delay_single_quote_subst"`'
+always_export_symbols='`$ECHO "X$always_export_symbols" | $Xsed -e "$delay_single_quote_subst"`'
+export_symbols_cmds='`$ECHO "X$export_symbols_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+exclude_expsyms='`$ECHO "X$exclude_expsyms" | $Xsed -e "$delay_single_quote_subst"`'
+include_expsyms='`$ECHO "X$include_expsyms" | $Xsed -e "$delay_single_quote_subst"`'
+prelink_cmds='`$ECHO "X$prelink_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+file_list_spec='`$ECHO "X$file_list_spec" | $Xsed -e "$delay_single_quote_subst"`'
+variables_saved_for_relink='`$ECHO "X$variables_saved_for_relink" | $Xsed -e "$delay_single_quote_subst"`'
+need_lib_prefix='`$ECHO "X$need_lib_prefix" | $Xsed -e "$delay_single_quote_subst"`'
+need_version='`$ECHO "X$need_version" | $Xsed -e "$delay_single_quote_subst"`'
+version_type='`$ECHO "X$version_type" | $Xsed -e "$delay_single_quote_subst"`'
+runpath_var='`$ECHO "X$runpath_var" | $Xsed -e "$delay_single_quote_subst"`'
+shlibpath_var='`$ECHO "X$shlibpath_var" | $Xsed -e "$delay_single_quote_subst"`'
+shlibpath_overrides_runpath='`$ECHO "X$shlibpath_overrides_runpath" | $Xsed -e "$delay_single_quote_subst"`'
+libname_spec='`$ECHO "X$libname_spec" | $Xsed -e "$delay_single_quote_subst"`'
+library_names_spec='`$ECHO "X$library_names_spec" | $Xsed -e "$delay_single_quote_subst"`'
+soname_spec='`$ECHO "X$soname_spec" | $Xsed -e "$delay_single_quote_subst"`'
+postinstall_cmds='`$ECHO "X$postinstall_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+postuninstall_cmds='`$ECHO "X$postuninstall_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+finish_cmds='`$ECHO "X$finish_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+finish_eval='`$ECHO "X$finish_eval" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_into_libs='`$ECHO "X$hardcode_into_libs" | $Xsed -e "$delay_single_quote_subst"`'
+sys_lib_search_path_spec='`$ECHO "X$sys_lib_search_path_spec" | $Xsed -e "$delay_single_quote_subst"`'
+sys_lib_dlsearch_path_spec='`$ECHO "X$sys_lib_dlsearch_path_spec" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_action='`$ECHO "X$hardcode_action" | $Xsed -e "$delay_single_quote_subst"`'
+enable_dlopen='`$ECHO "X$enable_dlopen" | $Xsed -e "$delay_single_quote_subst"`'
+enable_dlopen_self='`$ECHO "X$enable_dlopen_self" | $Xsed -e "$delay_single_quote_subst"`'
+enable_dlopen_self_static='`$ECHO "X$enable_dlopen_self_static" | $Xsed -e "$delay_single_quote_subst"`'
+old_striplib='`$ECHO "X$old_striplib" | $Xsed -e "$delay_single_quote_subst"`'
+striplib='`$ECHO "X$striplib" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_lib_search_dirs='`$ECHO "X$compiler_lib_search_dirs" | $Xsed -e "$delay_single_quote_subst"`'
+predep_objects='`$ECHO "X$predep_objects" | $Xsed -e "$delay_single_quote_subst"`'
+postdep_objects='`$ECHO "X$postdep_objects" | $Xsed -e "$delay_single_quote_subst"`'
+predeps='`$ECHO "X$predeps" | $Xsed -e "$delay_single_quote_subst"`'
+postdeps='`$ECHO "X$postdeps" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_lib_search_path='`$ECHO "X$compiler_lib_search_path" | $Xsed -e "$delay_single_quote_subst"`'
+LD_CXX='`$ECHO "X$LD_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_cmds_CXX='`$ECHO "X$old_archive_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_CXX='`$ECHO "X$compiler_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+GCC_CXX='`$ECHO "X$GCC_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_no_builtin_flag_CXX='`$ECHO "X$lt_prog_compiler_no_builtin_flag_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_wl_CXX='`$ECHO "X$lt_prog_compiler_wl_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_pic_CXX='`$ECHO "X$lt_prog_compiler_pic_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_static_CXX='`$ECHO "X$lt_prog_compiler_static_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_prog_compiler_c_o_CXX='`$ECHO "X$lt_cv_prog_compiler_c_o_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+archive_cmds_need_lc_CXX='`$ECHO "X$archive_cmds_need_lc_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+enable_shared_with_static_runtimes_CXX='`$ECHO "X$enable_shared_with_static_runtimes_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+export_dynamic_flag_spec_CXX='`$ECHO "X$export_dynamic_flag_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+whole_archive_flag_spec_CXX='`$ECHO "X$whole_archive_flag_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_needs_object_CXX='`$ECHO "X$compiler_needs_object_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_from_new_cmds_CXX='`$ECHO "X$old_archive_from_new_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_from_expsyms_cmds_CXX='`$ECHO "X$old_archive_from_expsyms_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+archive_cmds_CXX='`$ECHO "X$archive_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+archive_expsym_cmds_CXX='`$ECHO "X$archive_expsym_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+module_cmds_CXX='`$ECHO "X$module_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+module_expsym_cmds_CXX='`$ECHO "X$module_expsym_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+with_gnu_ld_CXX='`$ECHO "X$with_gnu_ld_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+allow_undefined_flag_CXX='`$ECHO "X$allow_undefined_flag_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+no_undefined_flag_CXX='`$ECHO "X$no_undefined_flag_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_flag_spec_CXX='`$ECHO "X$hardcode_libdir_flag_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_flag_spec_ld_CXX='`$ECHO "X$hardcode_libdir_flag_spec_ld_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_separator_CXX='`$ECHO "X$hardcode_libdir_separator_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_direct_CXX='`$ECHO "X$hardcode_direct_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_direct_absolute_CXX='`$ECHO "X$hardcode_direct_absolute_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_minus_L_CXX='`$ECHO "X$hardcode_minus_L_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_shlibpath_var_CXX='`$ECHO "X$hardcode_shlibpath_var_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_automatic_CXX='`$ECHO "X$hardcode_automatic_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+inherit_rpath_CXX='`$ECHO "X$inherit_rpath_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+link_all_deplibs_CXX='`$ECHO "X$link_all_deplibs_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+fix_srcfile_path_CXX='`$ECHO "X$fix_srcfile_path_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+always_export_symbols_CXX='`$ECHO "X$always_export_symbols_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+export_symbols_cmds_CXX='`$ECHO "X$export_symbols_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+exclude_expsyms_CXX='`$ECHO "X$exclude_expsyms_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+include_expsyms_CXX='`$ECHO "X$include_expsyms_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+prelink_cmds_CXX='`$ECHO "X$prelink_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+file_list_spec_CXX='`$ECHO "X$file_list_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_action_CXX='`$ECHO "X$hardcode_action_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_lib_search_dirs_CXX='`$ECHO "X$compiler_lib_search_dirs_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+predep_objects_CXX='`$ECHO "X$predep_objects_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+postdep_objects_CXX='`$ECHO "X$postdep_objects_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+predeps_CXX='`$ECHO "X$predeps_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+postdeps_CXX='`$ECHO "X$postdeps_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_lib_search_path_CXX='`$ECHO "X$compiler_lib_search_path_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+
+LTCC='$LTCC'
+LTCFLAGS='$LTCFLAGS'
+compiler='$compiler_DEFAULT'
+
+# Quote evaled strings.
+for var in SED \
+GREP \
+EGREP \
+FGREP \
+LD \
+NM \
+LN_S \
+lt_SP2NL \
+lt_NL2SP \
+reload_flag \
+OBJDUMP \
+deplibs_check_method \
+file_magic_cmd \
+AR \
+AR_FLAGS \
+STRIP \
+RANLIB \
+CC \
+CFLAGS \
+compiler \
+lt_cv_sys_global_symbol_pipe \
+lt_cv_sys_global_symbol_to_cdecl \
+lt_cv_sys_global_symbol_to_c_name_address \
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix \
+SHELL \
+ECHO \
+lt_prog_compiler_no_builtin_flag \
+lt_prog_compiler_wl \
+lt_prog_compiler_pic \
+lt_prog_compiler_static \
+lt_cv_prog_compiler_c_o \
+need_locks \
+DSYMUTIL \
+NMEDIT \
+LIPO \
+OTOOL \
+OTOOL64 \
+shrext_cmds \
+export_dynamic_flag_spec \
+whole_archive_flag_spec \
+compiler_needs_object \
+with_gnu_ld \
+allow_undefined_flag \
+no_undefined_flag \
+hardcode_libdir_flag_spec \
+hardcode_libdir_flag_spec_ld \
+hardcode_libdir_separator \
+fix_srcfile_path \
+exclude_expsyms \
+include_expsyms \
+file_list_spec \
+variables_saved_for_relink \
+libname_spec \
+library_names_spec \
+soname_spec \
+finish_eval \
+old_striplib \
+striplib \
+compiler_lib_search_dirs \
+predep_objects \
+postdep_objects \
+predeps \
+postdeps \
+compiler_lib_search_path \
+LD_CXX \
+compiler_CXX \
+lt_prog_compiler_no_builtin_flag_CXX \
+lt_prog_compiler_wl_CXX \
+lt_prog_compiler_pic_CXX \
+lt_prog_compiler_static_CXX \
+lt_cv_prog_compiler_c_o_CXX \
+export_dynamic_flag_spec_CXX \
+whole_archive_flag_spec_CXX \
+compiler_needs_object_CXX \
+with_gnu_ld_CXX \
+allow_undefined_flag_CXX \
+no_undefined_flag_CXX \
+hardcode_libdir_flag_spec_CXX \
+hardcode_libdir_flag_spec_ld_CXX \
+hardcode_libdir_separator_CXX \
+fix_srcfile_path_CXX \
+exclude_expsyms_CXX \
+include_expsyms_CXX \
+file_list_spec_CXX \
+compiler_lib_search_dirs_CXX \
+predep_objects_CXX \
+postdep_objects_CXX \
+predeps_CXX \
+postdeps_CXX \
+compiler_lib_search_path_CXX; do
+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in
+ *[\\\\\\\`\\"\\\$]*)
+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$sed_quote_subst\\"\\\`\\\\\\""
+ ;;
+ *)
+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\""
+ ;;
+ esac
+done
+
+# Double-quote double-evaled strings.
+for var in reload_cmds \
+old_postinstall_cmds \
+old_postuninstall_cmds \
+old_archive_cmds \
+extract_expsyms_cmds \
+old_archive_from_new_cmds \
+old_archive_from_expsyms_cmds \
+archive_cmds \
+archive_expsym_cmds \
+module_cmds \
+module_expsym_cmds \
+export_symbols_cmds \
+prelink_cmds \
+postinstall_cmds \
+postuninstall_cmds \
+finish_cmds \
+sys_lib_search_path_spec \
+sys_lib_dlsearch_path_spec \
+old_archive_cmds_CXX \
+old_archive_from_new_cmds_CXX \
+old_archive_from_expsyms_cmds_CXX \
+archive_cmds_CXX \
+archive_expsym_cmds_CXX \
+module_cmds_CXX \
+module_expsym_cmds_CXX \
+export_symbols_cmds_CXX \
+prelink_cmds_CXX; do
+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in
+ *[\\\\\\\`\\"\\\$]*)
+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$double_quote_subst\\" -e \\"\\\$sed_quote_subst\\" -e \\"\\\$delay_variable_subst\\"\\\`\\\\\\""
+ ;;
+ *)
+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\""
+ ;;
+ esac
+done
+
+# Fix-up fallback echo if it was mangled by the above quoting rules.
+case \$lt_ECHO in
+*'\\\$0 --fallback-echo"') lt_ECHO=\`\$ECHO "X\$lt_ECHO" | \$Xsed -e 's/\\\\\\\\\\\\\\\$0 --fallback-echo"\$/\$0 --fallback-echo"/'\`
+ ;;
+esac
+
+ac_aux_dir='$ac_aux_dir'
+xsi_shell='$xsi_shell'
+lt_shell_append='$lt_shell_append'
+
+# See if we are running on zsh, and set the options which allow our
+# commands through without removal of \ escapes INIT.
+if test -n "\${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+fi
+
+
+ PACKAGE='$PACKAGE'
+ VERSION='$VERSION'
+ TIMESTAMP='$TIMESTAMP'
+ RM='$RM'
+ ofile='$ofile'
+
+
+
+
+
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+
+# Handling of arguments.
+for ac_config_target in $ac_config_targets
+do
+ case $ac_config_target in
+ "config/config.h") CONFIG_HEADERS="$CONFIG_HEADERS config/config.h" ;;
+ "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+ "libtool") CONFIG_COMMANDS="$CONFIG_COMMANDS libtool" ;;
+ "control") CONFIG_FILES="$CONFIG_FILES control" ;;
+ "crac.spec") CONFIG_FILES="$CONFIG_FILES crac.spec" ;;
+ "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
+ "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
+ "scripts/Makefile") CONFIG_FILES="$CONFIG_FILES scripts/Makefile" ;;
+ "src/libReadsInfo/Makefile") CONFIG_FILES="$CONFIG_FILES src/libReadsInfo/Makefile" ;;
+ "src/libSSA/Makefile") CONFIG_FILES="$CONFIG_FILES src/libSSA/Makefile" ;;
+ "src/libgzstream/Makefile") CONFIG_FILES="$CONFIG_FILES src/libgzstream/Makefile" ;;
+ "doc/Makefile") CONFIG_FILES="$CONFIG_FILES doc/Makefile" ;;
+ "doc/package.texi") CONFIG_FILES="$CONFIG_FILES doc/package.texi" ;;
+ "man/Makefile") CONFIG_FILES="$CONFIG_FILES man/Makefile" ;;
+ "man/crac.1") CONFIG_FILES="$CONFIG_FILES man/crac.1" ;;
+ "scripts/crac-client") CONFIG_FILES="$CONFIG_FILES scripts/crac-client" ;;
+ "test_f/Makefile") CONFIG_FILES="$CONFIG_FILES test_f/Makefile" ;;
+ "test_f/bug/Makefile") CONFIG_FILES="$CONFIG_FILES test_f/bug/Makefile" ;;
+ "test_f/causes/Makefile") CONFIG_FILES="$CONFIG_FILES test_f/causes/Makefile" ;;
+ "test_f/cigar/Makefile") CONFIG_FILES="$CONFIG_FILES test_f/cigar/Makefile" ;;
+
+ *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5 ;;
+ esac
+done
+
+
+# If the user did not use the arguments to specify the items to instantiate,
+# then the envvar interface is used. Set only those that are not.
+# We use the long form for the default assignment because of an extremely
+# bizarre bug on SunOS 4.1.3.
+if $ac_need_defaults; then
+ test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
+ test "${CONFIG_HEADERS+set}" = set || CONFIG_HEADERS=$config_headers
+ test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands
+fi
+
+# Have a temporary directory for convenience. Make it in the build tree
+# simply because there is no reason against having it here, and in addition,
+# creating and moving files from /tmp can sometimes cause problems.
+# Hook for its removal unless debugging.
+# Note that there is a small window in which the directory will not be cleaned:
+# after its creation but before its name has been assigned to `$tmp'.
+$debug ||
+{
+ tmp=
+ trap 'exit_status=$?
+ { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status
+' 0
+ trap 'as_fn_exit 1' 1 2 13 15
+}
+# Create a (secure) tmp directory for tmp files.
+
+{
+ tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
+ test -n "$tmp" && test -d "$tmp"
+} ||
+{
+ tmp=./conf$$-$RANDOM
+ (umask 077 && mkdir "$tmp")
+} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
+
+# Set up the scripts for CONFIG_FILES section.
+# No need to generate them if there are no CONFIG_FILES.
+# This happens for instance with `./config.status config.h'.
+if test -n "$CONFIG_FILES"; then
+
+
+ac_cr=`echo X | tr X '\015'`
+# On cygwin, bash can eat \r inside `` if the user requested igncr.
+# But we know of no other shell where ac_cr would be empty at this
+# point, so we can use a bashism as a fallback.
+if test "x$ac_cr" = x; then
+ eval ac_cr=\$\'\\r\'
+fi
+ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
+if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
+ ac_cs_awk_cr='\\r'
+else
+ ac_cs_awk_cr=$ac_cr
+fi
+
+echo 'BEGIN {' >"$tmp/subs1.awk" &&
+_ACEOF
+
+
+{
+ echo "cat >conf$$subs.awk <<_ACEOF" &&
+ echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
+ echo "_ACEOF"
+} >conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'`
+ac_delim='%!_!# '
+for ac_last_try in false false false false false :; do
+ . ./conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+
+ ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
+ if test $ac_delim_n = $ac_delim_num; then
+ break
+ elif $ac_last_try; then
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ else
+ ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+ fi
+done
+rm -f conf$$subs.sh
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+cat >>"\$tmp/subs1.awk" <<\\_ACAWK &&
+_ACEOF
+sed -n '
+h
+s/^/S["/; s/!.*/"]=/
+p
+g
+s/^[^!]*!//
+:repl
+t repl
+s/'"$ac_delim"'$//
+t delim
+:nl
+h
+s/\(.\{148\}\)..*/\1/
+t more1
+s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/
+p
+n
+b repl
+:more1
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t nl
+:delim
+h
+s/\(.\{148\}\)..*/\1/
+t more2
+s/["\\]/\\&/g; s/^/"/; s/$/"/
+p
+b
+:more2
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t delim
+' <conf$$subs.awk | sed '
+/^[^""]/{
+ N
+ s/\n//
+}
+' >>$CONFIG_STATUS || ac_write_fail=1
+rm -f conf$$subs.awk
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+_ACAWK
+cat >>"\$tmp/subs1.awk" <<_ACAWK &&
+ for (key in S) S_is_set[key] = 1
+ FS = ""
+
+}
+{
+ line = $ 0
+ nfields = split(line, field, "@")
+ substed = 0
+ len = length(field[1])
+ for (i = 2; i < nfields; i++) {
+ key = field[i]
+ keylen = length(key)
+ if (S_is_set[key]) {
+ value = S[key]
+ line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3)
+ len += length(value) + length(field[++i])
+ substed = 1
+ } else
+ len += 1 + keylen
+ }
+
+ print line
+}
+
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
+ sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g"
+else
+ cat
+fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \
+ || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
+_ACEOF
+
+# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
+# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
+# trailing colons and then remove the whole line if VPATH becomes empty
+# (actually we leave an empty line to preserve line numbers).
+if test "x$srcdir" = x.; then
+ ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{
+h
+s///
+s/^/:/
+s/[ ]*$/:/
+s/:\$(srcdir):/:/g
+s/:\${srcdir}:/:/g
+s/:@srcdir@:/:/g
+s/^:*//
+s/:*$//
+x
+s/\(=[ ]*\).*/\1/
+G
+s/\n//
+s/^[^=]*=[ ]*$//
+}'
+fi
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+fi # test -n "$CONFIG_FILES"
+
+# Set up the scripts for CONFIG_HEADERS section.
+# No need to generate them if there are no CONFIG_HEADERS.
+# This happens for instance with `./config.status Makefile'.
+if test -n "$CONFIG_HEADERS"; then
+cat >"$tmp/defines.awk" <<\_ACAWK ||
+BEGIN {
+_ACEOF
+
+# Transform confdefs.h into an awk script `defines.awk', embedded as
+# here-document in config.status, that substitutes the proper values into
+# config.h.in to produce config.h.
+
+# Create a delimiter string that does not exist in confdefs.h, to ease
+# handling of long lines.
+ac_delim='%!_!# '
+for ac_last_try in false false :; do
+ ac_t=`sed -n "/$ac_delim/p" confdefs.h`
+ if test -z "$ac_t"; then
+ break
+ elif $ac_last_try; then
+ as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5
+ else
+ ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+ fi
+done
+
+# For the awk script, D is an array of macro values keyed by name,
+# likewise P contains macro parameters if any. Preserve backslash
+# newline sequences.
+
+ac_word_re=[_$as_cr_Letters][_$as_cr_alnum]*
+sed -n '
+s/.\{148\}/&'"$ac_delim"'/g
+t rset
+:rset
+s/^[ ]*#[ ]*define[ ][ ]*/ /
+t def
+d
+:def
+s/\\$//
+t bsnl
+s/["\\]/\\&/g
+s/^ \('"$ac_word_re"'\)\(([^()]*)\)[ ]*\(.*\)/P["\1"]="\2"\
+D["\1"]=" \3"/p
+s/^ \('"$ac_word_re"'\)[ ]*\(.*\)/D["\1"]=" \2"/p
+d
+:bsnl
+s/["\\]/\\&/g
+s/^ \('"$ac_word_re"'\)\(([^()]*)\)[ ]*\(.*\)/P["\1"]="\2"\
+D["\1"]=" \3\\\\\\n"\\/p
+t cont
+s/^ \('"$ac_word_re"'\)[ ]*\(.*\)/D["\1"]=" \2\\\\\\n"\\/p
+t cont
+d
+:cont
+n
+s/.\{148\}/&'"$ac_delim"'/g
+t clear
+:clear
+s/\\$//
+t bsnlc
+s/["\\]/\\&/g; s/^/"/; s/$/"/p
+d
+:bsnlc
+s/["\\]/\\&/g; s/^/"/; s/$/\\\\\\n"\\/p
+b cont
+' <confdefs.h | sed '
+s/'"$ac_delim"'/"\\\
+"/g' >>$CONFIG_STATUS || ac_write_fail=1
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ for (key in D) D_is_set[key] = 1
+ FS = ""
+}
+/^[\t ]*#[\t ]*(define|undef)[\t ]+$ac_word_re([\t (]|\$)/ {
+ line = \$ 0
+ split(line, arg, " ")
+ if (arg[1] == "#") {
+ defundef = arg[2]
+ mac1 = arg[3]
+ } else {
+ defundef = substr(arg[1], 2)
+ mac1 = arg[2]
+ }
+ split(mac1, mac2, "(") #)
+ macro = mac2[1]
+ prefix = substr(line, 1, index(line, defundef) - 1)
+ if (D_is_set[macro]) {
+ # Preserve the white space surrounding the "#".
+ print prefix "define", macro P[macro] D[macro]
+ next
+ } else {
+ # Replace #undef with comments. This is necessary, for example,
+ # in the case of _POSIX_SOURCE, which is predefined and required
+ # on some systems where configure will not decide to define it.
+ if (defundef == "undef") {
+ print "/*", prefix defundef, macro, "*/"
+ next
+ }
+ }
+}
+{ print }
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+ as_fn_error $? "could not setup config headers machinery" "$LINENO" 5
+fi # test -n "$CONFIG_HEADERS"
+
+
+eval set X " :F $CONFIG_FILES :H $CONFIG_HEADERS :C $CONFIG_COMMANDS"
+shift
+for ac_tag
+do
+ case $ac_tag in
+ :[FHLC]) ac_mode=$ac_tag; continue;;
+ esac
+ case $ac_mode$ac_tag in
+ :[FHL]*:*);;
+ :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5 ;;
+ :[FH]-) ac_tag=-:-;;
+ :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
+ esac
+ ac_save_IFS=$IFS
+ IFS=:
+ set x $ac_tag
+ IFS=$ac_save_IFS
+ shift
+ ac_file=$1
+ shift
+
+ case $ac_mode in
+ :L) ac_source=$1;;
+ :[FH])
+ ac_file_inputs=
+ for ac_f
+ do
+ case $ac_f in
+ -) ac_f="$tmp/stdin";;
+ *) # Look for the file first in the build tree, then in the source tree
+ # (if the path is not absolute). The absolute path cannot be DOS-style,
+ # because $ac_f cannot contain `:'.
+ test -f "$ac_f" ||
+ case $ac_f in
+ [\\/$]*) false;;
+ *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
+ esac ||
+ as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5 ;;
+ esac
+ case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
+ as_fn_append ac_file_inputs " '$ac_f'"
+ done
+
+ # Let's still pretend it is `configure' which instantiates (i.e., don't
+ # use $as_me), people would be surprised to read:
+ # /* config.h. Generated by config.status. */
+ configure_input='Generated from '`
+ $as_echo "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g'
+ `' by configure.'
+ if test x"$ac_file" != x-; then
+ configure_input="$ac_file. $configure_input"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5
+$as_echo "$as_me: creating $ac_file" >&6;}
+ fi
+ # Neutralize special characters interpreted by sed in replacement strings.
+ case $configure_input in #(
+ *\&* | *\|* | *\\* )
+ ac_sed_conf_input=`$as_echo "$configure_input" |
+ sed 's/[\\\\&|]/\\\\&/g'`;; #(
+ *) ac_sed_conf_input=$configure_input;;
+ esac
+
+ case $ac_tag in
+ *:-:* | *:-) cat >"$tmp/stdin" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;;
+ esac
+ ;;
+ esac
+
+ ac_dir=`$as_dirname -- "$ac_file" ||
+$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$ac_file" : 'X\(//\)[^/]' \| \
+ X"$ac_file" : 'X\(//\)$' \| \
+ X"$ac_file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$ac_file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir="$ac_dir"; as_fn_mkdir_p
+ ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+ ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
+ # A ".." for each directory in $ac_dir_suffix.
+ ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
+ case $ac_top_builddir_sub in
+ "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+ *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+ esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+ .) # We are building in place.
+ ac_srcdir=.
+ ac_top_srcdir=$ac_top_builddir_sub
+ ac_abs_top_srcdir=$ac_pwd ;;
+ [\\/]* | ?:[\\/]* ) # Absolute name.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir
+ ac_abs_top_srcdir=$srcdir ;;
+ *) # Relative name.
+ ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_build_prefix$srcdir
+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+
+ case $ac_mode in
+ :F)
+ #
+ # CONFIG_FILE
+ #
+
+ case $INSTALL in
+ [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;;
+ *) ac_INSTALL=$ac_top_build_prefix$INSTALL ;;
+ esac
+ ac_MKDIR_P=$MKDIR_P
+ case $MKDIR_P in
+ [\\/$]* | ?:[\\/]* ) ;;
+ */*) ac_MKDIR_P=$ac_top_build_prefix$MKDIR_P ;;
+ esac
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# If the template does not know about datarootdir, expand it.
+# FIXME: This hack should be removed a few years after 2.60.
+ac_datarootdir_hack=; ac_datarootdir_seen=
+ac_sed_dataroot='
+/datarootdir/ {
+ p
+ q
+}
+/@datadir@/p
+/@docdir@/p
+/@infodir@/p
+/@localedir@/p
+/@mandir@/p'
+case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
+*datarootdir*) ac_datarootdir_seen=yes;;
+*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
+$as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ ac_datarootdir_hack='
+ s&@datadir@&$datadir&g
+ s&@docdir@&$docdir&g
+ s&@infodir@&$infodir&g
+ s&@localedir@&$localedir&g
+ s&@mandir@&$mandir&g
+ s&\\\${datarootdir}&$datarootdir&g' ;;
+esac
+_ACEOF
+
+# Neutralize VPATH when `$srcdir' = `.'.
+# Shell code in configure.ac might set extrasub.
+# FIXME: do we really want to maintain this feature?
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_sed_extra="$ac_vpsub
+$extrasub
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+:t
+/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
+s|@configure_input@|$ac_sed_conf_input|;t t
+s&@top_builddir@&$ac_top_builddir_sub&;t t
+s&@top_build_prefix@&$ac_top_build_prefix&;t t
+s&@srcdir@&$ac_srcdir&;t t
+s&@abs_srcdir@&$ac_abs_srcdir&;t t
+s&@top_srcdir@&$ac_top_srcdir&;t t
+s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t
+s&@builddir@&$ac_builddir&;t t
+s&@abs_builddir@&$ac_abs_builddir&;t t
+s&@abs_top_builddir@&$ac_abs_top_builddir&;t t
+s&@INSTALL@&$ac_INSTALL&;t t
+s&@MKDIR_P@&$ac_MKDIR_P&;t t
+$ac_datarootdir_hack
+"
+eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$tmp/subs.awk" >$tmp/out \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+
+test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
+ { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } &&
+ { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } &&
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&5
+$as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&2;}
+
+ rm -f "$tmp/stdin"
+ case $ac_file in
+ -) cat "$tmp/out" && rm -f "$tmp/out";;
+ *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";;
+ esac \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ ;;
+ :H)
+ #
+ # CONFIG_HEADER
+ #
+ if test x"$ac_file" != x-; then
+ {
+ $as_echo "/* $configure_input */" \
+ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs"
+ } >"$tmp/config.h" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5
+$as_echo "$as_me: $ac_file is unchanged" >&6;}
+ else
+ rm -f "$ac_file"
+ mv "$tmp/config.h" "$ac_file" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ fi
+ else
+ $as_echo "/* $configure_input */" \
+ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \
+ || as_fn_error $? "could not create -" "$LINENO" 5
+ fi
+# Compute "$ac_file"'s index in $config_headers.
+_am_arg="$ac_file"
+_am_stamp_count=1
+for _am_header in $config_headers :; do
+ case $_am_header in
+ $_am_arg | $_am_arg:* )
+ break ;;
+ * )
+ _am_stamp_count=`expr $_am_stamp_count + 1` ;;
+ esac
+done
+echo "timestamp for $_am_arg" >`$as_dirname -- "$_am_arg" ||
+$as_expr X"$_am_arg" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$_am_arg" : 'X\(//\)[^/]' \| \
+ X"$_am_arg" : 'X\(//\)$' \| \
+ X"$_am_arg" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$_am_arg" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`/stamp-h$_am_stamp_count
+ ;;
+
+ :C) { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5
+$as_echo "$as_me: executing $ac_file commands" >&6;}
+ ;;
+ esac
+
+
+ case $ac_file$ac_mode in
+ "depfiles":C) test x"$AMDEP_TRUE" != x"" || {
+ # Autoconf 2.62 quotes --file arguments for eval, but not when files
+ # are listed without --file. Let's play safe and only enable the eval
+ # if we detect the quoting.
+ case $CONFIG_FILES in
+ *\'*) eval set x "$CONFIG_FILES" ;;
+ *) set x $CONFIG_FILES ;;
+ esac
+ shift
+ for mf
+ do
+ # Strip MF so we end up with the name of the file.
+ mf=`echo "$mf" | sed -e 's/:.*$//'`
+ # Check whether this is an Automake generated Makefile or not.
+ # We used to match only the files named `Makefile.in', but
+ # some people rename them; so instead we look at the file content.
+ # Grep'ing the first line is not enough: some people post-process
+ # each Makefile.in and add a new line on top of each file to say so.
+ # Grep'ing the whole file is not good either: AIX grep has a line
+ # limit of 2048, but all sed's we know have understand at least 4000.
+ if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
+ dirpart=`$as_dirname -- "$mf" ||
+$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$mf" : 'X\(//\)[^/]' \| \
+ X"$mf" : 'X\(//\)$' \| \
+ X"$mf" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$mf" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ else
+ continue
+ fi
+ # Extract the definition of DEPDIR, am__include, and am__quote
+ # from the Makefile without running `make'.
+ DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+ test -z "$DEPDIR" && continue
+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
+ test -z "am__include" && continue
+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # When using ansi2knr, U may be empty or an underscore; expand it
+ U=`sed -n 's/^U = //p' < "$mf"`
+ # Find all dependency output files, they are included files with
+ # $(DEPDIR) in their names. We invoke sed twice because it is the
+ # simplest approach to changing $(DEPDIR) to its actual value in the
+ # expansion.
+ for file in `sed -n "
+ s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+ # Make sure the directory exists.
+ test -f "$dirpart/$file" && continue
+ fdir=`$as_dirname -- "$file" ||
+$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$file" : 'X\(//\)[^/]' \| \
+ X"$file" : 'X\(//\)$' \| \
+ X"$file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir=$dirpart/$fdir; as_fn_mkdir_p
+ # echo "creating $dirpart/$file"
+ echo '# dummy' > "$dirpart/$file"
+ done
+ done
+}
+ ;;
+ "libtool":C)
+
+ # See if we are running on zsh, and set the options which allow our
+ # commands through without removal of \ escapes.
+ if test -n "${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+ fi
+
+ cfgfile="${ofile}T"
+ trap "$RM \"$cfgfile\"; exit 1" 1 2 15
+ $RM "$cfgfile"
+
+ cat <<_LT_EOF >> "$cfgfile"
+#! $SHELL
+
+# `$ECHO "$ofile" | sed 's%^.*/%%'` - Provide generalized library-building support services.
+# Generated automatically by $as_me ($PACKAGE$TIMESTAMP) $VERSION
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+# NOTE: Changes made to this file will be lost: look at ltmain.sh.
+#
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
+# 2006, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gordon Matzigkeit, 1996
+#
+# This file is part of GNU Libtool.
+#
+# GNU Libtool is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License as
+# published by the Free Software Foundation; either version 2 of
+# the License, or (at your option) any later version.
+#
+# As a special exception to the GNU General Public License,
+# if you distribute this file as part of a program or library that
+# is built using GNU Libtool, you may include this file under the
+# same distribution terms that you use for the rest of that program.
+#
+# GNU Libtool is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GNU Libtool; see the file COPYING. If not, a copy
+# can be downloaded from http://www.gnu.org/licenses/gpl.html, or
+# obtained by writing to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+
+# The names of the tagged configurations supported by this script.
+available_tags="CXX "
+
+# ### BEGIN LIBTOOL CONFIG
+
+# Whether or not to build shared libraries.
+build_libtool_libs=$enable_shared
+
+# Which release of libtool.m4 was used?
+macro_version=$macro_version
+macro_revision=$macro_revision
+
+# Whether or not to build static libraries.
+build_old_libs=$enable_static
+
+# What type of objects to build.
+pic_mode=$pic_mode
+
+# Whether or not to optimize for fast installation.
+fast_install=$enable_fast_install
+
+# The host system.
+host_alias=$host_alias
+host=$host
+host_os=$host_os
+
+# The build system.
+build_alias=$build_alias
+build=$build
+build_os=$build_os
+
+# A sed program that does not truncate output.
+SED=$lt_SED
+
+# Sed that helps us avoid accidentally triggering echo(1) options like -n.
+Xsed="\$SED -e 1s/^X//"
+
+# A grep program that handles long lines.
+GREP=$lt_GREP
+
+# An ERE matcher.
+EGREP=$lt_EGREP
+
+# A literal string matcher.
+FGREP=$lt_FGREP
+
+# A BSD- or MS-compatible name lister.
+NM=$lt_NM
+
+# Whether we need soft or hard links.
+LN_S=$lt_LN_S
+
+# What is the maximum length of a command?
+max_cmd_len=$max_cmd_len
+
+# Object file suffix (normally "o").
+objext=$ac_objext
+
+# Executable file suffix (normally "").
+exeext=$exeext
+
+# whether the shell understands "unset".
+lt_unset=$lt_unset
+
+# turn spaces into newlines.
+SP2NL=$lt_lt_SP2NL
+
+# turn newlines into spaces.
+NL2SP=$lt_lt_NL2SP
+
+# How to create reloadable object files.
+reload_flag=$lt_reload_flag
+reload_cmds=$lt_reload_cmds
+
+# An object symbol dumper.
+OBJDUMP=$lt_OBJDUMP
+
+# Method to check whether dependent libraries are shared objects.
+deplibs_check_method=$lt_deplibs_check_method
+
+# Command to use when deplibs_check_method == "file_magic".
+file_magic_cmd=$lt_file_magic_cmd
+
+# The archiver.
+AR=$lt_AR
+AR_FLAGS=$lt_AR_FLAGS
+
+# A symbol stripping program.
+STRIP=$lt_STRIP
+
+# Commands used to install an old-style archive.
+RANLIB=$lt_RANLIB
+old_postinstall_cmds=$lt_old_postinstall_cmds
+old_postuninstall_cmds=$lt_old_postuninstall_cmds
+
+# A C compiler.
+LTCC=$lt_CC
+
+# LTCC compiler flags.
+LTCFLAGS=$lt_CFLAGS
+
+# Take the output of nm and produce a listing of raw symbols and C names.
+global_symbol_pipe=$lt_lt_cv_sys_global_symbol_pipe
+
+# Transform the output of nm in a proper C declaration.
+global_symbol_to_cdecl=$lt_lt_cv_sys_global_symbol_to_cdecl
+
+# Transform the output of nm in a C name address pair.
+global_symbol_to_c_name_address=$lt_lt_cv_sys_global_symbol_to_c_name_address
+
+# Transform the output of nm in a C name address pair when lib prefix is needed.
+global_symbol_to_c_name_address_lib_prefix=$lt_lt_cv_sys_global_symbol_to_c_name_address_lib_prefix
+
+# The name of the directory that contains temporary libtool files.
+objdir=$objdir
+
+# Shell to use when invoking shell scripts.
+SHELL=$lt_SHELL
+
+# An echo program that does not interpret backslashes.
+ECHO=$lt_ECHO
+
+# Used to examine libraries when file_magic_cmd begins with "file".
+MAGIC_CMD=$MAGIC_CMD
+
+# Must we lock files when doing compilation?
+need_locks=$lt_need_locks
+
+# Tool to manipulate archived DWARF debug symbol files on Mac OS X.
+DSYMUTIL=$lt_DSYMUTIL
+
+# Tool to change global to local symbols on Mac OS X.
+NMEDIT=$lt_NMEDIT
+
+# Tool to manipulate fat objects and archives on Mac OS X.
+LIPO=$lt_LIPO
+
+# ldd/readelf like tool for Mach-O binaries on Mac OS X.
+OTOOL=$lt_OTOOL
+
+# ldd/readelf like tool for 64 bit Mach-O binaries on Mac OS X 10.4.
+OTOOL64=$lt_OTOOL64
+
+# Old archive suffix (normally "a").
+libext=$libext
+
+# Shared library suffix (normally ".so").
+shrext_cmds=$lt_shrext_cmds
+
+# The commands to extract the exported symbol list from a shared archive.
+extract_expsyms_cmds=$lt_extract_expsyms_cmds
+
+# Variables whose values should be saved in libtool wrapper scripts and
+# restored at link time.
+variables_saved_for_relink=$lt_variables_saved_for_relink
+
+# Do we need the "lib" prefix for modules?
+need_lib_prefix=$need_lib_prefix
+
+# Do we need a version for libraries?
+need_version=$need_version
+
+# Library versioning type.
+version_type=$version_type
+
+# Shared library runtime path variable.
+runpath_var=$runpath_var
+
+# Shared library path variable.
+shlibpath_var=$shlibpath_var
+
+# Is shlibpath searched before the hard-coded library search path?
+shlibpath_overrides_runpath=$shlibpath_overrides_runpath
+
+# Format of library name prefix.
+libname_spec=$lt_libname_spec
+
+# List of archive names. First name is the real one, the rest are links.
+# The last name is the one that the linker finds with -lNAME
+library_names_spec=$lt_library_names_spec
+
+# The coded name of the library, if different from the real name.
+soname_spec=$lt_soname_spec
+
+# Command to use after installation of a shared archive.
+postinstall_cmds=$lt_postinstall_cmds
+
+# Command to use after uninstallation of a shared archive.
+postuninstall_cmds=$lt_postuninstall_cmds
+
+# Commands used to finish a libtool library installation in a directory.
+finish_cmds=$lt_finish_cmds
+
+# As "finish_cmds", except a single script fragment to be evaled but
+# not shown.
+finish_eval=$lt_finish_eval
+
+# Whether we should hardcode library paths into libraries.
+hardcode_into_libs=$hardcode_into_libs
+
+# Compile-time system search path for libraries.
+sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+
+# Run-time system search path for libraries.
+sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec
+
+# Whether dlopen is supported.
+dlopen_support=$enable_dlopen
+
+# Whether dlopen of programs is supported.
+dlopen_self=$enable_dlopen_self
+
+# Whether dlopen of statically linked programs is supported.
+dlopen_self_static=$enable_dlopen_self_static
+
+# Commands to strip libraries.
+old_striplib=$lt_old_striplib
+striplib=$lt_striplib
+
+
+# The linker used to build libraries.
+LD=$lt_LD
+
+# Commands used to build an old-style archive.
+old_archive_cmds=$lt_old_archive_cmds
+
+# A language specific compiler.
+CC=$lt_compiler
+
+# Is the compiler the GNU compiler?
+with_gcc=$GCC
+
+# Compiler flag to turn off builtin functions.
+no_builtin_flag=$lt_lt_prog_compiler_no_builtin_flag
+
+# How to pass a linker flag through the compiler.
+wl=$lt_lt_prog_compiler_wl
+
+# Additional compiler flags for building library objects.
+pic_flag=$lt_lt_prog_compiler_pic
+
+# Compiler flag to prevent dynamic linking.
+link_static_flag=$lt_lt_prog_compiler_static
+
+# Does compiler simultaneously support -c and -o options?
+compiler_c_o=$lt_lt_cv_prog_compiler_c_o
+
+# Whether or not to add -lc for building shared libraries.
+build_libtool_need_lc=$archive_cmds_need_lc
+
+# Whether or not to disallow shared libs when runtime libs are static.
+allow_libtool_libs_with_static_runtimes=$enable_shared_with_static_runtimes
+
+# Compiler flag to allow reflexive dlopens.
+export_dynamic_flag_spec=$lt_export_dynamic_flag_spec
+
+# Compiler flag to generate shared objects directly from archives.
+whole_archive_flag_spec=$lt_whole_archive_flag_spec
+
+# Whether the compiler copes with passing no objects directly.
+compiler_needs_object=$lt_compiler_needs_object
+
+# Create an old-style archive from a shared archive.
+old_archive_from_new_cmds=$lt_old_archive_from_new_cmds
+
+# Create a temporary old-style archive to link instead of a shared archive.
+old_archive_from_expsyms_cmds=$lt_old_archive_from_expsyms_cmds
+
+# Commands used to build a shared archive.
+archive_cmds=$lt_archive_cmds
+archive_expsym_cmds=$lt_archive_expsym_cmds
+
+# Commands used to build a loadable module if different from building
+# a shared archive.
+module_cmds=$lt_module_cmds
+module_expsym_cmds=$lt_module_expsym_cmds
+
+# Whether we are building with GNU ld or not.
+with_gnu_ld=$lt_with_gnu_ld
+
+# Flag that allows shared libraries with undefined symbols to be built.
+allow_undefined_flag=$lt_allow_undefined_flag
+
+# Flag that enforces no undefined symbols.
+no_undefined_flag=$lt_no_undefined_flag
+
+# Flag to hardcode \$libdir into a binary during linking.
+# This must work even if \$libdir does not exist
+hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec
+
+# If ld is used when linking, flag to hardcode \$libdir into a binary
+# during linking. This must work even if \$libdir does not exist.
+hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld
+
+# Whether we need a single "-rpath" flag with a separated argument.
+hardcode_libdir_separator=$lt_hardcode_libdir_separator
+
+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes
+# DIR into the resulting binary.
+hardcode_direct=$hardcode_direct
+
+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes
+# DIR into the resulting binary and the resulting library dependency is
+# "absolute",i.e impossible to change by setting \${shlibpath_var} if the
+# library is relocated.
+hardcode_direct_absolute=$hardcode_direct_absolute
+
+# Set to "yes" if using the -LDIR flag during linking hardcodes DIR
+# into the resulting binary.
+hardcode_minus_L=$hardcode_minus_L
+
+# Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR
+# into the resulting binary.
+hardcode_shlibpath_var=$hardcode_shlibpath_var
+
+# Set to "yes" if building a shared library automatically hardcodes DIR
+# into the library and all subsequent libraries and executables linked
+# against it.
+hardcode_automatic=$hardcode_automatic
+
+# Set to yes if linker adds runtime paths of dependent libraries
+# to runtime path list.
+inherit_rpath=$inherit_rpath
+
+# Whether libtool must link a program against all its dependency libraries.
+link_all_deplibs=$link_all_deplibs
+
+# Fix the shell variable \$srcfile for the compiler.
+fix_srcfile_path=$lt_fix_srcfile_path
+
+# Set to "yes" if exported symbols are required.
+always_export_symbols=$always_export_symbols
+
+# The commands to list exported symbols.
+export_symbols_cmds=$lt_export_symbols_cmds
+
+# Symbols that should not be listed in the preloaded symbols.
+exclude_expsyms=$lt_exclude_expsyms
+
+# Symbols that must always be exported.
+include_expsyms=$lt_include_expsyms
+
+# Commands necessary for linking programs (against libraries) with templates.
+prelink_cmds=$lt_prelink_cmds
+
+# Specify filename containing input files.
+file_list_spec=$lt_file_list_spec
+
+# How to hardcode a shared library path into an executable.
+hardcode_action=$hardcode_action
+
+# The directories searched by this compiler when creating a shared library.
+compiler_lib_search_dirs=$lt_compiler_lib_search_dirs
+
+# Dependencies to place before and after the objects being linked to
+# create a shared library.
+predep_objects=$lt_predep_objects
+postdep_objects=$lt_postdep_objects
+predeps=$lt_predeps
+postdeps=$lt_postdeps
+
+# The library search path used internally by the compiler when linking
+# a shared library.
+compiler_lib_search_path=$lt_compiler_lib_search_path
+
+# ### END LIBTOOL CONFIG
+
+_LT_EOF
+
+ case $host_os in
+ aix3*)
+ cat <<\_LT_EOF >> "$cfgfile"
+# AIX sometimes has problems with the GCC collect2 program. For some
+# reason, if we set the COLLECT_NAMES environment variable, the problems
+# vanish in a puff of smoke.
+if test "X${COLLECT_NAMES+set}" != Xset; then
+ COLLECT_NAMES=
+ export COLLECT_NAMES
+fi
+_LT_EOF
+ ;;
+ esac
+
+
+ltmain="$ac_aux_dir/ltmain.sh"
+
+
+ # We use sed instead of cat because bash on DJGPP gets confused if
+ # if finds mixed CR/LF and LF-only lines. Since sed operates in
+ # text mode, it properly converts lines to CR/LF. This bash problem
+ # is reportedly fixed, but why not run on old versions too?
+ sed '/^# Generated shell functions inserted here/q' "$ltmain" >> "$cfgfile" \
+ || (rm -f "$cfgfile"; exit 1)
+
+ case $xsi_shell in
+ yes)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_dirname file append nondir_replacement
+# Compute the dirname of FILE. If nonempty, add APPEND to the result,
+# otherwise set result to NONDIR_REPLACEMENT.
+func_dirname ()
+{
+ case ${1} in
+ */*) func_dirname_result="${1%/*}${2}" ;;
+ * ) func_dirname_result="${3}" ;;
+ esac
+}
+
+# func_basename file
+func_basename ()
+{
+ func_basename_result="${1##*/}"
+}
+
+# func_dirname_and_basename file append nondir_replacement
+# perform func_basename and func_dirname in a single function
+# call:
+# dirname: Compute the dirname of FILE. If nonempty,
+# add APPEND to the result, otherwise set result
+# to NONDIR_REPLACEMENT.
+# value returned in "$func_dirname_result"
+# basename: Compute filename of FILE.
+# value retuned in "$func_basename_result"
+# Implementation must be kept synchronized with func_dirname
+# and func_basename. For efficiency, we do not delegate to
+# those functions but instead duplicate the functionality here.
+func_dirname_and_basename ()
+{
+ case ${1} in
+ */*) func_dirname_result="${1%/*}${2}" ;;
+ * ) func_dirname_result="${3}" ;;
+ esac
+ func_basename_result="${1##*/}"
+}
+
+# func_stripname prefix suffix name
+# strip PREFIX and SUFFIX off of NAME.
+# PREFIX and SUFFIX must not contain globbing or regex special
+# characters, hashes, percent signs, but SUFFIX may contain a leading
+# dot (in which case that matches only a dot).
+func_stripname ()
+{
+ # pdksh 5.2.14 does not do ${X%$Y} correctly if both X and Y are
+ # positional parameters, so assign one to ordinary parameter first.
+ func_stripname_result=${3}
+ func_stripname_result=${func_stripname_result#"${1}"}
+ func_stripname_result=${func_stripname_result%"${2}"}
+}
+
+# func_opt_split
+func_opt_split ()
+{
+ func_opt_split_opt=${1%%=*}
+ func_opt_split_arg=${1#*=}
+}
+
+# func_lo2o object
+func_lo2o ()
+{
+ case ${1} in
+ *.lo) func_lo2o_result=${1%.lo}.${objext} ;;
+ *) func_lo2o_result=${1} ;;
+ esac
+}
+
+# func_xform libobj-or-source
+func_xform ()
+{
+ func_xform_result=${1%.*}.lo
+}
+
+# func_arith arithmetic-term...
+func_arith ()
+{
+ func_arith_result=$(( $* ))
+}
+
+# func_len string
+# STRING may not start with a hyphen.
+func_len ()
+{
+ func_len_result=${#1}
+}
+
+_LT_EOF
+ ;;
+ *) # Bourne compatible functions.
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_dirname file append nondir_replacement
+# Compute the dirname of FILE. If nonempty, add APPEND to the result,
+# otherwise set result to NONDIR_REPLACEMENT.
+func_dirname ()
+{
+ # Extract subdirectory from the argument.
+ func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"`
+ if test "X$func_dirname_result" = "X${1}"; then
+ func_dirname_result="${3}"
+ else
+ func_dirname_result="$func_dirname_result${2}"
+ fi
+}
+
+# func_basename file
+func_basename ()
+{
+ func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"`
+}
+
+
+# func_stripname prefix suffix name
+# strip PREFIX and SUFFIX off of NAME.
+# PREFIX and SUFFIX must not contain globbing or regex special
+# characters, hashes, percent signs, but SUFFIX may contain a leading
+# dot (in which case that matches only a dot).
+# func_strip_suffix prefix name
+func_stripname ()
+{
+ case ${2} in
+ .*) func_stripname_result=`$ECHO "X${3}" \
+ | $Xsed -e "s%^${1}%%" -e "s%\\\\${2}\$%%"`;;
+ *) func_stripname_result=`$ECHO "X${3}" \
+ | $Xsed -e "s%^${1}%%" -e "s%${2}\$%%"`;;
+ esac
+}
+
+# sed scripts:
+my_sed_long_opt='1s/^\(-[^=]*\)=.*/\1/;q'
+my_sed_long_arg='1s/^-[^=]*=//'
+
+# func_opt_split
+func_opt_split ()
+{
+ func_opt_split_opt=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_opt"`
+ func_opt_split_arg=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_arg"`
+}
+
+# func_lo2o object
+func_lo2o ()
+{
+ func_lo2o_result=`$ECHO "X${1}" | $Xsed -e "$lo2o"`
+}
+
+# func_xform libobj-or-source
+func_xform ()
+{
+ func_xform_result=`$ECHO "X${1}" | $Xsed -e 's/\.[^.]*$/.lo/'`
+}
+
+# func_arith arithmetic-term...
+func_arith ()
+{
+ func_arith_result=`expr "$@"`
+}
+
+# func_len string
+# STRING may not start with a hyphen.
+func_len ()
+{
+ func_len_result=`expr "$1" : ".*" 2>/dev/null || echo $max_cmd_len`
+}
+
+_LT_EOF
+esac
+
+case $lt_shell_append in
+ yes)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$1+=\$2"
+}
+_LT_EOF
+ ;;
+ *)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$1=\$$1\$2"
+}
+
+_LT_EOF
+ ;;
+ esac
+
+
+ sed -n '/^# Generated shell functions inserted here/,$p' "$ltmain" >> "$cfgfile" \
+ || (rm -f "$cfgfile"; exit 1)
+
+ mv -f "$cfgfile" "$ofile" ||
+ (rm -f "$ofile" && cp "$cfgfile" "$ofile" && rm -f "$cfgfile")
+ chmod +x "$ofile"
+
+
+ cat <<_LT_EOF >> "$ofile"
+
+# ### BEGIN LIBTOOL TAG CONFIG: CXX
+
+# The linker used to build libraries.
+LD=$lt_LD_CXX
+
+# Commands used to build an old-style archive.
+old_archive_cmds=$lt_old_archive_cmds_CXX
+
+# A language specific compiler.
+CC=$lt_compiler_CXX
+
+# Is the compiler the GNU compiler?
+with_gcc=$GCC_CXX
+
+# Compiler flag to turn off builtin functions.
+no_builtin_flag=$lt_lt_prog_compiler_no_builtin_flag_CXX
+
+# How to pass a linker flag through the compiler.
+wl=$lt_lt_prog_compiler_wl_CXX
+
+# Additional compiler flags for building library objects.
+pic_flag=$lt_lt_prog_compiler_pic_CXX
+
+# Compiler flag to prevent dynamic linking.
+link_static_flag=$lt_lt_prog_compiler_static_CXX
+
+# Does compiler simultaneously support -c and -o options?
+compiler_c_o=$lt_lt_cv_prog_compiler_c_o_CXX
+
+# Whether or not to add -lc for building shared libraries.
+build_libtool_need_lc=$archive_cmds_need_lc_CXX
+
+# Whether or not to disallow shared libs when runtime libs are static.
+allow_libtool_libs_with_static_runtimes=$enable_shared_with_static_runtimes_CXX
+
+# Compiler flag to allow reflexive dlopens.
+export_dynamic_flag_spec=$lt_export_dynamic_flag_spec_CXX
+
+# Compiler flag to generate shared objects directly from archives.
+whole_archive_flag_spec=$lt_whole_archive_flag_spec_CXX
+
+# Whether the compiler copes with passing no objects directly.
+compiler_needs_object=$lt_compiler_needs_object_CXX
+
+# Create an old-style archive from a shared archive.
+old_archive_from_new_cmds=$lt_old_archive_from_new_cmds_CXX
+
+# Create a temporary old-style archive to link instead of a shared archive.
+old_archive_from_expsyms_cmds=$lt_old_archive_from_expsyms_cmds_CXX
+
+# Commands used to build a shared archive.
+archive_cmds=$lt_archive_cmds_CXX
+archive_expsym_cmds=$lt_archive_expsym_cmds_CXX
+
+# Commands used to build a loadable module if different from building
+# a shared archive.
+module_cmds=$lt_module_cmds_CXX
+module_expsym_cmds=$lt_module_expsym_cmds_CXX
+
+# Whether we are building with GNU ld or not.
+with_gnu_ld=$lt_with_gnu_ld_CXX
+
+# Flag that allows shared libraries with undefined symbols to be built.
+allow_undefined_flag=$lt_allow_undefined_flag_CXX
+
+# Flag that enforces no undefined symbols.
+no_undefined_flag=$lt_no_undefined_flag_CXX
+
+# Flag to hardcode \$libdir into a binary during linking.
+# This must work even if \$libdir does not exist
+hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec_CXX
+
+# If ld is used when linking, flag to hardcode \$libdir into a binary
+# during linking. This must work even if \$libdir does not exist.
+hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld_CXX
+
+# Whether we need a single "-rpath" flag with a separated argument.
+hardcode_libdir_separator=$lt_hardcode_libdir_separator_CXX
+
+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes
+# DIR into the resulting binary.
+hardcode_direct=$hardcode_direct_CXX
+
+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes
+# DIR into the resulting binary and the resulting library dependency is
+# "absolute",i.e impossible to change by setting \${shlibpath_var} if the
+# library is relocated.
+hardcode_direct_absolute=$hardcode_direct_absolute_CXX
+
+# Set to "yes" if using the -LDIR flag during linking hardcodes DIR
+# into the resulting binary.
+hardcode_minus_L=$hardcode_minus_L_CXX
+
+# Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR
+# into the resulting binary.
+hardcode_shlibpath_var=$hardcode_shlibpath_var_CXX
+
+# Set to "yes" if building a shared library automatically hardcodes DIR
+# into the library and all subsequent libraries and executables linked
+# against it.
+hardcode_automatic=$hardcode_automatic_CXX
+
+# Set to yes if linker adds runtime paths of dependent libraries
+# to runtime path list.
+inherit_rpath=$inherit_rpath_CXX
+
+# Whether libtool must link a program against all its dependency libraries.
+link_all_deplibs=$link_all_deplibs_CXX
+
+# Fix the shell variable \$srcfile for the compiler.
+fix_srcfile_path=$lt_fix_srcfile_path_CXX
+
+# Set to "yes" if exported symbols are required.
+always_export_symbols=$always_export_symbols_CXX
+
+# The commands to list exported symbols.
+export_symbols_cmds=$lt_export_symbols_cmds_CXX
+
+# Symbols that should not be listed in the preloaded symbols.
+exclude_expsyms=$lt_exclude_expsyms_CXX
+
+# Symbols that must always be exported.
+include_expsyms=$lt_include_expsyms_CXX
+
+# Commands necessary for linking programs (against libraries) with templates.
+prelink_cmds=$lt_prelink_cmds_CXX
+
+# Specify filename containing input files.
+file_list_spec=$lt_file_list_spec_CXX
+
+# How to hardcode a shared library path into an executable.
+hardcode_action=$hardcode_action_CXX
+
+# The directories searched by this compiler when creating a shared library.
+compiler_lib_search_dirs=$lt_compiler_lib_search_dirs_CXX
+
+# Dependencies to place before and after the objects being linked to
+# create a shared library.
+predep_objects=$lt_predep_objects_CXX
+postdep_objects=$lt_postdep_objects_CXX
+predeps=$lt_predeps_CXX
+postdeps=$lt_postdeps_CXX
+
+# The library search path used internally by the compiler when linking
+# a shared library.
+compiler_lib_search_path=$lt_compiler_lib_search_path_CXX
+
+# ### END LIBTOOL TAG CONFIG: CXX
+_LT_EOF
+
+ ;;
+ "control":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+ "crac.spec":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+ "Makefile":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+ "src/Makefile":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+ "scripts/Makefile":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+ "src/libReadsInfo/Makefile":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+ "src/libSSA/Makefile":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+ "src/libgzstream/Makefile":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+ "doc/Makefile":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+ "doc/package.texi":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+ "man/Makefile":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+ "man/crac.1":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+ "scripts/crac-client":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+ "test_f/Makefile":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+ "test_f/bug/Makefile":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+ "test_f/causes/Makefile":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+ "test_f/cigar/Makefile":F) \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+ ;;
+
+ esac
+done # for ac_tag
+
+
+as_fn_exit 0
+_ACEOF
+ac_clean_files=$ac_clean_files_save
+
+test $ac_write_fail = 0 ||
+ as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5
+
+
+# configure is writing to config.log, and then calls config.status.
+# config.status does its own redirection, appending to config.log.
+# Unfortunately, on DOS this fails, as config.log is still kept open
+# by configure, so config.status won't be able to write to it; its
+# output is simply discarded. So we exec the FD to /dev/null,
+# effectively closing config.log, so it can be properly (re)opened and
+# appended to by config.status. When coming back to configure, we
+# need to make the FD available again.
+if test "$no_create" != yes; then
+ ac_cs_success=:
+ ac_config_status_args=
+ test "$silent" = yes &&
+ ac_config_status_args="$ac_config_status_args --quiet"
+ exec 5>/dev/null
+ $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
+ exec 5>>config.log
+ # Use ||, not &&, to avoid exiting from the if with $? = 1, which
+ # would make configure fail if this is the last instruction.
+ $ac_cs_success || as_fn_exit 1
+fi
+
+#
+# CONFIG_SUBDIRS section.
+#
+if test "$no_recursion" != yes; then
+
+ # Remove --cache-file, --srcdir, and --disable-option-checking arguments
+ # so they do not pile up.
+ ac_sub_configure_args=
+ ac_prev=
+ eval "set x $ac_configure_args"
+ shift
+ for ac_arg
+ do
+ if test -n "$ac_prev"; then
+ ac_prev=
+ continue
+ fi
+ case $ac_arg in
+ -cache-file | --cache-file | --cache-fil | --cache-fi \
+ | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)
+ ac_prev=cache_file ;;
+ -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \
+ | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* \
+ | --c=*)
+ ;;
+ --config-cache | -C)
+ ;;
+ -srcdir | --srcdir | --srcdi | --srcd | --src | --sr)
+ ac_prev=srcdir ;;
+ -srcdir=* | --srcdir=* | --srcdi=* | --srcd=* | --src=* | --sr=*)
+ ;;
+ -prefix | --prefix | --prefi | --pref | --pre | --pr | --p)
+ ac_prev=prefix ;;
+ -prefix=* | --prefix=* | --prefi=* | --pref=* | --pre=* | --pr=* | --p=*)
+ ;;
+ --disable-option-checking)
+ ;;
+ *)
+ case $ac_arg in
+ *\'*) ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ as_fn_append ac_sub_configure_args " '$ac_arg'" ;;
+ esac
+ done
+
+ # Always prepend --prefix to ensure using the same prefix
+ # in subdir configurations.
+ ac_arg="--prefix=$prefix"
+ case $ac_arg in
+ *\'*) ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ ac_sub_configure_args="'$ac_arg' $ac_sub_configure_args"
+
+ # Pass --silent
+ if test "$silent" = yes; then
+ ac_sub_configure_args="--silent $ac_sub_configure_args"
+ fi
+
+ # Always prepend --disable-option-checking to silence warnings, since
+ # different subdirs can have different --enable and --with options.
+ ac_sub_configure_args="--disable-option-checking $ac_sub_configure_args"
+
+ ac_popdir=`pwd`
+ for ac_dir in : $subdirs; do test "x$ac_dir" = x: && continue
+
+ # Do not complain, so a configure script can configure whichever
+ # parts of a large source tree are present.
+ test -d "$srcdir/$ac_dir" || continue
+
+ ac_msg="=== configuring in $ac_dir (`pwd`/$ac_dir)"
+ $as_echo "$as_me:${as_lineno-$LINENO}: $ac_msg" >&5
+ $as_echo "$ac_msg" >&6
+ as_dir="$ac_dir"; as_fn_mkdir_p
+ ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+ ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
+ # A ".." for each directory in $ac_dir_suffix.
+ ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
+ case $ac_top_builddir_sub in
+ "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+ *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+ esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+ .) # We are building in place.
+ ac_srcdir=.
+ ac_top_srcdir=$ac_top_builddir_sub
+ ac_abs_top_srcdir=$ac_pwd ;;
+ [\\/]* | ?:[\\/]* ) # Absolute name.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir
+ ac_abs_top_srcdir=$srcdir ;;
+ *) # Relative name.
+ ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_build_prefix$srcdir
+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+
+ cd "$ac_dir"
+
+ # Check for guested configure; otherwise get Cygnus style configure.
+ if test -f "$ac_srcdir/configure.gnu"; then
+ ac_sub_configure=$ac_srcdir/configure.gnu
+ elif test -f "$ac_srcdir/configure"; then
+ ac_sub_configure=$ac_srcdir/configure
+ elif test -f "$ac_srcdir/configure.in"; then
+ # This should be Cygnus configure.
+ ac_sub_configure=$ac_aux_dir/configure
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: no configuration information is in $ac_dir" >&5
+$as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2;}
+ ac_sub_configure=
+ fi
+
+ # The recursion is here.
+ if test -n "$ac_sub_configure"; then
+ # Make the cache file name correct relative to the subdirectory.
+ case $cache_file in
+ [\\/]* | ?:[\\/]* ) ac_sub_cache_file=$cache_file ;;
+ *) # Relative name.
+ ac_sub_cache_file=$ac_top_build_prefix$cache_file ;;
+ esac
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: running $SHELL $ac_sub_configure $ac_sub_configure_args --cache-file=$ac_sub_cache_file --srcdir=$ac_srcdir" >&5
+$as_echo "$as_me: running $SHELL $ac_sub_configure $ac_sub_configure_args --cache-file=$ac_sub_cache_file --srcdir=$ac_srcdir" >&6;}
+ # The eval makes quoting arguments work.
+ eval "\$SHELL \"\$ac_sub_configure\" $ac_sub_configure_args \
+ --cache-file=\"\$ac_sub_cache_file\" --srcdir=\"\$ac_srcdir\"" ||
+ as_fn_error $? "$ac_sub_configure failed for $ac_dir" "$LINENO" 5
+ fi
+
+ cd "$ac_popdir"
+ done
+fi
+if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
+$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
+fi
+
diff --git a/configure.ac b/configure.ac
new file mode 100644
index 0000000..24e5099
--- /dev/null
+++ b/configure.ac
@@ -0,0 +1,426 @@
+dnl Process this file with autoconf to produce a configure script.
+
+dnl Copyright © 2010-2013 -- IRB/INSERM
+dnl (Institut de Recherches en Biothérapie /
+dnl Institut National de la Santé et de la Recherche
+dnl Médicale)
+dnl LIFL/INRIA
+dnl (Laboratoire d'Informatique Fondamentale de
+dnl Lille / Institut National de Recherche en
+dnl Informatique et Automatique)
+dnl LIRMM/CNRS
+dnl (Laboratoire d'Informatique, de Robotique et de
+dnl Microélectronique de Montpellier /
+dnl Centre National de la Recherche Scientifique)
+dnl LITIS
+dnl (Laboratoire d'Informatique, du Traitement de
+dnl l'Information et des Systèmes).
+dnl
+dnl Auteurs/Authors:
+dnl Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+dnl Mikaël SALSON <mikael.salson at lifl.fr>
+dnl Thérèse COMMES <commes at univ-montp2.fr>
+dnl Éric RIVALS <eric.rivals at lirmm.fr>
+dnl
+dnl Programmeurs
+dnl /Progammers:
+dnl Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+dnl Mikaël SALSON <mikael.salson at lifl.fr>
+dnl with additional contribution for the packaging of:
+dnl Alban MANCHERON <alban.mancheron at lirmm.fr>
+dnl
+dnl Contact: CRAC list <crac-bugs at lists.gforge.inria.fr>
+dnl -------------------------------------------------------------------------
+dnl
+dnl Ce fichier fait partie du programme CRAC.
+dnl
+dnl Ce logiciel est régi par la licence CeCILL soumise au droit français et
+dnl respectant les principes de diffusion des logiciels libres. Vous pouvez
+dnl utiliser, modifier et/ou redistribuer ce programme sous les conditions de
+dnl la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur
+dnl le site "http://www.cecill.info".
+dnl
+dnl En contrepartie de l'accessibilité au code source et des droits de copie,
+dnl de modification et de redistribution accordés par cette licence, il n'est
+dnl offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons,
+dnl seule une responsabilité restreinte pèse sur l'auteur du programme, le
+dnl titulaire des droits patrimoniaux et les concédants successifs.
+dnl
+dnl À cet égard l'attention de l'utilisateur est attirée sur les risques
+dnl associés au chargement, à l'utilisation, à la modification et/ou au
+dnl développement et à la reproduction du logiciel par l'utilisateur étant
+dnl donné sa spécificité de logiciel libre, qui peut le rendre complexe à
+dnl manipuler et qui le réserve donc à des développeurs et des professionnels
+dnl avertis possédant des connaissances informatiques approfondies. Les
+dnl utilisateurs sont donc invités à charger et tester l'adéquation du
+dnl logiciel à leurs besoins dans des conditions permettant d'assurer la
+dnl sécurité de leurs systêmes et ou de leurs données et, plus généralement,
+dnl à l'utiliser et l'exploiter dans les mêmes conditions de sécurité.
+dnl
+dnl Le fait que vous puissiez accéder à cet en-tête signifie que vous avez
+dnl pris connaissance de la licence CeCILL, et que vous en avez accepté les
+dnl termes.
+dnl
+dnl -------------------------------------------------------------------------
+dnl
+dnl This File is part of the CRAC program.
+dnl
+dnl This software is governed by the CeCILL license under French law and
+dnl abiding by the rules of distribution of free software. You can use,
+dnl modify and/ or redistribute the software under the terms of the CeCILL
+dnl license as circulated by CEA, CNRS and INRIA at the following URL
+dnl "http://www.cecill.info".
+dnl
+dnl As a counterpart to the access to the source code and rights to copy,
+dnl modify and redistribute granted by the license, users are provided only
+dnl with a limited warranty and the software's author, the holder of the
+dnl economic rights, and the successive licensors have only limited
+dnl liability.
+dnl
+dnl In this respect, the user's attention is drawn to the risks associated
+dnl with loading, using, modifying and/or developing or reproducing the
+dnl software by the user in light of its specific status of free software,
+dnl that may mean that it is complicated to manipulate, and that also
+dnl therefore means that it is reserved for developers and experienced
+dnl professionals having in-depth computer knowledge. Users are therefore
+dnl encouraged to load and test the software's suitability as regards their
+dnl requirements in conditions enabling the security of their systems and/or
+dnl data to be ensured and, more generally, to use and operate it in the same
+dnl conditions as regards security.
+dnl
+dnl The fact that you are presently reading this means that you have had
+dnl knowledge of the CeCILL license and that you accept its terms.
+
+dnl $Id$
+
+dnl Process this file with autoconf to produce a configure script.
+
+AC_PREREQ([2.64])
+m4_define([V_MAJOR], [1])
+m4_define([V_MINOR], [5])
+m4_define([V_MICRO], [0])
+
+AC_INIT(
+ [crac],
+ [V_MAJOR.V_MINOR.V_MICRO],
+ [crac-bugs at lists.gforge.inria.fr],
+ [crac],
+ [http://crac.gforge.inria.fr/])
+
+PACKAGE_DESCRIPTION="Crac is a tool to analyse RNA-Seq data provided by NGS"
+AC_SUBST([PACKAGE_DESCRIPTION])
+
+AC_CONFIG_SRCDIR([src/crac.cpp])
+AC_REVISION([$Revision$])
+AC_COPYRIGHT([
+*******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+*******************************************************************************
+])
+
+AS_IF([test x"$CFLAGS" == "x"], [CFLAGS=""])
+AS_IF([test x"$CPPFLAGS" == "x"], [CPPFLAGS=""])
+AS_IF([test x"$CXXFLAGS" == "x"], [CXXFLAGS=""])
+AS_IF([test x"$LDFLAGS" == "x"], [LDFLAGS=""])
+
+AC_CONFIG_AUX_DIR([config])
+
+dnl create a config.h file (Automake will add -DHAVE_CONFIG_H)
+AC_CONFIG_HEADERS([config/config.h])
+
+dnl Every other copy of the package version number gets its value from here
+AM_INIT_AUTOMAKE()
+
+AC_CANONICAL_HOST
+AC_LANG([C++])
+
+AC_CONFIG_MACRO_DIR([config/m4])
+
+dnl Checks for programs.
+AC_PROG_AWK
+AC_PROG_INSTALL
+AC_PROG_CC
+AC_PROG_CXX
+AC_PROG_CPP
+AC_PROG_MAKE_SET
+AC_PROG_LN_S
+
+AC_CHECK_PROG([TEXI2DVI], [texi2dvi], [texi2dvi])
+AC_CHECK_PROG([PDFTEX], [pdftex], [pdftex])
+AC_CHECK_PROG([KPSEWHICH], [kpsewhich], [kpsewhich])
+BUILD_DOC=false
+AS_IF([test "x$TEXI2DVI" != "xtexi2dvi" || test "x$PDFTEX" != "xpdftex"],
+ [BUILD_DOC=false
+ AC_MSG_WARN([The 'texi2dvi' or 'pdftex' program could not be found. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases.])])
+
+AS_IF([test "x$KPSEWHICH" != "xkpsewhich" || test "$(kpsewhich -show-path=fmt)" == "/nonesuch"],
+ [BUILD_DOC=false
+ AC_MSG_WARN([The 'texi2dvi' or 'pdftex' is missing a correct latex installation. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases.])])
+AM_CONDITIONAL([BUILD_DOC], [$BUILD_DOC])
+
+AC_SUBST([VERSION])
+
+dnl Disable shared library construction by default (must appear before LT_INIT)
+AC_DISABLE_SHARED
+
+LT_INIT
+LT_PATH_LD
+
+ISODATE=`date +%Y-%m-%d`
+AC_SUBST([ISODATE])
+
+ARCH=`uname -m | sed s/i.86/i386/ | sed s/x86_64/amd64/`
+AC_SUBST([ARCH])
+
+AC_PATH_PROG([DEB_BUILDER], [dpkg])
+AC_PATH_PROG([RPM_BUILDER], [rpmbuild])
+
+# Checks for libraries.
+AC_CHECK_LIB([m], [sqrt])
+AC_CHECK_LIB([pthread], [pthread_join])
+
+# Checks for header files.
+AC_FUNC_ALLOCA
+AC_HEADER_MAJOR
+AC_CHECK_HEADERS([\
+ fcntl.h inttypes.h libintl.h limits.h locale.h \
+ memory.h stdint.h stdlib.h string.h strings.h \
+ sys/file.h sys/param.h sys/time.h unistd.h utime.h \
+])
+
+# Checks for typedefs, structures, and compiler characteristics.
+AC_HEADER_STDBOOL
+AC_C_INLINE
+AC_TYPE_INT64_T
+AC_TYPE_OFF_T
+AC_TYPE_SIZE_T
+AC_CHECK_MEMBERS([struct stat.st_blksize])
+AC_TYPE_UINT32_T
+AC_TYPE_UINT8_T
+AC_CHECK_TYPES([ptrdiff_t])
+
+# Checks for library functions.
+AC_FUNC_MALLOC
+AC_FUNC_REALLOC
+AC_CHECK_FUNCS([\
+ floor gettimeofday memchr memmove memset \
+ mkfifo pow select sqrt strrchr strstr strtol \
+])
+
+
+CPPFLAGS="$CPPFLAGS -Wall -ansi -funroll-loops"
+
+dnl Add option --enable-debug (default to --disable-debug)
+AC_ARG_ENABLE([debug],
+ [AS_HELP_STRING([--enable-debug],
+ [enable debugging informations])],
+ [CPPFLAGS="$CPPFLAGS -g -O0"],
+ [CPPFLAGS="$CPPFLAGS -O4 -DNDEBUG"])
+
+dnl Add option --without-included-GkArrays (default --with-included-GkArrays=check)
+AC_ARG_WITH([included-GkArrays],
+ [AS_HELP_STRING([--without-included-GkArrays],
+ [don't use the GkArrays library included here])],
+ [],
+ [with_included_GkArrays="check"])
+
+dnl Add option --with-libGkArrays-prefix=PATH (default --without-libGkArrays-prefix)
+AC_ARG_WITH([libGkArrays-prefix],
+ [AS_HELP_STRING([--with-libGkArrays-prefix=DIR],
+ [search for libGkArrays in DIR/include/libGkArrays and DIR/lib])],
+ [LDFLAGS="$LDFLAGS -L$with_libGkArrays_prefix/lib"
+ CPPFLAGS="$CPPFLAGS -I$with_libGkArrays_prefix/include/libGkArrays"],
+ [with_libGkArrays_prefix=""])
+
+dnl Check if we need included GkArrays library.
+AS_IF([test "x$with_included_GkArrays" == "xcheck"],
+ [AS_IF([test "x$with_libGkArrays_prefix" != "x"],
+ [with_included_GkArrays="no"],
+ [with_included_GkArrays="yes"])])
+
+AS_IF([test "x$with_included_GkArrays" == "xyes"],
+ [AS_IF([test "x$with_libGkArrays_prefix" != "x"],
+ [AC_MSG_FAILURE([You can't use both --with-included-GkArrays and --with-libGkArrays-prefix options])])])
+
+dnl Add option --without-included-ProgressBar (default --with-included-ProgressBar=check)
+AC_ARG_WITH([included-ProgressBar],
+ [AS_HELP_STRING([--without-included-ProgressBar],
+ [don't use the ProgressBar library included here])],
+ [],
+ [with_included_ProgressBar="check"])
+
+dnl Add option --with-libProgressBar-prefix=PATH (default --without-libProgressBar-prefix)
+AC_ARG_WITH([libProgressBar-prefix],
+ [AS_HELP_STRING([--with-libProgressBar-prefix=DIR],
+ [search for libProgressBar in DIR/include/libProgressBar and DIR/lib])],
+ [LDFLAGS="$LDFLAGS -L$with_libProgressBar_prefix/lib"
+ CPPFLAGS="$CPPFLAGS -I$with_libProgressBar_prefix/include/libProgressBar"],
+ [with_libProgressBar_prefix=""])
+
+dnl Check if we need included ProgressBar library.
+PB_OK=0
+AS_IF([test "x$with_included_ProgressBar" == "xcheck"],
+ [AS_IF([test "x$with_libProgressBar_prefix" != "x"],
+ [with_included_ProgressBar="no"],
+ [with_included_ProgressBar="$with_included_GkArrays"])])
+
+AS_IF([test "x$with_included_ProgressBar" == "xyes"],
+ [AS_IF([test "x$with_libProgressBar_prefix" != "x"],
+ [AC_MSG_FAILURE([You can't use both --with-included-ProgressBar and --with-libProgressBar-prefix options])],
+ [AS_IF([test "x$with_included_GkArrays" != "xyes"],
+ [AC_MSG_FAILURE([You can't use both --with-included-ProgressBar and --without-included-GkArrays options])],
+ [PB_OK=1])
+ ])],
+ [AS_IF([test "x$with_libProgressBar_prefix" != "x"],
+ [PB_OK=1
+ LDFLAGS="$LDFLAGS -L$with_libProgressBar_prefix -L$with_libProgressBar_prefix/lib"
+ CPPFLAGS="$CPPFLAGS -I$with_libProgressBar_prefix -I$with_libProgressBar_prefix/include"],
+ [AC_CHECK_LIB([ProgressBar],
+ [libProgressBarVersion],
+ [PB_OK=1
+ ProgressBar_LIBS=-lProgressBar])])]) dnl Override the default behavior of AC_CHECK_LIB (we don't want -lProgressBar in LIBS).
+
+AS_IF([test "$PB_OK" == "1"], [AC_DEFINE([HAVE_LIBPROGRESSBAR], [1], [Define to 1 in order to Use libProgressBar])])
+
+dnl Set INCLUDED_PROGRESSBAR conditionnal for automake
+AM_CONDITIONAL([INCLUDED_PROGRESSBAR], [test "x$with_included_ProgressBar" == "xyes"])
+
+AC_CHECK_LIB([z], [gzread], ,
+ [AC_MSG_ERROR([zlib not found, see http://www.zlib.net])])
+
+AS_IF([test "x$with_included_GkArrays" != "xyes"],
+ [AC_CHECK_LIB([GkArrays],
+ [libGkArraysVersion],
+ [:],dnl Override the default behavior of AC_CHECK_LIB (we don't want -lGkArrays in LIBS).
+ [AC_MSG_FAILURE([[--without-included-GkArrays was given, but test for libGkArrays failed]])])],
+ [AC_CONFIG_SUBDIRS([src/libGkArrays])])
+
+dnl Set INCLUDED_GKARRAYS conditionnal for automake
+AM_CONDITIONAL([INCLUDED_GKARRAYS], [test "x$with_included_GkArrays" == xyes])
+
+dnl Forward options given to current configure script to libGkArrays configure script if needed
+AS_IF([test "x$enable_shared" == "xyes" ],
+ [AS_VAR_APPEND([ac_configure_args], [" --enable-shared"])],
+ [AS_VAR_APPEND([ac_configure_args], [" --disable-shared"])])
+AS_IF([test "x$enable_static" == "xyes" ],
+ [AS_VAR_APPEND([ac_configure_args], [" --enable-static"])],
+ [AS_VAR_APPEND([ac_configure_args], [" --disable-static"])])
+
+dnl Forward FLAGS to libGkArrays/libProgressBar configure scripts if needed
+AS_VAR_APPEND([ac_configure_args], [" CPPFLAGS=\"$CPPFLAGS\""])
+AS_VAR_APPEND([ac_configure_args], [" CFLAGS=\"$CFLAGS\""])
+AS_VAR_APPEND([ac_configure_args], [" CXXFLAGS=\"$CXXFLAGS\""])
+
+LDFLAGS="$LDFLAGS $ProgressBar_LIBS"
+CPPFLAGS="$CPPFLAGS $ProgressBar_CFLAGS"
+
+AC_CONFIG_FILES([\
+ control crac.spec \
+ Makefile src/Makefile scripts/Makefile \
+ src/libReadsInfo/Makefile src/libSSA/Makefile \
+ src/libgzstream/Makefile \
+ doc/Makefile doc/package.texi \
+ man/Makefile man/crac.1 \
+ scripts/crac-client \
+ test_f/Makefile test_f/bug/Makefile \
+ test_f/causes/Makefile test_f/cigar/Makefile \
+], [ \
+ test -f scripts/crac-client && chmod 755 scripts/crac-client ; \
+])
+
+AC_OUTPUT
diff --git a/control.in b/control.in
new file mode 100644
index 0000000..beb8d37
--- /dev/null
+++ b/control.in
@@ -0,0 +1,18 @@
+Package: @PACKAGE@
+Version: @PACKAGE_VERSION@
+Section: science
+Priority: optional
+Architecture: @ARCH@
+Essential: no
+Depends:
+Recommends:
+Suggests:
+Conflicts:
+Installed-Size: 0
+Maintainer: @PACKAGE_BUGREPORT@
+Provides: @PACKAGE@
+Homepage: @PACKAGE_URL@
+Description: [Biology] @PACKAGE_DESCRIPTION@
+ .
+ You may access further information on CRAC at @PACKAGE_URL@
+ .
diff --git a/crac.lsm.in b/crac.lsm.in
new file mode 100644
index 0000000..ef6380d
--- /dev/null
+++ b/crac.lsm.in
@@ -0,0 +1,21 @@
+Begin3
+Title: crac
+Version: @VERSION@
+Entered-date: @ISODATE@
+Description: Crac is a tool to analyse RNA-Seq data provided by NGS.
+ @configure_input@
+ Please edit crac.lsm.in to fix the Keywords and
+ Primary-site entries, add several more lines of
+ description here if appropriate, and to delete these
+ instructions.
+Keywords: [substitute your keywords here]
+Author: crac-bug at gforge.inria.fr (Nicolas PHILIPPE, Mikael SALSON, Alban MANCHERON)
+Maintained-by: crac-bug at gforge.inria.fr (Nicolas PHILIPPE, Mikael SALSON, Alban MANCHERON)
+Primary-site: metlab.unc.edu pub/Linux/apps/some/directory
+ 31k crac- at VERSION@.tar.gz
+ 500 crac.lsm
+Alternate-site:
+Original-site:
+Platforms:
+Copying-policy: GNU copyleft
+End
diff --git a/crac.spec.in b/crac.spec.in
new file mode 100644
index 0000000..b991785
--- /dev/null
+++ b/crac.spec.in
@@ -0,0 +1,179 @@
+###############################################################################
+# #
+# Copyright © 2010-2012 -- LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique). #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes) #
+# #
+# Auteurs/Authors: CRAC list <crac-bug at gforge.inria.fr> #
+# Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <therese.commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+
+# crac.spec
+#
+# Copyright (c) 2011-2012 Nicolas PHILIPPE, Mikael SALSON, Alban MANCHERON crac-bugs at listsgforge.inria.fr
+#
+%define name @PACKAGE@
+%define version @VERSION@
+%define release 1
+%define manifest %{_builddir}/%{name}-%{version}-%{release}.manifest
+
+# required items
+Name: %{name}
+Version: %{version}
+Release: %{release}
+License: CeCILL
+Group: Application/Misc
+
+# optional items
+#Vendor: Nicolas PHILIPPE, Mikael SALSON, Alban MANCHERON
+#Distribution:
+#Icon:
+#URL:
+#Packager: Nicolas PHILIPPE, Mikael SALSON, Alban MANCHERON crac-bug at gforge.inria.fr
+
+# source + patches
+Source: %{name}-%{version}.tar.gz
+#Source1:
+#Patch:
+#Patch1:
+
+# RPM info
+#Provides:
+#Requires:
+#Conflicts:
+#Prereq:
+
+#Prefix: /usr
+BuildRoot: /var/tmp/%{name}-%{version}
+
+Summary: Crac is a tool to analyse RNA-Seq data provided by NGS.
+
+%description
+We propose a novel way of analyzing reads that integrates
+genomic locations and local coverage, and delivers all above mentioned
+predictions in a single step. Our program, CRAC, uses a double k-mer profiling
+approach to detect candidate mutations, indels, splice or fusion junctions in
+each single read.
+
+%prep
+%setup -q
+#%patch0 -p1
+
+%build
+%configure
+make
+
+%install
+rm -rf $RPM_BUILD_ROOT
+mkdir -p $RPM_BUILD_ROOT
+make DESTDIR=%{buildroot} install
+
+# __os_install_post is implicitly expanded after the
+# %install section... do it now, and then disable it,
+# so all work is done before building manifest.
+
+%{?__os_install_post}
+%define __os_install_post %{nil}
+
+# build the file list automagically into %{manifest}
+
+cd $RPM_BUILD_ROOT
+rm -f %{manifest}
+find . -type d \
+ | sed '1,2d;s,^\.,\%attr(-\,root\,root) \%dir ,' >> %{manifest}
+find . -type f \
+ | sed 's,^\.,\%attr(-\,root\,root) ,' >> %{manifest}
+find . -type l \
+ | sed 's,^\.,\%attr(-\,root\,root) ,' >> %{manifest}
+
+#%pre
+#%post
+#%preun
+#%postun
+
+%clean
+rm -f %{manifest}
+rm -rf $RPM_BUILD_ROOT
+
+%files -f %{manifest}
+%defattr(-,root,root)
+#%doc README
+#%docdir
+#%config
+
+%changelog
diff --git a/doc/CeCILL.texi b/doc/CeCILL.texi
new file mode 100644
index 0000000..6c0bfc3
--- /dev/null
+++ b/doc/CeCILL.texi
@@ -0,0 +1,571 @@
+ at setfilename CeCILL.info
+ at documentencoding UTF-8
+
+ at unnumbered CeCILL FREE SOFTWARE LICENSE AGREEMENT
+
+ at copying
+CeCILL FREE SOFTWARE LICENSE AGREEMENT Version 2.0 dated 2006-09-05.
+
+Copyright @copyright{} 2006,
+
+ at itemize
+ at item
+Commissariat @`a l'@'Energie Atomique - @sc{c@'ea}, a public scientific, technical
+and industrial research establishment, having its principal place of
+business at 25 rue Leblanc, immeuble Le Ponant D, 75015 @sc{Paris}, France.
+
+ at item
+Centre National de la Recherche Scientifique - @sc{cnrs}, a public scientific
+and technological establishment, having its principal place of business
+at 3 rue Michel-Ange, 75794 @sc{Paris} @sc{cedex} 16, France.
+
+ at item
+Institut National de Recherche en Informatique et en Automatique -
+ at sc{inria}, a public scientific and technological establishment, having its
+principal place of business at Domaine de Voluceau, @sc{Rocquencourt},
+ at sc{bp} 105, 78153 @sc{Le Chesnay} @sc{cedex}, France.
+
+ at end itemize
+
+ at quotation
+Everyone is permitted to copy and distribute verbatim copies
+of this license document, but changing it is not allowed.
+ at end quotation
+
+ at end copying
+ at ifnotinfo
+ at insertcopying
+ at end ifnotinfo
+ at unnumberedsec Notice
+
+This Agreement is a Free Software license agreement that is the result
+of discussions between its authors in order to ensure compliance with
+the two main principles guiding its drafting:
+
+ at itemize
+ at item
+firstly, compliance with the principles governing the distribution
+of Free Software: access to source code, broad rights granted to
+users,
+ at item
+secondly, the election of a governing law, French law, with which
+it is conformant, both as regards the law of torts and
+intellectual property law, and the protection that it offers to
+both authors and holders of the economic rights over software.
+ at end itemize
+
+The authors of the @sc{c}@'e at sc{cill} (for C@'e[a] C[nrs] I[nria] L[ogiciel] L[ibre])
+license are:
+
+Commissariat @`a l'@'Energie Atomique - @sc{c@'ea}, a public scientific, technical
+and industrial research establishment, having its principal place of
+business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
+
+Centre National de la Recherche Scientifique - @sc{cnrs}, a public scientific
+and technological establishment, having its principal place of business
+at 3 rue Michel-Ange, 75794 @sc{Paris} @sc{cedex} 16, France.
+
+Institut National de Recherche en Informatique et en Automatique -
+ at sc{inria}, a public scientific and technological establishment, having its
+principal place of business at Domaine de Voluceau, @sc{Rocquencourt},
+ at sc{bp} 105, 78153 @sc{Le Chesnay} @sc{cedex}, France.
+
+ at unnumberedsec Preamble
+
+The purpose of this Free Software license agreement is to grant users
+the right to modify and redistribute the software governed by this
+license within the framework of an open source distribution model.
+
+The exercising of these rights is conditional upon certain obligations
+for users so as to preserve this status for all subsequent redistributions.
+
+In consideration of access to the source code and the rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors only have limited liability.
+
+In this respect, the risks associated with loading, using, modifying
+and/or developing or reproducing the software by the user are brought to
+the user's attention, given its Free Software status, which may make it
+complicated to use, with the result that its use is reserved for
+developers and experienced professionals having in-depth computer
+knowledge. Users are therefore encouraged to load and test the
+suitability of the software as regards their requirements in conditions
+enabling the security of their systems and/or data to be ensured and,
+more generally, to use and operate it in the same conditions of
+security. This Agreement may be freely reproduced and published,
+provided it is not altered, and that no provisions are either added or
+removed herefrom.
+
+This Agreement may apply to any or all software for which the holder of
+the economic rights decides to submit the use thereof to its provisions.
+
+
+ at unnumberedsec Article 1 - DEFINITIONS
+
+For the purpose of this Agreement, when the following expressions
+commence with a capital letter, they shall have the following meaning:
+
+ at strong{Agreement:} means this license agreement, and its possible
+subsequent versions and annexes.
+
+ at strong{Software:} means the software in its Object Code and/or Source Code form
+and, where applicable, its documentation, "as is" when the Licensee
+accepts the Agreement.
+
+ at strong{Initial Software:} means the Software in its Source Code and possibly its
+Object Code form and, where applicable, its documentation, "as is" when
+it is first distributed under the terms and conditions of the Agreement.
+
+ at strong{Modified Software:} means the Software modified by at least one
+Contribution.
+
+ at strong{Source Code:} means all the Software's instructions and program lines to
+which access is required so as to modify the Software.
+
+ at strong{Object Code:} means the binary files originating from the compilation of
+the Source Code.
+
+ at strong{Holder:} means the holder(s) of the economic rights over the Initial
+Software.
+
+ at strong{Licensee:} means the Software user(s) having accepted the Agreement.
+
+ at strong{Contributor:} means a Licensee having made at least one Contribution.
+
+ at strong{Licensor:} means the Holder, or any other individual or legal entity, who
+distributes the Software under the Agreement.
+
+ at strong{Contribution:} means any or all modifications, corrections, translations,
+adaptations and/or new functions integrated into the Software by any or
+all Contributors, as well as any or all Internal Modules.
+
+ at strong{Module:} means a set of sources files including their documentation that
+enables supplementary functions or services in addition to those offered
+by the Software.
+
+ at strong{External Module:} means any or all Modules, not derived from the
+Software, so that this Module and the Software run in separate address
+spaces, with one calling the other when they are run.
+
+ at strong{Internal Module:} means any or all Module, connected to the Software so
+that they both execute in the same address space.
+
+ at strong{GNU GPL:} means the @sc{gnu} General Public License version 2 or any
+subsequent version, as published by the Free Software Foundation Inc.
+
+ at strong{Parties:} mean both the Licensee and the Licensor.
+
+These expressions may be used both in singular and plural form.
+
+
+ at unnumberedsec Article 2 - PURPOSE
+
+The purpose of the Agreement is the grant by the Licensor to the
+Licensee of a non-exclusive, transferable and worldwide license for the
+Software as set forth in Article 5 hereinafter for the whole term of the
+protection granted by the rights over said Software.
+
+
+ at unnumberedsec Article 3 - ACCEPTANCE
+
+ at subheading 3.1
+The Licensee shall be deemed as having accepted the terms and
+conditions of this Agreement upon the occurrence of the first of the
+following events:
+
+ at itemize @w{}
+ at item (i)
+loading the Software by any or all means, notably, by
+downloading from a remote server, or by loading from a physical
+medium;
+
+ at item (ii)
+the first time the Licensee exercises any of the rights
+granted hereunder.
+ at end itemize
+
+ at subheading 3.2
+One copy of the Agreement, containing a notice relating to the
+characteristics of the Software, to the limited warranty, and to the
+fact that its use is restricted to experienced users has been provided
+to the Licensee prior to its acceptance as set forth in Article 3.1
+hereinabove, and the Licensee hereby acknowledges that it has read and
+understood it.
+
+ at unnumberedsec Article 4 - EFFECTIVE DATE AND TERM
+
+ at subheading 4.1 EFFECTIVE DATE
+
+The Agreement shall become effective on the date when it is accepted by
+the Licensee as set forth in Article 3.1.
+
+
+ at subheading 4.2 TERM
+
+The Agreement shall remain in force for the entire legal term of
+protection of the economic rights over the Software.
+
+
+ at unnumberedsec Article 5 - SCOPE OF RIGHTS GRANTED
+
+The Licensor hereby grants to the Licensee, who accepts, the following
+rights over the Software for any or all use, and for the term of the
+Agreement, on the basis of the terms and conditions set forth hereinafter.
+
+Besides, if the Licensor owns or comes to own one or more patents
+protecting all or part of the functions of the Software or of its
+components, the Licensor undertakes not to enforce the rights granted by
+these patents against successive Licensees using, exploiting or
+modifying the Software. If these patents are transferred, the Licensor
+undertakes to have the transferees subscribe to the obligations set
+forth in this paragraph.
+
+
+ at subheading 5.1 RIGHT OF USE
+
+The Licensee is authorized to use the Software, without any limitation
+as to its fields of application, with it being hereinafter specified
+that this comprises:
+
+ at subsubheading 5.1.1
+permanent or temporary reproduction of all or part of the Software
+by any or all means and in any or all form.
+
+ at subsubheading 5.1.2
+loading, displaying, running, or storing the Software on any or
+all medium.
+
+ at subsubheading 5.1.3
+entitlement to observe, study or test its operation so as to
+determine the ideas and principles behind any or all constituent
+elements of said Software. This shall apply when the Licensee
+carries out any or all loading, displaying, running, transmission
+or storage operation as regards the Software, that it is entitled
+to carry out hereunder.
+
+ at subheading 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
+
+The right to make Contributions includes the right to translate, adapt,
+arrange, or make any or all modifications to the Software, and the right
+to reproduce the resulting software.
+
+The Licensee is authorized to make any or all Contributions to the
+Software provided that it includes an explicit notice that it is the
+author of said Contribution and indicates the date of the creation thereof.
+
+
+ at subheading 5.3 RIGHT OF DISTRIBUTION
+
+In particular, the right of distribution includes the right to publish,
+transmit and communicate the Software to the general public on any or
+all medium, and by any or all means, and the right to market, either in
+consideration of a fee, or free of charge, one or more copies of the
+Software by any means.
+
+The Licensee is further authorized to distribute copies of the modified
+or unmodified Software to third parties according to the terms and
+conditions set forth hereinafter.
+
+
+ at subheading 5.4 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+
+The Licensee is authorized to distribute true copies of the Software in
+Source Code or Object Code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ at enumerate
+ at item
+a copy of the Agreement,
+
+ at item
+a notice relating to the limitation of both the Licensor's
+warranty and liability as set forth in Articles 8 and 9,
+ at end enumerate
+
+and that, in the event that only the Object Code of the Software is
+redistributed, the Licensee allows future Licensees unhindered access to
+the full Source Code of the Software by indicating how to access it, it
+being understood that the additional cost of acquiring the Source Code
+shall not exceed the cost of transferring the data.
+
+
+ at subheading 5.5 DISTRIBUTION OF MODIFIED SOFTWARE
+
+When the Licensee makes a Contribution to the Software, the terms and
+conditions for the distribution of the resulting Modified Software
+become subject to all the provisions of this Agreement.
+
+The Licensee is authorized to distribute the Modified Software, in
+source code or object code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied
+by:
+
+ at enumerate
+ at item
+a copy of the Agreement,
+
+ at item
+a notice relating to the limitation of both the Licensor's
+warranty and liability as set forth in Articles 8 and 9,
+ at end enumerate
+
+and that, in the event that only the object code of the Modified
+Software is redistributed, the Licensee allows future Licensees
+unhindered access to the full source code of the Modified Software by
+indicating how to access it, it being understood that the additional
+cost of acquiring the source code shall not exceed the cost of
+transferring the data.
+
+
+ at subheading 5.6 DISTRIBUTION OF EXTERNAL MODULES
+
+When the Licensee has developed an External Module, the terms and
+conditions of this Agreement do not apply to said External Module, that
+may be distributed under a separate license agreement.
+
+ at subheading 5.7 COMPATIBILITY WITH THE GNU GPL
+
+The Licensee can include a code that is subject to the provisions of one
+of the versions of the @sc{gnu gpl} in the Modified or unmodified Software,
+and distribute that entire code under the terms of the same version of
+the @sc{gnu gpl}.
+
+The Licensee can include the Modified or unmodified Software in a code
+that is subject to the provisions of one of the versions of the @sc{gnu gpl},
+and distribute that entire code under the terms of the same version of
+the @sc{gnu gpl}.
+
+
+ at unnumberedsec Article 6 - INTELLECTUAL PROPERTY
+
+
+ at subheading 6.1 OVER THE INITIAL SOFTWARE
+
+The Holder owns the economic rights over the Initial Software. Any or
+all use of the Initial Software is subject to compliance with the terms
+and conditions under which the Holder has elected to distribute its work
+and no one shall be entitled to modify the terms and conditions for the
+distribution of said Initial Software.
+
+The Holder undertakes that the Initial Software will remain ruled at
+least by this Agreement, for the duration set forth in Article 4.2.
+
+
+ at subheading 6.2 OVER THE CONTRIBUTIONS
+
+The Licensee who develops a Contribution is the owner of the
+intellectual property rights over this Contribution as defined by
+applicable law.
+
+
+ at subheading 6.3 OVER THE EXTERNAL MODULES
+
+The Licensee who develops an External Module is the owner of the
+intellectual property rights over this External Module as defined by
+applicable law and is free to choose the type of agreement that shall
+govern its distribution.
+
+
+ at subheading 6.4 JOINT PROVISIONS
+
+The Licensee expressly undertakes:
+
+ at enumerate
+ at item
+not to remove, or modify, in any manner, the intellectual property
+notices attached to the Software;
+
+ at item
+to reproduce said notices, in an identical manner, in the copies
+of the Software modified or not.
+ at end enumerate
+
+The Licensee undertakes not to directly or indirectly infringe the
+intellectual property rights of the Holder and/or Contributors on the
+Software and to take, where applicable, vis--b@`a-vis its staff, any and all-A
+measures required to ensure respect of said intellectual property rights
+of the Holder and/or Contributors.
+
+
+ at unnumberedsec Article 7 - RELATED SERVICES
+
+ at subheading 7.1
+Under no circumstances shall the Agreement oblige the Licensor to
+provide technical assistance or maintenance services for the Software.
+
+However, the Licensor is entitled to offer this type of services. The
+terms and conditions of such technical assistance, and/or such
+maintenance, shall be set forth in a separate instrument. Only the
+Licensor offering said maintenance and/or technical assistance services
+shall incur liability therefor.
+
+ at subheading 7.2
+Similarly, any Licensor is entitled to offer to its licensees, under
+its sole responsibility, a warranty, that shall only be binding upon
+itself, for the redistribution of the Software and/or the Modified
+Software, under terms and conditions that it is free to decide. Said
+warranty, and the financial terms and conditions of its application,
+shall be subject of a separate instrument executed between the Licensor
+and the Licensee.
+
+ at unnumberedsec Article 8 - LIABILITY
+
+ at subheading 8.1
+Subject to the provisions of Article 8.2, the Licensee shall be
+entitled to claim compensation for any direct loss it may have suffered
+from the Software as a result of a fault on the part of the relevant
+Licensor, subject to providing evidence thereof.
+
+ at subheading 8.2
+The Licensor's liability is limited to the commitments made under
+this Agreement and shall not be incurred as a result of in particular:
+(i) loss due the Licensee's total or partial failure to fulfill its
+obligations, (ii) direct or consequential loss that is suffered by the
+Licensee due to the use or performance of the Software, and (iii) more
+generally, any consequential loss. In particular the Parties expressly
+agree that any or all pecuniary or business loss (i.e. loss of data,
+loss of profits, operating loss, loss of customers or orders,
+opportunity cost, any disturbance to business activities) or any or all
+legal proceedings instituted against the Licensee by a third party,
+shall constitute consequential loss and shall not provide entitlement to
+any or all compensation from the Licensor.
+
+ at unnumberedsec Article 9 - WARRANTY
+
+ at subheading 9.1
+The Licensee acknowledges that the scientific and technical
+state-of-the-art when the Software was distributed did not enable all
+possible uses to be tested and verified, nor for the presence of
+possible defects to be detected. In this respect, the Licensee's
+attention has been drawn to the risks associated with loading, using,
+modifying and/or developing and reproducing the Software which are
+reserved for experienced users.
+
+The Licensee shall be responsible for verifying, by any or all means,
+the suitability of the product for its requirements, its good working
+order, and for ensuring that it shall not cause damage to either persons
+or properties.
+
+ at subheading 9.2
+The Licensor hereby represents, in good faith, that it is entitled
+to grant all the rights over the Software (including in particular the
+rights set forth in Article 5).
+
+ at subheading 9.3
+The Licensee acknowledges that the Software is supplied "as is" by
+the Licensor without any other express or tacit warranty, other than
+that provided for in Article 9.2 and, in particular, without any warranty
+as to its commercial value, its secured, safe, innovative or relevant
+nature.
+
+Specifically, the Licensor does not warrant that the Software is free
+from any error, that it will operate without interruption, that it will
+be compatible with the Licensee's own equipment and software
+configuration, nor that it will meet the Licensee's requirements.
+
+ at subheading 9.4
+The Licensor does not either expressly or tacitly warrant that the
+Software does not infringe any third party intellectual property right
+relating to a patent, software or any other property right. Therefore,
+the Licensor disclaims any and all liability towards the Licensee
+arising out of any or all proceedings for infringement that may be
+instituted in respect of the use, modification and redistribution of the
+Software. Nevertheless, should such proceedings be instituted against
+the Licensee, the Licensor shall provide it with technical and legal
+assistance for its defense. Such technical and legal assistance shall be
+decided on a case-by-case basis between the relevant Licensor and the
+Licensee pursuant to a memorandum of understanding. The Licensor
+disclaims any and all liability as regards the Licensee's use of the
+name of the Software. No warranty is given as regards the existence of
+prior rights over the name of the Software or as regards the existence
+of a trademark.
+
+ at unnumberedsec Article 10 - TERMINATION
+
+ at subheading 10.1
+In the event of a breach by the Licensee of its obligations
+hereunder, the Licensor may automatically terminate this Agreement
+thirty (30) days after notice has been sent to the Licensee and has
+remained ineffective.
+
+ at subheading 10.2
+A Licensee whose Agreement is terminated shall no longer be
+authorized to use, modify or distribute the Software. However, any
+licenses that it may have granted prior to termination of the Agreement
+shall remain valid subject to their having been granted in compliance
+with the terms and conditions hereof.
+
+ at unnumberedsec Article 11 - MISCELLANEOUS
+
+
+ at subheading 11.1 EXCUSABLE EVENTS
+
+Neither Party shall be liable for any or all delay, or failure to
+perform the Agreement, that may be attributable to an event of force
+majeure, an act of God or an outside cause, such as defective
+functioning or interruptions of the electricity or telecommunications
+networks, network paralysis following a virus attack, intervention by
+government authorities, natural disasters, water damage, earthquakes,
+fire, explosions, strikes and labor unrest, war, etc.
+
+ at subheading 11.2
+Any failure by either Party, on one or more occasions, to invoke
+one or more of the provisions hereof, shall under no circumstances be
+interpreted as being a waiver by the interested Party of its right to
+invoke said provision(s) subsequently.
+
+ at subheading 11.3
+The Agreement cancels and replaces any or all previous agreements,
+whether written or oral, between the Parties and having the same
+purpose, and constitutes the entirety of the agreement between said
+Parties concerning said purpose. No supplement or modification to the
+terms and conditions hereof shall be effective as between the Parties
+unless it is made in writing and signed by their duly authorized
+representatives.
+
+ at subheading 11.4
+In the event that one or more of the provisions hereof were to
+conflict with a current or future applicable act or legislative text,
+said act or legislative text shall prevail, and the Parties shall make
+the necessary amendments so as to comply with said act or legislative
+text. All other provisions shall remain effective. Similarly, invalidity
+of a provision of the Agreement, for any reason whatsoever, shall not
+cause the Agreement as a whole to be invalid.
+
+ at subheading 11.5 LANGUAGE
+
+The Agreement is drafted in both French and English and both versions
+are deemed authentic.
+
+
+ at unnumberedsec Article 12 - NEW VERSIONS OF THE AGREEMENT
+
+ at subheading 12.1
+Any person is authorized to duplicate and distribute copies of this
+Agreement.
+
+ at subheading 12.2
+So as to ensure coherence, the wording of this Agreement is
+protected and may only be modified by the authors of the License, who
+reserve the right to periodically publish updates or new versions of the
+Agreement, each with a separate number. These subsequent versions may
+address new issues encountered by Free Software.
+
+ at subheading 12.3
+Any Software distributed under a given version of the Agreement may
+only be subsequently distributed under the same version of the Agreement
+or a subsequent version, subject to the provisions of Article 5.3.4.
+
+ at unnumberedsec Article 13 - GOVERNING LAW AND JURISDICTION
+
+ at subheading 13.1
+The Agreement is governed by French law. The Parties agree to
+endeavor to seek an amicable solution to any disagreements or disputes
+that may arise during the performance of the Agreement.
+
+ at subheading 13.2
+Failing an amicable solution within two (2) months as from their
+occurrence, and unless emergency proceedings are necessary, the
+disagreements or disputes shall be referred to the Paris Courts having
+jurisdiction, by the more diligent Party.
diff --git a/doc/Makefile.am b/doc/Makefile.am
new file mode 100644
index 0000000..c77b832
--- /dev/null
+++ b/doc/Makefile.am
@@ -0,0 +1,131 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+
+
+# build and install the .info pages
+info_TEXINFOS = crac.texi
+crac_TEXINFOS = CeCILL.texi
+
+# Do not include package.texi in the distributed
+# source since it is generated from template.
+no_dist_crac_TEXINFOS = package.texi
+
+crac.info: crac.texi $(crac_TEXINFOS) $(no_dist_crac_TEXINFOS)
+crac.dvi: crac.texi $(crac_TEXINFOS) $(no_dist_crac_TEXINFOS)
+crac.pdf: crac.texi $(crac_TEXINFOS) $(no_dist_crac_TEXINFOS)
+crac.html: crac.texi $(crac_TEXINFOS) $(no_dist_crac_TEXINFOS)
+
+# Install the man page, but do not include it in
+# the distributed source since it is generated from template.
+#nodist_man_MANS = crac.1
+
+# Extra files to add in distributed sources
+#EXTRA_DIST = crac.1.in package.texi.in
+EXTRA_DIST = package.texi.in
+
+all-local: html pdf
+
+install-data-local: install-html install-pdf
+
+#MOSTLYCLEANFILES=$(no_dist_man_MANS) *~
+MOSTLYCLEANFILES=*~
+CLEANFILES=*~
+DISTCLEANFILES=*~
+MAINTAINERCLEANFILES=*~
diff --git a/doc/Makefile.in b/doc/Makefile.in
new file mode 100644
index 0000000..0087854
--- /dev/null
+++ b/doc/Makefile.in
@@ -0,0 +1,767 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+VPATH = @srcdir@
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+subdir = doc
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+TEXI2PDF = $(TEXI2DVI) --pdf --batch
+MAKEINFOHTML = $(MAKEINFO) --html
+AM_MAKEINFOHTMLFLAGS = $(AM_MAKEINFOFLAGS)
+DVIPS = dvips
+am__installdirs = "$(DESTDIR)$(infodir)"
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
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+
+# Do not include package.texi in the distributed
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+
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+
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+ else :; fi; \
+ done; \
+ done
+
+mostlyclean-aminfo:
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+ distclean-generic distclean-libtool distdir dvi dvi-am html \
+ html-am info info-am install install-am install-data \
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+ uninstall-ps-am
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+crac.dvi: crac.texi $(crac_TEXINFOS) $(no_dist_crac_TEXINFOS)
+crac.pdf: crac.texi $(crac_TEXINFOS) $(no_dist_crac_TEXINFOS)
+crac.html: crac.texi $(crac_TEXINFOS) $(no_dist_crac_TEXINFOS)
+
+all-local: html pdf
+
+install-data-local: install-html install-pdf
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/doc/crac.info b/doc/crac.info
new file mode 100644
index 0000000..83e3367
--- /dev/null
+++ b/doc/crac.info
@@ -0,0 +1,806 @@
+This is crac.info, produced by makeinfo version 4.13 from crac.texi.
+
+This file documents the `crac' command which Crac is a tool to analyse
+RNA-Seq data provided by NGS.
+
+ Copyright (C) 2011-2012 Nicolas PHILIPPE, Mikael SALSON, Alban
+MANCHERON
+
+ Permission is granted to make and distribute verbatim copies of this
+manual provided the copyright notice and this permission notice are
+preserved on all copies.
+
+ Permission is granted to copy and distribute modified versions of
+this manual under the conditions for verbatim copying, provided that
+the entire resulting derived work is distributed under the terms of a
+permission notice identical to this one.
+
+ Permission is granted to copy and distribute translations of this
+manual into another language, under the above conditions for modified
+versions, except that this permission notice may be stated in a
+translation approved by the Foundation.
+
+
+File: crac.info, Node: Top, Next: Instructions, Prev: (dir), Up: (dir)
+
+ This file documents the `crac' command to Crac is a tool to analyse
+RNA-Seq data provided by NGS..
+
+* Menu:
+
+* Instructions:: How to read this manual.
+* Copying:: How you can copy and share `crac'.
+* Overview:: Preliminary information.
+* Sample:: Sample output from `crac'.
+* Invoking crac:: How to run `crac'.
+* Problems:: Reporting bugs.
+* Concept Index:: Index of concepts.
+
+
+File: crac.info, Node: Instructions, Next: Copying, Prev: Top, Up: Top
+
+1 How to Read This Manual
+*************************
+
+To read this manual, begin at the beginning, reading from left to right
+and top to bottom, until you get to the end. Then stop. You may pause
+for a beer anywhere in the middle as well, if you wish. (Please note,
+however, that The King strongly advises against heavy use of
+prescription pharmaceuticals, based on his extensive personal and
+professional experience.)
+
+
+File: crac.info, Node: Copying, Next: Overview, Prev: Instructions, Up: Top
+
+CeCILL FREE SOFTWARE LICENSE AGREEMENT
+**************************************
+
+CeCILL FREE SOFTWARE LICENSE AGREEMENT Version 2.0 dated 2006-09-05.
+
+ Copyright (C) 2006,
+
+ * Commissariat à l'Énergie Atomique - CéA, a public scientific,
+ technical and industrial research establishment, having its
+ principal place of business at 25 rue Leblanc, immeuble Le Ponant
+ D, 75015 PARIS, France.
+
+ * Centre National de la Recherche Scientifique - CNRS, a public
+ scientific and technological establishment, having its principal
+ place of business at 3 rue Michel-Ange, 75794 PARIS CEDEX 16,
+ France.
+
+ * Institut National de Recherche en Informatique et en Automatique -
+ INRIA, a public scientific and technological establishment, having
+ its principal place of business at Domaine de Voluceau,
+ ROCQUENCOURT, BP 105, 78153 LE CHESNAY CEDEX, France.
+
+
+ Everyone is permitted to copy and distribute verbatim copies of
+ this license document, but changing it is not allowed.
+
+Notice
+======
+
+This Agreement is a Free Software license agreement that is the result
+of discussions between its authors in order to ensure compliance with
+the two main principles guiding its drafting:
+
+ * firstly, compliance with the principles governing the distribution
+ of Free Software: access to source code, broad rights granted to
+ users,
+
+ * secondly, the election of a governing law, French law, with which
+ it is conformant, both as regards the law of torts and
+ intellectual property law, and the protection that it offers to
+ both authors and holders of the economic rights over software.
+
+ The authors of the CéCILL (for Cé[a] C[nrs] I[nria] L[ogiciel]
+L[ibre]) license are:
+
+ Commissariat à l'Énergie Atomique - CéA, a public scientific,
+technical and industrial research establishment, having its principal
+place of business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris,
+France.
+
+ Centre National de la Recherche Scientifique - CNRS, a public
+scientific and technological establishment, having its principal place
+of business at 3 rue Michel-Ange, 75794 PARIS CEDEX 16, France.
+
+ Institut National de Recherche en Informatique et en Automatique -
+INRIA, a public scientific and technological establishment, having its
+principal place of business at Domaine de Voluceau, ROCQUENCOURT, BP
+105, 78153 LE CHESNAY CEDEX, France.
+
+Preamble
+========
+
+The purpose of this Free Software license agreement is to grant users
+the right to modify and redistribute the software governed by this
+license within the framework of an open source distribution model.
+
+ The exercising of these rights is conditional upon certain
+obligations for users so as to preserve this status for all subsequent
+redistributions.
+
+ In consideration of access to the source code and the rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors only have limited
+liability.
+
+ In this respect, the risks associated with loading, using, modifying
+and/or developing or reproducing the software by the user are brought to
+the user's attention, given its Free Software status, which may make it
+complicated to use, with the result that its use is reserved for
+developers and experienced professionals having in-depth computer
+knowledge. Users are therefore encouraged to load and test the
+suitability of the software as regards their requirements in conditions
+enabling the security of their systems and/or data to be ensured and,
+more generally, to use and operate it in the same conditions of
+security. This Agreement may be freely reproduced and published,
+provided it is not altered, and that no provisions are either added or
+removed herefrom.
+
+ This Agreement may apply to any or all software for which the holder
+of the economic rights decides to submit the use thereof to its
+provisions.
+
+Article 1 - DEFINITIONS
+=======================
+
+For the purpose of this Agreement, when the following expressions
+commence with a capital letter, they shall have the following meaning:
+
+ *Agreement:* means this license agreement, and its possible
+subsequent versions and annexes.
+
+ *Software:* means the software in its Object Code and/or Source Code
+form and, where applicable, its documentation, "as is" when the Licensee
+accepts the Agreement.
+
+ *Initial Software:* means the Software in its Source Code and
+possibly its Object Code form and, where applicable, its documentation,
+"as is" when it is first distributed under the terms and conditions of
+the Agreement.
+
+ *Modified Software:* means the Software modified by at least one
+Contribution.
+
+ *Source Code:* means all the Software's instructions and program
+lines to which access is required so as to modify the Software.
+
+ *Object Code:* means the binary files originating from the
+compilation of the Source Code.
+
+ *Holder:* means the holder(s) of the economic rights over the Initial
+Software.
+
+ *Licensee:* means the Software user(s) having accepted the Agreement.
+
+ *Contributor:* means a Licensee having made at least one
+Contribution.
+
+ *Licensor:* means the Holder, or any other individual or legal
+entity, who distributes the Software under the Agreement.
+
+ *Contribution:* means any or all modifications, corrections,
+translations, adaptations and/or new functions integrated into the
+Software by any or all Contributors, as well as any or all Internal
+Modules.
+
+ *Module:* means a set of sources files including their documentation
+that enables supplementary functions or services in addition to those
+offered by the Software.
+
+ *External Module:* means any or all Modules, not derived from the
+Software, so that this Module and the Software run in separate address
+spaces, with one calling the other when they are run.
+
+ *Internal Module:* means any or all Module, connected to the
+Software so that they both execute in the same address space.
+
+ *GNU GPL:* means the GNU General Public License version 2 or any
+subsequent version, as published by the Free Software Foundation Inc.
+
+ *Parties:* mean both the Licensee and the Licensor.
+
+ These expressions may be used both in singular and plural form.
+
+Article 2 - PURPOSE
+===================
+
+The purpose of the Agreement is the grant by the Licensor to the
+Licensee of a non-exclusive, transferable and worldwide license for the
+Software as set forth in Article 5 hereinafter for the whole term of the
+protection granted by the rights over said Software.
+
+Article 3 - ACCEPTANCE
+======================
+
+3.1
+---
+
+The Licensee shall be deemed as having accepted the terms and
+conditions of this Agreement upon the occurrence of the first of the
+following events:
+
+ (i) loading the Software by any or all means, notably, by
+ downloading from a remote server, or by loading from a physical
+ medium;
+
+ (ii) the first time the Licensee exercises any of the rights
+ granted hereunder.
+
+3.2
+---
+
+One copy of the Agreement, containing a notice relating to the
+characteristics of the Software, to the limited warranty, and to the
+fact that its use is restricted to experienced users has been provided
+to the Licensee prior to its acceptance as set forth in Article 3.1
+hereinabove, and the Licensee hereby acknowledges that it has read and
+understood it.
+
+Article 4 - EFFECTIVE DATE AND TERM
+===================================
+
+4.1 EFFECTIVE DATE
+------------------
+
+The Agreement shall become effective on the date when it is accepted by
+the Licensee as set forth in Article 3.1.
+
+4.2 TERM
+--------
+
+The Agreement shall remain in force for the entire legal term of
+protection of the economic rights over the Software.
+
+Article 5 - SCOPE OF RIGHTS GRANTED
+===================================
+
+The Licensor hereby grants to the Licensee, who accepts, the following
+rights over the Software for any or all use, and for the term of the
+Agreement, on the basis of the terms and conditions set forth
+hereinafter.
+
+ Besides, if the Licensor owns or comes to own one or more patents
+protecting all or part of the functions of the Software or of its
+components, the Licensor undertakes not to enforce the rights granted by
+these patents against successive Licensees using, exploiting or
+modifying the Software. If these patents are transferred, the Licensor
+undertakes to have the transferees subscribe to the obligations set
+forth in this paragraph.
+
+5.1 RIGHT OF USE
+----------------
+
+The Licensee is authorized to use the Software, without any limitation
+as to its fields of application, with it being hereinafter specified
+that this comprises:
+
+5.1.1
+.....
+
+permanent or temporary reproduction of all or part of the Software by
+any or all means and in any or all form.
+
+5.1.2
+.....
+
+loading, displaying, running, or storing the Software on any or all
+medium.
+
+5.1.3
+.....
+
+entitlement to observe, study or test its operation so as to determine
+the ideas and principles behind any or all constituent elements of said
+Software. This shall apply when the Licensee carries out any or all
+loading, displaying, running, transmission or storage operation as
+regards the Software, that it is entitled to carry out hereunder.
+
+5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
+-------------------------------------
+
+The right to make Contributions includes the right to translate, adapt,
+arrange, or make any or all modifications to the Software, and the right
+to reproduce the resulting software.
+
+ The Licensee is authorized to make any or all Contributions to the
+Software provided that it includes an explicit notice that it is the
+author of said Contribution and indicates the date of the creation
+thereof.
+
+5.3 RIGHT OF DISTRIBUTION
+-------------------------
+
+In particular, the right of distribution includes the right to publish,
+transmit and communicate the Software to the general public on any or
+all medium, and by any or all means, and the right to market, either in
+consideration of a fee, or free of charge, one or more copies of the
+Software by any means.
+
+ The Licensee is further authorized to distribute copies of the
+modified or unmodified Software to third parties according to the terms
+and conditions set forth hereinafter.
+
+5.4 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+-------------------------------------------------
+
+The Licensee is authorized to distribute true copies of the Software in
+Source Code or Object Code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ 1. a copy of the Agreement,
+
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+
+ and that, in the event that only the Object Code of the Software is
+redistributed, the Licensee allows future Licensees unhindered access to
+the full Source Code of the Software by indicating how to access it, it
+being understood that the additional cost of acquiring the Source Code
+shall not exceed the cost of transferring the data.
+
+5.5 DISTRIBUTION OF MODIFIED SOFTWARE
+-------------------------------------
+
+When the Licensee makes a Contribution to the Software, the terms and
+conditions for the distribution of the resulting Modified Software
+become subject to all the provisions of this Agreement.
+
+ The Licensee is authorized to distribute the Modified Software, in
+source code or object code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ 1. a copy of the Agreement,
+
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+
+ and that, in the event that only the object code of the Modified
+Software is redistributed, the Licensee allows future Licensees
+unhindered access to the full source code of the Modified Software by
+indicating how to access it, it being understood that the additional
+cost of acquiring the source code shall not exceed the cost of
+transferring the data.
+
+5.6 DISTRIBUTION OF EXTERNAL MODULES
+------------------------------------
+
+When the Licensee has developed an External Module, the terms and
+conditions of this Agreement do not apply to said External Module, that
+may be distributed under a separate license agreement.
+
+5.7 COMPATIBILITY WITH THE GNU GPL
+----------------------------------
+
+The Licensee can include a code that is subject to the provisions of one
+of the versions of the GNU GPL in the Modified or unmodified Software,
+and distribute that entire code under the terms of the same version of
+the GNU GPL.
+
+ The Licensee can include the Modified or unmodified Software in a
+code that is subject to the provisions of one of the versions of the
+GNU GPL, and distribute that entire code under the terms of the same
+version of the GNU GPL.
+
+Article 6 - INTELLECTUAL PROPERTY
+=================================
+
+6.1 OVER THE INITIAL SOFTWARE
+-----------------------------
+
+The Holder owns the economic rights over the Initial Software. Any or
+all use of the Initial Software is subject to compliance with the terms
+and conditions under which the Holder has elected to distribute its work
+and no one shall be entitled to modify the terms and conditions for the
+distribution of said Initial Software.
+
+ The Holder undertakes that the Initial Software will remain ruled at
+least by this Agreement, for the duration set forth in Article 4.2.
+
+6.2 OVER THE CONTRIBUTIONS
+--------------------------
+
+The Licensee who develops a Contribution is the owner of the
+intellectual property rights over this Contribution as defined by
+applicable law.
+
+6.3 OVER THE EXTERNAL MODULES
+-----------------------------
+
+The Licensee who develops an External Module is the owner of the
+intellectual property rights over this External Module as defined by
+applicable law and is free to choose the type of agreement that shall
+govern its distribution.
+
+6.4 JOINT PROVISIONS
+--------------------
+
+The Licensee expressly undertakes:
+
+ 1. not to remove, or modify, in any manner, the intellectual property
+ notices attached to the Software;
+
+ 2. to reproduce said notices, in an identical manner, in the copies
+ of the Software modified or not.
+
+ The Licensee undertakes not to directly or indirectly infringe the
+intellectual property rights of the Holder and/or Contributors on the
+Software and to take, where applicable, vis--bà-vis its staff, any
+and all-A measures required to ensure respect of said intellectual
+property rights of the Holder and/or Contributors.
+
+Article 7 - RELATED SERVICES
+============================
+
+7.1
+---
+
+Under no circumstances shall the Agreement oblige the Licensor to
+provide technical assistance or maintenance services for the Software.
+
+ However, the Licensor is entitled to offer this type of services. The
+terms and conditions of such technical assistance, and/or such
+maintenance, shall be set forth in a separate instrument. Only the
+Licensor offering said maintenance and/or technical assistance services
+shall incur liability therefor.
+
+7.2
+---
+
+Similarly, any Licensor is entitled to offer to its licensees, under
+its sole responsibility, a warranty, that shall only be binding upon
+itself, for the redistribution of the Software and/or the Modified
+Software, under terms and conditions that it is free to decide. Said
+warranty, and the financial terms and conditions of its application,
+shall be subject of a separate instrument executed between the Licensor
+and the Licensee.
+
+Article 8 - LIABILITY
+=====================
+
+8.1
+---
+
+Subject to the provisions of Article 8.2, the Licensee shall be
+entitled to claim compensation for any direct loss it may have suffered
+from the Software as a result of a fault on the part of the relevant
+Licensor, subject to providing evidence thereof.
+
+8.2
+---
+
+The Licensor's liability is limited to the commitments made under this
+Agreement and shall not be incurred as a result of in particular: (i)
+loss due the Licensee's total or partial failure to fulfill its
+obligations, (ii) direct or consequential loss that is suffered by the
+Licensee due to the use or performance of the Software, and (iii) more
+generally, any consequential loss. In particular the Parties expressly
+agree that any or all pecuniary or business loss (i.e. loss of data,
+loss of profits, operating loss, loss of customers or orders,
+opportunity cost, any disturbance to business activities) or any or all
+legal proceedings instituted against the Licensee by a third party,
+shall constitute consequential loss and shall not provide entitlement to
+any or all compensation from the Licensor.
+
+Article 9 - WARRANTY
+====================
+
+9.1
+---
+
+The Licensee acknowledges that the scientific and technical
+state-of-the-art when the Software was distributed did not enable all
+possible uses to be tested and verified, nor for the presence of
+possible defects to be detected. In this respect, the Licensee's
+attention has been drawn to the risks associated with loading, using,
+modifying and/or developing and reproducing the Software which are
+reserved for experienced users.
+
+ The Licensee shall be responsible for verifying, by any or all means,
+the suitability of the product for its requirements, its good working
+order, and for ensuring that it shall not cause damage to either persons
+or properties.
+
+9.2
+---
+
+The Licensor hereby represents, in good faith, that it is entitled to
+grant all the rights over the Software (including in particular the
+rights set forth in Article 5).
+
+9.3
+---
+
+The Licensee acknowledges that the Software is supplied "as is" by the
+Licensor without any other express or tacit warranty, other than that
+provided for in Article 9.2 and, in particular, without any warranty as
+to its commercial value, its secured, safe, innovative or relevant
+nature.
+
+ Specifically, the Licensor does not warrant that the Software is free
+from any error, that it will operate without interruption, that it will
+be compatible with the Licensee's own equipment and software
+configuration, nor that it will meet the Licensee's requirements.
+
+9.4
+---
+
+The Licensor does not either expressly or tacitly warrant that the
+Software does not infringe any third party intellectual property right
+relating to a patent, software or any other property right. Therefore,
+the Licensor disclaims any and all liability towards the Licensee
+arising out of any or all proceedings for infringement that may be
+instituted in respect of the use, modification and redistribution of the
+Software. Nevertheless, should such proceedings be instituted against
+the Licensee, the Licensor shall provide it with technical and legal
+assistance for its defense. Such technical and legal assistance shall be
+decided on a case-by-case basis between the relevant Licensor and the
+Licensee pursuant to a memorandum of understanding. The Licensor
+disclaims any and all liability as regards the Licensee's use of the
+name of the Software. No warranty is given as regards the existence of
+prior rights over the name of the Software or as regards the existence
+of a trademark.
+
+Article 10 - TERMINATION
+========================
+
+10.1
+----
+
+In the event of a breach by the Licensee of its obligations hereunder,
+the Licensor may automatically terminate this Agreement thirty (30)
+days after notice has been sent to the Licensee and has remained
+ineffective.
+
+10.2
+----
+
+A Licensee whose Agreement is terminated shall no longer be authorized
+to use, modify or distribute the Software. However, any licenses that
+it may have granted prior to termination of the Agreement shall remain
+valid subject to their having been granted in compliance with the terms
+and conditions hereof.
+
+Article 11 - MISCELLANEOUS
+==========================
+
+11.1 EXCUSABLE EVENTS
+---------------------
+
+Neither Party shall be liable for any or all delay, or failure to
+perform the Agreement, that may be attributable to an event of force
+majeure, an act of God or an outside cause, such as defective
+functioning or interruptions of the electricity or telecommunications
+networks, network paralysis following a virus attack, intervention by
+government authorities, natural disasters, water damage, earthquakes,
+fire, explosions, strikes and labor unrest, war, etc.
+
+11.2
+----
+
+Any failure by either Party, on one or more occasions, to invoke one or
+more of the provisions hereof, shall under no circumstances be
+interpreted as being a waiver by the interested Party of its right to
+invoke said provision(s) subsequently.
+
+11.3
+----
+
+The Agreement cancels and replaces any or all previous agreements,
+whether written or oral, between the Parties and having the same
+purpose, and constitutes the entirety of the agreement between said
+Parties concerning said purpose. No supplement or modification to the
+terms and conditions hereof shall be effective as between the Parties
+unless it is made in writing and signed by their duly authorized
+representatives.
+
+11.4
+----
+
+In the event that one or more of the provisions hereof were to conflict
+with a current or future applicable act or legislative text, said act
+or legislative text shall prevail, and the Parties shall make the
+necessary amendments so as to comply with said act or legislative text.
+All other provisions shall remain effective. Similarly, invalidity of a
+provision of the Agreement, for any reason whatsoever, shall not cause
+the Agreement as a whole to be invalid.
+
+11.5 LANGUAGE
+-------------
+
+The Agreement is drafted in both French and English and both versions
+are deemed authentic.
+
+Article 12 - NEW VERSIONS OF THE AGREEMENT
+==========================================
+
+12.1
+----
+
+Any person is authorized to duplicate and distribute copies of this
+Agreement.
+
+12.2
+----
+
+So as to ensure coherence, the wording of this Agreement is protected
+and may only be modified by the authors of the License, who reserve the
+right to periodically publish updates or new versions of the Agreement,
+each with a separate number. These subsequent versions may address new
+issues encountered by Free Software.
+
+12.3
+----
+
+Any Software distributed under a given version of the Agreement may
+only be subsequently distributed under the same version of the Agreement
+or a subsequent version, subject to the provisions of Article 5.3.4.
+
+Article 13 - GOVERNING LAW AND JURISDICTION
+===========================================
+
+13.1
+----
+
+The Agreement is governed by French law. The Parties agree to endeavor
+to seek an amicable solution to any disagreements or disputes that may
+arise during the performance of the Agreement.
+
+13.2
+----
+
+Failing an amicable solution within two (2) months as from their
+occurrence, and unless emergency proceedings are necessary, the
+disagreements or disputes shall be referred to the Paris Courts having
+jurisdiction, by the more diligent Party.
+
+
+File: crac.info, Node: Overview, Next: Sample, Prev: Copying, Up: Top
+
+2 Overview
+**********
+
+The GNU `crac' program produces a familiar, friendly greeting. It
+allows nonprogrammers to use a classic computer science tool which
+would otherwise be unavailable to them. Because it is protected by the
+GNU General Public License, users are free to share and change it.
+
+ GNU `crac' was written by Nicolas PHILIPPE, Mikael SALSON, Alban
+MANCHERON.
+
+
+File: crac.info, Node: Sample, Next: Invoking crac, Prev: Overview, Up: Top
+
+3 Sample Output
+***************
+
+Here are some realistic examples of running `crac'.
+
+ This is the output of the command `crac':
+
+ hello, world!
+
+ This is the output of the command `crac --help':
+
+ Usage: crac [OPTION...] [FILE...]
+ Crac is a tool to analyse RNA-Seq data provided by NGS.
+
+ --brief Shorten output
+ -i, --interactive Prompt for confirmation
+ -o, --output=FILE Send output to FILE instead of standard output
+ -q, --quiet, --silent Inhibit usual output
+ -v, --verbose Print more information
+ -?, --help Give this help list
+ --usage Give a short usage message
+ -V, --version Print program version
+
+ Report bugs to <crac-bug at gforge.inria.fr>.
+
+
+File: crac.info, Node: Invoking crac, Next: Problems, Prev: Sample, Up: Top
+
+4 Invoking `crac'
+*****************
+
+The format for running the `crac' program is:
+
+ crac OPTION ...
+
+ `crac' supports the following options:
+
+`--output=NAME'
+`-o NAME'
+ Write output to NAME instead of standard output.
+
+`--interactive'
+`-i'
+ Prompt for confirmation.
+
+`--quiet'
+`--silent'
+`-q'
+ Inhibit usual output.
+
+`--brief'
+ Shorten output.
+
+`--verbose'
+`-v'
+ Print more information.
+
+`--help'
+`-?'
+ Print an informative help message describing the options and then
+ exit successfully.
+
+`--usage'
+ Briefly list the options.
+
+`--version'
+`-V'
+ Print the version number of `crac' on the standard output and then
+ exit successfully.
+
+
+File: crac.info, Node: Problems, Next: Concept Index, Prev: Invoking crac, Up: Top
+
+5 Reporting Bugs
+****************
+
+If you find a bug in `crac', please send electronic mail to
+<crac-bug at gforge.inria.fr>. Include the version number, which you can
+find by running `crac --version'. Also include in your message the
+output that the program produced and the output you expected.
+
+ If you have other questions, comments or suggestions about `crac',
+contact the author via electronic mail to <crac-bug at gforge.inria.fr>.
+The author will try to help you out, although he may not have time to
+fix your problems.
+
+
+File: crac.info, Node: Concept Index, Prev: Problems, Up: Top
+
+Concept Index
+*************
+
+ [index ]
+* Menu:
+
+* bugs: Problems. (line 6)
+* getting help: Invoking crac. (line 6)
+* greetings: Overview. (line 6)
+* help: Invoking crac. (line 6)
+* how to read: Instructions. (line 6)
+* invoking: Invoking crac. (line 6)
+* manual, how to read: Instructions. (line 6)
+* options: Invoking crac. (line 6)
+* overview: Overview. (line 6)
+* problems: Problems. (line 6)
+* reading: Instructions. (line 6)
+* sample: Sample. (line 6)
+* tail recursion: Concept Index. (line 6)
+* usage: Invoking crac. (line 6)
+* version: Invoking crac. (line 6)
+
+
+
+Tag Table:
+Node: Top909
+Node: Instructions1488
+Node: Copying1988
+Node: Overview24958
+Node: Sample25412
+Node: Invoking crac26322
+Node: Problems27086
+Node: Concept Index27703
+
+End Tag Table
+
+
+Local Variables:
+coding: utf-8
+End:
diff --git a/doc/crac.texi b/doc/crac.texi
new file mode 100644
index 0000000..54b7aac
--- /dev/null
+++ b/doc/crac.texi
@@ -0,0 +1,218 @@
+\input texinfo @c -*-texinfo-*-
+ at c This file uses the @command command introduced in Texinfo 4.0.
+ at c %**start of header
+ at setfilename crac.info
+ at settitle Crac is a tool to analyse RNA-Seq data provided by NGS.
+ at finalout
+ at setchapternewpage odd
+ at c %**end of header
+
+ at set VERSION 0.1.0
+
+ at ifinfo
+This file documents the @command{crac} command which Crac is a tool to analyse RNA-Seq data provided by NGS.
+
+Copyright (C) 2011-2012 Nicolas PHILIPPE, Mikael SALSON, Alban MANCHERON
+
+Permission is granted to make and distribute verbatim copies of
+this manual provided the copyright notice and this permission notice
+are preserved on all copies.
+
+ at ignore
+Permission is granted to process this file through TeX and print the
+results, provided the printed document carries copying permission
+notice identical to this one except for the removal of this paragraph
+(this paragraph not being relevant to the printed manual).
+
+ at end ignore
+Permission is granted to copy and distribute modified versions of this
+manual under the conditions for verbatim copying, provided that the entire
+resulting derived work is distributed under the terms of a permission
+notice identical to this one.
+
+Permission is granted to copy and distribute translations of this manual
+into another language, under the above conditions for modified versions,
+except that this permission notice may be stated in a translation approved
+by the Foundation.
+ at end ifinfo
+
+ at titlepage
+ at title crac
+ at subtitle Crac is a tool to analyse RNA-Seq data provided by NGS.
+ at subtitle for crac Version @value{VERSION}
+ at author by Nicolas PHILIPPE, Mikael SALSON, Alban MANCHERON
+
+ at page
+ at vskip 0pt plus 1filll
+Copyright @copyright{} 2011-2012 Nicolas PHILIPPE, Mikael SALSON, Alban MANCHERON
+
+Permission is granted to make and distribute verbatim copies of
+this manual provided the copyright notice and this permission notice
+are preserved on all copies.
+
+Permission is granted to copy and distribute modified versions of this
+manual under the conditions for verbatim copying, provided that the entire
+resulting derived work is distributed under the terms of a permission
+notice identical to this one.
+
+Permission is granted to copy and distribute translations of this manual
+into another language, under the above conditions for modified versions,
+except that this permission notice may be stated in a translation approved
+by the Foundation.
+ at end titlepage
+
+ at c All the nodes can be updated using the EMACS command
+ at c texinfo-every-node-update, which is normally bound to C-c C-u C-e.
+ at node Top, Instructions, (dir), (dir)
+
+ at ifinfo
+This file documents the @command{crac} command to Crac is a tool to analyse RNA-Seq data provided by NGS..
+ at end ifinfo
+
+ at c All the menus can be updated with the EMACS command
+ at c texinfo-all-menus-update, which is normally bound to C-c C-u C-a.
+ at menu
+* Instructions:: How to read this manual.
+* Copying:: How you can copy and share @command{crac}.
+* Overview:: Preliminary information.
+* Sample:: Sample output from @command{crac}.
+* Invoking crac:: How to run @command{crac}.
+* Problems:: Reporting bugs.
+* Concept Index:: Index of concepts.
+ at end menu
+
+ at node Instructions, Copying, Top, Top
+ at chapter How to Read This Manual
+
+ at cindex reading
+ at cindex manual, how to read
+ at cindex how to read
+To read this manual, begin at the beginning, reading from left to right
+and top to bottom, until you get to the end. Then stop. You may pause
+for a beer anywhere in the middle as well, if you wish. (Please note,
+however, that The King strongly advises against heavy use of
+prescription pharmaceuticals, based on his extensive personal and
+professional experience.)
+
+ at node Copying, Overview, Instructions, Top
+ at include CeCILL.texi
+
+ at node Overview, Sample, Copying, Top
+ at chapter Overview
+ at cindex greetings
+ at cindex overview
+
+The GNU @command{crac} program produces a familiar, friendly greeting.
+It allows nonprogrammers to use a classic computer science tool which
+would otherwise be unavailable to them. Because it is protected by the
+GNU General Public License, users are free to share and change it.
+
+GNU @command{crac} was written by Nicolas PHILIPPE, Mikael SALSON, Alban MANCHERON.
+
+ at node Sample, Invoking crac, Overview, Top
+ at chapter Sample Output
+ at cindex sample
+
+Here are some realistic examples of running @command{crac}.
+
+This is the output of the command @samp{crac}:
+
+ at example
+hello, world!
+ at end example
+
+This is the output of the command @samp{crac --help}:
+
+ at example
+Usage: crac [OPTION...] [FILE...]
+Crac is a tool to analyse RNA-Seq data provided by NGS.
+
+ --brief Shorten output
+ -i, --interactive Prompt for confirmation
+ -o, --output=FILE Send output to FILE instead of standard output
+ -q, --quiet, --silent Inhibit usual output
+ -v, --verbose Print more information
+ -?, --help Give this help list
+ --usage Give a short usage message
+ -V, --version Print program version
+
+Report bugs to <crac-bug@@gforge.inria.fr>.
+ at end example
+
+ at node Invoking crac, Problems, Sample, Top
+ at chapter Invoking @command{crac}
+ at cindex invoking
+ at cindex version
+ at cindex options
+ at cindex usage
+ at cindex help
+ at cindex getting help
+
+The format for running the @command{crac} program is:
+
+ at example
+crac @var{option} @dots{}
+ at end example
+
+ at code{crac} supports the following options:
+
+ at c Formatting copied from the Texinfo 4.0 manual.
+ at table @code
+ at item --output=@var{name}
+ at itemx -o @var{name}
+Write output to @var{name} instead of standard output.
+
+ at item --interactive
+ at itemx -i
+Prompt for confirmation.
+
+ at item --quiet
+ at itemx --silent
+ at itemx -q
+Inhibit usual output.
+
+ at item --brief
+Shorten output.
+
+ at item --verbose
+ at itemx -v
+Print more information.
+
+ at item --help
+ at itemx -?
+Print an informative help message describing the options and then exit
+successfully.
+
+ at item --usage
+Briefly list the options.
+
+ at item --version
+ at itemx -V
+Print the version number of @command{crac} on the standard output
+and then exit successfully.
+ at end table
+
+ at node Problems, Concept Index, Invoking crac, Top
+ at chapter Reporting Bugs
+ at cindex bugs
+ at cindex problems
+
+If you find a bug in @command{crac}, please send electronic mail to
+ at email{crac-bug@@gforge.inria.fr}. Include the version number, which you can find by
+running @w{@samp{crac --version}}. Also include in your message the
+output that the program produced and the output you expected. at refill
+
+If you have other questions, comments or suggestions about
+ at command{crac}, contact the author via electronic mail to
+ at email{crac-bug@@gforge.inria.fr}. The author will try to help you out, although he
+may not have time to fix your problems.
+
+ at node Concept Index, , Problems, Top
+ at unnumbered Concept Index
+
+ at cindex tail recursion
+ at printindex cp
+
+ at shortcontents
+ at contents
+ at bye
diff --git a/doc/package.texi.in b/doc/package.texi.in
new file mode 100644
index 0000000..c53f183
--- /dev/null
+++ b/doc/package.texi.in
@@ -0,0 +1,2 @@
+ at set VERSION @PACKAGE_VERSION@
+ at set PACKAGE @PACKAGE@
diff --git a/man/Makefile.am b/man/Makefile.am
new file mode 100644
index 0000000..a1d4ab0
--- /dev/null
+++ b/man/Makefile.am
@@ -0,0 +1,110 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+# build and install the man page
+man_MANS = crac.1
+#nodist_man_MANS = crac.1
+
+# Extra files to add in distributed sources
+EXTRA_DIST = crac.1.in
+
+MOSTLYCLEANFILES=$(no_dist_man_MANS) *~
+CLEANFILES=*~
+DISTCLEANFILES=*~
+MAINTAINERCLEANFILES=*~
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new file mode 100644
index 0000000..e64039f
--- /dev/null
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+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
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+# En contrepartie de l'accessibilité au code source et des droits de copie, #
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+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
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+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
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+# ------------------------------------------------------------------------- #
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+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
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+# This software is governed by the CeCILL license under French law and #
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+# modify and/ or redistribute the software under the terms of the CeCILL #
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+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
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+# #
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+ -test -z "$(MOSTLYCLEANFILES)" || rm -f $(MOSTLYCLEANFILES)
+
+clean-generic:
+ -test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+ -test -z "$(DISTCLEANFILES)" || rm -f $(DISTCLEANFILES)
+
+maintainer-clean-generic:
+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+ -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
+clean: clean-am
+
+clean-am: clean-generic clean-libtool mostlyclean-am
+
+distclean: distclean-am
+ -rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am: install-man
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man: install-man1
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic mostlyclean-libtool
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-man
+
+uninstall-man: uninstall-man1
+
+.MAKE: install-am install-strip
+
+.PHONY: all all-am check check-am clean clean-generic clean-libtool \
+ distclean distclean-generic distclean-libtool distdir dvi \
+ dvi-am html html-am info info-am install install-am \
+ install-data install-data-am install-dvi install-dvi-am \
+ install-exec install-exec-am install-html install-html-am \
+ install-info install-info-am install-man install-man1 \
+ install-pdf install-pdf-am install-ps install-ps-am \
+ install-strip installcheck installcheck-am installdirs \
+ maintainer-clean maintainer-clean-generic mostlyclean \
+ mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
+ uninstall uninstall-am uninstall-man uninstall-man1
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/man/crac.1.in b/man/crac.1.in
new file mode 100644
index 0000000..5645e1d
--- /dev/null
+++ b/man/crac.1.in
@@ -0,0 +1,477 @@
+.\" hey, Emacs: -*- nroff -*-
+.\"
+.\" Copyright © 2010-2013 -- IRB/INSERM
+.\" (Institut de Recherches en Biothérapie /
+.\" Institut National de la Santé et de la Recherche
+.\" Médicale)
+.\" LIFL/INRIA
+.\" (Laboratoire d'Informatique Fondamentale de
+.\" Lille / Institut National de Recherche en
+.\" Informatique et Automatique)
+.\" LIRMM/CNRS
+.\" (Laboratoire d'Informatique, de Robotique et de
+.\" Microélectronique de Montpellier /
+.\" Centre National de la Recherche Scientifique)
+.\" LITIS
+.\" (Laboratoire d'Informatique, du Traitement de
+.\" l'Information et des Systèmes).
+.\"
+.\"
+.\" Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+.\" Mikaël SALSON <mikael.salson at lifl.fr>
+.\" Thérèse COMMES <commes at univ-montp2.fr>
+.\" Éric RIVALS <eric.rivals at lirmm.fr>
+.\"
+.\" Programmeurs
+.\" /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+.\" Mikaël SALSON <mikael.salson at lifl.fr>
+.\" with additional contribution for the packaging of:
+.\" Alban MANCHERON <alban.mancheron at lirmm.fr>
+.\"
+.\" Contact: CRAC list <crac-bugs at lists.gforge.inria.fr>
+.\"
+.\" -------------------------------------------------------------------------
+.\"
+.\" Ce fichier fait partie du programme CRAC.
+.\"
+.\" Crac est un outil d'analyse de données de RNA-Seq provenant des NGS.
+.\"
+.\" Ce logiciel est régi par la licence CeCILL soumise au droit français et
+.\" respectant les principes de diffusion des logiciels libres. Vous pouvez
+.\" utiliser, modifier et/ou redistribuer ce programme sous les conditions de
+.\" la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur
+.\" le site "http://www.cecill.info".
+.\"
+.\" En contrepartie de l'accessibilité au code source et des droits de copie,
+.\" de modification et de redistribution accordés par cette licence, il n'est
+.\" offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons,
+.\" seule une responsabilité restreinte pèse sur l'auteur du programme, le
+.\" titulaire des droits patrimoniaux et les concédants successifs.
+.\"
+.\" À cet égard l'attention de l'utilisateur est attirée sur les risques
+.\" associés au chargement, à l'utilisation, à la modification et/ou au
+.\" développement et à la reproduction du logiciel par l'utilisateur étant
+.\" donné sa spécificité de logiciel libre, qui peut le rendre complexe à
+.\" manipuler et qui le réserve donc à des développeurs et des professionnels
+.\" avertis possédant des connaissances informatiques approfondies. Les
+.\" utilisateurs sont donc invités à charger et tester l'adéquation du
+.\" logiciel à leurs besoins dans des conditions permettant d'assurer la
+.\" sécurité de leurs systêmes et ou de leurs données et, plus généralement,
+.\" à l'utiliser et l'exploiter dans les mêmes conditions de sécurité.
+.\"
+.\" Le fait que vous puissiez accéder à cet en-tête signifie que vous avez
+.\" pris connaissance de la licence CeCILL, et que vous en avez accepté les
+.\" termes.
+.\"
+.\" -------------------------------------------------------------------------
+.\"
+.\" This File is part of the CRAC program.
+.\"
+.\" Crac is a tool to analyse RNA-Seq data provided by NGS.
+.\"
+.\" This software is governed by the CeCILL license under French law and
+.\" abiding by the rules of distribution of free software. You can use,
+.\" modify and/ or redistribute the software under the terms of the CeCILL
+.\" license as circulated by CEA, CNRS and INRIA at the following URL
+.\" "http://www.cecill.info".
+.\"
+.\" As a counterpart to the access to the source code and rights to copy,
+.\" modify and redistribute granted by the license, users are provided only
+.\" with a limited warranty and the software's author, the holder of the
+.\" economic rights, and the successive licensors have only limited
+.\" liability.
+.\"
+.\" In this respect, the user's attention is drawn to the risks associated
+.\" with loading, using, modifying and/or developing or reproducing the
+.\" software by the user in light of its specific status of free software,
+.\" that may mean that it is complicated to manipulate, and that also
+.\" therefore means that it is reserved for developers and experienced
+.\" professionals having in-depth computer knowledge. Users are therefore
+.\" encouraged to load and test the software's suitability as regards their
+.\" requirements in conditions enabling the security of their systems and/or
+.\" data to be ensured and, more generally, to use and operate it in the same
+.\" conditions as regards security.
+.\"
+.\" The fact that you are presently reading this means that you have had
+.\" knowledge of the CeCILL license and that you accept its terms.
+.\"
+
+.TH @PACKAGE_NAME@ 1 "@ISODATE@"
+.\" Please update the above date whenever this man page is modified.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins (default)
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+ at PACKAGE_NAME@ v. @PACKAGE_VERSION@ \- @PACKAGE_DESCRIPTION at .
+
+.SH SYNOPSIS
+.B crac [ options ] \fB\-i\fR <index_file> \fB\-r\fR <reads_file1> [reads_file2]
+\fB\-k\fR <int> \fB\-o\fR <output_file>
+.PP
+.B crac \fB\-h\fR|\fB\-\-help\fR
+.br
+.B crac \fB\-f\fR|\fB\-\-full\-help\fR
+.br
+.B crac \fB\-v\fR|\fB\-\-version\fR
+
+.SH DESCRIPTION
+\fB at PACKAGE@\fP CRAC: an integrated approach to the analysis of RNA-seq reads
+.PP
+Whatever the biological questions it addresses, each RNA-seq analysis
+requires a computational prediction of either small scale mutations,
+indels, splice junctions or fusion RNAs. This prediction is currently
+performed using complex pipelines involving multiple tools for
+mapping, coverage computation, and prediction at distinct steps. We
+propose a novel way of analyzing reads that integrates genomic
+locations and local coverage, and delivers all above mentioned
+predictions in a single step. Our program, CRAC, uses a double k-mer
+profiling approach to detect candidate mutations, indels, splice or
+fusion junctions in each single read. Compared to existing tools,
+CRAC provides state of the art sensitivity and improved precision for
+all types of predictions, yielding high rates of true positive
+candidates (99.5% for splice junctions). When applied to four breast
+cancer libraries, CRAC recovered 74% of validated fusion RNAs and
+predicted reccurrent fusion junctions that were overseen in previous
+studies. Importantly, CRAC improves its predictive performance when
+supplied with e.g. 200 nt reads and should fit future needs of read
+analyses.
+.SH SPECIAL OPTIONS
+\fB at PACKAGE@\fP As a lot of softwares, there are many optional parameters in CRAC but only three are mandatory. This document is intended to guide users of CRAC to choose the more appropriate parameters according to their needs:
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+to print the principal help page of CRAC
+.TP
+\fB\-f\fR, \fB\-\-full\-help\fR
+to print the complete help page of CRAC
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+to print version of CRAC
+.SH USUAL ARGUMENTS
+.SS
+Mandatory options
+All these flags must be set.
+.TP
+\fB\-i\fR \fI<index_file>\fP
+is the name of the index previously built with the crac-index binary
+file. Note that crac-index construct the structure <index_file.ssa>
+with its configuration <index_file.conf> so only the prefix
+<index_file> must be specified (without extension) to consider the
+structure and the configuration files both in CRAC
+.TP
+\fB\-r\fR \fI<reads_file1> [reads_file2]\fP
+is the source(s) of the FASTA or FASTQ file(s) containing the
+reads. Note that the number of files depends if single or
+paired-reads. The input file may also be compressed using gzip
+.TP
+\fB\-k\fR \fI<int>\fP
+is the length of the k-mer to be used to map the reads on the
+reference <index_file>. Note that the condition (k < m) is necessary
+and reads (or both paired reads) are ignored if m < k. It must be
+chosen to ensure (as much as possible) that a k-mer has a very high
+probability to occur a single time on the genome
+.TP
+\fB\-o\fR, \fB\-\-sam\fR \fI<output\_file>\fP
+is the output file in SAM format (see the Documentation of SAM format
+in CRAC for more details) or print on STDOUT with "\-o \-" argument
+.SS
+Optional parameters
+.TP
+\fB\-\-stranded\fP
+must be specificied if reads are produced by a stranded protocol of RNA-Seq (not stranded by default)
+.TP
+\fB\-m\fR, \fB\-\-reads\-length\fR, \fB\-m\fR \fI<int>\fP
+must be specified for reads of fixed length. If the read length is
+fixed, we deeply recommend you to specify the read length, by using
+the -m parameter. CRAC will therefore be much faster. \-\-reads-length
+<int> is specified for variable or longer reads, reads shorter are
+ignored and reads longer are trimmed
+.TP
+\fB\-\-treat\-multiple\fR \fI<none>\fP
+display alignments with multiple locations (>max-duplication) rather
+than a single alignment per read in the SAM file
+.TP
+\fB\-\-nb\-threads\fR \fI<int>\fP
+is the number of threads to run crac, computational time is almost
+divided by the number of threads (one thread by default)
+.TP
+\fB\-\-max\-locs\fR \fI<int>\fP
+corresponds to the max number of occurrences retrieved in the index
+for a given k-mer: smaller is faster, but with a small value, you may
+miss some locations that would help CRAC detecting the right cause
+.TP
+\fB\-\-no\-ambiguity\fR \fI<none>\fP
+discard biological events (splice, svn, indel,
+chimera) which have several matches on the reference index.
+Indeed, if crac has identified a biological cause in the read that can
+match in differents places of the genome we classify this cause as a
+biological undetermined event.
+.SS
+Optional output arguments
+.TP
+\fB\-\-gz\fR \fI<none>\fP
+all output files specified after this argument are gzipped (included for the sam file if \-o/\-\-sam argument is specified after)
+.TP
+\fB\-\-summary\fR \fI<output\_file>\fP
+save some statistics about mapping and classification
+.SS
+Optional output homemade file formats
+.TP
+\fB\-\-all\fR \fI<base\_filename>\fP
+set output base filename for all causes following. Note that only a
+base\_filename must be specified. Then, the appropriate file extension
+is added for each cause (SNP, chimera, splice, etc) set output base
+filename for all causes following
+.TP
+\fB\-\-normal\fR \fI<output\_file>\fP
+save reads that do not contain any break
+.TP
+\fB\-\-almost\-normal\fR \fI<output\_file>\fP
+save reads that do not contain any break but with a variable support
+.TP
+\fB\-\-single\fR \fI<output\_file>\fP
+save reads which are located in this way: at least
+\-\-min\-percent\-single\-loc <float> of k\-mers are once located on the
+reference index
+.TP
+\fB\-\-duplicate\fR \fI<output\_file>\fP
+save reads which are located in this way: at least
+\-\-min\-percent\-duplication\-loc <float> of k\-mers are a few times on the
+reference index (ie. between \-\-min\-duplication <int> and
+\-\-max\-duplication <int> of locations)
+.TP
+\fB\-\-multiple\fR \fI<output\_file>\fP
+save reads which are located in this way: at least
+\-\-min\-percent\-multiple\-loc <float> of k\-mers are a many times on the
+reference index (ie. more than \-\-max\-duplication <int> of locations)
+.TP
+\fB\-\-none\fR \fI<output\_file>\fP
+ save reads which are not located on the reference index
+.TP
+\fB\-\-snv\fR \fI<output\_file>\fP
+save reads that contain at least a snv
+.TP
+\fB\-\-indel\fR \fI<output\_file>\fP
+save reads that contain at least a biological indel
+.TP
+\fB\-\-splice\fR \fI<output\_file>\fP
+save reads that contain at least a splicing junction
+.TP
+\fB\-\-weak\-splice\fR \fI<output\_file>\fP
+save reads that contain at least a low coverage splicing junction
+.TP
+\fB\-\-chimera\fR \fI<output\_file>\fP
+save reads that contain at least a chimera junction (junction on
+different chromosomes, strands or genes)
+.TP
+\fB\-\-paired\-end\-chimera\fR \fI<output\_file>\fP
+paired-end-chimera <output\_file>= save paired-end reads that contains a
+chimera in the non-sequenced part of the original fragment.
+.TP
+\fB\-\-biological\fR \fI<output\_file>\fP
+save reads that contain a biological cause but for which there is not
+enough informations to be more specific. Note that the biological
+cause is described for each read
+.TP
+\fB\-\-errors\fR \fI<output\_file>\fP
+save reads that contain at least a sequence error
+.TP
+\fB\-\-repeat\fR \fI<output\_file>\fP
+ save reads that contain a repeated sequence: at least
+ \-\-min\-percent\-repetition\-loc <float> percent of k-mers of a given
+ read are located at least \-\-min\-repetition <int> occurrences on the
+ reference index
+.TP
+\fB\-\-undetermined\fR \fI<output\_file>\fP
+save reads that contain an undetermined error: some k-mers are not
+located on the genome, but the reason for that could not be
+determined. Note that the error is described for each read
+.TP
+\fB\-\-nothing\fR \fI<output\_file>\fP
+save reads that are unclassified
+.SS
+Optional process for specific research
+.TP
+\fB\-\-deep\-snp\fR
+must be specified to increase sensitivity to find SNVs at the cost of
+more computations (only substitution, no indels YET). That process
+searches for SNV in border cases reads. Those reads would otherwise be
+classified in bioundetermined
+.TP
+\fB\-\-stringent\-chimera\fR
+must be specified to increase accuracy to find chimera junctions in
+exchange of sensitivity and computational times
+.SS
+Optional process launcher (once must be selected)
+.TP
+\fB\-\-emt\fR
+launch an exact matching processing of reads on the
+index. Either the argument specified with -k is equal to 0 which means that the
+entire read is perfectly mapped on the genome or only a factor of
+length k per read is mapped (the first one with a location) and the
+rest is sofclipped. With this process, reads are not indexed and it
+provides a low memory consumption. Note this kind of method is very
+useful for DGE reads mapping.
+
+.TP
+\fB\-\-server\fR
+launch a server to query a given read more precisely. That process is
+useful for debugging. Note that the output arguments will not be taken
+into account. Give an \-\-input\-name\-server <string> to set the input
+fifo name (classify.fifo by default) and give an \-\-output\-name\-server
+<string> to set the output fifo name (classify.out.fifo by
+default). The server can then be used through a client crac\-client
+.SS
+Additional settings for users
+.TP
+\fB\-\-detailed\-sam\fR
+more informations are added in SAM output file. See the Documentation
+of SAM format in CRAC for more details
+.TP
+\fB\-\-min\-percent\-single\-loc\fR \fI<float>\fR
+is, to consider a given read as uniquely mapped, the minimum
+proportion of k-mers that are uniquely mapped on the index (0.15 by
+default)
+.TP
+\fB\-\-min\-duplication\fR \fI<int>\fR
+is the minimum number of location to consider a duplicated k-mer (2 by
+default)
+.TP
+\fB\-\-max\-duplication\fR \fI<int>\fR
+is the maximum number of location to consider a duplicated k-mer (9 by
+default)
+.TP
+\fB\-\-min\-percent\-duplication\-loc\fR \fI<float>\fR
+is, to consider a given read as duplicated, the minimum proportion of
+k-mers that are duplicated on the index (0.15 by default)
+.TP
+\fB\-\-min\-percent\-multiple\-loc\fR \fI<float>\fR
+is, to consider a given read as “multiple”, the minimum proportion of
+k-mers that are multiple mapped on the index (0.50 by default)
+.TP
+\fB\-\-min\-repetition\fR \fI<int>\fR
+is the minimum number of locations to consider a repeated k-mer (20 by
+default)
+.TP
+\fB\-\-max\-percent\-repetition\-loc\fR \fI<float>\fR
+is, for a given read, the minimum proportion of k-mers that are
+repeated on the index to consider a repetition (0.20 by default)
+.TP
+\fB\-\-max\-splice\-length\fR \fI<int>\fR
+is the threshold to consider a splice, ie. a splice is reported if the
+junction length is below max\-splice\-length <int>, a chimera is
+considered otherwise (distance by default is 300Kb)
+.TP
+\fB\-\-max\-bio\-indel\fR \fI<int>\fR
+is the threshold to consider a biological indel, ie. an indel is
+reported if the gap length is below max\-bio\-indel, a splice is
+considered otherwise (distance by default is 15)
+.TP
+\fB\-\-max\-bases\-retrieved\fR \fI<int>\fR
+is the number of nucleotides to display in outputfile in case of
+insertion (15 by default)
+.TP
+\fB\-\-min\-support\-no\-cover\fR \fI<float>\fR
+is the minimum coverage to be able to report a biological cause. Note
+that if a single read contains a given substitution, it is difficult
+(if not impossible) to distinguish a sequence error and a biological
+cause (1.30 by default)
+.SS
+Additional settings for advanced users
+.TP
+\fB\-\-min\-break\-length\fR \fI<int>\fR
+is the minimal break length (as the percentage of k, the k-mer length)
+so that a cause can be reported. Theoretically, for a given cause, the
+break length is always >= (kmer_length \- 1). Otherwise, the break may
+be merged with a close enough break, or the break will be considered
+as undetermined. (0.5 by default)
+.TP
+\fB\-\-max\-bases\-randomly\-matched\fR \fI<int>\fR
+A k-mer overlapping an exon-exon junction, for example, may still
+match on the genome if the overlap is at the end of the read (without
+loss of generality). This is due to the fact that the nucleotides
+starting the second exon may be the same as the nucleotides starting
+the intron. Theoretically, there is a 0.25 probability that we have
+the same nucleotide at the first position of the intron and the
+exon. This option specifies how many nucleotides may be matched
+randomly at most
+.TP
+\fB\-\-max\-extension\-length\fR \fI<int>\fR
+is the maximum number of k-mers extended at each side of a read
+break. In fact, for a given break, k-mers with false locations can
+generate false biological causes, so the consistency is checked for
+each side of the break to discard false k-mers and readjust the good
+boundaries of the break (10 by default)
+.TP
+\fB\-\-nb\-tags\-info\-stored\fR \fI<int>\fR
+is a buffer to store informations for each thread during the computing
+phase (1000 by default). This value must be increased if threads work
+below their real capabilities. With \-\-nb\-threads 15, CPU usage must be
+about 1400%
+.TP
+\fB\-\-nb\-nucleotides\-snp\-comparison\fR \fI<int>\fR
+ is the minimum k\-mer length tolerated for the deep SNVs search (8 by
+ default)
+.PP
+.SH "SEE ALSO"
+The full documentation for
+.B @PACKAGE_NAME@
+is maintained as a org manual. If the
+.B info
+and
+.B @PACKAGE_NAME@
+programs are properly installed at your site, the command
+.IP
+.B info @PACKAGE_NAME@
+.PP
+should give you access to the complete manual.
+.SH AUTHOR
+.SS
+About the @PACKAGE_NAME@ package.
+You can contact
+Nicolas PHILIPPE, Mikael SALSON and Alban MANCHERON by sending an
+e-mail to <@PACKAGE_BUGREPORT@>.
+.TP 0
+CRAC is research project and achievement of:
+.br
+ Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+.br
+ Mikaël SALSON <mikael.salson at lifl.fr>
+.br
+ Thérèse COMMES <therese.commes at univ-montp2.fr>
+.br
+ Eric RIVALS <eric.rivals at lirmm.fr>
+.TP 0
+Supervision by:
+ Thérèse COMMES <therese.commes at univ-montp2.fr>
+ Eric RIVALS <eric.rivals at lirmm.fr>
+.TP 0
+Programming:
+ Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+ Mikaël SALSON <mikael.salson at lifl.fr>
+.br
+with additional contribution for the packaging of:
+ Alban MANCHERON <alban.mancheron at lirmm.fr>
+.SS
+About the @PACKAGE_NAME@ publication.
+You may cite the following paper if you use our tool:
+.TP 0
+Gk-arrays: Querying large read collections in main memory: a versatile
+data structure
+.br
+.B Philippe N., Salson M., Lecroq T., Leonard M., Commes T., Rivals E.
+.br
+BMC Bioinformatics 2011, 12:242.
+.TP 0
+Crac: An integrated RNA-Seq read analysis
+.br
+.B Philippe N., Salson M., Commes T., Rivals E.
+.br
+Genome Biology 2013; 14:R30.
diff --git a/scripts/Makefile.am b/scripts/Makefile.am
new file mode 100644
index 0000000..81433ba
--- /dev/null
+++ b/scripts/Makefile.am
@@ -0,0 +1,91 @@
+###############################################################################
+# #
+# #
+# Copyright © 2010-2012 -- LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique). #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes) #
+# #
+# Auteurs/Authors: CRAC list <crac-bug at gforge.inria.fr> #
+# Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <therese.commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+dist_bin_SCRIPTS = crac-client
+
+MOSTLYCLEANFILES=*~
+CLEANFILES=*~
+DISTCLEANFILES=*~
+MAINTAINERCLEANFILES=*~
diff --git a/scripts/Makefile.in b/scripts/Makefile.in
new file mode 100644
index 0000000..d2216ff
--- /dev/null
+++ b/scripts/Makefile.in
@@ -0,0 +1,521 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+###############################################################################
+# #
+# #
+# Copyright © 2010-2012 -- LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique). #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes) #
+# #
+# Auteurs/Authors: CRAC list <crac-bug at gforge.inria.fr> #
+# Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <therese.commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
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+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
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+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic mostlyclean-libtool
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-dist_binSCRIPTS
+
+.MAKE: install-am install-strip
+
+.PHONY: all all-am check check-am clean clean-generic clean-libtool \
+ distclean distclean-generic distclean-libtool distdir dvi \
+ dvi-am html html-am info info-am install install-am \
+ install-data install-data-am install-dist_binSCRIPTS \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-generic mostlyclean-libtool pdf pdf-am \
+ ps ps-am uninstall uninstall-am uninstall-dist_binSCRIPTS
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/scripts/crac-client b/scripts/crac-client
new file mode 100755
index 0000000..b004a88
--- /dev/null
+++ b/scripts/crac-client
@@ -0,0 +1,253 @@
+#!/bin/bash
+
+###############################################################################
+# #
+# #
+# Copyright © 2010-2012 -- LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique). #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes) #
+# #
+# Auteurs/Authors: CRAC list <crac-bug at gforge.inria.fr> #
+# Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <therese.commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+
+PIPE=`dirname $0`/classify.fifo
+PIPE_OUT=`dirname $0`/classify.out.fifo
+MAX_NB_ITER=100 # 100s
+if [ $# -gt 5 -o "$1" == "-h" -o "$1" == "--help" ]
+then
+ echo "Usage: $0 [-in <input_pipe>] [-out <output_pipe>] [-q]" >&2
+ exit 1
+fi
+
+QUIET=0
+while [ $# -gt 0 ]
+do
+ if [ "$1" == "-in" ]; then
+ PIPE=$2
+ shift
+ elif [ "$1" == "-out" ]; then
+ PIPE_OUT=$2
+ shift
+ elif [ "$1" == "-q" ]; then
+ QUIET=1
+ else
+ echo "Unknown option $1" >&2
+ fi
+ shift
+done
+
+if [ $QUIET -eq 0 ]; then
+ echo "This is the client of crac v. 1.5.0";
+fi
+
+[ -p $PIPE ] || PIPE=${PIPE/`dirname $0`/$PWD}
+[ -p $PIPE_OUT ] || PIPE_OUT=${PIPE_OUT/`dirname $0`/$PWD}
+
+if [ ! -p $PIPE -o ! -p $PIPE_OUT ]
+then
+ echo "$PIPE or $PIPE_OUT does not exist... Maybe you didn't launch crac --server?"
+ exit 1
+fi
+
+# Connecting
+echo -n "connect@$$" > $PIPE
+cat $PIPE_OUT > /dev/null
+
+SUBPIPE=`dirname $0`/in.$$.fifo
+SUBPIPE_OUT=`dirname $0`/out.$$.fifo
+NB_ITER=0
+
+[ -p $SUBPIPE ] || SUBPIPE=${SUBPIPE/`dirname $0`/`dirname $PIPE`}
+[ -p $SUBPIPE_OUT ] || SUBPIPE_OUT=${SUBPIPE_OUT/`dirname $0`/`dirname $PIPE_OUT`}
+
+while [ ! -p $SUBPIPE_OUT -a $NB_ITER -le $MAX_NB_ITER ]; do
+ sleep 0.1s
+ NB_ITER=$((NB_ITER+1))
+done
+
+if [ $NB_ITER -ge $MAX_NB_ITER ]; then
+ echo "Oops! Output pipe was not created.
+Maybe it has not been created in the directory I expected.
+Something going wrong, I'm leaving cowardly." >&2
+ exit 2
+fi
+
+if [ $QUIET -eq 0 ]; then
+ echo -n "> "
+fi
+while read line; do
+ set -- $line
+
+ PRINT=0
+ if [ "$1" == "help" ]; then
+ echo "* Set a variable: set <variable> <value>
+* Locate a pattern: locate <pattern>
+* Locate each k-mer in a sequence: klocate <k> <dna sequence>
+* Get information about a read: <read id>
+* Get information about a read (with its name): name <read name>
+* Get reads sharing the same k-factor as the one at position <pos> in <read id>: <read id>:<pos>
+* Get reads sharing a given factor: tag <factor>
+* Get reads that have a given factor at a given position: tag pos <position> <factor>
+* Retrieve a genome factor: genome [reverse] <chr_name:position> <length>
+* Get GkSA value: GkSA <pos>
+* Quit main server: quit
+* Quit only child server: <Ctrl>+D"
+ elif [ "$1" != "" -a "${1:0:1}" != ">" -a "${1:0:1}" != "#" ]; then
+ while [ $# -gt 0 ]; do
+ if [ "$1" == "set" -a $# -ge 3 ]
+ then
+ echo -n "set|$2|$3" > $SUBPIPE
+ shift 3
+ elif [ "$1" == "name" -a $# -ge 2 ]; then
+ echo -n "name|$2" > $SUBPIPE
+ shift 2
+ elif [ "$1" == "locate" -a $# -ge 2 ]; then
+ echo -n "loc|"`expr length $2`"|$2" > $SUBPIPE
+ shift 2
+ elif [ "$1" == "klocate" -a $# -ge 3 ]; then
+ k=$2
+ seq=$3
+ for (( i=0 ; $i < $((${#seq}-k+1)); i++ )); do
+ echo -n "loc|$k|"${seq:$i:$k} > $SUBPIPE
+ cat $SUBPIPE_OUT
+ done
+ PRINT=1
+ shift 3
+ elif [ "$1" == "tag" -a $# -ge 4 -a "$2" == "pos" ]; then
+ echo -n "tag|"`expr length $4`"|$4" > $SUBPIPE
+ cat $SUBPIPE_OUT | grep -Ewo "[0-9]+:$3" | awk -F: '{print $1}'
+ shift 4
+ PRINT=1
+ elif [ "$1" == "tag" -a $# -ge 2 ]; then
+ echo -n "tag|"`expr length $2`"|$2" > $SUBPIPE
+ shift 2
+ elif [ "$1" == "GkSA" -a $# -ge 2 ]; then
+ echo -n "GkSA|$2" > $SUBPIPE
+ shift 2
+ elif [ "$1" == "genome" -a $# -ge 3 ]; then
+ if [ "$2" == "reverse" ]; then
+ REV="true"
+ shift
+ else
+ REV="false"
+ fi
+ if [[ $2 == *:* ]]; then
+ chr=$(echo $2 | cut -d: -f1)
+ pos=$(echo $2 | cut -d: -f2)
+ if [ "$REV" == "true" ]; then
+ pos=-$pos
+ fi
+ echo -n "genome|$chr|$pos|$3" > $SUBPIPE
+ else
+ echo "Missing ``:''" >&2
+ fi
+ shift 3
+ elif [ "$1" == "quit" ]; then
+ echo -n "q" > $SUBPIPE
+ cat $SUBPIPE_OUT
+ echo -n "q" > $PIPE
+ cat $PIPE_OUT
+ exit 0
+ elif [ "$1" == "print" ]; then
+ shift
+ echo $*
+ shift $#
+ PRINT=1
+ elif [[ "$1" =~ ^[0-9]+$ ]] || [[ "$1" =~ ^[0-9]+:[0-9]+$ ]]; then
+ echo -n "$1" > $SUBPIPE
+ shift
+ else
+ echo "Unkown command."
+ shift
+ PRINT=1
+ fi
+ if [ $PRINT -eq 0 ]; then
+ cat $SUBPIPE_OUT
+ fi
+ done
+ fi
+ if [ $QUIET -eq 0 ]; then
+ echo -n "> "
+ fi
+done
+if [ $QUIET -eq 0 ]; then
+ echo
+fi
+echo -n "q" > $SUBPIPE
+cat $SUBPIPE_OUT > /dev/null
diff --git a/scripts/crac-client.in b/scripts/crac-client.in
new file mode 100755
index 0000000..a0b5436
--- /dev/null
+++ b/scripts/crac-client.in
@@ -0,0 +1,253 @@
+#!/bin/bash
+
+###############################################################################
+# #
+# #
+# Copyright © 2010-2012 -- LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique). #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes) #
+# #
+# Auteurs/Authors: CRAC list <crac-bug at gforge.inria.fr> #
+# Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <therese.commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+
+PIPE=`dirname $0`/classify.fifo
+PIPE_OUT=`dirname $0`/classify.out.fifo
+MAX_NB_ITER=100 # 100s
+if [ $# -gt 5 -o "$1" == "-h" -o "$1" == "--help" ]
+then
+ echo "Usage: $0 [-in <input_pipe>] [-out <output_pipe>] [-q]" >&2
+ exit 1
+fi
+
+QUIET=0
+while [ $# -gt 0 ]
+do
+ if [ "$1" == "-in" ]; then
+ PIPE=$2
+ shift
+ elif [ "$1" == "-out" ]; then
+ PIPE_OUT=$2
+ shift
+ elif [ "$1" == "-q" ]; then
+ QUIET=1
+ else
+ echo "Unknown option $1" >&2
+ fi
+ shift
+done
+
+if [ $QUIET -eq 0 ]; then
+ echo "This is the client of @PACKAGE_NAME@ v. @PACKAGE_VERSION@";
+fi
+
+[ -p $PIPE ] || PIPE=${PIPE/`dirname $0`/$PWD}
+[ -p $PIPE_OUT ] || PIPE_OUT=${PIPE_OUT/`dirname $0`/$PWD}
+
+if [ ! -p $PIPE -o ! -p $PIPE_OUT ]
+then
+ echo "$PIPE or $PIPE_OUT does not exist... Maybe you didn't launch @PACKAGE_NAME@ --server?"
+ exit 1
+fi
+
+# Connecting
+echo -n "connect@$$" > $PIPE
+cat $PIPE_OUT > /dev/null
+
+SUBPIPE=`dirname $0`/in.$$.fifo
+SUBPIPE_OUT=`dirname $0`/out.$$.fifo
+NB_ITER=0
+
+[ -p $SUBPIPE ] || SUBPIPE=${SUBPIPE/`dirname $0`/`dirname $PIPE`}
+[ -p $SUBPIPE_OUT ] || SUBPIPE_OUT=${SUBPIPE_OUT/`dirname $0`/`dirname $PIPE_OUT`}
+
+while [ ! -p $SUBPIPE_OUT -a $NB_ITER -le $MAX_NB_ITER ]; do
+ sleep 0.1s
+ NB_ITER=$((NB_ITER+1))
+done
+
+if [ $NB_ITER -ge $MAX_NB_ITER ]; then
+ echo "Oops! Output pipe was not created.
+Maybe it has not been created in the directory I expected.
+Something going wrong, I'm leaving cowardly." >&2
+ exit 2
+fi
+
+if [ $QUIET -eq 0 ]; then
+ echo -n "> "
+fi
+while read line; do
+ set -- $line
+
+ PRINT=0
+ if [ "$1" == "help" ]; then
+ echo "* Set a variable: set <variable> <value>
+* Locate a pattern: locate <pattern>
+* Locate each k-mer in a sequence: klocate <k> <dna sequence>
+* Get information about a read: <read id>
+* Get information about a read (with its name): name <read name>
+* Get reads sharing the same k-factor as the one at position <pos> in <read id>: <read id>:<pos>
+* Get reads sharing a given factor: tag <factor>
+* Get reads that have a given factor at a given position: tag pos <position> <factor>
+* Retrieve a genome factor: genome [reverse] <chr_name:position> <length>
+* Get GkSA value: GkSA <pos>
+* Quit main server: quit
+* Quit only child server: <Ctrl>+D"
+ elif [ "$1" != "" -a "${1:0:1}" != ">" -a "${1:0:1}" != "#" ]; then
+ while [ $# -gt 0 ]; do
+ if [ "$1" == "set" -a $# -ge 3 ]
+ then
+ echo -n "set|$2|$3" > $SUBPIPE
+ shift 3
+ elif [ "$1" == "name" -a $# -ge 2 ]; then
+ echo -n "name|$2" > $SUBPIPE
+ shift 2
+ elif [ "$1" == "locate" -a $# -ge 2 ]; then
+ echo -n "loc|"`expr length $2`"|$2" > $SUBPIPE
+ shift 2
+ elif [ "$1" == "klocate" -a $# -ge 3 ]; then
+ k=$2
+ seq=$3
+ for (( i=0 ; $i < $((${#seq}-k+1)); i++ )); do
+ echo -n "loc|$k|"${seq:$i:$k} > $SUBPIPE
+ cat $SUBPIPE_OUT
+ done
+ PRINT=1
+ shift 3
+ elif [ "$1" == "tag" -a $# -ge 4 -a "$2" == "pos" ]; then
+ echo -n "tag|"`expr length $4`"|$4" > $SUBPIPE
+ cat $SUBPIPE_OUT | grep -Ewo "[0-9]+:$3" | awk -F: '{print $1}'
+ shift 4
+ PRINT=1
+ elif [ "$1" == "tag" -a $# -ge 2 ]; then
+ echo -n "tag|"`expr length $2`"|$2" > $SUBPIPE
+ shift 2
+ elif [ "$1" == "GkSA" -a $# -ge 2 ]; then
+ echo -n "GkSA|$2" > $SUBPIPE
+ shift 2
+ elif [ "$1" == "genome" -a $# -ge 3 ]; then
+ if [ "$2" == "reverse" ]; then
+ REV="true"
+ shift
+ else
+ REV="false"
+ fi
+ if [[ $2 == *:* ]]; then
+ chr=$(echo $2 | cut -d: -f1)
+ pos=$(echo $2 | cut -d: -f2)
+ if [ "$REV" == "true" ]; then
+ pos=-$pos
+ fi
+ echo -n "genome|$chr|$pos|$3" > $SUBPIPE
+ else
+ echo "Missing ``:''" >&2
+ fi
+ shift 3
+ elif [ "$1" == "quit" ]; then
+ echo -n "q" > $SUBPIPE
+ cat $SUBPIPE_OUT
+ echo -n "q" > $PIPE
+ cat $PIPE_OUT
+ exit 0
+ elif [ "$1" == "print" ]; then
+ shift
+ echo $*
+ shift $#
+ PRINT=1
+ elif [[ "$1" =~ ^[0-9]+$ ]] || [[ "$1" =~ ^[0-9]+:[0-9]+$ ]]; then
+ echo -n "$1" > $SUBPIPE
+ shift
+ else
+ echo "Unkown command."
+ shift
+ PRINT=1
+ fi
+ if [ $PRINT -eq 0 ]; then
+ cat $SUBPIPE_OUT
+ fi
+ done
+ fi
+ if [ $QUIET -eq 0 ]; then
+ echo -n "> "
+ fi
+done
+if [ $QUIET -eq 0 ]; then
+ echo
+fi
+echo -n "q" > $SUBPIPE
+cat $SUBPIPE_OUT > /dev/null
diff --git a/src/CandidatBreak.cpp b/src/CandidatBreak.cpp
new file mode 100644
index 0000000..29cad69
--- /dev/null
+++ b/src/CandidatBreak.cpp
@@ -0,0 +1,322 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "CandidatBreak.h"
+#include "SupportBreak.h"
+#include <math.h>
+
+using namespace std;
+
+CandidatBreak::CandidatBreak(uint pos_start, uint loc_start, int strand_start,
+ uint pos_end, uint loc_end, int strand_end,
+ SupportBreak *sb, Parameters *p
+ ):pos_start_break(pos_start), loc_start_break(loc_start), strand_start_break(strand_start), pos_end_break(pos_end), loc_end_break(loc_end), strand_end_break(strand_end), supportBreak(sb), parameters(p) {
+ is_single_consistent = false;
+ single_distance = ~0;
+ is_duplicated = false;
+}
+
+CandidatBreak::CandidatBreak(const CandidatBreak &c):pos_start_break(c.pos_start_break), loc_start_break(c.loc_start_break), strand_start_break(c.strand_start_break), pos_end_break(c.pos_end_break), loc_end_break(c.loc_end_break), strand_end_break(c.strand_end_break), supportBreak(c.supportBreak), parameters(c.parameters) {
+ is_single_consistent = c.is_single_consistent;
+ is_duplicated = c.is_duplicated;
+ single_distance = c.single_distance;
+}
+
+CandidatBreak::~CandidatBreak(){}
+
+
+void CandidatBreak::checkSingleCorrespondence(uint pos_single, uint loc_single, int strand_single){
+ // case of loc_single does not exist
+ if (strand_single == 0){
+ is_single_consistent = false;
+ single_distance = ~0;
+ }else{
+ ulong chr_single = getGenome()->getIdChromosome(loc_single);
+ // if pos_single is before break, checking of strand and chr
+ if (strand_single == strand_start_break
+ && getPosEndBreak() > pos_single
+ && chr_single == getChrIdStartBreak()){
+ // compute the distance between loc_single and loc_start_break
+ if ((strand_single == 1 && pos_single <= getPosStartBreak())
+ || (strand_single == -1 && pos_single >= getPosStartBreak()))
+ single_distance = (long long int) getLocStartBreak() - loc_single;
+ else
+ single_distance = (long long int) loc_single - getLocStartBreak();
+ // is_single consistent iff single_distance >= 0 && single_distance <= parameters->max_splice_length
+ if (single_distance >= 0 && single_distance <= parameters->max_splice_length)
+ is_single_consistent = true;
+ else{
+ is_single_consistent = false;
+ single_distance = ~0;
+ }
+ }
+ // if pos_single is after break, checking of strand and chr
+ else if (strand_single == strand_end_break
+ && getPosStartBreak() < pos_single
+ && chr_single == getChrIdEndBreak()){
+ // compute the distance between loc_single and loc_start_break
+ if ((strand_single == 1 && pos_single >= getPosEndBreak())
+ || (strand_single == -1 && pos_single <= getPosEndBreak()))
+ single_distance = (long long int) loc_single - getLocEndBreak();
+ else
+ single_distance = (long long int) getLocEndBreak() - loc_single;
+ // is_single consistent iff single_distance >= 0
+ if (single_distance >= 0)
+ is_single_consistent = true;
+ else{
+ is_single_consistent = false;
+ single_distance = ~0;
+ }
+ }
+ // other cases: not single consistency
+ else{
+ is_single_consistent = false;
+ single_distance = ~0;
+ }
+ }
+}
+
+
+const uchar *CandidatBreak::getChrEndBreak(){
+ return getGenome()->getChromosome(loc_end_break);
+}
+
+
+ChrPosition *CandidatBreak::getChrPositionEndBreak(){
+ return getGenome()->getChrPos(loc_end_break,strand_end_break);
+}
+
+
+ChrPosition *CandidatBreak::getChrPositionStartBreak(){
+ return getGenome()->getChrPos(loc_start_break,strand_start_break);
+}
+
+ulong CandidatBreak::getChrIdEndBreak(){
+ return getGenome()->getIdChromosome(loc_end_break);
+}
+
+ulong CandidatBreak::getChrIdStartBreak(){
+ return getGenome()->getIdChromosome(loc_start_break);
+}
+
+const uchar *CandidatBreak::getChrStartBreak(){
+ return getGenome()->getChromosome(loc_start_break);
+}
+
+LocateOnGenome *CandidatBreak::getGenome(){
+ return supportBreak->getGenome();
+}
+
+gap_size_t CandidatBreak::getGenomeGapLength(){
+ if (strand_start_break != strand_end_break
+ || (getChrIdStartBreak() != getChrIdEndBreak()))
+ return min(labs(loc_end_break - loc_start_break),
+ labs(loc_start_break - loc_end_break)) - 1;
+ if (strand_end_break == -1)
+ return (gap_size_t)loc_start_break - (gap_size_t)loc_end_break-1;
+ return (gap_size_t)loc_end_break - (gap_size_t)loc_start_break-1;
+}
+
+uint CandidatBreak::getLength(){
+ return supportBreak->getLength();
+}
+
+uint CandidatBreak::getLocEndBreak(){
+ return loc_end_break;
+}
+
+uint CandidatBreak::getLocStartBreak(){
+ return loc_start_break;
+}
+
+uint CandidatBreak::getPosEndBreak(){
+ return pos_end_break;
+}
+
+uint CandidatBreak::getPosStartBreak(){
+ return pos_start_break;
+}
+
+uint CandidatBreak::getReadBreakLength(){
+ return (pos_end_break - pos_start_break + 1);
+}
+
+long long int CandidatBreak::getSingleDistance(){
+ return single_distance;
+}
+
+int CandidatBreak::getStrandEndBreak(){
+ return strand_end_break;
+}
+
+int CandidatBreak::getStrandStartBreak(){
+ return strand_start_break;
+}
+
+bool CandidatBreak::hasNoEndBreak(){
+ return (pos_end_break == (getLength() - 1));
+}
+
+bool CandidatBreak::hasNoStartBreak(){
+ return (pos_start_break == 0);
+}
+
+bool CandidatBreak::isDuplicated(){
+ return is_duplicated;
+}
+
+bool CandidatBreak::isNiceCandidat(){
+ return (isSameChr() && isSameStrand()
+ && (
+ (getStrandStartBreak() == 1 && (getLocStartBreak() + supportBreak->getThreshold() - 1) < getLocEndBreak())
+ || (getStrandStartBreak() == -1 && (getLocEndBreak() + supportBreak->getThreshold() - 1) < getLocStartBreak())
+ )
+ && (getGenomeGapLength() <= parameters->max_splice_length)
+ );
+}
+
+bool CandidatBreak::isSameChr(){
+ if (getChrIdStartBreak() != getChrIdEndBreak())
+ return false;
+ else
+ return true;
+}
+
+bool CandidatBreak::isSameStrand(){
+ if (strand_start_break != strand_end_break)
+ return false;
+ else
+ return true;
+}
+
+bool CandidatBreak::isSingleConsistent(){
+ return is_single_consistent;
+}
+
+void CandidatBreak::setDuplicated(bool flag){
+ is_duplicated = flag;
+}
+
+void CandidatBreak::setLocEndBreak(uint loc_end){
+ loc_end_break = loc_end;
+}
+
+void CandidatBreak::setLocStartBreak(uint loc_start){
+ loc_start_break = loc_start;
+}
+
+void CandidatBreak::setPosEndBreak(uint pos_end){
+ pos_end_break = pos_end;
+}
+
+void CandidatBreak::setPosStartBreak(uint pos_start){
+ pos_start_break = pos_start;
+}
+
+void CandidatBreak::setSingleConsistent(bool flag){
+ is_single_consistent = flag;
+}
+
+void CandidatBreak::setStrandEndBreak(int flag){
+ strand_end_break = flag;
+}
+
+void CandidatBreak::setStrandStartBreak(int flag){
+ strand_start_break = flag;
+}
diff --git a/src/CandidatBreak.h b/src/CandidatBreak.h
new file mode 100644
index 0000000..8302a96
--- /dev/null
+++ b/src/CandidatBreak.h
@@ -0,0 +1,332 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef CANDIDAT_BREAK_H
+#define CANDIDAT_BREAK_H
+
+#include <utility>
+#include "Parameters.h"
+#include "libSSA/locateOnGenome.h"
+#include "libSSA/chrPosition.h"
+#include "types.h"
+
+class SupportBreak;
+
+class CandidatBreak {
+
+ uint pos_start_break; /* Position in the support of the start of
+ the break.*/
+ uint loc_start_break; /* the last absolute location before the
+ break */
+
+ int strand_start_break; /* the strand of the start_break position */
+
+ uint pos_end_break; /* Position in the support of the end of
+ the break. */
+
+ uint loc_end_break; /* the first absolute location after the
+ break */
+
+
+ int strand_end_break; /* the strand of the end_break position*/
+
+ SupportBreak* supportBreak; /* The supportBreak we are working on. */
+
+ Parameters* parameters; /* Parameters chosen by the user or chosen
+ by default by the great developers. */
+
+ bool is_duplicated; /* true iff there are at least two possible causes for a same break */
+
+ bool is_single_consistent; /* true if the candidat locations follow the single location */
+
+ long long int single_distance; /* distance between (loc_start_break || loc_end_break) and loc_single in case of is_single_consistent */
+
+ public:
+
+ CandidatBreak(uint pos_start, uint loc_start, int strand_start,
+ uint pos_end, uint loc_end, int strand_end,
+ SupportBreak *sb, Parameters *p);
+
+
+ CandidatBreak(const CandidatBreak &c);
+
+ ~CandidatBreak();
+
+ /**
+ * Check the correspondence between Candidat and the single Location.
+ * - same strand
+ * - same chr
+ * - loc_single <= loc_start_break if loc_single is before break
+ * or loc_single => loc_end_break if loc_single is after break
+ */
+ void checkSingleCorrespondence(uint pos_single, uint loc_single, int strand_single);
+
+ /**
+ * @return chr for the pos_end_break
+ */
+ const uchar *getChrEndBreak();
+
+ /**
+ * @return a ChrPosition for the pos_end_break
+ */
+ ChrPosition *getChrPositionEndBreak();
+
+ /**
+ * @return a ChrPosition for the pos_start_break
+ */
+ ChrPosition *getChrPositionStartBreak();
+
+ /**
+ * @return chr id for the pos_end_break
+ */
+ ulong getChrIdEndBreak();
+
+ /**
+ * @return chr id for the pos_start_break
+ */
+ ulong getChrIdStartBreak();
+
+ /**
+ * @return chr for the pos_start_break
+ */
+ const uchar *getChrStartBreak();
+
+ /**
+ * @return the reference genome.
+ */
+ LocateOnGenome *getGenome();
+
+ /**
+ * @return the distance between loc_start_break and loc_end_break
+ * on the reference genome.
+ */
+ gap_size_t getGenomeGapLength();
+
+ /**
+ * @return the support length:
+ * supportBreak->getLength()
+ */
+ uint getLength();
+
+ /**
+ * @return loc_end_break
+ */
+ uint getLocEndBreak();
+
+ /**
+ * @return loc_start_break
+ */
+ uint getLocStartBreak();
+
+ /**
+ * @return pos_end_break
+ */
+ uint getPosEndBreak();
+
+ /**
+ * @return pos_start_break
+ */
+ uint getPosStartBreak();
+
+ /**
+ * @return the difference between pos_start_break and pos_end_break
+ * on the read (the break length).
+ */
+ uint getReadBreakLength();
+
+ /**
+ * @return single_distance;
+ */
+ long long int getSingleDistance();
+
+ /**
+ * @return strand_end_break
+ */
+ int getStrandEndBreak();
+
+ /**
+ * @return strand_start_break
+ */
+ int getStrandStartBreak();
+
+ /**
+ * @return true if pos_end_break == (getReadLength() -1)
+ */
+ bool hasNoEndBreak();
+
+ /**
+ * @return true if pos_start_break == 0
+ */
+ bool hasNoStartBreak();
+
+ /**
+ * @return true if the candidat is duplicated (two similar candidats
+ * for a same SupportBreak),
+ * false otherwise.
+ */
+ bool isDuplicated();
+
+ /**
+ * @return true is the candidat is a SNV, an indel or a splice,
+ * false is the candidat looks like a chimera.
+ */
+ bool isNiceCandidat();
+
+ /**
+ * @return true is loc_start_break and loc_end_break are on the same chr,
+ * false otherwise.
+ */
+ bool isSameChr();
+
+ /**
+ * @return true is loc_start_break and loc_end_break are on the same strand,
+ * false otherwise.
+ */
+ bool isSameStrand();
+
+ /**
+ * @return true is the candidat is single consistent
+ * (see checkSingleCorrespondence procedure)
+ * false otherwise.
+ */
+ bool isSingleConsistent();
+
+
+ /**
+ * isDuplicated = flag.
+ */
+ void setDuplicated(bool flag);
+
+ /**
+ * loc_end_break = loc_end.
+ */
+ void setLocEndBreak(uint loc_end);
+
+ /**
+ * loc_start_break = loc_start.
+ */
+ void setLocStartBreak(uint loc_start);
+
+ /**
+ * pos_end_break = pos_end.
+ */
+ void setPosEndBreak(uint pos_end);
+
+ /**
+ * pos_start_break = pos_start.
+ */
+ void setPosStartBreak(uint pos_start);
+
+ /**
+ * isSingleConsistent = flag.
+ */
+ void setSingleConsistent(bool flag);
+
+ /**
+ * strand_end_break = flag.
+ */
+ void setStrandEndBreak(int flag);
+
+ /**
+ * strand_start_break = flag.
+ */
+ void setStrandStartBreak(int flag);
+
+};
+#endif
diff --git a/src/Classifier.cpp b/src/Classifier.cpp
new file mode 100644
index 0000000..c13c831
--- /dev/null
+++ b/src/Classifier.cpp
@@ -0,0 +1,1202 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at univ-montp2.fr *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <Classifier.h>
+#include <iostream>
+#include <sstream>
+#include "utils.h"
+
+using namespace std;
+
+/****************************************
+* SingleReadClassifier *
+****************************************/
+
+SingleReadClassifier::SingleReadClassifier(uint tagId,
+ LocateOnGenome *genome,
+ gkArrays *tags,
+ Parameters *parameters):
+ tags(tags),genome(genome),parameters(parameters),tagId(tagId){
+ uint *S = tags->getSupport(tagId);
+ this->suppo = new Support(parameters, S, tagId, genome, tags);
+ this->taginfo = new TagInfo(genome, suppo);
+}
+
+SingleReadClassifier::~SingleReadClassifier() {
+ if (taginfo != NULL)
+ delete taginfo;
+ if (suppo != NULL)
+ delete suppo;
+}
+
+void SingleReadClassifier::classify() {
+ char *tag = tags->getTag(tagId);
+ int nb_tag_indel;
+ int nb_genome_indel;
+
+ if (tagId >= tags->getNbTags()) {
+ // TODO return NULL;
+ }
+
+ if (! suppo->isContinuous()
+ && ( suppo->isSingle() || suppo->isDuplicate() || suppo->isMultiple() )
+ ) {
+ // all cases with at least an interruption and where the read is not classify "single" or "duplicate"
+ // we have to do an other pass to find the interruption
+ for (uint i= 0 ; i < suppo->getNbBreaks() ; i++){
+ taginfo->setCurrentBreak(i);
+ SupportBreak *suppoBreak = suppo->getBreak(i);
+ nb_tag_indel = suppoBreak->getNbTagIndels();
+ nb_genome_indel = suppoBreak->getNbGenomeIndels();
+
+ // if (suppoBreak->isDuplicated()){
+ // cout << "DUPLICATION" << endl;
+ // }
+
+ if (! suppoBreak->hasLongEnoughTagBreak()) {
+ taginfo->addUndeterminedError("The break in the tag is too small (break length: %d)",
+ suppoBreak->getTagBreakLength());
+ } else if (suppoBreak->hasNoCover()) {
+ if (suppoBreak->isGenomeInsertion()
+ && parameters->max_bio_ins_del <= labs(nb_genome_indel)
+ && parameters->max_splice_length >= labs(nb_genome_indel)) {
+ // Splice with little support
+ // Todo: change the category
+ taginfo->addSpliceNoCover(nb_genome_indel);
+ } else {
+ taginfo->addUndeterminedError("The read (or the part of read) has no cover, we cannot deduce anything! (score in break:%.2f, score outside break:%.2f)",
+ suppoBreak->getScoreInsideBreak(), suppoBreak->getScoreOutsideBreak());
+ }
+ }
+ // Biological event
+ else if (suppoBreak->isBiologicalEvent()) {
+ // In this case we have a combination of biological reason and error
+ // But we can't really say anything on that.
+ if (suppoBreak->isDeviated()){
+ taginfo->addBioUndetermined(NULL,
+ suppoBreak->getPositionEndBreak(),
+ "Combination of error and biological reason (deviation score: %.2f)",
+ suppoBreak->getScoreInsideAverages());
+ } else if (suppoBreak->isRepeated()) {
+ // ambiguous cases (no limit start or end)
+ taginfo->addBioUndetermined(NULL, suppoBreak->getPositionStartBreak(),
+ "Repetition around the break");
+ }
+ else if (suppoBreak->hasNoStartBreak()){
+ taginfo->addBioUndetermined(suppoBreak->getLocationEndBreak()
+ ,suppoBreak->getPositionEndBreak()
+ ,"ambiguous case : no start break");
+ if (parameters->deep_snp_search) {
+ perform_deep_snp_search(suppoBreak, i);
+ }
+ }
+ else if (suppoBreak->hasNoEndBreak()){
+ taginfo->addBioUndetermined(suppoBreak->getLocationStartBreak()
+ ,suppoBreak->getPositionStartBreak()
+ ,"ambiguous case : no end break");
+ if (parameters->deep_snp_search) {
+ perform_deep_snp_search(suppoBreak, i);
+ }
+ }
+ // unambiguous cases
+ else {
+ // Check if the candidat is ambiguous or not
+ if (parameters->no_ambiguity && suppoBreak->isDuplicated()){
+ string message = "Biological event reclassication because of #no-ambiguity option. Probably several matches of the candidat on the genome.";
+ if(suppoBreak->isTagSubstitution()) {
+ message += " #snp";
+ } else if(suppoBreak->isTagIndel() || suppoBreak->isGenomeDeletion() ||
+ (suppoBreak->isGenomeInsertion() && parameters->max_bio_ins_del > labs(nb_genome_indel))) {
+ message += " #indel";
+ } else if(suppoBreak->isGenomeInsertion() && parameters->max_splice_length > labs(nb_genome_indel)) {
+ message += " #splice";
+ } else if(suppoBreak->isChimera()) {
+ message += " #chimera";
+ }
+ taginfo->addBioUndetermined(suppoBreak->getLocationStartBreak(),
+ suppoBreak->getPositionStartBreak(),
+ message.c_str());
+ }else{
+ // SNP
+ if (suppoBreak->isTagSubstitution()
+ && suppoBreak->isBiologicalIntraEvent()){
+ // two substituions
+ if (suppoBreak->getTagBreakLength() > suppo->getThreshold()) {
+ taginfo->addSNP(tag[suppoBreak->getPositionEndBreak()
+ -(suppoBreak->getTagBreakLength() - suppo->getThreshold())],
+ SECOND_SUBSTITUTION);
+ }
+
+ // one substitution
+ taginfo->addSNP(tag[suppoBreak->getPositionEndBreak()],
+ FIRST_SUBSTITUTION);
+ } // end if snp
+ // case biological tag ins/del
+ else if (suppoBreak->isTagIndel()
+ && suppoBreak->isBiologicalIntraEvent()){
+ // snp (insertion) at potsition j-1 into the tag (a snp is one sub, one ins or one del)
+ if (nb_tag_indel == 1){
+ taginfo->addSNP(tag[suppoBreak->getPositionEndBreak()],
+ INSERTION);
+ }
+ // insertion at position j-1 into the tag
+ else if (nb_tag_indel > 0){
+ taginfo->addBioTagIndel(nb_tag_indel,0);
+ }
+ // snp (deletion) at position j-1 into the tag
+ else if (nb_tag_indel == -1){
+ taginfo->addSNP(0, DELETION);
+ }
+ //deletion of lg ins_del_tag at position j-1 into the tag
+ else {
+ taginfo->addBioTagIndel(0,labs(nb_tag_indel));
+ }
+ } // end if tag indel
+ // case biological deletion in the genome
+ else if (suppoBreak->isGenomeDeletion()
+ && suppoBreak->isBiologicalIntraEvent()){
+ taginfo->addBioTagIndel(labs(nb_genome_indel),0);
+ } // end if genomeDeletion
+ // case biological insertion in the genome
+ else if (suppoBreak->isGenomeInsertion()){
+ // case insertion genome < max_bio_ins_del
+ if (parameters->max_bio_ins_del > labs(nb_genome_indel)){
+ taginfo->addBioTagIndel(0,labs(nb_genome_indel));
+ }
+ // case splice
+ else if (parameters->max_splice_length >= labs(nb_genome_indel)){
+ taginfo->addSplice(nb_genome_indel);
+ } else {
+ taginfo->addBioUndetermined(suppoBreak->getLocationStartBreak(),
+ suppoBreak->getPositionStartBreak(),
+ "Unknown type of genome insertion");
+ }
+ } // end if genomeInsertion
+ // case inter/intra transplicing (chimera)
+ else if (suppoBreak->isChimera()){
+ uint stringentChim = 0;
+ string message = "";
+ // If we are using stringent chimera option
+ if(parameters->stringent_chimera) {
+ stringentChim = isStringentChimera(suppoBreak,i);
+ message = "Chimera reclassication because of stringent-chimera option. Cause is: ";
+ switch(stringentChim) {
+ case 1:
+ message += "break_length";
+ break;
+ case 2:
+ message += "nb_merges";
+ break;
+ case 3:
+ message += "repeated_read";
+ break;
+ case 4:
+ message += "support_variation";
+ break;
+ case 5:
+ message += "kmer_verification";
+ break;
+ case 6:
+ message += "no_single_loc";
+ break;
+ }
+ }
+ if(stringentChim > 0) {
+ taginfo->addBioUndetermined(suppoBreak->getLocationStartBreak(),
+ suppoBreak->getPositionStartBreak(),
+ message.c_str());
+ } else {
+ taginfo->addSpliceInter();
+ }
+ } // end if chimera
+ // is continuous but no known biological reasons
+ // different cases of biological undetermined reasons
+ else{
+ if (suppoBreak->getTagBreakLength() >= suppo->getThreshold())
+ taginfo->addBioUndetermined(suppoBreak->getLocationEndBreak(),
+ suppoBreak->getPositionEndBreak(),
+ "The break in the tag is too large (%d). There may have several biological causes",
+ suppoBreak->getTagBreakLength());
+ // else if (suppoBreak->getBreakLength() > suppo->getThreshold())
+ // taginfo->addBioUndetermined(suppoBreak->getLocationEndBreak(),
+ // suppoBreak->getPositionEndBreak(),
+ // "The break is too large (%d). There may have several biological causes",
+ // suppoBreak->getBreakLength());
+ else if (suppoBreak->getTagBreakLength() < parameters->min_break_length)
+ taginfo->addBioUndetermined(suppoBreak->getLocationEndBreak(),
+ suppoBreak->getPositionEndBreak(),
+ "The break is too short (%d).",
+ suppoBreak->getTagBreakLength());
+ else if (! suppoBreak->isBiologicalIntraEvent()
+ && suppoBreak->isBiologicalInterEvent()) {
+ taginfo->addBioUndetermined(suppoBreak->getLocationEndBreak(),
+ suppoBreak->getPositionEndBreak(),
+ "Support is ok for an inter event but not for an intra.");
+ } else {
+ taginfo->addBioUndetermined(suppoBreak->getLocationEndBreak(),
+ suppoBreak->getPositionEndBreak(),
+ "This case was not expected.");
+ }
+ }
+ }
+ }
+ } // end if (isBiologicalEvent)
+ // --------> start of erronneous reason
+ else{
+ if (suppoBreak->isRepeated()) {
+ // In this case we have generally a few positions which are not located
+ // But we can't really say anything on that.
+ taginfo->addUndeterminedError("pos=%d-%d Repetitions around the break",
+ suppoBreak->getPositionStartBreak(),
+ suppoBreak->getPositionEndBreak());
+ }
+ // ambiguous cases (no limit start or end)
+ else if (suppoBreak->hasNoStartBreak()){
+ taginfo->addSeqErr(UNKNOWN_START_MISSING,
+ suppoBreak->getPositionEndBreak(),~0,~0,
+ suppoBreak->getScoreComputedIntraExon());
+ }else if(suppoBreak->hasNoEndBreak()){
+ uint pos = suppoBreak->getPositionStartBreak() + suppo->getThreshold() - 1;
+ taginfo->addSeqErr(UNKNOWN_END_MISSING,
+ pos >= tags->getTagLength(i) ? tags->getTagLength(i)-1 : pos,~0,~0,
+ suppoBreak->getScoreComputedIntraExon());
+ }
+ // seq error ---------------------------> (unambiguous choice)
+ else if (suppoBreak->isTagSubstitution()){
+ //two errors
+ if (suppoBreak->getTagBreakLength() > suppo->getThreshold()) {
+ uint shift = suppoBreak->getTagBreakLength() - suppo->getThreshold();
+ taginfo->addSeqErr(SECOND_SUBSTITUTION
+ ,suppoBreak->getPositionEndBreak()-shift,0,0,
+ suppoBreak->getScoreComputedIntraExon(),
+ 1,
+ getTagAtEndBreak(suppoBreak, tag, 1, -shift), 1);
+ }
+ // one error
+ taginfo->addSeqErr(FIRST_SUBSTITUTION,
+ suppoBreak->getPositionEndBreak(),0,0,
+ suppoBreak->getScoreComputedIntraExon(),
+ 1,
+ getTagAtEndBreak(suppoBreak, tag, 1), 1);
+
+ }
+ // case ins/del error into tag
+ else if (suppoBreak->isTagIndel()) {
+ // insertion of lg ins_del_tag
+ if (nb_tag_indel >= 0){
+ taginfo->addSeqErr(INSERTION,
+ suppoBreak->getPositionEndBreak(),
+ nb_tag_indel,0,
+ suppoBreak->getScoreComputedIntraExon(),
+ 0,
+ getTagAtEndBreak(suppoBreak, tag, nb_tag_indel),
+ nb_tag_indel);
+ }
+ //suppression of lg ins_del_tag
+ else{
+ taginfo->addSeqErr(DELETION
+ ,suppoBreak->getPositionEndBreak(),
+ 0,labs(nb_tag_indel),
+ suppoBreak->getScoreComputedIntraExon(),
+ labs(nb_tag_indel), NULL, ~0);
+ }
+ }
+ //insertion of lg ins_del_genome
+ else if (suppoBreak->isGenomeInsertion()) {
+ if (parameters->max_bio_ins_del < labs(nb_genome_indel)
+ && parameters->max_splice_length >= labs(nb_genome_indel)
+ // The following condition is there just to select
+ // splices with no cover.
+ // Otherwise it may be a false positive due to duplications
+ // and an error
+ && suppoBreak->getScoreOutsideBreak() <= parameters->max_support_out_no_cover) {
+ // Splice with little support
+ taginfo->addSpliceNoCover(nb_genome_indel);
+ }else {
+ ChrPosition *chrPos = suppoBreak->getLocationEndBreak();
+ taginfo->addUndeterminedError("position %d. Too many indels to be an error (probably a splice gap=%d, location=%s|%d,%u).", suppoBreak->getPositionEndBreak(), nb_genome_indel,suppoBreak->getChr(END_BREAK),
+ suppoBreak->getStrandLocation(END_BREAK), chrPos->getRelativePosition());
+ delete chrPos;
+ }
+ }
+ //suppresion of lg labs(ins_del_genome)
+ else if (suppoBreak->isGenomeDeletion()) {
+ taginfo->addSeqErr(INSERTION,
+ suppoBreak->getPositionEndBreak()
+ ,labs(nb_genome_indel),0,
+ suppoBreak->getScoreComputedInterExon(),
+ 0,
+ getTagAtEndBreak(suppoBreak, tag, labs(nb_genome_indel)),
+ labs(nb_genome_indel));
+ }
+ // is not continuous but no erroneous reason
+ else{
+ taginfo->addUndeterminedError("position = %d -> No location neither biological nor erroneous cause found (ins_del_tag: %d and ins_del_genome: %d, chr_before_break: %d and chr_after_break: %d, strand_before_break: %d and strand_after_break: %d)"
+ ,suppoBreak->getPositionEndBreak()
+ ,nb_tag_indel
+ ,nb_genome_indel
+ ,suppoBreak->getChrId(START_BREAK)
+ ,suppoBreak->getChrId(END_BREAK)
+ ,suppoBreak->getStrandLocation(START_BREAK)
+ ,suppoBreak->getStrandLocation(END_BREAK));
+ }
+ }
+ }
+ taginfo->setCurrentBreak(suppo->getNbBreaks());
+ }
+ delete [] tag;
+}
+
+uint SingleReadClassifier::getTagId() {
+ return tagId;
+}
+
+TagInfo *SingleReadClassifier::getTagInfo() {
+ return taginfo;
+}
+
+readIterator *SingleReadClassifier::setInfos(readIterator *readIt) {
+ taginfo->setReadName(readIt->getName());
+ taginfo->setReadQuality(readIt->getQuality());
+ taginfo->setReadNumber(readIt->getReadNumber());
+ ++(*readIt);
+ return readIt;
+}
+
+ostream &SingleReadClassifier::samOutput(ostream &os) {
+ taginfo->samOutput(os);
+ return os;
+}
+
+void SingleReadClassifier::writeOutputs(ostream *snp
+ , ostream *bioTagIndel
+ , ostream *seqErr
+ , ostream *splice
+ , ostream *spliceNoCover
+ , ostream *spliceInter
+ , ostream *undetermined
+ , ostream *repetition
+ , ostream *duplication
+ , ostream *nothing
+ , ostream *normal
+ , ostream *almostNormal
+ , ostream *multiple
+ , ostream *none
+ , ostream *bioUndermined
+ , ostream *single) {
+
+ uint i = taginfo->getReadNumber();
+
+ // First step : the mapping output
+ if (taginfo->hasNothing()){
+ if (nothing != NULL)
+ *nothing << i << " " << *taginfo << endl;
+ }else{
+ if (single != NULL)
+ if (taginfo->isSingle())
+ *single << i << " " << *taginfo << endl;
+ if (duplication != NULL)
+ if (taginfo->isDuplication())
+ *duplication << i << " " << *taginfo << endl ;
+ if (multiple != NULL)
+ if (taginfo->isMultiple())
+ *multiple << i << " " << *taginfo << endl;
+ if (none != NULL)
+ if (taginfo->isNone())
+ *none << i << " " << *taginfo << endl;
+ }
+
+ //Second step : the classification output
+ // if it is an erroneous tag then we uniquely write in the output errors file
+ if (taginfo->getNbSeqErr() > 0) {
+ if (seqErr != NULL)
+ for (uint j=0; j < taginfo->getNbSeqErr(); j++)
+ *seqErr << i << " " << *taginfo->getInfosSeqErr()[j] << " " << *taginfo << endl ;
+ }
+ // else{
+ if (normal != NULL)
+ if (taginfo->isNormal())
+ *normal << i << " " << *taginfo << endl;
+ if (almostNormal != NULL)
+ if (taginfo->isAlmostNormal())
+ *almostNormal << i << " " << *taginfo << endl;
+ if (snp != NULL)
+ for (uint j=0; j < taginfo->getNbSNP(); j++)
+ *snp << i << " " << *taginfo->getInfosSNP()[j] << " " << *taginfo << endl;
+ if (bioTagIndel != NULL)
+ for (uint j=0; j < taginfo->getNbBioTagIndel(); j++)
+ *bioTagIndel << i << " " << *taginfo->getInfosBioTagIndel()[j] << " " << *taginfo << endl;
+ if (repetition != NULL)
+ for (uint j=0; j < taginfo->getNbRepetition() ; j++)
+ *repetition << i << " " << *taginfo->getInfosRepetition()[j] << " " << *taginfo << endl;
+ if (undetermined != NULL)
+ for (uint j=0; j < taginfo->getNbUndeterminedError(); j++)
+ *undetermined << i << " " << *taginfo->getInfosUndeterminedError()[j] << " " << *taginfo << endl;
+ if (splice != NULL)
+ for (uint j=0; j < taginfo->getNbSplice(); j++)
+ *splice << i << " " << *taginfo->getInfosSplice()[j] << " " << *taginfo << endl ;
+ if (spliceNoCover != NULL)
+ for (uint j=0; j < taginfo->getNbSpliceNoCover(); j++)
+ *spliceNoCover << i << " " << *taginfo->getInfosSpliceNoCover()[j] << " " << *taginfo << endl;
+ if (spliceInter != NULL)
+ for (uint j=0; j < taginfo->getNbSpliceInter(); j++)
+ *spliceInter << i << " " << *taginfo->getInfosSpliceInter()[j] << " " << *taginfo << endl;
+ if (bioUndermined != NULL)
+ for (uint j=0; j < taginfo->getNbBioUndetermined(); j++)
+ *bioUndermined << i << " " << *taginfo->getInfosBioUndetermined()[j] << " " << *taginfo << endl ;
+}
+
+void SingleReadClassifier::updateStatistics(uint (*nb_classes)[NB_MASKS+1], uint *nb_explainable) {
+ int code = taginfo->getCode();
+ for (uint j=0; j < NB_MASKS; j++) {
+ if (code & (1<<j))
+ (*nb_classes)[j]++;
+ }
+ if (taginfo->isExplainable())
+ (*nb_explainable)++;
+ if (code == 0)
+ (*nb_classes)[NB_MASKS]++;
+}
+
+/// PRIVATE ///
+char *SingleReadClassifier::getTagAtEndBreak(SupportBreak *suppoBreak,
+ char *tag,
+ uint length,
+ uint shift) {
+ if (length > parameters->max_bases_retrieved)
+ return NULL;
+
+ uint pos = suppoBreak->getPositionEndBreak();
+ char *dna = new char[length+1];
+ dna[length] = 0;
+ strncpy(dna, &tag[pos+shift-length+1], length);
+ return dna;
+}
+
+void SingleReadClassifier::perform_deep_snp_search(SupportBreak *sbreak, uint break_num) {
+
+ if (! sbreak->isBiologicalEvent()
+ || sbreak->getScoreComputedIntraExon() > parameters->p_value_variation_biological)
+ return;
+ // For now, we currently search substitutions.
+
+ uint loc_break; // location of the k-mer before or after the break
+ uint loc_snp; // location of the putative SNP
+ // number of nucleotides for the comparison (the minimum is specified here,
+ // but that can be larger)
+ uint nb_nuc = parameters->number_nucleotides_snp_comparison;
+
+ uchar *test_qmer; // test q-mer from the read that (may) contain
+ // the SNP (the SNP is at the end of the q-mer in the case of a start break
+ // and at the start of the q-mer in the case of an end break)
+ uint loc_test_qmer; /* putative location of the test q-mer on the
+ * genome */
+ uchar *real_content; // real DNA from the genome, including the SNP that should correspond to test_qmer
+ uint pos_snp_in_qmer; // position of the putative SNP in the test q-mer
+ uint pos_of_test_qmer; // position of the modified q-mer in the read
+ int strand = 0;
+
+ // Variables used to update the break's informations
+ uint pos_start_break;
+ uint pos_end_break;
+ uint loc_start_break;
+ uint loc_end_break;
+
+ const char *read = taginfo->getTag();
+ uint read_length = taginfo->getSupportObject()->getTagLength();
+ if (sbreak->hasNoStartBreak()
+ && sbreak->getPositionEndBreak() >= nb_nuc ) {
+
+ nb_nuc = max(nb_nuc, sbreak->getPositionEndBreak());
+ test_qmer = new uchar[nb_nuc+2];
+
+ // End break's most likely location
+ // SNP should be one position before (on fwd strand)
+ pos_end_break = sbreak->getPositionEndBreak();
+ loc_end_break = loc_break = taginfo->getLocationEndBreak(break_num);
+ strand = taginfo->getChrPosEndBreak(break_num)->getStrand();
+ if (strand == -1) {
+ loc_end_break += taginfo->getThreshold() - nb_nuc;
+ }
+ pos_of_test_qmer = sbreak->getPositionEndBreak() - nb_nuc;
+ pos_start_break = pos_of_test_qmer + 1;
+ strncpy((char *)test_qmer,
+ &read[pos_of_test_qmer],
+ nb_nuc+1);
+ pos_snp_in_qmer = nb_nuc;
+ if (strand == 1) {
+ loc_test_qmer = loc_break - (1 + nb_nuc);
+ loc_snp = loc_break - 1;
+ loc_start_break = loc_test_qmer; // starts at the same position as the test-qmer
+ } else {
+ loc_test_qmer = loc_break + taginfo->getThreshold();
+ loc_snp = loc_test_qmer;
+ loc_start_break = loc_test_qmer + 1; // ends one position before the test q-mer
+
+ }
+ } else if (sbreak->hasNoEndBreak()
+ && sbreak->getPositionStartBreak() + taginfo->getThreshold() + nb_nuc <= read_length) {
+ nb_nuc = read_length - (sbreak->getPositionStartBreak() + taginfo->getThreshold());
+ test_qmer = new uchar[nb_nuc+2];
+
+ loc_break = taginfo->getLocationStartBreak(break_num);
+ pos_of_test_qmer = sbreak->getPositionStartBreak() + taginfo->getThreshold() - 1;
+ pos_end_break = pos_of_test_qmer;
+ pos_start_break = pos_end_break - nb_nuc + 1;
+ strand = taginfo->getChrPosStartBreak(break_num)->getStrand();
+ loc_start_break = loc_break + strand*(pos_start_break - sbreak->getPositionStartBreak());
+ if (strand == -1)
+ // If we are on the reverse strand, we must correct the position since the threshold changed
+ // (on the reverse strand, the position depends on the threshold)
+ loc_start_break += taginfo->getThreshold() - nb_nuc;
+
+ strncpy((char *)test_qmer,
+ &read[pos_of_test_qmer],
+ nb_nuc+1);
+ pos_snp_in_qmer = 0;
+
+ if (strand == 1) {
+ loc_test_qmer = loc_break + taginfo->getThreshold();
+ loc_snp = loc_test_qmer;
+ loc_end_break = loc_test_qmer + 1; // starts one position after the snp
+ } else {
+ loc_test_qmer = loc_break - 1 - nb_nuc;
+ loc_snp = loc_break - 1;
+ loc_end_break = loc_test_qmer; // ends at the same pos as the q-mer with the SNP
+ }
+ } else {
+ return;
+ }
+
+ test_qmer[nb_nuc + 1]=0;
+ real_content = genome->getGenomeSubstring(loc_test_qmer, nb_nuc+1, strand);
+
+ snp_type type = SNP_UNKNOWN;
+ bool match = true;
+ for (uint i=0, j=0; match && i <= nb_nuc && j <= nb_nuc; i++, j++) {
+ if (real_content[i] != test_qmer[j]) {
+ if (i == j && i == pos_snp_in_qmer)
+ type = SNP_SUBSTITUTION;
+ else
+ match = false;
+ }
+ }
+
+ ChrPosition *pchrPos = (genome->getChrPos(loc_snp, strand));
+ ChrPosition chrPos(*pchrPos);
+ delete pchrPos;
+ if (type == SNP_SUBSTITUTION && match) {
+ taginfo->changeGenericElement(INFO_BIOLOGICAL_UNDETERMINED, INFO_SNP,
+ MASK_BIOLOGICAL_UNDETERMINED, MASK_SNP,
+ break_num, 0,
+ new SNPInfo(chrPos, pos_of_test_qmer + pos_snp_in_qmer,
+ sbreak->getScoreComputedIntraExon(),
+ taginfo->isDuplicated(break_num),
+ test_qmer[pos_snp_in_qmer],
+ real_content[pos_snp_in_qmer]));
+ // Update break's informations
+ sbreak->setPositionStartBreak(pos_start_break);
+ sbreak->setPositionEndBreak(pos_end_break);
+ sbreak->setThreshold(nb_nuc);
+ sbreak->setLocationStartBreak(loc_start_break);
+ sbreak->setLocationEndBreak(loc_end_break);
+ sbreak->setStrandStartBreak(strand);
+ sbreak->setStrandEndBreak(strand);
+ sbreak->computeScore(pos_start_break, pos_end_break);
+ }
+ delete [] test_qmer;
+ free(real_content);
+}
+
+uint SingleReadClassifier::isStringentChimera(SupportBreak *sbreak, uint break_num) {
+
+ // TODO add tests for strigent-chimera option
+ uint is_strigent_chimera = 0;
+
+ // Check the size of support with higer expectations than usual
+ if (sbreak->getTagBreakLength() < parameters->stringent_chimera_min_break_length) {
+ is_strigent_chimera = 1;
+ }
+
+ // Check if the break where the chimera is from has a number of merges < to the related parameter
+ if(is_strigent_chimera == 0 && sbreak->getNbMerges() > parameters->stringent_chimera_max_number_of_merges) {
+ is_strigent_chimera = 2;
+ }
+
+ // Check if the break is in a repeated region
+ // TODO naive check, we should try to know how far is the repeat region
+ // from the chimera and add a min length parameter in const.h
+ if (is_strigent_chimera == 0 && taginfo->getSupportObject()->hasRepeat()) {
+ is_strigent_chimera = 3;
+ }
+
+ // Check interquartile range of support values in the break
+ if(is_strigent_chimera == 0 && (float)(sbreak->getInsideQuartile4() - sbreak->getInsideQuartile1()) > sbreak->getAverageHighInside()*PERCENT_SUPPORT_VARIATION_ALMOST_NORMAL) {
+ is_strigent_chimera = 4;
+ }
+
+ // Check if we found a single loc before and after the break within a window of k-1
+ if(is_strigent_chimera == 0){
+ int first_single_loc_before_break, first_single_loc_after_break;
+ uint startBreak = sbreak->getPositionStartBreak();
+ uint endBreak = sbreak->getPositionEndBreak();
+ int max_ext_length = parameters->threshold - (endBreak - startBreak + 1) - 1;
+
+ if(max_ext_length > 0) {
+ // First we try to find a single loc before the break
+ first_single_loc_before_break = startBreak - 1;
+ while (first_single_loc_before_break >= 0 &&
+ suppo->getNbLocs()[first_single_loc_before_break] != 1 &&
+ (int) (startBreak - first_single_loc_before_break) <= max_ext_length) {
+ first_single_loc_before_break--;
+ }
+
+ // First we try to find a single loc before the break
+ first_single_loc_after_break = endBreak + 1;
+ while (first_single_loc_after_break < (int) suppo->getLength() &&
+ suppo->getNbLocs()[first_single_loc_after_break] != 1 &&
+ (int) (first_single_loc_after_break - endBreak) <= max_ext_length) {
+ first_single_loc_after_break++;
+ }
+
+ if(first_single_loc_before_break < 0 || first_single_loc_after_break >= (int) suppo->getLength() ||
+ (first_single_loc_after_break - first_single_loc_before_break) >= (int) parameters->threshold) {
+ is_strigent_chimera = 6;
+ }
+ }
+ }
+
+ // Check a k_mer location profile after and before the chimera
+ if(is_strigent_chimera == 0) {
+ uint start_break = sbreak->getPositionStartBreak();
+ uint end_break = sbreak->getPositionEndBreak();
+ Support *suppo = taginfo->getSupportObject();
+ int before_pos = start_break - parameters->max_extension_length * 2;
+ bool loc_match_found = false;
+ uint nb_locs;
+
+ // if the k-mer before the chimera is in the support
+ if ( before_pos >= 0 && before_pos < (int) suppo->getLength()) {
+ if(suppo->getNbLocs()[before_pos] > 0) {
+ ChrPosition *start_break_pos = sbreak->getChrPosition(START_BREAK);
+ if(start_break_pos) {
+ ChrPosition *before_chrPos;
+ pair <uint, uint> before_range;
+ ulong *locs_before_pos;
+
+ if(start_break_pos->getStrand() == 1) {
+ before_range = suppo->getKmerRange(before_pos,FORWARD_STRAND);
+ }
+ else {
+ before_range = suppo->getKmerRange(before_pos,REVERSE_STRAND);
+ }
+
+ genome->getOccurrencesFMIndexRange(before_range.first,
+ before_range.second,
+ &locs_before_pos);
+
+ nb_locs = min(before_range.second - before_range.first + 1,genome->getNbLocations());
+ uint i = 0;
+ while(!loc_match_found && i < nb_locs) {
+ before_chrPos = genome->getChrPos(locs_before_pos[i],start_break_pos->getStrand());
+ long long int relativeDist = labs((long long int)before_chrPos->getRelativePosition() - (long long int)start_break_pos->getRelativePosition());
+ if (((before_chrPos->getRelativePosition() < start_break_pos->getRelativePosition()) == (start_break_pos->getStrand() == 1))
+ && strcmp(before_chrPos->getChrPosition(),start_break_pos->getChrPosition()) == 0
+ && relativeDist < parameters->max_splice_length) {
+ loc_match_found = true;
+ }
+ delete before_chrPos;
+ i++;
+ }
+ free(locs_before_pos);
+ if (!loc_match_found)
+ is_strigent_chimera = 5;
+ }
+ if (start_break_pos)
+ delete start_break_pos;
+ }
+ }
+ // if the k-mer after the chimera is still in the support
+ if (is_strigent_chimera == 0) {
+ int after_pos = end_break + parameters->max_extension_length * 2;
+ if (after_pos < (int) suppo->getLength() && after_pos >= 0) {
+ if(suppo->getNbLocs()[after_pos] > 0) {
+ ChrPosition *end_break_pos = sbreak->getChrPosition(END_BREAK);
+ if(end_break_pos) {
+ ChrPosition *after_chrPos;
+ pair <uint, uint> after_range;
+ ulong *locs_after_pos;
+
+ if(end_break_pos->getStrand() == 1) {
+ after_range = suppo->getKmerRange(after_pos,FORWARD_STRAND);
+ }
+ else {
+ after_range = suppo->getKmerRange(after_pos,REVERSE_STRAND);
+ }
+
+ genome->getOccurrencesFMIndexRange(after_range.first,
+ after_range.second,
+ &locs_after_pos);
+
+ nb_locs = min(after_range.second - after_range.first + 1,genome->getNbLocations());
+ uint i = 0;
+ loc_match_found = false;
+ while(!loc_match_found && i < nb_locs) {
+ after_chrPos = genome->getChrPos(locs_after_pos[i],end_break_pos->getStrand());
+ long long int relativeDist = labs((long long int)after_chrPos->getRelativePosition() - (long long int)end_break_pos->getRelativePosition());
+ if (((after_chrPos->getRelativePosition() > end_break_pos->getRelativePosition()) == (end_break_pos->getStrand() == 1))
+ && strcmp(after_chrPos->getChrPosition(),end_break_pos->getChrPosition()) == 0
+ && relativeDist < parameters->max_splice_length) {
+ loc_match_found = true;
+ }
+ delete after_chrPos;
+ i++;
+ }
+ free(locs_after_pos);
+ if (!loc_match_found)
+ is_strigent_chimera = 5;
+ }
+ if (end_break_pos)
+ delete end_break_pos;
+ }
+ }
+ }
+ }
+
+ return is_strigent_chimera;
+}
+
+/****************************************
+* PairedEndReadClassifier *
+****************************************/
+
+PairedEndReadClassifier::PairedEndReadClassifier(uint tagId1, uint tagId2,
+ LocateOnGenome *genome,
+ gkArrays *tags,
+ Parameters *parameters) {
+ this->tags = tags;
+ this->genome = genome;
+ this->parameters = parameters;
+ this->paired_end_chimera = 0;
+ classifier1 = new SingleReadClassifier(tagId1,genome,tags,parameters);
+ classifier2 = new SingleReadClassifier(tagId2,genome,tags,parameters);
+}
+
+PairedEndReadClassifier::~PairedEndReadClassifier() {
+ delete classifier1;
+ delete classifier2;
+}
+
+void PairedEndReadClassifier::classify() {
+ classifier1->classify();
+ classifier2->classify();
+
+ TagInfo *taginfo1 = classifier1->getTagInfo();
+ TagInfo *taginfo2 = classifier2->getTagInfo();
+
+ // reclassement of the chimera(s) in the first read
+ uint i = 0;
+ while (i < taginfo1->getNbSpliceInter()) {
+ if(!chimeraPairedEndCheck(taginfo1->getInfosSpliceInter()[i],classifier2)) {
+ taginfo1->removeSpliceInter(i,"Chimera reclassification because paired-end informations does not match the chimera.");
+ } else {
+ i++;
+ }
+ }
+
+ // reclassement of the chimera(s) in the second read
+ i = 0;
+ while (i < taginfo2->getNbSpliceInter()) {
+ if(!chimeraPairedEndCheck(taginfo2->getInfosSpliceInter()[i],classifier1)) {
+ taginfo2->removeSpliceInter(i,"Chimera reclassification because paired-end informations does not match the chimera.");
+ } else {
+ i++;
+ }
+ }
+
+ // Looking for paired-end chimera
+ if(taginfo1->isSingle() && taginfo2->isSingle() && !taginfo1->hasSpliceInterChr() && !taginfo2->hasSpliceInterChr()) {
+ ChrPosition *paire1 = taginfo1->getLocation();
+ ChrPosition *paire2 = taginfo2->getLocation();
+
+ if(paire1 != NULL && paire2 != NULL) {
+
+ if(strcmp(paire1->getChrPosition(), paire2->getChrPosition()) != 0) {
+ paired_end_chimera = 1;
+ } else {
+ if(paire1->getStrand() != paire2->getStrand()) {
+ long long int relativeDist = labs((long long int)paire1->getRelativePosition() - (long long int)paire2->getRelativePosition());
+ if((paire1->getStrand() == 1) && (paire1->getRelativePosition() > paire2->getRelativePosition() && relativeDist > taginfo2->getSupportLength())) {
+ paired_end_chimera = 3;
+ } else if((paire2->getStrand() == 1) && (paire2->getRelativePosition() > paire1->getRelativePosition() && relativeDist > taginfo1->getSupportLength())) {
+ paired_end_chimera = 3;
+ } else if(relativeDist > parameters->max_splice_length) {
+ paired_end_chimera = 2;
+ }
+ } else { // Paired-end read should be located on opposite strand according to the protocol
+ paired_end_chimera = 4;
+ }
+ }
+ }
+ }
+}
+
+ostream &PairedEndReadClassifier::samOutput(ostream &os) {
+ vector<SamLine*> *sam_lines1 = getFirstTagInfo()->getSamLines();
+ vector<SamLine*> *sam_lines2 = getSecondTagInfo()->getSamLines();
+
+ SamLine *primary_line1 = (*sam_lines1)[0];
+ SamLine *primary_line2 = (*sam_lines2)[0];
+
+
+ // If PE read is mapped we print paired-end additional fields
+ if(!primary_line2->isSegmentUnmapped()) {
+ ostringstream additionalInfos;
+ additionalInfos << "loc:" << getSecondTagInfo()->isSingle() << ':' << getSecondTagInfo()->isDuplication() << ':' << getSecondTagInfo()->isMultiple();
+ // If there is a chimera between both reads, we print that
+ // piece of information
+ if(this->hasPairedEndChimera()) {
+ additionalInfos << ";chimera:" << *getFirstTagInfo()->getLocation() << ':' << *getSecondTagInfo()->getLocation();
+ }
+ primary_line1->addOptionalField("XP",additionalInfos.str());
+ }
+
+
+ setPairedEndOptionalFields(*primary_line1,*primary_line2);
+ setPairedEndOptionalFields(*primary_line2,*primary_line1);
+
+ writeSamLines(os,*sam_lines1,*primary_line1,*primary_line2,true);
+ writeSamLines(os,*sam_lines2,*primary_line2,*primary_line1,false);
+
+ for (vector<SamLine*>::iterator it = sam_lines1->begin() ; it != sam_lines1->end(); ++it)
+ delete (*it);
+ delete sam_lines1;
+ for (vector<SamLine*>::iterator it = sam_lines2->begin() ; it != sam_lines2->end(); ++it)
+ delete (*it);
+ delete sam_lines2;
+
+ return os;
+}
+
+void PairedEndReadClassifier::setPairedEndOptionalFields(SamLine &line, const SamLine &paired_line) {
+ ostringstream string_stream;
+
+ line.addOptionalField("R2",paired_line.getSeq());
+ string_stream << paired_line.getCigar();
+ line.addOptionalField("MC",string_stream.str());
+ line.addOptionalField("MQ",paired_line.getMapQ());
+}
+
+void PairedEndReadClassifier::writeSamLines(ostream &os, vector<SamLine*> &sam_lines, SamLine &primary_line, SamLine &paired_primary_line, bool is_first_taginfo) {
+ // We add informations about paired-end in the SAM lines
+ // Setting flag bits for paired-end
+ for (vector<SamLine*>::iterator it = sam_lines.begin() ; it != sam_lines.end(); ++it) {
+ // Set FLAG
+ if(is_first_taginfo) {
+ (*it)->setFirstSegmentInTheTemplate();
+ } else {
+ (*it)->setLastSegmentInTheTemplate();
+ }
+ (*it)->setTemplateHavingMultipleSegments();
+ if(primary_line.isSegmentUnmapped() || paired_primary_line.isSegmentUnmapped()) {
+ (*it)->unsetEachSegmentsMapped();
+ } else {
+ (*it)->setEachSegmentsMapped();
+ }
+ if(paired_primary_line.isSegmentUnmapped())
+ (*it)->setNextSegmentUnmapped();
+ if(paired_primary_line.isSeqReverseComplemented())
+ (*it)->setNextSeqReverseComplemented();
+ // Set Pnext (field 7)
+ (*it)->setPnext(paired_primary_line.getPos());
+ // Set Rnext (field 8)
+ if((*it)->getRname() == paired_primary_line.getRname()) {
+ (*it)->setRnext("=");
+ } else {
+ (*it)->setRnext(paired_primary_line.getRname());
+ }
+ // Set TLEN (field 9)
+ // if both segment are mapped to the same reference
+ if(!primary_line.isSegmentUnmapped() && !paired_primary_line.isSegmentUnmapped()
+ && primary_line.getRname() == paired_primary_line.getRname()) {
+ int tlen = 0;
+ if(primary_line.getPos() < paired_primary_line.getPos()) {
+ tlen = (paired_primary_line.getPos() + paired_primary_line.getCigar().getReferenceAlignementLength()) - primary_line.getPos();
+ // Confused definition of tlen, should we compute a genomic distance
+ // or an exonic distance?
+ //tlen = (paired_primary_line.getPos() + paired_primary_line.getCigar().getNbDeletions())
+ // - (primary_line.getPos() + primary_line.getCigar().getNbPositionsRead());
+ } else if (primary_line.getPos() > paired_primary_line.getPos()) {
+ tlen = paired_primary_line.getPos() - (primary_line.getPos() + primary_line.getCigar().getReferenceAlignementLength());
+ //tlen = (paired_primary_line.getPos() + paired_primary_line.getCigar().getNbPositionsRead())
+ // - (primary_line.getPos() + primary_line.getCigar().getNbDeletions());
+ }
+ (*it)->setTlen(tlen);
+ //primary_line1->setTlen(primary_line1->getPos() - (primary_line2->getPos() + primary_line2->getCigar().getReferenceAlignementLength())
+ //primary_line2->setTlen(primary_line2->getPos() - (primary_line1->getPos() + primary_line1->getCigar().getReferenceAlignementLength())
+ }
+ (*it)->writeLine(os);
+ }
+}
+
+readIterator *PairedEndReadClassifier::setInfos(readIterator *readIt) {
+ classifier1->setInfos(readIt);
+ classifier2->setInfos(readIt);
+ return readIt;
+}
+
+
+void PairedEndReadClassifier::writeOutputs(ostream *snp
+ , ostream *bioTagIndel
+ , ostream *seqErr
+ , ostream *splice
+ , ostream *spliceNoCover
+ , ostream *spliceInter
+ , ostream *undetermined
+ , ostream *repetition
+ , ostream *duplication
+ , ostream *nothing
+ , ostream *normal
+ , ostream *almostNormal
+ , ostream *multiple
+ , ostream *none
+ , ostream *bioUndermined
+ , ostream *single) {
+
+ classifier1->writeOutputs(snp,
+ bioTagIndel,
+ seqErr,
+ splice,
+ spliceNoCover,
+ spliceInter,
+ undetermined,
+ repetition,
+ duplication,
+ nothing,
+ normal,
+ almostNormal,
+ multiple,
+ none,
+ bioUndermined,
+ single);
+
+ classifier2->writeOutputs(snp,
+ bioTagIndel,
+ seqErr,
+ splice,
+ spliceNoCover,
+ spliceInter,
+ undetermined,
+ repetition,
+ duplication,
+ nothing,
+ normal,
+ almostNormal,
+ multiple,
+ none,
+ bioUndermined,
+ single);
+}
+
+void PairedEndReadClassifier::updateStatistics(uint (*nb_classes)[NB_MASKS+1], uint *nb_explainable) {
+ classifier1->updateStatistics(nb_classes, nb_explainable);
+ classifier2->updateStatistics(nb_classes, nb_explainable);
+ if(this->hasPairedEndChimera()) {
+ (*nb_classes)[posBitInMask(MASK_PAIRED_END_CHIMERA)]++;
+ }
+}
+
+TagInfo *PairedEndReadClassifier::getFirstTagInfo() {
+ return classifier1->getTagInfo();
+}
+
+TagInfo *PairedEndReadClassifier::getSecondTagInfo() {
+ return classifier2->getTagInfo();
+}
+
+bool PairedEndReadClassifier::hasPairedEndChimera() {
+ return paired_end_chimera > 0;
+}
+
+void PairedEndReadClassifier::writePairedEndChimera(ostream *pairedEndChimera) {
+ // If there is a chimera between the paired-end tags
+ if(this->hasPairedEndChimera()) {
+ *pairedEndChimera << paired_end_chimera << " " << getFirstTagInfo()->getReadNumber() << " " << *getFirstTagInfo() << " " << getSecondTagInfo()->getReadNumber() << " " << *getSecondTagInfo() << endl;
+ }
+}
+
+/// PRIVATE ///
+bool PairedEndReadClassifier::chimeraPairedEndCheck(SpliceInterInfo *chimera,
+ SingleReadClassifier *pairedEndClassifier) {
+ TagInfo *pairedEndTag = pairedEndClassifier->getTagInfo();
+ ChrPosition P1 = chimera->getChrPosition(); // Position of the chimera before the break
+ ChrPosition P2 = chimera->getChromosomeDest(); // Position of the chimera before the break
+ ChrPosition *pairePos = NULL;
+
+ if (pairedEndTag->isSingle())
+ pairePos = pairedEndTag->getLocation(); // Position of the paired-end read only if it is the once (otherwise it is crap!!!)
+
+ bool isAValidChimera = false;
+
+ // If the paired-end read is located and has no chimera
+ if (pairePos != NULL && !pairedEndTag->hasSpliceInterChr()) {
+ // ------------------------------------
+ // 1. We use P1 position of the chimera
+ // ------------------------------------
+ // a) P1(+) Case
+ // ^ (P1)
+ // -------|\\\\\|--------- strand : +
+ // ======================================================= (ADN)
+ // -------------------- (paired-end read) strand : -
+ if (P1.getStrand() == 1) {
+ if (P1.getStrand() != pairePos->getStrand() &&
+ strcmp(P1.getChrPosition(), pairePos->getChrPosition()) == 0 &&
+ P1.getRelativePosition() >= pairePos->getRelativePosition() &&
+ (P1.getRelativePosition() - pairePos->getRelativePosition()) <= parameters->max_splice_length) {
+ isAValidChimera = true;
+ }
+ } else if (!isAValidChimera) {
+ // b) P1(-) Case
+ // (paired-end read) -------------------- strand : +
+ // ======================================================= (ADN)
+ // -------|\\\\\|--------- strand : -
+ // ^ (P1)
+ if (P1.getStrand() != pairePos->getStrand() &&
+ strcmp(P1.getChrPosition(), pairePos->getChrPosition()) == 0 &&
+ P1.getRelativePosition() <= pairePos->getRelativePosition() &&
+ (pairePos->getRelativePosition() - P1.getRelativePosition()) <= parameters->max_splice_length) {
+ isAValidChimera = true;
+ }
+ }
+ // ------------------------------------
+ // 2. We use P2 position of the chimera
+ // ------------------------------------
+ // a) P2(+) Case
+ // ^ (P2)
+ // -------|\\\\\|--------- strand : +
+ // ======================================================= (ADN)
+ // (paired-end read) -------------------- strand : -
+ if (P2.getStrand() == 1) {
+ if (P2.getStrand() != pairePos->getStrand() &&
+ strcmp(P2.getChrPosition(), pairePos->getChrPosition()) == 0 &&
+ P2.getRelativePosition() <= pairePos->getRelativePosition() &&
+ (pairePos->getRelativePosition() - P2.getRelativePosition()) <= parameters->max_splice_length) {
+ isAValidChimera = true;
+ }
+ } else if (!isAValidChimera) {
+ // b) P2(-) Case
+ // -------------------- (paired-end read) strand : +
+ // ======================================================= (ADN)
+ // -------|\\\\\|--------- strand : +
+ // ^ (P2)
+ if (P2.getStrand() != pairePos->getStrand() &&
+ strcmp(P2.getChrPosition(), pairePos->getChrPosition()) == 0 &&
+ P2.getRelativePosition() >= pairePos->getRelativePosition() &&
+ (P2.getRelativePosition() - pairePos->getRelativePosition()) <= parameters->max_splice_length) {
+ isAValidChimera = true;
+ }
+ }
+ } else {
+ // no assumption can be made about the paired-end tag, the chimera is not discarded
+ isAValidChimera = true;
+ }
+
+ return isAValidChimera;
+}
diff --git a/src/Classifier.h b/src/Classifier.h
new file mode 100644
index 0000000..2027dee
--- /dev/null
+++ b/src/Classifier.h
@@ -0,0 +1,398 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at univ-montp2.fr *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef CLASSIFIER_H
+#define CLASSIFIER_H
+
+#include <iostream>
+#include <gkArrays.h>
+#include "libReadsInfo/tagInfo.h"
+#include "Support.h"
+#include "const.h"
+#include "SupportBreak.h"
+#include <config.h>
+
+class Classifier {
+protected:
+ string output_sam;
+
+public:
+ virtual ~Classifier(){}
+
+ /*
+ * Classify read(s) depending of the implementation
+ * of Classifier
+ */
+ virtual void classify()=0;
+
+ /*
+ * Set Informations about read(s) using the readIteror
+ */
+ virtual readIterator *setInfos(readIterator *readIt)=0;
+
+ /**
+ * Write the line(s) in SAM file
+ */
+ virtual ostream &samOutput(ostream &os)=0;
+
+
+ /**
+ * Print specific information about classification in
+ * each file
+ */
+ virtual void writeOutputs(ostream *snp
+ , ostream *bioTagIndel
+ , ostream *seqErr
+ , ostream *splice
+ , ostream *spliceNoCover
+ , ostream *spliceInter
+ , ostream *undetermined
+ , ostream *repetition
+ , ostream *duplication
+ , ostream *nothing
+ , ostream *normal
+ , ostream *almostNormal
+ , ostream *multiple
+ , ostream *none
+ , ostream *bioUndermined
+ , ostream *single)=0;
+
+ /**
+ * Update statitics about classification
+ */
+ virtual void updateStatistics(uint (*nb_classes)[NB_MASKS+1], uint *nb_explainable)=0;
+
+};
+
+class SingleReadClassifier : public Classifier {
+private:
+ Support *suppo;
+ TagInfo *taginfo;
+ gkArrays *tags;
+ LocateOnGenome *genome;
+ Parameters *parameters;
+ uint tagId;
+
+public:
+ /**
+ * Constructor of SingleReadClassifier
+ *
+ * @param tagId the id of the tag in the gkArrays
+ * @param genome the LocateOnGenome object
+ * @param tags the gkArrays object
+ * @param parameters the parameters object
+ */
+ SingleReadClassifier(uint tagId, LocateOnGenome *genome, gkArrays *tags, Parameters *parameters);
+ ~SingleReadClassifier();
+
+ /**
+ * Classify the read contained if the classifier
+ */
+ virtual void classify();
+
+ /**
+ * Set Informations about the read using the iterator.
+ * This method also move the iterator one step further.
+ */
+ virtual readIterator *setInfos(readIterator *readIt);
+
+ /**
+ * Print the SAM line of the read in the file in arguement
+ *
+ * @param os the stream where the SAM line will be written
+ */
+ virtual ostream &samOutput(ostream &os);
+
+ /**
+ * Print informations about the classification of the read
+ * in the related stream
+ */
+ virtual void writeOutputs(ostream *snp
+ , ostream *bioTagIndel
+ , ostream *seqErr
+ , ostream *splice
+ , ostream *spliceNoCover
+ , ostream *spliceInter
+ , ostream *undetermined
+ , ostream *repetition
+ , ostream *duplication
+ , ostream *nothing
+ , ostream *normal
+ , ostream *almostNormal
+ , ostream *multiple
+ , ostream *none
+ , ostream *bioUndermined
+ , ostream *single);
+
+ /**
+ * Update the statistics about classification with the current classified read
+ *
+ * @param nb_classes the array containing statistics about each type of classification
+ * @param nb_explainable the number of read explainable
+ */
+ virtual void updateStatistics(uint (*nb_classes)[NB_MASKS+1], uint *nb_explainable);
+
+ /**
+ * @return the tag id of the read handled by the classifier
+ */
+ uint getTagId();
+
+ /**
+ * @return the tagInfo that has been created by the classifier.
+ */
+ TagInfo *getTagInfo();
+
+private:
+ /**
+ * Return a substring of the tag of length <length> and which
+ * ends at the position corresponding to the end of the break.
+ * The position retrieved can be shifted using value <shift>.
+ * length > params->max_bases_retrieved => result == NULL
+ */
+ char *getTagAtEndBreak(SupportBreak *suppoBreak, char *tag,
+ uint length, uint shift=0);
+
+ /**
+ * Try to find a SNP even is some information is lacking (eg. the break
+ * is not complete).
+ * This is done by naively retrieving the modified nucleotide on the genome
+ * and to check if we succeed to locate (a) k-mer(s) on the genome when
+ * correcting the faulty nucleotide.
+ * @post if a (or several) SNP(s) is/are found, the TagInfo is updated
+ * accordingly.
+ */
+ void perform_deep_snp_search(SupportBreak *, uint break_num);
+
+ /**
+ * Tests if the supportBreak that have been classified as a chimera
+ * is a stringent chimera according to stringent classification tests.
+ * This function stops when one of the test has failed and return a
+ * specific flag for this cause.
+ * This does not mean that the chimera has only failed this tests, but
+ * that this test is the first one that has failed.
+ *
+ * @return 0 if the chimera is stringent
+ * 1 if the chimera has a break_length too small
+ * 2 if the chimera comes from a break with too many merges
+ * 3 if the chimera is in a repeated zone
+ * 4 if the chimera has a high support variation
+ * 5 if the kmer verification test doesn't match the chimera
+ * 6 if no single loc have been found around the break
+ */
+ uint isStringentChimera(SupportBreak *, uint break_num);
+};
+
+class PairedEndReadClassifier : public Classifier {
+private:
+ gkArrays *tags;
+ LocateOnGenome *genome;
+ Parameters *parameters;
+ SingleReadClassifier *classifier1;
+ SingleReadClassifier *classifier2;
+ // 0 : nothing
+ // 1 : Class 1 chimera
+ // 2 : Class 2 chimera
+ // 3 : Class 3 chimera
+ // 4 : Class 4 chimera
+ uint paired_end_chimera;
+
+public:
+ /**
+ * Constructor of PairedEndReadClassifier
+ *
+ * @param tagId1 the id of the first tag of the pair in the gkArrays
+ * @param tagId2 the id of the second tag of the pair in the gkArrays
+ * @param genome the LocateOnGenome object
+ * @param tags the gkArrays object
+ * @param parameters the parameters object
+ */
+ PairedEndReadClassifier(uint tagId1, uint tagId2, LocateOnGenome *genome, gkArrays *tags, Parameters *parameters);
+ ~PairedEndReadClassifier();
+
+ /**
+ * Classify paired-end reads contained in the classifier
+ */
+ virtual void classify();
+
+ /**
+ * Set Informations about the paird-end reads using the iterator.
+ * This method also move the iterator two step further.
+ */
+ virtual readIterator *setInfos(readIterator *readIt);
+
+ /**
+ * Print two SAM lines corresponding to the paired-end reads classified by the
+ * Classifier in the output file in parameter
+ *
+ * @param os the stream where the SAM lines will be written
+ */
+ virtual ostream &samOutput(ostream &os);
+
+ /**
+ * Print informations about the classification of paired-end reads
+ * in the related stream
+ */
+ virtual void writeOutputs(ostream *snp
+ , ostream *bioTagIndel
+ , ostream *seqErr
+ , ostream *splice
+ , ostream *spliceNoCover
+ , ostream *spliceInter
+ , ostream *undetermined
+ , ostream *repetition
+ , ostream *duplication
+ , ostream *nothing
+ , ostream *normal
+ , ostream *almostNormal
+ , ostream *multiple
+ , ostream *none
+ , ostream *bioUndermined
+ , ostream *single);
+ /**
+ * Update the statistics about classification with the information about paired-end reads classified
+ *
+ * @param nb_classes the array containing statistics about each type of classification
+ * @param nb_explainable the number of read explainable
+ */
+ virtual void updateStatistics(uint (*nb_classes)[NB_MASKS+1], uint *nb_explainable);
+
+ /**
+ * If the paired-end tags contains a chimera in the non sequenced region
+ * between the tags informations about it in the pairedEndChimera file.
+ * Otherwise nothing is done.
+ */
+ void writePairedEndChimera(ostream *pairedEndChimera);
+
+ /**
+ * Return true if the paired-end tags contains a chimera in the non sequenced
+ * region between the tags.
+ */
+ bool hasPairedEndChimera();
+
+ /**
+ * @return the tagInfo that has been created by the classifier.
+ */
+ TagInfo *getFirstTagInfo();
+ TagInfo *getSecondTagInfo();
+
+private:
+ /**
+ * Check if a chimera is valid according to the informations
+ * about its paired read location.
+ *
+ * @param chimera the chimera to analyze
+ * @param pairedEndClassifier the paired read classfier
+ * @return true if chimera is valid, false if not.
+ */
+ bool chimeraPairedEndCheck(SpliceInterInfo *chimera, SingleReadClassifier *pairedEndClassifier);
+
+ /*
+ * Set @line optional fields deticated to store mate informations
+ */
+ void setPairedEndOptionalFields(SamLine &line, const SamLine &paired_line);
+
+ /**
+ * Write a vector of samlines to the output stream. According to the primary
+ * line and the paired-end read primary line the method update some flags to
+ * be SAM consistent.
+ */
+ void writeSamLines(ostream &os, vector<SamLine*> &sam_lines, SamLine &primary_line, SamLine &paired_primary_line, bool is_first_taginfo);
+};
+#endif
diff --git a/src/Makefile.am b/src/Makefile.am
new file mode 100644
index 0000000..aae065a
--- /dev/null
+++ b/src/Makefile.am
@@ -0,0 +1,154 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+
+bin_PROGRAMS=crac
+
+CRAC_LINKS = crac-index
+
+all-local: $(bin_PROGRAMS) $(CRAC_LINKS)
+
+
+SUBDIRS = libReadsInfo libSSA libgzstream
+if INCLUDED_GKARRAYS
+ SUBDIRS += libGkArrays
+endif
+
+crac_SOURCES = \
+ basic.h const.h types.h \
+ Classifier.cpp Classifier.h \
+ classifyTags.cpp classifyTags.h \
+ locateServer.cpp locateServer.h \
+ crac.cpp \
+ Parameters.cpp Parameters.h \
+ SupportBreak.cpp SupportBreak.h \
+ CandidatBreak.cpp CandidatBreak.h \
+ Support.cpp Support.h \
+ utils.cpp utils.h
+crac_LDADD = @abs_builddir@/libSSA/libSSA.a @abs_builddir@/libReadsInfo/libReadsInfo.a @abs_builddir@/libgzstream/libgzstream.a
+
+#crac_index_SOURCES = @abs_srcdir@/libSSA/cracIndex.cpp
+#crac_index_LDADD = @abs_builddir@/libSSA/libSSA.a
+
+crac-index: @abs_builddir@/libSSA/crac-index
+ $(LN_S) -f $^ $@
+
+crac-emt: @abs_builddir@/libSSA/crac-emt
+ $(LN_S) -f $^ $@
+
+
+AM_LDFLAGS = -lm -lpthread -lSSA -lReadsInfo -L at abs_builddir@/libSSA -L at abs_builddir@/libReadsInfo -L at abs_builddir@/libgzstream
+AM_CPPFLAGS = -I at abs_top_srcdir@ -I at abs_srcdir@ -I at abs_srcdir@/libSSA -I at abs_srcdir@/libSSA/karkkainen_bwt -I at abs_srcdir@/libgzstream # -IlibSSA -IlibReadsInfo
+
+if INCLUDED_GKARRAYS
+ AM_LDFLAGS += -L at abs_builddir@/libGkArrays/src/.libs
+ AM_CPPFLAGS += -I at abs_srcdir@/libGkArrays/src/
+if INCLUDED_PROGRESSBAR
+ AM_LDFLAGS += -L at abs_builddir@/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar
+ AM_CPPFLAGS += -I at abs_srcdir@/libGkArrays/src/libProgressBar-1.2.0/
+endif
+endif
+
+crac_LDFLAGS = -lGkArrays $(AM_LDFLAGS)
+
+
+MOSTLYCLEANFILES=*~
+CLEANFILES=*~ $(EXTRA_PROGRAMS) $(CRAC_LINKS)
+DISTCLEANFILES=*~
+MAINTAINERCLEANFILES=*~
diff --git a/src/Makefile.in b/src/Makefile.in
new file mode 100644
index 0000000..2995997
--- /dev/null
+++ b/src/Makefile.in
@@ -0,0 +1,839 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
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+mostlyclean-generic:
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+
+clean-generic:
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+ -test -z "$(DISTCLEANFILES)" || rm -f $(DISTCLEANFILES)
+
+maintainer-clean-generic:
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+ @echo "it deletes files that may require special tools to rebuild."
+ -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
+clean: clean-recursive
+
+clean-am: clean-binPROGRAMS clean-generic clean-libtool mostlyclean-am
+
+distclean: distclean-recursive
+ -rm -rf ./$(DEPDIR)
+ -rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+ distclean-tags
+
+dvi: dvi-recursive
+
+dvi-am:
+
+html: html-recursive
+
+html-am:
+
+info: info-recursive
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+
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+
+install-exec-am: install-binPROGRAMS
+
+install-html: install-html-recursive
+
+install-html-am:
+
+install-info: install-info-recursive
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-recursive
+
+install-pdf-am:
+
+install-ps: install-ps-recursive
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-recursive
+ -rm -rf ./$(DEPDIR)
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-recursive
+
+mostlyclean-am: mostlyclean-compile mostlyclean-generic \
+ mostlyclean-libtool
+
+pdf: pdf-recursive
+
+pdf-am:
+
+ps: ps-recursive
+
+ps-am:
+
+uninstall-am: uninstall-binPROGRAMS
+
+.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) ctags-recursive \
+ install-am install-strip tags-recursive
+
+.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
+ all all-am all-local check check-am clean clean-binPROGRAMS \
+ clean-generic clean-libtool ctags ctags-recursive distclean \
+ distclean-compile distclean-generic distclean-libtool \
+ distclean-tags distdir dvi dvi-am html html-am info info-am \
+ install install-am install-binPROGRAMS install-data \
+ install-data-am install-dvi install-dvi-am install-exec \
+ install-exec-am install-html install-html-am install-info \
+ install-info-am install-man install-pdf install-pdf-am \
+ install-ps install-ps-am install-strip installcheck \
+ installcheck-am installdirs installdirs-am maintainer-clean \
+ maintainer-clean-generic mostlyclean mostlyclean-compile \
+ mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
+ tags tags-recursive uninstall uninstall-am \
+ uninstall-binPROGRAMS
+
+
+all-local: $(bin_PROGRAMS) $(CRAC_LINKS)
+
+#crac_index_SOURCES = @abs_srcdir@/libSSA/cracIndex.cpp
+#crac_index_LDADD = @abs_builddir@/libSSA/libSSA.a
+
+crac-index: @abs_builddir@/libSSA/crac-index
+ $(LN_S) -f $^ $@
+
+crac-emt: @abs_builddir@/libSSA/crac-emt
+ $(LN_S) -f $^ $@
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/src/Parameters.cpp b/src/Parameters.cpp
new file mode 100644
index 0000000..1673e33
--- /dev/null
+++ b/src/Parameters.cpp
@@ -0,0 +1,195 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "Parameters.h"
+#include "const.h"
+
+using namespace std;
+
+Parameters::Parameters(uint threshold,
+ uint max_nb_located_occs,
+ uint max_splice_length,
+ uint max_bio_ins_del,
+ uint max_localisation_duplication,
+ uint min_localisation_duplication,
+ float percent_min_unique_repetition,
+ float percent_min_duplicate,
+ uint min_occ_repetition,
+ float percent_support_variation_almost_normal,
+ float p_value_variation_biological,
+ float score_intra_ambiguous,
+ float score_inter_ambiguous,
+ uint max_bases_randomly_matched,
+ uint min_bases_before_break,
+ uint max_bases_retrieved,
+ int max_extension_length,
+ uint support_score_window_length,
+ uint nb_bases_substracted_low_average,
+ uint nb_positions_check_ones,
+ uint nb_tags_info_stored,
+ uint nb_threads,
+ float min_support_no_cover,
+ float max_support_out_no_cover,
+ float max_ambiguous_average_high,
+ float min_perc_ones_inside,
+ float min_ratio_support_fall,
+ float max_nb_overlapping_breaks,
+ float percent_min_single,
+ float percent_min_multiple,
+ bool deep_snp_search,
+ uint number_nucleotides_snp_comparison,
+ bool detailed_sam,
+ uint max_verynice_merge,
+ bool stringent_chimera,
+ uint stringent_chimera_min_break_length,
+ uint stringent_chimera_max_number_of_merges,
+ bool no_ambiguity,
+ bool treat_multiple,
+ bool show_progressbar
+ ):
+ threshold(threshold)
+ ,max_nb_located_occs(max_nb_located_occs)
+ ,max_splice_length(max_splice_length)
+ ,max_bio_ins_del(max_bio_ins_del)
+ ,max_localisation_duplication(max_localisation_duplication)
+ ,min_localisation_duplication(min_localisation_duplication)
+ ,percent_min_unique_repetition(percent_min_unique_repetition)
+ ,percent_min_duplicate(percent_min_duplicate)
+ ,min_occ_repetition(min_occ_repetition)
+ ,percent_support_variation_almost_normal(percent_support_variation_almost_normal)
+ ,p_value_variation_biological(p_value_variation_biological)
+ ,score_intra_ambiguous(score_intra_ambiguous)
+ ,score_inter_ambiguous(score_inter_ambiguous)
+ ,max_bases_randomly_matched(max_bases_randomly_matched)
+ ,min_bases_before_break(min_bases_before_break)
+ ,max_bases_retrieved(max_bases_retrieved)
+ ,max_extension_length(max_extension_length)
+ ,support_score_window_length(support_score_window_length)
+ ,nb_bases_substracted_low_average(nb_bases_substracted_low_average)
+ ,nb_positions_check_ones(nb_positions_check_ones)
+ ,nb_tags_info_stored(nb_tags_info_stored)
+ ,nb_threads(nb_threads)
+ ,min_support_no_cover(min_support_no_cover)
+ ,max_support_out_no_cover(max_support_out_no_cover)
+ ,max_ambiguous_average_high(max_ambiguous_average_high)
+ ,min_perc_ones_inside(min_perc_ones_inside)
+ ,min_ratio_support_fall(min_ratio_support_fall)
+ ,max_nb_overlapping_breaks(max_nb_overlapping_breaks)
+ ,percent_min_single(percent_min_single)
+ ,percent_min_multiple(percent_min_multiple)
+ ,deep_snp_search(deep_snp_search)
+ ,number_nucleotides_snp_comparison(number_nucleotides_snp_comparison)
+ ,detailed_sam(detailed_sam)
+ ,max_verynice_merge(max_verynice_merge)
+ ,stringent_chimera(stringent_chimera)
+ ,stringent_chimera_max_number_of_merges(stringent_chimera_max_number_of_merges)
+ ,no_ambiguity(no_ambiguity)
+ ,treat_multiple(treat_multiple)
+ ,show_progressbar(show_progressbar)
+{
+ if (max_nb_located_occs < min_occ_repetition){
+ cerr << "max_nb_located_occs must be greater than min_loc_repetition" << endl << endl;
+ exit(2);
+ }
+}
+
+void Parameters::init() {
+ min_break_length = (uint) (MIN_BREAK_LENGTH*threshold);
+ stringent_chimera_min_break_length = (uint) (STRINGENT_CHIMERA_MIN_BREAK_LENGTH*threshold);
+}
diff --git a/src/Parameters.h b/src/Parameters.h
new file mode 100644
index 0000000..075f85a
--- /dev/null
+++ b/src/Parameters.h
@@ -0,0 +1,198 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef PARAMETERS_H
+#define PARAMETERS_H
+#include <cstdlib>
+#include <iostream>
+#include "types.h"
+#include "const.h"
+
+class Parameters {
+
+ public:
+ uint threshold;
+ uint max_nb_located_occs;
+ uint max_splice_length;
+ uint max_bio_ins_del;
+ uint max_localisation_duplication;
+ uint min_localisation_duplication;
+ float percent_min_unique_repetition;
+ float percent_min_duplicate;
+ uint min_occ_repetition;
+ float percent_support_variation_almost_normal;
+ float p_value_variation_biological;
+ float score_intra_ambiguous;
+ float score_inter_ambiguous;
+ uint max_bases_randomly_matched;
+ uint min_bases_before_break;
+ uint max_bases_retrieved;
+ uint min_break_length;
+ int max_extension_length;
+ uint support_score_window_length;
+ uint nb_bases_substracted_low_average;
+ uint nb_positions_check_ones;
+ uint nb_tags_info_stored;
+ uint nb_threads;
+ float min_support_no_cover;
+ float max_support_out_no_cover;
+ float max_ambiguous_average_high;
+ float min_perc_ones_inside;
+ float min_ratio_support_fall;
+ float max_nb_overlapping_breaks;
+ float percent_min_single;
+ float percent_min_multiple;
+ bool deep_snp_search;
+ uint number_nucleotides_snp_comparison;
+ bool detailed_sam;
+ uint max_verynice_merge;
+ bool stringent_chimera;
+ uint stringent_chimera_max_number_of_merges;
+ uint stringent_chimera_min_break_length;
+ bool no_ambiguity;
+ bool treat_multiple;
+ bool show_progressbar;
+
+ Parameters(uint threshold=~0,
+ uint max_nb_located_occs=MAX_NB_LOCATED_OCCS,
+ uint max_splice_length=MAX_SPLICE_LENGTH,
+ uint max_bio_ins_del=MAX_BIO_INS_DEL,
+ uint max_localisation_duplication=MAX_LOCALISATION_DUPLICATION,
+ uint min_localisation_duplication=MIN_LOCALISATION_DUPLICATION,
+ float percent_min_unique_repetition=PERCENT_MIN_UNIQUE_REPETITION,
+ float percent_min_duplicate=PERCENT_MIN_DUPLICATE,
+ uint min_occ_repetition=MIN_OCC_REPETITION,
+ float percent_support_variation_almost_normal=PERCENT_SUPPORT_VARIATION_ALMOST_NORMAL,
+ float p_value_variation_biological=P_VALUE_VARIATION_BIOLOGICAL,
+ float score_intra_ambiguous=SCORE_INTRA_AMBIGUOUS,
+ float score_inter_ambiguous=SCORE_INTER_AMBIGUOUS,
+ uint max_bases_randomly_matched=MAX_BASES_RANDOMLY_MATCHED,
+ uint min_bases_before_break=MIN_BASES_BEFORE_BREAK,
+ uint max_bases_retrieved = MAX_BASES_RETRIEVED,
+ int max_extension_length = MAX_EXTENSION_LENGTH,
+ uint support_score_window_length = SUPPORT_SCORE_WINDOW_LENGTH,
+ uint nb_bases_substracted_low_average = NB_BASES_SUBSTRACTED_LOW_AVERAGE,
+ uint nb_positions_check_ones = NB_POSITIONS_CHECK_ONES,
+ uint nb_tags_info_stored = NB_TAGS_INFO_STORED,
+ uint nb_threads = NB_THREADS,
+ float min_support_no_cover = MIN_SUPPORT_NO_COVER,
+ float max_support_out_no_cover = MAX_SUPPORT_OUT_NO_COVER,
+ float max_ambiguous_average_high = MAX_AMBIGUOUS_AVERAGE_HIGH,
+ float min_perc_ones_inside = MIN_PERCENTAGE_ONES_INSIDE,
+ float min_ratio_support_fall = MIN_RATIO_SUPPORT_FALL,
+ float max_nb_overlapping_breaks = MAX_NB_OVERLAPPING_BREAKS,
+ float percent_min_single = PERCENT_MIN_SINGLE,
+ float percent_min_multiple = PERCENT_MIN_MULTIPLE,
+ bool deep_snp_search = DEEP_SNP_SEARCH,
+ uint number_nucleotides_snp_comparison = NUMBER_NUCLEOTIDES_SNP_COMPARISON,
+ bool detailed_sam = DETAILED_SAM,
+ uint max_verynice_merge = MAX_VERYNICE_MERGE,
+ bool stringent_chimera = STRINGENT_CHIMERA,
+ uint stringent_chimera_min_break_length = STRINGENT_CHIMERA_MIN_BREAK_LENGTH,
+ uint stringent_chimera_max_number_of_merges = STRINGENT_CHIMERA_MAX_NUMBER_OF_MERGES,
+ bool no_ambiguity=NO_AMBIGUITY,
+ bool treat_multiple=TREAT_MULTIPLE,
+ bool show_progressbar=true
+ );
+
+ void init();
+
+};
+
+#endif
diff --git a/src/Support.cpp b/src/Support.cpp
new file mode 100644
index 0000000..1304eff
--- /dev/null
+++ b/src/Support.cpp
@@ -0,0 +1,887 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <stdlib.h>
+#include <utility>
+#include "Support.h"
+#include "utils.h"
+
+Support::Support(Parameters *p, uint *s, uint num
+ ,LocateOnGenome *g, gkArrays *ind):
+ parameters(p), support(s), tag_num(num), length(ind->getSupportLength(num)),
+ threshold(ind->getThreshold()), tag_length(ind->getTagLength(num)),
+ current_tag(ind->getTag(num)), genome(g), tags(ind), nb_pos_located(0) {
+
+
+ // cerr << "tag length: "<< tag_length << endl;
+ // cerr << "current_tag: " << current_tag << endl << endl;
+ ulong nb_occs_sens, nb_occs_antisens;
+// ulong *occs_sens, *occs_antisens;
+ ulong total_occ;
+ bool located = true;
+
+ ulong max_nb_breaks = 10;
+ breaks = (SupportBreak**)malloc(sizeof(SupportBreak*)*max_nb_breaks);
+ ulong pos_break=0;
+
+
+// pos_occ = new uint[tag_length-threshold+1];
+// strand_occ = new int[tag_length-threshold+1];
+
+
+ nb_locs = new uint[length];
+
+ start_pos_repeat = -1;
+ end_pos_repeat = -1;
+ nb_breaks = 0;
+ nb_single = 0;
+ nb_multiple = 0;
+ nb_duplicate = 0;
+ almostNormal = false;
+ nb_locs_max = 0;
+
+ ranges_forward = new pair<uint, uint>[length];
+ ranges_reverse = new pair<uint, uint>[length];
+
+ for (ulong j=0; j < length; j++) {
+ ranges_forward[j] = genome->getFMIndexRange((uchar *)¤t_tag[j],threshold);
+ nb_occs_sens = (ranges_forward[j].first <= ranges_forward[j].second) ?
+ (ranges_forward[j].second - ranges_forward[j].first + 1):0;
+
+ ranges_reverse[j] = genome->getFMIndexReverseRange((uchar *)¤t_tag[j],threshold);
+ nb_occs_antisens = (ranges_reverse[j].first <= ranges_reverse[j].second) ?
+ (ranges_reverse[j].second - ranges_reverse[j].first + 1):0;
+ nb_locs[j] = nb_occs_antisens + nb_occs_sens;
+ if (nb_locs_max < nb_locs[j])
+ nb_locs_max = nb_locs[j];
+ }
+
+ computeBestLocation(true);
+
+ // temporary repeat start, end and length
+ int minRepeat = 0;
+ int start_pos_r = -1;
+ int end_pos_r = -1;
+ for (ulong j=0; j < length; j++) {
+ total_occ = nb_locs[j];
+
+ // almost normal
+ if (!almostNormal && (j+1) < length) {
+ almostNormal = ((support[j] > support[j+1]
+ && support[j]*(1.0 - parameters->percent_support_variation_almost_normal) > support[j+1])
+ || (support[j] < support[j+1] && support[j]*1/(1.0 - parameters->percent_support_variation_almost_normal) < support[j+1]));
+ }
+ if (total_occ > 0) {
+ nb_pos_located++;
+ // end of repetition in case of repetition (we suppose one
+ // repetition per tag)
+ if (total_occ < parameters->min_occ_repetition
+ && start_pos_repeat != -1 && end_pos_repeat == -1 ){
+ end_pos_repeat = j-1;
+ }
+ // only the longest repetition is saved
+ if (end_pos_repeat == (int)(j-1)) {
+ if (getRepeatLength() > minRepeat){
+ minRepeat = getRepeatLength();
+ start_pos_r = start_pos_repeat;
+ end_pos_r = end_pos_repeat;
+ }
+ start_pos_repeat = -1;
+ end_pos_repeat = -1;
+ }
+
+ // duplication
+ if (total_occ <= parameters->max_localisation_duplication) {
+
+ if (total_occ >= parameters->min_localisation_duplication
+ && total_occ <= parameters->max_localisation_duplication) {
+ nb_duplicate++;
+ }
+ } else {
+ nb_multiple++;
+ if(start_pos_repeat == -1
+ && total_occ >= parameters->min_occ_repetition){
+ start_pos_repeat = j;
+ }
+ }
+
+ if (total_occ == 1){
+ nb_single++;
+ }
+
+ // We didn't attribute the score of the previous break
+ // and we're yet quite far from the break, so we attribute it right now!
+ if (! located) {
+ // We have more breaks than expected.
+ // We expand the array.
+ if (nb_breaks > max_nb_breaks) {
+ max_nb_breaks *= 2;
+ breaks = (SupportBreak**)realloc(breaks, sizeof(SupportBreak*)*max_nb_breaks);
+ }
+
+ breaks[nb_breaks-1] = new SupportBreak(pos_break, j-1,
+ this, parameters,ranges_forward,
+ ranges_reverse);
+ }
+
+ located = true;
+
+ }else{
+ if (located) {
+ nb_breaks++;
+ pos_break = j;
+ }
+ located = false;
+ }
+ }
+
+ // save the biggest repetition
+ if (getRepeatLength() <= minRepeat){
+ start_pos_repeat = start_pos_r;
+ end_pos_repeat = end_pos_r;
+ }
+
+ if (! located) {
+ if (nb_pos_located) {
+ // We have more breaks than expected.
+ // We expand the array.
+ if (nb_breaks > max_nb_breaks) {
+ max_nb_breaks *= 2;
+ breaks = (SupportBreak**)realloc(breaks, sizeof(SupportBreak*)*max_nb_breaks);
+ }
+ breaks[nb_breaks-1] = new SupportBreak(pos_break, length-1,
+ this, parameters,ranges_forward,
+ ranges_reverse);
+ } else {
+ nb_breaks--;
+ }
+ }
+
+ // Now we try to merge breaks
+ if (nb_breaks > 1) {
+ tryToMergeBreaks();
+ }
+
+ if (getLocation() == NULL) {
+ computeBestLocation(false);
+ }
+
+ almostNormal = almostNormal && ! hasRepeat() && isContinuous();
+}
+
+Support::Support(const Support &s): parameters(s.parameters), tag_num(s.tag_num),
+ length(s.length), threshold(s.threshold),
+ tag_length(s.tag_length), genome(s.genome),
+ tags(s.tags), nb_single(s.nb_single),
+ nb_multiple(s.nb_multiple), nb_duplicate(s.nb_duplicate),
+ nb_pos_located(s.nb_pos_located),
+ almostNormal(s.almostNormal),
+ start_pos_repeat(s.start_pos_repeat),
+ end_pos_repeat(s.end_pos_repeat), nb_breaks(s.nb_breaks)
+
+{
+ support = new uint[length];
+ nb_locs = new uint[length];
+ ranges_reverse = new pair<uint,uint>[length];
+ ranges_forward = new pair<uint,uint>[length];
+ for (uint i = 0; i < length; i++) {
+ support[i] = s.support[i];
+ nb_locs[i] = s.nb_locs[i];
+ ranges_forward[i] = s.ranges_forward[i];
+ ranges_reverse[i] = s.ranges_reverse[i];
+ }
+
+ current_tag = new char[tag_length+1];
+ for (uint i = 0; i <= tag_length; i++) {
+ current_tag[i] = s.current_tag[i];
+ }
+
+ pos = new ChrPosition(*(s.pos));
+ breaks = new SupportBreak*[nb_breaks];
+ for (uint i=0; i < nb_breaks; i++) {
+ breaks[i] = new SupportBreak(*(s.breaks[i]));
+ breaks[i]->setSupport(this);
+ breaks[i]->setRangesForward(ranges_forward);
+ breaks[i]->setRangesReverse(ranges_reverse);
+ }
+
+}
+
+Support::~Support() {
+ for (uint i=0; i < nb_breaks; i++) {
+ delete breaks[i];
+ }
+ delete [] ranges_forward;
+ delete [] ranges_reverse;
+// delete [] pos_occ;
+// delete [] strand_occ;
+ delete [] current_tag;
+ if (pos)
+ delete pos;
+ delete [] nb_locs;
+ delete [] support;
+ free(breaks);
+}
+
+SupportBreak *Support::getBreak(uint i, bool consider_strand) {
+ if (! consider_strand || ! getLocation()
+ || getLocation()->getStrand() == 1)
+ return breaks[i];
+ else
+ return breaks[getNbBreaks() - i - 1];
+}
+
+int Support::getEndPosRepeat() {
+ return end_pos_repeat;
+}
+
+gkArrays *Support::getIndexTags(){
+ return tags;
+}
+
+LocateOnGenome *Support::getGenome() {
+ return genome;
+}
+
+uint Support::getLength() {
+ return length;
+}
+
+ChrPosition *Support::getLocation(){
+ return pos;
+}
+
+pair<ChrPosition **, uint> Support::getLocations(uint &position_of_locations){
+ ChrPosition **locations = NULL;
+ position_of_locations = 0;
+ ulong *occs_fwd;
+ uint nb_occs_fwd=0;
+ ulong *occs_rev;
+ uint nb_occs_rev=0;
+ // multiple is initialized to nb_max_diplayed (--max-locs)
+ uint nb_locs_multiple = getGenome()->getNbLocations();
+
+ // we search the k-mer with the most occurrences
+ for (uint i=1 ; i<getLength() ; i++){
+ if (nb_locs[i] > nb_locs[position_of_locations])
+ position_of_locations = i;
+ }
+
+ // First, on forward strand
+ if (ranges_forward[position_of_locations].first <= ranges_forward[position_of_locations].second) {
+ genome->getOccurrencesFMIndexRange(ranges_forward[position_of_locations].first,
+ ranges_forward[position_of_locations].second,
+ &occs_fwd);
+ nb_occs_fwd = ranges_forward[position_of_locations].second - ranges_forward[position_of_locations].first + 1;
+ }
+ // We check that the number of occurrences is smaller than nb_locs_multiple before the reverse strand treatment
+ if (nb_occs_fwd < nb_locs_multiple) {
+ if (ranges_reverse[position_of_locations].first <= ranges_reverse[position_of_locations].second) {
+ genome->getOccurrencesFMIndexRange(ranges_reverse[position_of_locations].first,
+ ranges_reverse[position_of_locations].second,
+ &occs_rev);
+ nb_occs_rev = ranges_reverse[position_of_locations].second - ranges_reverse[position_of_locations].first + 1;
+ }
+
+ // Again, we check that the total number of occurrences is smaller than nb_locs_multiple
+ // and we adjust the nb_locs_multiple if the limit is not reached
+ if ((nb_occs_fwd+nb_occs_rev) < nb_locs_multiple)
+ nb_locs_multiple=nb_occs_rev+nb_occs_fwd;
+ }
+
+ // We save locations
+ if (nb_locs_multiple>0){
+ locations = (ChrPosition **)malloc(sizeof (ChrPosition *)*nb_locs_multiple);
+
+ uint nb_displayed = min(nb_occs_fwd,nb_locs_multiple);
+ for (uint i=0 ; i<nb_displayed ; i++){
+ locations[i] = getGenome()->getChrPos(occs_fwd[i],1);
+ }
+ for (uint i=nb_displayed ; i<nb_locs_multiple ; i++){
+ locations[i] = getGenome()->getChrPos(occs_rev[i-nb_displayed],-1);
+ }
+ }else{
+ position_of_locations = getTagLength();
+ }
+
+ // We delete tempory tables
+ if (nb_occs_fwd)
+ free(occs_fwd);
+ if (nb_occs_rev)
+ free(occs_rev);
+
+ return pair<ChrPosition **, uint>(locations,nb_locs_multiple);
+}
+
+uint Support::getNbBreaks() {
+ return nb_breaks;
+}
+
+uint Support::getNbDuplicate() {
+ return nb_duplicate;
+}
+
+uint *Support::getNbLocs() {
+ return nb_locs;
+}
+
+uint Support::getNbLocs(uint i) {
+ return nb_locs[i];
+}
+
+uint Support::getNbLocsMax() {
+ return nb_locs_max;
+}
+
+uint Support::getNbMultiple() {
+ return nb_multiple;
+}
+
+uint Support::getNbPositionsLocated() {
+ return nb_pos_located;
+}
+
+uint Support::getNbSingle() {
+ return nb_single;
+}
+
+Parameters *Support::getParameters() {
+ return parameters;
+}
+
+uint Support::getPositionOfLocation() {
+ return (getLocation() == NULL) ? getTagLength() : position_of_location;
+}
+
+pair<uint, uint> Support::getKmerRange(uint i, uint strand) {
+ if (i<length && i>=0) {
+ if (strand == FORWARD_STRAND)
+ return ranges_forward[i];
+ else
+ return ranges_reverse[i];
+ } else {
+ throw ILLEGAL_STATE_EXCEPTION;
+ }
+}
+
+int Support::getRepeatLength() {
+ if (getEndPosRepeat() == -1 && getStartPosRepeat() == -1)
+ return 0;
+ else if (getStartPosRepeat() == -1)
+ return getEndPosRepeat() + 1;
+ else if (getEndPosRepeat() == -1)
+ return (int)(getLength() - getStartPosRepeat() + 1);
+ else
+ return (int)(getEndPosRepeat() -getStartPosRepeat() + 1);
+}
+
+
+int Support::getStartPosRepeat() {
+ return start_pos_repeat;
+}
+
+uint *Support::getSupport() {
+ return support;
+}
+
+uint Support::getSupport(uint i) {
+ return support[i];
+}
+
+char *Support::getTag() {
+ return current_tag;
+}
+
+uint Support::getTagNum(){
+ return tag_num;
+}
+
+uint Support::getTagLength() {
+ return tag_length;
+}
+
+uint Support::getThreshold(){
+ return threshold;
+}
+
+bool Support::hasRepeat() {
+ return (getStartPosRepeat() != -1 || getEndPosRepeat() != -1)
+ && getRepeatLength() >= parameters->percent_min_unique_repetition*getNbPositionsLocated();
+}
+
+bool Support::isAlmostNormal(){
+ return almostNormal;
+}
+
+bool Support::isContinuous() {
+ return getLength() == (getNbMultiple() + getNbSingle() + getNbDuplicate());
+}
+
+bool Support::isDuplicate() {
+ return !isNone()
+ && getNbDuplicate() > 0
+ && getNbDuplicate() >= (uint) (parameters->percent_min_duplicate
+ * getNbPositionsLocated());
+}
+
+bool Support::isMultiple() {
+ return ! isNone()
+ && getNbMultiple() > 0
+ && getNbMultiple() >= (uint) (parameters->percent_min_multiple
+ * getNbPositionsLocated());
+}
+
+bool Support::isNone() {
+ bool is_none = (getNbSingle() == 0 && getNbMultiple() == 0 && getNbDuplicate() == 0);
+ if (nb_breaks == 1 && !is_none)
+ is_none = (breaks[0]->hasNoEndBreak()
+ && breaks[0]->hasNoStartBreak());
+ return is_none;
+}
+
+bool Support::isSingle() {
+ return !isNone()
+ && getNbSingle() > 0
+ && getNbSingle() >= (uint) (parameters->percent_min_single
+ * getNbPositionsLocated());
+}
+
+// PRIVATE
+void Support::computeBestLocation(bool only_single) {
+ // Look for a not isolated 1 in nb_locs
+ uint i;
+ uint longest_run = 0, current_run = 0;
+ uint start_longest_run = 0, start_current_run = 0;
+
+ bool in_run = false;
+ for (i=0; i < getLength(); i++) {
+ if ((only_single && nb_locs[i] == 1)
+ || (! only_single && nb_locs[i] > 0)){
+ if (in_run) {
+ current_run++;
+ } else {
+ in_run = true;
+ start_current_run = i;
+ current_run = 1;
+ }
+ } else if (in_run) {
+ in_run = false;
+ if (current_run > longest_run) {
+ longest_run = current_run;
+ start_longest_run = start_current_run;
+ }
+ }
+ }
+
+ if (in_run) {
+ if (current_run > longest_run) {
+ longest_run = current_run;
+ start_longest_run = start_current_run;
+ }
+ }
+
+ // Defines a chrPosition for the support so that we can display at least one
+ // genome location (if any).
+ if (longest_run > 0) {
+ // Best position of the 1 (in the middle of the run)
+ uint i = start_longest_run + (longest_run - 1)/2;
+ position_of_location = i;
+ ulong *occs;
+ if (ranges_forward[i].first <= ranges_forward[i].second) {
+ genome->getOccurrencesFMIndexRange(ranges_forward[i].first,
+ ranges_forward[i].second,
+ &occs);
+ pos = getGenome()->getChrPos(occs[0], 1);
+ } else {
+ genome->getOccurrencesFMIndexRange(ranges_reverse[i].first,
+ ranges_reverse[i].second,
+ &occs);
+ pos = getGenome()->getChrPos(occs[0], -1);
+ }
+ free(occs);
+ } else
+ pos = NULL;
+}
+
+void Support::tryToMergeBreaks() {
+ list<SupportBreak *> break_list;
+ list<bool> chimeric_breaks, short_chimeric_breaks;
+ list<SupportBreak *>::iterator it_b;
+ list<bool>::iterator it_chim;
+ list<bool>::iterator it_short;
+
+ for (uint i=0; i < nb_breaks; i++) {
+ break_list.push_back(breaks[i]);
+ }
+
+ // Filling arrays
+ for (uint i = 0; i < nb_breaks; i++) {
+ bool value = ! breaks[i]->isNiceBreak()
+ && ! breaks[i]->hasNoStartBreak() && ! breaks[i]->hasNoEndBreak();
+ chimeric_breaks.push_back(value);
+ short_chimeric_breaks.push_back(value &&
+ (! breaks[i]->hasLongEnoughTagBreak()));
+ }
+
+ it_b = break_list.begin();
+ it_chim = chimeric_breaks.begin();
+ it_short = short_chimeric_breaks.begin();
+
+
+ // Is the first break located?
+ // Should we do a loop?
+ if ((*it_b)->hasNoStartBreak() && ! (*((++it_b)--))->isNiceBreak()
+ && (*((++it_b)--))->getPositionStartBreak()
+ - (*it_b)->getPositionEndBreak() - 1
+ < parameters->min_bases_before_break) {
+ merge(break_list, chimeric_breaks, short_chimeric_breaks,
+ it_b, it_chim, it_short);
+ }
+
+ // Is the last break located?
+ // Should we do a loop?
+ it_b = break_list.begin();
+ it_chim = chimeric_breaks.begin();
+ it_short = short_chimeric_breaks.begin();
+ advance(it_b, break_list.size()-1);
+ if (break_list.size() > 2 ) {
+ advance(it_chim, break_list.size()-2);
+ advance(it_short, break_list.size()-2);
+ }
+
+ if (break_list.size() > 1 && (*it_b)->hasNoEndBreak()
+ && (*(--it_b)++)->isNiceBreak()
+ && (*it_b)->getPositionStartBreak()
+ - (*(--it_b)++)->getPositionEndBreak() - 1
+ < parameters->min_bases_before_break) {
+ merge(break_list, chimeric_breaks, short_chimeric_breaks,
+ --it_b, it_chim, it_short);
+ }
+
+ // Merging short chimeric breaks
+ it_b = break_list.begin();
+ it_chim = chimeric_breaks.begin();
+ it_short = short_chimeric_breaks.begin();
+
+ while (it_b != break_list.end()) {
+ if (*it_short) {
+ if (*it_b != break_list.front()
+ && (*it_b)->getPositionEndBreak()
+ - (*((--it_b)++))->getPositionStartBreak() + 1
+ <= parameters->max_nb_overlapping_breaks * getThreshold()
+ && (*((--it_b)++))->isNiceMerge(*it_b)) {
+ merge(break_list, chimeric_breaks, short_chimeric_breaks,
+ (--it_b), --it_chim, --it_short);
+ } else if (*it_b != break_list.back()
+ && (*((++it_b)--))->getPositionEndBreak()
+ - (*it_b)->getPositionStartBreak() + 1
+ <= parameters->max_nb_overlapping_breaks * getThreshold()
+ && (*it_b)->isNiceMerge(*(++it_b)--))
+ merge(break_list, chimeric_breaks, short_chimeric_breaks,
+ it_b, it_chim, it_short);
+
+ // else if (*it_b != break_list.front() && *(--it_short)++) {
+ // merge(break_list, chimeric_breaks, short_chimeric_breaks,
+ // --it_b, --it_chim, --it_short);
+ // }
+ else {
+ uint distance_left = 0, distance_right = 0;
+ uint short_distance_left = 0, short_distance_right = 0;
+ if (*it_b != break_list.front() && *(--it_chim)++) {
+ distance_left = (*it_b)->getPositionEndBreak()
+ - (*((--it_b)++))->getPositionStartBreak() + 1;
+ short_distance_left = (*it_b)->getPositionStartBreak()
+ - (*((--it_b)++))->getPositionEndBreak() + 1;
+ }
+ if (*it_b != break_list.back() && *(++it_chim)--) {
+ distance_right = (*((++it_b)--))->getPositionEndBreak()
+ - (*it_b)->getPositionStartBreak() + 1;
+ short_distance_right = (*((++it_b)--))->getPositionStartBreak()
+ - (*it_b)->getPositionEndBreak() + 1;
+ }
+ if (distance_left
+ && (distance_left
+ <= parameters->max_nb_overlapping_breaks * getThreshold()
+ || short_distance_left <= parameters->max_bases_randomly_matched)
+ && (distance_left < distance_right || ! distance_right))
+ merge(break_list, chimeric_breaks, short_chimeric_breaks,
+ (--it_b), --it_chim, --it_short);
+ else if (distance_right
+ && (distance_right
+ <= parameters->max_nb_overlapping_breaks * getThreshold()
+ || short_distance_right
+ <= parameters->max_bases_randomly_matched)
+ && (distance_right < distance_left || ! distance_left))
+ merge(break_list, chimeric_breaks, short_chimeric_breaks,
+ it_b, it_chim, it_short);
+
+ else if (*it_b != break_list.front()
+ && (*((--it_b)++))->hasNoStartBreak()
+ && (*it_b)->getPositionStartBreak()
+ - (*((--it_b)++))->getPositionEndBreak() + 1
+ <= parameters->max_bases_randomly_matched) {
+ merge(break_list, chimeric_breaks, short_chimeric_breaks,
+ (--it_b), --it_chim, --it_short);
+ } else if (*it_b != break_list.back() && (*(++it_b)--)->hasNoEndBreak()
+ && (*((++it_b)--))->getPositionStartBreak()
+ - (*it_b)->getPositionEndBreak() + 1
+ <= parameters->max_bases_randomly_matched)
+ merge(break_list, chimeric_breaks, short_chimeric_breaks,
+ it_b, it_chim, it_short);
+ else {
+ it_b++;
+ it_chim++;
+ it_short++;
+ }
+ }
+ } else {
+ it_b++;
+ it_chim++;
+ it_short++;
+ }
+ }
+
+ // for (uint i = 0; i < nb_breaks; i++) {
+ // printf("%d %d %d %d\n",i, chimeric_breaks[i], short_chimeric_breaks[i],
+ // merged_with[i]);
+ // }
+
+ // Merging chimeric_breaks
+ it_b = break_list.begin();
+ it_chim = chimeric_breaks.begin();
+ it_short = short_chimeric_breaks.begin();
+ while (it_b != break_list.end()) {
+ if (*it_chim) {
+ if (*it_b != break_list.front()&& (*((--it_b)++))->isNiceMerge(*it_b)
+ && ((*it_b)->getPositionEndBreak()
+ - (*((--it_b)++))->getPositionStartBreak() + 1
+ <= parameters->max_nb_overlapping_breaks * getThreshold()
+ || (*it_b)->getPositionStartBreak()
+ - (*((--it_b)++))->getPositionEndBreak() + 1
+ <= parameters->max_bases_randomly_matched)) {
+ merge(break_list, chimeric_breaks, short_chimeric_breaks,
+ (--it_b), --it_chim, --it_short);
+ } else if (*it_b != break_list.back()&& (*it_b)->isNiceMerge(*(++it_b)--)
+ && ((*((++it_b)--))->getPositionEndBreak()
+ - (*it_b)->getPositionStartBreak() + 1
+ <= parameters->max_nb_overlapping_breaks * getThreshold()
+ || (*((++it_b)--))->getPositionStartBreak()
+ - (*it_b)->getPositionEndBreak() + 1
+ <= parameters->max_bases_randomly_matched))
+ merge(break_list, chimeric_breaks, short_chimeric_breaks,
+ it_b, it_chim, it_short);
+
+ // If we have a chimeric break next to us, we merge it if it is not too
+ // far.
+ else if (*it_b != break_list.back() && *(++it_chim)--
+ && ((*((++it_b)--))->getPositionEndBreak()
+ - (*it_b)->getPositionStartBreak() + 1
+ <= parameters->max_nb_overlapping_breaks * getThreshold()
+ || (*((++it_b)--))->getPositionStartBreak()
+ - (*it_b)->getPositionEndBreak() + 1
+ <= parameters->max_bases_randomly_matched))
+ merge(break_list, chimeric_breaks, short_chimeric_breaks,
+ it_b, it_chim, it_short);
+
+ else if (*it_b != break_list.front()&& (*((--it_b)++))->hasNoStartBreak()
+ && (*it_b)->getPositionStartBreak()
+ - (*((--it_b)++))->getPositionEndBreak() + 1
+ <= parameters->max_bases_randomly_matched) {
+ merge(break_list, chimeric_breaks, short_chimeric_breaks,
+ (--it_b), --it_chim, --it_short);
+ } else if (*it_b != break_list.back()&& (*(++it_b)--)->hasNoEndBreak()
+ && (*((++it_b)--))->getPositionStartBreak()
+ - (*it_b)->getPositionEndBreak() + 1
+ <= parameters->max_bases_randomly_matched)
+ merge(break_list, chimeric_breaks, short_chimeric_breaks,
+ it_b, it_chim, it_short);
+ else {
+ it_b++;
+ it_chim++;
+ it_short++;
+ }
+ } else {
+ it_b++;
+ it_chim++;
+ it_short++;
+ }
+ }
+
+ // Merging other breaks
+ it_b = break_list.begin();
+ while (*it_b != break_list.back()) {
+ if (! (*it_b)->hasNoStartBreak() && ! (*((++it_b)--))->hasNoEndBreak()
+ && (*((++it_b)--))->getPositionEndBreak()
+ - (*it_b)->getPositionStartBreak() +1 <= getThreshold()
+ && (! (*it_b)->isVeryNiceBreak() || ! (*((++it_b)--))->isVeryNiceBreak())
+ && (*it_b)->isVeryNiceMerge(*((++it_b)--))) {
+ merge(break_list, chimeric_breaks, short_chimeric_breaks,
+ it_b, it_chim, it_short, true);
+ } else if ((*it_b)->getPositionEndBreak()
+ >= (*((++it_b)--))->getPositionStartBreak()) {
+ // If the breaks overlap, we merge them.
+ merge(break_list, chimeric_breaks, short_chimeric_breaks,
+ it_b, it_chim, it_short, true);
+ } else
+ it_b++;
+ }
+
+ // Just keep the necessary breaks
+ it_b = break_list.begin();
+ uint current_pos = 0;
+ while (it_b != break_list.end()) {
+ breaks[current_pos++] = *it_b;
+ it_b++;
+ }
+
+ if (break_list.size() < nb_breaks) {
+ // Realloc memory so that we don't take unnecessary memory
+ breaks = (SupportBreak **)realloc(breaks,
+ break_list.size() * sizeof(SupportBreak *));
+ nb_breaks = break_list.size();
+ }
+}
+
+void Support::merge(list<SupportBreak*> &break_list, list<bool> &chimeric_breaks,
+ list<bool> &short_chimeric_breaks,
+ list<SupportBreak*>::iterator &i,
+ list<bool>::iterator &chim,
+ list<bool>::iterator &shortB,
+ bool no_chim) {
+ uint pos_break = (*i)->getPositionStartBreak();
+ uint pos_end = (*((++i)--))->getPositionEndBreak();
+ uint nb_merges = (*i)->getNbMerges() + (*((++i)--))->getNbMerges() + 1;
+
+ // In the case where break i is at the start of the read
+ // maybe pos_break has been modified, so we need to find the original one.
+ if ((*i)->hasNoStartBreak() && pos_break == 0) {
+ while (pos_break < pos_end && getNbLocs()[pos_break] > 0)
+ pos_break++;
+ }
+ if ((*((++i)--))->hasNoEndBreak() && pos_end == getLength() - 1) {
+ while (pos_end > pos_break && getNbLocs()[pos_end] > 0)
+ pos_end--;
+ }
+
+ // cout << "Merging " << *i << endl;
+ // PRINT_VAR(pos_break);
+ // PRINT_VAR(pos_end);
+ delete (*i);
+ i = break_list.erase(i);
+ delete (*i);
+ i = break_list.erase(i);
+ i = break_list.insert(i, new SupportBreak(pos_break, pos_end, this, parameters,
+ ranges_forward, ranges_reverse,
+ nb_merges));
+
+ if (! no_chim) {
+ bool value = ! (*i)->isNiceBreak()
+ && ! (*i)->hasNoStartBreak()
+ && ! (*i)->hasNoEndBreak();
+
+ chim = chimeric_breaks.erase(chim);
+ chim = chimeric_breaks.erase(chim);
+ chim = chimeric_breaks.insert(chim, value);
+
+ shortB = short_chimeric_breaks.erase(shortB);
+ shortB = short_chimeric_breaks.erase(shortB);
+ shortB = short_chimeric_breaks.insert(shortB, value
+ && (! (*i)->hasLongEnoughTagBreak()));
+ }
+}
diff --git a/src/Support.h b/src/Support.h
new file mode 100644
index 0000000..1cb65e7
--- /dev/null
+++ b/src/Support.h
@@ -0,0 +1,462 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef SUPPORT_H
+#define SUPPORT_H
+#include <list>
+
+#include "libSSA/locateOnGenome.h"
+#include "Parameters.h"
+#include "SupportBreak.h"
+#include <gkArrays.h>
+
+using namespace std;
+using namespace gkarrays;
+
+class TagInfo;
+
+class Support {
+
+ Parameters *parameters; /* parameters to init constant values*/
+ uint *support; /* the support by itself */
+ uint tag_num; /* tag number */
+ uint length; /* support length */
+ uint threshold; /* size of the factors */
+ uint tag_length; /* length of the tag */
+ char *current_tag; /* tag corresponding to this support */
+ LocateOnGenome *genome; /* genome we are matching on */
+ gkArrays *tags; /* index of the tags */
+
+/* uint min_occ; /\* minimal number of occurrences for the support *\/ */
+/* uint max_occ; /\* maximal number of occurrences for the support *\/ */
+ uint nb_single; /* number of factors single located */
+ uint nb_multiple; /* number of factors located many times (>1) */
+ uint nb_duplicate; // number of duplicates
+ uint nb_pos_located; /* number of distinct factors that are located
+ (at most getLength()) */
+ bool almostNormal;
+
+ // The range support[start_pos_repeat ... end_pos_repeat] is such that
+ // each value is >= MIN_OCC_REPETITION
+ int start_pos_repeat; /* start position of the repeat in the support */
+ int end_pos_repeat; /* end position of the repeat in the support */
+
+
+ ChrPosition *pos; /* Position of an occurrence of one factor
+ and its strand (if any) */
+ uint position_of_location; /* Position in the read of the k-mer location */
+ uint position_of_locations; /* Position in the read of k-mer locations for
+ multiple treatment */
+
+ uint *nb_locs; /* number of occurrences of each factor are
+ located on the genome */
+
+ uint nb_locs_max; /* max value among the number of occurrences
+ computed in nb_locs */
+
+ uint nb_breaks; /* number of times consecutive factors are not
+ located on the genome */
+
+
+ SupportBreak **breaks;
+
+
+ pair <uint, uint> *ranges_forward; /* Range of occurrences, in the FM-index,
+ on the forward strand. */
+ pair <uint, uint> *ranges_reverse; /* Range of occurrences, in the FM-index,
+ on the reverse strand. */
+
+ public:
+
+ Support(Parameters *p, uint *s, uint tag_num
+ ,LocateOnGenome *g, gkArrays *i);
+
+ Support(const Support &);
+
+ ~Support();
+
+ // REQUESTS //
+
+ /**
+ * @pre i < j && i < nb_breaks && j < nb_breaks
+ * && i >= 0 && j >= 0
+ * @return true when two breaks can be merged.
+ * A break can be merged when we obvisouly have random
+ * locations in the middle of a larger break.
+ * This can be detected by checking if genome locations
+ * of both breaks are in the same region.
+ *
+ * We also consider that we can merge two breaks
+ * when one of them is on a border and (is a chimeric break
+ * or does not have a long enough break).
+ */
+ bool canMergeBreak(uint i, uint j);
+
+ /**
+ * @param i: the SupportBreak to return
+ * @param consider_strand: should we consider the strand when returning
+ * the break number i?
+ * @pre 0 <= i < nb_breaks
+ * @return the break number i in the read iff
+ * - we don't consider the strand,
+ * - it is on forward strand,
+ * - it is unknown
+ * the break number getNbBreaks() - i - 1, otherwise.
+ */
+ SupportBreak *getBreak(uint i, bool consider_strand=false);
+
+ /**
+ * @return end_pos_repeat
+ */
+ int getEndPosRepeat();
+
+ /**
+ * @return tags
+ */
+ gkArrays *getIndexTags();
+
+ /**
+ * @return genome
+ */
+ LocateOnGenome *getGenome();
+
+ /**
+ * @return the support length
+ */
+ uint getLength();
+
+ /**
+ * @return the 'best' location of a factor (of length getThreshold()) in the
+ * read.
+ * This is the location in the middle of a "run" of
+ * single-located factors. If no such location is found
+ * take a location in the middle of a run of located factors.
+ * If nothing is found return NULL
+ */
+ ChrPosition *getLocation();
+
+ /**
+ * @return all locations of a factor (of length getThreshold()) in
+ * the read and its numbers. This is the first factor with
+ * the most of occurrences on the reference. If too much
+ * locations return only getGenome()->getNbLocations()
+ * locations If nothing is found return a pair<ChrPosition
+ * **, uint> empty. In addition, position_of_locations is
+ * set after pair<ChrPosition **,uint> which determines
+ * position of the k-mer chosen for locations
+ */
+ pair<ChrPosition **, uint> getLocations(uint &position_of_locations);
+
+ /**
+ * @return min_occ
+ * @post min_occ > 0 iff getNbSingle()+getNbMultiple() == getLength()
+ */
+ /* uint getMinOcc(); */
+
+ /**
+ * @return max_occ
+ * @post max_occ == 0 iff isNone()
+ */
+/* uint getMaxOcc(); */
+
+ /**
+ * @return nb_breaks
+ */
+ uint getNbBreaks();
+
+ /**
+ * @return nb_duplicate
+ * @post getNbDuplicate() <= getNbMultiple()
+ */
+ uint getNbDuplicate();
+
+ /**
+ * @return nb_locs
+ */
+ uint *getNbLocs();
+
+ /**
+ * @return nb_locs at position i
+ */
+ uint getNbLocs(uint i);
+
+ /**
+ * @return the max value in nb_locs
+ */
+ uint getNbLocsMax();
+
+ /**
+ * @return nb_multiple
+ */
+ uint getNbMultiple();
+
+ /**
+ * @return the number of distinct positions where a factor of length
+ * getThreshold() is located.
+ */
+ uint getNbPositionsLocated();
+
+ /**
+ * @return nb_single
+ */
+ uint getNbSingle();
+
+ /**
+ * @return parameters
+ */
+ Parameters *getParameters();
+
+ /**
+ * getLocation() is the position of the k-mer at position
+ * getPositionOfLocation() in the read.
+ * Return getTagLength() if getLocation() == NULL
+ */
+ uint getPositionOfLocation();
+
+ /** Return the range of the k-mer at position i of
+ * the profile on a specific strand
+ *
+ * @param i the number of the kmer if the support
+ * @param strand the strand on wich we get the range
+ * @return the range of the kmer i in the genome index
+ */
+ pair<uint, uint> getKmerRange(uint i, uint strand);
+
+ /**
+ * @return the length of the repetitioon or 0 if not
+ */
+ int getRepeatLength();
+
+ /**
+ * @return start_pos_repeat, -1 if no repeat exists
+ */
+ int getStartPosRepeat();
+
+ /**
+ * @return support
+ */
+ uint *getSupport();
+
+ /**
+ * @return support at position i
+ */
+ uint getSupport(uint i);
+
+ /**
+ * @return the tag for this support
+ */
+ char *getTag();
+
+ /**
+ * @return the tag number
+ */
+ uint getTagNum();
+
+ /**
+ * @return the length of the current read
+ */
+ uint getTagLength();
+
+ /**
+ * @return threshold
+ */
+ uint getThreshold();
+
+ /**
+ * A repetition is built by a number of consecutive k-mers with
+ * a number of occurrence >= parameters->min_occ_repetition
+ * @return (getRepeatLength() >= percent_min_unique_repetition*getNbPositionsLocated())
+ *
+ */
+ bool hasRepeat();
+
+ /**
+ * @return isAlmostNormal
+ */
+ bool isAlmostNormal();
+
+ /**
+ * return getLength() == getNbMultiple()+getNbSingle()
+ */
+ bool isContinuous();
+
+ /**
+ * @return getNbDuplicate() >= params->percent_min_duplicate*getNbPositionsLocated()
+ */
+ bool isDuplicate();
+
+ /**
+ * @return ! isDuplicate
+ * && (getNbSingle() < parameters->percent_max_unique_multiple*getNbPositionsLocated()
+ */
+ bool isMultiple();
+
+ /**
+ * @return (nb_single == 0 && nb_multiple == 0)
+ * || (nb_breaks == 1 && breaks[0]->getPositionStartBreak() == 0
+ * && breaks[0]->getPositionEndBreak() == getLength()-1)
+ */
+ bool isNone();
+
+ /**
+ * @return !isNone() && !isMultiple() && !isDuplicate()
+ */
+ bool isSingle();
+ private:
+
+ /**
+ * Compute the best location either for k-mer only single located
+ * or for any k-mer.
+ * @param only_single if the parameter is true we only search for k-mers that
+ * are located unambiguously (ie. only once)
+ * @post getLocation() will return the location (if a suitable one was found)
+ * NULL otherwise
+ */
+ void computeBestLocation(bool only_single);
+
+ /**
+ * Will merge breaks using the following algorithm:
+ * If a break is at the beginning of the read and the next one
+ * ! isNiceBreak()
+ * -> merge them (if there are less than MIN_BASES_BEFORE_BREAK nt between them)
+ * If a break is at the end of the read and the previous one
+ * ! isNiceBreak()
+ * -> merge them (if there are less than MIN_BASES_BEFORE_BREAK nt between them)
+ * For each short chimeric break:
+ * if isNiceMerge() is true with the next or previous break and is not too far
+ * -> merge
+ * else if the next or previous break is chimeric
+ * merge with the closest one if it is not too far
+ * (< 2 * getThreshold)
+ * else if the next or previous break is at the start or at the
+ * end of the read
+ * -> merge
+ * For each chimeric break (not yet merged):
+ * if isNiceMerge() is true with the next or previous break and is not too far
+ * or if the next break is chimeric and not too far (< 2 * getThreshold())
+ * from the current break
+ * or if the next or previous break is at the start or at the
+ * end of the read
+ * -> merge
+ * For each break:
+ * Merge with the next one iff the resulting break isVeryNiceBreak(),
+ * the current break or the next one are not isVeryNiceBreak()
+ * and if the resulting break lengthis <= getThreshold().
+ * We also merge in the case two consecutive breaks are overlapping
+ */
+ void tryToMergeBreaks();
+
+ /**
+ * Merge break i vith break i+1.
+ * The other arrays are updated accordingly.
+ * @param no_chim: is it a chimeric break being merged?
+ * @post merged_with[i+1] == i
+ * breaks[i+1] == breaks[i]
+ * chimeric_breaks[i+1] == chimeric_breaks[i]
+ * short_chimeric_breaks[i+1] == short_chimeric_breaks[i]
+ */
+ void merge(list<SupportBreak*> &break_list, list<bool> &chimeric_breaks,
+ list<bool> &short_chimeric_breaks,
+ list<SupportBreak*>::iterator &i, list<bool>::iterator &chim,
+ list<bool>::iterator &shortB, bool no_chim=false);
+
+};
+
+#endif
+
diff --git a/src/SupportBreak.cpp b/src/SupportBreak.cpp
new file mode 100644
index 0000000..8fd4b70
--- /dev/null
+++ b/src/SupportBreak.cpp
@@ -0,0 +1,1621 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <string>
+#include <limits.h>
+#include "SupportBreak.h"
+#include "Support.h"
+#include "utils.h"
+#include <math.h>
+
+using namespace std;
+
+SupportBreak::SupportBreak(uint start, uint end,
+ Support *s, Parameters *p,
+ pair<uint, uint> *range_occs_forward,
+ pair<uint, uint> *range_occs_reverse,
+ uint nb_merges):
+ k(s->getThreshold()),
+ pos_start_break(start),pos_end_break(end),
+ support(s),parameters(p),
+ range_occs_fwd(range_occs_forward), range_occs_rev(range_occs_reverse),
+ nb_merges(nb_merges){
+ init();
+}
+
+SupportBreak::SupportBreak(SupportBreak &b1, SupportBreak &b2) {
+ SupportBreak *first, *last;
+ if (b1.support != b2.support) {
+ throw ILLEGAL_STATE_EXCEPTION;
+ }
+ if (b2.getPositionEndBreak() > b1.getPositionEndBreak()) {
+ first = &b1;
+ last = &b2;
+ } else {
+ first = &b2;
+ last = &b1;
+ }
+ uint pos_break = first->getPositionStartBreak();
+ uint pos_end = last->getPositionEndBreak();
+
+ if (first->hasNoStartBreak() && pos_break == 0) {
+ // If the k-mers are located, we have extended the breaks. We come back
+ // to the original positions so that the extension can be performed
+ // (again) after the merge without problem
+ while (pos_break < pos_end && first->support->getNbLocs()[pos_break] > 0)
+ pos_break++;
+ }
+ if (last->hasNoEndBreak() && pos_end == last->getLength() - 1) {
+ while (pos_end > pos_break && last->support->getNbLocs()[pos_end] > 0)
+ pos_end--;
+ }
+
+ k = b1.getThreshold();
+ pos_start_break = pos_break;
+ pos_end_break = pos_end;
+ support = first->support;
+ parameters = first->parameters;
+ range_occs_fwd = first->range_occs_fwd;
+ range_occs_rev = first->range_occs_rev;
+
+ init();
+}
+
+SupportBreak::~SupportBreak(){
+ for (uint i=0; i < nb_candidats; i++) {
+ delete candidats[i];
+ }
+ free(candidats);
+ if (candidat_chosen != NULL)
+ delete candidat_chosen;
+}
+
+void SupportBreak::computeScore(){
+ computeScore(pos_start_break, pos_end_break);
+}
+
+void SupportBreak::computeScore(uint pos_start, uint pos_end){
+ // we can not check a location after getLength()-1 in Support
+ uint max_pos_end = min(pos_end, support->getLength()-1);
+ uint max_pos_start = min(pos_start, support->getLength()-1);
+ // Computing score outside break
+ setInsideScore(max_pos_start, max_pos_end);
+
+ // Computing score outside break
+ setOutsideScore(max_pos_start, max_pos_end);
+}
+
+float SupportBreak::getAverageLowInside() {
+ return average_low_inside;
+}
+
+float SupportBreak::getAverageHighInside() {
+ return average_high_inside;
+}
+
+CandidatBreak *SupportBreak::getCandidatChosen(){
+ return candidat_chosen;
+}
+
+const uchar *SupportBreak::getChr(pos_location_break p){
+ if (((p == START_BREAK && hasNoStartBreak())
+ || (p == END_BREAK && hasNoEndBreak()))
+ )
+ return NULL;
+ if (p == START_BREAK)
+ return getGenome()->getChromosome(loc_start_break);
+ else
+ return getGenome()->getChromosome(loc_end_break);
+}
+
+
+ulong SupportBreak::getChrId(pos_location_break p){
+ if (((p == START_BREAK && hasNoStartBreak())
+ || (p == END_BREAK && hasNoEndBreak()))
+ )
+ return ~0;
+ if (p == START_BREAK)
+ return getGenome()->getIdChromosome(loc_start_break);
+ else
+ return getGenome()->getIdChromosome(loc_end_break);
+}
+
+ChrPosition *SupportBreak::getChrPosition(pos_location_break p){
+ if (((p == START_BREAK && hasNoStartBreak())
+ || (p == END_BREAK && hasNoEndBreak()))
+ )
+ return NULL;
+ if (p == START_BREAK) {
+ return getGenome()->getChrPos(loc_start_break,
+ strand_start_break);
+ }
+ else
+ return getGenome()->getChrPos(loc_end_break,strand_end_break);
+}
+
+
+LocateOnGenome *SupportBreak::getGenome(){
+ return support->getGenome();
+}
+
+gap_size_t SupportBreak::getGenomeGapLength(){
+ if (hasNoStartBreak() || hasNoEndBreak()
+ )
+ return GAP_SIZE_MAX;
+ if (strand_start_break != strand_end_break
+ || (getChrId(START_BREAK) != getChrId(END_BREAK)))
+ return min(labs((long long int) loc_end_break - loc_start_break),
+ labs((long long int) loc_start_break - loc_end_break)) - 1;
+ if (strand_end_break == -1)
+ return (gap_size_t)loc_start_break - (gap_size_t)loc_end_break-1;
+ return (gap_size_t)loc_end_break - (gap_size_t)loc_start_break-1;
+}
+
+uint SupportBreak::getInsideQuartile1() {
+ return inside_quartile1;
+}
+
+uint SupportBreak::getInsideQuartile4() {
+ return inside_quartile4;
+}
+
+float SupportBreak::getInsideScore(){
+ return score_during_break;
+}
+
+uint SupportBreak::getLength(){
+ return getTagLength() - getThreshold() + 1;
+}
+
+ChrPosition *SupportBreak::getLocationEndBreak() {
+ return getChrPosition(END_BREAK);
+}
+
+ChrPosition *SupportBreak::getLocationStartBreak() {
+ return getChrPosition(START_BREAK);
+}
+
+ulong SupportBreak::getNbCandidats(){
+ return nb_candidats;
+}
+
+uint SupportBreak::getNbMerges(){
+ return nb_merges;
+}
+
+int SupportBreak::getNbGenomeIndels(){
+ if (this->getGenomeGapLength() == GAP_SIZE_MAX)
+ return INT_MAX;
+ return (int)(this->getGenomeGapLength()
+ - (int)this->getTagBreakLength());
+}
+
+int SupportBreak::getNbTagIndels(){
+ //return (int)((int)this->getTagBreakLength()
+ // - (int)getThreshold());
+ return (int)((int)this->getTagBreakLength()
+ -this->getGenomeGapLength());
+}
+
+float SupportBreak::getOutsideScore(){
+ return score_outside_break;
+}
+
+uint SupportBreak::getPositionEndBreak(int strand){
+ if (strand == 1)
+ return pos_end_break;
+ return getLength() - 1 - getPositionStartBreak();
+}
+
+uint SupportBreak::getPositionEndBreakOnTheRead() {
+ if (! hasPositionEndBreakOnTheRead()) {
+ return getPositionEndBreak() + getThreshold() - 1;
+ }
+ return override_pos_end_break;
+}
+
+ulong SupportBreak::getPositionLocation(pos_location_break p){
+ if (((p == START_BREAK && hasNoStartBreak())
+ || (p == END_BREAK && hasNoEndBreak()))
+ // || isRepeated()
+ )
+ return ~0;
+ if (p == START_BREAK)
+ return loc_start_break;
+ else
+ return loc_end_break;
+}
+
+uint SupportBreak::getPositionStartBreak(int strand){
+ if (strand == 1)
+ return pos_start_break;
+ return getLength() - 1 - getPositionEndBreak();
+}
+
+
+CandidatBreak *SupportBreak::getPotentialCandidat(uint i){
+ return candidats[i];
+}
+
+pair<uint, uint> SupportBreak::getRangeEndBreak(uint strand) {
+ if (hasNoEndBreak())
+ throw ILLEGAL_STATE_EXCEPTION;
+
+ if (strand == FORWARD_STRAND)
+ return range_occs_fwd[pos_end_break+1];
+ else
+ return range_occs_rev[pos_end_break+1];
+
+}
+
+pair<uint, uint> SupportBreak::getRangeStartBreak(uint strand) {
+ if (hasNoStartBreak())
+ throw ILLEGAL_STATE_EXCEPTION;
+
+ if (strand == FORWARD_STRAND)
+ return range_occs_fwd[pos_start_break-1];
+ else
+ return range_occs_rev[pos_start_break-1];
+}
+
+float SupportBreak::getScoreInsideAverages() {
+ return score_inside_averages;
+}
+
+float SupportBreak::getScoreComputedIntraExon() {
+ // compute the distance between the curve and the point for the same outside
+ return (getThresholdForScoreIntraExon(score_outside_break)-score_during_break);
+}
+
+float SupportBreak::getScoreComputedInterExon(){
+ // compute the distance between the curve and the point for the same outside
+ return (getThresholdForScoreInterExon(score_outside_break)-score_during_break);
+}
+
+float SupportBreak::getScoreInsideBreak(){
+ return score_during_break;
+}
+
+float SupportBreak::getScoreOutsideBreak(){
+ return score_outside_break;
+}
+
+int SupportBreak::getStrandLocation(pos_location_break p){
+ if (((p == START_BREAK && hasNoStartBreak())
+ || (p == END_BREAK && hasNoEndBreak()))
+ // || isRepeated()
+ )
+ return 0;
+ if (p == START_BREAK)
+ return strand_start_break;
+ else
+ return strand_end_break;
+
+}
+
+uint SupportBreak::getTagBreakLength(){
+ return getPositionEndBreak()-getPositionStartBreak() + 1;
+}
+
+uint SupportBreak::getTagLength(){
+ return support->getTagLength();
+}
+
+uint SupportBreak::getThreshold(){
+ return k;
+}
+
+
+float SupportBreak::getThresholdForScoreInterExon(float score){
+// return (1-(log(score_during_break + M_E - (1+parameters->min_support_no_cover))
+// /log(score_outside_break + M_E - (1+parameters->min_support_no_cover))));
+ // float thresh = 981617 - 981610 * exp(-1.0*score_outside_break/60411843)
+// - 5.5 * exp(-1.0*score_outside_break/22.9);
+ //return 0.53793 + sqrt(0.24875 * score);
+ // return 0.22453 + sqrt(0.20354 * score);
+ return 0.51081 + sqrt(0.16758 * score);
+}
+
+float SupportBreak::getThresholdForScoreIntraExon(float score){
+// float thresh = 0.35+0.5 * score_outside_break;
+// float thresh = -4.063*pow(M_E,-score_outside_break/6.22)
+// - 3004 * pow(M_E,-score_outside_break/70240) + 3009;
+ //return 0.8 * pow(score_outside_break,5./6) + 0.13387;
+ //return 0.812 + 0.299 * pow(score,4./5);
+ //return 0.73566 + 0.16216 * pow(score,4./5);
+ //return 0.83566 + 0.16216 * pow(score,4./5);
+ // return 0.93330 + 0.18609 * pow(score,4./5);
+ //return -0.42376 + 1.17887 * pow(score,1./3) + 0.06945 * pow(score,5./6);
+ // return -0.33462 + 1.16893 * pow(score,1./3) + 0.04730 * pow(score,5./6);
+ // return -0.38608 + 0.85347 * pow(score,1./3) + 0.27864 * pow(score,5./6);
+ if (score <= 5)
+ return 0.19227 - 0.82749 * score + 1.51619 * pow(score,5./6);
+ else
+ return -2.40850 + 2.15859 * pow(score,1./3) + 0.15670 * pow(score,5./6);
+}
+
+// bool SupportBreak::hasLongEnoughTagBreak(){
+// return (getTagBreakLength() >= parameters->min_break_length);
+// }
+
+bool SupportBreak::hasLongEnoughTagBreak() {
+ return hasNoStartBreak() || hasNoEndBreak()
+ || getThreshold() < parameters->max_bases_randomly_matched
+ || getTagBreakLength() > getThreshold() - parameters->max_bases_randomly_matched;
+}
+
+bool SupportBreak::hasNoCover() {
+ return score_outside_break <= parameters->min_support_no_cover
+ && score_during_break <= parameters->min_support_no_cover;
+}
+
+bool SupportBreak::hasNoEndBreak(int strand) {
+ return (strand == 1
+ ? getPositionEndBreakOnTheRead() + 1 == getTagLength()
+ : hasNoStartBreak(1));
+}
+
+bool SupportBreak::hasNoStartBreak(int strand) {
+ return (strand == 1
+ ? getPositionStartBreak() == 0
+ : hasNoEndBreak(1));
+}
+
+bool SupportBreak::hasPositionEndBreakOnTheRead(int strand) {
+ return override_pos_end_break != 0;
+ // TODO
+}
+
+bool SupportBreak::isBiologicalEvent(){
+ return ! hasNoCover()
+ && (score_during_break >= score_outside_break
+ || isBiologicalIntraEvent()
+ || isBiologicalInterEvent()
+ );
+}
+
+bool SupportBreak::isBiologicalIntraEvent(){
+ return getScoreComputedIntraExon() <= parameters->p_value_variation_biological
+ && getChrId(START_BREAK) == getChrId(END_BREAK)
+ && getStrandLocation(START_BREAK) == getStrandLocation(END_BREAK)
+ && getGenomeGapLength() > 0
+ && getGenomeGapLength() <= (getTagBreakLength() + parameters->max_bio_ins_del);
+}
+
+bool SupportBreak::isBiologicalInterEvent(){
+ return getScoreComputedInterExon() <= parameters->p_value_variation_biological
+ && ! isBiologicalIntraEvent();
+}
+
+
+bool SupportBreak::isChimera(){
+ return
+ ((getChrId(START_BREAK) != getChrId(END_BREAK)
+ || getStrandLocation(START_BREAK) != getStrandLocation(END_BREAK)
+ || getGenomeGapLength() < 0
+ || labs(getGenomeGapLength()) > parameters->max_splice_length
+ )
+ && (getTagBreakLength() < getThreshold())
+ && hasLongEnoughTagBreak());
+}
+
+bool SupportBreak::isDeviated(){
+ return
+ getScoreInsideAverages() >= 0
+ || (getAverageLowInside() < 1+EPSILON
+ && getAverageHighInside() < parameters->max_ambiguous_average_high
+ && (isBiologicalEvent() && isSupportFalling()));
+}
+
+bool SupportBreak::isDuplicated(){
+ if (candidat_chosen == NULL)
+ return false;
+ else
+ return candidat_chosen->isDuplicated();
+}
+
+bool SupportBreak::isRepeated() {
+ return repeated;
+}
+
+bool SupportBreak::isGenomeDeletion(){
+ if (getTagBreakLength() <= parameters->max_bio_ins_del)
+ return false;
+ return (
+ getChrId(START_BREAK) == getChrId(END_BREAK)
+ && getStrandLocation(START_BREAK) == getStrandLocation(END_BREAK)
+ && getGenomeGapLength() > 0
+ && getGenomeGapLength() < getTagBreakLength() - parameters->max_bio_ins_del
+ );
+}
+
+bool SupportBreak::isGenomeInsertion(){
+ if (getTagBreakLength() > getThreshold() - 1)
+ return false;
+ return (
+ getChrId(START_BREAK) == getChrId(END_BREAK)
+ && getStrandLocation(START_BREAK) == getStrandLocation(END_BREAK)
+ && getGenomeGapLength() > getTagBreakLength() + parameters->max_bio_ins_del
+ && labs(getGenomeGapLength()) <= parameters->max_splice_length
+ );
+}
+
+bool SupportBreak::isNiceBreak() {
+ return (isVeryNiceBreak() || isGenomeInsertion()
+ || isGenomeDeletion())
+ && ! isChimera();
+ // return check_nice_merge(this, this, parameters->max_splice_length);
+}
+
+bool SupportBreak::isNiceMerge(SupportBreak *sb) {
+ return check_nice_merge(this, sb, false);
+}
+
+bool SupportBreak::isSupportFalling() {
+ return isSupportFallingRight() || isSupportFallingLeft();
+}
+
+bool SupportBreak::isSupportFallingLeft(int strand) {
+ return (strand == 1
+ ? (pc_ones_left_inside >= parameters->min_perc_ones_inside
+ && pc_ones_left_inside
+ >= parameters->min_ratio_support_fall * pc_ones_left_outside)
+ : isSupportFallingRight());
+}
+
+bool SupportBreak::isSupportFallingRight(int strand) {
+ return (strand == 1
+ ? (pc_ones_right_inside >= parameters->min_perc_ones_inside
+ && pc_ones_right_inside
+ >= parameters->min_ratio_support_fall * pc_ones_right_outside)
+ : isSupportFallingLeft());
+}
+
+bool SupportBreak::isTagSubstitution(){
+ return (getChrId(START_BREAK) == getChrId(END_BREAK)
+ && getStrandLocation(START_BREAK) == getStrandLocation(END_BREAK)
+ && getGenomeGapLength() == getTagBreakLength());
+}
+
+bool SupportBreak::isTagIndel(){
+ bool isAGoodTagBreakLength = true;
+ if (getNbTagIndels() < 0){
+ isAGoodTagBreakLength = (getTagBreakLength() < getThreshold());
+ }else{
+ isAGoodTagBreakLength = (getThreshold() + getNbTagIndels() > getGenomeGapLength());
+ }
+ return (isAGoodTagBreakLength
+ && getChrId(START_BREAK) == getChrId(END_BREAK)
+ && getStrandLocation(START_BREAK) == getStrandLocation(END_BREAK)
+ && ! isTagSubstitution()
+ && labs(getNbTagIndels()) <= parameters->max_bio_ins_del
+ && getGenomeGapLength() > 0);
+}
+
+bool SupportBreak::isVeryNiceBreak() {
+ return isTagIndel() || isTagSubstitution()
+ || (isGenomeInsertion()
+ && labs(getGenomeGapLength() <= parameters->max_verynice_merge));
+}
+
+bool SupportBreak::isVeryNiceMerge(SupportBreak *sb) {
+ return check_nice_merge(this, sb, true);
+}
+
+void SupportBreak::setInsideScore(){
+ setInsideScore(pos_start_break, pos_end_break);
+}
+
+void SupportBreak::setInsideScore(uint pos_start, uint pos_end){
+ uint nb_inside = 0;
+ score_during_break = 0;
+ for (uint i = pos_start ; i<=pos_end ; i++){
+ if (support->getNbLocs()[i] == 0) {
+ score_during_break += support->getSupport(i);
+ nb_inside++;
+ }
+ }
+
+ score_during_break /= nb_inside;
+}
+
+void SupportBreak::setLocationEndBreak(uint loc_end){
+ loc_end_break = loc_end;
+}
+
+void SupportBreak::setLocationStartBreak(uint loc_start){
+ loc_start_break = loc_start;
+}
+
+void SupportBreak::setOutsideScore() {
+ setOutsideScore(pos_start_break, pos_end_break);
+}
+
+void SupportBreak::setOutsideScore(uint pos_start, uint pos_end) {
+ uint pos_s, pos_e;
+ if (pos_start < parameters->support_score_window_length/2)
+ pos_s = 0;
+ else
+ pos_s = pos_start - parameters->support_score_window_length/2;
+ if (support->getLength()
+ < 1 + pos_end + parameters->support_score_window_length/2)
+ pos_e = support->getLength()-1;
+ else
+ pos_e = pos_end + parameters->support_score_window_length/2;
+
+ float newScore=0;
+ uint nb=0;
+ for (uint i = pos_s; i < pos_start; i++) {
+ if (support->getNbLocs()[i] == 0) {
+ nb = 0;
+ newScore = 0;
+ } else {
+ newScore += support->getSupport(i);
+ nb++;
+ }
+ }
+ for (uint i=pos_end+1; i <= pos_e
+ && support->getNbLocs()[i] != 0; i++) {
+ newScore += support->getSupport(i);
+ nb++;
+ }
+
+ if (nb > 0)
+ score_outside_break = newScore / nb;
+ else
+ score_outside_break = (support->getNbLocs()[pos_start]
+ + support->getNbLocs()[pos_end]) / 2.;
+
+ //make the process of stardard deviations
+ computeHighAndLowAverages(pos_start, pos_end);
+}
+
+void SupportBreak::setPositionEndBreak(uint pos_end){
+ pos_end_break = pos_end;
+}
+
+void SupportBreak::setPositionEndBreakOnTheRead(uint pos_end){
+ override_pos_end_break = pos_end;
+}
+
+void SupportBreak::setPositionStartBreak(uint pos_start){
+ pos_start_break = pos_start;
+}
+
+void SupportBreak::setRangesForward(pair<uint, uint> *p) {
+ range_occs_fwd = p;
+}
+
+void SupportBreak::setRangesReverse(pair<uint, uint> *p) {
+ range_occs_rev = p;
+}
+
+void SupportBreak::setStrandEndBreak(int strand_end){
+ strand_end_break = strand_end;
+}
+
+void SupportBreak::setStrandStartBreak(int strand_start){
+ strand_start_break = strand_start;
+}
+
+void SupportBreak::setSupport(Support *s) {
+ support = s;
+}
+
+void SupportBreak::setThreshold(uint k) {
+ this->k = k;
+}
+
+// PRIVATE
+
+void SupportBreak::init() {
+ strand_start_break = 0;
+ loc_start_break = ~0;
+ strand_end_break = 0;
+ loc_end_break = ~0;
+ override_pos_end_break = 0;
+ score_during_break = 0;
+ candidat_chosen = NULL;
+ repeated = false;
+
+ // maximal allocation to save candidats during extension process
+ int max_nb_candidats = parameters->max_extension_length + 1;
+ nb_candidats = 0;
+ candidats = (CandidatBreak**)malloc(sizeof(CandidatBreak*)*max_nb_candidats);
+
+ if (pos_start_break > 0 || pos_end_break < getLength() - 1)
+ fillWithClosestMatch();
+
+ if (candidat_chosen != NULL){
+ pos_start_break = candidat_chosen->getPosStartBreak();
+ loc_start_break = candidat_chosen->getLocStartBreak();
+ strand_start_break = candidat_chosen->getStrandStartBreak();
+ pos_end_break = candidat_chosen->getPosEndBreak();
+ loc_end_break = candidat_chosen->getLocEndBreak();
+ strand_end_break = candidat_chosen->getStrandEndBreak();
+ }
+
+ computeScore();
+}
+
+void SupportBreak::adjustBoundaries(){
+ // ulong nb_disp = getGenome()->getNbLocations();
+ ulong *locs_start_after, *locs_end_before;
+ ulong nb_elements_rev, nb_elements_fwd;
+ uint pos_start_extension = candidat_chosen->getPosStartBreak();
+ uint loc_start_extension = candidat_chosen->getLocStartBreak();
+ int strand_start_extension = candidat_chosen->getStrandStartBreak();
+ uint pos_end_extension = candidat_chosen->getPosEndBreak();
+ uint loc_end_extension = candidat_chosen->getLocEndBreak();
+ int strand_end_extension = candidat_chosen->getStrandEndBreak();
+
+ bool hasNoStartExtension = false;
+ bool hasNoEndExtension = false;
+ bool findStart = false;
+ bool findEnd = false;
+ bool findElement;
+
+ // a bioUndetermined candidat is notify if the extension process has not to
+ // be finished and the candidat looks like a chimera (it could be a false positive)
+ if (!candidat_chosen->isNiceCandidat() && (pos_start_extension == 0 || pos_end_extension == (getLength() - 1))){
+ if (pos_end_extension == (getLength() - 1)){
+ hasNoEndExtension = true;
+ }
+ if (pos_start_extension == 0){
+ hasNoStartExtension = true;
+ }
+ }
+
+ // Adjust the start break
+ if (!hasNoStartExtension){
+ if (strand_start_extension == -1){
+ while (range_occs_rev[pos_start_extension+1].first <=
+ range_occs_rev[pos_start_extension+1].second && !findStart){
+ getGenome()->
+ getOccurrencesFMIndexRange(range_occs_rev[pos_start_extension+1].first,
+ range_occs_rev[pos_start_extension+1].second,
+ &locs_start_after);
+
+ nb_elements_rev = range_occs_rev[pos_start_extension+1].second - range_occs_rev[pos_start_extension+1].first + 1;
+ // nb_elements_rev = min(range_occs_rev[pos_start_extension+1].second - range_occs_rev[pos_start_extension+1].first + 1,
+ // nb_disp);
+
+ findElement = false;
+ for (ulong j=0 ; j < nb_elements_rev && !findElement ; j++){
+ if (locs_start_after[j] + 1 == loc_start_extension){
+ findElement = true;
+ pos_start_extension++;
+ loc_start_extension--;
+ }
+ }
+
+ if (locs_start_after)
+ free(locs_start_after);
+
+ if (!findElement)
+ findStart = true;
+ }
+ }else{
+ while (range_occs_fwd[pos_start_extension+1].first <=
+ range_occs_fwd[pos_start_extension+1].second && !findStart){
+ getGenome()->
+ getOccurrencesFMIndexRange(range_occs_fwd[pos_start_extension+1].first,
+ range_occs_fwd[pos_start_extension+1].second,
+ &locs_start_after);
+
+ nb_elements_fwd = range_occs_fwd[pos_start_extension+1].second - range_occs_fwd[pos_start_extension+1].first + 1;
+ // nb_elements_fwd = min(range_occs_fwd[pos_start_extension+1].second - range_occs_fwd[pos_start_extension+1].first + 1,
+ // nb_disp);
+
+ findElement = false;
+ for (ulong j=0 ; j < nb_elements_fwd && !findElement ; j++){
+ if (locs_start_after[j] - 1 == loc_start_extension){
+ findElement = true;
+ pos_start_extension++;
+ loc_start_extension++;
+ }
+ }
+
+ if (locs_start_after)
+ free(locs_start_after);
+
+ if (!findElement)
+ findStart = true;
+ }
+ }
+ }
+
+ // Adjust the end break
+ if (!hasNoEndExtension){
+ if (strand_end_extension == -1){
+ while (range_occs_rev[pos_end_extension-1].first <=
+ range_occs_rev[pos_end_extension-1].second && !findEnd){
+ getGenome()->
+ getOccurrencesFMIndexRange(range_occs_rev[pos_end_extension-1].first,
+ range_occs_rev[pos_end_extension-1].second,
+ &locs_end_before);
+
+ nb_elements_rev = range_occs_rev[pos_end_extension-1].second - range_occs_rev[pos_end_extension-1].first + 1;
+ // nb_elements_rev = min(range_occs_rev[pos_end_extension-1].second - range_occs_rev[pos_end_extension-1].first + 1,
+ // nb_disp);
+
+ findElement = false;
+ for (ulong j=0 ; j < nb_elements_rev && !findElement ; j++){
+ if (locs_end_before[j] - 1 == loc_end_extension){
+ findElement = true;
+ pos_end_extension--;
+ loc_end_extension++;
+ }
+ }
+
+ if (locs_end_before)
+ free(locs_end_before);
+
+ if (!findElement)
+ findEnd = true;
+ }
+ }else if (strand_end_extension == 1){
+ while (range_occs_fwd[pos_end_extension-1].first <=
+ range_occs_fwd[pos_end_extension-1].second && !findEnd){
+ getGenome()->
+ getOccurrencesFMIndexRange(range_occs_fwd[pos_end_extension-1].first,
+ range_occs_fwd[pos_end_extension-1].second,
+ &locs_end_before);
+
+ nb_elements_fwd = range_occs_fwd[pos_end_extension-1].second - range_occs_fwd[pos_end_extension-1].first + 1;
+ // nb_elements_fwd = min(range_occs_fwd[pos_end_extension-1].second - range_occs_fwd[pos_end_extension-1].first + 1,
+ // nb_disp);
+
+ findElement = false;
+ for (ulong j=0 ; j < nb_elements_fwd && !findElement ; j++){
+ if (locs_end_before[j] + 1 == loc_end_extension){
+ findElement = true;
+ pos_end_extension--;
+ loc_end_extension--;
+ }
+ }
+
+ if (locs_end_before)
+ free(locs_end_before);
+
+ if (!findElement)
+ findEnd = true;
+ }
+ }
+ }
+
+ //////////////////// UPDATE NEW BONDARIES ////////////////////
+ if (!hasNoStartExtension){
+ candidat_chosen->setPosStartBreak(pos_start_extension+1);
+ candidat_chosen->setLocStartBreak(loc_start_extension);
+ }else{
+ candidat_chosen->setPosStartBreak(0);
+ candidat_chosen->setLocStartBreak(~0);
+ candidat_chosen->setStrandStartBreak(0);
+ }
+
+ if (!hasNoEndExtension){
+ candidat_chosen->setPosEndBreak(pos_end_extension-1);
+ candidat_chosen->setLocEndBreak(loc_end_extension);
+ }else{
+ candidat_chosen->setPosEndBreak(getLength() - 1);
+ candidat_chosen->setLocEndBreak(~0);
+ candidat_chosen->setStrandEndBreak(0);
+ }
+
+
+}
+
+
+bool SupportBreak::canCheckPositions(ulong start, ulong end) {
+ // We do not check the positions if we have a repetition just before
+ // or just after the break.
+ // A repetition artificially rises the score up which does not
+ // allow us to make a difference between a mutation or an error.
+ ulong nb_disp = getGenome()->getNbLocations();
+ return ((range_occs_fwd[start].second - range_occs_fwd[start].first+1
+ + range_occs_rev[start].second - range_occs_rev[start].first+1) < min(nb_disp+1,parameters->min_occ_repetition)
+ && (range_occs_fwd[end].second - range_occs_fwd[end].first +1
+ + range_occs_rev[end].second - range_occs_rev[end].first +1) < min(nb_disp+1,parameters->min_occ_repetition)
+ );
+}
+
+
+bool SupportBreak::check_nice_merge(SupportBreak *sb1, SupportBreak *sb2,
+ bool very_nice) {
+ SupportBreak *merged;
+ if (sb1 == sb2)
+ return (very_nice) ? sb1->isVeryNiceBreak() : sb1->isNiceBreak();
+
+ merged = new SupportBreak(*sb1, *sb2);
+
+ bool result = (very_nice) ? merged->isVeryNiceBreak() : merged->isNiceBreak();
+
+ delete merged;
+ return result;
+}
+
+void SupportBreak::computeHighAndLowAverages(uint pos_start, uint pos_end){
+ uint nb_outside = 0;
+ uint nb_inside = 0;
+ uint pos_start_out, pos_end_out;
+ if (pos_start < parameters->support_score_window_length/2)
+ pos_start_out = 0;
+ else
+ pos_start_out = pos_start - parameters->support_score_window_length/2;
+ if (support->getLength()
+ < 1 + pos_end + parameters->support_score_window_length/2)
+ pos_end_out = support->getLength()-1;
+ else
+ pos_end_out = pos_end + parameters->support_score_window_length/2;
+
+ //computing standard deviations
+ for (uint i = pos_start_out; i < pos_start ; i++) {
+ if (support->getNbLocs()[i] == 0){
+ nb_outside=0;
+ pos_start_out = i+1;
+ }else{
+ nb_outside++;
+ }
+ }
+
+ uint support_without_loc = 0;
+
+ // We only consider the support which are not located
+ // because it may bias the computation.
+ for (uint i = pos_start; i<=pos_end ; i++){
+ if (support->getNbLocs()[i] == 0
+ || (support_without_loc > 0
+ && support_without_loc >= support->getSupport(i))){
+ nb_inside++;
+ } else
+ support_without_loc = support->getSupport(i);
+ }
+ for (uint i=pos_end+1; i <= pos_end_out
+ && support->getNbLocs()[i] != 0; i++) {
+ nb_outside++;
+ }
+
+ uint *inside_elements = new uint[nb_inside];
+
+ nb_outside = 0;
+ nb_inside = 0;
+
+ support_without_loc = 0;
+
+ // We only consider the support which are not located
+ // because it may bias the computation.
+ for (uint i = pos_start; i<=pos_end ; i++){
+ if (support->getNbLocs()[i] == 0
+ || (support_without_loc > 0
+ && support_without_loc >= support->getSupport(i))){
+ inside_elements[nb_inside] = support->getSupport(i);
+ nb_inside++;
+ } else
+ support_without_loc = support->getSupport(i);
+ }
+ // Sorting the positions so that we can take
+ // the lowest ones and the highest ones.
+ qsort(inside_elements, nb_inside, sizeof(uint), comparUint);
+
+ // Get the first and last quartiles
+ inside_quartile1 = inside_elements[nb_inside/4];
+ inside_quartile4 = inside_elements[3*nb_inside/4];
+
+ average_low_inside = 0;
+ // An error affects getThreshold() factors, therefore
+ // if an error occurs inside a larger break, at least
+ // getThreshold() factors should be impacted.
+ // On the other hand, because of random locations,
+ // some factors containing the error may be located
+ // and thus may not appear in the inside support.
+ uint nb_low = min(getThreshold() - parameters->nb_bases_substracted_low_average,
+ nb_inside/2);
+ for (uint i = 0; i < nb_low; i++) {
+ average_low_inside += inside_elements[i];
+ }
+ average_high_inside = 0;
+ for (uint i = nb_inside/2; i < nb_inside; i++) {
+ average_high_inside += inside_elements[i];
+ }
+
+ average_high_inside /= nb_inside/2 + (nb_inside%2);
+ if (nb_low == 0)
+ average_low_inside = average_high_inside;
+ else
+ average_low_inside /= nb_low;
+
+ score_inside_averages = (getThresholdForScoreIntraExon(average_high_inside) - average_low_inside);
+
+
+ pc_ones_left_inside = pc_ones_left_outside = pc_ones_right_inside = pc_ones_right_outside = 0;
+
+ // If the low average is 1 (or almost), we have to check if these low
+ // values are due to a poorly supported read or to an error.
+ // If it is due to an error, it is likely that we have 1s in the support
+ // at a border inside the break, but higher values outside the break.
+ if (average_low_inside < 1+EPSILON) {
+ if (pos_start - pos_start_out > parameters->nb_positions_check_ones) {
+ pos_start_out = pos_start - parameters->nb_positions_check_ones;
+ }
+ if (pos_end_out - pos_end > parameters->nb_positions_check_ones) {
+ pos_end_out = pos_end + parameters->nb_positions_check_ones;
+ }
+
+ for (uint i = pos_start_out; i < pos_start; i++) {
+ if (support->getSupport(i) == 1)
+ pc_ones_left_outside++;
+ }
+ pc_ones_left_outside /= (pos_start - pos_start_out);
+
+ uint count = 0;
+ for (uint i = pos_start; count < parameters->nb_positions_check_ones
+ && i <= pos_end; i++) {
+ if (support->getNbLocs()[i] == 0){
+ if (support->getSupport(i) == 1)
+ pc_ones_left_inside++;
+ count++;
+ }
+ }
+ pc_ones_left_inside /= count;
+
+ count = 0;
+ for (uint i = pos_end; i > pos_start
+ && count < parameters->nb_positions_check_ones; i--) {
+ if (support->getNbLocs()[i] == 0){
+ if (support->getSupport(i) == 1)
+ pc_ones_right_inside++;
+ count++;
+ }
+ }
+ pc_ones_right_inside /= count;
+
+ for (uint i = pos_end+1; i <= pos_end_out; i++) {
+ if (support->getSupport(i) == 1)
+ pc_ones_right_outside++;
+ }
+ pc_ones_right_outside /= (pos_end_out - pos_end);
+ }
+
+ delete [] inside_elements;
+
+}
+
+void SupportBreak::fillWithClosestMatch() {
+ ulong *pos_occ;
+
+ if (hasNoStartBreak()) {
+ // We have no localisation before the break (beginning of the tag)
+ uint pos_after_break = pos_end_break+1;
+ loc_start_break = ~0;
+ strand_start_break = 0;
+ // getGenome()->setNbLocations(1);
+
+ // There are localisations on the forward strand
+ if (range_occs_fwd[pos_after_break].first <=
+ range_occs_fwd[pos_after_break].second) {
+ getGenome()->
+ getOccurrencesFMIndexRange(range_occs_fwd[pos_after_break].first,
+ range_occs_fwd[pos_after_break].second,
+ &pos_occ,0,1);
+ strand_end_break = 1;
+ } else {
+ // Localisations are on the reverse strand
+ getGenome()->
+ getOccurrencesFMIndexRange(range_occs_rev[pos_after_break].first,
+ range_occs_rev[pos_after_break].second,
+ &pos_occ,0,1);
+ strand_end_break = -1;
+ }
+ loc_end_break = pos_occ[0];
+ if (pos_occ)
+ free(pos_occ);
+
+ // getGenome()->setNbLocations(nb_disp);
+ } else if (hasNoEndBreak()) {
+ // We have no localisation before the break (beginning of the tag)
+ loc_end_break = ~0;
+ strand_end_break = 0;
+ uint pos_before_break = pos_start_break-1;
+
+ // getGenome()->setNbLocations(1);
+
+ // There are localisations on the forward strand
+ if (range_occs_fwd[pos_before_break].first <=
+ range_occs_fwd[pos_before_break].second) {
+ getGenome()->
+ getOccurrencesFMIndexRange(range_occs_fwd[pos_before_break].first,
+ range_occs_fwd[pos_before_break].second,
+ &pos_occ,0,1);
+ strand_start_break = 1;
+ } else {
+ // Localisations are on the reverse strand
+ getGenome()->
+ getOccurrencesFMIndexRange(range_occs_rev[pos_before_break].first,
+ range_occs_rev[pos_before_break].second,
+ &pos_occ,0,1);
+ strand_start_break = -1;
+ }
+ loc_start_break = pos_occ[0];
+ if (pos_occ)
+ free(pos_occ);
+
+ // getGenome()->setNbLocations(nb_disp);
+
+ }
+ // Both localisations before and after break are defined
+ else if (!hasNoEndBreak() && !hasNoStartBreak()) {
+
+ uint pos_end_extension = getPositionEndBreak();
+ uint pos_start_extension = getPositionStartBreak();
+
+ bool no_loc_before=false;
+ bool no_loc_after=false;
+
+ // from the break, we try to extend until max_extension_length
+ // while it is not on border case or it is not the best_candidate
+ // or it is not around a repetition
+ for (int i=0 ;
+ (i <= parameters->max_extension_length)
+ && (pos_end_extension < getLength()-1
+ || pos_start_extension > 0)
+ && (!no_loc_after || !no_loc_before)
+ && ! repeated ;
+ i++) {
+
+
+ ///////////////////////////////////////////////////////////////////////
+ /////////// CHECKING THE POSSIBILITY TO EXTEND FOR EACH SIDE //////////
+ ///////////////////////////////////////////////////////////////////////
+
+
+ // On the right, the extension is not possible if:
+ // i/ it is the read's end
+ if (pos_end_extension < (getLength() - 1) && ! no_loc_after)
+ pos_end_extension++;
+ else
+ no_loc_after = true;
+ // ii/ the extension is not coming inside an other break
+ if ((range_occs_fwd[pos_end_extension].first > range_occs_fwd[pos_end_extension].second)
+ && (range_occs_rev[pos_end_extension].first > range_occs_rev[pos_end_extension].second)) {
+ no_loc_after = true;
+ pos_end_extension--;
+ }
+
+ // On the right, the extension is not possible if:
+ // i/ it is the read's start
+ if (pos_start_extension > 0 && ! no_loc_before)
+ pos_start_extension--;
+ else
+ no_loc_before = true;
+ // ii/ the extension is not coming inside an other break
+ if ((range_occs_fwd[pos_start_extension].first > range_occs_fwd[pos_start_extension].second)
+ && (range_occs_rev[pos_start_extension].first > range_occs_rev[pos_start_extension].second)){
+ no_loc_before = true;
+ pos_start_extension++;
+ }
+
+ ///////////////////////////////////////////////////////////////////////
+
+ ///////////////////////////////////////////////////////////////////////
+ //////////// RUNNING UPDATELOCATION AND CHECKING CANDIDATS ////////////
+ ///////////////////////////////////////////////////////////////////////
+
+ if (!no_loc_before || !no_loc_after) {
+ if (! canCheckPositions(pos_start_extension, pos_end_extension)) {
+ repeated = true;
+ }
+ // only it is not around a repetition
+ else{
+ updateLocation(pos_start_extension, pos_end_extension);
+ }
+ }
+
+ ///////////////////////////////////////////////////////////////////////
+
+ }
+
+
+ ///////////////////////////////////////////////////////////////////////
+ /////////////////// CH0OSE THE BEST CANDIDAT///////////////////////////
+ ///////////////////////////////////////////////////////////////////////
+
+ // nb_candidats == 0 if there are directly a repetion at the first step of pos_start and pos_end breaks both.
+ if (nb_candidats > 0){
+ candidat_chosen = new CandidatBreak(*candidats[getBestCandidat()]);
+
+ // a candidat is necessarily chosen
+ if (candidat_chosen == NULL)
+ throw ILLEGAL_STATE_EXCEPTION;
+
+
+ // a candidat is chosen and (max_extension_length == 0), so we just must adjust PosStartBreak and posEndBreak
+ if (parameters->max_extension_length == 0){
+ candidat_chosen->setPosStartBreak(pos_start_extension+1);
+ candidat_chosen->setPosEndBreak(pos_end_extension-1);
+ }
+ // a candidat is chosen, so its boundaries are updated
+ else
+ adjustBoundaries();
+ }
+ }
+}
+
+
+ /**
+ * Return the position of the best_candidat :
+ * - nice_candidat (at least a splice)
+ * - single consistent
+ * - the minimal break on the genome
+ * And notify a duplicated candidat if the table contains several good candidats or (several not godd candidats)
+ */
+ ulong SupportBreak::getBestCandidat(CandidatBreak **potential_candidats, ulong nb_potential_candidats, bool after_extension){
+ ulong i_chosen = 0;
+ for (ulong i = 1 ; i < nb_potential_candidats ; i++){
+ // current candidat is a chimera
+ if (!potential_candidats[i_chosen]->isNiceCandidat()){
+ // new candidat is at least a splice, so it is better
+ if (potential_candidats[i]->isNiceCandidat()){
+ i_chosen = i;
+ }
+ // at least two different chimeras
+ else{
+ // in case of after extension, a same chimera is automatically extended
+ // but only if the new candidat is not duplicated or the two candidats are duplicated both
+ if (after_extension && (!potential_candidats[i]->isDuplicated()
+ //|| potential_candidats[i_chosen]->isDuplicated()
+ )
+ ){
+ i_chosen = i;
+ }
+ // normal process in case of not after extension
+ else{
+ if (!isSameCandidat(potential_candidats,i,i_chosen)){
+ potential_candidats[i_chosen]->setDuplicated(true);
+ potential_candidats[i]->setDuplicated(true);
+
+ // new candidat is also a chimera but it is consistent with the
+ // single map, so it is better
+ if (!potential_candidats[i_chosen]->isSingleConsistent() && potential_candidats[i]->isSingleConsistent()){
+ i_chosen = i;
+ }
+ // two different chimeras (both single or both not), so:
+ // In case of after the extension process, the good one depends of getBreakLength
+ else if (!potential_candidats[i_chosen]->isSingleConsistent() || potential_candidats[i]->isSingleConsistent()) {
+ if (after_extension){
+ if (potential_candidats[i]->getReadBreakLength() < getThreshold() && hasLongEnoughTagBreak()){
+ i_chosen = i;
+ }
+ }
+ // else we try to do a choice
+ else{
+ // we keep the candidat with the smallest single_distance
+ if (potential_candidats[i]->isSingleConsistent()
+ && potential_candidats[i]->getSingleDistance() < potential_candidats[i_chosen]->getSingleDistance()) {
+ i_chosen = i;
+ }
+ // or we keep the candidat with the smallest gap on the genome
+ else if ((
+ !potential_candidats[i]->isSingleConsistent()
+ || (potential_candidats[i]->getSingleDistance() == potential_candidats[i_chosen]->getSingleDistance())
+ )
+ &&
+ (
+ labs((long long int) potential_candidats[i]->getGenomeGapLength()-potential_candidats[i]->getReadBreakLength())
+ < labs((long long int)(potential_candidats[i_chosen]->getGenomeGapLength()-potential_candidats[i_chosen]->getReadBreakLength()))
+ )
+ ){
+ i_chosen = i;
+ }
+ }
+ }
+ }
+ }
+ } // end at least two different chimeras
+ }
+ // current candidat is at least a splice
+ else{
+ // new candidat is also at least a splice
+ if (potential_candidats[i]->isNiceCandidat()){
+ // new candidat is also a "NiceCandidat" but it is consistent with the
+ // single map, so it is better
+ if (!potential_candidats[i_chosen]->isSingleConsistent() && potential_candidats[i]->isSingleConsistent()){
+ i_chosen = i;
+ }
+ // two different "NiceCandidat" (both single or both not), so it is a duplicated cause
+ else if (!potential_candidats[i_chosen]->isSingleConsistent() || potential_candidats[i]->isSingleConsistent()) {
+ if (!isSameCandidat(potential_candidats,i,i_chosen)){
+ potential_candidats[i_chosen]->setDuplicated(true);
+ potential_candidats[i]->setDuplicated(true);
+
+ // if both single consistency, we keep the candidat with the smallest single_distance
+ if (potential_candidats[i]->isSingleConsistent()
+ && potential_candidats[i]->getSingleDistance() < potential_candidats[i_chosen]->getSingleDistance()) {
+ i_chosen = i;
+ }
+ // we keep the candidat with the smallest gap on the genome
+ else if ((
+ !potential_candidats[i]->isSingleConsistent()
+ || (potential_candidats[i]->getSingleDistance() == potential_candidats[i_chosen]->getSingleDistance())
+ )
+ &&
+ (
+ (potential_candidats[i]->getGenomeGapLength()-potential_candidats[i]->getReadBreakLength())
+ < (potential_candidats[i_chosen]->getGenomeGapLength()-potential_candidats[i_chosen]->getReadBreakLength())
+ )
+ ){
+ i_chosen = i;
+ }
+ }
+ }
+ }
+ }
+ }
+ // in case of after extension, we have not a good candidat and we have extend to the bitter end or to the bitter start
+ // so we keep the last candidat to easily check no_start and no_end break in adjust process
+ if (after_extension && !potential_candidats[i_chosen]->isNiceCandidat()
+ && (potential_candidats[nb_potential_candidats-1]->getPosEndBreak() == (getLength() - 1) || potential_candidats[nb_potential_candidats-1]->getPosStartBreak() == 0)
+ ) {
+ i_chosen = nb_potential_candidats-1;
+ }
+
+ return i_chosen;
+}
+
+ulong SupportBreak::getBestCandidat(){
+ return getBestCandidat(this->candidats, this->nb_candidats, true);
+}
+
+bool SupportBreak::isSameCandidat(CandidatBreak **potential_candidats,ulong pos_i, ulong pos_j){
+ return isSameCandidatEnd(potential_candidats, pos_i, pos_j) && isSameCandidatStart(potential_candidats, pos_i, pos_j);
+}
+
+bool SupportBreak::isSameCandidatEnd(CandidatBreak **potential_candidats,ulong pos_i, ulong pos_j){
+ long long int diff_end = labs((long long int) potential_candidats[pos_j]->getPosEndBreak() - potential_candidats[pos_i]->getPosEndBreak());
+ // Two candidats are not the same if there are differents strand
+ if (potential_candidats[pos_i]->getStrandEndBreak() != potential_candidats[pos_j]->getStrandEndBreak())
+ return false;
+ // or different chr
+ if (potential_candidats[pos_i]->getChrIdEndBreak() != potential_candidats[pos_j]->getChrIdEndBreak())
+ return false;
+ // or the same with an extension step (or not if the extension is not longer possible before or after the break)
+ if (
+ (
+ (potential_candidats[pos_i]->getPosEndBreak() != potential_candidats[pos_j]->getPosEndBreak()
+ || potential_candidats[pos_i]->getLocEndBreak() != potential_candidats[pos_j]->getLocEndBreak()
+ )
+ && labs((long long int) potential_candidats[pos_i]->getLocEndBreak() - potential_candidats[pos_j]->getLocEndBreak()) != diff_end
+ )
+ )
+ return false;
+ // else two candidats are the same
+ return true;
+}
+
+bool SupportBreak::isSameCandidatStart(CandidatBreak **potential_candidats,ulong pos_i, ulong pos_j){
+ long long int diff_start = labs((long long int) potential_candidats[pos_j]->getPosStartBreak() - potential_candidats[pos_i]->getPosStartBreak());
+ // Two candidats are not the same if there are differents strand
+ if (potential_candidats[pos_i]->getStrandStartBreak() != potential_candidats[pos_j]->getStrandStartBreak())
+ return false;
+ // or different chr
+ if (potential_candidats[pos_i]->getChrIdStartBreak() != potential_candidats[pos_j]->getChrIdStartBreak())
+ return false;
+ // or the same with an extension step (or not if the extension is not longer possible before or after the break)
+ if (
+ (
+ (potential_candidats[pos_i]->getPosStartBreak() != potential_candidats[pos_j]->getPosStartBreak()
+ || potential_candidats[pos_i]->getLocStartBreak() != potential_candidats[pos_j]->getLocStartBreak()
+ )
+ && labs((long long int) potential_candidats[pos_i]->getLocStartBreak() - potential_candidats[pos_j]->getLocStartBreak()) != diff_start
+ )
+ )
+ return false;
+ // else two candidats are the same
+ return true;
+}
+
+void SupportBreak::saveCandidates(uint pos_before_break, uint pos_after_break,
+ ulong *pos_occ_start, uint nb_loc_start,
+ int strand_start, ulong *pos_occ_end,
+ uint nb_loc_end, int strand_end, CandidatBreak ***potential_candidats, ulong &nb_potential, ulong &nb_potential_max) {
+
+ uint i, j;
+
+ if (nb_potential == 0)
+ *potential_candidats = (CandidatBreak**)malloc(sizeof(CandidatBreak*)*nb_potential_max);
+
+ uint loc_occ_single = ~0;
+ int strand_occ_single = 0;
+ uint pos_occ_single = ~0;
+
+ // get single_loc features
+ if (support->getLocation() != NULL){
+ loc_occ_single = getGenome()->getAbsolutePosition(support->getLocation());
+ strand_occ_single = support->getLocation()->getStrand();
+ pos_occ_single = support->getPositionOfLocation();
+ }
+
+ ///////// TEMPORARY SAVE ALL CANDIDATS FOR AN EXTENSION STEP //////////
+
+ i = 0; j = 0;
+ while (i < nb_loc_start && j < nb_loc_end) {
+ if (nb_potential >= nb_potential_max) {
+ nb_potential_max *= 2;
+ *potential_candidats = (CandidatBreak**)realloc(*potential_candidats, sizeof(CandidatBreak*)*nb_potential_max);
+
+ }
+ CandidatBreak *temp_candidat = new CandidatBreak(pos_before_break, pos_occ_start[i], strand_start, pos_after_break, pos_occ_end[j], strand_end, this, parameters);
+ temp_candidat->checkSingleCorrespondence(pos_occ_single, loc_occ_single, strand_occ_single);
+ (*potential_candidats)[nb_potential] = temp_candidat;
+ nb_potential++;
+ if (i < (nb_loc_start - 1))
+ i++;
+ else{
+ j++;
+ i=0;
+ }
+ }
+}
+
+
+
+void SupportBreak::updateLocation(uint pos_before_break,
+ uint pos_after_break){
+
+ // maximum number of locations defined in parameter by user
+ //ulong nb_disp = getGenome()->getNbLocations();
+
+ ulong *pos_occ_start_fwd, *pos_occ_end_fwd;
+ ulong *pos_occ_start_rev, *pos_occ_end_rev;
+ uint nb_loc_start_fwd=0, nb_loc_end_fwd=0;
+ uint nb_loc_start_rev=0, nb_loc_end_rev=0;
+
+ CandidatBreak **potential_candidats;
+ ulong nb_potential_candidats=0;
+ ulong max_potential_candidats = parameters->min_occ_repetition;
+
+ bool has_start_forward_strand = false;
+ bool has_start_reverse_strand = false;
+ bool has_end_forward_strand = false;
+ bool has_end_reverse_strand = false;
+
+ // Locating at start forward
+ if (range_occs_fwd[pos_before_break].first <=
+ range_occs_fwd[pos_before_break].second){
+ has_start_forward_strand = true;
+ getGenome()->
+ getOccurrencesFMIndexRange(range_occs_fwd[pos_before_break].first,
+ range_occs_fwd[pos_before_break].second,
+ &pos_occ_start_fwd);
+ nb_loc_start_fwd = range_occs_fwd[pos_before_break].second - range_occs_fwd[pos_before_break].first+1;
+ }
+
+ // Locating at end forward
+ if (range_occs_fwd[pos_after_break].first <=
+ range_occs_fwd[pos_after_break].second) {
+ has_end_forward_strand = true;
+ getGenome()->
+ getOccurrencesFMIndexRange(range_occs_fwd[pos_after_break].first,
+ range_occs_fwd[pos_after_break].second,
+ &pos_occ_end_fwd);
+ nb_loc_end_fwd = range_occs_fwd[pos_after_break].second - range_occs_fwd[pos_after_break].first+1;
+ }
+
+ // Locating at start reverse
+ if (range_occs_rev[pos_before_break].first <=
+ range_occs_rev[pos_before_break].second){
+ has_start_reverse_strand = true;
+ getGenome()->
+ getOccurrencesFMIndexRange(range_occs_rev[pos_before_break].first,
+ range_occs_rev[pos_before_break].second,
+ &pos_occ_start_rev);
+ nb_loc_start_rev = range_occs_rev[pos_before_break].second - range_occs_rev[pos_before_break].first+1;
+ }
+
+ // Locating at end reverse
+ if (range_occs_rev[pos_after_break].first <=
+ range_occs_rev[pos_after_break].second) {
+ has_end_reverse_strand = true;
+ getGenome()->
+ getOccurrencesFMIndexRange(range_occs_rev[pos_after_break].first,
+ range_occs_rev[pos_after_break].second,
+ &pos_occ_end_rev);
+ nb_loc_end_rev = range_occs_rev[pos_after_break].second - range_occs_rev[pos_after_break].first+1;
+ }
+
+ ///// A GOOD CANDIDAT IS PROBABLE IF START/END ARE ON THE SAME STRAND ////
+ if ((has_start_forward_strand && has_end_forward_strand)
+ || (has_start_reverse_strand && has_end_reverse_strand)){
+ //save candidats on forward strand
+ if (has_start_forward_strand && has_end_forward_strand){
+ saveCandidates(pos_before_break, pos_after_break,
+ pos_occ_start_fwd, nb_loc_start_fwd,1,
+ pos_occ_end_fwd, nb_loc_end_fwd,1,
+ &potential_candidats, nb_potential_candidats,max_potential_candidats);
+ }
+ //save candidats on reverse strand
+ if (has_start_reverse_strand && has_end_reverse_strand){
+ saveCandidates(pos_before_break, pos_after_break,
+ pos_occ_start_rev, nb_loc_start_rev,-1,
+ pos_occ_end_rev, nb_loc_end_rev,-1,
+ &potential_candidats, nb_potential_candidats, max_potential_candidats);
+ }
+ }
+
+ // test if there is a good candidat (at least a splice)
+ bool isIntermediarySplice = false;
+ if (nb_potential_candidats > 0){
+ ulong i_chosen = getBestCandidat(potential_candidats, nb_potential_candidats);
+ if (i_chosen != 0){
+ delete potential_candidats[0];
+ potential_candidats[0] = new CandidatBreak(*potential_candidats[i_chosen]);
+ }
+ for (ulong i=1; i < nb_potential_candidats; i++) {
+ delete potential_candidats[i];
+ }
+ nb_potential_candidats = 1;
+ isIntermediarySplice = potential_candidats[0]->isNiceCandidat();
+ }
+
+ /////////////////// WE SAVE SOME CHIMERAS //////////////////
+ // get other chimeras if there is not at least an intermediary splice
+ if (nb_potential_candidats == 0 || !isIntermediarySplice){
+ if (has_start_forward_strand && has_end_reverse_strand){
+ saveCandidates(pos_before_break, pos_after_break,
+ pos_occ_start_fwd, nb_loc_start_fwd,1,
+ pos_occ_end_rev, nb_loc_end_rev,-1,
+ &potential_candidats, nb_potential_candidats, max_potential_candidats);
+ }
+ if (has_start_reverse_strand && has_end_forward_strand){
+ saveCandidates(pos_before_break, pos_after_break,
+ pos_occ_start_rev, nb_loc_start_rev,-1,
+ pos_occ_end_fwd, nb_loc_end_fwd,1,
+ &potential_candidats, nb_potential_candidats, max_potential_candidats);
+ }
+ }
+
+ ////////////////////////////////////////////////////////////////////////
+ /////////////////// SAVE THE BEST CANDIDAT AT THIS STEP /////////////////
+ ////////////////////////////////////////////////////////////////////////
+
+ if (nb_potential_candidats > 0){
+ ulong i_chosen = 0;
+ // a new candidat is chosen only if it is not an at least intermediary splice
+ if (!isIntermediarySplice && nb_potential_candidats > 1){
+ i_chosen = getBestCandidat(potential_candidats, nb_potential_candidats);
+ }
+ candidats[nb_candidats] = new CandidatBreak(*potential_candidats[i_chosen]);
+ nb_candidats++;
+ }
+
+ /////////////////// DELETE THE TEMPORARY TABLE /////////////////////////
+
+ if (has_start_forward_strand)
+ free(pos_occ_start_fwd);
+ if (has_end_forward_strand)
+ free(pos_occ_end_fwd);
+ if (has_start_reverse_strand)
+ free(pos_occ_start_rev);
+ if (has_end_reverse_strand)
+ free(pos_occ_end_rev);
+
+ for (ulong i=0; i < nb_potential_candidats; i++) {
+ delete potential_candidats[i];
+ }
+ free(potential_candidats);
+}
+
+
+ostream &operator<<(ostream &os, SupportBreak &sb) {
+ os << "[break={" << sb.getPositionStartBreak() << ","
+ << sb.getPositionEndBreak() << "};gap={"
+ << sb.getPositionStartBreak() << ","
+ << sb.getPositionEndBreak() << "};loc={";
+ if (sb.getLocationStartBreak())
+ os << *sb.getLocationStartBreak();
+ else
+ os << "undef";
+ os << ",";
+ if (sb.getLocationEndBreak())
+ os << *sb.getLocationEndBreak();
+ else
+ os << "undef";
+ os << "}]" << endl;
+ return os;
+}
diff --git a/src/SupportBreak.h b/src/SupportBreak.h
new file mode 100644
index 0000000..5429458
--- /dev/null
+++ b/src/SupportBreak.h
@@ -0,0 +1,812 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef SUPPORT_BREAK_H
+#define SUPPORT_BREAK_H
+#include <utility>
+#include "Parameters.h"
+#include "CandidatBreak.h"
+#include "libSSA/chrPosition.h"
+#include "libSSA/locateOnGenome.h"
+#include "types.h"
+
+class Support;
+
+class SupportBreak {
+
+ CandidatBreak **candidats;
+ ulong nb_candidats;
+ CandidatBreak *candidat_chosen;
+
+ uint k; /* Threshold, size of k-mer used */
+ /* bool duplicated; /\* true iff there are two possible causes *\/ */
+
+ bool repeated; /* true iff the break is in a repeated region.
+ In that case, loc_{start,end}_break are not
+ defined. */
+
+ uint pos_start_break; /* Position in the support of the start
+ of the break. */
+ uint pos_end_break; /* Position in the support of the end
+ of the break.*/
+
+ uint override_pos_end_break; /* Position in read of the end
+ of the break. (ie. pos_end_break + k - 1) */
+
+ float score_outside_break; /* the score (can be median, average
+ or whatever we can think about)
+ of the support, just before or
+ after the break. */
+
+ float score_during_break; /* Well, that's self-speaking, isn't it? */
+
+ float average_low_inside; /* Average of the lowest values inside the break */
+ float average_high_inside; /* Average of the highest values inside the break */
+ float pc_ones_left_inside, /* Percentage of 1s in the support on the */
+ pc_ones_left_outside, /* border of the breaks */
+ pc_ones_right_inside,
+ pc_ones_right_outside;
+ float score_inside_averages; /* Score between the two averages */
+
+ Support *support; /* The support we are working on. */
+
+ Parameters* parameters; /* Parameters chosen by the user or chosen
+ by default by the great developers. */
+
+ pair<uint, uint> *range_occs_fwd; /* Range of the occurrences on the
+ forward strand. */
+
+ pair<uint, uint> *range_occs_rev; /* Range of the occurrences on the
+ reverse strand. */
+
+ uint loc_end_break; /* the first absolute location after the
+ break */
+
+ uint loc_start_break; /* the last absolute location before the
+ break */
+
+ uint nb_loc_end; /* the number of location at the current pos after the break */
+ uint nb_loc_start; /* the number of location at the current pos before the break */
+
+ int strand_end_break; /* the strand of the end_break position*/
+
+ int strand_start_break; /* the strand of the start_break position */
+
+ uint inside_quartile1; /* first quartile of the support
+ * inside the break*/
+ uint inside_quartile4; /* last quartile of the support
+ * inside the break*/
+ uint nb_merges; /* the number of merges that have been done to create this break */
+
+ public:
+
+ SupportBreak(uint start, uint end,
+ Support *s, Parameters *p,
+ pair<uint, uint> *range_occs_forward,
+ pair<uint, uint> *range_occs_reverse,
+ uint nb_merges = 0);
+
+ /**
+ * Merge the two breaks in parameters.
+ */
+ SupportBreak(SupportBreak &b1, SupportBreak &b2);
+
+ ~SupportBreak();
+
+ /**
+ * Computes score inside and outside break. It depends of
+ * pos_start_break and pos_end_break
+ */
+ void computeScore();
+
+ /**
+ * @param pos_start: a position to define a start break
+ * @param pos_end: a position to define an end break
+ * Computes score inside and outside break between a pos_start and a
+ * pos_end defined in argument.
+ */
+ void computeScore(uint pos_start, uint pos_end);
+
+ /**
+ * @return the average low support inside the break
+ */
+ float getAverageLowInside();
+
+ /**
+ * @return the average high support inside the break
+ */
+ float getAverageHighInside();
+
+ /**
+ * @return the candidat chosen for the break
+ */
+ CandidatBreak *getCandidatChosen();
+
+ /**
+ * @return the candidat number i among the potential candidats
+ */
+ CandidatBreak *getPotentialCandidat(uint i);
+
+ /**
+ * @param: position of the location
+ * @return the chromosome corresponding to the position
+ * in the genome of the factor before
+ * or after the break.
+ * ~0 if p == START_BREAK && getPositionStartBreak() == 0
+ * || p == END_BREAK && getPositionEndBreak() == support->getLength()
+ */
+ const uchar *getChr(pos_location_break);
+
+
+ /**
+ * @param: position of the location
+ * @return the ID of the chromosome corresponding to the position
+ * in the genome of the factor before
+ * or after the break.
+ * ~0 if p == START_BREAK && getPositionStartBreak() == 0
+ * || p == END_BREAK && getPositionEndBreak() == support->getLength()
+ */
+ ulong getChrId(pos_location_break);
+
+ /**
+ * @param: position of the location
+ * @return a ChrPosition object corresponding to the position
+ * in the genome of the factor before
+ * or after the break.
+ * NULL if p == START_BREAK && getPositionStartBreak() == 0
+ * || p == END_BREAK && getPositionEndBreak() == support->getLength()
+ */
+ ChrPosition *getChrPosition(pos_location_break p);
+
+
+ /**
+ * @return genome
+ */
+ LocateOnGenome *getGenome();
+
+ /**
+ * @return The gap length between the location of the factors on the
+ * genome, before the break and after the break. If no factor is
+ * located before or after the break return 0.
+ */
+ gap_size_t getGenomeGapLength();
+
+ /**
+ * @return the value delimiting the first and second quartile of the
+ * support inside the break (ie. 25% of the values are lower or
+ * equal than getInsideQuartile1())
+ */
+ uint getInsideQuartile1();
+
+ /**
+ * @return the value delimiting the third and fourth quartile of the
+ * support inside the break (ie. 25% of the values are greater or
+ * equal than getInsideQuartile1())
+ */
+ uint getInsideQuartile4();
+
+ /**
+ * @return the score inside the break i.e. the average of support
+ * of each pos inside the break.
+ */
+ float getInsideScore();
+
+ /**
+ * @return the location of the factor just after the break.
+ */
+ ChrPosition *getLocationEndBreak();
+
+ /**
+ * @return the location of the factor just before the break.
+ */
+ ChrPosition *getLocationStartBreak();
+
+
+ /**
+ * @return length of the support as seen using the current threshold getThreshold().
+ * getLength() + support->getThreshold() - getThreshold() == support->getLength()
+ */
+ uint getLength();
+
+ /**
+ * @return the number of candidats saved during the extension process
+ */
+ ulong getNbCandidats();
+
+ /**
+ * @return the number of merge processed to create this break
+ */
+ uint getNbMerges();
+
+ /**
+ * Return the number of indels on the genome.
+ * @return getGenomeGapLength() - support->getTagBreakLength()
+ * , if getGenomeGapLength() > 0
+ * INT_MAX, otherwise.
+ */
+ int getNbGenomeIndels();
+
+ /**
+ * Return the number of indels in the tag.
+ * @return getTagBreakLength() - support->getGenomeGapLength()
+ */
+ int getNbTagIndels();
+
+ /**
+ * @return the score outiside the break i.e.
+ * the average of support for each position outside the break
+ */
+ float getOutsideScore();
+
+ /**
+ * @param strand: if -1 consider the break is on the other strand
+ * @return pos_end_break (ie. position where the k-mer begins after the break)
+ * or getSupportLength() - 1 - getPositionStartBreak() (if strand == -1)
+ */
+ uint getPositionEndBreak(int strand=1);
+
+ /**
+ * @return pos_end_break + k -1 or override_pos_end_break (ie. the
+ * real pos_end_break in more detailed search)
+ */
+ uint getPositionEndBreakOnTheRead();
+
+ /**
+ * @param: position of the location
+ * @return absolute posittion in the genome
+ * corresponding the factor before
+ * or after the break.
+ * ~0 if p == START_BREAK && getPositionStartBreak() == 0
+ * || p == END_BREAK && getPositionEndBreak() == support->getLength()
+ */
+ ulong getPositionLocation(pos_location_break);
+
+ /**
+ * @param strand: the strand we must consider to return the position
+ * @return pos_start_break or getSupportLength() - 1 - getPositionEndBreak()
+ * if strand == -1
+ */
+ uint getPositionStartBreak(int strand=1);
+
+ /**
+ * @param i: i == FORWARD_STRAND || i == REVERSE_STRAND
+ * @return range_occurrences[END_BREAK][i]
+ */
+ pair<uint, uint> getRangeEndBreak(uint i);
+
+ /**
+ * @param i: i == FORWARD_STRAND || i == REVERSE_STRAND
+ * @return range_occurrences[START_BREAK][i]
+ */
+ pair<uint, uint> getRangeStartBreak(uint i);
+
+ /**
+ * Compute the score to evaluate the coverage between two exons from
+ * getScoreInsideBreak() and getScoreOutsideBreak(). @return a
+ * float between -1 and 1 (-1: biological reason, 0: not different, 1: error)
+ */
+ float getScoreComputedInterExon();
+
+ /**
+ * Compute the score to evaluate the coverage inside an exon from
+ * getScoreInsideBreak() and getScoreOutsideBreak(). @return a
+ * float between -1 and 1 (-1: biological reason, 0: not different, 1: error)
+ */
+ float getScoreComputedIntraExon();
+
+ /**
+ * @return the score computed between the average of the 50% highest values and
+ * the average of the 50% lowest values, inside the break
+ */
+ float getScoreInsideAverages();
+
+ /**
+ * @return score_inside_break
+ */
+ float getScoreInsideBreak();
+
+ /**
+ * @return score_outside_break
+ */
+ float getScoreOutsideBreak();
+
+ /**
+ * @param: position of the location
+ * @return strand in the genome
+ * corresponding the factor before
+ * or after the break.
+ * 0 if p == START_BREAK && getPositionStartBreak() == 0
+ * || p == END_BREAK && getPositionEndBreak() == support->getLength()
+ */
+ int getStrandLocation(pos_location_break);
+
+ /**
+ * The break length between the the break and after the break, in the tag.
+ * @return getPositionEndBreak()-getPositionStartBreak() + 1
+ */
+ uint getTagBreakLength();
+
+ /**
+ * @return the length of the current read
+ */
+ uint getTagLength();
+
+ /**
+ * @param : the score outside the break
+ * @return a score computed by a
+ * function from the score to define the threshold between errors
+ * and biological reasons like chimera or splice.
+ */
+ float getThresholdForScoreInterExon(float score);
+
+ /**
+ * @return the threshold (ie. the k-mer length)
+ */
+ uint getThreshold();
+
+ /**
+ * @param : the score outside the break
+ * @return a score computed by a function from the score to
+ * define the threshold between errors and biological reasons
+ * like snp or short indel.
+ */
+ float getThresholdForScoreIntraExon(float score);
+
+ /**
+ * Return true if the support has no cover
+ * @return score_outside_break <= 1 + EPSILON
+ * && score_inside_break <= 1 + EPSILON
+ */
+ bool hasNoCover();
+
+ /**
+ * @return true if the getTagBreakLength() is long enough
+ * or if there is no start/end break (in that case we don't know
+ * where the break starts/finishes).
+ * There is no good reason for it to be less than
+ * getThreshold() - parameters->max_bases_randomly_matched.
+ */
+ bool hasLongEnoughTagBreak();
+
+ /**
+ * @return true if getPositionEndBreak() + 1 == support->getLength()
+ * or if hasNoStartBreak() (when strand == 1)
+ */
+ bool hasNoEndBreak(int strand=1);
+
+ /**
+ * @return true if getPositionStartBreak() == 0 (when strand == 1)
+ * or if hasNoEndBreak() (when strand == -1)
+ */
+ bool hasNoStartBreak(int strand=1);
+
+ /**
+ * @return true iff we have set the end position of the break on the read
+ * using setPositionEndBreakOnTheRead()
+ */
+ bool hasPositionEndBreakOnTheRead(int strand=1);
+
+ /**
+ * @return return ! hasNoCover()
+ * && (score_during_break >= score_outside_break
+ * || isBiologicalIntraEvent()
+ * || isBiologicalInterEvent())
+ */
+ bool isBiologicalEvent();
+
+ /**
+ * @return getScoreComputedIntraExon()
+ * <= parameters->p_value_variation_biological
+ * && !isTagIndel() && !isTagSubstitution()
+ */
+ bool isBiologicalIntraEvent();
+
+ /**
+ * @return getScoreComputedInterExon() <=
+ * parameters->p_value_variation_biological
+ * && !isChimera()
+ */
+ bool isBiologicalInterEvent();
+
+ /**
+ * For a chimera the break length in the tag
+ * cannot be greater than threshold - 1.
+ * There is a chimera is two parts of the read
+ * are not located on the same strand or not on
+ * the same chromosome or when the break on the
+ * genome is larger than parameters->max_splice_length
+ * or when the break length is long enough
+ * @return true if the break is a chimera
+ */
+ bool isChimera();
+
+ /**
+ * @return true if a part of the support is low because of an error
+ * occuring at the same time as a mutation
+ */
+ bool isDeviated();
+
+ /**
+ * @return true if the cause is duplicated, i.e. there are two
+ * possible splice or SNV
+ */
+ bool isDuplicated();
+
+ /**
+ * A genome deletion must be larger than
+ * parameters->max_bio_ins_del bases
+ * (otherwise we consider it to be a tag deletion).
+ * A genome deletion is characterised by a larger break
+ * in the tag than in the genome.
+ * @return true if the break is a genome deletion
+ */
+ bool isGenomeDeletion();
+
+ /**
+ * For a genome insertion the break length in the tag
+ * cannot be greater than threshold - 1.
+ * Moreover, the insertion length must be greater than
+ * parameters->max_bio_ins_del (otherwise it is
+ * considered as an insertion in the tag).
+ * @return true if the break is a genome insertion
+ */
+ bool isGenomeInsertion();
+
+ /**
+ * @return true iff
+ * - locations are defined both before and after the break
+ * - both locations are on the same strand and on the same chromosome
+ * - genome gap length is not larger than parameters->max_splice_length
+ * and is coherent with the strand.
+ */
+ bool isNiceBreak();
+
+ /**
+ * @return true iff merging *this and *sb will produce a break
+ * where isNiceBreak() == true.
+ */
+ bool isNiceMerge(SupportBreak *sb);
+
+ /**
+ * @return true iff the break is in a repeated region and we didn't find
+ * a ``nice'' location (ie. locations before and after the break must be close).
+ */
+ bool isRepeated();
+
+ /**
+ * @return true if the support falls on the left or on the right border of
+ * the break between the inside and outside.
+ */
+ bool isSupportFalling();
+
+ /**
+ * @return true if the support falls on the left border of the break
+ * between the inside and outside (when strand == 1).
+ * Return isSupportFallingRight() when strand == -1
+ */
+ bool isSupportFallingLeft(int strand=1);
+
+ /**
+ * @return true if the support falls on the right border of the break
+ * between the inside and outside (when strand == 1)
+ * Return isSupportFallingLeft() when strand == -1
+ */
+ bool isSupportFallingRight(int strand = 1);
+
+ /**
+ * The TagBreakLength must be equal to the GenomeGapLength.
+ * We don't compare the tag break length to the threshold since
+ * we may have several substitutions in a raw leading to a larger gap.
+ * @return true if the break is a substitution
+ */
+ bool isTagSubstitution();
+
+ /**
+ * An indel in a tag corresponds to an indel (length != 0)
+ * whose maximal length is parameters->max_bio_ins_del.
+ * In case of tag deletion the break length of tag must be less
+ * than threshold.
+ * With tag indel, the gap on the genome can't be negative. It would be
+ * a chimera.
+ * @return true if the break is a short indel
+ */
+ bool isTagIndel();
+
+ /**
+ * @return true iff
+ * - locations are defined both before and after the break
+ * - both locations are on the same strand and on the same chromosome
+ * - genome gap length is not larger than parameters->max_intron_length
+ * and is coherent with the strand.
+ */
+ bool isVeryNiceBreak();
+
+ /**
+ * @return true iff merging *this and *sb will produce a break
+ * where isVeryNiceBreak() == true.
+ */
+ bool isVeryNiceMerge(SupportBreak *sb);
+
+
+ /**
+ * Compute the inside score between pos_start_break and
+ * pos_end_break. An average support values inside the break is
+ * computed (only pos with a getNbLocs() == 0 are considered).
+ */
+ void setInsideScore();
+
+
+ /**
+ * @param pos_start: a position to define a start break
+ * @param pos_end: a position to define an end break
+ * Compute the inside score between pos_start and pos_end. An average
+ * support values inside the break is computed (only pos with a
+ * getNbLocs() == 0 are considered because it may bias the
+ * computation).
+ */
+ void setInsideScore(uint pos_start, uint pos_end);
+
+ /**
+ * loc_end_break = loc_end.
+ */
+ void setLocationEndBreak(uint loc_end);
+
+ /**
+ * loc_start_break = loc_start.
+ */
+ void setLocationStartBreak(uint loc_start);
+
+ /**
+ * pos_end_break = pos_end
+ */
+ void setPositionEndBreak(uint pos_end);
+
+ /**
+ * override_pos_end_break = pos_end
+ */
+ void setPositionEndBreakOnTheRead(uint pos_end);
+
+ /**
+ * pos_start_break = pos_start
+ */
+ void setPositionStartBreak(uint pos_start);
+
+ /**
+ * @post getThreshold() == k
+ */
+ void setThreshold(uint k);
+
+ /**
+ * Compute the outside score between the pos_start_break and the
+ * pos_end_break. An average of (at most)
+ * parameters->support_score_window_length support values outside
+ * the break is computed.
+ */
+ void setOutsideScore();
+
+ /**
+ * @param pos_start: a position to define a start break
+ * @param pos_end: a position to define an end break
+ * Compute the outside score between pos_start and pos_end. An
+ * average of (at most) parameters->support_score_window_length
+ * support values outside the break is computed.
+ */
+ void setOutsideScore(uint pos_start, uint pos_end);
+
+ /**
+ * Sets the forward range.
+ */
+ void setRangesForward(pair<uint, uint> *);
+
+ /**
+ * strand_end_break = strand_end.
+ */
+ void setStrandEndBreak(int strand_end);
+
+ /**
+ * strand_start_break = strand_start.
+ */
+ void setStrandStartBreak(int strand_start);
+
+ /**
+ * Sets the reverse range.
+ */
+ void setRangesReverse(pair<uint, uint> *);
+
+ /**
+ * Sets the support.
+ */
+ void setSupport(Support *);
+
+ private:
+
+ /**
+ * Adjust the boundaries of getCandidatChosen because
+ * it has not necessary the good ones after the extension process
+ */
+ void adjustBoundaries();
+
+
+ /**
+ * Return true if we can check locations at positions start and end
+ */
+ bool canCheckPositions(ulong start, ulong end);
+
+
+ /**
+ * Merge the two breaks and check if the result is nice (or very nice if
+ * the boolean is set at true)
+ */
+ bool check_nice_merge(SupportBreak *sb1, SupportBreak *sb2,
+ bool very_nice);
+
+
+ /**
+ * @param pos_start: a position to define a start break
+ * @param pos_end: a position to define an end break
+ * Sort the inside support between pos_start and pos_end. Compute
+ * the average on the low and on the high values and compute the
+ * score between those two averages.
+ */
+ void computeHighAndLowAverages(uint pos_start, uint pos_end);
+
+
+ /**
+ * Method to choose the best location.
+ */
+ void fillWithClosestMatch();
+
+
+ /**
+ * @param a table of candidats
+ * @return the position of best candidat among the table of potential candidats during a step of the extension
+ * the best candidat is :
+ * - nice_candidat (at least a splice)
+ * - single consistent
+ * - the minimal gap on the genome
+ * And notify a duplicated candidat if the table contains several good candidats
+ */
+ ulong getBestCandidat(CandidatBreak** potential_candidats, ulong nb_potential_candidats, bool after_extension = false);
+
+ /**
+ * @return getBestCandidat(this->candidats,this->nb_candidats,true) after the extension process
+ */
+ ulong getBestCandidat();
+
+ /**
+ * Initialises the members (called by the different constructors);
+ */
+ void init();
+
+ /**
+ * @return (potential_candidats[pos_i] eq potential_candidats[pos_j]) ? true : false
+ */
+ bool isSameCandidat(CandidatBreak **potential_candidats, ulong pos_i, ulong pos_j);
+
+ /**
+ * @return (potential_candidats[pos_i].end eq potential_candidats[pos_j].end) ? true : false
+ */
+ bool isSameCandidatEnd(CandidatBreak **potential_candidats, ulong pos_i, ulong pos_j);
+
+ /**
+ * @return (potential_candidats[pos_i].start eq potential_candidats[pos_j].start) ? true : false
+ */
+ bool isSameCandidatStart(CandidatBreak **potential_candidats, ulong pos_i, ulong pos_j);
+
+ /**
+ * Save the best candadidat for each extension step of the extension
+ */
+ void saveCandidates(uint pos_before_break, uint pos_after_break,
+ ulong *pos_occ_start, uint nb_loc_start,
+ int strand_start, ulong *pos_occ_end,
+ uint nb_loc_end, int strand_end,
+ CandidatBreak ***potential_candidats,
+ ulong &nb_potential, ulong &nb_potential_max);
+
+ /**
+ * Method to select potential candidats during the extension process.
+ */
+ void updateLocation(uint pos_before_break,
+ uint pos_after_break);
+
+
+};
+
+ostream &operator<<(ostream &, SupportBreak &);
+#endif
diff --git a/src/basic.h b/src/basic.h
new file mode 100644
index 0000000..2ba72b0
--- /dev/null
+++ b/src/basic.h
@@ -0,0 +1,191 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef BASICSINCLUDED
+#define BASICSINCLUDED
+
+#include <sys/types.h>
+#include <sys/resource.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#define mask31 0x0000001F
+
+#define max(x,y) ((x)>(y)?(x):(y))
+#define min(x,y) ((x)<(y)?(x):(y))
+
+
+
+
+/*numero de bits del entero de la maquina*/
+#define W 32
+/* W-1 */
+#define Wminusone 31
+/*numero de bits del entero de la maquina*/
+#define WW 64
+/*bits para hacer la mascara para contar mas rapido*/
+#define bitsM 8
+/*bytes que hacen una palabra */
+#define BW 4
+#define size_uchar 256
+
+
+/* bits needed to represent a number between 0 and n */
+inline uint bits (uint n){
+ uint b = 0;
+ while (n) { b++; n >>= 1; }
+ return b;
+}
+
+/* reads bit p from e */
+#define bitget(e,p) ((((e)[(p)/W] >> ((p)%W))) & 1)
+/* sets bit p in e */
+#define bitset(e,p) ((e)[(p)/W] |= (1<<((p)%W)))
+/* cleans bit p in e */
+#define bitclean(e,p) ((e)[(p)/W] &= ~(1<<((p)%W)))
+
+/* numero de enteros necesarios para representar e elementos de largo n */
+#define enteros(e,n) ((e)*(n))/W+(((e)*(n))%W > 0)
+
+inline ulong GetField(ulong *A, register ulong len, register ulong index) {
+ register ulong i=index*len/W, j=index*len-W*i, result;
+ if (j+len <= W)
+ result = (A[i] << (W-j-len)) >> (W-len);
+ else {
+ result = A[i] >> j;
+ result = result | (A[i+1] << (WW-j-len)) >> (W-len);
+ }
+ return result;
+}
+
+inline void SetField(ulong *A,register ulong len, register ulong index,register ulong x) {
+ ulong i=index*len/W, j=index*len-i*W;
+ ulong mask = ((j+len) < W ? ~0u << (j+len) : 0) | ((W-j) < W ? ~0u >> (W-j) : 0);
+ A[i] = (A[i] & mask) | x << j;
+ if (j+len>W) {
+ mask = ((~0u) << (len+j-W));
+ A[i+1] = (A[i+1] & mask)| x >> (W-j);
+ }
+}
+
+inline unsigned GetFieldW32(unsigned *A,register unsigned index) {
+ return A[index];
+}
+
+inline void SetField32(unsigned *A, register unsigned index,register unsigned x) {
+ A[index]=x;
+}
+
+inline unsigned GetFieldW16(unsigned *A,register unsigned index) {
+ register unsigned i=index/2, j=(index&1)<<4, result;
+ result = (A[i] << (16-j)) >> (16);
+ return result;
+}
+
+inline unsigned GetFieldW4(unsigned *A,register unsigned index) {
+ register unsigned i=index/8, j=(index&0x7)<<2;
+ /*register unsigned i=index/8, j=index*4-32*i; */
+ return (A[i] << (28-j)) >> (28);
+}
+
+
+
+#endif
+
diff --git a/src/classifyTags.cpp b/src/classifyTags.cpp
new file mode 100644
index 0000000..02fafef
--- /dev/null
+++ b/src/classifyTags.cpp
@@ -0,0 +1,542 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at univ-montp2.fr *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "classifyTags.h"
+#include "utils.h"
+#include "libReadsInfo/tagInfo.h"
+#include "Support.h"
+#include "SupportBreak.h"
+#include <config.h>
+#include <pthread.h>
+#include <cstdlib>
+#include <string>
+#include <sstream>
+
+#ifdef HAVE_LIBPROGRESSBAR
+#include <sys/ioctl.h>
+#include <libProgressBar/progressBar.h>
+#endif
+
+using namespace std;
+
+ClassifyTags::ClassifyTags(LocateOnGenome *genome,
+ gkArrays *tags,
+ Parameters *param):
+ genome(genome),tags(tags),parameters(param)
+{}
+
+void ClassifyTags::classify(ostream *snp
+ , ostream *bioTagIndel
+ , ostream *seqErr
+ , ostream *splice
+ , ostream *spliceNoCover
+ , ostream *spliceInter
+ , ostream *undetermined
+ , ostream *repetition
+ , ostream *duplication
+ , ostream *nothing
+ , ostream *normal
+ , ostream *almostNormal
+ , ostream *multiple
+ , ostream *none
+ , ostream *bioUndermined
+ , ostream *single
+ , ostream *sam
+ , ostream *pairedEndChimera) {
+ Classifier *classifier;
+ pthread_t threads[parameters->nb_threads];
+ classify_thread_t params[parameters->nb_threads];
+ readIterator *readIt = tags->getReads()->begin();
+ Classifier **store_tagsInfo[parameters->nb_threads-1];
+ sem_t remaining_seats[parameters->nb_threads-1];
+ sem_t processed_tags[parameters->nb_threads-1];
+ uint *positions = NULL;
+ uint nb_tagsInfo;
+ bool isPairedEnd = tags->getReads()->isPairedEnd();
+
+
+#ifdef HAVE_LIBPROGRESSBAR
+ DoccY::ProgressBar *PB = NULL;
+ unsigned int maxval = 0;
+ unsigned int cpt = 0;
+ unsigned int reset_cpt = 0;
+ if (parameters->show_progressbar) {
+ unsigned int cols = 80;
+#ifdef TIOCGSIZE
+ struct ttysize ts;
+ cols = ioctl(STDIN_FILENO, TIOCGSIZE, &ts) ? 80 : ts.ts_cols;
+#elif defined(TIOCGWINSZ)
+ struct winsize ts;
+ cols = ioctl(STDIN_FILENO, TIOCGWINSZ, &ts) ? 80 : ts.ws_col;
+#endif /* TIOCGSIZE */
+
+ maxval = cols ? cols : 100;
+ reset_cpt = tags->getNbTags() / maxval;
+ PB = new DoccY::ProgressBar("Processing Reads", maxval, cols, cerr, false);
+ PB->ShowPercent();
+ PB->ShowTime();
+ PB->update();
+ }
+#endif
+
+ for (uint i=0; i <= NB_MASKS; i++)
+ nb_classes[i] = 0;
+
+ nb_explainable=0;
+
+ if (parameters->nb_threads > 1) {
+ nb_tagsInfo = parameters->nb_tags_info_stored;
+
+ positions = new uint[parameters->nb_threads - 1];
+
+ for (uint j = 0; j < parameters->nb_threads - 1; j++) {
+ positions[j] = 0;
+ params[j].classify = this;
+ sem_init(&remaining_seats[j],0,nb_tagsInfo-1);
+ sem_init(&processed_tags[j],0,0);
+ params[j].remaining_seats = &remaining_seats[j];
+ params[j].processed_tags = &processed_tags[j];
+ params[j].total_seats = nb_tagsInfo;
+ if(isPairedEnd) {
+ store_tagsInfo[j] = (Classifier**)calloc(nb_tagsInfo, sizeof(PairedEndReadClassifier*));
+ } else {
+ store_tagsInfo[j] = (Classifier**)calloc(nb_tagsInfo, sizeof(SingleReadClassifier*));
+ }
+ params[j].seats = store_tagsInfo[j];
+ params[j].thread_num = j;
+ params[j].nb_threads = parameters->nb_threads-1;
+ }
+ } else {
+ nb_tagsInfo = 1;
+ }
+
+ if (parameters->nb_threads > 1) {
+ // Launching threads
+ for (uint j = 0; j < parameters->nb_threads - 1; j++) {
+ pthread_create(&threads[j], NULL, fillInfos, ¶ms[j]);
+ }
+ }
+
+ uint i = 0;
+ while (!readIt->isFinished()) {
+ if (parameters->nb_threads > 1) {
+ uint j;
+ if(isPairedEnd && i > 0) {
+ j = i/2 % (parameters->nb_threads - 1);
+ }
+ else {
+ j = i % (parameters->nb_threads - 1);
+ }
+ sem_wait(&processed_tags[j]);
+ classifier = store_tagsInfo[j][positions[j]];
+ sem_post(&remaining_seats[j]);
+ positions[j] = (positions[j] + 1) % nb_tagsInfo;
+ } else {
+ if(isPairedEnd) {
+ classifier = new PairedEndReadClassifier(i,i+1,genome,tags,parameters);
+ } else {
+ classifier = new SingleReadClassifier(i,genome,tags,parameters);
+ }
+ classifier->classify();
+ }
+
+ classifier->setInfos(readIt);
+ classifier->writeOutputs(snp,
+ bioTagIndel,
+ seqErr,
+ splice,
+ spliceNoCover,
+ spliceInter,
+ undetermined,
+ repetition,
+ duplication,
+ nothing,
+ normal,
+ almostNormal,
+ multiple,
+ none,
+ bioUndermined,
+ single);
+ classifier->samOutput(*sam);
+ if(isPairedEnd && pairedEndChimera != NULL)
+ ((PairedEndReadClassifier*)classifier)->writePairedEndChimera(pairedEndChimera);
+ classifier->updateStatistics(&nb_classes,&nb_explainable);
+ delete classifier;
+
+ // If we are using paired-end tags, increments loop ind by 2
+ if(isPairedEnd) {
+ i += 2;
+#ifdef HAVE_LIBPROGRESSBAR
+ cpt += 2;
+#endif
+ } else {
+ i++;
+#ifdef HAVE_LIBPROGRESSBAR
+ cpt++;
+#endif
+ }
+#ifdef HAVE_LIBPROGRESSBAR
+ if ((cpt >= reset_cpt) && parameters->show_progressbar) {
+ PB->Step();
+ cpt = 0;
+ }
+#endif
+ }
+#ifdef HAVE_LIBPROGRESSBAR
+ if (parameters->show_progressbar) {
+ PB->SetVal(maxval);
+ PB->update(false);
+ cerr << endl;
+ delete PB;
+ }
+#endif
+
+ // deleting the iterator
+ delete readIt;
+ for (uint j = 0; j < parameters->nb_threads - 1; j++) {
+ free(store_tagsInfo[j]);
+ sem_destroy(&remaining_seats[j]);
+ }
+ for (uint j = 0; j < parameters->nb_threads - 1; j++) {
+ pthread_join(threads[j], NULL);
+ }
+
+ if (positions)
+ delete [] positions;
+}
+
+LocateOnGenome *ClassifyTags::getGenomeIndex() {
+ return genome;
+}
+
+Parameters *ClassifyTags::getParameters() {
+ return parameters;
+}
+
+gkArrays *ClassifyTags::getReadIndex() {
+ return tags;
+}
+
+uint ClassifyTags::getNbNone() {
+ return nb_classes[posBitInMask(MASK_NONE)];
+}
+
+uint ClassifyTags::getNbMultiple() {
+ return nb_classes[posBitInMask(MASK_MULTIPLE)];
+}
+
+uint ClassifyTags::getNbSingle() {
+ return nb_classes[posBitInMask(MASK_SINGLE)];
+}
+
+uint ClassifyTags::getNbAlmostNormal() {
+ return nb_classes[posBitInMask(MASK_ALMOST_NORMAL)];
+}
+
+uint ClassifyTags::getNbExplainable() {
+ return nb_explainable;
+}
+
+uint ClassifyTags::getNbNormal() {
+ return nb_classes[posBitInMask(MASK_NORMAL)];
+}
+
+uint ClassifyTags::getNbDuplication() {
+ return nb_classes[posBitInMask(MASK_DUPLICATION)];
+}
+
+uint ClassifyTags::getNbSNP() {
+ return nb_classes[posBitInMask(MASK_SNP)];
+}
+
+uint ClassifyTags::getNbBioTagIndel() {
+ return nb_classes[posBitInMask(MASK_BIOLOGICAL_TAG_INDEL)];
+}
+
+uint ClassifyTags::getNbBioUndetermined() {
+ return nb_classes[posBitInMask(MASK_BIOLOGICAL_UNDETERMINED)];
+}
+
+uint ClassifyTags::getNbSeqErr() {
+ return nb_classes[posBitInMask(MASK_SEQ_ERR)];
+}
+
+
+uint ClassifyTags::getNbRepetition() {
+ return nb_classes[posBitInMask(MASK_REPETITION)];
+}
+
+uint ClassifyTags::getNbSplice() {
+ return nb_classes[posBitInMask(MASK_SPLICE)];
+}
+
+uint ClassifyTags::getNbSpliceIntra() {
+ return nb_classes[posBitInMask(MASK_INTRA_TRANSPLICING)];
+}
+
+uint ClassifyTags::getNbSpliceInter() {
+ return nb_classes[posBitInMask(MASK_INTER_TRANSPLICING)];
+}
+
+uint ClassifyTags::getNbSpliceNoCover() {
+ return nb_classes[posBitInMask(MASK_SPLICE_NO_COVER)];
+}
+
+uint ClassifyTags::getNbNothing() {
+ return nb_classes[NB_MASKS];
+}
+
+uint ClassifyTags::getNbUndetermined() {
+ return nb_classes[posBitInMask(MASK_UNDETERMINED_ERROR)];
+}
+
+uint ClassifyTags::getNbPairedEndChimera() {
+ return nb_classes[posBitInMask(MASK_PAIRED_END_CHIMERA)];
+}
+
+void ClassifyTags::getHeaders(ostream *snp
+ , ostream *bioTagIndel
+ , ostream *seqErr
+ , ostream *splice
+ , ostream *spliceNoCover
+ , ostream *spliceInter
+ , ostream *undetermined
+ , ostream *repetition
+ , ostream *duplication
+ , ostream *nothing
+ , ostream *normal
+ , ostream *almostNormal
+ , ostream *multiple
+ , ostream *none
+ , ostream *bioUndermined
+ , ostream *single
+ , ostream *pairedEndChimera) {
+
+ stringstream headerTemplate;
+ headerTemplate << "#CRAC version " << PACKAGE_VERSION << endl;
+ headerTemplate << "#Created on " <<__DATE__ << endl << "#" << endl;
+
+ string chrPosPatternInfo = "#A pattern [ chr|strand,pos ] is an occurrence of location on the index (genome or reference)";
+
+ // For SNV
+ if (snp){
+ *snp << headerTemplate.str() << chrPosPatternInfo << endl;
+ *snp << "#A tag \"single\" is noted if there is one possibility of SNV, a tag \"duplicate\" is noted otherwise" << endl;
+ *snp << "#read_id tag_snv loc_snv_on_genome pos_snv_on_read snv crac_score single_loc_on_genome(private) pos_single_loc_on_read(private) read p_support p_loc" << endl;
+ }
+ // For indels
+ if (bioTagIndel){
+ *bioTagIndel << headerTemplate.str() << chrPosPatternInfo << endl;
+ *bioTagIndel << "#A tag \"single\" is noted if there is one possibility of indel, a tag \"duplicate\" is noted otherwise" << endl;
+ *bioTagIndel << "#read_id tag_indel loc_indel_on_genome pos_start_indel_on_read nb_of_insertion nb_of_deletion single_loc_on_genome(private) pos_single_loc_on_read(private) read p_support p_loc" << endl;
+ }
+ // For error
+ if (seqErr){
+ *seqErr << headerTemplate.str() << chrPosPatternInfo << endl;
+ *seqErr << "#A tag \"single\" is noted if there is one possibility of error, a tag \"duplicate\" is noted otherwise" << endl;
+ *seqErr << "#Two different formats for error: "<< endl;
+ *seqErr << "#read_id tag_error loc_error_on_genome pos_ponctual_error_on_read error crac_score single_loc_on_genome(private) pos_single_loc_on_read(private) read p_support p_loc" << endl;
+ *seqErr << "#or" << endl;
+ *seqErr << "#read_id tag_error loc_error_on_genome pos_start_indel_error_on_read nb_of_insertion nb_of_deletion single_loc_on_genome(private) pos_single_loc_on_read(private) read p_support p_loc" << endl;
+ }
+ // For splice and splice_no_cover
+ if (splice){
+ *splice << headerTemplate.str() << chrPosPatternInfo << endl;
+ *splice << "#A tag \"single\" is noted if there is one possibility of splice, a tag \"duplicate\" is noted otherwise" << endl;
+ *splice << "#read_id tag_splice loc_end_first_exon_on_genome pos_junction_on_read splice_length single_loc_on_genome(private) pos_single_loc_on_read(private) read p_support p_loc" << endl;
+ }
+
+ if (spliceNoCover) {
+ *spliceNoCover << headerTemplate.str() << chrPosPatternInfo << endl;
+ *spliceNoCover << "#A tag \"single\" is noted if there is one possibility of splice, a tag \"duplicate\" is noted otherwise" << endl;
+ *spliceNoCover << "#read_id tag_splice loc_end_first_exon_on_genome pos_junction_on_read splice_length single_loc_on_genome(private) pos_single_loc_on_read(private) read p_support p_loc" << endl;
+ }
+ // For chimera
+ if (spliceInter){
+ *spliceInter << headerTemplate.str() << chrPosPatternInfo << endl;
+ *spliceInter << "#A tag \"single\" is noted if there is one possibility of chimera, a tag \"duplicate\" is noted otherwise" << endl;
+ *spliceInter << "#read_id tag_chimera loc_end_first_exon_on_genome loc_start_second_exon_on_genome pos_junction_on_read single_loc_on_genome(private) pos_single_loc_on_read(private) read p_support p_loc" << endl;
+ }
+
+ if (pairedEndChimera){
+ *pairedEndChimera << headerTemplate.str() << chrPosPatternInfo << endl;
+ *pairedEndChimera << "#A paire of paired-end tags classified as \"single\" are noted if there is one possibility of chimera between them" << endl;
+ *pairedEndChimera << "#chimera_class read_id1 single_loc_on_genome1(private) pos_single_loc_on_read1(private) read1 p_support1 p_loc1 read_id2 single_loc_on_genome2(private) pos_single_loc_on_read2(private) read2 p_support2 p_loc2" << endl;
+ }
+
+ // For undetermined cause and bioUndermined
+ if (undetermined){
+ *undetermined << headerTemplate.str() << chrPosPatternInfo << endl;
+ *undetermined << "#read_id undetermined_cause_features single_loc_on_genome(private) pos_single_loc_on_read(private) read p_support p_loc" << endl;
+ }
+ if (bioUndermined) {
+ *bioUndermined << headerTemplate.str() << chrPosPatternInfo << endl;
+ *bioUndermined << "#read_id bioUndetermined_cause_features single_loc_on_genome(private) pos_single_loc_on_read(private) read p_support p_loc" << endl;
+ }
+ // For repetition
+ if (repetition){
+ *repetition << headerTemplate.str() << chrPosPatternInfo << endl;
+ *repetition << "#read_id pos_start_repeat_on_read pos_end_repeat_on_read single_loc_on_genome(private) pos_single_loc_on_read(private) read p_support p_loc" << endl;
+ }
+ // For duplication and multiple
+ if (duplication){
+ *duplication << headerTemplate.str() << chrPosPatternInfo << endl;
+ *duplication << "#read_id occurrence_loc_on_genome(private) pos_loc_on_read(private) read p_support p_loc" << endl;
+ }
+ if (multiple) {
+ *multiple << headerTemplate.str() << chrPosPatternInfo << endl;
+ *multiple << "#read_id one_occurrence_loc_on_genome(private) pos_loc_on_read(private) read p_support p_loc" << endl;
+ }
+ // For nothing
+ if (nothing){
+ *nothing << headerTemplate.str();
+ *nothing << "#read_id read p_support p_loc" << endl;
+ }
+ // For normal and almostNormal
+ if (normal){
+ *normal << headerTemplate.str() << chrPosPatternInfo << endl;
+ *normal << "#read_id single_loc_on_genome(private) pos_single_loc_on_read(private) read p_support p_loc" << endl;
+ }
+ if (almostNormal) {
+ *almostNormal << headerTemplate.str() << chrPosPatternInfo << endl;
+ *almostNormal << "#read_id single_loc_on_genome(private) pos_single_loc_on_read(private) read p_support p_loc" << endl;
+ }
+ // For none
+ if (none){
+ *none << headerTemplate.str() << chrPosPatternInfo << endl;
+ *none << "#read_id [loc_on_genome(private) pos_loc_on_read(private)] read p_support p_loc" << endl;
+ }
+ // For single
+ if (single){
+ *single << headerTemplate.str() << chrPosPatternInfo << endl;
+ *single << "#read_id single_loc_on_genome(private) pos_single_loc_on_read(private) read p_support p_loc" << endl;
+ }
+}
+
+/// PRIVATE ///
+
+void *fillInfos(void *args) {
+ classify_thread_t params = ((classify_thread_t *)args)[0];
+ uint id = params.thread_num;
+ uintSA nb_reads = params.classify->getReadIndex()->getNbTags();
+ bool isPairedEnd = params.classify->getReadIndex()->getReads()->isPairedEnd();
+ uint current_pos = 0;
+ uint k = id;
+ uint increment = params.nb_threads;
+ if(isPairedEnd) {
+ k = 2*k;
+ increment = 2*increment;
+ }
+ for (; k < nb_reads; k += increment) {
+ // We need one seat for the current read
+ if (isPairedEnd) {
+ params.seats[current_pos] = new PairedEndReadClassifier(k,k+1,params.classify->getGenomeIndex(),params.classify->getReadIndex(),params.classify->getParameters());
+ } else {
+ params.seats[current_pos] = new SingleReadClassifier(k,params.classify->getGenomeIndex(),params.classify->getReadIndex(),params.classify->getParameters());
+ }
+ params.seats[current_pos]->classify();
+ //params.seats[current_pos]->generateSAM();
+ sem_post(params.processed_tags);
+ sem_wait(params.remaining_seats);
+ current_pos = (current_pos + 1) % params.total_seats;
+ }
+ pthread_exit(NULL);
+ return NULL;
+}
diff --git a/src/classifyTags.h b/src/classifyTags.h
new file mode 100644
index 0000000..c330468
--- /dev/null
+++ b/src/classifyTags.h
@@ -0,0 +1,232 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at univ-montp2.fr *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef CLASSIFY_TAGS
+#define CLASSIFY_TAGS
+#include <cstdlib>
+#include <gkArrays.h>
+#include "const.h"
+#include "Parameters.h"
+#include "libReadsInfo/tagInfo.h"
+#include "libSSA/locateOnGenome.h"
+#include "Classifier.h"
+#include <semaphore.h>
+
+using namespace std;
+using namespace gkarrays;
+
+class ClassifyTags {
+
+ private:
+ LocateOnGenome *genome;
+ gkArrays *tags;
+ Parameters *parameters;
+
+ /* Statistics */
+ uint nb_classes[NB_MASKS+1];
+ uint nb_explainable;
+
+ public:
+ ClassifyTags(LocateOnGenome *genome,
+ gkArrays *tags,
+ Parameters *param);
+
+ /* Member access */
+ LocateOnGenome *getGenomeIndex();
+ Parameters *getParameters();
+ gkArrays *getReadIndex();
+
+ /* Statistics */
+ uint getNbNone();
+ uint getNbMultiple();
+ uint getNbExplainable();
+ uint getNbAlmostNormal();
+ uint getNbNormal();
+ uint getNbDuplication();
+ uint getNbSingle();
+ uint getNbSNP();
+ uint getNbBioTagIndel();
+ uint getNbSeqErr();
+ uint getNbRepetition();
+ uint getNbSplice();
+ uint getNbSpliceIntra();
+ uint getNbSpliceInter();
+ uint getNbSpliceNoCover();
+ uint getNbNothing();
+ uint getNbUndetermined();
+ uint getNbBioUndetermined();
+ uint getNbPairedEndChimera();
+
+
+ /**
+ * variables used for duplication:
+ * - max_localisation_duplication
+ * - min_localisation_duplication
+ * - percent_min_unique_repetition
+ */
+
+ void classify(ostream *snp=NULL
+ , ostream *bioTagIndel=NULL
+ , ostream *seqErr=NULL
+ , ostream *splice=NULL
+ , ostream *spliceIntra=NULL
+ , ostream *spliceInter=NULL
+ , ostream *undetermined=NULL
+ , ostream *repetition=NULL
+ , ostream *duplication=NULL
+ , ostream *nothing=NULL
+ , ostream *normal=NULL
+ , ostream *almostNormal=NULL
+ , ostream *multiple = NULL
+ , ostream *none = NULL
+ , ostream *bioUndermined = NULL
+ , ostream *single = NULL
+ , ostream *sam = NULL
+ , ostream *pairedEndChimera = NULL);
+
+
+ /**
+ * get headers for all ostreams
+ */
+ void getHeaders(ostream *snp=NULL
+ , ostream *bioTagIndel=NULL
+ , ostream *seqErr=NULL
+ , ostream *splice=NULL
+ , ostream *spliceIntra=NULL
+ , ostream *spliceInter=NULL
+ , ostream *undetermined=NULL
+ , ostream *repetition=NULL
+ , ostream *duplication=NULL
+ , ostream *nothing=NULL
+ , ostream *normal=NULL
+ , ostream *almostNormal=NULL
+ , ostream *multiple = NULL
+ , ostream *none = NULL
+ , ostream *bioUndermined = NULL
+ , ostream *single = NULL
+ , ostream *pairedEndChimera = NULL);
+
+
+
+ private:
+
+ friend void *fillInfos(void *);
+
+};
+
+/**
+ * Function called when creating a thread.
+ * It fills a part of _store_tagsInfo array.
+ */
+void *fillInfos(void *);
+
+
+typedef struct classify_thread_s {
+ ClassifyTags *classify;
+ sem_t *remaining_seats; /* Number of remaining cells for storing tagInfo */
+ sem_t *processed_tags;
+ Classifier **seats; /* Seats where the TagInfo are stored */
+ uint thread_num;
+ uint total_seats; /* Total number of seats */
+ uint nb_threads; /* Number of threads classifying tags */
+} classify_thread_t;
+
+
+#endif
diff --git a/src/const.h b/src/const.h
new file mode 100644
index 0000000..31e10d5
--- /dev/null
+++ b/src/const.h
@@ -0,0 +1,327 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef CONST_H
+#define CONST_H
+
+#define MAX_NB_LOCATED_OCCS 300 /* Maximal number of occurrences we
+ * get the actual locations */
+#define MAX_SPLICE_LENGTH 300000 /* Maximal genomic insertion length between the locations
+ * before and after a break */
+#define MAX_BIO_INS_DEL 15 /* Maximal length of short biological indel */
+#define MAX_LOCALISATION_DUPLICATION 9 /* Maximal number of occurrences for a factor
+ * to be considered as duplicated
+ */
+#define MIN_LOCALISATION_DUPLICATION 2 /* Minimal number of occurrences for a factor
+ * to be considered as duplicated
+ */
+#define PERCENT_MIN_UNIQUE_REPETITION 0.05 /* For classifying as repetition, minimal percentage of factors located once */
+
+
+#define PERCENT_MIN_DUPLICATE 0.15 /* To be classified as duplicate, a support must
+ * have at least this percentage of factors
+ * located at most MAX_LOCALISATION_DUPLICATION on the genome
+ */
+
+#define PERCENT_MIN_SINGLE 0.15 /* To be classified as single, a support
+ * must have at least this percent of
+ * single-located factors
+ */
+
+#define PERCENT_MIN_MULTIPLE 0.50 /* To be classified as single, a support
+ * must have at least this percent of
+ * multiple-located factors > MAX_LOCALISATION_DUPLICATION
+ */
+
+
+#define MIN_OCC_REPETITION 20 /* Minimal number of occurrences to a located k-mer to consider a repetition */
+
+#define PERCENT_SUPPORT_VARIATION_ALMOST_NORMAL 0.25 /* 25% */
+#define P_VALUE_VARIATION_BIOLOGICAL 0. /* P-Value which is the relation of two average
+ * to determine whether we have a sequence error
+ * or a biological explanation. */
+
+#define TREAT_MULTIPLE false /* treat multiple alignments
+ (>max-duplication) rather than considering a no-alignment in the
+ SAM file */
+
+#define NO_AMBIGUITY false /* discard biological events (splice, snv, indel, chimera)
+ which have several matches on the reference index */
+
+#define SCORE_INTRA_AMBIGUOUS 0.9 /* Maximal score for intra biological causes
+ under which, the support must fall
+ to be an error. */
+
+#define SCORE_INTER_AMBIGUOUS 0.7 /* Maximal score for inter biological causes
+ * under which, the support must fall
+ * to be an error. */
+
+#define MAX_BASES_RANDOMLY_MATCHED 10 /* Maximal number of bases we may match, before the
+ * expected position (e.g. for genome ins/del,
+ * there is 0.25 probability to match a factor of
+ * the tag one position, before the one expected)*/
+
+#define MIN_BASES_BEFORE_BREAK 3 /* Minimal number of bases we must have to consider a
+ new break */
+
+#define MAX_BASES_RETRIEVED 15 /* is the number of nucleotides to display in outputfile in case of
+ insertion. */
+
+#define MAX_EXTENSION_LENGTH 10 /* A break is extended right and left by, at most,
+ MAX_EXTENSION_LENGTH bases. */
+
+#define SUPPORT_SCORE_WINDOW_LENGTH 16
+
+
+#define MIN_SUPPORT_NO_COVER 1.3 /* Value below which the read is considered to
+ be not supported enough for drawing conclusions.*/
+
+#define MIN_BREAK_LENGTH 0.5 /* a minimal break length is required for a biological cause */
+
+
+#define MAX_SUPPORT_OUT_NO_COVER 3.0 /* value below which the outside score break is considered to
+ be not enough for drawing conclusions. */
+
+
+#define MAX_AMBIGUOUS_AVERAGE_HIGH 1.6 /* Value below which high inside average
+ of a support is considered as
+ possibly ambiguous and needs
+ extra test to ensure that there is
+ (not) an error. */
+
+#define MAX_VERYNICE_MERGE 5000 /* Maximal insertion length to consider a very nice
+ merge. For example if we have two canditats: one
+ with an insertion of 10 Kbp and an other of 40 bp,
+ so the first is nice and the second is very nice.
+ */
+
+#define NB_BASES_SUBSTRACTED_LOW_AVERAGE 5 /* Number of positions that are
+ substracted from the threshold
+ to know how many positions we have
+ to consider when computing the
+ low average inside the support */
+
+#define NB_POSITIONS_CHECK_ONES 5 /* Designate the number of positions for which
+ we have
+ to count the number of ones at a border
+ inside the support (the same number is
+ taken outside the support).
+ */
+
+#define MIN_PERCENTAGE_ONES_INSIDE 0.5 /* The minimal percentage of ones
+ that must be in the support inside the
+ break, near its border
+ (0.5 is 50%)
+ */
+
+#define MIN_RATIO_SUPPORT_FALL 1.5 /* Minimal ratio we must have between
+ the percentage of ones inside and
+ outside the support.
+ A ratio of 1.5 would mean
+ that the percentage of ones inside must be
+ at least 1.5 times the outside one.
+ */
+
+#define NB_TAGS_INFO_STORED 1000 /* Number of TagInfo stored at a given moment,
+ per thread,
+ for accelerating the process
+ (for multi-threading)
+ */
+
+#define NB_THREADS 1 /* Number of threads by default */
+
+#define MAX_NB_OVERLAPPING_BREAKS 2 /* Number of overlapping breaks
+ 'allowed'. This is for merging
+ breaks and is used to know
+ what is the maximal distance we allow.
+ The distance allowed will be
+ MAX_NB_OVERLAPPING_BREAKS * threshold
+ */
+
+#define DEEP_SNP_SEARCH false /* If true, will search SNPs in the breaks that
+ are not complete at the start or at the end of
+ the read. */
+#define NUMBER_NUCLEOTIDES_SNP_COMPARISON 8 /* Only used if DEEP_SNP_SEARCH is
+ true.
+ Corresponds to the number of extra
+ nucleotides that are compared
+ after (or brefore) the SNP
+ to make sure that there is only
+ one substitution (and that
+ it is not a more complicated
+ cause)
+ */
+#define DETAILED_SAM false /* Output detailed information for each
+ break in the SAM output
+ */
+#define INPUT_FIFO "classify.fifo" /* Default name for the input fifo
+ for the main server
+ */
+#define OUTPUT_FIFO "classify.out.fifo" /* Default name for the output
+ fifo for the main server
+ */
+
+#define EPSILON 0.01 /* A small value (to make the difference when
+ comparing floats for example)
+ */
+
+#define DELAY_BEFORE_READ_IS_PROCESSED 1000 /* Time in microseconds to wait
+ before a read has been
+ processed so that we can output
+ it */
+
+#define NB_MASKS 19
+#define MASK_NOTHING 0
+#define MASK_MULTIPLE 1 /* the tag is located multiple times (and is not a DUPLICATION) */
+#define MASK_CLASSIFIED 2
+#define MASK_DUPLICATION 4
+#define MASK_ALMOST_NORMAL 8 /* as normal but something goes down at the end, for example */
+#define MASK_NORMAL 16
+#define MASK_SNP 32
+#define MASK_SEQ_ERR 64
+#define MASK_REPETITION 128 /* a factor of the tag is repeated (but not the whole tag, apart from DUPLICATIONs) */
+#define MASK_SPLICE 256
+#define MASK_INTRA_TRANSPLICING 512
+#define MASK_INTER_TRANSPLICING 1024
+#define MASK_NONE 2048 /* not located */
+#define MASK_BIOLOGICAL_UNDETERMINED 4096 /* Maybe splice or SNP
+ but we cannot conclude
+ using the data*/
+#define MASK_BIOLOGICAL_TAG_INDEL 8192
+#define MASK_UNDETERMINED_ERROR 16384 /* There is an error but we cannot
+ tell what it is really due to
+ */
+#define MASK_SINGLE 32768
+#define MASK_SPLICE_NO_COVER 65536
+#define MASK_PAIRED_END_CHIMERA 131072
+
+#define INFO_NB_TYPES 11
+#define INFO_SNP 0
+#define INFO_SEQ_ERR 1
+#define INFO_SPLICE 2
+#define INFO_INTRASPLICE 3
+#define INFO_INTERSPLICE 4
+#define INFO_BIOLOGICAL_UNDETERMINED 5
+#define INFO_REPETITION 6
+#define INFO_DUPLICATION 7
+#define INFO_BIOLOGICAL_TAG_INDEL 8
+#define INFO_UNDETERMINED_ERROR 9
+#define INFO_SPLICE_NO_COVER 10
+
+
+#define NB_ELEMENTS_PER_TYPE 3 /* Internal constant for the number of cells
+ to allocate in tagInfo for info_each_type */
+#define NB_INFO_STORED 6 /* Internal constant for the number of cells to allocate
+ in tagInfo for types_in_order */
+#define NB_INFO_BREAKS 4 /* Internal constant for the number of cells
+ allocated in tagInfo for storing
+ the number of causes per break. */
+#define NB_CIGAR_ELEM 6
+
+#define STRINGENT_CHIMERA false
+#define STRINGENT_CHIMERA_MAX_NUMBER_OF_MERGES 1 /* Maximum number of merges to construct the break where the stringent chimera
+ has been found */
+#define STRINGENT_CHIMERA_MIN_BREAK_LENGTH 0.75 /* Minimal break length is required for a chimera cause */
+
+#define MAX_SIZE_MESSAGE_UNDETERMINED_ERROR 256
+
+/* Exceptions */
+#define ILLEGAL_STATE_EXCEPTION 1
+
+#endif
diff --git a/src/crac.cpp b/src/crac.cpp
new file mode 100644
index 0000000..9b78a99
--- /dev/null
+++ b/src/crac.cpp
@@ -0,0 +1,1016 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at univ-montp2.fr *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <iostream>
+#include <fstream>
+#include <ostream>
+#include <string>
+#include <cstdlib>
+#include <algorithm>
+#include "types.h"
+#include "utils.h"
+#include <gkArrays.h>
+#include <gkArraysTypes.h>
+#include "classifyTags.h"
+#include "libSSA/locateOnGenome.h"
+#include "locateTags.h"
+#include "libSSA/cracIndex.h"
+#include "Parameters.h"
+#include "locateServer.h"
+#include <cstdio>
+#include <unistd.h>
+#include <getopt.h>
+#include <sys/stat.h>
+#ifdef HAVE_CONFIG_H
+# include <config.h>
+#endif
+#include <gzstream.h>
+
+using namespace std;
+
+#define SNP 8
+#define BIOTAG 9
+#define SEQERR 10
+#define SPLICE 11
+#define SPLICE_NOCOVER 12
+#define CHIMERA 13
+#define UNDETERMINED 14
+#define REPETITION 15
+#define DUPLICATION 16
+#define NOTHING 17
+#define NORMAL 18
+#define ALMOSTNORMAL 19
+#define MULTIPLE 20
+#define NONE 21
+#define BIOUNDETERMINED 22
+#define SINGLE 23
+
+#define MAX_SPLICE 24
+#define MAX_BIO_INDEL 25
+// #define MAX_SEQERR_INDEL 26
+#define MAX_DUPLICATION 27 /* Maximal number of occurrences for a factor
+ to be considered as duplicated */
+#define MIN_DUPLICATION 28 /* Minimal number of occurrences for a factor
+ to be considered as duplicated */
+#define PERCENT_MIN_SINGLE_REPETITION 29 /* For classifying as repetition, minimal percentage of factors located once */
+#define PERCENT_MIN_MULTIPLE_CST 30 /* To be classified as single, a support
+ * must have at least PERCENT_MIN_SINGLE%
+ * single-located factors
+ */
+#define PERCENT_MIN_DUPLICATION 31 /* To be classified as duplicate, a support must
+ have at least this percentage of factors
+ located at most MAX_LOCALISATION_DUPLICATION on the genome */
+#define MIN_LOC_REPETITION 32 /* Minimal number of occurrences of a factor, for being a repetition */
+#define PERCENT_VARIATION_COVERAGE 33 /* 50% */
+#define P_VALUE_VARIATION_COVERAGE 34 /* P-Value which is the relation of two average
+ * to determine whether we have a sequence error
+ * or a biological explanation. */
+#define MAX_BIOLOGICAL_DEVIATION 35 /* Maximal deviation allowed for the support
+ * inside the break, to consider it as a biological event*/
+
+#define MAX_RANDOMLY_MATCHED 36 /* Maximal number of bases we may match, before the
+ * expected position (e.g. for genome ins/del,
+ * there is 0.25 probability to match a factor of
+ * the tag one position, before the one expected)*/
+
+#define MAX_EXTENSION 38 /* A break is extended right and left by, at most,
+ * MAX_EXTENSION_LENGTH bases. */
+#define MIN_BEFORE_BREAK 39 /* Minimal number of bases we must have to consider a
+ new break */
+#define MAX_RETRIEVED 40 /* Maximal number of bases retrieve for information
+ * when discovering a sequence error. */
+
+#define SUPPORT_SCORE_WINDOW 41
+
+#define MINIMUM_SUPPORT_NO_COVER 42
+
+#define MINIMUM_BREAK_LENGTH 43
+
+#define MAXIMUM_SUPPORT_OUT_NO_COVER 44
+
+#define MAX_AMBIGUOUS_AVG_HIGH 45
+#define NB_BASES_SUBSTRACTED_LOW_AVG 46
+#define NB_POS_CHECK_ONES 47
+#define MIN_PERC_ONES_INSIDE 48
+#define MIN_RATIO_SUPPORT_FALL_CST 49
+#define NB_TAGS_INFO_CST 50
+#define NB_THREADS_CST 51
+
+#define ALL_OUTPUT 52
+
+#define MAX_NB_OVERLAPPING_BREAKS_CST 53
+#define PERCENT_MIN_SINGLE_CST 54 /* To be classified as single, a support
+ * must have at least PERCENT_MIN_SINGLE%
+ * single-located factors
+ */
+#define SCORE_INTRA_AMBIGUOUS_CST 55
+#define SCORE_INTER_AMBIGUOUS_CST 56
+
+#define SAM 57
+
+#define DEEP_SNP_SEARCH_CST 58
+#define NUMBER_NUCLEOTIDES_SNP_COMPARISON_CST 59
+#define DETAILED_SAM_CST 60
+#define SERVER_CST 61
+#define INPUT_FIFO_CST 62
+//63 for '?'
+#define OUTPUT_FIFO_CST 64
+
+#define MAX_VERYNICE_MERGE_CST 65
+#define MAX_NB_LOCATED_OCCS_CST 66 // -n
+
+#define READS_LENGTH 67
+#define IS_STRANDED_CST 68
+
+#define DGE 69
+#define STRINGENT_CHIMERA_CST 70
+#define NO_AMBIGUITY_CST 71
+#define PAIRED_END_CHIMERA 72
+#define GZ_OUTPUT 73
+#define SUMMARY 74
+#define PROGRESSBAR 75
+#define TREAT_MULTIPLE_CST 76
+
+void print_help() {
+ printf(PACKAGE_STRING);
+ printf("\tCompiled on %s.\n\n",__DATE__);
+
+ printf(" -h, --help <none> print this help and exit\n");
+ printf(" -f, --full-help <none> print a complete help and exit\n");
+ printf(" -v <none> print version and exit\n\n");
+
+ printf("Mandatory arguments\n");
+ printf(" -i <FILE> set genome index file (without the extension filename)\n");
+ printf(" -r <FILE> [FILE2] set read file. Specify FILE2 in case of paired-end reads\n");
+ printf(" -k <INT> set k-mer length\n");
+ printf(" -o, --sam <FILE> set SAM output filename or print on STDOUT with \"-o -\" argument\n\n");
+
+
+ printf("Optional arguments\n");
+ printf(" * Protocol\n");
+ printf(" --stranded <none> set the read mapping with for a strand specific library (DEFAULT non-strand specific)\n\n");
+ printf(" * Efficiency\n");
+ printf(" --nb-threads <INT> set the number of worker threads (DEFAULT %d)\n", NB_THREADS);
+ printf(" --reads-length, -m <INT> set read length in case of all reads have the same length to optimize\n\
+ CPU and memory times\n");
+ printf(" --treat-multiple <none> write alignments with multiple locations (>max-duplication and <=max-locs) in the SAM file rather than only one occurrence\n");
+ printf(" --max-locs <INT> set the maximum number of locations on the reference index (DEFAULT %d)\n\n", MAX_NB_LOCATED_OCCS);
+ printf(" * Accuracy\n");
+ printf(" --no-ambiguity <none> discard biological events (splice, snv, indel, chimera) which have several matches on the reference index\n\n");
+}
+
+void print_fullhelp() {
+ print_help();
+ printf("\nOptional output arguments\n");
+ printf(" --all <FILE> set output base filename for all homemade file formats (see man page for more details)\n\
+ in addition to SAM output \n");
+ printf(" --gz <none> all output files specified after this argument are gzipped (included SAM output file)\n");
+ printf(" --summary <FILE> set output summary file with some statistics about mapping and classification\n");
+#ifdef HAVE_LIBPROGRESSBAR
+ printf(" --show-progressbar <none> show a progress bar for the process times on STDERR\n\n");
+#else
+ printf("\n");
+#endif
+
+ // printf(" * Mapping\n");
+ // printf(" --single <FILE> set output single file\n");
+ // printf(" --duplicate <FILE> set output duplication file\n");
+ // printf(" --multiple <FILE> set output multiple file\n");
+ // printf(" --none <FILE> set output none file\n");
+ // printf(" --normal <FILE> set output normal file\n");
+ // printf(" --almost-normal <FILE> set output almost normal file\n\n");
+
+ // printf(" * Biological causes\n");
+ // printf(" --snv <FILE> set output SNV file\n");
+ // printf(" --indel <FILE> set output short indel file\n");
+ // printf(" --splice <FILE> set output splice junction file\n");
+ // printf(" --weak-splice <FILE> set output coverless splice junction file\n");
+ // printf(" --chimera <FILE> set output chimera junction file\n");
+ // printf(" --paired-end-chimera <FILE> set output for paired-end chimera file\n");
+ // printf(" --biological <FILE> set output bio-undetermined file\n\n");
+
+ // printf(" * Sequence errors\n");
+ // printf(" --errors <FILE> set output sequence errors file\n\n");
+
+ // printf(" * Repetition\n");
+ // printf(" --repeat <FILE> set output repetition file\n\n");
+
+ // printf(" * Other causes\n");
+ // printf(" --undetermined <FILE> set output undetermined file\n");
+ // printf(" --nothing <FILE> set output nothing file\n\n");
+
+ printf("Optional process for specific research\n");
+ printf(" --deep-snv <none> will search hard to find SNPs\n");
+ printf(" --stringent-chimera <none> will search chimeras with more accuracy (but less sensitivity)\n\n");
+
+ printf("Optional process launcher (once must be selected)\n");
+ printf(" * Exact matching tool\n");
+ printf(" --emt <none> launch CRAC-emt for exact mapping of short reads\n\n");
+ printf(" * Server tool (for debugging) \n");
+ printf(" --server <none> launch CRAC server,the output arguments will\n\
+ not be taken into account\n");
+ printf(" --input-name-server <STRING> DEFAULT %s\n", INPUT_FIFO);
+ printf(" --output-name-server <STRING> DEFAULT %s\n\n", OUTPUT_FIFO);
+ printf("Additional settings for users\n");
+ printf(" * Sam output file\n");
+ printf(" --detailed-sam <none> more informations are added in SAM output file\n\n");
+
+ printf(" * Mapping\n");
+ printf(" --min-percent-single-loc <FLOAT> DEFAULT %.2f\n", PERCENT_MIN_SINGLE);
+ printf(" --min-duplication <INT> DEFAULT %d\n", MIN_LOCALISATION_DUPLICATION);
+ printf(" --max-duplication <INT> DEFAULT %d\n", MAX_LOCALISATION_DUPLICATION);
+ printf(" --min-percent-duplication-loc <FLOAT> DEFAULT %.2f\n", PERCENT_MIN_DUPLICATE);
+ printf(" --min-percent-multiple-loc <FLOAT> DEFAULT %.2f\n", PERCENT_MIN_MULTIPLE);
+ printf(" --min-repetition <INT> DEFAULT %d\n", MIN_OCC_REPETITION);
+ printf(" --min-percent-repetition-loc <FLOAT> DEFAULT %.2f\n\n", PERCENT_MIN_UNIQUE_REPETITION);
+
+
+ printf(" * Biological causes\n");
+ printf(" --max-splice-length <INT> DEFAULT %d\n", MAX_SPLICE_LENGTH);
+ printf(" --max-bio-indel <INT> DEFAULT %d\n", MAX_BIO_INS_DEL);
+ printf(" --max-bases-retrieved <INT> DEFAULT %d\n\n", MAX_BASES_RETRIEVED);
+
+ printf(" * Undetermined\n");
+ printf(" --min-support-no-cover <FLOAT> DEFAULT %.2f\n\n", MIN_SUPPORT_NO_COVER);
+
+
+ printf("Additional settings for advanced users\n");
+ printf(" * Break verification and fusion (merging mirage breaks)\n");
+ printf(" --min-break-length <FLOAT> DEFAULT %.2f\n", MIN_BREAK_LENGTH);
+ printf(" --max-bases-randomly-matched <INT> DEFAULT %d\n", MAX_BASES_RANDOMLY_MATCHED);
+ printf(" --max-extension-length <INT> DEFAULT %d\n\n", MAX_EXTENSION_LENGTH);
+
+ printf(" * Threading\n");
+ printf(" --nb-tags-info-stored <INT> DEFAULT %d\n\n", NB_TAGS_INFO_STORED);
+
+ printf(" * Deep SNV search option\n");
+ printf(" --nb-nucleotides-snv-comparison <INT> DEFAULT %d\n\n", NUMBER_NUCLEOTIDES_SNP_COMPARISON);
+
+ // printf(" --percent-variation-coverage <FLOAT> DEFAULT %.2f\n", PERCENT_SUPPORT_VARIATION_ALMOST_NORMAL);
+ // printf(" --p-value-variation-coverage <FLOAT> DEFAULT %.2f\n", P_VALUE_VARIATION_BIOLOGICAL);
+ // printf(" --score-intra-ambiguous <FLOAT> DEFAULT %.2f\n", SCORE_INTRA_AMBIGUOUS);
+ // printf(" --score-inter-ambiguous <FLOAT> DEFAULT %.2f\n", SCORE_INTER_AMBIGUOUS);
+ // printf(" --min-bases-before-break <INT> DEFAULT %d\n", MIN_BASES_BEFORE_BREAK);
+ // printf(" --support-score-window-length <INT> DEFAULT %d\n", SUPPORT_SCORE_WINDOW_LENGTH);
+ // printf(" --max-support-out-no-cover <FLOAT> DEFAULT %.2f\n", MAX_SUPPORT_OUT_NO_COVER);
+ // printf(" --max-ambiguous-high-average <FLOAT> DEFAULT %.2f\n", MAX_AMBIGUOUS_AVERAGE_HIGH);
+ // printf(" --max-verynice-merge <INT> DEFAULT %d\n", MAX_VERYNICE_MERGE);
+ // printf(" --nb-bases-substracted-low <INT> DEFAULT %d\n", NB_BASES_SUBSTRACTED_LOW_AVERAGE);
+ // printf(" --nb-positions-check-ones <INT> DEFAULT %d\n", NB_POSITIONS_CHECK_ONES);
+ // printf(" --min-perc-ones-inside <FLOAT> DEFAULT %.2f\n", MIN_PERCENTAGE_ONES_INSIDE);
+ // printf(" --min-ratio-support-fall <FLOAT> DEFAULT %.2f\n", MIN_RATIO_SUPPORT_FALL);
+ // printf(" --max-nb-overlapping-breaks <INT> DEFAULT %d\n\n", MAX_NB_OVERLAPPING_BREAKS);
+
+}
+
+void print_version() {
+ printf("CRAC version " PACKAGE_VERSION "\n\n");
+ printf("/******************************************************************************\n");
+ printf("* *\n");
+ printf("* Copyright © 2010-2013 -- IRB/INSERM *\n");
+ printf("* (Institut de Recherches en Biothérapie / *\n");
+ printf("* Institut National de la Santé et de la Recherche *\n");
+ printf("* Médicale) *\n");
+ printf("* LIFL/INRIA *\n");
+ printf("* (Laboratoire d'Informatique Fondamentale de *\n");
+ printf("* Lille / Institut National de Recherche en *\n");
+ printf("* Informatique et Automatique) *\n");
+ printf("* LIRMM/CNRS *\n");
+ printf("* (Laboratoire d'Informatique, de Robotique et de *\n");
+ printf("* Microélectronique de Montpellier / *\n");
+ printf("* Centre National de la Recherche Scientifique) *\n");
+ printf("* LITIS *\n");
+ printf("* (Laboratoire d'Informatique, du Traitement de *\n");
+ printf("* l'Information et des Systèmes). *\n");
+ printf("* *\n");
+ printf("* *\n");
+ printf("* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *\n");
+ printf("* Mikaël SALSON <mikael.salson at lifl.fr> *\n");
+ printf("* Thérèse COMMES <commesd at univ-montp2.fr> *\n");
+ printf("* Éric RIVALS <eric.rivals at lirmm.fr> *\n");
+ printf("* *\n");
+ printf("* Programmeurs *\n");
+ printf("* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *\n");
+ printf("* Mikaël SALSON <mikael.salson at lifl.fr> *\n");
+ printf("* Jérôme AUDOUX <jerome.audoux at univ-montp2.fr *\n");
+ printf("* with additional contribution for the packaging of: *\n");
+ printf("* Alban MANCHERON <alban.mancheron at lirmm.fr> *\n");
+ printf("* *\n");
+ printf("* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *\n");
+ printf("* *\n");
+ printf("/******************************************************************************\n");
+}
+
+void writeSamHeader(ostream *sam
+ , LocateOnGenome *genome
+ , int argc
+ , char **argv
+ , string sam_filename) {
+ *sam << "@HD\tVN:1.4\tSO:unsorted" << endl;
+ // Display information on sequence names and lengths
+ for (uint i=0; i < genome->getGenomeInfo()->getNbChr(); i++) {
+ *sam << "@SQ\tSN:" << genome->getGenomeInfo()->getChrName(i)
+ << "\tLN:" << genome->getGenomeInfo()->getChrLength(i) << endl;
+ }
+ struct tm tm;
+ char tmp[120];
+ time_t t;
+ time(&t);
+ localtime_r(&t,&tm);
+ sprintf(tmp,"%i-%02i-%02iT%02i:%02i:%02i", tm.tm_year + 1900, tm.tm_mon+1, tm.tm_mday, tm.tm_hour, tm.tm_min, tm.tm_sec);
+ *sam << "@RG\tID:" << rand() << "\tSM:" << sam_filename << "\tDT:" << tmp << endl;
+ *sam << "@PG\tID:crac\tPN:crac\tVN:" << PACKAGE_VERSION;
+ if (argc) {
+ *sam << "\tCL:";
+ for (int i=0; i < argc; i++)
+ *sam << argv[i] << " ";
+ *sam << endl;
+ }
+}
+
+int main(int argc, char **argv) {
+ fstream file;
+ int nb_streams;
+ ostream *streams[19] = {NULL,NULL,NULL
+ ,NULL,NULL,NULL
+ ,NULL,NULL,NULL
+ ,NULL,NULL,NULL
+ ,NULL,NULL, NULL
+ ,NULL,NULL,NULL
+ ,NULL};
+ const char *extensions[19] = {
+ "snp", "indel", "error", "splice",
+ "coverlessSplice", "chimera", "undetermined", "repetition",
+ "duplication", "nothing", "normal", "almostNormal", "multiple",
+ "none", "bioUndetermined", "single", "sam", "pairedEndChimera",
+ "summary"
+ };
+ nb_streams = 19;
+
+ bool gzOutput = false;
+ gkArrays *indexTags = NULL;
+ ulong pattern_length = 0;
+ bool is_stranded = false;
+ ClassifyTags *ct;
+ LocateOnGenome *log = NULL;
+ Parameters *params = new Parameters();
+ params->show_progressbar = false;
+ uint threshold = ~0;
+ char *reads = 0;
+ char *reads2 = 0;
+ char *indexGenome = 0;
+ char *fileBasename = 0;
+ char *filename = 0;
+ uint max_length = 0;
+ int nb_streams_to_init = 0;
+ bool use_server = false;
+ bool use_emt = false;
+ bool use_paired_end_chimera = false;
+ bool use_all_outputs = false;
+ bool find_output_file = false;
+ char *fifo_input_name = NULL;
+ char *fifo_output_name = NULL;
+ string sam_filename;
+ ostream *summary = NULL;
+
+ int option_index = 0;
+ int opt;
+
+ static const char *short_options = "hi:r:o:k:m:fv";
+
+ static struct option long_options[] = {
+ { "help", no_argument, NULL, 'h' },
+ { "full-help", no_argument, NULL, 'f' },
+ { "version", no_argument, NULL, 'v' },
+ { "all", required_argument, NULL, ALL_OUTPUT},
+ { "reads-length", required_argument, NULL, READS_LENGTH},
+ { "stranded", no_argument, NULL, IS_STRANDED_CST},
+ { "sam", required_argument, NULL, SAM },
+ { "snv", required_argument, NULL, SNP },
+ { "indel", required_argument, NULL, BIOTAG },
+ { "errors", required_argument, NULL, SEQERR },
+ { "splice", required_argument, NULL, SPLICE },
+ { "weak-splice", required_argument, NULL, SPLICE_NOCOVER },
+ { "chimera", required_argument, NULL, CHIMERA },
+ { "undetermined", required_argument, NULL, UNDETERMINED },
+ { "repeat", required_argument, NULL, REPETITION },
+ { "duplicate", required_argument, NULL, DUPLICATION },
+ { "nothing", required_argument, NULL, NOTHING },
+ { "normal", required_argument, NULL, NORMAL },
+ { "almost-normal", required_argument, NULL, ALMOSTNORMAL },
+ { "multiple", required_argument, NULL, MULTIPLE},
+ { "none", required_argument, NULL, NONE },
+ { "biological", required_argument, NULL, BIOUNDETERMINED },
+ { "single", required_argument, NULL, SINGLE },
+ { "max-locs", required_argument, NULL, MAX_NB_LOCATED_OCCS_CST},
+ { "max-splice-length", required_argument, NULL, MAX_SPLICE },
+ { "max-bio-indel", required_argument, NULL, MAX_BIO_INDEL },
+ { "min-duplication", required_argument, NULL, MIN_DUPLICATION },
+ { "max-duplication", required_argument, NULL, MAX_DUPLICATION },
+ { "min-percent-multiple-loc", required_argument, NULL, PERCENT_MIN_MULTIPLE_CST },
+ { "min-percent-duplication-loc", required_argument, NULL, PERCENT_MIN_DUPLICATION },
+ { "min-percent-single-loc", required_argument, NULL, PERCENT_MIN_SINGLE_CST},
+ { "min-percent-repetition-loc", required_argument, NULL, PERCENT_MIN_SINGLE_REPETITION },
+ { "max-verynice-merge", required_argument, NULL, MAX_VERYNICE_MERGE_CST },
+ { "min-repetition", required_argument, NULL, MIN_LOC_REPETITION },
+ { "percent-variation-coverage", required_argument, NULL, PERCENT_VARIATION_COVERAGE },
+ { "p-value-variation-coverage", required_argument, NULL, P_VALUE_VARIATION_COVERAGE },
+ { "score-intra-ambiguous", required_argument, NULL, SCORE_INTRA_AMBIGUOUS_CST},
+ { "score-inter-ambiguous", required_argument, NULL, SCORE_INTER_AMBIGUOUS_CST},
+ { "max-bio-deviation", required_argument, NULL, MAX_BIOLOGICAL_DEVIATION },
+ { "max-bases-randomly-matched", required_argument, NULL, MAX_RANDOMLY_MATCHED },
+ { "min-bases-before-break", required_argument, NULL, MIN_BEFORE_BREAK },
+ { "max-bases-retrieved", required_argument, NULL, MAX_RETRIEVED },
+ { "max-extension-length", required_argument, NULL, MAX_EXTENSION },
+ { "support-score-window-length", required_argument, NULL, SUPPORT_SCORE_WINDOW },
+ { "min-support-no-cover", required_argument, NULL, MINIMUM_SUPPORT_NO_COVER },
+ { "min-break-length", required_argument, NULL, MINIMUM_BREAK_LENGTH },
+ { "max-support-out-no-cover", required_argument, NULL, MAXIMUM_SUPPORT_OUT_NO_COVER },
+ { "max-ambiguous-high-average", required_argument, NULL, MAX_AMBIGUOUS_AVG_HIGH },
+ { "nb-bases-substracted-low", required_argument, NULL, NB_BASES_SUBSTRACTED_LOW_AVG },
+ { "nb-positions-check-ones", required_argument, NULL, NB_POS_CHECK_ONES },
+ { "min-perc-ones-inside", required_argument, NULL, MIN_PERC_ONES_INSIDE },
+ { "min-ratio-support-fall", required_argument, NULL, MIN_RATIO_SUPPORT_FALL_CST },
+ { "nb-tags-info-stored", required_argument, NULL, NB_TAGS_INFO_CST},
+ { "nb-threads", required_argument, NULL, NB_THREADS_CST},
+ { "max-nb-overlapping-breaks", required_argument, NULL,
+ MAX_NB_OVERLAPPING_BREAKS_CST},
+ { "deep-snv", no_argument, NULL, DEEP_SNP_SEARCH_CST},
+ { "nb-nucleotides-snv-comparison", required_argument, NULL,
+ NUMBER_NUCLEOTIDES_SNP_COMPARISON_CST},
+ { "detailed-sam", no_argument, NULL, DETAILED_SAM_CST},
+ { "server", no_argument, NULL, SERVER_CST},
+ { "input-name-server", required_argument, NULL, INPUT_FIFO_CST},
+ { "output-name-server", required_argument, NULL, OUTPUT_FIFO_CST},
+ { "emt", no_argument, NULL, DGE },
+ { "stringent-chimera", no_argument, NULL, STRINGENT_CHIMERA_CST },
+ { "no-ambiguity", no_argument, NULL, NO_AMBIGUITY_CST },
+ { "paired-end-chimera", required_argument, NULL, PAIRED_END_CHIMERA },
+ { "gz", no_argument, NULL, GZ_OUTPUT},
+ { "summary", required_argument, NULL, SUMMARY },
+#ifdef HAVE_LIBPROGRESSBAR
+ { "show-progressbar", no_argument, NULL, PROGRESSBAR },
+#endif
+ { "treat-multiple", no_argument, NULL, TREAT_MULTIPLE_CST },
+ { 0, 0, 0, 0 } //terminator
+ };
+
+ while ((opt = getopt_long(argc, argv, short_options, long_options, &option_index)) != -1){
+ switch(opt) {
+
+ case 'h':
+ print_help();
+ exit(0);
+ case 'f' :
+ print_fullhelp();
+ exit(0);
+ case 'v' :
+ print_version();
+ exit(0);
+ case 'i':
+ indexGenome = optarg;
+ break;
+ case 'r':
+ reads = optarg;
+ break;
+ case 'k':
+ threshold = atoi(optarg);
+ params->threshold = threshold;
+ break;
+ case 'o':
+ sam_filename = (const char *)optarg;
+ if (strcmp(sam_filename.c_str(),"-") != 0){
+ streams[16] = create_stream(gzOutput, optarg);
+ }else{
+ streams[16] = &cout;
+ }
+ break;
+ case 'm':
+ pattern_length = atol(optarg);
+ break;
+ case ALL_OUTPUT:
+ fileBasename = optarg;
+ use_all_outputs = true;
+ break;
+ case READS_LENGTH:
+ pattern_length = atol(optarg);
+ break;
+ case IS_STRANDED_CST:
+ is_stranded = true;
+ break;
+ case MAX_NB_LOCATED_OCCS_CST:
+ params->max_nb_located_occs = atol(optarg);
+ break;
+ case SNP:
+ streams[0] = create_stream(gzOutput, optarg);
+ break;
+ case BIOTAG:
+ streams[1] = create_stream(gzOutput, optarg);
+ break;
+ case SEQERR:
+ streams[2] = create_stream(gzOutput, optarg);
+ break;
+ case SPLICE:
+ streams[3] = create_stream(gzOutput, optarg);
+ break;
+ case SPLICE_NOCOVER:
+ streams[4] = create_stream(gzOutput, optarg);
+ break;
+ case CHIMERA:
+ streams[5] = create_stream(gzOutput, optarg);
+ break;
+ case UNDETERMINED:
+ streams[6] = create_stream(gzOutput, optarg);
+ break;
+ case REPETITION:
+ streams[7] = create_stream(gzOutput, optarg);
+ break;
+ case DUPLICATION:
+ streams[8] = create_stream(gzOutput, optarg);
+ break;
+ case NOTHING:
+ streams[9] = create_stream(gzOutput, optarg);
+ break;
+ case NORMAL:
+ streams[10] = create_stream(gzOutput, optarg);
+ break;
+ case ALMOSTNORMAL:
+ streams[11] = create_stream(gzOutput, optarg);
+ break;
+ case MULTIPLE:
+ streams[12] = create_stream(gzOutput, optarg);
+ break;
+ case NONE:
+ streams[13] = create_stream(gzOutput, optarg);
+ break;
+ case BIOUNDETERMINED:
+ streams[14] = create_stream(gzOutput, optarg);
+ break;
+ case SINGLE:
+ streams[15] = create_stream(gzOutput, optarg);
+ break;
+ case SAM:
+ streams[16] = create_stream(gzOutput, optarg);
+ sam_filename = (const char *)optarg;
+ break;
+ case PAIRED_END_CHIMERA:
+ streams[17] = create_stream(gzOutput, optarg);
+ use_paired_end_chimera = true;
+ break;
+ case SUMMARY:
+ streams[18] = create_stream(gzOutput, optarg);
+ summary = streams[18];
+ break;
+ case MAX_SPLICE:
+ params->max_splice_length = atoi(optarg);
+ break;
+ case MAX_BIO_INDEL:
+ params->max_bio_ins_del = atoi(optarg);
+ break;
+ case MAX_DUPLICATION:
+ params->max_localisation_duplication = atoi(optarg);
+ break;
+ case MIN_DUPLICATION:
+ params->min_localisation_duplication = atoi(optarg);
+ break;
+ case PERCENT_MIN_SINGLE_REPETITION:
+ params->percent_min_unique_repetition = atof(optarg);
+ break;
+ case PERCENT_MIN_SINGLE_CST:
+ params->percent_min_single = atof(optarg);
+ break;
+ case PERCENT_MIN_MULTIPLE_CST:
+ params->percent_min_multiple = atof(optarg);
+ break;
+ case PERCENT_MIN_DUPLICATION:
+ params->percent_min_duplicate = atof(optarg);
+ break;
+ case MIN_LOC_REPETITION:
+ params->min_occ_repetition = atoi(optarg);
+ break;
+ case PERCENT_VARIATION_COVERAGE:
+ params->percent_support_variation_almost_normal = atof(optarg);
+ break;
+ case P_VALUE_VARIATION_COVERAGE:
+ params->p_value_variation_biological = atof(optarg);
+ break;
+ case SCORE_INTRA_AMBIGUOUS_CST:
+ params->score_intra_ambiguous = atof(optarg);
+ break;
+ case SCORE_INTER_AMBIGUOUS_CST:
+ params->score_inter_ambiguous = atof(optarg);
+ break;
+ case MAX_RANDOMLY_MATCHED:
+ params->max_bases_randomly_matched = atoi(optarg);
+ break;
+ case MAX_VERYNICE_MERGE_CST:
+ params->max_verynice_merge = atoi(optarg);
+ break;
+ case MIN_BEFORE_BREAK:
+ params->min_bases_before_break = atoi(optarg);
+ break;
+ case MAX_RETRIEVED:
+ params->max_bases_retrieved = atoi(optarg);
+ break;
+ case MAX_EXTENSION:
+ params->max_extension_length = atoi(optarg);
+ break;
+ case SUPPORT_SCORE_WINDOW:
+ params->support_score_window_length = atoi(optarg);
+ break;
+ case MINIMUM_SUPPORT_NO_COVER:
+ params->min_support_no_cover = atof(optarg);
+ break;
+ case MINIMUM_BREAK_LENGTH:
+ params->min_break_length = atoi(optarg);
+ break;
+ case MAXIMUM_SUPPORT_OUT_NO_COVER:
+ params->max_support_out_no_cover = atof(optarg);
+ break;
+ case MAX_AMBIGUOUS_AVG_HIGH:
+ params->max_ambiguous_average_high = atof(optarg);
+ break;
+ case NB_BASES_SUBSTRACTED_LOW_AVG:
+ params->nb_bases_substracted_low_average = atoi(optarg);
+ break;
+ case NB_POS_CHECK_ONES:
+ params->nb_positions_check_ones = atoi(optarg);
+ break;
+ case MIN_PERC_ONES_INSIDE:
+ params->min_perc_ones_inside = atof(optarg);
+ break;
+ case MIN_RATIO_SUPPORT_FALL_CST:
+ params->min_ratio_support_fall = atof(optarg);
+ break;
+ case NB_TAGS_INFO_CST:
+ params->nb_tags_info_stored = atoi(optarg);
+ break;
+ case NB_THREADS_CST:
+ params->nb_threads = atoi(optarg);
+ break;
+ case MAX_NB_OVERLAPPING_BREAKS_CST:
+ params->max_nb_overlapping_breaks = atof(optarg);
+ break;
+ case DEEP_SNP_SEARCH_CST:
+ params->deep_snp_search = true;
+ break;
+ case NUMBER_NUCLEOTIDES_SNP_COMPARISON_CST:
+ params->number_nucleotides_snp_comparison = atoi(optarg);
+ break;
+ case DETAILED_SAM_CST:
+ params->detailed_sam = true;
+ break;
+ case SERVER_CST:
+ use_server=true;
+ break;
+ case STRINGENT_CHIMERA_CST:
+ params->stringent_chimera = true;
+ break;
+ case INPUT_FIFO_CST:
+ fifo_input_name = new char[strlen(optarg)+1];
+ strcpy(fifo_input_name, optarg);
+ break;
+ case OUTPUT_FIFO_CST:
+ fifo_output_name = new char[strlen(optarg)+1];
+ strcpy(fifo_output_name, optarg);
+ break;
+ case DGE:
+ use_emt=true;
+ break;
+ case GZ_OUTPUT:
+ gzOutput = true;
+ break;
+ case NO_AMBIGUITY_CST:
+ params->no_ambiguity=true;
+ break;
+ case PROGRESSBAR:
+ params->show_progressbar = true;
+ break;
+ case TREAT_MULTIPLE_CST:
+ params->treat_multiple=true;
+ break;
+ case '?':
+ print_help();
+ exit(1);
+ default:
+ print_help();
+ exit(1);
+ }
+ }
+
+ // Init parameters with values we have fixed with options
+ params->init();
+
+ // little hack to get the second file argument of -r option when doing paired-end
+ if (optind < argc)
+ {
+ reads2 = argv[optind++];
+ }
+
+ // Init output files if we use --all option
+ if(use_all_outputs) {
+ nb_streams_to_init = nb_streams;
+ // If we are not using paired-end reads we dont create the last stream which is
+ // dedicated for paired-end reads only
+ if(reads2 == NULL) {
+ nb_streams_to_init--;
+ }
+ max_length = 0;
+ for (int i = 0; i < nb_streams_to_init; i++) {
+ uint current_length = strlen(extensions[i]);
+ if (current_length > max_length)
+ max_length = current_length;
+ }
+ filename = new char[strlen(fileBasename)+max_length+2];
+ for (int i=0; i < nb_streams_to_init; i++) {
+ sprintf(filename, "%s.%s", fileBasename, extensions[i]);
+ streams[i] = create_stream(gzOutput, filename);
+ if (i==16)
+ sam_filename = filename;
+ }
+ delete [] filename;
+ }
+
+ if (indexGenome == NULL || reads == 0 ||
+ threshold == (uint)~0 || (streams[16] == NULL && !use_server)){
+ print_help();
+ cerr << endl << "Missing at least a mandatory argument among: -i <index> -r <reads> -k <k_length> -o <output_SAM>" << endl << endl;
+ exit(1);
+ }else{
+ for (int i=0; i < nb_streams && !find_output_file ; i++) {
+ if (streams[i] != NULL){
+ find_output_file = true;
+ }
+ }
+ if (!find_output_file && !use_server){
+ print_help();
+ cerr << endl << "Obviously, you must specify at least one output argument" << endl << endl;
+ exit(1);
+ }
+ // check if the there is paired-end input file when using paired-end options
+ if (reads2 == NULL && use_paired_end_chimera) {
+ print_help();
+ cerr << endl << "Please specify a second read input file if you want to use a specific option for paired-end tags." << endl;
+ }
+ }
+
+ // Checking fifos for server
+ if (use_server) {
+ struct stat buf;
+ // If no name was specified, use default ones.
+ if (! fifo_input_name)
+ fifo_input_name = (char *)INPUT_FIFO;
+ if (! fifo_output_name)
+ fifo_output_name = (char *)OUTPUT_FIFO;
+
+ if (stat(fifo_input_name,&buf) == 0 || stat(fifo_output_name,&buf) == 0) {
+ cerr << fifo_input_name << " or " << fifo_output_name << " already exist."
+ << endl << "Please specity another name or delete the existing files." << endl;
+ exit(4);
+ }
+ }
+
+ // Launching exact-matching for reads mapping
+ if (use_emt){
+ if (reads2 != NULL)
+ cerr << "Warning: CRAC--emt version does not support paired-ends protocol, only the first input file "<<reads <<" is considered" << endl;
+ if (summary != NULL)
+ *summary << "Running CRAC-emt version " <<PACKAGE_VERSION <<" optimized for exact mapping reads " << endl << endl;
+ // Indexation of the genome
+ if (threshold > 0)
+ cerr << "Warning: Running CRAC--emt with k=" << threshold << " which means that it only maps the first located kmer of length "<< threshold <<" for each read" << endl;
+ else
+ cerr << "Warning: Running CRAC--emt with k=0 to map the entire reads" << endl;
+ log = new LocateOnGenome((uchar *)indexGenome);
+ log->setNbLocations(params->max_nb_located_occs);
+ log->startChrono();
+ LocateTags *lt;
+ lt = new LocateTags(log, params, reads, threshold);
+ // put headers in the sam file
+ writeSamHeader(streams[16],log,argc,argv,sam_filename);
+ // launch the locate process
+ lt->locate(streams[16]);
+
+ if (summary != NULL) {
+ *summary << "Time to locate all tags: "<< log->getElapsedTime() << " s" << endl;
+ *summary << endl << "----------------------------------" << endl;
+ *summary << " Some STATISTICS " << endl;
+ *summary << endl << "----------------------------------" << endl;
+ *summary << "Total number of reads analyzed: " << lt->getNbTags() << endl << endl;
+ *summary << "Single: " << lt->getNbSingle() << " (" << lt->getNbSingle()*100./lt->getNbTags() << "%)" << endl;
+ *summary << "Multiple: " << lt->getNbMultiple() << " (" << lt->getNbMultiple()*100./lt->getNbTags() << "%)" << endl;
+ *summary << "None: " << lt->getNbNone() << " (" << lt->getNbNone()*100./lt->getNbTags() << "%)" << endl;
+ }
+ delete lt;
+ }
+ // Launching CRAC for RNA-Seq mapping
+ else{
+ // Indexation of reads
+ float start = getChrono();
+ // If we have pairedEnd reads we create gkArrays using both reads files
+ try {
+ if (reads2 != 0) {
+ if (summary != NULL)
+ *summary << "Running CRAC using paired-end files." << endl;
+ indexTags = new gkArrays(reads, reads2, threshold, false, pattern_length, is_stranded, params->nb_threads, params->show_progressbar);
+ } else {
+ indexTags = new gkArrays(reads, threshold, false, pattern_length, is_stranded, params->nb_threads, params->show_progressbar);
+ }
+ } catch (bad_alloc e) {
+ cerr << "You do not have enough memory to store all the reads. Aborting" << endl;
+ exit(42);
+ }
+
+ if (summary != NULL){
+ if (indexTags->isLarge()){
+ *summary << "Running CRAC version " <<PACKAGE_VERSION <<" optimized for large data set ";
+ if (pattern_length){
+ *summary << "and fixed read length " ;
+ }else{
+ *summary << "and variable read length ";
+ }
+ }else{
+ *summary << "Running CRAC version " <<PACKAGE_VERSION <<" optimized for small data set < 4Gbp (eg. less than 50M reads of 75 bp) ";
+ if (pattern_length){
+ *summary << "and fixed read length " ;
+ }else{
+ *summary << "and variable read length " ;
+ }
+ }
+ if (is_stranded)
+ *summary << "for a strand specific library." << endl;
+ else
+ *summary << "for a non-strand specific library." << endl;
+
+ *summary << endl << "Time to index all reads: " << (getChrono()-start)/1000000. << " s" << endl;
+ }
+
+ // Indexation of the genome
+ log = new LocateOnGenome((uchar *)indexGenome);
+ log->setNbLocations(params->max_nb_located_occs);
+
+ // classify the reads
+ ct = new ClassifyTags(log, indexTags, params);
+ if (use_server) {
+ locateServer(ct, fifo_input_name, fifo_output_name);
+ } else {
+ log->startChrono();
+ // put headers in the sam file
+ writeSamHeader(streams[16],log,argc,argv,sam_filename);
+ // put headers with feature for each files
+ ct->getHeaders(streams[0], streams[1], streams[2], streams[3],
+ streams[4], streams[5], streams[6], streams[7],
+ streams[8], streams[9], streams[10], streams[11],
+ streams[12], streams[13], streams[14], streams[15],
+ streams[17]);
+ // and classify
+ ct->classify(streams[0], streams[1], streams[2], streams[3],
+ streams[4], streams[5], streams[6], streams[7],
+ streams[8], streams[9], streams[10], streams[11],
+ streams[12], streams[13], streams[14], streams[15],
+ streams[16], streams[17] );
+
+ if (summary != NULL){
+ *summary << "Time to classify all reads: "<< log->getElapsedTime() << " s" << endl;
+
+ // making statistics on STDOUT
+ *summary << endl << "----------------------------------" << endl;
+ *summary << " Some STATISTICS " << endl;
+ *summary << endl << "----------------------------------" << endl;
+ *summary << "Total number of reads analyzed: " << indexTags->getNbTags() << endl << endl;
+ *summary << "Single: " << ct->getNbSingle() << " (" << ct->getNbSingle()*100./indexTags->getNbTags() << "%)" << endl;
+ *summary << "Multiple: " << ct->getNbMultiple() << " (" << ct->getNbMultiple()*100./indexTags->getNbTags() << "%)" << endl;
+ *summary << "None: " << ct->getNbNone() << " (" << ct->getNbNone()*100./indexTags->getNbTags() << "%)" << endl;
+ *summary << "Duplication: " << ct->getNbDuplication() << " (" << ct->getNbDuplication()*100./indexTags->getNbTags() << "%)" << endl;
+
+ *summary << endl << "Warning: the sum of the four previous categories may not be equal to 100%." << endl << " This is normal: reads are considered by chunks." << endl << " In a given read, a chunk may appear multiple times, while another just appears once." << endl ;
+ *summary << endl << "----------------------------------" << endl;
+
+ *summary << "Explainable: " << ct->getNbExplainable() << " (" << ct->getNbExplainable()*100./indexTags->getNbTags() << "%)" << endl << endl;
+
+ *summary << "Repetition: " << ct->getNbRepetition() << " (" << ct->getNbRepetition()*100./indexTags->getNbTags() << "%)" << endl ;
+ *summary << "Normal: " << ct->getNbNormal() << " (" << ct->getNbNormal()*100./indexTags->getNbTags() << "%)" << endl ;
+ *summary << "Almost-Normal: " << ct->getNbAlmostNormal() << " (" << ct->getNbAlmostNormal()*100./indexTags->getNbTags() << "%)" << endl ;
+ *summary << "Sequence-Errors: " << ct->getNbSeqErr() << " (" << ct->getNbSeqErr()*100./indexTags->getNbTags() << "%)" << endl ;
+ *summary << "SNV: " << ct->getNbSNP() << " (" << ct->getNbSNP()*100./indexTags->getNbTags() << "%)" << endl ;
+ *summary << "Short-Indel: " << ct->getNbBioTagIndel() << " (" << ct->getNbBioTagIndel()*100./indexTags->getNbTags() << "%)" << endl ;
+ *summary << "Splice: " << ct->getNbSplice() << " (" << ct->getNbSplice()*100./indexTags->getNbTags() << "%)" << endl ;
+ *summary << "Weak-Splice: " << ct->getNbSpliceNoCover() << " (" << ct->getNbSpliceNoCover()*100./indexTags->getNbTags() << "%)" << endl ;
+ *summary << "Chimera: " << ct->getNbSpliceInter() << " (" << ct->getNbSpliceInter()*100./indexTags->getNbTags() << "%)" << endl ;
+ if(reads2 != NULL) {
+ *summary << "Paired-end Chimera: " << ct->getNbPairedEndChimera() << " (" << ct->getNbPairedEndChimera()*100./indexTags->getNbTags() << "%)" << endl ;
+ }
+ *summary << "Bio-Undetermined: " << ct->getNbBioUndetermined() << " (" << ct->getNbBioUndetermined()*100./indexTags->getNbTags() << "%)" << endl ;
+ *summary << "Undetermined: " << ct->getNbUndetermined() << " (" << ct->getNbUndetermined()*100./indexTags->getNbTags() << "%)" << endl ;
+ // *summary << "Nothing: " << ct->getNbNothing() << " (" << ct->getNbNothing()*100./indexTags->getNbTags() << "%)" << endl ;
+ }
+ }
+ delete ct;
+ }
+
+ for (int i = 0; i < nb_streams; i++) {
+ if (streams[i] != NULL && streams[i] != &cout)
+ delete streams[i];
+ }
+ delete indexTags;
+ delete params;
+ delete log;
+ return 0;
+}
diff --git a/src/libGkArrays/AUTHORS b/src/libGkArrays/AUTHORS
new file mode 100644
index 0000000..d147cc7
--- /dev/null
+++ b/src/libGkArrays/AUTHORS
@@ -0,0 +1,19 @@
+Nicolas PHILIPPE, Mikael SALSON, Alban MANCHERON, Thierry LECROQ, Eric RIVALS <crac-gkarrays at lists.gforge.inria.fr>
+
+libGkArrays is a part of research activities of:
+ Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+ Mikaël SALSON <mikael.salson at lifl.fr>
+ Thierry LECROQ <thierry.lecroq at univ-rouen.fr>
+ Martine LÉONARD <martine.leonard at univ-rouen.fr>
+ Eric RIVALS <eric.rivals at lirmm.fr>
+
+Supervision by:
+ Thierry LECROQ <thierry.lecroq at univ-rouen.fr>
+ Eric RIVALS <eric.rivals at lirmm.fr>
+
+Programming:
+ Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+ Mikaël SALSON <mikael.salson at lifl.fr>
+
+with additional contribution for the packaging of:
+ Alban MANCHERON <alban.mancheron at lirmm.fr>
diff --git a/src/libGkArrays/COPYING b/src/libGkArrays/COPYING
new file mode 100644
index 0000000..0bb3771
--- /dev/null
+++ b/src/libGkArrays/COPYING
@@ -0,0 +1,1047 @@
+***********************************************************************
+******* English translation of the french licence is thereafter *******
+***********************************************************************
+
+CONTRAT DE LICENCE DE LOGICIEL LIBRE CeCILL-C
+
+
+ Avertissement
+
+Ce contrat est une licence de logiciel libre issue d'une concertation
+entre ses auteurs afin que le respect de deux grands principes préside à
+sa rédaction:
+
+ * d'une part, le respect des principes de diffusion des logiciels
+ libres: accès au code source, droits étendus conférés aux
+ utilisateurs,
+ * d'autre part, la désignation d'un droit applicable, le droit
+ français, auquel elle est conforme, tant au regard du droit de la
+ responsabilité civile que du droit de la propriété intellectuelle
+ et de la protection qu'il offre aux auteurs et titulaires des
+ droits patrimoniaux sur un logiciel.
+
+Les auteurs de la licence CeCILL-C (pour Ce[a] C[nrs] I[nria] L[ogiciel]
+L[ibre]) sont:
+
+Commissariat à l'Energie Atomique - CEA, établissement public de
+recherche à caractère scientifique, technique et industriel, dont le
+siège est situé 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris.
+
+Centre National de la Recherche Scientifique - CNRS, établissement
+public à caractère scientifique et technologique, dont le siège est
+situé 3 rue Michel-Ange, 75794 Paris cedex 16.
+
+Institut National de Recherche en Informatique et en Automatique -
+INRIA, établissement public à caractère scientifique et technologique,
+dont le siège est situé Domaine de Voluceau, Rocquencourt, BP 105, 78153
+Le Chesnay cedex.
+
+
+ Préambule
+
+Ce contrat est une licence de logiciel libre dont l'objectif est de
+conférer aux utilisateurs la liberté de modifier et de réutiliser le
+logiciel régi par cette licence.
+
+L'exercice de cette liberté est assorti d'une obligation de remettre à
+la disposition de la communauté les modifications apportées au code
+source du logiciel afin de contribuer à son évolution.
+
+L'accessibilité au code source et les droits de copie, de modification
+et de redistribution qui découlent de ce contrat ont pour contrepartie
+de n'offrir aux utilisateurs qu'une garantie limitée et de ne faire
+peser sur l'auteur du logiciel, le titulaire des droits patrimoniaux et
+les concédants successifs qu'une responsabilité restreinte.
+
+A cet égard l'attention de l'utilisateur est attirée sur les risques
+associés au chargement, à l'utilisation, à la modification et/ou au
+développement et à la reproduction du logiciel par l'utilisateur étant
+donné sa spécificité de logiciel libre, qui peut le rendre complexe à
+manipuler et qui le réserve donc à des développeurs ou des
+professionnels avertis possédant des connaissances informatiques
+approfondies. Les utilisateurs sont donc invités à charger et tester
+l'adéquation du logiciel à leurs besoins dans des conditions permettant
+d'assurer la sécurité de leurs systèmes et/ou de leurs données et, plus
+généralement, à l'utiliser et l'exploiter dans les mêmes conditions de
+sécurité. Ce contrat peut être reproduit et diffusé librement, sous
+réserve de le conserver en l'état, sans ajout ni suppression de clauses.
+
+Ce contrat est susceptible de s'appliquer à tout logiciel dont le
+titulaire des droits patrimoniaux décide de soumettre l'exploitation aux
+dispositions qu'il contient.
+
+
+ Article 1 - DEFINITIONS
+
+Dans ce contrat, les termes suivants, lorsqu'ils seront écrits avec une
+lettre capitale, auront la signification suivante:
+
+Contrat: désigne le présent contrat de licence, ses éventuelles versions
+postérieures et annexes.
+
+Logiciel: désigne le logiciel sous sa forme de Code Objet et/ou de Code
+Source et le cas échéant sa documentation, dans leur état au moment de
+l'acceptation du Contrat par le Licencié.
+
+Logiciel Initial: désigne le Logiciel sous sa forme de Code Source et
+éventuellement de Code Objet et le cas échéant sa documentation, dans
+leur état au moment de leur première diffusion sous les termes du Contrat.
+
+Logiciel Modifié: désigne le Logiciel modifié par au moins une
+Contribution Intégrée.
+
+Code Source: désigne l'ensemble des instructions et des lignes de
+programme du Logiciel et auquel l'accès est nécessaire en vue de
+modifier le Logiciel.
+
+Code Objet: désigne les fichiers binaires issus de la compilation du
+Code Source.
+
+Titulaire: désigne le ou les détenteurs des droits patrimoniaux d'auteur
+sur le Logiciel Initial.
+
+Licencié: désigne le ou les utilisateurs du Logiciel ayant accepté le
+Contrat.
+
+Contributeur: désigne le Licencié auteur d'au moins une Contribution
+Intégrée.
+
+Concédant: désigne le Titulaire ou toute personne physique ou morale
+distribuant le Logiciel sous le Contrat.
+
+Contribution Intégrée: désigne l'ensemble des modifications,
+corrections, traductions, adaptations et/ou nouvelles fonctionnalités
+intégrées dans le Code Source par tout Contributeur.
+
+Module Lié: désigne un ensemble de fichiers sources y compris leur
+documentation qui, sans modification du Code Source, permet de réaliser
+des fonctionnalités ou services supplémentaires à ceux fournis par le
+Logiciel.
+
+Logiciel Dérivé: désigne toute combinaison du Logiciel, modifié ou non,
+et d'un Module Lié.
+
+Parties: désigne collectivement le Licencié et le Concédant.
+
+Ces termes s'entendent au singulier comme au pluriel.
+
+
+ Article 2 - OBJET
+
+Le Contrat a pour objet la concession par le Concédant au Licencié d'une
+licence non exclusive, cessible et mondiale du Logiciel telle que
+définie ci-après à l'article 5 pour toute la durée de protection des droits
+portant sur ce Logiciel.
+
+
+ Article 3 - ACCEPTATION
+
+3.1 L'acceptation par le Licencié des termes du Contrat est réputée
+acquise du fait du premier des faits suivants:
+
+ * (i) le chargement du Logiciel par tout moyen notamment par
+ téléchargement à partir d'un serveur distant ou par chargement à
+ partir d'un support physique;
+ * (ii) le premier exercice par le Licencié de l'un quelconque des
+ droits concédés par le Contrat.
+
+3.2 Un exemplaire du Contrat, contenant notamment un avertissement
+relatif aux spécificités du Logiciel, à la restriction de garantie et à
+la limitation à un usage par des utilisateurs expérimentés a été mis à
+disposition du Licencié préalablement à son acceptation telle que
+définie à l'article 3.1 ci dessus et le Licencié reconnaît en avoir pris
+connaissance.
+
+
+ Article 4 - ENTREE EN VIGUEUR ET DUREE
+
+
+ 4.1 ENTREE EN VIGUEUR
+
+Le Contrat entre en vigueur à la date de son acceptation par le Licencié
+telle que définie en 3.1.
+
+
+ 4.2 DUREE
+
+Le Contrat produira ses effets pendant toute la durée légale de
+protection des droits patrimoniaux portant sur le Logiciel.
+
+
+ Article 5 - ETENDUE DES DROITS CONCEDES
+
+Le Concédant concède au Licencié, qui accepte, les droits suivants sur
+le Logiciel pour toutes destinations et pour la durée du Contrat dans
+les conditions ci-après détaillées.
+
+Par ailleurs, si le Concédant détient ou venait à détenir un ou
+plusieurs brevets d'invention protégeant tout ou partie des
+fonctionnalités du Logiciel ou de ses composants, il s'engage à ne pas
+opposer les éventuels droits conférés par ces brevets aux Licenciés
+successifs qui utiliseraient, exploiteraient ou modifieraient le
+Logiciel. En cas de cession de ces brevets, le Concédant s'engage à
+faire reprendre les obligations du présent alinéa aux cessionnaires.
+
+
+ 5.1 DROIT D'UTILISATION
+
+Le Licencié est autorisé à utiliser le Logiciel, sans restriction quant
+aux domaines d'application, étant ci-après précisé que cela comporte:
+
+ 1. la reproduction permanente ou provisoire du Logiciel en tout ou
+ partie par tout moyen et sous toute forme.
+
+ 2. le chargement, l'affichage, l'exécution, ou le stockage du
+ Logiciel sur tout support.
+
+ 3. la possibilité d'en observer, d'en étudier, ou d'en tester le
+ fonctionnement afin de déterminer les idées et principes qui sont
+ à la base de n'importe quel élément de ce Logiciel; et ceci,
+ lorsque le Licencié effectue toute opération de chargement,
+ d'affichage, d'exécution, de transmission ou de stockage du
+ Logiciel qu'il est en droit d'effectuer en vertu du Contrat.
+
+
+ 5.2 DROIT DE MODIFICATION
+
+Le droit de modification comporte le droit de traduire, d'adapter,
+d'arranger ou d'apporter toute autre modification au Logiciel et le
+droit de reproduire le logiciel en résultant. Il comprend en particulier
+le droit de créer un Logiciel Dérivé.
+
+Le Licencié est autorisé à apporter toute modification au Logiciel sous
+réserve de mentionner, de façon explicite, son nom en tant qu'auteur de
+cette modification et la date de création de celle-ci.
+
+
+ 5.3 DROIT DE DISTRIBUTION
+
+Le droit de distribution comporte notamment le droit de diffuser, de
+transmettre et de communiquer le Logiciel au public sur tout support et
+par tout moyen ainsi que le droit de mettre sur le marché à titre
+onéreux ou gratuit, un ou des exemplaires du Logiciel par tout procédé.
+
+Le Licencié est autorisé à distribuer des copies du Logiciel, modifié ou
+non, à des tiers dans les conditions ci-après détaillées.
+
+
+ 5.3.1 DISTRIBUTION DU LOGICIEL SANS MODIFICATION
+
+Le Licencié est autorisé à distribuer des copies conformes du Logiciel,
+sous forme de Code Source ou de Code Objet, à condition que cette
+distribution respecte les dispositions du Contrat dans leur totalité et
+soit accompagnée:
+
+ 1. d'un exemplaire du Contrat,
+
+ 2. d'un avertissement relatif à la restriction de garantie et de
+ responsabilité du Concédant telle que prévue aux articles 8
+ et 9,
+
+et que, dans le cas où seul le Code Objet du Logiciel est redistribué,
+le Licencié permette un accès effectif au Code Source complet du
+Logiciel pendant au moins toute la durée de sa distribution du Logiciel,
+étant entendu que le coût additionnel d'acquisition du Code Source ne
+devra pas excéder le simple coût de transfert des données.
+
+
+ 5.3.2 DISTRIBUTION DU LOGICIEL MODIFIE
+
+Lorsque le Licencié apporte une Contribution Intégrée au Logiciel, les
+conditions de distribution du Logiciel Modifié en résultant sont alors
+soumises à l'intégralité des dispositions du Contrat.
+
+Le Licencié est autorisé à distribuer le Logiciel Modifié sous forme de
+code source ou de code objet, à condition que cette distribution
+respecte les dispositions du Contrat dans leur totalité et soit
+accompagnée:
+
+ 1. d'un exemplaire du Contrat,
+
+ 2. d'un avertissement relatif à la restriction de garantie et de
+ responsabilité du Concédant telle que prévue aux articles 8
+ et 9,
+
+et que, dans le cas où seul le code objet du Logiciel Modifié est
+redistribué, le Licencié permette un accès effectif à son code source
+complet pendant au moins toute la durée de sa distribution du Logiciel
+Modifié, étant entendu que le coût additionnel d'acquisition du code
+source ne devra pas excéder le simple coût de transfert des données.
+
+
+ 5.3.3 DISTRIBUTION DU LOGICIEL DERIVE
+
+Lorsque le Licencié crée un Logiciel Dérivé, ce Logiciel Dérivé peut
+être distribué sous un contrat de licence autre que le présent Contrat à
+condition de respecter les obligations de mention des droits sur le
+Logiciel telles que définies à l'article 6.4. Dans le cas où la création du
+Logiciel Dérivé a nécessité une modification du Code Source le licencié
+s'engage à ce que:
+
+ 1. le Logiciel Modifié correspondant à cette modification soit régi
+ par le présent Contrat,
+ 2. les Contributions Intégrées dont le Logiciel Modifié résulte
+ soient clairement identifiées et documentées,
+ 3. le Licencié permette un accès effectif au code source du Logiciel
+ Modifié, pendant au moins toute la durée de la distribution du
+ Logiciel Dérivé, de telle sorte que ces modifications puissent
+ être reprises dans une version ultérieure du Logiciel, étant
+ entendu que le coût additionnel d'acquisition du code source du
+ Logiciel Modifié ne devra pas excéder le simple coût du transfert
+ des données.
+
+
+ 5.3.4 COMPATIBILITE AVEC LA LICENCE CeCILL
+
+Lorsqu'un Logiciel Modifié contient une Contribution Intégrée soumise au
+contrat de licence CeCILL, ou lorsqu'un Logiciel Dérivé contient un
+Module Lié soumis au contrat de licence CeCILL, les stipulations prévues
+au troisième item de l'article 6.4 sont facultatives.
+
+
+ Article 6 - PROPRIETE INTELLECTUELLE
+
+
+ 6.1 SUR LE LOGICIEL INITIAL
+
+Le Titulaire est détenteur des droits patrimoniaux sur le Logiciel
+Initial. Toute utilisation du Logiciel Initial est soumise au respect
+des conditions dans lesquelles le Titulaire a choisi de diffuser son
+oeuvre et nul autre n'a la faculté de modifier les conditions de
+diffusion de ce Logiciel Initial.
+
+Le Titulaire s'engage à ce que le Logiciel Initial reste au moins régi
+par le Contrat et ce, pour la durée visée à l'article 4.2.
+
+
+ 6.2 SUR LES CONTRIBUTIONS INTEGREES
+
+Le Licencié qui a développé une Contribution Intégrée est titulaire sur
+celle-ci des droits de propriété intellectuelle dans les conditions
+définies par la législation applicable.
+
+
+ 6.3 SUR LES MODULES LIES
+
+Le Licencié qui a développé un Module Lié est titulaire sur celui-ci des
+droits de propriété intellectuelle dans les conditions définies par la
+législation applicable et reste libre du choix du contrat régissant sa
+diffusion dans les conditions définies à l'article 5.3.3.
+
+
+ 6.4 MENTIONS DES DROITS
+
+Le Licencié s'engage expressément:
+
+ 1. à ne pas supprimer ou modifier de quelque manière que ce soit les
+ mentions de propriété intellectuelle apposées sur le Logiciel;
+
+ 2. à reproduire à l'identique lesdites mentions de propriété
+ intellectuelle sur les copies du Logiciel modifié ou non;
+
+ 3. à faire en sorte que l'utilisation du Logiciel, ses mentions de
+ propriété intellectuelle et le fait qu'il est régi par le Contrat
+ soient indiqués dans un texte facilement accessible notamment
+ depuis l'interface de tout Logiciel Dérivé.
+
+Le Licencié s'engage à ne pas porter atteinte, directement ou
+indirectement, aux droits de propriété intellectuelle du Titulaire et/ou
+des Contributeurs sur le Logiciel et à prendre, le cas échéant, à
+l'égard de son personnel toutes les mesures nécessaires pour assurer le
+respect des dits droits de propriété intellectuelle du Titulaire et/ou
+des Contributeurs.
+
+
+ Article 7 - SERVICES ASSOCIES
+
+7.1 Le Contrat n'oblige en aucun cas le Concédant à la réalisation de
+prestations d'assistance technique ou de maintenance du Logiciel.
+
+Cependant le Concédant reste libre de proposer ce type de services. Les
+termes et conditions d'une telle assistance technique et/ou d'une telle
+maintenance seront alors déterminés dans un acte séparé. Ces actes de
+maintenance et/ou assistance technique n'engageront que la seule
+responsabilité du Concédant qui les propose.
+
+7.2 De même, tout Concédant est libre de proposer, sous sa seule
+responsabilité, à ses licenciés une garantie, qui n'engagera que lui,
+lors de la redistribution du Logiciel et/ou du Logiciel Modifié et ce,
+dans les conditions qu'il souhaite. Cette garantie et les modalités
+financières de son application feront l'objet d'un acte séparé entre le
+Concédant et le Licencié.
+
+
+ Article 8 - RESPONSABILITE
+
+8.1 Sous réserve des dispositions de l'article 8.2, le Licencié a la
+faculté, sous réserve de prouver la faute du Concédant concerné, de
+solliciter la réparation du préjudice direct qu'il subirait du fait du
+Logiciel et dont il apportera la preuve.
+
+8.2 La responsabilité du Concédant est limitée aux engagements pris en
+application du Contrat et ne saurait être engagée en raison notamment:
+(i) des dommages dus à l'inexécution, totale ou partielle, de ses
+obligations par le Licencié, (ii) des dommages directs ou indirects
+découlant de l'utilisation ou des performances du Logiciel subis par le
+Licencié et (iii) plus généralement d'un quelconque dommage indirect. En
+particulier, les Parties conviennent expressément que tout préjudice
+financier ou commercial (par exemple perte de données, perte de
+bénéfices, perte d'exploitation, perte de clientèle ou de commandes,
+manque à gagner, trouble commercial quelconque) ou toute action dirigée
+contre le Licencié par un tiers, constitue un dommage indirect et
+n'ouvre pas droit à réparation par le Concédant.
+
+
+ Article 9 - GARANTIE
+
+9.1 Le Licencié reconnaît que l'état actuel des connaissances
+scientifiques et techniques au moment de la mise en circulation du
+Logiciel ne permet pas d'en tester et d'en vérifier toutes les
+utilisations ni de détecter l'existence d'éventuels défauts. L'attention
+du Licencié a été attirée sur ce point sur les risques associés au
+chargement, à l'utilisation, la modification et/ou au développement et à
+la reproduction du Logiciel qui sont réservés à des utilisateurs avertis.
+
+Il relève de la responsabilité du Licencié de contrôler, par tous
+moyens, l'adéquation du produit à ses besoins, son bon fonctionnement et
+de s'assurer qu'il ne causera pas de dommages aux personnes et aux biens.
+
+9.2 Le Concédant déclare de bonne foi être en droit de concéder
+l'ensemble des droits attachés au Logiciel (comprenant notamment les
+droits visés à l'article 5).
+
+9.3 Le Licencié reconnaît que le Logiciel est fourni "en l'état" par le
+Concédant sans autre garantie, expresse ou tacite, que celle prévue à
+l'article 9.2 et notamment sans aucune garantie sur sa valeur commerciale,
+son caractère sécurisé, innovant ou pertinent.
+
+En particulier, le Concédant ne garantit pas que le Logiciel est exempt
+d'erreur, qu'il fonctionnera sans interruption, qu'il sera compatible
+avec l'équipement du Licencié et sa configuration logicielle ni qu'il
+remplira les besoins du Licencié.
+
+9.4 Le Concédant ne garantit pas, de manière expresse ou tacite, que le
+Logiciel ne porte pas atteinte à un quelconque droit de propriété
+intellectuelle d'un tiers portant sur un brevet, un logiciel ou sur tout
+autre droit de propriété. Ainsi, le Concédant exclut toute garantie au
+profit du Licencié contre les actions en contrefaçon qui pourraient être
+diligentées au titre de l'utilisation, de la modification, et de la
+redistribution du Logiciel. Néanmoins, si de telles actions sont
+exercées contre le Licencié, le Concédant lui apportera son aide
+technique et juridique pour sa défense. Cette aide technique et
+juridique est déterminée au cas par cas entre le Concédant concerné et
+le Licencié dans le cadre d'un protocole d'accord. Le Concédant dégage
+toute responsabilité quant à l'utilisation de la dénomination du
+Logiciel par le Licencié. Aucune garantie n'est apportée quant à
+l'existence de droits antérieurs sur le nom du Logiciel et sur
+l'existence d'une marque.
+
+
+ Article 10 - RESILIATION
+
+10.1 En cas de manquement par le Licencié aux obligations mises à sa
+charge par le Contrat, le Concédant pourra résilier de plein droit le
+Contrat trente (30) jours après notification adressée au Licencié et
+restée sans effet.
+
+10.2 Le Licencié dont le Contrat est résilié n'est plus autorisé à
+utiliser, modifier ou distribuer le Logiciel. Cependant, toutes les
+licences qu'il aura concédées antérieurement à la résiliation du Contrat
+resteront valides sous réserve qu'elles aient été effectuées en
+conformité avec le Contrat.
+
+
+ Article 11 - DISPOSITIONS DIVERSES
+
+
+ 11.1 CAUSE EXTERIEURE
+
+Aucune des Parties ne sera responsable d'un retard ou d'une défaillance
+d'exécution du Contrat qui serait dû à un cas de force majeure, un cas
+fortuit ou une cause extérieure, telle que, notamment, le mauvais
+fonctionnement ou les interruptions du réseau électrique ou de
+télécommunication, la paralysie du réseau liée à une attaque
+informatique, l'intervention des autorités gouvernementales, les
+catastrophes naturelles, les dégâts des eaux, les tremblements de terre,
+le feu, les explosions, les grèves et les conflits sociaux, l'état de
+guerre...
+
+11.2 Le fait, par l'une ou l'autre des Parties, d'omettre en une ou
+plusieurs occasions de se prévaloir d'une ou plusieurs dispositions du
+Contrat, ne pourra en aucun cas impliquer renonciation par la Partie
+intéressée à s'en prévaloir ultérieurement.
+
+11.3 Le Contrat annule et remplace toute convention antérieure, écrite
+ou orale, entre les Parties sur le même objet et constitue l'accord
+entier entre les Parties sur cet objet. Aucune addition ou modification
+aux termes du Contrat n'aura d'effet à l'égard des Parties à moins
+d'être faite par écrit et signée par leurs représentants dûment habilités.
+
+11.4 Dans l'hypothèse où une ou plusieurs des dispositions du Contrat
+s'avèrerait contraire à une loi ou à un texte applicable, existants ou
+futurs, cette loi ou ce texte prévaudrait, et les Parties feraient les
+amendements nécessaires pour se conformer à cette loi ou à ce texte.
+Toutes les autres dispositions resteront en vigueur. De même, la
+nullité, pour quelque raison que ce soit, d'une des dispositions du
+Contrat ne saurait entraîner la nullité de l'ensemble du Contrat.
+
+
+ 11.5 LANGUE
+
+Le Contrat est rédigé en langue française et en langue anglaise, ces
+deux versions faisant également foi.
+
+
+ Article 12 - NOUVELLES VERSIONS DU CONTRAT
+
+12.1 Toute personne est autorisée à copier et distribuer des copies de
+ce Contrat.
+
+12.2 Afin d'en préserver la cohérence, le texte du Contrat est protégé
+et ne peut être modifié que par les auteurs de la licence, lesquels se
+réservent le droit de publier périodiquement des mises à jour ou de
+nouvelles versions du Contrat, qui posséderont chacune un numéro
+distinct. Ces versions ultérieures seront susceptibles de prendre en
+compte de nouvelles problématiques rencontrées par les logiciels libres.
+
+12.3 Tout Logiciel diffusé sous une version donnée du Contrat ne pourra
+faire l'objet d'une diffusion ultérieure que sous la même version du
+Contrat ou une version postérieure.
+
+
+ Article 13 - LOI APPLICABLE ET COMPETENCE TERRITORIALE
+
+13.1 Le Contrat est régi par la loi française. Les Parties conviennent
+de tenter de régler à l'amiable les différends ou litiges qui
+viendraient à se produire par suite ou à l'occasion du Contrat.
+
+13.2 A défaut d'accord amiable dans un délai de deux (2) mois à compter
+de leur survenance et sauf situation relevant d'une procédure d'urgence,
+les différends ou litiges seront portés par la Partie la plus diligente
+devant les Tribunaux compétents de Paris.
+
+
+Version 1.0 du 2006-09-05.
+
+***********************************************************************
+***********************************************************************
+***********************************************************************
+
+CeCILL-C FREE SOFTWARE LICENSE AGREEMENT
+
+
+ Notice
+
+This Agreement is a Free Software license agreement that is the result
+of discussions between its authors in order to ensure compliance with
+the two main principles guiding its drafting:
+
+ * firstly, compliance with the principles governing the distribution
+ of Free Software: access to source code, broad rights granted to
+ users,
+ * secondly, the election of a governing law, French law, with which
+ it is conformant, both as regards the law of torts and
+ intellectual property law, and the protection that it offers to
+ both authors and holders of the economic rights over software.
+
+The authors of the CeCILL-C (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
+license are:
+
+Commissariat à l'Energie Atomique - CEA, a public scientific, technical
+and industrial research establishment, having its principal place of
+business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
+
+Centre National de la Recherche Scientifique - CNRS, a public scientific
+and technological establishment, having its principal place of business
+at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
+
+Institut National de Recherche en Informatique et en Automatique -
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+
+Version 1.0 dated 2006-09-05.
+
+***********************************************************************
diff --git a/src/libGkArrays/ChangeLog b/src/libGkArrays/ChangeLog
new file mode 100644
index 0000000..5cd0794
--- /dev/null
+++ b/src/libGkArrays/ChangeLog
@@ -0,0 +1,482 @@
+2013-11-29 mancheron
+
+ * [r2735] configure.ac, src/Makefile.am, src/gkArrays.cpp,
+ src/gkCFPSBuilder.cpp, src/gkIFABuilder.cpp, src/gkSABuilder.cpp,
+ src/libProgressBar-1.1.2, src/libProgressBar-1.2.0,
+ src/libProgressBar-1.2.0/ChangeLog,
+ src/libProgressBar-1.2.0/Makefile.am,
+ src/libProgressBar-1.2.0/Makefile.in,
+ src/libProgressBar-1.2.0/configure,
+ src/libProgressBar-1.2.0/configure.in,
+ src/libProgressBar-1.2.0/doc/Makefile.in,
+ src/libProgressBar-1.2.0/doc/libProgressBar.3,
+ src/libProgressBar-1.2.0/libProgressBar/Makefile.in,
+ src/libProgressBar-1.2.0/libProgressBar/progressBar.cpp,
+ src/libProgressBar-1.2.0/libProgressBar/progressBar.h,
+ src/libProgressBar-1.2.0/libProgressBar/testPB.cpp: Updating
+ libProgressBar library. Enhance display. Remove pkg-config usage
+ to detect library since some people dislike it.
+
+2013-11-28 mancheron
+
+ * [r2730] ChangeLog:
+ * [r2729] src/gkSABuilder.cpp,
+ src/libProgressBar-1.1.2/doc/libProgressBar.3: Bug Fix:
+ Multithreading displayed the progress bar twice for SA
+ construction.
+ * [r2728] ., configure.ac, src/Makefile.am, src/gkArrays.cpp,
+ src/gkArrays.h, src/gkCFPSBuilder.cpp, src/gkIFABuilder.cpp,
+ src/gkSABuilder.cpp, src/libProgressBar-1.1.2: New release
+
+2013-09-30 salson
+
+ * [r2564] GkSABuilder: Prevent loop variables to go out the
+ boundaries
+
+2013-09-28 salson
+
+ * [r2559] Release 2.0.6: - Correction in quicksort algorithm: pivot
+ choice changed to avoid long computations in very specific cases
+ * [r2558] GkSABuilder: Remove med function not needed anymore
+ (pivot choice method changed)
+ * [r2557] gkSABuilder: Change the way pivot is chosen: pick one
+ randomly.
+
+ Choosing the median could generate some highly inefficient
+ processing in specific conditions (array sorted in reverse order)
+ * [r2555] Release 2.0.5: - Fixed a bug when processing (very) large
+ files. A uint value should have been a uintSA - Fixed some
+ autotools issues
+
+2013-09-27 salson
+
+ * [r2554] GkIFABuilder: uintSA instead of uint
+
+ Using a uint provoked an overflow on very large files, when
+ computing i+j (which was therefore done as a uint).
+
+2013-05-21 salson
+
+ * [r2446] GkArrays: Check for libpthread in GkArrays
+ * [r2445] GkArrays: Remove config.h.in file
+
+2013-05-07 nphilippe
+
+ * [r2424] -fixed typo error in configure.ac -remove AC_PROG_RANLIB
+ obsolete
+
+2013-04-29 salson
+
+ * [r2395] GkArrays: remove Makefile.in, configure scripts and so
+ on. Generate them usign aclocal && autoconf && autoheader &&
+ automake --add-missing
+
+2013-04-19 nphilippe
+
+ * [r2352]
+
+2013-04-19 salson
+
+ * [r2349] GkArrays: Typo in configure.ac (space missing) and check
+ that kpsewhich exists
+
+2013-04-17 salson
+
+ * [r2288] Release 2.0.3: - Bug correction on the number of bits
+ used with the bitvector version - Bug correction on the size of
+ an array, that could cause segfault in very specific cases - Some
+ compilation warnings removed
+ * [r2287] GkArrays: Array values'' must be of size nb_kmers+1 just
+ in case all the kmers are distinct
+
+2013-04-16 salson
+
+ * [r2274] GkArrays: gkSABuilder uses the new SolArray constructor
+ since gkSA is not really a permutation (GkSA length is not the
+ maximal value that can be stored in the array
+ * [r2273] GkArrays: solArrays have another constructor that take as
+ a parameter the maximal value that can be stored in the array
+ * [r2272] GkArrays: computation of number of bits needed for an
+ array did not work depending on the endianness
+ * [r2271] GkArrays: Use bitvectors in consistency tests.
+
+2013-04-13 salson
+
+ * [r2270] GkArrays: filename parameters to the constructors are now
+ const char*
+
+2013-04-12 salson
+
+ * [r2261] GkArrays: Remove compilation warnings
+
+2013-04-12 nphilippe
+
+ * [r2258] new release 2.0.2
+
+2013-04-10 jaudoux
+
+ * [r2245] [BUG] Correction of bug #15561 paired-end iterators were
+ having a trouble in numbering.
+
+2013-04-05 salson
+
+ * [r2223] GkArrays: Bug #15583 corrected (concerning problems in
+ tests/Makefile.am). Version 2.0.1 issued
+
+2013-04-05 nphilippe
+
+ * [r2222] configure.ac
+
+2013-04-03 jaudoux
+
+ * [r2192] Correct the read numeration of readsIterator. The first
+ tag has now the id 0.
+
+2013-03-21 salson
+
+ * [r2127] GkArrays: Changelog of version 2.0.0
+ * [r2126] GkArrays: testGkArrays.cpp: Added some comments to
+ explain the possibilities with the constructor
+ * [r2125] GkArrays: src/Makefiles: Many headers must be installed
+ * [r2124] GkArrays: Code cleanup
+ * [r2123] GkArrays: Example for new users
+ * [r2122] GkArrays: Tests: Add tests for bit vectors. Add
+ information in case of failed tests
+ * [r2121] GkArrays: Bit vector implementation by Alban Mancheron
+ included, replaced former one. Beware: we only use bit vectors on
+ a multiple of 8bits to avoid race conditions with multi-threading
+ * [r2118] GkArrays: Add a --coverage option in configure script to
+ compute the code coverage
+
+2013-03-20 nphilippe
+
+ * [r2117] put Solarray type for values table and modify code in
+ function
+
+2013-03-20 jaudoux
+
+ * [r2115] Add a method in readsReader to get the read number
+
+2013-03-20 salson
+
+ * [r2113] GkArrays: Javadoc: specify that arrays on the output are
+ sorted
+
+2013-03-18 salson
+
+ * [r2104] GkArrays: Unit tests: Produce a .tap file when tests are
+ launched [file testing.h forgotten]
+ * [r2103] GkArrays: Unit tests: Produce a .tap file when tests are
+ launched
+
+2013-03-12 salson
+
+ * [r2100] GkArrays: Keep a N in dataset files.
+
+2013-03-11 salson
+
+ * [r2099] GkArrays: Makefile.in file deleted during a previous
+ commit, put back on the SVN
+
+2013-03-10 nphilippe
+
+ * [r2095] last cleanup for gk-arrays 2.0.0
+
+2013-03-08 salson
+
+ * [r2094] GkArrays: Fixed some Javadoc problems (typos in the
+ command name, parameter not documented, unknown parameter
+ documented, ...)
+
+2013-03-08 jaudoux
+
+ * [r2089] * New headers for each soure file * Change copyright year
+ * Add IRB/INSERM in copyright * Add a name of developpers in a
+ specific part * Tests added for pairedEnd classes * Builtables
+ can now be run using pairedEnd reads * New methods in readsReader
+ for switching between paired-end reads
+
+2013-03-07 salson
+
+ * [r2083] GkArrays: Changed the delay for waiting the children. It
+ is now small (for the start) and increases until it reaches an
+ upper bound Moved the place sem_post is put. sem_post must be
+ executed each time we leave a thread. Since we may launch the
+ insertion sort in a thread, sem_post had to be executed after
+ that too.
+
+2013-03-06 salson
+
+ * [r2082] GkArrays: - Removed two unnecessary variables (not used
+ anymore) - Removed a comparison between signed and unsigned
+ interger
+
+2013-03-03 salson
+
+ * [r2048] GkArrays: GkSABuilder: quicksort has now a better
+ parallel implementation and uses all the available resources (but
+ not more)
+ * [r2047] Bug #15429 corrected: use of uintSA rather than uint for
+ the end position of a read in C_R.
+
+2013-03-01 jaudoux
+
+ * [r2037] Add an ifndef declaration in readsReader class.
+
+2013-03-01 nphilippe
+
+ * [r2035] -oops
+
+2013-03-01 jaudoux
+
+ * [r2034] Add missing comments and JavaDoc in readsReader class and
+ gkarrays class.
+
+2013-03-01 nphilippe
+
+ * [r2033] Version 1.3.1 with the following modifs: - integration of
+ paired reads - threading of gkIFA and gkSA - modification of
+ architecture
+
+2013-02-28 salson
+
+ * [r2032] GkArrays: Benchmarks: Evaluate performance depending on
+ the constant values
+ * [r2022] Gkarrays tests: Also perform tests on multi-threaded
+ implementation. On the variable and fixed consistency, check also
+ with changing values of k and with the stranded or non-stranded
+ implementation
+ * [r2021] GkArrays: Constant changed for the minimal size to call a
+ thread. This size has been changed according to the benchmarks
+ performed.
+
+2013-02-27 jaudoux
+
+ * [r2015] Integration of stranded for paired-end reads in values
+ array. Reverse complement the first read of each pair and keep
+ the second read of the pair as forward
+ * [r2013] Bug correction on paired-end iterator.
+
+2013-02-26 jaudoux
+
+ * [r2010] Function getPair now return -1 if data are not paired-end
+ * [r2009] - Add header to files : readsReader.h readsReader.cpp -
+ Correcting the function to reverse complement reads when using
+ paired-end - Add the function getPair(uint i), to get the read
+ associated to an other when using paired-end data
+ * [r2008] Correcting warnings display in case of paired-end. Only
+ show them the first time we run trough the reads files
+
+2013-02-25 salson
+
+ * [r2007] Bug correction: read_lengths is of type uint64_t and not
+ size_t, therefore we must specify the type uint64_t to Calloc
+ * [r2006] Tests: NDEBUG must not be set so that tests work
+
+2013-02-25 jaudoux
+
+ * [r2002] Correct the way to discard reads when using paired-end
+ files : - if one of the read has its length < k or <
+ expectedLength, both reads are discarded - Display the number of
+ tags discarded with informations about wich tag was in cause
+
+2013-02-25 nphilippe
+
+ * [r2000] change version with an integreted paired reads management
+
+2013-02-25 jaudoux
+
+ * [r1999] Add paired-end files management : - files management is
+ no longer in gkarrays.h class but in the new class readsReader.h
+ - for reading FASTA and FASTQ files, create an readReader object
+ using the simple file constructor for singleRead or double file
+ constructor for pairedEnd. - Use method begin() of readsReader in
+ order to get an generic iterator for getting reads - Don't forget
+ to delete the iterator.
+
+2013-02-24 salson
+
+ * [r1993] Tests: constant DATADIR was removed during a merge,
+ recovered
+ * [r1992] Added benchmarks to test the best values for the
+ constants
+ * [r1991] * Replaced the hard-coded value for the minimal size of
+ the array to call a thread, by a constant * Added ifndef in
+ const.h to allow defining the constant at compilation time
+
+2013-02-23 salson
+
+ * [r1990] GkArrays: getGkCFALength() now really returns GkCFA
+ length, ie. the number of distinct factors
+ * [r1989] Building GkSA: quicksort must not be launched on an empty
+ range
+ * [r1988] Tests: getGkCFALength() now really returns GkCFA length,
+ ie. the number of distinct factors
+ * [r1987] * Updated call to GkArrays constructor: we do consider
+ the dataset is stranded (otherwise the tests would fail) * Solved
+ memory leaks
+
+2013-02-18 nphilippe
+
+ * [r1973] add isLarge() and isStranded() in gkArrays.h
+ * [r1972] test for MAC configuration
+
+2013-02-17 nphilippe
+
+ * [r1970] add isLarge() and isStranded() in gkArrays.h
+ * [r1969] add isLarge() and isStranded() in gkArrays.h
+ * [r1968] add missing file
+ * [r1967] add missing file
+ * [r1966] add missing file
+ * [r1963] - cleanup libdivsufsort
+ * [r1962] - integration of gk-arrays stranded with a direct
+ construction of gkIFA and gkCFPS from values array - optimization
+ of the parallelization of gkSA
+ * [r1961] code cleanup and mv int64 -> uint64
+
+2013-02-15 salson
+
+ * [r1927] configure.ac: Added -g flag at compilation
+ * [r1926] Unit test: check consistency → corrected a memory leak
+ * [r1921] GkArrays: Actually, getGkCFALength() had no good reason
+ to return the size of nb_commons. Given its name, the function
+ must return the number of element in GkCFA
+ * [r1920] GkArrays: size_t was used for storing bits, which was a
+ pretty bad idea for 32-bit architecture
+ * [r1919] testConsistency: Changed the order of the tests. Start by
+ the query of the table, and finish by more complex queries
+
+2013-02-14 salson
+
+ * [r1918] Tests: Now compile with distcheck.
+ * [r1913] readIterator: add a isFinished() method to know when the
+ file has been completely read
+ * [r1912] GkArrays: unit tests. Added unit tests for the GkArrays,
+ to check that variable and fixed-length implementation give the
+ same result and to test that all the results in the GkArrays are
+ consistent. Some little datasets have been added. They should be
+ completed in the future.
+ * [r1911] GkArrays: the comment of getGkCFALength() was not
+ accurate enough: the number returned is not exactly the number of
+ distinct k-mers. There is one more cell, to deal with the sum
+ properly.
+ * [r1910] GkArrays: in getGkSA(), no reason for transforming the
+ P-position in Q-position: the comment said the opposite. I
+ checked that no other function would be impacted
+ * [r1908] Autotools file updates for creating version 1.1.0
+ * [r1907] GkArrays: Removed code duplication by using another class
+ that makes the choice between a large and a small array
+
+2013-02-11 nphilippe
+
+ * [r1885] bug fixed between configure.ac and doc
+ * [r1884] bug fixed between configure.ac and doc
+
+2013-02-11 salson
+
+ * [r1881] Gk-Arrays: Add solArray type to deal with arrays
+ containing 32-bit or 64-bit integers
+
+2013-02-10 salson
+
+ * [r1873] variableAndFixedLength: Int overflow when computing
+ position queried in getTagNum. Replaced int type for uintSA
+ * [r1872] variableAndFixedLength: Test getTagNum function on each
+ position of the read concatenation, check that the results are
+ correct; test read length for each read and check the result is
+ correct
+ * [r1871] Delete PRINT_VAR that were in the middle of the code!
+ Sorry for the disturbance...
+
+2013-02-09 salson
+
+ * [r1870] GkArrays test case: add output information on assert
+ failure
+ * [r1869] Disable NDEBUG macro so that asserts are evaluated
+
+2013-02-04 salson
+
+ * [r1841] Added a tests directory with a test to check that
+ variable and fixed length implementations give the same results
+ * [r1840] New assert macro for displaying a message (with variable
+ values for instance)
+ * [r1839] Code of getGkCFALength()
+ * [r1838] Added a getGkCFALength() method that returns the number
+ of elements in GkCFA
+
+2013-01-30 salson
+
+ * [r1824] Cancel previous commit and modified getTagFactor code so
+ that we can retrieve substrings of length < 4
+ * [r1823] Add a pre-condition to getTagFactor() and getTextFactor()
+ to tell that the shortest factor must be of length 4 at least
+
+2012-07-02 salson
+
+ * [r1708] Changing minor version to 1.0.1
+
+2012-06-29 salson
+
+ * [r1707] * Added comments to detail class and function roles *
+ Added static method isDiscarded in gkArrays to know if a read is
+ discarded * Bug corrected in readIterator: now we do not take
+ into account reads that should be discarded -> parameters have
+ been added to the constructors so that we can determine if a read
+ must be discarded
+
+2012-05-18 salson
+
+ * [r1631] Updated documentation: remove reference to four library
+ versions and added procedure for installing
+ * [r1630] Adding Doxygen configuration file
+ * [r1629] Do not display anymore the bit version. That is
+ meaningless now.
+ * [r1628] Bug: kseq/kseq.h was not included with 'make install'.
+ Solved.
+
+2012-04-26 nphilippe
+
+ * [r1613] bug fixed about the limit between large et small SA
+
+2012-04-25 nphilippe
+
+ * [r1612] bug fixed about the limit between large et small SA
+
+2012-04-05 salson
+
+ * [r1591] Solved memory leaks
+
+2012-04-04 salson
+
+ * [r1581] * Bug correction: in readIterator finished was not
+ modified properly * Bug correction: in readIterator seq was not
+ initialised properly (first item was missed)
+
+2012-04-03 nphilippe
+
+ * [r1578]
+ * [r1577] add iterators in input file
+
+2012-04-02 nphilippe
+
+ * [r1566] one lib for all version (fixed,variable,32bits,64 bits)
+ * [r1565] one lib for all version (fixed,variable,32bits,64 bits)
+ * [r1564] one lib for all version (fixed,variable,32bits,64 bits)
+ * [r1563] one lib for all version (fixed,variable,32bits,64 bits)
+ * [r1562] one lib for all version (fixed,variable,32bits,64 bits)
+ * [r1561] one lib for all version (fixed,variable,32bits,64 bits)
+ * [r1560] one lib for all version (fixed,variable,32bits,64 bits)
+ * [r1558] pour le developpement
+ * [r1550] update svn struct
+
+2011-07-11 salson
+
+ * [r781] Release 0.2.0
+ * [r780] Not the newest
+
+2011-07-10 salson
+
+ * [r775] Right version of the release (hopefully)
+ * [r768] Release 0.2.0 of GkArrays
+ * [r767] Gk arrays tag directory
+
diff --git a/src/libGkArrays/INSTALL b/src/libGkArrays/INSTALL
new file mode 100644
index 0000000..7d1c323
--- /dev/null
+++ b/src/libGkArrays/INSTALL
@@ -0,0 +1,365 @@
+Installation Instructions
+*************************
+
+Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005,
+2006, 2007, 2008, 2009 Free Software Foundation, Inc.
+
+ Copying and distribution of this file, with or without modification,
+are permitted in any medium without royalty provided the copyright
+notice and this notice are preserved. This file is offered as-is,
+without warranty of any kind.
+
+Basic Installation
+==================
+
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+=====================
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+ ./configure CC=c99 CFLAGS=-g LIBS=-lposix
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+====================================
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+==================
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+
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+================
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+
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diff --git a/src/libGkArrays/Makefile.am b/src/libGkArrays/Makefile.am
new file mode 100644
index 0000000..e6cd9e8
--- /dev/null
+++ b/src/libGkArrays/Makefile.am
@@ -0,0 +1,191 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thierry LECROQ <thierry.lecroq at univ-rouen.fr> #
+# Martine LÉONARD <Martine.Leonard at univ-rouen.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie de la librairie Gk-arrays. #
+# #
+# La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de #
+# lectures de séquences issues du séquençage haut-débit. #
+# #
+# Ce logiciel est régi par la licence CeCILL-C soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
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+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the Gk-arrays library. #
+# #
+# The Gk-arrays library aims at indexing k-factors from a huge set of #
+# sequencing reads. #
+# #
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+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
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+# Ce fichier fait partie de la librairie Gk-arrays. #
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+# La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de #
+# lectures de séquences issues du séquençage haut-débit. #
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diff --git a/src/libGkArrays/NEWS b/src/libGkArrays/NEWS
new file mode 100644
index 0000000..e69de29
diff --git a/src/libGkArrays/README b/src/libGkArrays/README
new file mode 100644
index 0000000..a8bea90
--- /dev/null
+++ b/src/libGkArrays/README
@@ -0,0 +1,143 @@
+Gk-arrays - Package
+
+Gk-arrays are a data structure to index the k-mers in a collection of
+reads (short sequences provided by Next Generation Sequencing
+machines). Similarly, the well known suffix tree is a data structure
+to index the (sub)words of a text. Given a parameter k, the Gk-arrays
+index all k-mers occurrences in the input collection of reads (given
+as a file with lot of short sequences, some of them can be identical,
+but have different names). Once the index is built and kept in memory,
+the program can asks queries to the index.
+
+An example of query type, among 7 types: given a position in the
+collection, compute the number of reads that share this
+k-mer. Gk-arrays are designed to answer multiple, even numerous
+(thousands, millions of) queries. Compared to other possible
+solutions, like hash tables, Gk-arrays are efficient in terms of
+memory and both of construction and query time.
+
+Reads are qproduced by sequencing machines in the context of genomics projects (for genome, transcriptome, epigenome, meta-genome or meta-transcriptome sequencing). Millions of reads can be in a single run, and this represents a novel challenge for indexing algorithms.
+
+Gk-arrays accept files where all reads have the same length, but also
+files with reads of varying length. The files can be in FASTA/FASTQ
+format.
+
+Gk-arrays - Source code
+
+This page provides access to the code of a C++ library to build and
+use Gk-arrays. This code is freely available under a GPL-compliant
+CeCILL-C license.
+
+Gk-arrays - Installation
+
+For installing the library just type:
+configure
+make
+(sudo make install)
+
+After the compilation succeded you can find a more complete documentation
+inside the doc directory.
+
+-------------------------------------------------------------------------
+
+Copyright © 2010-2013 -- IRB/INSERM
+ (Institut de Recherches en Biothérapie /
+ Institut National de la Santé et de la Recherche
+ Médicale)
+ LIFL/INRIA
+ (Laboratoire d'Informatique Fondamentale de
+ Lille / Institut National de Recherche en
+ Informatique et Automatique)
+ LIRMM/CNRS
+ (Laboratoire d'Informatique, de Robotique et de
+ Microélectronique de Montpellier /
+ Centre National de la Recherche Scientifique)
+ LITIS
+ (Laboratoire d'Informatique, du Traitement de
+ l'Information et des Systèmes).
+
+
+Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+ Mikaël SALSON <mikael.salson at lifl.fr>
+ Thierry LECROQ <thierry.lecroq at univ-rouen.fr>
+ Martine LÉONARD <Martine.Leonard at univ-rouen.fr>
+ Éric RIVALS <eric.rivals at lirmm.fr>
+
+Programmeurs
+ /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+ Mikaël SALSON <mikael.salson at lifl.fr>
+with additional contribution for the packaging of:
+ Alban MANCHERON <alban.mancheron at lirmm.fr>
+
+Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr>
+
+-------------------------------------------------------------------------
+
+Ce fichier fait partie de la librairie Gk-arrays.
+
+La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de
+lectures de séquences issues du séquençage haut-débit.
+
+Ce logiciel est régi par la licence CeCILL-C soumise au droit français et
+respectant les principes de diffusion des logiciels libres. Vous pouvez
+utiliser, modifier et/ou redistribuer ce programme sous les conditions de
+la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur
+le site "http://www.cecill.info".
+
+En contrepartie de l'accessibilité au code source et des droits de copie,
+de modification et de redistribution accordés par cette licence, il n'est
+offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons,
+seule une responsabilité restreinte pèse sur l'auteur du programme, le
+titulaire des droits patrimoniaux et les concédants successifs.
+
+À cet égard l'attention de l'utilisateur est attirée sur les risques
+associés au chargement, à l'utilisation, à la modification et/ou au
+développement et à la reproduction du logiciel par l'utilisateur étant
+donné sa spécificité de logiciel libre, qui peut le rendre complexe à
+manipuler et qui le réserve donc à des développeurs et des professionnels
+avertis possédant des connaissances informatiques approfondies. Les
+utilisateurs sont donc invités à charger et tester l'adéquation du
+logiciel à leurs besoins dans des conditions permettant d'assurer la
+sécurité de leurs systêmes et ou de leurs données et, plus généralement,
+à l'utiliser et l'exploiter dans les mêmes conditions de sécurité.
+
+Le fait que vous puissiez accéder à cet en-tête signifie que vous avez
+pris connaissance de la licence CeCILL-C, et que vous en avez accepté les
+termes.
+
+-------------------------------------------------------------------------
+
+This File is part of the Gk-arrays library.
+
+The Gk-arrays library aims at indexing k-factors from a huge set of
+sequencing reads.
+
+This software is governed by the CeCILL-C license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL-C
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the same
+conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL-C license and that you accept its terms.
+
+-------------------------------------------------------------------------
+
+Les commentaires sont les bienvenus/Comments are welcome.
diff --git a/src/libGkArrays/aclocal.m4 b/src/libGkArrays/aclocal.m4
new file mode 100644
index 0000000..c5edfb1
--- /dev/null
+++ b/src/libGkArrays/aclocal.m4
@@ -0,0 +1,8917 @@
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+# VARNAME. Any other value will be used directly.
+m4_define([_LT_DECL],
+[lt_if_append_uniq([lt_decl_varnames], [$2], [, ],
+ [lt_dict_add_subkey([lt_decl_dict], [$2], [libtool_name],
+ [m4_ifval([$1], [$1], [$2])])
+ lt_dict_add_subkey([lt_decl_dict], [$2], [value], [$3])
+ m4_ifval([$4],
+ [lt_dict_add_subkey([lt_decl_dict], [$2], [description], [$4])])
+ lt_dict_add_subkey([lt_decl_dict], [$2],
+ [tagged?], [m4_ifval([$5], [yes], [no])])])
+])
+
+
+# _LT_TAGDECL([CONFIGNAME], VARNAME, VALUE, [DESCRIPTION])
+# --------------------------------------------------------
+m4_define([_LT_TAGDECL], [_LT_DECL([$1], [$2], [$3], [$4], [yes])])
+
+
+# lt_decl_tag_varnames([SEPARATOR], [VARNAME1...])
+# ------------------------------------------------
+m4_define([lt_decl_tag_varnames],
+[_lt_decl_filter([tagged?], [yes], $@)])
+
+
+# _lt_decl_filter(SUBKEY, VALUE, [SEPARATOR], [VARNAME1..])
+# ---------------------------------------------------------
+m4_define([_lt_decl_filter],
+[m4_case([$#],
+ [0], [m4_fatal([$0: too few arguments: $#])],
+ [1], [m4_fatal([$0: too few arguments: $#: $1])],
+ [2], [lt_dict_filter([lt_decl_dict], [$1], [$2], [], lt_decl_varnames)],
+ [3], [lt_dict_filter([lt_decl_dict], [$1], [$2], [$3], lt_decl_varnames)],
+ [lt_dict_filter([lt_decl_dict], $@)])[]dnl
+])
+
+
+# lt_decl_quote_varnames([SEPARATOR], [VARNAME1...])
+# --------------------------------------------------
+m4_define([lt_decl_quote_varnames],
+[_lt_decl_filter([value], [1], $@)])
+
+
+# lt_decl_dquote_varnames([SEPARATOR], [VARNAME1...])
+# ---------------------------------------------------
+m4_define([lt_decl_dquote_varnames],
+[_lt_decl_filter([value], [2], $@)])
+
+
+# lt_decl_varnames_tagged([SEPARATOR], [VARNAME1...])
+# ---------------------------------------------------
+m4_define([lt_decl_varnames_tagged],
+[m4_assert([$# <= 2])dnl
+_$0(m4_quote(m4_default([$1], [[, ]])),
+ m4_ifval([$2], [[$2]], [m4_dquote(lt_decl_tag_varnames)]),
+ m4_split(m4_normalize(m4_quote(_LT_TAGS)), [ ]))])
+m4_define([_lt_decl_varnames_tagged],
+[m4_ifval([$3], [lt_combine([$1], [$2], [_], $3)])])
+
+
+# lt_decl_all_varnames([SEPARATOR], [VARNAME1...])
+# ------------------------------------------------
+m4_define([lt_decl_all_varnames],
+[_$0(m4_quote(m4_default([$1], [[, ]])),
+ m4_if([$2], [],
+ m4_quote(lt_decl_varnames),
+ m4_quote(m4_shift($@))))[]dnl
+])
+m4_define([_lt_decl_all_varnames],
+[lt_join($@, lt_decl_varnames_tagged([$1],
+ lt_decl_tag_varnames([[, ]], m4_shift($@))))dnl
+])
+
+
+# _LT_CONFIG_STATUS_DECLARE([VARNAME])
+# ------------------------------------
+# Quote a variable value, and forward it to `config.status' so that its
+# declaration there will have the same value as in `configure'. VARNAME
+# must have a single quote delimited value for this to work.
+m4_define([_LT_CONFIG_STATUS_DECLARE],
+[$1='`$ECHO "X$][$1" | $Xsed -e "$delay_single_quote_subst"`'])
+
+
+# _LT_CONFIG_STATUS_DECLARATIONS
+# ------------------------------
+# We delimit libtool config variables with single quotes, so when
+# we write them to config.status, we have to be sure to quote all
+# embedded single quotes properly. In configure, this macro expands
+# each variable declared with _LT_DECL (and _LT_TAGDECL) into:
+#
+# <var>='`$ECHO "X$<var>" | $Xsed -e "$delay_single_quote_subst"`'
+m4_defun([_LT_CONFIG_STATUS_DECLARATIONS],
+[m4_foreach([_lt_var], m4_quote(lt_decl_all_varnames),
+ [m4_n([_LT_CONFIG_STATUS_DECLARE(_lt_var)])])])
+
+
+# _LT_LIBTOOL_TAGS
+# ----------------
+# Output comment and list of tags supported by the script
+m4_defun([_LT_LIBTOOL_TAGS],
+[_LT_FORMAT_COMMENT([The names of the tagged configurations supported by this script])dnl
+available_tags="_LT_TAGS"dnl
+])
+
+
+# _LT_LIBTOOL_DECLARE(VARNAME, [TAG])
+# -----------------------------------
+# Extract the dictionary values for VARNAME (optionally with TAG) and
+# expand to a commented shell variable setting:
+#
+# # Some comment about what VAR is for.
+# visible_name=$lt_internal_name
+m4_define([_LT_LIBTOOL_DECLARE],
+[_LT_FORMAT_COMMENT(m4_quote(lt_dict_fetch([lt_decl_dict], [$1],
+ [description])))[]dnl
+m4_pushdef([_libtool_name],
+ m4_quote(lt_dict_fetch([lt_decl_dict], [$1], [libtool_name])))[]dnl
+m4_case(m4_quote(lt_dict_fetch([lt_decl_dict], [$1], [value])),
+ [0], [_libtool_name=[$]$1],
+ [1], [_libtool_name=$lt_[]$1],
+ [2], [_libtool_name=$lt_[]$1],
+ [_libtool_name=lt_dict_fetch([lt_decl_dict], [$1], [value])])[]dnl
+m4_ifval([$2], [_$2])[]m4_popdef([_libtool_name])[]dnl
+])
+
+
+# _LT_LIBTOOL_CONFIG_VARS
+# -----------------------
+# Produce commented declarations of non-tagged libtool config variables
+# suitable for insertion in the LIBTOOL CONFIG section of the `libtool'
+# script. Tagged libtool config variables (even for the LIBTOOL CONFIG
+# section) are produced by _LT_LIBTOOL_TAG_VARS.
+m4_defun([_LT_LIBTOOL_CONFIG_VARS],
+[m4_foreach([_lt_var],
+ m4_quote(_lt_decl_filter([tagged?], [no], [], lt_decl_varnames)),
+ [m4_n([_LT_LIBTOOL_DECLARE(_lt_var)])])])
+
+
+# _LT_LIBTOOL_TAG_VARS(TAG)
+# -------------------------
+m4_define([_LT_LIBTOOL_TAG_VARS],
+[m4_foreach([_lt_var], m4_quote(lt_decl_tag_varnames),
+ [m4_n([_LT_LIBTOOL_DECLARE(_lt_var, [$1])])])])
+
+
+# _LT_TAGVAR(VARNAME, [TAGNAME])
+# ------------------------------
+m4_define([_LT_TAGVAR], [m4_ifval([$2], [$1_$2], [$1])])
+
+
+# _LT_CONFIG_COMMANDS
+# -------------------
+# Send accumulated output to $CONFIG_STATUS. Thanks to the lists of
+# variables for single and double quote escaping we saved from calls
+# to _LT_DECL, we can put quote escaped variables declarations
+# into `config.status', and then the shell code to quote escape them in
+# for loops in `config.status'. Finally, any additional code accumulated
+# from calls to _LT_CONFIG_LIBTOOL_INIT is expanded.
+m4_defun([_LT_CONFIG_COMMANDS],
+[AC_PROVIDE_IFELSE([LT_OUTPUT],
+ dnl If the libtool generation code has been placed in $CONFIG_LT,
+ dnl instead of duplicating it all over again into config.status,
+ dnl then we will have config.status run $CONFIG_LT later, so it
+ dnl needs to know what name is stored there:
+ [AC_CONFIG_COMMANDS([libtool],
+ [$SHELL $CONFIG_LT || AS_EXIT(1)], [CONFIG_LT='$CONFIG_LT'])],
+ dnl If the libtool generation code is destined for config.status,
+ dnl expand the accumulated commands and init code now:
+ [AC_CONFIG_COMMANDS([libtool],
+ [_LT_OUTPUT_LIBTOOL_COMMANDS], [_LT_OUTPUT_LIBTOOL_COMMANDS_INIT])])
+])#_LT_CONFIG_COMMANDS
+
+
+# Initialize.
+m4_define([_LT_OUTPUT_LIBTOOL_COMMANDS_INIT],
+[
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+sed_quote_subst='$sed_quote_subst'
+double_quote_subst='$double_quote_subst'
+delay_variable_subst='$delay_variable_subst'
+_LT_CONFIG_STATUS_DECLARATIONS
+LTCC='$LTCC'
+LTCFLAGS='$LTCFLAGS'
+compiler='$compiler_DEFAULT'
+
+# Quote evaled strings.
+for var in lt_decl_all_varnames([[ \
+]], lt_decl_quote_varnames); do
+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in
+ *[[\\\\\\\`\\"\\\$]]*)
+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$sed_quote_subst\\"\\\`\\\\\\""
+ ;;
+ *)
+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\""
+ ;;
+ esac
+done
+
+# Double-quote double-evaled strings.
+for var in lt_decl_all_varnames([[ \
+]], lt_decl_dquote_varnames); do
+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in
+ *[[\\\\\\\`\\"\\\$]]*)
+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$double_quote_subst\\" -e \\"\\\$sed_quote_subst\\" -e \\"\\\$delay_variable_subst\\"\\\`\\\\\\""
+ ;;
+ *)
+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\""
+ ;;
+ esac
+done
+
+# Fix-up fallback echo if it was mangled by the above quoting rules.
+case \$lt_ECHO in
+*'\\\[$]0 --fallback-echo"')dnl "
+ lt_ECHO=\`\$ECHO "X\$lt_ECHO" | \$Xsed -e 's/\\\\\\\\\\\\\\\[$]0 --fallback-echo"\[$]/\[$]0 --fallback-echo"/'\`
+ ;;
+esac
+
+_LT_OUTPUT_LIBTOOL_INIT
+])
+
+
+# LT_OUTPUT
+# ---------
+# This macro allows early generation of the libtool script (before
+# AC_OUTPUT is called), incase it is used in configure for compilation
+# tests.
+AC_DEFUN([LT_OUTPUT],
+[: ${CONFIG_LT=./config.lt}
+AC_MSG_NOTICE([creating $CONFIG_LT])
+cat >"$CONFIG_LT" <<_LTEOF
+#! $SHELL
+# Generated by $as_me.
+# Run this file to recreate a libtool stub with the current configuration.
+
+lt_cl_silent=false
+SHELL=\${CONFIG_SHELL-$SHELL}
+_LTEOF
+
+cat >>"$CONFIG_LT" <<\_LTEOF
+AS_SHELL_SANITIZE
+_AS_PREPARE
+
+exec AS_MESSAGE_FD>&1
+exec AS_MESSAGE_LOG_FD>>config.log
+{
+ echo
+ AS_BOX([Running $as_me.])
+} >&AS_MESSAGE_LOG_FD
+
+lt_cl_help="\
+\`$as_me' creates a local libtool stub from the current configuration,
+for use in further configure time tests before the real libtool is
+generated.
+
+Usage: $[0] [[OPTIONS]]
+
+ -h, --help print this help, then exit
+ -V, --version print version number, then exit
+ -q, --quiet do not print progress messages
+ -d, --debug don't remove temporary files
+
+Report bugs to <bug-libtool at gnu.org>."
+
+lt_cl_version="\
+m4_ifset([AC_PACKAGE_NAME], [AC_PACKAGE_NAME ])config.lt[]dnl
+m4_ifset([AC_PACKAGE_VERSION], [ AC_PACKAGE_VERSION])
+configured by $[0], generated by m4_PACKAGE_STRING.
+
+Copyright (C) 2008 Free Software Foundation, Inc.
+This config.lt script is free software; the Free Software Foundation
+gives unlimited permision to copy, distribute and modify it."
+
+while test $[#] != 0
+do
+ case $[1] in
+ --version | --v* | -V )
+ echo "$lt_cl_version"; exit 0 ;;
+ --help | --h* | -h )
+ echo "$lt_cl_help"; exit 0 ;;
+ --debug | --d* | -d )
+ debug=: ;;
+ --quiet | --q* | --silent | --s* | -q )
+ lt_cl_silent=: ;;
+
+ -*) AC_MSG_ERROR([unrecognized option: $[1]
+Try \`$[0] --help' for more information.]) ;;
+
+ *) AC_MSG_ERROR([unrecognized argument: $[1]
+Try \`$[0] --help' for more information.]) ;;
+ esac
+ shift
+done
+
+if $lt_cl_silent; then
+ exec AS_MESSAGE_FD>/dev/null
+fi
+_LTEOF
+
+cat >>"$CONFIG_LT" <<_LTEOF
+_LT_OUTPUT_LIBTOOL_COMMANDS_INIT
+_LTEOF
+
+cat >>"$CONFIG_LT" <<\_LTEOF
+AC_MSG_NOTICE([creating $ofile])
+_LT_OUTPUT_LIBTOOL_COMMANDS
+AS_EXIT(0)
+_LTEOF
+chmod +x "$CONFIG_LT"
+
+# configure is writing to config.log, but config.lt does its own redirection,
+# appending to config.log, which fails on DOS, as config.log is still kept
+# open by configure. Here we exec the FD to /dev/null, effectively closing
+# config.log, so it can be properly (re)opened and appended to by config.lt.
+if test "$no_create" != yes; then
+ lt_cl_success=:
+ test "$silent" = yes &&
+ lt_config_lt_args="$lt_config_lt_args --quiet"
+ exec AS_MESSAGE_LOG_FD>/dev/null
+ $SHELL "$CONFIG_LT" $lt_config_lt_args || lt_cl_success=false
+ exec AS_MESSAGE_LOG_FD>>config.log
+ $lt_cl_success || AS_EXIT(1)
+fi
+])# LT_OUTPUT
+
+
+# _LT_CONFIG(TAG)
+# ---------------
+# If TAG is the built-in tag, create an initial libtool script with a
+# default configuration from the untagged config vars. Otherwise add code
+# to config.status for appending the configuration named by TAG from the
+# matching tagged config vars.
+m4_defun([_LT_CONFIG],
+[m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+_LT_CONFIG_SAVE_COMMANDS([
+ m4_define([_LT_TAG], m4_if([$1], [], [C], [$1]))dnl
+ m4_if(_LT_TAG, [C], [
+ # See if we are running on zsh, and set the options which allow our
+ # commands through without removal of \ escapes.
+ if test -n "${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+ fi
+
+ cfgfile="${ofile}T"
+ trap "$RM \"$cfgfile\"; exit 1" 1 2 15
+ $RM "$cfgfile"
+
+ cat <<_LT_EOF >> "$cfgfile"
+#! $SHELL
+
+# `$ECHO "$ofile" | sed 's%^.*/%%'` - Provide generalized library-building support services.
+# Generated automatically by $as_me ($PACKAGE$TIMESTAMP) $VERSION
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+# NOTE: Changes made to this file will be lost: look at ltmain.sh.
+#
+_LT_COPYING
+_LT_LIBTOOL_TAGS
+
+# ### BEGIN LIBTOOL CONFIG
+_LT_LIBTOOL_CONFIG_VARS
+_LT_LIBTOOL_TAG_VARS
+# ### END LIBTOOL CONFIG
+
+_LT_EOF
+
+ case $host_os in
+ aix3*)
+ cat <<\_LT_EOF >> "$cfgfile"
+# AIX sometimes has problems with the GCC collect2 program. For some
+# reason, if we set the COLLECT_NAMES environment variable, the problems
+# vanish in a puff of smoke.
+if test "X${COLLECT_NAMES+set}" != Xset; then
+ COLLECT_NAMES=
+ export COLLECT_NAMES
+fi
+_LT_EOF
+ ;;
+ esac
+
+ _LT_PROG_LTMAIN
+
+ # We use sed instead of cat because bash on DJGPP gets confused if
+ # if finds mixed CR/LF and LF-only lines. Since sed operates in
+ # text mode, it properly converts lines to CR/LF. This bash problem
+ # is reportedly fixed, but why not run on old versions too?
+ sed '/^# Generated shell functions inserted here/q' "$ltmain" >> "$cfgfile" \
+ || (rm -f "$cfgfile"; exit 1)
+
+ _LT_PROG_XSI_SHELLFNS
+
+ sed -n '/^# Generated shell functions inserted here/,$p' "$ltmain" >> "$cfgfile" \
+ || (rm -f "$cfgfile"; exit 1)
+
+ mv -f "$cfgfile" "$ofile" ||
+ (rm -f "$ofile" && cp "$cfgfile" "$ofile" && rm -f "$cfgfile")
+ chmod +x "$ofile"
+],
+[cat <<_LT_EOF >> "$ofile"
+
+dnl Unfortunately we have to use $1 here, since _LT_TAG is not expanded
+dnl in a comment (ie after a #).
+# ### BEGIN LIBTOOL TAG CONFIG: $1
+_LT_LIBTOOL_TAG_VARS(_LT_TAG)
+# ### END LIBTOOL TAG CONFIG: $1
+_LT_EOF
+])dnl /m4_if
+],
+[m4_if([$1], [], [
+ PACKAGE='$PACKAGE'
+ VERSION='$VERSION'
+ TIMESTAMP='$TIMESTAMP'
+ RM='$RM'
+ ofile='$ofile'], [])
+])dnl /_LT_CONFIG_SAVE_COMMANDS
+])# _LT_CONFIG
+
+
+# LT_SUPPORTED_TAG(TAG)
+# ---------------------
+# Trace this macro to discover what tags are supported by the libtool
+# --tag option, using:
+# autoconf --trace 'LT_SUPPORTED_TAG:$1'
+AC_DEFUN([LT_SUPPORTED_TAG], [])
+
+
+# C support is built-in for now
+m4_define([_LT_LANG_C_enabled], [])
+m4_define([_LT_TAGS], [])
+
+
+# LT_LANG(LANG)
+# -------------
+# Enable libtool support for the given language if not already enabled.
+AC_DEFUN([LT_LANG],
+[AC_BEFORE([$0], [LT_OUTPUT])dnl
+m4_case([$1],
+ [C], [_LT_LANG(C)],
+ [C++], [_LT_LANG(CXX)],
+ [Java], [_LT_LANG(GCJ)],
+ [Fortran 77], [_LT_LANG(F77)],
+ [Fortran], [_LT_LANG(FC)],
+ [Windows Resource], [_LT_LANG(RC)],
+ [m4_ifdef([_LT_LANG_]$1[_CONFIG],
+ [_LT_LANG($1)],
+ [m4_fatal([$0: unsupported language: "$1"])])])dnl
+])# LT_LANG
+
+
+# _LT_LANG(LANGNAME)
+# ------------------
+m4_defun([_LT_LANG],
+[m4_ifdef([_LT_LANG_]$1[_enabled], [],
+ [LT_SUPPORTED_TAG([$1])dnl
+ m4_append([_LT_TAGS], [$1 ])dnl
+ m4_define([_LT_LANG_]$1[_enabled], [])dnl
+ _LT_LANG_$1_CONFIG($1)])dnl
+])# _LT_LANG
+
+
+# _LT_LANG_DEFAULT_CONFIG
+# -----------------------
+m4_defun([_LT_LANG_DEFAULT_CONFIG],
+[AC_PROVIDE_IFELSE([AC_PROG_CXX],
+ [LT_LANG(CXX)],
+ [m4_define([AC_PROG_CXX], defn([AC_PROG_CXX])[LT_LANG(CXX)])])
+
+AC_PROVIDE_IFELSE([AC_PROG_F77],
+ [LT_LANG(F77)],
+ [m4_define([AC_PROG_F77], defn([AC_PROG_F77])[LT_LANG(F77)])])
+
+AC_PROVIDE_IFELSE([AC_PROG_FC],
+ [LT_LANG(FC)],
+ [m4_define([AC_PROG_FC], defn([AC_PROG_FC])[LT_LANG(FC)])])
+
+dnl The call to [A][M_PROG_GCJ] is quoted like that to stop aclocal
+dnl pulling things in needlessly.
+AC_PROVIDE_IFELSE([AC_PROG_GCJ],
+ [LT_LANG(GCJ)],
+ [AC_PROVIDE_IFELSE([A][M_PROG_GCJ],
+ [LT_LANG(GCJ)],
+ [AC_PROVIDE_IFELSE([LT_PROG_GCJ],
+ [LT_LANG(GCJ)],
+ [m4_ifdef([AC_PROG_GCJ],
+ [m4_define([AC_PROG_GCJ], defn([AC_PROG_GCJ])[LT_LANG(GCJ)])])
+ m4_ifdef([A][M_PROG_GCJ],
+ [m4_define([A][M_PROG_GCJ], defn([A][M_PROG_GCJ])[LT_LANG(GCJ)])])
+ m4_ifdef([LT_PROG_GCJ],
+ [m4_define([LT_PROG_GCJ], defn([LT_PROG_GCJ])[LT_LANG(GCJ)])])])])])
+
+AC_PROVIDE_IFELSE([LT_PROG_RC],
+ [LT_LANG(RC)],
+ [m4_define([LT_PROG_RC], defn([LT_PROG_RC])[LT_LANG(RC)])])
+])# _LT_LANG_DEFAULT_CONFIG
+
+# Obsolete macros:
+AU_DEFUN([AC_LIBTOOL_CXX], [LT_LANG(C++)])
+AU_DEFUN([AC_LIBTOOL_F77], [LT_LANG(Fortran 77)])
+AU_DEFUN([AC_LIBTOOL_FC], [LT_LANG(Fortran)])
+AU_DEFUN([AC_LIBTOOL_GCJ], [LT_LANG(Java)])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_CXX], [])
+dnl AC_DEFUN([AC_LIBTOOL_F77], [])
+dnl AC_DEFUN([AC_LIBTOOL_FC], [])
+dnl AC_DEFUN([AC_LIBTOOL_GCJ], [])
+
+
+# _LT_TAG_COMPILER
+# ----------------
+m4_defun([_LT_TAG_COMPILER],
+[AC_REQUIRE([AC_PROG_CC])dnl
+
+_LT_DECL([LTCC], [CC], [1], [A C compiler])dnl
+_LT_DECL([LTCFLAGS], [CFLAGS], [1], [LTCC compiler flags])dnl
+_LT_TAGDECL([CC], [compiler], [1], [A language specific compiler])dnl
+_LT_TAGDECL([with_gcc], [GCC], [0], [Is the compiler the GNU compiler?])dnl
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+])# _LT_TAG_COMPILER
+
+
+# _LT_COMPILER_BOILERPLATE
+# ------------------------
+# Check for compiler boilerplate output or warnings with
+# the simple compiler test code.
+m4_defun([_LT_COMPILER_BOILERPLATE],
+[m4_require([_LT_DECL_SED])dnl
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$RM conftest*
+])# _LT_COMPILER_BOILERPLATE
+
+
+# _LT_LINKER_BOILERPLATE
+# ----------------------
+# Check for linker boilerplate output or warnings with
+# the simple link test code.
+m4_defun([_LT_LINKER_BOILERPLATE],
+[m4_require([_LT_DECL_SED])dnl
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$RM -r conftest*
+])# _LT_LINKER_BOILERPLATE
+
+# _LT_REQUIRED_DARWIN_CHECKS
+# -------------------------
+m4_defun_once([_LT_REQUIRED_DARWIN_CHECKS],[
+ case $host_os in
+ rhapsody* | darwin*)
+ AC_CHECK_TOOL([DSYMUTIL], [dsymutil], [:])
+ AC_CHECK_TOOL([NMEDIT], [nmedit], [:])
+ AC_CHECK_TOOL([LIPO], [lipo], [:])
+ AC_CHECK_TOOL([OTOOL], [otool], [:])
+ AC_CHECK_TOOL([OTOOL64], [otool64], [:])
+ _LT_DECL([], [DSYMUTIL], [1],
+ [Tool to manipulate archived DWARF debug symbol files on Mac OS X])
+ _LT_DECL([], [NMEDIT], [1],
+ [Tool to change global to local symbols on Mac OS X])
+ _LT_DECL([], [LIPO], [1],
+ [Tool to manipulate fat objects and archives on Mac OS X])
+ _LT_DECL([], [OTOOL], [1],
+ [ldd/readelf like tool for Mach-O binaries on Mac OS X])
+ _LT_DECL([], [OTOOL64], [1],
+ [ldd/readelf like tool for 64 bit Mach-O binaries on Mac OS X 10.4])
+
+ AC_CACHE_CHECK([for -single_module linker flag],[lt_cv_apple_cc_single_mod],
+ [lt_cv_apple_cc_single_mod=no
+ if test -z "${LT_MULTI_MODULE}"; then
+ # By default we will add the -single_module flag. You can override
+ # by either setting the environment variable LT_MULTI_MODULE
+ # non-empty at configure time, or by adding -multi_module to the
+ # link flags.
+ rm -rf libconftest.dylib*
+ echo "int foo(void){return 1;}" > conftest.c
+ echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+-dynamiclib -Wl,-single_module conftest.c" >&AS_MESSAGE_LOG_FD
+ $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+ -dynamiclib -Wl,-single_module conftest.c 2>conftest.err
+ _lt_result=$?
+ if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then
+ lt_cv_apple_cc_single_mod=yes
+ else
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ fi
+ rm -rf libconftest.dylib*
+ rm -f conftest.*
+ fi])
+ AC_CACHE_CHECK([for -exported_symbols_list linker flag],
+ [lt_cv_ld_exported_symbols_list],
+ [lt_cv_ld_exported_symbols_list=no
+ save_LDFLAGS=$LDFLAGS
+ echo "_main" > conftest.sym
+ LDFLAGS="$LDFLAGS -Wl,-exported_symbols_list,conftest.sym"
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([],[])],
+ [lt_cv_ld_exported_symbols_list=yes],
+ [lt_cv_ld_exported_symbols_list=no])
+ LDFLAGS="$save_LDFLAGS"
+ ])
+ case $host_os in
+ rhapsody* | darwin1.[[012]])
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}suppress' ;;
+ darwin1.*)
+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+ darwin*) # darwin 5.x on
+ # if running on 10.5 or later, the deployment target defaults
+ # to the OS version, if on x86, and 10.4, the deployment
+ # target defaults to 10.4. Don't you love it?
+ case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in
+ 10.0,*86*-darwin8*|10.0,*-darwin[[91]]*)
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+ 10.[[012]]*)
+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+ 10.*)
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+ esac
+ ;;
+ esac
+ if test "$lt_cv_apple_cc_single_mod" = "yes"; then
+ _lt_dar_single_mod='$single_module'
+ fi
+ if test "$lt_cv_ld_exported_symbols_list" = "yes"; then
+ _lt_dar_export_syms=' ${wl}-exported_symbols_list,$output_objdir/${libname}-symbols.expsym'
+ else
+ _lt_dar_export_syms='~$NMEDIT -s $output_objdir/${libname}-symbols.expsym ${lib}'
+ fi
+ if test "$DSYMUTIL" != ":"; then
+ _lt_dsymutil='~$DSYMUTIL $lib || :'
+ else
+ _lt_dsymutil=
+ fi
+ ;;
+ esac
+])
+
+
+# _LT_DARWIN_LINKER_FEATURES
+# --------------------------
+# Checks for linker and compiler features on darwin
+m4_defun([_LT_DARWIN_LINKER_FEATURES],
+[
+ m4_require([_LT_REQUIRED_DARWIN_CHECKS])
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_automatic, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=''
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(allow_undefined_flag, $1)="$_lt_dar_allow_undefined"
+ case $cc_basename in
+ ifort*) _lt_dar_can_shared=yes ;;
+ *) _lt_dar_can_shared=$GCC ;;
+ esac
+ if test "$_lt_dar_can_shared" = "yes"; then
+ output_verbose_link_cmd=echo
+ _LT_TAGVAR(archive_cmds, $1)="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}"
+ _LT_TAGVAR(module_cmds, $1)="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}"
+ _LT_TAGVAR(archive_expsym_cmds, $1)="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}"
+ _LT_TAGVAR(module_expsym_cmds, $1)="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}"
+ m4_if([$1], [CXX],
+[ if test "$lt_cv_apple_cc_single_mod" != "yes"; then
+ _LT_TAGVAR(archive_cmds, $1)="\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dsymutil}"
+ _LT_TAGVAR(archive_expsym_cmds, $1)="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dar_export_syms}${_lt_dsymutil}"
+ fi
+],[])
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+])
+
+# _LT_SYS_MODULE_PATH_AIX
+# -----------------------
+# Links a minimal program and checks the executable
+# for the system default hardcoded library path. In most cases,
+# this is /usr/lib:/lib, but when the MPI compilers are used
+# the location of the communication and MPI libs are included too.
+# If we don't find anything, use the default library path according
+# to the aix ld manual.
+m4_defun([_LT_SYS_MODULE_PATH_AIX],
+[m4_require([_LT_DECL_SED])dnl
+AC_LINK_IFELSE(AC_LANG_PROGRAM,[
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi],[])
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+])# _LT_SYS_MODULE_PATH_AIX
+
+
+# _LT_SHELL_INIT(ARG)
+# -------------------
+m4_define([_LT_SHELL_INIT],
+[ifdef([AC_DIVERSION_NOTICE],
+ [AC_DIVERT_PUSH(AC_DIVERSION_NOTICE)],
+ [AC_DIVERT_PUSH(NOTICE)])
+$1
+AC_DIVERT_POP
+])# _LT_SHELL_INIT
+
+
+# _LT_PROG_ECHO_BACKSLASH
+# -----------------------
+# Add some code to the start of the generated configure script which
+# will find an echo command which doesn't interpret backslashes.
+m4_defun([_LT_PROG_ECHO_BACKSLASH],
+[_LT_SHELL_INIT([
+# Check that we are running under the correct shell.
+SHELL=${CONFIG_SHELL-/bin/sh}
+
+case X$lt_ECHO in
+X*--fallback-echo)
+ # Remove one level of quotation (which was required for Make).
+ ECHO=`echo "$lt_ECHO" | sed 's,\\\\\[$]\\[$]0,'[$]0','`
+ ;;
+esac
+
+ECHO=${lt_ECHO-echo}
+if test "X[$]1" = X--no-reexec; then
+ # Discard the --no-reexec flag, and continue.
+ shift
+elif test "X[$]1" = X--fallback-echo; then
+ # Avoid inline document here, it may be left over
+ :
+elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' ; then
+ # Yippee, $ECHO works!
+ :
+else
+ # Restart under the correct shell.
+ exec $SHELL "[$]0" --no-reexec ${1+"[$]@"}
+fi
+
+if test "X[$]1" = X--fallback-echo; then
+ # used as fallback echo
+ shift
+ cat <<_LT_EOF
+[$]*
+_LT_EOF
+ exit 0
+fi
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test -z "$lt_ECHO"; then
+ if test "X${echo_test_string+set}" != Xset; then
+ # find a string as large as possible, as long as the shell can cope with it
+ for cmd in 'sed 50q "[$]0"' 'sed 20q "[$]0"' 'sed 10q "[$]0"' 'sed 2q "[$]0"' 'echo test'; do
+ # expected sizes: less than 2Kb, 1Kb, 512 bytes, 16 bytes, ...
+ if { echo_test_string=`eval $cmd`; } 2>/dev/null &&
+ { test "X$echo_test_string" = "X$echo_test_string"; } 2>/dev/null
+ then
+ break
+ fi
+ done
+ fi
+
+ if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ :
+ else
+ # The Solaris, AIX, and Digital Unix default echo programs unquote
+ # backslashes. This makes it impossible to quote backslashes using
+ # echo "$something" | sed 's/\\/\\\\/g'
+ #
+ # So, first we look for a working echo in the user's PATH.
+
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for dir in $PATH /usr/ucb; do
+ IFS="$lt_save_ifs"
+ if (test -f $dir/echo || test -f $dir/echo$ac_exeext) &&
+ test "X`($dir/echo '\t') 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`($dir/echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ ECHO="$dir/echo"
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+
+ if test "X$ECHO" = Xecho; then
+ # We didn't find a better echo, so look for alternatives.
+ if test "X`{ print -r '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ print -r "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ # This shell has a builtin print -r that does the trick.
+ ECHO='print -r'
+ elif { test -f /bin/ksh || test -f /bin/ksh$ac_exeext; } &&
+ test "X$CONFIG_SHELL" != X/bin/ksh; then
+ # If we have ksh, try running configure again with it.
+ ORIGINAL_CONFIG_SHELL=${CONFIG_SHELL-/bin/sh}
+ export ORIGINAL_CONFIG_SHELL
+ CONFIG_SHELL=/bin/ksh
+ export CONFIG_SHELL
+ exec $CONFIG_SHELL "[$]0" --no-reexec ${1+"[$]@"}
+ else
+ # Try using printf.
+ ECHO='printf %s\n'
+ if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ # Cool, printf works
+ :
+ elif echo_testing_string=`($ORIGINAL_CONFIG_SHELL "[$]0" --fallback-echo '\t') 2>/dev/null` &&
+ test "X$echo_testing_string" = 'X\t' &&
+ echo_testing_string=`($ORIGINAL_CONFIG_SHELL "[$]0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ CONFIG_SHELL=$ORIGINAL_CONFIG_SHELL
+ export CONFIG_SHELL
+ SHELL="$CONFIG_SHELL"
+ export SHELL
+ ECHO="$CONFIG_SHELL [$]0 --fallback-echo"
+ elif echo_testing_string=`($CONFIG_SHELL "[$]0" --fallback-echo '\t') 2>/dev/null` &&
+ test "X$echo_testing_string" = 'X\t' &&
+ echo_testing_string=`($CONFIG_SHELL "[$]0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ ECHO="$CONFIG_SHELL [$]0 --fallback-echo"
+ else
+ # maybe with a smaller string...
+ prev=:
+
+ for cmd in 'echo test' 'sed 2q "[$]0"' 'sed 10q "[$]0"' 'sed 20q "[$]0"' 'sed 50q "[$]0"'; do
+ if { test "X$echo_test_string" = "X`eval $cmd`"; } 2>/dev/null
+ then
+ break
+ fi
+ prev="$cmd"
+ done
+
+ if test "$prev" != 'sed 50q "[$]0"'; then
+ echo_test_string=`eval $prev`
+ export echo_test_string
+ exec ${ORIGINAL_CONFIG_SHELL-${CONFIG_SHELL-/bin/sh}} "[$]0" ${1+"[$]@"}
+ else
+ # Oops. We lost completely, so just stick with echo.
+ ECHO=echo
+ fi
+ fi
+ fi
+ fi
+ fi
+fi
+
+# Copy echo and quote the copy suitably for passing to libtool from
+# the Makefile, instead of quoting the original, which is used later.
+lt_ECHO=$ECHO
+if test "X$lt_ECHO" = "X$CONFIG_SHELL [$]0 --fallback-echo"; then
+ lt_ECHO="$CONFIG_SHELL \\\$\[$]0 --fallback-echo"
+fi
+
+AC_SUBST(lt_ECHO)
+])
+_LT_DECL([], [SHELL], [1], [Shell to use when invoking shell scripts])
+_LT_DECL([], [ECHO], [1],
+ [An echo program that does not interpret backslashes])
+])# _LT_PROG_ECHO_BACKSLASH
+
+
+# _LT_ENABLE_LOCK
+# ---------------
+m4_defun([_LT_ENABLE_LOCK],
+[AC_ARG_ENABLE([libtool-lock],
+ [AS_HELP_STRING([--disable-libtool-lock],
+ [avoid locking (might break parallel builds)])])
+test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes
+
+# Some flags need to be propagated to the compiler or linker for good
+# libtool support.
+case $host in
+ia64-*-hpux*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *ELF-32*)
+ HPUX_IA64_MODE="32"
+ ;;
+ *ELF-64*)
+ HPUX_IA64_MODE="64"
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+*-*-irix6*)
+ # Find out which ABI we are using.
+ echo '[#]line __oline__ "configure"' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *32-bit*)
+ LD="${LD-ld} -melf32bsmip"
+ ;;
+ *N32*)
+ LD="${LD-ld} -melf32bmipn32"
+ ;;
+ *64-bit*)
+ LD="${LD-ld} -melf64bmip"
+ ;;
+ esac
+ else
+ case `/usr/bin/file conftest.$ac_objext` in
+ *32-bit*)
+ LD="${LD-ld} -32"
+ ;;
+ *N32*)
+ LD="${LD-ld} -n32"
+ ;;
+ *64-bit*)
+ LD="${LD-ld} -64"
+ ;;
+ esac
+ fi
+ fi
+ rm -rf conftest*
+ ;;
+
+x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \
+s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ case `/usr/bin/file conftest.o` in
+ *32-bit*)
+ case $host in
+ x86_64-*kfreebsd*-gnu)
+ LD="${LD-ld} -m elf_i386_fbsd"
+ ;;
+ x86_64-*linux*)
+ LD="${LD-ld} -m elf_i386"
+ ;;
+ ppc64-*linux*|powerpc64-*linux*)
+ LD="${LD-ld} -m elf32ppclinux"
+ ;;
+ s390x-*linux*)
+ LD="${LD-ld} -m elf_s390"
+ ;;
+ sparc64-*linux*)
+ LD="${LD-ld} -m elf32_sparc"
+ ;;
+ esac
+ ;;
+ *64-bit*)
+ case $host in
+ x86_64-*kfreebsd*-gnu)
+ LD="${LD-ld} -m elf_x86_64_fbsd"
+ ;;
+ x86_64-*linux*)
+ LD="${LD-ld} -m elf_x86_64"
+ ;;
+ ppc*-*linux*|powerpc*-*linux*)
+ LD="${LD-ld} -m elf64ppc"
+ ;;
+ s390*-*linux*|s390*-*tpf*)
+ LD="${LD-ld} -m elf64_s390"
+ ;;
+ sparc*-*linux*)
+ LD="${LD-ld} -m elf64_sparc"
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+
+*-*-sco3.2v5*)
+ # On SCO OpenServer 5, we need -belf to get full-featured binaries.
+ SAVE_CFLAGS="$CFLAGS"
+ CFLAGS="$CFLAGS -belf"
+ AC_CACHE_CHECK([whether the C compiler needs -belf], lt_cv_cc_needs_belf,
+ [AC_LANG_PUSH(C)
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[]],[[]])],[lt_cv_cc_needs_belf=yes],[lt_cv_cc_needs_belf=no])
+ AC_LANG_POP])
+ if test x"$lt_cv_cc_needs_belf" != x"yes"; then
+ # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf
+ CFLAGS="$SAVE_CFLAGS"
+ fi
+ ;;
+sparc*-*solaris*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ case `/usr/bin/file conftest.o` in
+ *64-bit*)
+ case $lt_cv_prog_gnu_ld in
+ yes*) LD="${LD-ld} -m elf64_sparc" ;;
+ *)
+ if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then
+ LD="${LD-ld} -64"
+ fi
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+esac
+
+need_locks="$enable_libtool_lock"
+])# _LT_ENABLE_LOCK
+
+
+# _LT_CMD_OLD_ARCHIVE
+# -------------------
+m4_defun([_LT_CMD_OLD_ARCHIVE],
+[AC_CHECK_TOOL(AR, ar, false)
+test -z "$AR" && AR=ar
+test -z "$AR_FLAGS" && AR_FLAGS=cru
+_LT_DECL([], [AR], [1], [The archiver])
+_LT_DECL([], [AR_FLAGS], [1])
+
+AC_CHECK_TOOL(STRIP, strip, :)
+test -z "$STRIP" && STRIP=:
+_LT_DECL([], [STRIP], [1], [A symbol stripping program])
+
+AC_CHECK_TOOL(RANLIB, ranlib, :)
+test -z "$RANLIB" && RANLIB=:
+_LT_DECL([], [RANLIB], [1],
+ [Commands used to install an old-style archive])
+
+# Determine commands to create old-style static archives.
+old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs'
+old_postinstall_cmds='chmod 644 $oldlib'
+old_postuninstall_cmds=
+
+if test -n "$RANLIB"; then
+ case $host_os in
+ openbsd*)
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib"
+ ;;
+ *)
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib"
+ ;;
+ esac
+ old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib"
+fi
+_LT_DECL([], [old_postinstall_cmds], [2])
+_LT_DECL([], [old_postuninstall_cmds], [2])
+_LT_TAGDECL([], [old_archive_cmds], [2],
+ [Commands used to build an old-style archive])
+])# _LT_CMD_OLD_ARCHIVE
+
+
+# _LT_COMPILER_OPTION(MESSAGE, VARIABLE-NAME, FLAGS,
+# [OUTPUT-FILE], [ACTION-SUCCESS], [ACTION-FAILURE])
+# ----------------------------------------------------------------
+# Check whether the given compiler option works
+AC_DEFUN([_LT_COMPILER_OPTION],
+[m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_SED])dnl
+AC_CACHE_CHECK([$1], [$2],
+ [$2=no
+ m4_if([$4], , [ac_outfile=conftest.$ac_objext], [ac_outfile=$4])
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+ lt_compiler_flag="$3"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ # The option is referenced via a variable to avoid confusing sed.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [[^ ]]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:__oline__: $lt_compile\"" >&AS_MESSAGE_LOG_FD)
+ (eval "$lt_compile" 2>conftest.err)
+ ac_status=$?
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ echo "$as_me:__oline__: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
+ if (exit $ac_status) && test -s "$ac_outfile"; then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings other than the usual output.
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+ $2=yes
+ fi
+ fi
+ $RM conftest*
+])
+
+if test x"[$]$2" = xyes; then
+ m4_if([$5], , :, [$5])
+else
+ m4_if([$6], , :, [$6])
+fi
+])# _LT_COMPILER_OPTION
+
+# Old name:
+AU_ALIAS([AC_LIBTOOL_COMPILER_OPTION], [_LT_COMPILER_OPTION])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_COMPILER_OPTION], [])
+
+
+# _LT_LINKER_OPTION(MESSAGE, VARIABLE-NAME, FLAGS,
+# [ACTION-SUCCESS], [ACTION-FAILURE])
+# ----------------------------------------------------
+# Check whether the given linker option works
+AC_DEFUN([_LT_LINKER_OPTION],
+[m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_SED])dnl
+AC_CACHE_CHECK([$1], [$2],
+ [$2=no
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS $3"
+ echo "$lt_simple_link_test_code" > conftest.$ac_ext
+ if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+ # The linker can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ if test -s conftest.err; then
+ # Append any errors to the config.log.
+ cat conftest.err 1>&AS_MESSAGE_LOG_FD
+ $ECHO "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if diff conftest.exp conftest.er2 >/dev/null; then
+ $2=yes
+ fi
+ else
+ $2=yes
+ fi
+ fi
+ $RM -r conftest*
+ LDFLAGS="$save_LDFLAGS"
+])
+
+if test x"[$]$2" = xyes; then
+ m4_if([$4], , :, [$4])
+else
+ m4_if([$5], , :, [$5])
+fi
+])# _LT_LINKER_OPTION
+
+# Old name:
+AU_ALIAS([AC_LIBTOOL_LINKER_OPTION], [_LT_LINKER_OPTION])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_LINKER_OPTION], [])
+
+
+# LT_CMD_MAX_LEN
+#---------------
+AC_DEFUN([LT_CMD_MAX_LEN],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+# find the maximum length of command line arguments
+AC_MSG_CHECKING([the maximum length of command line arguments])
+AC_CACHE_VAL([lt_cv_sys_max_cmd_len], [dnl
+ i=0
+ teststring="ABCD"
+
+ case $build_os in
+ msdosdjgpp*)
+ # On DJGPP, this test can blow up pretty badly due to problems in libc
+ # (any single argument exceeding 2000 bytes causes a buffer overrun
+ # during glob expansion). Even if it were fixed, the result of this
+ # check would be larger than it should be.
+ lt_cv_sys_max_cmd_len=12288; # 12K is about right
+ ;;
+
+ gnu*)
+ # Under GNU Hurd, this test is not required because there is
+ # no limit to the length of command line arguments.
+ # Libtool will interpret -1 as no limit whatsoever
+ lt_cv_sys_max_cmd_len=-1;
+ ;;
+
+ cygwin* | mingw* | cegcc*)
+ # On Win9x/ME, this test blows up -- it succeeds, but takes
+ # about 5 minutes as the teststring grows exponentially.
+ # Worse, since 9x/ME are not pre-emptively multitasking,
+ # you end up with a "frozen" computer, even though with patience
+ # the test eventually succeeds (with a max line length of 256k).
+ # Instead, let's just punt: use the minimum linelength reported by
+ # all of the supported platforms: 8192 (on NT/2K/XP).
+ lt_cv_sys_max_cmd_len=8192;
+ ;;
+
+ amigaos*)
+ # On AmigaOS with pdksh, this test takes hours, literally.
+ # So we just punt and use a minimum line length of 8192.
+ lt_cv_sys_max_cmd_len=8192;
+ ;;
+
+ netbsd* | freebsd* | openbsd* | darwin* | dragonfly*)
+ # This has been around since 386BSD, at least. Likely further.
+ if test -x /sbin/sysctl; then
+ lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax`
+ elif test -x /usr/sbin/sysctl; then
+ lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax`
+ else
+ lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs
+ fi
+ # And add a safety zone
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+ ;;
+
+ interix*)
+ # We know the value 262144 and hardcode it with a safety zone (like BSD)
+ lt_cv_sys_max_cmd_len=196608
+ ;;
+
+ osf*)
+ # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure
+ # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not
+ # nice to cause kernel panics so lets avoid the loop below.
+ # First set a reasonable default.
+ lt_cv_sys_max_cmd_len=16384
+ #
+ if test -x /sbin/sysconfig; then
+ case `/sbin/sysconfig -q proc exec_disable_arg_limit` in
+ *1*) lt_cv_sys_max_cmd_len=-1 ;;
+ esac
+ fi
+ ;;
+ sco3.2v5*)
+ lt_cv_sys_max_cmd_len=102400
+ ;;
+ sysv5* | sco5v6* | sysv4.2uw2*)
+ kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null`
+ if test -n "$kargmax"; then
+ lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[[ ]]//'`
+ else
+ lt_cv_sys_max_cmd_len=32768
+ fi
+ ;;
+ *)
+ lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null`
+ if test -n "$lt_cv_sys_max_cmd_len"; then
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+ else
+ # Make teststring a little bigger before we do anything with it.
+ # a 1K string should be a reasonable start.
+ for i in 1 2 3 4 5 6 7 8 ; do
+ teststring=$teststring$teststring
+ done
+ SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}}
+ # If test is not a shell built-in, we'll probably end up computing a
+ # maximum length that is only half of the actual maximum length, but
+ # we can't tell.
+ while { test "X"`$SHELL [$]0 --fallback-echo "X$teststring$teststring" 2>/dev/null` \
+ = "XX$teststring$teststring"; } >/dev/null 2>&1 &&
+ test $i != 17 # 1/2 MB should be enough
+ do
+ i=`expr $i + 1`
+ teststring=$teststring$teststring
+ done
+ # Only check the string length outside the loop.
+ lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1`
+ teststring=
+ # Add a significant safety factor because C++ compilers can tack on
+ # massive amounts of additional arguments before passing them to the
+ # linker. It appears as though 1/2 is a usable value.
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2`
+ fi
+ ;;
+ esac
+])
+if test -n $lt_cv_sys_max_cmd_len ; then
+ AC_MSG_RESULT($lt_cv_sys_max_cmd_len)
+else
+ AC_MSG_RESULT(none)
+fi
+max_cmd_len=$lt_cv_sys_max_cmd_len
+_LT_DECL([], [max_cmd_len], [0],
+ [What is the maximum length of a command?])
+])# LT_CMD_MAX_LEN
+
+# Old name:
+AU_ALIAS([AC_LIBTOOL_SYS_MAX_CMD_LEN], [LT_CMD_MAX_LEN])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_SYS_MAX_CMD_LEN], [])
+
+
+# _LT_HEADER_DLFCN
+# ----------------
+m4_defun([_LT_HEADER_DLFCN],
+[AC_CHECK_HEADERS([dlfcn.h], [], [], [AC_INCLUDES_DEFAULT])dnl
+])# _LT_HEADER_DLFCN
+
+
+# _LT_TRY_DLOPEN_SELF (ACTION-IF-TRUE, ACTION-IF-TRUE-W-USCORE,
+# ACTION-IF-FALSE, ACTION-IF-CROSS-COMPILING)
+# ----------------------------------------------------------------
+m4_defun([_LT_TRY_DLOPEN_SELF],
+[m4_require([_LT_HEADER_DLFCN])dnl
+if test "$cross_compiling" = yes; then :
+ [$4]
+else
+ lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
+ lt_status=$lt_dlunknown
+ cat > conftest.$ac_ext <<_LT_EOF
+[#line __oline__ "configure"
+#include "confdefs.h"
+
+#if HAVE_DLFCN_H
+#include <dlfcn.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef RTLD_GLOBAL
+# define LT_DLGLOBAL RTLD_GLOBAL
+#else
+# ifdef DL_GLOBAL
+# define LT_DLGLOBAL DL_GLOBAL
+# else
+# define LT_DLGLOBAL 0
+# endif
+#endif
+
+/* We may have to define LT_DLLAZY_OR_NOW in the command line if we
+ find out it does not work in some platform. */
+#ifndef LT_DLLAZY_OR_NOW
+# ifdef RTLD_LAZY
+# define LT_DLLAZY_OR_NOW RTLD_LAZY
+# else
+# ifdef DL_LAZY
+# define LT_DLLAZY_OR_NOW DL_LAZY
+# else
+# ifdef RTLD_NOW
+# define LT_DLLAZY_OR_NOW RTLD_NOW
+# else
+# ifdef DL_NOW
+# define LT_DLLAZY_OR_NOW DL_NOW
+# else
+# define LT_DLLAZY_OR_NOW 0
+# endif
+# endif
+# endif
+# endif
+#endif
+
+void fnord() { int i=42;}
+int main ()
+{
+ void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW);
+ int status = $lt_dlunknown;
+
+ if (self)
+ {
+ if (dlsym (self,"fnord")) status = $lt_dlno_uscore;
+ else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore;
+ /* dlclose (self); */
+ }
+ else
+ puts (dlerror ());
+
+ return status;
+}]
+_LT_EOF
+ if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext} 2>/dev/null; then
+ (./conftest; exit; ) >&AS_MESSAGE_LOG_FD 2>/dev/null
+ lt_status=$?
+ case x$lt_status in
+ x$lt_dlno_uscore) $1 ;;
+ x$lt_dlneed_uscore) $2 ;;
+ x$lt_dlunknown|x*) $3 ;;
+ esac
+ else :
+ # compilation failed
+ $3
+ fi
+fi
+rm -fr conftest*
+])# _LT_TRY_DLOPEN_SELF
+
+
+# LT_SYS_DLOPEN_SELF
+# ------------------
+AC_DEFUN([LT_SYS_DLOPEN_SELF],
+[m4_require([_LT_HEADER_DLFCN])dnl
+if test "x$enable_dlopen" != xyes; then
+ enable_dlopen=unknown
+ enable_dlopen_self=unknown
+ enable_dlopen_self_static=unknown
+else
+ lt_cv_dlopen=no
+ lt_cv_dlopen_libs=
+
+ case $host_os in
+ beos*)
+ lt_cv_dlopen="load_add_on"
+ lt_cv_dlopen_libs=
+ lt_cv_dlopen_self=yes
+ ;;
+
+ mingw* | pw32* | cegcc*)
+ lt_cv_dlopen="LoadLibrary"
+ lt_cv_dlopen_libs=
+ ;;
+
+ cygwin*)
+ lt_cv_dlopen="dlopen"
+ lt_cv_dlopen_libs=
+ ;;
+
+ darwin*)
+ # if libdl is installed we need to link against it
+ AC_CHECK_LIB([dl], [dlopen],
+ [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"],[
+ lt_cv_dlopen="dyld"
+ lt_cv_dlopen_libs=
+ lt_cv_dlopen_self=yes
+ ])
+ ;;
+
+ *)
+ AC_CHECK_FUNC([shl_load],
+ [lt_cv_dlopen="shl_load"],
+ [AC_CHECK_LIB([dld], [shl_load],
+ [lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-ldld"],
+ [AC_CHECK_FUNC([dlopen],
+ [lt_cv_dlopen="dlopen"],
+ [AC_CHECK_LIB([dl], [dlopen],
+ [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"],
+ [AC_CHECK_LIB([svld], [dlopen],
+ [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld"],
+ [AC_CHECK_LIB([dld], [dld_link],
+ [lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-ldld"])
+ ])
+ ])
+ ])
+ ])
+ ])
+ ;;
+ esac
+
+ if test "x$lt_cv_dlopen" != xno; then
+ enable_dlopen=yes
+ else
+ enable_dlopen=no
+ fi
+
+ case $lt_cv_dlopen in
+ dlopen)
+ save_CPPFLAGS="$CPPFLAGS"
+ test "x$ac_cv_header_dlfcn_h" = xyes && CPPFLAGS="$CPPFLAGS -DHAVE_DLFCN_H"
+
+ save_LDFLAGS="$LDFLAGS"
+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\"
+
+ save_LIBS="$LIBS"
+ LIBS="$lt_cv_dlopen_libs $LIBS"
+
+ AC_CACHE_CHECK([whether a program can dlopen itself],
+ lt_cv_dlopen_self, [dnl
+ _LT_TRY_DLOPEN_SELF(
+ lt_cv_dlopen_self=yes, lt_cv_dlopen_self=yes,
+ lt_cv_dlopen_self=no, lt_cv_dlopen_self=cross)
+ ])
+
+ if test "x$lt_cv_dlopen_self" = xyes; then
+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\"
+ AC_CACHE_CHECK([whether a statically linked program can dlopen itself],
+ lt_cv_dlopen_self_static, [dnl
+ _LT_TRY_DLOPEN_SELF(
+ lt_cv_dlopen_self_static=yes, lt_cv_dlopen_self_static=yes,
+ lt_cv_dlopen_self_static=no, lt_cv_dlopen_self_static=cross)
+ ])
+ fi
+
+ CPPFLAGS="$save_CPPFLAGS"
+ LDFLAGS="$save_LDFLAGS"
+ LIBS="$save_LIBS"
+ ;;
+ esac
+
+ case $lt_cv_dlopen_self in
+ yes|no) enable_dlopen_self=$lt_cv_dlopen_self ;;
+ *) enable_dlopen_self=unknown ;;
+ esac
+
+ case $lt_cv_dlopen_self_static in
+ yes|no) enable_dlopen_self_static=$lt_cv_dlopen_self_static ;;
+ *) enable_dlopen_self_static=unknown ;;
+ esac
+fi
+_LT_DECL([dlopen_support], [enable_dlopen], [0],
+ [Whether dlopen is supported])
+_LT_DECL([dlopen_self], [enable_dlopen_self], [0],
+ [Whether dlopen of programs is supported])
+_LT_DECL([dlopen_self_static], [enable_dlopen_self_static], [0],
+ [Whether dlopen of statically linked programs is supported])
+])# LT_SYS_DLOPEN_SELF
+
+# Old name:
+AU_ALIAS([AC_LIBTOOL_DLOPEN_SELF], [LT_SYS_DLOPEN_SELF])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_DLOPEN_SELF], [])
+
+
+# _LT_COMPILER_C_O([TAGNAME])
+# ---------------------------
+# Check to see if options -c and -o are simultaneously supported by compiler.
+# This macro does not hard code the compiler like AC_PROG_CC_C_O.
+m4_defun([_LT_COMPILER_C_O],
+[m4_require([_LT_DECL_SED])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_TAG_COMPILER])dnl
+AC_CACHE_CHECK([if $compiler supports -c -o file.$ac_objext],
+ [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)],
+ [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [[^ ]]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:__oline__: $lt_compile\"" >&AS_MESSAGE_LOG_FD)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&AS_MESSAGE_LOG_FD
+ echo "$as_me:__oline__: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ _LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=yes
+ fi
+ fi
+ chmod u+w . 2>&AS_MESSAGE_LOG_FD
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+])
+_LT_TAGDECL([compiler_c_o], [lt_cv_prog_compiler_c_o], [1],
+ [Does compiler simultaneously support -c and -o options?])
+])# _LT_COMPILER_C_O
+
+
+# _LT_COMPILER_FILE_LOCKS([TAGNAME])
+# ----------------------------------
+# Check to see if we can do hard links to lock some files if needed
+m4_defun([_LT_COMPILER_FILE_LOCKS],
+[m4_require([_LT_ENABLE_LOCK])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+_LT_COMPILER_C_O([$1])
+
+hard_links="nottested"
+if test "$_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)" = no && test "$need_locks" != no; then
+ # do not overwrite the value of need_locks provided by the user
+ AC_MSG_CHECKING([if we can lock with hard links])
+ hard_links=yes
+ $RM conftest*
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ touch conftest.a
+ ln conftest.a conftest.b 2>&5 || hard_links=no
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ AC_MSG_RESULT([$hard_links])
+ if test "$hard_links" = no; then
+ AC_MSG_WARN([`$CC' does not support `-c -o', so `make -j' may be unsafe])
+ need_locks=warn
+ fi
+else
+ need_locks=no
+fi
+_LT_DECL([], [need_locks], [1], [Must we lock files when doing compilation?])
+])# _LT_COMPILER_FILE_LOCKS
+
+
+# _LT_CHECK_OBJDIR
+# ----------------
+m4_defun([_LT_CHECK_OBJDIR],
+[AC_CACHE_CHECK([for objdir], [lt_cv_objdir],
+[rm -f .libs 2>/dev/null
+mkdir .libs 2>/dev/null
+if test -d .libs; then
+ lt_cv_objdir=.libs
+else
+ # MS-DOS does not allow filenames that begin with a dot.
+ lt_cv_objdir=_libs
+fi
+rmdir .libs 2>/dev/null])
+objdir=$lt_cv_objdir
+_LT_DECL([], [objdir], [0],
+ [The name of the directory that contains temporary libtool files])dnl
+m4_pattern_allow([LT_OBJDIR])dnl
+AC_DEFINE_UNQUOTED(LT_OBJDIR, "$lt_cv_objdir/",
+ [Define to the sub-directory in which libtool stores uninstalled libraries.])
+])# _LT_CHECK_OBJDIR
+
+
+# _LT_LINKER_HARDCODE_LIBPATH([TAGNAME])
+# --------------------------------------
+# Check hardcoding attributes.
+m4_defun([_LT_LINKER_HARDCODE_LIBPATH],
+[AC_MSG_CHECKING([how to hardcode library paths into programs])
+_LT_TAGVAR(hardcode_action, $1)=
+if test -n "$_LT_TAGVAR(hardcode_libdir_flag_spec, $1)" ||
+ test -n "$_LT_TAGVAR(runpath_var, $1)" ||
+ test "X$_LT_TAGVAR(hardcode_automatic, $1)" = "Xyes" ; then
+
+ # We can hardcode non-existent directories.
+ if test "$_LT_TAGVAR(hardcode_direct, $1)" != no &&
+ # If the only mechanism to avoid hardcoding is shlibpath_var, we
+ # have to relink, otherwise we might link with an installed library
+ # when we should be linking with a yet-to-be-installed one
+ ## test "$_LT_TAGVAR(hardcode_shlibpath_var, $1)" != no &&
+ test "$_LT_TAGVAR(hardcode_minus_L, $1)" != no; then
+ # Linking always hardcodes the temporary library directory.
+ _LT_TAGVAR(hardcode_action, $1)=relink
+ else
+ # We can link without hardcoding, and we can hardcode nonexisting dirs.
+ _LT_TAGVAR(hardcode_action, $1)=immediate
+ fi
+else
+ # We cannot hardcode anything, or else we can only hardcode existing
+ # directories.
+ _LT_TAGVAR(hardcode_action, $1)=unsupported
+fi
+AC_MSG_RESULT([$_LT_TAGVAR(hardcode_action, $1)])
+
+if test "$_LT_TAGVAR(hardcode_action, $1)" = relink ||
+ test "$_LT_TAGVAR(inherit_rpath, $1)" = yes; then
+ # Fast installation is not supported
+ enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+ test "$enable_shared" = no; then
+ # Fast installation is not necessary
+ enable_fast_install=needless
+fi
+_LT_TAGDECL([], [hardcode_action], [0],
+ [How to hardcode a shared library path into an executable])
+])# _LT_LINKER_HARDCODE_LIBPATH
+
+
+# _LT_CMD_STRIPLIB
+# ----------------
+m4_defun([_LT_CMD_STRIPLIB],
+[m4_require([_LT_DECL_EGREP])
+striplib=
+old_striplib=
+AC_MSG_CHECKING([whether stripping libraries is possible])
+if test -n "$STRIP" && $STRIP -V 2>&1 | $GREP "GNU strip" >/dev/null; then
+ test -z "$old_striplib" && old_striplib="$STRIP --strip-debug"
+ test -z "$striplib" && striplib="$STRIP --strip-unneeded"
+ AC_MSG_RESULT([yes])
+else
+# FIXME - insert some real tests, host_os isn't really good enough
+ case $host_os in
+ darwin*)
+ if test -n "$STRIP" ; then
+ striplib="$STRIP -x"
+ old_striplib="$STRIP -S"
+ AC_MSG_RESULT([yes])
+ else
+ AC_MSG_RESULT([no])
+ fi
+ ;;
+ *)
+ AC_MSG_RESULT([no])
+ ;;
+ esac
+fi
+_LT_DECL([], [old_striplib], [1], [Commands to strip libraries])
+_LT_DECL([], [striplib], [1])
+])# _LT_CMD_STRIPLIB
+
+
+# _LT_SYS_DYNAMIC_LINKER([TAG])
+# -----------------------------
+# PORTME Fill in your ld.so characteristics
+m4_defun([_LT_SYS_DYNAMIC_LINKER],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+m4_require([_LT_DECL_EGREP])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_OBJDUMP])dnl
+m4_require([_LT_DECL_SED])dnl
+AC_MSG_CHECKING([dynamic linker characteristics])
+m4_if([$1],
+ [], [
+if test "$GCC" = yes; then
+ case $host_os in
+ darwin*) lt_awk_arg="/^libraries:/,/LR/" ;;
+ *) lt_awk_arg="/^libraries:/" ;;
+ esac
+ lt_search_path_spec=`$CC -print-search-dirs | awk $lt_awk_arg | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$lt_search_path_spec" | $GREP ';' >/dev/null ; then
+ # if the path contains ";" then we assume it to be the separator
+ # otherwise default to the standard path separator (i.e. ":") - it is
+ # assumed that no part of a normal pathname contains ";" but that should
+ # okay in the real world where ";" in dirpaths is itself problematic.
+ lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ # Ok, now we have the path, separated by spaces, we can step through it
+ # and add multilib dir if necessary.
+ lt_tmp_lt_search_path_spec=
+ lt_multi_os_dir=`$CC $CPPFLAGS $CFLAGS $LDFLAGS -print-multi-os-directory 2>/dev/null`
+ for lt_sys_path in $lt_search_path_spec; do
+ if test -d "$lt_sys_path/$lt_multi_os_dir"; then
+ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path/$lt_multi_os_dir"
+ else
+ test -d "$lt_sys_path" && \
+ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path"
+ fi
+ done
+ lt_search_path_spec=`$ECHO $lt_tmp_lt_search_path_spec | awk '
+BEGIN {RS=" "; FS="/|\n";} {
+ lt_foo="";
+ lt_count=0;
+ for (lt_i = NF; lt_i > 0; lt_i--) {
+ if ($lt_i != "" && $lt_i != ".") {
+ if ($lt_i == "..") {
+ lt_count++;
+ } else {
+ if (lt_count == 0) {
+ lt_foo="/" $lt_i lt_foo;
+ } else {
+ lt_count--;
+ }
+ }
+ }
+ }
+ if (lt_foo != "") { lt_freq[[lt_foo]]++; }
+ if (lt_freq[[lt_foo]] == 1) { print lt_foo; }
+}'`
+ sys_lib_search_path_spec=`$ECHO $lt_search_path_spec`
+else
+ sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib"
+fi])
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+ shlibpath_var=LIBPATH
+
+ # AIX 3 has no versioning support, so we append a major version to the name.
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+
+aix[[4-9]]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ hardcode_into_libs=yes
+ if test "$host_cpu" = ia64; then
+ # AIX 5 supports IA64
+ library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ else
+ # With GCC up to 2.95.x, collect2 would create an import file
+ # for dependence libraries. The import file would start with
+ # the line `#! .'. This would cause the generated library to
+ # depend on `.', always an invalid library. This was fixed in
+ # development snapshots of GCC prior to 3.0.
+ case $host_os in
+ aix4 | aix4.[[01]] | aix4.[[01]].*)
+ if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+ echo ' yes '
+ echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then
+ :
+ else
+ can_build_shared=no
+ fi
+ ;;
+ esac
+ # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+ # soname into executable. Probably we can add versioning support to
+ # collect2, so additional links can be useful in future.
+ if test "$aix_use_runtimelinking" = yes; then
+ # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+ # instead of lib<name>.a to let people know that these are not
+ # typical AIX shared libraries.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ else
+ # We preserve .a as extension for shared libraries through AIX4.2
+ # and later when we are not doing run time linking.
+ library_names_spec='${libname}${release}.a $libname.a'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ fi
+ shlibpath_var=LIBPATH
+ fi
+ ;;
+
+amigaos*)
+ case $host_cpu in
+ powerpc)
+ # Since July 2007 AmigaOS4 officially supports .so libraries.
+ # When compiling the executable, add -use-dynld -Lsobjs: to the compileline.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ ;;
+ m68k)
+ library_names_spec='$libname.ixlibrary $libname.a'
+ # Create ${libname}_ixlibrary.a entries in /sys/libs.
+ finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$ECHO "X$lib" | $Xsed -e '\''s%^.*/\([[^/]]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+ ;;
+ esac
+ ;;
+
+beos*)
+ library_names_spec='${libname}${shared_ext}'
+ dynamic_linker="$host_os ld.so"
+ shlibpath_var=LIBRARY_PATH
+ ;;
+
+bsdi[[45]]*)
+ version_type=linux
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+ sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+ # the default ld.so.conf also contains /usr/contrib/lib and
+ # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+ # libtool to hard-code these into programs
+ ;;
+
+cygwin* | mingw* | pw32* | cegcc*)
+ version_type=windows
+ shrext_cmds=".dll"
+ need_version=no
+ need_lib_prefix=no
+
+ case $GCC,$host_os in
+ yes,cygwin* | yes,mingw* | yes,pw32* | yes,cegcc*)
+ library_names_spec='$libname.dll.a'
+ # DLL is installed to $(libdir)/../bin by postinstall_cmds
+ postinstall_cmds='base_file=`basename \${file}`~
+ dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i; echo \$dlname'\''`~
+ dldir=$destdir/`dirname \$dlpath`~
+ test -d \$dldir || mkdir -p \$dldir~
+ $install_prog $dir/$dlname \$dldir/$dlname~
+ chmod a+x \$dldir/$dlname~
+ if test -n '\''$stripme'\'' && test -n '\''$striplib'\''; then
+ eval '\''$striplib \$dldir/$dlname'\'' || exit \$?;
+ fi'
+ postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+ dlpath=$dir/\$dldll~
+ $RM \$dlpath'
+ shlibpath_overrides_runpath=yes
+
+ case $host_os in
+ cygwin*)
+ # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+ soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+ ;;
+ mingw* | cegcc*)
+ # MinGW DLLs use traditional 'lib' prefix
+ soname_spec='${libname}`echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec=`$CC -print-search-dirs | $GREP "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$sys_lib_search_path_spec" | [$GREP ';[c-zC-Z]:/' >/dev/null]; then
+ # It is most probably a Windows format PATH printed by
+ # mingw gcc, but we are running on Cygwin. Gcc prints its search
+ # path with ; separators, and with drive letters. We can handle the
+ # drive letters (cygwin fileutils understands them), so leave them,
+ # especially as we might pass files found there to a mingw objdump,
+ # which wouldn't understand a cygwinified path. Ahh.
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ ;;
+ pw32*)
+ # pw32 DLLs use 'pw' prefix rather than 'lib'
+ library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}'
+ ;;
+ esac
+ ;;
+
+ *)
+ library_names_spec='${libname}`echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext} $libname.lib'
+ ;;
+ esac
+ dynamic_linker='Win32 ld.exe'
+ # FIXME: first we should search . and the directory the executable is in
+ shlibpath_var=PATH
+ ;;
+
+darwin* | rhapsody*)
+ dynamic_linker="$host_os dyld"
+ version_type=darwin
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+ soname_spec='${libname}${release}${major}$shared_ext'
+ shlibpath_overrides_runpath=yes
+ shlibpath_var=DYLD_LIBRARY_PATH
+ shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+m4_if([$1], [],[
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /usr/local/lib"])
+ sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+ ;;
+
+dgux*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+freebsd1*)
+ dynamic_linker=no
+ ;;
+
+freebsd* | dragonfly*)
+ # DragonFly does not have aout. When/if they implement a new
+ # versioning mechanism, adjust this.
+ if test -x /usr/bin/objformat; then
+ objformat=`/usr/bin/objformat`
+ else
+ case $host_os in
+ freebsd[[123]]*) objformat=aout ;;
+ *) objformat=elf ;;
+ esac
+ fi
+ version_type=freebsd-$objformat
+ case $version_type in
+ freebsd-elf*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ need_version=no
+ need_lib_prefix=no
+ ;;
+ freebsd-*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+ need_version=yes
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_os in
+ freebsd2*)
+ shlibpath_overrides_runpath=yes
+ ;;
+ freebsd3.[[01]]* | freebsdelf3.[[01]]*)
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ freebsd3.[[2-9]]* | freebsdelf3.[[2-9]]* | \
+ freebsd4.[[0-5]] | freebsdelf4.[[0-5]] | freebsd4.1.1 | freebsdelf4.1.1)
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+ *) # from 4.6 on, and DragonFly
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ esac
+ ;;
+
+gnu*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ hardcode_into_libs=yes
+ ;;
+
+hpux9* | hpux10* | hpux11*)
+ # Give a soname corresponding to the major version so that dld.sl refuses to
+ # link against other versions.
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ case $host_cpu in
+ ia64*)
+ shrext_cmds='.so'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.so"
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ if test "X$HPUX_IA64_MODE" = X32; then
+ sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+ else
+ sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+ fi
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ hppa*64*)
+ shrext_cmds='.sl'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ *)
+ shrext_cmds='.sl'
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=SHLIB_PATH
+ shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+ esac
+ # HP-UX runs *really* slowly unless shared libraries are mode 555.
+ postinstall_cmds='chmod 555 $lib'
+ ;;
+
+interix[[3-9]]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $host_os in
+ nonstopux*) version_type=nonstopux ;;
+ *)
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ version_type=linux
+ else
+ version_type=irix
+ fi ;;
+ esac
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+ case $host_os in
+ irix5* | nonstopux*)
+ libsuff= shlibsuff=
+ ;;
+ *)
+ case $LD in # libtool.m4 will add one of these switches to LD
+ *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+ libsuff= shlibsuff= libmagic=32-bit;;
+ *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+ libsuff=32 shlibsuff=N32 libmagic=N32;;
+ *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+ libsuff=64 shlibsuff=64 libmagic=64-bit;;
+ *) libsuff= shlibsuff= libmagic=never-match;;
+ esac
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+ sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+ hardcode_into_libs=yes
+ ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+ dynamic_linker=no
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ # Some binutils ld are patched to set DT_RUNPATH
+ save_LDFLAGS=$LDFLAGS
+ save_libdir=$libdir
+ eval "libdir=/foo; wl=\"$_LT_TAGVAR(lt_prog_compiler_wl, $1)\"; \
+ LDFLAGS=\"\$LDFLAGS $_LT_TAGVAR(hardcode_libdir_flag_spec, $1)\""
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([],[])],
+ [AS_IF([ ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null],
+ [shlibpath_overrides_runpath=yes])])
+ LDFLAGS=$save_LDFLAGS
+ libdir=$save_libdir
+
+ # This implies no fast_install, which is unacceptable.
+ # Some rework will be needed to allow for fast_install
+ # before this can be enabled.
+ hardcode_into_libs=yes
+
+ # Append ld.so.conf contents to the search path
+ if test -f /etc/ld.so.conf; then
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \[$]2)); skip = 1; } { if (!skip) print \[$]0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ fi
+
+ # We used to test for /lib/ld.so.1 and disable shared libraries on
+ # powerpc, because MkLinux only supported shared libraries with the
+ # GNU dynamic linker. Since this was broken with cross compilers,
+ # most powerpc-linux boxes support dynamic linking these days and
+ # people can always --disable-shared, the test was removed, and we
+ # assume the GNU/Linux dynamic linker is in use.
+ dynamic_linker='GNU/Linux ld.so'
+ ;;
+
+netbsdelf*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='NetBSD ld.elf_so'
+ ;;
+
+netbsd*)
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ dynamic_linker='NetBSD (a.out) ld.so'
+ else
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='NetBSD ld.elf_so'
+ fi
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+
+newsos6)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ ;;
+
+*nto* | *qnx*)
+ version_type=qnx
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='ldqnx.so'
+ ;;
+
+openbsd*)
+ version_type=sunos
+ sys_lib_dlsearch_path_spec="/usr/lib"
+ need_lib_prefix=no
+ # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+ case $host_os in
+ openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+ *) need_version=no ;;
+ esac
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ case $host_os in
+ openbsd2.[[89]] | openbsd2.[[89]].*)
+ shlibpath_overrides_runpath=no
+ ;;
+ *)
+ shlibpath_overrides_runpath=yes
+ ;;
+ esac
+ else
+ shlibpath_overrides_runpath=yes
+ fi
+ ;;
+
+os2*)
+ libname_spec='$name'
+ shrext_cmds=".dll"
+ need_lib_prefix=no
+ library_names_spec='$libname${shared_ext} $libname.a'
+ dynamic_linker='OS/2 ld.exe'
+ shlibpath_var=LIBPATH
+ ;;
+
+osf3* | osf4* | osf5*)
+ version_type=osf
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+ sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+ ;;
+
+rdos*)
+ dynamic_linker=no
+ ;;
+
+solaris*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ # ldd complains unless libraries are executable
+ postinstall_cmds='chmod +x $lib'
+ ;;
+
+sunos4*)
+ version_type=sunos
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ if test "$with_gnu_ld" = yes; then
+ need_lib_prefix=no
+ fi
+ need_version=yes
+ ;;
+
+sysv4 | sysv4.3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_vendor in
+ sni)
+ shlibpath_overrides_runpath=no
+ need_lib_prefix=no
+ runpath_var=LD_RUN_PATH
+ ;;
+ siemens)
+ need_lib_prefix=no
+ ;;
+ motorola)
+ need_lib_prefix=no
+ need_version=no
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+ ;;
+ esac
+ ;;
+
+sysv4*MP*)
+ if test -d /usr/nec ;then
+ version_type=linux
+ library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+ soname_spec='$libname${shared_ext}.$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ fi
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ version_type=freebsd-elf
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ if test "$with_gnu_ld" = yes; then
+ sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+ else
+ sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+ case $host_os in
+ sco3.2v5*)
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+ ;;
+ esac
+ fi
+ sys_lib_dlsearch_path_spec='/usr/lib'
+ ;;
+
+tpf*)
+ # TPF is a cross-target only. Preferred cross-host = GNU/Linux.
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+uts4*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+*)
+ dynamic_linker=no
+ ;;
+esac
+AC_MSG_RESULT([$dynamic_linker])
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+ variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+
+if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then
+ sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec"
+fi
+if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then
+ sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec"
+fi
+
+_LT_DECL([], [variables_saved_for_relink], [1],
+ [Variables whose values should be saved in libtool wrapper scripts and
+ restored at link time])
+_LT_DECL([], [need_lib_prefix], [0],
+ [Do we need the "lib" prefix for modules?])
+_LT_DECL([], [need_version], [0], [Do we need a version for libraries?])
+_LT_DECL([], [version_type], [0], [Library versioning type])
+_LT_DECL([], [runpath_var], [0], [Shared library runtime path variable])
+_LT_DECL([], [shlibpath_var], [0],[Shared library path variable])
+_LT_DECL([], [shlibpath_overrides_runpath], [0],
+ [Is shlibpath searched before the hard-coded library search path?])
+_LT_DECL([], [libname_spec], [1], [Format of library name prefix])
+_LT_DECL([], [library_names_spec], [1],
+ [[List of archive names. First name is the real one, the rest are links.
+ The last name is the one that the linker finds with -lNAME]])
+_LT_DECL([], [soname_spec], [1],
+ [[The coded name of the library, if different from the real name]])
+_LT_DECL([], [postinstall_cmds], [2],
+ [Command to use after installation of a shared archive])
+_LT_DECL([], [postuninstall_cmds], [2],
+ [Command to use after uninstallation of a shared archive])
+_LT_DECL([], [finish_cmds], [2],
+ [Commands used to finish a libtool library installation in a directory])
+_LT_DECL([], [finish_eval], [1],
+ [[As "finish_cmds", except a single script fragment to be evaled but
+ not shown]])
+_LT_DECL([], [hardcode_into_libs], [0],
+ [Whether we should hardcode library paths into libraries])
+_LT_DECL([], [sys_lib_search_path_spec], [2],
+ [Compile-time system search path for libraries])
+_LT_DECL([], [sys_lib_dlsearch_path_spec], [2],
+ [Run-time system search path for libraries])
+])# _LT_SYS_DYNAMIC_LINKER
+
+
+# _LT_PATH_TOOL_PREFIX(TOOL)
+# --------------------------
+# find a file program which can recognize shared library
+AC_DEFUN([_LT_PATH_TOOL_PREFIX],
+[m4_require([_LT_DECL_EGREP])dnl
+AC_MSG_CHECKING([for $1])
+AC_CACHE_VAL(lt_cv_path_MAGIC_CMD,
+[case $MAGIC_CMD in
+[[\\/*] | ?:[\\/]*])
+ lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path.
+ ;;
+*)
+ lt_save_MAGIC_CMD="$MAGIC_CMD"
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+dnl $ac_dummy forces splitting on constant user-supplied paths.
+dnl POSIX.2 word splitting is done only on the output of word expansions,
+dnl not every word. This closes a longstanding sh security hole.
+ ac_dummy="m4_if([$2], , $PATH, [$2])"
+ for ac_dir in $ac_dummy; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f $ac_dir/$1; then
+ lt_cv_path_MAGIC_CMD="$ac_dir/$1"
+ if test -n "$file_magic_test_file"; then
+ case $deplibs_check_method in
+ "file_magic "*)
+ file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"`
+ MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+ if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null |
+ $EGREP "$file_magic_regex" > /dev/null; then
+ :
+ else
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the command libtool uses to detect shared libraries,
+*** $file_magic_cmd, produces output that libtool cannot recognize.
+*** The result is that libtool may fail to recognize shared libraries
+*** as such. This will affect the creation of libtool libraries that
+*** depend on shared libraries, but programs linked with such libtool
+*** libraries will work regardless of this problem. Nevertheless, you
+*** may want to report the problem to your system manager and/or to
+*** bug-libtool at gnu.org
+
+_LT_EOF
+ fi ;;
+ esac
+ fi
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+ MAGIC_CMD="$lt_save_MAGIC_CMD"
+ ;;
+esac])
+MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+if test -n "$MAGIC_CMD"; then
+ AC_MSG_RESULT($MAGIC_CMD)
+else
+ AC_MSG_RESULT(no)
+fi
+_LT_DECL([], [MAGIC_CMD], [0],
+ [Used to examine libraries when file_magic_cmd begins with "file"])dnl
+])# _LT_PATH_TOOL_PREFIX
+
+# Old name:
+AU_ALIAS([AC_PATH_TOOL_PREFIX], [_LT_PATH_TOOL_PREFIX])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_PATH_TOOL_PREFIX], [])
+
+
+# _LT_PATH_MAGIC
+# --------------
+# find a file program which can recognize a shared library
+m4_defun([_LT_PATH_MAGIC],
+[_LT_PATH_TOOL_PREFIX(${ac_tool_prefix}file, /usr/bin$PATH_SEPARATOR$PATH)
+if test -z "$lt_cv_path_MAGIC_CMD"; then
+ if test -n "$ac_tool_prefix"; then
+ _LT_PATH_TOOL_PREFIX(file, /usr/bin$PATH_SEPARATOR$PATH)
+ else
+ MAGIC_CMD=:
+ fi
+fi
+])# _LT_PATH_MAGIC
+
+
+# LT_PATH_LD
+# ----------
+# find the pathname to the GNU or non-GNU linker
+AC_DEFUN([LT_PATH_LD],
+[AC_REQUIRE([AC_PROG_CC])dnl
+AC_REQUIRE([AC_CANONICAL_HOST])dnl
+AC_REQUIRE([AC_CANONICAL_BUILD])dnl
+m4_require([_LT_DECL_SED])dnl
+m4_require([_LT_DECL_EGREP])dnl
+
+AC_ARG_WITH([gnu-ld],
+ [AS_HELP_STRING([--with-gnu-ld],
+ [assume the C compiler uses GNU ld @<:@default=no@:>@])],
+ [test "$withval" = no || with_gnu_ld=yes],
+ [with_gnu_ld=no])dnl
+
+ac_prog=ld
+if test "$GCC" = yes; then
+ # Check if gcc -print-prog-name=ld gives a path.
+ AC_MSG_CHECKING([for ld used by $CC])
+ case $host in
+ *-*-mingw*)
+ # gcc leaves a trailing carriage return which upsets mingw
+ ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+ *)
+ ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+ esac
+ case $ac_prog in
+ # Accept absolute paths.
+ [[\\/]]* | ?:[[\\/]]*)
+ re_direlt='/[[^/]][[^/]]*/\.\./'
+ # Canonicalize the pathname of ld
+ ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'`
+ while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do
+ ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"`
+ done
+ test -z "$LD" && LD="$ac_prog"
+ ;;
+ "")
+ # If it fails, then pretend we aren't using GCC.
+ ac_prog=ld
+ ;;
+ *)
+ # If it is relative, then search for the first ld in PATH.
+ with_gnu_ld=unknown
+ ;;
+ esac
+elif test "$with_gnu_ld" = yes; then
+ AC_MSG_CHECKING([for GNU ld])
+else
+ AC_MSG_CHECKING([for non-GNU ld])
+fi
+AC_CACHE_VAL(lt_cv_path_LD,
+[if test -z "$LD"; then
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+ lt_cv_path_LD="$ac_dir/$ac_prog"
+ # Check to see if the program is GNU ld. I'd rather use --version,
+ # but apparently some variants of GNU ld only accept -v.
+ # Break only if it was the GNU/non-GNU ld that we prefer.
+ case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+ *GNU* | *'with BFD'*)
+ test "$with_gnu_ld" != no && break
+ ;;
+ *)
+ test "$with_gnu_ld" != yes && break
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+else
+ lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi])
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+ AC_MSG_RESULT($LD)
+else
+ AC_MSG_RESULT(no)
+fi
+test -z "$LD" && AC_MSG_ERROR([no acceptable ld found in \$PATH])
+_LT_PATH_LD_GNU
+AC_SUBST([LD])
+
+_LT_TAGDECL([], [LD], [1], [The linker used to build libraries])
+])# LT_PATH_LD
+
+# Old names:
+AU_ALIAS([AM_PROG_LD], [LT_PATH_LD])
+AU_ALIAS([AC_PROG_LD], [LT_PATH_LD])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AM_PROG_LD], [])
+dnl AC_DEFUN([AC_PROG_LD], [])
+
+
+# _LT_PATH_LD_GNU
+#- --------------
+m4_defun([_LT_PATH_LD_GNU],
+[AC_CACHE_CHECK([if the linker ($LD) is GNU ld], lt_cv_prog_gnu_ld,
+[# I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+ lt_cv_prog_gnu_ld=yes
+ ;;
+*)
+ lt_cv_prog_gnu_ld=no
+ ;;
+esac])
+with_gnu_ld=$lt_cv_prog_gnu_ld
+])# _LT_PATH_LD_GNU
+
+
+# _LT_CMD_RELOAD
+# --------------
+# find reload flag for linker
+# -- PORTME Some linkers may need a different reload flag.
+m4_defun([_LT_CMD_RELOAD],
+[AC_CACHE_CHECK([for $LD option to reload object files],
+ lt_cv_ld_reload_flag,
+ [lt_cv_ld_reload_flag='-r'])
+reload_flag=$lt_cv_ld_reload_flag
+case $reload_flag in
+"" | " "*) ;;
+*) reload_flag=" $reload_flag" ;;
+esac
+reload_cmds='$LD$reload_flag -o $output$reload_objs'
+case $host_os in
+ darwin*)
+ if test "$GCC" = yes; then
+ reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs'
+ else
+ reload_cmds='$LD$reload_flag -o $output$reload_objs'
+ fi
+ ;;
+esac
+_LT_DECL([], [reload_flag], [1], [How to create reloadable object files])dnl
+_LT_DECL([], [reload_cmds], [2])dnl
+])# _LT_CMD_RELOAD
+
+
+# _LT_CHECK_MAGIC_METHOD
+# ----------------------
+# how to check for library dependencies
+# -- PORTME fill in with the dynamic library characteristics
+m4_defun([_LT_CHECK_MAGIC_METHOD],
+[m4_require([_LT_DECL_EGREP])
+m4_require([_LT_DECL_OBJDUMP])
+AC_CACHE_CHECK([how to recognize dependent libraries],
+lt_cv_deplibs_check_method,
+[lt_cv_file_magic_cmd='$MAGIC_CMD'
+lt_cv_file_magic_test_file=
+lt_cv_deplibs_check_method='unknown'
+# Need to set the preceding variable on all platforms that support
+# interlibrary dependencies.
+# 'none' -- dependencies not supported.
+# `unknown' -- same as none, but documents that we really don't know.
+# 'pass_all' -- all dependencies passed with no checks.
+# 'test_compile' -- check by making test program.
+# 'file_magic [[regex]]' -- check by looking for files in library path
+# which responds to the $file_magic_cmd with a given extended regex.
+# If you have `file' or equivalent on your system and you're not sure
+# whether `pass_all' will *always* work, you probably want this one.
+
+case $host_os in
+aix[[4-9]]*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+beos*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+bsdi[[45]]*)
+ lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (shared object|dynamic lib)'
+ lt_cv_file_magic_cmd='/usr/bin/file -L'
+ lt_cv_file_magic_test_file=/shlib/libc.so
+ ;;
+
+cygwin*)
+ # func_win32_libid is a shell function defined in ltmain.sh
+ lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+ lt_cv_file_magic_cmd='func_win32_libid'
+ ;;
+
+mingw* | pw32*)
+ # Base MSYS/MinGW do not provide the 'file' command needed by
+ # func_win32_libid shell function, so use a weaker test based on 'objdump',
+ # unless we find 'file', for example because we are cross-compiling.
+ if ( file / ) >/dev/null 2>&1; then
+ lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+ lt_cv_file_magic_cmd='func_win32_libid'
+ else
+ lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?'
+ lt_cv_file_magic_cmd='$OBJDUMP -f'
+ fi
+ ;;
+
+cegcc)
+ # use the weaker test based on 'objdump'. See mingw*.
+ lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?'
+ lt_cv_file_magic_cmd='$OBJDUMP -f'
+ ;;
+
+darwin* | rhapsody*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+freebsd* | dragonfly*)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
+ case $host_cpu in
+ i*86 )
+ # Not sure whether the presence of OpenBSD here was a mistake.
+ # Let's accept both of them until this is cleared up.
+ lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[[3-9]]86 (compact )?demand paged shared library'
+ lt_cv_file_magic_cmd=/usr/bin/file
+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*`
+ ;;
+ esac
+ else
+ lt_cv_deplibs_check_method=pass_all
+ fi
+ ;;
+
+gnu*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+hpux10.20* | hpux11*)
+ lt_cv_file_magic_cmd=/usr/bin/file
+ case $host_cpu in
+ ia64*)
+ lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|ELF-[[0-9]][[0-9]]) shared object file - IA64'
+ lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so
+ ;;
+ hppa*64*)
+ [lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]']
+ lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl
+ ;;
+ *)
+ lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|PA-RISC[[0-9]].[[0-9]]) shared library'
+ lt_cv_file_magic_test_file=/usr/lib/libc.sl
+ ;;
+ esac
+ ;;
+
+interix[[3-9]]*)
+ # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|\.a)$'
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $LD in
+ *-32|*"-32 ") libmagic=32-bit;;
+ *-n32|*"-n32 ") libmagic=N32;;
+ *-64|*"-64 ") libmagic=64-bit;;
+ *) libmagic=never-match;;
+ esac
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$'
+ else
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|_pic\.a)$'
+ fi
+ ;;
+
+newos6*)
+ lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (executable|dynamic lib)'
+ lt_cv_file_magic_cmd=/usr/bin/file
+ lt_cv_file_magic_test_file=/usr/lib/libnls.so
+ ;;
+
+*nto* | *qnx*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+openbsd*)
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|\.so|_pic\.a)$'
+ else
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$'
+ fi
+ ;;
+
+osf3* | osf4* | osf5*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+rdos*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+solaris*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+sysv4 | sysv4.3*)
+ case $host_vendor in
+ motorola)
+ lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (shared object|dynamic lib) M[[0-9]][[0-9]]* Version [[0-9]]'
+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*`
+ ;;
+ ncr)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ sequent)
+ lt_cv_file_magic_cmd='/bin/file'
+ lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB (shared object|dynamic lib )'
+ ;;
+ sni)
+ lt_cv_file_magic_cmd='/bin/file'
+ lt_cv_deplibs_check_method="file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB dynamic lib"
+ lt_cv_file_magic_test_file=/lib/libc.so
+ ;;
+ siemens)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ pc)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ esac
+ ;;
+
+tpf*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+esac
+])
+file_magic_cmd=$lt_cv_file_magic_cmd
+deplibs_check_method=$lt_cv_deplibs_check_method
+test -z "$deplibs_check_method" && deplibs_check_method=unknown
+
+_LT_DECL([], [deplibs_check_method], [1],
+ [Method to check whether dependent libraries are shared objects])
+_LT_DECL([], [file_magic_cmd], [1],
+ [Command to use when deplibs_check_method == "file_magic"])
+])# _LT_CHECK_MAGIC_METHOD
+
+
+# LT_PATH_NM
+# ----------
+# find the pathname to a BSD- or MS-compatible name lister
+AC_DEFUN([LT_PATH_NM],
+[AC_REQUIRE([AC_PROG_CC])dnl
+AC_CACHE_CHECK([for BSD- or MS-compatible name lister (nm)], lt_cv_path_NM,
+[if test -n "$NM"; then
+ # Let the user override the test.
+ lt_cv_path_NM="$NM"
+else
+ lt_nm_to_check="${ac_tool_prefix}nm"
+ if test -n "$ac_tool_prefix" && test "$build" = "$host"; then
+ lt_nm_to_check="$lt_nm_to_check nm"
+ fi
+ for lt_tmp_nm in $lt_nm_to_check; do
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ tmp_nm="$ac_dir/$lt_tmp_nm"
+ if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then
+ # Check to see if the nm accepts a BSD-compat flag.
+ # Adding the `sed 1q' prevents false positives on HP-UX, which says:
+ # nm: unknown option "B" ignored
+ # Tru64's nm complains that /dev/null is an invalid object file
+ case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in
+ */dev/null* | *'Invalid file or object type'*)
+ lt_cv_path_NM="$tmp_nm -B"
+ break
+ ;;
+ *)
+ case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in
+ */dev/null*)
+ lt_cv_path_NM="$tmp_nm -p"
+ break
+ ;;
+ *)
+ lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but
+ continue # so that we can try to find one that supports BSD flags
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+ done
+ : ${lt_cv_path_NM=no}
+fi])
+if test "$lt_cv_path_NM" != "no"; then
+ NM="$lt_cv_path_NM"
+else
+ # Didn't find any BSD compatible name lister, look for dumpbin.
+ AC_CHECK_TOOLS(DUMPBIN, ["dumpbin -symbols" "link -dump -symbols"], :)
+ AC_SUBST([DUMPBIN])
+ if test "$DUMPBIN" != ":"; then
+ NM="$DUMPBIN"
+ fi
+fi
+test -z "$NM" && NM=nm
+AC_SUBST([NM])
+_LT_DECL([], [NM], [1], [A BSD- or MS-compatible name lister])dnl
+
+AC_CACHE_CHECK([the name lister ($NM) interface], [lt_cv_nm_interface],
+ [lt_cv_nm_interface="BSD nm"
+ echo "int some_variable = 0;" > conftest.$ac_ext
+ (eval echo "\"\$as_me:__oline__: $ac_compile\"" >&AS_MESSAGE_LOG_FD)
+ (eval "$ac_compile" 2>conftest.err)
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ (eval echo "\"\$as_me:__oline__: $NM \\\"conftest.$ac_objext\\\"\"" >&AS_MESSAGE_LOG_FD)
+ (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out)
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ (eval echo "\"\$as_me:__oline__: output\"" >&AS_MESSAGE_LOG_FD)
+ cat conftest.out >&AS_MESSAGE_LOG_FD
+ if $GREP 'External.*some_variable' conftest.out > /dev/null; then
+ lt_cv_nm_interface="MS dumpbin"
+ fi
+ rm -f conftest*])
+])# LT_PATH_NM
+
+# Old names:
+AU_ALIAS([AM_PROG_NM], [LT_PATH_NM])
+AU_ALIAS([AC_PROG_NM], [LT_PATH_NM])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AM_PROG_NM], [])
+dnl AC_DEFUN([AC_PROG_NM], [])
+
+
+# LT_LIB_M
+# --------
+# check for math library
+AC_DEFUN([LT_LIB_M],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+LIBM=
+case $host in
+*-*-beos* | *-*-cygwin* | *-*-pw32* | *-*-darwin*)
+ # These system don't have libm, or don't need it
+ ;;
+*-ncr-sysv4.3*)
+ AC_CHECK_LIB(mw, _mwvalidcheckl, LIBM="-lmw")
+ AC_CHECK_LIB(m, cos, LIBM="$LIBM -lm")
+ ;;
+*)
+ AC_CHECK_LIB(m, cos, LIBM="-lm")
+ ;;
+esac
+AC_SUBST([LIBM])
+])# LT_LIB_M
+
+# Old name:
+AU_ALIAS([AC_CHECK_LIBM], [LT_LIB_M])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_CHECK_LIBM], [])
+
+
+# _LT_COMPILER_NO_RTTI([TAGNAME])
+# -------------------------------
+m4_defun([_LT_COMPILER_NO_RTTI],
+[m4_require([_LT_TAG_COMPILER])dnl
+
+_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=
+
+if test "$GCC" = yes; then
+ _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin'
+
+ _LT_COMPILER_OPTION([if $compiler supports -fno-rtti -fno-exceptions],
+ lt_cv_prog_compiler_rtti_exceptions,
+ [-fno-rtti -fno-exceptions], [],
+ [_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)="$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1) -fno-rtti -fno-exceptions"])
+fi
+_LT_TAGDECL([no_builtin_flag], [lt_prog_compiler_no_builtin_flag], [1],
+ [Compiler flag to turn off builtin functions])
+])# _LT_COMPILER_NO_RTTI
+
+
+# _LT_CMD_GLOBAL_SYMBOLS
+# ----------------------
+m4_defun([_LT_CMD_GLOBAL_SYMBOLS],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+AC_REQUIRE([AC_PROG_CC])dnl
+AC_REQUIRE([LT_PATH_NM])dnl
+AC_REQUIRE([LT_PATH_LD])dnl
+m4_require([_LT_DECL_SED])dnl
+m4_require([_LT_DECL_EGREP])dnl
+m4_require([_LT_TAG_COMPILER])dnl
+
+# Check for command to grab the raw symbol name followed by C symbol from nm.
+AC_MSG_CHECKING([command to parse $NM output from $compiler object])
+AC_CACHE_VAL([lt_cv_sys_global_symbol_pipe],
+[
+# These are sane defaults that work on at least a few old systems.
+# [They come from Ultrix. What could be older than Ultrix?!! ;)]
+
+# Character class describing NM global symbol codes.
+symcode='[[BCDEGRST]]'
+
+# Regexp to match symbols that can be accessed directly from C.
+sympat='\([[_A-Za-z]][[_A-Za-z0-9]]*\)'
+
+# Define system-specific variables.
+case $host_os in
+aix*)
+ symcode='[[BCDT]]'
+ ;;
+cygwin* | mingw* | pw32* | cegcc*)
+ symcode='[[ABCDGISTW]]'
+ ;;
+hpux*)
+ if test "$host_cpu" = ia64; then
+ symcode='[[ABCDEGRST]]'
+ fi
+ ;;
+irix* | nonstopux*)
+ symcode='[[BCDEGRST]]'
+ ;;
+osf*)
+ symcode='[[BCDEGQRST]]'
+ ;;
+solaris*)
+ symcode='[[BDRT]]'
+ ;;
+sco3.2v5*)
+ symcode='[[DT]]'
+ ;;
+sysv4.2uw2*)
+ symcode='[[DT]]'
+ ;;
+sysv5* | sco5v6* | unixware* | OpenUNIX*)
+ symcode='[[ABDT]]'
+ ;;
+sysv4)
+ symcode='[[DFNSTU]]'
+ ;;
+esac
+
+# If we're using GNU nm, then use its standard symbol codes.
+case `$NM -V 2>&1` in
+*GNU* | *'with BFD'*)
+ symcode='[[ABCDGIRSTW]]' ;;
+esac
+
+# Transform an extracted symbol line into a proper C declaration.
+# Some systems (esp. on ia64) link data and code symbols differently,
+# so use this general approach.
+lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'"
+
+# Transform an extracted symbol line into symbol name and symbol address
+lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p'"
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \(lib[[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"lib\2\", (void *) \&\2},/p'"
+
+# Handle CRLF in mingw tool chain
+opt_cr=
+case $build_os in
+mingw*)
+ opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp
+ ;;
+esac
+
+# Try without a prefix underscore, then with it.
+for ac_symprfx in "" "_"; do
+
+ # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol.
+ symxfrm="\\1 $ac_symprfx\\2 \\2"
+
+ # Write the raw and C identifiers.
+ if test "$lt_cv_nm_interface" = "MS dumpbin"; then
+ # Fake it for dumpbin and say T for any non-static function
+ # and D for any global variable.
+ # Also find C++ and __fastcall symbols from MSVC++,
+ # which start with @ or ?.
+ lt_cv_sys_global_symbol_pipe="$AWK ['"\
+" {last_section=section; section=\$ 3};"\
+" /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\
+" \$ 0!~/External *\|/{next};"\
+" / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\
+" {if(hide[section]) next};"\
+" {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\
+" {split(\$ 0, a, /\||\r/); split(a[2], s)};"\
+" s[1]~/^[@?]/{print s[1], s[1]; next};"\
+" s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\
+" ' prfx=^$ac_symprfx]"
+ else
+ lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[[ ]]\($symcode$symcode*\)[[ ]][[ ]]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'"
+ fi
+
+ # Check to see that the pipe works correctly.
+ pipe_works=no
+
+ rm -f conftest*
+ cat > conftest.$ac_ext <<_LT_EOF
+#ifdef __cplusplus
+extern "C" {
+#endif
+char nm_test_var;
+void nm_test_func(void);
+void nm_test_func(void){}
+#ifdef __cplusplus
+}
+#endif
+int main(){nm_test_var='a';nm_test_func();return(0);}
+_LT_EOF
+
+ if AC_TRY_EVAL(ac_compile); then
+ # Now try to grab the symbols.
+ nlist=conftest.nm
+ if AC_TRY_EVAL(NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) && test -s "$nlist"; then
+ # Try sorting and uniquifying the output.
+ if sort "$nlist" | uniq > "$nlist"T; then
+ mv -f "$nlist"T "$nlist"
+ else
+ rm -f "$nlist"T
+ fi
+
+ # Make sure that we snagged all the symbols we need.
+ if $GREP ' nm_test_var$' "$nlist" >/dev/null; then
+ if $GREP ' nm_test_func$' "$nlist" >/dev/null; then
+ cat <<_LT_EOF > conftest.$ac_ext
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+_LT_EOF
+ # Now generate the symbol file.
+ eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext'
+
+ cat <<_LT_EOF >> conftest.$ac_ext
+
+/* The mapping between symbol names and symbols. */
+const struct {
+ const char *name;
+ void *address;
+}
+lt__PROGRAM__LTX_preloaded_symbols[[]] =
+{
+ { "@PROGRAM@", (void *) 0 },
+_LT_EOF
+ $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext
+ cat <<\_LT_EOF >> conftest.$ac_ext
+ {0, (void *) 0}
+};
+
+/* This works around a problem in FreeBSD linker */
+#ifdef FREEBSD_WORKAROUND
+static const void *lt_preloaded_setup() {
+ return lt__PROGRAM__LTX_preloaded_symbols;
+}
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+_LT_EOF
+ # Now try linking the two files.
+ mv conftest.$ac_objext conftstm.$ac_objext
+ lt_save_LIBS="$LIBS"
+ lt_save_CFLAGS="$CFLAGS"
+ LIBS="conftstm.$ac_objext"
+ CFLAGS="$CFLAGS$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)"
+ if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext}; then
+ pipe_works=yes
+ fi
+ LIBS="$lt_save_LIBS"
+ CFLAGS="$lt_save_CFLAGS"
+ else
+ echo "cannot find nm_test_func in $nlist" >&AS_MESSAGE_LOG_FD
+ fi
+ else
+ echo "cannot find nm_test_var in $nlist" >&AS_MESSAGE_LOG_FD
+ fi
+ else
+ echo "cannot run $lt_cv_sys_global_symbol_pipe" >&AS_MESSAGE_LOG_FD
+ fi
+ else
+ echo "$progname: failed program was:" >&AS_MESSAGE_LOG_FD
+ cat conftest.$ac_ext >&5
+ fi
+ rm -rf conftest* conftst*
+
+ # Do not use the global_symbol_pipe unless it works.
+ if test "$pipe_works" = yes; then
+ break
+ else
+ lt_cv_sys_global_symbol_pipe=
+ fi
+done
+])
+if test -z "$lt_cv_sys_global_symbol_pipe"; then
+ lt_cv_sys_global_symbol_to_cdecl=
+fi
+if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then
+ AC_MSG_RESULT(failed)
+else
+ AC_MSG_RESULT(ok)
+fi
+
+_LT_DECL([global_symbol_pipe], [lt_cv_sys_global_symbol_pipe], [1],
+ [Take the output of nm and produce a listing of raw symbols and C names])
+_LT_DECL([global_symbol_to_cdecl], [lt_cv_sys_global_symbol_to_cdecl], [1],
+ [Transform the output of nm in a proper C declaration])
+_LT_DECL([global_symbol_to_c_name_address],
+ [lt_cv_sys_global_symbol_to_c_name_address], [1],
+ [Transform the output of nm in a C name address pair])
+_LT_DECL([global_symbol_to_c_name_address_lib_prefix],
+ [lt_cv_sys_global_symbol_to_c_name_address_lib_prefix], [1],
+ [Transform the output of nm in a C name address pair when lib prefix is needed])
+]) # _LT_CMD_GLOBAL_SYMBOLS
+
+
+# _LT_COMPILER_PIC([TAGNAME])
+# ---------------------------
+m4_defun([_LT_COMPILER_PIC],
+[m4_require([_LT_TAG_COMPILER])dnl
+_LT_TAGVAR(lt_prog_compiler_wl, $1)=
+_LT_TAGVAR(lt_prog_compiler_pic, $1)=
+_LT_TAGVAR(lt_prog_compiler_static, $1)=
+
+AC_MSG_CHECKING([for $compiler option to produce PIC])
+m4_if([$1], [CXX], [
+ # C++ specific cases for pic, static, wl, etc.
+ if test "$GXX" = yes; then
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+
+ case $host_os in
+ aix*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ m68k)
+ # FIXME: we need at least 68020 code to build shared libraries, but
+ # adding the `-m68020' flag to GCC prevents building anything better,
+ # like `-m68040'.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4'
+ ;;
+ esac
+ ;;
+
+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+ # PIC is the default for these OSes.
+ ;;
+ mingw* | cygwin* | os2* | pw32* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ # Although the cygwin gcc ignores -fPIC, still need this for old-style
+ # (--disable-auto-import) libraries
+ m4_if([$1], [GCJ], [],
+ [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT'])
+ ;;
+ darwin* | rhapsody*)
+ # PIC is the default on this platform
+ # Common symbols not allowed in MH_DYLIB files
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common'
+ ;;
+ *djgpp*)
+ # DJGPP does not support shared libraries at all
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ ;;
+ interix[[3-9]]*)
+ # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+ # Instead, we relocate shared libraries at runtime.
+ ;;
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic
+ fi
+ ;;
+ hpux*)
+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit
+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag
+ # sets the default TLS model and affects inlining.
+ case $host_cpu in
+ hppa*64*)
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ esac
+ ;;
+ *qnx* | *nto*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared'
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ esac
+ else
+ case $host_os in
+ aix[[4-9]]*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ else
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp'
+ fi
+ ;;
+ chorus*)
+ case $cc_basename in
+ cxch68*)
+ # Green Hills C++ Compiler
+ # _LT_TAGVAR(lt_prog_compiler_static, $1)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a"
+ ;;
+ esac
+ ;;
+ dgux*)
+ case $cc_basename in
+ ec++*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ ;;
+ ghcx*)
+ # Green Hills C++ Compiler
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ freebsd* | dragonfly*)
+ # FreeBSD uses GNU C++
+ ;;
+ hpux9* | hpux10* | hpux11*)
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive'
+ if test "$host_cpu" != ia64; then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z'
+ fi
+ ;;
+ aCC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive'
+ case $host_cpu in
+ hppa*64*|ia64*)
+ # +Z the default
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z'
+ ;;
+ esac
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ interix*)
+ # This is c89, which is MS Visual C++ (no shared libs)
+ # Anyone wants to do a port?
+ ;;
+ irix5* | irix6* | nonstopux*)
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ # CC pic flag -KPIC is the default.
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ KCC*)
+ # KAI C++ Compiler
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ ecpc* )
+ # old Intel C++ for x86_64 which still supported -KPIC.
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ icpc* )
+ # Intel C++, used to be incompatible with GCC.
+ # ICC 10 doesn't accept -KPIC any more.
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ pgCC* | pgcpp*)
+ # Portland Group C++ compiler
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+ cxx*)
+ # Compaq C++
+ # Make sure the PIC flag is empty. It appears that all Alpha
+ # Linux and Compaq Tru64 Unix objects are PIC.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+ xlc* | xlC*)
+ # IBM XL 8.0 on PPC
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink'
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld '
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+ lynxos*)
+ ;;
+ m88k*)
+ ;;
+ mvs*)
+ case $cc_basename in
+ cxx*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-W c,exportall'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ netbsd* | netbsdelf*-gnu)
+ ;;
+ *qnx* | *nto*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared'
+ ;;
+ osf3* | osf4* | osf5*)
+ case $cc_basename in
+ KCC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,'
+ ;;
+ RCC*)
+ # Rational C++ 2.4.1
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ ;;
+ cxx*)
+ # Digital/Compaq C++
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # Make sure the PIC flag is empty. It appears that all Alpha
+ # Linux and Compaq Tru64 Unix objects are PIC.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ psos*)
+ ;;
+ solaris*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.2, 5.x and Centerline C++
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld '
+ ;;
+ gcx*)
+ # Green Hills C++ Compiler
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ sunos4*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.x
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+ lcc*)
+ # Lucid
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+ esac
+ ;;
+ tandem*)
+ case $cc_basename in
+ NCC*)
+ # NonStop-UX NCC 3.20
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ vxworks*)
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+ ;;
+ esac
+ fi
+],
+[
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+
+ case $host_os in
+ aix*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ m68k)
+ # FIXME: we need at least 68020 code to build shared libraries, but
+ # adding the `-m68020' flag to GCC prevents building anything better,
+ # like `-m68040'.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4'
+ ;;
+ esac
+ ;;
+
+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+ # PIC is the default for these OSes.
+ ;;
+
+ mingw* | cygwin* | pw32* | os2* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ # Although the cygwin gcc ignores -fPIC, still need this for old-style
+ # (--disable-auto-import) libraries
+ m4_if([$1], [GCJ], [],
+ [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT'])
+ ;;
+
+ darwin* | rhapsody*)
+ # PIC is the default on this platform
+ # Common symbols not allowed in MH_DYLIB files
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common'
+ ;;
+
+ hpux*)
+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit
+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag
+ # sets the default TLS model and affects inlining.
+ case $host_cpu in
+ hppa*64*)
+ # +Z the default
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ esac
+ ;;
+
+ interix[[3-9]]*)
+ # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+ # Instead, we relocate shared libraries at runtime.
+ ;;
+
+ msdosdjgpp*)
+ # Just because we use GCC doesn't mean we suddenly get shared libraries
+ # on systems that don't support them.
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+ enable_shared=no
+ ;;
+
+ *nto* | *qnx*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic
+ fi
+ ;;
+
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ esac
+ else
+ # PORTME Check for flag to pass linker flags through the system compiler.
+ case $host_os in
+ aix*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ else
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp'
+ fi
+ ;;
+
+ mingw* | cygwin* | pw32* | os2* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ m4_if([$1], [GCJ], [],
+ [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT'])
+ ;;
+
+ hpux9* | hpux10* | hpux11*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+ # not for PA HP-UX.
+ case $host_cpu in
+ hppa*64*|ia64*)
+ # +Z the default
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z'
+ ;;
+ esac
+ # Is there a better lt_prog_compiler_static that works with the bundled CC?
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive'
+ ;;
+
+ irix5* | irix6* | nonstopux*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # PIC (with -KPIC) is the default.
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ # old Intel for x86_64 which still supported -KPIC.
+ ecc*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ # icc used to be incompatible with GCC.
+ # ICC 10 doesn't accept -KPIC any more.
+ icc* | ifort*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ # Lahey Fortran 8.1.
+ lf95*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='--shared'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='--static'
+ ;;
+ pgcc* | pgf77* | pgf90* | pgf95*)
+ # Portland Group compilers (*not* the Pentium gcc compiler,
+ # which looks to be a dead project)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+ ccc*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # All Alpha code is PIC.
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+ xl*)
+ # IBM XL C 8.0/Fortran 10.1 on PPC
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink'
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C 5.9
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ ;;
+ *Sun\ F*)
+ # Sun Fortran 8.3 passes all unrecognized flags to the linker
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)=''
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+
+ newsos6)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ *nto* | *qnx*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared'
+ ;;
+
+ osf3* | osf4* | osf5*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # All OSF/1 code is PIC.
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+
+ rdos*)
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+
+ solaris*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ case $cc_basename in
+ f77* | f90* | f95*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ';;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,';;
+ esac
+ ;;
+
+ sunos4*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld '
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ sysv4 | sysv4.2uw2* | sysv4.3*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec ;then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-Kconform_pic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ fi
+ ;;
+
+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ unicos*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+ ;;
+
+ uts4*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ *)
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+ ;;
+ esac
+ fi
+])
+case $host_os in
+ # For platforms which do not support PIC, -DPIC is meaningless:
+ *djgpp*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)="$_LT_TAGVAR(lt_prog_compiler_pic, $1)@&t at m4_if([$1],[],[ -DPIC],[m4_if([$1],[CXX],[ -DPIC],[])])"
+ ;;
+esac
+AC_MSG_RESULT([$_LT_TAGVAR(lt_prog_compiler_pic, $1)])
+_LT_TAGDECL([wl], [lt_prog_compiler_wl], [1],
+ [How to pass a linker flag through the compiler])
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$_LT_TAGVAR(lt_prog_compiler_pic, $1)"; then
+ _LT_COMPILER_OPTION([if $compiler PIC flag $_LT_TAGVAR(lt_prog_compiler_pic, $1) works],
+ [_LT_TAGVAR(lt_cv_prog_compiler_pic_works, $1)],
+ [$_LT_TAGVAR(lt_prog_compiler_pic, $1)@&t at m4_if([$1],[],[ -DPIC],[m4_if([$1],[CXX],[ -DPIC],[])])], [],
+ [case $_LT_TAGVAR(lt_prog_compiler_pic, $1) in
+ "" | " "*) ;;
+ *) _LT_TAGVAR(lt_prog_compiler_pic, $1)=" $_LT_TAGVAR(lt_prog_compiler_pic, $1)" ;;
+ esac],
+ [_LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no])
+fi
+_LT_TAGDECL([pic_flag], [lt_prog_compiler_pic], [1],
+ [Additional compiler flags for building library objects])
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$_LT_TAGVAR(lt_prog_compiler_wl, $1) eval lt_tmp_static_flag=\"$_LT_TAGVAR(lt_prog_compiler_static, $1)\"
+_LT_LINKER_OPTION([if $compiler static flag $lt_tmp_static_flag works],
+ _LT_TAGVAR(lt_cv_prog_compiler_static_works, $1),
+ $lt_tmp_static_flag,
+ [],
+ [_LT_TAGVAR(lt_prog_compiler_static, $1)=])
+_LT_TAGDECL([link_static_flag], [lt_prog_compiler_static], [1],
+ [Compiler flag to prevent dynamic linking])
+])# _LT_COMPILER_PIC
+
+
+# _LT_LINKER_SHLIBS([TAGNAME])
+# ----------------------------
+# See if the linker supports building shared libraries.
+m4_defun([_LT_LINKER_SHLIBS],
+[AC_REQUIRE([LT_PATH_LD])dnl
+AC_REQUIRE([LT_PATH_NM])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_EGREP])dnl
+m4_require([_LT_DECL_SED])dnl
+m4_require([_LT_CMD_GLOBAL_SYMBOLS])dnl
+m4_require([_LT_TAG_COMPILER])dnl
+AC_MSG_CHECKING([whether the $compiler linker ($LD) supports shared libraries])
+m4_if([$1], [CXX], [
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ case $host_os in
+ aix[[4-9]]*)
+ # If we're using GNU nm, then we don't want the "-C" option.
+ # -C means demangle to AIX nm, but means don't demangle with GNU nm
+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ else
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ fi
+ ;;
+ pw32*)
+ _LT_TAGVAR(export_symbols_cmds, $1)="$ltdll_cmds"
+ ;;
+ cygwin* | mingw* | cegcc*)
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]][[ ]]/s/.*[[ ]]\([[^ ]]*\)/\1 DATA/;/^.*[[ ]]__nm__/s/^.*[[ ]]__nm__\([[^ ]]*\)[[ ]][[^ ]]*/\1 DATA/;/^I[[ ]]/d;/^[[AITW]][[ ]]/s/.* //'\'' | sort | uniq > $export_symbols'
+ ;;
+ linux* | k*bsd*-gnu)
+ _LT_TAGVAR(link_all_deplibs, $1)=no
+ ;;
+ *)
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ ;;
+ esac
+ _LT_TAGVAR(exclude_expsyms, $1)=['_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*']
+], [
+ runpath_var=
+ _LT_TAGVAR(allow_undefined_flag, $1)=
+ _LT_TAGVAR(always_export_symbols, $1)=no
+ _LT_TAGVAR(archive_cmds, $1)=
+ _LT_TAGVAR(archive_expsym_cmds, $1)=
+ _LT_TAGVAR(compiler_needs_object, $1)=no
+ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)=
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ _LT_TAGVAR(hardcode_automatic, $1)=no
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+ _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=
+ _LT_TAGVAR(hardcode_minus_L, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
+ _LT_TAGVAR(inherit_rpath, $1)=no
+ _LT_TAGVAR(link_all_deplibs, $1)=unknown
+ _LT_TAGVAR(module_cmds, $1)=
+ _LT_TAGVAR(module_expsym_cmds, $1)=
+ _LT_TAGVAR(old_archive_from_new_cmds, $1)=
+ _LT_TAGVAR(old_archive_from_expsyms_cmds, $1)=
+ _LT_TAGVAR(thread_safe_flag_spec, $1)=
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ # include_expsyms should be a list of space-separated symbols to be *always*
+ # included in the symbol list
+ _LT_TAGVAR(include_expsyms, $1)=
+ # exclude_expsyms can be an extended regexp of symbols to exclude
+ # it will be wrapped by ` (' and `)$', so one must not match beginning or
+ # end of line. Example: `a|bc|.*d.*' will exclude the symbols `a' and `bc',
+ # as well as any symbol that contains `d'.
+ _LT_TAGVAR(exclude_expsyms, $1)=['_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*']
+ # Although _GLOBAL_OFFSET_TABLE_ is a valid symbol C name, most a.out
+ # platforms (ab)use it in PIC code, but their linkers get confused if
+ # the symbol is explicitly referenced. Since portable code cannot
+ # rely on this symbol name, it's probably fine to never include it in
+ # preloaded symbol tables.
+ # Exclude shared library initialization/finalization symbols.
+dnl Note also adjust exclude_expsyms for C++ above.
+ extract_expsyms_cmds=
+
+ case $host_os in
+ cygwin* | mingw* | pw32* | cegcc*)
+ # FIXME: the MSVC++ port hasn't been tested in a loooong time
+ # When not using gcc, we currently assume that we are using
+ # Microsoft Visual C++.
+ if test "$GCC" != yes; then
+ with_gnu_ld=no
+ fi
+ ;;
+ interix*)
+ # we just hope/assume this is gcc and not c89 (= MSVC++)
+ with_gnu_ld=yes
+ ;;
+ openbsd*)
+ with_gnu_ld=no
+ ;;
+ linux* | k*bsd*-gnu)
+ _LT_TAGVAR(link_all_deplibs, $1)=no
+ ;;
+ esac
+
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ if test "$with_gnu_ld" = yes; then
+ # If archive_cmds runs LD, not CC, wlarc should be empty
+ wlarc='${wl}'
+
+ # Set some defaults for GNU ld with shared library support. These
+ # are reset later if shared libraries are not supported. Putting them
+ # here allows them to be overridden if necessary.
+ runpath_var=LD_RUN_PATH
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+ # ancient GNU ld didn't support --whole-archive et. al.
+ if $LD --help 2>&1 | $GREP 'no-whole-archive' > /dev/null; then
+ _LT_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ else
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ fi
+ supports_anon_versioning=no
+ case `$LD -v 2>&1` in
+ *GNU\ gold*) supports_anon_versioning=yes ;;
+ *\ [[01]].* | *\ 2.[[0-9]].* | *\ 2.10.*) ;; # catch versions < 2.11
+ *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ...
+ *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ...
+ *\ 2.11.*) ;; # other 2.11 versions
+ *) supports_anon_versioning=yes ;;
+ esac
+
+ # See if GNU ld supports shared libraries.
+ case $host_os in
+ aix[[3-9]]*)
+ # On AIX/PPC, the GNU linker is very broken
+ if test "$host_cpu" != ia64; then
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the GNU linker, at least up to release 2.9.1, is reported
+*** to be unable to reliably create shared libraries on AIX.
+*** Therefore, libtool is disabling shared libraries support. If you
+*** really care for shared libraries, you may want to modify your PATH
+*** so that a non-GNU linker is found, and then restart.
+
+_LT_EOF
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)=''
+ ;;
+ m68k)
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ ;;
+ esac
+ ;;
+
+ beos*)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ # Joseph Beckenbach <jrb3 at best.com> says some releases of gcc
+ # support --undefined. This deserves some investigation. FIXME
+ _LT_TAGVAR(archive_cmds, $1)='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # _LT_TAGVAR(hardcode_libdir_flag_spec, $1) is actually meaningless,
+ # as there is no search path for DLLs.
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ _LT_TAGVAR(always_export_symbols, $1)=no
+ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]][[ ]]/s/.*[[ ]]\([[^ ]]*\)/\1 DATA/'\'' | $SED -e '\''/^[[AITW]][[ ]]/s/.*[[ ]]//'\'' | sort | uniq > $export_symbols'
+
+ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ # If the export-symbols file already is a .def file (1st line
+ # is EXPORTS), use it as is; otherwise, prepend...
+ _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+ cp $export_symbols $output_objdir/$soname.def;
+ else
+ echo EXPORTS > $output_objdir/$soname.def;
+ cat $export_symbols >> $output_objdir/$soname.def;
+ fi~
+ $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ interix[[3-9]]*)
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+ # Instead, shared libraries are loaded at an image base (0x10000000 by
+ # default) and relocated if they conflict, which is a slow very memory
+ # consuming and fragmenting process. To avoid this, we pick a random,
+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+ # time. Moving up from 0x10000000 also allows more sbrk(2) space.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ ;;
+
+ gnu* | linux* | tpf* | k*bsd*-gnu | kopensolaris*-gnu)
+ tmp_diet=no
+ if test "$host_os" = linux-dietlibc; then
+ case $cc_basename in
+ diet\ *) tmp_diet=yes;; # linux-dietlibc with static linking (!diet-dyn)
+ esac
+ fi
+ if $LD --help 2>&1 | $EGREP ': supported targets:.* elf' > /dev/null \
+ && test "$tmp_diet" = no
+ then
+ tmp_addflag=
+ tmp_sharedflag='-shared'
+ case $cc_basename,$host_cpu in
+ pgcc*) # Portland Group C compiler
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ tmp_addflag=' $pic_flag'
+ ;;
+ pgf77* | pgf90* | pgf95*) # Portland Group f77 and f90 compilers
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ tmp_addflag=' $pic_flag -Mnomain' ;;
+ ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64
+ tmp_addflag=' -i_dynamic' ;;
+ efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64
+ tmp_addflag=' -i_dynamic -nofor_main' ;;
+ ifc* | ifort*) # Intel Fortran compiler
+ tmp_addflag=' -nofor_main' ;;
+ lf95*) # Lahey Fortran 8.1
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ tmp_sharedflag='--shared' ;;
+ xl[[cC]]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ tmp_sharedflag='-qmkshrobj'
+ tmp_addflag= ;;
+ esac
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*) # Sun C 5.9
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ _LT_TAGVAR(compiler_needs_object, $1)=yes
+ tmp_sharedflag='-G' ;;
+ *Sun\ F*) # Sun Fortran 8.3
+ tmp_sharedflag='-G' ;;
+ esac
+ _LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+
+ if test "x$supports_anon_versioning" = xyes; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+ fi
+
+ case $cc_basename in
+ xlf*)
+ # IBM XL Fortran 10.1 on PPC cannot create shared libs itself
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='--whole-archive$convenience --no-whole-archive'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+ _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='-rpath $libdir'
+ _LT_TAGVAR(archive_cmds, $1)='$LD -shared $libobjs $deplibs $compiler_flags -soname $soname -o $lib'
+ if test "x$supports_anon_versioning" = xyes; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $LD -shared $libobjs $deplibs $compiler_flags -soname $soname -version-script $output_objdir/$libname.ver -o $lib'
+ fi
+ ;;
+ esac
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
+ wlarc=
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ fi
+ ;;
+
+ solaris*)
+ if $LD -v 2>&1 | $GREP 'BFD 2\.8' > /dev/null; then
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: The releases 2.8.* of the GNU linker cannot reliably
+*** create shared libraries on Solaris systems. Therefore, libtool
+*** is disabling shared libraries support. We urge you to upgrade GNU
+*** binutils to release 2.9.1 or newer. Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+ elif $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*)
+ case `$LD -v 2>&1` in
+ *\ [[01]].* | *\ 2.[[0-9]].* | *\ 2.1[[0-5]].*)
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not
+*** reliably create shared libraries on SCO systems. Therefore, libtool
+*** is disabling shared libraries support. We urge you to upgrade GNU
+*** binutils to release 2.16.91.0.3 or newer. Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+ ;;
+ *)
+ # For security reasons, it is highly recommended that you always
+ # use absolute paths for naming shared libraries, and exclude the
+ # DT_RUNPATH tag from executables and libraries. But doing so
+ # requires that you compile everything twice, which is a pain.
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+ ;;
+
+ sunos4*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ wlarc=
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ *)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+
+ if test "$_LT_TAGVAR(ld_shlibs, $1)" = no; then
+ runpath_var=
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)=
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ fi
+ else
+ # PORTME fill in a description of your system's linker (not GNU ld)
+ case $host_os in
+ aix3*)
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ _LT_TAGVAR(always_export_symbols, $1)=yes
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname'
+ # Note: this linker hardcodes the directories in LIBPATH if there
+ # are no directories specified by -L.
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then
+ # Neither direct hardcoding nor static linking is supported with a
+ # broken collect2.
+ _LT_TAGVAR(hardcode_direct, $1)=unsupported
+ fi
+ ;;
+
+ aix[[4-9]]*)
+ if test "$host_cpu" = ia64; then
+ # On IA64, the linker does run time linking by default, so we don't
+ # have to do anything special.
+ aix_use_runtimelinking=no
+ exp_sym_flag='-Bexport'
+ no_entry_flag=""
+ else
+ # If we're using GNU nm, then we don't want the "-C" option.
+ # -C means demangle to AIX nm, but means don't demangle with GNU nm
+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ else
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ fi
+ aix_use_runtimelinking=no
+
+ # Test if we are trying to use run time linking or normal
+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+ # need to do runtime linking.
+ case $host_os in aix4.[[23]]|aix4.[[23]].*|aix[[5-9]]*)
+ for ld_flag in $LDFLAGS; do
+ if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then
+ aix_use_runtimelinking=yes
+ break
+ fi
+ done
+ ;;
+ esac
+
+ exp_sym_flag='-bexport'
+ no_entry_flag='-bnoentry'
+ fi
+
+ # When large executables or shared objects are built, AIX ld can
+ # have problems creating the table of contents. If linking a library
+ # or program results in "error TOC overflow" add -mminimal-toc to
+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not
+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+ _LT_TAGVAR(archive_cmds, $1)=''
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=':'
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(file_list_spec, $1)='${wl}-f,'
+
+ if test "$GCC" = yes; then
+ case $host_os in aix4.[[012]]|aix4.[[012]].*)
+ # We only want to do this on AIX 4.2 and lower, the check
+ # below for broken collect2 doesn't work under 4.3+
+ collect2name=`${CC} -print-prog-name=collect2`
+ if test -f "$collect2name" &&
+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null
+ then
+ # We have reworked collect2
+ :
+ else
+ # We have old collect2
+ _LT_TAGVAR(hardcode_direct, $1)=unsupported
+ # It fails to find uninstalled libraries when the uninstalled
+ # path is not listed in the libpath. Setting hardcode_minus_L
+ # to unsupported forces relinking
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=
+ fi
+ ;;
+ esac
+ shared_flag='-shared'
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag="$shared_flag "'${wl}-G'
+ fi
+ _LT_TAGVAR(link_all_deplibs, $1)=no
+ else
+ # not using gcc
+ if test "$host_cpu" = ia64; then
+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+ # chokes on -Wl,-G. The following line is correct:
+ shared_flag='-G'
+ else
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag='${wl}-G'
+ else
+ shared_flag='${wl}-bM:SRE'
+ fi
+ fi
+ fi
+
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-bexpall'
+ # It seems that -bexpall does not export symbols beginning with
+ # underscore (_), so it is better to generate a list of symbols to export.
+ _LT_TAGVAR(always_export_symbols, $1)=yes
+ if test "$aix_use_runtimelinking" = yes; then
+ # Warning - without using the other runtime loading flags (-brtl),
+ # -berok will link without error, but may produce a broken library.
+ _LT_TAGVAR(allow_undefined_flag, $1)='-berok'
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ _LT_SYS_MODULE_PATH_AIX
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+ else
+ if test "$host_cpu" = ia64; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $libdir:/usr/lib:/lib'
+ _LT_TAGVAR(allow_undefined_flag, $1)="-z nodefs"
+ _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+ else
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ _LT_SYS_MODULE_PATH_AIX
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+ # Warning - without using the other run time loading flags,
+ # -berok will link without error, but may produce a broken library.
+ _LT_TAGVAR(no_undefined_flag, $1)=' ${wl}-bernotok'
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-berok'
+ # Exported symbols can be pulled into shared objects from archives
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='$convenience'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=yes
+ # This is similar to how AIX traditionally builds its shared libraries.
+ _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+ fi
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)=''
+ ;;
+ m68k)
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ ;;
+ esac
+ ;;
+
+ bsdi[[45]]*)
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)=-rdynamic
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # When not using gcc, we currently assume that we are using
+ # Microsoft Visual C++.
+ # hardcode_libdir_flag_spec is actually meaningless, as there is
+ # no search path for DLLs.
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=' '
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ # Tell ltmain to make .lib files, not .a files.
+ libext=lib
+ # Tell ltmain to make .dll files, not .so files.
+ shrext_cmds=".dll"
+ # FIXME: Setting linknames here is a bad hack.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -o $lib $libobjs $compiler_flags `$ECHO "X$deplibs" | $Xsed -e '\''s/ -lc$//'\''` -link -dll~linknames='
+ # The linker will automatically build a .lib file if we build a DLL.
+ _LT_TAGVAR(old_archive_from_new_cmds, $1)='true'
+ # FIXME: Should let the user specify the lib program.
+ _LT_TAGVAR(old_archive_cmds, $1)='lib -OUT:$oldlib$oldobjs$old_deplibs'
+ _LT_TAGVAR(fix_srcfile_path, $1)='`cygpath -w "$srcfile"`'
+ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+ ;;
+
+ darwin* | rhapsody*)
+ _LT_DARWIN_LINKER_FEATURES($1)
+ ;;
+
+ dgux*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ freebsd1*)
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor
+ # support. Future versions do this automatically, but an explicit c++rt0.o
+ # does not break anything, and helps significantly (at the cost of a little
+ # extra space).
+ freebsd2.2*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ # Unfortunately, older versions of FreeBSD 2 do not have this feature.
+ freebsd2*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ # FreeBSD 3 and greater uses gcc -shared to do shared libraries.
+ freebsd* | dragonfly*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ hpux9*)
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ fi
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ ;;
+
+ hpux10*)
+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags'
+ fi
+ if test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='+b $libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ fi
+ ;;
+
+ hpux11*)
+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+ case $host_cpu in
+ hppa*64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ ia64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ else
+ case $host_cpu in
+ hppa*64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ ia64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ fi
+ if test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ case $host_cpu in
+ hppa*64*|ia64*)
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+ *)
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ ;;
+ esac
+ fi
+ ;;
+
+ irix5* | irix6* | nonstopux*)
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ # Try to use the -exported_symbol ld option, if it does not
+ # work, assume that -exports_file does not work either and
+ # implicitly export all symbols.
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null"
+ AC_LINK_IFELSE(int foo(void) {},
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib'
+ )
+ LDFLAGS="$save_LDFLAGS"
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib'
+ fi
+ _LT_TAGVAR(archive_cmds_need_lc, $1)='no'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(inherit_rpath, $1)=yes
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ ;;
+
+ netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF
+ fi
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ newsos6)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ *nto* | *qnx*)
+ ;;
+
+ openbsd*)
+ if test -f /usr/libexec/ld.so; then
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ else
+ case $host_os in
+ openbsd[[01]].* | openbsd2.[[0-7]] | openbsd2.[[0-7]].*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ ;;
+ esac
+ fi
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ os2*)
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ _LT_TAGVAR(archive_cmds, $1)='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def'
+ _LT_TAGVAR(old_archive_from_new_cmds, $1)='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def'
+ ;;
+
+ osf3*)
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ else
+ _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ fi
+ _LT_TAGVAR(archive_cmds_need_lc, $1)='no'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ ;;
+
+ osf4* | osf5*) # as osf3* with the addition of -msym flag
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ else
+ _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~
+ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp'
+
+ # Both c and cxx compiler support -rpath directly
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir'
+ fi
+ _LT_TAGVAR(archive_cmds_need_lc, $1)='no'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ ;;
+
+ solaris*)
+ _LT_TAGVAR(no_undefined_flag, $1)=' -z defs'
+ if test "$GCC" = yes; then
+ wlarc='${wl}'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp'
+ else
+ case `$CC -V 2>&1` in
+ *"Compilers 5.0"*)
+ wlarc=''
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp'
+ ;;
+ *)
+ wlarc='${wl}'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp'
+ ;;
+ esac
+ fi
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ case $host_os in
+ solaris2.[[0-5]] | solaris2.[[0-5]].*) ;;
+ *)
+ # The compiler driver will combine and reorder linker options,
+ # but understands `-z linker_flag'. GCC discards it without `$wl',
+ # but is careful enough not to reorder.
+ # Supported since Solaris 2.6 (maybe 2.5.1?)
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract'
+ else
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='-z allextract$convenience -z defaultextract'
+ fi
+ ;;
+ esac
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ ;;
+
+ sunos4*)
+ if test "x$host_vendor" = xsequent; then
+ # Use $CC to link under sequent, because it throws in some extra .o
+ # files that make .init and .fini sections work.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags'
+ fi
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ sysv4)
+ case $host_vendor in
+ sni)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_direct, $1)=yes # is this really true???
+ ;;
+ siemens)
+ ## LD is ld it makes a PLAMLIB
+ ## CC just makes a GrossModule.
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(reload_cmds, $1)='$CC -r -o $output$reload_objs'
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ ;;
+ motorola)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_direct, $1)=no #Motorola manual says yes, but my tests say they lie
+ ;;
+ esac
+ runpath_var='LD_RUN_PATH'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ sysv4.3*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='-Bexport'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ runpath_var=LD_RUN_PATH
+ hardcode_runpath_var=yes
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ fi
+ ;;
+
+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[[01]].[[10]]* | unixware7* | sco3.2v5.0.[[024]]*)
+ _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ runpath_var='LD_RUN_PATH'
+
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ fi
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6*)
+ # Note: We can NOT use -z defs as we might desire, because we do not
+ # link with -lc, and that would cause any symbols used from libc to
+ # always be unresolved, which means just about no library would
+ # ever link correctly. If we're not using GNU ld we use -z text
+ # though, which does catch some bad symbols but isn't as heavy-handed
+ # as -z defs.
+ _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+ _LT_TAGVAR(allow_undefined_flag, $1)='${wl}-z,nodefs'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R,$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=':'
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Bexport'
+ runpath_var='LD_RUN_PATH'
+
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ fi
+ ;;
+
+ uts4*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ *)
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+
+ if test x$host_vendor = xsni; then
+ case $host in
+ sysv4 | sysv4.2uw2* | sysv4.3* | sysv5*)
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Blargedynsym'
+ ;;
+ esac
+ fi
+ fi
+])
+AC_MSG_RESULT([$_LT_TAGVAR(ld_shlibs, $1)])
+test "$_LT_TAGVAR(ld_shlibs, $1)" = no && can_build_shared=no
+
+_LT_TAGVAR(with_gnu_ld, $1)=$with_gnu_ld
+
+_LT_DECL([], [libext], [0], [Old archive suffix (normally "a")])dnl
+_LT_DECL([], [shrext_cmds], [1], [Shared library suffix (normally ".so")])dnl
+_LT_DECL([], [extract_expsyms_cmds], [2],
+ [The commands to extract the exported symbol list from a shared archive])
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$_LT_TAGVAR(archive_cmds_need_lc, $1)" in
+x|xyes)
+ # Assume -lc should be added
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=yes
+
+ if test "$enable_shared" = yes && test "$GCC" = yes; then
+ case $_LT_TAGVAR(archive_cmds, $1) in
+ *'~'*)
+ # FIXME: we may have to deal with multi-command sequences.
+ ;;
+ '$CC '*)
+ # Test whether the compiler implicitly links with -lc since on some
+ # systems, -lgcc has to come before -lc. If gcc already passes -lc
+ # to ld, don't add -lc before -lgcc.
+ AC_MSG_CHECKING([whether -lc should be explicitly linked in])
+ $RM conftest*
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ if AC_TRY_EVAL(ac_compile) 2>conftest.err; then
+ soname=conftest
+ lib=conftest
+ libobjs=conftest.$ac_objext
+ deplibs=
+ wl=$_LT_TAGVAR(lt_prog_compiler_wl, $1)
+ pic_flag=$_LT_TAGVAR(lt_prog_compiler_pic, $1)
+ compiler_flags=-v
+ linker_flags=-v
+ verstring=
+ output_objdir=.
+ libname=conftest
+ lt_save_allow_undefined_flag=$_LT_TAGVAR(allow_undefined_flag, $1)
+ _LT_TAGVAR(allow_undefined_flag, $1)=
+ if AC_TRY_EVAL(_LT_TAGVAR(archive_cmds, $1) 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1)
+ then
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ else
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=yes
+ fi
+ _LT_TAGVAR(allow_undefined_flag, $1)=$lt_save_allow_undefined_flag
+ else
+ cat conftest.err 1>&5
+ fi
+ $RM conftest*
+ AC_MSG_RESULT([$_LT_TAGVAR(archive_cmds_need_lc, $1)])
+ ;;
+ esac
+ fi
+ ;;
+esac
+
+_LT_TAGDECL([build_libtool_need_lc], [archive_cmds_need_lc], [0],
+ [Whether or not to add -lc for building shared libraries])
+_LT_TAGDECL([allow_libtool_libs_with_static_runtimes],
+ [enable_shared_with_static_runtimes], [0],
+ [Whether or not to disallow shared libs when runtime libs are static])
+_LT_TAGDECL([], [export_dynamic_flag_spec], [1],
+ [Compiler flag to allow reflexive dlopens])
+_LT_TAGDECL([], [whole_archive_flag_spec], [1],
+ [Compiler flag to generate shared objects directly from archives])
+_LT_TAGDECL([], [compiler_needs_object], [1],
+ [Whether the compiler copes with passing no objects directly])
+_LT_TAGDECL([], [old_archive_from_new_cmds], [2],
+ [Create an old-style archive from a shared archive])
+_LT_TAGDECL([], [old_archive_from_expsyms_cmds], [2],
+ [Create a temporary old-style archive to link instead of a shared archive])
+_LT_TAGDECL([], [archive_cmds], [2], [Commands used to build a shared archive])
+_LT_TAGDECL([], [archive_expsym_cmds], [2])
+_LT_TAGDECL([], [module_cmds], [2],
+ [Commands used to build a loadable module if different from building
+ a shared archive.])
+_LT_TAGDECL([], [module_expsym_cmds], [2])
+_LT_TAGDECL([], [with_gnu_ld], [1],
+ [Whether we are building with GNU ld or not])
+_LT_TAGDECL([], [allow_undefined_flag], [1],
+ [Flag that allows shared libraries with undefined symbols to be built])
+_LT_TAGDECL([], [no_undefined_flag], [1],
+ [Flag that enforces no undefined symbols])
+_LT_TAGDECL([], [hardcode_libdir_flag_spec], [1],
+ [Flag to hardcode $libdir into a binary during linking.
+ This must work even if $libdir does not exist])
+_LT_TAGDECL([], [hardcode_libdir_flag_spec_ld], [1],
+ [[If ld is used when linking, flag to hardcode $libdir into a binary
+ during linking. This must work even if $libdir does not exist]])
+_LT_TAGDECL([], [hardcode_libdir_separator], [1],
+ [Whether we need a single "-rpath" flag with a separated argument])
+_LT_TAGDECL([], [hardcode_direct], [0],
+ [Set to "yes" if using DIR/libNAME${shared_ext} during linking hardcodes
+ DIR into the resulting binary])
+_LT_TAGDECL([], [hardcode_direct_absolute], [0],
+ [Set to "yes" if using DIR/libNAME${shared_ext} during linking hardcodes
+ DIR into the resulting binary and the resulting library dependency is
+ "absolute", i.e impossible to change by setting ${shlibpath_var} if the
+ library is relocated])
+_LT_TAGDECL([], [hardcode_minus_L], [0],
+ [Set to "yes" if using the -LDIR flag during linking hardcodes DIR
+ into the resulting binary])
+_LT_TAGDECL([], [hardcode_shlibpath_var], [0],
+ [Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR
+ into the resulting binary])
+_LT_TAGDECL([], [hardcode_automatic], [0],
+ [Set to "yes" if building a shared library automatically hardcodes DIR
+ into the library and all subsequent libraries and executables linked
+ against it])
+_LT_TAGDECL([], [inherit_rpath], [0],
+ [Set to yes if linker adds runtime paths of dependent libraries
+ to runtime path list])
+_LT_TAGDECL([], [link_all_deplibs], [0],
+ [Whether libtool must link a program against all its dependency libraries])
+_LT_TAGDECL([], [fix_srcfile_path], [1],
+ [Fix the shell variable $srcfile for the compiler])
+_LT_TAGDECL([], [always_export_symbols], [0],
+ [Set to "yes" if exported symbols are required])
+_LT_TAGDECL([], [export_symbols_cmds], [2],
+ [The commands to list exported symbols])
+_LT_TAGDECL([], [exclude_expsyms], [1],
+ [Symbols that should not be listed in the preloaded symbols])
+_LT_TAGDECL([], [include_expsyms], [1],
+ [Symbols that must always be exported])
+_LT_TAGDECL([], [prelink_cmds], [2],
+ [Commands necessary for linking programs (against libraries) with templates])
+_LT_TAGDECL([], [file_list_spec], [1],
+ [Specify filename containing input files])
+dnl FIXME: Not yet implemented
+dnl _LT_TAGDECL([], [thread_safe_flag_spec], [1],
+dnl [Compiler flag to generate thread safe objects])
+])# _LT_LINKER_SHLIBS
+
+
+# _LT_LANG_C_CONFIG([TAG])
+# ------------------------
+# Ensure that the configuration variables for a C compiler are suitably
+# defined. These variables are subsequently used by _LT_CONFIG to write
+# the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_C_CONFIG],
+[m4_require([_LT_DECL_EGREP])dnl
+lt_save_CC="$CC"
+AC_LANG_PUSH(C)
+
+# Source file extension for C test sources.
+ac_ext=c
+
+# Object file extension for compiled C test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="int some_variable = 0;"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='int main(){return(0);}'
+
+_LT_TAG_COMPILER
+# Save the default compiler, since it gets overwritten when the other
+# tags are being tested, and _LT_TAGVAR(compiler, []) is a NOP.
+compiler_DEFAULT=$CC
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+if test -n "$compiler"; then
+ _LT_COMPILER_NO_RTTI($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_SYS_DYNAMIC_LINKER($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+ LT_SYS_DLOPEN_SELF
+ _LT_CMD_STRIPLIB
+
+ # Report which library types will actually be built
+ AC_MSG_CHECKING([if libtool supports shared libraries])
+ AC_MSG_RESULT([$can_build_shared])
+
+ AC_MSG_CHECKING([whether to build shared libraries])
+ test "$can_build_shared" = "no" && enable_shared=no
+
+ # On AIX, shared libraries and static libraries use the same namespace, and
+ # are all built from PIC.
+ case $host_os in
+ aix3*)
+ test "$enable_shared" = yes && enable_static=no
+ if test -n "$RANLIB"; then
+ archive_cmds="$archive_cmds~\$RANLIB \$lib"
+ postinstall_cmds='$RANLIB $lib'
+ fi
+ ;;
+
+ aix[[4-9]]*)
+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+ test "$enable_shared" = yes && enable_static=no
+ fi
+ ;;
+ esac
+ AC_MSG_RESULT([$enable_shared])
+
+ AC_MSG_CHECKING([whether to build static libraries])
+ # Make sure either enable_shared or enable_static is yes.
+ test "$enable_shared" = yes || enable_static=yes
+ AC_MSG_RESULT([$enable_static])
+
+ _LT_CONFIG($1)
+fi
+AC_LANG_POP
+CC="$lt_save_CC"
+])# _LT_LANG_C_CONFIG
+
+
+# _LT_PROG_CXX
+# ------------
+# Since AC_PROG_CXX is broken, in that it returns g++ if there is no c++
+# compiler, we have our own version here.
+m4_defun([_LT_PROG_CXX],
+[
+pushdef([AC_MSG_ERROR], [_lt_caught_CXX_error=yes])
+AC_PROG_CXX
+if test -n "$CXX" && ( test "X$CXX" != "Xno" &&
+ ( (test "X$CXX" = "Xg++" && `g++ -v >/dev/null 2>&1` ) ||
+ (test "X$CXX" != "Xg++"))) ; then
+ AC_PROG_CXXCPP
+else
+ _lt_caught_CXX_error=yes
+fi
+popdef([AC_MSG_ERROR])
+])# _LT_PROG_CXX
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([_LT_PROG_CXX], [])
+
+
+# _LT_LANG_CXX_CONFIG([TAG])
+# --------------------------
+# Ensure that the configuration variables for a C++ compiler are suitably
+# defined. These variables are subsequently used by _LT_CONFIG to write
+# the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_CXX_CONFIG],
+[AC_REQUIRE([_LT_PROG_CXX])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_EGREP])dnl
+
+AC_LANG_PUSH(C++)
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+_LT_TAGVAR(allow_undefined_flag, $1)=
+_LT_TAGVAR(always_export_symbols, $1)=no
+_LT_TAGVAR(archive_expsym_cmds, $1)=
+_LT_TAGVAR(compiler_needs_object, $1)=no
+_LT_TAGVAR(export_dynamic_flag_spec, $1)=
+_LT_TAGVAR(hardcode_direct, $1)=no
+_LT_TAGVAR(hardcode_direct_absolute, $1)=no
+_LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+_LT_TAGVAR(hardcode_libdir_separator, $1)=
+_LT_TAGVAR(hardcode_minus_L, $1)=no
+_LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
+_LT_TAGVAR(hardcode_automatic, $1)=no
+_LT_TAGVAR(inherit_rpath, $1)=no
+_LT_TAGVAR(module_cmds, $1)=
+_LT_TAGVAR(module_expsym_cmds, $1)=
+_LT_TAGVAR(link_all_deplibs, $1)=unknown
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+_LT_TAGVAR(no_undefined_flag, $1)=
+_LT_TAGVAR(whole_archive_flag_spec, $1)=
+_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+
+# Source file extension for C++ test sources.
+ac_ext=cpp
+
+# Object file extension for compiled C++ test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# No sense in running all these tests if we already determined that
+# the CXX compiler isn't working. Some variables (like enable_shared)
+# are currently assumed to apply to all compilers on this platform,
+# and will be corrupted by setting them based on a non-working compiler.
+if test "$_lt_caught_CXX_error" != yes; then
+ # Code to be used in simple compile tests
+ lt_simple_compile_test_code="int some_variable = 0;"
+
+ # Code to be used in simple link tests
+ lt_simple_link_test_code='int main(int, char *[[]]) { return(0); }'
+
+ # ltmain only uses $CC for tagged configurations so make sure $CC is set.
+ _LT_TAG_COMPILER
+
+ # save warnings/boilerplate of simple test code
+ _LT_COMPILER_BOILERPLATE
+ _LT_LINKER_BOILERPLATE
+
+ # Allow CC to be a program name with arguments.
+ lt_save_CC=$CC
+ lt_save_LD=$LD
+ lt_save_GCC=$GCC
+ GCC=$GXX
+ lt_save_with_gnu_ld=$with_gnu_ld
+ lt_save_path_LD=$lt_cv_path_LD
+ if test -n "${lt_cv_prog_gnu_ldcxx+set}"; then
+ lt_cv_prog_gnu_ld=$lt_cv_prog_gnu_ldcxx
+ else
+ $as_unset lt_cv_prog_gnu_ld
+ fi
+ if test -n "${lt_cv_path_LDCXX+set}"; then
+ lt_cv_path_LD=$lt_cv_path_LDCXX
+ else
+ $as_unset lt_cv_path_LD
+ fi
+ test -z "${LDCXX+set}" || LD=$LDCXX
+ CC=${CXX-"c++"}
+ compiler=$CC
+ _LT_TAGVAR(compiler, $1)=$CC
+ _LT_CC_BASENAME([$compiler])
+
+ if test -n "$compiler"; then
+ # We don't want -fno-exception when compiling C++ code, so set the
+ # no_builtin_flag separately
+ if test "$GXX" = yes; then
+ _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin'
+ else
+ _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=
+ fi
+
+ if test "$GXX" = yes; then
+ # Set up default GNU C++ configuration
+
+ LT_PATH_LD
+
+ # Check if GNU C++ uses GNU ld as the underlying linker, since the
+ # archiving commands below assume that GNU ld is being used.
+ if test "$with_gnu_ld" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+
+ # If archive_cmds runs LD, not CC, wlarc should be empty
+ # XXX I think wlarc can be eliminated in ltcf-cxx, but I need to
+ # investigate it a little bit more. (MM)
+ wlarc='${wl}'
+
+ # ancient GNU ld didn't support --whole-archive et. al.
+ if eval "`$CC -print-prog-name=ld` --help 2>&1" |
+ $GREP 'no-whole-archive' > /dev/null; then
+ _LT_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ else
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ fi
+ else
+ with_gnu_ld=no
+ wlarc=
+
+ # A generic and very simple default shared library creation
+ # command for GNU C++ for the case where it uses the native
+ # linker, instead of GNU ld. If possible, this setting should
+ # overridden to take advantage of the native linker features on
+ # the platform it is being used on.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+ fi
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+
+ else
+ GXX=no
+ with_gnu_ld=no
+ wlarc=
+ fi
+
+ # PORTME: fill in a description of your system's C++ link characteristics
+ AC_MSG_CHECKING([whether the $compiler linker ($LD) supports shared libraries])
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ case $host_os in
+ aix3*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ aix[[4-9]]*)
+ if test "$host_cpu" = ia64; then
+ # On IA64, the linker does run time linking by default, so we don't
+ # have to do anything special.
+ aix_use_runtimelinking=no
+ exp_sym_flag='-Bexport'
+ no_entry_flag=""
+ else
+ aix_use_runtimelinking=no
+
+ # Test if we are trying to use run time linking or normal
+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+ # need to do runtime linking.
+ case $host_os in aix4.[[23]]|aix4.[[23]].*|aix[[5-9]]*)
+ for ld_flag in $LDFLAGS; do
+ case $ld_flag in
+ *-brtl*)
+ aix_use_runtimelinking=yes
+ break
+ ;;
+ esac
+ done
+ ;;
+ esac
+
+ exp_sym_flag='-bexport'
+ no_entry_flag='-bnoentry'
+ fi
+
+ # When large executables or shared objects are built, AIX ld can
+ # have problems creating the table of contents. If linking a library
+ # or program results in "error TOC overflow" add -mminimal-toc to
+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not
+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+ _LT_TAGVAR(archive_cmds, $1)=''
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=':'
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(file_list_spec, $1)='${wl}-f,'
+
+ if test "$GXX" = yes; then
+ case $host_os in aix4.[[012]]|aix4.[[012]].*)
+ # We only want to do this on AIX 4.2 and lower, the check
+ # below for broken collect2 doesn't work under 4.3+
+ collect2name=`${CC} -print-prog-name=collect2`
+ if test -f "$collect2name" &&
+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null
+ then
+ # We have reworked collect2
+ :
+ else
+ # We have old collect2
+ _LT_TAGVAR(hardcode_direct, $1)=unsupported
+ # It fails to find uninstalled libraries when the uninstalled
+ # path is not listed in the libpath. Setting hardcode_minus_L
+ # to unsupported forces relinking
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=
+ fi
+ esac
+ shared_flag='-shared'
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag="$shared_flag "'${wl}-G'
+ fi
+ else
+ # not using gcc
+ if test "$host_cpu" = ia64; then
+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+ # chokes on -Wl,-G. The following line is correct:
+ shared_flag='-G'
+ else
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag='${wl}-G'
+ else
+ shared_flag='${wl}-bM:SRE'
+ fi
+ fi
+ fi
+
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-bexpall'
+ # It seems that -bexpall does not export symbols beginning with
+ # underscore (_), so it is better to generate a list of symbols to
+ # export.
+ _LT_TAGVAR(always_export_symbols, $1)=yes
+ if test "$aix_use_runtimelinking" = yes; then
+ # Warning - without using the other runtime loading flags (-brtl),
+ # -berok will link without error, but may produce a broken library.
+ _LT_TAGVAR(allow_undefined_flag, $1)='-berok'
+ # Determine the default libpath from the value encoded in an empty
+ # executable.
+ _LT_SYS_MODULE_PATH_AIX
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+ else
+ if test "$host_cpu" = ia64; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $libdir:/usr/lib:/lib'
+ _LT_TAGVAR(allow_undefined_flag, $1)="-z nodefs"
+ _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+ else
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ _LT_SYS_MODULE_PATH_AIX
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+ # Warning - without using the other run time loading flags,
+ # -berok will link without error, but may produce a broken library.
+ _LT_TAGVAR(no_undefined_flag, $1)=' ${wl}-bernotok'
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-berok'
+ # Exported symbols can be pulled into shared objects from archives
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='$convenience'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=yes
+ # This is similar to how AIX traditionally builds its shared
+ # libraries.
+ _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+ fi
+ fi
+ ;;
+
+ beos*)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ # Joseph Beckenbach <jrb3 at best.com> says some releases of gcc
+ # support --undefined. This deserves some investigation. FIXME
+ _LT_TAGVAR(archive_cmds, $1)='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ chorus*)
+ case $cc_basename in
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # _LT_TAGVAR(hardcode_libdir_flag_spec, $1) is actually meaningless,
+ # as there is no search path for DLLs.
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ _LT_TAGVAR(always_export_symbols, $1)=no
+ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+
+ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ # If the export-symbols file already is a .def file (1st line
+ # is EXPORTS), use it as is; otherwise, prepend...
+ _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+ cp $export_symbols $output_objdir/$soname.def;
+ else
+ echo EXPORTS > $output_objdir/$soname.def;
+ cat $export_symbols >> $output_objdir/$soname.def;
+ fi~
+ $CC -shared -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ darwin* | rhapsody*)
+ _LT_DARWIN_LINKER_FEATURES($1)
+ ;;
+
+ dgux*)
+ case $cc_basename in
+ ec++*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ ghcx*)
+ # Green Hills C++ Compiler
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ freebsd[[12]]*)
+ # C++ shared libraries reported to be fairly broken before
+ # switch to ELF
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ freebsd-elf*)
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ ;;
+
+ freebsd* | dragonfly*)
+ # FreeBSD 3 and later use GNU C++ and GNU ld with standard ELF
+ # conventions
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ ;;
+
+ gnu*)
+ ;;
+
+ hpux9*)
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes # Not in the search PATH,
+ # but as the default
+ # location of the library.
+
+ case $cc_basename in
+ CC*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ aCC*)
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -b ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $EGREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -shared -nostdlib -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ else
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+ ;;
+
+ hpux10*|hpux11*)
+ if test $with_gnu_ld = no; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ case $host_cpu in
+ hppa*64*|ia64*)
+ ;;
+ *)
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ ;;
+ esac
+ fi
+ case $host_cpu in
+ hppa*64*|ia64*)
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+ *)
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes # Not in the search PATH,
+ # but as the default
+ # location of the library.
+ ;;
+ esac
+
+ case $cc_basename in
+ CC*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ aCC*)
+ case $host_cpu in
+ hppa*64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ ia64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ esac
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $GREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ if test $with_gnu_ld = no; then
+ case $host_cpu in
+ hppa*64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ ia64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ esac
+ fi
+ else
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+ ;;
+
+ interix[[3-9]]*)
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+ # Instead, shared libraries are loaded at an image base (0x10000000 by
+ # default) and relocated if they conflict, which is a slow very memory
+ # consuming and fragmenting process. To avoid this, we pick a random,
+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+ # time. Moving up from 0x10000000 also allows more sbrk(2) space.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ ;;
+ irix5* | irix6*)
+ case $cc_basename in
+ CC*)
+ # SGI C++
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -all -multigot $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+
+ # Archives containing C++ object files must be created using
+ # "CC -ar", where "CC" is the IRIX C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC -ar -WR,-u -o $oldlib $oldobjs'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ if test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` -o $lib'
+ fi
+ fi
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ ;;
+ esac
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(inherit_rpath, $1)=yes
+ ;;
+
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ KCC*)
+ # Kuck and Associates, Inc. (KAI) C++ Compiler
+
+ # KCC will only create a shared library if the output file
+ # ends with ".so" (or ".sl" for HP-UX), so rename the library
+ # to its proper name (with version) after linking.
+ _LT_TAGVAR(archive_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib ${wl}-retain-symbols-file,$export_symbols; mv \$templib $lib'
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 | $GREP "ld"`; rm -f libconftest$shared_ext; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+
+ # Archives containing C++ object files must be created using
+ # "CC -Bstatic", where "CC" is the KAI C++ compiler.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC -Bstatic -o $oldlib $oldobjs'
+ ;;
+ icpc* | ecpc* )
+ # Intel C++
+ with_gnu_ld=yes
+ # version 8.0 and above of icpc choke on multiply defined symbols
+ # if we add $predep_objects and $postdep_objects, however 7.1 and
+ # earlier do not add the objects themselves.
+ case `$CC -V 2>&1` in
+ *"Version 7."*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ ;;
+ *) # Version 8.0 or newer
+ tmp_idyn=
+ case $host_cpu in
+ ia64*) tmp_idyn=' -i_dynamic';;
+ esac
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ ;;
+ esac
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive$convenience ${wl}--no-whole-archive'
+ ;;
+ pgCC* | pgcpp*)
+ # Portland Group C++ compiler
+ case `$CC -V` in
+ *pgCC\ [[1-5]]* | *pgcpp\ [[1-5]]*)
+ _LT_TAGVAR(prelink_cmds, $1)='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $objs $libobjs $compile_deplibs~
+ compile_command="$compile_command `find $tpldir -name \*.o | $NL2SP`"'
+ _LT_TAGVAR(old_archive_cmds, $1)='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $oldobjs$old_deplibs~
+ $AR $AR_FLAGS $oldlib$oldobjs$old_deplibs `find $tpldir -name \*.o | $NL2SP`~
+ $RANLIB $oldlib'
+ _LT_TAGVAR(archive_cmds, $1)='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~
+ $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~
+ $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+ ;;
+ *) # Version 6 will use weak symbols
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+ ;;
+ esac
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}--rpath ${wl}$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ ;;
+ cxx*)
+ # Compaq C++
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib ${wl}-retain-symbols-file $wl$export_symbols'
+
+ runpath_var=LD_RUN_PATH
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld .*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ xl*)
+ # IBM XL 8.0 on PPC, with GNU ld
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ if test "x$supports_anon_versioning" = xyes; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+ fi
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+ _LT_TAGVAR(no_undefined_flag, $1)=' -zdefs'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file ${wl}$export_symbols'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ _LT_TAGVAR(compiler_needs_object, $1)=yes
+
+ # Not sure whether something based on
+ # $CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1
+ # would be better.
+ output_verbose_link_cmd='echo'
+
+ # Archives containing C++ object files must be created using
+ # "CC -xar", where "CC" is the Sun C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC -xar -o $oldlib $oldobjs'
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+
+ lynxos*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ m88k*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ mvs*)
+ case $cc_basename in
+ cxx*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ netbsd*)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $predep_objects $libobjs $deplibs $postdep_objects $linker_flags'
+ wlarc=
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ fi
+ # Workaround some broken pre-1.5 toolchains
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP conftest.$objext | $SED -e "s:-lgcc -lc -lgcc::"'
+ ;;
+
+ *nto* | *qnx*)
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ ;;
+
+ openbsd2*)
+ # C++ shared libraries are fairly broken
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ openbsd*)
+ if test -f /usr/libexec/ld.so; then
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file,$export_symbols -o $lib'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ _LT_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ fi
+ output_verbose_link_cmd=echo
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ osf3* | osf4* | osf5*)
+ case $cc_basename in
+ KCC*)
+ # Kuck and Associates, Inc. (KAI) C++ Compiler
+
+ # KCC will only create a shared library if the output file
+ # ends with ".so" (or ".sl" for HP-UX), so rename the library
+ # to its proper name (with version) after linking.
+ _LT_TAGVAR(archive_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo "$lib" | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ # Archives containing C++ object files must be created using
+ # the KAI C++ compiler.
+ case $host in
+ osf3*) _LT_TAGVAR(old_archive_cmds, $1)='$CC -Bstatic -o $oldlib $oldobjs' ;;
+ *) _LT_TAGVAR(old_archive_cmds, $1)='$CC -o $oldlib $oldobjs' ;;
+ esac
+ ;;
+ RCC*)
+ # Rational C++ 2.4.1
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ cxx*)
+ case $host in
+ osf3*)
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $soname `test -n "$verstring" && $ECHO "X${wl}-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ ;;
+ *)
+ _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done~
+ echo "-hidden">> $lib.exp~
+ $CC -shared$allow_undefined_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname ${wl}-input ${wl}$lib.exp `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~
+ $RM $lib.exp'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir'
+ ;;
+ esac
+
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld" | $GREP -v "ld:"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld.*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+ case $host in
+ osf3*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ ;;
+ esac
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+
+ else
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+ ;;
+
+ psos*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ sunos4*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.x
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ lcc*)
+ # Lucid
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ solaris*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.2, 5.x and Centerline C++
+ _LT_TAGVAR(archive_cmds_need_lc,$1)=yes
+ _LT_TAGVAR(no_undefined_flag, $1)=' -zdefs'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G${allow_undefined_flag} ${wl}-M ${wl}$lib.exp -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ case $host_os in
+ solaris2.[[0-5]] | solaris2.[[0-5]].*) ;;
+ *)
+ # The compiler driver will combine and reorder linker options,
+ # but understands `-z linker_flag'.
+ # Supported since Solaris 2.6 (maybe 2.5.1?)
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='-z allextract$convenience -z defaultextract'
+ ;;
+ esac
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+
+ output_verbose_link_cmd='echo'
+
+ # Archives containing C++ object files must be created using
+ # "CC -xar", where "CC" is the Sun C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC -xar -o $oldlib $oldobjs'
+ ;;
+ gcx*)
+ # Green Hills C++ Compiler
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+
+ # The C++ compiler must be used to create the archive.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC $LDFLAGS -archive -o $oldlib $oldobjs'
+ ;;
+ *)
+ # GNU C++ compiler with Solaris linker
+ if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(no_undefined_flag, $1)=' ${wl}-z ${wl}defs'
+ if $CC --version | $GREP -v '^2\.7' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -shared -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+ else
+ # g++ 2.7 appears to require `-G' NOT `-shared' on this
+ # platform.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -G $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+ fi
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $wl$libdir'
+ case $host_os in
+ solaris2.[[0-5]] | solaris2.[[0-5]].*) ;;
+ *)
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract'
+ ;;
+ esac
+ fi
+ ;;
+ esac
+ ;;
+
+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[[01]].[[10]]* | unixware7* | sco3.2v5.0.[[024]]*)
+ _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ runpath_var='LD_RUN_PATH'
+
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6*)
+ # Note: We can NOT use -z defs as we might desire, because we do not
+ # link with -lc, and that would cause any symbols used from libc to
+ # always be unresolved, which means just about no library would
+ # ever link correctly. If we're not using GNU ld we use -z text
+ # though, which does catch some bad symbols but isn't as heavy-handed
+ # as -z defs.
+ _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+ _LT_TAGVAR(allow_undefined_flag, $1)='${wl}-z,nodefs'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R,$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=':'
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Bexport'
+ runpath_var='LD_RUN_PATH'
+
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ ;;
+
+ tandem*)
+ case $cc_basename in
+ NCC*)
+ # NonStop-UX NCC 3.20
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ vxworks*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+
+ AC_MSG_RESULT([$_LT_TAGVAR(ld_shlibs, $1)])
+ test "$_LT_TAGVAR(ld_shlibs, $1)" = no && can_build_shared=no
+
+ _LT_TAGVAR(GCC, $1)="$GXX"
+ _LT_TAGVAR(LD, $1)="$LD"
+
+ ## CAVEAT EMPTOR:
+ ## There is no encapsulation within the following macros, do not change
+ ## the running order or otherwise move them around unless you know exactly
+ ## what you are doing...
+ _LT_SYS_HIDDEN_LIBDEPS($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_SYS_DYNAMIC_LINKER($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+ fi # test -n "$compiler"
+
+ CC=$lt_save_CC
+ LDCXX=$LD
+ LD=$lt_save_LD
+ GCC=$lt_save_GCC
+ with_gnu_ld=$lt_save_with_gnu_ld
+ lt_cv_path_LDCXX=$lt_cv_path_LD
+ lt_cv_path_LD=$lt_save_path_LD
+ lt_cv_prog_gnu_ldcxx=$lt_cv_prog_gnu_ld
+ lt_cv_prog_gnu_ld=$lt_save_with_gnu_ld
+fi # test "$_lt_caught_CXX_error" != yes
+
+AC_LANG_POP
+])# _LT_LANG_CXX_CONFIG
+
+
+# _LT_SYS_HIDDEN_LIBDEPS([TAGNAME])
+# ---------------------------------
+# Figure out "hidden" library dependencies from verbose
+# compiler output when linking a shared library.
+# Parse the compiler output and extract the necessary
+# objects, libraries and library flags.
+m4_defun([_LT_SYS_HIDDEN_LIBDEPS],
+[m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+# Dependencies to place before and after the object being linked:
+_LT_TAGVAR(predep_objects, $1)=
+_LT_TAGVAR(postdep_objects, $1)=
+_LT_TAGVAR(predeps, $1)=
+_LT_TAGVAR(postdeps, $1)=
+_LT_TAGVAR(compiler_lib_search_path, $1)=
+
+dnl we can't use the lt_simple_compile_test_code here,
+dnl because it contains code intended for an executable,
+dnl not a library. It's possible we should let each
+dnl tag define a new lt_????_link_test_code variable,
+dnl but it's only used here...
+m4_if([$1], [], [cat > conftest.$ac_ext <<_LT_EOF
+int a;
+void foo (void) { a = 0; }
+_LT_EOF
+], [$1], [CXX], [cat > conftest.$ac_ext <<_LT_EOF
+class Foo
+{
+public:
+ Foo (void) { a = 0; }
+private:
+ int a;
+};
+_LT_EOF
+], [$1], [F77], [cat > conftest.$ac_ext <<_LT_EOF
+ subroutine foo
+ implicit none
+ integer*4 a
+ a=0
+ return
+ end
+_LT_EOF
+], [$1], [FC], [cat > conftest.$ac_ext <<_LT_EOF
+ subroutine foo
+ implicit none
+ integer a
+ a=0
+ return
+ end
+_LT_EOF
+], [$1], [GCJ], [cat > conftest.$ac_ext <<_LT_EOF
+public class foo {
+ private int a;
+ public void bar (void) {
+ a = 0;
+ }
+};
+_LT_EOF
+])
+dnl Parse the compiler output and extract the necessary
+dnl objects, libraries and library flags.
+if AC_TRY_EVAL(ac_compile); then
+ # Parse the compiler output and extract the necessary
+ # objects, libraries and library flags.
+
+ # Sentinel used to keep track of whether or not we are before
+ # the conftest object file.
+ pre_test_object_deps_done=no
+
+ for p in `eval "$output_verbose_link_cmd"`; do
+ case $p in
+
+ -L* | -R* | -l*)
+ # Some compilers place space between "-{L,R}" and the path.
+ # Remove the space.
+ if test $p = "-L" ||
+ test $p = "-R"; then
+ prev=$p
+ continue
+ else
+ prev=
+ fi
+
+ if test "$pre_test_object_deps_done" = no; then
+ case $p in
+ -L* | -R*)
+ # Internal compiler library paths should come after those
+ # provided the user. The postdeps already come after the
+ # user supplied libs so there is no need to process them.
+ if test -z "$_LT_TAGVAR(compiler_lib_search_path, $1)"; then
+ _LT_TAGVAR(compiler_lib_search_path, $1)="${prev}${p}"
+ else
+ _LT_TAGVAR(compiler_lib_search_path, $1)="${_LT_TAGVAR(compiler_lib_search_path, $1)} ${prev}${p}"
+ fi
+ ;;
+ # The "-l" case would never come before the object being
+ # linked, so don't bother handling this case.
+ esac
+ else
+ if test -z "$_LT_TAGVAR(postdeps, $1)"; then
+ _LT_TAGVAR(postdeps, $1)="${prev}${p}"
+ else
+ _LT_TAGVAR(postdeps, $1)="${_LT_TAGVAR(postdeps, $1)} ${prev}${p}"
+ fi
+ fi
+ ;;
+
+ *.$objext)
+ # This assumes that the test object file only shows up
+ # once in the compiler output.
+ if test "$p" = "conftest.$objext"; then
+ pre_test_object_deps_done=yes
+ continue
+ fi
+
+ if test "$pre_test_object_deps_done" = no; then
+ if test -z "$_LT_TAGVAR(predep_objects, $1)"; then
+ _LT_TAGVAR(predep_objects, $1)="$p"
+ else
+ _LT_TAGVAR(predep_objects, $1)="$_LT_TAGVAR(predep_objects, $1) $p"
+ fi
+ else
+ if test -z "$_LT_TAGVAR(postdep_objects, $1)"; then
+ _LT_TAGVAR(postdep_objects, $1)="$p"
+ else
+ _LT_TAGVAR(postdep_objects, $1)="$_LT_TAGVAR(postdep_objects, $1) $p"
+ fi
+ fi
+ ;;
+
+ *) ;; # Ignore the rest.
+
+ esac
+ done
+
+ # Clean up.
+ rm -f a.out a.exe
+else
+ echo "libtool.m4: error: problem compiling $1 test program"
+fi
+
+$RM -f confest.$objext
+
+# PORTME: override above test on systems where it is broken
+m4_if([$1], [CXX],
+[case $host_os in
+interix[[3-9]]*)
+ # Interix 3.5 installs completely hosed .la files for C++, so rather than
+ # hack all around it, let's just trust "g++" to DTRT.
+ _LT_TAGVAR(predep_objects,$1)=
+ _LT_TAGVAR(postdep_objects,$1)=
+ _LT_TAGVAR(postdeps,$1)=
+ ;;
+
+linux*)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+
+ # The more standards-conforming stlport4 library is
+ # incompatible with the Cstd library. Avoid specifying
+ # it if it's in CXXFLAGS. Ignore libCrun as
+ # -library=stlport4 depends on it.
+ case " $CXX $CXXFLAGS " in
+ *" -library=stlport4 "*)
+ solaris_use_stlport4=yes
+ ;;
+ esac
+
+ if test "$solaris_use_stlport4" != yes; then
+ _LT_TAGVAR(postdeps,$1)='-library=Cstd -library=Crun'
+ fi
+ ;;
+ esac
+ ;;
+
+solaris*)
+ case $cc_basename in
+ CC*)
+ # The more standards-conforming stlport4 library is
+ # incompatible with the Cstd library. Avoid specifying
+ # it if it's in CXXFLAGS. Ignore libCrun as
+ # -library=stlport4 depends on it.
+ case " $CXX $CXXFLAGS " in
+ *" -library=stlport4 "*)
+ solaris_use_stlport4=yes
+ ;;
+ esac
+
+ # Adding this requires a known-good setup of shared libraries for
+ # Sun compiler versions before 5.6, else PIC objects from an old
+ # archive will be linked into the output, leading to subtle bugs.
+ if test "$solaris_use_stlport4" != yes; then
+ _LT_TAGVAR(postdeps,$1)='-library=Cstd -library=Crun'
+ fi
+ ;;
+ esac
+ ;;
+esac
+])
+
+case " $_LT_TAGVAR(postdeps, $1) " in
+*" -lc "*) _LT_TAGVAR(archive_cmds_need_lc, $1)=no ;;
+esac
+ _LT_TAGVAR(compiler_lib_search_dirs, $1)=
+if test -n "${_LT_TAGVAR(compiler_lib_search_path, $1)}"; then
+ _LT_TAGVAR(compiler_lib_search_dirs, $1)=`echo " ${_LT_TAGVAR(compiler_lib_search_path, $1)}" | ${SED} -e 's! -L! !g' -e 's!^ !!'`
+fi
+_LT_TAGDECL([], [compiler_lib_search_dirs], [1],
+ [The directories searched by this compiler when creating a shared library])
+_LT_TAGDECL([], [predep_objects], [1],
+ [Dependencies to place before and after the objects being linked to
+ create a shared library])
+_LT_TAGDECL([], [postdep_objects], [1])
+_LT_TAGDECL([], [predeps], [1])
+_LT_TAGDECL([], [postdeps], [1])
+_LT_TAGDECL([], [compiler_lib_search_path], [1],
+ [The library search path used internally by the compiler when linking
+ a shared library])
+])# _LT_SYS_HIDDEN_LIBDEPS
+
+
+# _LT_PROG_F77
+# ------------
+# Since AC_PROG_F77 is broken, in that it returns the empty string
+# if there is no fortran compiler, we have our own version here.
+m4_defun([_LT_PROG_F77],
+[
+pushdef([AC_MSG_ERROR], [_lt_disable_F77=yes])
+AC_PROG_F77
+if test -z "$F77" || test "X$F77" = "Xno"; then
+ _lt_disable_F77=yes
+fi
+popdef([AC_MSG_ERROR])
+])# _LT_PROG_F77
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([_LT_PROG_F77], [])
+
+
+# _LT_LANG_F77_CONFIG([TAG])
+# --------------------------
+# Ensure that the configuration variables for a Fortran 77 compiler are
+# suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_F77_CONFIG],
+[AC_REQUIRE([_LT_PROG_F77])dnl
+AC_LANG_PUSH(Fortran 77)
+
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+_LT_TAGVAR(allow_undefined_flag, $1)=
+_LT_TAGVAR(always_export_symbols, $1)=no
+_LT_TAGVAR(archive_expsym_cmds, $1)=
+_LT_TAGVAR(export_dynamic_flag_spec, $1)=
+_LT_TAGVAR(hardcode_direct, $1)=no
+_LT_TAGVAR(hardcode_direct_absolute, $1)=no
+_LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+_LT_TAGVAR(hardcode_libdir_separator, $1)=
+_LT_TAGVAR(hardcode_minus_L, $1)=no
+_LT_TAGVAR(hardcode_automatic, $1)=no
+_LT_TAGVAR(inherit_rpath, $1)=no
+_LT_TAGVAR(module_cmds, $1)=
+_LT_TAGVAR(module_expsym_cmds, $1)=
+_LT_TAGVAR(link_all_deplibs, $1)=unknown
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+_LT_TAGVAR(no_undefined_flag, $1)=
+_LT_TAGVAR(whole_archive_flag_spec, $1)=
+_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+
+# Source file extension for f77 test sources.
+ac_ext=f
+
+# Object file extension for compiled f77 test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# No sense in running all these tests if we already determined that
+# the F77 compiler isn't working. Some variables (like enable_shared)
+# are currently assumed to apply to all compilers on this platform,
+# and will be corrupted by setting them based on a non-working compiler.
+if test "$_lt_disable_F77" != yes; then
+ # Code to be used in simple compile tests
+ lt_simple_compile_test_code="\
+ subroutine t
+ return
+ end
+"
+
+ # Code to be used in simple link tests
+ lt_simple_link_test_code="\
+ program t
+ end
+"
+
+ # ltmain only uses $CC for tagged configurations so make sure $CC is set.
+ _LT_TAG_COMPILER
+
+ # save warnings/boilerplate of simple test code
+ _LT_COMPILER_BOILERPLATE
+ _LT_LINKER_BOILERPLATE
+
+ # Allow CC to be a program name with arguments.
+ lt_save_CC="$CC"
+ lt_save_GCC=$GCC
+ CC=${F77-"f77"}
+ compiler=$CC
+ _LT_TAGVAR(compiler, $1)=$CC
+ _LT_CC_BASENAME([$compiler])
+ GCC=$G77
+ if test -n "$compiler"; then
+ AC_MSG_CHECKING([if libtool supports shared libraries])
+ AC_MSG_RESULT([$can_build_shared])
+
+ AC_MSG_CHECKING([whether to build shared libraries])
+ test "$can_build_shared" = "no" && enable_shared=no
+
+ # On AIX, shared libraries and static libraries use the same namespace, and
+ # are all built from PIC.
+ case $host_os in
+ aix3*)
+ test "$enable_shared" = yes && enable_static=no
+ if test -n "$RANLIB"; then
+ archive_cmds="$archive_cmds~\$RANLIB \$lib"
+ postinstall_cmds='$RANLIB $lib'
+ fi
+ ;;
+ aix[[4-9]]*)
+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+ test "$enable_shared" = yes && enable_static=no
+ fi
+ ;;
+ esac
+ AC_MSG_RESULT([$enable_shared])
+
+ AC_MSG_CHECKING([whether to build static libraries])
+ # Make sure either enable_shared or enable_static is yes.
+ test "$enable_shared" = yes || enable_static=yes
+ AC_MSG_RESULT([$enable_static])
+
+ _LT_TAGVAR(GCC, $1)="$G77"
+ _LT_TAGVAR(LD, $1)="$LD"
+
+ ## CAVEAT EMPTOR:
+ ## There is no encapsulation within the following macros, do not change
+ ## the running order or otherwise move them around unless you know exactly
+ ## what you are doing...
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_SYS_DYNAMIC_LINKER($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+ fi # test -n "$compiler"
+
+ GCC=$lt_save_GCC
+ CC="$lt_save_CC"
+fi # test "$_lt_disable_F77" != yes
+
+AC_LANG_POP
+])# _LT_LANG_F77_CONFIG
+
+
+# _LT_PROG_FC
+# -----------
+# Since AC_PROG_FC is broken, in that it returns the empty string
+# if there is no fortran compiler, we have our own version here.
+m4_defun([_LT_PROG_FC],
+[
+pushdef([AC_MSG_ERROR], [_lt_disable_FC=yes])
+AC_PROG_FC
+if test -z "$FC" || test "X$FC" = "Xno"; then
+ _lt_disable_FC=yes
+fi
+popdef([AC_MSG_ERROR])
+])# _LT_PROG_FC
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([_LT_PROG_FC], [])
+
+
+# _LT_LANG_FC_CONFIG([TAG])
+# -------------------------
+# Ensure that the configuration variables for a Fortran compiler are
+# suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_FC_CONFIG],
+[AC_REQUIRE([_LT_PROG_FC])dnl
+AC_LANG_PUSH(Fortran)
+
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+_LT_TAGVAR(allow_undefined_flag, $1)=
+_LT_TAGVAR(always_export_symbols, $1)=no
+_LT_TAGVAR(archive_expsym_cmds, $1)=
+_LT_TAGVAR(export_dynamic_flag_spec, $1)=
+_LT_TAGVAR(hardcode_direct, $1)=no
+_LT_TAGVAR(hardcode_direct_absolute, $1)=no
+_LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+_LT_TAGVAR(hardcode_libdir_separator, $1)=
+_LT_TAGVAR(hardcode_minus_L, $1)=no
+_LT_TAGVAR(hardcode_automatic, $1)=no
+_LT_TAGVAR(inherit_rpath, $1)=no
+_LT_TAGVAR(module_cmds, $1)=
+_LT_TAGVAR(module_expsym_cmds, $1)=
+_LT_TAGVAR(link_all_deplibs, $1)=unknown
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+_LT_TAGVAR(no_undefined_flag, $1)=
+_LT_TAGVAR(whole_archive_flag_spec, $1)=
+_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+
+# Source file extension for fc test sources.
+ac_ext=${ac_fc_srcext-f}
+
+# Object file extension for compiled fc test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# No sense in running all these tests if we already determined that
+# the FC compiler isn't working. Some variables (like enable_shared)
+# are currently assumed to apply to all compilers on this platform,
+# and will be corrupted by setting them based on a non-working compiler.
+if test "$_lt_disable_FC" != yes; then
+ # Code to be used in simple compile tests
+ lt_simple_compile_test_code="\
+ subroutine t
+ return
+ end
+"
+
+ # Code to be used in simple link tests
+ lt_simple_link_test_code="\
+ program t
+ end
+"
+
+ # ltmain only uses $CC for tagged configurations so make sure $CC is set.
+ _LT_TAG_COMPILER
+
+ # save warnings/boilerplate of simple test code
+ _LT_COMPILER_BOILERPLATE
+ _LT_LINKER_BOILERPLATE
+
+ # Allow CC to be a program name with arguments.
+ lt_save_CC="$CC"
+ lt_save_GCC=$GCC
+ CC=${FC-"f95"}
+ compiler=$CC
+ GCC=$ac_cv_fc_compiler_gnu
+
+ _LT_TAGVAR(compiler, $1)=$CC
+ _LT_CC_BASENAME([$compiler])
+
+ if test -n "$compiler"; then
+ AC_MSG_CHECKING([if libtool supports shared libraries])
+ AC_MSG_RESULT([$can_build_shared])
+
+ AC_MSG_CHECKING([whether to build shared libraries])
+ test "$can_build_shared" = "no" && enable_shared=no
+
+ # On AIX, shared libraries and static libraries use the same namespace, and
+ # are all built from PIC.
+ case $host_os in
+ aix3*)
+ test "$enable_shared" = yes && enable_static=no
+ if test -n "$RANLIB"; then
+ archive_cmds="$archive_cmds~\$RANLIB \$lib"
+ postinstall_cmds='$RANLIB $lib'
+ fi
+ ;;
+ aix[[4-9]]*)
+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+ test "$enable_shared" = yes && enable_static=no
+ fi
+ ;;
+ esac
+ AC_MSG_RESULT([$enable_shared])
+
+ AC_MSG_CHECKING([whether to build static libraries])
+ # Make sure either enable_shared or enable_static is yes.
+ test "$enable_shared" = yes || enable_static=yes
+ AC_MSG_RESULT([$enable_static])
+
+ _LT_TAGVAR(GCC, $1)="$ac_cv_fc_compiler_gnu"
+ _LT_TAGVAR(LD, $1)="$LD"
+
+ ## CAVEAT EMPTOR:
+ ## There is no encapsulation within the following macros, do not change
+ ## the running order or otherwise move them around unless you know exactly
+ ## what you are doing...
+ _LT_SYS_HIDDEN_LIBDEPS($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_SYS_DYNAMIC_LINKER($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+ fi # test -n "$compiler"
+
+ GCC=$lt_save_GCC
+ CC="$lt_save_CC"
+fi # test "$_lt_disable_FC" != yes
+
+AC_LANG_POP
+])# _LT_LANG_FC_CONFIG
+
+
+# _LT_LANG_GCJ_CONFIG([TAG])
+# --------------------------
+# Ensure that the configuration variables for the GNU Java Compiler compiler
+# are suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_GCJ_CONFIG],
+[AC_REQUIRE([LT_PROG_GCJ])dnl
+AC_LANG_SAVE
+
+# Source file extension for Java test sources.
+ac_ext=java
+
+# Object file extension for compiled Java test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="class foo {}"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='public class conftest { public static void main(String[[]] argv) {}; }'
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+_LT_TAG_COMPILER
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+# Allow CC to be a program name with arguments.
+lt_save_CC="$CC"
+lt_save_GCC=$GCC
+GCC=yes
+CC=${GCJ-"gcj"}
+compiler=$CC
+_LT_TAGVAR(compiler, $1)=$CC
+_LT_TAGVAR(LD, $1)="$LD"
+_LT_CC_BASENAME([$compiler])
+
+# GCJ did not exist at the time GCC didn't implicitly link libc in.
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+
+if test -n "$compiler"; then
+ _LT_COMPILER_NO_RTTI($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+fi
+
+AC_LANG_RESTORE
+
+GCC=$lt_save_GCC
+CC="$lt_save_CC"
+])# _LT_LANG_GCJ_CONFIG
+
+
+# _LT_LANG_RC_CONFIG([TAG])
+# -------------------------
+# Ensure that the configuration variables for the Windows resource compiler
+# are suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_RC_CONFIG],
+[AC_REQUIRE([LT_PROG_RC])dnl
+AC_LANG_SAVE
+
+# Source file extension for RC test sources.
+ac_ext=rc
+
+# Object file extension for compiled RC test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code='sample MENU { MENUITEM "&Soup", 100, CHECKED }'
+
+# Code to be used in simple link tests
+lt_simple_link_test_code="$lt_simple_compile_test_code"
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+_LT_TAG_COMPILER
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+# Allow CC to be a program name with arguments.
+lt_save_CC="$CC"
+lt_save_GCC=$GCC
+GCC=
+CC=${RC-"windres"}
+compiler=$CC
+_LT_TAGVAR(compiler, $1)=$CC
+_LT_CC_BASENAME([$compiler])
+_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=yes
+
+if test -n "$compiler"; then
+ :
+ _LT_CONFIG($1)
+fi
+
+GCC=$lt_save_GCC
+AC_LANG_RESTORE
+CC="$lt_save_CC"
+])# _LT_LANG_RC_CONFIG
+
+
+# LT_PROG_GCJ
+# -----------
+AC_DEFUN([LT_PROG_GCJ],
+[m4_ifdef([AC_PROG_GCJ], [AC_PROG_GCJ],
+ [m4_ifdef([A][M_PROG_GCJ], [A][M_PROG_GCJ],
+ [AC_CHECK_TOOL(GCJ, gcj,)
+ test "x${GCJFLAGS+set}" = xset || GCJFLAGS="-g -O2"
+ AC_SUBST(GCJFLAGS)])])[]dnl
+])
+
+# Old name:
+AU_ALIAS([LT_AC_PROG_GCJ], [LT_PROG_GCJ])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([LT_AC_PROG_GCJ], [])
+
+
+# LT_PROG_RC
+# ----------
+AC_DEFUN([LT_PROG_RC],
+[AC_CHECK_TOOL(RC, windres,)
+])
+
+# Old name:
+AU_ALIAS([LT_AC_PROG_RC], [LT_PROG_RC])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([LT_AC_PROG_RC], [])
+
+
+# _LT_DECL_EGREP
+# --------------
+# If we don't have a new enough Autoconf to choose the best grep
+# available, choose the one first in the user's PATH.
+m4_defun([_LT_DECL_EGREP],
+[AC_REQUIRE([AC_PROG_EGREP])dnl
+AC_REQUIRE([AC_PROG_FGREP])dnl
+test -z "$GREP" && GREP=grep
+_LT_DECL([], [GREP], [1], [A grep program that handles long lines])
+_LT_DECL([], [EGREP], [1], [An ERE matcher])
+_LT_DECL([], [FGREP], [1], [A literal string matcher])
+dnl Non-bleeding-edge autoconf doesn't subst GREP, so do it here too
+AC_SUBST([GREP])
+])
+
+
+# _LT_DECL_OBJDUMP
+# --------------
+# If we don't have a new enough Autoconf to choose the best objdump
+# available, choose the one first in the user's PATH.
+m4_defun([_LT_DECL_OBJDUMP],
+[AC_CHECK_TOOL(OBJDUMP, objdump, false)
+test -z "$OBJDUMP" && OBJDUMP=objdump
+_LT_DECL([], [OBJDUMP], [1], [An object symbol dumper])
+AC_SUBST([OBJDUMP])
+])
+
+
+# _LT_DECL_SED
+# ------------
+# Check for a fully-functional sed program, that truncates
+# as few characters as possible. Prefer GNU sed if found.
+m4_defun([_LT_DECL_SED],
+[AC_PROG_SED
+test -z "$SED" && SED=sed
+Xsed="$SED -e 1s/^X//"
+_LT_DECL([], [SED], [1], [A sed program that does not truncate output])
+_LT_DECL([], [Xsed], ["\$SED -e 1s/^X//"],
+ [Sed that helps us avoid accidentally triggering echo(1) options like -n])
+])# _LT_DECL_SED
+
+m4_ifndef([AC_PROG_SED], [
+# NOTE: This macro has been submitted for inclusion into #
+# GNU Autoconf as AC_PROG_SED. When it is available in #
+# a released version of Autoconf we should remove this #
+# macro and use it instead. #
+
+m4_defun([AC_PROG_SED],
+[AC_MSG_CHECKING([for a sed that does not truncate output])
+AC_CACHE_VAL(lt_cv_path_SED,
+[# Loop through the user's path and test for sed and gsed.
+# Then use that list of sed's as ones to test for truncation.
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for lt_ac_prog in sed gsed; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$lt_ac_prog$ac_exec_ext"; then
+ lt_ac_sed_list="$lt_ac_sed_list $as_dir/$lt_ac_prog$ac_exec_ext"
+ fi
+ done
+ done
+done
+IFS=$as_save_IFS
+lt_ac_max=0
+lt_ac_count=0
+# Add /usr/xpg4/bin/sed as it is typically found on Solaris
+# along with /bin/sed that truncates output.
+for lt_ac_sed in $lt_ac_sed_list /usr/xpg4/bin/sed; do
+ test ! -f $lt_ac_sed && continue
+ cat /dev/null > conftest.in
+ lt_ac_count=0
+ echo $ECHO_N "0123456789$ECHO_C" >conftest.in
+ # Check for GNU sed and select it if it is found.
+ if "$lt_ac_sed" --version 2>&1 < /dev/null | grep 'GNU' > /dev/null; then
+ lt_cv_path_SED=$lt_ac_sed
+ break
+ fi
+ while true; do
+ cat conftest.in conftest.in >conftest.tmp
+ mv conftest.tmp conftest.in
+ cp conftest.in conftest.nl
+ echo >>conftest.nl
+ $lt_ac_sed -e 's/a$//' < conftest.nl >conftest.out || break
+ cmp -s conftest.out conftest.nl || break
+ # 10000 chars as input seems more than enough
+ test $lt_ac_count -gt 10 && break
+ lt_ac_count=`expr $lt_ac_count + 1`
+ if test $lt_ac_count -gt $lt_ac_max; then
+ lt_ac_max=$lt_ac_count
+ lt_cv_path_SED=$lt_ac_sed
+ fi
+ done
+done
+])
+SED=$lt_cv_path_SED
+AC_SUBST([SED])
+AC_MSG_RESULT([$SED])
+])#AC_PROG_SED
+])#m4_ifndef
+
+# Old name:
+AU_ALIAS([LT_AC_PROG_SED], [AC_PROG_SED])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([LT_AC_PROG_SED], [])
+
+
+# _LT_CHECK_SHELL_FEATURES
+# ------------------------
+# Find out whether the shell is Bourne or XSI compatible,
+# or has some other useful features.
+m4_defun([_LT_CHECK_SHELL_FEATURES],
+[AC_MSG_CHECKING([whether the shell understands some XSI constructs])
+# Try some XSI features
+xsi_shell=no
+( _lt_dummy="a/b/c"
+ test "${_lt_dummy##*/},${_lt_dummy%/*},"${_lt_dummy%"$_lt_dummy"}, \
+ = c,a/b,, \
+ && eval 'test $(( 1 + 1 )) -eq 2 \
+ && test "${#_lt_dummy}" -eq 5' ) >/dev/null 2>&1 \
+ && xsi_shell=yes
+AC_MSG_RESULT([$xsi_shell])
+_LT_CONFIG_LIBTOOL_INIT([xsi_shell='$xsi_shell'])
+
+AC_MSG_CHECKING([whether the shell understands "+="])
+lt_shell_append=no
+( foo=bar; set foo baz; eval "$[1]+=\$[2]" && test "$foo" = barbaz ) \
+ >/dev/null 2>&1 \
+ && lt_shell_append=yes
+AC_MSG_RESULT([$lt_shell_append])
+_LT_CONFIG_LIBTOOL_INIT([lt_shell_append='$lt_shell_append'])
+
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+ lt_unset=unset
+else
+ lt_unset=false
+fi
+_LT_DECL([], [lt_unset], [0], [whether the shell understands "unset"])dnl
+
+# test EBCDIC or ASCII
+case `echo X|tr X '\101'` in
+ A) # ASCII based system
+ # \n is not interpreted correctly by Solaris 8 /usr/ucb/tr
+ lt_SP2NL='tr \040 \012'
+ lt_NL2SP='tr \015\012 \040\040'
+ ;;
+ *) # EBCDIC based system
+ lt_SP2NL='tr \100 \n'
+ lt_NL2SP='tr \r\n \100\100'
+ ;;
+esac
+_LT_DECL([SP2NL], [lt_SP2NL], [1], [turn spaces into newlines])dnl
+_LT_DECL([NL2SP], [lt_NL2SP], [1], [turn newlines into spaces])dnl
+])# _LT_CHECK_SHELL_FEATURES
+
+
+# _LT_PROG_XSI_SHELLFNS
+# ---------------------
+# Bourne and XSI compatible variants of some useful shell functions.
+m4_defun([_LT_PROG_XSI_SHELLFNS],
+[case $xsi_shell in
+ yes)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_dirname file append nondir_replacement
+# Compute the dirname of FILE. If nonempty, add APPEND to the result,
+# otherwise set result to NONDIR_REPLACEMENT.
+func_dirname ()
+{
+ case ${1} in
+ */*) func_dirname_result="${1%/*}${2}" ;;
+ * ) func_dirname_result="${3}" ;;
+ esac
+}
+
+# func_basename file
+func_basename ()
+{
+ func_basename_result="${1##*/}"
+}
+
+# func_dirname_and_basename file append nondir_replacement
+# perform func_basename and func_dirname in a single function
+# call:
+# dirname: Compute the dirname of FILE. If nonempty,
+# add APPEND to the result, otherwise set result
+# to NONDIR_REPLACEMENT.
+# value returned in "$func_dirname_result"
+# basename: Compute filename of FILE.
+# value retuned in "$func_basename_result"
+# Implementation must be kept synchronized with func_dirname
+# and func_basename. For efficiency, we do not delegate to
+# those functions but instead duplicate the functionality here.
+func_dirname_and_basename ()
+{
+ case ${1} in
+ */*) func_dirname_result="${1%/*}${2}" ;;
+ * ) func_dirname_result="${3}" ;;
+ esac
+ func_basename_result="${1##*/}"
+}
+
+# func_stripname prefix suffix name
+# strip PREFIX and SUFFIX off of NAME.
+# PREFIX and SUFFIX must not contain globbing or regex special
+# characters, hashes, percent signs, but SUFFIX may contain a leading
+# dot (in which case that matches only a dot).
+func_stripname ()
+{
+ # pdksh 5.2.14 does not do ${X%$Y} correctly if both X and Y are
+ # positional parameters, so assign one to ordinary parameter first.
+ func_stripname_result=${3}
+ func_stripname_result=${func_stripname_result#"${1}"}
+ func_stripname_result=${func_stripname_result%"${2}"}
+}
+
+# func_opt_split
+func_opt_split ()
+{
+ func_opt_split_opt=${1%%=*}
+ func_opt_split_arg=${1#*=}
+}
+
+# func_lo2o object
+func_lo2o ()
+{
+ case ${1} in
+ *.lo) func_lo2o_result=${1%.lo}.${objext} ;;
+ *) func_lo2o_result=${1} ;;
+ esac
+}
+
+# func_xform libobj-or-source
+func_xform ()
+{
+ func_xform_result=${1%.*}.lo
+}
+
+# func_arith arithmetic-term...
+func_arith ()
+{
+ func_arith_result=$(( $[*] ))
+}
+
+# func_len string
+# STRING may not start with a hyphen.
+func_len ()
+{
+ func_len_result=${#1}
+}
+
+_LT_EOF
+ ;;
+ *) # Bourne compatible functions.
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_dirname file append nondir_replacement
+# Compute the dirname of FILE. If nonempty, add APPEND to the result,
+# otherwise set result to NONDIR_REPLACEMENT.
+func_dirname ()
+{
+ # Extract subdirectory from the argument.
+ func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"`
+ if test "X$func_dirname_result" = "X${1}"; then
+ func_dirname_result="${3}"
+ else
+ func_dirname_result="$func_dirname_result${2}"
+ fi
+}
+
+# func_basename file
+func_basename ()
+{
+ func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"`
+}
+
+dnl func_dirname_and_basename
+dnl A portable version of this function is already defined in general.m4sh
+dnl so there is no need for it here.
+
+# func_stripname prefix suffix name
+# strip PREFIX and SUFFIX off of NAME.
+# PREFIX and SUFFIX must not contain globbing or regex special
+# characters, hashes, percent signs, but SUFFIX may contain a leading
+# dot (in which case that matches only a dot).
+# func_strip_suffix prefix name
+func_stripname ()
+{
+ case ${2} in
+ .*) func_stripname_result=`$ECHO "X${3}" \
+ | $Xsed -e "s%^${1}%%" -e "s%\\\\${2}\$%%"`;;
+ *) func_stripname_result=`$ECHO "X${3}" \
+ | $Xsed -e "s%^${1}%%" -e "s%${2}\$%%"`;;
+ esac
+}
+
+# sed scripts:
+my_sed_long_opt='1s/^\(-[[^=]]*\)=.*/\1/;q'
+my_sed_long_arg='1s/^-[[^=]]*=//'
+
+# func_opt_split
+func_opt_split ()
+{
+ func_opt_split_opt=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_opt"`
+ func_opt_split_arg=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_arg"`
+}
+
+# func_lo2o object
+func_lo2o ()
+{
+ func_lo2o_result=`$ECHO "X${1}" | $Xsed -e "$lo2o"`
+}
+
+# func_xform libobj-or-source
+func_xform ()
+{
+ func_xform_result=`$ECHO "X${1}" | $Xsed -e 's/\.[[^.]]*$/.lo/'`
+}
+
+# func_arith arithmetic-term...
+func_arith ()
+{
+ func_arith_result=`expr "$[@]"`
+}
+
+# func_len string
+# STRING may not start with a hyphen.
+func_len ()
+{
+ func_len_result=`expr "$[1]" : ".*" 2>/dev/null || echo $max_cmd_len`
+}
+
+_LT_EOF
+esac
+
+case $lt_shell_append in
+ yes)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$[1]+=\$[2]"
+}
+_LT_EOF
+ ;;
+ *)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$[1]=\$$[1]\$[2]"
+}
+
+_LT_EOF
+ ;;
+ esac
+])
+
+# Helper functions for option handling. -*- Autoconf -*-
+#
+# Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gary V. Vaughan, 2004
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+# serial 6 ltoptions.m4
+
+# This is to help aclocal find these macros, as it can't see m4_define.
+AC_DEFUN([LTOPTIONS_VERSION], [m4_if([1])])
+
+
+# _LT_MANGLE_OPTION(MACRO-NAME, OPTION-NAME)
+# ------------------------------------------
+m4_define([_LT_MANGLE_OPTION],
+[[_LT_OPTION_]m4_bpatsubst($1__$2, [[^a-zA-Z0-9_]], [_])])
+
+
+# _LT_SET_OPTION(MACRO-NAME, OPTION-NAME)
+# ---------------------------------------
+# Set option OPTION-NAME for macro MACRO-NAME, and if there is a
+# matching handler defined, dispatch to it. Other OPTION-NAMEs are
+# saved as a flag.
+m4_define([_LT_SET_OPTION],
+[m4_define(_LT_MANGLE_OPTION([$1], [$2]))dnl
+m4_ifdef(_LT_MANGLE_DEFUN([$1], [$2]),
+ _LT_MANGLE_DEFUN([$1], [$2]),
+ [m4_warning([Unknown $1 option `$2'])])[]dnl
+])
+
+
+# _LT_IF_OPTION(MACRO-NAME, OPTION-NAME, IF-SET, [IF-NOT-SET])
+# ------------------------------------------------------------
+# Execute IF-SET if OPTION is set, IF-NOT-SET otherwise.
+m4_define([_LT_IF_OPTION],
+[m4_ifdef(_LT_MANGLE_OPTION([$1], [$2]), [$3], [$4])])
+
+
+# _LT_UNLESS_OPTIONS(MACRO-NAME, OPTION-LIST, IF-NOT-SET)
+# -------------------------------------------------------
+# Execute IF-NOT-SET unless all options in OPTION-LIST for MACRO-NAME
+# are set.
+m4_define([_LT_UNLESS_OPTIONS],
+[m4_foreach([_LT_Option], m4_split(m4_normalize([$2])),
+ [m4_ifdef(_LT_MANGLE_OPTION([$1], _LT_Option),
+ [m4_define([$0_found])])])[]dnl
+m4_ifdef([$0_found], [m4_undefine([$0_found])], [$3
+])[]dnl
+])
+
+
+# _LT_SET_OPTIONS(MACRO-NAME, OPTION-LIST)
+# ----------------------------------------
+# OPTION-LIST is a space-separated list of Libtool options associated
+# with MACRO-NAME. If any OPTION has a matching handler declared with
+# LT_OPTION_DEFINE, dispatch to that macro; otherwise complain about
+# the unknown option and exit.
+m4_defun([_LT_SET_OPTIONS],
+[# Set options
+m4_foreach([_LT_Option], m4_split(m4_normalize([$2])),
+ [_LT_SET_OPTION([$1], _LT_Option)])
+
+m4_if([$1],[LT_INIT],[
+ dnl
+ dnl Simply set some default values (i.e off) if boolean options were not
+ dnl specified:
+ _LT_UNLESS_OPTIONS([LT_INIT], [dlopen], [enable_dlopen=no
+ ])
+ _LT_UNLESS_OPTIONS([LT_INIT], [win32-dll], [enable_win32_dll=no
+ ])
+ dnl
+ dnl If no reference was made to various pairs of opposing options, then
+ dnl we run the default mode handler for the pair. For example, if neither
+ dnl `shared' nor `disable-shared' was passed, we enable building of shared
+ dnl archives by default:
+ _LT_UNLESS_OPTIONS([LT_INIT], [shared disable-shared], [_LT_ENABLE_SHARED])
+ _LT_UNLESS_OPTIONS([LT_INIT], [static disable-static], [_LT_ENABLE_STATIC])
+ _LT_UNLESS_OPTIONS([LT_INIT], [pic-only no-pic], [_LT_WITH_PIC])
+ _LT_UNLESS_OPTIONS([LT_INIT], [fast-install disable-fast-install],
+ [_LT_ENABLE_FAST_INSTALL])
+ ])
+])# _LT_SET_OPTIONS
+
+
+
+# _LT_MANGLE_DEFUN(MACRO-NAME, OPTION-NAME)
+# -----------------------------------------
+m4_define([_LT_MANGLE_DEFUN],
+[[_LT_OPTION_DEFUN_]m4_bpatsubst(m4_toupper([$1__$2]), [[^A-Z0-9_]], [_])])
+
+
+# LT_OPTION_DEFINE(MACRO-NAME, OPTION-NAME, CODE)
+# -----------------------------------------------
+m4_define([LT_OPTION_DEFINE],
+[m4_define(_LT_MANGLE_DEFUN([$1], [$2]), [$3])[]dnl
+])# LT_OPTION_DEFINE
+
+
+# dlopen
+# ------
+LT_OPTION_DEFINE([LT_INIT], [dlopen], [enable_dlopen=yes
+])
+
+AU_DEFUN([AC_LIBTOOL_DLOPEN],
+[_LT_SET_OPTION([LT_INIT], [dlopen])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you
+put the `dlopen' option into LT_INIT's first parameter.])
+])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_DLOPEN], [])
+
+
+# win32-dll
+# ---------
+# Declare package support for building win32 dll's.
+LT_OPTION_DEFINE([LT_INIT], [win32-dll],
+[enable_win32_dll=yes
+
+case $host in
+*-*-cygwin* | *-*-mingw* | *-*-pw32* | *-cegcc*)
+ AC_CHECK_TOOL(AS, as, false)
+ AC_CHECK_TOOL(DLLTOOL, dlltool, false)
+ AC_CHECK_TOOL(OBJDUMP, objdump, false)
+ ;;
+esac
+
+test -z "$AS" && AS=as
+_LT_DECL([], [AS], [0], [Assembler program])dnl
+
+test -z "$DLLTOOL" && DLLTOOL=dlltool
+_LT_DECL([], [DLLTOOL], [0], [DLL creation program])dnl
+
+test -z "$OBJDUMP" && OBJDUMP=objdump
+_LT_DECL([], [OBJDUMP], [0], [Object dumper program])dnl
+])# win32-dll
+
+AU_DEFUN([AC_LIBTOOL_WIN32_DLL],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+_LT_SET_OPTION([LT_INIT], [win32-dll])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you
+put the `win32-dll' option into LT_INIT's first parameter.])
+])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_WIN32_DLL], [])
+
+
+# _LT_ENABLE_SHARED([DEFAULT])
+# ----------------------------
+# implement the --enable-shared flag, and supports the `shared' and
+# `disable-shared' LT_INIT options.
+# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'.
+m4_define([_LT_ENABLE_SHARED],
+[m4_define([_LT_ENABLE_SHARED_DEFAULT], [m4_if($1, no, no, yes)])dnl
+AC_ARG_ENABLE([shared],
+ [AS_HELP_STRING([--enable-shared@<:@=PKGS@:>@],
+ [build shared libraries @<:@default=]_LT_ENABLE_SHARED_DEFAULT[@:>@])],
+ [p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_shared=yes ;;
+ no) enable_shared=no ;;
+ *)
+ enable_shared=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_shared=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac],
+ [enable_shared=]_LT_ENABLE_SHARED_DEFAULT)
+
+ _LT_DECL([build_libtool_libs], [enable_shared], [0],
+ [Whether or not to build shared libraries])
+])# _LT_ENABLE_SHARED
+
+LT_OPTION_DEFINE([LT_INIT], [shared], [_LT_ENABLE_SHARED([yes])])
+LT_OPTION_DEFINE([LT_INIT], [disable-shared], [_LT_ENABLE_SHARED([no])])
+
+# Old names:
+AC_DEFUN([AC_ENABLE_SHARED],
+[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[shared])
+])
+
+AC_DEFUN([AC_DISABLE_SHARED],
+[_LT_SET_OPTION([LT_INIT], [disable-shared])
+])
+
+AU_DEFUN([AM_ENABLE_SHARED], [AC_ENABLE_SHARED($@)])
+AU_DEFUN([AM_DISABLE_SHARED], [AC_DISABLE_SHARED($@)])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AM_ENABLE_SHARED], [])
+dnl AC_DEFUN([AM_DISABLE_SHARED], [])
+
+
+
+# _LT_ENABLE_STATIC([DEFAULT])
+# ----------------------------
+# implement the --enable-static flag, and support the `static' and
+# `disable-static' LT_INIT options.
+# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'.
+m4_define([_LT_ENABLE_STATIC],
+[m4_define([_LT_ENABLE_STATIC_DEFAULT], [m4_if($1, no, no, yes)])dnl
+AC_ARG_ENABLE([static],
+ [AS_HELP_STRING([--enable-static@<:@=PKGS@:>@],
+ [build static libraries @<:@default=]_LT_ENABLE_STATIC_DEFAULT[@:>@])],
+ [p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_static=yes ;;
+ no) enable_static=no ;;
+ *)
+ enable_static=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_static=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac],
+ [enable_static=]_LT_ENABLE_STATIC_DEFAULT)
+
+ _LT_DECL([build_old_libs], [enable_static], [0],
+ [Whether or not to build static libraries])
+])# _LT_ENABLE_STATIC
+
+LT_OPTION_DEFINE([LT_INIT], [static], [_LT_ENABLE_STATIC([yes])])
+LT_OPTION_DEFINE([LT_INIT], [disable-static], [_LT_ENABLE_STATIC([no])])
+
+# Old names:
+AC_DEFUN([AC_ENABLE_STATIC],
+[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[static])
+])
+
+AC_DEFUN([AC_DISABLE_STATIC],
+[_LT_SET_OPTION([LT_INIT], [disable-static])
+])
+
+AU_DEFUN([AM_ENABLE_STATIC], [AC_ENABLE_STATIC($@)])
+AU_DEFUN([AM_DISABLE_STATIC], [AC_DISABLE_STATIC($@)])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AM_ENABLE_STATIC], [])
+dnl AC_DEFUN([AM_DISABLE_STATIC], [])
+
+
+
+# _LT_ENABLE_FAST_INSTALL([DEFAULT])
+# ----------------------------------
+# implement the --enable-fast-install flag, and support the `fast-install'
+# and `disable-fast-install' LT_INIT options.
+# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'.
+m4_define([_LT_ENABLE_FAST_INSTALL],
+[m4_define([_LT_ENABLE_FAST_INSTALL_DEFAULT], [m4_if($1, no, no, yes)])dnl
+AC_ARG_ENABLE([fast-install],
+ [AS_HELP_STRING([--enable-fast-install@<:@=PKGS@:>@],
+ [optimize for fast installation @<:@default=]_LT_ENABLE_FAST_INSTALL_DEFAULT[@:>@])],
+ [p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_fast_install=yes ;;
+ no) enable_fast_install=no ;;
+ *)
+ enable_fast_install=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_fast_install=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac],
+ [enable_fast_install=]_LT_ENABLE_FAST_INSTALL_DEFAULT)
+
+_LT_DECL([fast_install], [enable_fast_install], [0],
+ [Whether or not to optimize for fast installation])dnl
+])# _LT_ENABLE_FAST_INSTALL
+
+LT_OPTION_DEFINE([LT_INIT], [fast-install], [_LT_ENABLE_FAST_INSTALL([yes])])
+LT_OPTION_DEFINE([LT_INIT], [disable-fast-install], [_LT_ENABLE_FAST_INSTALL([no])])
+
+# Old names:
+AU_DEFUN([AC_ENABLE_FAST_INSTALL],
+[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[fast-install])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you put
+the `fast-install' option into LT_INIT's first parameter.])
+])
+
+AU_DEFUN([AC_DISABLE_FAST_INSTALL],
+[_LT_SET_OPTION([LT_INIT], [disable-fast-install])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you put
+the `disable-fast-install' option into LT_INIT's first parameter.])
+])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_ENABLE_FAST_INSTALL], [])
+dnl AC_DEFUN([AM_DISABLE_FAST_INSTALL], [])
+
+
+# _LT_WITH_PIC([MODE])
+# --------------------
+# implement the --with-pic flag, and support the `pic-only' and `no-pic'
+# LT_INIT options.
+# MODE is either `yes' or `no'. If omitted, it defaults to `both'.
+m4_define([_LT_WITH_PIC],
+[AC_ARG_WITH([pic],
+ [AS_HELP_STRING([--with-pic],
+ [try to use only PIC/non-PIC objects @<:@default=use both@:>@])],
+ [pic_mode="$withval"],
+ [pic_mode=default])
+
+test -z "$pic_mode" && pic_mode=m4_default([$1], [default])
+
+_LT_DECL([], [pic_mode], [0], [What type of objects to build])dnl
+])# _LT_WITH_PIC
+
+LT_OPTION_DEFINE([LT_INIT], [pic-only], [_LT_WITH_PIC([yes])])
+LT_OPTION_DEFINE([LT_INIT], [no-pic], [_LT_WITH_PIC([no])])
+
+# Old name:
+AU_DEFUN([AC_LIBTOOL_PICMODE],
+[_LT_SET_OPTION([LT_INIT], [pic-only])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you
+put the `pic-only' option into LT_INIT's first parameter.])
+])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_PICMODE], [])
+
+
+m4_define([_LTDL_MODE], [])
+LT_OPTION_DEFINE([LTDL_INIT], [nonrecursive],
+ [m4_define([_LTDL_MODE], [nonrecursive])])
+LT_OPTION_DEFINE([LTDL_INIT], [recursive],
+ [m4_define([_LTDL_MODE], [recursive])])
+LT_OPTION_DEFINE([LTDL_INIT], [subproject],
+ [m4_define([_LTDL_MODE], [subproject])])
+
+m4_define([_LTDL_TYPE], [])
+LT_OPTION_DEFINE([LTDL_INIT], [installable],
+ [m4_define([_LTDL_TYPE], [installable])])
+LT_OPTION_DEFINE([LTDL_INIT], [convenience],
+ [m4_define([_LTDL_TYPE], [convenience])])
+
+# ltsugar.m4 -- libtool m4 base layer. -*-Autoconf-*-
+#
+# Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gary V. Vaughan, 2004
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+# serial 6 ltsugar.m4
+
+# This is to help aclocal find these macros, as it can't see m4_define.
+AC_DEFUN([LTSUGAR_VERSION], [m4_if([0.1])])
+
+
+# lt_join(SEP, ARG1, [ARG2...])
+# -----------------------------
+# Produce ARG1SEPARG2...SEPARGn, omitting [] arguments and their
+# associated separator.
+# Needed until we can rely on m4_join from Autoconf 2.62, since all earlier
+# versions in m4sugar had bugs.
+m4_define([lt_join],
+[m4_if([$#], [1], [],
+ [$#], [2], [[$2]],
+ [m4_if([$2], [], [], [[$2]_])$0([$1], m4_shift(m4_shift($@)))])])
+m4_define([_lt_join],
+[m4_if([$#$2], [2], [],
+ [m4_if([$2], [], [], [[$1$2]])$0([$1], m4_shift(m4_shift($@)))])])
+
+
+# lt_car(LIST)
+# lt_cdr(LIST)
+# ------------
+# Manipulate m4 lists.
+# These macros are necessary as long as will still need to support
+# Autoconf-2.59 which quotes differently.
+m4_define([lt_car], [[$1]])
+m4_define([lt_cdr],
+[m4_if([$#], 0, [m4_fatal([$0: cannot be called without arguments])],
+ [$#], 1, [],
+ [m4_dquote(m4_shift($@))])])
+m4_define([lt_unquote], $1)
+
+
+# lt_append(MACRO-NAME, STRING, [SEPARATOR])
+# ------------------------------------------
+# Redefine MACRO-NAME to hold its former content plus `SEPARATOR'`STRING'.
+# Note that neither SEPARATOR nor STRING are expanded; they are appended
+# to MACRO-NAME as is (leaving the expansion for when MACRO-NAME is invoked).
+# No SEPARATOR is output if MACRO-NAME was previously undefined (different
+# than defined and empty).
+#
+# This macro is needed until we can rely on Autoconf 2.62, since earlier
+# versions of m4sugar mistakenly expanded SEPARATOR but not STRING.
+m4_define([lt_append],
+[m4_define([$1],
+ m4_ifdef([$1], [m4_defn([$1])[$3]])[$2])])
+
+
+
+# lt_combine(SEP, PREFIX-LIST, INFIX, SUFFIX1, [SUFFIX2...])
+# ----------------------------------------------------------
+# Produce a SEP delimited list of all paired combinations of elements of
+# PREFIX-LIST with SUFFIX1 through SUFFIXn. Each element of the list
+# has the form PREFIXmINFIXSUFFIXn.
+# Needed until we can rely on m4_combine added in Autoconf 2.62.
+m4_define([lt_combine],
+[m4_if(m4_eval([$# > 3]), [1],
+ [m4_pushdef([_Lt_sep], [m4_define([_Lt_sep], m4_defn([lt_car]))])]]dnl
+[[m4_foreach([_Lt_prefix], [$2],
+ [m4_foreach([_Lt_suffix],
+ ]m4_dquote(m4_dquote(m4_shift(m4_shift(m4_shift($@)))))[,
+ [_Lt_sep([$1])[]m4_defn([_Lt_prefix])[$3]m4_defn([_Lt_suffix])])])])])
+
+
+# lt_if_append_uniq(MACRO-NAME, VARNAME, [SEPARATOR], [UNIQ], [NOT-UNIQ])
+# -----------------------------------------------------------------------
+# Iff MACRO-NAME does not yet contain VARNAME, then append it (delimited
+# by SEPARATOR if supplied) and expand UNIQ, else NOT-UNIQ.
+m4_define([lt_if_append_uniq],
+[m4_ifdef([$1],
+ [m4_if(m4_index([$3]m4_defn([$1])[$3], [$3$2$3]), [-1],
+ [lt_append([$1], [$2], [$3])$4],
+ [$5])],
+ [lt_append([$1], [$2], [$3])$4])])
+
+
+# lt_dict_add(DICT, KEY, VALUE)
+# -----------------------------
+m4_define([lt_dict_add],
+[m4_define([$1($2)], [$3])])
+
+
+# lt_dict_add_subkey(DICT, KEY, SUBKEY, VALUE)
+# --------------------------------------------
+m4_define([lt_dict_add_subkey],
+[m4_define([$1($2:$3)], [$4])])
+
+
+# lt_dict_fetch(DICT, KEY, [SUBKEY])
+# ----------------------------------
+m4_define([lt_dict_fetch],
+[m4_ifval([$3],
+ m4_ifdef([$1($2:$3)], [m4_defn([$1($2:$3)])]),
+ m4_ifdef([$1($2)], [m4_defn([$1($2)])]))])
+
+
+# lt_if_dict_fetch(DICT, KEY, [SUBKEY], VALUE, IF-TRUE, [IF-FALSE])
+# -----------------------------------------------------------------
+m4_define([lt_if_dict_fetch],
+[m4_if(lt_dict_fetch([$1], [$2], [$3]), [$4],
+ [$5],
+ [$6])])
+
+
+# lt_dict_filter(DICT, [SUBKEY], VALUE, [SEPARATOR], KEY, [...])
+# --------------------------------------------------------------
+m4_define([lt_dict_filter],
+[m4_if([$5], [], [],
+ [lt_join(m4_quote(m4_default([$4], [[, ]])),
+ lt_unquote(m4_split(m4_normalize(m4_foreach(_Lt_key, lt_car([m4_shiftn(4, $@)]),
+ [lt_if_dict_fetch([$1], _Lt_key, [$2], [$3], [_Lt_key ])])))))])[]dnl
+])
+
+# ltversion.m4 -- version numbers -*- Autoconf -*-
+#
+# Copyright (C) 2004 Free Software Foundation, Inc.
+# Written by Scott James Remnant, 2004
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+# Generated from ltversion.in.
+
+# serial 3017 ltversion.m4
+# This file is part of GNU Libtool
+
+m4_define([LT_PACKAGE_VERSION], [2.2.6b])
+m4_define([LT_PACKAGE_REVISION], [1.3017])
+
+AC_DEFUN([LTVERSION_VERSION],
+[macro_version='2.2.6b'
+macro_revision='1.3017'
+_LT_DECL(, macro_version, 0, [Which release of libtool.m4 was used?])
+_LT_DECL(, macro_revision, 0)
+])
+
+# lt~obsolete.m4 -- aclocal satisfying obsolete definitions. -*-Autoconf-*-
+#
+# Copyright (C) 2004, 2005, 2007 Free Software Foundation, Inc.
+# Written by Scott James Remnant, 2004.
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+# serial 4 lt~obsolete.m4
+
+# These exist entirely to fool aclocal when bootstrapping libtool.
+#
+# In the past libtool.m4 has provided macros via AC_DEFUN (or AU_DEFUN)
+# which have later been changed to m4_define as they aren't part of the
+# exported API, or moved to Autoconf or Automake where they belong.
+#
+# The trouble is, aclocal is a bit thick. It'll see the old AC_DEFUN
+# in /usr/share/aclocal/libtool.m4 and remember it, then when it sees us
+# using a macro with the same name in our local m4/libtool.m4 it'll
+# pull the old libtool.m4 in (it doesn't see our shiny new m4_define
+# and doesn't know about Autoconf macros at all.)
+#
+# So we provide this file, which has a silly filename so it's always
+# included after everything else. This provides aclocal with the
+# AC_DEFUNs it wants, but when m4 processes it, it doesn't do anything
+# because those macros already exist, or will be overwritten later.
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diff --git a/src/libGkArrays/config/config.guess b/src/libGkArrays/config/config.guess
new file mode 100755
index 0000000..d622a44
--- /dev/null
+++ b/src/libGkArrays/config/config.guess
@@ -0,0 +1,1530 @@
+#! /bin/sh
+# Attempt to guess a canonical system name.
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
+# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,
+# 2011, 2012 Free Software Foundation, Inc.
+
+timestamp='2012-02-10'
+
+# This file is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+
+# Originally written by Per Bothner. Please send patches (context
+# diff format) to <config-patches at gnu.org> and include a ChangeLog
+# entry.
+#
+# This script attempts to guess a canonical system name similar to
+# config.sub. If it succeeds, it prints the system name on stdout, and
+# exits with 0. Otherwise, it exits with 1.
+#
+# You can get the latest version of this script from:
+# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
+
+me=`echo "$0" | sed -e 's,.*/,,'`
+
+usage="\
+Usage: $0 [OPTION]
+
+Output the configuration name of the system \`$me' is run on.
+
+Operation modes:
+ -h, --help print this help, then exit
+ -t, --time-stamp print date of last modification, then exit
+ -v, --version print version number, then exit
+
+Report bugs and patches to <config-patches at gnu.org>."
+
+version="\
+GNU config.guess ($timestamp)
+
+Originally written by Per Bothner.
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000,
+2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012
+Free Software Foundation, Inc.
+
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+
+help="
+Try \`$me --help' for more information."
+
+# Parse command line
+while test $# -gt 0 ; do
+ case $1 in
+ --time-stamp | --time* | -t )
+ echo "$timestamp" ; exit ;;
+ --version | -v )
+ echo "$version" ; exit ;;
+ --help | --h* | -h )
+ echo "$usage"; exit ;;
+ -- ) # Stop option processing
+ shift; break ;;
+ - ) # Use stdin as input.
+ break ;;
+ -* )
+ echo "$me: invalid option $1$help" >&2
+ exit 1 ;;
+ * )
+ break ;;
+ esac
+done
+
+if test $# != 0; then
+ echo "$me: too many arguments$help" >&2
+ exit 1
+fi
+
+trap 'exit 1' 1 2 15
+
+# CC_FOR_BUILD -- compiler used by this script. Note that the use of a
+# compiler to aid in system detection is discouraged as it requires
+# temporary files to be created and, as you can see below, it is a
+# headache to deal with in a portable fashion.
+
+# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still
+# use `HOST_CC' if defined, but it is deprecated.
+
+# Portable tmp directory creation inspired by the Autoconf team.
+
+set_cc_for_build='
+trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ;
+trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ;
+: ${TMPDIR=/tmp} ;
+ { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
+ { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||
+ { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } ||
+ { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ;
+dummy=$tmp/dummy ;
+tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ;
+case $CC_FOR_BUILD,$HOST_CC,$CC in
+ ,,) echo "int x;" > $dummy.c ;
+ for c in cc gcc c89 c99 ; do
+ if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then
+ CC_FOR_BUILD="$c"; break ;
+ fi ;
+ done ;
+ if test x"$CC_FOR_BUILD" = x ; then
+ CC_FOR_BUILD=no_compiler_found ;
+ fi
+ ;;
+ ,,*) CC_FOR_BUILD=$CC ;;
+ ,*,*) CC_FOR_BUILD=$HOST_CC ;;
+esac ; set_cc_for_build= ;'
+
+# This is needed to find uname on a Pyramid OSx when run in the BSD universe.
+# (ghazi at noc.rutgers.edu 1994-08-24)
+if (test -f /.attbin/uname) >/dev/null 2>&1 ; then
+ PATH=$PATH:/.attbin ; export PATH
+fi
+
+UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown
+UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
+UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown
+UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
+
+# Note: order is significant - the case branches are not exclusive.
+
+case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
+ *:NetBSD:*:*)
+ # NetBSD (nbsd) targets should (where applicable) match one or
+ # more of the tuples: *-*-netbsdelf*, *-*-netbsdaout*,
+ # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently
+ # switched to ELF, *-*-netbsd* would select the old
+ # object file format. This provides both forward
+ # compatibility and a consistent mechanism for selecting the
+ # object file format.
+ #
+ # Note: NetBSD doesn't particularly care about the vendor
+ # portion of the name. We always set it to "unknown".
+ sysctl="sysctl -n hw.machine_arch"
+ UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \
+ /usr/sbin/$sysctl 2>/dev/null || echo unknown)`
+ case "${UNAME_MACHINE_ARCH}" in
+ armeb) machine=armeb-unknown ;;
+ arm*) machine=arm-unknown ;;
+ sh3el) machine=shl-unknown ;;
+ sh3eb) machine=sh-unknown ;;
+ sh5el) machine=sh5le-unknown ;;
+ *) machine=${UNAME_MACHINE_ARCH}-unknown ;;
+ esac
+ # The Operating System including object format, if it has switched
+ # to ELF recently, or will in the future.
+ case "${UNAME_MACHINE_ARCH}" in
+ arm*|i386|m68k|ns32k|sh3*|sparc|vax)
+ eval $set_cc_for_build
+ if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep -q __ELF__
+ then
+ # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout).
+ # Return netbsd for either. FIX?
+ os=netbsd
+ else
+ os=netbsdelf
+ fi
+ ;;
+ *)
+ os=netbsd
+ ;;
+ esac
+ # The OS release
+ # Debian GNU/NetBSD machines have a different userland, and
+ # thus, need a distinct triplet. However, they do not need
+ # kernel version information, so it can be replaced with a
+ # suitable tag, in the style of linux-gnu.
+ case "${UNAME_VERSION}" in
+ Debian*)
+ release='-gnu'
+ ;;
+ *)
+ release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'`
+ ;;
+ esac
+ # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM:
+ # contains redundant information, the shorter form:
+ # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used.
+ echo "${machine}-${os}${release}"
+ exit ;;
+ *:OpenBSD:*:*)
+ UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'`
+ echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE}
+ exit ;;
+ *:ekkoBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE}
+ exit ;;
+ *:SolidBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-solidbsd${UNAME_RELEASE}
+ exit ;;
+ macppc:MirBSD:*:*)
+ echo powerpc-unknown-mirbsd${UNAME_RELEASE}
+ exit ;;
+ *:MirBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE}
+ exit ;;
+ alpha:OSF1:*:*)
+ case $UNAME_RELEASE in
+ *4.0)
+ UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
+ ;;
+ *5.*)
+ UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
+ ;;
+ esac
+ # According to Compaq, /usr/sbin/psrinfo has been available on
+ # OSF/1 and Tru64 systems produced since 1995. I hope that
+ # covers most systems running today. This code pipes the CPU
+ # types through head -n 1, so we only detect the type of CPU 0.
+ ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
+ case "$ALPHA_CPU_TYPE" in
+ "EV4 (21064)")
+ UNAME_MACHINE="alpha" ;;
+ "EV4.5 (21064)")
+ UNAME_MACHINE="alpha" ;;
+ "LCA4 (21066/21068)")
+ UNAME_MACHINE="alpha" ;;
+ "EV5 (21164)")
+ UNAME_MACHINE="alphaev5" ;;
+ "EV5.6 (21164A)")
+ UNAME_MACHINE="alphaev56" ;;
+ "EV5.6 (21164PC)")
+ UNAME_MACHINE="alphapca56" ;;
+ "EV5.7 (21164PC)")
+ UNAME_MACHINE="alphapca57" ;;
+ "EV6 (21264)")
+ UNAME_MACHINE="alphaev6" ;;
+ "EV6.7 (21264A)")
+ UNAME_MACHINE="alphaev67" ;;
+ "EV6.8CB (21264C)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.8AL (21264B)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.8CX (21264D)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.9A (21264/EV69A)")
+ UNAME_MACHINE="alphaev69" ;;
+ "EV7 (21364)")
+ UNAME_MACHINE="alphaev7" ;;
+ "EV7.9 (21364A)")
+ UNAME_MACHINE="alphaev79" ;;
+ esac
+ # A Pn.n version is a patched version.
+ # A Vn.n version is a released version.
+ # A Tn.n version is a released field test version.
+ # A Xn.n version is an unreleased experimental baselevel.
+ # 1.2 uses "1.2" for uname -r.
+ echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
+ # Reset EXIT trap before exiting to avoid spurious non-zero exit code.
+ exitcode=$?
+ trap '' 0
+ exit $exitcode ;;
+ Alpha\ *:Windows_NT*:*)
+ # How do we know it's Interix rather than the generic POSIX subsystem?
+ # Should we change UNAME_MACHINE based on the output of uname instead
+ # of the specific Alpha model?
+ echo alpha-pc-interix
+ exit ;;
+ 21064:Windows_NT:50:3)
+ echo alpha-dec-winnt3.5
+ exit ;;
+ Amiga*:UNIX_System_V:4.0:*)
+ echo m68k-unknown-sysv4
+ exit ;;
+ *:[Aa]miga[Oo][Ss]:*:*)
+ echo ${UNAME_MACHINE}-unknown-amigaos
+ exit ;;
+ *:[Mm]orph[Oo][Ss]:*:*)
+ echo ${UNAME_MACHINE}-unknown-morphos
+ exit ;;
+ *:OS/390:*:*)
+ echo i370-ibm-openedition
+ exit ;;
+ *:z/VM:*:*)
+ echo s390-ibm-zvmoe
+ exit ;;
+ *:OS400:*:*)
+ echo powerpc-ibm-os400
+ exit ;;
+ arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
+ echo arm-acorn-riscix${UNAME_RELEASE}
+ exit ;;
+ arm:riscos:*:*|arm:RISCOS:*:*)
+ echo arm-unknown-riscos
+ exit ;;
+ SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*)
+ echo hppa1.1-hitachi-hiuxmpp
+ exit ;;
+ Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*)
+ # akee at wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE.
+ if test "`(/bin/universe) 2>/dev/null`" = att ; then
+ echo pyramid-pyramid-sysv3
+ else
+ echo pyramid-pyramid-bsd
+ fi
+ exit ;;
+ NILE*:*:*:dcosx)
+ echo pyramid-pyramid-svr4
+ exit ;;
+ DRS?6000:unix:4.0:6*)
+ echo sparc-icl-nx6
+ exit ;;
+ DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*)
+ case `/usr/bin/uname -p` in
+ sparc) echo sparc-icl-nx7; exit ;;
+ esac ;;
+ s390x:SunOS:*:*)
+ echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4H:SunOS:5.*:*)
+ echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
+ echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*)
+ echo i386-pc-auroraux${UNAME_RELEASE}
+ exit ;;
+ i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*)
+ eval $set_cc_for_build
+ SUN_ARCH="i386"
+ # If there is a compiler, see if it is configured for 64-bit objects.
+ # Note that the Sun cc does not turn __LP64__ into 1 like gcc does.
+ # This test works for both compilers.
+ if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
+ if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \
+ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_64BIT_ARCH >/dev/null
+ then
+ SUN_ARCH="x86_64"
+ fi
+ fi
+ echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4*:SunOS:6*:*)
+ # According to config.sub, this is the proper way to canonicalize
+ # SunOS6. Hard to guess exactly what SunOS6 will be like, but
+ # it's likely to be more like Solaris than SunOS4.
+ echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4*:SunOS:*:*)
+ case "`/usr/bin/arch -k`" in
+ Series*|S4*)
+ UNAME_RELEASE=`uname -v`
+ ;;
+ esac
+ # Japanese Language versions have a version number like `4.1.3-JL'.
+ echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'`
+ exit ;;
+ sun3*:SunOS:*:*)
+ echo m68k-sun-sunos${UNAME_RELEASE}
+ exit ;;
+ sun*:*:4.2BSD:*)
+ UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
+ test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3
+ case "`/bin/arch`" in
+ sun3)
+ echo m68k-sun-sunos${UNAME_RELEASE}
+ ;;
+ sun4)
+ echo sparc-sun-sunos${UNAME_RELEASE}
+ ;;
+ esac
+ exit ;;
+ aushp:SunOS:*:*)
+ echo sparc-auspex-sunos${UNAME_RELEASE}
+ exit ;;
+ # The situation for MiNT is a little confusing. The machine name
+ # can be virtually everything (everything which is not
+ # "atarist" or "atariste" at least should have a processor
+ # > m68000). The system name ranges from "MiNT" over "FreeMiNT"
+ # to the lowercase version "mint" (or "freemint"). Finally
+ # the system name "TOS" denotes a system which is actually not
+ # MiNT. But MiNT is downward compatible to TOS, so this should
+ # be no problem.
+ atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit ;;
+ atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit ;;
+ *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit ;;
+ milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
+ echo m68k-milan-mint${UNAME_RELEASE}
+ exit ;;
+ hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
+ echo m68k-hades-mint${UNAME_RELEASE}
+ exit ;;
+ *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
+ echo m68k-unknown-mint${UNAME_RELEASE}
+ exit ;;
+ m68k:machten:*:*)
+ echo m68k-apple-machten${UNAME_RELEASE}
+ exit ;;
+ powerpc:machten:*:*)
+ echo powerpc-apple-machten${UNAME_RELEASE}
+ exit ;;
+ RISC*:Mach:*:*)
+ echo mips-dec-mach_bsd4.3
+ exit ;;
+ RISC*:ULTRIX:*:*)
+ echo mips-dec-ultrix${UNAME_RELEASE}
+ exit ;;
+ VAX*:ULTRIX*:*:*)
+ echo vax-dec-ultrix${UNAME_RELEASE}
+ exit ;;
+ 2020:CLIX:*:* | 2430:CLIX:*:*)
+ echo clipper-intergraph-clix${UNAME_RELEASE}
+ exit ;;
+ mips:*:*:UMIPS | mips:*:*:RISCos)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+#ifdef __cplusplus
+#include <stdio.h> /* for printf() prototype */
+ int main (int argc, char *argv[]) {
+#else
+ int main (argc, argv) int argc; char *argv[]; {
+#endif
+ #if defined (host_mips) && defined (MIPSEB)
+ #if defined (SYSTYPE_SYSV)
+ printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0);
+ #endif
+ #if defined (SYSTYPE_SVR4)
+ printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0);
+ #endif
+ #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD)
+ printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0);
+ #endif
+ #endif
+ exit (-1);
+ }
+EOF
+ $CC_FOR_BUILD -o $dummy $dummy.c &&
+ dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` &&
+ SYSTEM_NAME=`$dummy $dummyarg` &&
+ { echo "$SYSTEM_NAME"; exit; }
+ echo mips-mips-riscos${UNAME_RELEASE}
+ exit ;;
+ Motorola:PowerMAX_OS:*:*)
+ echo powerpc-motorola-powermax
+ exit ;;
+ Motorola:*:4.3:PL8-*)
+ echo powerpc-harris-powermax
+ exit ;;
+ Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*)
+ echo powerpc-harris-powermax
+ exit ;;
+ Night_Hawk:Power_UNIX:*:*)
+ echo powerpc-harris-powerunix
+ exit ;;
+ m88k:CX/UX:7*:*)
+ echo m88k-harris-cxux7
+ exit ;;
+ m88k:*:4*:R4*)
+ echo m88k-motorola-sysv4
+ exit ;;
+ m88k:*:3*:R3*)
+ echo m88k-motorola-sysv3
+ exit ;;
+ AViiON:dgux:*:*)
+ # DG/UX returns AViiON for all architectures
+ UNAME_PROCESSOR=`/usr/bin/uname -p`
+ if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ]
+ then
+ if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \
+ [ ${TARGET_BINARY_INTERFACE}x = x ]
+ then
+ echo m88k-dg-dgux${UNAME_RELEASE}
+ else
+ echo m88k-dg-dguxbcs${UNAME_RELEASE}
+ fi
+ else
+ echo i586-dg-dgux${UNAME_RELEASE}
+ fi
+ exit ;;
+ M88*:DolphinOS:*:*) # DolphinOS (SVR3)
+ echo m88k-dolphin-sysv3
+ exit ;;
+ M88*:*:R3*:*)
+ # Delta 88k system running SVR3
+ echo m88k-motorola-sysv3
+ exit ;;
+ XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3)
+ echo m88k-tektronix-sysv3
+ exit ;;
+ Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD)
+ echo m68k-tektronix-bsd
+ exit ;;
+ *:IRIX*:*:*)
+ echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'`
+ exit ;;
+ ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX.
+ echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id
+ exit ;; # Note that: echo "'`uname -s`'" gives 'AIX '
+ i*86:AIX:*:*)
+ echo i386-ibm-aix
+ exit ;;
+ ia64:AIX:*:*)
+ if [ -x /usr/bin/oslevel ] ; then
+ IBM_REV=`/usr/bin/oslevel`
+ else
+ IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
+ fi
+ echo ${UNAME_MACHINE}-ibm-aix${IBM_REV}
+ exit ;;
+ *:AIX:2:3)
+ if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #include <sys/systemcfg.h>
+
+ main()
+ {
+ if (!__power_pc())
+ exit(1);
+ puts("powerpc-ibm-aix3.2.5");
+ exit(0);
+ }
+EOF
+ if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy`
+ then
+ echo "$SYSTEM_NAME"
+ else
+ echo rs6000-ibm-aix3.2.5
+ fi
+ elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then
+ echo rs6000-ibm-aix3.2.4
+ else
+ echo rs6000-ibm-aix3.2
+ fi
+ exit ;;
+ *:AIX:*:[4567])
+ IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
+ if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
+ IBM_ARCH=rs6000
+ else
+ IBM_ARCH=powerpc
+ fi
+ if [ -x /usr/bin/oslevel ] ; then
+ IBM_REV=`/usr/bin/oslevel`
+ else
+ IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
+ fi
+ echo ${IBM_ARCH}-ibm-aix${IBM_REV}
+ exit ;;
+ *:AIX:*:*)
+ echo rs6000-ibm-aix
+ exit ;;
+ ibmrt:4.4BSD:*|romp-ibm:BSD:*)
+ echo romp-ibm-bsd4.4
+ exit ;;
+ ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and
+ echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to
+ exit ;; # report: romp-ibm BSD 4.3
+ *:BOSX:*:*)
+ echo rs6000-bull-bosx
+ exit ;;
+ DPX/2?00:B.O.S.:*:*)
+ echo m68k-bull-sysv3
+ exit ;;
+ 9000/[34]??:4.3bsd:1.*:*)
+ echo m68k-hp-bsd
+ exit ;;
+ hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*)
+ echo m68k-hp-bsd4.4
+ exit ;;
+ 9000/[34678]??:HP-UX:*:*)
+ HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
+ case "${UNAME_MACHINE}" in
+ 9000/31? ) HP_ARCH=m68000 ;;
+ 9000/[34]?? ) HP_ARCH=m68k ;;
+ 9000/[678][0-9][0-9])
+ if [ -x /usr/bin/getconf ]; then
+ sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
+ sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
+ case "${sc_cpu_version}" in
+ 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
+ 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
+ 532) # CPU_PA_RISC2_0
+ case "${sc_kernel_bits}" in
+ 32) HP_ARCH="hppa2.0n" ;;
+ 64) HP_ARCH="hppa2.0w" ;;
+ '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20
+ esac ;;
+ esac
+ fi
+ if [ "${HP_ARCH}" = "" ]; then
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+
+ #define _HPUX_SOURCE
+ #include <stdlib.h>
+ #include <unistd.h>
+
+ int main ()
+ {
+ #if defined(_SC_KERNEL_BITS)
+ long bits = sysconf(_SC_KERNEL_BITS);
+ #endif
+ long cpu = sysconf (_SC_CPU_VERSION);
+
+ switch (cpu)
+ {
+ case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
+ case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
+ case CPU_PA_RISC2_0:
+ #if defined(_SC_KERNEL_BITS)
+ switch (bits)
+ {
+ case 64: puts ("hppa2.0w"); break;
+ case 32: puts ("hppa2.0n"); break;
+ default: puts ("hppa2.0"); break;
+ } break;
+ #else /* !defined(_SC_KERNEL_BITS) */
+ puts ("hppa2.0"); break;
+ #endif
+ default: puts ("hppa1.0"); break;
+ }
+ exit (0);
+ }
+EOF
+ (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
+ test -z "$HP_ARCH" && HP_ARCH=hppa
+ fi ;;
+ esac
+ if [ ${HP_ARCH} = "hppa2.0w" ]
+ then
+ eval $set_cc_for_build
+
+ # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating
+ # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler
+ # generating 64-bit code. GNU and HP use different nomenclature:
+ #
+ # $ CC_FOR_BUILD=cc ./config.guess
+ # => hppa2.0w-hp-hpux11.23
+ # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess
+ # => hppa64-hp-hpux11.23
+
+ if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) |
+ grep -q __LP64__
+ then
+ HP_ARCH="hppa2.0w"
+ else
+ HP_ARCH="hppa64"
+ fi
+ fi
+ echo ${HP_ARCH}-hp-hpux${HPUX_REV}
+ exit ;;
+ ia64:HP-UX:*:*)
+ HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
+ echo ia64-hp-hpux${HPUX_REV}
+ exit ;;
+ 3050*:HI-UX:*:*)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #include <unistd.h>
+ int
+ main ()
+ {
+ long cpu = sysconf (_SC_CPU_VERSION);
+ /* The order matters, because CPU_IS_HP_MC68K erroneously returns
+ true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct
+ results, however. */
+ if (CPU_IS_PA_RISC (cpu))
+ {
+ switch (cpu)
+ {
+ case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break;
+ case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break;
+ case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break;
+ default: puts ("hppa-hitachi-hiuxwe2"); break;
+ }
+ }
+ else if (CPU_IS_HP_MC68K (cpu))
+ puts ("m68k-hitachi-hiuxwe2");
+ else puts ("unknown-hitachi-hiuxwe2");
+ exit (0);
+ }
+EOF
+ $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` &&
+ { echo "$SYSTEM_NAME"; exit; }
+ echo unknown-hitachi-hiuxwe2
+ exit ;;
+ 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* )
+ echo hppa1.1-hp-bsd
+ exit ;;
+ 9000/8??:4.3bsd:*:*)
+ echo hppa1.0-hp-bsd
+ exit ;;
+ *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*)
+ echo hppa1.0-hp-mpeix
+ exit ;;
+ hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* )
+ echo hppa1.1-hp-osf
+ exit ;;
+ hp8??:OSF1:*:*)
+ echo hppa1.0-hp-osf
+ exit ;;
+ i*86:OSF1:*:*)
+ if [ -x /usr/sbin/sysversion ] ; then
+ echo ${UNAME_MACHINE}-unknown-osf1mk
+ else
+ echo ${UNAME_MACHINE}-unknown-osf1
+ fi
+ exit ;;
+ parisc*:Lites*:*:*)
+ echo hppa1.1-hp-lites
+ exit ;;
+ C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*)
+ echo c1-convex-bsd
+ exit ;;
+ C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*)
+ if getsysinfo -f scalar_acc
+ then echo c32-convex-bsd
+ else echo c2-convex-bsd
+ fi
+ exit ;;
+ C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*)
+ echo c34-convex-bsd
+ exit ;;
+ C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*)
+ echo c38-convex-bsd
+ exit ;;
+ C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*)
+ echo c4-convex-bsd
+ exit ;;
+ CRAY*Y-MP:*:*:*)
+ echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*[A-Z]90:*:*:*)
+ echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \
+ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \
+ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \
+ -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*TS:*:*:*)
+ echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*T3E:*:*:*)
+ echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*SV1:*:*:*)
+ echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ *:UNICOS/mp:*:*)
+ echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
+ FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
+ FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
+ echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+ exit ;;
+ 5000:UNIX_System_V:4.*:*)
+ FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
+ echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+ exit ;;
+ i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
+ echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE}
+ exit ;;
+ sparc*:BSD/OS:*:*)
+ echo sparc-unknown-bsdi${UNAME_RELEASE}
+ exit ;;
+ *:BSD/OS:*:*)
+ echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE}
+ exit ;;
+ *:FreeBSD:*:*)
+ UNAME_PROCESSOR=`/usr/bin/uname -p`
+ case ${UNAME_PROCESSOR} in
+ amd64)
+ echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+ *)
+ echo ${UNAME_PROCESSOR}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+ esac
+ exit ;;
+ i*:CYGWIN*:*)
+ echo ${UNAME_MACHINE}-pc-cygwin
+ exit ;;
+ *:MINGW*:*)
+ echo ${UNAME_MACHINE}-pc-mingw32
+ exit ;;
+ i*:MSYS*:*)
+ echo ${UNAME_MACHINE}-pc-msys
+ exit ;;
+ i*:windows32*:*)
+ # uname -m includes "-pc" on this system.
+ echo ${UNAME_MACHINE}-mingw32
+ exit ;;
+ i*:PW*:*)
+ echo ${UNAME_MACHINE}-pc-pw32
+ exit ;;
+ *:Interix*:*)
+ case ${UNAME_MACHINE} in
+ x86)
+ echo i586-pc-interix${UNAME_RELEASE}
+ exit ;;
+ authenticamd | genuineintel | EM64T)
+ echo x86_64-unknown-interix${UNAME_RELEASE}
+ exit ;;
+ IA64)
+ echo ia64-unknown-interix${UNAME_RELEASE}
+ exit ;;
+ esac ;;
+ [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*)
+ echo i${UNAME_MACHINE}-pc-mks
+ exit ;;
+ 8664:Windows_NT:*)
+ echo x86_64-pc-mks
+ exit ;;
+ i*:Windows_NT*:* | Pentium*:Windows_NT*:*)
+ # How do we know it's Interix rather than the generic POSIX subsystem?
+ # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we
+ # UNAME_MACHINE based on the output of uname instead of i386?
+ echo i586-pc-interix
+ exit ;;
+ i*:UWIN*:*)
+ echo ${UNAME_MACHINE}-pc-uwin
+ exit ;;
+ amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*)
+ echo x86_64-unknown-cygwin
+ exit ;;
+ p*:CYGWIN*:*)
+ echo powerpcle-unknown-cygwin
+ exit ;;
+ prep*:SunOS:5.*:*)
+ echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ *:GNU:*:*)
+ # the GNU system
+ echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
+ exit ;;
+ *:GNU/*:*:*)
+ # other systems with GNU libc and userland
+ echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu
+ exit ;;
+ i*86:Minix:*:*)
+ echo ${UNAME_MACHINE}-pc-minix
+ exit ;;
+ aarch64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ aarch64_be:Linux:*:*)
+ UNAME_MACHINE=aarch64_be
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ alpha:Linux:*:*)
+ case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
+ EV5) UNAME_MACHINE=alphaev5 ;;
+ EV56) UNAME_MACHINE=alphaev56 ;;
+ PCA56) UNAME_MACHINE=alphapca56 ;;
+ PCA57) UNAME_MACHINE=alphapca56 ;;
+ EV6) UNAME_MACHINE=alphaev6 ;;
+ EV67) UNAME_MACHINE=alphaev67 ;;
+ EV68*) UNAME_MACHINE=alphaev68 ;;
+ esac
+ objdump --private-headers /bin/sh | grep -q ld.so.1
+ if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi
+ echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC}
+ exit ;;
+ arm*:Linux:*:*)
+ eval $set_cc_for_build
+ if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep -q __ARM_EABI__
+ then
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ else
+ if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep -q __ARM_PCS_VFP
+ then
+ echo ${UNAME_MACHINE}-unknown-linux-gnueabi
+ else
+ echo ${UNAME_MACHINE}-unknown-linux-gnueabihf
+ fi
+ fi
+ exit ;;
+ avr32*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ cris:Linux:*:*)
+ echo ${UNAME_MACHINE}-axis-linux-gnu
+ exit ;;
+ crisv32:Linux:*:*)
+ echo ${UNAME_MACHINE}-axis-linux-gnu
+ exit ;;
+ frv:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ hexagon:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ i*86:Linux:*:*)
+ LIBC=gnu
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #ifdef __dietlibc__
+ LIBC=dietlibc
+ #endif
+EOF
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'`
+ echo "${UNAME_MACHINE}-pc-linux-${LIBC}"
+ exit ;;
+ ia64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ m32r*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ m68*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ mips:Linux:*:* | mips64:Linux:*:*)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #undef CPU
+ #undef ${UNAME_MACHINE}
+ #undef ${UNAME_MACHINE}el
+ #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
+ CPU=${UNAME_MACHINE}el
+ #else
+ #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
+ CPU=${UNAME_MACHINE}
+ #else
+ CPU=
+ #endif
+ #endif
+EOF
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'`
+ test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
+ ;;
+ or32:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ padre:Linux:*:*)
+ echo sparc-unknown-linux-gnu
+ exit ;;
+ parisc64:Linux:*:* | hppa64:Linux:*:*)
+ echo hppa64-unknown-linux-gnu
+ exit ;;
+ parisc:Linux:*:* | hppa:Linux:*:*)
+ # Look for CPU level
+ case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
+ PA7*) echo hppa1.1-unknown-linux-gnu ;;
+ PA8*) echo hppa2.0-unknown-linux-gnu ;;
+ *) echo hppa-unknown-linux-gnu ;;
+ esac
+ exit ;;
+ ppc64:Linux:*:*)
+ echo powerpc64-unknown-linux-gnu
+ exit ;;
+ ppc:Linux:*:*)
+ echo powerpc-unknown-linux-gnu
+ exit ;;
+ s390:Linux:*:* | s390x:Linux:*:*)
+ echo ${UNAME_MACHINE}-ibm-linux
+ exit ;;
+ sh64*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ sh*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ sparc:Linux:*:* | sparc64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ tile*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ vax:Linux:*:*)
+ echo ${UNAME_MACHINE}-dec-linux-gnu
+ exit ;;
+ x86_64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ xtensa*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ i*86:DYNIX/ptx:4*:*)
+ # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
+ # earlier versions are messed up and put the nodename in both
+ # sysname and nodename.
+ echo i386-sequent-sysv4
+ exit ;;
+ i*86:UNIX_SV:4.2MP:2.*)
+ # Unixware is an offshoot of SVR4, but it has its own version
+ # number series starting with 2...
+ # I am not positive that other SVR4 systems won't match this,
+ # I just have to hope. -- rms.
+ # Use sysv4.2uw... so that sysv4* matches it.
+ echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION}
+ exit ;;
+ i*86:OS/2:*:*)
+ # If we were able to find `uname', then EMX Unix compatibility
+ # is probably installed.
+ echo ${UNAME_MACHINE}-pc-os2-emx
+ exit ;;
+ i*86:XTS-300:*:STOP)
+ echo ${UNAME_MACHINE}-unknown-stop
+ exit ;;
+ i*86:atheos:*:*)
+ echo ${UNAME_MACHINE}-unknown-atheos
+ exit ;;
+ i*86:syllable:*:*)
+ echo ${UNAME_MACHINE}-pc-syllable
+ exit ;;
+ i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*)
+ echo i386-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ i*86:*DOS:*:*)
+ echo ${UNAME_MACHINE}-pc-msdosdjgpp
+ exit ;;
+ i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*)
+ UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'`
+ if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
+ echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL}
+ else
+ echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL}
+ fi
+ exit ;;
+ i*86:*:5:[678]*)
+ # UnixWare 7.x, OpenUNIX and OpenServer 6.
+ case `/bin/uname -X | grep "^Machine"` in
+ *486*) UNAME_MACHINE=i486 ;;
+ *Pentium) UNAME_MACHINE=i586 ;;
+ *Pent*|*Celeron) UNAME_MACHINE=i686 ;;
+ esac
+ echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}
+ exit ;;
+ i*86:*:3.2:*)
+ if test -f /usr/options/cb.name; then
+ UNAME_REL=`sed -n 's/.*Version //p' </usr/options/cb.name`
+ echo ${UNAME_MACHINE}-pc-isc$UNAME_REL
+ elif /bin/uname -X 2>/dev/null >/dev/null ; then
+ UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')`
+ (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486
+ (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \
+ && UNAME_MACHINE=i586
+ (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \
+ && UNAME_MACHINE=i686
+ (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \
+ && UNAME_MACHINE=i686
+ echo ${UNAME_MACHINE}-pc-sco$UNAME_REL
+ else
+ echo ${UNAME_MACHINE}-pc-sysv32
+ fi
+ exit ;;
+ pc:*:*:*)
+ # Left here for compatibility:
+ # uname -m prints for DJGPP always 'pc', but it prints nothing about
+ # the processor, so we play safe by assuming i586.
+ # Note: whatever this is, it MUST be the same as what config.sub
+ # prints for the "djgpp" host, or else GDB configury will decide that
+ # this is a cross-build.
+ echo i586-pc-msdosdjgpp
+ exit ;;
+ Intel:Mach:3*:*)
+ echo i386-pc-mach3
+ exit ;;
+ paragon:*:*:*)
+ echo i860-intel-osf1
+ exit ;;
+ i860:*:4.*:*) # i860-SVR4
+ if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then
+ echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4
+ else # Add other i860-SVR4 vendors below as they are discovered.
+ echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4
+ fi
+ exit ;;
+ mini*:CTIX:SYS*5:*)
+ # "miniframe"
+ echo m68010-convergent-sysv
+ exit ;;
+ mc68k:UNIX:SYSTEM5:3.51m)
+ echo m68k-convergent-sysv
+ exit ;;
+ M680?0:D-NIX:5.3:*)
+ echo m68k-diab-dnix
+ exit ;;
+ M68*:*:R3V[5678]*:*)
+ test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;;
+ 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0)
+ OS_REL=''
+ test -r /etc/.relid \
+ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
+ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
+ 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4; exit; } ;;
+ NCR*:*:4.2:* | MPRAS*:*:4.2:*)
+ OS_REL='.3'
+ test -r /etc/.relid \
+ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
+ && { echo i586-ncr-sysv4.3${OS_REL}; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \
+ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
+ m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
+ echo m68k-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ mc68030:UNIX_System_V:4.*:*)
+ echo m68k-atari-sysv4
+ exit ;;
+ TSUNAMI:LynxOS:2.*:*)
+ echo sparc-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ rs6000:LynxOS:2.*:*)
+ echo rs6000-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*)
+ echo powerpc-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ SM[BE]S:UNIX_SV:*:*)
+ echo mips-dde-sysv${UNAME_RELEASE}
+ exit ;;
+ RM*:ReliantUNIX-*:*:*)
+ echo mips-sni-sysv4
+ exit ;;
+ RM*:SINIX-*:*:*)
+ echo mips-sni-sysv4
+ exit ;;
+ *:SINIX-*:*:*)
+ if uname -p 2>/dev/null >/dev/null ; then
+ UNAME_MACHINE=`(uname -p) 2>/dev/null`
+ echo ${UNAME_MACHINE}-sni-sysv4
+ else
+ echo ns32k-sni-sysv
+ fi
+ exit ;;
+ PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
+ # says <Richard.M.Bartel at ccMail.Census.GOV>
+ echo i586-unisys-sysv4
+ exit ;;
+ *:UNIX_System_V:4*:FTX*)
+ # From Gerald Hewes <hewes at openmarket.com>.
+ # How about differentiating between stratus architectures? -djm
+ echo hppa1.1-stratus-sysv4
+ exit ;;
+ *:*:*:FTX*)
+ # From seanf at swdc.stratus.com.
+ echo i860-stratus-sysv4
+ exit ;;
+ i*86:VOS:*:*)
+ # From Paul.Green at stratus.com.
+ echo ${UNAME_MACHINE}-stratus-vos
+ exit ;;
+ *:VOS:*:*)
+ # From Paul.Green at stratus.com.
+ echo hppa1.1-stratus-vos
+ exit ;;
+ mc68*:A/UX:*:*)
+ echo m68k-apple-aux${UNAME_RELEASE}
+ exit ;;
+ news*:NEWS-OS:6*:*)
+ echo mips-sony-newsos6
+ exit ;;
+ R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
+ if [ -d /usr/nec ]; then
+ echo mips-nec-sysv${UNAME_RELEASE}
+ else
+ echo mips-unknown-sysv${UNAME_RELEASE}
+ fi
+ exit ;;
+ BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only.
+ echo powerpc-be-beos
+ exit ;;
+ BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only.
+ echo powerpc-apple-beos
+ exit ;;
+ BePC:BeOS:*:*) # BeOS running on Intel PC compatible.
+ echo i586-pc-beos
+ exit ;;
+ BePC:Haiku:*:*) # Haiku running on Intel PC compatible.
+ echo i586-pc-haiku
+ exit ;;
+ SX-4:SUPER-UX:*:*)
+ echo sx4-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-5:SUPER-UX:*:*)
+ echo sx5-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-6:SUPER-UX:*:*)
+ echo sx6-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-7:SUPER-UX:*:*)
+ echo sx7-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-8:SUPER-UX:*:*)
+ echo sx8-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-8R:SUPER-UX:*:*)
+ echo sx8r-nec-superux${UNAME_RELEASE}
+ exit ;;
+ Power*:Rhapsody:*:*)
+ echo powerpc-apple-rhapsody${UNAME_RELEASE}
+ exit ;;
+ *:Rhapsody:*:*)
+ echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE}
+ exit ;;
+ *:Darwin:*:*)
+ UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown
+ case $UNAME_PROCESSOR in
+ i386)
+ eval $set_cc_for_build
+ if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
+ if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
+ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_64BIT_ARCH >/dev/null
+ then
+ UNAME_PROCESSOR="x86_64"
+ fi
+ fi ;;
+ unknown) UNAME_PROCESSOR=powerpc ;;
+ esac
+ echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
+ exit ;;
+ *:procnto*:*:* | *:QNX:[0123456789]*:*)
+ UNAME_PROCESSOR=`uname -p`
+ if test "$UNAME_PROCESSOR" = "x86"; then
+ UNAME_PROCESSOR=i386
+ UNAME_MACHINE=pc
+ fi
+ echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE}
+ exit ;;
+ *:QNX:*:4*)
+ echo i386-pc-qnx
+ exit ;;
+ NEO-?:NONSTOP_KERNEL:*:*)
+ echo neo-tandem-nsk${UNAME_RELEASE}
+ exit ;;
+ NSE-?:NONSTOP_KERNEL:*:*)
+ echo nse-tandem-nsk${UNAME_RELEASE}
+ exit ;;
+ NSR-?:NONSTOP_KERNEL:*:*)
+ echo nsr-tandem-nsk${UNAME_RELEASE}
+ exit ;;
+ *:NonStop-UX:*:*)
+ echo mips-compaq-nonstopux
+ exit ;;
+ BS2000:POSIX*:*:*)
+ echo bs2000-siemens-sysv
+ exit ;;
+ DS/*:UNIX_System_V:*:*)
+ echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE}
+ exit ;;
+ *:Plan9:*:*)
+ # "uname -m" is not consistent, so use $cputype instead. 386
+ # is converted to i386 for consistency with other x86
+ # operating systems.
+ if test "$cputype" = "386"; then
+ UNAME_MACHINE=i386
+ else
+ UNAME_MACHINE="$cputype"
+ fi
+ echo ${UNAME_MACHINE}-unknown-plan9
+ exit ;;
+ *:TOPS-10:*:*)
+ echo pdp10-unknown-tops10
+ exit ;;
+ *:TENEX:*:*)
+ echo pdp10-unknown-tenex
+ exit ;;
+ KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*)
+ echo pdp10-dec-tops20
+ exit ;;
+ XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*)
+ echo pdp10-xkl-tops20
+ exit ;;
+ *:TOPS-20:*:*)
+ echo pdp10-unknown-tops20
+ exit ;;
+ *:ITS:*:*)
+ echo pdp10-unknown-its
+ exit ;;
+ SEI:*:*:SEIUX)
+ echo mips-sei-seiux${UNAME_RELEASE}
+ exit ;;
+ *:DragonFly:*:*)
+ echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
+ exit ;;
+ *:*VMS:*:*)
+ UNAME_MACHINE=`(uname -p) 2>/dev/null`
+ case "${UNAME_MACHINE}" in
+ A*) echo alpha-dec-vms ; exit ;;
+ I*) echo ia64-dec-vms ; exit ;;
+ V*) echo vax-dec-vms ; exit ;;
+ esac ;;
+ *:XENIX:*:SysV)
+ echo i386-pc-xenix
+ exit ;;
+ i*86:skyos:*:*)
+ echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//'
+ exit ;;
+ i*86:rdos:*:*)
+ echo ${UNAME_MACHINE}-pc-rdos
+ exit ;;
+ i*86:AROS:*:*)
+ echo ${UNAME_MACHINE}-pc-aros
+ exit ;;
+ x86_64:VMkernel:*:*)
+ echo ${UNAME_MACHINE}-unknown-esx
+ exit ;;
+esac
+
+#echo '(No uname command or uname output not recognized.)' 1>&2
+#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2
+
+eval $set_cc_for_build
+cat >$dummy.c <<EOF
+#ifdef _SEQUENT_
+# include <sys/types.h>
+# include <sys/utsname.h>
+#endif
+main ()
+{
+#if defined (sony)
+#if defined (MIPSEB)
+ /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed,
+ I don't know.... */
+ printf ("mips-sony-bsd\n"); exit (0);
+#else
+#include <sys/param.h>
+ printf ("m68k-sony-newsos%s\n",
+#ifdef NEWSOS4
+ "4"
+#else
+ ""
+#endif
+ ); exit (0);
+#endif
+#endif
+
+#if defined (__arm) && defined (__acorn) && defined (__unix)
+ printf ("arm-acorn-riscix\n"); exit (0);
+#endif
+
+#if defined (hp300) && !defined (hpux)
+ printf ("m68k-hp-bsd\n"); exit (0);
+#endif
+
+#if defined (NeXT)
+#if !defined (__ARCHITECTURE__)
+#define __ARCHITECTURE__ "m68k"
+#endif
+ int version;
+ version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`;
+ if (version < 4)
+ printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version);
+ else
+ printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version);
+ exit (0);
+#endif
+
+#if defined (MULTIMAX) || defined (n16)
+#if defined (UMAXV)
+ printf ("ns32k-encore-sysv\n"); exit (0);
+#else
+#if defined (CMU)
+ printf ("ns32k-encore-mach\n"); exit (0);
+#else
+ printf ("ns32k-encore-bsd\n"); exit (0);
+#endif
+#endif
+#endif
+
+#if defined (__386BSD__)
+ printf ("i386-pc-bsd\n"); exit (0);
+#endif
+
+#if defined (sequent)
+#if defined (i386)
+ printf ("i386-sequent-dynix\n"); exit (0);
+#endif
+#if defined (ns32000)
+ printf ("ns32k-sequent-dynix\n"); exit (0);
+#endif
+#endif
+
+#if defined (_SEQUENT_)
+ struct utsname un;
+
+ uname(&un);
+
+ if (strncmp(un.version, "V2", 2) == 0) {
+ printf ("i386-sequent-ptx2\n"); exit (0);
+ }
+ if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */
+ printf ("i386-sequent-ptx1\n"); exit (0);
+ }
+ printf ("i386-sequent-ptx\n"); exit (0);
+
+#endif
+
+#if defined (vax)
+# if !defined (ultrix)
+# include <sys/param.h>
+# if defined (BSD)
+# if BSD == 43
+ printf ("vax-dec-bsd4.3\n"); exit (0);
+# else
+# if BSD == 199006
+ printf ("vax-dec-bsd4.3reno\n"); exit (0);
+# else
+ printf ("vax-dec-bsd\n"); exit (0);
+# endif
+# endif
+# else
+ printf ("vax-dec-bsd\n"); exit (0);
+# endif
+# else
+ printf ("vax-dec-ultrix\n"); exit (0);
+# endif
+#endif
+
+#if defined (alliant) && defined (i860)
+ printf ("i860-alliant-bsd\n"); exit (0);
+#endif
+
+ exit (1);
+}
+EOF
+
+$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` &&
+ { echo "$SYSTEM_NAME"; exit; }
+
+# Apollos put the system type in the environment.
+
+test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; }
+
+# Convex versions that predate uname can use getsysinfo(1)
+
+if [ -x /usr/convex/getsysinfo ]
+then
+ case `getsysinfo -f cpu_type` in
+ c1*)
+ echo c1-convex-bsd
+ exit ;;
+ c2*)
+ if getsysinfo -f scalar_acc
+ then echo c32-convex-bsd
+ else echo c2-convex-bsd
+ fi
+ exit ;;
+ c34*)
+ echo c34-convex-bsd
+ exit ;;
+ c38*)
+ echo c38-convex-bsd
+ exit ;;
+ c4*)
+ echo c4-convex-bsd
+ exit ;;
+ esac
+fi
+
+cat >&2 <<EOF
+$0: unable to guess system type
+
+This script, last modified $timestamp, has failed to recognize
+the operating system you are using. It is advised that you
+download the most up to date version of the config scripts from
+
+ http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
+and
+ http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
+
+If the version you run ($0) is already up to date, please
+send the following data and any information you think might be
+pertinent to <config-patches at gnu.org> in order to provide the needed
+information to handle your system.
+
+config.guess timestamp = $timestamp
+
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null`
+
+hostinfo = `(hostinfo) 2>/dev/null`
+/bin/universe = `(/bin/universe) 2>/dev/null`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null`
+/bin/arch = `(/bin/arch) 2>/dev/null`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null`
+
+UNAME_MACHINE = ${UNAME_MACHINE}
+UNAME_RELEASE = ${UNAME_RELEASE}
+UNAME_SYSTEM = ${UNAME_SYSTEM}
+UNAME_VERSION = ${UNAME_VERSION}
+EOF
+
+exit 1
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "timestamp='"
+# time-stamp-format: "%:y-%02m-%02d"
+# time-stamp-end: "'"
+# End:
diff --git a/src/libGkArrays/config/config.h.in b/src/libGkArrays/config/config.h.in
new file mode 100644
index 0000000..0fac70b
--- /dev/null
+++ b/src/libGkArrays/config/config.h.in
@@ -0,0 +1,145 @@
+/* config/config.h.in. Generated from configure.ac by autoheader. */
+
+/* Define to 1 if you have the <dlfcn.h> header file. */
+#undef HAVE_DLFCN_H
+
+/* Define to 1 if you have the `gettimeofday' function. */
+#undef HAVE_GETTIMEOFDAY
+
+/* Define to 1 if you have the <inttypes.h> header file. */
+#undef HAVE_INTTYPES_H
+
+/* Define to 1 in order to Use libProgressBar */
+#undef HAVE_LIBPROGRESSBAR
+
+/* Define to 1 if you have the `pthread' library (-lpthread). */
+#undef HAVE_LIBPTHREAD
+
+/* Define to 1 if you have the `z' library (-lz). */
+#undef HAVE_LIBZ
+
+/* Define to 1 if your system has a GNU libc compatible `malloc' function, and
+ to 0 otherwise. */
+#undef HAVE_MALLOC
+
+/* Define to 1 if you have the <memory.h> header file. */
+#undef HAVE_MEMORY_H
+
+/* Define to 1 if you have the `memset' function. */
+#undef HAVE_MEMSET
+
+/* Define to 1 if your system has a GNU libc compatible `realloc' function,
+ and to 0 otherwise. */
+#undef HAVE_REALLOC
+
+/* Define to 1 if you have the `select' function. */
+#undef HAVE_SELECT
+
+/* Define to 1 if stdbool.h conforms to C99. */
+#undef HAVE_STDBOOL_H
+
+/* Define to 1 if you have the <stdint.h> header file. */
+#undef HAVE_STDINT_H
+
+/* Define to 1 if you have the <stdlib.h> header file. */
+#undef HAVE_STDLIB_H
+
+/* Define to 1 if you have the <strings.h> header file. */
+#undef HAVE_STRINGS_H
+
+/* Define to 1 if you have the <string.h> header file. */
+#undef HAVE_STRING_H
+
+/* Define to 1 if you have the <sys/stat.h> header file. */
+#undef HAVE_SYS_STAT_H
+
+/* Define to 1 if you have the <sys/time.h> header file. */
+#undef HAVE_SYS_TIME_H
+
+/* Define to 1 if you have the <sys/types.h> header file. */
+#undef HAVE_SYS_TYPES_H
+
+/* Define to 1 if you have the <unistd.h> header file. */
+#undef HAVE_UNISTD_H
+
+/* Define to 1 if the system has the type `unsigned long long int'. */
+#undef HAVE_UNSIGNED_LONG_LONG_INT
+
+/* Define to 1 if the system has the type `_Bool'. */
+#undef HAVE__BOOL
+
+/* Define to the sub-directory in which libtool stores uninstalled libraries.
+ */
+#undef LT_OBJDIR
+
+/* Output the factors' number of occurences */
+#undef OUTPUT_NB_OCC_FACTORS
+
+/* Name of package */
+#undef PACKAGE
+
+/* Define to the address where bug reports for this package should be sent. */
+#undef PACKAGE_BUGREPORT
+
+/* Define to the full name of this package. */
+#undef PACKAGE_NAME
+
+/* Define to the full name and version of this package. */
+#undef PACKAGE_STRING
+
+/* Define to the one symbol short name of this package. */
+#undef PACKAGE_TARNAME
+
+/* Define to the home page for this package. */
+#undef PACKAGE_URL
+
+/* Define to the version of this package. */
+#undef PACKAGE_VERSION
+
+/* Define to 1 if you have the ANSI C header files. */
+#undef STDC_HEADERS
+
+/* Version number of package */
+#undef VERSION
+
+/* Define for Solaris 2.5.1 so the uint32_t typedef from <sys/synch.h>,
+ <pthread.h>, or <semaphore.h> is not used. If the typedef were allowed, the
+ #define below would cause a syntax error. */
+#undef _UINT32_T
+
+/* Define for Solaris 2.5.1 so the uint64_t typedef from <sys/synch.h>,
+ <pthread.h>, or <semaphore.h> is not used. If the typedef were allowed, the
+ #define below would cause a syntax error. */
+#undef _UINT64_T
+
+/* Define for Solaris 2.5.1 so the uint8_t typedef from <sys/synch.h>,
+ <pthread.h>, or <semaphore.h> is not used. If the typedef were allowed, the
+ #define below would cause a syntax error. */
+#undef _UINT8_T
+
+/* Define to `__inline__' or `__inline' if that's what the C compiler
+ calls it, or to nothing if 'inline' is not supported under any name. */
+#ifndef __cplusplus
+#undef inline
+#endif
+
+/* Define to rpl_malloc if the replacement function should be used. */
+#undef malloc
+
+/* Define to rpl_realloc if the replacement function should be used. */
+#undef realloc
+
+/* Define to `unsigned int' if <sys/types.h> does not define. */
+#undef size_t
+
+/* Define to the type of an unsigned integer type of width exactly 32 bits if
+ such a type exists and the standard includes do not define it. */
+#undef uint32_t
+
+/* Define to the type of an unsigned integer type of width exactly 64 bits if
+ such a type exists and the standard includes do not define it. */
+#undef uint64_t
+
+/* Define to the type of an unsigned integer type of width exactly 8 bits if
+ such a type exists and the standard includes do not define it. */
+#undef uint8_t
diff --git a/src/libGkArrays/config/config.sub b/src/libGkArrays/config/config.sub
new file mode 100755
index 0000000..c894da4
--- /dev/null
+++ b/src/libGkArrays/config/config.sub
@@ -0,0 +1,1773 @@
+#! /bin/sh
+# Configuration validation subroutine script.
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
+# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,
+# 2011, 2012 Free Software Foundation, Inc.
+
+timestamp='2012-02-10'
+
+# This file is (in principle) common to ALL GNU software.
+# The presence of a machine in this file suggests that SOME GNU software
+# can handle that machine. It does not imply ALL GNU software can.
+#
+# This file is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+
+# Please send patches to <config-patches at gnu.org>. Submit a context
+# diff and a properly formatted GNU ChangeLog entry.
+#
+# Configuration subroutine to validate and canonicalize a configuration type.
+# Supply the specified configuration type as an argument.
+# If it is invalid, we print an error message on stderr and exit with code 1.
+# Otherwise, we print the canonical config type on stdout and succeed.
+
+# You can get the latest version of this script from:
+# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
+
+# This file is supposed to be the same for all GNU packages
+# and recognize all the CPU types, system types and aliases
+# that are meaningful with *any* GNU software.
+# Each package is responsible for reporting which valid configurations
+# it does not support. The user should be able to distinguish
+# a failure to support a valid configuration from a meaningless
+# configuration.
+
+# The goal of this file is to map all the various variations of a given
+# machine specification into a single specification in the form:
+# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM
+# or in some cases, the newer four-part form:
+# CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM
+# It is wrong to echo any other type of specification.
+
+me=`echo "$0" | sed -e 's,.*/,,'`
+
+usage="\
+Usage: $0 [OPTION] CPU-MFR-OPSYS
+ $0 [OPTION] ALIAS
+
+Canonicalize a configuration name.
+
+Operation modes:
+ -h, --help print this help, then exit
+ -t, --time-stamp print date of last modification, then exit
+ -v, --version print version number, then exit
+
+Report bugs and patches to <config-patches at gnu.org>."
+
+version="\
+GNU config.sub ($timestamp)
+
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000,
+2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012
+Free Software Foundation, Inc.
+
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+
+help="
+Try \`$me --help' for more information."
+
+# Parse command line
+while test $# -gt 0 ; do
+ case $1 in
+ --time-stamp | --time* | -t )
+ echo "$timestamp" ; exit ;;
+ --version | -v )
+ echo "$version" ; exit ;;
+ --help | --h* | -h )
+ echo "$usage"; exit ;;
+ -- ) # Stop option processing
+ shift; break ;;
+ - ) # Use stdin as input.
+ break ;;
+ -* )
+ echo "$me: invalid option $1$help"
+ exit 1 ;;
+
+ *local*)
+ # First pass through any local machine types.
+ echo $1
+ exit ;;
+
+ * )
+ break ;;
+ esac
+done
+
+case $# in
+ 0) echo "$me: missing argument$help" >&2
+ exit 1;;
+ 1) ;;
+ *) echo "$me: too many arguments$help" >&2
+ exit 1;;
+esac
+
+# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any).
+# Here we must recognize all the valid KERNEL-OS combinations.
+maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
+case $maybe_os in
+ nto-qnx* | linux-gnu* | linux-android* | linux-dietlibc | linux-newlib* | \
+ linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | \
+ knetbsd*-gnu* | netbsd*-gnu* | \
+ kopensolaris*-gnu* | \
+ storm-chaos* | os2-emx* | rtmk-nova*)
+ os=-$maybe_os
+ basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
+ ;;
+ android-linux)
+ os=-linux-android
+ basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`-unknown
+ ;;
+ *)
+ basic_machine=`echo $1 | sed 's/-[^-]*$//'`
+ if [ $basic_machine != $1 ]
+ then os=`echo $1 | sed 's/.*-/-/'`
+ else os=; fi
+ ;;
+esac
+
+### Let's recognize common machines as not being operating systems so
+### that things like config.sub decstation-3100 work. We also
+### recognize some manufacturers as not being operating systems, so we
+### can provide default operating systems below.
+case $os in
+ -sun*os*)
+ # Prevent following clause from handling this invalid input.
+ ;;
+ -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \
+ -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \
+ -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \
+ -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
+ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
+ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
+ -apple | -axis | -knuth | -cray | -microblaze)
+ os=
+ basic_machine=$1
+ ;;
+ -bluegene*)
+ os=-cnk
+ ;;
+ -sim | -cisco | -oki | -wec | -winbond)
+ os=
+ basic_machine=$1
+ ;;
+ -scout)
+ ;;
+ -wrs)
+ os=-vxworks
+ basic_machine=$1
+ ;;
+ -chorusos*)
+ os=-chorusos
+ basic_machine=$1
+ ;;
+ -chorusrdb)
+ os=-chorusrdb
+ basic_machine=$1
+ ;;
+ -hiux*)
+ os=-hiuxwe2
+ ;;
+ -sco6)
+ os=-sco5v6
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco5)
+ os=-sco3.2v5
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco4)
+ os=-sco3.2v4
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco3.2.[4-9]*)
+ os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco3.2v[4-9]*)
+ # Don't forget version if it is 3.2v4 or newer.
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco5v6*)
+ # Don't forget version if it is 3.2v4 or newer.
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco*)
+ os=-sco3.2v2
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -udk*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -isc)
+ os=-isc2.2
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -clix*)
+ basic_machine=clipper-intergraph
+ ;;
+ -isc*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -lynx*)
+ os=-lynxos
+ ;;
+ -ptx*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'`
+ ;;
+ -windowsnt*)
+ os=`echo $os | sed -e 's/windowsnt/winnt/'`
+ ;;
+ -psos*)
+ os=-psos
+ ;;
+ -mint | -mint[0-9]*)
+ basic_machine=m68k-atari
+ os=-mint
+ ;;
+esac
+
+# Decode aliases for certain CPU-COMPANY combinations.
+case $basic_machine in
+ # Recognize the basic CPU types without company name.
+ # Some are omitted here because they have special meanings below.
+ 1750a | 580 \
+ | a29k \
+ | aarch64 | aarch64_be \
+ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \
+ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \
+ | am33_2.0 \
+ | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \
+ | be32 | be64 \
+ | bfin \
+ | c4x | clipper \
+ | d10v | d30v | dlx | dsp16xx \
+ | epiphany \
+ | fido | fr30 | frv \
+ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
+ | hexagon \
+ | i370 | i860 | i960 | ia64 \
+ | ip2k | iq2000 \
+ | le32 | le64 \
+ | lm32 \
+ | m32c | m32r | m32rle | m68000 | m68k | m88k \
+ | maxq | mb | microblaze | mcore | mep | metag \
+ | mips | mipsbe | mipseb | mipsel | mipsle \
+ | mips16 \
+ | mips64 | mips64el \
+ | mips64octeon | mips64octeonel \
+ | mips64orion | mips64orionel \
+ | mips64r5900 | mips64r5900el \
+ | mips64vr | mips64vrel \
+ | mips64vr4100 | mips64vr4100el \
+ | mips64vr4300 | mips64vr4300el \
+ | mips64vr5000 | mips64vr5000el \
+ | mips64vr5900 | mips64vr5900el \
+ | mipsisa32 | mipsisa32el \
+ | mipsisa32r2 | mipsisa32r2el \
+ | mipsisa64 | mipsisa64el \
+ | mipsisa64r2 | mipsisa64r2el \
+ | mipsisa64sb1 | mipsisa64sb1el \
+ | mipsisa64sr71k | mipsisa64sr71kel \
+ | mipstx39 | mipstx39el \
+ | mn10200 | mn10300 \
+ | moxie \
+ | mt \
+ | msp430 \
+ | nds32 | nds32le | nds32be \
+ | nios | nios2 \
+ | ns16k | ns32k \
+ | open8 \
+ | or32 \
+ | pdp10 | pdp11 | pj | pjl \
+ | powerpc | powerpc64 | powerpc64le | powerpcle \
+ | pyramid \
+ | rl78 | rx \
+ | score \
+ | sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
+ | sh64 | sh64le \
+ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \
+ | sparcv8 | sparcv9 | sparcv9b | sparcv9v \
+ | spu \
+ | tahoe | tic4x | tic54x | tic55x | tic6x | tic80 | tron \
+ | ubicom32 \
+ | v850 | v850e | v850e1 | v850e2 | v850es | v850e2v3 \
+ | we32k \
+ | x86 | xc16x | xstormy16 | xtensa \
+ | z8k | z80)
+ basic_machine=$basic_machine-unknown
+ ;;
+ c54x)
+ basic_machine=tic54x-unknown
+ ;;
+ c55x)
+ basic_machine=tic55x-unknown
+ ;;
+ c6x)
+ basic_machine=tic6x-unknown
+ ;;
+ m6811 | m68hc11 | m6812 | m68hc12 | m68hcs12x | picochip)
+ basic_machine=$basic_machine-unknown
+ os=-none
+ ;;
+ m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k)
+ ;;
+ ms1)
+ basic_machine=mt-unknown
+ ;;
+
+ strongarm | thumb | xscale)
+ basic_machine=arm-unknown
+ ;;
+ xgate)
+ basic_machine=$basic_machine-unknown
+ os=-none
+ ;;
+ xscaleeb)
+ basic_machine=armeb-unknown
+ ;;
+
+ xscaleel)
+ basic_machine=armel-unknown
+ ;;
+
+ # We use `pc' rather than `unknown'
+ # because (1) that's what they normally are, and
+ # (2) the word "unknown" tends to confuse beginning users.
+ i*86 | x86_64)
+ basic_machine=$basic_machine-pc
+ ;;
+ # Object if more than one company name word.
+ *-*-*)
+ echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
+ exit 1
+ ;;
+ # Recognize the basic CPU types with company name.
+ 580-* \
+ | a29k-* \
+ | aarch64-* | aarch64_be-* \
+ | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \
+ | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \
+ | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \
+ | arm-* | armbe-* | armle-* | armeb-* | armv*-* \
+ | avr-* | avr32-* \
+ | be32-* | be64-* \
+ | bfin-* | bs2000-* \
+ | c[123]* | c30-* | [cjt]90-* | c4x-* \
+ | clipper-* | craynv-* | cydra-* \
+ | d10v-* | d30v-* | dlx-* \
+ | elxsi-* \
+ | f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \
+ | h8300-* | h8500-* \
+ | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
+ | hexagon-* \
+ | i*86-* | i860-* | i960-* | ia64-* \
+ | ip2k-* | iq2000-* \
+ | le32-* | le64-* \
+ | lm32-* \
+ | m32c-* | m32r-* | m32rle-* \
+ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
+ | m88110-* | m88k-* | maxq-* | mcore-* | metag-* | microblaze-* \
+ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
+ | mips16-* \
+ | mips64-* | mips64el-* \
+ | mips64octeon-* | mips64octeonel-* \
+ | mips64orion-* | mips64orionel-* \
+ | mips64r5900-* | mips64r5900el-* \
+ | mips64vr-* | mips64vrel-* \
+ | mips64vr4100-* | mips64vr4100el-* \
+ | mips64vr4300-* | mips64vr4300el-* \
+ | mips64vr5000-* | mips64vr5000el-* \
+ | mips64vr5900-* | mips64vr5900el-* \
+ | mipsisa32-* | mipsisa32el-* \
+ | mipsisa32r2-* | mipsisa32r2el-* \
+ | mipsisa64-* | mipsisa64el-* \
+ | mipsisa64r2-* | mipsisa64r2el-* \
+ | mipsisa64sb1-* | mipsisa64sb1el-* \
+ | mipsisa64sr71k-* | mipsisa64sr71kel-* \
+ | mipstx39-* | mipstx39el-* \
+ | mmix-* \
+ | mt-* \
+ | msp430-* \
+ | nds32-* | nds32le-* | nds32be-* \
+ | nios-* | nios2-* \
+ | none-* | np1-* | ns16k-* | ns32k-* \
+ | open8-* \
+ | orion-* \
+ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
+ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* \
+ | pyramid-* \
+ | rl78-* | romp-* | rs6000-* | rx-* \
+ | sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \
+ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \
+ | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \
+ | sparclite-* \
+ | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | sv1-* | sx?-* \
+ | tahoe-* \
+ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
+ | tile*-* \
+ | tron-* \
+ | ubicom32-* \
+ | v850-* | v850e-* | v850e1-* | v850es-* | v850e2-* | v850e2v3-* \
+ | vax-* \
+ | we32k-* \
+ | x86-* | x86_64-* | xc16x-* | xps100-* \
+ | xstormy16-* | xtensa*-* \
+ | ymp-* \
+ | z8k-* | z80-*)
+ ;;
+ # Recognize the basic CPU types without company name, with glob match.
+ xtensa*)
+ basic_machine=$basic_machine-unknown
+ ;;
+ # Recognize the various machine names and aliases which stand
+ # for a CPU type and a company and sometimes even an OS.
+ 386bsd)
+ basic_machine=i386-unknown
+ os=-bsd
+ ;;
+ 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc)
+ basic_machine=m68000-att
+ ;;
+ 3b*)
+ basic_machine=we32k-att
+ ;;
+ a29khif)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ abacus)
+ basic_machine=abacus-unknown
+ ;;
+ adobe68k)
+ basic_machine=m68010-adobe
+ os=-scout
+ ;;
+ alliant | fx80)
+ basic_machine=fx80-alliant
+ ;;
+ altos | altos3068)
+ basic_machine=m68k-altos
+ ;;
+ am29k)
+ basic_machine=a29k-none
+ os=-bsd
+ ;;
+ amd64)
+ basic_machine=x86_64-pc
+ ;;
+ amd64-*)
+ basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ amdahl)
+ basic_machine=580-amdahl
+ os=-sysv
+ ;;
+ amiga | amiga-*)
+ basic_machine=m68k-unknown
+ ;;
+ amigaos | amigados)
+ basic_machine=m68k-unknown
+ os=-amigaos
+ ;;
+ amigaunix | amix)
+ basic_machine=m68k-unknown
+ os=-sysv4
+ ;;
+ apollo68)
+ basic_machine=m68k-apollo
+ os=-sysv
+ ;;
+ apollo68bsd)
+ basic_machine=m68k-apollo
+ os=-bsd
+ ;;
+ aros)
+ basic_machine=i386-pc
+ os=-aros
+ ;;
+ aux)
+ basic_machine=m68k-apple
+ os=-aux
+ ;;
+ balance)
+ basic_machine=ns32k-sequent
+ os=-dynix
+ ;;
+ blackfin)
+ basic_machine=bfin-unknown
+ os=-linux
+ ;;
+ blackfin-*)
+ basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'`
+ os=-linux
+ ;;
+ bluegene*)
+ basic_machine=powerpc-ibm
+ os=-cnk
+ ;;
+ c54x-*)
+ basic_machine=tic54x-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ c55x-*)
+ basic_machine=tic55x-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ c6x-*)
+ basic_machine=tic6x-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ c90)
+ basic_machine=c90-cray
+ os=-unicos
+ ;;
+ cegcc)
+ basic_machine=arm-unknown
+ os=-cegcc
+ ;;
+ convex-c1)
+ basic_machine=c1-convex
+ os=-bsd
+ ;;
+ convex-c2)
+ basic_machine=c2-convex
+ os=-bsd
+ ;;
+ convex-c32)
+ basic_machine=c32-convex
+ os=-bsd
+ ;;
+ convex-c34)
+ basic_machine=c34-convex
+ os=-bsd
+ ;;
+ convex-c38)
+ basic_machine=c38-convex
+ os=-bsd
+ ;;
+ cray | j90)
+ basic_machine=j90-cray
+ os=-unicos
+ ;;
+ craynv)
+ basic_machine=craynv-cray
+ os=-unicosmp
+ ;;
+ cr16 | cr16-*)
+ basic_machine=cr16-unknown
+ os=-elf
+ ;;
+ crds | unos)
+ basic_machine=m68k-crds
+ ;;
+ crisv32 | crisv32-* | etraxfs*)
+ basic_machine=crisv32-axis
+ ;;
+ cris | cris-* | etrax*)
+ basic_machine=cris-axis
+ ;;
+ crx)
+ basic_machine=crx-unknown
+ os=-elf
+ ;;
+ da30 | da30-*)
+ basic_machine=m68k-da30
+ ;;
+ decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn)
+ basic_machine=mips-dec
+ ;;
+ decsystem10* | dec10*)
+ basic_machine=pdp10-dec
+ os=-tops10
+ ;;
+ decsystem20* | dec20*)
+ basic_machine=pdp10-dec
+ os=-tops20
+ ;;
+ delta | 3300 | motorola-3300 | motorola-delta \
+ | 3300-motorola | delta-motorola)
+ basic_machine=m68k-motorola
+ ;;
+ delta88)
+ basic_machine=m88k-motorola
+ os=-sysv3
+ ;;
+ dicos)
+ basic_machine=i686-pc
+ os=-dicos
+ ;;
+ djgpp)
+ basic_machine=i586-pc
+ os=-msdosdjgpp
+ ;;
+ dpx20 | dpx20-*)
+ basic_machine=rs6000-bull
+ os=-bosx
+ ;;
+ dpx2* | dpx2*-bull)
+ basic_machine=m68k-bull
+ os=-sysv3
+ ;;
+ ebmon29k)
+ basic_machine=a29k-amd
+ os=-ebmon
+ ;;
+ elxsi)
+ basic_machine=elxsi-elxsi
+ os=-bsd
+ ;;
+ encore | umax | mmax)
+ basic_machine=ns32k-encore
+ ;;
+ es1800 | OSE68k | ose68k | ose | OSE)
+ basic_machine=m68k-ericsson
+ os=-ose
+ ;;
+ fx2800)
+ basic_machine=i860-alliant
+ ;;
+ genix)
+ basic_machine=ns32k-ns
+ ;;
+ gmicro)
+ basic_machine=tron-gmicro
+ os=-sysv
+ ;;
+ go32)
+ basic_machine=i386-pc
+ os=-go32
+ ;;
+ h3050r* | hiux*)
+ basic_machine=hppa1.1-hitachi
+ os=-hiuxwe2
+ ;;
+ h8300hms)
+ basic_machine=h8300-hitachi
+ os=-hms
+ ;;
+ h8300xray)
+ basic_machine=h8300-hitachi
+ os=-xray
+ ;;
+ h8500hms)
+ basic_machine=h8500-hitachi
+ os=-hms
+ ;;
+ harris)
+ basic_machine=m88k-harris
+ os=-sysv3
+ ;;
+ hp300-*)
+ basic_machine=m68k-hp
+ ;;
+ hp300bsd)
+ basic_machine=m68k-hp
+ os=-bsd
+ ;;
+ hp300hpux)
+ basic_machine=m68k-hp
+ os=-hpux
+ ;;
+ hp3k9[0-9][0-9] | hp9[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hp9k2[0-9][0-9] | hp9k31[0-9])
+ basic_machine=m68000-hp
+ ;;
+ hp9k3[2-9][0-9])
+ basic_machine=m68k-hp
+ ;;
+ hp9k6[0-9][0-9] | hp6[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hp9k7[0-79][0-9] | hp7[0-79][0-9])
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k78[0-9] | hp78[0-9])
+ # FIXME: really hppa2.0-hp
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893)
+ # FIXME: really hppa2.0-hp
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[0-9][13679] | hp8[0-9][13679])
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[0-9][0-9] | hp8[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hppa-next)
+ os=-nextstep3
+ ;;
+ hppaosf)
+ basic_machine=hppa1.1-hp
+ os=-osf
+ ;;
+ hppro)
+ basic_machine=hppa1.1-hp
+ os=-proelf
+ ;;
+ i370-ibm* | ibm*)
+ basic_machine=i370-ibm
+ ;;
+ i*86v32)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv32
+ ;;
+ i*86v4*)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv4
+ ;;
+ i*86v)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv
+ ;;
+ i*86sol2)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-solaris2
+ ;;
+ i386mach)
+ basic_machine=i386-mach
+ os=-mach
+ ;;
+ i386-vsta | vsta)
+ basic_machine=i386-unknown
+ os=-vsta
+ ;;
+ iris | iris4d)
+ basic_machine=mips-sgi
+ case $os in
+ -irix*)
+ ;;
+ *)
+ os=-irix4
+ ;;
+ esac
+ ;;
+ isi68 | isi)
+ basic_machine=m68k-isi
+ os=-sysv
+ ;;
+ m68knommu)
+ basic_machine=m68k-unknown
+ os=-linux
+ ;;
+ m68knommu-*)
+ basic_machine=m68k-`echo $basic_machine | sed 's/^[^-]*-//'`
+ os=-linux
+ ;;
+ m88k-omron*)
+ basic_machine=m88k-omron
+ ;;
+ magnum | m3230)
+ basic_machine=mips-mips
+ os=-sysv
+ ;;
+ merlin)
+ basic_machine=ns32k-utek
+ os=-sysv
+ ;;
+ microblaze)
+ basic_machine=microblaze-xilinx
+ ;;
+ mingw32)
+ basic_machine=i386-pc
+ os=-mingw32
+ ;;
+ mingw32ce)
+ basic_machine=arm-unknown
+ os=-mingw32ce
+ ;;
+ miniframe)
+ basic_machine=m68000-convergent
+ ;;
+ *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*)
+ basic_machine=m68k-atari
+ os=-mint
+ ;;
+ mips3*-*)
+ basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`
+ ;;
+ mips3*)
+ basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown
+ ;;
+ monitor)
+ basic_machine=m68k-rom68k
+ os=-coff
+ ;;
+ morphos)
+ basic_machine=powerpc-unknown
+ os=-morphos
+ ;;
+ msdos)
+ basic_machine=i386-pc
+ os=-msdos
+ ;;
+ ms1-*)
+ basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'`
+ ;;
+ msys)
+ basic_machine=i386-pc
+ os=-msys
+ ;;
+ mvs)
+ basic_machine=i370-ibm
+ os=-mvs
+ ;;
+ nacl)
+ basic_machine=le32-unknown
+ os=-nacl
+ ;;
+ ncr3000)
+ basic_machine=i486-ncr
+ os=-sysv4
+ ;;
+ netbsd386)
+ basic_machine=i386-unknown
+ os=-netbsd
+ ;;
+ netwinder)
+ basic_machine=armv4l-rebel
+ os=-linux
+ ;;
+ news | news700 | news800 | news900)
+ basic_machine=m68k-sony
+ os=-newsos
+ ;;
+ news1000)
+ basic_machine=m68030-sony
+ os=-newsos
+ ;;
+ news-3600 | risc-news)
+ basic_machine=mips-sony
+ os=-newsos
+ ;;
+ necv70)
+ basic_machine=v70-nec
+ os=-sysv
+ ;;
+ next | m*-next )
+ basic_machine=m68k-next
+ case $os in
+ -nextstep* )
+ ;;
+ -ns2*)
+ os=-nextstep2
+ ;;
+ *)
+ os=-nextstep3
+ ;;
+ esac
+ ;;
+ nh3000)
+ basic_machine=m68k-harris
+ os=-cxux
+ ;;
+ nh[45]000)
+ basic_machine=m88k-harris
+ os=-cxux
+ ;;
+ nindy960)
+ basic_machine=i960-intel
+ os=-nindy
+ ;;
+ mon960)
+ basic_machine=i960-intel
+ os=-mon960
+ ;;
+ nonstopux)
+ basic_machine=mips-compaq
+ os=-nonstopux
+ ;;
+ np1)
+ basic_machine=np1-gould
+ ;;
+ neo-tandem)
+ basic_machine=neo-tandem
+ ;;
+ nse-tandem)
+ basic_machine=nse-tandem
+ ;;
+ nsr-tandem)
+ basic_machine=nsr-tandem
+ ;;
+ op50n-* | op60c-*)
+ basic_machine=hppa1.1-oki
+ os=-proelf
+ ;;
+ openrisc | openrisc-*)
+ basic_machine=or32-unknown
+ ;;
+ os400)
+ basic_machine=powerpc-ibm
+ os=-os400
+ ;;
+ OSE68000 | ose68000)
+ basic_machine=m68000-ericsson
+ os=-ose
+ ;;
+ os68k)
+ basic_machine=m68k-none
+ os=-os68k
+ ;;
+ pa-hitachi)
+ basic_machine=hppa1.1-hitachi
+ os=-hiuxwe2
+ ;;
+ paragon)
+ basic_machine=i860-intel
+ os=-osf
+ ;;
+ parisc)
+ basic_machine=hppa-unknown
+ os=-linux
+ ;;
+ parisc-*)
+ basic_machine=hppa-`echo $basic_machine | sed 's/^[^-]*-//'`
+ os=-linux
+ ;;
+ pbd)
+ basic_machine=sparc-tti
+ ;;
+ pbb)
+ basic_machine=m68k-tti
+ ;;
+ pc532 | pc532-*)
+ basic_machine=ns32k-pc532
+ ;;
+ pc98)
+ basic_machine=i386-pc
+ ;;
+ pc98-*)
+ basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentium | p5 | k5 | k6 | nexgen | viac3)
+ basic_machine=i586-pc
+ ;;
+ pentiumpro | p6 | 6x86 | athlon | athlon_*)
+ basic_machine=i686-pc
+ ;;
+ pentiumii | pentium2 | pentiumiii | pentium3)
+ basic_machine=i686-pc
+ ;;
+ pentium4)
+ basic_machine=i786-pc
+ ;;
+ pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
+ basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentiumpro-* | p6-* | 6x86-* | athlon-*)
+ basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
+ basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentium4-*)
+ basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pn)
+ basic_machine=pn-gould
+ ;;
+ power) basic_machine=power-ibm
+ ;;
+ ppc | ppcbe) basic_machine=powerpc-unknown
+ ;;
+ ppc-* | ppcbe-*)
+ basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppcle | powerpclittle | ppc-le | powerpc-little)
+ basic_machine=powerpcle-unknown
+ ;;
+ ppcle-* | powerpclittle-*)
+ basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppc64) basic_machine=powerpc64-unknown
+ ;;
+ ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppc64le | powerpc64little | ppc64-le | powerpc64-little)
+ basic_machine=powerpc64le-unknown
+ ;;
+ ppc64le-* | powerpc64little-*)
+ basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ps2)
+ basic_machine=i386-ibm
+ ;;
+ pw32)
+ basic_machine=i586-unknown
+ os=-pw32
+ ;;
+ rdos)
+ basic_machine=i386-pc
+ os=-rdos
+ ;;
+ rom68k)
+ basic_machine=m68k-rom68k
+ os=-coff
+ ;;
+ rm[46]00)
+ basic_machine=mips-siemens
+ ;;
+ rtpc | rtpc-*)
+ basic_machine=romp-ibm
+ ;;
+ s390 | s390-*)
+ basic_machine=s390-ibm
+ ;;
+ s390x | s390x-*)
+ basic_machine=s390x-ibm
+ ;;
+ sa29200)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ sb1)
+ basic_machine=mipsisa64sb1-unknown
+ ;;
+ sb1el)
+ basic_machine=mipsisa64sb1el-unknown
+ ;;
+ sde)
+ basic_machine=mipsisa32-sde
+ os=-elf
+ ;;
+ sei)
+ basic_machine=mips-sei
+ os=-seiux
+ ;;
+ sequent)
+ basic_machine=i386-sequent
+ ;;
+ sh)
+ basic_machine=sh-hitachi
+ os=-hms
+ ;;
+ sh5el)
+ basic_machine=sh5le-unknown
+ ;;
+ sh64)
+ basic_machine=sh64-unknown
+ ;;
+ sparclite-wrs | simso-wrs)
+ basic_machine=sparclite-wrs
+ os=-vxworks
+ ;;
+ sps7)
+ basic_machine=m68k-bull
+ os=-sysv2
+ ;;
+ spur)
+ basic_machine=spur-unknown
+ ;;
+ st2000)
+ basic_machine=m68k-tandem
+ ;;
+ stratus)
+ basic_machine=i860-stratus
+ os=-sysv4
+ ;;
+ strongarm-* | thumb-*)
+ basic_machine=arm-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ sun2)
+ basic_machine=m68000-sun
+ ;;
+ sun2os3)
+ basic_machine=m68000-sun
+ os=-sunos3
+ ;;
+ sun2os4)
+ basic_machine=m68000-sun
+ os=-sunos4
+ ;;
+ sun3os3)
+ basic_machine=m68k-sun
+ os=-sunos3
+ ;;
+ sun3os4)
+ basic_machine=m68k-sun
+ os=-sunos4
+ ;;
+ sun4os3)
+ basic_machine=sparc-sun
+ os=-sunos3
+ ;;
+ sun4os4)
+ basic_machine=sparc-sun
+ os=-sunos4
+ ;;
+ sun4sol2)
+ basic_machine=sparc-sun
+ os=-solaris2
+ ;;
+ sun3 | sun3-*)
+ basic_machine=m68k-sun
+ ;;
+ sun4)
+ basic_machine=sparc-sun
+ ;;
+ sun386 | sun386i | roadrunner)
+ basic_machine=i386-sun
+ ;;
+ sv1)
+ basic_machine=sv1-cray
+ os=-unicos
+ ;;
+ symmetry)
+ basic_machine=i386-sequent
+ os=-dynix
+ ;;
+ t3e)
+ basic_machine=alphaev5-cray
+ os=-unicos
+ ;;
+ t90)
+ basic_machine=t90-cray
+ os=-unicos
+ ;;
+ tile*)
+ basic_machine=$basic_machine-unknown
+ os=-linux-gnu
+ ;;
+ tx39)
+ basic_machine=mipstx39-unknown
+ ;;
+ tx39el)
+ basic_machine=mipstx39el-unknown
+ ;;
+ toad1)
+ basic_machine=pdp10-xkl
+ os=-tops20
+ ;;
+ tower | tower-32)
+ basic_machine=m68k-ncr
+ ;;
+ tpf)
+ basic_machine=s390x-ibm
+ os=-tpf
+ ;;
+ udi29k)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ ultra3)
+ basic_machine=a29k-nyu
+ os=-sym1
+ ;;
+ v810 | necv810)
+ basic_machine=v810-nec
+ os=-none
+ ;;
+ vaxv)
+ basic_machine=vax-dec
+ os=-sysv
+ ;;
+ vms)
+ basic_machine=vax-dec
+ os=-vms
+ ;;
+ vpp*|vx|vx-*)
+ basic_machine=f301-fujitsu
+ ;;
+ vxworks960)
+ basic_machine=i960-wrs
+ os=-vxworks
+ ;;
+ vxworks68)
+ basic_machine=m68k-wrs
+ os=-vxworks
+ ;;
+ vxworks29k)
+ basic_machine=a29k-wrs
+ os=-vxworks
+ ;;
+ w65*)
+ basic_machine=w65-wdc
+ os=-none
+ ;;
+ w89k-*)
+ basic_machine=hppa1.1-winbond
+ os=-proelf
+ ;;
+ xbox)
+ basic_machine=i686-pc
+ os=-mingw32
+ ;;
+ xps | xps100)
+ basic_machine=xps100-honeywell
+ ;;
+ xscale-* | xscalee[bl]-*)
+ basic_machine=`echo $basic_machine | sed 's/^xscale/arm/'`
+ ;;
+ ymp)
+ basic_machine=ymp-cray
+ os=-unicos
+ ;;
+ z8k-*-coff)
+ basic_machine=z8k-unknown
+ os=-sim
+ ;;
+ z80-*-coff)
+ basic_machine=z80-unknown
+ os=-sim
+ ;;
+ none)
+ basic_machine=none-none
+ os=-none
+ ;;
+
+# Here we handle the default manufacturer of certain CPU types. It is in
+# some cases the only manufacturer, in others, it is the most popular.
+ w89k)
+ basic_machine=hppa1.1-winbond
+ ;;
+ op50n)
+ basic_machine=hppa1.1-oki
+ ;;
+ op60c)
+ basic_machine=hppa1.1-oki
+ ;;
+ romp)
+ basic_machine=romp-ibm
+ ;;
+ mmix)
+ basic_machine=mmix-knuth
+ ;;
+ rs6000)
+ basic_machine=rs6000-ibm
+ ;;
+ vax)
+ basic_machine=vax-dec
+ ;;
+ pdp10)
+ # there are many clones, so DEC is not a safe bet
+ basic_machine=pdp10-unknown
+ ;;
+ pdp11)
+ basic_machine=pdp11-dec
+ ;;
+ we32k)
+ basic_machine=we32k-att
+ ;;
+ sh[1234] | sh[24]a | sh[24]aeb | sh[34]eb | sh[1234]le | sh[23]ele)
+ basic_machine=sh-unknown
+ ;;
+ sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v)
+ basic_machine=sparc-sun
+ ;;
+ cydra)
+ basic_machine=cydra-cydrome
+ ;;
+ orion)
+ basic_machine=orion-highlevel
+ ;;
+ orion105)
+ basic_machine=clipper-highlevel
+ ;;
+ mac | mpw | mac-mpw)
+ basic_machine=m68k-apple
+ ;;
+ pmac | pmac-mpw)
+ basic_machine=powerpc-apple
+ ;;
+ *-unknown)
+ # Make sure to match an already-canonicalized machine name.
+ ;;
+ *)
+ echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
+ exit 1
+ ;;
+esac
+
+# Here we canonicalize certain aliases for manufacturers.
+case $basic_machine in
+ *-digital*)
+ basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'`
+ ;;
+ *-commodore*)
+ basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'`
+ ;;
+ *)
+ ;;
+esac
+
+# Decode manufacturer-specific aliases for certain operating systems.
+
+if [ x"$os" != x"" ]
+then
+case $os in
+ # First match some system type aliases
+ # that might get confused with valid system types.
+ # -solaris* is a basic system type, with this one exception.
+ -auroraux)
+ os=-auroraux
+ ;;
+ -solaris1 | -solaris1.*)
+ os=`echo $os | sed -e 's|solaris1|sunos4|'`
+ ;;
+ -solaris)
+ os=-solaris2
+ ;;
+ -svr4*)
+ os=-sysv4
+ ;;
+ -unixware*)
+ os=-sysv4.2uw
+ ;;
+ -gnu/linux*)
+ os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
+ ;;
+ # First accept the basic system types.
+ # The portable systems comes first.
+ # Each alternative MUST END IN A *, to match a version number.
+ # -sysv* is not here because it comes later, after sysvr4.
+ -gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
+ | -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\
+ | -hpux* | -unos* | -osf* | -luna* | -dgux* | -auroraux* | -solaris* \
+ | -sym* | -kopensolaris* \
+ | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
+ | -aos* | -aros* \
+ | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
+ | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
+ | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \
+ | -openbsd* | -solidbsd* \
+ | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \
+ | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
+ | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
+ | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
+ | -chorusos* | -chorusrdb* | -cegcc* \
+ | -cygwin* | -msys* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
+ | -mingw32* | -linux-gnu* | -linux-android* \
+ | -linux-newlib* | -linux-uclibc* \
+ | -uxpv* | -beos* | -mpeix* | -udk* \
+ | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \
+ | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \
+ | -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \
+ | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
+ | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
+ | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
+ | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es*)
+ # Remember, each alternative MUST END IN *, to match a version number.
+ ;;
+ -qnx*)
+ case $basic_machine in
+ x86-* | i*86-*)
+ ;;
+ *)
+ os=-nto$os
+ ;;
+ esac
+ ;;
+ -nto-qnx*)
+ ;;
+ -nto*)
+ os=`echo $os | sed -e 's|nto|nto-qnx|'`
+ ;;
+ -sim | -es1800* | -hms* | -xray | -os68k* | -none* | -v88r* \
+ | -windows* | -osx | -abug | -netware* | -os9* | -beos* | -haiku* \
+ | -macos* | -mpw* | -magic* | -mmixware* | -mon960* | -lnews*)
+ ;;
+ -mac*)
+ os=`echo $os | sed -e 's|mac|macos|'`
+ ;;
+ -linux-dietlibc)
+ os=-linux-dietlibc
+ ;;
+ -linux*)
+ os=`echo $os | sed -e 's|linux|linux-gnu|'`
+ ;;
+ -sunos5*)
+ os=`echo $os | sed -e 's|sunos5|solaris2|'`
+ ;;
+ -sunos6*)
+ os=`echo $os | sed -e 's|sunos6|solaris3|'`
+ ;;
+ -opened*)
+ os=-openedition
+ ;;
+ -os400*)
+ os=-os400
+ ;;
+ -wince*)
+ os=-wince
+ ;;
+ -osfrose*)
+ os=-osfrose
+ ;;
+ -osf*)
+ os=-osf
+ ;;
+ -utek*)
+ os=-bsd
+ ;;
+ -dynix*)
+ os=-bsd
+ ;;
+ -acis*)
+ os=-aos
+ ;;
+ -atheos*)
+ os=-atheos
+ ;;
+ -syllable*)
+ os=-syllable
+ ;;
+ -386bsd)
+ os=-bsd
+ ;;
+ -ctix* | -uts*)
+ os=-sysv
+ ;;
+ -nova*)
+ os=-rtmk-nova
+ ;;
+ -ns2 )
+ os=-nextstep2
+ ;;
+ -nsk*)
+ os=-nsk
+ ;;
+ # Preserve the version number of sinix5.
+ -sinix5.*)
+ os=`echo $os | sed -e 's|sinix|sysv|'`
+ ;;
+ -sinix*)
+ os=-sysv4
+ ;;
+ -tpf*)
+ os=-tpf
+ ;;
+ -triton*)
+ os=-sysv3
+ ;;
+ -oss*)
+ os=-sysv3
+ ;;
+ -svr4)
+ os=-sysv4
+ ;;
+ -svr3)
+ os=-sysv3
+ ;;
+ -sysvr4)
+ os=-sysv4
+ ;;
+ # This must come after -sysvr4.
+ -sysv*)
+ ;;
+ -ose*)
+ os=-ose
+ ;;
+ -es1800*)
+ os=-ose
+ ;;
+ -xenix)
+ os=-xenix
+ ;;
+ -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
+ os=-mint
+ ;;
+ -aros*)
+ os=-aros
+ ;;
+ -kaos*)
+ os=-kaos
+ ;;
+ -zvmoe)
+ os=-zvmoe
+ ;;
+ -dicos*)
+ os=-dicos
+ ;;
+ -nacl*)
+ ;;
+ -none)
+ ;;
+ *)
+ # Get rid of the `-' at the beginning of $os.
+ os=`echo $os | sed 's/[^-]*-//'`
+ echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2
+ exit 1
+ ;;
+esac
+else
+
+# Here we handle the default operating systems that come with various machines.
+# The value should be what the vendor currently ships out the door with their
+# machine or put another way, the most popular os provided with the machine.
+
+# Note that if you're going to try to match "-MANUFACTURER" here (say,
+# "-sun"), then you have to tell the case statement up towards the top
+# that MANUFACTURER isn't an operating system. Otherwise, code above
+# will signal an error saying that MANUFACTURER isn't an operating
+# system, and we'll never get to this point.
+
+case $basic_machine in
+ score-*)
+ os=-elf
+ ;;
+ spu-*)
+ os=-elf
+ ;;
+ *-acorn)
+ os=-riscix1.2
+ ;;
+ arm*-rebel)
+ os=-linux
+ ;;
+ arm*-semi)
+ os=-aout
+ ;;
+ c4x-* | tic4x-*)
+ os=-coff
+ ;;
+ tic54x-*)
+ os=-coff
+ ;;
+ tic55x-*)
+ os=-coff
+ ;;
+ tic6x-*)
+ os=-coff
+ ;;
+ # This must come before the *-dec entry.
+ pdp10-*)
+ os=-tops20
+ ;;
+ pdp11-*)
+ os=-none
+ ;;
+ *-dec | vax-*)
+ os=-ultrix4.2
+ ;;
+ m68*-apollo)
+ os=-domain
+ ;;
+ i386-sun)
+ os=-sunos4.0.2
+ ;;
+ m68000-sun)
+ os=-sunos3
+ ;;
+ m68*-cisco)
+ os=-aout
+ ;;
+ mep-*)
+ os=-elf
+ ;;
+ mips*-cisco)
+ os=-elf
+ ;;
+ mips*-*)
+ os=-elf
+ ;;
+ or32-*)
+ os=-coff
+ ;;
+ *-tti) # must be before sparc entry or we get the wrong os.
+ os=-sysv3
+ ;;
+ sparc-* | *-sun)
+ os=-sunos4.1.1
+ ;;
+ *-be)
+ os=-beos
+ ;;
+ *-haiku)
+ os=-haiku
+ ;;
+ *-ibm)
+ os=-aix
+ ;;
+ *-knuth)
+ os=-mmixware
+ ;;
+ *-wec)
+ os=-proelf
+ ;;
+ *-winbond)
+ os=-proelf
+ ;;
+ *-oki)
+ os=-proelf
+ ;;
+ *-hp)
+ os=-hpux
+ ;;
+ *-hitachi)
+ os=-hiux
+ ;;
+ i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent)
+ os=-sysv
+ ;;
+ *-cbm)
+ os=-amigaos
+ ;;
+ *-dg)
+ os=-dgux
+ ;;
+ *-dolphin)
+ os=-sysv3
+ ;;
+ m68k-ccur)
+ os=-rtu
+ ;;
+ m88k-omron*)
+ os=-luna
+ ;;
+ *-next )
+ os=-nextstep
+ ;;
+ *-sequent)
+ os=-ptx
+ ;;
+ *-crds)
+ os=-unos
+ ;;
+ *-ns)
+ os=-genix
+ ;;
+ i370-*)
+ os=-mvs
+ ;;
+ *-next)
+ os=-nextstep3
+ ;;
+ *-gould)
+ os=-sysv
+ ;;
+ *-highlevel)
+ os=-bsd
+ ;;
+ *-encore)
+ os=-bsd
+ ;;
+ *-sgi)
+ os=-irix
+ ;;
+ *-siemens)
+ os=-sysv4
+ ;;
+ *-masscomp)
+ os=-rtu
+ ;;
+ f30[01]-fujitsu | f700-fujitsu)
+ os=-uxpv
+ ;;
+ *-rom68k)
+ os=-coff
+ ;;
+ *-*bug)
+ os=-coff
+ ;;
+ *-apple)
+ os=-macos
+ ;;
+ *-atari*)
+ os=-mint
+ ;;
+ *)
+ os=-none
+ ;;
+esac
+fi
+
+# Here we handle the case where we know the os, and the CPU type, but not the
+# manufacturer. We pick the logical manufacturer.
+vendor=unknown
+case $basic_machine in
+ *-unknown)
+ case $os in
+ -riscix*)
+ vendor=acorn
+ ;;
+ -sunos*)
+ vendor=sun
+ ;;
+ -cnk*|-aix*)
+ vendor=ibm
+ ;;
+ -beos*)
+ vendor=be
+ ;;
+ -hpux*)
+ vendor=hp
+ ;;
+ -mpeix*)
+ vendor=hp
+ ;;
+ -hiux*)
+ vendor=hitachi
+ ;;
+ -unos*)
+ vendor=crds
+ ;;
+ -dgux*)
+ vendor=dg
+ ;;
+ -luna*)
+ vendor=omron
+ ;;
+ -genix*)
+ vendor=ns
+ ;;
+ -mvs* | -opened*)
+ vendor=ibm
+ ;;
+ -os400*)
+ vendor=ibm
+ ;;
+ -ptx*)
+ vendor=sequent
+ ;;
+ -tpf*)
+ vendor=ibm
+ ;;
+ -vxsim* | -vxworks* | -windiss*)
+ vendor=wrs
+ ;;
+ -aux*)
+ vendor=apple
+ ;;
+ -hms*)
+ vendor=hitachi
+ ;;
+ -mpw* | -macos*)
+ vendor=apple
+ ;;
+ -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
+ vendor=atari
+ ;;
+ -vos*)
+ vendor=stratus
+ ;;
+ esac
+ basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"`
+ ;;
+esac
+
+echo $basic_machine$os
+exit
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "timestamp='"
+# time-stamp-format: "%:y-%02m-%02d"
+# time-stamp-end: "'"
+# End:
diff --git a/src/libGkArrays/config/depcomp b/src/libGkArrays/config/depcomp
new file mode 100755
index 0000000..df8eea7
--- /dev/null
+++ b/src/libGkArrays/config/depcomp
@@ -0,0 +1,630 @@
+#! /bin/sh
+# depcomp - compile a program generating dependencies as side-effects
+
+scriptversion=2009-04-28.21; # UTC
+
+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free
+# Software Foundation, Inc.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# Originally written by Alexandre Oliva <oliva at dcc.unicamp.br>.
+
+case $1 in
+ '')
+ echo "$0: No command. Try \`$0 --help' for more information." 1>&2
+ exit 1;
+ ;;
+ -h | --h*)
+ cat <<\EOF
+Usage: depcomp [--help] [--version] PROGRAM [ARGS]
+
+Run PROGRAMS ARGS to compile a file, generating dependencies
+as side-effects.
+
+Environment variables:
+ depmode Dependency tracking mode.
+ source Source file read by `PROGRAMS ARGS'.
+ object Object file output by `PROGRAMS ARGS'.
+ DEPDIR directory where to store dependencies.
+ depfile Dependency file to output.
+ tmpdepfile Temporary file to use when outputing dependencies.
+ libtool Whether libtool is used (yes/no).
+
+Report bugs to <bug-automake at gnu.org>.
+EOF
+ exit $?
+ ;;
+ -v | --v*)
+ echo "depcomp $scriptversion"
+ exit $?
+ ;;
+esac
+
+if test -z "$depmode" || test -z "$source" || test -z "$object"; then
+ echo "depcomp: Variables source, object and depmode must be set" 1>&2
+ exit 1
+fi
+
+# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
+depfile=${depfile-`echo "$object" |
+ sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
+tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
+
+rm -f "$tmpdepfile"
+
+# Some modes work just like other modes, but use different flags. We
+# parameterize here, but still list the modes in the big case below,
+# to make depend.m4 easier to write. Note that we *cannot* use a case
+# here, because this file can only contain one case statement.
+if test "$depmode" = hp; then
+ # HP compiler uses -M and no extra arg.
+ gccflag=-M
+ depmode=gcc
+fi
+
+if test "$depmode" = dashXmstdout; then
+ # This is just like dashmstdout with a different argument.
+ dashmflag=-xM
+ depmode=dashmstdout
+fi
+
+cygpath_u="cygpath -u -f -"
+if test "$depmode" = msvcmsys; then
+ # This is just like msvisualcpp but w/o cygpath translation.
+ # Just convert the backslash-escaped backslashes to single forward
+ # slashes to satisfy depend.m4
+ cygpath_u="sed s,\\\\\\\\,/,g"
+ depmode=msvisualcpp
+fi
+
+case "$depmode" in
+gcc3)
+## gcc 3 implements dependency tracking that does exactly what
+## we want. Yay! Note: for some reason libtool 1.4 doesn't like
+## it if -MD -MP comes after the -MF stuff. Hmm.
+## Unfortunately, FreeBSD c89 acceptance of flags depends upon
+## the command line argument order; so add the flags where they
+## appear in depend2.am. Note that the slowdown incurred here
+## affects only configure: in makefiles, %FASTDEP% shortcuts this.
+ for arg
+ do
+ case $arg in
+ -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;;
+ *) set fnord "$@" "$arg" ;;
+ esac
+ shift # fnord
+ shift # $arg
+ done
+ "$@"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ mv "$tmpdepfile" "$depfile"
+ ;;
+
+gcc)
+## There are various ways to get dependency output from gcc. Here's
+## why we pick this rather obscure method:
+## - Don't want to use -MD because we'd like the dependencies to end
+## up in a subdir. Having to rename by hand is ugly.
+## (We might end up doing this anyway to support other compilers.)
+## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
+## -MM, not -M (despite what the docs say).
+## - Using -M directly means running the compiler twice (even worse
+## than renaming).
+ if test -z "$gccflag"; then
+ gccflag=-MD,
+ fi
+ "$@" -Wp,"$gccflag$tmpdepfile"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
+## The second -e expression handles DOS-style file names with drive letters.
+ sed -e 's/^[^:]*: / /' \
+ -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
+## This next piece of magic avoids the `deleted header file' problem.
+## The problem is that when a header file which appears in a .P file
+## is deleted, the dependency causes make to die (because there is
+## typically no way to rebuild the header). We avoid this by adding
+## dummy dependencies for each header file. Too bad gcc doesn't do
+## this for us directly.
+ tr ' ' '
+' < "$tmpdepfile" |
+## Some versions of gcc put a space before the `:'. On the theory
+## that the space means something, we add a space to the output as
+## well.
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+hp)
+ # This case exists only to let depend.m4 do its work. It works by
+ # looking at the text of this script. This case will never be run,
+ # since it is checked for above.
+ exit 1
+ ;;
+
+sgi)
+ if test "$libtool" = yes; then
+ "$@" "-Wp,-MDupdate,$tmpdepfile"
+ else
+ "$@" -MDupdate "$tmpdepfile"
+ fi
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+
+ if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
+ echo "$object : \\" > "$depfile"
+
+ # Clip off the initial element (the dependent). Don't try to be
+ # clever and replace this with sed code, as IRIX sed won't handle
+ # lines with more than a fixed number of characters (4096 in
+ # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
+ # the IRIX cc adds comments like `#:fec' to the end of the
+ # dependency line.
+ tr ' ' '
+' < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
+ tr '
+' ' ' >> "$depfile"
+ echo >> "$depfile"
+
+ # The second pass generates a dummy entry for each header file.
+ tr ' ' '
+' < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
+ >> "$depfile"
+ else
+ # The sourcefile does not contain any dependencies, so just
+ # store a dummy comment line, to avoid errors with the Makefile
+ # "include basename.Plo" scheme.
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+aix)
+ # The C for AIX Compiler uses -M and outputs the dependencies
+ # in a .u file. In older versions, this file always lives in the
+ # current directory. Also, the AIX compiler puts `$object:' at the
+ # start of each line; $object doesn't have directory information.
+ # Version 6 uses the directory in both cases.
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+ if test "$libtool" = yes; then
+ tmpdepfile1=$dir$base.u
+ tmpdepfile2=$base.u
+ tmpdepfile3=$dir.libs/$base.u
+ "$@" -Wc,-M
+ else
+ tmpdepfile1=$dir$base.u
+ tmpdepfile2=$dir$base.u
+ tmpdepfile3=$dir$base.u
+ "$@" -M
+ fi
+ stat=$?
+
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ if test -f "$tmpdepfile"; then
+ # Each line is of the form `foo.o: dependent.h'.
+ # Do two passes, one to just change these to
+ # `$object: dependent.h' and one to simply `dependent.h:'.
+ sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+ # That's a tab and a space in the [].
+ sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
+ else
+ # The sourcefile does not contain any dependencies, so just
+ # store a dummy comment line, to avoid errors with the Makefile
+ # "include basename.Plo" scheme.
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+icc)
+ # Intel's C compiler understands `-MD -MF file'. However on
+ # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
+ # ICC 7.0 will fill foo.d with something like
+ # foo.o: sub/foo.c
+ # foo.o: sub/foo.h
+ # which is wrong. We want:
+ # sub/foo.o: sub/foo.c
+ # sub/foo.o: sub/foo.h
+ # sub/foo.c:
+ # sub/foo.h:
+ # ICC 7.1 will output
+ # foo.o: sub/foo.c sub/foo.h
+ # and will wrap long lines using \ :
+ # foo.o: sub/foo.c ... \
+ # sub/foo.h ... \
+ # ...
+
+ "$@" -MD -MF "$tmpdepfile"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+ # Each line is of the form `foo.o: dependent.h',
+ # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
+ # Do two passes, one to just change these to
+ # `$object: dependent.h' and one to simply `dependent.h:'.
+ sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
+ # Some versions of the HPUX 10.20 sed can't process this invocation
+ # correctly. Breaking it into two sed invocations is a workaround.
+ sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
+ sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+hp2)
+ # The "hp" stanza above does not work with aCC (C++) and HP's ia64
+ # compilers, which have integrated preprocessors. The correct option
+ # to use with these is +Maked; it writes dependencies to a file named
+ # 'foo.d', which lands next to the object file, wherever that
+ # happens to be.
+ # Much of this is similar to the tru64 case; see comments there.
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+ if test "$libtool" = yes; then
+ tmpdepfile1=$dir$base.d
+ tmpdepfile2=$dir.libs/$base.d
+ "$@" -Wc,+Maked
+ else
+ tmpdepfile1=$dir$base.d
+ tmpdepfile2=$dir$base.d
+ "$@" +Maked
+ fi
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ if test -f "$tmpdepfile"; then
+ sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
+ # Add `dependent.h:' lines.
+ sed -ne '2,${
+ s/^ *//
+ s/ \\*$//
+ s/$/:/
+ p
+ }' "$tmpdepfile" >> "$depfile"
+ else
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile" "$tmpdepfile2"
+ ;;
+
+tru64)
+ # The Tru64 compiler uses -MD to generate dependencies as a side
+ # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
+ # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
+ # dependencies in `foo.d' instead, so we check for that too.
+ # Subdirectories are respected.
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+
+ if test "$libtool" = yes; then
+ # With Tru64 cc, shared objects can also be used to make a
+ # static library. This mechanism is used in libtool 1.4 series to
+ # handle both shared and static libraries in a single compilation.
+ # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
+ #
+ # With libtool 1.5 this exception was removed, and libtool now
+ # generates 2 separate objects for the 2 libraries. These two
+ # compilations output dependencies in $dir.libs/$base.o.d and
+ # in $dir$base.o.d. We have to check for both files, because
+ # one of the two compilations can be disabled. We should prefer
+ # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
+ # automatically cleaned when .libs/ is deleted, while ignoring
+ # the former would cause a distcleancheck panic.
+ tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
+ tmpdepfile2=$dir$base.o.d # libtool 1.5
+ tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
+ tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
+ "$@" -Wc,-MD
+ else
+ tmpdepfile1=$dir$base.o.d
+ tmpdepfile2=$dir$base.d
+ tmpdepfile3=$dir$base.d
+ tmpdepfile4=$dir$base.d
+ "$@" -MD
+ fi
+
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ if test -f "$tmpdepfile"; then
+ sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+ # That's a tab and a space in the [].
+ sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
+ else
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+#nosideeffect)
+ # This comment above is used by automake to tell side-effect
+ # dependency tracking mechanisms from slower ones.
+
+dashmstdout)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout, regardless of -o.
+ "$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
+ # Remove `-o $object'.
+ IFS=" "
+ for arg
+ do
+ case $arg in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift # fnord
+ shift # $arg
+ ;;
+ esac
+ done
+
+ test -z "$dashmflag" && dashmflag=-M
+ # Require at least two characters before searching for `:'
+ # in the target name. This is to cope with DOS-style filenames:
+ # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
+ "$@" $dashmflag |
+ sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
+ rm -f "$depfile"
+ cat < "$tmpdepfile" > "$depfile"
+ tr ' ' '
+' < "$tmpdepfile" | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+dashXmstdout)
+ # This case only exists to satisfy depend.m4. It is never actually
+ # run, as this mode is specially recognized in the preamble.
+ exit 1
+ ;;
+
+makedepend)
+ "$@" || exit $?
+ # Remove any Libtool call
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+ # X makedepend
+ shift
+ cleared=no eat=no
+ for arg
+ do
+ case $cleared in
+ no)
+ set ""; shift
+ cleared=yes ;;
+ esac
+ if test $eat = yes; then
+ eat=no
+ continue
+ fi
+ case "$arg" in
+ -D*|-I*)
+ set fnord "$@" "$arg"; shift ;;
+ # Strip any option that makedepend may not understand. Remove
+ # the object too, otherwise makedepend will parse it as a source file.
+ -arch)
+ eat=yes ;;
+ -*|$object)
+ ;;
+ *)
+ set fnord "$@" "$arg"; shift ;;
+ esac
+ done
+ obj_suffix=`echo "$object" | sed 's/^.*\././'`
+ touch "$tmpdepfile"
+ ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
+ rm -f "$depfile"
+ cat < "$tmpdepfile" > "$depfile"
+ sed '1,2d' "$tmpdepfile" | tr ' ' '
+' | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile" "$tmpdepfile".bak
+ ;;
+
+cpp)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout.
+ "$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
+ # Remove `-o $object'.
+ IFS=" "
+ for arg
+ do
+ case $arg in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift # fnord
+ shift # $arg
+ ;;
+ esac
+ done
+
+ "$@" -E |
+ sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
+ -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
+ sed '$ s: \\$::' > "$tmpdepfile"
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ cat < "$tmpdepfile" >> "$depfile"
+ sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+msvisualcpp)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout.
+ "$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
+ IFS=" "
+ for arg
+ do
+ case "$arg" in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
+ "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
+ set fnord "$@"
+ shift
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift
+ shift
+ ;;
+ esac
+ done
+ "$@" -E 2>/dev/null |
+ sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
+ echo " " >> "$depfile"
+ sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+msvcmsys)
+ # This case exists only to let depend.m4 do its work. It works by
+ # looking at the text of this script. This case will never be run,
+ # since it is checked for above.
+ exit 1
+ ;;
+
+none)
+ exec "$@"
+ ;;
+
+*)
+ echo "Unknown depmode $depmode" 1>&2
+ exit 1
+ ;;
+esac
+
+exit 0
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/src/libGkArrays/config/install-sh b/src/libGkArrays/config/install-sh
new file mode 100755
index 0000000..6781b98
--- /dev/null
+++ b/src/libGkArrays/config/install-sh
@@ -0,0 +1,520 @@
+#!/bin/sh
+# install - install a program, script, or datafile
+
+scriptversion=2009-04-28.21; # UTC
+
+# This originates from X11R5 (mit/util/scripts/install.sh), which was
+# later released in X11R6 (xc/config/util/install.sh) with the
+# following copyright and license.
+#
+# Copyright (C) 1994 X Consortium
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to
+# deal in the Software without restriction, including without limitation the
+# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+# sell copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
+# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
+# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Except as contained in this notice, the name of the X Consortium shall not
+# be used in advertising or otherwise to promote the sale, use or other deal-
+# ings in this Software without prior written authorization from the X Consor-
+# tium.
+#
+#
+# FSF changes to this file are in the public domain.
+#
+# Calling this script install-sh is preferred over install.sh, to prevent
+# `make' implicit rules from creating a file called install from it
+# when there is no Makefile.
+#
+# This script is compatible with the BSD install script, but was written
+# from scratch.
+
+nl='
+'
+IFS=" "" $nl"
+
+# set DOITPROG to echo to test this script
+
+# Don't use :- since 4.3BSD and earlier shells don't like it.
+doit=${DOITPROG-}
+if test -z "$doit"; then
+ doit_exec=exec
+else
+ doit_exec=$doit
+fi
+
+# Put in absolute file names if you don't have them in your path;
+# or use environment vars.
+
+chgrpprog=${CHGRPPROG-chgrp}
+chmodprog=${CHMODPROG-chmod}
+chownprog=${CHOWNPROG-chown}
+cmpprog=${CMPPROG-cmp}
+cpprog=${CPPROG-cp}
+mkdirprog=${MKDIRPROG-mkdir}
+mvprog=${MVPROG-mv}
+rmprog=${RMPROG-rm}
+stripprog=${STRIPPROG-strip}
+
+posix_glob='?'
+initialize_posix_glob='
+ test "$posix_glob" != "?" || {
+ if (set -f) 2>/dev/null; then
+ posix_glob=
+ else
+ posix_glob=:
+ fi
+ }
+'
+
+posix_mkdir=
+
+# Desired mode of installed file.
+mode=0755
+
+chgrpcmd=
+chmodcmd=$chmodprog
+chowncmd=
+mvcmd=$mvprog
+rmcmd="$rmprog -f"
+stripcmd=
+
+src=
+dst=
+dir_arg=
+dst_arg=
+
+copy_on_change=false
+no_target_directory=
+
+usage="\
+Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
+ or: $0 [OPTION]... SRCFILES... DIRECTORY
+ or: $0 [OPTION]... -t DIRECTORY SRCFILES...
+ or: $0 [OPTION]... -d DIRECTORIES...
+
+In the 1st form, copy SRCFILE to DSTFILE.
+In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
+In the 4th, create DIRECTORIES.
+
+Options:
+ --help display this help and exit.
+ --version display version info and exit.
+
+ -c (ignored)
+ -C install only if different (preserve the last data modification time)
+ -d create directories instead of installing files.
+ -g GROUP $chgrpprog installed files to GROUP.
+ -m MODE $chmodprog installed files to MODE.
+ -o USER $chownprog installed files to USER.
+ -s $stripprog installed files.
+ -t DIRECTORY install into DIRECTORY.
+ -T report an error if DSTFILE is a directory.
+
+Environment variables override the default commands:
+ CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG
+ RMPROG STRIPPROG
+"
+
+while test $# -ne 0; do
+ case $1 in
+ -c) ;;
+
+ -C) copy_on_change=true;;
+
+ -d) dir_arg=true;;
+
+ -g) chgrpcmd="$chgrpprog $2"
+ shift;;
+
+ --help) echo "$usage"; exit $?;;
+
+ -m) mode=$2
+ case $mode in
+ *' '* | *' '* | *'
+'* | *'*'* | *'?'* | *'['*)
+ echo "$0: invalid mode: $mode" >&2
+ exit 1;;
+ esac
+ shift;;
+
+ -o) chowncmd="$chownprog $2"
+ shift;;
+
+ -s) stripcmd=$stripprog;;
+
+ -t) dst_arg=$2
+ shift;;
+
+ -T) no_target_directory=true;;
+
+ --version) echo "$0 $scriptversion"; exit $?;;
+
+ --) shift
+ break;;
+
+ -*) echo "$0: invalid option: $1" >&2
+ exit 1;;
+
+ *) break;;
+ esac
+ shift
+done
+
+if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
+ # When -d is used, all remaining arguments are directories to create.
+ # When -t is used, the destination is already specified.
+ # Otherwise, the last argument is the destination. Remove it from $@.
+ for arg
+ do
+ if test -n "$dst_arg"; then
+ # $@ is not empty: it contains at least $arg.
+ set fnord "$@" "$dst_arg"
+ shift # fnord
+ fi
+ shift # arg
+ dst_arg=$arg
+ done
+fi
+
+if test $# -eq 0; then
+ if test -z "$dir_arg"; then
+ echo "$0: no input file specified." >&2
+ exit 1
+ fi
+ # It's OK to call `install-sh -d' without argument.
+ # This can happen when creating conditional directories.
+ exit 0
+fi
+
+if test -z "$dir_arg"; then
+ trap '(exit $?); exit' 1 2 13 15
+
+ # Set umask so as not to create temps with too-generous modes.
+ # However, 'strip' requires both read and write access to temps.
+ case $mode in
+ # Optimize common cases.
+ *644) cp_umask=133;;
+ *755) cp_umask=22;;
+
+ *[0-7])
+ if test -z "$stripcmd"; then
+ u_plus_rw=
+ else
+ u_plus_rw='% 200'
+ fi
+ cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
+ *)
+ if test -z "$stripcmd"; then
+ u_plus_rw=
+ else
+ u_plus_rw=,u+rw
+ fi
+ cp_umask=$mode$u_plus_rw;;
+ esac
+fi
+
+for src
+do
+ # Protect names starting with `-'.
+ case $src in
+ -*) src=./$src;;
+ esac
+
+ if test -n "$dir_arg"; then
+ dst=$src
+ dstdir=$dst
+ test -d "$dstdir"
+ dstdir_status=$?
+ else
+
+ # Waiting for this to be detected by the "$cpprog $src $dsttmp" command
+ # might cause directories to be created, which would be especially bad
+ # if $src (and thus $dsttmp) contains '*'.
+ if test ! -f "$src" && test ! -d "$src"; then
+ echo "$0: $src does not exist." >&2
+ exit 1
+ fi
+
+ if test -z "$dst_arg"; then
+ echo "$0: no destination specified." >&2
+ exit 1
+ fi
+
+ dst=$dst_arg
+ # Protect names starting with `-'.
+ case $dst in
+ -*) dst=./$dst;;
+ esac
+
+ # If destination is a directory, append the input filename; won't work
+ # if double slashes aren't ignored.
+ if test -d "$dst"; then
+ if test -n "$no_target_directory"; then
+ echo "$0: $dst_arg: Is a directory" >&2
+ exit 1
+ fi
+ dstdir=$dst
+ dst=$dstdir/`basename "$src"`
+ dstdir_status=0
+ else
+ # Prefer dirname, but fall back on a substitute if dirname fails.
+ dstdir=`
+ (dirname "$dst") 2>/dev/null ||
+ expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$dst" : 'X\(//\)[^/]' \| \
+ X"$dst" : 'X\(//\)$' \| \
+ X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
+ echo X"$dst" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'
+ `
+
+ test -d "$dstdir"
+ dstdir_status=$?
+ fi
+ fi
+
+ obsolete_mkdir_used=false
+
+ if test $dstdir_status != 0; then
+ case $posix_mkdir in
+ '')
+ # Create intermediate dirs using mode 755 as modified by the umask.
+ # This is like FreeBSD 'install' as of 1997-10-28.
+ umask=`umask`
+ case $stripcmd.$umask in
+ # Optimize common cases.
+ *[2367][2367]) mkdir_umask=$umask;;
+ .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
+
+ *[0-7])
+ mkdir_umask=`expr $umask + 22 \
+ - $umask % 100 % 40 + $umask % 20 \
+ - $umask % 10 % 4 + $umask % 2
+ `;;
+ *) mkdir_umask=$umask,go-w;;
+ esac
+
+ # With -d, create the new directory with the user-specified mode.
+ # Otherwise, rely on $mkdir_umask.
+ if test -n "$dir_arg"; then
+ mkdir_mode=-m$mode
+ else
+ mkdir_mode=
+ fi
+
+ posix_mkdir=false
+ case $umask in
+ *[123567][0-7][0-7])
+ # POSIX mkdir -p sets u+wx bits regardless of umask, which
+ # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
+ ;;
+ *)
+ tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
+ trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
+
+ if (umask $mkdir_umask &&
+ exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
+ then
+ if test -z "$dir_arg" || {
+ # Check for POSIX incompatibilities with -m.
+ # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
+ # other-writeable bit of parent directory when it shouldn't.
+ # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
+ ls_ld_tmpdir=`ls -ld "$tmpdir"`
+ case $ls_ld_tmpdir in
+ d????-?r-*) different_mode=700;;
+ d????-?--*) different_mode=755;;
+ *) false;;
+ esac &&
+ $mkdirprog -m$different_mode -p -- "$tmpdir" && {
+ ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
+ test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
+ }
+ }
+ then posix_mkdir=:
+ fi
+ rmdir "$tmpdir/d" "$tmpdir"
+ else
+ # Remove any dirs left behind by ancient mkdir implementations.
+ rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
+ fi
+ trap '' 0;;
+ esac;;
+ esac
+
+ if
+ $posix_mkdir && (
+ umask $mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
+ )
+ then :
+ else
+
+ # The umask is ridiculous, or mkdir does not conform to POSIX,
+ # or it failed possibly due to a race condition. Create the
+ # directory the slow way, step by step, checking for races as we go.
+
+ case $dstdir in
+ /*) prefix='/';;
+ -*) prefix='./';;
+ *) prefix='';;
+ esac
+
+ eval "$initialize_posix_glob"
+
+ oIFS=$IFS
+ IFS=/
+ $posix_glob set -f
+ set fnord $dstdir
+ shift
+ $posix_glob set +f
+ IFS=$oIFS
+
+ prefixes=
+
+ for d
+ do
+ test -z "$d" && continue
+
+ prefix=$prefix$d
+ if test -d "$prefix"; then
+ prefixes=
+ else
+ if $posix_mkdir; then
+ (umask=$mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
+ # Don't fail if two instances are running concurrently.
+ test -d "$prefix" || exit 1
+ else
+ case $prefix in
+ *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
+ *) qprefix=$prefix;;
+ esac
+ prefixes="$prefixes '$qprefix'"
+ fi
+ fi
+ prefix=$prefix/
+ done
+
+ if test -n "$prefixes"; then
+ # Don't fail if two instances are running concurrently.
+ (umask $mkdir_umask &&
+ eval "\$doit_exec \$mkdirprog $prefixes") ||
+ test -d "$dstdir" || exit 1
+ obsolete_mkdir_used=true
+ fi
+ fi
+ fi
+
+ if test -n "$dir_arg"; then
+ { test -z "$chowncmd" || $doit $chowncmd "$dst"; } &&
+ { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } &&
+ { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false ||
+ test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1
+ else
+
+ # Make a couple of temp file names in the proper directory.
+ dsttmp=$dstdir/_inst.$$_
+ rmtmp=$dstdir/_rm.$$_
+
+ # Trap to clean up those temp files at exit.
+ trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
+
+ # Copy the file name to the temp name.
+ (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") &&
+
+ # and set any options; do chmod last to preserve setuid bits.
+ #
+ # If any of these fail, we abort the whole thing. If we want to
+ # ignore errors from any of these, just make sure not to ignore
+ # errors from the above "$doit $cpprog $src $dsttmp" command.
+ #
+ { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&
+ { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&
+ { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&
+ { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
+
+ # If -C, don't bother to copy if it wouldn't change the file.
+ if $copy_on_change &&
+ old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
+ new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
+
+ eval "$initialize_posix_glob" &&
+ $posix_glob set -f &&
+ set X $old && old=:$2:$4:$5:$6 &&
+ set X $new && new=:$2:$4:$5:$6 &&
+ $posix_glob set +f &&
+
+ test "$old" = "$new" &&
+ $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
+ then
+ rm -f "$dsttmp"
+ else
+ # Rename the file to the real destination.
+ $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||
+
+ # The rename failed, perhaps because mv can't rename something else
+ # to itself, or perhaps because mv is so ancient that it does not
+ # support -f.
+ {
+ # Now remove or move aside any old file at destination location.
+ # We try this two ways since rm can't unlink itself on some
+ # systems and the destination file might be busy for other
+ # reasons. In this case, the final cleanup might fail but the new
+ # file should still install successfully.
+ {
+ test ! -f "$dst" ||
+ $doit $rmcmd -f "$dst" 2>/dev/null ||
+ { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
+ { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
+ } ||
+ { echo "$0: cannot unlink or rename $dst" >&2
+ (exit 1); exit 1
+ }
+ } &&
+
+ # Now rename the file to the real destination.
+ $doit $mvcmd "$dsttmp" "$dst"
+ }
+ fi || exit 1
+
+ trap '' 0
+ fi
+done
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/src/libGkArrays/config/ltmain.sh b/src/libGkArrays/config/ltmain.sh
new file mode 100755
index 0000000..d88da2c
--- /dev/null
+++ b/src/libGkArrays/config/ltmain.sh
@@ -0,0 +1,8413 @@
+# Generated from ltmain.m4sh.
+
+# ltmain.sh (GNU libtool) 2.2.6b
+# Written by Gordon Matzigkeit <gord at gnu.ai.mit.edu>, 1996
+
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, 2006, 2007 2008 Free Software Foundation, Inc.
+# This is free software; see the source for copying conditions. There is NO
+# warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+# GNU Libtool is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# As a special exception to the GNU General Public License,
+# if you distribute this file as part of a program or library that
+# is built using GNU Libtool, you may include this file under the
+# same distribution terms that you use for the rest of that program.
+#
+# GNU Libtool is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GNU Libtool; see the file COPYING. If not, a copy
+# can be downloaded from http://www.gnu.org/licenses/gpl.html,
+# or obtained by writing to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# Usage: $progname [OPTION]... [MODE-ARG]...
+#
+# Provide generalized library-building support services.
+#
+# --config show all configuration variables
+# --debug enable verbose shell tracing
+# -n, --dry-run display commands without modifying any files
+# --features display basic configuration information and exit
+# --mode=MODE use operation mode MODE
+# --preserve-dup-deps don't remove duplicate dependency libraries
+# --quiet, --silent don't print informational messages
+# --tag=TAG use configuration variables from tag TAG
+# -v, --verbose print informational messages (default)
+# --version print version information
+# -h, --help print short or long help message
+#
+# MODE must be one of the following:
+#
+# clean remove files from the build directory
+# compile compile a source file into a libtool object
+# execute automatically set library path, then run a program
+# finish complete the installation of libtool libraries
+# install install libraries or executables
+# link create a library or an executable
+# uninstall remove libraries from an installed directory
+#
+# MODE-ARGS vary depending on the MODE.
+# Try `$progname --help --mode=MODE' for a more detailed description of MODE.
+#
+# When reporting a bug, please describe a test case to reproduce it and
+# include the following information:
+#
+# host-triplet: $host
+# shell: $SHELL
+# compiler: $LTCC
+# compiler flags: $LTCFLAGS
+# linker: $LD (gnu? $with_gnu_ld)
+# $progname: (GNU libtool) 2.2.6b Debian-2.2.6b-2
+# automake: $automake_version
+# autoconf: $autoconf_version
+#
+# Report bugs to <bug-libtool at gnu.org>.
+
+PROGRAM=ltmain.sh
+PACKAGE=libtool
+VERSION="2.2.6b Debian-2.2.6b-2"
+TIMESTAMP=""
+package_revision=1.3017
+
+# Be Bourne compatible
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in *posix*) set -o posix;; esac
+fi
+BIN_SH=xpg4; export BIN_SH # for Tru64
+DUALCASE=1; export DUALCASE # for MKS sh
+
+# NLS nuisances: We save the old values to restore during execute mode.
+# Only set LANG and LC_ALL to C if already set.
+# These must not be set unconditionally because not all systems understand
+# e.g. LANG=C (notably SCO).
+lt_user_locale=
+lt_safe_locale=
+for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES
+do
+ eval "if test \"\${$lt_var+set}\" = set; then
+ save_$lt_var=\$$lt_var
+ $lt_var=C
+ export $lt_var
+ lt_user_locale=\"$lt_var=\\\$save_\$lt_var; \$lt_user_locale\"
+ lt_safe_locale=\"$lt_var=C; \$lt_safe_locale\"
+ fi"
+done
+
+$lt_unset CDPATH
+
+
+
+
+
+: ${CP="cp -f"}
+: ${ECHO="echo"}
+: ${EGREP="/bin/grep -E"}
+: ${FGREP="/bin/grep -F"}
+: ${GREP="/bin/grep"}
+: ${LN_S="ln -s"}
+: ${MAKE="make"}
+: ${MKDIR="mkdir"}
+: ${MV="mv -f"}
+: ${RM="rm -f"}
+: ${SED="/bin/sed"}
+: ${SHELL="${CONFIG_SHELL-/bin/sh}"}
+: ${Xsed="$SED -e 1s/^X//"}
+
+# Global variables:
+EXIT_SUCCESS=0
+EXIT_FAILURE=1
+EXIT_MISMATCH=63 # $? = 63 is used to indicate version mismatch to missing.
+EXIT_SKIP=77 # $? = 77 is used to indicate a skipped test to automake.
+
+exit_status=$EXIT_SUCCESS
+
+# Make sure IFS has a sensible default
+lt_nl='
+'
+IFS=" $lt_nl"
+
+dirname="s,/[^/]*$,,"
+basename="s,^.*/,,"
+
+# func_dirname_and_basename file append nondir_replacement
+# perform func_basename and func_dirname in a single function
+# call:
+# dirname: Compute the dirname of FILE. If nonempty,
+# add APPEND to the result, otherwise set result
+# to NONDIR_REPLACEMENT.
+# value returned in "$func_dirname_result"
+# basename: Compute filename of FILE.
+# value retuned in "$func_basename_result"
+# Implementation must be kept synchronized with func_dirname
+# and func_basename. For efficiency, we do not delegate to
+# those functions but instead duplicate the functionality here.
+func_dirname_and_basename ()
+{
+ # Extract subdirectory from the argument.
+ func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"`
+ if test "X$func_dirname_result" = "X${1}"; then
+ func_dirname_result="${3}"
+ else
+ func_dirname_result="$func_dirname_result${2}"
+ fi
+ func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"`
+}
+
+# Generated shell functions inserted here.
+
+# Work around backward compatibility issue on IRIX 6.5. On IRIX 6.4+, sh
+# is ksh but when the shell is invoked as "sh" and the current value of
+# the _XPG environment variable is not equal to 1 (one), the special
+# positional parameter $0, within a function call, is the name of the
+# function.
+progpath="$0"
+
+# The name of this program:
+# In the unlikely event $progname began with a '-', it would play havoc with
+# func_echo (imagine progname=-n), so we prepend ./ in that case:
+func_dirname_and_basename "$progpath"
+progname=$func_basename_result
+case $progname in
+ -*) progname=./$progname ;;
+esac
+
+# Make sure we have an absolute path for reexecution:
+case $progpath in
+ [\\/]*|[A-Za-z]:\\*) ;;
+ *[\\/]*)
+ progdir=$func_dirname_result
+ progdir=`cd "$progdir" && pwd`
+ progpath="$progdir/$progname"
+ ;;
+ *)
+ save_IFS="$IFS"
+ IFS=:
+ for progdir in $PATH; do
+ IFS="$save_IFS"
+ test -x "$progdir/$progname" && break
+ done
+ IFS="$save_IFS"
+ test -n "$progdir" || progdir=`pwd`
+ progpath="$progdir/$progname"
+ ;;
+esac
+
+# Sed substitution that helps us do robust quoting. It backslashifies
+# metacharacters that are still active within double-quoted strings.
+Xsed="${SED}"' -e 1s/^X//'
+sed_quote_subst='s/\([`"$\\]\)/\\\1/g'
+
+# Same as above, but do not quote variable references.
+double_quote_subst='s/\(["`\\]\)/\\\1/g'
+
+# Re-`\' parameter expansions in output of double_quote_subst that were
+# `\'-ed in input to the same. If an odd number of `\' preceded a '$'
+# in input to double_quote_subst, that '$' was protected from expansion.
+# Since each input `\' is now two `\'s, look for any number of runs of
+# four `\'s followed by two `\'s and then a '$'. `\' that '$'.
+bs='\\'
+bs2='\\\\'
+bs4='\\\\\\\\'
+dollar='\$'
+sed_double_backslash="\
+ s/$bs4/&\\
+/g
+ s/^$bs2$dollar/$bs&/
+ s/\\([^$bs]\\)$bs2$dollar/\\1$bs2$bs$dollar/g
+ s/\n//g"
+
+# Standard options:
+opt_dry_run=false
+opt_help=false
+opt_quiet=false
+opt_verbose=false
+opt_warning=:
+
+# func_echo arg...
+# Echo program name prefixed message, along with the current mode
+# name if it has been set yet.
+func_echo ()
+{
+ $ECHO "$progname${mode+: }$mode: $*"
+}
+
+# func_verbose arg...
+# Echo program name prefixed message in verbose mode only.
+func_verbose ()
+{
+ $opt_verbose && func_echo ${1+"$@"}
+
+ # A bug in bash halts the script if the last line of a function
+ # fails when set -e is in force, so we need another command to
+ # work around that:
+ :
+}
+
+# func_error arg...
+# Echo program name prefixed message to standard error.
+func_error ()
+{
+ $ECHO "$progname${mode+: }$mode: "${1+"$@"} 1>&2
+}
+
+# func_warning arg...
+# Echo program name prefixed warning message to standard error.
+func_warning ()
+{
+ $opt_warning && $ECHO "$progname${mode+: }$mode: warning: "${1+"$@"} 1>&2
+
+ # bash bug again:
+ :
+}
+
+# func_fatal_error arg...
+# Echo program name prefixed message to standard error, and exit.
+func_fatal_error ()
+{
+ func_error ${1+"$@"}
+ exit $EXIT_FAILURE
+}
+
+# func_fatal_help arg...
+# Echo program name prefixed message to standard error, followed by
+# a help hint, and exit.
+func_fatal_help ()
+{
+ func_error ${1+"$@"}
+ func_fatal_error "$help"
+}
+help="Try \`$progname --help' for more information." ## default
+
+
+# func_grep expression filename
+# Check whether EXPRESSION matches any line of FILENAME, without output.
+func_grep ()
+{
+ $GREP "$1" "$2" >/dev/null 2>&1
+}
+
+
+# func_mkdir_p directory-path
+# Make sure the entire path to DIRECTORY-PATH is available.
+func_mkdir_p ()
+{
+ my_directory_path="$1"
+ my_dir_list=
+
+ if test -n "$my_directory_path" && test "$opt_dry_run" != ":"; then
+
+ # Protect directory names starting with `-'
+ case $my_directory_path in
+ -*) my_directory_path="./$my_directory_path" ;;
+ esac
+
+ # While some portion of DIR does not yet exist...
+ while test ! -d "$my_directory_path"; do
+ # ...make a list in topmost first order. Use a colon delimited
+ # list incase some portion of path contains whitespace.
+ my_dir_list="$my_directory_path:$my_dir_list"
+
+ # If the last portion added has no slash in it, the list is done
+ case $my_directory_path in */*) ;; *) break ;; esac
+
+ # ...otherwise throw away the child directory and loop
+ my_directory_path=`$ECHO "X$my_directory_path" | $Xsed -e "$dirname"`
+ done
+ my_dir_list=`$ECHO "X$my_dir_list" | $Xsed -e 's,:*$,,'`
+
+ save_mkdir_p_IFS="$IFS"; IFS=':'
+ for my_dir in $my_dir_list; do
+ IFS="$save_mkdir_p_IFS"
+ # mkdir can fail with a `File exist' error if two processes
+ # try to create one of the directories concurrently. Don't
+ # stop in that case!
+ $MKDIR "$my_dir" 2>/dev/null || :
+ done
+ IFS="$save_mkdir_p_IFS"
+
+ # Bail out if we (or some other process) failed to create a directory.
+ test -d "$my_directory_path" || \
+ func_fatal_error "Failed to create \`$1'"
+ fi
+}
+
+
+# func_mktempdir [string]
+# Make a temporary directory that won't clash with other running
+# libtool processes, and avoids race conditions if possible. If
+# given, STRING is the basename for that directory.
+func_mktempdir ()
+{
+ my_template="${TMPDIR-/tmp}/${1-$progname}"
+
+ if test "$opt_dry_run" = ":"; then
+ # Return a directory name, but don't create it in dry-run mode
+ my_tmpdir="${my_template}-$$"
+ else
+
+ # If mktemp works, use that first and foremost
+ my_tmpdir=`mktemp -d "${my_template}-XXXXXXXX" 2>/dev/null`
+
+ if test ! -d "$my_tmpdir"; then
+ # Failing that, at least try and use $RANDOM to avoid a race
+ my_tmpdir="${my_template}-${RANDOM-0}$$"
+
+ save_mktempdir_umask=`umask`
+ umask 0077
+ $MKDIR "$my_tmpdir"
+ umask $save_mktempdir_umask
+ fi
+
+ # If we're not in dry-run mode, bomb out on failure
+ test -d "$my_tmpdir" || \
+ func_fatal_error "cannot create temporary directory \`$my_tmpdir'"
+ fi
+
+ $ECHO "X$my_tmpdir" | $Xsed
+}
+
+
+# func_quote_for_eval arg
+# Aesthetically quote ARG to be evaled later.
+# This function returns two values: FUNC_QUOTE_FOR_EVAL_RESULT
+# is double-quoted, suitable for a subsequent eval, whereas
+# FUNC_QUOTE_FOR_EVAL_UNQUOTED_RESULT has merely all characters
+# which are still active within double quotes backslashified.
+func_quote_for_eval ()
+{
+ case $1 in
+ *[\\\`\"\$]*)
+ func_quote_for_eval_unquoted_result=`$ECHO "X$1" | $Xsed -e "$sed_quote_subst"` ;;
+ *)
+ func_quote_for_eval_unquoted_result="$1" ;;
+ esac
+
+ case $func_quote_for_eval_unquoted_result in
+ # Double-quote args containing shell metacharacters to delay
+ # word splitting, command substitution and and variable
+ # expansion for a subsequent eval.
+ # Many Bourne shells cannot handle close brackets correctly
+ # in scan sets, so we specify it separately.
+ *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"")
+ func_quote_for_eval_result="\"$func_quote_for_eval_unquoted_result\""
+ ;;
+ *)
+ func_quote_for_eval_result="$func_quote_for_eval_unquoted_result"
+ esac
+}
+
+
+# func_quote_for_expand arg
+# Aesthetically quote ARG to be evaled later; same as above,
+# but do not quote variable references.
+func_quote_for_expand ()
+{
+ case $1 in
+ *[\\\`\"]*)
+ my_arg=`$ECHO "X$1" | $Xsed \
+ -e "$double_quote_subst" -e "$sed_double_backslash"` ;;
+ *)
+ my_arg="$1" ;;
+ esac
+
+ case $my_arg in
+ # Double-quote args containing shell metacharacters to delay
+ # word splitting and command substitution for a subsequent eval.
+ # Many Bourne shells cannot handle close brackets correctly
+ # in scan sets, so we specify it separately.
+ *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"")
+ my_arg="\"$my_arg\""
+ ;;
+ esac
+
+ func_quote_for_expand_result="$my_arg"
+}
+
+
+# func_show_eval cmd [fail_exp]
+# Unless opt_silent is true, then output CMD. Then, if opt_dryrun is
+# not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP
+# is given, then evaluate it.
+func_show_eval ()
+{
+ my_cmd="$1"
+ my_fail_exp="${2-:}"
+
+ ${opt_silent-false} || {
+ func_quote_for_expand "$my_cmd"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+
+ if ${opt_dry_run-false}; then :; else
+ eval "$my_cmd"
+ my_status=$?
+ if test "$my_status" -eq 0; then :; else
+ eval "(exit $my_status); $my_fail_exp"
+ fi
+ fi
+}
+
+
+# func_show_eval_locale cmd [fail_exp]
+# Unless opt_silent is true, then output CMD. Then, if opt_dryrun is
+# not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP
+# is given, then evaluate it. Use the saved locale for evaluation.
+func_show_eval_locale ()
+{
+ my_cmd="$1"
+ my_fail_exp="${2-:}"
+
+ ${opt_silent-false} || {
+ func_quote_for_expand "$my_cmd"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+
+ if ${opt_dry_run-false}; then :; else
+ eval "$lt_user_locale
+ $my_cmd"
+ my_status=$?
+ eval "$lt_safe_locale"
+ if test "$my_status" -eq 0; then :; else
+ eval "(exit $my_status); $my_fail_exp"
+ fi
+ fi
+}
+
+
+
+
+
+# func_version
+# Echo version message to standard output and exit.
+func_version ()
+{
+ $SED -n '/^# '$PROGRAM' (GNU /,/# warranty; / {
+ s/^# //
+ s/^# *$//
+ s/\((C)\)[ 0-9,-]*\( [1-9][0-9]*\)/\1\2/
+ p
+ }' < "$progpath"
+ exit $?
+}
+
+# func_usage
+# Echo short help message to standard output and exit.
+func_usage ()
+{
+ $SED -n '/^# Usage:/,/# -h/ {
+ s/^# //
+ s/^# *$//
+ s/\$progname/'$progname'/
+ p
+ }' < "$progpath"
+ $ECHO
+ $ECHO "run \`$progname --help | more' for full usage"
+ exit $?
+}
+
+# func_help
+# Echo long help message to standard output and exit.
+func_help ()
+{
+ $SED -n '/^# Usage:/,/# Report bugs to/ {
+ s/^# //
+ s/^# *$//
+ s*\$progname*'$progname'*
+ s*\$host*'"$host"'*
+ s*\$SHELL*'"$SHELL"'*
+ s*\$LTCC*'"$LTCC"'*
+ s*\$LTCFLAGS*'"$LTCFLAGS"'*
+ s*\$LD*'"$LD"'*
+ s/\$with_gnu_ld/'"$with_gnu_ld"'/
+ s/\$automake_version/'"`(automake --version) 2>/dev/null |$SED 1q`"'/
+ s/\$autoconf_version/'"`(autoconf --version) 2>/dev/null |$SED 1q`"'/
+ p
+ }' < "$progpath"
+ exit $?
+}
+
+# func_missing_arg argname
+# Echo program name prefixed message to standard error and set global
+# exit_cmd.
+func_missing_arg ()
+{
+ func_error "missing argument for $1"
+ exit_cmd=exit
+}
+
+exit_cmd=:
+
+
+
+
+
+# Check that we have a working $ECHO.
+if test "X$1" = X--no-reexec; then
+ # Discard the --no-reexec flag, and continue.
+ shift
+elif test "X$1" = X--fallback-echo; then
+ # Avoid inline document here, it may be left over
+ :
+elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t'; then
+ # Yippee, $ECHO works!
+ :
+else
+ # Restart under the correct shell, and then maybe $ECHO will work.
+ exec $SHELL "$progpath" --no-reexec ${1+"$@"}
+fi
+
+if test "X$1" = X--fallback-echo; then
+ # used as fallback echo
+ shift
+ cat <<EOF
+$*
+EOF
+ exit $EXIT_SUCCESS
+fi
+
+magic="%%%MAGIC variable%%%"
+magic_exe="%%%MAGIC EXE variable%%%"
+
+# Global variables.
+# $mode is unset
+nonopt=
+execute_dlfiles=
+preserve_args=
+lo2o="s/\\.lo\$/.${objext}/"
+o2lo="s/\\.${objext}\$/.lo/"
+extracted_archives=
+extracted_serial=0
+
+opt_dry_run=false
+opt_duplicate_deps=false
+opt_silent=false
+opt_debug=:
+
+# If this variable is set in any of the actions, the command in it
+# will be execed at the end. This prevents here-documents from being
+# left over by shells.
+exec_cmd=
+
+# func_fatal_configuration arg...
+# Echo program name prefixed message to standard error, followed by
+# a configuration failure hint, and exit.
+func_fatal_configuration ()
+{
+ func_error ${1+"$@"}
+ func_error "See the $PACKAGE documentation for more information."
+ func_fatal_error "Fatal configuration error."
+}
+
+
+# func_config
+# Display the configuration for all the tags in this script.
+func_config ()
+{
+ re_begincf='^# ### BEGIN LIBTOOL'
+ re_endcf='^# ### END LIBTOOL'
+
+ # Default configuration.
+ $SED "1,/$re_begincf CONFIG/d;/$re_endcf CONFIG/,\$d" < "$progpath"
+
+ # Now print the configurations for the tags.
+ for tagname in $taglist; do
+ $SED -n "/$re_begincf TAG CONFIG: $tagname\$/,/$re_endcf TAG CONFIG: $tagname\$/p" < "$progpath"
+ done
+
+ exit $?
+}
+
+# func_features
+# Display the features supported by this script.
+func_features ()
+{
+ $ECHO "host: $host"
+ if test "$build_libtool_libs" = yes; then
+ $ECHO "enable shared libraries"
+ else
+ $ECHO "disable shared libraries"
+ fi
+ if test "$build_old_libs" = yes; then
+ $ECHO "enable static libraries"
+ else
+ $ECHO "disable static libraries"
+ fi
+
+ exit $?
+}
+
+# func_enable_tag tagname
+# Verify that TAGNAME is valid, and either flag an error and exit, or
+# enable the TAGNAME tag. We also add TAGNAME to the global $taglist
+# variable here.
+func_enable_tag ()
+{
+ # Global variable:
+ tagname="$1"
+
+ re_begincf="^# ### BEGIN LIBTOOL TAG CONFIG: $tagname\$"
+ re_endcf="^# ### END LIBTOOL TAG CONFIG: $tagname\$"
+ sed_extractcf="/$re_begincf/,/$re_endcf/p"
+
+ # Validate tagname.
+ case $tagname in
+ *[!-_A-Za-z0-9,/]*)
+ func_fatal_error "invalid tag name: $tagname"
+ ;;
+ esac
+
+ # Don't test for the "default" C tag, as we know it's
+ # there but not specially marked.
+ case $tagname in
+ CC) ;;
+ *)
+ if $GREP "$re_begincf" "$progpath" >/dev/null 2>&1; then
+ taglist="$taglist $tagname"
+
+ # Evaluate the configuration. Be careful to quote the path
+ # and the sed script, to avoid splitting on whitespace, but
+ # also don't use non-portable quotes within backquotes within
+ # quotes we have to do it in 2 steps:
+ extractedcf=`$SED -n -e "$sed_extractcf" < "$progpath"`
+ eval "$extractedcf"
+ else
+ func_error "ignoring unknown tag $tagname"
+ fi
+ ;;
+ esac
+}
+
+# Parse options once, thoroughly. This comes as soon as possible in
+# the script to make things like `libtool --version' happen quickly.
+{
+
+ # Shorthand for --mode=foo, only valid as the first argument
+ case $1 in
+ clean|clea|cle|cl)
+ shift; set dummy --mode clean ${1+"$@"}; shift
+ ;;
+ compile|compil|compi|comp|com|co|c)
+ shift; set dummy --mode compile ${1+"$@"}; shift
+ ;;
+ execute|execut|execu|exec|exe|ex|e)
+ shift; set dummy --mode execute ${1+"$@"}; shift
+ ;;
+ finish|finis|fini|fin|fi|f)
+ shift; set dummy --mode finish ${1+"$@"}; shift
+ ;;
+ install|instal|insta|inst|ins|in|i)
+ shift; set dummy --mode install ${1+"$@"}; shift
+ ;;
+ link|lin|li|l)
+ shift; set dummy --mode link ${1+"$@"}; shift
+ ;;
+ uninstall|uninstal|uninsta|uninst|unins|unin|uni|un|u)
+ shift; set dummy --mode uninstall ${1+"$@"}; shift
+ ;;
+ esac
+
+ # Parse non-mode specific arguments:
+ while test "$#" -gt 0; do
+ opt="$1"
+ shift
+
+ case $opt in
+ --config) func_config ;;
+
+ --debug) preserve_args="$preserve_args $opt"
+ func_echo "enabling shell trace mode"
+ opt_debug='set -x'
+ $opt_debug
+ ;;
+
+ -dlopen) test "$#" -eq 0 && func_missing_arg "$opt" && break
+ execute_dlfiles="$execute_dlfiles $1"
+ shift
+ ;;
+
+ --dry-run | -n) opt_dry_run=: ;;
+ --features) func_features ;;
+ --finish) mode="finish" ;;
+
+ --mode) test "$#" -eq 0 && func_missing_arg "$opt" && break
+ case $1 in
+ # Valid mode arguments:
+ clean) ;;
+ compile) ;;
+ execute) ;;
+ finish) ;;
+ install) ;;
+ link) ;;
+ relink) ;;
+ uninstall) ;;
+
+ # Catch anything else as an error
+ *) func_error "invalid argument for $opt"
+ exit_cmd=exit
+ break
+ ;;
+ esac
+
+ mode="$1"
+ shift
+ ;;
+
+ --preserve-dup-deps)
+ opt_duplicate_deps=: ;;
+
+ --quiet|--silent) preserve_args="$preserve_args $opt"
+ opt_silent=:
+ ;;
+
+ --verbose| -v) preserve_args="$preserve_args $opt"
+ opt_silent=false
+ ;;
+
+ --tag) test "$#" -eq 0 && func_missing_arg "$opt" && break
+ preserve_args="$preserve_args $opt $1"
+ func_enable_tag "$1" # tagname is set here
+ shift
+ ;;
+
+ # Separate optargs to long options:
+ -dlopen=*|--mode=*|--tag=*)
+ func_opt_split "$opt"
+ set dummy "$func_opt_split_opt" "$func_opt_split_arg" ${1+"$@"}
+ shift
+ ;;
+
+ -\?|-h) func_usage ;;
+ --help) opt_help=: ;;
+ --version) func_version ;;
+
+ -*) func_fatal_help "unrecognized option \`$opt'" ;;
+
+ *) nonopt="$opt"
+ break
+ ;;
+ esac
+ done
+
+
+ case $host in
+ *cygwin* | *mingw* | *pw32* | *cegcc*)
+ # don't eliminate duplications in $postdeps and $predeps
+ opt_duplicate_compiler_generated_deps=:
+ ;;
+ *)
+ opt_duplicate_compiler_generated_deps=$opt_duplicate_deps
+ ;;
+ esac
+
+ # Having warned about all mis-specified options, bail out if
+ # anything was wrong.
+ $exit_cmd $EXIT_FAILURE
+}
+
+# func_check_version_match
+# Ensure that we are using m4 macros, and libtool script from the same
+# release of libtool.
+func_check_version_match ()
+{
+ if test "$package_revision" != "$macro_revision"; then
+ if test "$VERSION" != "$macro_version"; then
+ if test -z "$macro_version"; then
+ cat >&2 <<_LT_EOF
+$progname: Version mismatch error. This is $PACKAGE $VERSION, but the
+$progname: definition of this LT_INIT comes from an older release.
+$progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION
+$progname: and run autoconf again.
+_LT_EOF
+ else
+ cat >&2 <<_LT_EOF
+$progname: Version mismatch error. This is $PACKAGE $VERSION, but the
+$progname: definition of this LT_INIT comes from $PACKAGE $macro_version.
+$progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION
+$progname: and run autoconf again.
+_LT_EOF
+ fi
+ else
+ cat >&2 <<_LT_EOF
+$progname: Version mismatch error. This is $PACKAGE $VERSION, revision $package_revision,
+$progname: but the definition of this LT_INIT comes from revision $macro_revision.
+$progname: You should recreate aclocal.m4 with macros from revision $package_revision
+$progname: of $PACKAGE $VERSION and run autoconf again.
+_LT_EOF
+ fi
+
+ exit $EXIT_MISMATCH
+ fi
+}
+
+
+## ----------- ##
+## Main. ##
+## ----------- ##
+
+$opt_help || {
+ # Sanity checks first:
+ func_check_version_match
+
+ if test "$build_libtool_libs" != yes && test "$build_old_libs" != yes; then
+ func_fatal_configuration "not configured to build any kind of library"
+ fi
+
+ test -z "$mode" && func_fatal_error "error: you must specify a MODE."
+
+
+ # Darwin sucks
+ eval std_shrext=\"$shrext_cmds\"
+
+
+ # Only execute mode is allowed to have -dlopen flags.
+ if test -n "$execute_dlfiles" && test "$mode" != execute; then
+ func_error "unrecognized option \`-dlopen'"
+ $ECHO "$help" 1>&2
+ exit $EXIT_FAILURE
+ fi
+
+ # Change the help message to a mode-specific one.
+ generic_help="$help"
+ help="Try \`$progname --help --mode=$mode' for more information."
+}
+
+
+# func_lalib_p file
+# True iff FILE is a libtool `.la' library or `.lo' object file.
+# This function is only a basic sanity check; it will hardly flush out
+# determined imposters.
+func_lalib_p ()
+{
+ test -f "$1" &&
+ $SED -e 4q "$1" 2>/dev/null \
+ | $GREP "^# Generated by .*$PACKAGE" > /dev/null 2>&1
+}
+
+# func_lalib_unsafe_p file
+# True iff FILE is a libtool `.la' library or `.lo' object file.
+# This function implements the same check as func_lalib_p without
+# resorting to external programs. To this end, it redirects stdin and
+# closes it afterwards, without saving the original file descriptor.
+# As a safety measure, use it only where a negative result would be
+# fatal anyway. Works if `file' does not exist.
+func_lalib_unsafe_p ()
+{
+ lalib_p=no
+ if test -f "$1" && test -r "$1" && exec 5<&0 <"$1"; then
+ for lalib_p_l in 1 2 3 4
+ do
+ read lalib_p_line
+ case "$lalib_p_line" in
+ \#\ Generated\ by\ *$PACKAGE* ) lalib_p=yes; break;;
+ esac
+ done
+ exec 0<&5 5<&-
+ fi
+ test "$lalib_p" = yes
+}
+
+# func_ltwrapper_script_p file
+# True iff FILE is a libtool wrapper script
+# This function is only a basic sanity check; it will hardly flush out
+# determined imposters.
+func_ltwrapper_script_p ()
+{
+ func_lalib_p "$1"
+}
+
+# func_ltwrapper_executable_p file
+# True iff FILE is a libtool wrapper executable
+# This function is only a basic sanity check; it will hardly flush out
+# determined imposters.
+func_ltwrapper_executable_p ()
+{
+ func_ltwrapper_exec_suffix=
+ case $1 in
+ *.exe) ;;
+ *) func_ltwrapper_exec_suffix=.exe ;;
+ esac
+ $GREP "$magic_exe" "$1$func_ltwrapper_exec_suffix" >/dev/null 2>&1
+}
+
+# func_ltwrapper_scriptname file
+# Assumes file is an ltwrapper_executable
+# uses $file to determine the appropriate filename for a
+# temporary ltwrapper_script.
+func_ltwrapper_scriptname ()
+{
+ func_ltwrapper_scriptname_result=""
+ if func_ltwrapper_executable_p "$1"; then
+ func_dirname_and_basename "$1" "" "."
+ func_stripname '' '.exe' "$func_basename_result"
+ func_ltwrapper_scriptname_result="$func_dirname_result/$objdir/${func_stripname_result}_ltshwrapper"
+ fi
+}
+
+# func_ltwrapper_p file
+# True iff FILE is a libtool wrapper script or wrapper executable
+# This function is only a basic sanity check; it will hardly flush out
+# determined imposters.
+func_ltwrapper_p ()
+{
+ func_ltwrapper_script_p "$1" || func_ltwrapper_executable_p "$1"
+}
+
+
+# func_execute_cmds commands fail_cmd
+# Execute tilde-delimited COMMANDS.
+# If FAIL_CMD is given, eval that upon failure.
+# FAIL_CMD may read-access the current command in variable CMD!
+func_execute_cmds ()
+{
+ $opt_debug
+ save_ifs=$IFS; IFS='~'
+ for cmd in $1; do
+ IFS=$save_ifs
+ eval cmd=\"$cmd\"
+ func_show_eval "$cmd" "${2-:}"
+ done
+ IFS=$save_ifs
+}
+
+
+# func_source file
+# Source FILE, adding directory component if necessary.
+# Note that it is not necessary on cygwin/mingw to append a dot to
+# FILE even if both FILE and FILE.exe exist: automatic-append-.exe
+# behavior happens only for exec(3), not for open(2)! Also, sourcing
+# `FILE.' does not work on cygwin managed mounts.
+func_source ()
+{
+ $opt_debug
+ case $1 in
+ */* | *\\*) . "$1" ;;
+ *) . "./$1" ;;
+ esac
+}
+
+
+# func_infer_tag arg
+# Infer tagged configuration to use if any are available and
+# if one wasn't chosen via the "--tag" command line option.
+# Only attempt this if the compiler in the base compile
+# command doesn't match the default compiler.
+# arg is usually of the form 'gcc ...'
+func_infer_tag ()
+{
+ $opt_debug
+ if test -n "$available_tags" && test -z "$tagname"; then
+ CC_quoted=
+ for arg in $CC; do
+ func_quote_for_eval "$arg"
+ CC_quoted="$CC_quoted $func_quote_for_eval_result"
+ done
+ case $@ in
+ # Blanks in the command may have been stripped by the calling shell,
+ # but not from the CC environment variable when configure was run.
+ " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*) ;;
+ # Blanks at the start of $base_compile will cause this to fail
+ # if we don't check for them as well.
+ *)
+ for z in $available_tags; do
+ if $GREP "^# ### BEGIN LIBTOOL TAG CONFIG: $z$" < "$progpath" > /dev/null; then
+ # Evaluate the configuration.
+ eval "`${SED} -n -e '/^# ### BEGIN LIBTOOL TAG CONFIG: '$z'$/,/^# ### END LIBTOOL TAG CONFIG: '$z'$/p' < $progpath`"
+ CC_quoted=
+ for arg in $CC; do
+ # Double-quote args containing other shell metacharacters.
+ func_quote_for_eval "$arg"
+ CC_quoted="$CC_quoted $func_quote_for_eval_result"
+ done
+ case "$@ " in
+ " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*)
+ # The compiler in the base compile command matches
+ # the one in the tagged configuration.
+ # Assume this is the tagged configuration we want.
+ tagname=$z
+ break
+ ;;
+ esac
+ fi
+ done
+ # If $tagname still isn't set, then no tagged configuration
+ # was found and let the user know that the "--tag" command
+ # line option must be used.
+ if test -z "$tagname"; then
+ func_echo "unable to infer tagged configuration"
+ func_fatal_error "specify a tag with \`--tag'"
+# else
+# func_verbose "using $tagname tagged configuration"
+ fi
+ ;;
+ esac
+ fi
+}
+
+
+
+# func_write_libtool_object output_name pic_name nonpic_name
+# Create a libtool object file (analogous to a ".la" file),
+# but don't create it if we're doing a dry run.
+func_write_libtool_object ()
+{
+ write_libobj=${1}
+ if test "$build_libtool_libs" = yes; then
+ write_lobj=\'${2}\'
+ else
+ write_lobj=none
+ fi
+
+ if test "$build_old_libs" = yes; then
+ write_oldobj=\'${3}\'
+ else
+ write_oldobj=none
+ fi
+
+ $opt_dry_run || {
+ cat >${write_libobj}T <<EOF
+# $write_libobj - a libtool object file
+# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object=$write_lobj
+
+# Name of the non-PIC object
+non_pic_object=$write_oldobj
+
+EOF
+ $MV "${write_libobj}T" "${write_libobj}"
+ }
+}
+
+# func_mode_compile arg...
+func_mode_compile ()
+{
+ $opt_debug
+ # Get the compilation command and the source file.
+ base_compile=
+ srcfile="$nonopt" # always keep a non-empty value in "srcfile"
+ suppress_opt=yes
+ suppress_output=
+ arg_mode=normal
+ libobj=
+ later=
+ pie_flag=
+
+ for arg
+ do
+ case $arg_mode in
+ arg )
+ # do not "continue". Instead, add this to base_compile
+ lastarg="$arg"
+ arg_mode=normal
+ ;;
+
+ target )
+ libobj="$arg"
+ arg_mode=normal
+ continue
+ ;;
+
+ normal )
+ # Accept any command-line options.
+ case $arg in
+ -o)
+ test -n "$libobj" && \
+ func_fatal_error "you cannot specify \`-o' more than once"
+ arg_mode=target
+ continue
+ ;;
+
+ -pie | -fpie | -fPIE)
+ pie_flag="$pie_flag $arg"
+ continue
+ ;;
+
+ -shared | -static | -prefer-pic | -prefer-non-pic)
+ later="$later $arg"
+ continue
+ ;;
+
+ -no-suppress)
+ suppress_opt=no
+ continue
+ ;;
+
+ -Xcompiler)
+ arg_mode=arg # the next one goes into the "base_compile" arg list
+ continue # The current "srcfile" will either be retained or
+ ;; # replaced later. I would guess that would be a bug.
+
+ -Wc,*)
+ func_stripname '-Wc,' '' "$arg"
+ args=$func_stripname_result
+ lastarg=
+ save_ifs="$IFS"; IFS=','
+ for arg in $args; do
+ IFS="$save_ifs"
+ func_quote_for_eval "$arg"
+ lastarg="$lastarg $func_quote_for_eval_result"
+ done
+ IFS="$save_ifs"
+ func_stripname ' ' '' "$lastarg"
+ lastarg=$func_stripname_result
+
+ # Add the arguments to base_compile.
+ base_compile="$base_compile $lastarg"
+ continue
+ ;;
+
+ *)
+ # Accept the current argument as the source file.
+ # The previous "srcfile" becomes the current argument.
+ #
+ lastarg="$srcfile"
+ srcfile="$arg"
+ ;;
+ esac # case $arg
+ ;;
+ esac # case $arg_mode
+
+ # Aesthetically quote the previous argument.
+ func_quote_for_eval "$lastarg"
+ base_compile="$base_compile $func_quote_for_eval_result"
+ done # for arg
+
+ case $arg_mode in
+ arg)
+ func_fatal_error "you must specify an argument for -Xcompile"
+ ;;
+ target)
+ func_fatal_error "you must specify a target with \`-o'"
+ ;;
+ *)
+ # Get the name of the library object.
+ test -z "$libobj" && {
+ func_basename "$srcfile"
+ libobj="$func_basename_result"
+ }
+ ;;
+ esac
+
+ # Recognize several different file suffixes.
+ # If the user specifies -o file.o, it is replaced with file.lo
+ case $libobj in
+ *.[cCFSifmso] | \
+ *.ada | *.adb | *.ads | *.asm | \
+ *.c++ | *.cc | *.ii | *.class | *.cpp | *.cxx | \
+ *.[fF][09]? | *.for | *.java | *.obj | *.sx)
+ func_xform "$libobj"
+ libobj=$func_xform_result
+ ;;
+ esac
+
+ case $libobj in
+ *.lo) func_lo2o "$libobj"; obj=$func_lo2o_result ;;
+ *)
+ func_fatal_error "cannot determine name of library object from \`$libobj'"
+ ;;
+ esac
+
+ func_infer_tag $base_compile
+
+ for arg in $later; do
+ case $arg in
+ -shared)
+ test "$build_libtool_libs" != yes && \
+ func_fatal_configuration "can not build a shared library"
+ build_old_libs=no
+ continue
+ ;;
+
+ -static)
+ build_libtool_libs=no
+ build_old_libs=yes
+ continue
+ ;;
+
+ -prefer-pic)
+ pic_mode=yes
+ continue
+ ;;
+
+ -prefer-non-pic)
+ pic_mode=no
+ continue
+ ;;
+ esac
+ done
+
+ func_quote_for_eval "$libobj"
+ test "X$libobj" != "X$func_quote_for_eval_result" \
+ && $ECHO "X$libobj" | $GREP '[]~#^*{};<>?"'"'"' &()|`$[]' \
+ && func_warning "libobj name \`$libobj' may not contain shell special characters."
+ func_dirname_and_basename "$obj" "/" ""
+ objname="$func_basename_result"
+ xdir="$func_dirname_result"
+ lobj=${xdir}$objdir/$objname
+
+ test -z "$base_compile" && \
+ func_fatal_help "you must specify a compilation command"
+
+ # Delete any leftover library objects.
+ if test "$build_old_libs" = yes; then
+ removelist="$obj $lobj $libobj ${libobj}T"
+ else
+ removelist="$lobj $libobj ${libobj}T"
+ fi
+
+ # On Cygwin there's no "real" PIC flag so we must build both object types
+ case $host_os in
+ cygwin* | mingw* | pw32* | os2* | cegcc*)
+ pic_mode=default
+ ;;
+ esac
+ if test "$pic_mode" = no && test "$deplibs_check_method" != pass_all; then
+ # non-PIC code in shared libraries is not supported
+ pic_mode=default
+ fi
+
+ # Calculate the filename of the output object if compiler does
+ # not support -o with -c
+ if test "$compiler_c_o" = no; then
+ output_obj=`$ECHO "X$srcfile" | $Xsed -e 's%^.*/%%' -e 's%\.[^.]*$%%'`.${objext}
+ lockfile="$output_obj.lock"
+ else
+ output_obj=
+ need_locks=no
+ lockfile=
+ fi
+
+ # Lock this critical section if it is needed
+ # We use this script file to make the link, it avoids creating a new file
+ if test "$need_locks" = yes; then
+ until $opt_dry_run || ln "$progpath" "$lockfile" 2>/dev/null; do
+ func_echo "Waiting for $lockfile to be removed"
+ sleep 2
+ done
+ elif test "$need_locks" = warn; then
+ if test -f "$lockfile"; then
+ $ECHO "\
+*** ERROR, $lockfile exists and contains:
+`cat $lockfile 2>/dev/null`
+
+This indicates that another process is trying to use the same
+temporary object file, and libtool could not work around it because
+your compiler does not support \`-c' and \`-o' together. If you
+repeat this compilation, it may succeed, by chance, but you had better
+avoid parallel builds (make -j) in this platform, or get a better
+compiler."
+
+ $opt_dry_run || $RM $removelist
+ exit $EXIT_FAILURE
+ fi
+ removelist="$removelist $output_obj"
+ $ECHO "$srcfile" > "$lockfile"
+ fi
+
+ $opt_dry_run || $RM $removelist
+ removelist="$removelist $lockfile"
+ trap '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' 1 2 15
+
+ if test -n "$fix_srcfile_path"; then
+ eval srcfile=\"$fix_srcfile_path\"
+ fi
+ func_quote_for_eval "$srcfile"
+ qsrcfile=$func_quote_for_eval_result
+
+ # Only build a PIC object if we are building libtool libraries.
+ if test "$build_libtool_libs" = yes; then
+ # Without this assignment, base_compile gets emptied.
+ fbsd_hideous_sh_bug=$base_compile
+
+ if test "$pic_mode" != no; then
+ command="$base_compile $qsrcfile $pic_flag"
+ else
+ # Don't build PIC code
+ command="$base_compile $qsrcfile"
+ fi
+
+ func_mkdir_p "$xdir$objdir"
+
+ if test -z "$output_obj"; then
+ # Place PIC objects in $objdir
+ command="$command -o $lobj"
+ fi
+
+ func_show_eval_locale "$command" \
+ 'test -n "$output_obj" && $RM $removelist; exit $EXIT_FAILURE'
+
+ if test "$need_locks" = warn &&
+ test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then
+ $ECHO "\
+*** ERROR, $lockfile contains:
+`cat $lockfile 2>/dev/null`
+
+but it should contain:
+$srcfile
+
+This indicates that another process is trying to use the same
+temporary object file, and libtool could not work around it because
+your compiler does not support \`-c' and \`-o' together. If you
+repeat this compilation, it may succeed, by chance, but you had better
+avoid parallel builds (make -j) in this platform, or get a better
+compiler."
+
+ $opt_dry_run || $RM $removelist
+ exit $EXIT_FAILURE
+ fi
+
+ # Just move the object if needed, then go on to compile the next one
+ if test -n "$output_obj" && test "X$output_obj" != "X$lobj"; then
+ func_show_eval '$MV "$output_obj" "$lobj"' \
+ 'error=$?; $opt_dry_run || $RM $removelist; exit $error'
+ fi
+
+ # Allow error messages only from the first compilation.
+ if test "$suppress_opt" = yes; then
+ suppress_output=' >/dev/null 2>&1'
+ fi
+ fi
+
+ # Only build a position-dependent object if we build old libraries.
+ if test "$build_old_libs" = yes; then
+ if test "$pic_mode" != yes; then
+ # Don't build PIC code
+ command="$base_compile $qsrcfile$pie_flag"
+ else
+ command="$base_compile $qsrcfile $pic_flag"
+ fi
+ if test "$compiler_c_o" = yes; then
+ command="$command -o $obj"
+ fi
+
+ # Suppress compiler output if we already did a PIC compilation.
+ command="$command$suppress_output"
+ func_show_eval_locale "$command" \
+ '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE'
+
+ if test "$need_locks" = warn &&
+ test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then
+ $ECHO "\
+*** ERROR, $lockfile contains:
+`cat $lockfile 2>/dev/null`
+
+but it should contain:
+$srcfile
+
+This indicates that another process is trying to use the same
+temporary object file, and libtool could not work around it because
+your compiler does not support \`-c' and \`-o' together. If you
+repeat this compilation, it may succeed, by chance, but you had better
+avoid parallel builds (make -j) in this platform, or get a better
+compiler."
+
+ $opt_dry_run || $RM $removelist
+ exit $EXIT_FAILURE
+ fi
+
+ # Just move the object if needed
+ if test -n "$output_obj" && test "X$output_obj" != "X$obj"; then
+ func_show_eval '$MV "$output_obj" "$obj"' \
+ 'error=$?; $opt_dry_run || $RM $removelist; exit $error'
+ fi
+ fi
+
+ $opt_dry_run || {
+ func_write_libtool_object "$libobj" "$objdir/$objname" "$objname"
+
+ # Unlock the critical section if it was locked
+ if test "$need_locks" != no; then
+ removelist=$lockfile
+ $RM "$lockfile"
+ fi
+ }
+
+ exit $EXIT_SUCCESS
+}
+
+$opt_help || {
+test "$mode" = compile && func_mode_compile ${1+"$@"}
+}
+
+func_mode_help ()
+{
+ # We need to display help for each of the modes.
+ case $mode in
+ "")
+ # Generic help is extracted from the usage comments
+ # at the start of this file.
+ func_help
+ ;;
+
+ clean)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=clean RM [RM-OPTION]... FILE...
+
+Remove files from the build directory.
+
+RM is the name of the program to use to delete files associated with each FILE
+(typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed
+to RM.
+
+If FILE is a libtool library, object or program, all the files associated
+with it are deleted. Otherwise, only FILE itself is deleted using RM."
+ ;;
+
+ compile)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=compile COMPILE-COMMAND... SOURCEFILE
+
+Compile a source file into a libtool library object.
+
+This mode accepts the following additional options:
+
+ -o OUTPUT-FILE set the output file name to OUTPUT-FILE
+ -no-suppress do not suppress compiler output for multiple passes
+ -prefer-pic try to building PIC objects only
+ -prefer-non-pic try to building non-PIC objects only
+ -shared do not build a \`.o' file suitable for static linking
+ -static only build a \`.o' file suitable for static linking
+
+COMPILE-COMMAND is a command to be used in creating a \`standard' object file
+from the given SOURCEFILE.
+
+The output file name is determined by removing the directory component from
+SOURCEFILE, then substituting the C source code suffix \`.c' with the
+library object suffix, \`.lo'."
+ ;;
+
+ execute)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=execute COMMAND [ARGS]...
+
+Automatically set library path, then run a program.
+
+This mode accepts the following additional options:
+
+ -dlopen FILE add the directory containing FILE to the library path
+
+This mode sets the library path environment variable according to \`-dlopen'
+flags.
+
+If any of the ARGS are libtool executable wrappers, then they are translated
+into their corresponding uninstalled binary, and any of their required library
+directories are added to the library path.
+
+Then, COMMAND is executed, with ARGS as arguments."
+ ;;
+
+ finish)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=finish [LIBDIR]...
+
+Complete the installation of libtool libraries.
+
+Each LIBDIR is a directory that contains libtool libraries.
+
+The commands that this mode executes may require superuser privileges. Use
+the \`--dry-run' option if you just want to see what would be executed."
+ ;;
+
+ install)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=install INSTALL-COMMAND...
+
+Install executables or libraries.
+
+INSTALL-COMMAND is the installation command. The first component should be
+either the \`install' or \`cp' program.
+
+The following components of INSTALL-COMMAND are treated specially:
+
+ -inst-prefix PREFIX-DIR Use PREFIX-DIR as a staging area for installation
+
+The rest of the components are interpreted as arguments to that command (only
+BSD-compatible install options are recognized)."
+ ;;
+
+ link)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=link LINK-COMMAND...
+
+Link object files or libraries together to form another library, or to
+create an executable program.
+
+LINK-COMMAND is a command using the C compiler that you would use to create
+a program from several object files.
+
+The following components of LINK-COMMAND are treated specially:
+
+ -all-static do not do any dynamic linking at all
+ -avoid-version do not add a version suffix if possible
+ -dlopen FILE \`-dlpreopen' FILE if it cannot be dlopened at runtime
+ -dlpreopen FILE link in FILE and add its symbols to lt_preloaded_symbols
+ -export-dynamic allow symbols from OUTPUT-FILE to be resolved with dlsym(3)
+ -export-symbols SYMFILE
+ try to export only the symbols listed in SYMFILE
+ -export-symbols-regex REGEX
+ try to export only the symbols matching REGEX
+ -LLIBDIR search LIBDIR for required installed libraries
+ -lNAME OUTPUT-FILE requires the installed library libNAME
+ -module build a library that can dlopened
+ -no-fast-install disable the fast-install mode
+ -no-install link a not-installable executable
+ -no-undefined declare that a library does not refer to external symbols
+ -o OUTPUT-FILE create OUTPUT-FILE from the specified objects
+ -objectlist FILE Use a list of object files found in FILE to specify objects
+ -precious-files-regex REGEX
+ don't remove output files matching REGEX
+ -release RELEASE specify package release information
+ -rpath LIBDIR the created library will eventually be installed in LIBDIR
+ -R[ ]LIBDIR add LIBDIR to the runtime path of programs and libraries
+ -shared only do dynamic linking of libtool libraries
+ -shrext SUFFIX override the standard shared library file extension
+ -static do not do any dynamic linking of uninstalled libtool libraries
+ -static-libtool-libs
+ do not do any dynamic linking of libtool libraries
+ -version-info CURRENT[:REVISION[:AGE]]
+ specify library version info [each variable defaults to 0]
+ -weak LIBNAME declare that the target provides the LIBNAME interface
+
+All other options (arguments beginning with \`-') are ignored.
+
+Every other argument is treated as a filename. Files ending in \`.la' are
+treated as uninstalled libtool libraries, other files are standard or library
+object files.
+
+If the OUTPUT-FILE ends in \`.la', then a libtool library is created,
+only library objects (\`.lo' files) may be specified, and \`-rpath' is
+required, except when creating a convenience library.
+
+If OUTPUT-FILE ends in \`.a' or \`.lib', then a standard library is created
+using \`ar' and \`ranlib', or on Windows using \`lib'.
+
+If OUTPUT-FILE ends in \`.lo' or \`.${objext}', then a reloadable object file
+is created, otherwise an executable program is created."
+ ;;
+
+ uninstall)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=uninstall RM [RM-OPTION]... FILE...
+
+Remove libraries from an installation directory.
+
+RM is the name of the program to use to delete files associated with each FILE
+(typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed
+to RM.
+
+If FILE is a libtool library, all the files associated with it are deleted.
+Otherwise, only FILE itself is deleted using RM."
+ ;;
+
+ *)
+ func_fatal_help "invalid operation mode \`$mode'"
+ ;;
+ esac
+
+ $ECHO
+ $ECHO "Try \`$progname --help' for more information about other modes."
+
+ exit $?
+}
+
+ # Now that we've collected a possible --mode arg, show help if necessary
+ $opt_help && func_mode_help
+
+
+# func_mode_execute arg...
+func_mode_execute ()
+{
+ $opt_debug
+ # The first argument is the command name.
+ cmd="$nonopt"
+ test -z "$cmd" && \
+ func_fatal_help "you must specify a COMMAND"
+
+ # Handle -dlopen flags immediately.
+ for file in $execute_dlfiles; do
+ test -f "$file" \
+ || func_fatal_help "\`$file' is not a file"
+
+ dir=
+ case $file in
+ *.la)
+ # Check to see that this really is a libtool archive.
+ func_lalib_unsafe_p "$file" \
+ || func_fatal_help "\`$lib' is not a valid libtool archive"
+
+ # Read the libtool library.
+ dlname=
+ library_names=
+ func_source "$file"
+
+ # Skip this library if it cannot be dlopened.
+ if test -z "$dlname"; then
+ # Warn if it was a shared library.
+ test -n "$library_names" && \
+ func_warning "\`$file' was not linked with \`-export-dynamic'"
+ continue
+ fi
+
+ func_dirname "$file" "" "."
+ dir="$func_dirname_result"
+
+ if test -f "$dir/$objdir/$dlname"; then
+ dir="$dir/$objdir"
+ else
+ if test ! -f "$dir/$dlname"; then
+ func_fatal_error "cannot find \`$dlname' in \`$dir' or \`$dir/$objdir'"
+ fi
+ fi
+ ;;
+
+ *.lo)
+ # Just add the directory containing the .lo file.
+ func_dirname "$file" "" "."
+ dir="$func_dirname_result"
+ ;;
+
+ *)
+ func_warning "\`-dlopen' is ignored for non-libtool libraries and objects"
+ continue
+ ;;
+ esac
+
+ # Get the absolute pathname.
+ absdir=`cd "$dir" && pwd`
+ test -n "$absdir" && dir="$absdir"
+
+ # Now add the directory to shlibpath_var.
+ if eval "test -z \"\$$shlibpath_var\""; then
+ eval "$shlibpath_var=\"\$dir\""
+ else
+ eval "$shlibpath_var=\"\$dir:\$$shlibpath_var\""
+ fi
+ done
+
+ # This variable tells wrapper scripts just to set shlibpath_var
+ # rather than running their programs.
+ libtool_execute_magic="$magic"
+
+ # Check if any of the arguments is a wrapper script.
+ args=
+ for file
+ do
+ case $file in
+ -*) ;;
+ *)
+ # Do a test to see if this is really a libtool program.
+ if func_ltwrapper_script_p "$file"; then
+ func_source "$file"
+ # Transform arg to wrapped name.
+ file="$progdir/$program"
+ elif func_ltwrapper_executable_p "$file"; then
+ func_ltwrapper_scriptname "$file"
+ func_source "$func_ltwrapper_scriptname_result"
+ # Transform arg to wrapped name.
+ file="$progdir/$program"
+ fi
+ ;;
+ esac
+ # Quote arguments (to preserve shell metacharacters).
+ func_quote_for_eval "$file"
+ args="$args $func_quote_for_eval_result"
+ done
+
+ if test "X$opt_dry_run" = Xfalse; then
+ if test -n "$shlibpath_var"; then
+ # Export the shlibpath_var.
+ eval "export $shlibpath_var"
+ fi
+
+ # Restore saved environment variables
+ for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES
+ do
+ eval "if test \"\${save_$lt_var+set}\" = set; then
+ $lt_var=\$save_$lt_var; export $lt_var
+ else
+ $lt_unset $lt_var
+ fi"
+ done
+
+ # Now prepare to actually exec the command.
+ exec_cmd="\$cmd$args"
+ else
+ # Display what would be done.
+ if test -n "$shlibpath_var"; then
+ eval "\$ECHO \"\$shlibpath_var=\$$shlibpath_var\""
+ $ECHO "export $shlibpath_var"
+ fi
+ $ECHO "$cmd$args"
+ exit $EXIT_SUCCESS
+ fi
+}
+
+test "$mode" = execute && func_mode_execute ${1+"$@"}
+
+
+# func_mode_finish arg...
+func_mode_finish ()
+{
+ $opt_debug
+ libdirs="$nonopt"
+ admincmds=
+
+ if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then
+ for dir
+ do
+ libdirs="$libdirs $dir"
+ done
+
+ for libdir in $libdirs; do
+ if test -n "$finish_cmds"; then
+ # Do each command in the finish commands.
+ func_execute_cmds "$finish_cmds" 'admincmds="$admincmds
+'"$cmd"'"'
+ fi
+ if test -n "$finish_eval"; then
+ # Do the single finish_eval.
+ eval cmds=\"$finish_eval\"
+ $opt_dry_run || eval "$cmds" || admincmds="$admincmds
+ $cmds"
+ fi
+ done
+ fi
+
+ # Exit here if they wanted silent mode.
+ $opt_silent && exit $EXIT_SUCCESS
+
+ $ECHO "X----------------------------------------------------------------------" | $Xsed
+ $ECHO "Libraries have been installed in:"
+ for libdir in $libdirs; do
+ $ECHO " $libdir"
+ done
+ $ECHO
+ $ECHO "If you ever happen to want to link against installed libraries"
+ $ECHO "in a given directory, LIBDIR, you must either use libtool, and"
+ $ECHO "specify the full pathname of the library, or use the \`-LLIBDIR'"
+ $ECHO "flag during linking and do at least one of the following:"
+ if test -n "$shlibpath_var"; then
+ $ECHO " - add LIBDIR to the \`$shlibpath_var' environment variable"
+ $ECHO " during execution"
+ fi
+ if test -n "$runpath_var"; then
+ $ECHO " - add LIBDIR to the \`$runpath_var' environment variable"
+ $ECHO " during linking"
+ fi
+ if test -n "$hardcode_libdir_flag_spec"; then
+ libdir=LIBDIR
+ eval flag=\"$hardcode_libdir_flag_spec\"
+
+ $ECHO " - use the \`$flag' linker flag"
+ fi
+ if test -n "$admincmds"; then
+ $ECHO " - have your system administrator run these commands:$admincmds"
+ fi
+ if test -f /etc/ld.so.conf; then
+ $ECHO " - have your system administrator add LIBDIR to \`/etc/ld.so.conf'"
+ fi
+ $ECHO
+
+ $ECHO "See any operating system documentation about shared libraries for"
+ case $host in
+ solaris2.[6789]|solaris2.1[0-9])
+ $ECHO "more information, such as the ld(1), crle(1) and ld.so(8) manual"
+ $ECHO "pages."
+ ;;
+ *)
+ $ECHO "more information, such as the ld(1) and ld.so(8) manual pages."
+ ;;
+ esac
+ $ECHO "X----------------------------------------------------------------------" | $Xsed
+ exit $EXIT_SUCCESS
+}
+
+test "$mode" = finish && func_mode_finish ${1+"$@"}
+
+
+# func_mode_install arg...
+func_mode_install ()
+{
+ $opt_debug
+ # There may be an optional sh(1) argument at the beginning of
+ # install_prog (especially on Windows NT).
+ if test "$nonopt" = "$SHELL" || test "$nonopt" = /bin/sh ||
+ # Allow the use of GNU shtool's install command.
+ $ECHO "X$nonopt" | $GREP shtool >/dev/null; then
+ # Aesthetically quote it.
+ func_quote_for_eval "$nonopt"
+ install_prog="$func_quote_for_eval_result "
+ arg=$1
+ shift
+ else
+ install_prog=
+ arg=$nonopt
+ fi
+
+ # The real first argument should be the name of the installation program.
+ # Aesthetically quote it.
+ func_quote_for_eval "$arg"
+ install_prog="$install_prog$func_quote_for_eval_result"
+
+ # We need to accept at least all the BSD install flags.
+ dest=
+ files=
+ opts=
+ prev=
+ install_type=
+ isdir=no
+ stripme=
+ for arg
+ do
+ if test -n "$dest"; then
+ files="$files $dest"
+ dest=$arg
+ continue
+ fi
+
+ case $arg in
+ -d) isdir=yes ;;
+ -f)
+ case " $install_prog " in
+ *[\\\ /]cp\ *) ;;
+ *) prev=$arg ;;
+ esac
+ ;;
+ -g | -m | -o)
+ prev=$arg
+ ;;
+ -s)
+ stripme=" -s"
+ continue
+ ;;
+ -*)
+ ;;
+ *)
+ # If the previous option needed an argument, then skip it.
+ if test -n "$prev"; then
+ prev=
+ else
+ dest=$arg
+ continue
+ fi
+ ;;
+ esac
+
+ # Aesthetically quote the argument.
+ func_quote_for_eval "$arg"
+ install_prog="$install_prog $func_quote_for_eval_result"
+ done
+
+ test -z "$install_prog" && \
+ func_fatal_help "you must specify an install program"
+
+ test -n "$prev" && \
+ func_fatal_help "the \`$prev' option requires an argument"
+
+ if test -z "$files"; then
+ if test -z "$dest"; then
+ func_fatal_help "no file or destination specified"
+ else
+ func_fatal_help "you must specify a destination"
+ fi
+ fi
+
+ # Strip any trailing slash from the destination.
+ func_stripname '' '/' "$dest"
+ dest=$func_stripname_result
+
+ # Check to see that the destination is a directory.
+ test -d "$dest" && isdir=yes
+ if test "$isdir" = yes; then
+ destdir="$dest"
+ destname=
+ else
+ func_dirname_and_basename "$dest" "" "."
+ destdir="$func_dirname_result"
+ destname="$func_basename_result"
+
+ # Not a directory, so check to see that there is only one file specified.
+ set dummy $files; shift
+ test "$#" -gt 1 && \
+ func_fatal_help "\`$dest' is not a directory"
+ fi
+ case $destdir in
+ [\\/]* | [A-Za-z]:[\\/]*) ;;
+ *)
+ for file in $files; do
+ case $file in
+ *.lo) ;;
+ *)
+ func_fatal_help "\`$destdir' must be an absolute directory name"
+ ;;
+ esac
+ done
+ ;;
+ esac
+
+ # This variable tells wrapper scripts just to set variables rather
+ # than running their programs.
+ libtool_install_magic="$magic"
+
+ staticlibs=
+ future_libdirs=
+ current_libdirs=
+ for file in $files; do
+
+ # Do each installation.
+ case $file in
+ *.$libext)
+ # Do the static libraries later.
+ staticlibs="$staticlibs $file"
+ ;;
+
+ *.la)
+ # Check to see that this really is a libtool archive.
+ func_lalib_unsafe_p "$file" \
+ || func_fatal_help "\`$file' is not a valid libtool archive"
+
+ library_names=
+ old_library=
+ relink_command=
+ func_source "$file"
+
+ # Add the libdir to current_libdirs if it is the destination.
+ if test "X$destdir" = "X$libdir"; then
+ case "$current_libdirs " in
+ *" $libdir "*) ;;
+ *) current_libdirs="$current_libdirs $libdir" ;;
+ esac
+ else
+ # Note the libdir as a future libdir.
+ case "$future_libdirs " in
+ *" $libdir "*) ;;
+ *) future_libdirs="$future_libdirs $libdir" ;;
+ esac
+ fi
+
+ func_dirname "$file" "/" ""
+ dir="$func_dirname_result"
+ dir="$dir$objdir"
+
+ if test -n "$relink_command"; then
+ # Determine the prefix the user has applied to our future dir.
+ inst_prefix_dir=`$ECHO "X$destdir" | $Xsed -e "s%$libdir\$%%"`
+
+ # Don't allow the user to place us outside of our expected
+ # location b/c this prevents finding dependent libraries that
+ # are installed to the same prefix.
+ # At present, this check doesn't affect windows .dll's that
+ # are installed into $libdir/../bin (currently, that works fine)
+ # but it's something to keep an eye on.
+ test "$inst_prefix_dir" = "$destdir" && \
+ func_fatal_error "error: cannot install \`$file' to a directory not ending in $libdir"
+
+ if test -n "$inst_prefix_dir"; then
+ # Stick the inst_prefix_dir data into the link command.
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%"`
+ else
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%%"`
+ fi
+
+ func_warning "relinking \`$file'"
+ func_show_eval "$relink_command" \
+ 'func_fatal_error "error: relink \`$file'\'' with the above command before installing it"'
+ fi
+
+ # See the names of the shared library.
+ set dummy $library_names; shift
+ if test -n "$1"; then
+ realname="$1"
+ shift
+
+ srcname="$realname"
+ test -n "$relink_command" && srcname="$realname"T
+
+ # Install the shared library and build the symlinks.
+ func_show_eval "$install_prog $dir/$srcname $destdir/$realname" \
+ 'exit $?'
+ tstripme="$stripme"
+ case $host_os in
+ cygwin* | mingw* | pw32* | cegcc*)
+ case $realname in
+ *.dll.a)
+ tstripme=""
+ ;;
+ esac
+ ;;
+ esac
+ if test -n "$tstripme" && test -n "$striplib"; then
+ func_show_eval "$striplib $destdir/$realname" 'exit $?'
+ fi
+
+ if test "$#" -gt 0; then
+ # Delete the old symlinks, and create new ones.
+ # Try `ln -sf' first, because the `ln' binary might depend on
+ # the symlink we replace! Solaris /bin/ln does not understand -f,
+ # so we also need to try rm && ln -s.
+ for linkname
+ do
+ test "$linkname" != "$realname" \
+ && func_show_eval "(cd $destdir && { $LN_S -f $realname $linkname || { $RM $linkname && $LN_S $realname $linkname; }; })"
+ done
+ fi
+
+ # Do each command in the postinstall commands.
+ lib="$destdir/$realname"
+ func_execute_cmds "$postinstall_cmds" 'exit $?'
+ fi
+
+ # Install the pseudo-library for information purposes.
+ func_basename "$file"
+ name="$func_basename_result"
+ instname="$dir/$name"i
+ func_show_eval "$install_prog $instname $destdir/$name" 'exit $?'
+
+ # Maybe install the static library, too.
+ test -n "$old_library" && staticlibs="$staticlibs $dir/$old_library"
+ ;;
+
+ *.lo)
+ # Install (i.e. copy) a libtool object.
+
+ # Figure out destination file name, if it wasn't already specified.
+ if test -n "$destname"; then
+ destfile="$destdir/$destname"
+ else
+ func_basename "$file"
+ destfile="$func_basename_result"
+ destfile="$destdir/$destfile"
+ fi
+
+ # Deduce the name of the destination old-style object file.
+ case $destfile in
+ *.lo)
+ func_lo2o "$destfile"
+ staticdest=$func_lo2o_result
+ ;;
+ *.$objext)
+ staticdest="$destfile"
+ destfile=
+ ;;
+ *)
+ func_fatal_help "cannot copy a libtool object to \`$destfile'"
+ ;;
+ esac
+
+ # Install the libtool object if requested.
+ test -n "$destfile" && \
+ func_show_eval "$install_prog $file $destfile" 'exit $?'
+
+ # Install the old object if enabled.
+ if test "$build_old_libs" = yes; then
+ # Deduce the name of the old-style object file.
+ func_lo2o "$file"
+ staticobj=$func_lo2o_result
+ func_show_eval "$install_prog \$staticobj \$staticdest" 'exit $?'
+ fi
+ exit $EXIT_SUCCESS
+ ;;
+
+ *)
+ # Figure out destination file name, if it wasn't already specified.
+ if test -n "$destname"; then
+ destfile="$destdir/$destname"
+ else
+ func_basename "$file"
+ destfile="$func_basename_result"
+ destfile="$destdir/$destfile"
+ fi
+
+ # If the file is missing, and there is a .exe on the end, strip it
+ # because it is most likely a libtool script we actually want to
+ # install
+ stripped_ext=""
+ case $file in
+ *.exe)
+ if test ! -f "$file"; then
+ func_stripname '' '.exe' "$file"
+ file=$func_stripname_result
+ stripped_ext=".exe"
+ fi
+ ;;
+ esac
+
+ # Do a test to see if this is really a libtool program.
+ case $host in
+ *cygwin* | *mingw*)
+ if func_ltwrapper_executable_p "$file"; then
+ func_ltwrapper_scriptname "$file"
+ wrapper=$func_ltwrapper_scriptname_result
+ else
+ func_stripname '' '.exe' "$file"
+ wrapper=$func_stripname_result
+ fi
+ ;;
+ *)
+ wrapper=$file
+ ;;
+ esac
+ if func_ltwrapper_script_p "$wrapper"; then
+ notinst_deplibs=
+ relink_command=
+
+ func_source "$wrapper"
+
+ # Check the variables that should have been set.
+ test -z "$generated_by_libtool_version" && \
+ func_fatal_error "invalid libtool wrapper script \`$wrapper'"
+
+ finalize=yes
+ for lib in $notinst_deplibs; do
+ # Check to see that each library is installed.
+ libdir=
+ if test -f "$lib"; then
+ func_source "$lib"
+ fi
+ libfile="$libdir/"`$ECHO "X$lib" | $Xsed -e 's%^.*/%%g'` ### testsuite: skip nested quoting test
+ if test -n "$libdir" && test ! -f "$libfile"; then
+ func_warning "\`$lib' has not been installed in \`$libdir'"
+ finalize=no
+ fi
+ done
+
+ relink_command=
+ func_source "$wrapper"
+
+ outputname=
+ if test "$fast_install" = no && test -n "$relink_command"; then
+ $opt_dry_run || {
+ if test "$finalize" = yes; then
+ tmpdir=`func_mktempdir`
+ func_basename "$file$stripped_ext"
+ file="$func_basename_result"
+ outputname="$tmpdir/$file"
+ # Replace the output file specification.
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e 's%@OUTPUT@%'"$outputname"'%g'`
+
+ $opt_silent || {
+ func_quote_for_expand "$relink_command"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+ if eval "$relink_command"; then :
+ else
+ func_error "error: relink \`$file' with the above command before installing it"
+ $opt_dry_run || ${RM}r "$tmpdir"
+ continue
+ fi
+ file="$outputname"
+ else
+ func_warning "cannot relink \`$file'"
+ fi
+ }
+ else
+ # Install the binary that we compiled earlier.
+ file=`$ECHO "X$file$stripped_ext" | $Xsed -e "s%\([^/]*\)$%$objdir/\1%"`
+ fi
+ fi
+
+ # remove .exe since cygwin /usr/bin/install will append another
+ # one anyway
+ case $install_prog,$host in
+ */usr/bin/install*,*cygwin*)
+ case $file:$destfile in
+ *.exe:*.exe)
+ # this is ok
+ ;;
+ *.exe:*)
+ destfile=$destfile.exe
+ ;;
+ *:*.exe)
+ func_stripname '' '.exe' "$destfile"
+ destfile=$func_stripname_result
+ ;;
+ esac
+ ;;
+ esac
+ func_show_eval "$install_prog\$stripme \$file \$destfile" 'exit $?'
+ $opt_dry_run || if test -n "$outputname"; then
+ ${RM}r "$tmpdir"
+ fi
+ ;;
+ esac
+ done
+
+ for file in $staticlibs; do
+ func_basename "$file"
+ name="$func_basename_result"
+
+ # Set up the ranlib parameters.
+ oldlib="$destdir/$name"
+
+ func_show_eval "$install_prog \$file \$oldlib" 'exit $?'
+
+ if test -n "$stripme" && test -n "$old_striplib"; then
+ func_show_eval "$old_striplib $oldlib" 'exit $?'
+ fi
+
+ # Do each command in the postinstall commands.
+ func_execute_cmds "$old_postinstall_cmds" 'exit $?'
+ done
+
+ test -n "$future_libdirs" && \
+ func_warning "remember to run \`$progname --finish$future_libdirs'"
+
+ if test -n "$current_libdirs"; then
+ # Maybe just do a dry run.
+ $opt_dry_run && current_libdirs=" -n$current_libdirs"
+ exec_cmd='$SHELL $progpath $preserve_args --finish$current_libdirs'
+ else
+ exit $EXIT_SUCCESS
+ fi
+}
+
+test "$mode" = install && func_mode_install ${1+"$@"}
+
+
+# func_generate_dlsyms outputname originator pic_p
+# Extract symbols from dlprefiles and create ${outputname}S.o with
+# a dlpreopen symbol table.
+func_generate_dlsyms ()
+{
+ $opt_debug
+ my_outputname="$1"
+ my_originator="$2"
+ my_pic_p="${3-no}"
+ my_prefix=`$ECHO "$my_originator" | sed 's%[^a-zA-Z0-9]%_%g'`
+ my_dlsyms=
+
+ if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
+ if test -n "$NM" && test -n "$global_symbol_pipe"; then
+ my_dlsyms="${my_outputname}S.c"
+ else
+ func_error "not configured to extract global symbols from dlpreopened files"
+ fi
+ fi
+
+ if test -n "$my_dlsyms"; then
+ case $my_dlsyms in
+ "") ;;
+ *.c)
+ # Discover the nlist of each of the dlfiles.
+ nlist="$output_objdir/${my_outputname}.nm"
+
+ func_show_eval "$RM $nlist ${nlist}S ${nlist}T"
+
+ # Parse the name list into a source file.
+ func_verbose "creating $output_objdir/$my_dlsyms"
+
+ $opt_dry_run || $ECHO > "$output_objdir/$my_dlsyms" "\
+/* $my_dlsyms - symbol resolution table for \`$my_outputname' dlsym emulation. */
+/* Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION */
+
+#ifdef __cplusplus
+extern \"C\" {
+#endif
+
+/* External symbol declarations for the compiler. */\
+"
+
+ if test "$dlself" = yes; then
+ func_verbose "generating symbol list for \`$output'"
+
+ $opt_dry_run || echo ': @PROGRAM@ ' > "$nlist"
+
+ # Add our own program objects to the symbol list.
+ progfiles=`$ECHO "X$objs$old_deplibs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+ for progfile in $progfiles; do
+ func_verbose "extracting global C symbols from \`$progfile'"
+ $opt_dry_run || eval "$NM $progfile | $global_symbol_pipe >> '$nlist'"
+ done
+
+ if test -n "$exclude_expsyms"; then
+ $opt_dry_run || {
+ eval '$EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T'
+ eval '$MV "$nlist"T "$nlist"'
+ }
+ fi
+
+ if test -n "$export_symbols_regex"; then
+ $opt_dry_run || {
+ eval '$EGREP -e "$export_symbols_regex" "$nlist" > "$nlist"T'
+ eval '$MV "$nlist"T "$nlist"'
+ }
+ fi
+
+ # Prepare the list of exported symbols
+ if test -z "$export_symbols"; then
+ export_symbols="$output_objdir/$outputname.exp"
+ $opt_dry_run || {
+ $RM $export_symbols
+ eval "${SED} -n -e '/^: @PROGRAM@ $/d' -e 's/^.* \(.*\)$/\1/p' "'< "$nlist" > "$export_symbols"'
+ case $host in
+ *cygwin* | *mingw* | *cegcc* )
+ eval "echo EXPORTS "'> "$output_objdir/$outputname.def"'
+ eval 'cat "$export_symbols" >> "$output_objdir/$outputname.def"'
+ ;;
+ esac
+ }
+ else
+ $opt_dry_run || {
+ eval "${SED} -e 's/\([].[*^$]\)/\\\\\1/g' -e 's/^/ /' -e 's/$/$/'"' < "$export_symbols" > "$output_objdir/$outputname.exp"'
+ eval '$GREP -f "$output_objdir/$outputname.exp" < "$nlist" > "$nlist"T'
+ eval '$MV "$nlist"T "$nlist"'
+ case $host in
+ *cygwin | *mingw* | *cegcc* )
+ eval "echo EXPORTS "'> "$output_objdir/$outputname.def"'
+ eval 'cat "$nlist" >> "$output_objdir/$outputname.def"'
+ ;;
+ esac
+ }
+ fi
+ fi
+
+ for dlprefile in $dlprefiles; do
+ func_verbose "extracting global C symbols from \`$dlprefile'"
+ func_basename "$dlprefile"
+ name="$func_basename_result"
+ $opt_dry_run || {
+ eval '$ECHO ": $name " >> "$nlist"'
+ eval "$NM $dlprefile 2>/dev/null | $global_symbol_pipe >> '$nlist'"
+ }
+ done
+
+ $opt_dry_run || {
+ # Make sure we have at least an empty file.
+ test -f "$nlist" || : > "$nlist"
+
+ if test -n "$exclude_expsyms"; then
+ $EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T
+ $MV "$nlist"T "$nlist"
+ fi
+
+ # Try sorting and uniquifying the output.
+ if $GREP -v "^: " < "$nlist" |
+ if sort -k 3 </dev/null >/dev/null 2>&1; then
+ sort -k 3
+ else
+ sort +2
+ fi |
+ uniq > "$nlist"S; then
+ :
+ else
+ $GREP -v "^: " < "$nlist" > "$nlist"S
+ fi
+
+ if test -f "$nlist"S; then
+ eval "$global_symbol_to_cdecl"' < "$nlist"S >> "$output_objdir/$my_dlsyms"'
+ else
+ $ECHO '/* NONE */' >> "$output_objdir/$my_dlsyms"
+ fi
+
+ $ECHO >> "$output_objdir/$my_dlsyms" "\
+
+/* The mapping between symbol names and symbols. */
+typedef struct {
+ const char *name;
+ void *address;
+} lt_dlsymlist;
+"
+ case $host in
+ *cygwin* | *mingw* | *cegcc* )
+ $ECHO >> "$output_objdir/$my_dlsyms" "\
+/* DATA imports from DLLs on WIN32 con't be const, because
+ runtime relocations are performed -- see ld's documentation
+ on pseudo-relocs. */"
+ lt_dlsym_const= ;;
+ *osf5*)
+ echo >> "$output_objdir/$my_dlsyms" "\
+/* This system does not cope well with relocations in const data */"
+ lt_dlsym_const= ;;
+ *)
+ lt_dlsym_const=const ;;
+ esac
+
+ $ECHO >> "$output_objdir/$my_dlsyms" "\
+extern $lt_dlsym_const lt_dlsymlist
+lt_${my_prefix}_LTX_preloaded_symbols[];
+$lt_dlsym_const lt_dlsymlist
+lt_${my_prefix}_LTX_preloaded_symbols[] =
+{\
+ { \"$my_originator\", (void *) 0 },"
+
+ case $need_lib_prefix in
+ no)
+ eval "$global_symbol_to_c_name_address" < "$nlist" >> "$output_objdir/$my_dlsyms"
+ ;;
+ *)
+ eval "$global_symbol_to_c_name_address_lib_prefix" < "$nlist" >> "$output_objdir/$my_dlsyms"
+ ;;
+ esac
+ $ECHO >> "$output_objdir/$my_dlsyms" "\
+ {0, (void *) 0}
+};
+
+/* This works around a problem in FreeBSD linker */
+#ifdef FREEBSD_WORKAROUND
+static const void *lt_preloaded_setup() {
+ return lt_${my_prefix}_LTX_preloaded_symbols;
+}
+#endif
+
+#ifdef __cplusplus
+}
+#endif\
+"
+ } # !$opt_dry_run
+
+ pic_flag_for_symtable=
+ case "$compile_command " in
+ *" -static "*) ;;
+ *)
+ case $host in
+ # compiling the symbol table file with pic_flag works around
+ # a FreeBSD bug that causes programs to crash when -lm is
+ # linked before any other PIC object. But we must not use
+ # pic_flag when linking with -static. The problem exists in
+ # FreeBSD 2.2.6 and is fixed in FreeBSD 3.1.
+ *-*-freebsd2*|*-*-freebsd3.0*|*-*-freebsdelf3.0*)
+ pic_flag_for_symtable=" $pic_flag -DFREEBSD_WORKAROUND" ;;
+ *-*-hpux*)
+ pic_flag_for_symtable=" $pic_flag" ;;
+ *)
+ if test "X$my_pic_p" != Xno; then
+ pic_flag_for_symtable=" $pic_flag"
+ fi
+ ;;
+ esac
+ ;;
+ esac
+ symtab_cflags=
+ for arg in $LTCFLAGS; do
+ case $arg in
+ -pie | -fpie | -fPIE) ;;
+ *) symtab_cflags="$symtab_cflags $arg" ;;
+ esac
+ done
+
+ # Now compile the dynamic symbol file.
+ func_show_eval '(cd $output_objdir && $LTCC$symtab_cflags -c$no_builtin_flag$pic_flag_for_symtable "$my_dlsyms")' 'exit $?'
+
+ # Clean up the generated files.
+ func_show_eval '$RM "$output_objdir/$my_dlsyms" "$nlist" "${nlist}S" "${nlist}T"'
+
+ # Transform the symbol file into the correct name.
+ symfileobj="$output_objdir/${my_outputname}S.$objext"
+ case $host in
+ *cygwin* | *mingw* | *cegcc* )
+ if test -f "$output_objdir/$my_outputname.def"; then
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"`
+ finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"`
+ else
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"`
+ finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"`
+ fi
+ ;;
+ *)
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"`
+ finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"`
+ ;;
+ esac
+ ;;
+ *)
+ func_fatal_error "unknown suffix for \`$my_dlsyms'"
+ ;;
+ esac
+ else
+ # We keep going just in case the user didn't refer to
+ # lt_preloaded_symbols. The linker will fail if global_symbol_pipe
+ # really was required.
+
+ # Nullify the symbol file.
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e "s% @SYMFILE@%%"`
+ finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s% @SYMFILE@%%"`
+ fi
+}
+
+# func_win32_libid arg
+# return the library type of file 'arg'
+#
+# Need a lot of goo to handle *both* DLLs and import libs
+# Has to be a shell function in order to 'eat' the argument
+# that is supplied when $file_magic_command is called.
+func_win32_libid ()
+{
+ $opt_debug
+ win32_libid_type="unknown"
+ win32_fileres=`file -L $1 2>/dev/null`
+ case $win32_fileres in
+ *ar\ archive\ import\ library*) # definitely import
+ win32_libid_type="x86 archive import"
+ ;;
+ *ar\ archive*) # could be an import, or static
+ if eval $OBJDUMP -f $1 | $SED -e '10q' 2>/dev/null |
+ $EGREP 'file format pe-i386(.*architecture: i386)?' >/dev/null ; then
+ win32_nmres=`eval $NM -f posix -A $1 |
+ $SED -n -e '
+ 1,100{
+ / I /{
+ s,.*,import,
+ p
+ q
+ }
+ }'`
+ case $win32_nmres in
+ import*) win32_libid_type="x86 archive import";;
+ *) win32_libid_type="x86 archive static";;
+ esac
+ fi
+ ;;
+ *DLL*)
+ win32_libid_type="x86 DLL"
+ ;;
+ *executable*) # but shell scripts are "executable" too...
+ case $win32_fileres in
+ *MS\ Windows\ PE\ Intel*)
+ win32_libid_type="x86 DLL"
+ ;;
+ esac
+ ;;
+ esac
+ $ECHO "$win32_libid_type"
+}
+
+
+
+# func_extract_an_archive dir oldlib
+func_extract_an_archive ()
+{
+ $opt_debug
+ f_ex_an_ar_dir="$1"; shift
+ f_ex_an_ar_oldlib="$1"
+ func_show_eval "(cd \$f_ex_an_ar_dir && $AR x \"\$f_ex_an_ar_oldlib\")" 'exit $?'
+ if ($AR t "$f_ex_an_ar_oldlib" | sort | sort -uc >/dev/null 2>&1); then
+ :
+ else
+ func_fatal_error "object name conflicts in archive: $f_ex_an_ar_dir/$f_ex_an_ar_oldlib"
+ fi
+}
+
+
+# func_extract_archives gentop oldlib ...
+func_extract_archives ()
+{
+ $opt_debug
+ my_gentop="$1"; shift
+ my_oldlibs=${1+"$@"}
+ my_oldobjs=""
+ my_xlib=""
+ my_xabs=""
+ my_xdir=""
+
+ for my_xlib in $my_oldlibs; do
+ # Extract the objects.
+ case $my_xlib in
+ [\\/]* | [A-Za-z]:[\\/]*) my_xabs="$my_xlib" ;;
+ *) my_xabs=`pwd`"/$my_xlib" ;;
+ esac
+ func_basename "$my_xlib"
+ my_xlib="$func_basename_result"
+ my_xlib_u=$my_xlib
+ while :; do
+ case " $extracted_archives " in
+ *" $my_xlib_u "*)
+ func_arith $extracted_serial + 1
+ extracted_serial=$func_arith_result
+ my_xlib_u=lt$extracted_serial-$my_xlib ;;
+ *) break ;;
+ esac
+ done
+ extracted_archives="$extracted_archives $my_xlib_u"
+ my_xdir="$my_gentop/$my_xlib_u"
+
+ func_mkdir_p "$my_xdir"
+
+ case $host in
+ *-darwin*)
+ func_verbose "Extracting $my_xabs"
+ # Do not bother doing anything if just a dry run
+ $opt_dry_run || {
+ darwin_orig_dir=`pwd`
+ cd $my_xdir || exit $?
+ darwin_archive=$my_xabs
+ darwin_curdir=`pwd`
+ darwin_base_archive=`basename "$darwin_archive"`
+ darwin_arches=`$LIPO -info "$darwin_archive" 2>/dev/null | $GREP Architectures 2>/dev/null || true`
+ if test -n "$darwin_arches"; then
+ darwin_arches=`$ECHO "$darwin_arches" | $SED -e 's/.*are://'`
+ darwin_arch=
+ func_verbose "$darwin_base_archive has multiple architectures $darwin_arches"
+ for darwin_arch in $darwin_arches ; do
+ func_mkdir_p "unfat-$$/${darwin_base_archive}-${darwin_arch}"
+ $LIPO -thin $darwin_arch -output "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" "${darwin_archive}"
+ cd "unfat-$$/${darwin_base_archive}-${darwin_arch}"
+ func_extract_an_archive "`pwd`" "${darwin_base_archive}"
+ cd "$darwin_curdir"
+ $RM "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}"
+ done # $darwin_arches
+ ## Okay now we've a bunch of thin objects, gotta fatten them up :)
+ darwin_filelist=`find unfat-$$ -type f -name \*.o -print -o -name \*.lo -print | $SED -e "$basename" | sort -u`
+ darwin_file=
+ darwin_files=
+ for darwin_file in $darwin_filelist; do
+ darwin_files=`find unfat-$$ -name $darwin_file -print | $NL2SP`
+ $LIPO -create -output "$darwin_file" $darwin_files
+ done # $darwin_filelist
+ $RM -rf unfat-$$
+ cd "$darwin_orig_dir"
+ else
+ cd $darwin_orig_dir
+ func_extract_an_archive "$my_xdir" "$my_xabs"
+ fi # $darwin_arches
+ } # !$opt_dry_run
+ ;;
+ *)
+ func_extract_an_archive "$my_xdir" "$my_xabs"
+ ;;
+ esac
+ my_oldobjs="$my_oldobjs "`find $my_xdir -name \*.$objext -print -o -name \*.lo -print | $NL2SP`
+ done
+
+ func_extract_archives_result="$my_oldobjs"
+}
+
+
+
+# func_emit_wrapper_part1 [arg=no]
+#
+# Emit the first part of a libtool wrapper script on stdout.
+# For more information, see the description associated with
+# func_emit_wrapper(), below.
+func_emit_wrapper_part1 ()
+{
+ func_emit_wrapper_part1_arg1=no
+ if test -n "$1" ; then
+ func_emit_wrapper_part1_arg1=$1
+ fi
+
+ $ECHO "\
+#! $SHELL
+
+# $output - temporary wrapper script for $objdir/$outputname
+# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
+#
+# The $output program cannot be directly executed until all the libtool
+# libraries that it depends on are installed.
+#
+# This wrapper script should never be moved out of the build directory.
+# If it is, it will not operate correctly.
+
+# Sed substitution that helps us do robust quoting. It backslashifies
+# metacharacters that are still active within double-quoted strings.
+Xsed='${SED} -e 1s/^X//'
+sed_quote_subst='$sed_quote_subst'
+
+# Be Bourne compatible
+if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Zsh 3.x and 4.x performs word splitting on \${1+\"\$@\"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '\${1+\"\$@\"}'='\"\$@\"'
+ setopt NO_GLOB_SUBST
+else
+ case \`(set -o) 2>/dev/null\` in *posix*) set -o posix;; esac
+fi
+BIN_SH=xpg4; export BIN_SH # for Tru64
+DUALCASE=1; export DUALCASE # for MKS sh
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+relink_command=\"$relink_command\"
+
+# This environment variable determines our operation mode.
+if test \"\$libtool_install_magic\" = \"$magic\"; then
+ # install mode needs the following variables:
+ generated_by_libtool_version='$macro_version'
+ notinst_deplibs='$notinst_deplibs'
+else
+ # When we are sourced in execute mode, \$file and \$ECHO are already set.
+ if test \"\$libtool_execute_magic\" != \"$magic\"; then
+ ECHO=\"$qecho\"
+ file=\"\$0\"
+ # Make sure echo works.
+ if test \"X\$1\" = X--no-reexec; then
+ # Discard the --no-reexec flag, and continue.
+ shift
+ elif test \"X\`{ \$ECHO '\t'; } 2>/dev/null\`\" = 'X\t'; then
+ # Yippee, \$ECHO works!
+ :
+ else
+ # Restart under the correct shell, and then maybe \$ECHO will work.
+ exec $SHELL \"\$0\" --no-reexec \${1+\"\$@\"}
+ fi
+ fi\
+"
+ $ECHO "\
+
+ # Find the directory that this script lives in.
+ thisdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*$%%'\`
+ test \"x\$thisdir\" = \"x\$file\" && thisdir=.
+
+ # Follow symbolic links until we get to the real thisdir.
+ file=\`ls -ld \"\$file\" | ${SED} -n 's/.*-> //p'\`
+ while test -n \"\$file\"; do
+ destdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*\$%%'\`
+
+ # If there was a directory component, then change thisdir.
+ if test \"x\$destdir\" != \"x\$file\"; then
+ case \"\$destdir\" in
+ [\\\\/]* | [A-Za-z]:[\\\\/]*) thisdir=\"\$destdir\" ;;
+ *) thisdir=\"\$thisdir/\$destdir\" ;;
+ esac
+ fi
+
+ file=\`\$ECHO \"X\$file\" | \$Xsed -e 's%^.*/%%'\`
+ file=\`ls -ld \"\$thisdir/\$file\" | ${SED} -n 's/.*-> //p'\`
+ done
+"
+}
+# end: func_emit_wrapper_part1
+
+# func_emit_wrapper_part2 [arg=no]
+#
+# Emit the second part of a libtool wrapper script on stdout.
+# For more information, see the description associated with
+# func_emit_wrapper(), below.
+func_emit_wrapper_part2 ()
+{
+ func_emit_wrapper_part2_arg1=no
+ if test -n "$1" ; then
+ func_emit_wrapper_part2_arg1=$1
+ fi
+
+ $ECHO "\
+
+ # Usually 'no', except on cygwin/mingw when embedded into
+ # the cwrapper.
+ WRAPPER_SCRIPT_BELONGS_IN_OBJDIR=$func_emit_wrapper_part2_arg1
+ if test \"\$WRAPPER_SCRIPT_BELONGS_IN_OBJDIR\" = \"yes\"; then
+ # special case for '.'
+ if test \"\$thisdir\" = \".\"; then
+ thisdir=\`pwd\`
+ fi
+ # remove .libs from thisdir
+ case \"\$thisdir\" in
+ *[\\\\/]$objdir ) thisdir=\`\$ECHO \"X\$thisdir\" | \$Xsed -e 's%[\\\\/][^\\\\/]*$%%'\` ;;
+ $objdir ) thisdir=. ;;
+ esac
+ fi
+
+ # Try to get the absolute directory name.
+ absdir=\`cd \"\$thisdir\" && pwd\`
+ test -n \"\$absdir\" && thisdir=\"\$absdir\"
+"
+
+ if test "$fast_install" = yes; then
+ $ECHO "\
+ program=lt-'$outputname'$exeext
+ progdir=\"\$thisdir/$objdir\"
+
+ if test ! -f \"\$progdir/\$program\" ||
+ { file=\`ls -1dt \"\$progdir/\$program\" \"\$progdir/../\$program\" 2>/dev/null | ${SED} 1q\`; \\
+ test \"X\$file\" != \"X\$progdir/\$program\"; }; then
+
+ file=\"\$\$-\$program\"
+
+ if test ! -d \"\$progdir\"; then
+ $MKDIR \"\$progdir\"
+ else
+ $RM \"\$progdir/\$file\"
+ fi"
+
+ $ECHO "\
+
+ # relink executable if necessary
+ if test -n \"\$relink_command\"; then
+ if relink_command_output=\`eval \$relink_command 2>&1\`; then :
+ else
+ $ECHO \"\$relink_command_output\" >&2
+ $RM \"\$progdir/\$file\"
+ exit 1
+ fi
+ fi
+
+ $MV \"\$progdir/\$file\" \"\$progdir/\$program\" 2>/dev/null ||
+ { $RM \"\$progdir/\$program\";
+ $MV \"\$progdir/\$file\" \"\$progdir/\$program\"; }
+ $RM \"\$progdir/\$file\"
+ fi"
+ else
+ $ECHO "\
+ program='$outputname'
+ progdir=\"\$thisdir/$objdir\"
+"
+ fi
+
+ $ECHO "\
+
+ if test -f \"\$progdir/\$program\"; then"
+
+ # Export our shlibpath_var if we have one.
+ if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then
+ $ECHO "\
+ # Add our own library path to $shlibpath_var
+ $shlibpath_var=\"$temp_rpath\$$shlibpath_var\"
+
+ # Some systems cannot cope with colon-terminated $shlibpath_var
+ # The second colon is a workaround for a bug in BeOS R4 sed
+ $shlibpath_var=\`\$ECHO \"X\$$shlibpath_var\" | \$Xsed -e 's/::*\$//'\`
+
+ export $shlibpath_var
+"
+ fi
+
+ # fixup the dll searchpath if we need to.
+ if test -n "$dllsearchpath"; then
+ $ECHO "\
+ # Add the dll search path components to the executable PATH
+ PATH=$dllsearchpath:\$PATH
+"
+ fi
+
+ $ECHO "\
+ if test \"\$libtool_execute_magic\" != \"$magic\"; then
+ # Run the actual program with our arguments.
+"
+ case $host in
+ # Backslashes separate directories on plain windows
+ *-*-mingw | *-*-os2* | *-cegcc*)
+ $ECHO "\
+ exec \"\$progdir\\\\\$program\" \${1+\"\$@\"}
+"
+ ;;
+
+ *)
+ $ECHO "\
+ exec \"\$progdir/\$program\" \${1+\"\$@\"}
+"
+ ;;
+ esac
+ $ECHO "\
+ \$ECHO \"\$0: cannot exec \$program \$*\" 1>&2
+ exit 1
+ fi
+ else
+ # The program doesn't exist.
+ \$ECHO \"\$0: error: \\\`\$progdir/\$program' does not exist\" 1>&2
+ \$ECHO \"This script is just a wrapper for \$program.\" 1>&2
+ $ECHO \"See the $PACKAGE documentation for more information.\" 1>&2
+ exit 1
+ fi
+fi\
+"
+}
+# end: func_emit_wrapper_part2
+
+
+# func_emit_wrapper [arg=no]
+#
+# Emit a libtool wrapper script on stdout.
+# Don't directly open a file because we may want to
+# incorporate the script contents within a cygwin/mingw
+# wrapper executable. Must ONLY be called from within
+# func_mode_link because it depends on a number of variables
+# set therein.
+#
+# ARG is the value that the WRAPPER_SCRIPT_BELONGS_IN_OBJDIR
+# variable will take. If 'yes', then the emitted script
+# will assume that the directory in which it is stored is
+# the $objdir directory. This is a cygwin/mingw-specific
+# behavior.
+func_emit_wrapper ()
+{
+ func_emit_wrapper_arg1=no
+ if test -n "$1" ; then
+ func_emit_wrapper_arg1=$1
+ fi
+
+ # split this up so that func_emit_cwrapperexe_src
+ # can call each part independently.
+ func_emit_wrapper_part1 "${func_emit_wrapper_arg1}"
+ func_emit_wrapper_part2 "${func_emit_wrapper_arg1}"
+}
+
+
+# func_to_host_path arg
+#
+# Convert paths to host format when used with build tools.
+# Intended for use with "native" mingw (where libtool itself
+# is running under the msys shell), or in the following cross-
+# build environments:
+# $build $host
+# mingw (msys) mingw [e.g. native]
+# cygwin mingw
+# *nix + wine mingw
+# where wine is equipped with the `winepath' executable.
+# In the native mingw case, the (msys) shell automatically
+# converts paths for any non-msys applications it launches,
+# but that facility isn't available from inside the cwrapper.
+# Similar accommodations are necessary for $host mingw and
+# $build cygwin. Calling this function does no harm for other
+# $host/$build combinations not listed above.
+#
+# ARG is the path (on $build) that should be converted to
+# the proper representation for $host. The result is stored
+# in $func_to_host_path_result.
+func_to_host_path ()
+{
+ func_to_host_path_result="$1"
+ if test -n "$1" ; then
+ case $host in
+ *mingw* )
+ lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g'
+ case $build in
+ *mingw* ) # actually, msys
+ # awkward: cmd appends spaces to result
+ lt_sed_strip_trailing_spaces="s/[ ]*\$//"
+ func_to_host_path_tmp1=`( cmd //c echo "$1" |\
+ $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""`
+ func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ ;;
+ *cygwin* )
+ func_to_host_path_tmp1=`cygpath -w "$1"`
+ func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ ;;
+ * )
+ # Unfortunately, winepath does not exit with a non-zero
+ # error code, so we are forced to check the contents of
+ # stdout. On the other hand, if the command is not
+ # found, the shell will set an exit code of 127 and print
+ # *an error message* to stdout. So we must check for both
+ # error code of zero AND non-empty stdout, which explains
+ # the odd construction:
+ func_to_host_path_tmp1=`winepath -w "$1" 2>/dev/null`
+ if test "$?" -eq 0 && test -n "${func_to_host_path_tmp1}"; then
+ func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ else
+ # Allow warning below.
+ func_to_host_path_result=""
+ fi
+ ;;
+ esac
+ if test -z "$func_to_host_path_result" ; then
+ func_error "Could not determine host path corresponding to"
+ func_error " '$1'"
+ func_error "Continuing, but uninstalled executables may not work."
+ # Fallback:
+ func_to_host_path_result="$1"
+ fi
+ ;;
+ esac
+ fi
+}
+# end: func_to_host_path
+
+# func_to_host_pathlist arg
+#
+# Convert pathlists to host format when used with build tools.
+# See func_to_host_path(), above. This function supports the
+# following $build/$host combinations (but does no harm for
+# combinations not listed here):
+# $build $host
+# mingw (msys) mingw [e.g. native]
+# cygwin mingw
+# *nix + wine mingw
+#
+# Path separators are also converted from $build format to
+# $host format. If ARG begins or ends with a path separator
+# character, it is preserved (but converted to $host format)
+# on output.
+#
+# ARG is a pathlist (on $build) that should be converted to
+# the proper representation on $host. The result is stored
+# in $func_to_host_pathlist_result.
+func_to_host_pathlist ()
+{
+ func_to_host_pathlist_result="$1"
+ if test -n "$1" ; then
+ case $host in
+ *mingw* )
+ lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g'
+ # Remove leading and trailing path separator characters from
+ # ARG. msys behavior is inconsistent here, cygpath turns them
+ # into '.;' and ';.', and winepath ignores them completely.
+ func_to_host_pathlist_tmp2="$1"
+ # Once set for this call, this variable should not be
+ # reassigned. It is used in tha fallback case.
+ func_to_host_pathlist_tmp1=`echo "$func_to_host_pathlist_tmp2" |\
+ $SED -e 's|^:*||' -e 's|:*$||'`
+ case $build in
+ *mingw* ) # Actually, msys.
+ # Awkward: cmd appends spaces to result.
+ lt_sed_strip_trailing_spaces="s/[ ]*\$//"
+ func_to_host_pathlist_tmp2=`( cmd //c echo "$func_to_host_pathlist_tmp1" |\
+ $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""`
+ func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ ;;
+ *cygwin* )
+ func_to_host_pathlist_tmp2=`cygpath -w -p "$func_to_host_pathlist_tmp1"`
+ func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ ;;
+ * )
+ # unfortunately, winepath doesn't convert pathlists
+ func_to_host_pathlist_result=""
+ func_to_host_pathlist_oldIFS=$IFS
+ IFS=:
+ for func_to_host_pathlist_f in $func_to_host_pathlist_tmp1 ; do
+ IFS=$func_to_host_pathlist_oldIFS
+ if test -n "$func_to_host_pathlist_f" ; then
+ func_to_host_path "$func_to_host_pathlist_f"
+ if test -n "$func_to_host_path_result" ; then
+ if test -z "$func_to_host_pathlist_result" ; then
+ func_to_host_pathlist_result="$func_to_host_path_result"
+ else
+ func_to_host_pathlist_result="$func_to_host_pathlist_result;$func_to_host_path_result"
+ fi
+ fi
+ fi
+ IFS=:
+ done
+ IFS=$func_to_host_pathlist_oldIFS
+ ;;
+ esac
+ if test -z "$func_to_host_pathlist_result" ; then
+ func_error "Could not determine the host path(s) corresponding to"
+ func_error " '$1'"
+ func_error "Continuing, but uninstalled executables may not work."
+ # Fallback. This may break if $1 contains DOS-style drive
+ # specifications. The fix is not to complicate the expression
+ # below, but for the user to provide a working wine installation
+ # with winepath so that path translation in the cross-to-mingw
+ # case works properly.
+ lt_replace_pathsep_nix_to_dos="s|:|;|g"
+ func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp1" |\
+ $SED -e "$lt_replace_pathsep_nix_to_dos"`
+ fi
+ # Now, add the leading and trailing path separators back
+ case "$1" in
+ :* ) func_to_host_pathlist_result=";$func_to_host_pathlist_result"
+ ;;
+ esac
+ case "$1" in
+ *: ) func_to_host_pathlist_result="$func_to_host_pathlist_result;"
+ ;;
+ esac
+ ;;
+ esac
+ fi
+}
+# end: func_to_host_pathlist
+
+# func_emit_cwrapperexe_src
+# emit the source code for a wrapper executable on stdout
+# Must ONLY be called from within func_mode_link because
+# it depends on a number of variable set therein.
+func_emit_cwrapperexe_src ()
+{
+ cat <<EOF
+
+/* $cwrappersource - temporary wrapper executable for $objdir/$outputname
+ Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
+
+ The $output program cannot be directly executed until all the libtool
+ libraries that it depends on are installed.
+
+ This wrapper executable should never be moved out of the build directory.
+ If it is, it will not operate correctly.
+
+ Currently, it simply execs the wrapper *script* "$SHELL $output",
+ but could eventually absorb all of the scripts functionality and
+ exec $objdir/$outputname directly.
+*/
+EOF
+ cat <<"EOF"
+#include <stdio.h>
+#include <stdlib.h>
+#ifdef _MSC_VER
+# include <direct.h>
+# include <process.h>
+# include <io.h>
+# define setmode _setmode
+#else
+# include <unistd.h>
+# include <stdint.h>
+# ifdef __CYGWIN__
+# include <io.h>
+# define HAVE_SETENV
+# ifdef __STRICT_ANSI__
+char *realpath (const char *, char *);
+int putenv (char *);
+int setenv (const char *, const char *, int);
+# endif
+# endif
+#endif
+#include <malloc.h>
+#include <stdarg.h>
+#include <assert.h>
+#include <string.h>
+#include <ctype.h>
+#include <errno.h>
+#include <fcntl.h>
+#include <sys/stat.h>
+
+#if defined(PATH_MAX)
+# define LT_PATHMAX PATH_MAX
+#elif defined(MAXPATHLEN)
+# define LT_PATHMAX MAXPATHLEN
+#else
+# define LT_PATHMAX 1024
+#endif
+
+#ifndef S_IXOTH
+# define S_IXOTH 0
+#endif
+#ifndef S_IXGRP
+# define S_IXGRP 0
+#endif
+
+#ifdef _MSC_VER
+# define S_IXUSR _S_IEXEC
+# define stat _stat
+# ifndef _INTPTR_T_DEFINED
+# define intptr_t int
+# endif
+#endif
+
+#ifndef DIR_SEPARATOR
+# define DIR_SEPARATOR '/'
+# define PATH_SEPARATOR ':'
+#endif
+
+#if defined (_WIN32) || defined (__MSDOS__) || defined (__DJGPP__) || \
+ defined (__OS2__)
+# define HAVE_DOS_BASED_FILE_SYSTEM
+# define FOPEN_WB "wb"
+# ifndef DIR_SEPARATOR_2
+# define DIR_SEPARATOR_2 '\\'
+# endif
+# ifndef PATH_SEPARATOR_2
+# define PATH_SEPARATOR_2 ';'
+# endif
+#endif
+
+#ifndef DIR_SEPARATOR_2
+# define IS_DIR_SEPARATOR(ch) ((ch) == DIR_SEPARATOR)
+#else /* DIR_SEPARATOR_2 */
+# define IS_DIR_SEPARATOR(ch) \
+ (((ch) == DIR_SEPARATOR) || ((ch) == DIR_SEPARATOR_2))
+#endif /* DIR_SEPARATOR_2 */
+
+#ifndef PATH_SEPARATOR_2
+# define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR)
+#else /* PATH_SEPARATOR_2 */
+# define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR_2)
+#endif /* PATH_SEPARATOR_2 */
+
+#ifdef __CYGWIN__
+# define FOPEN_WB "wb"
+#endif
+
+#ifndef FOPEN_WB
+# define FOPEN_WB "w"
+#endif
+#ifndef _O_BINARY
+# define _O_BINARY 0
+#endif
+
+#define XMALLOC(type, num) ((type *) xmalloc ((num) * sizeof(type)))
+#define XFREE(stale) do { \
+ if (stale) { free ((void *) stale); stale = 0; } \
+} while (0)
+
+#undef LTWRAPPER_DEBUGPRINTF
+#if defined DEBUGWRAPPER
+# define LTWRAPPER_DEBUGPRINTF(args) ltwrapper_debugprintf args
+static void
+ltwrapper_debugprintf (const char *fmt, ...)
+{
+ va_list args;
+ va_start (args, fmt);
+ (void) vfprintf (stderr, fmt, args);
+ va_end (args);
+}
+#else
+# define LTWRAPPER_DEBUGPRINTF(args)
+#endif
+
+const char *program_name = NULL;
+
+void *xmalloc (size_t num);
+char *xstrdup (const char *string);
+const char *base_name (const char *name);
+char *find_executable (const char *wrapper);
+char *chase_symlinks (const char *pathspec);
+int make_executable (const char *path);
+int check_executable (const char *path);
+char *strendzap (char *str, const char *pat);
+void lt_fatal (const char *message, ...);
+void lt_setenv (const char *name, const char *value);
+char *lt_extend_str (const char *orig_value, const char *add, int to_end);
+void lt_opt_process_env_set (const char *arg);
+void lt_opt_process_env_prepend (const char *arg);
+void lt_opt_process_env_append (const char *arg);
+int lt_split_name_value (const char *arg, char** name, char** value);
+void lt_update_exe_path (const char *name, const char *value);
+void lt_update_lib_path (const char *name, const char *value);
+
+static const char *script_text_part1 =
+EOF
+
+ func_emit_wrapper_part1 yes |
+ $SED -e 's/\([\\"]\)/\\\1/g' \
+ -e 's/^/ "/' -e 's/$/\\n"/'
+ echo ";"
+ cat <<EOF
+
+static const char *script_text_part2 =
+EOF
+ func_emit_wrapper_part2 yes |
+ $SED -e 's/\([\\"]\)/\\\1/g' \
+ -e 's/^/ "/' -e 's/$/\\n"/'
+ echo ";"
+
+ cat <<EOF
+const char * MAGIC_EXE = "$magic_exe";
+const char * LIB_PATH_VARNAME = "$shlibpath_var";
+EOF
+
+ if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then
+ func_to_host_pathlist "$temp_rpath"
+ cat <<EOF
+const char * LIB_PATH_VALUE = "$func_to_host_pathlist_result";
+EOF
+ else
+ cat <<"EOF"
+const char * LIB_PATH_VALUE = "";
+EOF
+ fi
+
+ if test -n "$dllsearchpath"; then
+ func_to_host_pathlist "$dllsearchpath:"
+ cat <<EOF
+const char * EXE_PATH_VARNAME = "PATH";
+const char * EXE_PATH_VALUE = "$func_to_host_pathlist_result";
+EOF
+ else
+ cat <<"EOF"
+const char * EXE_PATH_VARNAME = "";
+const char * EXE_PATH_VALUE = "";
+EOF
+ fi
+
+ if test "$fast_install" = yes; then
+ cat <<EOF
+const char * TARGET_PROGRAM_NAME = "lt-$outputname"; /* hopefully, no .exe */
+EOF
+ else
+ cat <<EOF
+const char * TARGET_PROGRAM_NAME = "$outputname"; /* hopefully, no .exe */
+EOF
+ fi
+
+
+ cat <<"EOF"
+
+#define LTWRAPPER_OPTION_PREFIX "--lt-"
+#define LTWRAPPER_OPTION_PREFIX_LENGTH 5
+
+static const size_t opt_prefix_len = LTWRAPPER_OPTION_PREFIX_LENGTH;
+static const char *ltwrapper_option_prefix = LTWRAPPER_OPTION_PREFIX;
+
+static const char *dumpscript_opt = LTWRAPPER_OPTION_PREFIX "dump-script";
+
+static const size_t env_set_opt_len = LTWRAPPER_OPTION_PREFIX_LENGTH + 7;
+static const char *env_set_opt = LTWRAPPER_OPTION_PREFIX "env-set";
+ /* argument is putenv-style "foo=bar", value of foo is set to bar */
+
+static const size_t env_prepend_opt_len = LTWRAPPER_OPTION_PREFIX_LENGTH + 11;
+static const char *env_prepend_opt = LTWRAPPER_OPTION_PREFIX "env-prepend";
+ /* argument is putenv-style "foo=bar", new value of foo is bar${foo} */
+
+static const size_t env_append_opt_len = LTWRAPPER_OPTION_PREFIX_LENGTH + 10;
+static const char *env_append_opt = LTWRAPPER_OPTION_PREFIX "env-append";
+ /* argument is putenv-style "foo=bar", new value of foo is ${foo}bar */
+
+int
+main (int argc, char *argv[])
+{
+ char **newargz;
+ int newargc;
+ char *tmp_pathspec;
+ char *actual_cwrapper_path;
+ char *actual_cwrapper_name;
+ char *target_name;
+ char *lt_argv_zero;
+ intptr_t rval = 127;
+
+ int i;
+
+ program_name = (char *) xstrdup (base_name (argv[0]));
+ LTWRAPPER_DEBUGPRINTF (("(main) argv[0] : %s\n", argv[0]));
+ LTWRAPPER_DEBUGPRINTF (("(main) program_name : %s\n", program_name));
+
+ /* very simple arg parsing; don't want to rely on getopt */
+ for (i = 1; i < argc; i++)
+ {
+ if (strcmp (argv[i], dumpscript_opt) == 0)
+ {
+EOF
+ case "$host" in
+ *mingw* | *cygwin* )
+ # make stdout use "unix" line endings
+ echo " setmode(1,_O_BINARY);"
+ ;;
+ esac
+
+ cat <<"EOF"
+ printf ("%s", script_text_part1);
+ printf ("%s", script_text_part2);
+ return 0;
+ }
+ }
+
+ newargz = XMALLOC (char *, argc + 1);
+ tmp_pathspec = find_executable (argv[0]);
+ if (tmp_pathspec == NULL)
+ lt_fatal ("Couldn't find %s", argv[0]);
+ LTWRAPPER_DEBUGPRINTF (("(main) found exe (before symlink chase) at : %s\n",
+ tmp_pathspec));
+
+ actual_cwrapper_path = chase_symlinks (tmp_pathspec);
+ LTWRAPPER_DEBUGPRINTF (("(main) found exe (after symlink chase) at : %s\n",
+ actual_cwrapper_path));
+ XFREE (tmp_pathspec);
+
+ actual_cwrapper_name = xstrdup( base_name (actual_cwrapper_path));
+ strendzap (actual_cwrapper_path, actual_cwrapper_name);
+
+ /* wrapper name transforms */
+ strendzap (actual_cwrapper_name, ".exe");
+ tmp_pathspec = lt_extend_str (actual_cwrapper_name, ".exe", 1);
+ XFREE (actual_cwrapper_name);
+ actual_cwrapper_name = tmp_pathspec;
+ tmp_pathspec = 0;
+
+ /* target_name transforms -- use actual target program name; might have lt- prefix */
+ target_name = xstrdup (base_name (TARGET_PROGRAM_NAME));
+ strendzap (target_name, ".exe");
+ tmp_pathspec = lt_extend_str (target_name, ".exe", 1);
+ XFREE (target_name);
+ target_name = tmp_pathspec;
+ tmp_pathspec = 0;
+
+ LTWRAPPER_DEBUGPRINTF (("(main) libtool target name: %s\n",
+ target_name));
+EOF
+
+ cat <<EOF
+ newargz[0] =
+ XMALLOC (char, (strlen (actual_cwrapper_path) +
+ strlen ("$objdir") + 1 + strlen (actual_cwrapper_name) + 1));
+ strcpy (newargz[0], actual_cwrapper_path);
+ strcat (newargz[0], "$objdir");
+ strcat (newargz[0], "/");
+EOF
+
+ cat <<"EOF"
+ /* stop here, and copy so we don't have to do this twice */
+ tmp_pathspec = xstrdup (newargz[0]);
+
+ /* do NOT want the lt- prefix here, so use actual_cwrapper_name */
+ strcat (newargz[0], actual_cwrapper_name);
+
+ /* DO want the lt- prefix here if it exists, so use target_name */
+ lt_argv_zero = lt_extend_str (tmp_pathspec, target_name, 1);
+ XFREE (tmp_pathspec);
+ tmp_pathspec = NULL;
+EOF
+
+ case $host_os in
+ mingw*)
+ cat <<"EOF"
+ {
+ char* p;
+ while ((p = strchr (newargz[0], '\\')) != NULL)
+ {
+ *p = '/';
+ }
+ while ((p = strchr (lt_argv_zero, '\\')) != NULL)
+ {
+ *p = '/';
+ }
+ }
+EOF
+ ;;
+ esac
+
+ cat <<"EOF"
+ XFREE (target_name);
+ XFREE (actual_cwrapper_path);
+ XFREE (actual_cwrapper_name);
+
+ lt_setenv ("BIN_SH", "xpg4"); /* for Tru64 */
+ lt_setenv ("DUALCASE", "1"); /* for MSK sh */
+ lt_update_lib_path (LIB_PATH_VARNAME, LIB_PATH_VALUE);
+ lt_update_exe_path (EXE_PATH_VARNAME, EXE_PATH_VALUE);
+
+ newargc=0;
+ for (i = 1; i < argc; i++)
+ {
+ if (strncmp (argv[i], env_set_opt, env_set_opt_len) == 0)
+ {
+ if (argv[i][env_set_opt_len] == '=')
+ {
+ const char *p = argv[i] + env_set_opt_len + 1;
+ lt_opt_process_env_set (p);
+ }
+ else if (argv[i][env_set_opt_len] == '\0' && i + 1 < argc)
+ {
+ lt_opt_process_env_set (argv[++i]); /* don't copy */
+ }
+ else
+ lt_fatal ("%s missing required argument", env_set_opt);
+ continue;
+ }
+ if (strncmp (argv[i], env_prepend_opt, env_prepend_opt_len) == 0)
+ {
+ if (argv[i][env_prepend_opt_len] == '=')
+ {
+ const char *p = argv[i] + env_prepend_opt_len + 1;
+ lt_opt_process_env_prepend (p);
+ }
+ else if (argv[i][env_prepend_opt_len] == '\0' && i + 1 < argc)
+ {
+ lt_opt_process_env_prepend (argv[++i]); /* don't copy */
+ }
+ else
+ lt_fatal ("%s missing required argument", env_prepend_opt);
+ continue;
+ }
+ if (strncmp (argv[i], env_append_opt, env_append_opt_len) == 0)
+ {
+ if (argv[i][env_append_opt_len] == '=')
+ {
+ const char *p = argv[i] + env_append_opt_len + 1;
+ lt_opt_process_env_append (p);
+ }
+ else if (argv[i][env_append_opt_len] == '\0' && i + 1 < argc)
+ {
+ lt_opt_process_env_append (argv[++i]); /* don't copy */
+ }
+ else
+ lt_fatal ("%s missing required argument", env_append_opt);
+ continue;
+ }
+ if (strncmp (argv[i], ltwrapper_option_prefix, opt_prefix_len) == 0)
+ {
+ /* however, if there is an option in the LTWRAPPER_OPTION_PREFIX
+ namespace, but it is not one of the ones we know about and
+ have already dealt with, above (inluding dump-script), then
+ report an error. Otherwise, targets might begin to believe
+ they are allowed to use options in the LTWRAPPER_OPTION_PREFIX
+ namespace. The first time any user complains about this, we'll
+ need to make LTWRAPPER_OPTION_PREFIX a configure-time option
+ or a configure.ac-settable value.
+ */
+ lt_fatal ("Unrecognized option in %s namespace: '%s'",
+ ltwrapper_option_prefix, argv[i]);
+ }
+ /* otherwise ... */
+ newargz[++newargc] = xstrdup (argv[i]);
+ }
+ newargz[++newargc] = NULL;
+
+ LTWRAPPER_DEBUGPRINTF (("(main) lt_argv_zero : %s\n", (lt_argv_zero ? lt_argv_zero : "<NULL>")));
+ for (i = 0; i < newargc; i++)
+ {
+ LTWRAPPER_DEBUGPRINTF (("(main) newargz[%d] : %s\n", i, (newargz[i] ? newargz[i] : "<NULL>")));
+ }
+
+EOF
+
+ case $host_os in
+ mingw*)
+ cat <<"EOF"
+ /* execv doesn't actually work on mingw as expected on unix */
+ rval = _spawnv (_P_WAIT, lt_argv_zero, (const char * const *) newargz);
+ if (rval == -1)
+ {
+ /* failed to start process */
+ LTWRAPPER_DEBUGPRINTF (("(main) failed to launch target \"%s\": errno = %d\n", lt_argv_zero, errno));
+ return 127;
+ }
+ return rval;
+EOF
+ ;;
+ *)
+ cat <<"EOF"
+ execv (lt_argv_zero, newargz);
+ return rval; /* =127, but avoids unused variable warning */
+EOF
+ ;;
+ esac
+
+ cat <<"EOF"
+}
+
+void *
+xmalloc (size_t num)
+{
+ void *p = (void *) malloc (num);
+ if (!p)
+ lt_fatal ("Memory exhausted");
+
+ return p;
+}
+
+char *
+xstrdup (const char *string)
+{
+ return string ? strcpy ((char *) xmalloc (strlen (string) + 1),
+ string) : NULL;
+}
+
+const char *
+base_name (const char *name)
+{
+ const char *base;
+
+#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
+ /* Skip over the disk name in MSDOS pathnames. */
+ if (isalpha ((unsigned char) name[0]) && name[1] == ':')
+ name += 2;
+#endif
+
+ for (base = name; *name; name++)
+ if (IS_DIR_SEPARATOR (*name))
+ base = name + 1;
+ return base;
+}
+
+int
+check_executable (const char *path)
+{
+ struct stat st;
+
+ LTWRAPPER_DEBUGPRINTF (("(check_executable) : %s\n",
+ path ? (*path ? path : "EMPTY!") : "NULL!"));
+ if ((!path) || (!*path))
+ return 0;
+
+ if ((stat (path, &st) >= 0)
+ && (st.st_mode & (S_IXUSR | S_IXGRP | S_IXOTH)))
+ return 1;
+ else
+ return 0;
+}
+
+int
+make_executable (const char *path)
+{
+ int rval = 0;
+ struct stat st;
+
+ LTWRAPPER_DEBUGPRINTF (("(make_executable) : %s\n",
+ path ? (*path ? path : "EMPTY!") : "NULL!"));
+ if ((!path) || (!*path))
+ return 0;
+
+ if (stat (path, &st) >= 0)
+ {
+ rval = chmod (path, st.st_mode | S_IXOTH | S_IXGRP | S_IXUSR);
+ }
+ return rval;
+}
+
+/* Searches for the full path of the wrapper. Returns
+ newly allocated full path name if found, NULL otherwise
+ Does not chase symlinks, even on platforms that support them.
+*/
+char *
+find_executable (const char *wrapper)
+{
+ int has_slash = 0;
+ const char *p;
+ const char *p_next;
+ /* static buffer for getcwd */
+ char tmp[LT_PATHMAX + 1];
+ int tmp_len;
+ char *concat_name;
+
+ LTWRAPPER_DEBUGPRINTF (("(find_executable) : %s\n",
+ wrapper ? (*wrapper ? wrapper : "EMPTY!") : "NULL!"));
+
+ if ((wrapper == NULL) || (*wrapper == '\0'))
+ return NULL;
+
+ /* Absolute path? */
+#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
+ if (isalpha ((unsigned char) wrapper[0]) && wrapper[1] == ':')
+ {
+ concat_name = xstrdup (wrapper);
+ if (check_executable (concat_name))
+ return concat_name;
+ XFREE (concat_name);
+ }
+ else
+ {
+#endif
+ if (IS_DIR_SEPARATOR (wrapper[0]))
+ {
+ concat_name = xstrdup (wrapper);
+ if (check_executable (concat_name))
+ return concat_name;
+ XFREE (concat_name);
+ }
+#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
+ }
+#endif
+
+ for (p = wrapper; *p; p++)
+ if (*p == '/')
+ {
+ has_slash = 1;
+ break;
+ }
+ if (!has_slash)
+ {
+ /* no slashes; search PATH */
+ const char *path = getenv ("PATH");
+ if (path != NULL)
+ {
+ for (p = path; *p; p = p_next)
+ {
+ const char *q;
+ size_t p_len;
+ for (q = p; *q; q++)
+ if (IS_PATH_SEPARATOR (*q))
+ break;
+ p_len = q - p;
+ p_next = (*q == '\0' ? q : q + 1);
+ if (p_len == 0)
+ {
+ /* empty path: current directory */
+ if (getcwd (tmp, LT_PATHMAX) == NULL)
+ lt_fatal ("getcwd failed");
+ tmp_len = strlen (tmp);
+ concat_name =
+ XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1);
+ memcpy (concat_name, tmp, tmp_len);
+ concat_name[tmp_len] = '/';
+ strcpy (concat_name + tmp_len + 1, wrapper);
+ }
+ else
+ {
+ concat_name =
+ XMALLOC (char, p_len + 1 + strlen (wrapper) + 1);
+ memcpy (concat_name, p, p_len);
+ concat_name[p_len] = '/';
+ strcpy (concat_name + p_len + 1, wrapper);
+ }
+ if (check_executable (concat_name))
+ return concat_name;
+ XFREE (concat_name);
+ }
+ }
+ /* not found in PATH; assume curdir */
+ }
+ /* Relative path | not found in path: prepend cwd */
+ if (getcwd (tmp, LT_PATHMAX) == NULL)
+ lt_fatal ("getcwd failed");
+ tmp_len = strlen (tmp);
+ concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1);
+ memcpy (concat_name, tmp, tmp_len);
+ concat_name[tmp_len] = '/';
+ strcpy (concat_name + tmp_len + 1, wrapper);
+
+ if (check_executable (concat_name))
+ return concat_name;
+ XFREE (concat_name);
+ return NULL;
+}
+
+char *
+chase_symlinks (const char *pathspec)
+{
+#ifndef S_ISLNK
+ return xstrdup (pathspec);
+#else
+ char buf[LT_PATHMAX];
+ struct stat s;
+ char *tmp_pathspec = xstrdup (pathspec);
+ char *p;
+ int has_symlinks = 0;
+ while (strlen (tmp_pathspec) && !has_symlinks)
+ {
+ LTWRAPPER_DEBUGPRINTF (("checking path component for symlinks: %s\n",
+ tmp_pathspec));
+ if (lstat (tmp_pathspec, &s) == 0)
+ {
+ if (S_ISLNK (s.st_mode) != 0)
+ {
+ has_symlinks = 1;
+ break;
+ }
+
+ /* search backwards for last DIR_SEPARATOR */
+ p = tmp_pathspec + strlen (tmp_pathspec) - 1;
+ while ((p > tmp_pathspec) && (!IS_DIR_SEPARATOR (*p)))
+ p--;
+ if ((p == tmp_pathspec) && (!IS_DIR_SEPARATOR (*p)))
+ {
+ /* no more DIR_SEPARATORS left */
+ break;
+ }
+ *p = '\0';
+ }
+ else
+ {
+ char *errstr = strerror (errno);
+ lt_fatal ("Error accessing file %s (%s)", tmp_pathspec, errstr);
+ }
+ }
+ XFREE (tmp_pathspec);
+
+ if (!has_symlinks)
+ {
+ return xstrdup (pathspec);
+ }
+
+ tmp_pathspec = realpath (pathspec, buf);
+ if (tmp_pathspec == 0)
+ {
+ lt_fatal ("Could not follow symlinks for %s", pathspec);
+ }
+ return xstrdup (tmp_pathspec);
+#endif
+}
+
+char *
+strendzap (char *str, const char *pat)
+{
+ size_t len, patlen;
+
+ assert (str != NULL);
+ assert (pat != NULL);
+
+ len = strlen (str);
+ patlen = strlen (pat);
+
+ if (patlen <= len)
+ {
+ str += len - patlen;
+ if (strcmp (str, pat) == 0)
+ *str = '\0';
+ }
+ return str;
+}
+
+static void
+lt_error_core (int exit_status, const char *mode,
+ const char *message, va_list ap)
+{
+ fprintf (stderr, "%s: %s: ", program_name, mode);
+ vfprintf (stderr, message, ap);
+ fprintf (stderr, ".\n");
+
+ if (exit_status >= 0)
+ exit (exit_status);
+}
+
+void
+lt_fatal (const char *message, ...)
+{
+ va_list ap;
+ va_start (ap, message);
+ lt_error_core (EXIT_FAILURE, "FATAL", message, ap);
+ va_end (ap);
+}
+
+void
+lt_setenv (const char *name, const char *value)
+{
+ LTWRAPPER_DEBUGPRINTF (("(lt_setenv) setting '%s' to '%s'\n",
+ (name ? name : "<NULL>"),
+ (value ? value : "<NULL>")));
+ {
+#ifdef HAVE_SETENV
+ /* always make a copy, for consistency with !HAVE_SETENV */
+ char *str = xstrdup (value);
+ setenv (name, str, 1);
+#else
+ int len = strlen (name) + 1 + strlen (value) + 1;
+ char *str = XMALLOC (char, len);
+ sprintf (str, "%s=%s", name, value);
+ if (putenv (str) != EXIT_SUCCESS)
+ {
+ XFREE (str);
+ }
+#endif
+ }
+}
+
+char *
+lt_extend_str (const char *orig_value, const char *add, int to_end)
+{
+ char *new_value;
+ if (orig_value && *orig_value)
+ {
+ int orig_value_len = strlen (orig_value);
+ int add_len = strlen (add);
+ new_value = XMALLOC (char, add_len + orig_value_len + 1);
+ if (to_end)
+ {
+ strcpy (new_value, orig_value);
+ strcpy (new_value + orig_value_len, add);
+ }
+ else
+ {
+ strcpy (new_value, add);
+ strcpy (new_value + add_len, orig_value);
+ }
+ }
+ else
+ {
+ new_value = xstrdup (add);
+ }
+ return new_value;
+}
+
+int
+lt_split_name_value (const char *arg, char** name, char** value)
+{
+ const char *p;
+ int len;
+ if (!arg || !*arg)
+ return 1;
+
+ p = strchr (arg, (int)'=');
+
+ if (!p)
+ return 1;
+
+ *value = xstrdup (++p);
+
+ len = strlen (arg) - strlen (*value);
+ *name = XMALLOC (char, len);
+ strncpy (*name, arg, len-1);
+ (*name)[len - 1] = '\0';
+
+ return 0;
+}
+
+void
+lt_opt_process_env_set (const char *arg)
+{
+ char *name = NULL;
+ char *value = NULL;
+
+ if (lt_split_name_value (arg, &name, &value) != 0)
+ {
+ XFREE (name);
+ XFREE (value);
+ lt_fatal ("bad argument for %s: '%s'", env_set_opt, arg);
+ }
+
+ lt_setenv (name, value);
+ XFREE (name);
+ XFREE (value);
+}
+
+void
+lt_opt_process_env_prepend (const char *arg)
+{
+ char *name = NULL;
+ char *value = NULL;
+ char *new_value = NULL;
+
+ if (lt_split_name_value (arg, &name, &value) != 0)
+ {
+ XFREE (name);
+ XFREE (value);
+ lt_fatal ("bad argument for %s: '%s'", env_prepend_opt, arg);
+ }
+
+ new_value = lt_extend_str (getenv (name), value, 0);
+ lt_setenv (name, new_value);
+ XFREE (new_value);
+ XFREE (name);
+ XFREE (value);
+}
+
+void
+lt_opt_process_env_append (const char *arg)
+{
+ char *name = NULL;
+ char *value = NULL;
+ char *new_value = NULL;
+
+ if (lt_split_name_value (arg, &name, &value) != 0)
+ {
+ XFREE (name);
+ XFREE (value);
+ lt_fatal ("bad argument for %s: '%s'", env_append_opt, arg);
+ }
+
+ new_value = lt_extend_str (getenv (name), value, 1);
+ lt_setenv (name, new_value);
+ XFREE (new_value);
+ XFREE (name);
+ XFREE (value);
+}
+
+void
+lt_update_exe_path (const char *name, const char *value)
+{
+ LTWRAPPER_DEBUGPRINTF (("(lt_update_exe_path) modifying '%s' by prepending '%s'\n",
+ (name ? name : "<NULL>"),
+ (value ? value : "<NULL>")));
+
+ if (name && *name && value && *value)
+ {
+ char *new_value = lt_extend_str (getenv (name), value, 0);
+ /* some systems can't cope with a ':'-terminated path #' */
+ int len = strlen (new_value);
+ while (((len = strlen (new_value)) > 0) && IS_PATH_SEPARATOR (new_value[len-1]))
+ {
+ new_value[len-1] = '\0';
+ }
+ lt_setenv (name, new_value);
+ XFREE (new_value);
+ }
+}
+
+void
+lt_update_lib_path (const char *name, const char *value)
+{
+ LTWRAPPER_DEBUGPRINTF (("(lt_update_lib_path) modifying '%s' by prepending '%s'\n",
+ (name ? name : "<NULL>"),
+ (value ? value : "<NULL>")));
+
+ if (name && *name && value && *value)
+ {
+ char *new_value = lt_extend_str (getenv (name), value, 0);
+ lt_setenv (name, new_value);
+ XFREE (new_value);
+ }
+}
+
+
+EOF
+}
+# end: func_emit_cwrapperexe_src
+
+# func_mode_link arg...
+func_mode_link ()
+{
+ $opt_debug
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*)
+ # It is impossible to link a dll without this setting, and
+ # we shouldn't force the makefile maintainer to figure out
+ # which system we are compiling for in order to pass an extra
+ # flag for every libtool invocation.
+ # allow_undefined=no
+
+ # FIXME: Unfortunately, there are problems with the above when trying
+ # to make a dll which has undefined symbols, in which case not
+ # even a static library is built. For now, we need to specify
+ # -no-undefined on the libtool link line when we can be certain
+ # that all symbols are satisfied, otherwise we get a static library.
+ allow_undefined=yes
+ ;;
+ *)
+ allow_undefined=yes
+ ;;
+ esac
+ libtool_args=$nonopt
+ base_compile="$nonopt $@"
+ compile_command=$nonopt
+ finalize_command=$nonopt
+
+ compile_rpath=
+ finalize_rpath=
+ compile_shlibpath=
+ finalize_shlibpath=
+ convenience=
+ old_convenience=
+ deplibs=
+ old_deplibs=
+ compiler_flags=
+ linker_flags=
+ dllsearchpath=
+ lib_search_path=`pwd`
+ inst_prefix_dir=
+ new_inherited_linker_flags=
+
+ avoid_version=no
+ dlfiles=
+ dlprefiles=
+ dlself=no
+ export_dynamic=no
+ export_symbols=
+ export_symbols_regex=
+ generated=
+ libobjs=
+ ltlibs=
+ module=no
+ no_install=no
+ objs=
+ non_pic_objects=
+ precious_files_regex=
+ prefer_static_libs=no
+ preload=no
+ prev=
+ prevarg=
+ release=
+ rpath=
+ xrpath=
+ perm_rpath=
+ temp_rpath=
+ thread_safe=no
+ vinfo=
+ vinfo_number=no
+ weak_libs=
+ single_module="${wl}-single_module"
+ func_infer_tag $base_compile
+
+ # We need to know -static, to get the right output filenames.
+ for arg
+ do
+ case $arg in
+ -shared)
+ test "$build_libtool_libs" != yes && \
+ func_fatal_configuration "can not build a shared library"
+ build_old_libs=no
+ break
+ ;;
+ -all-static | -static | -static-libtool-libs)
+ case $arg in
+ -all-static)
+ if test "$build_libtool_libs" = yes && test -z "$link_static_flag"; then
+ func_warning "complete static linking is impossible in this configuration"
+ fi
+ if test -n "$link_static_flag"; then
+ dlopen_self=$dlopen_self_static
+ fi
+ prefer_static_libs=yes
+ ;;
+ -static)
+ if test -z "$pic_flag" && test -n "$link_static_flag"; then
+ dlopen_self=$dlopen_self_static
+ fi
+ prefer_static_libs=built
+ ;;
+ -static-libtool-libs)
+ if test -z "$pic_flag" && test -n "$link_static_flag"; then
+ dlopen_self=$dlopen_self_static
+ fi
+ prefer_static_libs=yes
+ ;;
+ esac
+ build_libtool_libs=no
+ build_old_libs=yes
+ break
+ ;;
+ esac
+ done
+
+ # See if our shared archives depend on static archives.
+ test -n "$old_archive_from_new_cmds" && build_old_libs=yes
+
+ # Go through the arguments, transforming them on the way.
+ while test "$#" -gt 0; do
+ arg="$1"
+ shift
+ func_quote_for_eval "$arg"
+ qarg=$func_quote_for_eval_unquoted_result
+ func_append libtool_args " $func_quote_for_eval_result"
+
+ # If the previous option needs an argument, assign it.
+ if test -n "$prev"; then
+ case $prev in
+ output)
+ func_append compile_command " @OUTPUT@"
+ func_append finalize_command " @OUTPUT@"
+ ;;
+ esac
+
+ case $prev in
+ dlfiles|dlprefiles)
+ if test "$preload" = no; then
+ # Add the symbol object into the linking commands.
+ func_append compile_command " @SYMFILE@"
+ func_append finalize_command " @SYMFILE@"
+ preload=yes
+ fi
+ case $arg in
+ *.la | *.lo) ;; # We handle these cases below.
+ force)
+ if test "$dlself" = no; then
+ dlself=needless
+ export_dynamic=yes
+ fi
+ prev=
+ continue
+ ;;
+ self)
+ if test "$prev" = dlprefiles; then
+ dlself=yes
+ elif test "$prev" = dlfiles && test "$dlopen_self" != yes; then
+ dlself=yes
+ else
+ dlself=needless
+ export_dynamic=yes
+ fi
+ prev=
+ continue
+ ;;
+ *)
+ if test "$prev" = dlfiles; then
+ dlfiles="$dlfiles $arg"
+ else
+ dlprefiles="$dlprefiles $arg"
+ fi
+ prev=
+ continue
+ ;;
+ esac
+ ;;
+ expsyms)
+ export_symbols="$arg"
+ test -f "$arg" \
+ || func_fatal_error "symbol file \`$arg' does not exist"
+ prev=
+ continue
+ ;;
+ expsyms_regex)
+ export_symbols_regex="$arg"
+ prev=
+ continue
+ ;;
+ framework)
+ case $host in
+ *-*-darwin*)
+ case "$deplibs " in
+ *" $qarg.ltframework "*) ;;
+ *) deplibs="$deplibs $qarg.ltframework" # this is fixed later
+ ;;
+ esac
+ ;;
+ esac
+ prev=
+ continue
+ ;;
+ inst_prefix)
+ inst_prefix_dir="$arg"
+ prev=
+ continue
+ ;;
+ objectlist)
+ if test -f "$arg"; then
+ save_arg=$arg
+ moreargs=
+ for fil in `cat "$save_arg"`
+ do
+# moreargs="$moreargs $fil"
+ arg=$fil
+ # A libtool-controlled object.
+
+ # Check to see that this really is a libtool object.
+ if func_lalib_unsafe_p "$arg"; then
+ pic_object=
+ non_pic_object=
+
+ # Read the .lo file
+ func_source "$arg"
+
+ if test -z "$pic_object" ||
+ test -z "$non_pic_object" ||
+ test "$pic_object" = none &&
+ test "$non_pic_object" = none; then
+ func_fatal_error "cannot find name of object for \`$arg'"
+ fi
+
+ # Extract subdirectory from the argument.
+ func_dirname "$arg" "/" ""
+ xdir="$func_dirname_result"
+
+ if test "$pic_object" != none; then
+ # Prepend the subdirectory the object is found in.
+ pic_object="$xdir$pic_object"
+
+ if test "$prev" = dlfiles; then
+ if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then
+ dlfiles="$dlfiles $pic_object"
+ prev=
+ continue
+ else
+ # If libtool objects are unsupported, then we need to preload.
+ prev=dlprefiles
+ fi
+ fi
+
+ # CHECK ME: I think I busted this. -Ossama
+ if test "$prev" = dlprefiles; then
+ # Preload the old-style object.
+ dlprefiles="$dlprefiles $pic_object"
+ prev=
+ fi
+
+ # A PIC object.
+ func_append libobjs " $pic_object"
+ arg="$pic_object"
+ fi
+
+ # Non-PIC object.
+ if test "$non_pic_object" != none; then
+ # Prepend the subdirectory the object is found in.
+ non_pic_object="$xdir$non_pic_object"
+
+ # A standard non-PIC object
+ func_append non_pic_objects " $non_pic_object"
+ if test -z "$pic_object" || test "$pic_object" = none ; then
+ arg="$non_pic_object"
+ fi
+ else
+ # If the PIC object exists, use it instead.
+ # $xdir was prepended to $pic_object above.
+ non_pic_object="$pic_object"
+ func_append non_pic_objects " $non_pic_object"
+ fi
+ else
+ # Only an error if not doing a dry-run.
+ if $opt_dry_run; then
+ # Extract subdirectory from the argument.
+ func_dirname "$arg" "/" ""
+ xdir="$func_dirname_result"
+
+ func_lo2o "$arg"
+ pic_object=$xdir$objdir/$func_lo2o_result
+ non_pic_object=$xdir$func_lo2o_result
+ func_append libobjs " $pic_object"
+ func_append non_pic_objects " $non_pic_object"
+ else
+ func_fatal_error "\`$arg' is not a valid libtool object"
+ fi
+ fi
+ done
+ else
+ func_fatal_error "link input file \`$arg' does not exist"
+ fi
+ arg=$save_arg
+ prev=
+ continue
+ ;;
+ precious_regex)
+ precious_files_regex="$arg"
+ prev=
+ continue
+ ;;
+ release)
+ release="-$arg"
+ prev=
+ continue
+ ;;
+ rpath | xrpath)
+ # We need an absolute path.
+ case $arg in
+ [\\/]* | [A-Za-z]:[\\/]*) ;;
+ *)
+ func_fatal_error "only absolute run-paths are allowed"
+ ;;
+ esac
+ if test "$prev" = rpath; then
+ case "$rpath " in
+ *" $arg "*) ;;
+ *) rpath="$rpath $arg" ;;
+ esac
+ else
+ case "$xrpath " in
+ *" $arg "*) ;;
+ *) xrpath="$xrpath $arg" ;;
+ esac
+ fi
+ prev=
+ continue
+ ;;
+ shrext)
+ shrext_cmds="$arg"
+ prev=
+ continue
+ ;;
+ weak)
+ weak_libs="$weak_libs $arg"
+ prev=
+ continue
+ ;;
+ xcclinker)
+ linker_flags="$linker_flags $qarg"
+ compiler_flags="$compiler_flags $qarg"
+ prev=
+ func_append compile_command " $qarg"
+ func_append finalize_command " $qarg"
+ continue
+ ;;
+ xcompiler)
+ compiler_flags="$compiler_flags $qarg"
+ prev=
+ func_append compile_command " $qarg"
+ func_append finalize_command " $qarg"
+ continue
+ ;;
+ xlinker)
+ linker_flags="$linker_flags $qarg"
+ compiler_flags="$compiler_flags $wl$qarg"
+ prev=
+ func_append compile_command " $wl$qarg"
+ func_append finalize_command " $wl$qarg"
+ continue
+ ;;
+ *)
+ eval "$prev=\"\$arg\""
+ prev=
+ continue
+ ;;
+ esac
+ fi # test -n "$prev"
+
+ prevarg="$arg"
+
+ case $arg in
+ -all-static)
+ if test -n "$link_static_flag"; then
+ # See comment for -static flag below, for more details.
+ func_append compile_command " $link_static_flag"
+ func_append finalize_command " $link_static_flag"
+ fi
+ continue
+ ;;
+
+ -allow-undefined)
+ # FIXME: remove this flag sometime in the future.
+ func_fatal_error "\`-allow-undefined' must not be used because it is the default"
+ ;;
+
+ -avoid-version)
+ avoid_version=yes
+ continue
+ ;;
+
+ -dlopen)
+ prev=dlfiles
+ continue
+ ;;
+
+ -dlpreopen)
+ prev=dlprefiles
+ continue
+ ;;
+
+ -export-dynamic)
+ export_dynamic=yes
+ continue
+ ;;
+
+ -export-symbols | -export-symbols-regex)
+ if test -n "$export_symbols" || test -n "$export_symbols_regex"; then
+ func_fatal_error "more than one -exported-symbols argument is not allowed"
+ fi
+ if test "X$arg" = "X-export-symbols"; then
+ prev=expsyms
+ else
+ prev=expsyms_regex
+ fi
+ continue
+ ;;
+
+ -framework)
+ prev=framework
+ continue
+ ;;
+
+ -inst-prefix-dir)
+ prev=inst_prefix
+ continue
+ ;;
+
+ # The native IRIX linker understands -LANG:*, -LIST:* and -LNO:*
+ # so, if we see these flags be careful not to treat them like -L
+ -L[A-Z][A-Z]*:*)
+ case $with_gcc/$host in
+ no/*-*-irix* | /*-*-irix*)
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ ;;
+ esac
+ continue
+ ;;
+
+ -L*)
+ func_stripname '-L' '' "$arg"
+ dir=$func_stripname_result
+ if test -z "$dir"; then
+ if test "$#" -gt 0; then
+ func_fatal_error "require no space between \`-L' and \`$1'"
+ else
+ func_fatal_error "need path for \`-L' option"
+ fi
+ fi
+ # We need an absolute path.
+ case $dir in
+ [\\/]* | [A-Za-z]:[\\/]*) ;;
+ *)
+ absdir=`cd "$dir" && pwd`
+ test -z "$absdir" && \
+ func_fatal_error "cannot determine absolute directory name of \`$dir'"
+ dir="$absdir"
+ ;;
+ esac
+ case "$deplibs " in
+ *" -L$dir "*) ;;
+ *)
+ deplibs="$deplibs -L$dir"
+ lib_search_path="$lib_search_path $dir"
+ ;;
+ esac
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*)
+ testbindir=`$ECHO "X$dir" | $Xsed -e 's*/lib$*/bin*'`
+ case :$dllsearchpath: in
+ *":$dir:"*) ;;
+ ::) dllsearchpath=$dir;;
+ *) dllsearchpath="$dllsearchpath:$dir";;
+ esac
+ case :$dllsearchpath: in
+ *":$testbindir:"*) ;;
+ ::) dllsearchpath=$testbindir;;
+ *) dllsearchpath="$dllsearchpath:$testbindir";;
+ esac
+ ;;
+ esac
+ continue
+ ;;
+
+ -l*)
+ if test "X$arg" = "X-lc" || test "X$arg" = "X-lm"; then
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-beos* | *-cegcc*)
+ # These systems don't actually have a C or math library (as such)
+ continue
+ ;;
+ *-*-os2*)
+ # These systems don't actually have a C library (as such)
+ test "X$arg" = "X-lc" && continue
+ ;;
+ *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
+ # Do not include libc due to us having libc/libc_r.
+ test "X$arg" = "X-lc" && continue
+ ;;
+ *-*-rhapsody* | *-*-darwin1.[012])
+ # Rhapsody C and math libraries are in the System framework
+ deplibs="$deplibs System.ltframework"
+ continue
+ ;;
+ *-*-sco3.2v5* | *-*-sco5v6*)
+ # Causes problems with __ctype
+ test "X$arg" = "X-lc" && continue
+ ;;
+ *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*)
+ # Compiler inserts libc in the correct place for threads to work
+ test "X$arg" = "X-lc" && continue
+ ;;
+ esac
+ elif test "X$arg" = "X-lc_r"; then
+ case $host in
+ *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
+ # Do not include libc_r directly, use -pthread flag.
+ continue
+ ;;
+ esac
+ fi
+ deplibs="$deplibs $arg"
+ continue
+ ;;
+
+ -module)
+ module=yes
+ continue
+ ;;
+
+ # Tru64 UNIX uses -model [arg] to determine the layout of C++
+ # classes, name mangling, and exception handling.
+ # Darwin uses the -arch flag to determine output architecture.
+ -model|-arch|-isysroot)
+ compiler_flags="$compiler_flags $arg"
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ prev=xcompiler
+ continue
+ ;;
+
+ -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads)
+ compiler_flags="$compiler_flags $arg"
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ case "$new_inherited_linker_flags " in
+ *" $arg "*) ;;
+ * ) new_inherited_linker_flags="$new_inherited_linker_flags $arg" ;;
+ esac
+ continue
+ ;;
+
+ -multi_module)
+ single_module="${wl}-multi_module"
+ continue
+ ;;
+
+ -no-fast-install)
+ fast_install=no
+ continue
+ ;;
+
+ -no-install)
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-darwin* | *-cegcc*)
+ # The PATH hackery in wrapper scripts is required on Windows
+ # and Darwin in order for the loader to find any dlls it needs.
+ func_warning "\`-no-install' is ignored for $host"
+ func_warning "assuming \`-no-fast-install' instead"
+ fast_install=no
+ ;;
+ *) no_install=yes ;;
+ esac
+ continue
+ ;;
+
+ -no-undefined)
+ allow_undefined=no
+ continue
+ ;;
+
+ -objectlist)
+ prev=objectlist
+ continue
+ ;;
+
+ -o) prev=output ;;
+
+ -precious-files-regex)
+ prev=precious_regex
+ continue
+ ;;
+
+ -release)
+ prev=release
+ continue
+ ;;
+
+ -rpath)
+ prev=rpath
+ continue
+ ;;
+
+ -R)
+ prev=xrpath
+ continue
+ ;;
+
+ -R*)
+ func_stripname '-R' '' "$arg"
+ dir=$func_stripname_result
+ # We need an absolute path.
+ case $dir in
+ [\\/]* | [A-Za-z]:[\\/]*) ;;
+ *)
+ func_fatal_error "only absolute run-paths are allowed"
+ ;;
+ esac
+ case "$xrpath " in
+ *" $dir "*) ;;
+ *) xrpath="$xrpath $dir" ;;
+ esac
+ continue
+ ;;
+
+ -shared)
+ # The effects of -shared are defined in a previous loop.
+ continue
+ ;;
+
+ -shrext)
+ prev=shrext
+ continue
+ ;;
+
+ -static | -static-libtool-libs)
+ # The effects of -static are defined in a previous loop.
+ # We used to do the same as -all-static on platforms that
+ # didn't have a PIC flag, but the assumption that the effects
+ # would be equivalent was wrong. It would break on at least
+ # Digital Unix and AIX.
+ continue
+ ;;
+
+ -thread-safe)
+ thread_safe=yes
+ continue
+ ;;
+
+ -version-info)
+ prev=vinfo
+ continue
+ ;;
+
+ -version-number)
+ prev=vinfo
+ vinfo_number=yes
+ continue
+ ;;
+
+ -weak)
+ prev=weak
+ continue
+ ;;
+
+ -Wc,*)
+ func_stripname '-Wc,' '' "$arg"
+ args=$func_stripname_result
+ arg=
+ save_ifs="$IFS"; IFS=','
+ for flag in $args; do
+ IFS="$save_ifs"
+ func_quote_for_eval "$flag"
+ arg="$arg $wl$func_quote_for_eval_result"
+ compiler_flags="$compiler_flags $func_quote_for_eval_result"
+ done
+ IFS="$save_ifs"
+ func_stripname ' ' '' "$arg"
+ arg=$func_stripname_result
+ ;;
+
+ -Wl,*)
+ func_stripname '-Wl,' '' "$arg"
+ args=$func_stripname_result
+ arg=
+ save_ifs="$IFS"; IFS=','
+ for flag in $args; do
+ IFS="$save_ifs"
+ func_quote_for_eval "$flag"
+ arg="$arg $wl$func_quote_for_eval_result"
+ compiler_flags="$compiler_flags $wl$func_quote_for_eval_result"
+ linker_flags="$linker_flags $func_quote_for_eval_result"
+ done
+ IFS="$save_ifs"
+ func_stripname ' ' '' "$arg"
+ arg=$func_stripname_result
+ ;;
+
+ -Xcompiler)
+ prev=xcompiler
+ continue
+ ;;
+
+ -Xlinker)
+ prev=xlinker
+ continue
+ ;;
+
+ -XCClinker)
+ prev=xcclinker
+ continue
+ ;;
+
+ # -msg_* for osf cc
+ -msg_*)
+ func_quote_for_eval "$arg"
+ arg="$func_quote_for_eval_result"
+ ;;
+
+ # -64, -mips[0-9] enable 64-bit mode on the SGI compiler
+ # -r[0-9][0-9]* specifies the processor on the SGI compiler
+ # -xarch=*, -xtarget=* enable 64-bit mode on the Sun compiler
+ # +DA*, +DD* enable 64-bit mode on the HP compiler
+ # -q* pass through compiler args for the IBM compiler
+ # -m*, -t[45]*, -txscale* pass through architecture-specific
+ # compiler args for GCC
+ # -F/path gives path to uninstalled frameworks, gcc on darwin
+ # -p, -pg, --coverage, -fprofile-* pass through profiling flag for GCC
+ # @file GCC response files
+ -64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*| \
+ -t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*)
+ func_quote_for_eval "$arg"
+ arg="$func_quote_for_eval_result"
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ compiler_flags="$compiler_flags $arg"
+ continue
+ ;;
+
+ # Some other compiler flag.
+ -* | +*)
+ func_quote_for_eval "$arg"
+ arg="$func_quote_for_eval_result"
+ ;;
+
+ *.$objext)
+ # A standard object.
+ objs="$objs $arg"
+ ;;
+
+ *.lo)
+ # A libtool-controlled object.
+
+ # Check to see that this really is a libtool object.
+ if func_lalib_unsafe_p "$arg"; then
+ pic_object=
+ non_pic_object=
+
+ # Read the .lo file
+ func_source "$arg"
+
+ if test -z "$pic_object" ||
+ test -z "$non_pic_object" ||
+ test "$pic_object" = none &&
+ test "$non_pic_object" = none; then
+ func_fatal_error "cannot find name of object for \`$arg'"
+ fi
+
+ # Extract subdirectory from the argument.
+ func_dirname "$arg" "/" ""
+ xdir="$func_dirname_result"
+
+ if test "$pic_object" != none; then
+ # Prepend the subdirectory the object is found in.
+ pic_object="$xdir$pic_object"
+
+ if test "$prev" = dlfiles; then
+ if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then
+ dlfiles="$dlfiles $pic_object"
+ prev=
+ continue
+ else
+ # If libtool objects are unsupported, then we need to preload.
+ prev=dlprefiles
+ fi
+ fi
+
+ # CHECK ME: I think I busted this. -Ossama
+ if test "$prev" = dlprefiles; then
+ # Preload the old-style object.
+ dlprefiles="$dlprefiles $pic_object"
+ prev=
+ fi
+
+ # A PIC object.
+ func_append libobjs " $pic_object"
+ arg="$pic_object"
+ fi
+
+ # Non-PIC object.
+ if test "$non_pic_object" != none; then
+ # Prepend the subdirectory the object is found in.
+ non_pic_object="$xdir$non_pic_object"
+
+ # A standard non-PIC object
+ func_append non_pic_objects " $non_pic_object"
+ if test -z "$pic_object" || test "$pic_object" = none ; then
+ arg="$non_pic_object"
+ fi
+ else
+ # If the PIC object exists, use it instead.
+ # $xdir was prepended to $pic_object above.
+ non_pic_object="$pic_object"
+ func_append non_pic_objects " $non_pic_object"
+ fi
+ else
+ # Only an error if not doing a dry-run.
+ if $opt_dry_run; then
+ # Extract subdirectory from the argument.
+ func_dirname "$arg" "/" ""
+ xdir="$func_dirname_result"
+
+ func_lo2o "$arg"
+ pic_object=$xdir$objdir/$func_lo2o_result
+ non_pic_object=$xdir$func_lo2o_result
+ func_append libobjs " $pic_object"
+ func_append non_pic_objects " $non_pic_object"
+ else
+ func_fatal_error "\`$arg' is not a valid libtool object"
+ fi
+ fi
+ ;;
+
+ *.$libext)
+ # An archive.
+ deplibs="$deplibs $arg"
+ old_deplibs="$old_deplibs $arg"
+ continue
+ ;;
+
+ *.la)
+ # A libtool-controlled library.
+
+ if test "$prev" = dlfiles; then
+ # This library was specified with -dlopen.
+ dlfiles="$dlfiles $arg"
+ prev=
+ elif test "$prev" = dlprefiles; then
+ # The library was specified with -dlpreopen.
+ dlprefiles="$dlprefiles $arg"
+ prev=
+ else
+ deplibs="$deplibs $arg"
+ fi
+ continue
+ ;;
+
+ # Some other compiler argument.
+ *)
+ # Unknown arguments in both finalize_command and compile_command need
+ # to be aesthetically quoted because they are evaled later.
+ func_quote_for_eval "$arg"
+ arg="$func_quote_for_eval_result"
+ ;;
+ esac # arg
+
+ # Now actually substitute the argument into the commands.
+ if test -n "$arg"; then
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ fi
+ done # argument parsing loop
+
+ test -n "$prev" && \
+ func_fatal_help "the \`$prevarg' option requires an argument"
+
+ if test "$export_dynamic" = yes && test -n "$export_dynamic_flag_spec"; then
+ eval arg=\"$export_dynamic_flag_spec\"
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ fi
+
+ oldlibs=
+ # calculate the name of the file, without its directory
+ func_basename "$output"
+ outputname="$func_basename_result"
+ libobjs_save="$libobjs"
+
+ if test -n "$shlibpath_var"; then
+ # get the directories listed in $shlibpath_var
+ eval shlib_search_path=\`\$ECHO \"X\${$shlibpath_var}\" \| \$Xsed -e \'s/:/ /g\'\`
+ else
+ shlib_search_path=
+ fi
+ eval sys_lib_search_path=\"$sys_lib_search_path_spec\"
+ eval sys_lib_dlsearch_path=\"$sys_lib_dlsearch_path_spec\"
+
+ func_dirname "$output" "/" ""
+ output_objdir="$func_dirname_result$objdir"
+ # Create the object directory.
+ func_mkdir_p "$output_objdir"
+
+ # Determine the type of output
+ case $output in
+ "")
+ func_fatal_help "you must specify an output file"
+ ;;
+ *.$libext) linkmode=oldlib ;;
+ *.lo | *.$objext) linkmode=obj ;;
+ *.la) linkmode=lib ;;
+ *) linkmode=prog ;; # Anything else should be a program.
+ esac
+
+ specialdeplibs=
+
+ libs=
+ # Find all interdependent deplibs by searching for libraries
+ # that are linked more than once (e.g. -la -lb -la)
+ for deplib in $deplibs; do
+ if $opt_duplicate_deps ; then
+ case "$libs " in
+ *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+ esac
+ fi
+ libs="$libs $deplib"
+ done
+
+ if test "$linkmode" = lib; then
+ libs="$predeps $libs $compiler_lib_search_path $postdeps"
+
+ # Compute libraries that are listed more than once in $predeps
+ # $postdeps and mark them as special (i.e., whose duplicates are
+ # not to be eliminated).
+ pre_post_deps=
+ if $opt_duplicate_compiler_generated_deps; then
+ for pre_post_dep in $predeps $postdeps; do
+ case "$pre_post_deps " in
+ *" $pre_post_dep "*) specialdeplibs="$specialdeplibs $pre_post_deps" ;;
+ esac
+ pre_post_deps="$pre_post_deps $pre_post_dep"
+ done
+ fi
+ pre_post_deps=
+ fi
+
+ deplibs=
+ newdependency_libs=
+ newlib_search_path=
+ need_relink=no # whether we're linking any uninstalled libtool libraries
+ notinst_deplibs= # not-installed libtool libraries
+ notinst_path= # paths that contain not-installed libtool libraries
+
+ case $linkmode in
+ lib)
+ passes="conv dlpreopen link"
+ for file in $dlfiles $dlprefiles; do
+ case $file in
+ *.la) ;;
+ *)
+ func_fatal_help "libraries can \`-dlopen' only libtool libraries: $file"
+ ;;
+ esac
+ done
+ ;;
+ prog)
+ compile_deplibs=
+ finalize_deplibs=
+ alldeplibs=no
+ newdlfiles=
+ newdlprefiles=
+ passes="conv scan dlopen dlpreopen link"
+ ;;
+ *) passes="conv"
+ ;;
+ esac
+
+ for pass in $passes; do
+ # The preopen pass in lib mode reverses $deplibs; put it back here
+ # so that -L comes before libs that need it for instance...
+ if test "$linkmode,$pass" = "lib,link"; then
+ ## FIXME: Find the place where the list is rebuilt in the wrong
+ ## order, and fix it there properly
+ tmp_deplibs=
+ for deplib in $deplibs; do
+ tmp_deplibs="$deplib $tmp_deplibs"
+ done
+ deplibs="$tmp_deplibs"
+ fi
+
+ if test "$linkmode,$pass" = "lib,link" ||
+ test "$linkmode,$pass" = "prog,scan"; then
+ libs="$deplibs"
+ deplibs=
+ fi
+ if test "$linkmode" = prog; then
+ case $pass in
+ dlopen) libs="$dlfiles" ;;
+ dlpreopen) libs="$dlprefiles" ;;
+ link)
+ libs="$deplibs %DEPLIBS%"
+ test "X$link_all_deplibs" != Xno && libs="$libs $dependency_libs"
+ ;;
+ esac
+ fi
+ if test "$linkmode,$pass" = "lib,dlpreopen"; then
+ # Collect and forward deplibs of preopened libtool libs
+ for lib in $dlprefiles; do
+ # Ignore non-libtool-libs
+ dependency_libs=
+ case $lib in
+ *.la) func_source "$lib" ;;
+ esac
+
+ # Collect preopened libtool deplibs, except any this library
+ # has declared as weak libs
+ for deplib in $dependency_libs; do
+ deplib_base=`$ECHO "X$deplib" | $Xsed -e "$basename"`
+ case " $weak_libs " in
+ *" $deplib_base "*) ;;
+ *) deplibs="$deplibs $deplib" ;;
+ esac
+ done
+ done
+ libs="$dlprefiles"
+ fi
+ if test "$pass" = dlopen; then
+ # Collect dlpreopened libraries
+ save_deplibs="$deplibs"
+ deplibs=
+ fi
+
+ for deplib in $libs; do
+ lib=
+ found=no
+ case $deplib in
+ -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads)
+ if test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ compiler_flags="$compiler_flags $deplib"
+ if test "$linkmode" = lib ; then
+ case "$new_inherited_linker_flags " in
+ *" $deplib "*) ;;
+ * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;;
+ esac
+ fi
+ fi
+ continue
+ ;;
+ -l*)
+ if test "$linkmode" != lib && test "$linkmode" != prog; then
+ func_warning "\`-l' is ignored for archives/objects"
+ continue
+ fi
+ func_stripname '-l' '' "$deplib"
+ name=$func_stripname_result
+ if test "$linkmode" = lib; then
+ searchdirs="$newlib_search_path $lib_search_path $compiler_lib_search_dirs $sys_lib_search_path $shlib_search_path"
+ else
+ searchdirs="$newlib_search_path $lib_search_path $sys_lib_search_path $shlib_search_path"
+ fi
+ for searchdir in $searchdirs; do
+ for search_ext in .la $std_shrext .so .a; do
+ # Search the libtool library
+ lib="$searchdir/lib${name}${search_ext}"
+ if test -f "$lib"; then
+ if test "$search_ext" = ".la"; then
+ found=yes
+ else
+ found=no
+ fi
+ break 2
+ fi
+ done
+ done
+ if test "$found" != yes; then
+ # deplib doesn't seem to be a libtool library
+ if test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ deplibs="$deplib $deplibs"
+ test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs"
+ fi
+ continue
+ else # deplib is a libtool library
+ # If $allow_libtool_libs_with_static_runtimes && $deplib is a stdlib,
+ # We need to do some special things here, and not later.
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $deplib "*)
+ if func_lalib_p "$lib"; then
+ library_names=
+ old_library=
+ func_source "$lib"
+ for l in $old_library $library_names; do
+ ll="$l"
+ done
+ if test "X$ll" = "X$old_library" ; then # only static version available
+ found=no
+ func_dirname "$lib" "" "."
+ ladir="$func_dirname_result"
+ lib=$ladir/$old_library
+ if test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ deplibs="$deplib $deplibs"
+ test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs"
+ fi
+ continue
+ fi
+ fi
+ ;;
+ *) ;;
+ esac
+ fi
+ fi
+ ;; # -l
+ *.ltframework)
+ if test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ deplibs="$deplib $deplibs"
+ if test "$linkmode" = lib ; then
+ case "$new_inherited_linker_flags " in
+ *" $deplib "*) ;;
+ * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;;
+ esac
+ fi
+ fi
+ continue
+ ;;
+ -L*)
+ case $linkmode in
+ lib)
+ deplibs="$deplib $deplibs"
+ test "$pass" = conv && continue
+ newdependency_libs="$deplib $newdependency_libs"
+ func_stripname '-L' '' "$deplib"
+ newlib_search_path="$newlib_search_path $func_stripname_result"
+ ;;
+ prog)
+ if test "$pass" = conv; then
+ deplibs="$deplib $deplibs"
+ continue
+ fi
+ if test "$pass" = scan; then
+ deplibs="$deplib $deplibs"
+ else
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ fi
+ func_stripname '-L' '' "$deplib"
+ newlib_search_path="$newlib_search_path $func_stripname_result"
+ ;;
+ *)
+ func_warning "\`-L' is ignored for archives/objects"
+ ;;
+ esac # linkmode
+ continue
+ ;; # -L
+ -R*)
+ if test "$pass" = link; then
+ func_stripname '-R' '' "$deplib"
+ dir=$func_stripname_result
+ # Make sure the xrpath contains only unique directories.
+ case "$xrpath " in
+ *" $dir "*) ;;
+ *) xrpath="$xrpath $dir" ;;
+ esac
+ fi
+ deplibs="$deplib $deplibs"
+ continue
+ ;;
+ *.la) lib="$deplib" ;;
+ *.$libext)
+ if test "$pass" = conv; then
+ deplibs="$deplib $deplibs"
+ continue
+ fi
+ case $linkmode in
+ lib)
+ # Linking convenience modules into shared libraries is allowed,
+ # but linking other static libraries is non-portable.
+ case " $dlpreconveniencelibs " in
+ *" $deplib "*) ;;
+ *)
+ valid_a_lib=no
+ case $deplibs_check_method in
+ match_pattern*)
+ set dummy $deplibs_check_method; shift
+ match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"`
+ if eval "\$ECHO \"X$deplib\"" 2>/dev/null | $Xsed -e 10q \
+ | $EGREP "$match_pattern_regex" > /dev/null; then
+ valid_a_lib=yes
+ fi
+ ;;
+ pass_all)
+ valid_a_lib=yes
+ ;;
+ esac
+ if test "$valid_a_lib" != yes; then
+ $ECHO
+ $ECHO "*** Warning: Trying to link with static lib archive $deplib."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have"
+ $ECHO "*** because the file extensions .$libext of this argument makes me believe"
+ $ECHO "*** that it is just a static archive that I should not use here."
+ else
+ $ECHO
+ $ECHO "*** Warning: Linking the shared library $output against the"
+ $ECHO "*** static library $deplib is not portable!"
+ deplibs="$deplib $deplibs"
+ fi
+ ;;
+ esac
+ continue
+ ;;
+ prog)
+ if test "$pass" != link; then
+ deplibs="$deplib $deplibs"
+ else
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ fi
+ continue
+ ;;
+ esac # linkmode
+ ;; # *.$libext
+ *.lo | *.$objext)
+ if test "$pass" = conv; then
+ deplibs="$deplib $deplibs"
+ elif test "$linkmode" = prog; then
+ if test "$pass" = dlpreopen || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then
+ # If there is no dlopen support or we're linking statically,
+ # we need to preload.
+ newdlprefiles="$newdlprefiles $deplib"
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ newdlfiles="$newdlfiles $deplib"
+ fi
+ fi
+ continue
+ ;;
+ %DEPLIBS%)
+ alldeplibs=yes
+ continue
+ ;;
+ esac # case $deplib
+
+ if test "$found" = yes || test -f "$lib"; then :
+ else
+ func_fatal_error "cannot find the library \`$lib' or unhandled argument \`$deplib'"
+ fi
+
+ # Check to see that this really is a libtool archive.
+ func_lalib_unsafe_p "$lib" \
+ || func_fatal_error "\`$lib' is not a valid libtool archive"
+
+ func_dirname "$lib" "" "."
+ ladir="$func_dirname_result"
+
+ dlname=
+ dlopen=
+ dlpreopen=
+ libdir=
+ library_names=
+ old_library=
+ inherited_linker_flags=
+ # If the library was installed with an old release of libtool,
+ # it will not redefine variables installed, or shouldnotlink
+ installed=yes
+ shouldnotlink=no
+ avoidtemprpath=
+
+
+ # Read the .la file
+ func_source "$lib"
+
+ # Convert "-framework foo" to "foo.ltframework"
+ if test -n "$inherited_linker_flags"; then
+ tmp_inherited_linker_flags=`$ECHO "X$inherited_linker_flags" | $Xsed -e 's/-framework \([^ $]*\)/\1.ltframework/g'`
+ for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
+ case " $new_inherited_linker_flags " in
+ *" $tmp_inherited_linker_flag "*) ;;
+ *) new_inherited_linker_flags="$new_inherited_linker_flags $tmp_inherited_linker_flag";;
+ esac
+ done
+ fi
+ dependency_libs=`$ECHO "X $dependency_libs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ if test "$linkmode,$pass" = "lib,link" ||
+ test "$linkmode,$pass" = "prog,scan" ||
+ { test "$linkmode" != prog && test "$linkmode" != lib; }; then
+ test -n "$dlopen" && dlfiles="$dlfiles $dlopen"
+ test -n "$dlpreopen" && dlprefiles="$dlprefiles $dlpreopen"
+ fi
+
+ if test "$pass" = conv; then
+ # Only check for convenience libraries
+ deplibs="$lib $deplibs"
+ if test -z "$libdir"; then
+ if test -z "$old_library"; then
+ func_fatal_error "cannot find name of link library for \`$lib'"
+ fi
+ # It is a libtool convenience library, so add in its objects.
+ convenience="$convenience $ladir/$objdir/$old_library"
+ old_convenience="$old_convenience $ladir/$objdir/$old_library"
+ tmp_libs=
+ for deplib in $dependency_libs; do
+ deplibs="$deplib $deplibs"
+ if $opt_duplicate_deps ; then
+ case "$tmp_libs " in
+ *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+ esac
+ fi
+ tmp_libs="$tmp_libs $deplib"
+ done
+ elif test "$linkmode" != prog && test "$linkmode" != lib; then
+ func_fatal_error "\`$lib' is not a convenience library"
+ fi
+ continue
+ fi # $pass = conv
+
+
+ # Get the name of the library we link against.
+ linklib=
+ for l in $old_library $library_names; do
+ linklib="$l"
+ done
+ if test -z "$linklib"; then
+ func_fatal_error "cannot find name of link library for \`$lib'"
+ fi
+
+ # This library was specified with -dlopen.
+ if test "$pass" = dlopen; then
+ if test -z "$libdir"; then
+ func_fatal_error "cannot -dlopen a convenience library: \`$lib'"
+ fi
+ if test -z "$dlname" ||
+ test "$dlopen_support" != yes ||
+ test "$build_libtool_libs" = no; then
+ # If there is no dlname, no dlopen support or we're linking
+ # statically, we need to preload. We also need to preload any
+ # dependent libraries so libltdl's deplib preloader doesn't
+ # bomb out in the load deplibs phase.
+ dlprefiles="$dlprefiles $lib $dependency_libs"
+ else
+ newdlfiles="$newdlfiles $lib"
+ fi
+ continue
+ fi # $pass = dlopen
+
+ # We need an absolute path.
+ case $ladir in
+ [\\/]* | [A-Za-z]:[\\/]*) abs_ladir="$ladir" ;;
+ *)
+ abs_ladir=`cd "$ladir" && pwd`
+ if test -z "$abs_ladir"; then
+ func_warning "cannot determine absolute directory name of \`$ladir'"
+ func_warning "passing it literally to the linker, although it might fail"
+ abs_ladir="$ladir"
+ fi
+ ;;
+ esac
+ func_basename "$lib"
+ laname="$func_basename_result"
+
+ # Find the relevant object directory and library name.
+ if test "X$installed" = Xyes; then
+ if test ! -f "$libdir/$linklib" && test -f "$abs_ladir/$linklib"; then
+ func_warning "library \`$lib' was moved."
+ dir="$ladir"
+ absdir="$abs_ladir"
+ libdir="$abs_ladir"
+ else
+ dir="$libdir"
+ absdir="$libdir"
+ fi
+ test "X$hardcode_automatic" = Xyes && avoidtemprpath=yes
+ else
+ if test ! -f "$ladir/$objdir/$linklib" && test -f "$abs_ladir/$linklib"; then
+ dir="$ladir"
+ absdir="$abs_ladir"
+ # Remove this search path later
+ notinst_path="$notinst_path $abs_ladir"
+ else
+ dir="$ladir/$objdir"
+ absdir="$abs_ladir/$objdir"
+ # Remove this search path later
+ notinst_path="$notinst_path $abs_ladir"
+ fi
+ fi # $installed = yes
+ func_stripname 'lib' '.la' "$laname"
+ name=$func_stripname_result
+
+ # This library was specified with -dlpreopen.
+ if test "$pass" = dlpreopen; then
+ if test -z "$libdir" && test "$linkmode" = prog; then
+ func_fatal_error "only libraries may -dlpreopen a convenience library: \`$lib'"
+ fi
+ # Prefer using a static library (so that no silly _DYNAMIC symbols
+ # are required to link).
+ if test -n "$old_library"; then
+ newdlprefiles="$newdlprefiles $dir/$old_library"
+ # Keep a list of preopened convenience libraries to check
+ # that they are being used correctly in the link pass.
+ test -z "$libdir" && \
+ dlpreconveniencelibs="$dlpreconveniencelibs $dir/$old_library"
+ # Otherwise, use the dlname, so that lt_dlopen finds it.
+ elif test -n "$dlname"; then
+ newdlprefiles="$newdlprefiles $dir/$dlname"
+ else
+ newdlprefiles="$newdlprefiles $dir/$linklib"
+ fi
+ fi # $pass = dlpreopen
+
+ if test -z "$libdir"; then
+ # Link the convenience library
+ if test "$linkmode" = lib; then
+ deplibs="$dir/$old_library $deplibs"
+ elif test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$dir/$old_library $compile_deplibs"
+ finalize_deplibs="$dir/$old_library $finalize_deplibs"
+ else
+ deplibs="$lib $deplibs" # used for prog,scan pass
+ fi
+ continue
+ fi
+
+
+ if test "$linkmode" = prog && test "$pass" != link; then
+ newlib_search_path="$newlib_search_path $ladir"
+ deplibs="$lib $deplibs"
+
+ linkalldeplibs=no
+ if test "$link_all_deplibs" != no || test -z "$library_names" ||
+ test "$build_libtool_libs" = no; then
+ linkalldeplibs=yes
+ fi
+
+ tmp_libs=
+ for deplib in $dependency_libs; do
+ case $deplib in
+ -L*) func_stripname '-L' '' "$deplib"
+ newlib_search_path="$newlib_search_path $func_stripname_result"
+ ;;
+ esac
+ # Need to link against all dependency_libs?
+ if test "$linkalldeplibs" = yes; then
+ deplibs="$deplib $deplibs"
+ else
+ # Need to hardcode shared library paths
+ # or/and link against static libraries
+ newdependency_libs="$deplib $newdependency_libs"
+ fi
+ if $opt_duplicate_deps ; then
+ case "$tmp_libs " in
+ *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+ esac
+ fi
+ tmp_libs="$tmp_libs $deplib"
+ done # for deplib
+ continue
+ fi # $linkmode = prog...
+
+ if test "$linkmode,$pass" = "prog,link"; then
+ if test -n "$library_names" &&
+ { { test "$prefer_static_libs" = no ||
+ test "$prefer_static_libs,$installed" = "built,yes"; } ||
+ test -z "$old_library"; }; then
+ # We need to hardcode the library path
+ if test -n "$shlibpath_var" && test -z "$avoidtemprpath" ; then
+ # Make sure the rpath contains only unique directories.
+ case "$temp_rpath:" in
+ *"$absdir:"*) ;;
+ *) temp_rpath="$temp_rpath$absdir:" ;;
+ esac
+ fi
+
+ # Hardcode the library path.
+ # Skip directories that are in the system default run-time
+ # search path.
+ case " $sys_lib_dlsearch_path " in
+ *" $absdir "*) ;;
+ *)
+ case "$compile_rpath " in
+ *" $absdir "*) ;;
+ *) compile_rpath="$compile_rpath $absdir"
+ esac
+ ;;
+ esac
+ case " $sys_lib_dlsearch_path " in
+ *" $libdir "*) ;;
+ *)
+ case "$finalize_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_rpath="$finalize_rpath $libdir"
+ esac
+ ;;
+ esac
+ fi # $linkmode,$pass = prog,link...
+
+ if test "$alldeplibs" = yes &&
+ { test "$deplibs_check_method" = pass_all ||
+ { test "$build_libtool_libs" = yes &&
+ test -n "$library_names"; }; }; then
+ # We only need to search for static libraries
+ continue
+ fi
+ fi
+
+ link_static=no # Whether the deplib will be linked statically
+ use_static_libs=$prefer_static_libs
+ if test "$use_static_libs" = built && test "$installed" = yes; then
+ use_static_libs=no
+ fi
+ if test -n "$library_names" &&
+ { test "$use_static_libs" = no || test -z "$old_library"; }; then
+ case $host in
+ *cygwin* | *mingw* | *cegcc*)
+ # No point in relinking DLLs because paths are not encoded
+ notinst_deplibs="$notinst_deplibs $lib"
+ need_relink=no
+ ;;
+ *)
+ if test "$installed" = no; then
+ notinst_deplibs="$notinst_deplibs $lib"
+ need_relink=yes
+ fi
+ ;;
+ esac
+ # This is a shared library
+
+ # Warn about portability, can't link against -module's on some
+ # systems (darwin). Don't bleat about dlopened modules though!
+ dlopenmodule=""
+ for dlpremoduletest in $dlprefiles; do
+ if test "X$dlpremoduletest" = "X$lib"; then
+ dlopenmodule="$dlpremoduletest"
+ break
+ fi
+ done
+ if test -z "$dlopenmodule" && test "$shouldnotlink" = yes && test "$pass" = link; then
+ $ECHO
+ if test "$linkmode" = prog; then
+ $ECHO "*** Warning: Linking the executable $output against the loadable module"
+ else
+ $ECHO "*** Warning: Linking the shared library $output against the loadable module"
+ fi
+ $ECHO "*** $linklib is not portable!"
+ fi
+ if test "$linkmode" = lib &&
+ test "$hardcode_into_libs" = yes; then
+ # Hardcode the library path.
+ # Skip directories that are in the system default run-time
+ # search path.
+ case " $sys_lib_dlsearch_path " in
+ *" $absdir "*) ;;
+ *)
+ case "$compile_rpath " in
+ *" $absdir "*) ;;
+ *) compile_rpath="$compile_rpath $absdir"
+ esac
+ ;;
+ esac
+ case " $sys_lib_dlsearch_path " in
+ *" $libdir "*) ;;
+ *)
+ case "$finalize_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_rpath="$finalize_rpath $libdir"
+ esac
+ ;;
+ esac
+ fi
+
+ if test -n "$old_archive_from_expsyms_cmds"; then
+ # figure out the soname
+ set dummy $library_names
+ shift
+ realname="$1"
+ shift
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ # use dlname if we got it. it's perfectly good, no?
+ if test -n "$dlname"; then
+ soname="$dlname"
+ elif test -n "$soname_spec"; then
+ # bleh windows
+ case $host in
+ *cygwin* | mingw* | *cegcc*)
+ func_arith $current - $age
+ major=$func_arith_result
+ versuffix="-$major"
+ ;;
+ esac
+ eval soname=\"$soname_spec\"
+ else
+ soname="$realname"
+ fi
+
+ # Make a new name for the extract_expsyms_cmds to use
+ soroot="$soname"
+ func_basename "$soroot"
+ soname="$func_basename_result"
+ func_stripname 'lib' '.dll' "$soname"
+ newlib=libimp-$func_stripname_result.a
+
+ # If the library has no export list, then create one now
+ if test -f "$output_objdir/$soname-def"; then :
+ else
+ func_verbose "extracting exported symbol list from \`$soname'"
+ func_execute_cmds "$extract_expsyms_cmds" 'exit $?'
+ fi
+
+ # Create $newlib
+ if test -f "$output_objdir/$newlib"; then :; else
+ func_verbose "generating import library for \`$soname'"
+ func_execute_cmds "$old_archive_from_expsyms_cmds" 'exit $?'
+ fi
+ # make sure the library variables are pointing to the new library
+ dir=$output_objdir
+ linklib=$newlib
+ fi # test -n "$old_archive_from_expsyms_cmds"
+
+ if test "$linkmode" = prog || test "$mode" != relink; then
+ add_shlibpath=
+ add_dir=
+ add=
+ lib_linked=yes
+ case $hardcode_action in
+ immediate | unsupported)
+ if test "$hardcode_direct" = no; then
+ add="$dir/$linklib"
+ case $host in
+ *-*-sco3.2v5.0.[024]*) add_dir="-L$dir" ;;
+ *-*-sysv4*uw2*) add_dir="-L$dir" ;;
+ *-*-sysv5OpenUNIX* | *-*-sysv5UnixWare7.[01].[10]* | \
+ *-*-unixware7*) add_dir="-L$dir" ;;
+ *-*-darwin* )
+ # if the lib is a (non-dlopened) module then we can not
+ # link against it, someone is ignoring the earlier warnings
+ if /usr/bin/file -L $add 2> /dev/null |
+ $GREP ": [^:]* bundle" >/dev/null ; then
+ if test "X$dlopenmodule" != "X$lib"; then
+ $ECHO "*** Warning: lib $linklib is a module, not a shared library"
+ if test -z "$old_library" ; then
+ $ECHO
+ $ECHO "*** And there doesn't seem to be a static archive available"
+ $ECHO "*** The link will probably fail, sorry"
+ else
+ add="$dir/$old_library"
+ fi
+ elif test -n "$old_library"; then
+ add="$dir/$old_library"
+ fi
+ fi
+ esac
+ elif test "$hardcode_minus_L" = no; then
+ case $host in
+ *-*-sunos*) add_shlibpath="$dir" ;;
+ esac
+ add_dir="-L$dir"
+ add="-l$name"
+ elif test "$hardcode_shlibpath_var" = no; then
+ add_shlibpath="$dir"
+ add="-l$name"
+ else
+ lib_linked=no
+ fi
+ ;;
+ relink)
+ if test "$hardcode_direct" = yes &&
+ test "$hardcode_direct_absolute" = no; then
+ add="$dir/$linklib"
+ elif test "$hardcode_minus_L" = yes; then
+ add_dir="-L$dir"
+ # Try looking first in the location we're being installed to.
+ if test -n "$inst_prefix_dir"; then
+ case $libdir in
+ [\\/]*)
+ add_dir="$add_dir -L$inst_prefix_dir$libdir"
+ ;;
+ esac
+ fi
+ add="-l$name"
+ elif test "$hardcode_shlibpath_var" = yes; then
+ add_shlibpath="$dir"
+ add="-l$name"
+ else
+ lib_linked=no
+ fi
+ ;;
+ *) lib_linked=no ;;
+ esac
+
+ if test "$lib_linked" != yes; then
+ func_fatal_configuration "unsupported hardcode properties"
+ fi
+
+ if test -n "$add_shlibpath"; then
+ case :$compile_shlibpath: in
+ *":$add_shlibpath:"*) ;;
+ *) compile_shlibpath="$compile_shlibpath$add_shlibpath:" ;;
+ esac
+ fi
+ if test "$linkmode" = prog; then
+ test -n "$add_dir" && compile_deplibs="$add_dir $compile_deplibs"
+ test -n "$add" && compile_deplibs="$add $compile_deplibs"
+ else
+ test -n "$add_dir" && deplibs="$add_dir $deplibs"
+ test -n "$add" && deplibs="$add $deplibs"
+ if test "$hardcode_direct" != yes &&
+ test "$hardcode_minus_L" != yes &&
+ test "$hardcode_shlibpath_var" = yes; then
+ case :$finalize_shlibpath: in
+ *":$libdir:"*) ;;
+ *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;;
+ esac
+ fi
+ fi
+ fi
+
+ if test "$linkmode" = prog || test "$mode" = relink; then
+ add_shlibpath=
+ add_dir=
+ add=
+ # Finalize command for both is simple: just hardcode it.
+ if test "$hardcode_direct" = yes &&
+ test "$hardcode_direct_absolute" = no; then
+ add="$libdir/$linklib"
+ elif test "$hardcode_minus_L" = yes; then
+ add_dir="-L$libdir"
+ add="-l$name"
+ elif test "$hardcode_shlibpath_var" = yes; then
+ case :$finalize_shlibpath: in
+ *":$libdir:"*) ;;
+ *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;;
+ esac
+ add="-l$name"
+ elif test "$hardcode_automatic" = yes; then
+ if test -n "$inst_prefix_dir" &&
+ test -f "$inst_prefix_dir$libdir/$linklib" ; then
+ add="$inst_prefix_dir$libdir/$linklib"
+ else
+ add="$libdir/$linklib"
+ fi
+ else
+ # We cannot seem to hardcode it, guess we'll fake it.
+ add_dir="-L$libdir"
+ # Try looking first in the location we're being installed to.
+ if test -n "$inst_prefix_dir"; then
+ case $libdir in
+ [\\/]*)
+ add_dir="$add_dir -L$inst_prefix_dir$libdir"
+ ;;
+ esac
+ fi
+ add="-l$name"
+ fi
+
+ if test "$linkmode" = prog; then
+ test -n "$add_dir" && finalize_deplibs="$add_dir $finalize_deplibs"
+ test -n "$add" && finalize_deplibs="$add $finalize_deplibs"
+ else
+ test -n "$add_dir" && deplibs="$add_dir $deplibs"
+ test -n "$add" && deplibs="$add $deplibs"
+ fi
+ fi
+ elif test "$linkmode" = prog; then
+ # Here we assume that one of hardcode_direct or hardcode_minus_L
+ # is not unsupported. This is valid on all known static and
+ # shared platforms.
+ if test "$hardcode_direct" != unsupported; then
+ test -n "$old_library" && linklib="$old_library"
+ compile_deplibs="$dir/$linklib $compile_deplibs"
+ finalize_deplibs="$dir/$linklib $finalize_deplibs"
+ else
+ compile_deplibs="-l$name -L$dir $compile_deplibs"
+ finalize_deplibs="-l$name -L$dir $finalize_deplibs"
+ fi
+ elif test "$build_libtool_libs" = yes; then
+ # Not a shared library
+ if test "$deplibs_check_method" != pass_all; then
+ # We're trying link a shared library against a static one
+ # but the system doesn't support it.
+
+ # Just print a warning and add the library to dependency_libs so
+ # that the program can be linked against the static library.
+ $ECHO
+ $ECHO "*** Warning: This system can not link to static lib archive $lib."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have."
+ if test "$module" = yes; then
+ $ECHO "*** But as you try to build a module library, libtool will still create "
+ $ECHO "*** a static module, that should work as long as the dlopening application"
+ $ECHO "*** is linked with the -dlopen flag to resolve symbols at runtime."
+ if test -z "$global_symbol_pipe"; then
+ $ECHO
+ $ECHO "*** However, this would only work if libtool was able to extract symbol"
+ $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could"
+ $ECHO "*** not find such a program. So, this module is probably useless."
+ $ECHO "*** \`nm' from GNU binutils and a full rebuild may help."
+ fi
+ if test "$build_old_libs" = no; then
+ build_libtool_libs=module
+ build_old_libs=yes
+ else
+ build_libtool_libs=no
+ fi
+ fi
+ else
+ deplibs="$dir/$old_library $deplibs"
+ link_static=yes
+ fi
+ fi # link shared/static library?
+
+ if test "$linkmode" = lib; then
+ if test -n "$dependency_libs" &&
+ { test "$hardcode_into_libs" != yes ||
+ test "$build_old_libs" = yes ||
+ test "$link_static" = yes; }; then
+ # Extract -R from dependency_libs
+ temp_deplibs=
+ for libdir in $dependency_libs; do
+ case $libdir in
+ -R*) func_stripname '-R' '' "$libdir"
+ temp_xrpath=$func_stripname_result
+ case " $xrpath " in
+ *" $temp_xrpath "*) ;;
+ *) xrpath="$xrpath $temp_xrpath";;
+ esac;;
+ *) temp_deplibs="$temp_deplibs $libdir";;
+ esac
+ done
+ dependency_libs="$temp_deplibs"
+ fi
+
+ newlib_search_path="$newlib_search_path $absdir"
+ # Link against this library
+ test "$link_static" = no && newdependency_libs="$abs_ladir/$laname $newdependency_libs"
+ # ... and its dependency_libs
+ tmp_libs=
+ for deplib in $dependency_libs; do
+ newdependency_libs="$deplib $newdependency_libs"
+ if $opt_duplicate_deps ; then
+ case "$tmp_libs " in
+ *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+ esac
+ fi
+ tmp_libs="$tmp_libs $deplib"
+ done
+
+ if test "$link_all_deplibs" != no; then
+ # Add the search paths of all dependency libraries
+ for deplib in $dependency_libs; do
+ path=
+ case $deplib in
+ -L*) path="$deplib" ;;
+ *.la)
+ func_dirname "$deplib" "" "."
+ dir="$func_dirname_result"
+ # We need an absolute path.
+ case $dir in
+ [\\/]* | [A-Za-z]:[\\/]*) absdir="$dir" ;;
+ *)
+ absdir=`cd "$dir" && pwd`
+ if test -z "$absdir"; then
+ func_warning "cannot determine absolute directory name of \`$dir'"
+ absdir="$dir"
+ fi
+ ;;
+ esac
+ if $GREP "^installed=no" $deplib > /dev/null; then
+ case $host in
+ *-*-darwin*)
+ depdepl=
+ eval deplibrary_names=`${SED} -n -e 's/^library_names=\(.*\)$/\1/p' $deplib`
+ if test -n "$deplibrary_names" ; then
+ for tmp in $deplibrary_names ; do
+ depdepl=$tmp
+ done
+ if test -f "$absdir/$objdir/$depdepl" ; then
+ depdepl="$absdir/$objdir/$depdepl"
+ darwin_install_name=`${OTOOL} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'`
+ if test -z "$darwin_install_name"; then
+ darwin_install_name=`${OTOOL64} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'`
+ fi
+ compiler_flags="$compiler_flags ${wl}-dylib_file ${wl}${darwin_install_name}:${depdepl}"
+ linker_flags="$linker_flags -dylib_file ${darwin_install_name}:${depdepl}"
+ path=
+ fi
+ fi
+ ;;
+ *)
+ path="-L$absdir/$objdir"
+ ;;
+ esac
+ else
+ eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib`
+ test -z "$libdir" && \
+ func_fatal_error "\`$deplib' is not a valid libtool archive"
+ test "$absdir" != "$libdir" && \
+ func_warning "\`$deplib' seems to be moved"
+
+ path="-L$absdir"
+ fi
+ ;;
+ esac
+ case " $deplibs " in
+ *" $path "*) ;;
+ *) deplibs="$path $deplibs" ;;
+ esac
+ done
+ fi # link_all_deplibs != no
+ fi # linkmode = lib
+ done # for deplib in $libs
+ if test "$pass" = link; then
+ if test "$linkmode" = "prog"; then
+ compile_deplibs="$new_inherited_linker_flags $compile_deplibs"
+ finalize_deplibs="$new_inherited_linker_flags $finalize_deplibs"
+ else
+ compiler_flags="$compiler_flags "`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ fi
+ fi
+ dependency_libs="$newdependency_libs"
+ if test "$pass" = dlpreopen; then
+ # Link the dlpreopened libraries before other libraries
+ for deplib in $save_deplibs; do
+ deplibs="$deplib $deplibs"
+ done
+ fi
+ if test "$pass" != dlopen; then
+ if test "$pass" != conv; then
+ # Make sure lib_search_path contains only unique directories.
+ lib_search_path=
+ for dir in $newlib_search_path; do
+ case "$lib_search_path " in
+ *" $dir "*) ;;
+ *) lib_search_path="$lib_search_path $dir" ;;
+ esac
+ done
+ newlib_search_path=
+ fi
+
+ if test "$linkmode,$pass" != "prog,link"; then
+ vars="deplibs"
+ else
+ vars="compile_deplibs finalize_deplibs"
+ fi
+ for var in $vars dependency_libs; do
+ # Add libraries to $var in reverse order
+ eval tmp_libs=\"\$$var\"
+ new_libs=
+ for deplib in $tmp_libs; do
+ # FIXME: Pedantically, this is the right thing to do, so
+ # that some nasty dependency loop isn't accidentally
+ # broken:
+ #new_libs="$deplib $new_libs"
+ # Pragmatically, this seems to cause very few problems in
+ # practice:
+ case $deplib in
+ -L*) new_libs="$deplib $new_libs" ;;
+ -R*) ;;
+ *)
+ # And here is the reason: when a library appears more
+ # than once as an explicit dependence of a library, or
+ # is implicitly linked in more than once by the
+ # compiler, it is considered special, and multiple
+ # occurrences thereof are not removed. Compare this
+ # with having the same library being listed as a
+ # dependency of multiple other libraries: in this case,
+ # we know (pedantically, we assume) the library does not
+ # need to be listed more than once, so we keep only the
+ # last copy. This is not always right, but it is rare
+ # enough that we require users that really mean to play
+ # such unportable linking tricks to link the library
+ # using -Wl,-lname, so that libtool does not consider it
+ # for duplicate removal.
+ case " $specialdeplibs " in
+ *" $deplib "*) new_libs="$deplib $new_libs" ;;
+ *)
+ case " $new_libs " in
+ *" $deplib "*) ;;
+ *) new_libs="$deplib $new_libs" ;;
+ esac
+ ;;
+ esac
+ ;;
+ esac
+ done
+ tmp_libs=
+ for deplib in $new_libs; do
+ case $deplib in
+ -L*)
+ case " $tmp_libs " in
+ *" $deplib "*) ;;
+ *) tmp_libs="$tmp_libs $deplib" ;;
+ esac
+ ;;
+ *) tmp_libs="$tmp_libs $deplib" ;;
+ esac
+ done
+ eval $var=\"$tmp_libs\"
+ done # for var
+ fi
+ # Last step: remove runtime libs from dependency_libs
+ # (they stay in deplibs)
+ tmp_libs=
+ for i in $dependency_libs ; do
+ case " $predeps $postdeps $compiler_lib_search_path " in
+ *" $i "*)
+ i=""
+ ;;
+ esac
+ if test -n "$i" ; then
+ tmp_libs="$tmp_libs $i"
+ fi
+ done
+ dependency_libs=$tmp_libs
+ done # for pass
+ if test "$linkmode" = prog; then
+ dlfiles="$newdlfiles"
+ fi
+ if test "$linkmode" = prog || test "$linkmode" = lib; then
+ dlprefiles="$newdlprefiles"
+ fi
+
+ case $linkmode in
+ oldlib)
+ if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
+ func_warning "\`-dlopen' is ignored for archives"
+ fi
+
+ case " $deplibs" in
+ *\ -l* | *\ -L*)
+ func_warning "\`-l' and \`-L' are ignored for archives" ;;
+ esac
+
+ test -n "$rpath" && \
+ func_warning "\`-rpath' is ignored for archives"
+
+ test -n "$xrpath" && \
+ func_warning "\`-R' is ignored for archives"
+
+ test -n "$vinfo" && \
+ func_warning "\`-version-info/-version-number' is ignored for archives"
+
+ test -n "$release" && \
+ func_warning "\`-release' is ignored for archives"
+
+ test -n "$export_symbols$export_symbols_regex" && \
+ func_warning "\`-export-symbols' is ignored for archives"
+
+ # Now set the variables for building old libraries.
+ build_libtool_libs=no
+ oldlibs="$output"
+ objs="$objs$old_deplibs"
+ ;;
+
+ lib)
+ # Make sure we only generate libraries of the form `libNAME.la'.
+ case $outputname in
+ lib*)
+ func_stripname 'lib' '.la' "$outputname"
+ name=$func_stripname_result
+ eval shared_ext=\"$shrext_cmds\"
+ eval libname=\"$libname_spec\"
+ ;;
+ *)
+ test "$module" = no && \
+ func_fatal_help "libtool library \`$output' must begin with \`lib'"
+
+ if test "$need_lib_prefix" != no; then
+ # Add the "lib" prefix for modules if required
+ func_stripname '' '.la' "$outputname"
+ name=$func_stripname_result
+ eval shared_ext=\"$shrext_cmds\"
+ eval libname=\"$libname_spec\"
+ else
+ func_stripname '' '.la' "$outputname"
+ libname=$func_stripname_result
+ fi
+ ;;
+ esac
+
+ if test -n "$objs"; then
+ if test "$deplibs_check_method" != pass_all; then
+ func_fatal_error "cannot build libtool library \`$output' from non-libtool objects on this host:$objs"
+ else
+ $ECHO
+ $ECHO "*** Warning: Linking the shared library $output against the non-libtool"
+ $ECHO "*** objects $objs is not portable!"
+ libobjs="$libobjs $objs"
+ fi
+ fi
+
+ test "$dlself" != no && \
+ func_warning "\`-dlopen self' is ignored for libtool libraries"
+
+ set dummy $rpath
+ shift
+ test "$#" -gt 1 && \
+ func_warning "ignoring multiple \`-rpath's for a libtool library"
+
+ install_libdir="$1"
+
+ oldlibs=
+ if test -z "$rpath"; then
+ if test "$build_libtool_libs" = yes; then
+ # Building a libtool convenience library.
+ # Some compilers have problems with a `.al' extension so
+ # convenience libraries should have the same extension an
+ # archive normally would.
+ oldlibs="$output_objdir/$libname.$libext $oldlibs"
+ build_libtool_libs=convenience
+ build_old_libs=yes
+ fi
+
+ test -n "$vinfo" && \
+ func_warning "\`-version-info/-version-number' is ignored for convenience libraries"
+
+ test -n "$release" && \
+ func_warning "\`-release' is ignored for convenience libraries"
+ else
+
+ # Parse the version information argument.
+ save_ifs="$IFS"; IFS=':'
+ set dummy $vinfo 0 0 0
+ shift
+ IFS="$save_ifs"
+
+ test -n "$7" && \
+ func_fatal_help "too many parameters to \`-version-info'"
+
+ # convert absolute version numbers to libtool ages
+ # this retains compatibility with .la files and attempts
+ # to make the code below a bit more comprehensible
+
+ case $vinfo_number in
+ yes)
+ number_major="$1"
+ number_minor="$2"
+ number_revision="$3"
+ #
+ # There are really only two kinds -- those that
+ # use the current revision as the major version
+ # and those that subtract age and use age as
+ # a minor version. But, then there is irix
+ # which has an extra 1 added just for fun
+ #
+ case $version_type in
+ darwin|linux|osf|windows|none)
+ func_arith $number_major + $number_minor
+ current=$func_arith_result
+ age="$number_minor"
+ revision="$number_revision"
+ ;;
+ freebsd-aout|freebsd-elf|sunos)
+ current="$number_major"
+ revision="$number_minor"
+ age="0"
+ ;;
+ irix|nonstopux)
+ func_arith $number_major + $number_minor
+ current=$func_arith_result
+ age="$number_minor"
+ revision="$number_minor"
+ lt_irix_increment=no
+ ;;
+ *)
+ func_fatal_configuration "$modename: unknown library version type \`$version_type'"
+ ;;
+ esac
+ ;;
+ no)
+ current="$1"
+ revision="$2"
+ age="$3"
+ ;;
+ esac
+
+ # Check that each of the things are valid numbers.
+ case $current in
+ 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
+ *)
+ func_error "CURRENT \`$current' must be a nonnegative integer"
+ func_fatal_error "\`$vinfo' is not valid version information"
+ ;;
+ esac
+
+ case $revision in
+ 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
+ *)
+ func_error "REVISION \`$revision' must be a nonnegative integer"
+ func_fatal_error "\`$vinfo' is not valid version information"
+ ;;
+ esac
+
+ case $age in
+ 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
+ *)
+ func_error "AGE \`$age' must be a nonnegative integer"
+ func_fatal_error "\`$vinfo' is not valid version information"
+ ;;
+ esac
+
+ if test "$age" -gt "$current"; then
+ func_error "AGE \`$age' is greater than the current interface number \`$current'"
+ func_fatal_error "\`$vinfo' is not valid version information"
+ fi
+
+ # Calculate the version variables.
+ major=
+ versuffix=
+ verstring=
+ case $version_type in
+ none) ;;
+
+ darwin)
+ # Like Linux, but with the current version available in
+ # verstring for coding it into the library header
+ func_arith $current - $age
+ major=.$func_arith_result
+ versuffix="$major.$age.$revision"
+ # Darwin ld doesn't like 0 for these options...
+ func_arith $current + 1
+ minor_current=$func_arith_result
+ xlcverstring="${wl}-compatibility_version ${wl}$minor_current ${wl}-current_version ${wl}$minor_current.$revision"
+ verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
+ ;;
+
+ freebsd-aout)
+ major=".$current"
+ versuffix=".$current.$revision";
+ ;;
+
+ freebsd-elf)
+ major=".$current"
+ versuffix=".$current"
+ ;;
+
+ irix | nonstopux)
+ if test "X$lt_irix_increment" = "Xno"; then
+ func_arith $current - $age
+ else
+ func_arith $current - $age + 1
+ fi
+ major=$func_arith_result
+
+ case $version_type in
+ nonstopux) verstring_prefix=nonstopux ;;
+ *) verstring_prefix=sgi ;;
+ esac
+ verstring="$verstring_prefix$major.$revision"
+
+ # Add in all the interfaces that we are compatible with.
+ loop=$revision
+ while test "$loop" -ne 0; do
+ func_arith $revision - $loop
+ iface=$func_arith_result
+ func_arith $loop - 1
+ loop=$func_arith_result
+ verstring="$verstring_prefix$major.$iface:$verstring"
+ done
+
+ # Before this point, $major must not contain `.'.
+ major=.$major
+ versuffix="$major.$revision"
+ ;;
+
+ linux)
+ func_arith $current - $age
+ major=.$func_arith_result
+ versuffix="$major.$age.$revision"
+ ;;
+
+ osf)
+ func_arith $current - $age
+ major=.$func_arith_result
+ versuffix=".$current.$age.$revision"
+ verstring="$current.$age.$revision"
+
+ # Add in all the interfaces that we are compatible with.
+ loop=$age
+ while test "$loop" -ne 0; do
+ func_arith $current - $loop
+ iface=$func_arith_result
+ func_arith $loop - 1
+ loop=$func_arith_result
+ verstring="$verstring:${iface}.0"
+ done
+
+ # Make executables depend on our current version.
+ verstring="$verstring:${current}.0"
+ ;;
+
+ qnx)
+ major=".$current"
+ versuffix=".$current"
+ ;;
+
+ sunos)
+ major=".$current"
+ versuffix=".$current.$revision"
+ ;;
+
+ windows)
+ # Use '-' rather than '.', since we only want one
+ # extension on DOS 8.3 filesystems.
+ func_arith $current - $age
+ major=$func_arith_result
+ versuffix="-$major"
+ ;;
+
+ *)
+ func_fatal_configuration "unknown library version type \`$version_type'"
+ ;;
+ esac
+
+ # Clear the version info if we defaulted, and they specified a release.
+ if test -z "$vinfo" && test -n "$release"; then
+ major=
+ case $version_type in
+ darwin)
+ # we can't check for "0.0" in archive_cmds due to quoting
+ # problems, so we reset it completely
+ verstring=
+ ;;
+ *)
+ verstring="0.0"
+ ;;
+ esac
+ if test "$need_version" = no; then
+ versuffix=
+ else
+ versuffix=".0.0"
+ fi
+ fi
+
+ # Remove version info from name if versioning should be avoided
+ if test "$avoid_version" = yes && test "$need_version" = no; then
+ major=
+ versuffix=
+ verstring=""
+ fi
+
+ # Check to see if the archive will have undefined symbols.
+ if test "$allow_undefined" = yes; then
+ if test "$allow_undefined_flag" = unsupported; then
+ func_warning "undefined symbols not allowed in $host shared libraries"
+ build_libtool_libs=no
+ build_old_libs=yes
+ fi
+ else
+ # Don't allow undefined symbols.
+ allow_undefined_flag="$no_undefined_flag"
+ fi
+
+ fi
+
+ func_generate_dlsyms "$libname" "$libname" "yes"
+ libobjs="$libobjs $symfileobj"
+ test "X$libobjs" = "X " && libobjs=
+
+ if test "$mode" != relink; then
+ # Remove our outputs, but don't remove object files since they
+ # may have been created when compiling PIC objects.
+ removelist=
+ tempremovelist=`$ECHO "$output_objdir/*"`
+ for p in $tempremovelist; do
+ case $p in
+ *.$objext | *.gcno)
+ ;;
+ $output_objdir/$outputname | $output_objdir/$libname.* | $output_objdir/${libname}${release}.*)
+ if test "X$precious_files_regex" != "X"; then
+ if $ECHO "$p" | $EGREP -e "$precious_files_regex" >/dev/null 2>&1
+ then
+ continue
+ fi
+ fi
+ removelist="$removelist $p"
+ ;;
+ *) ;;
+ esac
+ done
+ test -n "$removelist" && \
+ func_show_eval "${RM}r \$removelist"
+ fi
+
+ # Now set the variables for building old libraries.
+ if test "$build_old_libs" = yes && test "$build_libtool_libs" != convenience ; then
+ oldlibs="$oldlibs $output_objdir/$libname.$libext"
+
+ # Transform .lo files to .o files.
+ oldobjs="$objs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}'$/d' -e "$lo2o" | $NL2SP`
+ fi
+
+ # Eliminate all temporary directories.
+ #for path in $notinst_path; do
+ # lib_search_path=`$ECHO "X$lib_search_path " | $Xsed -e "s% $path % %g"`
+ # deplibs=`$ECHO "X$deplibs " | $Xsed -e "s% -L$path % %g"`
+ # dependency_libs=`$ECHO "X$dependency_libs " | $Xsed -e "s% -L$path % %g"`
+ #done
+
+ if test -n "$xrpath"; then
+ # If the user specified any rpath flags, then add them.
+ temp_xrpath=
+ for libdir in $xrpath; do
+ temp_xrpath="$temp_xrpath -R$libdir"
+ case "$finalize_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_rpath="$finalize_rpath $libdir" ;;
+ esac
+ done
+ if test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes; then
+ dependency_libs="$temp_xrpath $dependency_libs"
+ fi
+ fi
+
+ # Make sure dlfiles contains only unique files that won't be dlpreopened
+ old_dlfiles="$dlfiles"
+ dlfiles=
+ for lib in $old_dlfiles; do
+ case " $dlprefiles $dlfiles " in
+ *" $lib "*) ;;
+ *) dlfiles="$dlfiles $lib" ;;
+ esac
+ done
+
+ # Make sure dlprefiles contains only unique files
+ old_dlprefiles="$dlprefiles"
+ dlprefiles=
+ for lib in $old_dlprefiles; do
+ case "$dlprefiles " in
+ *" $lib "*) ;;
+ *) dlprefiles="$dlprefiles $lib" ;;
+ esac
+ done
+
+ if test "$build_libtool_libs" = yes; then
+ if test -n "$rpath"; then
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-beos* | *-cegcc*)
+ # these systems don't actually have a c library (as such)!
+ ;;
+ *-*-rhapsody* | *-*-darwin1.[012])
+ # Rhapsody C library is in the System framework
+ deplibs="$deplibs System.ltframework"
+ ;;
+ *-*-netbsd*)
+ # Don't link with libc until the a.out ld.so is fixed.
+ ;;
+ *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
+ # Do not include libc due to us having libc/libc_r.
+ ;;
+ *-*-sco3.2v5* | *-*-sco5v6*)
+ # Causes problems with __ctype
+ ;;
+ *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*)
+ # Compiler inserts libc in the correct place for threads to work
+ ;;
+ *)
+ # Add libc to deplibs on all other systems if necessary.
+ if test "$build_libtool_need_lc" = "yes"; then
+ deplibs="$deplibs -lc"
+ fi
+ ;;
+ esac
+ fi
+
+ # Transform deplibs into only deplibs that can be linked in shared.
+ name_save=$name
+ libname_save=$libname
+ release_save=$release
+ versuffix_save=$versuffix
+ major_save=$major
+ # I'm not sure if I'm treating the release correctly. I think
+ # release should show up in the -l (ie -lgmp5) so we don't want to
+ # add it in twice. Is that correct?
+ release=""
+ versuffix=""
+ major=""
+ newdeplibs=
+ droppeddeps=no
+ case $deplibs_check_method in
+ pass_all)
+ # Don't check for shared/static. Everything works.
+ # This might be a little naive. We might want to check
+ # whether the library exists or not. But this is on
+ # osf3 & osf4 and I'm not really sure... Just
+ # implementing what was already the behavior.
+ newdeplibs=$deplibs
+ ;;
+ test_compile)
+ # This code stresses the "libraries are programs" paradigm to its
+ # limits. Maybe even breaks it. We compile a program, linking it
+ # against the deplibs as a proxy for the library. Then we can check
+ # whether they linked in statically or dynamically with ldd.
+ $opt_dry_run || $RM conftest.c
+ cat > conftest.c <<EOF
+ int main() { return 0; }
+EOF
+ $opt_dry_run || $RM conftest
+ if $LTCC $LTCFLAGS -o conftest conftest.c $deplibs; then
+ ldd_output=`ldd conftest`
+ for i in $deplibs; do
+ case $i in
+ -l*)
+ func_stripname -l '' "$i"
+ name=$func_stripname_result
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $i "*)
+ newdeplibs="$newdeplibs $i"
+ i=""
+ ;;
+ esac
+ fi
+ if test -n "$i" ; then
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ deplib_matches=`eval "\\$ECHO \"$library_names_spec\""`
+ set dummy $deplib_matches; shift
+ deplib_match=$1
+ if test `expr "$ldd_output" : ".*$deplib_match"` -ne 0 ; then
+ newdeplibs="$newdeplibs $i"
+ else
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning: dynamic linker does not accept needed library $i."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which I believe you do not have"
+ $ECHO "*** because a test_compile did reveal that the linker did not use it for"
+ $ECHO "*** its dynamic dependency list that programs get resolved with at runtime."
+ fi
+ fi
+ ;;
+ *)
+ newdeplibs="$newdeplibs $i"
+ ;;
+ esac
+ done
+ else
+ # Error occurred in the first compile. Let's try to salvage
+ # the situation: Compile a separate program for each library.
+ for i in $deplibs; do
+ case $i in
+ -l*)
+ func_stripname -l '' "$i"
+ name=$func_stripname_result
+ $opt_dry_run || $RM conftest
+ if $LTCC $LTCFLAGS -o conftest conftest.c $i; then
+ ldd_output=`ldd conftest`
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $i "*)
+ newdeplibs="$newdeplibs $i"
+ i=""
+ ;;
+ esac
+ fi
+ if test -n "$i" ; then
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ deplib_matches=`eval "\\$ECHO \"$library_names_spec\""`
+ set dummy $deplib_matches; shift
+ deplib_match=$1
+ if test `expr "$ldd_output" : ".*$deplib_match"` -ne 0 ; then
+ newdeplibs="$newdeplibs $i"
+ else
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning: dynamic linker does not accept needed library $i."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have"
+ $ECHO "*** because a test_compile did reveal that the linker did not use this one"
+ $ECHO "*** as a dynamic dependency that programs can get resolved with at runtime."
+ fi
+ fi
+ else
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning! Library $i is needed by this library but I was not able to"
+ $ECHO "*** make it link in! You will probably need to install it or some"
+ $ECHO "*** library that it depends on before this library will be fully"
+ $ECHO "*** functional. Installing it before continuing would be even better."
+ fi
+ ;;
+ *)
+ newdeplibs="$newdeplibs $i"
+ ;;
+ esac
+ done
+ fi
+ ;;
+ file_magic*)
+ set dummy $deplibs_check_method; shift
+ file_magic_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"`
+ for a_deplib in $deplibs; do
+ case $a_deplib in
+ -l*)
+ func_stripname -l '' "$a_deplib"
+ name=$func_stripname_result
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $a_deplib "*)
+ newdeplibs="$newdeplibs $a_deplib"
+ a_deplib=""
+ ;;
+ esac
+ fi
+ if test -n "$a_deplib" ; then
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do
+ potential_libs=`ls $i/$libname[.-]* 2>/dev/null`
+ for potent_lib in $potential_libs; do
+ # Follow soft links.
+ if ls -lLd "$potent_lib" 2>/dev/null |
+ $GREP " -> " >/dev/null; then
+ continue
+ fi
+ # The statement above tries to avoid entering an
+ # endless loop below, in case of cyclic links.
+ # We might still enter an endless loop, since a link
+ # loop can be closed while we follow links,
+ # but so what?
+ potlib="$potent_lib"
+ while test -h "$potlib" 2>/dev/null; do
+ potliblink=`ls -ld $potlib | ${SED} 's/.* -> //'`
+ case $potliblink in
+ [\\/]* | [A-Za-z]:[\\/]*) potlib="$potliblink";;
+ *) potlib=`$ECHO "X$potlib" | $Xsed -e 's,[^/]*$,,'`"$potliblink";;
+ esac
+ done
+ if eval $file_magic_cmd \"\$potlib\" 2>/dev/null |
+ $SED -e 10q |
+ $EGREP "$file_magic_regex" > /dev/null; then
+ newdeplibs="$newdeplibs $a_deplib"
+ a_deplib=""
+ break 2
+ fi
+ done
+ done
+ fi
+ if test -n "$a_deplib" ; then
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning: linker path does not have real file for library $a_deplib."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have"
+ $ECHO "*** because I did check the linker path looking for a file starting"
+ if test -z "$potlib" ; then
+ $ECHO "*** with $libname but no candidates were found. (...for file magic test)"
+ else
+ $ECHO "*** with $libname and none of the candidates passed a file format test"
+ $ECHO "*** using a file magic. Last file checked: $potlib"
+ fi
+ fi
+ ;;
+ *)
+ # Add a -L argument.
+ newdeplibs="$newdeplibs $a_deplib"
+ ;;
+ esac
+ done # Gone through all deplibs.
+ ;;
+ match_pattern*)
+ set dummy $deplibs_check_method; shift
+ match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"`
+ for a_deplib in $deplibs; do
+ case $a_deplib in
+ -l*)
+ func_stripname -l '' "$a_deplib"
+ name=$func_stripname_result
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $a_deplib "*)
+ newdeplibs="$newdeplibs $a_deplib"
+ a_deplib=""
+ ;;
+ esac
+ fi
+ if test -n "$a_deplib" ; then
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do
+ potential_libs=`ls $i/$libname[.-]* 2>/dev/null`
+ for potent_lib in $potential_libs; do
+ potlib="$potent_lib" # see symlink-check above in file_magic test
+ if eval "\$ECHO \"X$potent_lib\"" 2>/dev/null | $Xsed -e 10q | \
+ $EGREP "$match_pattern_regex" > /dev/null; then
+ newdeplibs="$newdeplibs $a_deplib"
+ a_deplib=""
+ break 2
+ fi
+ done
+ done
+ fi
+ if test -n "$a_deplib" ; then
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning: linker path does not have real file for library $a_deplib."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have"
+ $ECHO "*** because I did check the linker path looking for a file starting"
+ if test -z "$potlib" ; then
+ $ECHO "*** with $libname but no candidates were found. (...for regex pattern test)"
+ else
+ $ECHO "*** with $libname and none of the candidates passed a file format test"
+ $ECHO "*** using a regex pattern. Last file checked: $potlib"
+ fi
+ fi
+ ;;
+ *)
+ # Add a -L argument.
+ newdeplibs="$newdeplibs $a_deplib"
+ ;;
+ esac
+ done # Gone through all deplibs.
+ ;;
+ none | unknown | *)
+ newdeplibs=""
+ tmp_deplibs=`$ECHO "X $deplibs" | $Xsed \
+ -e 's/ -lc$//' -e 's/ -[LR][^ ]*//g'`
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ for i in $predeps $postdeps ; do
+ # can't use Xsed below, because $i might contain '/'
+ tmp_deplibs=`$ECHO "X $tmp_deplibs" | $Xsed -e "s,$i,,"`
+ done
+ fi
+ if $ECHO "X $tmp_deplibs" | $Xsed -e 's/[ ]//g' |
+ $GREP . >/dev/null; then
+ $ECHO
+ if test "X$deplibs_check_method" = "Xnone"; then
+ $ECHO "*** Warning: inter-library dependencies are not supported in this platform."
+ else
+ $ECHO "*** Warning: inter-library dependencies are not known to be supported."
+ fi
+ $ECHO "*** All declared inter-library dependencies are being dropped."
+ droppeddeps=yes
+ fi
+ ;;
+ esac
+ versuffix=$versuffix_save
+ major=$major_save
+ release=$release_save
+ libname=$libname_save
+ name=$name_save
+
+ case $host in
+ *-*-rhapsody* | *-*-darwin1.[012])
+ # On Rhapsody replace the C library with the System framework
+ newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's/ -lc / System.ltframework /'`
+ ;;
+ esac
+
+ if test "$droppeddeps" = yes; then
+ if test "$module" = yes; then
+ $ECHO
+ $ECHO "*** Warning: libtool could not satisfy all declared inter-library"
+ $ECHO "*** dependencies of module $libname. Therefore, libtool will create"
+ $ECHO "*** a static module, that should work as long as the dlopening"
+ $ECHO "*** application is linked with the -dlopen flag."
+ if test -z "$global_symbol_pipe"; then
+ $ECHO
+ $ECHO "*** However, this would only work if libtool was able to extract symbol"
+ $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could"
+ $ECHO "*** not find such a program. So, this module is probably useless."
+ $ECHO "*** \`nm' from GNU binutils and a full rebuild may help."
+ fi
+ if test "$build_old_libs" = no; then
+ oldlibs="$output_objdir/$libname.$libext"
+ build_libtool_libs=module
+ build_old_libs=yes
+ else
+ build_libtool_libs=no
+ fi
+ else
+ $ECHO "*** The inter-library dependencies that have been dropped here will be"
+ $ECHO "*** automatically added whenever a program is linked with this library"
+ $ECHO "*** or is declared to -dlopen it."
+
+ if test "$allow_undefined" = no; then
+ $ECHO
+ $ECHO "*** Since this library must not contain undefined symbols,"
+ $ECHO "*** because either the platform does not support them or"
+ $ECHO "*** it was explicitly requested with -no-undefined,"
+ $ECHO "*** libtool will only create a static version of it."
+ if test "$build_old_libs" = no; then
+ oldlibs="$output_objdir/$libname.$libext"
+ build_libtool_libs=module
+ build_old_libs=yes
+ else
+ build_libtool_libs=no
+ fi
+ fi
+ fi
+ fi
+ # Done checking deplibs!
+ deplibs=$newdeplibs
+ fi
+ # Time to change all our "foo.ltframework" stuff back to "-framework foo"
+ case $host in
+ *-*-darwin*)
+ newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ new_inherited_linker_flags=`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ deplibs=`$ECHO "X $deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ ;;
+ esac
+
+ # move library search paths that coincide with paths to not yet
+ # installed libraries to the beginning of the library search list
+ new_libs=
+ for path in $notinst_path; do
+ case " $new_libs " in
+ *" -L$path/$objdir "*) ;;
+ *)
+ case " $deplibs " in
+ *" -L$path/$objdir "*)
+ new_libs="$new_libs -L$path/$objdir" ;;
+ esac
+ ;;
+ esac
+ done
+ for deplib in $deplibs; do
+ case $deplib in
+ -L*)
+ case " $new_libs " in
+ *" $deplib "*) ;;
+ *) new_libs="$new_libs $deplib" ;;
+ esac
+ ;;
+ *) new_libs="$new_libs $deplib" ;;
+ esac
+ done
+ deplibs="$new_libs"
+
+ # All the library-specific variables (install_libdir is set above).
+ library_names=
+ old_library=
+ dlname=
+
+ # Test again, we may have decided not to build it any more
+ if test "$build_libtool_libs" = yes; then
+ if test "$hardcode_into_libs" = yes; then
+ # Hardcode the library paths
+ hardcode_libdirs=
+ dep_rpath=
+ rpath="$finalize_rpath"
+ test "$mode" != relink && rpath="$compile_rpath$rpath"
+ for libdir in $rpath; do
+ if test -n "$hardcode_libdir_flag_spec"; then
+ if test -n "$hardcode_libdir_separator"; then
+ if test -z "$hardcode_libdirs"; then
+ hardcode_libdirs="$libdir"
+ else
+ # Just accumulate the unique libdirs.
+ case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
+ *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
+ ;;
+ *)
+ hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir"
+ ;;
+ esac
+ fi
+ else
+ eval flag=\"$hardcode_libdir_flag_spec\"
+ dep_rpath="$dep_rpath $flag"
+ fi
+ elif test -n "$runpath_var"; then
+ case "$perm_rpath " in
+ *" $libdir "*) ;;
+ *) perm_rpath="$perm_rpath $libdir" ;;
+ esac
+ fi
+ done
+ # Substitute the hardcoded libdirs into the rpath.
+ if test -n "$hardcode_libdir_separator" &&
+ test -n "$hardcode_libdirs"; then
+ libdir="$hardcode_libdirs"
+ if test -n "$hardcode_libdir_flag_spec_ld"; then
+ eval dep_rpath=\"$hardcode_libdir_flag_spec_ld\"
+ else
+ eval dep_rpath=\"$hardcode_libdir_flag_spec\"
+ fi
+ fi
+ if test -n "$runpath_var" && test -n "$perm_rpath"; then
+ # We should set the runpath_var.
+ rpath=
+ for dir in $perm_rpath; do
+ rpath="$rpath$dir:"
+ done
+ eval "$runpath_var='$rpath\$$runpath_var'; export $runpath_var"
+ fi
+ test -n "$dep_rpath" && deplibs="$dep_rpath $deplibs"
+ fi
+
+ shlibpath="$finalize_shlibpath"
+ test "$mode" != relink && shlibpath="$compile_shlibpath$shlibpath"
+ if test -n "$shlibpath"; then
+ eval "$shlibpath_var='$shlibpath\$$shlibpath_var'; export $shlibpath_var"
+ fi
+
+ # Get the real and link names of the library.
+ eval shared_ext=\"$shrext_cmds\"
+ eval library_names=\"$library_names_spec\"
+ set dummy $library_names
+ shift
+ realname="$1"
+ shift
+
+ if test -n "$soname_spec"; then
+ eval soname=\"$soname_spec\"
+ else
+ soname="$realname"
+ fi
+ if test -z "$dlname"; then
+ dlname=$soname
+ fi
+
+ lib="$output_objdir/$realname"
+ linknames=
+ for link
+ do
+ linknames="$linknames $link"
+ done
+
+ # Use standard objects if they are pic
+ test -z "$pic_flag" && libobjs=`$ECHO "X$libobjs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+ test "X$libobjs" = "X " && libobjs=
+
+ delfiles=
+ if test -n "$export_symbols" && test -n "$include_expsyms"; then
+ $opt_dry_run || cp "$export_symbols" "$output_objdir/$libname.uexp"
+ export_symbols="$output_objdir/$libname.uexp"
+ delfiles="$delfiles $export_symbols"
+ fi
+
+ orig_export_symbols=
+ case $host_os in
+ cygwin* | mingw* | cegcc*)
+ if test -n "$export_symbols" && test -z "$export_symbols_regex"; then
+ # exporting using user supplied symfile
+ if test "x`$SED 1q $export_symbols`" != xEXPORTS; then
+ # and it's NOT already a .def file. Must figure out
+ # which of the given symbols are data symbols and tag
+ # them as such. So, trigger use of export_symbols_cmds.
+ # export_symbols gets reassigned inside the "prepare
+ # the list of exported symbols" if statement, so the
+ # include_expsyms logic still works.
+ orig_export_symbols="$export_symbols"
+ export_symbols=
+ always_export_symbols=yes
+ fi
+ fi
+ ;;
+ esac
+
+ # Prepare the list of exported symbols
+ if test -z "$export_symbols"; then
+ if test "$always_export_symbols" = yes || test -n "$export_symbols_regex"; then
+ func_verbose "generating symbol list for \`$libname.la'"
+ export_symbols="$output_objdir/$libname.exp"
+ $opt_dry_run || $RM $export_symbols
+ cmds=$export_symbols_cmds
+ save_ifs="$IFS"; IFS='~'
+ for cmd in $cmds; do
+ IFS="$save_ifs"
+ eval cmd=\"$cmd\"
+ func_len " $cmd"
+ len=$func_len_result
+ if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then
+ func_show_eval "$cmd" 'exit $?'
+ skipped_export=false
+ else
+ # The command line is too long to execute in one step.
+ func_verbose "using reloadable object file for export list..."
+ skipped_export=:
+ # Break out early, otherwise skipped_export may be
+ # set to false by a later but shorter cmd.
+ break
+ fi
+ done
+ IFS="$save_ifs"
+ if test -n "$export_symbols_regex" && test "X$skipped_export" != "X:"; then
+ func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"'
+ func_show_eval '$MV "${export_symbols}T" "$export_symbols"'
+ fi
+ fi
+ fi
+
+ if test -n "$export_symbols" && test -n "$include_expsyms"; then
+ tmp_export_symbols="$export_symbols"
+ test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols"
+ $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"'
+ fi
+
+ if test "X$skipped_export" != "X:" && test -n "$orig_export_symbols"; then
+ # The given exports_symbols file has to be filtered, so filter it.
+ func_verbose "filter symbol list for \`$libname.la' to tag DATA exports"
+ # FIXME: $output_objdir/$libname.filter potentially contains lots of
+ # 's' commands which not all seds can handle. GNU sed should be fine
+ # though. Also, the filter scales superlinearly with the number of
+ # global variables. join(1) would be nice here, but unfortunately
+ # isn't a blessed tool.
+ $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter
+ delfiles="$delfiles $export_symbols $output_objdir/$libname.filter"
+ export_symbols=$output_objdir/$libname.def
+ $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols
+ fi
+
+ tmp_deplibs=
+ for test_deplib in $deplibs; do
+ case " $convenience " in
+ *" $test_deplib "*) ;;
+ *)
+ tmp_deplibs="$tmp_deplibs $test_deplib"
+ ;;
+ esac
+ done
+ deplibs="$tmp_deplibs"
+
+ if test -n "$convenience"; then
+ if test -n "$whole_archive_flag_spec" &&
+ test "$compiler_needs_object" = yes &&
+ test -z "$libobjs"; then
+ # extract the archives, so we have objects to list.
+ # TODO: could optimize this to just extract one archive.
+ whole_archive_flag_spec=
+ fi
+ if test -n "$whole_archive_flag_spec"; then
+ save_libobjs=$libobjs
+ eval libobjs=\"\$libobjs $whole_archive_flag_spec\"
+ test "X$libobjs" = "X " && libobjs=
+ else
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $convenience
+ libobjs="$libobjs $func_extract_archives_result"
+ test "X$libobjs" = "X " && libobjs=
+ fi
+ fi
+
+ if test "$thread_safe" = yes && test -n "$thread_safe_flag_spec"; then
+ eval flag=\"$thread_safe_flag_spec\"
+ linker_flags="$linker_flags $flag"
+ fi
+
+ # Make a backup of the uninstalled library when relinking
+ if test "$mode" = relink; then
+ $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}U && $MV $realname ${realname}U)' || exit $?
+ fi
+
+ # Do each of the archive commands.
+ if test "$module" = yes && test -n "$module_cmds" ; then
+ if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then
+ eval test_cmds=\"$module_expsym_cmds\"
+ cmds=$module_expsym_cmds
+ else
+ eval test_cmds=\"$module_cmds\"
+ cmds=$module_cmds
+ fi
+ else
+ if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then
+ eval test_cmds=\"$archive_expsym_cmds\"
+ cmds=$archive_expsym_cmds
+ else
+ eval test_cmds=\"$archive_cmds\"
+ cmds=$archive_cmds
+ fi
+ fi
+
+ if test "X$skipped_export" != "X:" &&
+ func_len " $test_cmds" &&
+ len=$func_len_result &&
+ test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then
+ :
+ else
+ # The command line is too long to link in one step, link piecewise
+ # or, if using GNU ld and skipped_export is not :, use a linker
+ # script.
+
+ # Save the value of $output and $libobjs because we want to
+ # use them later. If we have whole_archive_flag_spec, we
+ # want to use save_libobjs as it was before
+ # whole_archive_flag_spec was expanded, because we can't
+ # assume the linker understands whole_archive_flag_spec.
+ # This may have to be revisited, in case too many
+ # convenience libraries get linked in and end up exceeding
+ # the spec.
+ if test -z "$convenience" || test -z "$whole_archive_flag_spec"; then
+ save_libobjs=$libobjs
+ fi
+ save_output=$output
+ output_la=`$ECHO "X$output" | $Xsed -e "$basename"`
+
+ # Clear the reloadable object creation command queue and
+ # initialize k to one.
+ test_cmds=
+ concat_cmds=
+ objlist=
+ last_robj=
+ k=1
+
+ if test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "$with_gnu_ld" = yes; then
+ output=${output_objdir}/${output_la}.lnkscript
+ func_verbose "creating GNU ld script: $output"
+ $ECHO 'INPUT (' > $output
+ for obj in $save_libobjs
+ do
+ $ECHO "$obj" >> $output
+ done
+ $ECHO ')' >> $output
+ delfiles="$delfiles $output"
+ elif test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "X$file_list_spec" != X; then
+ output=${output_objdir}/${output_la}.lnk
+ func_verbose "creating linker input file list: $output"
+ : > $output
+ set x $save_libobjs
+ shift
+ firstobj=
+ if test "$compiler_needs_object" = yes; then
+ firstobj="$1 "
+ shift
+ fi
+ for obj
+ do
+ $ECHO "$obj" >> $output
+ done
+ delfiles="$delfiles $output"
+ output=$firstobj\"$file_list_spec$output\"
+ else
+ if test -n "$save_libobjs"; then
+ func_verbose "creating reloadable object files..."
+ output=$output_objdir/$output_la-${k}.$objext
+ eval test_cmds=\"$reload_cmds\"
+ func_len " $test_cmds"
+ len0=$func_len_result
+ len=$len0
+
+ # Loop over the list of objects to be linked.
+ for obj in $save_libobjs
+ do
+ func_len " $obj"
+ func_arith $len + $func_len_result
+ len=$func_arith_result
+ if test "X$objlist" = X ||
+ test "$len" -lt "$max_cmd_len"; then
+ func_append objlist " $obj"
+ else
+ # The command $test_cmds is almost too long, add a
+ # command to the queue.
+ if test "$k" -eq 1 ; then
+ # The first file doesn't have a previous command to add.
+ eval concat_cmds=\"$reload_cmds $objlist $last_robj\"
+ else
+ # All subsequent reloadable object files will link in
+ # the last one created.
+ eval concat_cmds=\"\$concat_cmds~$reload_cmds $objlist $last_robj~\$RM $last_robj\"
+ fi
+ last_robj=$output_objdir/$output_la-${k}.$objext
+ func_arith $k + 1
+ k=$func_arith_result
+ output=$output_objdir/$output_la-${k}.$objext
+ objlist=$obj
+ func_len " $last_robj"
+ func_arith $len0 + $func_len_result
+ len=$func_arith_result
+ fi
+ done
+ # Handle the remaining objects by creating one last
+ # reloadable object file. All subsequent reloadable object
+ # files will link in the last one created.
+ test -z "$concat_cmds" || concat_cmds=$concat_cmds~
+ eval concat_cmds=\"\${concat_cmds}$reload_cmds $objlist $last_robj\"
+ if test -n "$last_robj"; then
+ eval concat_cmds=\"\${concat_cmds}~\$RM $last_robj\"
+ fi
+ delfiles="$delfiles $output"
+
+ else
+ output=
+ fi
+
+ if ${skipped_export-false}; then
+ func_verbose "generating symbol list for \`$libname.la'"
+ export_symbols="$output_objdir/$libname.exp"
+ $opt_dry_run || $RM $export_symbols
+ libobjs=$output
+ # Append the command to create the export file.
+ test -z "$concat_cmds" || concat_cmds=$concat_cmds~
+ eval concat_cmds=\"\$concat_cmds$export_symbols_cmds\"
+ if test -n "$last_robj"; then
+ eval concat_cmds=\"\$concat_cmds~\$RM $last_robj\"
+ fi
+ fi
+
+ test -n "$save_libobjs" &&
+ func_verbose "creating a temporary reloadable object file: $output"
+
+ # Loop through the commands generated above and execute them.
+ save_ifs="$IFS"; IFS='~'
+ for cmd in $concat_cmds; do
+ IFS="$save_ifs"
+ $opt_silent || {
+ func_quote_for_expand "$cmd"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+ $opt_dry_run || eval "$cmd" || {
+ lt_exit=$?
+
+ # Restore the uninstalled library and exit
+ if test "$mode" = relink; then
+ ( cd "$output_objdir" && \
+ $RM "${realname}T" && \
+ $MV "${realname}U" "$realname" )
+ fi
+
+ exit $lt_exit
+ }
+ done
+ IFS="$save_ifs"
+
+ if test -n "$export_symbols_regex" && ${skipped_export-false}; then
+ func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"'
+ func_show_eval '$MV "${export_symbols}T" "$export_symbols"'
+ fi
+ fi
+
+ if ${skipped_export-false}; then
+ if test -n "$export_symbols" && test -n "$include_expsyms"; then
+ tmp_export_symbols="$export_symbols"
+ test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols"
+ $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"'
+ fi
+
+ if test -n "$orig_export_symbols"; then
+ # The given exports_symbols file has to be filtered, so filter it.
+ func_verbose "filter symbol list for \`$libname.la' to tag DATA exports"
+ # FIXME: $output_objdir/$libname.filter potentially contains lots of
+ # 's' commands which not all seds can handle. GNU sed should be fine
+ # though. Also, the filter scales superlinearly with the number of
+ # global variables. join(1) would be nice here, but unfortunately
+ # isn't a blessed tool.
+ $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter
+ delfiles="$delfiles $export_symbols $output_objdir/$libname.filter"
+ export_symbols=$output_objdir/$libname.def
+ $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols
+ fi
+ fi
+
+ libobjs=$output
+ # Restore the value of output.
+ output=$save_output
+
+ if test -n "$convenience" && test -n "$whole_archive_flag_spec"; then
+ eval libobjs=\"\$libobjs $whole_archive_flag_spec\"
+ test "X$libobjs" = "X " && libobjs=
+ fi
+ # Expand the library linking commands again to reset the
+ # value of $libobjs for piecewise linking.
+
+ # Do each of the archive commands.
+ if test "$module" = yes && test -n "$module_cmds" ; then
+ if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then
+ cmds=$module_expsym_cmds
+ else
+ cmds=$module_cmds
+ fi
+ else
+ if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then
+ cmds=$archive_expsym_cmds
+ else
+ cmds=$archive_cmds
+ fi
+ fi
+ fi
+
+ if test -n "$delfiles"; then
+ # Append the command to remove temporary files to $cmds.
+ eval cmds=\"\$cmds~\$RM $delfiles\"
+ fi
+
+ # Add any objects from preloaded convenience libraries
+ if test -n "$dlprefiles"; then
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $dlprefiles
+ libobjs="$libobjs $func_extract_archives_result"
+ test "X$libobjs" = "X " && libobjs=
+ fi
+
+ save_ifs="$IFS"; IFS='~'
+ for cmd in $cmds; do
+ IFS="$save_ifs"
+ eval cmd=\"$cmd\"
+ $opt_silent || {
+ func_quote_for_expand "$cmd"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+ $opt_dry_run || eval "$cmd" || {
+ lt_exit=$?
+
+ # Restore the uninstalled library and exit
+ if test "$mode" = relink; then
+ ( cd "$output_objdir" && \
+ $RM "${realname}T" && \
+ $MV "${realname}U" "$realname" )
+ fi
+
+ exit $lt_exit
+ }
+ done
+ IFS="$save_ifs"
+
+ # Restore the uninstalled library and exit
+ if test "$mode" = relink; then
+ $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}T && $MV $realname ${realname}T && $MV ${realname}U $realname)' || exit $?
+
+ if test -n "$convenience"; then
+ if test -z "$whole_archive_flag_spec"; then
+ func_show_eval '${RM}r "$gentop"'
+ fi
+ fi
+
+ exit $EXIT_SUCCESS
+ fi
+
+ # Create links to the real library.
+ for linkname in $linknames; do
+ if test "$realname" != "$linkname"; then
+ func_show_eval '(cd "$output_objdir" && $RM "$linkname" && $LN_S "$realname" "$linkname")' 'exit $?'
+ fi
+ done
+
+ # If -module or -export-dynamic was specified, set the dlname.
+ if test "$module" = yes || test "$export_dynamic" = yes; then
+ # On all known operating systems, these are identical.
+ dlname="$soname"
+ fi
+ fi
+ ;;
+
+ obj)
+ if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
+ func_warning "\`-dlopen' is ignored for objects"
+ fi
+
+ case " $deplibs" in
+ *\ -l* | *\ -L*)
+ func_warning "\`-l' and \`-L' are ignored for objects" ;;
+ esac
+
+ test -n "$rpath" && \
+ func_warning "\`-rpath' is ignored for objects"
+
+ test -n "$xrpath" && \
+ func_warning "\`-R' is ignored for objects"
+
+ test -n "$vinfo" && \
+ func_warning "\`-version-info' is ignored for objects"
+
+ test -n "$release" && \
+ func_warning "\`-release' is ignored for objects"
+
+ case $output in
+ *.lo)
+ test -n "$objs$old_deplibs" && \
+ func_fatal_error "cannot build library object \`$output' from non-libtool objects"
+
+ libobj=$output
+ func_lo2o "$libobj"
+ obj=$func_lo2o_result
+ ;;
+ *)
+ libobj=
+ obj="$output"
+ ;;
+ esac
+
+ # Delete the old objects.
+ $opt_dry_run || $RM $obj $libobj
+
+ # Objects from convenience libraries. This assumes
+ # single-version convenience libraries. Whenever we create
+ # different ones for PIC/non-PIC, this we'll have to duplicate
+ # the extraction.
+ reload_conv_objs=
+ gentop=
+ # reload_cmds runs $LD directly, so let us get rid of
+ # -Wl from whole_archive_flag_spec and hope we can get by with
+ # turning comma into space..
+ wl=
+
+ if test -n "$convenience"; then
+ if test -n "$whole_archive_flag_spec"; then
+ eval tmp_whole_archive_flags=\"$whole_archive_flag_spec\"
+ reload_conv_objs=$reload_objs\ `$ECHO "X$tmp_whole_archive_flags" | $Xsed -e 's|,| |g'`
+ else
+ gentop="$output_objdir/${obj}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $convenience
+ reload_conv_objs="$reload_objs $func_extract_archives_result"
+ fi
+ fi
+
+ # Create the old-style object.
+ reload_objs="$objs$old_deplibs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}$'/d' -e '/\.lib$/d' -e "$lo2o" | $NL2SP`" $reload_conv_objs" ### testsuite: skip nested quoting test
+
+ output="$obj"
+ func_execute_cmds "$reload_cmds" 'exit $?'
+
+ # Exit if we aren't doing a library object file.
+ if test -z "$libobj"; then
+ if test -n "$gentop"; then
+ func_show_eval '${RM}r "$gentop"'
+ fi
+
+ exit $EXIT_SUCCESS
+ fi
+
+ if test "$build_libtool_libs" != yes; then
+ if test -n "$gentop"; then
+ func_show_eval '${RM}r "$gentop"'
+ fi
+
+ # Create an invalid libtool object if no PIC, so that we don't
+ # accidentally link it into a program.
+ # $show "echo timestamp > $libobj"
+ # $opt_dry_run || eval "echo timestamp > $libobj" || exit $?
+ exit $EXIT_SUCCESS
+ fi
+
+ if test -n "$pic_flag" || test "$pic_mode" != default; then
+ # Only do commands if we really have different PIC objects.
+ reload_objs="$libobjs $reload_conv_objs"
+ output="$libobj"
+ func_execute_cmds "$reload_cmds" 'exit $?'
+ fi
+
+ if test -n "$gentop"; then
+ func_show_eval '${RM}r "$gentop"'
+ fi
+
+ exit $EXIT_SUCCESS
+ ;;
+
+ prog)
+ case $host in
+ *cygwin*) func_stripname '' '.exe' "$output"
+ output=$func_stripname_result.exe;;
+ esac
+ test -n "$vinfo" && \
+ func_warning "\`-version-info' is ignored for programs"
+
+ test -n "$release" && \
+ func_warning "\`-release' is ignored for programs"
+
+ test "$preload" = yes \
+ && test "$dlopen_support" = unknown \
+ && test "$dlopen_self" = unknown \
+ && test "$dlopen_self_static" = unknown && \
+ func_warning "\`LT_INIT([dlopen])' not used. Assuming no dlopen support."
+
+ case $host in
+ *-*-rhapsody* | *-*-darwin1.[012])
+ # On Rhapsody replace the C library is the System framework
+ compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'`
+ finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'`
+ ;;
+ esac
+
+ case $host in
+ *-*-darwin*)
+ # Don't allow lazy linking, it breaks C++ global constructors
+ # But is supposedly fixed on 10.4 or later (yay!).
+ if test "$tagname" = CXX ; then
+ case ${MACOSX_DEPLOYMENT_TARGET-10.0} in
+ 10.[0123])
+ compile_command="$compile_command ${wl}-bind_at_load"
+ finalize_command="$finalize_command ${wl}-bind_at_load"
+ ;;
+ esac
+ fi
+ # Time to change all our "foo.ltframework" stuff back to "-framework foo"
+ compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ ;;
+ esac
+
+
+ # move library search paths that coincide with paths to not yet
+ # installed libraries to the beginning of the library search list
+ new_libs=
+ for path in $notinst_path; do
+ case " $new_libs " in
+ *" -L$path/$objdir "*) ;;
+ *)
+ case " $compile_deplibs " in
+ *" -L$path/$objdir "*)
+ new_libs="$new_libs -L$path/$objdir" ;;
+ esac
+ ;;
+ esac
+ done
+ for deplib in $compile_deplibs; do
+ case $deplib in
+ -L*)
+ case " $new_libs " in
+ *" $deplib "*) ;;
+ *) new_libs="$new_libs $deplib" ;;
+ esac
+ ;;
+ *) new_libs="$new_libs $deplib" ;;
+ esac
+ done
+ compile_deplibs="$new_libs"
+
+
+ compile_command="$compile_command $compile_deplibs"
+ finalize_command="$finalize_command $finalize_deplibs"
+
+ if test -n "$rpath$xrpath"; then
+ # If the user specified any rpath flags, then add them.
+ for libdir in $rpath $xrpath; do
+ # This is the magic to use -rpath.
+ case "$finalize_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_rpath="$finalize_rpath $libdir" ;;
+ esac
+ done
+ fi
+
+ # Now hardcode the library paths
+ rpath=
+ hardcode_libdirs=
+ for libdir in $compile_rpath $finalize_rpath; do
+ if test -n "$hardcode_libdir_flag_spec"; then
+ if test -n "$hardcode_libdir_separator"; then
+ if test -z "$hardcode_libdirs"; then
+ hardcode_libdirs="$libdir"
+ else
+ # Just accumulate the unique libdirs.
+ case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
+ *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
+ ;;
+ *)
+ hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir"
+ ;;
+ esac
+ fi
+ else
+ eval flag=\"$hardcode_libdir_flag_spec\"
+ rpath="$rpath $flag"
+ fi
+ elif test -n "$runpath_var"; then
+ case "$perm_rpath " in
+ *" $libdir "*) ;;
+ *) perm_rpath="$perm_rpath $libdir" ;;
+ esac
+ fi
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*)
+ testbindir=`${ECHO} "$libdir" | ${SED} -e 's*/lib$*/bin*'`
+ case :$dllsearchpath: in
+ *":$libdir:"*) ;;
+ ::) dllsearchpath=$libdir;;
+ *) dllsearchpath="$dllsearchpath:$libdir";;
+ esac
+ case :$dllsearchpath: in
+ *":$testbindir:"*) ;;
+ ::) dllsearchpath=$testbindir;;
+ *) dllsearchpath="$dllsearchpath:$testbindir";;
+ esac
+ ;;
+ esac
+ done
+ # Substitute the hardcoded libdirs into the rpath.
+ if test -n "$hardcode_libdir_separator" &&
+ test -n "$hardcode_libdirs"; then
+ libdir="$hardcode_libdirs"
+ eval rpath=\" $hardcode_libdir_flag_spec\"
+ fi
+ compile_rpath="$rpath"
+
+ rpath=
+ hardcode_libdirs=
+ for libdir in $finalize_rpath; do
+ if test -n "$hardcode_libdir_flag_spec"; then
+ if test -n "$hardcode_libdir_separator"; then
+ if test -z "$hardcode_libdirs"; then
+ hardcode_libdirs="$libdir"
+ else
+ # Just accumulate the unique libdirs.
+ case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
+ *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
+ ;;
+ *)
+ hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir"
+ ;;
+ esac
+ fi
+ else
+ eval flag=\"$hardcode_libdir_flag_spec\"
+ rpath="$rpath $flag"
+ fi
+ elif test -n "$runpath_var"; then
+ case "$finalize_perm_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_perm_rpath="$finalize_perm_rpath $libdir" ;;
+ esac
+ fi
+ done
+ # Substitute the hardcoded libdirs into the rpath.
+ if test -n "$hardcode_libdir_separator" &&
+ test -n "$hardcode_libdirs"; then
+ libdir="$hardcode_libdirs"
+ eval rpath=\" $hardcode_libdir_flag_spec\"
+ fi
+ finalize_rpath="$rpath"
+
+ if test -n "$libobjs" && test "$build_old_libs" = yes; then
+ # Transform all the library objects into standard objects.
+ compile_command=`$ECHO "X$compile_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+ finalize_command=`$ECHO "X$finalize_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+ fi
+
+ func_generate_dlsyms "$outputname" "@PROGRAM@" "no"
+
+ # template prelinking step
+ if test -n "$prelink_cmds"; then
+ func_execute_cmds "$prelink_cmds" 'exit $?'
+ fi
+
+ wrappers_required=yes
+ case $host in
+ *cygwin* | *mingw* )
+ if test "$build_libtool_libs" != yes; then
+ wrappers_required=no
+ fi
+ ;;
+ *cegcc)
+ # Disable wrappers for cegcc, we are cross compiling anyway.
+ wrappers_required=no
+ ;;
+ *)
+ if test "$need_relink" = no || test "$build_libtool_libs" != yes; then
+ wrappers_required=no
+ fi
+ ;;
+ esac
+ if test "$wrappers_required" = no; then
+ # Replace the output file specification.
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'`
+ link_command="$compile_command$compile_rpath"
+
+ # We have no uninstalled library dependencies, so finalize right now.
+ exit_status=0
+ func_show_eval "$link_command" 'exit_status=$?'
+
+ # Delete the generated files.
+ if test -f "$output_objdir/${outputname}S.${objext}"; then
+ func_show_eval '$RM "$output_objdir/${outputname}S.${objext}"'
+ fi
+
+ exit $exit_status
+ fi
+
+ if test -n "$compile_shlibpath$finalize_shlibpath"; then
+ compile_command="$shlibpath_var=\"$compile_shlibpath$finalize_shlibpath\$$shlibpath_var\" $compile_command"
+ fi
+ if test -n "$finalize_shlibpath"; then
+ finalize_command="$shlibpath_var=\"$finalize_shlibpath\$$shlibpath_var\" $finalize_command"
+ fi
+
+ compile_var=
+ finalize_var=
+ if test -n "$runpath_var"; then
+ if test -n "$perm_rpath"; then
+ # We should set the runpath_var.
+ rpath=
+ for dir in $perm_rpath; do
+ rpath="$rpath$dir:"
+ done
+ compile_var="$runpath_var=\"$rpath\$$runpath_var\" "
+ fi
+ if test -n "$finalize_perm_rpath"; then
+ # We should set the runpath_var.
+ rpath=
+ for dir in $finalize_perm_rpath; do
+ rpath="$rpath$dir:"
+ done
+ finalize_var="$runpath_var=\"$rpath\$$runpath_var\" "
+ fi
+ fi
+
+ if test "$no_install" = yes; then
+ # We don't need to create a wrapper script.
+ link_command="$compile_var$compile_command$compile_rpath"
+ # Replace the output file specification.
+ link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'`
+ # Delete the old output file.
+ $opt_dry_run || $RM $output
+ # Link the executable and exit
+ func_show_eval "$link_command" 'exit $?'
+ exit $EXIT_SUCCESS
+ fi
+
+ if test "$hardcode_action" = relink; then
+ # Fast installation is not supported
+ link_command="$compile_var$compile_command$compile_rpath"
+ relink_command="$finalize_var$finalize_command$finalize_rpath"
+
+ func_warning "this platform does not like uninstalled shared libraries"
+ func_warning "\`$output' will be relinked during installation"
+ else
+ if test "$fast_install" != no; then
+ link_command="$finalize_var$compile_command$finalize_rpath"
+ if test "$fast_install" = yes; then
+ relink_command=`$ECHO "X$compile_var$compile_command$compile_rpath" | $Xsed -e 's%@OUTPUT@%\$progdir/\$file%g'`
+ else
+ # fast_install is set to needless
+ relink_command=
+ fi
+ else
+ link_command="$compile_var$compile_command$compile_rpath"
+ relink_command="$finalize_var$finalize_command$finalize_rpath"
+ fi
+ fi
+
+ # Replace the output file specification.
+ link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output_objdir/$outputname"'%g'`
+
+ # Delete the old output files.
+ $opt_dry_run || $RM $output $output_objdir/$outputname $output_objdir/lt-$outputname
+
+ func_show_eval "$link_command" 'exit $?'
+
+ # Now create the wrapper script.
+ func_verbose "creating $output"
+
+ # Quote the relink command for shipping.
+ if test -n "$relink_command"; then
+ # Preserve any variables that may affect compiler behavior
+ for var in $variables_saved_for_relink; do
+ if eval test -z \"\${$var+set}\"; then
+ relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command"
+ elif eval var_value=\$$var; test -z "$var_value"; then
+ relink_command="$var=; export $var; $relink_command"
+ else
+ func_quote_for_eval "$var_value"
+ relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command"
+ fi
+ done
+ relink_command="(cd `pwd`; $relink_command)"
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e "$sed_quote_subst"`
+ fi
+
+ # Quote $ECHO for shipping.
+ if test "X$ECHO" = "X$SHELL $progpath --fallback-echo"; then
+ case $progpath in
+ [\\/]* | [A-Za-z]:[\\/]*) qecho="$SHELL $progpath --fallback-echo";;
+ *) qecho="$SHELL `pwd`/$progpath --fallback-echo";;
+ esac
+ qecho=`$ECHO "X$qecho" | $Xsed -e "$sed_quote_subst"`
+ else
+ qecho=`$ECHO "X$ECHO" | $Xsed -e "$sed_quote_subst"`
+ fi
+
+ # Only actually do things if not in dry run mode.
+ $opt_dry_run || {
+ # win32 will think the script is a binary if it has
+ # a .exe suffix, so we strip it off here.
+ case $output in
+ *.exe) func_stripname '' '.exe' "$output"
+ output=$func_stripname_result ;;
+ esac
+ # test for cygwin because mv fails w/o .exe extensions
+ case $host in
+ *cygwin*)
+ exeext=.exe
+ func_stripname '' '.exe' "$outputname"
+ outputname=$func_stripname_result ;;
+ *) exeext= ;;
+ esac
+ case $host in
+ *cygwin* | *mingw* )
+ func_dirname_and_basename "$output" "" "."
+ output_name=$func_basename_result
+ output_path=$func_dirname_result
+ cwrappersource="$output_path/$objdir/lt-$output_name.c"
+ cwrapper="$output_path/$output_name.exe"
+ $RM $cwrappersource $cwrapper
+ trap "$RM $cwrappersource $cwrapper; exit $EXIT_FAILURE" 1 2 15
+
+ func_emit_cwrapperexe_src > $cwrappersource
+
+ # The wrapper executable is built using the $host compiler,
+ # because it contains $host paths and files. If cross-
+ # compiling, it, like the target executable, must be
+ # executed on the $host or under an emulation environment.
+ $opt_dry_run || {
+ $LTCC $LTCFLAGS -o $cwrapper $cwrappersource
+ $STRIP $cwrapper
+ }
+
+ # Now, create the wrapper script for func_source use:
+ func_ltwrapper_scriptname $cwrapper
+ $RM $func_ltwrapper_scriptname_result
+ trap "$RM $func_ltwrapper_scriptname_result; exit $EXIT_FAILURE" 1 2 15
+ $opt_dry_run || {
+ # note: this script will not be executed, so do not chmod.
+ if test "x$build" = "x$host" ; then
+ $cwrapper --lt-dump-script > $func_ltwrapper_scriptname_result
+ else
+ func_emit_wrapper no > $func_ltwrapper_scriptname_result
+ fi
+ }
+ ;;
+ * )
+ $RM $output
+ trap "$RM $output; exit $EXIT_FAILURE" 1 2 15
+
+ func_emit_wrapper no > $output
+ chmod +x $output
+ ;;
+ esac
+ }
+ exit $EXIT_SUCCESS
+ ;;
+ esac
+
+ # See if we need to build an old-fashioned archive.
+ for oldlib in $oldlibs; do
+
+ if test "$build_libtool_libs" = convenience; then
+ oldobjs="$libobjs_save $symfileobj"
+ addlibs="$convenience"
+ build_libtool_libs=no
+ else
+ if test "$build_libtool_libs" = module; then
+ oldobjs="$libobjs_save"
+ build_libtool_libs=no
+ else
+ oldobjs="$old_deplibs $non_pic_objects"
+ if test "$preload" = yes && test -f "$symfileobj"; then
+ oldobjs="$oldobjs $symfileobj"
+ fi
+ fi
+ addlibs="$old_convenience"
+ fi
+
+ if test -n "$addlibs"; then
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $addlibs
+ oldobjs="$oldobjs $func_extract_archives_result"
+ fi
+
+ # Do each command in the archive commands.
+ if test -n "$old_archive_from_new_cmds" && test "$build_libtool_libs" = yes; then
+ cmds=$old_archive_from_new_cmds
+ else
+
+ # Add any objects from preloaded convenience libraries
+ if test -n "$dlprefiles"; then
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $dlprefiles
+ oldobjs="$oldobjs $func_extract_archives_result"
+ fi
+
+ # POSIX demands no paths to be encoded in archives. We have
+ # to avoid creating archives with duplicate basenames if we
+ # might have to extract them afterwards, e.g., when creating a
+ # static archive out of a convenience library, or when linking
+ # the entirety of a libtool archive into another (currently
+ # not supported by libtool).
+ if (for obj in $oldobjs
+ do
+ func_basename "$obj"
+ $ECHO "$func_basename_result"
+ done | sort | sort -uc >/dev/null 2>&1); then
+ :
+ else
+ $ECHO "copying selected object files to avoid basename conflicts..."
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+ func_mkdir_p "$gentop"
+ save_oldobjs=$oldobjs
+ oldobjs=
+ counter=1
+ for obj in $save_oldobjs
+ do
+ func_basename "$obj"
+ objbase="$func_basename_result"
+ case " $oldobjs " in
+ " ") oldobjs=$obj ;;
+ *[\ /]"$objbase "*)
+ while :; do
+ # Make sure we don't pick an alternate name that also
+ # overlaps.
+ newobj=lt$counter-$objbase
+ func_arith $counter + 1
+ counter=$func_arith_result
+ case " $oldobjs " in
+ *[\ /]"$newobj "*) ;;
+ *) if test ! -f "$gentop/$newobj"; then break; fi ;;
+ esac
+ done
+ func_show_eval "ln $obj $gentop/$newobj || cp $obj $gentop/$newobj"
+ oldobjs="$oldobjs $gentop/$newobj"
+ ;;
+ *) oldobjs="$oldobjs $obj" ;;
+ esac
+ done
+ fi
+ eval cmds=\"$old_archive_cmds\"
+
+ func_len " $cmds"
+ len=$func_len_result
+ if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then
+ cmds=$old_archive_cmds
+ else
+ # the command line is too long to link in one step, link in parts
+ func_verbose "using piecewise archive linking..."
+ save_RANLIB=$RANLIB
+ RANLIB=:
+ objlist=
+ concat_cmds=
+ save_oldobjs=$oldobjs
+ oldobjs=
+ # Is there a better way of finding the last object in the list?
+ for obj in $save_oldobjs
+ do
+ last_oldobj=$obj
+ done
+ eval test_cmds=\"$old_archive_cmds\"
+ func_len " $test_cmds"
+ len0=$func_len_result
+ len=$len0
+ for obj in $save_oldobjs
+ do
+ func_len " $obj"
+ func_arith $len + $func_len_result
+ len=$func_arith_result
+ func_append objlist " $obj"
+ if test "$len" -lt "$max_cmd_len"; then
+ :
+ else
+ # the above command should be used before it gets too long
+ oldobjs=$objlist
+ if test "$obj" = "$last_oldobj" ; then
+ RANLIB=$save_RANLIB
+ fi
+ test -z "$concat_cmds" || concat_cmds=$concat_cmds~
+ eval concat_cmds=\"\${concat_cmds}$old_archive_cmds\"
+ objlist=
+ len=$len0
+ fi
+ done
+ RANLIB=$save_RANLIB
+ oldobjs=$objlist
+ if test "X$oldobjs" = "X" ; then
+ eval cmds=\"\$concat_cmds\"
+ else
+ eval cmds=\"\$concat_cmds~\$old_archive_cmds\"
+ fi
+ fi
+ fi
+ func_execute_cmds "$cmds" 'exit $?'
+ done
+
+ test -n "$generated" && \
+ func_show_eval "${RM}r$generated"
+
+ # Now create the libtool archive.
+ case $output in
+ *.la)
+ old_library=
+ test "$build_old_libs" = yes && old_library="$libname.$libext"
+ func_verbose "creating $output"
+
+ # Preserve any variables that may affect compiler behavior
+ for var in $variables_saved_for_relink; do
+ if eval test -z \"\${$var+set}\"; then
+ relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command"
+ elif eval var_value=\$$var; test -z "$var_value"; then
+ relink_command="$var=; export $var; $relink_command"
+ else
+ func_quote_for_eval "$var_value"
+ relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command"
+ fi
+ done
+ # Quote the link command for shipping.
+ relink_command="(cd `pwd`; $SHELL $progpath $preserve_args --mode=relink $libtool_args @inst_prefix_dir@)"
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e "$sed_quote_subst"`
+ if test "$hardcode_automatic" = yes ; then
+ relink_command=
+ fi
+
+ # Only create the output if not a dry run.
+ $opt_dry_run || {
+ for installed in no yes; do
+ if test "$installed" = yes; then
+ if test -z "$install_libdir"; then
+ break
+ fi
+ output="$output_objdir/$outputname"i
+ # Replace all uninstalled libtool libraries with the installed ones
+ newdependency_libs=
+ for deplib in $dependency_libs; do
+ case $deplib in
+ *.la)
+ func_basename "$deplib"
+ name="$func_basename_result"
+ eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib`
+ test -z "$libdir" && \
+ func_fatal_error "\`$deplib' is not a valid libtool archive"
+ newdependency_libs="$newdependency_libs $libdir/$name"
+ ;;
+ *) newdependency_libs="$newdependency_libs $deplib" ;;
+ esac
+ done
+ dependency_libs="$newdependency_libs"
+ newdlfiles=
+
+ for lib in $dlfiles; do
+ case $lib in
+ *.la)
+ func_basename "$lib"
+ name="$func_basename_result"
+ eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib`
+ test -z "$libdir" && \
+ func_fatal_error "\`$lib' is not a valid libtool archive"
+ newdlfiles="$newdlfiles $libdir/$name"
+ ;;
+ *) newdlfiles="$newdlfiles $lib" ;;
+ esac
+ done
+ dlfiles="$newdlfiles"
+ newdlprefiles=
+ for lib in $dlprefiles; do
+ case $lib in
+ *.la)
+ # Only pass preopened files to the pseudo-archive (for
+ # eventual linking with the app. that links it) if we
+ # didn't already link the preopened objects directly into
+ # the library:
+ func_basename "$lib"
+ name="$func_basename_result"
+ eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib`
+ test -z "$libdir" && \
+ func_fatal_error "\`$lib' is not a valid libtool archive"
+ newdlprefiles="$newdlprefiles $libdir/$name"
+ ;;
+ esac
+ done
+ dlprefiles="$newdlprefiles"
+ else
+ newdlfiles=
+ for lib in $dlfiles; do
+ case $lib in
+ [\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;;
+ *) abs=`pwd`"/$lib" ;;
+ esac
+ newdlfiles="$newdlfiles $abs"
+ done
+ dlfiles="$newdlfiles"
+ newdlprefiles=
+ for lib in $dlprefiles; do
+ case $lib in
+ [\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;;
+ *) abs=`pwd`"/$lib" ;;
+ esac
+ newdlprefiles="$newdlprefiles $abs"
+ done
+ dlprefiles="$newdlprefiles"
+ fi
+ $RM $output
+ # place dlname in correct position for cygwin
+ tdlname=$dlname
+ case $host,$output,$installed,$module,$dlname in
+ *cygwin*,*lai,yes,no,*.dll | *mingw*,*lai,yes,no,*.dll | *cegcc*,*lai,yes,no,*.dll) tdlname=../bin/$dlname ;;
+ esac
+ $ECHO > $output "\
+# $outputname - a libtool library file
+# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# The name that we can dlopen(3).
+dlname='$tdlname'
+
+# Names of this library.
+library_names='$library_names'
+
+# The name of the static archive.
+old_library='$old_library'
+
+# Linker flags that can not go in dependency_libs.
+inherited_linker_flags='$new_inherited_linker_flags'
+
+# Libraries that this one depends upon.
+dependency_libs='$dependency_libs'
+
+# Names of additional weak libraries provided by this library
+weak_library_names='$weak_libs'
+
+# Version information for $libname.
+current=$current
+age=$age
+revision=$revision
+
+# Is this an already installed library?
+installed=$installed
+
+# Should we warn about portability when linking against -modules?
+shouldnotlink=$module
+
+# Files to dlopen/dlpreopen
+dlopen='$dlfiles'
+dlpreopen='$dlprefiles'
+
+# Directory that this library needs to be installed in:
+libdir='$install_libdir'"
+ if test "$installed" = no && test "$need_relink" = yes; then
+ $ECHO >> $output "\
+relink_command=\"$relink_command\""
+ fi
+ done
+ }
+
+ # Do a symbolic link so that the libtool archive can be found in
+ # LD_LIBRARY_PATH before the program is installed.
+ func_show_eval '( cd "$output_objdir" && $RM "$outputname" && $LN_S "../$outputname" "$outputname" )' 'exit $?'
+ ;;
+ esac
+ exit $EXIT_SUCCESS
+}
+
+{ test "$mode" = link || test "$mode" = relink; } &&
+ func_mode_link ${1+"$@"}
+
+
+# func_mode_uninstall arg...
+func_mode_uninstall ()
+{
+ $opt_debug
+ RM="$nonopt"
+ files=
+ rmforce=
+ exit_status=0
+
+ # This variable tells wrapper scripts just to set variables rather
+ # than running their programs.
+ libtool_install_magic="$magic"
+
+ for arg
+ do
+ case $arg in
+ -f) RM="$RM $arg"; rmforce=yes ;;
+ -*) RM="$RM $arg" ;;
+ *) files="$files $arg" ;;
+ esac
+ done
+
+ test -z "$RM" && \
+ func_fatal_help "you must specify an RM program"
+
+ rmdirs=
+
+ origobjdir="$objdir"
+ for file in $files; do
+ func_dirname "$file" "" "."
+ dir="$func_dirname_result"
+ if test "X$dir" = X.; then
+ objdir="$origobjdir"
+ else
+ objdir="$dir/$origobjdir"
+ fi
+ func_basename "$file"
+ name="$func_basename_result"
+ test "$mode" = uninstall && objdir="$dir"
+
+ # Remember objdir for removal later, being careful to avoid duplicates
+ if test "$mode" = clean; then
+ case " $rmdirs " in
+ *" $objdir "*) ;;
+ *) rmdirs="$rmdirs $objdir" ;;
+ esac
+ fi
+
+ # Don't error if the file doesn't exist and rm -f was used.
+ if { test -L "$file"; } >/dev/null 2>&1 ||
+ { test -h "$file"; } >/dev/null 2>&1 ||
+ test -f "$file"; then
+ :
+ elif test -d "$file"; then
+ exit_status=1
+ continue
+ elif test "$rmforce" = yes; then
+ continue
+ fi
+
+ rmfiles="$file"
+
+ case $name in
+ *.la)
+ # Possibly a libtool archive, so verify it.
+ if func_lalib_p "$file"; then
+ func_source $dir/$name
+
+ # Delete the libtool libraries and symlinks.
+ for n in $library_names; do
+ rmfiles="$rmfiles $objdir/$n"
+ done
+ test -n "$old_library" && rmfiles="$rmfiles $objdir/$old_library"
+
+ case "$mode" in
+ clean)
+ case " $library_names " in
+ # " " in the beginning catches empty $dlname
+ *" $dlname "*) ;;
+ *) rmfiles="$rmfiles $objdir/$dlname" ;;
+ esac
+ test -n "$libdir" && rmfiles="$rmfiles $objdir/$name $objdir/${name}i"
+ ;;
+ uninstall)
+ if test -n "$library_names"; then
+ # Do each command in the postuninstall commands.
+ func_execute_cmds "$postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1'
+ fi
+
+ if test -n "$old_library"; then
+ # Do each command in the old_postuninstall commands.
+ func_execute_cmds "$old_postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1'
+ fi
+ # FIXME: should reinstall the best remaining shared library.
+ ;;
+ esac
+ fi
+ ;;
+
+ *.lo)
+ # Possibly a libtool object, so verify it.
+ if func_lalib_p "$file"; then
+
+ # Read the .lo file
+ func_source $dir/$name
+
+ # Add PIC object to the list of files to remove.
+ if test -n "$pic_object" &&
+ test "$pic_object" != none; then
+ rmfiles="$rmfiles $dir/$pic_object"
+ fi
+
+ # Add non-PIC object to the list of files to remove.
+ if test -n "$non_pic_object" &&
+ test "$non_pic_object" != none; then
+ rmfiles="$rmfiles $dir/$non_pic_object"
+ fi
+ fi
+ ;;
+
+ *)
+ if test "$mode" = clean ; then
+ noexename=$name
+ case $file in
+ *.exe)
+ func_stripname '' '.exe' "$file"
+ file=$func_stripname_result
+ func_stripname '' '.exe' "$name"
+ noexename=$func_stripname_result
+ # $file with .exe has already been added to rmfiles,
+ # add $file without .exe
+ rmfiles="$rmfiles $file"
+ ;;
+ esac
+ # Do a test to see if this is a libtool program.
+ if func_ltwrapper_p "$file"; then
+ if func_ltwrapper_executable_p "$file"; then
+ func_ltwrapper_scriptname "$file"
+ relink_command=
+ func_source $func_ltwrapper_scriptname_result
+ rmfiles="$rmfiles $func_ltwrapper_scriptname_result"
+ else
+ relink_command=
+ func_source $dir/$noexename
+ fi
+
+ # note $name still contains .exe if it was in $file originally
+ # as does the version of $file that was added into $rmfiles
+ rmfiles="$rmfiles $objdir/$name $objdir/${name}S.${objext}"
+ if test "$fast_install" = yes && test -n "$relink_command"; then
+ rmfiles="$rmfiles $objdir/lt-$name"
+ fi
+ if test "X$noexename" != "X$name" ; then
+ rmfiles="$rmfiles $objdir/lt-${noexename}.c"
+ fi
+ fi
+ fi
+ ;;
+ esac
+ func_show_eval "$RM $rmfiles" 'exit_status=1'
+ done
+ objdir="$origobjdir"
+
+ # Try to remove the ${objdir}s in the directories where we deleted files
+ for dir in $rmdirs; do
+ if test -d "$dir"; then
+ func_show_eval "rmdir $dir >/dev/null 2>&1"
+ fi
+ done
+
+ exit $exit_status
+}
+
+{ test "$mode" = uninstall || test "$mode" = clean; } &&
+ func_mode_uninstall ${1+"$@"}
+
+test -z "$mode" && {
+ help="$generic_help"
+ func_fatal_help "you must specify a MODE"
+}
+
+test -z "$exec_cmd" && \
+ func_fatal_help "invalid operation mode \`$mode'"
+
+if test -n "$exec_cmd"; then
+ eval exec "$exec_cmd"
+ exit $EXIT_FAILURE
+fi
+
+exit $exit_status
+
+
+# The TAGs below are defined such that we never get into a situation
+# in which we disable both kinds of libraries. Given conflicting
+# choices, we go for a static library, that is the most portable,
+# since we can't tell whether shared libraries were disabled because
+# the user asked for that or because the platform doesn't support
+# them. This is particularly important on AIX, because we don't
+# support having both static and shared libraries enabled at the same
+# time on that platform, so we default to a shared-only configuration.
+# If a disable-shared tag is given, we'll fallback to a static-only
+# configuration. But we'll never go from static-only to shared-only.
+
+# ### BEGIN LIBTOOL TAG CONFIG: disable-shared
+build_libtool_libs=no
+build_old_libs=yes
+# ### END LIBTOOL TAG CONFIG: disable-shared
+
+# ### BEGIN LIBTOOL TAG CONFIG: disable-static
+build_old_libs=`case $build_libtool_libs in yes) echo no;; *) echo yes;; esac`
+# ### END LIBTOOL TAG CONFIG: disable-static
+
+# Local Variables:
+# mode:shell-script
+# sh-indentation:2
+# End:
+# vi:sw=2
+
diff --git a/src/libGkArrays/config/missing b/src/libGkArrays/config/missing
new file mode 100755
index 0000000..28055d2
--- /dev/null
+++ b/src/libGkArrays/config/missing
@@ -0,0 +1,376 @@
+#! /bin/sh
+# Common stub for a few missing GNU programs while installing.
+
+scriptversion=2009-04-28.21; # UTC
+
+# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
+# 2008, 2009 Free Software Foundation, Inc.
+# Originally by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+if test $# -eq 0; then
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+fi
+
+run=:
+sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
+sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
+
+# In the cases where this matters, `missing' is being run in the
+# srcdir already.
+if test -f configure.ac; then
+ configure_ac=configure.ac
+else
+ configure_ac=configure.in
+fi
+
+msg="missing on your system"
+
+case $1 in
+--run)
+ # Try to run requested program, and just exit if it succeeds.
+ run=
+ shift
+ "$@" && exit 0
+ # Exit code 63 means version mismatch. This often happens
+ # when the user try to use an ancient version of a tool on
+ # a file that requires a minimum version. In this case we
+ # we should proceed has if the program had been absent, or
+ # if --run hadn't been passed.
+ if test $? = 63; then
+ run=:
+ msg="probably too old"
+ fi
+ ;;
+
+ -h|--h|--he|--hel|--help)
+ echo "\
+$0 [OPTION]... PROGRAM [ARGUMENT]...
+
+Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
+error status if there is no known handling for PROGRAM.
+
+Options:
+ -h, --help display this help and exit
+ -v, --version output version information and exit
+ --run try to run the given command, and emulate it if it fails
+
+Supported PROGRAM values:
+ aclocal touch file \`aclocal.m4'
+ autoconf touch file \`configure'
+ autoheader touch file \`config.h.in'
+ autom4te touch the output file, or create a stub one
+ automake touch all \`Makefile.in' files
+ bison create \`y.tab.[ch]', if possible, from existing .[ch]
+ flex create \`lex.yy.c', if possible, from existing .c
+ help2man touch the output file
+ lex create \`lex.yy.c', if possible, from existing .c
+ makeinfo touch the output file
+ tar try tar, gnutar, gtar, then tar without non-portable flags
+ yacc create \`y.tab.[ch]', if possible, from existing .[ch]
+
+Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
+\`g' are ignored when checking the name.
+
+Send bug reports to <bug-automake at gnu.org>."
+ exit $?
+ ;;
+
+ -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
+ echo "missing $scriptversion (GNU Automake)"
+ exit $?
+ ;;
+
+ -*)
+ echo 1>&2 "$0: Unknown \`$1' option"
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+ ;;
+
+esac
+
+# normalize program name to check for.
+program=`echo "$1" | sed '
+ s/^gnu-//; t
+ s/^gnu//; t
+ s/^g//; t'`
+
+# Now exit if we have it, but it failed. Also exit now if we
+# don't have it and --version was passed (most likely to detect
+# the program). This is about non-GNU programs, so use $1 not
+# $program.
+case $1 in
+ lex*|yacc*)
+ # Not GNU programs, they don't have --version.
+ ;;
+
+ tar*)
+ if test -n "$run"; then
+ echo 1>&2 "ERROR: \`tar' requires --run"
+ exit 1
+ elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+ exit 1
+ fi
+ ;;
+
+ *)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+ # Could not run --version or --help. This is probably someone
+ # running `$TOOL --version' or `$TOOL --help' to check whether
+ # $TOOL exists and not knowing $TOOL uses missing.
+ exit 1
+ fi
+ ;;
+esac
+
+# If it does not exist, or fails to run (possibly an outdated version),
+# try to emulate it.
+case $program in
+ aclocal*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acinclude.m4' or \`${configure_ac}'. You might want
+ to install the \`Automake' and \`Perl' packages. Grab them from
+ any GNU archive site."
+ touch aclocal.m4
+ ;;
+
+ autoconf*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`${configure_ac}'. You might want to install the
+ \`Autoconf' and \`GNU m4' packages. Grab them from any GNU
+ archive site."
+ touch configure
+ ;;
+
+ autoheader*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acconfig.h' or \`${configure_ac}'. You might want
+ to install the \`Autoconf' and \`GNU m4' packages. Grab them
+ from any GNU archive site."
+ files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
+ test -z "$files" && files="config.h"
+ touch_files=
+ for f in $files; do
+ case $f in
+ *:*) touch_files="$touch_files "`echo "$f" |
+ sed -e 's/^[^:]*://' -e 's/:.*//'`;;
+ *) touch_files="$touch_files $f.in";;
+ esac
+ done
+ touch $touch_files
+ ;;
+
+ automake*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
+ You might want to install the \`Automake' and \`Perl' packages.
+ Grab them from any GNU archive site."
+ find . -type f -name Makefile.am -print |
+ sed 's/\.am$/.in/' |
+ while read f; do touch "$f"; done
+ ;;
+
+ autom4te*)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, but is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them.
+ You can get \`$1' as part of \`Autoconf' from any GNU
+ archive site."
+
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo "#! /bin/sh"
+ echo "# Created by GNU Automake missing as a replacement of"
+ echo "# $ $@"
+ echo "exit 0"
+ chmod +x $file
+ exit 1
+ fi
+ ;;
+
+ bison*|yacc*)
+ echo 1>&2 "\
+WARNING: \`$1' $msg. You should only need it if
+ you modified a \`.y' file. You may need the \`Bison' package
+ in order for those modifications to take effect. You can get
+ \`Bison' from any GNU archive site."
+ rm -f y.tab.c y.tab.h
+ if test $# -ne 1; then
+ eval LASTARG="\${$#}"
+ case $LASTARG in
+ *.y)
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" y.tab.c
+ fi
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" y.tab.h
+ fi
+ ;;
+ esac
+ fi
+ if test ! -f y.tab.h; then
+ echo >y.tab.h
+ fi
+ if test ! -f y.tab.c; then
+ echo 'main() { return 0; }' >y.tab.c
+ fi
+ ;;
+
+ lex*|flex*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.l' file. You may need the \`Flex' package
+ in order for those modifications to take effect. You can get
+ \`Flex' from any GNU archive site."
+ rm -f lex.yy.c
+ if test $# -ne 1; then
+ eval LASTARG="\${$#}"
+ case $LASTARG in
+ *.l)
+ SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" lex.yy.c
+ fi
+ ;;
+ esac
+ fi
+ if test ! -f lex.yy.c; then
+ echo 'main() { return 0; }' >lex.yy.c
+ fi
+ ;;
+
+ help2man*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a dependency of a manual page. You may need the
+ \`Help2man' package in order for those modifications to take
+ effect. You can get \`Help2man' from any GNU archive site."
+
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo ".ab help2man is required to generate this page"
+ exit $?
+ fi
+ ;;
+
+ makeinfo*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.texi' or \`.texinfo' file, or any other file
+ indirectly affecting the aspect of the manual. The spurious
+ call might also be the consequence of using a buggy \`make' (AIX,
+ DU, IRIX). You might want to install the \`Texinfo' package or
+ the \`GNU make' package. Grab either from any GNU archive site."
+ # The file to touch is that specified with -o ...
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -z "$file"; then
+ # ... or it is the one specified with @setfilename ...
+ infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
+ file=`sed -n '
+ /^@setfilename/{
+ s/.* \([^ ]*\) *$/\1/
+ p
+ q
+ }' $infile`
+ # ... or it is derived from the source name (dir/f.texi becomes f.info)
+ test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
+ fi
+ # If the file does not exist, the user really needs makeinfo;
+ # let's fail without touching anything.
+ test -f $file || exit 1
+ touch $file
+ ;;
+
+ tar*)
+ shift
+
+ # We have already tried tar in the generic part.
+ # Look for gnutar/gtar before invocation to avoid ugly error
+ # messages.
+ if (gnutar --version > /dev/null 2>&1); then
+ gnutar "$@" && exit 0
+ fi
+ if (gtar --version > /dev/null 2>&1); then
+ gtar "$@" && exit 0
+ fi
+ firstarg="$1"
+ if shift; then
+ case $firstarg in
+ *o*)
+ firstarg=`echo "$firstarg" | sed s/o//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ case $firstarg in
+ *h*)
+ firstarg=`echo "$firstarg" | sed s/h//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ fi
+
+ echo 1>&2 "\
+WARNING: I can't seem to be able to run \`tar' with the given arguments.
+ You may want to install GNU tar or Free paxutils, or check the
+ command line arguments."
+ exit 1
+ ;;
+
+ *)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, and is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them. Check the \`README' file,
+ it often tells you about the needed prerequisites for installing
+ this package. You may also peek at any GNU archive site, in case
+ some other package would contain this missing \`$1' program."
+ exit 1
+ ;;
+esac
+
+exit 0
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/src/libGkArrays/config/texinfo.tex b/src/libGkArrays/config/texinfo.tex
new file mode 100644
index 0000000..9140826
--- /dev/null
+++ b/src/libGkArrays/config/texinfo.tex
@@ -0,0 +1,9291 @@
+% texinfo.tex -- TeX macros to handle Texinfo files.
+%
+% Load plain if necessary, i.e., if running under initex.
+\expandafter\ifx\csname fmtname\endcsname\relax\input plain\fi
+%
+\def\texinfoversion{2009-08-14.15}
+%
+% Copyright 1985, 1986, 1988, 1990, 1991, 1992, 1993, 1994, 1995,
+% 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006,
+% 2007, 2008, 2009 Free Software Foundation, Inc.
+%
+% This texinfo.tex file is free software: you can redistribute it and/or
+% modify it under the terms of the GNU General Public License as
+% published by the Free Software Foundation, either version 3 of the
+% License, or (at your option) any later version.
+%
+% This texinfo.tex file is distributed in the hope that it will be
+% useful, but WITHOUT ANY WARRANTY; without even the implied warranty
+% of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program. If not, see <http://www.gnu.org/licenses/>.
+%
+% As a special exception, when this file is read by TeX when processing
+% a Texinfo source document, you may use the result without
+% restriction. (This has been our intent since Texinfo was invented.)
+%
+% Please try the latest version of texinfo.tex before submitting bug
+% reports; you can get the latest version from:
+% http://www.gnu.org/software/texinfo/ (the Texinfo home page), or
+% ftp://tug.org/tex/texinfo.tex
+% (and all CTAN mirrors, see http://www.ctan.org).
+% The texinfo.tex in any given distribution could well be out
+% of date, so if that's what you're using, please check.
+%
+% Send bug reports to bug-texinfo at gnu.org. Please include including a
+% complete document in each bug report with which we can reproduce the
+% problem. Patches are, of course, greatly appreciated.
+%
+% To process a Texinfo manual with TeX, it's most reliable to use the
+% texi2dvi shell script that comes with the distribution. For a simple
+% manual foo.texi, however, you can get away with this:
+% tex foo.texi
+% texindex foo.??
+% tex foo.texi
+% tex foo.texi
+% dvips foo.dvi -o # or whatever; this makes foo.ps.
+% The extra TeX runs get the cross-reference information correct.
+% Sometimes one run after texindex suffices, and sometimes you need more
+% than two; texi2dvi does it as many times as necessary.
+%
+% It is possible to adapt texinfo.tex for other languages, to some
+% extent. You can get the existing language-specific files from the
+% full Texinfo distribution.
+%
+% The GNU Texinfo home page is http://www.gnu.org/software/texinfo.
+
+
+\message{Loading texinfo [version \texinfoversion]:}
+
+% If in a .fmt file, print the version number
+% and turn on active characters that we couldn't do earlier because
+% they might have appeared in the input file name.
+\everyjob{\message{[Texinfo version \texinfoversion]}%
+ \catcode`+=\active \catcode`\_=\active}
+
+
+\chardef\other=12
+
+% We never want plain's \outer definition of \+ in Texinfo.
+% For @tex, we can use \tabalign.
+\let\+ = \relax
+
+% Save some plain tex macros whose names we will redefine.
+\let\ptexb=\b
+\let\ptexbullet=\bullet
+\let\ptexc=\c
+\let\ptexcomma=\,
+\let\ptexdot=\.
+\let\ptexdots=\dots
+\let\ptexend=\end
+\let\ptexequiv=\equiv
+\let\ptexexclam=\!
+\let\ptexfootnote=\footnote
+\let\ptexgtr=>
+\let\ptexhat=^
+\let\ptexi=\i
+\let\ptexindent=\indent
+\let\ptexinsert=\insert
+\let\ptexlbrace=\{
+\let\ptexless=<
+\let\ptexnewwrite\newwrite
+\let\ptexnoindent=\noindent
+\let\ptexplus=+
+\let\ptexrbrace=\}
+\let\ptexslash=\/
+\let\ptexstar=\*
+\let\ptext=\t
+\let\ptextop=\top
+{\catcode`\'=\active
+\global\let\ptexquoteright'}% Math-mode def from plain.tex.
+\let\ptexraggedright=\raggedright
+
+% If this character appears in an error message or help string, it
+% starts a new line in the output.
+\newlinechar = `^^J
+
+% Use TeX 3.0's \inputlineno to get the line number, for better error
+% messages, but if we're using an old version of TeX, don't do anything.
+%
+\ifx\inputlineno\thisisundefined
+ \let\linenumber = \empty % Pre-3.0.
+\else
+ \def\linenumber{l.\the\inputlineno:\space}
+\fi
+
+% Set up fixed words for English if not already set.
+\ifx\putwordAppendix\undefined \gdef\putwordAppendix{Appendix}\fi
+\ifx\putwordChapter\undefined \gdef\putwordChapter{Chapter}\fi
+\ifx\putwordfile\undefined \gdef\putwordfile{file}\fi
+\ifx\putwordin\undefined \gdef\putwordin{in}\fi
+\ifx\putwordIndexIsEmpty\undefined \gdef\putwordIndexIsEmpty{(Index is empty)}\fi
+\ifx\putwordIndexNonexistent\undefined \gdef\putwordIndexNonexistent{(Index is nonexistent)}\fi
+\ifx\putwordInfo\undefined \gdef\putwordInfo{Info}\fi
+\ifx\putwordInstanceVariableof\undefined \gdef\putwordInstanceVariableof{Instance Variable of}\fi
+\ifx\putwordMethodon\undefined \gdef\putwordMethodon{Method on}\fi
+\ifx\putwordNoTitle\undefined \gdef\putwordNoTitle{No Title}\fi
+\ifx\putwordof\undefined \gdef\putwordof{of}\fi
+\ifx\putwordon\undefined \gdef\putwordon{on}\fi
+\ifx\putwordpage\undefined \gdef\putwordpage{page}\fi
+\ifx\putwordsection\undefined \gdef\putwordsection{section}\fi
+\ifx\putwordSection\undefined \gdef\putwordSection{Section}\fi
+\ifx\putwordsee\undefined \gdef\putwordsee{see}\fi
+\ifx\putwordSee\undefined \gdef\putwordSee{See}\fi
+\ifx\putwordShortTOC\undefined \gdef\putwordShortTOC{Short Contents}\fi
+\ifx\putwordTOC\undefined \gdef\putwordTOC{Table of Contents}\fi
+%
+\ifx\putwordMJan\undefined \gdef\putwordMJan{January}\fi
+\ifx\putwordMFeb\undefined \gdef\putwordMFeb{February}\fi
+\ifx\putwordMMar\undefined \gdef\putwordMMar{March}\fi
+\ifx\putwordMApr\undefined \gdef\putwordMApr{April}\fi
+\ifx\putwordMMay\undefined \gdef\putwordMMay{May}\fi
+\ifx\putwordMJun\undefined \gdef\putwordMJun{June}\fi
+\ifx\putwordMJul\undefined \gdef\putwordMJul{July}\fi
+\ifx\putwordMAug\undefined \gdef\putwordMAug{August}\fi
+\ifx\putwordMSep\undefined \gdef\putwordMSep{September}\fi
+\ifx\putwordMOct\undefined \gdef\putwordMOct{October}\fi
+\ifx\putwordMNov\undefined \gdef\putwordMNov{November}\fi
+\ifx\putwordMDec\undefined \gdef\putwordMDec{December}\fi
+%
+\ifx\putwordDefmac\undefined \gdef\putwordDefmac{Macro}\fi
+\ifx\putwordDefspec\undefined \gdef\putwordDefspec{Special Form}\fi
+\ifx\putwordDefvar\undefined \gdef\putwordDefvar{Variable}\fi
+\ifx\putwordDefopt\undefined \gdef\putwordDefopt{User Option}\fi
+\ifx\putwordDeffunc\undefined \gdef\putwordDeffunc{Function}\fi
+
+% Since the category of space is not known, we have to be careful.
+\chardef\spacecat = 10
+\def\spaceisspace{\catcode`\ =\spacecat}
+
+% sometimes characters are active, so we need control sequences.
+\chardef\colonChar = `\:
+\chardef\commaChar = `\,
+\chardef\dashChar = `\-
+\chardef\dotChar = `\.
+\chardef\exclamChar= `\!
+\chardef\lquoteChar= `\`
+\chardef\questChar = `\?
+\chardef\rquoteChar= `\'
+\chardef\semiChar = `\;
+\chardef\underChar = `\_
+
+% Ignore a token.
+%
+\def\gobble#1{}
+
+% The following is used inside several \edef's.
+\def\makecsname#1{\expandafter\noexpand\csname#1\endcsname}
+
+% Hyphenation fixes.
+\hyphenation{
+ Flor-i-da Ghost-script Ghost-view Mac-OS Post-Script
+ ap-pen-dix bit-map bit-maps
+ data-base data-bases eshell fall-ing half-way long-est man-u-script
+ man-u-scripts mini-buf-fer mini-buf-fers over-view par-a-digm
+ par-a-digms rath-er rec-tan-gu-lar ro-bot-ics se-vere-ly set-up spa-ces
+ spell-ing spell-ings
+ stand-alone strong-est time-stamp time-stamps which-ever white-space
+ wide-spread wrap-around
+}
+
+% Margin to add to right of even pages, to left of odd pages.
+\newdimen\bindingoffset
+\newdimen\normaloffset
+\newdimen\pagewidth \newdimen\pageheight
+
+% For a final copy, take out the rectangles
+% that mark overfull boxes (in case you have decided
+% that the text looks ok even though it passes the margin).
+%
+\def\finalout{\overfullrule=0pt}
+
+% @| inserts a changebar to the left of the current line. It should
+% surround any changed text. This approach does *not* work if the
+% change spans more than two lines of output. To handle that, we would
+% have adopt a much more difficult approach (putting marks into the main
+% vertical list for the beginning and end of each change).
+%
+\def\|{%
+ % \vadjust can only be used in horizontal mode.
+ \leavevmode
+ %
+ % Append this vertical mode material after the current line in the output.
+ \vadjust{%
+ % We want to insert a rule with the height and depth of the current
+ % leading; that is exactly what \strutbox is supposed to record.
+ \vskip-\baselineskip
+ %
+ % \vadjust-items are inserted at the left edge of the type. So
+ % the \llap here moves out into the left-hand margin.
+ \llap{%
+ %
+ % For a thicker or thinner bar, change the `1pt'.
+ \vrule height\baselineskip width1pt
+ %
+ % This is the space between the bar and the text.
+ \hskip 12pt
+ }%
+ }%
+}
+
+% Sometimes it is convenient to have everything in the transcript file
+% and nothing on the terminal. We don't just call \tracingall here,
+% since that produces some useless output on the terminal. We also make
+% some effort to order the tracing commands to reduce output in the log
+% file; cf. trace.sty in LaTeX.
+%
+\def\gloggingall{\begingroup \globaldefs = 1 \loggingall \endgroup}%
+\def\loggingall{%
+ \tracingstats2
+ \tracingpages1
+ \tracinglostchars2 % 2 gives us more in etex
+ \tracingparagraphs1
+ \tracingoutput1
+ \tracingmacros2
+ \tracingrestores1
+ \showboxbreadth\maxdimen \showboxdepth\maxdimen
+ \ifx\eTeXversion\undefined\else % etex gives us more logging
+ \tracingscantokens1
+ \tracingifs1
+ \tracinggroups1
+ \tracingnesting2
+ \tracingassigns1
+ \fi
+ \tracingcommands3 % 3 gives us more in etex
+ \errorcontextlines16
+}%
+
+% add check for \lastpenalty to plain's definitions. If the last thing
+% we did was a \nobreak, we don't want to insert more space.
+%
+\def\smallbreak{\ifnum\lastpenalty<10000\par\ifdim\lastskip<\smallskipamount
+ \removelastskip\penalty-50\smallskip\fi\fi}
+\def\medbreak{\ifnum\lastpenalty<10000\par\ifdim\lastskip<\medskipamount
+ \removelastskip\penalty-100\medskip\fi\fi}
+\def\bigbreak{\ifnum\lastpenalty<10000\par\ifdim\lastskip<\bigskipamount
+ \removelastskip\penalty-200\bigskip\fi\fi}
+
+% For @cropmarks command.
+% Do @cropmarks to get crop marks.
+%
+\newif\ifcropmarks
+\let\cropmarks = \cropmarkstrue
+%
+% Dimensions to add cropmarks at corners.
+% Added by P. A. MacKay, 12 Nov. 1986
+%
+\newdimen\outerhsize \newdimen\outervsize % set by the paper size routines
+\newdimen\cornerlong \cornerlong=1pc
+\newdimen\cornerthick \cornerthick=.3pt
+\newdimen\topandbottommargin \topandbottommargin=.75in
+
+% Output a mark which sets \thischapter, \thissection and \thiscolor.
+% We dump everything together because we only have one kind of mark.
+% This works because we only use \botmark / \topmark, not \firstmark.
+%
+% A mark contains a subexpression of the \ifcase ... \fi construct.
+% \get*marks macros below extract the needed part using \ifcase.
+%
+% Another complication is to let the user choose whether \thischapter
+% (\thissection) refers to the chapter (section) in effect at the top
+% of a page, or that at the bottom of a page. The solution is
+% described on page 260 of The TeXbook. It involves outputting two
+% marks for the sectioning macros, one before the section break, and
+% one after. I won't pretend I can describe this better than DEK...
+\def\domark{%
+ \toks0=\expandafter{\lastchapterdefs}%
+ \toks2=\expandafter{\lastsectiondefs}%
+ \toks4=\expandafter{\prevchapterdefs}%
+ \toks6=\expandafter{\prevsectiondefs}%
+ \toks8=\expandafter{\lastcolordefs}%
+ \mark{%
+ \the\toks0 \the\toks2
+ \noexpand\or \the\toks4 \the\toks6
+ \noexpand\else \the\toks8
+ }%
+}
+% \topmark doesn't work for the very first chapter (after the title
+% page or the contents), so we use \firstmark there -- this gets us
+% the mark with the chapter defs, unless the user sneaks in, e.g.,
+% @setcolor (or @url, or @link, etc.) between @contents and the very
+% first @chapter.
+\def\gettopheadingmarks{%
+ \ifcase0\topmark\fi
+ \ifx\thischapter\empty \ifcase0\firstmark\fi \fi
+}
+\def\getbottomheadingmarks{\ifcase1\botmark\fi}
+\def\getcolormarks{\ifcase2\topmark\fi}
+
+% Avoid "undefined control sequence" errors.
+\def\lastchapterdefs{}
+\def\lastsectiondefs{}
+\def\prevchapterdefs{}
+\def\prevsectiondefs{}
+\def\lastcolordefs{}
+
+% Main output routine.
+\chardef\PAGE = 255
+\output = {\onepageout{\pagecontents\PAGE}}
+
+\newbox\headlinebox
+\newbox\footlinebox
+
+% \onepageout takes a vbox as an argument. Note that \pagecontents
+% does insertions, but you have to call it yourself.
+\def\onepageout#1{%
+ \ifcropmarks \hoffset=0pt \else \hoffset=\normaloffset \fi
+ %
+ \ifodd\pageno \advance\hoffset by \bindingoffset
+ \else \advance\hoffset by -\bindingoffset\fi
+ %
+ % Do this outside of the \shipout so @code etc. will be expanded in
+ % the headline as they should be, not taken literally (outputting ''code).
+ \ifodd\pageno \getoddheadingmarks \else \getevenheadingmarks \fi
+ \setbox\headlinebox = \vbox{\let\hsize=\pagewidth \makeheadline}%
+ \ifodd\pageno \getoddfootingmarks \else \getevenfootingmarks \fi
+ \setbox\footlinebox = \vbox{\let\hsize=\pagewidth \makefootline}%
+ %
+ {%
+ % Have to do this stuff outside the \shipout because we want it to
+ % take effect in \write's, yet the group defined by the \vbox ends
+ % before the \shipout runs.
+ %
+ \indexdummies % don't expand commands in the output.
+ \normalturnoffactive % \ in index entries must not stay \, e.g., if
+ % the page break happens to be in the middle of an example.
+ % We don't want .vr (or whatever) entries like this:
+ % \entry{{\tt \indexbackslash }acronym}{32}{\code {\acronym}}
+ % "\acronym" won't work when it's read back in;
+ % it needs to be
+ % {\code {{\tt \backslashcurfont }acronym}
+ \shipout\vbox{%
+ % Do this early so pdf references go to the beginning of the page.
+ \ifpdfmakepagedest \pdfdest name{\the\pageno} xyz\fi
+ %
+ \ifcropmarks \vbox to \outervsize\bgroup
+ \hsize = \outerhsize
+ \vskip-\topandbottommargin
+ \vtop to0pt{%
+ \line{\ewtop\hfil\ewtop}%
+ \nointerlineskip
+ \line{%
+ \vbox{\moveleft\cornerthick\nstop}%
+ \hfill
+ \vbox{\moveright\cornerthick\nstop}%
+ }%
+ \vss}%
+ \vskip\topandbottommargin
+ \line\bgroup
+ \hfil % center the page within the outer (page) hsize.
+ \ifodd\pageno\hskip\bindingoffset\fi
+ \vbox\bgroup
+ \fi
+ %
+ \unvbox\headlinebox
+ \pagebody{#1}%
+ \ifdim\ht\footlinebox > 0pt
+ % Only leave this space if the footline is nonempty.
+ % (We lessened \vsize for it in \oddfootingyyy.)
+ % The \baselineskip=24pt in plain's \makefootline has no effect.
+ \vskip 24pt
+ \unvbox\footlinebox
+ \fi
+ %
+ \ifcropmarks
+ \egroup % end of \vbox\bgroup
+ \hfil\egroup % end of (centering) \line\bgroup
+ \vskip\topandbottommargin plus1fill minus1fill
+ \boxmaxdepth = \cornerthick
+ \vbox to0pt{\vss
+ \line{%
+ \vbox{\moveleft\cornerthick\nsbot}%
+ \hfill
+ \vbox{\moveright\cornerthick\nsbot}%
+ }%
+ \nointerlineskip
+ \line{\ewbot\hfil\ewbot}%
+ }%
+ \egroup % \vbox from first cropmarks clause
+ \fi
+ }% end of \shipout\vbox
+ }% end of group with \indexdummies
+ \advancepageno
+ \ifnum\outputpenalty>-20000 \else\dosupereject\fi
+}
+
+\newinsert\margin \dimen\margin=\maxdimen
+
+\def\pagebody#1{\vbox to\pageheight{\boxmaxdepth=\maxdepth #1}}
+{\catcode`\@ =11
+\gdef\pagecontents#1{\ifvoid\topins\else\unvbox\topins\fi
+% marginal hacks, juha at viisa.uucp (Juha Takala)
+\ifvoid\margin\else % marginal info is present
+ \rlap{\kern\hsize\vbox to\z@{\kern1pt\box\margin \vss}}\fi
+\dimen@=\dp#1\relax \unvbox#1\relax
+\ifvoid\footins\else\vskip\skip\footins\footnoterule \unvbox\footins\fi
+\ifr at ggedbottom \kern-\dimen@ \vfil \fi}
+}
+
+% Here are the rules for the cropmarks. Note that they are
+% offset so that the space between them is truly \outerhsize or \outervsize
+% (P. A. MacKay, 12 November, 1986)
+%
+\def\ewtop{\vrule height\cornerthick depth0pt width\cornerlong}
+\def\nstop{\vbox
+ {\hrule height\cornerthick depth\cornerlong width\cornerthick}}
+\def\ewbot{\vrule height0pt depth\cornerthick width\cornerlong}
+\def\nsbot{\vbox
+ {\hrule height\cornerlong depth\cornerthick width\cornerthick}}
+
+% Parse an argument, then pass it to #1. The argument is the rest of
+% the input line (except we remove a trailing comment). #1 should be a
+% macro which expects an ordinary undelimited TeX argument.
+%
+\def\parsearg{\parseargusing{}}
+\def\parseargusing#1#2{%
+ \def\argtorun{#2}%
+ \begingroup
+ \obeylines
+ \spaceisspace
+ #1%
+ \parseargline\empty% Insert the \empty token, see \finishparsearg below.
+}
+
+{\obeylines %
+ \gdef\parseargline#1^^M{%
+ \endgroup % End of the group started in \parsearg.
+ \argremovecomment #1\comment\ArgTerm%
+ }%
+}
+
+% First remove any @comment, then any @c comment.
+\def\argremovecomment#1\comment#2\ArgTerm{\argremovec #1\c\ArgTerm}
+\def\argremovec#1\c#2\ArgTerm{\argcheckspaces#1\^^M\ArgTerm}
+
+% Each occurrence of `\^^M' or `<space>\^^M' is replaced by a single space.
+%
+% \argremovec might leave us with trailing space, e.g.,
+% @end itemize @c foo
+% This space token undergoes the same procedure and is eventually removed
+% by \finishparsearg.
+%
+\def\argcheckspaces#1\^^M{\argcheckspacesX#1\^^M \^^M}
+\def\argcheckspacesX#1 \^^M{\argcheckspacesY#1\^^M}
+\def\argcheckspacesY#1\^^M#2\^^M#3\ArgTerm{%
+ \def\temp{#3}%
+ \ifx\temp\empty
+ % Do not use \next, perhaps the caller of \parsearg uses it; reuse \temp:
+ \let\temp\finishparsearg
+ \else
+ \let\temp\argcheckspaces
+ \fi
+ % Put the space token in:
+ \temp#1 #3\ArgTerm
+}
+
+% If a _delimited_ argument is enclosed in braces, they get stripped; so
+% to get _exactly_ the rest of the line, we had to prevent such situation.
+% We prepended an \empty token at the very beginning and we expand it now,
+% just before passing the control to \argtorun.
+% (Similarly, we have to think about #3 of \argcheckspacesY above: it is
+% either the null string, or it ends with \^^M---thus there is no danger
+% that a pair of braces would be stripped.
+%
+% But first, we have to remove the trailing space token.
+%
+\def\finishparsearg#1 \ArgTerm{\expandafter\argtorun\expandafter{#1}}
+
+% \parseargdef\foo{...}
+% is roughly equivalent to
+% \def\foo{\parsearg\Xfoo}
+% \def\Xfoo#1{...}
+%
+% Actually, I use \csname\string\foo\endcsname, ie. \\foo, as it is my
+% favourite TeX trick. --kasal, 16nov03
+
+\def\parseargdef#1{%
+ \expandafter \doparseargdef \csname\string#1\endcsname #1%
+}
+\def\doparseargdef#1#2{%
+ \def#2{\parsearg#1}%
+ \def#1##1%
+}
+
+% Several utility definitions with active space:
+{
+ \obeyspaces
+ \gdef\obeyedspace{ }
+
+ % Make each space character in the input produce a normal interword
+ % space in the output. Don't allow a line break at this space, as this
+ % is used only in environments like @example, where each line of input
+ % should produce a line of output anyway.
+ %
+ \gdef\sepspaces{\obeyspaces\let =\tie}
+
+ % If an index command is used in an @example environment, any spaces
+ % therein should become regular spaces in the raw index file, not the
+ % expansion of \tie (\leavevmode \penalty \@M \ ).
+ \gdef\unsepspaces{\let =\space}
+}
+
+
+\def\flushcr{\ifx\par\lisppar \def\next##1{}\else \let\next=\relax \fi \next}
+
+% Define the framework for environments in texinfo.tex. It's used like this:
+%
+% \envdef\foo{...}
+% \def\Efoo{...}
+%
+% It's the responsibility of \envdef to insert \begingroup before the
+% actual body; @end closes the group after calling \Efoo. \envdef also
+% defines \thisenv, so the current environment is known; @end checks
+% whether the environment name matches. The \checkenv macro can also be
+% used to check whether the current environment is the one expected.
+%
+% Non-false conditionals (@iftex, @ifset) don't fit into this, so they
+% are not treated as environments; they don't open a group. (The
+% implementation of @end takes care not to call \endgroup in this
+% special case.)
+
+
+% At run-time, environments start with this:
+\def\startenvironment#1{\begingroup\def\thisenv{#1}}
+% initialize
+\let\thisenv\empty
+
+% ... but they get defined via ``\envdef\foo{...}'':
+\long\def\envdef#1#2{\def#1{\startenvironment#1#2}}
+\def\envparseargdef#1#2{\parseargdef#1{\startenvironment#1#2}}
+
+% Check whether we're in the right environment:
+\def\checkenv#1{%
+ \def\temp{#1}%
+ \ifx\thisenv\temp
+ \else
+ \badenverr
+ \fi
+}
+
+% Environment mismatch, #1 expected:
+\def\badenverr{%
+ \errhelp = \EMsimple
+ \errmessage{This command can appear only \inenvironment\temp,
+ not \inenvironment\thisenv}%
+}
+\def\inenvironment#1{%
+ \ifx#1\empty
+ out of any environment%
+ \else
+ in environment \expandafter\string#1%
+ \fi
+}
+
+% @end foo executes the definition of \Efoo.
+% But first, it executes a specialized version of \checkenv
+%
+\parseargdef\end{%
+ \if 1\csname iscond.#1\endcsname
+ \else
+ % The general wording of \badenverr may not be ideal, but... --kasal, 06nov03
+ \expandafter\checkenv\csname#1\endcsname
+ \csname E#1\endcsname
+ \endgroup
+ \fi
+}
+
+\newhelp\EMsimple{Press RETURN to continue.}
+
+
+%% Simple single-character @ commands
+
+% @@ prints an @
+% Kludge this until the fonts are right (grr).
+\def\@{{\tt\char64}}
+
+% This is turned off because it was never documented
+% and you can use @w{...} around a quote to suppress ligatures.
+%% Define @` and @' to be the same as ` and '
+%% but suppressing ligatures.
+%\def\`{{`}}
+%\def\'{{'}}
+
+% Used to generate quoted braces.
+\def\mylbrace {{\tt\char123}}
+\def\myrbrace {{\tt\char125}}
+\let\{=\mylbrace
+\let\}=\myrbrace
+\begingroup
+ % Definitions to produce \{ and \} commands for indices,
+ % and @{ and @} for the aux/toc files.
+ \catcode`\{ = \other \catcode`\} = \other
+ \catcode`\[ = 1 \catcode`\] = 2
+ \catcode`\! = 0 \catcode`\\ = \other
+ !gdef!lbracecmd[\{]%
+ !gdef!rbracecmd[\}]%
+ !gdef!lbraceatcmd[@{]%
+ !gdef!rbraceatcmd[@}]%
+!endgroup
+
+% @comma{} to avoid , parsing problems.
+\let\comma = ,
+
+% Accents: @, @dotaccent @ringaccent @ubaraccent @udotaccent
+% Others are defined by plain TeX: @` @' @" @^ @~ @= @u @v @H.
+\let\, = \c
+\let\dotaccent = \.
+\def\ringaccent#1{{\accent23 #1}}
+\let\tieaccent = \t
+\let\ubaraccent = \b
+\let\udotaccent = \d
+
+% Other special characters: @questiondown @exclamdown @ordf @ordm
+% Plain TeX defines: @AA @AE @O @OE @L (plus lowercase versions) @ss.
+\def\questiondown{?`}
+\def\exclamdown{!`}
+\def\ordf{\leavevmode\raise1ex\hbox{\selectfonts\lllsize \underbar{a}}}
+\def\ordm{\leavevmode\raise1ex\hbox{\selectfonts\lllsize \underbar{o}}}
+
+% Dotless i and dotless j, used for accents.
+\def\imacro{i}
+\def\jmacro{j}
+\def\dotless#1{%
+ \def\temp{#1}%
+ \ifx\temp\imacro \ifmmode\imath \else\ptexi \fi
+ \else\ifx\temp\jmacro \ifmmode\jmath \else\j \fi
+ \else \errmessage{@dotless can be used only with i or j}%
+ \fi\fi
+}
+
+% The \TeX{} logo, as in plain, but resetting the spacing so that a
+% period following counts as ending a sentence. (Idea found in latex.)
+%
+\edef\TeX{\TeX \spacefactor=1000 }
+
+% @LaTeX{} logo. Not quite the same results as the definition in
+% latex.ltx, since we use a different font for the raised A; it's most
+% convenient for us to use an explicitly smaller font, rather than using
+% the \scriptstyle font (since we don't reset \scriptstyle and
+% \scriptscriptstyle).
+%
+\def\LaTeX{%
+ L\kern-.36em
+ {\setbox0=\hbox{T}%
+ \vbox to \ht0{\hbox{\selectfonts\lllsize A}\vss}}%
+ \kern-.15em
+ \TeX
+}
+
+% Be sure we're in horizontal mode when doing a tie, since we make space
+% equivalent to this in @example-like environments. Otherwise, a space
+% at the beginning of a line will start with \penalty -- and
+% since \penalty is valid in vertical mode, we'd end up putting the
+% penalty on the vertical list instead of in the new paragraph.
+{\catcode`@ = 11
+ % Avoid using \@M directly, because that causes trouble
+ % if the definition is written into an index file.
+ \global\let\tiepenalty = \@M
+ \gdef\tie{\leavevmode\penalty\tiepenalty\ }
+}
+
+% @: forces normal size whitespace following.
+\def\:{\spacefactor=1000 }
+
+% @* forces a line break.
+\def\*{\hfil\break\hbox{}\ignorespaces}
+
+% @/ allows a line break.
+\let\/=\allowbreak
+
+% @. is an end-of-sentence period.
+\def\.{.\spacefactor=\endofsentencespacefactor\space}
+
+% @! is an end-of-sentence bang.
+\def\!{!\spacefactor=\endofsentencespacefactor\space}
+
+% @? is an end-of-sentence query.
+\def\?{?\spacefactor=\endofsentencespacefactor\space}
+
+% @frenchspacing on|off says whether to put extra space after punctuation.
+%
+\def\onword{on}
+\def\offword{off}
+%
+\parseargdef\frenchspacing{%
+ \def\temp{#1}%
+ \ifx\temp\onword \plainfrenchspacing
+ \else\ifx\temp\offword \plainnonfrenchspacing
+ \else
+ \errhelp = \EMsimple
+ \errmessage{Unknown @frenchspacing option `\temp', must be on/off}%
+ \fi\fi
+}
+
+% @w prevents a word break. Without the \leavevmode, @w at the
+% beginning of a paragraph, when TeX is still in vertical mode, would
+% produce a whole line of output instead of starting the paragraph.
+\def\w#1{\leavevmode\hbox{#1}}
+
+% @group ... @end group forces ... to be all on one page, by enclosing
+% it in a TeX vbox. We use \vtop instead of \vbox to construct the box
+% to keep its height that of a normal line. According to the rules for
+% \topskip (p.114 of the TeXbook), the glue inserted is
+% max (\topskip - \ht (first item), 0). If that height is large,
+% therefore, no glue is inserted, and the space between the headline and
+% the text is small, which looks bad.
+%
+% Another complication is that the group might be very large. This can
+% cause the glue on the previous page to be unduly stretched, because it
+% does not have much material. In this case, it's better to add an
+% explicit \vfill so that the extra space is at the bottom. The
+% threshold for doing this is if the group is more than \vfilllimit
+% percent of a page (\vfilllimit can be changed inside of @tex).
+%
+\newbox\groupbox
+\def\vfilllimit{0.7}
+%
+\envdef\group{%
+ \ifnum\catcode`\^^M=\active \else
+ \errhelp = \groupinvalidhelp
+ \errmessage{@group invalid in context where filling is enabled}%
+ \fi
+ \startsavinginserts
+ %
+ \setbox\groupbox = \vtop\bgroup
+ % Do @comment since we are called inside an environment such as
+ % @example, where each end-of-line in the input causes an
+ % end-of-line in the output. We don't want the end-of-line after
+ % the `@group' to put extra space in the output. Since @group
+ % should appear on a line by itself (according to the Texinfo
+ % manual), we don't worry about eating any user text.
+ \comment
+}
+%
+% The \vtop produces a box with normal height and large depth; thus, TeX puts
+% \baselineskip glue before it, and (when the next line of text is done)
+% \lineskip glue after it. Thus, space below is not quite equal to space
+% above. But it's pretty close.
+\def\Egroup{%
+ % To get correct interline space between the last line of the group
+ % and the first line afterwards, we have to propagate \prevdepth.
+ \endgraf % Not \par, as it may have been set to \lisppar.
+ \global\dimen1 = \prevdepth
+ \egroup % End the \vtop.
+ % \dimen0 is the vertical size of the group's box.
+ \dimen0 = \ht\groupbox \advance\dimen0 by \dp\groupbox
+ % \dimen2 is how much space is left on the page (more or less).
+ \dimen2 = \pageheight \advance\dimen2 by -\pagetotal
+ % if the group doesn't fit on the current page, and it's a big big
+ % group, force a page break.
+ \ifdim \dimen0 > \dimen2
+ \ifdim \pagetotal < \vfilllimit\pageheight
+ \page
+ \fi
+ \fi
+ \box\groupbox
+ \prevdepth = \dimen1
+ \checkinserts
+}
+%
+% TeX puts in an \escapechar (i.e., `@') at the beginning of the help
+% message, so this ends up printing `@group can only ...'.
+%
+\newhelp\groupinvalidhelp{%
+group can only be used in environments such as @example,^^J%
+where each line of input produces a line of output.}
+
+% @need space-in-mils
+% forces a page break if there is not space-in-mils remaining.
+
+\newdimen\mil \mil=0.001in
+
+% Old definition--didn't work.
+%\parseargdef\need{\par %
+%% This method tries to make TeX break the page naturally
+%% if the depth of the box does not fit.
+%{\baselineskip=0pt%
+%\vtop to #1\mil{\vfil}\kern -#1\mil\nobreak
+%\prevdepth=-1000pt
+%}}
+
+\parseargdef\need{%
+ % Ensure vertical mode, so we don't make a big box in the middle of a
+ % paragraph.
+ \par
+ %
+ % If the @need value is less than one line space, it's useless.
+ \dimen0 = #1\mil
+ \dimen2 = \ht\strutbox
+ \advance\dimen2 by \dp\strutbox
+ \ifdim\dimen0 > \dimen2
+ %
+ % Do a \strut just to make the height of this box be normal, so the
+ % normal leading is inserted relative to the preceding line.
+ % And a page break here is fine.
+ \vtop to #1\mil{\strut\vfil}%
+ %
+ % TeX does not even consider page breaks if a penalty added to the
+ % main vertical list is 10000 or more. But in order to see if the
+ % empty box we just added fits on the page, we must make it consider
+ % page breaks. On the other hand, we don't want to actually break the
+ % page after the empty box. So we use a penalty of 9999.
+ %
+ % There is an extremely small chance that TeX will actually break the
+ % page at this \penalty, if there are no other feasible breakpoints in
+ % sight. (If the user is using lots of big @group commands, which
+ % almost-but-not-quite fill up a page, TeX will have a hard time doing
+ % good page breaking, for example.) However, I could not construct an
+ % example where a page broke at this \penalty; if it happens in a real
+ % document, then we can reconsider our strategy.
+ \penalty9999
+ %
+ % Back up by the size of the box, whether we did a page break or not.
+ \kern -#1\mil
+ %
+ % Do not allow a page break right after this kern.
+ \nobreak
+ \fi
+}
+
+% @br forces paragraph break (and is undocumented).
+
+\let\br = \par
+
+% @page forces the start of a new page.
+%
+\def\page{\par\vfill\supereject}
+
+% @exdent text....
+% outputs text on separate line in roman font, starting at standard page margin
+
+% This records the amount of indent in the innermost environment.
+% That's how much \exdent should take out.
+\newskip\exdentamount
+
+% This defn is used inside fill environments such as @defun.
+\parseargdef\exdent{\hfil\break\hbox{\kern -\exdentamount{\rm#1}}\hfil\break}
+
+% This defn is used inside nofill environments such as @example.
+\parseargdef\nofillexdent{{\advance \leftskip by -\exdentamount
+ \leftline{\hskip\leftskip{\rm#1}}}}
+
+% @inmargin{WHICH}{TEXT} puts TEXT in the WHICH margin next to the current
+% paragraph. For more general purposes, use the \margin insertion
+% class. WHICH is `l' or `r'.
+%
+\newskip\inmarginspacing \inmarginspacing=1cm
+\def\strutdepth{\dp\strutbox}
+%
+\def\doinmargin#1#2{\strut\vadjust{%
+ \nobreak
+ \kern-\strutdepth
+ \vtop to \strutdepth{%
+ \baselineskip=\strutdepth
+ \vss
+ % if you have multiple lines of stuff to put here, you'll need to
+ % make the vbox yourself of the appropriate size.
+ \ifx#1l%
+ \llap{\ignorespaces #2\hskip\inmarginspacing}%
+ \else
+ \rlap{\hskip\hsize \hskip\inmarginspacing \ignorespaces #2}%
+ \fi
+ \null
+ }%
+}}
+\def\inleftmargin{\doinmargin l}
+\def\inrightmargin{\doinmargin r}
+%
+% @inmargin{TEXT [, RIGHT-TEXT]}
+% (if RIGHT-TEXT is given, use TEXT for left page, RIGHT-TEXT for right;
+% else use TEXT for both).
+%
+\def\inmargin#1{\parseinmargin #1,,\finish}
+\def\parseinmargin#1,#2,#3\finish{% not perfect, but better than nothing.
+ \setbox0 = \hbox{\ignorespaces #2}%
+ \ifdim\wd0 > 0pt
+ \def\lefttext{#1}% have both texts
+ \def\righttext{#2}%
+ \else
+ \def\lefttext{#1}% have only one text
+ \def\righttext{#1}%
+ \fi
+ %
+ \ifodd\pageno
+ \def\temp{\inrightmargin\righttext}% odd page -> outside is right margin
+ \else
+ \def\temp{\inleftmargin\lefttext}%
+ \fi
+ \temp
+}
+
+% @include FILE -- \input text of FILE.
+%
+\def\include{\parseargusing\filenamecatcodes\includezzz}
+\def\includezzz#1{%
+ \pushthisfilestack
+ \def\thisfile{#1}%
+ {%
+ \makevalueexpandable % we want to expand any @value in FILE.
+ \turnoffactive % and allow special characters in the expansion
+ \indexnofonts % Allow `@@' and other weird things in file names.
+ \edef\temp{\noexpand\input #1 }%
+ %
+ % This trickery is to read FILE outside of a group, in case it makes
+ % definitions, etc.
+ \expandafter
+ }\temp
+ \popthisfilestack
+}
+\def\filenamecatcodes{%
+ \catcode`\\=\other
+ \catcode`~=\other
+ \catcode`^=\other
+ \catcode`_=\other
+ \catcode`|=\other
+ \catcode`<=\other
+ \catcode`>=\other
+ \catcode`+=\other
+ \catcode`-=\other
+ \catcode`\`=\other
+ \catcode`\'=\other
+}
+
+\def\pushthisfilestack{%
+ \expandafter\pushthisfilestackX\popthisfilestack\StackTerm
+}
+\def\pushthisfilestackX{%
+ \expandafter\pushthisfilestackY\thisfile\StackTerm
+}
+\def\pushthisfilestackY #1\StackTerm #2\StackTerm {%
+ \gdef\popthisfilestack{\gdef\thisfile{#1}\gdef\popthisfilestack{#2}}%
+}
+
+\def\popthisfilestack{\errthisfilestackempty}
+\def\errthisfilestackempty{\errmessage{Internal error:
+ the stack of filenames is empty.}}
+
+\def\thisfile{}
+
+% @center line
+% outputs that line, centered.
+%
+\parseargdef\center{%
+ \ifhmode
+ \let\next\centerH
+ \else
+ \let\next\centerV
+ \fi
+ \next{\hfil \ignorespaces#1\unskip \hfil}%
+}
+\def\centerH#1{%
+ {%
+ \hfil\break
+ \advance\hsize by -\leftskip
+ \advance\hsize by -\rightskip
+ \line{#1}%
+ \break
+ }%
+}
+\def\centerV#1{\line{\kern\leftskip #1\kern\rightskip}}
+
+% @sp n outputs n lines of vertical space
+
+\parseargdef\sp{\vskip #1\baselineskip}
+
+% @comment ...line which is ignored...
+% @c is the same as @comment
+% @ignore ... @end ignore is another way to write a comment
+
+\def\comment{\begingroup \catcode`\^^M=\other%
+\catcode`\@=\other \catcode`\{=\other \catcode`\}=\other%
+\commentxxx}
+{\catcode`\^^M=\other \gdef\commentxxx#1^^M{\endgroup}}
+
+\let\c=\comment
+
+% @paragraphindent NCHARS
+% We'll use ems for NCHARS, close enough.
+% NCHARS can also be the word `asis' or `none'.
+% We cannot feasibly implement @paragraphindent asis, though.
+%
+\def\asisword{asis} % no translation, these are keywords
+\def\noneword{none}
+%
+\parseargdef\paragraphindent{%
+ \def\temp{#1}%
+ \ifx\temp\asisword
+ \else
+ \ifx\temp\noneword
+ \defaultparindent = 0pt
+ \else
+ \defaultparindent = #1em
+ \fi
+ \fi
+ \parindent = \defaultparindent
+}
+
+% @exampleindent NCHARS
+% We'll use ems for NCHARS like @paragraphindent.
+% It seems @exampleindent asis isn't necessary, but
+% I preserve it to make it similar to @paragraphindent.
+\parseargdef\exampleindent{%
+ \def\temp{#1}%
+ \ifx\temp\asisword
+ \else
+ \ifx\temp\noneword
+ \lispnarrowing = 0pt
+ \else
+ \lispnarrowing = #1em
+ \fi
+ \fi
+}
+
+% @firstparagraphindent WORD
+% If WORD is `none', then suppress indentation of the first paragraph
+% after a section heading. If WORD is `insert', then do indent at such
+% paragraphs.
+%
+% The paragraph indentation is suppressed or not by calling
+% \suppressfirstparagraphindent, which the sectioning commands do.
+% We switch the definition of this back and forth according to WORD.
+% By default, we suppress indentation.
+%
+\def\suppressfirstparagraphindent{\dosuppressfirstparagraphindent}
+\def\insertword{insert}
+%
+\parseargdef\firstparagraphindent{%
+ \def\temp{#1}%
+ \ifx\temp\noneword
+ \let\suppressfirstparagraphindent = \dosuppressfirstparagraphindent
+ \else\ifx\temp\insertword
+ \let\suppressfirstparagraphindent = \relax
+ \else
+ \errhelp = \EMsimple
+ \errmessage{Unknown @firstparagraphindent option `\temp'}%
+ \fi\fi
+}
+
+% Here is how we actually suppress indentation. Redefine \everypar to
+% \kern backwards by \parindent, and then reset itself to empty.
+%
+% We also make \indent itself not actually do anything until the next
+% paragraph.
+%
+\gdef\dosuppressfirstparagraphindent{%
+ \gdef\indent{%
+ \restorefirstparagraphindent
+ \indent
+ }%
+ \gdef\noindent{%
+ \restorefirstparagraphindent
+ \noindent
+ }%
+ \global\everypar = {%
+ \kern -\parindent
+ \restorefirstparagraphindent
+ }%
+}
+
+\gdef\restorefirstparagraphindent{%
+ \global \let \indent = \ptexindent
+ \global \let \noindent = \ptexnoindent
+ \global \everypar = {}%
+}
+
+
+% @asis just yields its argument. Used with @table, for example.
+%
+\def\asis#1{#1}
+
+% @math outputs its argument in math mode.
+%
+% One complication: _ usually means subscripts, but it could also mean
+% an actual _ character, as in @math{@var{some_variable} + 1}. So make
+% _ active, and distinguish by seeing if the current family is \slfam,
+% which is what @var uses.
+{
+ \catcode`\_ = \active
+ \gdef\mathunderscore{%
+ \catcode`\_=\active
+ \def_{\ifnum\fam=\slfam \_\else\sb\fi}%
+ }
+}
+% Another complication: we want \\ (and @\) to output a \ character.
+% FYI, plain.tex uses \\ as a temporary control sequence (why?), but
+% this is not advertised and we don't care. Texinfo does not
+% otherwise define @\.
+%
+% The \mathchar is class=0=ordinary, family=7=ttfam, position=5C=\.
+\def\mathbackslash{\ifnum\fam=\ttfam \mathchar"075C \else\backslash \fi}
+%
+\def\math{%
+ \tex
+ \mathunderscore
+ \let\\ = \mathbackslash
+ \mathactive
+ % make the texinfo accent commands work in math mode
+ \let\"=\ddot
+ \let\'=\acute
+ \let\==\bar
+ \let\^=\hat
+ \let\`=\grave
+ \let\u=\breve
+ \let\v=\check
+ \let\~=\tilde
+ \let\dotaccent=\dot
+ $\finishmath
+}
+\def\finishmath#1{#1$\endgroup} % Close the group opened by \tex.
+
+% Some active characters (such as <) are spaced differently in math.
+% We have to reset their definitions in case the @math was an argument
+% to a command which sets the catcodes (such as @item or @section).
+%
+{
+ \catcode`^ = \active
+ \catcode`< = \active
+ \catcode`> = \active
+ \catcode`+ = \active
+ \catcode`' = \active
+ \gdef\mathactive{%
+ \let^ = \ptexhat
+ \let< = \ptexless
+ \let> = \ptexgtr
+ \let+ = \ptexplus
+ \let' = \ptexquoteright
+ }
+}
+
+% Some math mode symbols.
+\def\bullet{$\ptexbullet$}
+\def\geq{\ifmmode \ge\else $\ge$\fi}
+\def\leq{\ifmmode \le\else $\le$\fi}
+\def\minus{\ifmmode -\else $-$\fi}
+
+% @dots{} outputs an ellipsis using the current font.
+% We do .5em per period so that it has the same spacing in the cm
+% typewriter fonts as three actual period characters; on the other hand,
+% in other typewriter fonts three periods are wider than 1.5em. So do
+% whichever is larger.
+%
+\def\dots{%
+ \leavevmode
+ \setbox0=\hbox{...}% get width of three periods
+ \ifdim\wd0 > 1.5em
+ \dimen0 = \wd0
+ \else
+ \dimen0 = 1.5em
+ \fi
+ \hbox to \dimen0{%
+ \hskip 0pt plus.25fil
+ .\hskip 0pt plus1fil
+ .\hskip 0pt plus1fil
+ .\hskip 0pt plus.5fil
+ }%
+}
+
+% @enddots{} is an end-of-sentence ellipsis.
+%
+\def\enddots{%
+ \dots
+ \spacefactor=\endofsentencespacefactor
+}
+
+% @comma{} is so commas can be inserted into text without messing up
+% Texinfo's parsing.
+%
+\let\comma = ,
+
+% @refill is a no-op.
+\let\refill=\relax
+
+% If working on a large document in chapters, it is convenient to
+% be able to disable indexing, cross-referencing, and contents, for test runs.
+% This is done with @novalidate (before @setfilename).
+%
+\newif\iflinks \linkstrue % by default we want the aux files.
+\let\novalidate = \linksfalse
+
+% @setfilename is done at the beginning of every texinfo file.
+% So open here the files we need to have open while reading the input.
+% This makes it possible to make a .fmt file for texinfo.
+\def\setfilename{%
+ \fixbackslash % Turn off hack to swallow `\input texinfo'.
+ \iflinks
+ \tryauxfile
+ % Open the new aux file. TeX will close it automatically at exit.
+ \immediate\openout\auxfile=\jobname.aux
+ \fi % \openindices needs to do some work in any case.
+ \openindices
+ \let\setfilename=\comment % Ignore extra @setfilename cmds.
+ %
+ % If texinfo.cnf is present on the system, read it.
+ % Useful for site-wide @afourpaper, etc.
+ \openin 1 texinfo.cnf
+ \ifeof 1 \else \input texinfo.cnf \fi
+ \closein 1
+ %
+ \comment % Ignore the actual filename.
+}
+
+% Called from \setfilename.
+%
+\def\openindices{%
+ \newindex{cp}%
+ \newcodeindex{fn}%
+ \newcodeindex{vr}%
+ \newcodeindex{tp}%
+ \newcodeindex{ky}%
+ \newcodeindex{pg}%
+}
+
+% @bye.
+\outer\def\bye{\pagealignmacro\tracingstats=1\ptexend}
+
+
+\message{pdf,}
+% adobe `portable' document format
+\newcount\tempnum
+\newcount\lnkcount
+\newtoks\filename
+\newcount\filenamelength
+\newcount\pgn
+\newtoks\toksA
+\newtoks\toksB
+\newtoks\toksC
+\newtoks\toksD
+\newbox\boxA
+\newcount\countA
+\newif\ifpdf
+\newif\ifpdfmakepagedest
+
+% when pdftex is run in dvi mode, \pdfoutput is defined (so \pdfoutput=1
+% can be set). So we test for \relax and 0 as well as \undefined,
+% borrowed from ifpdf.sty.
+\ifx\pdfoutput\undefined
+\else
+ \ifx\pdfoutput\relax
+ \else
+ \ifcase\pdfoutput
+ \else
+ \pdftrue
+ \fi
+ \fi
+\fi
+
+% PDF uses PostScript string constants for the names of xref targets,
+% for display in the outlines, and in other places. Thus, we have to
+% double any backslashes. Otherwise, a name like "\node" will be
+% interpreted as a newline (\n), followed by o, d, e. Not good.
+% http://www.ntg.nl/pipermail/ntg-pdftex/2004-July/000654.html
+% (and related messages, the final outcome is that it is up to the TeX
+% user to double the backslashes and otherwise make the string valid, so
+% that's what we do).
+
+% double active backslashes.
+%
+{\catcode`\@=0 \catcode`\\=\active
+ @gdef at activebackslashdouble{%
+ @catcode`@\=@active
+ @let\=@doublebackslash}
+}
+
+% To handle parens, we must adopt a different approach, since parens are
+% not active characters. hyperref.dtx (which has the same problem as
+% us) handles it with this amazing macro to replace tokens, with minor
+% changes for Texinfo. It is included here under the GPL by permission
+% from the author, Heiko Oberdiek.
+%
+% #1 is the tokens to replace.
+% #2 is the replacement.
+% #3 is the control sequence with the string.
+%
+\def\HyPsdSubst#1#2#3{%
+ \def\HyPsdReplace##1#1##2\END{%
+ ##1%
+ \ifx\\##2\\%
+ \else
+ #2%
+ \HyReturnAfterFi{%
+ \HyPsdReplace##2\END
+ }%
+ \fi
+ }%
+ \xdef#3{\expandafter\HyPsdReplace#3#1\END}%
+}
+\long\def\HyReturnAfterFi#1\fi{\fi#1}
+
+% #1 is a control sequence in which to do the replacements.
+\def\backslashparens#1{%
+ \xdef#1{#1}% redefine it as its expansion; the definition is simply
+ % \lastnode when called from \setref -> \pdfmkdest.
+ \HyPsdSubst{(}{\realbackslash(}{#1}%
+ \HyPsdSubst{)}{\realbackslash)}{#1}%
+}
+
+\newhelp\nopdfimagehelp{Texinfo supports .png, .jpg, .jpeg, and .pdf images
+with PDF output, and none of those formats could be found. (.eps cannot
+be supported due to the design of the PDF format; use regular TeX (DVI
+output) for that.)}
+
+\ifpdf
+ %
+ % Color manipulation macros based on pdfcolor.tex,
+ % except using rgb instead of cmyk; the latter is said to render as a
+ % very dark gray on-screen and a very dark halftone in print, instead
+ % of actual black.
+ \def\rgbDarkRed{0.50 0.09 0.12}
+ \def\rgbBlack{0 0 0}
+ %
+ % k sets the color for filling (usual text, etc.);
+ % K sets the color for stroking (thin rules, e.g., normal _'s).
+ \def\pdfsetcolor#1{\pdfliteral{#1 rg #1 RG}}
+ %
+ % Set color, and create a mark which defines \thiscolor accordingly,
+ % so that \makeheadline knows which color to restore.
+ \def\setcolor#1{%
+ \xdef\lastcolordefs{\gdef\noexpand\thiscolor{#1}}%
+ \domark
+ \pdfsetcolor{#1}%
+ }
+ %
+ \def\maincolor{\rgbBlack}
+ \pdfsetcolor{\maincolor}
+ \edef\thiscolor{\maincolor}
+ \def\lastcolordefs{}
+ %
+ \def\makefootline{%
+ \baselineskip24pt
+ \line{\pdfsetcolor{\maincolor}\the\footline}%
+ }
+ %
+ \def\makeheadline{%
+ \vbox to 0pt{%
+ \vskip-22.5pt
+ \line{%
+ \vbox to8.5pt{}%
+ % Extract \thiscolor definition from the marks.
+ \getcolormarks
+ % Typeset the headline with \maincolor, then restore the color.
+ \pdfsetcolor{\maincolor}\the\headline\pdfsetcolor{\thiscolor}%
+ }%
+ \vss
+ }%
+ \nointerlineskip
+ }
+ %
+ %
+ \pdfcatalog{/PageMode /UseOutlines}
+ %
+ % #1 is image name, #2 width (might be empty/whitespace), #3 height (ditto).
+ \def\dopdfimage#1#2#3{%
+ \def\imagewidth{#2}\setbox0 = \hbox{\ignorespaces #2}%
+ \def\imageheight{#3}\setbox2 = \hbox{\ignorespaces #3}%
+ %
+ % pdftex (and the PDF format) support .png, .jpg, .pdf (among
+ % others). Let's try in that order.
+ \let\pdfimgext=\empty
+ \begingroup
+ \openin 1 #1.png \ifeof 1
+ \openin 1 #1.jpg \ifeof 1
+ \openin 1 #1.jpeg \ifeof 1
+ \openin 1 #1.JPG \ifeof 1
+ \openin 1 #1.pdf \ifeof 1
+ \openin 1 #1.PDF \ifeof 1
+ \errhelp = \nopdfimagehelp
+ \errmessage{Could not find image file #1 for pdf}%
+ \else \gdef\pdfimgext{PDF}%
+ \fi
+ \else \gdef\pdfimgext{pdf}%
+ \fi
+ \else \gdef\pdfimgext{JPG}%
+ \fi
+ \else \gdef\pdfimgext{jpeg}%
+ \fi
+ \else \gdef\pdfimgext{jpg}%
+ \fi
+ \else \gdef\pdfimgext{png}%
+ \fi
+ \closein 1
+ \endgroup
+ %
+ % without \immediate, ancient pdftex seg faults when the same image is
+ % included twice. (Version 3.14159-pre-1.0-unofficial-20010704.)
+ \ifnum\pdftexversion < 14
+ \immediate\pdfimage
+ \else
+ \immediate\pdfximage
+ \fi
+ \ifdim \wd0 >0pt width \imagewidth \fi
+ \ifdim \wd2 >0pt height \imageheight \fi
+ \ifnum\pdftexversion<13
+ #1.\pdfimgext
+ \else
+ {#1.\pdfimgext}%
+ \fi
+ \ifnum\pdftexversion < 14 \else
+ \pdfrefximage \pdflastximage
+ \fi}
+ %
+ \def\pdfmkdest#1{{%
+ % We have to set dummies so commands such as @code, and characters
+ % such as \, aren't expanded when present in a section title.
+ \indexnofonts
+ \turnoffactive
+ \activebackslashdouble
+ \makevalueexpandable
+ \def\pdfdestname{#1}%
+ \backslashparens\pdfdestname
+ \safewhatsit{\pdfdest name{\pdfdestname} xyz}%
+ }}
+ %
+ % used to mark target names; must be expandable.
+ \def\pdfmkpgn#1{#1}
+ %
+ % by default, use a color that is dark enough to print on paper as
+ % nearly black, but still distinguishable for online viewing.
+ \def\urlcolor{\rgbDarkRed}
+ \def\linkcolor{\rgbDarkRed}
+ \def\endlink{\setcolor{\maincolor}\pdfendlink}
+ %
+ % Adding outlines to PDF; macros for calculating structure of outlines
+ % come from Petr Olsak
+ \def\expnumber#1{\expandafter\ifx\csname#1\endcsname\relax 0%
+ \else \csname#1\endcsname \fi}
+ \def\advancenumber#1{\tempnum=\expnumber{#1}\relax
+ \advance\tempnum by 1
+ \expandafter\xdef\csname#1\endcsname{\the\tempnum}}
+ %
+ % #1 is the section text, which is what will be displayed in the
+ % outline by the pdf viewer. #2 is the pdf expression for the number
+ % of subentries (or empty, for subsubsections). #3 is the node text,
+ % which might be empty if this toc entry had no corresponding node.
+ % #4 is the page number
+ %
+ \def\dopdfoutline#1#2#3#4{%
+ % Generate a link to the node text if that exists; else, use the
+ % page number. We could generate a destination for the section
+ % text in the case where a section has no node, but it doesn't
+ % seem worth the trouble, since most documents are normally structured.
+ \def\pdfoutlinedest{#3}%
+ \ifx\pdfoutlinedest\empty
+ \def\pdfoutlinedest{#4}%
+ \else
+ % Doubled backslashes in the name.
+ {\activebackslashdouble \xdef\pdfoutlinedest{#3}%
+ \backslashparens\pdfoutlinedest}%
+ \fi
+ %
+ % Also double the backslashes in the display string.
+ {\activebackslashdouble \xdef\pdfoutlinetext{#1}%
+ \backslashparens\pdfoutlinetext}%
+ %
+ \pdfoutline goto name{\pdfmkpgn{\pdfoutlinedest}}#2{\pdfoutlinetext}%
+ }
+ %
+ \def\pdfmakeoutlines{%
+ \begingroup
+ % Thanh's hack / proper braces in bookmarks
+ \edef\mylbrace{\iftrue \string{\else}\fi}\let\{=\mylbrace
+ \edef\myrbrace{\iffalse{\else\string}\fi}\let\}=\myrbrace
+ %
+ % Read toc silently, to get counts of subentries for \pdfoutline.
+ \def\numchapentry##1##2##3##4{%
+ \def\thischapnum{##2}%
+ \def\thissecnum{0}%
+ \def\thissubsecnum{0}%
+ }%
+ \def\numsecentry##1##2##3##4{%
+ \advancenumber{chap\thischapnum}%
+ \def\thissecnum{##2}%
+ \def\thissubsecnum{0}%
+ }%
+ \def\numsubsecentry##1##2##3##4{%
+ \advancenumber{sec\thissecnum}%
+ \def\thissubsecnum{##2}%
+ }%
+ \def\numsubsubsecentry##1##2##3##4{%
+ \advancenumber{subsec\thissubsecnum}%
+ }%
+ \def\thischapnum{0}%
+ \def\thissecnum{0}%
+ \def\thissubsecnum{0}%
+ %
+ % use \def rather than \let here because we redefine \chapentry et
+ % al. a second time, below.
+ \def\appentry{\numchapentry}%
+ \def\appsecentry{\numsecentry}%
+ \def\appsubsecentry{\numsubsecentry}%
+ \def\appsubsubsecentry{\numsubsubsecentry}%
+ \def\unnchapentry{\numchapentry}%
+ \def\unnsecentry{\numsecentry}%
+ \def\unnsubsecentry{\numsubsecentry}%
+ \def\unnsubsubsecentry{\numsubsubsecentry}%
+ \readdatafile{toc}%
+ %
+ % Read toc second time, this time actually producing the outlines.
+ % The `-' means take the \expnumber as the absolute number of
+ % subentries, which we calculated on our first read of the .toc above.
+ %
+ % We use the node names as the destinations.
+ \def\numchapentry##1##2##3##4{%
+ \dopdfoutline{##1}{count-\expnumber{chap##2}}{##3}{##4}}%
+ \def\numsecentry##1##2##3##4{%
+ \dopdfoutline{##1}{count-\expnumber{sec##2}}{##3}{##4}}%
+ \def\numsubsecentry##1##2##3##4{%
+ \dopdfoutline{##1}{count-\expnumber{subsec##2}}{##3}{##4}}%
+ \def\numsubsubsecentry##1##2##3##4{% count is always zero
+ \dopdfoutline{##1}{}{##3}{##4}}%
+ %
+ % PDF outlines are displayed using system fonts, instead of
+ % document fonts. Therefore we cannot use special characters,
+ % since the encoding is unknown. For example, the eogonek from
+ % Latin 2 (0xea) gets translated to a | character. Info from
+ % Staszek Wawrykiewicz, 19 Jan 2004 04:09:24 +0100.
+ %
+ % xx to do this right, we have to translate 8-bit characters to
+ % their "best" equivalent, based on the @documentencoding. Right
+ % now, I guess we'll just let the pdf reader have its way.
+ \indexnofonts
+ \setupdatafile
+ \catcode`\\=\active \otherbackslash
+ \input \tocreadfilename
+ \endgroup
+ }
+ %
+ \def\skipspaces#1{\def\PP{#1}\def\D{|}%
+ \ifx\PP\D\let\nextsp\relax
+ \else\let\nextsp\skipspaces
+ \ifx\p\space\else\addtokens{\filename}{\PP}%
+ \advance\filenamelength by 1
+ \fi
+ \fi
+ \nextsp}
+ \def\getfilename#1{\filenamelength=0\expandafter\skipspaces#1|\relax}
+ \ifnum\pdftexversion < 14
+ \let \startlink \pdfannotlink
+ \else
+ \let \startlink \pdfstartlink
+ \fi
+ % make a live url in pdf output.
+ \def\pdfurl#1{%
+ \begingroup
+ % it seems we really need yet another set of dummies; have not
+ % tried to figure out what each command should do in the context
+ % of @url. for now, just make @/ a no-op, that's the only one
+ % people have actually reported a problem with.
+ %
+ \normalturnoffactive
+ \def\@{@}%
+ \let\/=\empty
+ \makevalueexpandable
+ % do we want to go so far as to use \indexnofonts instead of just
+ % special-casing \var here?
+ \def\var##1{##1}%
+ %
+ \leavevmode\setcolor{\urlcolor}%
+ \startlink attr{/Border [0 0 0]}%
+ user{/Subtype /Link /A << /S /URI /URI (#1) >>}%
+ \endgroup}
+ \def\pdfgettoks#1.{\setbox\boxA=\hbox{\toksA={#1.}\toksB={}\maketoks}}
+ \def\addtokens#1#2{\edef\addtoks{\noexpand#1={\the#1#2}}\addtoks}
+ \def\adn#1{\addtokens{\toksC}{#1}\global\countA=1\let\next=\maketoks}
+ \def\poptoks#1#2|ENDTOKS|{\let\first=#1\toksD={#1}\toksA={#2}}
+ \def\maketoks{%
+ \expandafter\poptoks\the\toksA|ENDTOKS|\relax
+ \ifx\first0\adn0
+ \else\ifx\first1\adn1 \else\ifx\first2\adn2 \else\ifx\first3\adn3
+ \else\ifx\first4\adn4 \else\ifx\first5\adn5 \else\ifx\first6\adn6
+ \else\ifx\first7\adn7 \else\ifx\first8\adn8 \else\ifx\first9\adn9
+ \else
+ \ifnum0=\countA\else\makelink\fi
+ \ifx\first.\let\next=\done\else
+ \let\next=\maketoks
+ \addtokens{\toksB}{\the\toksD}
+ \ifx\first,\addtokens{\toksB}{\space}\fi
+ \fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \next}
+ \def\makelink{\addtokens{\toksB}%
+ {\noexpand\pdflink{\the\toksC}}\toksC={}\global\countA=0}
+ \def\pdflink#1{%
+ \startlink attr{/Border [0 0 0]} goto name{\pdfmkpgn{#1}}
+ \setcolor{\linkcolor}#1\endlink}
+ \def\done{\edef\st{\global\noexpand\toksA={\the\toksB}}\st}
+\else
+ % non-pdf mode
+ \let\pdfmkdest = \gobble
+ \let\pdfurl = \gobble
+ \let\endlink = \relax
+ \let\setcolor = \gobble
+ \let\pdfsetcolor = \gobble
+ \let\pdfmakeoutlines = \relax
+\fi % \ifx\pdfoutput
+
+
+\message{fonts,}
+
+% Change the current font style to #1, remembering it in \curfontstyle.
+% For now, we do not accumulate font styles: @b{@i{foo}} prints foo in
+% italics, not bold italics.
+%
+\def\setfontstyle#1{%
+ \def\curfontstyle{#1}% not as a control sequence, because we are \edef'd.
+ \csname ten#1\endcsname % change the current font
+}
+
+% Select #1 fonts with the current style.
+%
+\def\selectfonts#1{\csname #1fonts\endcsname \csname\curfontstyle\endcsname}
+
+\def\rm{\fam=0 \setfontstyle{rm}}
+\def\it{\fam=\itfam \setfontstyle{it}}
+\def\sl{\fam=\slfam \setfontstyle{sl}}
+\def\bf{\fam=\bffam \setfontstyle{bf}}\def\bfstylename{bf}
+\def\tt{\fam=\ttfam \setfontstyle{tt}}
+
+% Unfortunately, we have to override this for titles and the like, since
+% in those cases "rm" is bold. Sigh.
+\def\rmisbold{\rm\def\curfontstyle{bf}}
+
+% Texinfo sort of supports the sans serif font style, which plain TeX does not.
+% So we set up a \sf.
+\newfam\sffam
+\def\sf{\fam=\sffam \setfontstyle{sf}}
+\let\li = \sf % Sometimes we call it \li, not \sf.
+
+% We don't need math for this font style.
+\def\ttsl{\setfontstyle{ttsl}}
+
+
+% Default leading.
+\newdimen\textleading \textleading = 13.2pt
+
+% Set the baselineskip to #1, and the lineskip and strut size
+% correspondingly. There is no deep meaning behind these magic numbers
+% used as factors; they just match (closely enough) what Knuth defined.
+%
+\def\lineskipfactor{.08333}
+\def\strutheightpercent{.70833}
+\def\strutdepthpercent {.29167}
+%
+% can get a sort of poor man's double spacing by redefining this.
+\def\baselinefactor{1}
+%
+\def\setleading#1{%
+ \dimen0 = #1\relax
+ \normalbaselineskip = \baselinefactor\dimen0
+ \normallineskip = \lineskipfactor\normalbaselineskip
+ \normalbaselines
+ \setbox\strutbox =\hbox{%
+ \vrule width0pt height\strutheightpercent\baselineskip
+ depth \strutdepthpercent \baselineskip
+ }%
+}
+
+% PDF CMaps. See also LaTeX's t1.cmap.
+%
+% do nothing with this by default.
+\expandafter\let\csname cmapOT1\endcsname\gobble
+\expandafter\let\csname cmapOT1IT\endcsname\gobble
+\expandafter\let\csname cmapOT1TT\endcsname\gobble
+
+% if we are producing pdf, and we have \pdffontattr, then define cmaps.
+% (\pdffontattr was introduced many years ago, but people still run
+% older pdftex's; it's easy to conditionalize, so we do.)
+\ifpdf \ifx\pdffontattr\undefined \else
+ \begingroup
+ \catcode`\^^M=\active \def^^M{^^J}% Output line endings as the ^^J char.
+ \catcode`\%=12 \immediate\pdfobj stream {%!PS-Adobe-3.0 Resource-CMap
+%%DocumentNeededResources: ProcSet (CIDInit)
+%%IncludeResource: ProcSet (CIDInit)
+%%BeginResource: CMap (TeX-OT1-0)
+%%Title: (TeX-OT1-0 TeX OT1 0)
+%%Version: 1.000
+%%EndComments
+/CIDInit /ProcSet findresource begin
+12 dict begin
+begincmap
+/CIDSystemInfo
+<< /Registry (TeX)
+/Ordering (OT1)
+/Supplement 0
+>> def
+/CMapName /TeX-OT1-0 def
+/CMapType 2 def
+1 begincodespacerange
+<00> <7F>
+endcodespacerange
+8 beginbfrange
+<00> <01> <0393>
+<09> <0A> <03A8>
+<23> <26> <0023>
+<28> <3B> <0028>
+<3F> <5B> <003F>
+<5D> <5E> <005D>
+<61> <7A> <0061>
+<7B> <7C> <2013>
+endbfrange
+40 beginbfchar
+<02> <0398>
+<03> <039B>
+<04> <039E>
+<05> <03A0>
+<06> <03A3>
+<07> <03D2>
+<08> <03A6>
+<0B> <00660066>
+<0C> <00660069>
+<0D> <0066006C>
+<0E> <006600660069>
+<0F> <00660066006C>
+<10> <0131>
+<11> <0237>
+<12> <0060>
+<13> <00B4>
+<14> <02C7>
+<15> <02D8>
+<16> <00AF>
+<17> <02DA>
+<18> <00B8>
+<19> <00DF>
+<1A> <00E6>
+<1B> <0153>
+<1C> <00F8>
+<1D> <00C6>
+<1E> <0152>
+<1F> <00D8>
+<21> <0021>
+<22> <201D>
+<27> <2019>
+<3C> <00A1>
+<3D> <003D>
+<3E> <00BF>
+<5C> <201C>
+<5F> <02D9>
+<60> <2018>
+<7D> <02DD>
+<7E> <007E>
+<7F> <00A8>
+endbfchar
+endcmap
+CMapName currentdict /CMap defineresource pop
+end
+end
+%%EndResource
+%%EOF
+ }\endgroup
+ \expandafter\edef\csname cmapOT1\endcsname#1{%
+ \pdffontattr#1{/ToUnicode \the\pdflastobj\space 0 R}%
+ }%
+%
+% \cmapOT1IT
+ \begingroup
+ \catcode`\^^M=\active \def^^M{^^J}% Output line endings as the ^^J char.
+ \catcode`\%=12 \immediate\pdfobj stream {%!PS-Adobe-3.0 Resource-CMap
+%%DocumentNeededResources: ProcSet (CIDInit)
+%%IncludeResource: ProcSet (CIDInit)
+%%BeginResource: CMap (TeX-OT1IT-0)
+%%Title: (TeX-OT1IT-0 TeX OT1IT 0)
+%%Version: 1.000
+%%EndComments
+/CIDInit /ProcSet findresource begin
+12 dict begin
+begincmap
+/CIDSystemInfo
+<< /Registry (TeX)
+/Ordering (OT1IT)
+/Supplement 0
+>> def
+/CMapName /TeX-OT1IT-0 def
+/CMapType 2 def
+1 begincodespacerange
+<00> <7F>
+endcodespacerange
+8 beginbfrange
+<00> <01> <0393>
+<09> <0A> <03A8>
+<25> <26> <0025>
+<28> <3B> <0028>
+<3F> <5B> <003F>
+<5D> <5E> <005D>
+<61> <7A> <0061>
+<7B> <7C> <2013>
+endbfrange
+42 beginbfchar
+<02> <0398>
+<03> <039B>
+<04> <039E>
+<05> <03A0>
+<06> <03A3>
+<07> <03D2>
+<08> <03A6>
+<0B> <00660066>
+<0C> <00660069>
+<0D> <0066006C>
+<0E> <006600660069>
+<0F> <00660066006C>
+<10> <0131>
+<11> <0237>
+<12> <0060>
+<13> <00B4>
+<14> <02C7>
+<15> <02D8>
+<16> <00AF>
+<17> <02DA>
+<18> <00B8>
+<19> <00DF>
+<1A> <00E6>
+<1B> <0153>
+<1C> <00F8>
+<1D> <00C6>
+<1E> <0152>
+<1F> <00D8>
+<21> <0021>
+<22> <201D>
+<23> <0023>
+<24> <00A3>
+<27> <2019>
+<3C> <00A1>
+<3D> <003D>
+<3E> <00BF>
+<5C> <201C>
+<5F> <02D9>
+<60> <2018>
+<7D> <02DD>
+<7E> <007E>
+<7F> <00A8>
+endbfchar
+endcmap
+CMapName currentdict /CMap defineresource pop
+end
+end
+%%EndResource
+%%EOF
+ }\endgroup
+ \expandafter\edef\csname cmapOT1IT\endcsname#1{%
+ \pdffontattr#1{/ToUnicode \the\pdflastobj\space 0 R}%
+ }%
+%
+% \cmapOT1TT
+ \begingroup
+ \catcode`\^^M=\active \def^^M{^^J}% Output line endings as the ^^J char.
+ \catcode`\%=12 \immediate\pdfobj stream {%!PS-Adobe-3.0 Resource-CMap
+%%DocumentNeededResources: ProcSet (CIDInit)
+%%IncludeResource: ProcSet (CIDInit)
+%%BeginResource: CMap (TeX-OT1TT-0)
+%%Title: (TeX-OT1TT-0 TeX OT1TT 0)
+%%Version: 1.000
+%%EndComments
+/CIDInit /ProcSet findresource begin
+12 dict begin
+begincmap
+/CIDSystemInfo
+<< /Registry (TeX)
+/Ordering (OT1TT)
+/Supplement 0
+>> def
+/CMapName /TeX-OT1TT-0 def
+/CMapType 2 def
+1 begincodespacerange
+<00> <7F>
+endcodespacerange
+5 beginbfrange
+<00> <01> <0393>
+<09> <0A> <03A8>
+<21> <26> <0021>
+<28> <5F> <0028>
+<61> <7E> <0061>
+endbfrange
+32 beginbfchar
+<02> <0398>
+<03> <039B>
+<04> <039E>
+<05> <03A0>
+<06> <03A3>
+<07> <03D2>
+<08> <03A6>
+<0B> <2191>
+<0C> <2193>
+<0D> <0027>
+<0E> <00A1>
+<0F> <00BF>
+<10> <0131>
+<11> <0237>
+<12> <0060>
+<13> <00B4>
+<14> <02C7>
+<15> <02D8>
+<16> <00AF>
+<17> <02DA>
+<18> <00B8>
+<19> <00DF>
+<1A> <00E6>
+<1B> <0153>
+<1C> <00F8>
+<1D> <00C6>
+<1E> <0152>
+<1F> <00D8>
+<20> <2423>
+<27> <2019>
+<60> <2018>
+<7F> <00A8>
+endbfchar
+endcmap
+CMapName currentdict /CMap defineresource pop
+end
+end
+%%EndResource
+%%EOF
+ }\endgroup
+ \expandafter\edef\csname cmapOT1TT\endcsname#1{%
+ \pdffontattr#1{/ToUnicode \the\pdflastobj\space 0 R}%
+ }%
+\fi\fi
+
+
+% Set the font macro #1 to the font named #2, adding on the
+% specified font prefix (normally `cm').
+% #3 is the font's design size, #4 is a scale factor, #5 is the CMap
+% encoding (currently only OT1, OT1IT and OT1TT are allowed, pass
+% empty to omit).
+\def\setfont#1#2#3#4#5{%
+ \font#1=\fontprefix#2#3 scaled #4
+ \csname cmap#5\endcsname#1%
+}
+% This is what gets called when #5 of \setfont is empty.
+\let\cmap\gobble
+% emacs-page end of cmaps
+
+% Use cm as the default font prefix.
+% To specify the font prefix, you must define \fontprefix
+% before you read in texinfo.tex.
+\ifx\fontprefix\undefined
+\def\fontprefix{cm}
+\fi
+% Support font families that don't use the same naming scheme as CM.
+\def\rmshape{r}
+\def\rmbshape{bx} %where the normal face is bold
+\def\bfshape{b}
+\def\bxshape{bx}
+\def\ttshape{tt}
+\def\ttbshape{tt}
+\def\ttslshape{sltt}
+\def\itshape{ti}
+\def\itbshape{bxti}
+\def\slshape{sl}
+\def\slbshape{bxsl}
+\def\sfshape{ss}
+\def\sfbshape{ss}
+\def\scshape{csc}
+\def\scbshape{csc}
+
+% Definitions for a main text size of 11pt. This is the default in
+% Texinfo.
+%
+\def\definetextfontsizexi{%
+% Text fonts (11.2pt, magstep1).
+\def\textnominalsize{11pt}
+\edef\mainmagstep{\magstephalf}
+\setfont\textrm\rmshape{10}{\mainmagstep}{OT1}
+\setfont\texttt\ttshape{10}{\mainmagstep}{OT1TT}
+\setfont\textbf\bfshape{10}{\mainmagstep}{OT1}
+\setfont\textit\itshape{10}{\mainmagstep}{OT1IT}
+\setfont\textsl\slshape{10}{\mainmagstep}{OT1}
+\setfont\textsf\sfshape{10}{\mainmagstep}{OT1}
+\setfont\textsc\scshape{10}{\mainmagstep}{OT1}
+\setfont\textttsl\ttslshape{10}{\mainmagstep}{OT1TT}
+\font\texti=cmmi10 scaled \mainmagstep
+\font\textsy=cmsy10 scaled \mainmagstep
+\def\textecsize{1095}
+
+% A few fonts for @defun names and args.
+\setfont\defbf\bfshape{10}{\magstep1}{OT1}
+\setfont\deftt\ttshape{10}{\magstep1}{OT1TT}
+\setfont\defttsl\ttslshape{10}{\magstep1}{OT1TT}
+\def\df{\let\tentt=\deftt \let\tenbf = \defbf \let\tenttsl=\defttsl \bf}
+
+% Fonts for indices, footnotes, small examples (9pt).
+\def\smallnominalsize{9pt}
+\setfont\smallrm\rmshape{9}{1000}{OT1}
+\setfont\smalltt\ttshape{9}{1000}{OT1TT}
+\setfont\smallbf\bfshape{10}{900}{OT1}
+\setfont\smallit\itshape{9}{1000}{OT1IT}
+\setfont\smallsl\slshape{9}{1000}{OT1}
+\setfont\smallsf\sfshape{9}{1000}{OT1}
+\setfont\smallsc\scshape{10}{900}{OT1}
+\setfont\smallttsl\ttslshape{10}{900}{OT1TT}
+\font\smalli=cmmi9
+\font\smallsy=cmsy9
+\def\smallecsize{0900}
+
+% Fonts for small examples (8pt).
+\def\smallernominalsize{8pt}
+\setfont\smallerrm\rmshape{8}{1000}{OT1}
+\setfont\smallertt\ttshape{8}{1000}{OT1TT}
+\setfont\smallerbf\bfshape{10}{800}{OT1}
+\setfont\smallerit\itshape{8}{1000}{OT1IT}
+\setfont\smallersl\slshape{8}{1000}{OT1}
+\setfont\smallersf\sfshape{8}{1000}{OT1}
+\setfont\smallersc\scshape{10}{800}{OT1}
+\setfont\smallerttsl\ttslshape{10}{800}{OT1TT}
+\font\smalleri=cmmi8
+\font\smallersy=cmsy8
+\def\smallerecsize{0800}
+
+% Fonts for title page (20.4pt):
+\def\titlenominalsize{20pt}
+\setfont\titlerm\rmbshape{12}{\magstep3}{OT1}
+\setfont\titleit\itbshape{10}{\magstep4}{OT1IT}
+\setfont\titlesl\slbshape{10}{\magstep4}{OT1}
+\setfont\titlett\ttbshape{12}{\magstep3}{OT1TT}
+\setfont\titlettsl\ttslshape{10}{\magstep4}{OT1TT}
+\setfont\titlesf\sfbshape{17}{\magstep1}{OT1}
+\let\titlebf=\titlerm
+\setfont\titlesc\scbshape{10}{\magstep4}{OT1}
+\font\titlei=cmmi12 scaled \magstep3
+\font\titlesy=cmsy10 scaled \magstep4
+\def\titleecsize{2074}
+
+% Chapter (and unnumbered) fonts (17.28pt).
+\def\chapnominalsize{17pt}
+\setfont\chaprm\rmbshape{12}{\magstep2}{OT1}
+\setfont\chapit\itbshape{10}{\magstep3}{OT1IT}
+\setfont\chapsl\slbshape{10}{\magstep3}{OT1}
+\setfont\chaptt\ttbshape{12}{\magstep2}{OT1TT}
+\setfont\chapttsl\ttslshape{10}{\magstep3}{OT1TT}
+\setfont\chapsf\sfbshape{17}{1000}{OT1}
+\let\chapbf=\chaprm
+\setfont\chapsc\scbshape{10}{\magstep3}{OT1}
+\font\chapi=cmmi12 scaled \magstep2
+\font\chapsy=cmsy10 scaled \magstep3
+\def\chapecsize{1728}
+
+% Section fonts (14.4pt).
+\def\secnominalsize{14pt}
+\setfont\secrm\rmbshape{12}{\magstep1}{OT1}
+\setfont\secit\itbshape{10}{\magstep2}{OT1IT}
+\setfont\secsl\slbshape{10}{\magstep2}{OT1}
+\setfont\sectt\ttbshape{12}{\magstep1}{OT1TT}
+\setfont\secttsl\ttslshape{10}{\magstep2}{OT1TT}
+\setfont\secsf\sfbshape{12}{\magstep1}{OT1}
+\let\secbf\secrm
+\setfont\secsc\scbshape{10}{\magstep2}{OT1}
+\font\seci=cmmi12 scaled \magstep1
+\font\secsy=cmsy10 scaled \magstep2
+\def\sececsize{1440}
+
+% Subsection fonts (13.15pt).
+\def\ssecnominalsize{13pt}
+\setfont\ssecrm\rmbshape{12}{\magstephalf}{OT1}
+\setfont\ssecit\itbshape{10}{1315}{OT1IT}
+\setfont\ssecsl\slbshape{10}{1315}{OT1}
+\setfont\ssectt\ttbshape{12}{\magstephalf}{OT1TT}
+\setfont\ssecttsl\ttslshape{10}{1315}{OT1TT}
+\setfont\ssecsf\sfbshape{12}{\magstephalf}{OT1}
+\let\ssecbf\ssecrm
+\setfont\ssecsc\scbshape{10}{1315}{OT1}
+\font\sseci=cmmi12 scaled \magstephalf
+\font\ssecsy=cmsy10 scaled 1315
+\def\ssececsize{1200}
+
+% Reduced fonts for @acro in text (10pt).
+\def\reducednominalsize{10pt}
+\setfont\reducedrm\rmshape{10}{1000}{OT1}
+\setfont\reducedtt\ttshape{10}{1000}{OT1TT}
+\setfont\reducedbf\bfshape{10}{1000}{OT1}
+\setfont\reducedit\itshape{10}{1000}{OT1IT}
+\setfont\reducedsl\slshape{10}{1000}{OT1}
+\setfont\reducedsf\sfshape{10}{1000}{OT1}
+\setfont\reducedsc\scshape{10}{1000}{OT1}
+\setfont\reducedttsl\ttslshape{10}{1000}{OT1TT}
+\font\reducedi=cmmi10
+\font\reducedsy=cmsy10
+\def\reducedecsize{1000}
+
+% reset the current fonts
+\textfonts
+\rm
+} % end of 11pt text font size definitions
+
+
+% Definitions to make the main text be 10pt Computer Modern, with
+% section, chapter, etc., sizes following suit. This is for the GNU
+% Press printing of the Emacs 22 manual. Maybe other manuals in the
+% future. Used with @smallbook, which sets the leading to 12pt.
+%
+\def\definetextfontsizex{%
+% Text fonts (10pt).
+\def\textnominalsize{10pt}
+\edef\mainmagstep{1000}
+\setfont\textrm\rmshape{10}{\mainmagstep}{OT1}
+\setfont\texttt\ttshape{10}{\mainmagstep}{OT1TT}
+\setfont\textbf\bfshape{10}{\mainmagstep}{OT1}
+\setfont\textit\itshape{10}{\mainmagstep}{OT1IT}
+\setfont\textsl\slshape{10}{\mainmagstep}{OT1}
+\setfont\textsf\sfshape{10}{\mainmagstep}{OT1}
+\setfont\textsc\scshape{10}{\mainmagstep}{OT1}
+\setfont\textttsl\ttslshape{10}{\mainmagstep}{OT1TT}
+\font\texti=cmmi10 scaled \mainmagstep
+\font\textsy=cmsy10 scaled \mainmagstep
+\def\textecsize{1000}
+
+% A few fonts for @defun names and args.
+\setfont\defbf\bfshape{10}{\magstephalf}{OT1}
+\setfont\deftt\ttshape{10}{\magstephalf}{OT1TT}
+\setfont\defttsl\ttslshape{10}{\magstephalf}{OT1TT}
+\def\df{\let\tentt=\deftt \let\tenbf = \defbf \let\tenttsl=\defttsl \bf}
+
+% Fonts for indices, footnotes, small examples (9pt).
+\def\smallnominalsize{9pt}
+\setfont\smallrm\rmshape{9}{1000}{OT1}
+\setfont\smalltt\ttshape{9}{1000}{OT1TT}
+\setfont\smallbf\bfshape{10}{900}{OT1}
+\setfont\smallit\itshape{9}{1000}{OT1IT}
+\setfont\smallsl\slshape{9}{1000}{OT1}
+\setfont\smallsf\sfshape{9}{1000}{OT1}
+\setfont\smallsc\scshape{10}{900}{OT1}
+\setfont\smallttsl\ttslshape{10}{900}{OT1TT}
+\font\smalli=cmmi9
+\font\smallsy=cmsy9
+\def\smallecsize{0900}
+
+% Fonts for small examples (8pt).
+\def\smallernominalsize{8pt}
+\setfont\smallerrm\rmshape{8}{1000}{OT1}
+\setfont\smallertt\ttshape{8}{1000}{OT1TT}
+\setfont\smallerbf\bfshape{10}{800}{OT1}
+\setfont\smallerit\itshape{8}{1000}{OT1IT}
+\setfont\smallersl\slshape{8}{1000}{OT1}
+\setfont\smallersf\sfshape{8}{1000}{OT1}
+\setfont\smallersc\scshape{10}{800}{OT1}
+\setfont\smallerttsl\ttslshape{10}{800}{OT1TT}
+\font\smalleri=cmmi8
+\font\smallersy=cmsy8
+\def\smallerecsize{0800}
+
+% Fonts for title page (20.4pt):
+\def\titlenominalsize{20pt}
+\setfont\titlerm\rmbshape{12}{\magstep3}{OT1}
+\setfont\titleit\itbshape{10}{\magstep4}{OT1IT}
+\setfont\titlesl\slbshape{10}{\magstep4}{OT1}
+\setfont\titlett\ttbshape{12}{\magstep3}{OT1TT}
+\setfont\titlettsl\ttslshape{10}{\magstep4}{OT1TT}
+\setfont\titlesf\sfbshape{17}{\magstep1}{OT1}
+\let\titlebf=\titlerm
+\setfont\titlesc\scbshape{10}{\magstep4}{OT1}
+\font\titlei=cmmi12 scaled \magstep3
+\font\titlesy=cmsy10 scaled \magstep4
+\def\titleecsize{2074}
+
+% Chapter fonts (14.4pt).
+\def\chapnominalsize{14pt}
+\setfont\chaprm\rmbshape{12}{\magstep1}{OT1}
+\setfont\chapit\itbshape{10}{\magstep2}{OT1IT}
+\setfont\chapsl\slbshape{10}{\magstep2}{OT1}
+\setfont\chaptt\ttbshape{12}{\magstep1}{OT1TT}
+\setfont\chapttsl\ttslshape{10}{\magstep2}{OT1TT}
+\setfont\chapsf\sfbshape{12}{\magstep1}{OT1}
+\let\chapbf\chaprm
+\setfont\chapsc\scbshape{10}{\magstep2}{OT1}
+\font\chapi=cmmi12 scaled \magstep1
+\font\chapsy=cmsy10 scaled \magstep2
+\def\chapecsize{1440}
+
+% Section fonts (12pt).
+\def\secnominalsize{12pt}
+\setfont\secrm\rmbshape{12}{1000}{OT1}
+\setfont\secit\itbshape{10}{\magstep1}{OT1IT}
+\setfont\secsl\slbshape{10}{\magstep1}{OT1}
+\setfont\sectt\ttbshape{12}{1000}{OT1TT}
+\setfont\secttsl\ttslshape{10}{\magstep1}{OT1TT}
+\setfont\secsf\sfbshape{12}{1000}{OT1}
+\let\secbf\secrm
+\setfont\secsc\scbshape{10}{\magstep1}{OT1}
+\font\seci=cmmi12
+\font\secsy=cmsy10 scaled \magstep1
+\def\sececsize{1200}
+
+% Subsection fonts (10pt).
+\def\ssecnominalsize{10pt}
+\setfont\ssecrm\rmbshape{10}{1000}{OT1}
+\setfont\ssecit\itbshape{10}{1000}{OT1IT}
+\setfont\ssecsl\slbshape{10}{1000}{OT1}
+\setfont\ssectt\ttbshape{10}{1000}{OT1TT}
+\setfont\ssecttsl\ttslshape{10}{1000}{OT1TT}
+\setfont\ssecsf\sfbshape{10}{1000}{OT1}
+\let\ssecbf\ssecrm
+\setfont\ssecsc\scbshape{10}{1000}{OT1}
+\font\sseci=cmmi10
+\font\ssecsy=cmsy10
+\def\ssececsize{1000}
+
+% Reduced fonts for @acro in text (9pt).
+\def\reducednominalsize{9pt}
+\setfont\reducedrm\rmshape{9}{1000}{OT1}
+\setfont\reducedtt\ttshape{9}{1000}{OT1TT}
+\setfont\reducedbf\bfshape{10}{900}{OT1}
+\setfont\reducedit\itshape{9}{1000}{OT1IT}
+\setfont\reducedsl\slshape{9}{1000}{OT1}
+\setfont\reducedsf\sfshape{9}{1000}{OT1}
+\setfont\reducedsc\scshape{10}{900}{OT1}
+\setfont\reducedttsl\ttslshape{10}{900}{OT1TT}
+\font\reducedi=cmmi9
+\font\reducedsy=cmsy9
+\def\reducedecsize{0900}
+
+% reduce space between paragraphs
+\divide\parskip by 2
+
+% reset the current fonts
+\textfonts
+\rm
+} % end of 10pt text font size definitions
+
+
+% We provide the user-level command
+% @fonttextsize 10
+% (or 11) to redefine the text font size. pt is assumed.
+%
+\def\xword{10}
+\def\xiword{11}
+%
+\parseargdef\fonttextsize{%
+ \def\textsizearg{#1}%
+ \wlog{doing @fonttextsize \textsizearg}%
+ %
+ % Set \globaldefs so that documents can use this inside @tex, since
+ % makeinfo 4.8 does not support it, but we need it nonetheless.
+ %
+ \begingroup \globaldefs=1
+ \ifx\textsizearg\xword \definetextfontsizex
+ \else \ifx\textsizearg\xiword \definetextfontsizexi
+ \else
+ \errhelp=\EMsimple
+ \errmessage{@fonttextsize only supports `10' or `11', not `\textsizearg'}
+ \fi\fi
+ \endgroup
+}
+
+
+% In order for the font changes to affect most math symbols and letters,
+% we have to define the \textfont of the standard families. Since
+% texinfo doesn't allow for producing subscripts and superscripts except
+% in the main text, we don't bother to reset \scriptfont and
+% \scriptscriptfont (which would also require loading a lot more fonts).
+%
+\def\resetmathfonts{%
+ \textfont0=\tenrm \textfont1=\teni \textfont2=\tensy
+ \textfont\itfam=\tenit \textfont\slfam=\tensl \textfont\bffam=\tenbf
+ \textfont\ttfam=\tentt \textfont\sffam=\tensf
+}
+
+% The font-changing commands redefine the meanings of \tenSTYLE, instead
+% of just \STYLE. We do this because \STYLE needs to also set the
+% current \fam for math mode. Our \STYLE (e.g., \rm) commands hardwire
+% \tenSTYLE to set the current font.
+%
+% Each font-changing command also sets the names \lsize (one size lower)
+% and \lllsize (three sizes lower). These relative commands are used in
+% the LaTeX logo and acronyms.
+%
+% This all needs generalizing, badly.
+%
+\def\textfonts{%
+ \let\tenrm=\textrm \let\tenit=\textit \let\tensl=\textsl
+ \let\tenbf=\textbf \let\tentt=\texttt \let\smallcaps=\textsc
+ \let\tensf=\textsf \let\teni=\texti \let\tensy=\textsy
+ \let\tenttsl=\textttsl
+ \def\curfontsize{text}%
+ \def\lsize{reduced}\def\lllsize{smaller}%
+ \resetmathfonts \setleading{\textleading}}
+\def\titlefonts{%
+ \let\tenrm=\titlerm \let\tenit=\titleit \let\tensl=\titlesl
+ \let\tenbf=\titlebf \let\tentt=\titlett \let\smallcaps=\titlesc
+ \let\tensf=\titlesf \let\teni=\titlei \let\tensy=\titlesy
+ \let\tenttsl=\titlettsl
+ \def\curfontsize{title}%
+ \def\lsize{chap}\def\lllsize{subsec}%
+ \resetmathfonts \setleading{25pt}}
+\def\titlefont#1{{\titlefonts\rmisbold #1}}
+\def\chapfonts{%
+ \let\tenrm=\chaprm \let\tenit=\chapit \let\tensl=\chapsl
+ \let\tenbf=\chapbf \let\tentt=\chaptt \let\smallcaps=\chapsc
+ \let\tensf=\chapsf \let\teni=\chapi \let\tensy=\chapsy
+ \let\tenttsl=\chapttsl
+ \def\curfontsize{chap}%
+ \def\lsize{sec}\def\lllsize{text}%
+ \resetmathfonts \setleading{19pt}}
+\def\secfonts{%
+ \let\tenrm=\secrm \let\tenit=\secit \let\tensl=\secsl
+ \let\tenbf=\secbf \let\tentt=\sectt \let\smallcaps=\secsc
+ \let\tensf=\secsf \let\teni=\seci \let\tensy=\secsy
+ \let\tenttsl=\secttsl
+ \def\curfontsize{sec}%
+ \def\lsize{subsec}\def\lllsize{reduced}%
+ \resetmathfonts \setleading{16pt}}
+\def\subsecfonts{%
+ \let\tenrm=\ssecrm \let\tenit=\ssecit \let\tensl=\ssecsl
+ \let\tenbf=\ssecbf \let\tentt=\ssectt \let\smallcaps=\ssecsc
+ \let\tensf=\ssecsf \let\teni=\sseci \let\tensy=\ssecsy
+ \let\tenttsl=\ssecttsl
+ \def\curfontsize{ssec}%
+ \def\lsize{text}\def\lllsize{small}%
+ \resetmathfonts \setleading{15pt}}
+\let\subsubsecfonts = \subsecfonts
+\def\reducedfonts{%
+ \let\tenrm=\reducedrm \let\tenit=\reducedit \let\tensl=\reducedsl
+ \let\tenbf=\reducedbf \let\tentt=\reducedtt \let\reducedcaps=\reducedsc
+ \let\tensf=\reducedsf \let\teni=\reducedi \let\tensy=\reducedsy
+ \let\tenttsl=\reducedttsl
+ \def\curfontsize{reduced}%
+ \def\lsize{small}\def\lllsize{smaller}%
+ \resetmathfonts \setleading{10.5pt}}
+\def\smallfonts{%
+ \let\tenrm=\smallrm \let\tenit=\smallit \let\tensl=\smallsl
+ \let\tenbf=\smallbf \let\tentt=\smalltt \let\smallcaps=\smallsc
+ \let\tensf=\smallsf \let\teni=\smalli \let\tensy=\smallsy
+ \let\tenttsl=\smallttsl
+ \def\curfontsize{small}%
+ \def\lsize{smaller}\def\lllsize{smaller}%
+ \resetmathfonts \setleading{10.5pt}}
+\def\smallerfonts{%
+ \let\tenrm=\smallerrm \let\tenit=\smallerit \let\tensl=\smallersl
+ \let\tenbf=\smallerbf \let\tentt=\smallertt \let\smallcaps=\smallersc
+ \let\tensf=\smallersf \let\teni=\smalleri \let\tensy=\smallersy
+ \let\tenttsl=\smallerttsl
+ \def\curfontsize{smaller}%
+ \def\lsize{smaller}\def\lllsize{smaller}%
+ \resetmathfonts \setleading{9.5pt}}
+
+% Fonts for short table of contents.
+\setfont\shortcontrm\rmshape{12}{1000}{OT1}
+\setfont\shortcontbf\bfshape{10}{\magstep1}{OT1} % no cmb12
+\setfont\shortcontsl\slshape{12}{1000}{OT1}
+\setfont\shortconttt\ttshape{12}{1000}{OT1TT}
+
+% Define these just so they can be easily changed for other fonts.
+\def\angleleft{$\langle$}
+\def\angleright{$\rangle$}
+
+% Set the fonts to use with the @small... environments.
+\let\smallexamplefonts = \smallfonts
+
+% About \smallexamplefonts. If we use \smallfonts (9pt), @smallexample
+% can fit this many characters:
+% 8.5x11=86 smallbook=72 a4=90 a5=69
+% If we use \scriptfonts (8pt), then we can fit this many characters:
+% 8.5x11=90+ smallbook=80 a4=90+ a5=77
+% For me, subjectively, the few extra characters that fit aren't worth
+% the additional smallness of 8pt. So I'm making the default 9pt.
+%
+% By the way, for comparison, here's what fits with @example (10pt):
+% 8.5x11=71 smallbook=60 a4=75 a5=58
+% --karl, 24jan03.
+
+% Set up the default fonts, so we can use them for creating boxes.
+%
+\definetextfontsizexi
+
+
+\message{markup,}
+
+% Check if we are currently using a typewriter font. Since all the
+% Computer Modern typewriter fonts have zero interword stretch (and
+% shrink), and it is reasonable to expect all typewriter fonts to have
+% this property, we can check that font parameter.
+%
+\def\ifmonospace{\ifdim\fontdimen3\font=0pt }
+
+% Markup style infrastructure. \defmarkupstylesetup\INITMACRO will
+% define and register \INITMACRO to be called on markup style changes.
+% \INITMACRO can check \currentmarkupstyle for the innermost
+% style and the set of \ifmarkupSTYLE switches for all styles
+% currently in effect.
+\newif\ifmarkupvar
+\newif\ifmarkupsamp
+\newif\ifmarkupkey
+%\newif\ifmarkupfile % @file == @samp.
+%\newif\ifmarkupoption % @option == @samp.
+\newif\ifmarkupcode
+\newif\ifmarkupkbd
+%\newif\ifmarkupenv % @env == @code.
+%\newif\ifmarkupcommand % @command == @code.
+\newif\ifmarkuptex % @tex (and part of @math, for now).
+\newif\ifmarkupexample
+\newif\ifmarkupverb
+\newif\ifmarkupverbatim
+
+\let\currentmarkupstyle\empty
+
+\def\setupmarkupstyle#1{%
+ \csname markup#1true\endcsname
+ \def\currentmarkupstyle{#1}%
+ \markupstylesetup
+}
+
+\let\markupstylesetup\empty
+
+\def\defmarkupstylesetup#1{%
+ \expandafter\def\expandafter\markupstylesetup
+ \expandafter{\markupstylesetup #1}%
+ \def#1%
+}
+
+% Markup style setup for left and right quotes.
+\defmarkupstylesetup\markupsetuplq{%
+ \expandafter\let\expandafter \temp \csname markupsetuplq\currentmarkupstyle\endcsname
+ \ifx\temp\relax \markupsetuplqdefault \else \temp \fi
+}
+
+\defmarkupstylesetup\markupsetuprq{%
+ \expandafter\let\expandafter \temp \csname markupsetuprq\currentmarkupstyle\endcsname
+ \ifx\temp\relax \markupsetuprqdefault \else \temp \fi
+}
+
+{
+\catcode`\'=\active
+\catcode`\`=\active
+
+\gdef\markupsetuplqdefault{\let`\lq}
+\gdef\markupsetuprqdefault{\let'\rq}
+
+\gdef\markupsetcodequoteleft{\let`\codequoteleft}
+\gdef\markupsetcodequoteright{\let'\codequoteright}
+
+\gdef\markupsetnoligaturesquoteleft{\let`\noligaturesquoteleft}
+}
+
+\let\markupsetuplqcode \markupsetcodequoteleft
+\let\markupsetuprqcode \markupsetcodequoteright
+\let\markupsetuplqexample \markupsetcodequoteleft
+\let\markupsetuprqexample \markupsetcodequoteright
+\let\markupsetuplqverb \markupsetcodequoteleft
+\let\markupsetuprqverb \markupsetcodequoteright
+\let\markupsetuplqverbatim \markupsetcodequoteleft
+\let\markupsetuprqverbatim \markupsetcodequoteright
+
+\let\markupsetuplqsamp \markupsetnoligaturesquoteleft
+\let\markupsetuplqkbd \markupsetnoligaturesquoteleft
+
+% Allow an option to not replace quotes with a regular directed right
+% quote/apostrophe (char 0x27), but instead use the undirected quote
+% from cmtt (char 0x0d). The undirected quote is ugly, so don't make it
+% the default, but it works for pasting with more pdf viewers (at least
+% evince), the lilypond developers report. xpdf does work with the
+% regular 0x27.
+%
+\def\codequoteright{%
+ \expandafter\ifx\csname SETtxicodequoteundirected\endcsname\relax
+ \expandafter\ifx\csname SETcodequoteundirected\endcsname\relax
+ '%
+ \else \char'15 \fi
+ \else \char'15 \fi
+}
+%
+% and a similar option for the left quote char vs. a grave accent.
+% Modern fonts display ASCII 0x60 as a grave accent, so some people like
+% the code environments to do likewise.
+%
+\def\codequoteleft{%
+ \expandafter\ifx\csname SETtxicodequotebacktick\endcsname\relax
+ \expandafter\ifx\csname SETcodequotebacktick\endcsname\relax
+ % [Knuth] pp. 380,381,391
+ % \relax disables Spanish ligatures ?` and !` of \tt font.
+ \relax`%
+ \else \char'22 \fi
+ \else \char'22 \fi
+}
+
+% [Knuth] pp. 380,381,391, disable Spanish ligatures ?` and !` of \tt font.
+\def\noligaturesquoteleft{\relax\lq}
+
+% Count depth in font-changes, for error checks
+\newcount\fontdepth \fontdepth=0
+
+%% Add scribe-like font environments, plus @l for inline lisp (usually sans
+%% serif) and @ii for TeX italic
+
+% \smartitalic{ARG} outputs arg in italics, followed by an italic correction
+% unless the following character is such as not to need one.
+\def\smartitalicx{\ifx\next,\else\ifx\next-\else\ifx\next.\else
+ \ptexslash\fi\fi\fi}
+\def\smartslanted#1{{\ifusingtt\ttsl\sl #1}\futurelet\next\smartitalicx}
+\def\smartitalic#1{{\ifusingtt\ttsl\it #1}\futurelet\next\smartitalicx}
+
+% like \smartslanted except unconditionally uses \ttsl.
+% @var is set to this for defun arguments.
+\def\ttslanted#1{{\ttsl #1}\futurelet\next\smartitalicx}
+
+% @cite is like \smartslanted except unconditionally use \sl. We never want
+% ttsl for book titles, do we?
+\def\cite#1{{\sl #1}\futurelet\next\smartitalicx}
+
+\let\i=\smartitalic
+\let\slanted=\smartslanted
+\def\var#1{{\setupmarkupstyle{var}\smartslanted{#1}}}
+\let\dfn=\smartslanted
+\let\emph=\smartitalic
+
+% Explicit font changes: @r, @sc, undocumented @ii.
+\def\r#1{{\rm #1}} % roman font
+\def\sc#1{{\smallcaps#1}} % smallcaps font
+\def\ii#1{{\it #1}} % italic font
+
+% @b, explicit bold. Also @strong.
+\def\b#1{{\bf #1}}
+\let\strong=\b
+
+% @sansserif, explicit sans.
+\def\sansserif#1{{\sf #1}}
+
+% We can't just use \exhyphenpenalty, because that only has effect at
+% the end of a paragraph. Restore normal hyphenation at the end of the
+% group within which \nohyphenation is presumably called.
+%
+\def\nohyphenation{\hyphenchar\font = -1 \aftergroup\restorehyphenation}
+\def\restorehyphenation{\hyphenchar\font = `- }
+
+% Set sfcode to normal for the chars that usually have another value.
+% Can't use plain's \frenchspacing because it uses the `\x notation, and
+% sometimes \x has an active definition that messes things up.
+%
+\catcode`@=11
+ \def\plainfrenchspacing{%
+ \sfcode\dotChar =\@m \sfcode\questChar=\@m \sfcode\exclamChar=\@m
+ \sfcode\colonChar=\@m \sfcode\semiChar =\@m \sfcode\commaChar =\@m
+ \def\endofsentencespacefactor{1000}% for @. and friends
+ }
+ \def\plainnonfrenchspacing{%
+ \sfcode`\.3000\sfcode`\?3000\sfcode`\!3000
+ \sfcode`\:2000\sfcode`\;1500\sfcode`\,1250
+ \def\endofsentencespacefactor{3000}% for @. and friends
+ }
+\catcode`@=\other
+\def\endofsentencespacefactor{3000}% default
+
+% @t, explicit typewriter.
+\def\t#1{%
+ {\tt \rawbackslash \plainfrenchspacing #1}%
+ \null
+}
+
+% @samp.
+\def\samp#1{{\setupmarkupstyle{samp}\lq\tclose{#1}\rq\null}}
+
+% definition of @key that produces a lozenge. Doesn't adjust to text size.
+%\setfont\keyrm\rmshape{8}{1000}{OT1}
+%\font\keysy=cmsy9
+%\def\key#1{{\keyrm\textfont2=\keysy \leavevmode\hbox{%
+% \raise0.4pt\hbox{\angleleft}\kern-.08em\vtop{%
+% \vbox{\hrule\kern-0.4pt
+% \hbox{\raise0.4pt\hbox{\vphantom{\angleleft}}#1}}%
+% \kern-0.4pt\hrule}%
+% \kern-.06em\raise0.4pt\hbox{\angleright}}}}
+
+% definition of @key with no lozenge. If the current font is already
+% monospace, don't change it; that way, we respect @kbdinputstyle. But
+% if it isn't monospace, then use \tt.
+%
+\def\key#1{{\setupmarkupstyle{key}%
+ \nohyphenation
+ \ifmonospace\else\tt\fi
+ #1}\null}
+
+% ctrl is no longer a Texinfo command.
+\def\ctrl #1{{\tt \rawbackslash \hat}#1}
+
+% @file, @option are the same as @samp.
+\let\file=\samp
+\let\option=\samp
+
+% @code is a modification of @t,
+% which makes spaces the same size as normal in the surrounding text.
+\def\tclose#1{%
+ {%
+ % Change normal interword space to be same as for the current font.
+ \spaceskip = \fontdimen2\font
+ %
+ % Switch to typewriter.
+ \tt
+ %
+ % But `\ ' produces the large typewriter interword space.
+ \def\ {{\spaceskip = 0pt{} }}%
+ %
+ % Turn off hyphenation.
+ \nohyphenation
+ %
+ \rawbackslash
+ \plainfrenchspacing
+ #1%
+ }%
+ \null
+}
+
+% We *must* turn on hyphenation at `-' and `_' in @code.
+% Otherwise, it is too hard to avoid overfull hboxes
+% in the Emacs manual, the Library manual, etc.
+
+% Unfortunately, TeX uses one parameter (\hyphenchar) to control
+% both hyphenation at - and hyphenation within words.
+% We must therefore turn them both off (\tclose does that)
+% and arrange explicitly to hyphenate at a dash.
+% -- rms.
+{
+ \catcode`\-=\active \catcode`\_=\active
+ \catcode`\'=\active \catcode`\`=\active
+ \global\let'=\rq \global\let`=\lq % default definitions
+ %
+ \global\def\code{\begingroup
+ \setupmarkupstyle{code}%
+ % The following should really be moved into \setupmarkupstyle handlers.
+ \catcode\dashChar=\active \catcode\underChar=\active
+ \ifallowcodebreaks
+ \let-\codedash
+ \let_\codeunder
+ \else
+ \let-\realdash
+ \let_\realunder
+ \fi
+ \codex
+ }
+}
+
+\def\realdash{-}
+\def\codedash{-\discretionary{}{}{}}
+\def\codeunder{%
+ % this is all so @math{@code{var_name}+1} can work. In math mode, _
+ % is "active" (mathcode"8000) and \normalunderscore (or \char95, etc.)
+ % will therefore expand the active definition of _, which is us
+ % (inside @code that is), therefore an endless loop.
+ \ifusingtt{\ifmmode
+ \mathchar"075F % class 0=ordinary, family 7=ttfam, pos 0x5F=_.
+ \else\normalunderscore \fi
+ \discretionary{}{}{}}%
+ {\_}%
+}
+\def\codex #1{\tclose{#1}\endgroup}
+
+% An additional complication: the above will allow breaks after, e.g.,
+% each of the four underscores in __typeof__. This is undesirable in
+% some manuals, especially if they don't have long identifiers in
+% general. @allowcodebreaks provides a way to control this.
+%
+\newif\ifallowcodebreaks \allowcodebreakstrue
+
+\def\keywordtrue{true}
+\def\keywordfalse{false}
+
+\parseargdef\allowcodebreaks{%
+ \def\txiarg{#1}%
+ \ifx\txiarg\keywordtrue
+ \allowcodebreakstrue
+ \else\ifx\txiarg\keywordfalse
+ \allowcodebreaksfalse
+ \else
+ \errhelp = \EMsimple
+ \errmessage{Unknown @allowcodebreaks option `\txiarg'}%
+ \fi\fi
+}
+
+% @kbd is like @code, except that if the argument is just one @key command,
+% then @kbd has no effect.
+\def\kbd#1{{\setupmarkupstyle{kbd}\def\look{#1}\expandafter\kbdfoo\look??\par}}
+
+% @kbdinputstyle -- arg is `distinct' (@kbd uses slanted tty font always),
+% `example' (@kbd uses ttsl only inside of @example and friends),
+% or `code' (@kbd uses normal tty font always).
+\parseargdef\kbdinputstyle{%
+ \def\txiarg{#1}%
+ \ifx\txiarg\worddistinct
+ \gdef\kbdexamplefont{\ttsl}\gdef\kbdfont{\ttsl}%
+ \else\ifx\txiarg\wordexample
+ \gdef\kbdexamplefont{\ttsl}\gdef\kbdfont{\tt}%
+ \else\ifx\txiarg\wordcode
+ \gdef\kbdexamplefont{\tt}\gdef\kbdfont{\tt}%
+ \else
+ \errhelp = \EMsimple
+ \errmessage{Unknown @kbdinputstyle option `\txiarg'}%
+ \fi\fi\fi
+}
+\def\worddistinct{distinct}
+\def\wordexample{example}
+\def\wordcode{code}
+
+% Default is `distinct'.
+\kbdinputstyle distinct
+
+\def\xkey{\key}
+\def\kbdfoo#1#2#3\par{\def\one{#1}\def\three{#3}\def\threex{??}%
+\ifx\one\xkey\ifx\threex\three \key{#2}%
+\else{\tclose{\kbdfont\setupmarkupstyle{kbd}\look}}\fi
+\else{\tclose{\kbdfont\setupmarkupstyle{kbd}\look}}\fi}
+
+% For @indicateurl, @env, @command quotes seem unnecessary, so use \code.
+\let\indicateurl=\code
+\let\env=\code
+\let\command=\code
+
+% @clicksequence{File @click{} Open ...}
+\def\clicksequence#1{\begingroup #1\endgroup}
+
+% @clickstyle @arrow (by default)
+\parseargdef\clickstyle{\def\click{#1}}
+\def\click{\arrow}
+
+% @uref (abbreviation for `urlref') takes an optional (comma-separated)
+% second argument specifying the text to display and an optional third
+% arg as text to display instead of (rather than in addition to) the url
+% itself. First (mandatory) arg is the url. Perhaps eventually put in
+% a hypertex \special here.
+%
+\def\uref#1{\douref #1,,,\finish}
+\def\douref#1,#2,#3,#4\finish{\begingroup
+ \unsepspaces
+ \pdfurl{#1}%
+ \setbox0 = \hbox{\ignorespaces #3}%
+ \ifdim\wd0 > 0pt
+ \unhbox0 % third arg given, show only that
+ \else
+ \setbox0 = \hbox{\ignorespaces #2}%
+ \ifdim\wd0 > 0pt
+ \ifpdf
+ \unhbox0 % PDF: 2nd arg given, show only it
+ \else
+ \unhbox0\ (\code{#1})% DVI: 2nd arg given, show both it and url
+ \fi
+ \else
+ \code{#1}% only url given, so show it
+ \fi
+ \fi
+ \endlink
+\endgroup}
+
+% @url synonym for @uref, since that's how everyone uses it.
+%
+\let\url=\uref
+
+% rms does not like angle brackets --karl, 17may97.
+% So now @email is just like @uref, unless we are pdf.
+%
+%\def\email#1{\angleleft{\tt #1}\angleright}
+\ifpdf
+ \def\email#1{\doemail#1,,\finish}
+ \def\doemail#1,#2,#3\finish{\begingroup
+ \unsepspaces
+ \pdfurl{mailto:#1}%
+ \setbox0 = \hbox{\ignorespaces #2}%
+ \ifdim\wd0>0pt\unhbox0\else\code{#1}\fi
+ \endlink
+ \endgroup}
+\else
+ \let\email=\uref
+\fi
+
+% Typeset a dimension, e.g., `in' or `pt'. The only reason for the
+% argument is to make the input look right: @dmn{pt} instead of @dmn{}pt.
+%
+\def\dmn#1{\thinspace #1}
+
+% @l was never documented to mean ``switch to the Lisp font'',
+% and it is not used as such in any manual I can find. We need it for
+% Polish suppressed-l. --karl, 22sep96.
+%\def\l#1{{\li #1}\null}
+
+% @acronym for "FBI", "NATO", and the like.
+% We print this one point size smaller, since it's intended for
+% all-uppercase.
+%
+\def\acronym#1{\doacronym #1,,\finish}
+\def\doacronym#1,#2,#3\finish{%
+ {\selectfonts\lsize #1}%
+ \def\temp{#2}%
+ \ifx\temp\empty \else
+ \space ({\unsepspaces \ignorespaces \temp \unskip})%
+ \fi
+}
+
+% @abbr for "Comput. J." and the like.
+% No font change, but don't do end-of-sentence spacing.
+%
+\def\abbr#1{\doabbr #1,,\finish}
+\def\doabbr#1,#2,#3\finish{%
+ {\plainfrenchspacing #1}%
+ \def\temp{#2}%
+ \ifx\temp\empty \else
+ \space ({\unsepspaces \ignorespaces \temp \unskip})%
+ \fi
+}
+
+
+\message{glyphs,}
+
+% @point{}, @result{}, @expansion{}, @print{}, @equiv{}.
+%
+% Since these characters are used in examples, they should be an even number of
+% \tt widths. Each \tt character is 1en, so two makes it 1em.
+%
+\def\point{$\star$}
+\def\arrow{\leavevmode\raise.05ex\hbox to 1em{\hfil$\rightarrow$\hfil}}
+\def\result{\leavevmode\raise.05ex\hbox to 1em{\hfil$\Rightarrow$\hfil}}
+\def\expansion{\leavevmode\hbox to 1em{\hfil$\mapsto$\hfil}}
+\def\print{\leavevmode\lower.1ex\hbox to 1em{\hfil$\dashv$\hfil}}
+\def\equiv{\leavevmode\hbox to 1em{\hfil$\ptexequiv$\hfil}}
+
+% The @error{} command.
+% Adapted from the TeXbook's \boxit.
+%
+\newbox\errorbox
+%
+{\tentt \global\dimen0 = 3em}% Width of the box.
+\dimen2 = .55pt % Thickness of rules
+% The text. (`r' is open on the right, `e' somewhat less so on the left.)
+\setbox0 = \hbox{\kern-.75pt \reducedsf error\kern-1.5pt}
+%
+\setbox\errorbox=\hbox to \dimen0{\hfil
+ \hsize = \dimen0 \advance\hsize by -5.8pt % Space to left+right.
+ \advance\hsize by -2\dimen2 % Rules.
+ \vbox{%
+ \hrule height\dimen2
+ \hbox{\vrule width\dimen2 \kern3pt % Space to left of text.
+ \vtop{\kern2.4pt \box0 \kern2.4pt}% Space above/below.
+ \kern3pt\vrule width\dimen2}% Space to right.
+ \hrule height\dimen2}
+ \hfil}
+%
+\def\error{\leavevmode\lower.7ex\copy\errorbox}
+
+% @pounds{} is a sterling sign, which Knuth put in the CM italic font.
+%
+\def\pounds{{\it\$}}
+
+% @euro{} comes from a separate font, depending on the current style.
+% We use the free feym* fonts from the eurosym package by Henrik
+% Theiling, which support regular, slanted, bold and bold slanted (and
+% "outlined" (blackboard board, sort of) versions, which we don't need).
+% It is available from http://www.ctan.org/tex-archive/fonts/eurosym.
+%
+% Although only regular is the truly official Euro symbol, we ignore
+% that. The Euro is designed to be slightly taller than the regular
+% font height.
+%
+% feymr - regular
+% feymo - slanted
+% feybr - bold
+% feybo - bold slanted
+%
+% There is no good (free) typewriter version, to my knowledge.
+% A feymr10 euro is ~7.3pt wide, while a normal cmtt10 char is ~5.25pt wide.
+% Hmm.
+%
+% Also doesn't work in math. Do we need to do math with euro symbols?
+% Hope not.
+%
+%
+\def\euro{{\eurofont e}}
+\def\eurofont{%
+ % We set the font at each command, rather than predefining it in
+ % \textfonts and the other font-switching commands, so that
+ % installations which never need the symbol don't have to have the
+ % font installed.
+ %
+ % There is only one designed size (nominal 10pt), so we always scale
+ % that to the current nominal size.
+ %
+ % By the way, simply using "at 1em" works for cmr10 and the like, but
+ % does not work for cmbx10 and other extended/shrunken fonts.
+ %
+ \def\eurosize{\csname\curfontsize nominalsize\endcsname}%
+ %
+ \ifx\curfontstyle\bfstylename
+ % bold:
+ \font\thiseurofont = \ifusingit{feybo10}{feybr10} at \eurosize
+ \else
+ % regular:
+ \font\thiseurofont = \ifusingit{feymo10}{feymr10} at \eurosize
+ \fi
+ \thiseurofont
+}
+
+% Glyphs from the EC fonts. We don't use \let for the aliases, because
+% sometimes we redefine the original macro, and the alias should reflect
+% the redefinition.
+%
+% Use LaTeX names for the Icelandic letters.
+\def\DH{{\ecfont \char"D0}} % Eth
+\def\dh{{\ecfont \char"F0}} % eth
+\def\TH{{\ecfont \char"DE}} % Thorn
+\def\th{{\ecfont \char"FE}} % thorn
+%
+\def\guillemetleft{{\ecfont \char"13}}
+\def\guillemotleft{\guillemetleft}
+\def\guillemetright{{\ecfont \char"14}}
+\def\guillemotright{\guillemetright}
+\def\guilsinglleft{{\ecfont \char"0E}}
+\def\guilsinglright{{\ecfont \char"0F}}
+\def\quotedblbase{{\ecfont \char"12}}
+\def\quotesinglbase{{\ecfont \char"0D}}
+%
+% This positioning is not perfect (see the ogonek LaTeX package), but
+% we have the precomposed glyphs for the most common cases. We put the
+% tests to use those glyphs in the single \ogonek macro so we have fewer
+% dummy definitions to worry about for index entries, etc.
+%
+% ogonek is also used with other letters in Lithuanian (IOU), but using
+% the precomposed glyphs for those is not so easy since they aren't in
+% the same EC font.
+\def\ogonek#1{{%
+ \def\temp{#1}%
+ \ifx\temp\macrocharA\Aogonek
+ \else\ifx\temp\macrochara\aogonek
+ \else\ifx\temp\macrocharE\Eogonek
+ \else\ifx\temp\macrochare\eogonek
+ \else
+ \ecfont \setbox0=\hbox{#1}%
+ \ifdim\ht0=1ex\accent"0C #1%
+ \else\ooalign{\unhbox0\crcr\hidewidth\char"0C \hidewidth}%
+ \fi
+ \fi\fi\fi\fi
+ }%
+}
+\def\Aogonek{{\ecfont \char"81}}\def\macrocharA{A}
+\def\aogonek{{\ecfont \char"A1}}\def\macrochara{a}
+\def\Eogonek{{\ecfont \char"86}}\def\macrocharE{E}
+\def\eogonek{{\ecfont \char"A6}}\def\macrochare{e}
+%
+% Use the ec* fonts (cm-super in outline format) for non-CM glyphs.
+\def\ecfont{%
+ % We can't distinguish serif/sans and italic/slanted, but this
+ % is used for crude hacks anyway (like adding French and German
+ % quotes to documents typeset with CM, where we lose kerning), so
+ % hopefully nobody will notice/care.
+ \edef\ecsize{\csname\curfontsize ecsize\endcsname}%
+ \edef\nominalsize{\csname\curfontsize nominalsize\endcsname}%
+ \ifx\curfontstyle\bfstylename
+ % bold:
+ \font\thisecfont = ecb\ifusingit{i}{x}\ecsize \space at \nominalsize
+ \else
+ % regular:
+ \font\thisecfont = ec\ifusingit{ti}{rm}\ecsize \space at \nominalsize
+ \fi
+ \thisecfont
+}
+
+% @registeredsymbol - R in a circle. The font for the R should really
+% be smaller yet, but lllsize is the best we can do for now.
+% Adapted from the plain.tex definition of \copyright.
+%
+\def\registeredsymbol{%
+ $^{{\ooalign{\hfil\raise.07ex\hbox{\selectfonts\lllsize R}%
+ \hfil\crcr\Orb}}%
+ }$%
+}
+
+% @textdegree - the normal degrees sign.
+%
+\def\textdegree{$^\circ$}
+
+% Laurent Siebenmann reports \Orb undefined with:
+% Textures 1.7.7 (preloaded format=plain 93.10.14) (68K) 16 APR 2004 02:38
+% so we'll define it if necessary.
+%
+\ifx\Orb\undefined
+\def\Orb{\mathhexbox20D}
+\fi
+
+% Quotes.
+\chardef\quotedblleft="5C
+\chardef\quotedblright=`\"
+\chardef\quoteleft=`\`
+\chardef\quoteright=`\'
+
+
+\message{page headings,}
+
+\newskip\titlepagetopglue \titlepagetopglue = 1.5in
+\newskip\titlepagebottomglue \titlepagebottomglue = 2pc
+
+% First the title page. Must do @settitle before @titlepage.
+\newif\ifseenauthor
+\newif\iffinishedtitlepage
+
+% Do an implicit @contents or @shortcontents after @end titlepage if the
+% user says @setcontentsaftertitlepage or @setshortcontentsaftertitlepage.
+%
+\newif\ifsetcontentsaftertitlepage
+ \let\setcontentsaftertitlepage = \setcontentsaftertitlepagetrue
+\newif\ifsetshortcontentsaftertitlepage
+ \let\setshortcontentsaftertitlepage = \setshortcontentsaftertitlepagetrue
+
+\parseargdef\shorttitlepage{\begingroup\hbox{}\vskip 1.5in \chaprm \centerline{#1}%
+ \endgroup\page\hbox{}\page}
+
+\envdef\titlepage{%
+ % Open one extra group, as we want to close it in the middle of \Etitlepage.
+ \begingroup
+ \parindent=0pt \textfonts
+ % Leave some space at the very top of the page.
+ \vglue\titlepagetopglue
+ % No rule at page bottom unless we print one at the top with @title.
+ \finishedtitlepagetrue
+ %
+ % Most title ``pages'' are actually two pages long, with space
+ % at the top of the second. We don't want the ragged left on the second.
+ \let\oldpage = \page
+ \def\page{%
+ \iffinishedtitlepage\else
+ \finishtitlepage
+ \fi
+ \let\page = \oldpage
+ \page
+ \null
+ }%
+}
+
+\def\Etitlepage{%
+ \iffinishedtitlepage\else
+ \finishtitlepage
+ \fi
+ % It is important to do the page break before ending the group,
+ % because the headline and footline are only empty inside the group.
+ % If we use the new definition of \page, we always get a blank page
+ % after the title page, which we certainly don't want.
+ \oldpage
+ \endgroup
+ %
+ % Need this before the \...aftertitlepage checks so that if they are
+ % in effect the toc pages will come out with page numbers.
+ \HEADINGSon
+ %
+ % If they want short, they certainly want long too.
+ \ifsetshortcontentsaftertitlepage
+ \shortcontents
+ \contents
+ \global\let\shortcontents = \relax
+ \global\let\contents = \relax
+ \fi
+ %
+ \ifsetcontentsaftertitlepage
+ \contents
+ \global\let\contents = \relax
+ \global\let\shortcontents = \relax
+ \fi
+}
+
+\def\finishtitlepage{%
+ \vskip4pt \hrule height 2pt width \hsize
+ \vskip\titlepagebottomglue
+ \finishedtitlepagetrue
+}
+
+%%% Macros to be used within @titlepage:
+
+\let\subtitlerm=\tenrm
+\def\subtitlefont{\subtitlerm \normalbaselineskip = 13pt \normalbaselines}
+
+\parseargdef\title{%
+ \checkenv\titlepage
+ \leftline{\titlefonts\rmisbold #1}
+ % print a rule at the page bottom also.
+ \finishedtitlepagefalse
+ \vskip4pt \hrule height 4pt width \hsize \vskip4pt
+}
+
+\parseargdef\subtitle{%
+ \checkenv\titlepage
+ {\subtitlefont \rightline{#1}}%
+}
+
+% @author should come last, but may come many times.
+% It can also be used inside @quotation.
+%
+\parseargdef\author{%
+ \def\temp{\quotation}%
+ \ifx\thisenv\temp
+ \def\quotationauthor{#1}% printed in \Equotation.
+ \else
+ \checkenv\titlepage
+ \ifseenauthor\else \vskip 0pt plus 1filll \seenauthortrue \fi
+ {\secfonts\rmisbold \leftline{#1}}%
+ \fi
+}
+
+
+%%% Set up page headings and footings.
+
+\let\thispage=\folio
+
+\newtoks\evenheadline % headline on even pages
+\newtoks\oddheadline % headline on odd pages
+\newtoks\evenfootline % footline on even pages
+\newtoks\oddfootline % footline on odd pages
+
+% Now make TeX use those variables
+\headline={{\textfonts\rm \ifodd\pageno \the\oddheadline
+ \else \the\evenheadline \fi}}
+\footline={{\textfonts\rm \ifodd\pageno \the\oddfootline
+ \else \the\evenfootline \fi}\HEADINGShook}
+\let\HEADINGShook=\relax
+
+% Commands to set those variables.
+% For example, this is what @headings on does
+% @evenheading @thistitle|@thispage|@thischapter
+% @oddheading @thischapter|@thispage|@thistitle
+% @evenfooting @thisfile||
+% @oddfooting ||@thisfile
+
+
+\def\evenheading{\parsearg\evenheadingxxx}
+\def\evenheadingxxx #1{\evenheadingyyy #1\|\|\|\|\finish}
+\def\evenheadingyyy #1\|#2\|#3\|#4\finish{%
+\global\evenheadline={\rlap{\centerline{#2}}\line{#1\hfil#3}}}
+
+\def\oddheading{\parsearg\oddheadingxxx}
+\def\oddheadingxxx #1{\oddheadingyyy #1\|\|\|\|\finish}
+\def\oddheadingyyy #1\|#2\|#3\|#4\finish{%
+\global\oddheadline={\rlap{\centerline{#2}}\line{#1\hfil#3}}}
+
+\parseargdef\everyheading{\oddheadingxxx{#1}\evenheadingxxx{#1}}%
+
+\def\evenfooting{\parsearg\evenfootingxxx}
+\def\evenfootingxxx #1{\evenfootingyyy #1\|\|\|\|\finish}
+\def\evenfootingyyy #1\|#2\|#3\|#4\finish{%
+\global\evenfootline={\rlap{\centerline{#2}}\line{#1\hfil#3}}}
+
+\def\oddfooting{\parsearg\oddfootingxxx}
+\def\oddfootingxxx #1{\oddfootingyyy #1\|\|\|\|\finish}
+\def\oddfootingyyy #1\|#2\|#3\|#4\finish{%
+ \global\oddfootline = {\rlap{\centerline{#2}}\line{#1\hfil#3}}%
+ %
+ % Leave some space for the footline. Hopefully ok to assume
+ % @evenfooting will not be used by itself.
+ \global\advance\pageheight by -12pt
+ \global\advance\vsize by -12pt
+}
+
+\parseargdef\everyfooting{\oddfootingxxx{#1}\evenfootingxxx{#1}}
+
+% @evenheadingmarks top \thischapter <- chapter at the top of a page
+% @evenheadingmarks bottom \thischapter <- chapter at the bottom of a page
+%
+% The same set of arguments for:
+%
+% @oddheadingmarks
+% @evenfootingmarks
+% @oddfootingmarks
+% @everyheadingmarks
+% @everyfootingmarks
+
+\def\evenheadingmarks{\headingmarks{even}{heading}}
+\def\oddheadingmarks{\headingmarks{odd}{heading}}
+\def\evenfootingmarks{\headingmarks{even}{footing}}
+\def\oddfootingmarks{\headingmarks{odd}{footing}}
+\def\everyheadingmarks#1 {\headingmarks{even}{heading}{#1}
+ \headingmarks{odd}{heading}{#1} }
+\def\everyfootingmarks#1 {\headingmarks{even}{footing}{#1}
+ \headingmarks{odd}{footing}{#1} }
+% #1 = even/odd, #2 = heading/footing, #3 = top/bottom.
+\def\headingmarks#1#2#3 {%
+ \expandafter\let\expandafter\temp \csname get#3headingmarks\endcsname
+ \global\expandafter\let\csname get#1#2marks\endcsname \temp
+}
+
+\everyheadingmarks bottom
+\everyfootingmarks bottom
+
+% @headings double turns headings on for double-sided printing.
+% @headings single turns headings on for single-sided printing.
+% @headings off turns them off.
+% @headings on same as @headings double, retained for compatibility.
+% @headings after turns on double-sided headings after this page.
+% @headings doubleafter turns on double-sided headings after this page.
+% @headings singleafter turns on single-sided headings after this page.
+% By default, they are off at the start of a document,
+% and turned `on' after @end titlepage.
+
+\def\headings #1 {\csname HEADINGS#1\endcsname}
+
+\def\HEADINGSoff{%
+\global\evenheadline={\hfil} \global\evenfootline={\hfil}
+\global\oddheadline={\hfil} \global\oddfootline={\hfil}}
+\HEADINGSoff
+% When we turn headings on, set the page number to 1.
+% For double-sided printing, put current file name in lower left corner,
+% chapter name on inside top of right hand pages, document
+% title on inside top of left hand pages, and page numbers on outside top
+% edge of all pages.
+\def\HEADINGSdouble{%
+\global\pageno=1
+\global\evenfootline={\hfil}
+\global\oddfootline={\hfil}
+\global\evenheadline={\line{\folio\hfil\thistitle}}
+\global\oddheadline={\line{\thischapter\hfil\folio}}
+\global\let\contentsalignmacro = \chapoddpage
+}
+\let\contentsalignmacro = \chappager
+
+% For single-sided printing, chapter title goes across top left of page,
+% page number on top right.
+\def\HEADINGSsingle{%
+\global\pageno=1
+\global\evenfootline={\hfil}
+\global\oddfootline={\hfil}
+\global\evenheadline={\line{\thischapter\hfil\folio}}
+\global\oddheadline={\line{\thischapter\hfil\folio}}
+\global\let\contentsalignmacro = \chappager
+}
+\def\HEADINGSon{\HEADINGSdouble}
+
+\def\HEADINGSafter{\let\HEADINGShook=\HEADINGSdoublex}
+\let\HEADINGSdoubleafter=\HEADINGSafter
+\def\HEADINGSdoublex{%
+\global\evenfootline={\hfil}
+\global\oddfootline={\hfil}
+\global\evenheadline={\line{\folio\hfil\thistitle}}
+\global\oddheadline={\line{\thischapter\hfil\folio}}
+\global\let\contentsalignmacro = \chapoddpage
+}
+
+\def\HEADINGSsingleafter{\let\HEADINGShook=\HEADINGSsinglex}
+\def\HEADINGSsinglex{%
+\global\evenfootline={\hfil}
+\global\oddfootline={\hfil}
+\global\evenheadline={\line{\thischapter\hfil\folio}}
+\global\oddheadline={\line{\thischapter\hfil\folio}}
+\global\let\contentsalignmacro = \chappager
+}
+
+% Subroutines used in generating headings
+% This produces Day Month Year style of output.
+% Only define if not already defined, in case a txi-??.tex file has set
+% up a different format (e.g., txi-cs.tex does this).
+\ifx\today\undefined
+\def\today{%
+ \number\day\space
+ \ifcase\month
+ \or\putwordMJan\or\putwordMFeb\or\putwordMMar\or\putwordMApr
+ \or\putwordMMay\or\putwordMJun\or\putwordMJul\or\putwordMAug
+ \or\putwordMSep\or\putwordMOct\or\putwordMNov\or\putwordMDec
+ \fi
+ \space\number\year}
+\fi
+
+% @settitle line... specifies the title of the document, for headings.
+% It generates no output of its own.
+\def\thistitle{\putwordNoTitle}
+\def\settitle{\parsearg{\gdef\thistitle}}
+
+
+\message{tables,}
+% Tables -- @table, @ftable, @vtable, @item(x).
+
+% default indentation of table text
+\newdimen\tableindent \tableindent=.8in
+% default indentation of @itemize and @enumerate text
+\newdimen\itemindent \itemindent=.3in
+% margin between end of table item and start of table text.
+\newdimen\itemmargin \itemmargin=.1in
+
+% used internally for \itemindent minus \itemmargin
+\newdimen\itemmax
+
+% Note @table, @ftable, and @vtable define @item, @itemx, etc., with
+% these defs.
+% They also define \itemindex
+% to index the item name in whatever manner is desired (perhaps none).
+
+\newif\ifitemxneedsnegativevskip
+
+\def\itemxpar{\par\ifitemxneedsnegativevskip\nobreak\vskip-\parskip\nobreak\fi}
+
+\def\internalBitem{\smallbreak \parsearg\itemzzz}
+\def\internalBitemx{\itemxpar \parsearg\itemzzz}
+
+\def\itemzzz #1{\begingroup %
+ \advance\hsize by -\rightskip
+ \advance\hsize by -\tableindent
+ \setbox0=\hbox{\itemindicate{#1}}%
+ \itemindex{#1}%
+ \nobreak % This prevents a break before @itemx.
+ %
+ % If the item text does not fit in the space we have, put it on a line
+ % by itself, and do not allow a page break either before or after that
+ % line. We do not start a paragraph here because then if the next
+ % command is, e.g., @kindex, the whatsit would get put into the
+ % horizontal list on a line by itself, resulting in extra blank space.
+ \ifdim \wd0>\itemmax
+ %
+ % Make this a paragraph so we get the \parskip glue and wrapping,
+ % but leave it ragged-right.
+ \begingroup
+ \advance\leftskip by-\tableindent
+ \advance\hsize by\tableindent
+ \advance\rightskip by0pt plus1fil
+ \leavevmode\unhbox0\par
+ \endgroup
+ %
+ % We're going to be starting a paragraph, but we don't want the
+ % \parskip glue -- logically it's part of the @item we just started.
+ \nobreak \vskip-\parskip
+ %
+ % Stop a page break at the \parskip glue coming up. However, if
+ % what follows is an environment such as @example, there will be no
+ % \parskip glue; then the negative vskip we just inserted would
+ % cause the example and the item to crash together. So we use this
+ % bizarre value of 10001 as a signal to \aboveenvbreak to insert
+ % \parskip glue after all. Section titles are handled this way also.
+ %
+ \penalty 10001
+ \endgroup
+ \itemxneedsnegativevskipfalse
+ \else
+ % The item text fits into the space. Start a paragraph, so that the
+ % following text (if any) will end up on the same line.
+ \noindent
+ % Do this with kerns and \unhbox so that if there is a footnote in
+ % the item text, it can migrate to the main vertical list and
+ % eventually be printed.
+ \nobreak\kern-\tableindent
+ \dimen0 = \itemmax \advance\dimen0 by \itemmargin \advance\dimen0 by -\wd0
+ \unhbox0
+ \nobreak\kern\dimen0
+ \endgroup
+ \itemxneedsnegativevskiptrue
+ \fi
+}
+
+\def\item{\errmessage{@item while not in a list environment}}
+\def\itemx{\errmessage{@itemx while not in a list environment}}
+
+% @table, @ftable, @vtable.
+\envdef\table{%
+ \let\itemindex\gobble
+ \tablecheck{table}%
+}
+\envdef\ftable{%
+ \def\itemindex ##1{\doind {fn}{\code{##1}}}%
+ \tablecheck{ftable}%
+}
+\envdef\vtable{%
+ \def\itemindex ##1{\doind {vr}{\code{##1}}}%
+ \tablecheck{vtable}%
+}
+\def\tablecheck#1{%
+ \ifnum \the\catcode`\^^M=\active
+ \endgroup
+ \errmessage{This command won't work in this context; perhaps the problem is
+ that we are \inenvironment\thisenv}%
+ \def\next{\doignore{#1}}%
+ \else
+ \let\next\tablex
+ \fi
+ \next
+}
+\def\tablex#1{%
+ \def\itemindicate{#1}%
+ \parsearg\tabley
+}
+\def\tabley#1{%
+ {%
+ \makevalueexpandable
+ \edef\temp{\noexpand\tablez #1\space\space\space}%
+ \expandafter
+ }\temp \endtablez
+}
+\def\tablez #1 #2 #3 #4\endtablez{%
+ \aboveenvbreak
+ \ifnum 0#1>0 \advance \leftskip by #1\mil \fi
+ \ifnum 0#2>0 \tableindent=#2\mil \fi
+ \ifnum 0#3>0 \advance \rightskip by #3\mil \fi
+ \itemmax=\tableindent
+ \advance \itemmax by -\itemmargin
+ \advance \leftskip by \tableindent
+ \exdentamount=\tableindent
+ \parindent = 0pt
+ \parskip = \smallskipamount
+ \ifdim \parskip=0pt \parskip=2pt \fi
+ \let\item = \internalBitem
+ \let\itemx = \internalBitemx
+}
+\def\Etable{\endgraf\afterenvbreak}
+\let\Eftable\Etable
+\let\Evtable\Etable
+\let\Eitemize\Etable
+\let\Eenumerate\Etable
+
+% This is the counter used by @enumerate, which is really @itemize
+
+\newcount \itemno
+
+\envdef\itemize{\parsearg\doitemize}
+
+\def\doitemize#1{%
+ \aboveenvbreak
+ \itemmax=\itemindent
+ \advance\itemmax by -\itemmargin
+ \advance\leftskip by \itemindent
+ \exdentamount=\itemindent
+ \parindent=0pt
+ \parskip=\smallskipamount
+ \ifdim\parskip=0pt \parskip=2pt \fi
+ %
+ % Try typesetting the item mark that if the document erroneously says
+ % something like @itemize @samp (intending @table), there's an error
+ % right away at the @itemize. It's not the best error message in the
+ % world, but it's better than leaving it to the @item. This means if
+ % the user wants an empty mark, they have to say @w{} not just @w.
+ \def\itemcontents{#1}%
+ \setbox0 = \hbox{\itemcontents}%
+ %
+ % @itemize with no arg is equivalent to @itemize @bullet.
+ \ifx\itemcontents\empty\def\itemcontents{\bullet}\fi
+ %
+ \let\item=\itemizeitem
+}
+
+% Definition of @item while inside @itemize and @enumerate.
+%
+\def\itemizeitem{%
+ \advance\itemno by 1 % for enumerations
+ {\let\par=\endgraf \smallbreak}% reasonable place to break
+ {%
+ % If the document has an @itemize directly after a section title, a
+ % \nobreak will be last on the list, and \sectionheading will have
+ % done a \vskip-\parskip. In that case, we don't want to zero
+ % parskip, or the item text will crash with the heading. On the
+ % other hand, when there is normal text preceding the item (as there
+ % usually is), we do want to zero parskip, or there would be too much
+ % space. In that case, we won't have a \nobreak before. At least
+ % that's the theory.
+ \ifnum\lastpenalty<10000 \parskip=0in \fi
+ \noindent
+ \hbox to 0pt{\hss \itemcontents \kern\itemmargin}%
+ %
+ \vadjust{\penalty 1200}}% not good to break after first line of item.
+ \flushcr
+}
+
+% \splitoff TOKENS\endmark defines \first to be the first token in
+% TOKENS, and \rest to be the remainder.
+%
+\def\splitoff#1#2\endmark{\def\first{#1}\def\rest{#2}}%
+
+% Allow an optional argument of an uppercase letter, lowercase letter,
+% or number, to specify the first label in the enumerated list. No
+% argument is the same as `1'.
+%
+\envparseargdef\enumerate{\enumeratey #1 \endenumeratey}
+\def\enumeratey #1 #2\endenumeratey{%
+ % If we were given no argument, pretend we were given `1'.
+ \def\thearg{#1}%
+ \ifx\thearg\empty \def\thearg{1}\fi
+ %
+ % Detect if the argument is a single token. If so, it might be a
+ % letter. Otherwise, the only valid thing it can be is a number.
+ % (We will always have one token, because of the test we just made.
+ % This is a good thing, since \splitoff doesn't work given nothing at
+ % all -- the first parameter is undelimited.)
+ \expandafter\splitoff\thearg\endmark
+ \ifx\rest\empty
+ % Only one token in the argument. It could still be anything.
+ % A ``lowercase letter'' is one whose \lccode is nonzero.
+ % An ``uppercase letter'' is one whose \lccode is both nonzero, and
+ % not equal to itself.
+ % Otherwise, we assume it's a number.
+ %
+ % We need the \relax at the end of the \ifnum lines to stop TeX from
+ % continuing to look for a <number>.
+ %
+ \ifnum\lccode\expandafter`\thearg=0\relax
+ \numericenumerate % a number (we hope)
+ \else
+ % It's a letter.
+ \ifnum\lccode\expandafter`\thearg=\expandafter`\thearg\relax
+ \lowercaseenumerate % lowercase letter
+ \else
+ \uppercaseenumerate % uppercase letter
+ \fi
+ \fi
+ \else
+ % Multiple tokens in the argument. We hope it's a number.
+ \numericenumerate
+ \fi
+}
+
+% An @enumerate whose labels are integers. The starting integer is
+% given in \thearg.
+%
+\def\numericenumerate{%
+ \itemno = \thearg
+ \startenumeration{\the\itemno}%
+}
+
+% The starting (lowercase) letter is in \thearg.
+\def\lowercaseenumerate{%
+ \itemno = \expandafter`\thearg
+ \startenumeration{%
+ % Be sure we're not beyond the end of the alphabet.
+ \ifnum\itemno=0
+ \errmessage{No more lowercase letters in @enumerate; get a bigger
+ alphabet}%
+ \fi
+ \char\lccode\itemno
+ }%
+}
+
+% The starting (uppercase) letter is in \thearg.
+\def\uppercaseenumerate{%
+ \itemno = \expandafter`\thearg
+ \startenumeration{%
+ % Be sure we're not beyond the end of the alphabet.
+ \ifnum\itemno=0
+ \errmessage{No more uppercase letters in @enumerate; get a bigger
+ alphabet}
+ \fi
+ \char\uccode\itemno
+ }%
+}
+
+% Call \doitemize, adding a period to the first argument and supplying the
+% common last two arguments. Also subtract one from the initial value in
+% \itemno, since @item increments \itemno.
+%
+\def\startenumeration#1{%
+ \advance\itemno by -1
+ \doitemize{#1.}\flushcr
+}
+
+% @alphaenumerate and @capsenumerate are abbreviations for giving an arg
+% to @enumerate.
+%
+\def\alphaenumerate{\enumerate{a}}
+\def\capsenumerate{\enumerate{A}}
+\def\Ealphaenumerate{\Eenumerate}
+\def\Ecapsenumerate{\Eenumerate}
+
+
+% @multitable macros
+% Amy Hendrickson, 8/18/94, 3/6/96
+%
+% @multitable ... @end multitable will make as many columns as desired.
+% Contents of each column will wrap at width given in preamble. Width
+% can be specified either with sample text given in a template line,
+% or in percent of \hsize, the current width of text on page.
+
+% Table can continue over pages but will only break between lines.
+
+% To make preamble:
+%
+% Either define widths of columns in terms of percent of \hsize:
+% @multitable @columnfractions .25 .3 .45
+% @item ...
+%
+% Numbers following @columnfractions are the percent of the total
+% current hsize to be used for each column. You may use as many
+% columns as desired.
+
+
+% Or use a template:
+% @multitable {Column 1 template} {Column 2 template} {Column 3 template}
+% @item ...
+% using the widest term desired in each column.
+
+% Each new table line starts with @item, each subsequent new column
+% starts with @tab. Empty columns may be produced by supplying @tab's
+% with nothing between them for as many times as empty columns are needed,
+% ie, @tab at tab@tab will produce two empty columns.
+
+% @item, @tab do not need to be on their own lines, but it will not hurt
+% if they are.
+
+% Sample multitable:
+
+% @multitable {Column 1 template} {Column 2 template} {Column 3 template}
+% @item first col stuff @tab second col stuff @tab third col
+% @item
+% first col stuff
+% @tab
+% second col stuff
+% @tab
+% third col
+% @item first col stuff @tab second col stuff
+% @tab Many paragraphs of text may be used in any column.
+%
+% They will wrap at the width determined by the template.
+% @item at tab@tab This will be in third column.
+% @end multitable
+
+% Default dimensions may be reset by user.
+% @multitableparskip is vertical space between paragraphs in table.
+% @multitableparindent is paragraph indent in table.
+% @multitablecolmargin is horizontal space to be left between columns.
+% @multitablelinespace is space to leave between table items, baseline
+% to baseline.
+% 0pt means it depends on current normal line spacing.
+%
+\newskip\multitableparskip
+\newskip\multitableparindent
+\newdimen\multitablecolspace
+\newskip\multitablelinespace
+\multitableparskip=0pt
+\multitableparindent=6pt
+\multitablecolspace=12pt
+\multitablelinespace=0pt
+
+% Macros used to set up halign preamble:
+%
+\let\endsetuptable\relax
+\def\xendsetuptable{\endsetuptable}
+\let\columnfractions\relax
+\def\xcolumnfractions{\columnfractions}
+\newif\ifsetpercent
+
+% #1 is the @columnfraction, usually a decimal number like .5, but might
+% be just 1. We just use it, whatever it is.
+%
+\def\pickupwholefraction#1 {%
+ \global\advance\colcount by 1
+ \expandafter\xdef\csname col\the\colcount\endcsname{#1\hsize}%
+ \setuptable
+}
+
+\newcount\colcount
+\def\setuptable#1{%
+ \def\firstarg{#1}%
+ \ifx\firstarg\xendsetuptable
+ \let\go = \relax
+ \else
+ \ifx\firstarg\xcolumnfractions
+ \global\setpercenttrue
+ \else
+ \ifsetpercent
+ \let\go\pickupwholefraction
+ \else
+ \global\advance\colcount by 1
+ \setbox0=\hbox{#1\unskip\space}% Add a normal word space as a
+ % separator; typically that is always in the input, anyway.
+ \expandafter\xdef\csname col\the\colcount\endcsname{\the\wd0}%
+ \fi
+ \fi
+ \ifx\go\pickupwholefraction
+ % Put the argument back for the \pickupwholefraction call, so
+ % we'll always have a period there to be parsed.
+ \def\go{\pickupwholefraction#1}%
+ \else
+ \let\go = \setuptable
+ \fi%
+ \fi
+ \go
+}
+
+% multitable-only commands.
+%
+% @headitem starts a heading row, which we typeset in bold.
+% Assignments have to be global since we are inside the implicit group
+% of an alignment entry. \everycr resets \everytab so we don't have to
+% undo it ourselves.
+\def\headitemfont{\b}% for people to use in the template row; not changeable
+\def\headitem{%
+ \checkenv\multitable
+ \crcr
+ \global\everytab={\bf}% can't use \headitemfont since the parsing differs
+ \the\everytab % for the first item
+}%
+%
+% A \tab used to include \hskip1sp. But then the space in a template
+% line is not enough. That is bad. So let's go back to just `&' until
+% we again encounter the problem the 1sp was intended to solve.
+% --karl, nathan at acm.org, 20apr99.
+\def\tab{\checkenv\multitable &\the\everytab}%
+
+% @multitable ... @end multitable definitions:
+%
+\newtoks\everytab % insert after every tab.
+%
+\envdef\multitable{%
+ \vskip\parskip
+ \startsavinginserts
+ %
+ % @item within a multitable starts a normal row.
+ % We use \def instead of \let so that if one of the multitable entries
+ % contains an @itemize, we don't choke on the \item (seen as \crcr aka
+ % \endtemplate) expanding \doitemize.
+ \def\item{\crcr}%
+ %
+ \tolerance=9500
+ \hbadness=9500
+ \setmultitablespacing
+ \parskip=\multitableparskip
+ \parindent=\multitableparindent
+ \overfullrule=0pt
+ \global\colcount=0
+ %
+ \everycr = {%
+ \noalign{%
+ \global\everytab={}%
+ \global\colcount=0 % Reset the column counter.
+ % Check for saved footnotes, etc.
+ \checkinserts
+ % Keeps underfull box messages off when table breaks over pages.
+ %\filbreak
+ % Maybe so, but it also creates really weird page breaks when the
+ % table breaks over pages. Wouldn't \vfil be better? Wait until the
+ % problem manifests itself, so it can be fixed for real --karl.
+ }%
+ }%
+ %
+ \parsearg\domultitable
+}
+\def\domultitable#1{%
+ % To parse everything between @multitable and @item:
+ \setuptable#1 \endsetuptable
+ %
+ % This preamble sets up a generic column definition, which will
+ % be used as many times as user calls for columns.
+ % \vtop will set a single line and will also let text wrap and
+ % continue for many paragraphs if desired.
+ \halign\bgroup &%
+ \global\advance\colcount by 1
+ \multistrut
+ \vtop{%
+ % Use the current \colcount to find the correct column width:
+ \hsize=\expandafter\csname col\the\colcount\endcsname
+ %
+ % In order to keep entries from bumping into each other
+ % we will add a \leftskip of \multitablecolspace to all columns after
+ % the first one.
+ %
+ % If a template has been used, we will add \multitablecolspace
+ % to the width of each template entry.
+ %
+ % If the user has set preamble in terms of percent of \hsize we will
+ % use that dimension as the width of the column, and the \leftskip
+ % will keep entries from bumping into each other. Table will start at
+ % left margin and final column will justify at right margin.
+ %
+ % Make sure we don't inherit \rightskip from the outer environment.
+ \rightskip=0pt
+ \ifnum\colcount=1
+ % The first column will be indented with the surrounding text.
+ \advance\hsize by\leftskip
+ \else
+ \ifsetpercent \else
+ % If user has not set preamble in terms of percent of \hsize
+ % we will advance \hsize by \multitablecolspace.
+ \advance\hsize by \multitablecolspace
+ \fi
+ % In either case we will make \leftskip=\multitablecolspace:
+ \leftskip=\multitablecolspace
+ \fi
+ % Ignoring space at the beginning and end avoids an occasional spurious
+ % blank line, when TeX decides to break the line at the space before the
+ % box from the multistrut, so the strut ends up on a line by itself.
+ % For example:
+ % @multitable @columnfractions .11 .89
+ % @item @code{#}
+ % @tab Legal holiday which is valid in major parts of the whole country.
+ % Is automatically provided with highlighting sequences respectively
+ % marking characters.
+ \noindent\ignorespaces##\unskip\multistrut
+ }\cr
+}
+\def\Emultitable{%
+ \crcr
+ \egroup % end the \halign
+ \global\setpercentfalse
+}
+
+\def\setmultitablespacing{%
+ \def\multistrut{\strut}% just use the standard line spacing
+ %
+ % Compute \multitablelinespace (if not defined by user) for use in
+ % \multitableparskip calculation. We used define \multistrut based on
+ % this, but (ironically) that caused the spacing to be off.
+ % See bug-texinfo report from Werner Lemberg, 31 Oct 2004 12:52:20 +0100.
+\ifdim\multitablelinespace=0pt
+\setbox0=\vbox{X}\global\multitablelinespace=\the\baselineskip
+\global\advance\multitablelinespace by-\ht0
+\fi
+%% Test to see if parskip is larger than space between lines of
+%% table. If not, do nothing.
+%% If so, set to same dimension as multitablelinespace.
+\ifdim\multitableparskip>\multitablelinespace
+\global\multitableparskip=\multitablelinespace
+\global\advance\multitableparskip-7pt %% to keep parskip somewhat smaller
+ %% than skip between lines in the table.
+\fi%
+\ifdim\multitableparskip=0pt
+\global\multitableparskip=\multitablelinespace
+\global\advance\multitableparskip-7pt %% to keep parskip somewhat smaller
+ %% than skip between lines in the table.
+\fi}
+
+
+\message{conditionals,}
+
+% @iftex, @ifnotdocbook, @ifnothtml, @ifnotinfo, @ifnotplaintext,
+% @ifnotxml always succeed. They currently do nothing; we don't
+% attempt to check whether the conditionals are properly nested. But we
+% have to remember that they are conditionals, so that @end doesn't
+% attempt to close an environment group.
+%
+\def\makecond#1{%
+ \expandafter\let\csname #1\endcsname = \relax
+ \expandafter\let\csname iscond.#1\endcsname = 1
+}
+\makecond{iftex}
+\makecond{ifnotdocbook}
+\makecond{ifnothtml}
+\makecond{ifnotinfo}
+\makecond{ifnotplaintext}
+\makecond{ifnotxml}
+
+% Ignore @ignore, @ifhtml, @ifinfo, and the like.
+%
+\def\direntry{\doignore{direntry}}
+\def\documentdescription{\doignore{documentdescription}}
+\def\docbook{\doignore{docbook}}
+\def\html{\doignore{html}}
+\def\ifdocbook{\doignore{ifdocbook}}
+\def\ifhtml{\doignore{ifhtml}}
+\def\ifinfo{\doignore{ifinfo}}
+\def\ifnottex{\doignore{ifnottex}}
+\def\ifplaintext{\doignore{ifplaintext}}
+\def\ifxml{\doignore{ifxml}}
+\def\ignore{\doignore{ignore}}
+\def\menu{\doignore{menu}}
+\def\xml{\doignore{xml}}
+
+% Ignore text until a line `@end #1', keeping track of nested conditionals.
+%
+% A count to remember the depth of nesting.
+\newcount\doignorecount
+
+\def\doignore#1{\begingroup
+ % Scan in ``verbatim'' mode:
+ \obeylines
+ \catcode`\@ = \other
+ \catcode`\{ = \other
+ \catcode`\} = \other
+ %
+ % Make sure that spaces turn into tokens that match what \doignoretext wants.
+ \spaceisspace
+ %
+ % Count number of #1's that we've seen.
+ \doignorecount = 0
+ %
+ % Swallow text until we reach the matching `@end #1'.
+ \dodoignore{#1}%
+}
+
+{ \catcode`_=11 % We want to use \_STOP_ which cannot appear in texinfo source.
+ \obeylines %
+ %
+ \gdef\dodoignore#1{%
+ % #1 contains the command name as a string, e.g., `ifinfo'.
+ %
+ % Define a command to find the next `@end #1'.
+ \long\def\doignoretext##1^^M at end #1{%
+ \doignoretextyyy##1^^M@#1\_STOP_}%
+ %
+ % And this command to find another #1 command, at the beginning of a
+ % line. (Otherwise, we would consider a line `@c @ifset', for
+ % example, to count as an @ifset for nesting.)
+ \long\def\doignoretextyyy##1^^M@#1##2\_STOP_{\doignoreyyy{##2}\_STOP_}%
+ %
+ % And now expand that command.
+ \doignoretext ^^M%
+ }%
+}
+
+\def\doignoreyyy#1{%
+ \def\temp{#1}%
+ \ifx\temp\empty % Nothing found.
+ \let\next\doignoretextzzz
+ \else % Found a nested condition, ...
+ \advance\doignorecount by 1
+ \let\next\doignoretextyyy % ..., look for another.
+ % If we're here, #1 ends with ^^M\ifinfo (for example).
+ \fi
+ \next #1% the token \_STOP_ is present just after this macro.
+}
+
+% We have to swallow the remaining "\_STOP_".
+%
+\def\doignoretextzzz#1{%
+ \ifnum\doignorecount = 0 % We have just found the outermost @end.
+ \let\next\enddoignore
+ \else % Still inside a nested condition.
+ \advance\doignorecount by -1
+ \let\next\doignoretext % Look for the next @end.
+ \fi
+ \next
+}
+
+% Finish off ignored text.
+{ \obeylines%
+ % Ignore anything after the last `@end #1'; this matters in verbatim
+ % environments, where otherwise the newline after an ignored conditional
+ % would result in a blank line in the output.
+ \gdef\enddoignore#1^^M{\endgroup\ignorespaces}%
+}
+
+
+% @set VAR sets the variable VAR to an empty value.
+% @set VAR REST-OF-LINE sets VAR to the value REST-OF-LINE.
+%
+% Since we want to separate VAR from REST-OF-LINE (which might be
+% empty), we can't just use \parsearg; we have to insert a space of our
+% own to delimit the rest of the line, and then take it out again if we
+% didn't need it.
+% We rely on the fact that \parsearg sets \catcode`\ =10.
+%
+\parseargdef\set{\setyyy#1 \endsetyyy}
+\def\setyyy#1 #2\endsetyyy{%
+ {%
+ \makevalueexpandable
+ \def\temp{#2}%
+ \edef\next{\gdef\makecsname{SET#1}}%
+ \ifx\temp\empty
+ \next{}%
+ \else
+ \setzzz#2\endsetzzz
+ \fi
+ }%
+}
+% Remove the trailing space \setxxx inserted.
+\def\setzzz#1 \endsetzzz{\next{#1}}
+
+% @clear VAR clears (i.e., unsets) the variable VAR.
+%
+\parseargdef\clear{%
+ {%
+ \makevalueexpandable
+ \global\expandafter\let\csname SET#1\endcsname=\relax
+ }%
+}
+
+% @value{foo} gets the text saved in variable foo.
+\def\value{\begingroup\makevalueexpandable\valuexxx}
+\def\valuexxx#1{\expandablevalue{#1}\endgroup}
+{
+ \catcode`\- = \active \catcode`\_ = \active
+ %
+ \gdef\makevalueexpandable{%
+ \let\value = \expandablevalue
+ % We don't want these characters active, ...
+ \catcode`\-=\other \catcode`\_=\other
+ % ..., but we might end up with active ones in the argument if
+ % we're called from @code, as @code{@value{foo-bar_}}, though.
+ % So \let them to their normal equivalents.
+ \let-\realdash \let_\normalunderscore
+ }
+}
+
+% We have this subroutine so that we can handle at least some @value's
+% properly in indexes (we call \makevalueexpandable in \indexdummies).
+% The command has to be fully expandable (if the variable is set), since
+% the result winds up in the index file. This means that if the
+% variable's value contains other Texinfo commands, it's almost certain
+% it will fail (although perhaps we could fix that with sufficient work
+% to do a one-level expansion on the result, instead of complete).
+%
+\def\expandablevalue#1{%
+ \expandafter\ifx\csname SET#1\endcsname\relax
+ {[No value for ``#1'']}%
+ \message{Variable `#1', used in @value, is not set.}%
+ \else
+ \csname SET#1\endcsname
+ \fi
+}
+
+% @ifset VAR ... @end ifset reads the `...' iff VAR has been defined
+% with @set.
+%
+% To get special treatment of `@end ifset,' call \makeond and the redefine.
+%
+\makecond{ifset}
+\def\ifset{\parsearg{\doifset{\let\next=\ifsetfail}}}
+\def\doifset#1#2{%
+ {%
+ \makevalueexpandable
+ \let\next=\empty
+ \expandafter\ifx\csname SET#2\endcsname\relax
+ #1% If not set, redefine \next.
+ \fi
+ \expandafter
+ }\next
+}
+\def\ifsetfail{\doignore{ifset}}
+
+% @ifclear VAR ... @end ifclear reads the `...' iff VAR has never been
+% defined with @set, or has been undefined with @clear.
+%
+% The `\else' inside the `\doifset' parameter is a trick to reuse the
+% above code: if the variable is not set, do nothing, if it is set,
+% then redefine \next to \ifclearfail.
+%
+\makecond{ifclear}
+\def\ifclear{\parsearg{\doifset{\else \let\next=\ifclearfail}}}
+\def\ifclearfail{\doignore{ifclear}}
+
+% @dircategory CATEGORY -- specify a category of the dir file
+% which this file should belong to. Ignore this in TeX.
+\let\dircategory=\comment
+
+% @defininfoenclose.
+\let\definfoenclose=\comment
+
+
+\message{indexing,}
+% Index generation facilities
+
+% Define \newwrite to be identical to plain tex's \newwrite
+% except not \outer, so it can be used within macros and \if's.
+\edef\newwrite{\makecsname{ptexnewwrite}}
+
+% \newindex {foo} defines an index named foo.
+% It automatically defines \fooindex such that
+% \fooindex ...rest of line... puts an entry in the index foo.
+% It also defines \fooindfile to be the number of the output channel for
+% the file that accumulates this index. The file's extension is foo.
+% The name of an index should be no more than 2 characters long
+% for the sake of vms.
+%
+\def\newindex#1{%
+ \iflinks
+ \expandafter\newwrite \csname#1indfile\endcsname
+ \openout \csname#1indfile\endcsname \jobname.#1 % Open the file
+ \fi
+ \expandafter\xdef\csname#1index\endcsname{% % Define @#1index
+ \noexpand\doindex{#1}}
+}
+
+% @defindex foo == \newindex{foo}
+%
+\def\defindex{\parsearg\newindex}
+
+% Define @defcodeindex, like @defindex except put all entries in @code.
+%
+\def\defcodeindex{\parsearg\newcodeindex}
+%
+\def\newcodeindex#1{%
+ \iflinks
+ \expandafter\newwrite \csname#1indfile\endcsname
+ \openout \csname#1indfile\endcsname \jobname.#1
+ \fi
+ \expandafter\xdef\csname#1index\endcsname{%
+ \noexpand\docodeindex{#1}}%
+}
+
+
+% @synindex foo bar makes index foo feed into index bar.
+% Do this instead of @defindex foo if you don't want it as a separate index.
+%
+% @syncodeindex foo bar similar, but put all entries made for index foo
+% inside @code.
+%
+\def\synindex#1 #2 {\dosynindex\doindex{#1}{#2}}
+\def\syncodeindex#1 #2 {\dosynindex\docodeindex{#1}{#2}}
+
+% #1 is \doindex or \docodeindex, #2 the index getting redefined (foo),
+% #3 the target index (bar).
+\def\dosynindex#1#2#3{%
+ % Only do \closeout if we haven't already done it, else we'll end up
+ % closing the target index.
+ \expandafter \ifx\csname donesynindex#2\endcsname \relax
+ % The \closeout helps reduce unnecessary open files; the limit on the
+ % Acorn RISC OS is a mere 16 files.
+ \expandafter\closeout\csname#2indfile\endcsname
+ \expandafter\let\csname donesynindex#2\endcsname = 1
+ \fi
+ % redefine \fooindfile:
+ \expandafter\let\expandafter\temp\expandafter=\csname#3indfile\endcsname
+ \expandafter\let\csname#2indfile\endcsname=\temp
+ % redefine \fooindex:
+ \expandafter\xdef\csname#2index\endcsname{\noexpand#1{#3}}%
+}
+
+% Define \doindex, the driver for all \fooindex macros.
+% Argument #1 is generated by the calling \fooindex macro,
+% and it is "foo", the name of the index.
+
+% \doindex just uses \parsearg; it calls \doind for the actual work.
+% This is because \doind is more useful to call from other macros.
+
+% There is also \dosubind {index}{topic}{subtopic}
+% which makes an entry in a two-level index such as the operation index.
+
+\def\doindex#1{\edef\indexname{#1}\parsearg\singleindexer}
+\def\singleindexer #1{\doind{\indexname}{#1}}
+
+% like the previous two, but they put @code around the argument.
+\def\docodeindex#1{\edef\indexname{#1}\parsearg\singlecodeindexer}
+\def\singlecodeindexer #1{\doind{\indexname}{\code{#1}}}
+
+% Take care of Texinfo commands that can appear in an index entry.
+% Since there are some commands we want to expand, and others we don't,
+% we have to laboriously prevent expansion for those that we don't.
+%
+\def\indexdummies{%
+ \escapechar = `\\ % use backslash in output files.
+ \def\@{@}% change to @@ when we switch to @ as escape char in index files.
+ \def\ {\realbackslash\space }%
+ %
+ % Need these in case \tex is in effect and \{ is a \delimiter again.
+ % But can't use \lbracecmd and \rbracecmd because texindex assumes
+ % braces and backslashes are used only as delimiters.
+ \let\{ = \mylbrace
+ \let\} = \myrbrace
+ %
+ % I don't entirely understand this, but when an index entry is
+ % generated from a macro call, the \endinput which \scanmacro inserts
+ % causes processing to be prematurely terminated. This is,
+ % apparently, because \indexsorttmp is fully expanded, and \endinput
+ % is an expandable command. The redefinition below makes \endinput
+ % disappear altogether for that purpose -- although logging shows that
+ % processing continues to some further point. On the other hand, it
+ % seems \endinput does not hurt in the printed index arg, since that
+ % is still getting written without apparent harm.
+ %
+ % Sample source (mac-idx3.tex, reported by Graham Percival to
+ % help-texinfo, 22may06):
+ % @macro funindex {WORD}
+ % @findex xyz
+ % @end macro
+ % ...
+ % @funindex commtest
+ %
+ % The above is not enough to reproduce the bug, but it gives the flavor.
+ %
+ % Sample whatsit resulting:
+ % . at write3{\entry{xyz}{@folio }{@code {xyz at endinput }}}
+ %
+ % So:
+ \let\endinput = \empty
+ %
+ % Do the redefinitions.
+ \commondummies
+}
+
+% For the aux and toc files, @ is the escape character. So we want to
+% redefine everything using @ as the escape character (instead of
+% \realbackslash, still used for index files). When everything uses @,
+% this will be simpler.
+%
+\def\atdummies{%
+ \def\@{@@}%
+ \def\ {@ }%
+ \let\{ = \lbraceatcmd
+ \let\} = \rbraceatcmd
+ %
+ % Do the redefinitions.
+ \commondummies
+ \otherbackslash
+}
+
+% Called from \indexdummies and \atdummies.
+%
+\def\commondummies{%
+ %
+ % \definedummyword defines \#1 as \string\#1\space, thus effectively
+ % preventing its expansion. This is used only for control% words,
+ % not control letters, because the \space would be incorrect for
+ % control characters, but is needed to separate the control word
+ % from whatever follows.
+ %
+ % For control letters, we have \definedummyletter, which omits the
+ % space.
+ %
+ % These can be used both for control words that take an argument and
+ % those that do not. If it is followed by {arg} in the input, then
+ % that will dutifully get written to the index (or wherever).
+ %
+ \def\definedummyword ##1{\def##1{\string##1\space}}%
+ \def\definedummyletter##1{\def##1{\string##1}}%
+ \let\definedummyaccent\definedummyletter
+ %
+ \commondummiesnofonts
+ %
+ \definedummyletter\_%
+ %
+ % Non-English letters.
+ \definedummyword\AA
+ \definedummyword\AE
+ \definedummyword\DH
+ \definedummyword\L
+ \definedummyword\O
+ \definedummyword\OE
+ \definedummyword\TH
+ \definedummyword\aa
+ \definedummyword\ae
+ \definedummyword\dh
+ \definedummyword\exclamdown
+ \definedummyword\l
+ \definedummyword\o
+ \definedummyword\oe
+ \definedummyword\ordf
+ \definedummyword\ordm
+ \definedummyword\questiondown
+ \definedummyword\ss
+ \definedummyword\th
+ %
+ % Although these internal commands shouldn't show up, sometimes they do.
+ \definedummyword\bf
+ \definedummyword\gtr
+ \definedummyword\hat
+ \definedummyword\less
+ \definedummyword\sf
+ \definedummyword\sl
+ \definedummyword\tclose
+ \definedummyword\tt
+ %
+ \definedummyword\LaTeX
+ \definedummyword\TeX
+ %
+ % Assorted special characters.
+ \definedummyword\bullet
+ \definedummyword\comma
+ \definedummyword\copyright
+ \definedummyword\registeredsymbol
+ \definedummyword\dots
+ \definedummyword\enddots
+ \definedummyword\equiv
+ \definedummyword\error
+ \definedummyword\euro
+ \definedummyword\guillemetleft
+ \definedummyword\guillemetright
+ \definedummyword\guilsinglleft
+ \definedummyword\guilsinglright
+ \definedummyword\expansion
+ \definedummyword\minus
+ \definedummyword\ogonek
+ \definedummyword\pounds
+ \definedummyword\point
+ \definedummyword\print
+ \definedummyword\quotedblbase
+ \definedummyword\quotedblleft
+ \definedummyword\quotedblright
+ \definedummyword\quoteleft
+ \definedummyword\quoteright
+ \definedummyword\quotesinglbase
+ \definedummyword\result
+ \definedummyword\textdegree
+ %
+ % We want to disable all macros so that they are not expanded by \write.
+ \macrolist
+ %
+ \normalturnoffactive
+ %
+ % Handle some cases of @value -- where it does not contain any
+ % (non-fully-expandable) commands.
+ \makevalueexpandable
+}
+
+% \commondummiesnofonts: common to \commondummies and \indexnofonts.
+%
+\def\commondummiesnofonts{%
+ % Control letters and accents.
+ \definedummyletter\!%
+ \definedummyaccent\"%
+ \definedummyaccent\'%
+ \definedummyletter\*%
+ \definedummyaccent\,%
+ \definedummyletter\.%
+ \definedummyletter\/%
+ \definedummyletter\:%
+ \definedummyaccent\=%
+ \definedummyletter\?%
+ \definedummyaccent\^%
+ \definedummyaccent\`%
+ \definedummyaccent\~%
+ \definedummyword\u
+ \definedummyword\v
+ \definedummyword\H
+ \definedummyword\dotaccent
+ \definedummyword\ogonek
+ \definedummyword\ringaccent
+ \definedummyword\tieaccent
+ \definedummyword\ubaraccent
+ \definedummyword\udotaccent
+ \definedummyword\dotless
+ %
+ % Texinfo font commands.
+ \definedummyword\b
+ \definedummyword\i
+ \definedummyword\r
+ \definedummyword\sc
+ \definedummyword\t
+ %
+ % Commands that take arguments.
+ \definedummyword\acronym
+ \definedummyword\cite
+ \definedummyword\code
+ \definedummyword\command
+ \definedummyword\dfn
+ \definedummyword\email
+ \definedummyword\emph
+ \definedummyword\env
+ \definedummyword\file
+ \definedummyword\kbd
+ \definedummyword\key
+ \definedummyword\math
+ \definedummyword\option
+ \definedummyword\pxref
+ \definedummyword\ref
+ \definedummyword\samp
+ \definedummyword\strong
+ \definedummyword\tie
+ \definedummyword\uref
+ \definedummyword\url
+ \definedummyword\var
+ \definedummyword\verb
+ \definedummyword\w
+ \definedummyword\xref
+}
+
+% \indexnofonts is used when outputting the strings to sort the index
+% by, and when constructing control sequence names. It eliminates all
+% control sequences and just writes whatever the best ASCII sort string
+% would be for a given command (usually its argument).
+%
+\def\indexnofonts{%
+ % Accent commands should become @asis.
+ \def\definedummyaccent##1{\let##1\asis}%
+ % We can just ignore other control letters.
+ \def\definedummyletter##1{\let##1\empty}%
+ % Hopefully, all control words can become @asis.
+ \let\definedummyword\definedummyaccent
+ %
+ \commondummiesnofonts
+ %
+ % Don't no-op \tt, since it isn't a user-level command
+ % and is used in the definitions of the active chars like <, >, |, etc.
+ % Likewise with the other plain tex font commands.
+ %\let\tt=\asis
+ %
+ \def\ { }%
+ \def\@{@}%
+ % how to handle braces?
+ \def\_{\normalunderscore}%
+ %
+ % Non-English letters.
+ \def\AA{AA}%
+ \def\AE{AE}%
+ \def\DH{DZZ}%
+ \def\L{L}%
+ \def\OE{OE}%
+ \def\O{O}%
+ \def\TH{ZZZ}%
+ \def\aa{aa}%
+ \def\ae{ae}%
+ \def\dh{dzz}%
+ \def\exclamdown{!}%
+ \def\l{l}%
+ \def\oe{oe}%
+ \def\ordf{a}%
+ \def\ordm{o}%
+ \def\o{o}%
+ \def\questiondown{?}%
+ \def\ss{ss}%
+ \def\th{zzz}%
+ %
+ \def\LaTeX{LaTeX}%
+ \def\TeX{TeX}%
+ %
+ % Assorted special characters.
+ % (The following {} will end up in the sort string, but that's ok.)
+ \def\bullet{bullet}%
+ \def\comma{,}%
+ \def\copyright{copyright}%
+ \def\dots{...}%
+ \def\enddots{...}%
+ \def\equiv{==}%
+ \def\error{error}%
+ \def\euro{euro}%
+ \def\expansion{==>}%
+ \def\guillemetleft{<<}%
+ \def\guillemetright{>>}%
+ \def\guilsinglleft{<}%
+ \def\guilsinglright{>}%
+ \def\minus{-}%
+ \def\point{.}%
+ \def\pounds{pounds}%
+ \def\print{-|}%
+ \def\quotedblbase{"}%
+ \def\quotedblleft{"}%
+ \def\quotedblright{"}%
+ \def\quoteleft{`}%
+ \def\quoteright{'}%
+ \def\quotesinglbase{,}%
+ \def\registeredsymbol{R}%
+ \def\result{=>}%
+ \def\textdegree{o}%
+ %
+ % We need to get rid of all macros, leaving only the arguments (if present).
+ % Of course this is not nearly correct, but it is the best we can do for now.
+ % makeinfo does not expand macros in the argument to @deffn, which ends up
+ % writing an index entry, and texindex isn't prepared for an index sort entry
+ % that starts with \.
+ %
+ % Since macro invocations are followed by braces, we can just redefine them
+ % to take a single TeX argument. The case of a macro invocation that
+ % goes to end-of-line is not handled.
+ %
+ \macrolist
+}
+
+\let\indexbackslash=0 %overridden during \printindex.
+\let\SETmarginindex=\relax % put index entries in margin (undocumented)?
+
+% Most index entries go through here, but \dosubind is the general case.
+% #1 is the index name, #2 is the entry text.
+\def\doind#1#2{\dosubind{#1}{#2}{}}
+
+% Workhorse for all \fooindexes.
+% #1 is name of index, #2 is stuff to put there, #3 is subentry --
+% empty if called from \doind, as we usually are (the main exception
+% is with most defuns, which call us directly).
+%
+\def\dosubind#1#2#3{%
+ \iflinks
+ {%
+ % Store the main index entry text (including the third arg).
+ \toks0 = {#2}%
+ % If third arg is present, precede it with a space.
+ \def\thirdarg{#3}%
+ \ifx\thirdarg\empty \else
+ \toks0 = \expandafter{\the\toks0 \space #3}%
+ \fi
+ %
+ \edef\writeto{\csname#1indfile\endcsname}%
+ %
+ \safewhatsit\dosubindwrite
+ }%
+ \fi
+}
+
+% Write the entry in \toks0 to the index file:
+%
+\def\dosubindwrite{%
+ % Put the index entry in the margin if desired.
+ \ifx\SETmarginindex\relax\else
+ \insert\margin{\hbox{\vrule height8pt depth3pt width0pt \the\toks0}}%
+ \fi
+ %
+ % Remember, we are within a group.
+ \indexdummies % Must do this here, since \bf, etc expand at this stage
+ \def\backslashcurfont{\indexbackslash}% \indexbackslash isn't defined now
+ % so it will be output as is; and it will print as backslash.
+ %
+ % Process the index entry with all font commands turned off, to
+ % get the string to sort by.
+ {\indexnofonts
+ \edef\temp{\the\toks0}% need full expansion
+ \xdef\indexsorttmp{\temp}%
+ }%
+ %
+ % Set up the complete index entry, with both the sort key and
+ % the original text, including any font commands. We write
+ % three arguments to \entry to the .?? file (four in the
+ % subentry case), texindex reduces to two when writing the .??s
+ % sorted result.
+ \edef\temp{%
+ \write\writeto{%
+ \string\entry{\indexsorttmp}{\noexpand\folio}{\the\toks0}}%
+ }%
+ \temp
+}
+
+% Take care of unwanted page breaks/skips around a whatsit:
+%
+% If a skip is the last thing on the list now, preserve it
+% by backing up by \lastskip, doing the \write, then inserting
+% the skip again. Otherwise, the whatsit generated by the
+% \write or \pdfdest will make \lastskip zero. The result is that
+% sequences like this:
+% @end defun
+% @tindex whatever
+% @defun ...
+% will have extra space inserted, because the \medbreak in the
+% start of the @defun won't see the skip inserted by the @end of
+% the previous defun.
+%
+% But don't do any of this if we're not in vertical mode. We
+% don't want to do a \vskip and prematurely end a paragraph.
+%
+% Avoid page breaks due to these extra skips, too.
+%
+% But wait, there is a catch there:
+% We'll have to check whether \lastskip is zero skip. \ifdim is not
+% sufficient for this purpose, as it ignores stretch and shrink parts
+% of the skip. The only way seems to be to check the textual
+% representation of the skip.
+%
+% The following is almost like \def\zeroskipmacro{0.0pt} except that
+% the ``p'' and ``t'' characters have catcode \other, not 11 (letter).
+%
+\edef\zeroskipmacro{\expandafter\the\csname z at skip\endcsname}
+%
+\newskip\whatsitskip
+\newcount\whatsitpenalty
+%
+% ..., ready, GO:
+%
+\def\safewhatsit#1{%
+\ifhmode
+ #1%
+\else
+ % \lastskip and \lastpenalty cannot both be nonzero simultaneously.
+ \whatsitskip = \lastskip
+ \edef\lastskipmacro{\the\lastskip}%
+ \whatsitpenalty = \lastpenalty
+ %
+ % If \lastskip is nonzero, that means the last item was a
+ % skip. And since a skip is discardable, that means this
+ % -\whatsitskip glue we're inserting is preceded by a
+ % non-discardable item, therefore it is not a potential
+ % breakpoint, therefore no \nobreak needed.
+ \ifx\lastskipmacro\zeroskipmacro
+ \else
+ \vskip-\whatsitskip
+ \fi
+ %
+ #1%
+ %
+ \ifx\lastskipmacro\zeroskipmacro
+ % If \lastskip was zero, perhaps the last item was a penalty, and
+ % perhaps it was >=10000, e.g., a \nobreak. In that case, we want
+ % to re-insert the same penalty (values >10000 are used for various
+ % signals); since we just inserted a non-discardable item, any
+ % following glue (such as a \parskip) would be a breakpoint. For example:
+ %
+ % @deffn deffn-whatever
+ % @vindex index-whatever
+ % Description.
+ % would allow a break between the index-whatever whatsit
+ % and the "Description." paragraph.
+ \ifnum\whatsitpenalty>9999 \penalty\whatsitpenalty \fi
+ \else
+ % On the other hand, if we had a nonzero \lastskip,
+ % this make-up glue would be preceded by a non-discardable item
+ % (the whatsit from the \write), so we must insert a \nobreak.
+ \nobreak\vskip\whatsitskip
+ \fi
+\fi
+}
+
+% The index entry written in the file actually looks like
+% \entry {sortstring}{page}{topic}
+% or
+% \entry {sortstring}{page}{topic}{subtopic}
+% The texindex program reads in these files and writes files
+% containing these kinds of lines:
+% \initial {c}
+% before the first topic whose initial is c
+% \entry {topic}{pagelist}
+% for a topic that is used without subtopics
+% \primary {topic}
+% for the beginning of a topic that is used with subtopics
+% \secondary {subtopic}{pagelist}
+% for each subtopic.
+
+% Define the user-accessible indexing commands
+% @findex, @vindex, @kindex, @cindex.
+
+\def\findex {\fnindex}
+\def\kindex {\kyindex}
+\def\cindex {\cpindex}
+\def\vindex {\vrindex}
+\def\tindex {\tpindex}
+\def\pindex {\pgindex}
+
+\def\cindexsub {\begingroup\obeylines\cindexsub}
+{\obeylines %
+\gdef\cindexsub "#1" #2^^M{\endgroup %
+\dosubind{cp}{#2}{#1}}}
+
+% Define the macros used in formatting output of the sorted index material.
+
+% @printindex causes a particular index (the ??s file) to get printed.
+% It does not print any chapter heading (usually an @unnumbered).
+%
+\parseargdef\printindex{\begingroup
+ \dobreak \chapheadingskip{10000}%
+ %
+ \smallfonts \rm
+ \tolerance = 9500
+ \plainfrenchspacing
+ \everypar = {}% don't want the \kern\-parindent from indentation suppression.
+ %
+ % See if the index file exists and is nonempty.
+ % Change catcode of @ here so that if the index file contains
+ % \initial {@}
+ % as its first line, TeX doesn't complain about mismatched braces
+ % (because it thinks @} is a control sequence).
+ \catcode`\@ = 11
+ \openin 1 \jobname.#1s
+ \ifeof 1
+ % \enddoublecolumns gets confused if there is no text in the index,
+ % and it loses the chapter title and the aux file entries for the
+ % index. The easiest way to prevent this problem is to make sure
+ % there is some text.
+ \putwordIndexNonexistent
+ \else
+ %
+ % If the index file exists but is empty, then \openin leaves \ifeof
+ % false. We have to make TeX try to read something from the file, so
+ % it can discover if there is anything in it.
+ \read 1 to \temp
+ \ifeof 1
+ \putwordIndexIsEmpty
+ \else
+ % Index files are almost Texinfo source, but we use \ as the escape
+ % character. It would be better to use @, but that's too big a change
+ % to make right now.
+ \def\indexbackslash{\backslashcurfont}%
+ \catcode`\\ = 0
+ \escapechar = `\\
+ \begindoublecolumns
+ \input \jobname.#1s
+ \enddoublecolumns
+ \fi
+ \fi
+ \closein 1
+\endgroup}
+
+% These macros are used by the sorted index file itself.
+% Change them to control the appearance of the index.
+
+\def\initial#1{{%
+ % Some minor font changes for the special characters.
+ \let\tentt=\sectt \let\tt=\sectt \let\sf=\sectt
+ %
+ % Remove any glue we may have, we'll be inserting our own.
+ \removelastskip
+ %
+ % We like breaks before the index initials, so insert a bonus.
+ \nobreak
+ \vskip 0pt plus 3\baselineskip
+ \penalty 0
+ \vskip 0pt plus -3\baselineskip
+ %
+ % Typeset the initial. Making this add up to a whole number of
+ % baselineskips increases the chance of the dots lining up from column
+ % to column. It still won't often be perfect, because of the stretch
+ % we need before each entry, but it's better.
+ %
+ % No shrink because it confuses \balancecolumns.
+ \vskip 1.67\baselineskip plus .5\baselineskip
+ \leftline{\secbf #1}%
+ % Do our best not to break after the initial.
+ \nobreak
+ \vskip .33\baselineskip plus .1\baselineskip
+}}
+
+% \entry typesets a paragraph consisting of the text (#1), dot leaders, and
+% then page number (#2) flushed to the right margin. It is used for index
+% and table of contents entries. The paragraph is indented by \leftskip.
+%
+% A straightforward implementation would start like this:
+% \def\entry#1#2{...
+% But this freezes the catcodes in the argument, and can cause problems to
+% @code, which sets - active. This problem was fixed by a kludge---
+% ``-'' was active throughout whole index, but this isn't really right.
+%
+% The right solution is to prevent \entry from swallowing the whole text.
+% --kasal, 21nov03
+\def\entry{%
+ \begingroup
+ %
+ % Start a new paragraph if necessary, so our assignments below can't
+ % affect previous text.
+ \par
+ %
+ % Do not fill out the last line with white space.
+ \parfillskip = 0in
+ %
+ % No extra space above this paragraph.
+ \parskip = 0in
+ %
+ % Do not prefer a separate line ending with a hyphen to fewer lines.
+ \finalhyphendemerits = 0
+ %
+ % \hangindent is only relevant when the entry text and page number
+ % don't both fit on one line. In that case, bob suggests starting the
+ % dots pretty far over on the line. Unfortunately, a large
+ % indentation looks wrong when the entry text itself is broken across
+ % lines. So we use a small indentation and put up with long leaders.
+ %
+ % \hangafter is reset to 1 (which is the value we want) at the start
+ % of each paragraph, so we need not do anything with that.
+ \hangindent = 2em
+ %
+ % When the entry text needs to be broken, just fill out the first line
+ % with blank space.
+ \rightskip = 0pt plus1fil
+ %
+ % A bit of stretch before each entry for the benefit of balancing
+ % columns.
+ \vskip 0pt plus1pt
+ %
+ % Swallow the left brace of the text (first parameter):
+ \afterassignment\doentry
+ \let\temp =
+}
+\def\doentry{%
+ \bgroup % Instead of the swallowed brace.
+ \noindent
+ \aftergroup\finishentry
+ % And now comes the text of the entry.
+}
+\def\finishentry#1{%
+ % #1 is the page number.
+ %
+ % The following is kludged to not output a line of dots in the index if
+ % there are no page numbers. The next person who breaks this will be
+ % cursed by a Unix daemon.
+ \setbox\boxA = \hbox{#1}%
+ \ifdim\wd\boxA = 0pt
+ \ %
+ \else
+ %
+ % If we must, put the page number on a line of its own, and fill out
+ % this line with blank space. (The \hfil is overwhelmed with the
+ % fill leaders glue in \indexdotfill if the page number does fit.)
+ \hfil\penalty50
+ \null\nobreak\indexdotfill % Have leaders before the page number.
+ %
+ % The `\ ' here is removed by the implicit \unskip that TeX does as
+ % part of (the primitive) \par. Without it, a spurious underfull
+ % \hbox ensues.
+ \ifpdf
+ \pdfgettoks#1.%
+ \ \the\toksA
+ \else
+ \ #1%
+ \fi
+ \fi
+ \par
+ \endgroup
+}
+
+% Like plain.tex's \dotfill, except uses up at least 1 em.
+\def\indexdotfill{\cleaders
+ \hbox{$\mathsurround=0pt \mkern1.5mu.\mkern1.5mu$}\hskip 1em plus 1fill}
+
+\def\primary #1{\line{#1\hfil}}
+
+\newskip\secondaryindent \secondaryindent=0.5cm
+\def\secondary#1#2{{%
+ \parfillskip=0in
+ \parskip=0in
+ \hangindent=1in
+ \hangafter=1
+ \noindent\hskip\secondaryindent\hbox{#1}\indexdotfill
+ \ifpdf
+ \pdfgettoks#2.\ \the\toksA % The page number ends the paragraph.
+ \else
+ #2
+ \fi
+ \par
+}}
+
+% Define two-column mode, which we use to typeset indexes.
+% Adapted from the TeXbook, page 416, which is to say,
+% the manmac.tex format used to print the TeXbook itself.
+\catcode`\@=11
+
+\newbox\partialpage
+\newdimen\doublecolumnhsize
+
+\def\begindoublecolumns{\begingroup % ended by \enddoublecolumns
+ % Grab any single-column material above us.
+ \output = {%
+ %
+ % Here is a possibility not foreseen in manmac: if we accumulate a
+ % whole lot of material, we might end up calling this \output
+ % routine twice in a row (see the doublecol-lose test, which is
+ % essentially a couple of indexes with @setchapternewpage off). In
+ % that case we just ship out what is in \partialpage with the normal
+ % output routine. Generally, \partialpage will be empty when this
+ % runs and this will be a no-op. See the indexspread.tex test case.
+ \ifvoid\partialpage \else
+ \onepageout{\pagecontents\partialpage}%
+ \fi
+ %
+ \global\setbox\partialpage = \vbox{%
+ % Unvbox the main output page.
+ \unvbox\PAGE
+ \kern-\topskip \kern\baselineskip
+ }%
+ }%
+ \eject % run that output routine to set \partialpage
+ %
+ % Use the double-column output routine for subsequent pages.
+ \output = {\doublecolumnout}%
+ %
+ % Change the page size parameters. We could do this once outside this
+ % routine, in each of @smallbook, @afourpaper, and the default 8.5x11
+ % format, but then we repeat the same computation. Repeating a couple
+ % of assignments once per index is clearly meaningless for the
+ % execution time, so we may as well do it in one place.
+ %
+ % First we halve the line length, less a little for the gutter between
+ % the columns. We compute the gutter based on the line length, so it
+ % changes automatically with the paper format. The magic constant
+ % below is chosen so that the gutter has the same value (well, +-<1pt)
+ % as it did when we hard-coded it.
+ %
+ % We put the result in a separate register, \doublecolumhsize, so we
+ % can restore it in \pagesofar, after \hsize itself has (potentially)
+ % been clobbered.
+ %
+ \doublecolumnhsize = \hsize
+ \advance\doublecolumnhsize by -.04154\hsize
+ \divide\doublecolumnhsize by 2
+ \hsize = \doublecolumnhsize
+ %
+ % Double the \vsize as well. (We don't need a separate register here,
+ % since nobody clobbers \vsize.)
+ \vsize = 2\vsize
+}
+
+% The double-column output routine for all double-column pages except
+% the last.
+%
+\def\doublecolumnout{%
+ \splittopskip=\topskip \splitmaxdepth=\maxdepth
+ % Get the available space for the double columns -- the normal
+ % (undoubled) page height minus any material left over from the
+ % previous page.
+ \dimen@ = \vsize
+ \divide\dimen@ by 2
+ \advance\dimen@ by -\ht\partialpage
+ %
+ % box0 will be the left-hand column, box2 the right.
+ \setbox0=\vsplit255 to\dimen@ \setbox2=\vsplit255 to\dimen@
+ \onepageout\pagesofar
+ \unvbox255
+ \penalty\outputpenalty
+}
+%
+% Re-output the contents of the output page -- any previous material,
+% followed by the two boxes we just split, in box0 and box2.
+\def\pagesofar{%
+ \unvbox\partialpage
+ %
+ \hsize = \doublecolumnhsize
+ \wd0=\hsize \wd2=\hsize
+ \hbox to\pagewidth{\box0\hfil\box2}%
+}
+%
+% All done with double columns.
+\def\enddoublecolumns{%
+ % The following penalty ensures that the page builder is exercised
+ % _before_ we change the output routine. This is necessary in the
+ % following situation:
+ %
+ % The last section of the index consists only of a single entry.
+ % Before this section, \pagetotal is less than \pagegoal, so no
+ % break occurs before the last section starts. However, the last
+ % section, consisting of \initial and the single \entry, does not
+ % fit on the page and has to be broken off. Without the following
+ % penalty the page builder will not be exercised until \eject
+ % below, and by that time we'll already have changed the output
+ % routine to the \balancecolumns version, so the next-to-last
+ % double-column page will be processed with \balancecolumns, which
+ % is wrong: The two columns will go to the main vertical list, with
+ % the broken-off section in the recent contributions. As soon as
+ % the output routine finishes, TeX starts reconsidering the page
+ % break. The two columns and the broken-off section both fit on the
+ % page, because the two columns now take up only half of the page
+ % goal. When TeX sees \eject from below which follows the final
+ % section, it invokes the new output routine that we've set after
+ % \balancecolumns below; \onepageout will try to fit the two columns
+ % and the final section into the vbox of \pageheight (see
+ % \pagebody), causing an overfull box.
+ %
+ % Note that glue won't work here, because glue does not exercise the
+ % page builder, unlike penalties (see The TeXbook, pp. 280-281).
+ \penalty0
+ %
+ \output = {%
+ % Split the last of the double-column material. Leave it on the
+ % current page, no automatic page break.
+ \balancecolumns
+ %
+ % If we end up splitting too much material for the current page,
+ % though, there will be another page break right after this \output
+ % invocation ends. Having called \balancecolumns once, we do not
+ % want to call it again. Therefore, reset \output to its normal
+ % definition right away. (We hope \balancecolumns will never be
+ % called on to balance too much material, but if it is, this makes
+ % the output somewhat more palatable.)
+ \global\output = {\onepageout{\pagecontents\PAGE}}%
+ }%
+ \eject
+ \endgroup % started in \begindoublecolumns
+ %
+ % \pagegoal was set to the doubled \vsize above, since we restarted
+ % the current page. We're now back to normal single-column
+ % typesetting, so reset \pagegoal to the normal \vsize (after the
+ % \endgroup where \vsize got restored).
+ \pagegoal = \vsize
+}
+%
+% Called at the end of the double column material.
+\def\balancecolumns{%
+ \setbox0 = \vbox{\unvbox255}% like \box255 but more efficient, see p.120.
+ \dimen@ = \ht0
+ \advance\dimen@ by \topskip
+ \advance\dimen@ by-\baselineskip
+ \divide\dimen@ by 2 % target to split to
+ %debug\message{final 2-column material height=\the\ht0, target=\the\dimen at .}%
+ \splittopskip = \topskip
+ % Loop until we get a decent breakpoint.
+ {%
+ \vbadness = 10000
+ \loop
+ \global\setbox3 = \copy0
+ \global\setbox1 = \vsplit3 to \dimen@
+ \ifdim\ht3>\dimen@
+ \global\advance\dimen@ by 1pt
+ \repeat
+ }%
+ %debug\message{split to \the\dimen@, column heights: \the\ht1, \the\ht3.}%
+ \setbox0=\vbox to\dimen@{\unvbox1}%
+ \setbox2=\vbox to\dimen@{\unvbox3}%
+ %
+ \pagesofar
+}
+\catcode`\@ = \other
+
+
+\message{sectioning,}
+% Chapters, sections, etc.
+
+% \unnumberedno is an oxymoron, of course. But we count the unnumbered
+% sections so that we can refer to them unambiguously in the pdf
+% outlines by their "section number". We avoid collisions with chapter
+% numbers by starting them at 10000. (If a document ever has 10000
+% chapters, we're in trouble anyway, I'm sure.)
+\newcount\unnumberedno \unnumberedno = 10000
+\newcount\chapno
+\newcount\secno \secno=0
+\newcount\subsecno \subsecno=0
+\newcount\subsubsecno \subsubsecno=0
+
+% This counter is funny since it counts through charcodes of letters A, B, ...
+\newcount\appendixno \appendixno = `\@
+%
+% \def\appendixletter{\char\the\appendixno}
+% We do the following ugly conditional instead of the above simple
+% construct for the sake of pdftex, which needs the actual
+% letter in the expansion, not just typeset.
+%
+\def\appendixletter{%
+ \ifnum\appendixno=`A A%
+ \else\ifnum\appendixno=`B B%
+ \else\ifnum\appendixno=`C C%
+ \else\ifnum\appendixno=`D D%
+ \else\ifnum\appendixno=`E E%
+ \else\ifnum\appendixno=`F F%
+ \else\ifnum\appendixno=`G G%
+ \else\ifnum\appendixno=`H H%
+ \else\ifnum\appendixno=`I I%
+ \else\ifnum\appendixno=`J J%
+ \else\ifnum\appendixno=`K K%
+ \else\ifnum\appendixno=`L L%
+ \else\ifnum\appendixno=`M M%
+ \else\ifnum\appendixno=`N N%
+ \else\ifnum\appendixno=`O O%
+ \else\ifnum\appendixno=`P P%
+ \else\ifnum\appendixno=`Q Q%
+ \else\ifnum\appendixno=`R R%
+ \else\ifnum\appendixno=`S S%
+ \else\ifnum\appendixno=`T T%
+ \else\ifnum\appendixno=`U U%
+ \else\ifnum\appendixno=`V V%
+ \else\ifnum\appendixno=`W W%
+ \else\ifnum\appendixno=`X X%
+ \else\ifnum\appendixno=`Y Y%
+ \else\ifnum\appendixno=`Z Z%
+ % The \the is necessary, despite appearances, because \appendixletter is
+ % expanded while writing the .toc file. \char\appendixno is not
+ % expandable, thus it is written literally, thus all appendixes come out
+ % with the same letter (or @) in the toc without it.
+ \else\char\the\appendixno
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi}
+
+% Each @chapter defines these (using marks) as the number+name, number
+% and name of the chapter. Page headings and footings can use
+% these. @section does likewise.
+\def\thischapter{}
+\def\thischapternum{}
+\def\thischaptername{}
+\def\thissection{}
+\def\thissectionnum{}
+\def\thissectionname{}
+
+\newcount\absseclevel % used to calculate proper heading level
+\newcount\secbase\secbase=0 % @raisesections/@lowersections modify this count
+
+% @raisesections: treat @section as chapter, @subsection as section, etc.
+\def\raisesections{\global\advance\secbase by -1}
+\let\up=\raisesections % original BFox name
+
+% @lowersections: treat @chapter as section, @section as subsection, etc.
+\def\lowersections{\global\advance\secbase by 1}
+\let\down=\lowersections % original BFox name
+
+% we only have subsub.
+\chardef\maxseclevel = 3
+%
+% A numbered section within an unnumbered changes to unnumbered too.
+% To achive this, remember the "biggest" unnum. sec. we are currently in:
+\chardef\unmlevel = \maxseclevel
+%
+% Trace whether the current chapter is an appendix or not:
+% \chapheadtype is "N" or "A", unnumbered chapters are ignored.
+\def\chapheadtype{N}
+
+% Choose a heading macro
+% #1 is heading type
+% #2 is heading level
+% #3 is text for heading
+\def\genhead#1#2#3{%
+ % Compute the abs. sec. level:
+ \absseclevel=#2
+ \advance\absseclevel by \secbase
+ % Make sure \absseclevel doesn't fall outside the range:
+ \ifnum \absseclevel < 0
+ \absseclevel = 0
+ \else
+ \ifnum \absseclevel > 3
+ \absseclevel = 3
+ \fi
+ \fi
+ % The heading type:
+ \def\headtype{#1}%
+ \if \headtype U%
+ \ifnum \absseclevel < \unmlevel
+ \chardef\unmlevel = \absseclevel
+ \fi
+ \else
+ % Check for appendix sections:
+ \ifnum \absseclevel = 0
+ \edef\chapheadtype{\headtype}%
+ \else
+ \if \headtype A\if \chapheadtype N%
+ \errmessage{@appendix... within a non-appendix chapter}%
+ \fi\fi
+ \fi
+ % Check for numbered within unnumbered:
+ \ifnum \absseclevel > \unmlevel
+ \def\headtype{U}%
+ \else
+ \chardef\unmlevel = 3
+ \fi
+ \fi
+ % Now print the heading:
+ \if \headtype U%
+ \ifcase\absseclevel
+ \unnumberedzzz{#3}%
+ \or \unnumberedseczzz{#3}%
+ \or \unnumberedsubseczzz{#3}%
+ \or \unnumberedsubsubseczzz{#3}%
+ \fi
+ \else
+ \if \headtype A%
+ \ifcase\absseclevel
+ \appendixzzz{#3}%
+ \or \appendixsectionzzz{#3}%
+ \or \appendixsubseczzz{#3}%
+ \or \appendixsubsubseczzz{#3}%
+ \fi
+ \else
+ \ifcase\absseclevel
+ \chapterzzz{#3}%
+ \or \seczzz{#3}%
+ \or \numberedsubseczzz{#3}%
+ \or \numberedsubsubseczzz{#3}%
+ \fi
+ \fi
+ \fi
+ \suppressfirstparagraphindent
+}
+
+% an interface:
+\def\numhead{\genhead N}
+\def\apphead{\genhead A}
+\def\unnmhead{\genhead U}
+
+% @chapter, @appendix, @unnumbered. Increment top-level counter, reset
+% all lower-level sectioning counters to zero.
+%
+% Also set \chaplevelprefix, which we prepend to @float sequence numbers
+% (e.g., figures), q.v. By default (before any chapter), that is empty.
+\let\chaplevelprefix = \empty
+%
+\outer\parseargdef\chapter{\numhead0{#1}} % normally numhead0 calls chapterzzz
+\def\chapterzzz#1{%
+ % section resetting is \global in case the chapter is in a group, such
+ % as an @include file.
+ \global\secno=0 \global\subsecno=0 \global\subsubsecno=0
+ \global\advance\chapno by 1
+ %
+ % Used for \float.
+ \gdef\chaplevelprefix{\the\chapno.}%
+ \resetallfloatnos
+ %
+ % \putwordChapter can contain complex things in translations.
+ \toks0=\expandafter{\putwordChapter}%
+ \message{\the\toks0 \space \the\chapno}%
+ %
+ % Write the actual heading.
+ \chapmacro{#1}{Ynumbered}{\the\chapno}%
+ %
+ % So @section and the like are numbered underneath this chapter.
+ \global\let\section = \numberedsec
+ \global\let\subsection = \numberedsubsec
+ \global\let\subsubsection = \numberedsubsubsec
+}
+
+\outer\parseargdef\appendix{\apphead0{#1}} % normally calls appendixzzz
+%
+\def\appendixzzz#1{%
+ \global\secno=0 \global\subsecno=0 \global\subsubsecno=0
+ \global\advance\appendixno by 1
+ \gdef\chaplevelprefix{\appendixletter.}%
+ \resetallfloatnos
+ %
+ % \putwordAppendix can contain complex things in translations.
+ \toks0=\expandafter{\putwordAppendix}%
+ \message{\the\toks0 \space \appendixletter}%
+ %
+ \chapmacro{#1}{Yappendix}{\appendixletter}%
+ %
+ \global\let\section = \appendixsec
+ \global\let\subsection = \appendixsubsec
+ \global\let\subsubsection = \appendixsubsubsec
+}
+
+\outer\parseargdef\unnumbered{\unnmhead0{#1}} % normally unnmhead0 calls unnumberedzzz
+\def\unnumberedzzz#1{%
+ \global\secno=0 \global\subsecno=0 \global\subsubsecno=0
+ \global\advance\unnumberedno by 1
+ %
+ % Since an unnumbered has no number, no prefix for figures.
+ \global\let\chaplevelprefix = \empty
+ \resetallfloatnos
+ %
+ % This used to be simply \message{#1}, but TeX fully expands the
+ % argument to \message. Therefore, if #1 contained @-commands, TeX
+ % expanded them. For example, in `@unnumbered The @cite{Book}', TeX
+ % expanded @cite (which turns out to cause errors because \cite is meant
+ % to be executed, not expanded).
+ %
+ % Anyway, we don't want the fully-expanded definition of @cite to appear
+ % as a result of the \message, we just want `@cite' itself. We use
+ % \the<toks register> to achieve this: TeX expands \the<toks> only once,
+ % simply yielding the contents of <toks register>. (We also do this for
+ % the toc entries.)
+ \toks0 = {#1}%
+ \message{(\the\toks0)}%
+ %
+ \chapmacro{#1}{Ynothing}{\the\unnumberedno}%
+ %
+ \global\let\section = \unnumberedsec
+ \global\let\subsection = \unnumberedsubsec
+ \global\let\subsubsection = \unnumberedsubsubsec
+}
+
+% @centerchap is like @unnumbered, but the heading is centered.
+\outer\parseargdef\centerchap{%
+ % Well, we could do the following in a group, but that would break
+ % an assumption that \chapmacro is called at the outermost level.
+ % Thus we are safer this way: --kasal, 24feb04
+ \let\centerparametersmaybe = \centerparameters
+ \unnmhead0{#1}%
+ \let\centerparametersmaybe = \relax
+}
+
+% @top is like @unnumbered.
+\let\top\unnumbered
+
+% Sections.
+\outer\parseargdef\numberedsec{\numhead1{#1}} % normally calls seczzz
+\def\seczzz#1{%
+ \global\subsecno=0 \global\subsubsecno=0 \global\advance\secno by 1
+ \sectionheading{#1}{sec}{Ynumbered}{\the\chapno.\the\secno}%
+}
+
+\outer\parseargdef\appendixsection{\apphead1{#1}} % normally calls appendixsectionzzz
+\def\appendixsectionzzz#1{%
+ \global\subsecno=0 \global\subsubsecno=0 \global\advance\secno by 1
+ \sectionheading{#1}{sec}{Yappendix}{\appendixletter.\the\secno}%
+}
+\let\appendixsec\appendixsection
+
+\outer\parseargdef\unnumberedsec{\unnmhead1{#1}} % normally calls unnumberedseczzz
+\def\unnumberedseczzz#1{%
+ \global\subsecno=0 \global\subsubsecno=0 \global\advance\secno by 1
+ \sectionheading{#1}{sec}{Ynothing}{\the\unnumberedno.\the\secno}%
+}
+
+% Subsections.
+\outer\parseargdef\numberedsubsec{\numhead2{#1}} % normally calls numberedsubseczzz
+\def\numberedsubseczzz#1{%
+ \global\subsubsecno=0 \global\advance\subsecno by 1
+ \sectionheading{#1}{subsec}{Ynumbered}{\the\chapno.\the\secno.\the\subsecno}%
+}
+
+\outer\parseargdef\appendixsubsec{\apphead2{#1}} % normally calls appendixsubseczzz
+\def\appendixsubseczzz#1{%
+ \global\subsubsecno=0 \global\advance\subsecno by 1
+ \sectionheading{#1}{subsec}{Yappendix}%
+ {\appendixletter.\the\secno.\the\subsecno}%
+}
+
+\outer\parseargdef\unnumberedsubsec{\unnmhead2{#1}} %normally calls unnumberedsubseczzz
+\def\unnumberedsubseczzz#1{%
+ \global\subsubsecno=0 \global\advance\subsecno by 1
+ \sectionheading{#1}{subsec}{Ynothing}%
+ {\the\unnumberedno.\the\secno.\the\subsecno}%
+}
+
+% Subsubsections.
+\outer\parseargdef\numberedsubsubsec{\numhead3{#1}} % normally numberedsubsubseczzz
+\def\numberedsubsubseczzz#1{%
+ \global\advance\subsubsecno by 1
+ \sectionheading{#1}{subsubsec}{Ynumbered}%
+ {\the\chapno.\the\secno.\the\subsecno.\the\subsubsecno}%
+}
+
+\outer\parseargdef\appendixsubsubsec{\apphead3{#1}} % normally appendixsubsubseczzz
+\def\appendixsubsubseczzz#1{%
+ \global\advance\subsubsecno by 1
+ \sectionheading{#1}{subsubsec}{Yappendix}%
+ {\appendixletter.\the\secno.\the\subsecno.\the\subsubsecno}%
+}
+
+\outer\parseargdef\unnumberedsubsubsec{\unnmhead3{#1}} %normally unnumberedsubsubseczzz
+\def\unnumberedsubsubseczzz#1{%
+ \global\advance\subsubsecno by 1
+ \sectionheading{#1}{subsubsec}{Ynothing}%
+ {\the\unnumberedno.\the\secno.\the\subsecno.\the\subsubsecno}%
+}
+
+% These macros control what the section commands do, according
+% to what kind of chapter we are in (ordinary, appendix, or unnumbered).
+% Define them by default for a numbered chapter.
+\let\section = \numberedsec
+\let\subsection = \numberedsubsec
+\let\subsubsection = \numberedsubsubsec
+
+% Define @majorheading, @heading and @subheading
+
+% NOTE on use of \vbox for chapter headings, section headings, and such:
+% 1) We use \vbox rather than the earlier \line to permit
+% overlong headings to fold.
+% 2) \hyphenpenalty is set to 10000 because hyphenation in a
+% heading is obnoxious; this forbids it.
+% 3) Likewise, headings look best if no \parindent is used, and
+% if justification is not attempted. Hence \raggedright.
+
+\def\majorheading{%
+ {\advance\chapheadingskip by 10pt \chapbreak }%
+ \parsearg\chapheadingzzz
+}
+
+\def\chapheading{\chapbreak \parsearg\chapheadingzzz}
+\def\chapheadingzzz#1{%
+ {\chapfonts \vbox{\hyphenpenalty=10000\tolerance=5000
+ \parindent=0pt\ptexraggedright
+ \rmisbold #1\hfill}}%
+ \bigskip \par\penalty 200\relax
+ \suppressfirstparagraphindent
+}
+
+% @heading, @subheading, @subsubheading.
+\parseargdef\heading{\sectionheading{#1}{sec}{Yomitfromtoc}{}
+ \suppressfirstparagraphindent}
+\parseargdef\subheading{\sectionheading{#1}{subsec}{Yomitfromtoc}{}
+ \suppressfirstparagraphindent}
+\parseargdef\subsubheading{\sectionheading{#1}{subsubsec}{Yomitfromtoc}{}
+ \suppressfirstparagraphindent}
+
+% These macros generate a chapter, section, etc. heading only
+% (including whitespace, linebreaking, etc. around it),
+% given all the information in convenient, parsed form.
+
+%%% Args are the skip and penalty (usually negative)
+\def\dobreak#1#2{\par\ifdim\lastskip<#1\removelastskip\penalty#2\vskip#1\fi}
+
+%%% Define plain chapter starts, and page on/off switching for it
+% Parameter controlling skip before chapter headings (if needed)
+
+\newskip\chapheadingskip
+
+\def\chapbreak{\dobreak \chapheadingskip {-4000}}
+\def\chappager{\par\vfill\supereject}
+% Because \domark is called before \chapoddpage, the filler page will
+% get the headings for the next chapter, which is wrong. But we don't
+% care -- we just disable all headings on the filler page.
+\def\chapoddpage{%
+ \chappager
+ \ifodd\pageno \else
+ \begingroup
+ \evenheadline={\hfil}\evenfootline={\hfil}%
+ \oddheadline={\hfil}\oddfootline={\hfil}%
+ \hbox to 0pt{}%
+ \chappager
+ \endgroup
+ \fi
+}
+
+\def\setchapternewpage #1 {\csname CHAPPAG#1\endcsname}
+
+\def\CHAPPAGoff{%
+\global\let\contentsalignmacro = \chappager
+\global\let\pchapsepmacro=\chapbreak
+\global\let\pagealignmacro=\chappager}
+
+\def\CHAPPAGon{%
+\global\let\contentsalignmacro = \chappager
+\global\let\pchapsepmacro=\chappager
+\global\let\pagealignmacro=\chappager
+\global\def\HEADINGSon{\HEADINGSsingle}}
+
+\def\CHAPPAGodd{%
+\global\let\contentsalignmacro = \chapoddpage
+\global\let\pchapsepmacro=\chapoddpage
+\global\let\pagealignmacro=\chapoddpage
+\global\def\HEADINGSon{\HEADINGSdouble}}
+
+\CHAPPAGon
+
+% Chapter opening.
+%
+% #1 is the text, #2 is the section type (Ynumbered, Ynothing,
+% Yappendix, Yomitfromtoc), #3 the chapter number.
+%
+% To test against our argument.
+\def\Ynothingkeyword{Ynothing}
+\def\Yomitfromtockeyword{Yomitfromtoc}
+\def\Yappendixkeyword{Yappendix}
+%
+\def\chapmacro#1#2#3{%
+ % Insert the first mark before the heading break (see notes for \domark).
+ \let\prevchapterdefs=\lastchapterdefs
+ \let\prevsectiondefs=\lastsectiondefs
+ \gdef\lastsectiondefs{\gdef\thissectionname{}\gdef\thissectionnum{}%
+ \gdef\thissection{}}%
+ %
+ \def\temptype{#2}%
+ \ifx\temptype\Ynothingkeyword
+ \gdef\lastchapterdefs{\gdef\thischaptername{#1}\gdef\thischapternum{}%
+ \gdef\thischapter{\thischaptername}}%
+ \else\ifx\temptype\Yomitfromtockeyword
+ \gdef\lastchapterdefs{\gdef\thischaptername{#1}\gdef\thischapternum{}%
+ \gdef\thischapter{}}%
+ \else\ifx\temptype\Yappendixkeyword
+ \toks0={#1}%
+ \xdef\lastchapterdefs{%
+ \gdef\noexpand\thischaptername{\the\toks0}%
+ \gdef\noexpand\thischapternum{\appendixletter}%
+ % \noexpand\putwordAppendix avoids expanding indigestible
+ % commands in some of the translations.
+ \gdef\noexpand\thischapter{\noexpand\putwordAppendix{}
+ \noexpand\thischapternum:
+ \noexpand\thischaptername}%
+ }%
+ \else
+ \toks0={#1}%
+ \xdef\lastchapterdefs{%
+ \gdef\noexpand\thischaptername{\the\toks0}%
+ \gdef\noexpand\thischapternum{\the\chapno}%
+ % \noexpand\putwordChapter avoids expanding indigestible
+ % commands in some of the translations.
+ \gdef\noexpand\thischapter{\noexpand\putwordChapter{}
+ \noexpand\thischapternum:
+ \noexpand\thischaptername}%
+ }%
+ \fi\fi\fi
+ %
+ % Output the mark. Pass it through \safewhatsit, to take care of
+ % the preceding space.
+ \safewhatsit\domark
+ %
+ % Insert the chapter heading break.
+ \pchapsepmacro
+ %
+ % Now the second mark, after the heading break. No break points
+ % between here and the heading.
+ \let\prevchapterdefs=\lastchapterdefs
+ \let\prevsectiondefs=\lastsectiondefs
+ \domark
+ %
+ {%
+ \chapfonts \rmisbold
+ %
+ % Have to define \lastsection before calling \donoderef, because the
+ % xref code eventually uses it. On the other hand, it has to be called
+ % after \pchapsepmacro, or the headline will change too soon.
+ \gdef\lastsection{#1}%
+ %
+ % Only insert the separating space if we have a chapter/appendix
+ % number, and don't print the unnumbered ``number''.
+ \ifx\temptype\Ynothingkeyword
+ \setbox0 = \hbox{}%
+ \def\toctype{unnchap}%
+ \else\ifx\temptype\Yomitfromtockeyword
+ \setbox0 = \hbox{}% contents like unnumbered, but no toc entry
+ \def\toctype{omit}%
+ \else\ifx\temptype\Yappendixkeyword
+ \setbox0 = \hbox{\putwordAppendix{} #3\enspace}%
+ \def\toctype{app}%
+ \else
+ \setbox0 = \hbox{#3\enspace}%
+ \def\toctype{numchap}%
+ \fi\fi\fi
+ %
+ % Write the toc entry for this chapter. Must come before the
+ % \donoderef, because we include the current node name in the toc
+ % entry, and \donoderef resets it to empty.
+ \writetocentry{\toctype}{#1}{#3}%
+ %
+ % For pdftex, we have to write out the node definition (aka, make
+ % the pdfdest) after any page break, but before the actual text has
+ % been typeset. If the destination for the pdf outline is after the
+ % text, then jumping from the outline may wind up with the text not
+ % being visible, for instance under high magnification.
+ \donoderef{#2}%
+ %
+ % Typeset the actual heading.
+ \nobreak % Avoid page breaks at the interline glue.
+ \vbox{\hyphenpenalty=10000 \tolerance=5000 \parindent=0pt \ptexraggedright
+ \hangindent=\wd0 \centerparametersmaybe
+ \unhbox0 #1\par}%
+ }%
+ \nobreak\bigskip % no page break after a chapter title
+ \nobreak
+}
+
+% @centerchap -- centered and unnumbered.
+\let\centerparametersmaybe = \relax
+\def\centerparameters{%
+ \advance\rightskip by 3\rightskip
+ \leftskip = \rightskip
+ \parfillskip = 0pt
+}
+
+
+% I don't think this chapter style is supported any more, so I'm not
+% updating it with the new noderef stuff. We'll see. --karl, 11aug03.
+%
+\def\setchapterstyle #1 {\csname CHAPF#1\endcsname}
+%
+\def\unnchfopen #1{%
+\chapoddpage {\chapfonts \vbox{\hyphenpenalty=10000\tolerance=5000
+ \parindent=0pt\ptexraggedright
+ \rmisbold #1\hfill}}\bigskip \par\nobreak
+}
+\def\chfopen #1#2{\chapoddpage {\chapfonts
+\vbox to 3in{\vfil \hbox to\hsize{\hfil #2} \hbox to\hsize{\hfil #1} \vfil}}%
+\par\penalty 5000 %
+}
+\def\centerchfopen #1{%
+\chapoddpage {\chapfonts \vbox{\hyphenpenalty=10000\tolerance=5000
+ \parindent=0pt
+ \hfill {\rmisbold #1}\hfill}}\bigskip \par\nobreak
+}
+\def\CHAPFopen{%
+ \global\let\chapmacro=\chfopen
+ \global\let\centerchapmacro=\centerchfopen}
+
+
+% Section titles. These macros combine the section number parts and
+% call the generic \sectionheading to do the printing.
+%
+\newskip\secheadingskip
+\def\secheadingbreak{\dobreak \secheadingskip{-1000}}
+
+% Subsection titles.
+\newskip\subsecheadingskip
+\def\subsecheadingbreak{\dobreak \subsecheadingskip{-500}}
+
+% Subsubsection titles.
+\def\subsubsecheadingskip{\subsecheadingskip}
+\def\subsubsecheadingbreak{\subsecheadingbreak}
+
+
+% Print any size, any type, section title.
+%
+% #1 is the text, #2 is the section level (sec/subsec/subsubsec), #3 is
+% the section type for xrefs (Ynumbered, Ynothing, Yappendix), #4 is the
+% section number.
+%
+\def\seckeyword{sec}
+%
+\def\sectionheading#1#2#3#4{%
+ {%
+ % Switch to the right set of fonts.
+ \csname #2fonts\endcsname \rmisbold
+ %
+ \def\sectionlevel{#2}%
+ \def\temptype{#3}%
+ %
+ % Insert first mark before the heading break (see notes for \domark).
+ \let\prevsectiondefs=\lastsectiondefs
+ \ifx\temptype\Ynothingkeyword
+ \ifx\sectionlevel\seckeyword
+ \gdef\lastsectiondefs{\gdef\thissectionname{#1}\gdef\thissectionnum{}%
+ \gdef\thissection{\thissectionname}}%
+ \fi
+ \else\ifx\temptype\Yomitfromtockeyword
+ % Don't redefine \thissection.
+ \else\ifx\temptype\Yappendixkeyword
+ \ifx\sectionlevel\seckeyword
+ \toks0={#1}%
+ \xdef\lastsectiondefs{%
+ \gdef\noexpand\thissectionname{\the\toks0}%
+ \gdef\noexpand\thissectionnum{#4}%
+ % \noexpand\putwordSection avoids expanding indigestible
+ % commands in some of the translations.
+ \gdef\noexpand\thissection{\noexpand\putwordSection{}
+ \noexpand\thissectionnum:
+ \noexpand\thissectionname}%
+ }%
+ \fi
+ \else
+ \ifx\sectionlevel\seckeyword
+ \toks0={#1}%
+ \xdef\lastsectiondefs{%
+ \gdef\noexpand\thissectionname{\the\toks0}%
+ \gdef\noexpand\thissectionnum{#4}%
+ % \noexpand\putwordSection avoids expanding indigestible
+ % commands in some of the translations.
+ \gdef\noexpand\thissection{\noexpand\putwordSection{}
+ \noexpand\thissectionnum:
+ \noexpand\thissectionname}%
+ }%
+ \fi
+ \fi\fi\fi
+ %
+ % Go into vertical mode. Usually we'll already be there, but we
+ % don't want the following whatsit to end up in a preceding paragraph
+ % if the document didn't happen to have a blank line.
+ \par
+ %
+ % Output the mark. Pass it through \safewhatsit, to take care of
+ % the preceding space.
+ \safewhatsit\domark
+ %
+ % Insert space above the heading.
+ \csname #2headingbreak\endcsname
+ %
+ % Now the second mark, after the heading break. No break points
+ % between here and the heading.
+ \let\prevsectiondefs=\lastsectiondefs
+ \domark
+ %
+ % Only insert the space after the number if we have a section number.
+ \ifx\temptype\Ynothingkeyword
+ \setbox0 = \hbox{}%
+ \def\toctype{unn}%
+ \gdef\lastsection{#1}%
+ \else\ifx\temptype\Yomitfromtockeyword
+ % for @headings -- no section number, don't include in toc,
+ % and don't redefine \lastsection.
+ \setbox0 = \hbox{}%
+ \def\toctype{omit}%
+ \let\sectionlevel=\empty
+ \else\ifx\temptype\Yappendixkeyword
+ \setbox0 = \hbox{#4\enspace}%
+ \def\toctype{app}%
+ \gdef\lastsection{#1}%
+ \else
+ \setbox0 = \hbox{#4\enspace}%
+ \def\toctype{num}%
+ \gdef\lastsection{#1}%
+ \fi\fi\fi
+ %
+ % Write the toc entry (before \donoderef). See comments in \chapmacro.
+ \writetocentry{\toctype\sectionlevel}{#1}{#4}%
+ %
+ % Write the node reference (= pdf destination for pdftex).
+ % Again, see comments in \chapmacro.
+ \donoderef{#3}%
+ %
+ % Interline glue will be inserted when the vbox is completed.
+ % That glue will be a valid breakpoint for the page, since it'll be
+ % preceded by a whatsit (usually from the \donoderef, or from the
+ % \writetocentry if there was no node). We don't want to allow that
+ % break, since then the whatsits could end up on page n while the
+ % section is on page n+1, thus toc/etc. are wrong. Debian bug 276000.
+ \nobreak
+ %
+ % Output the actual section heading.
+ \vbox{\hyphenpenalty=10000 \tolerance=5000 \parindent=0pt \ptexraggedright
+ \hangindent=\wd0 % zero if no section number
+ \unhbox0 #1}%
+ }%
+ % Add extra space after the heading -- half of whatever came above it.
+ % Don't allow stretch, though.
+ \kern .5 \csname #2headingskip\endcsname
+ %
+ % Do not let the kern be a potential breakpoint, as it would be if it
+ % was followed by glue.
+ \nobreak
+ %
+ % We'll almost certainly start a paragraph next, so don't let that
+ % glue accumulate. (Not a breakpoint because it's preceded by a
+ % discardable item.)
+ \vskip-\parskip
+ %
+ % This is purely so the last item on the list is a known \penalty >
+ % 10000. This is so \startdefun can avoid allowing breakpoints after
+ % section headings. Otherwise, it would insert a valid breakpoint between:
+ %
+ % @section sec-whatever
+ % @deffn def-whatever
+ \penalty 10001
+}
+
+
+\message{toc,}
+% Table of contents.
+\newwrite\tocfile
+
+% Write an entry to the toc file, opening it if necessary.
+% Called from @chapter, etc.
+%
+% Example usage: \writetocentry{sec}{Section Name}{\the\chapno.\the\secno}
+% We append the current node name (if any) and page number as additional
+% arguments for the \{chap,sec,...}entry macros which will eventually
+% read this. The node name is used in the pdf outlines as the
+% destination to jump to.
+%
+% We open the .toc file for writing here instead of at @setfilename (or
+% any other fixed time) so that @contents can be anywhere in the document.
+% But if #1 is `omit', then we don't do anything. This is used for the
+% table of contents chapter openings themselves.
+%
+\newif\iftocfileopened
+\def\omitkeyword{omit}%
+%
+\def\writetocentry#1#2#3{%
+ \edef\writetoctype{#1}%
+ \ifx\writetoctype\omitkeyword \else
+ \iftocfileopened\else
+ \immediate\openout\tocfile = \jobname.toc
+ \global\tocfileopenedtrue
+ \fi
+ %
+ \iflinks
+ {\atdummies
+ \edef\temp{%
+ \write\tocfile{@#1entry{#2}{#3}{\lastnode}{\noexpand\folio}}}%
+ \temp
+ }%
+ \fi
+ \fi
+ %
+ % Tell \shipout to create a pdf destination on each page, if we're
+ % writing pdf. These are used in the table of contents. We can't
+ % just write one on every page because the title pages are numbered
+ % 1 and 2 (the page numbers aren't printed), and so are the first
+ % two pages of the document. Thus, we'd have two destinations named
+ % `1', and two named `2'.
+ \ifpdf \global\pdfmakepagedesttrue \fi
+}
+
+
+% These characters do not print properly in the Computer Modern roman
+% fonts, so we must take special care. This is more or less redundant
+% with the Texinfo input format setup at the end of this file.
+%
+\def\activecatcodes{%
+ \catcode`\"=\active
+ \catcode`\$=\active
+ \catcode`\<=\active
+ \catcode`\>=\active
+ \catcode`\\=\active
+ \catcode`\^=\active
+ \catcode`\_=\active
+ \catcode`\|=\active
+ \catcode`\~=\active
+}
+
+
+% Read the toc file, which is essentially Texinfo input.
+\def\readtocfile{%
+ \setupdatafile
+ \activecatcodes
+ \input \tocreadfilename
+}
+
+\newskip\contentsrightmargin \contentsrightmargin=1in
+\newcount\savepageno
+\newcount\lastnegativepageno \lastnegativepageno = -1
+
+% Prepare to read what we've written to \tocfile.
+%
+\def\startcontents#1{%
+ % If @setchapternewpage on, and @headings double, the contents should
+ % start on an odd page, unlike chapters. Thus, we maintain
+ % \contentsalignmacro in parallel with \pagealignmacro.
+ % From: Torbjorn Granlund <tege at matematik.su.se>
+ \contentsalignmacro
+ \immediate\closeout\tocfile
+ %
+ % Don't need to put `Contents' or `Short Contents' in the headline.
+ % It is abundantly clear what they are.
+ \chapmacro{#1}{Yomitfromtoc}{}%
+ %
+ \savepageno = \pageno
+ \begingroup % Set up to handle contents files properly.
+ \raggedbottom % Worry more about breakpoints than the bottom.
+ \advance\hsize by -\contentsrightmargin % Don't use the full line length.
+ %
+ % Roman numerals for page numbers.
+ \ifnum \pageno>0 \global\pageno = \lastnegativepageno \fi
+}
+
+% redefined for the two-volume lispref. We always output on
+% \jobname.toc even if this is redefined.
+%
+\def\tocreadfilename{\jobname.toc}
+
+% Normal (long) toc.
+%
+\def\contents{%
+ \startcontents{\putwordTOC}%
+ \openin 1 \tocreadfilename\space
+ \ifeof 1 \else
+ \readtocfile
+ \fi
+ \vfill \eject
+ \contentsalignmacro % in case @setchapternewpage odd is in effect
+ \ifeof 1 \else
+ \pdfmakeoutlines
+ \fi
+ \closein 1
+ \endgroup
+ \lastnegativepageno = \pageno
+ \global\pageno = \savepageno
+}
+
+% And just the chapters.
+\def\summarycontents{%
+ \startcontents{\putwordShortTOC}%
+ %
+ \let\numchapentry = \shortchapentry
+ \let\appentry = \shortchapentry
+ \let\unnchapentry = \shortunnchapentry
+ % We want a true roman here for the page numbers.
+ \secfonts
+ \let\rm=\shortcontrm \let\bf=\shortcontbf
+ \let\sl=\shortcontsl \let\tt=\shortconttt
+ \rm
+ \hyphenpenalty = 10000
+ \advance\baselineskip by 1pt % Open it up a little.
+ \def\numsecentry##1##2##3##4{}
+ \let\appsecentry = \numsecentry
+ \let\unnsecentry = \numsecentry
+ \let\numsubsecentry = \numsecentry
+ \let\appsubsecentry = \numsecentry
+ \let\unnsubsecentry = \numsecentry
+ \let\numsubsubsecentry = \numsecentry
+ \let\appsubsubsecentry = \numsecentry
+ \let\unnsubsubsecentry = \numsecentry
+ \openin 1 \tocreadfilename\space
+ \ifeof 1 \else
+ \readtocfile
+ \fi
+ \closein 1
+ \vfill \eject
+ \contentsalignmacro % in case @setchapternewpage odd is in effect
+ \endgroup
+ \lastnegativepageno = \pageno
+ \global\pageno = \savepageno
+}
+\let\shortcontents = \summarycontents
+
+% Typeset the label for a chapter or appendix for the short contents.
+% The arg is, e.g., `A' for an appendix, or `3' for a chapter.
+%
+\def\shortchaplabel#1{%
+ % This space should be enough, since a single number is .5em, and the
+ % widest letter (M) is 1em, at least in the Computer Modern fonts.
+ % But use \hss just in case.
+ % (This space doesn't include the extra space that gets added after
+ % the label; that gets put in by \shortchapentry above.)
+ %
+ % We'd like to right-justify chapter numbers, but that looks strange
+ % with appendix letters. And right-justifying numbers and
+ % left-justifying letters looks strange when there is less than 10
+ % chapters. Have to read the whole toc once to know how many chapters
+ % there are before deciding ...
+ \hbox to 1em{#1\hss}%
+}
+
+% These macros generate individual entries in the table of contents.
+% The first argument is the chapter or section name.
+% The last argument is the page number.
+% The arguments in between are the chapter number, section number, ...
+
+% Chapters, in the main contents.
+\def\numchapentry#1#2#3#4{\dochapentry{#2\labelspace#1}{#4}}
+%
+% Chapters, in the short toc.
+% See comments in \dochapentry re vbox and related settings.
+\def\shortchapentry#1#2#3#4{%
+ \tocentry{\shortchaplabel{#2}\labelspace #1}{\doshortpageno\bgroup#4\egroup}%
+}
+
+% Appendices, in the main contents.
+% Need the word Appendix, and a fixed-size box.
+%
+\def\appendixbox#1{%
+ % We use M since it's probably the widest letter.
+ \setbox0 = \hbox{\putwordAppendix{} M}%
+ \hbox to \wd0{\putwordAppendix{} #1\hss}}
+%
+\def\appentry#1#2#3#4{\dochapentry{\appendixbox{#2}\labelspace#1}{#4}}
+
+% Unnumbered chapters.
+\def\unnchapentry#1#2#3#4{\dochapentry{#1}{#4}}
+\def\shortunnchapentry#1#2#3#4{\tocentry{#1}{\doshortpageno\bgroup#4\egroup}}
+
+% Sections.
+\def\numsecentry#1#2#3#4{\dosecentry{#2\labelspace#1}{#4}}
+\let\appsecentry=\numsecentry
+\def\unnsecentry#1#2#3#4{\dosecentry{#1}{#4}}
+
+% Subsections.
+\def\numsubsecentry#1#2#3#4{\dosubsecentry{#2\labelspace#1}{#4}}
+\let\appsubsecentry=\numsubsecentry
+\def\unnsubsecentry#1#2#3#4{\dosubsecentry{#1}{#4}}
+
+% And subsubsections.
+\def\numsubsubsecentry#1#2#3#4{\dosubsubsecentry{#2\labelspace#1}{#4}}
+\let\appsubsubsecentry=\numsubsubsecentry
+\def\unnsubsubsecentry#1#2#3#4{\dosubsubsecentry{#1}{#4}}
+
+% This parameter controls the indentation of the various levels.
+% Same as \defaultparindent.
+\newdimen\tocindent \tocindent = 15pt
+
+% Now for the actual typesetting. In all these, #1 is the text and #2 is the
+% page number.
+%
+% If the toc has to be broken over pages, we want it to be at chapters
+% if at all possible; hence the \penalty.
+\def\dochapentry#1#2{%
+ \penalty-300 \vskip1\baselineskip plus.33\baselineskip minus.25\baselineskip
+ \begingroup
+ \chapentryfonts
+ \tocentry{#1}{\dopageno\bgroup#2\egroup}%
+ \endgroup
+ \nobreak\vskip .25\baselineskip plus.1\baselineskip
+}
+
+\def\dosecentry#1#2{\begingroup
+ \secentryfonts \leftskip=\tocindent
+ \tocentry{#1}{\dopageno\bgroup#2\egroup}%
+\endgroup}
+
+\def\dosubsecentry#1#2{\begingroup
+ \subsecentryfonts \leftskip=2\tocindent
+ \tocentry{#1}{\dopageno\bgroup#2\egroup}%
+\endgroup}
+
+\def\dosubsubsecentry#1#2{\begingroup
+ \subsubsecentryfonts \leftskip=3\tocindent
+ \tocentry{#1}{\dopageno\bgroup#2\egroup}%
+\endgroup}
+
+% We use the same \entry macro as for the index entries.
+\let\tocentry = \entry
+
+% Space between chapter (or whatever) number and the title.
+\def\labelspace{\hskip1em \relax}
+
+\def\dopageno#1{{\rm #1}}
+\def\doshortpageno#1{{\rm #1}}
+
+\def\chapentryfonts{\secfonts \rm}
+\def\secentryfonts{\textfonts}
+\def\subsecentryfonts{\textfonts}
+\def\subsubsecentryfonts{\textfonts}
+
+
+\message{environments,}
+% @foo ... @end foo.
+
+% @tex ... @end tex escapes into raw Tex temporarily.
+% One exception: @ is still an escape character, so that @end tex works.
+% But \@ or @@ will get a plain tex @ character.
+
+\envdef\tex{%
+ \setupmarkupstyle{tex}%
+ \catcode `\\=0 \catcode `\{=1 \catcode `\}=2
+ \catcode `\$=3 \catcode `\&=4 \catcode `\#=6
+ \catcode `\^=7 \catcode `\_=8 \catcode `\~=\active \let~=\tie
+ \catcode `\%=14
+ \catcode `\+=\other
+ \catcode `\"=\other
+ \catcode `\|=\other
+ \catcode `\<=\other
+ \catcode `\>=\other
+ \catcode`\`=\other
+ \catcode`\'=\other
+ \escapechar=`\\
+ %
+ \let\b=\ptexb
+ \let\bullet=\ptexbullet
+ \let\c=\ptexc
+ \let\,=\ptexcomma
+ \let\.=\ptexdot
+ \let\dots=\ptexdots
+ \let\equiv=\ptexequiv
+ \let\!=\ptexexclam
+ \let\i=\ptexi
+ \let\indent=\ptexindent
+ \let\noindent=\ptexnoindent
+ \let\{=\ptexlbrace
+ \let\+=\tabalign
+ \let\}=\ptexrbrace
+ \let\/=\ptexslash
+ \let\*=\ptexstar
+ \let\t=\ptext
+ \expandafter \let\csname top\endcsname=\ptextop % outer
+ \let\frenchspacing=\plainfrenchspacing
+ %
+ \def\endldots{\mathinner{\ldots\ldots\ldots\ldots}}%
+ \def\enddots{\relax\ifmmode\endldots\else$\mathsurround=0pt \endldots\,$\fi}%
+ \def\@{@}%
+}
+% There is no need to define \Etex.
+
+% Define @lisp ... @end lisp.
+% @lisp environment forms a group so it can rebind things,
+% including the definition of @end lisp (which normally is erroneous).
+
+% Amount to narrow the margins by for @lisp.
+\newskip\lispnarrowing \lispnarrowing=0.4in
+
+% This is the definition that ^^M gets inside @lisp, @example, and other
+% such environments. \null is better than a space, since it doesn't
+% have any width.
+\def\lisppar{\null\endgraf}
+
+% This space is always present above and below environments.
+\newskip\envskipamount \envskipamount = 0pt
+
+% Make spacing and below environment symmetrical. We use \parskip here
+% to help in doing that, since in @example-like environments \parskip
+% is reset to zero; thus the \afterenvbreak inserts no space -- but the
+% start of the next paragraph will insert \parskip.
+%
+\def\aboveenvbreak{{%
+ % =10000 instead of <10000 because of a special case in \itemzzz and
+ % \sectionheading, q.v.
+ \ifnum \lastpenalty=10000 \else
+ \advance\envskipamount by \parskip
+ \endgraf
+ \ifdim\lastskip<\envskipamount
+ \removelastskip
+ % it's not a good place to break if the last penalty was \nobreak
+ % or better ...
+ \ifnum\lastpenalty<10000 \penalty-50 \fi
+ \vskip\envskipamount
+ \fi
+ \fi
+}}
+
+\let\afterenvbreak = \aboveenvbreak
+
+% \nonarrowing is a flag. If "set", @lisp etc don't narrow margins; it will
+% also clear it, so that its embedded environments do the narrowing again.
+\let\nonarrowing=\relax
+
+% @cartouche ... @end cartouche: draw rectangle w/rounded corners around
+% environment contents.
+\font\circle=lcircle10
+\newdimen\circthick
+\newdimen\cartouter\newdimen\cartinner
+\newskip\normbskip\newskip\normpskip\newskip\normlskip
+\circthick=\fontdimen8\circle
+%
+\def\ctl{{\circle\char'013\hskip -6pt}}% 6pt from pl file: 1/2charwidth
+\def\ctr{{\hskip 6pt\circle\char'010}}
+\def\cbl{{\circle\char'012\hskip -6pt}}
+\def\cbr{{\hskip 6pt\circle\char'011}}
+\def\carttop{\hbox to \cartouter{\hskip\lskip
+ \ctl\leaders\hrule height\circthick\hfil\ctr
+ \hskip\rskip}}
+\def\cartbot{\hbox to \cartouter{\hskip\lskip
+ \cbl\leaders\hrule height\circthick\hfil\cbr
+ \hskip\rskip}}
+%
+\newskip\lskip\newskip\rskip
+
+\envdef\cartouche{%
+ \ifhmode\par\fi % can't be in the midst of a paragraph.
+ \startsavinginserts
+ \lskip=\leftskip \rskip=\rightskip
+ \leftskip=0pt\rightskip=0pt % we want these *outside*.
+ \cartinner=\hsize \advance\cartinner by-\lskip
+ \advance\cartinner by-\rskip
+ \cartouter=\hsize
+ \advance\cartouter by 18.4pt % allow for 3pt kerns on either
+ % side, and for 6pt waste from
+ % each corner char, and rule thickness
+ \normbskip=\baselineskip \normpskip=\parskip \normlskip=\lineskip
+ % Flag to tell @lisp, etc., not to narrow margin.
+ \let\nonarrowing = t%
+ \vbox\bgroup
+ \baselineskip=0pt\parskip=0pt\lineskip=0pt
+ \carttop
+ \hbox\bgroup
+ \hskip\lskip
+ \vrule\kern3pt
+ \vbox\bgroup
+ \kern3pt
+ \hsize=\cartinner
+ \baselineskip=\normbskip
+ \lineskip=\normlskip
+ \parskip=\normpskip
+ \vskip -\parskip
+ \comment % For explanation, see the end of \def\group.
+}
+\def\Ecartouche{%
+ \ifhmode\par\fi
+ \kern3pt
+ \egroup
+ \kern3pt\vrule
+ \hskip\rskip
+ \egroup
+ \cartbot
+ \egroup
+ \checkinserts
+}
+
+
+% This macro is called at the beginning of all the @example variants,
+% inside a group.
+\newdimen\nonfillparindent
+\def\nonfillstart{%
+ \aboveenvbreak
+ \hfuzz = 12pt % Don't be fussy
+ \sepspaces % Make spaces be word-separators rather than space tokens.
+ \let\par = \lisppar % don't ignore blank lines
+ \obeylines % each line of input is a line of output
+ \parskip = 0pt
+ % Turn off paragraph indentation but redefine \indent to emulate
+ % the normal \indent.
+ \nonfillparindent=\parindent
+ \parindent = 0pt
+ \let\indent\nonfillindent
+ %
+ \emergencystretch = 0pt % don't try to avoid overfull boxes
+ \ifx\nonarrowing\relax
+ \advance \leftskip by \lispnarrowing
+ \exdentamount=\lispnarrowing
+ \else
+ \let\nonarrowing = \relax
+ \fi
+ \let\exdent=\nofillexdent
+}
+
+\begingroup
+\obeyspaces
+% We want to swallow spaces (but not other tokens) after the fake
+% @indent in our nonfill-environments, where spaces are normally
+% active and set to @tie, resulting in them not being ignored after
+% @indent.
+\gdef\nonfillindent{\futurelet\temp\nonfillindentcheck}%
+\gdef\nonfillindentcheck{%
+\ifx\temp %
+\expandafter\nonfillindentgobble%
+\else%
+\leavevmode\nonfillindentbox%
+\fi%
+}%
+\endgroup
+\def\nonfillindentgobble#1{\nonfillindent}
+\def\nonfillindentbox{\hbox to \nonfillparindent{\hss}}
+
+% If you want all examples etc. small: @set dispenvsize small.
+% If you want even small examples the full size: @set dispenvsize nosmall.
+% This affects the following displayed environments:
+% @example, @display, @format, @lisp
+%
+\def\smallword{small}
+\def\nosmallword{nosmall}
+\let\SETdispenvsize\relax
+\def\setnormaldispenv{%
+ \ifx\SETdispenvsize\smallword
+ % end paragraph for sake of leading, in case document has no blank
+ % line. This is redundant with what happens in \aboveenvbreak, but
+ % we need to do it before changing the fonts, and it's inconvenient
+ % to change the fonts afterward.
+ \ifnum \lastpenalty=10000 \else \endgraf \fi
+ \smallexamplefonts \rm
+ \fi
+}
+\def\setsmalldispenv{%
+ \ifx\SETdispenvsize\nosmallword
+ \else
+ \ifnum \lastpenalty=10000 \else \endgraf \fi
+ \smallexamplefonts \rm
+ \fi
+}
+
+% We often define two environments, @foo and @smallfoo.
+% Let's do it by one command:
+\def\makedispenv #1#2{
+ \expandafter\envdef\csname#1\endcsname {\setnormaldispenv #2}
+ \expandafter\envdef\csname small#1\endcsname {\setsmalldispenv #2}
+ \expandafter\let\csname E#1\endcsname \afterenvbreak
+ \expandafter\let\csname Esmall#1\endcsname \afterenvbreak
+}
+
+% Define two synonyms:
+\def\maketwodispenvs #1#2#3{
+ \makedispenv{#1}{#3}
+ \makedispenv{#2}{#3}
+}
+
+% @lisp: indented, narrowed, typewriter font; @example: same as @lisp.
+%
+% @smallexample and @smalllisp: use smaller fonts.
+% Originally contributed by Pavel at xerox.
+%
+\maketwodispenvs {lisp}{example}{%
+ \nonfillstart
+ \tt\setupmarkupstyle{example}%
+ \let\kbdfont = \kbdexamplefont % Allow @kbd to do something special.
+ \gobble % eat return
+}
+% @display/@smalldisplay: same as @lisp except keep current font.
+%
+\makedispenv {display}{%
+ \nonfillstart
+ \gobble
+}
+
+% @format/@smallformat: same as @display except don't narrow margins.
+%
+\makedispenv{format}{%
+ \let\nonarrowing = t%
+ \nonfillstart
+ \gobble
+}
+
+% @flushleft: same as @format, but doesn't obey \SETdispenvsize.
+\envdef\flushleft{%
+ \let\nonarrowing = t%
+ \nonfillstart
+ \gobble
+}
+\let\Eflushleft = \afterenvbreak
+
+% @flushright.
+%
+\envdef\flushright{%
+ \let\nonarrowing = t%
+ \nonfillstart
+ \advance\leftskip by 0pt plus 1fill
+ \gobble
+}
+\let\Eflushright = \afterenvbreak
+
+
+% @raggedright does more-or-less normal line breaking but no right
+% justification. From plain.tex.
+\envdef\raggedright{%
+ \rightskip0pt plus2em \spaceskip.3333em \xspaceskip.5em\relax
+}
+\let\Eraggedright\par
+
+\envdef\raggedleft{%
+ \parindent=0pt \leftskip0pt plus2em
+ \spaceskip.3333em \xspaceskip.5em \parfillskip=0pt
+ \hbadness=10000 % Last line will usually be underfull, so turn off
+ % badness reporting.
+}
+\let\Eraggedleft\par
+
+\envdef\raggedcenter{%
+ \parindent=0pt \rightskip0pt plus1em \leftskip0pt plus1em
+ \spaceskip.3333em \xspaceskip.5em \parfillskip=0pt
+ \hbadness=10000 % Last line will usually be underfull, so turn off
+ % badness reporting.
+}
+\let\Eraggedcenter\par
+
+
+% @quotation does normal linebreaking (hence we can't use \nonfillstart)
+% and narrows the margins. We keep \parskip nonzero in general, since
+% we're doing normal filling. So, when using \aboveenvbreak and
+% \afterenvbreak, temporarily make \parskip 0.
+%
+\def\quotationstart{%
+ {\parskip=0pt \aboveenvbreak}% because \aboveenvbreak inserts \parskip
+ \parindent=0pt
+ %
+ % @cartouche defines \nonarrowing to inhibit narrowing at next level down.
+ \ifx\nonarrowing\relax
+ \advance\leftskip by \lispnarrowing
+ \advance\rightskip by \lispnarrowing
+ \exdentamount = \lispnarrowing
+ \else
+ \let\nonarrowing = \relax
+ \fi
+ \parsearg\quotationlabel
+}
+
+\envdef\quotation{%
+ \setnormaldispenv
+ \quotationstart
+}
+
+\envdef\smallquotation{%
+ \setsmalldispenv
+ \quotationstart
+}
+\let\Esmallquotation = \Equotation
+
+% We have retained a nonzero parskip for the environment, since we're
+% doing normal filling.
+%
+\def\Equotation{%
+ \par
+ \ifx\quotationauthor\undefined\else
+ % indent a bit.
+ \leftline{\kern 2\leftskip \sl ---\quotationauthor}%
+ \fi
+ {\parskip=0pt \afterenvbreak}%
+}
+
+% If we're given an argument, typeset it in bold with a colon after.
+\def\quotationlabel#1{%
+ \def\temp{#1}%
+ \ifx\temp\empty \else
+ {\bf #1: }%
+ \fi
+}
+
+
+% LaTeX-like @verbatim... at end verbatim and @verb{<char>...<char>}
+% If we want to allow any <char> as delimiter,
+% we need the curly braces so that makeinfo sees the @verb command, eg:
+% `@verbx...x' would look like the '@verbx' command. --janneke at gnu.org
+%
+% [Knuth]: Donald Ervin Knuth, 1996. The TeXbook.
+%
+% [Knuth] p.344; only we need to do the other characters Texinfo sets
+% active too. Otherwise, they get lost as the first character on a
+% verbatim line.
+\def\dospecials{%
+ \do\ \do\\\do\{\do\}\do\$\do\&%
+ \do\#\do\^\do\^^K\do\_\do\^^A\do\%\do\~%
+ \do\<\do\>\do\|\do\@\do+\do\"%
+ % Don't do the quotes -- if we do, @set txicodequoteundirected and
+ % @set txicodequotebacktick will not have effect on @verb and
+ % @verbatim, and ?` and !` ligatures won't get disabled.
+ %\do\`\do\'%
+}
+%
+% [Knuth] p. 380
+\def\uncatcodespecials{%
+ \def\do##1{\catcode`##1=\other}\dospecials}
+%
+% Setup for the @verb command.
+%
+% Eight spaces for a tab
+\begingroup
+ \catcode`\^^I=\active
+ \gdef\tabeightspaces{\catcode`\^^I=\active\def^^I{\ \ \ \ \ \ \ \ }}
+\endgroup
+%
+\def\setupverb{%
+ \tt % easiest (and conventionally used) font for verbatim
+ \def\par{\leavevmode\endgraf}%
+ \setupmarkupstyle{verb}%
+ \tabeightspaces
+ % Respect line breaks,
+ % print special symbols as themselves, and
+ % make each space count
+ % must do in this order:
+ \obeylines \uncatcodespecials \sepspaces
+}
+
+% Setup for the @verbatim environment
+%
+% Real tab expansion
+\newdimen\tabw \setbox0=\hbox{\tt\space} \tabw=8\wd0 % tab amount
+%
+\def\starttabbox{\setbox0=\hbox\bgroup}
+%
+\begingroup
+ \catcode`\^^I=\active
+ \gdef\tabexpand{%
+ \catcode`\^^I=\active
+ \def^^I{\leavevmode\egroup
+ \dimen0=\wd0 % the width so far, or since the previous tab
+ \divide\dimen0 by\tabw
+ \multiply\dimen0 by\tabw % compute previous multiple of \tabw
+ \advance\dimen0 by\tabw % advance to next multiple of \tabw
+ \wd0=\dimen0 \box0 \starttabbox
+ }%
+ }
+\endgroup
+
+% start the verbatim environment.
+\def\setupverbatim{%
+ \let\nonarrowing = t%
+ \nonfillstart
+ % Easiest (and conventionally used) font for verbatim
+ \tt
+ \def\par{\leavevmode\egroup\box0\endgraf}%
+ \tabexpand
+ \setupmarkupstyle{verbatim}%
+ % Respect line breaks,
+ % print special symbols as themselves, and
+ % make each space count
+ % must do in this order:
+ \obeylines \uncatcodespecials \sepspaces
+ \everypar{\starttabbox}%
+}
+
+% Do the @verb magic: verbatim text is quoted by unique
+% delimiter characters. Before first delimiter expect a
+% right brace, after last delimiter expect closing brace:
+%
+% \def\doverb'{'<char>#1<char>'}'{#1}
+%
+% [Knuth] p. 382; only eat outer {}
+\begingroup
+ \catcode`[=1\catcode`]=2\catcode`\{=\other\catcode`\}=\other
+ \gdef\doverb{#1[\def\next##1#1}[##1\endgroup]\next]
+\endgroup
+%
+\def\verb{\begingroup\setupverb\doverb}
+%
+%
+% Do the @verbatim magic: define the macro \doverbatim so that
+% the (first) argument ends when '@end verbatim' is reached, ie:
+%
+% \def\doverbatim#1 at end verbatim{#1}
+%
+% For Texinfo it's a lot easier than for LaTeX,
+% because texinfo's \verbatim doesn't stop at '\end{verbatim}':
+% we need not redefine '\', '{' and '}'.
+%
+% Inspired by LaTeX's verbatim command set [latex.ltx]
+%
+\begingroup
+ \catcode`\ =\active
+ \obeylines %
+ % ignore everything up to the first ^^M, that's the newline at the end
+ % of the @verbatim input line itself. Otherwise we get an extra blank
+ % line in the output.
+ \xdef\doverbatim#1^^M#2 at end verbatim{#2\noexpand\end\gobble verbatim}%
+ % We really want {...\end verbatim} in the body of the macro, but
+ % without the active space; thus we have to use \xdef and \gobble.
+\endgroup
+%
+\envdef\verbatim{%
+ \setupverbatim\doverbatim
+}
+\let\Everbatim = \afterenvbreak
+
+
+% @verbatiminclude FILE - insert text of file in verbatim environment.
+%
+\def\verbatiminclude{\parseargusing\filenamecatcodes\doverbatiminclude}
+%
+\def\doverbatiminclude#1{%
+ {%
+ \makevalueexpandable
+ \setupverbatim
+ \indexnofonts % Allow `@@' and other weird things in file names.
+ \input #1
+ \afterenvbreak
+ }%
+}
+
+% @copying ... @end copying.
+% Save the text away for @insertcopying later.
+%
+% We save the uninterpreted tokens, rather than creating a box.
+% Saving the text in a box would be much easier, but then all the
+% typesetting commands (@smallbook, font changes, etc.) have to be done
+% beforehand -- and a) we want @copying to be done first in the source
+% file; b) letting users define the frontmatter in as flexible order as
+% possible is very desirable.
+%
+\def\copying{\checkenv{}\begingroup\scanargctxt\docopying}
+\def\docopying#1 at end copying{\endgroup\def\copyingtext{#1}}
+%
+\def\insertcopying{%
+ \begingroup
+ \parindent = 0pt % paragraph indentation looks wrong on title page
+ \scanexp\copyingtext
+ \endgroup
+}
+
+
+\message{defuns,}
+% @defun etc.
+
+\newskip\defbodyindent \defbodyindent=.4in
+\newskip\defargsindent \defargsindent=50pt
+\newskip\deflastargmargin \deflastargmargin=18pt
+\newcount\defunpenalty
+
+% Start the processing of @deffn:
+\def\startdefun{%
+ \ifnum\lastpenalty<10000
+ \medbreak
+ \defunpenalty=10003 % Will keep this @deffn together with the
+ % following @def command, see below.
+ \else
+ % If there are two @def commands in a row, we'll have a \nobreak,
+ % which is there to keep the function description together with its
+ % header. But if there's nothing but headers, we need to allow a
+ % break somewhere. Check specifically for penalty 10002, inserted
+ % by \printdefunline, instead of 10000, since the sectioning
+ % commands also insert a nobreak penalty, and we don't want to allow
+ % a break between a section heading and a defun.
+ %
+ % As a minor refinement, we avoid "club" headers by signalling
+ % with penalty of 10003 after the very first @deffn in the
+ % sequence (see above), and penalty of 10002 after any following
+ % @def command.
+ \ifnum\lastpenalty=10002 \penalty2000 \else \defunpenalty=10002 \fi
+ %
+ % Similarly, after a section heading, do not allow a break.
+ % But do insert the glue.
+ \medskip % preceded by discardable penalty, so not a breakpoint
+ \fi
+ %
+ \parindent=0in
+ \advance\leftskip by \defbodyindent
+ \exdentamount=\defbodyindent
+}
+
+\def\dodefunx#1{%
+ % First, check whether we are in the right environment:
+ \checkenv#1%
+ %
+ % As above, allow line break if we have multiple x headers in a row.
+ % It's not a great place, though.
+ \ifnum\lastpenalty=10002 \penalty3000 \else \defunpenalty=10002 \fi
+ %
+ % And now, it's time to reuse the body of the original defun:
+ \expandafter\gobbledefun#1%
+}
+\def\gobbledefun#1\startdefun{}
+
+% \printdefunline \deffnheader{text}
+%
+\def\printdefunline#1#2{%
+ \begingroup
+ % call \deffnheader:
+ #1#2 \endheader
+ % common ending:
+ \interlinepenalty = 10000
+ \advance\rightskip by 0pt plus 1fil
+ \endgraf
+ \nobreak\vskip -\parskip
+ \penalty\defunpenalty % signal to \startdefun and \dodefunx
+ % Some of the @defun-type tags do not enable magic parentheses,
+ % rendering the following check redundant. But we don't optimize.
+ \checkparencounts
+ \endgroup
+}
+
+\def\Edefun{\endgraf\medbreak}
+
+% \makedefun{deffn} creates \deffn, \deffnx and \Edeffn;
+% the only thing remaining is to define \deffnheader.
+%
+\def\makedefun#1{%
+ \expandafter\let\csname E#1\endcsname = \Edefun
+ \edef\temp{\noexpand\domakedefun
+ \makecsname{#1}\makecsname{#1x}\makecsname{#1header}}%
+ \temp
+}
+
+% \domakedefun \deffn \deffnx \deffnheader
+%
+% Define \deffn and \deffnx, without parameters.
+% \deffnheader has to be defined explicitly.
+%
+\def\domakedefun#1#2#3{%
+ \envdef#1{%
+ \startdefun
+ \parseargusing\activeparens{\printdefunline#3}%
+ }%
+ \def#2{\dodefunx#1}%
+ \def#3%
+}
+
+%%% Untyped functions:
+
+% @deffn category name args
+\makedefun{deffn}{\deffngeneral{}}
+
+% @deffn category class name args
+\makedefun{defop}#1 {\defopon{#1\ \putwordon}}
+
+% \defopon {category on}class name args
+\def\defopon#1#2 {\deffngeneral{\putwordon\ \code{#2}}{#1\ \code{#2}} }
+
+% \deffngeneral {subind}category name args
+%
+\def\deffngeneral#1#2 #3 #4\endheader{%
+ % Remember that \dosubind{fn}{foo}{} is equivalent to \doind{fn}{foo}.
+ \dosubind{fn}{\code{#3}}{#1}%
+ \defname{#2}{}{#3}\magicamp\defunargs{#4\unskip}%
+}
+
+%%% Typed functions:
+
+% @deftypefn category type name args
+\makedefun{deftypefn}{\deftypefngeneral{}}
+
+% @deftypeop category class type name args
+\makedefun{deftypeop}#1 {\deftypeopon{#1\ \putwordon}}
+
+% \deftypeopon {category on}class type name args
+\def\deftypeopon#1#2 {\deftypefngeneral{\putwordon\ \code{#2}}{#1\ \code{#2}} }
+
+% \deftypefngeneral {subind}category type name args
+%
+\def\deftypefngeneral#1#2 #3 #4 #5\endheader{%
+ \dosubind{fn}{\code{#4}}{#1}%
+ \defname{#2}{#3}{#4}\defunargs{#5\unskip}%
+}
+
+%%% Typed variables:
+
+% @deftypevr category type var args
+\makedefun{deftypevr}{\deftypecvgeneral{}}
+
+% @deftypecv category class type var args
+\makedefun{deftypecv}#1 {\deftypecvof{#1\ \putwordof}}
+
+% \deftypecvof {category of}class type var args
+\def\deftypecvof#1#2 {\deftypecvgeneral{\putwordof\ \code{#2}}{#1\ \code{#2}} }
+
+% \deftypecvgeneral {subind}category type var args
+%
+\def\deftypecvgeneral#1#2 #3 #4 #5\endheader{%
+ \dosubind{vr}{\code{#4}}{#1}%
+ \defname{#2}{#3}{#4}\defunargs{#5\unskip}%
+}
+
+%%% Untyped variables:
+
+% @defvr category var args
+\makedefun{defvr}#1 {\deftypevrheader{#1} {} }
+
+% @defcv category class var args
+\makedefun{defcv}#1 {\defcvof{#1\ \putwordof}}
+
+% \defcvof {category of}class var args
+\def\defcvof#1#2 {\deftypecvof{#1}#2 {} }
+
+%%% Type:
+% @deftp category name args
+\makedefun{deftp}#1 #2 #3\endheader{%
+ \doind{tp}{\code{#2}}%
+ \defname{#1}{}{#2}\defunargs{#3\unskip}%
+}
+
+% Remaining @defun-like shortcuts:
+\makedefun{defun}{\deffnheader{\putwordDeffunc} }
+\makedefun{defmac}{\deffnheader{\putwordDefmac} }
+\makedefun{defspec}{\deffnheader{\putwordDefspec} }
+\makedefun{deftypefun}{\deftypefnheader{\putwordDeffunc} }
+\makedefun{defvar}{\defvrheader{\putwordDefvar} }
+\makedefun{defopt}{\defvrheader{\putwordDefopt} }
+\makedefun{deftypevar}{\deftypevrheader{\putwordDefvar} }
+\makedefun{defmethod}{\defopon\putwordMethodon}
+\makedefun{deftypemethod}{\deftypeopon\putwordMethodon}
+\makedefun{defivar}{\defcvof\putwordInstanceVariableof}
+\makedefun{deftypeivar}{\deftypecvof\putwordInstanceVariableof}
+
+% \defname, which formats the name of the @def (not the args).
+% #1 is the category, such as "Function".
+% #2 is the return type, if any.
+% #3 is the function name.
+%
+% We are followed by (but not passed) the arguments, if any.
+%
+\def\defname#1#2#3{%
+ % Get the values of \leftskip and \rightskip as they were outside the @def...
+ \advance\leftskip by -\defbodyindent
+ %
+ % How we'll format the type name. Putting it in brackets helps
+ % distinguish it from the body text that may end up on the next line
+ % just below it.
+ \def\temp{#1}%
+ \setbox0=\hbox{\kern\deflastargmargin \ifx\temp\empty\else [\rm\temp]\fi}
+ %
+ % Figure out line sizes for the paragraph shape.
+ % The first line needs space for \box0; but if \rightskip is nonzero,
+ % we need only space for the part of \box0 which exceeds it:
+ \dimen0=\hsize \advance\dimen0 by -\wd0 \advance\dimen0 by \rightskip
+ % The continuations:
+ \dimen2=\hsize \advance\dimen2 by -\defargsindent
+ % (plain.tex says that \dimen1 should be used only as global.)
+ \parshape 2 0in \dimen0 \defargsindent \dimen2
+ %
+ % Put the type name to the right margin.
+ \noindent
+ \hbox to 0pt{%
+ \hfil\box0 \kern-\hsize
+ % \hsize has to be shortened this way:
+ \kern\leftskip
+ % Intentionally do not respect \rightskip, since we need the space.
+ }%
+ %
+ % Allow all lines to be underfull without complaint:
+ \tolerance=10000 \hbadness=10000
+ \exdentamount=\defbodyindent
+ {%
+ % defun fonts. We use typewriter by default (used to be bold) because:
+ % . we're printing identifiers, they should be in tt in principle.
+ % . in languages with many accents, such as Czech or French, it's
+ % common to leave accents off identifiers. The result looks ok in
+ % tt, but exceedingly strange in rm.
+ % . we don't want -- and --- to be treated as ligatures.
+ % . this still does not fix the ?` and !` ligatures, but so far no
+ % one has made identifiers using them :).
+ \df \tt
+ \def\temp{#2}% return value type
+ \ifx\temp\empty\else \tclose{\temp} \fi
+ #3% output function name
+ }%
+ {\rm\enskip}% hskip 0.5 em of \tenrm
+ %
+ \boldbrax
+ % arguments will be output next, if any.
+}
+
+% Print arguments in slanted roman (not ttsl), inconsistently with using
+% tt for the name. This is because literal text is sometimes needed in
+% the argument list (groff manual), and ttsl and tt are not very
+% distinguishable. Prevent hyphenation at `-' chars.
+%
+\def\defunargs#1{%
+ % use sl by default (not ttsl),
+ % tt for the names.
+ \df \sl \hyphenchar\font=0
+ %
+ % On the other hand, if an argument has two dashes (for instance), we
+ % want a way to get ttsl. Let's try @var for that.
+ \def\var##1{{\setupmarkupstyle{var}\ttslanted{##1}}}%
+ #1%
+ \sl\hyphenchar\font=45
+}
+
+% We want ()&[] to print specially on the defun line.
+%
+\def\activeparens{%
+ \catcode`\(=\active \catcode`\)=\active
+ \catcode`\[=\active \catcode`\]=\active
+ \catcode`\&=\active
+}
+
+% Make control sequences which act like normal parenthesis chars.
+\let\lparen = ( \let\rparen = )
+
+% Be sure that we always have a definition for `(', etc. For example,
+% if the fn name has parens in it, \boldbrax will not be in effect yet,
+% so TeX would otherwise complain about undefined control sequence.
+{
+ \activeparens
+ \global\let(=\lparen \global\let)=\rparen
+ \global\let[=\lbrack \global\let]=\rbrack
+ \global\let& = \&
+
+ \gdef\boldbrax{\let(=\opnr\let)=\clnr\let[=\lbrb\let]=\rbrb}
+ \gdef\magicamp{\let&=\amprm}
+}
+
+\newcount\parencount
+
+% If we encounter &foo, then turn on ()-hacking afterwards
+\newif\ifampseen
+\def\amprm#1 {\ampseentrue{\bf\ }}
+
+\def\parenfont{%
+ \ifampseen
+ % At the first level, print parens in roman,
+ % otherwise use the default font.
+ \ifnum \parencount=1 \rm \fi
+ \else
+ % The \sf parens (in \boldbrax) actually are a little bolder than
+ % the contained text. This is especially needed for [ and ] .
+ \sf
+ \fi
+}
+\def\infirstlevel#1{%
+ \ifampseen
+ \ifnum\parencount=1
+ #1%
+ \fi
+ \fi
+}
+\def\bfafterword#1 {#1 \bf}
+
+\def\opnr{%
+ \global\advance\parencount by 1
+ {\parenfont(}%
+ \infirstlevel \bfafterword
+}
+\def\clnr{%
+ {\parenfont)}%
+ \infirstlevel \sl
+ \global\advance\parencount by -1
+}
+
+\newcount\brackcount
+\def\lbrb{%
+ \global\advance\brackcount by 1
+ {\bf[}%
+}
+\def\rbrb{%
+ {\bf]}%
+ \global\advance\brackcount by -1
+}
+
+\def\checkparencounts{%
+ \ifnum\parencount=0 \else \badparencount \fi
+ \ifnum\brackcount=0 \else \badbrackcount \fi
+}
+% these should not use \errmessage; the glibc manual, at least, actually
+% has such constructs (when documenting function pointers).
+\def\badparencount{%
+ \message{Warning: unbalanced parentheses in @def...}%
+ \global\parencount=0
+}
+\def\badbrackcount{%
+ \message{Warning: unbalanced square brackets in @def...}%
+ \global\brackcount=0
+}
+
+
+\message{macros,}
+% @macro.
+
+% To do this right we need a feature of e-TeX, \scantokens,
+% which we arrange to emulate with a temporary file in ordinary TeX.
+\ifx\eTeXversion\undefined
+ \newwrite\macscribble
+ \def\scantokens#1{%
+ \toks0={#1}%
+ \immediate\openout\macscribble=\jobname.tmp
+ \immediate\write\macscribble{\the\toks0}%
+ \immediate\closeout\macscribble
+ \input \jobname.tmp
+ }
+\fi
+
+\def\scanmacro#1{%
+ \begingroup
+ \newlinechar`\^^M
+ \let\xeatspaces\eatspaces
+ % Undo catcode changes of \startcontents and \doprintindex
+ % When called from @insertcopying or (short)caption, we need active
+ % backslash to get it printed correctly. Previously, we had
+ % \catcode`\\=\other instead. We'll see whether a problem appears
+ % with macro expansion. --kasal, 19aug04
+ \catcode`\@=0 \catcode`\\=\active \escapechar=`\@
+ % ... and \example
+ \spaceisspace
+ %
+ % Append \endinput to make sure that TeX does not see the ending newline.
+ % I've verified that it is necessary both for e-TeX and for ordinary TeX
+ % --kasal, 29nov03
+ \scantokens{#1\endinput}%
+ \endgroup
+}
+
+\def\scanexp#1{%
+ \edef\temp{\noexpand\scanmacro{#1}}%
+ \temp
+}
+
+\newcount\paramno % Count of parameters
+\newtoks\macname % Macro name
+\newif\ifrecursive % Is it recursive?
+
+% List of all defined macros in the form
+% \definedummyword\macro1\definedummyword\macro2...
+% Currently is also contains all @aliases; the list can be split
+% if there is a need.
+\def\macrolist{}
+
+% Add the macro to \macrolist
+\def\addtomacrolist#1{\expandafter \addtomacrolistxxx \csname#1\endcsname}
+\def\addtomacrolistxxx#1{%
+ \toks0 = \expandafter{\macrolist\definedummyword#1}%
+ \xdef\macrolist{\the\toks0}%
+}
+
+% Utility routines.
+% This does \let #1 = #2, with \csnames; that is,
+% \let \csname#1\endcsname = \csname#2\endcsname
+% (except of course we have to play expansion games).
+%
+\def\cslet#1#2{%
+ \expandafter\let
+ \csname#1\expandafter\endcsname
+ \csname#2\endcsname
+}
+
+% Trim leading and trailing spaces off a string.
+% Concepts from aro-bend problem 15 (see CTAN).
+{\catcode`\@=11
+\gdef\eatspaces #1{\expandafter\trim@\expandafter{#1 }}
+\gdef\trim@ #1{\trim@@ @#1 @ #1 @ @@}
+\gdef\trim@@ #1@ #2@ #3@@{\trim@@@\empty #2 @}
+\def\unbrace#1{#1}
+\unbrace{\gdef\trim@@@ #1 } #2@{#1}
+}
+
+% Trim a single trailing ^^M off a string.
+{\catcode`\^^M=\other \catcode`\Q=3%
+\gdef\eatcr #1{\eatcra #1Q^^MQ}%
+\gdef\eatcra#1^^MQ{\eatcrb#1Q}%
+\gdef\eatcrb#1Q#2Q{#1}%
+}
+
+% Macro bodies are absorbed as an argument in a context where
+% all characters are catcode 10, 11 or 12, except \ which is active
+% (as in normal texinfo). It is necessary to change the definition of \.
+
+% Non-ASCII encodings make 8-bit characters active, so un-activate
+% them to avoid their expansion. Must do this non-globally, to
+% confine the change to the current group.
+
+% It's necessary to have hard CRs when the macro is executed. This is
+% done by making ^^M (\endlinechar) catcode 12 when reading the macro
+% body, and then making it the \newlinechar in \scanmacro.
+
+\def\scanctxt{%
+ \catcode`\"=\other
+ \catcode`\+=\other
+ \catcode`\<=\other
+ \catcode`\>=\other
+ \catcode`\@=\other
+ \catcode`\^=\other
+ \catcode`\_=\other
+ \catcode`\|=\other
+ \catcode`\~=\other
+ \ifx\declaredencoding\ascii \else \setnonasciicharscatcodenonglobal\other \fi
+}
+
+\def\scanargctxt{%
+ \scanctxt
+ \catcode`\\=\other
+ \catcode`\^^M=\other
+}
+
+\def\macrobodyctxt{%
+ \scanctxt
+ \catcode`\{=\other
+ \catcode`\}=\other
+ \catcode`\^^M=\other
+ \usembodybackslash
+}
+
+\def\macroargctxt{%
+ \scanctxt
+ \catcode`\\=\other
+}
+
+% \mbodybackslash is the definition of \ in @macro bodies.
+% It maps \foo\ => \csname macarg.foo\endcsname => #N
+% where N is the macro parameter number.
+% We define \csname macarg.\endcsname to be \realbackslash, so
+% \\ in macro replacement text gets you a backslash.
+
+{\catcode`@=0 @catcode`@\=@active
+ @gdef at usembodybackslash{@let\=@mbodybackslash}
+ @gdef at mbodybackslash#1\{@csname macarg.#1 at endcsname}
+}
+\expandafter\def\csname macarg.\endcsname{\realbackslash}
+
+\def\macro{\recursivefalse\parsearg\macroxxx}
+\def\rmacro{\recursivetrue\parsearg\macroxxx}
+
+\def\macroxxx#1{%
+ \getargs{#1}% now \macname is the macname and \argl the arglist
+ \ifx\argl\empty % no arguments
+ \paramno=0%
+ \else
+ \expandafter\parsemargdef \argl;%
+ \fi
+ \if1\csname ismacro.\the\macname\endcsname
+ \message{Warning: redefining \the\macname}%
+ \else
+ \expandafter\ifx\csname \the\macname\endcsname \relax
+ \else \errmessage{Macro name \the\macname\space already defined}\fi
+ \global\cslet{macsave.\the\macname}{\the\macname}%
+ \global\expandafter\let\csname ismacro.\the\macname\endcsname=1%
+ \addtomacrolist{\the\macname}%
+ \fi
+ \begingroup \macrobodyctxt
+ \ifrecursive \expandafter\parsermacbody
+ \else \expandafter\parsemacbody
+ \fi}
+
+\parseargdef\unmacro{%
+ \if1\csname ismacro.#1\endcsname
+ \global\cslet{#1}{macsave.#1}%
+ \global\expandafter\let \csname ismacro.#1\endcsname=0%
+ % Remove the macro name from \macrolist:
+ \begingroup
+ \expandafter\let\csname#1\endcsname \relax
+ \let\definedummyword\unmacrodo
+ \xdef\macrolist{\macrolist}%
+ \endgroup
+ \else
+ \errmessage{Macro #1 not defined}%
+ \fi
+}
+
+% Called by \do from \dounmacro on each macro. The idea is to omit any
+% macro definitions that have been changed to \relax.
+%
+\def\unmacrodo#1{%
+ \ifx #1\relax
+ % remove this
+ \else
+ \noexpand\definedummyword \noexpand#1%
+ \fi
+}
+
+% This makes use of the obscure feature that if the last token of a
+% <parameter list> is #, then the preceding argument is delimited by
+% an opening brace, and that opening brace is not consumed.
+\def\getargs#1{\getargsxxx#1{}}
+\def\getargsxxx#1#{\getmacname #1 \relax\getmacargs}
+\def\getmacname #1 #2\relax{\macname={#1}}
+\def\getmacargs#1{\def\argl{#1}}
+
+% Parse the optional {params} list. Set up \paramno and \paramlist
+% so \defmacro knows what to do. Define \macarg.blah for each blah
+% in the params list, to be ##N where N is the position in that list.
+% That gets used by \mbodybackslash (above).
+
+% We need to get `macro parameter char #' into several definitions.
+% The technique used is stolen from LaTeX: let \hash be something
+% unexpandable, insert that wherever you need a #, and then redefine
+% it to # just before using the token list produced.
+%
+% The same technique is used to protect \eatspaces till just before
+% the macro is used.
+
+\def\parsemargdef#1;{\paramno=0\def\paramlist{}%
+ \let\hash\relax\let\xeatspaces\relax\parsemargdefxxx#1,;,}
+\def\parsemargdefxxx#1,{%
+ \if#1;\let\next=\relax
+ \else \let\next=\parsemargdefxxx
+ \advance\paramno by 1%
+ \expandafter\edef\csname macarg.\eatspaces{#1}\endcsname
+ {\xeatspaces{\hash\the\paramno}}%
+ \edef\paramlist{\paramlist\hash\the\paramno,}%
+ \fi\next}
+
+% These two commands read recursive and nonrecursive macro bodies.
+% (They're different since rec and nonrec macros end differently.)
+
+\long\def\parsemacbody#1 at end macro%
+{\xdef\temp{\eatcr{#1}}\endgroup\defmacro}%
+\long\def\parsermacbody#1 at end rmacro%
+{\xdef\temp{\eatcr{#1}}\endgroup\defmacro}%
+
+% This defines the macro itself. There are six cases: recursive and
+% nonrecursive macros of zero, one, and many arguments.
+% Much magic with \expandafter here.
+% \xdef is used so that macro definitions will survive the file
+% they're defined in; @include reads the file inside a group.
+\def\defmacro{%
+ \let\hash=##% convert placeholders to macro parameter chars
+ \ifrecursive
+ \ifcase\paramno
+ % 0
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \noexpand\scanmacro{\temp}}%
+ \or % 1
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \bgroup\noexpand\macroargctxt
+ \noexpand\braceorline
+ \expandafter\noexpand\csname\the\macname xxx\endcsname}%
+ \expandafter\xdef\csname\the\macname xxx\endcsname##1{%
+ \egroup\noexpand\scanmacro{\temp}}%
+ \else % many
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \bgroup\noexpand\macroargctxt
+ \noexpand\csname\the\macname xx\endcsname}%
+ \expandafter\xdef\csname\the\macname xx\endcsname##1{%
+ \expandafter\noexpand\csname\the\macname xxx\endcsname ##1,}%
+ \expandafter\expandafter
+ \expandafter\xdef
+ \expandafter\expandafter
+ \csname\the\macname xxx\endcsname
+ \paramlist{\egroup\noexpand\scanmacro{\temp}}%
+ \fi
+ \else
+ \ifcase\paramno
+ % 0
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \noexpand\norecurse{\the\macname}%
+ \noexpand\scanmacro{\temp}\egroup}%
+ \or % 1
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \bgroup\noexpand\macroargctxt
+ \noexpand\braceorline
+ \expandafter\noexpand\csname\the\macname xxx\endcsname}%
+ \expandafter\xdef\csname\the\macname xxx\endcsname##1{%
+ \egroup
+ \noexpand\norecurse{\the\macname}%
+ \noexpand\scanmacro{\temp}\egroup}%
+ \else % many
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \bgroup\noexpand\macroargctxt
+ \expandafter\noexpand\csname\the\macname xx\endcsname}%
+ \expandafter\xdef\csname\the\macname xx\endcsname##1{%
+ \expandafter\noexpand\csname\the\macname xxx\endcsname ##1,}%
+ \expandafter\expandafter
+ \expandafter\xdef
+ \expandafter\expandafter
+ \csname\the\macname xxx\endcsname
+ \paramlist{%
+ \egroup
+ \noexpand\norecurse{\the\macname}%
+ \noexpand\scanmacro{\temp}\egroup}%
+ \fi
+ \fi}
+
+\def\norecurse#1{\bgroup\cslet{#1}{macsave.#1}}
+
+% \braceorline decides whether the next nonwhitespace character is a
+% {. If so it reads up to the closing }, if not, it reads the whole
+% line. Whatever was read is then fed to the next control sequence
+% as an argument (by \parsebrace or \parsearg)
+\def\braceorline#1{\let\macnamexxx=#1\futurelet\nchar\braceorlinexxx}
+\def\braceorlinexxx{%
+ \ifx\nchar\bgroup\else
+ \expandafter\parsearg
+ \fi \macnamexxx}
+
+
+% @alias.
+% We need some trickery to remove the optional spaces around the equal
+% sign. Just make them active and then expand them all to nothing.
+\def\alias{\parseargusing\obeyspaces\aliasxxx}
+\def\aliasxxx #1{\aliasyyy#1\relax}
+\def\aliasyyy #1=#2\relax{%
+ {%
+ \expandafter\let\obeyedspace=\empty
+ \addtomacrolist{#1}%
+ \xdef\next{\global\let\makecsname{#1}=\makecsname{#2}}%
+ }%
+ \next
+}
+
+
+\message{cross references,}
+
+\newwrite\auxfile
+\newif\ifhavexrefs % True if xref values are known.
+\newif\ifwarnedxrefs % True if we warned once that they aren't known.
+
+% @inforef is relatively simple.
+\def\inforef #1{\inforefzzz #1,,,,**}
+\def\inforefzzz #1,#2,#3,#4**{\putwordSee{} \putwordInfo{} \putwordfile{} \file{\ignorespaces #3{}},
+ node \samp{\ignorespaces#1{}}}
+
+% @node's only job in TeX is to define \lastnode, which is used in
+% cross-references. The @node line might or might not have commas, and
+% might or might not have spaces before the first comma, like:
+% @node foo , bar , ...
+% We don't want such trailing spaces in the node name.
+%
+\parseargdef\node{\checkenv{}\donode #1 ,\finishnodeparse}
+%
+% also remove a trailing comma, in case of something like this:
+% @node Help-Cross, , , Cross-refs
+\def\donode#1 ,#2\finishnodeparse{\dodonode #1,\finishnodeparse}
+\def\dodonode#1,#2\finishnodeparse{\gdef\lastnode{#1}}
+
+\let\nwnode=\node
+\let\lastnode=\empty
+
+% Write a cross-reference definition for the current node. #1 is the
+% type (Ynumbered, Yappendix, Ynothing).
+%
+\def\donoderef#1{%
+ \ifx\lastnode\empty\else
+ \setref{\lastnode}{#1}%
+ \global\let\lastnode=\empty
+ \fi
+}
+
+% @anchor{NAME} -- define xref target at arbitrary point.
+%
+\newcount\savesfregister
+%
+\def\savesf{\relax \ifhmode \savesfregister=\spacefactor \fi}
+\def\restoresf{\relax \ifhmode \spacefactor=\savesfregister \fi}
+\def\anchor#1{\savesf \setref{#1}{Ynothing}\restoresf \ignorespaces}
+
+% \setref{NAME}{SNT} defines a cross-reference point NAME (a node or an
+% anchor), which consists of three parts:
+% 1) NAME-title - the current sectioning name taken from \lastsection,
+% or the anchor name.
+% 2) NAME-snt - section number and type, passed as the SNT arg, or
+% empty for anchors.
+% 3) NAME-pg - the page number.
+%
+% This is called from \donoderef, \anchor, and \dofloat. In the case of
+% floats, there is an additional part, which is not written here:
+% 4) NAME-lof - the text as it should appear in a @listoffloats.
+%
+\def\setref#1#2{%
+ \pdfmkdest{#1}%
+ \iflinks
+ {%
+ \atdummies % preserve commands, but don't expand them
+ \edef\writexrdef##1##2{%
+ \write\auxfile{@xrdef{#1-% #1 of \setref, expanded by the \edef
+ ##1}{##2}}% these are parameters of \writexrdef
+ }%
+ \toks0 = \expandafter{\lastsection}%
+ \immediate \writexrdef{title}{\the\toks0 }%
+ \immediate \writexrdef{snt}{\csname #2\endcsname}% \Ynumbered etc.
+ \safewhatsit{\writexrdef{pg}{\folio}}% will be written later, during \shipout
+ }%
+ \fi
+}
+
+% @xref, @pxref, and @ref generate cross-references. For \xrefX, #1 is
+% the node name, #2 the name of the Info cross-reference, #3 the printed
+% node name, #4 the name of the Info file, #5 the name of the printed
+% manual. All but the node name can be omitted.
+%
+\def\pxref#1{\putwordsee{} \xrefX[#1,,,,,,,]}
+\def\xref#1{\putwordSee{} \xrefX[#1,,,,,,,]}
+\def\ref#1{\xrefX[#1,,,,,,,]}
+\def\xrefX[#1,#2,#3,#4,#5,#6]{\begingroup
+ \unsepspaces
+ \def\printedmanual{\ignorespaces #5}%
+ \def\printedrefname{\ignorespaces #3}%
+ \setbox1=\hbox{\printedmanual\unskip}%
+ \setbox0=\hbox{\printedrefname\unskip}%
+ \ifdim \wd0 = 0pt
+ % No printed node name was explicitly given.
+ \expandafter\ifx\csname SETxref-automatic-section-title\endcsname\relax
+ % Use the node name inside the square brackets.
+ \def\printedrefname{\ignorespaces #1}%
+ \else
+ % Use the actual chapter/section title appear inside
+ % the square brackets. Use the real section title if we have it.
+ \ifdim \wd1 > 0pt
+ % It is in another manual, so we don't have it.
+ \def\printedrefname{\ignorespaces #1}%
+ \else
+ \ifhavexrefs
+ % We know the real title if we have the xref values.
+ \def\printedrefname{\refx{#1-title}{}}%
+ \else
+ % Otherwise just copy the Info node name.
+ \def\printedrefname{\ignorespaces #1}%
+ \fi%
+ \fi
+ \fi
+ \fi
+ %
+ % Make link in pdf output.
+ \ifpdf
+ {\indexnofonts
+ \turnoffactive
+ % This expands tokens, so do it after making catcode changes, so _
+ % etc. don't get their TeX definitions.
+ \getfilename{#4}%
+ %
+ % See comments at \activebackslashdouble.
+ {\activebackslashdouble \xdef\pdfxrefdest{#1}%
+ \backslashparens\pdfxrefdest}%
+ %
+ \leavevmode
+ \startlink attr{/Border [0 0 0]}%
+ \ifnum\filenamelength>0
+ goto file{\the\filename.pdf} name{\pdfxrefdest}%
+ \else
+ goto name{\pdfmkpgn{\pdfxrefdest}}%
+ \fi
+ }%
+ \setcolor{\linkcolor}%
+ \fi
+ %
+ % Float references are printed completely differently: "Figure 1.2"
+ % instead of "[somenode], p.3". We distinguish them by the
+ % LABEL-title being set to a magic string.
+ {%
+ % Have to otherify everything special to allow the \csname to
+ % include an _ in the xref name, etc.
+ \indexnofonts
+ \turnoffactive
+ \expandafter\global\expandafter\let\expandafter\Xthisreftitle
+ \csname XR#1-title\endcsname
+ }%
+ \iffloat\Xthisreftitle
+ % If the user specified the print name (third arg) to the ref,
+ % print it instead of our usual "Figure 1.2".
+ \ifdim\wd0 = 0pt
+ \refx{#1-snt}{}%
+ \else
+ \printedrefname
+ \fi
+ %
+ % if the user also gave the printed manual name (fifth arg), append
+ % "in MANUALNAME".
+ \ifdim \wd1 > 0pt
+ \space \putwordin{} \cite{\printedmanual}%
+ \fi
+ \else
+ % node/anchor (non-float) references.
+ %
+ % If we use \unhbox0 and \unhbox1 to print the node names, TeX does not
+ % insert empty discretionaries after hyphens, which means that it will
+ % not find a line break at a hyphen in a node names. Since some manuals
+ % are best written with fairly long node names, containing hyphens, this
+ % is a loss. Therefore, we give the text of the node name again, so it
+ % is as if TeX is seeing it for the first time.
+ \ifdim \wd1 > 0pt
+ \putwordSection{} ``\printedrefname'' \putwordin{} \cite{\printedmanual}%
+ \else
+ % _ (for example) has to be the character _ for the purposes of the
+ % control sequence corresponding to the node, but it has to expand
+ % into the usual \leavevmode...\vrule stuff for purposes of
+ % printing. So we \turnoffactive for the \refx-snt, back on for the
+ % printing, back off for the \refx-pg.
+ {\turnoffactive
+ % Only output a following space if the -snt ref is nonempty; for
+ % @unnumbered and @anchor, it won't be.
+ \setbox2 = \hbox{\ignorespaces \refx{#1-snt}{}}%
+ \ifdim \wd2 > 0pt \refx{#1-snt}\space\fi
+ }%
+ % output the `[mynode]' via a macro so it can be overridden.
+ \xrefprintnodename\printedrefname
+ %
+ % But we always want a comma and a space:
+ ,\space
+ %
+ % output the `page 3'.
+ \turnoffactive \putwordpage\tie\refx{#1-pg}{}%
+ \fi
+ \fi
+ \endlink
+\endgroup}
+
+% This macro is called from \xrefX for the `[nodename]' part of xref
+% output. It's a separate macro only so it can be changed more easily,
+% since square brackets don't work well in some documents. Particularly
+% one that Bob is working on :).
+%
+\def\xrefprintnodename#1{[#1]}
+
+% Things referred to by \setref.
+%
+\def\Ynothing{}
+\def\Yomitfromtoc{}
+\def\Ynumbered{%
+ \ifnum\secno=0
+ \putwordChapter at tie \the\chapno
+ \else \ifnum\subsecno=0
+ \putwordSection at tie \the\chapno.\the\secno
+ \else \ifnum\subsubsecno=0
+ \putwordSection at tie \the\chapno.\the\secno.\the\subsecno
+ \else
+ \putwordSection at tie \the\chapno.\the\secno.\the\subsecno.\the\subsubsecno
+ \fi\fi\fi
+}
+\def\Yappendix{%
+ \ifnum\secno=0
+ \putwordAppendix at tie @char\the\appendixno{}%
+ \else \ifnum\subsecno=0
+ \putwordSection at tie @char\the\appendixno.\the\secno
+ \else \ifnum\subsubsecno=0
+ \putwordSection at tie @char\the\appendixno.\the\secno.\the\subsecno
+ \else
+ \putwordSection at tie
+ @char\the\appendixno.\the\secno.\the\subsecno.\the\subsubsecno
+ \fi\fi\fi
+}
+
+% Define \refx{NAME}{SUFFIX} to reference a cross-reference string named NAME.
+% If its value is nonempty, SUFFIX is output afterward.
+%
+\def\refx#1#2{%
+ {%
+ \indexnofonts
+ \otherbackslash
+ \expandafter\global\expandafter\let\expandafter\thisrefX
+ \csname XR#1\endcsname
+ }%
+ \ifx\thisrefX\relax
+ % If not defined, say something at least.
+ \angleleft un\-de\-fined\angleright
+ \iflinks
+ \ifhavexrefs
+ \message{\linenumber Undefined cross reference `#1'.}%
+ \else
+ \ifwarnedxrefs\else
+ \global\warnedxrefstrue
+ \message{Cross reference values unknown; you must run TeX again.}%
+ \fi
+ \fi
+ \fi
+ \else
+ % It's defined, so just use it.
+ \thisrefX
+ \fi
+ #2% Output the suffix in any case.
+}
+
+% This is the macro invoked by entries in the aux file. Usually it's
+% just a \def (we prepend XR to the control sequence name to avoid
+% collisions). But if this is a float type, we have more work to do.
+%
+\def\xrdef#1#2{%
+ {% The node name might contain 8-bit characters, which in our current
+ % implementation are changed to commands like @'e. Don't let these
+ % mess up the control sequence name.
+ \indexnofonts
+ \turnoffactive
+ \xdef\safexrefname{#1}%
+ }%
+ %
+ \expandafter\gdef\csname XR\safexrefname\endcsname{#2}% remember this xref
+ %
+ % Was that xref control sequence that we just defined for a float?
+ \expandafter\iffloat\csname XR\safexrefname\endcsname
+ % it was a float, and we have the (safe) float type in \iffloattype.
+ \expandafter\let\expandafter\floatlist
+ \csname floatlist\iffloattype\endcsname
+ %
+ % Is this the first time we've seen this float type?
+ \expandafter\ifx\floatlist\relax
+ \toks0 = {\do}% yes, so just \do
+ \else
+ % had it before, so preserve previous elements in list.
+ \toks0 = \expandafter{\floatlist\do}%
+ \fi
+ %
+ % Remember this xref in the control sequence \floatlistFLOATTYPE,
+ % for later use in \listoffloats.
+ \expandafter\xdef\csname floatlist\iffloattype\endcsname{\the\toks0
+ {\safexrefname}}%
+ \fi
+}
+
+% Read the last existing aux file, if any. No error if none exists.
+%
+\def\tryauxfile{%
+ \openin 1 \jobname.aux
+ \ifeof 1 \else
+ \readdatafile{aux}%
+ \global\havexrefstrue
+ \fi
+ \closein 1
+}
+
+\def\setupdatafile{%
+ \catcode`\^^@=\other
+ \catcode`\^^A=\other
+ \catcode`\^^B=\other
+ \catcode`\^^C=\other
+ \catcode`\^^D=\other
+ \catcode`\^^E=\other
+ \catcode`\^^F=\other
+ \catcode`\^^G=\other
+ \catcode`\^^H=\other
+ \catcode`\^^K=\other
+ \catcode`\^^L=\other
+ \catcode`\^^N=\other
+ \catcode`\^^P=\other
+ \catcode`\^^Q=\other
+ \catcode`\^^R=\other
+ \catcode`\^^S=\other
+ \catcode`\^^T=\other
+ \catcode`\^^U=\other
+ \catcode`\^^V=\other
+ \catcode`\^^W=\other
+ \catcode`\^^X=\other
+ \catcode`\^^Z=\other
+ \catcode`\^^[=\other
+ \catcode`\^^\=\other
+ \catcode`\^^]=\other
+ \catcode`\^^^=\other
+ \catcode`\^^_=\other
+ % It was suggested to set the catcode of ^ to 7, which would allow ^^e4 etc.
+ % in xref tags, i.e., node names. But since ^^e4 notation isn't
+ % supported in the main text, it doesn't seem desirable. Furthermore,
+ % that is not enough: for node names that actually contain a ^
+ % character, we would end up writing a line like this: 'xrdef {'hat
+ % b-title}{'hat b} and \xrdef does a \csname...\endcsname on the first
+ % argument, and \hat is not an expandable control sequence. It could
+ % all be worked out, but why? Either we support ^^ or we don't.
+ %
+ % The other change necessary for this was to define \auxhat:
+ % \def\auxhat{\def^{'hat }}% extra space so ok if followed by letter
+ % and then to call \auxhat in \setq.
+ %
+ \catcode`\^=\other
+ %
+ % Special characters. Should be turned off anyway, but...
+ \catcode`\~=\other
+ \catcode`\[=\other
+ \catcode`\]=\other
+ \catcode`\"=\other
+ \catcode`\_=\other
+ \catcode`\|=\other
+ \catcode`\<=\other
+ \catcode`\>=\other
+ \catcode`\$=\other
+ \catcode`\#=\other
+ \catcode`\&=\other
+ \catcode`\%=\other
+ \catcode`+=\other % avoid \+ for paranoia even though we've turned it off
+ %
+ % This is to support \ in node names and titles, since the \
+ % characters end up in a \csname. It's easier than
+ % leaving it active and making its active definition an actual \
+ % character. What I don't understand is why it works in the *value*
+ % of the xrdef. Seems like it should be a catcode12 \, and that
+ % should not typeset properly. But it works, so I'm moving on for
+ % now. --karl, 15jan04.
+ \catcode`\\=\other
+ %
+ % Make the characters 128-255 be printing characters.
+ {%
+ \count1=128
+ \def\loop{%
+ \catcode\count1=\other
+ \advance\count1 by 1
+ \ifnum \count1<256 \loop \fi
+ }%
+ }%
+ %
+ % @ is our escape character in .aux files, and we need braces.
+ \catcode`\{=1
+ \catcode`\}=2
+ \catcode`\@=0
+}
+
+\def\readdatafile#1{%
+\begingroup
+ \setupdatafile
+ \input\jobname.#1
+\endgroup}
+
+
+\message{insertions,}
+% including footnotes.
+
+\newcount \footnoteno
+
+% The trailing space in the following definition for supereject is
+% vital for proper filling; pages come out unaligned when you do a
+% pagealignmacro call if that space before the closing brace is
+% removed. (Generally, numeric constants should always be followed by a
+% space to prevent strange expansion errors.)
+\def\supereject{\par\penalty -20000\footnoteno =0 }
+
+% @footnotestyle is meaningful for info output only.
+\let\footnotestyle=\comment
+
+{\catcode `\@=11
+%
+% Auto-number footnotes. Otherwise like plain.
+\gdef\footnote{%
+ \let\indent=\ptexindent
+ \let\noindent=\ptexnoindent
+ \global\advance\footnoteno by \@ne
+ \edef\thisfootno{$^{\the\footnoteno}$}%
+ %
+ % In case the footnote comes at the end of a sentence, preserve the
+ % extra spacing after we do the footnote number.
+ \let\@sf\empty
+ \ifhmode\edef\@sf{\spacefactor\the\spacefactor}\ptexslash\fi
+ %
+ % Remove inadvertent blank space before typesetting the footnote number.
+ \unskip
+ \thisfootno\@sf
+ \dofootnote
+}%
+
+% Don't bother with the trickery in plain.tex to not require the
+% footnote text as a parameter. Our footnotes don't need to be so general.
+%
+% Oh yes, they do; otherwise, @ifset (and anything else that uses
+% \parseargline) fails inside footnotes because the tokens are fixed when
+% the footnote is read. --karl, 16nov96.
+%
+\gdef\dofootnote{%
+ \insert\footins\bgroup
+ % We want to typeset this text as a normal paragraph, even if the
+ % footnote reference occurs in (for example) a display environment.
+ % So reset some parameters.
+ \hsize=\pagewidth
+ \interlinepenalty\interfootnotelinepenalty
+ \splittopskip\ht\strutbox % top baseline for broken footnotes
+ \splitmaxdepth\dp\strutbox
+ \floatingpenalty\@MM
+ \leftskip\z at skip
+ \rightskip\z at skip
+ \spaceskip\z at skip
+ \xspaceskip\z at skip
+ \parindent\defaultparindent
+ %
+ \smallfonts \rm
+ %
+ % Because we use hanging indentation in footnotes, a @noindent appears
+ % to exdent this text, so make it be a no-op. makeinfo does not use
+ % hanging indentation so @noindent can still be needed within footnote
+ % text after an @example or the like (not that this is good style).
+ \let\noindent = \relax
+ %
+ % Hang the footnote text off the number. Use \everypar in case the
+ % footnote extends for more than one paragraph.
+ \everypar = {\hang}%
+ \textindent{\thisfootno}%
+ %
+ % Don't crash into the line above the footnote text. Since this
+ % expands into a box, it must come within the paragraph, lest it
+ % provide a place where TeX can split the footnote.
+ \footstrut
+ \futurelet\next\fo at t
+}
+}%end \catcode `\@=11
+
+% In case a @footnote appears in a vbox, save the footnote text and create
+% the real \insert just after the vbox finished. Otherwise, the insertion
+% would be lost.
+% Similarly, if a @footnote appears inside an alignment, save the footnote
+% text to a box and make the \insert when a row of the table is finished.
+% And the same can be done for other insert classes. --kasal, 16nov03.
+
+% Replace the \insert primitive by a cheating macro.
+% Deeper inside, just make sure that the saved insertions are not spilled
+% out prematurely.
+%
+\def\startsavinginserts{%
+ \ifx \insert\ptexinsert
+ \let\insert\saveinsert
+ \else
+ \let\checkinserts\relax
+ \fi
+}
+
+% This \insert replacement works for both \insert\footins{foo} and
+% \insert\footins\bgroup foo\egroup, but it doesn't work for \insert27{foo}.
+%
+\def\saveinsert#1{%
+ \edef\next{\noexpand\savetobox \makeSAVEname#1}%
+ \afterassignment\next
+ % swallow the left brace
+ \let\temp =
+}
+\def\makeSAVEname#1{\makecsname{SAVE\expandafter\gobble\string#1}}
+\def\savetobox#1{\global\setbox#1 = \vbox\bgroup \unvbox#1}
+
+\def\checksaveins#1{\ifvoid#1\else \placesaveins#1\fi}
+
+\def\placesaveins#1{%
+ \ptexinsert \csname\expandafter\gobblesave\string#1\endcsname
+ {\box#1}%
+}
+
+% eat @SAVE -- beware, all of them have catcode \other:
+{
+ \def\dospecials{\do S\do A\do V\do E} \uncatcodespecials % ;-)
+ \gdef\gobblesave @SAVE{}
+}
+
+% initialization:
+\def\newsaveins #1{%
+ \edef\next{\noexpand\newsaveinsX \makeSAVEname#1}%
+ \next
+}
+\def\newsaveinsX #1{%
+ \csname newbox\endcsname #1%
+ \expandafter\def\expandafter\checkinserts\expandafter{\checkinserts
+ \checksaveins #1}%
+}
+
+% initialize:
+\let\checkinserts\empty
+\newsaveins\footins
+\newsaveins\margin
+
+
+% @image. We use the macros from epsf.tex to support this.
+% If epsf.tex is not installed and @image is used, we complain.
+%
+% Check for and read epsf.tex up front. If we read it only at @image
+% time, we might be inside a group, and then its definitions would get
+% undone and the next image would fail.
+\openin 1 = epsf.tex
+\ifeof 1 \else
+ % Do not bother showing banner with epsf.tex v2.7k (available in
+ % doc/epsf.tex and on ctan).
+ \def\epsfannounce{\toks0 = }%
+ \input epsf.tex
+\fi
+\closein 1
+%
+% We will only complain once about lack of epsf.tex.
+\newif\ifwarnednoepsf
+\newhelp\noepsfhelp{epsf.tex must be installed for images to
+ work. It is also included in the Texinfo distribution, or you can get
+ it from ftp://tug.org/tex/epsf.tex.}
+%
+\def\image#1{%
+ \ifx\epsfbox\undefined
+ \ifwarnednoepsf \else
+ \errhelp = \noepsfhelp
+ \errmessage{epsf.tex not found, images will be ignored}%
+ \global\warnednoepsftrue
+ \fi
+ \else
+ \imagexxx #1,,,,,\finish
+ \fi
+}
+%
+% Arguments to @image:
+% #1 is (mandatory) image filename; we tack on .eps extension.
+% #2 is (optional) width, #3 is (optional) height.
+% #4 is (ignored optional) html alt text.
+% #5 is (ignored optional) extension.
+% #6 is just the usual extra ignored arg for parsing this stuff.
+\newif\ifimagevmode
+\def\imagexxx#1,#2,#3,#4,#5,#6\finish{\begingroup
+ \catcode`\^^M = 5 % in case we're inside an example
+ \normalturnoffactive % allow _ et al. in names
+ % If the image is by itself, center it.
+ \ifvmode
+ \imagevmodetrue
+ \nobreak\medskip
+ % Usually we'll have text after the image which will insert
+ % \parskip glue, so insert it here too to equalize the space
+ % above and below.
+ \nobreak\vskip\parskip
+ \nobreak
+ \fi
+ %
+ % Leave vertical mode so that indentation from an enclosing
+ % environment such as @quotation is respected. On the other hand, if
+ % it's at the top level, we don't want the normal paragraph indentation.
+ \noindent
+ %
+ % Output the image.
+ \ifpdf
+ \dopdfimage{#1}{#2}{#3}%
+ \else
+ % \epsfbox itself resets \epsf?size at each figure.
+ \setbox0 = \hbox{\ignorespaces #2}\ifdim\wd0 > 0pt \epsfxsize=#2\relax \fi
+ \setbox0 = \hbox{\ignorespaces #3}\ifdim\wd0 > 0pt \epsfysize=#3\relax \fi
+ \epsfbox{#1.eps}%
+ \fi
+ %
+ \ifimagevmode \medskip \fi % space after the standalone image
+\endgroup}
+
+
+% @float FLOATTYPE,LABEL,LOC ... @end float for displayed figures, tables,
+% etc. We don't actually implement floating yet, we always include the
+% float "here". But it seemed the best name for the future.
+%
+\envparseargdef\float{\eatcommaspace\eatcommaspace\dofloat#1, , ,\finish}
+
+% There may be a space before second and/or third parameter; delete it.
+\def\eatcommaspace#1, {#1,}
+
+% #1 is the optional FLOATTYPE, the text label for this float, typically
+% "Figure", "Table", "Example", etc. Can't contain commas. If omitted,
+% this float will not be numbered and cannot be referred to.
+%
+% #2 is the optional xref label. Also must be present for the float to
+% be referable.
+%
+% #3 is the optional positioning argument; for now, it is ignored. It
+% will somehow specify the positions allowed to float to (here, top, bottom).
+%
+% We keep a separate counter for each FLOATTYPE, which we reset at each
+% chapter-level command.
+\let\resetallfloatnos=\empty
+%
+\def\dofloat#1,#2,#3,#4\finish{%
+ \let\thiscaption=\empty
+ \let\thisshortcaption=\empty
+ %
+ % don't lose footnotes inside @float.
+ %
+ % BEWARE: when the floats start float, we have to issue warning whenever an
+ % insert appears inside a float which could possibly float. --kasal, 26may04
+ %
+ \startsavinginserts
+ %
+ % We can't be used inside a paragraph.
+ \par
+ %
+ \vtop\bgroup
+ \def\floattype{#1}%
+ \def\floatlabel{#2}%
+ \def\floatloc{#3}% we do nothing with this yet.
+ %
+ \ifx\floattype\empty
+ \let\safefloattype=\empty
+ \else
+ {%
+ % the floattype might have accents or other special characters,
+ % but we need to use it in a control sequence name.
+ \indexnofonts
+ \turnoffactive
+ \xdef\safefloattype{\floattype}%
+ }%
+ \fi
+ %
+ % If label is given but no type, we handle that as the empty type.
+ \ifx\floatlabel\empty \else
+ % We want each FLOATTYPE to be numbered separately (Figure 1,
+ % Table 1, Figure 2, ...). (And if no label, no number.)
+ %
+ \expandafter\getfloatno\csname\safefloattype floatno\endcsname
+ \global\advance\floatno by 1
+ %
+ {%
+ % This magic value for \lastsection is output by \setref as the
+ % XREFLABEL-title value. \xrefX uses it to distinguish float
+ % labels (which have a completely different output format) from
+ % node and anchor labels. And \xrdef uses it to construct the
+ % lists of floats.
+ %
+ \edef\lastsection{\floatmagic=\safefloattype}%
+ \setref{\floatlabel}{Yfloat}%
+ }%
+ \fi
+ %
+ % start with \parskip glue, I guess.
+ \vskip\parskip
+ %
+ % Don't suppress indentation if a float happens to start a section.
+ \restorefirstparagraphindent
+}
+
+% we have these possibilities:
+% @float Foo,lbl & @caption{Cap}: Foo 1.1: Cap
+% @float Foo,lbl & no caption: Foo 1.1
+% @float Foo & @caption{Cap}: Foo: Cap
+% @float Foo & no caption: Foo
+% @float ,lbl & Caption{Cap}: 1.1: Cap
+% @float ,lbl & no caption: 1.1
+% @float & @caption{Cap}: Cap
+% @float & no caption:
+%
+\def\Efloat{%
+ \let\floatident = \empty
+ %
+ % In all cases, if we have a float type, it comes first.
+ \ifx\floattype\empty \else \def\floatident{\floattype}\fi
+ %
+ % If we have an xref label, the number comes next.
+ \ifx\floatlabel\empty \else
+ \ifx\floattype\empty \else % if also had float type, need tie first.
+ \appendtomacro\floatident{\tie}%
+ \fi
+ % the number.
+ \appendtomacro\floatident{\chaplevelprefix\the\floatno}%
+ \fi
+ %
+ % Start the printed caption with what we've constructed in
+ % \floatident, but keep it separate; we need \floatident again.
+ \let\captionline = \floatident
+ %
+ \ifx\thiscaption\empty \else
+ \ifx\floatident\empty \else
+ \appendtomacro\captionline{: }% had ident, so need a colon between
+ \fi
+ %
+ % caption text.
+ \appendtomacro\captionline{\scanexp\thiscaption}%
+ \fi
+ %
+ % If we have anything to print, print it, with space before.
+ % Eventually this needs to become an \insert.
+ \ifx\captionline\empty \else
+ \vskip.5\parskip
+ \captionline
+ %
+ % Space below caption.
+ \vskip\parskip
+ \fi
+ %
+ % If have an xref label, write the list of floats info. Do this
+ % after the caption, to avoid chance of it being a breakpoint.
+ \ifx\floatlabel\empty \else
+ % Write the text that goes in the lof to the aux file as
+ % \floatlabel-lof. Besides \floatident, we include the short
+ % caption if specified, else the full caption if specified, else nothing.
+ {%
+ \atdummies
+ %
+ % since we read the caption text in the macro world, where ^^M
+ % is turned into a normal character, we have to scan it back, so
+ % we don't write the literal three characters "^^M" into the aux file.
+ \scanexp{%
+ \xdef\noexpand\gtemp{%
+ \ifx\thisshortcaption\empty
+ \thiscaption
+ \else
+ \thisshortcaption
+ \fi
+ }%
+ }%
+ \immediate\write\auxfile{@xrdef{\floatlabel-lof}{\floatident
+ \ifx\gtemp\empty \else : \gtemp \fi}}%
+ }%
+ \fi
+ \egroup % end of \vtop
+ %
+ % place the captured inserts
+ %
+ % BEWARE: when the floats start floating, we have to issue warning
+ % whenever an insert appears inside a float which could possibly
+ % float. --kasal, 26may04
+ %
+ \checkinserts
+}
+
+% Append the tokens #2 to the definition of macro #1, not expanding either.
+%
+\def\appendtomacro#1#2{%
+ \expandafter\def\expandafter#1\expandafter{#1#2}%
+}
+
+% @caption, @shortcaption
+%
+\def\caption{\docaption\thiscaption}
+\def\shortcaption{\docaption\thisshortcaption}
+\def\docaption{\checkenv\float \bgroup\scanargctxt\defcaption}
+\def\defcaption#1#2{\egroup \def#1{#2}}
+
+% The parameter is the control sequence identifying the counter we are
+% going to use. Create it if it doesn't exist and assign it to \floatno.
+\def\getfloatno#1{%
+ \ifx#1\relax
+ % Haven't seen this figure type before.
+ \csname newcount\endcsname #1%
+ %
+ % Remember to reset this floatno at the next chap.
+ \expandafter\gdef\expandafter\resetallfloatnos
+ \expandafter{\resetallfloatnos #1=0 }%
+ \fi
+ \let\floatno#1%
+}
+
+% \setref calls this to get the XREFLABEL-snt value. We want an @xref
+% to the FLOATLABEL to expand to "Figure 3.1". We call \setref when we
+% first read the @float command.
+%
+\def\Yfloat{\floattype at tie \chaplevelprefix\the\floatno}%
+
+% Magic string used for the XREFLABEL-title value, so \xrefX can
+% distinguish floats from other xref types.
+\def\floatmagic{!!float!!}
+
+% #1 is the control sequence we are passed; we expand into a conditional
+% which is true if #1 represents a float ref. That is, the magic
+% \lastsection value which we \setref above.
+%
+\def\iffloat#1{\expandafter\doiffloat#1==\finish}
+%
+% #1 is (maybe) the \floatmagic string. If so, #2 will be the
+% (safe) float type for this float. We set \iffloattype to #2.
+%
+\def\doiffloat#1=#2=#3\finish{%
+ \def\temp{#1}%
+ \def\iffloattype{#2}%
+ \ifx\temp\floatmagic
+}
+
+% @listoffloats FLOATTYPE - print a list of floats like a table of contents.
+%
+\parseargdef\listoffloats{%
+ \def\floattype{#1}% floattype
+ {%
+ % the floattype might have accents or other special characters,
+ % but we need to use it in a control sequence name.
+ \indexnofonts
+ \turnoffactive
+ \xdef\safefloattype{\floattype}%
+ }%
+ %
+ % \xrdef saves the floats as a \do-list in \floatlistSAFEFLOATTYPE.
+ \expandafter\ifx\csname floatlist\safefloattype\endcsname \relax
+ \ifhavexrefs
+ % if the user said @listoffloats foo but never @float foo.
+ \message{\linenumber No `\safefloattype' floats to list.}%
+ \fi
+ \else
+ \begingroup
+ \leftskip=\tocindent % indent these entries like a toc
+ \let\do=\listoffloatsdo
+ \csname floatlist\safefloattype\endcsname
+ \endgroup
+ \fi
+}
+
+% This is called on each entry in a list of floats. We're passed the
+% xref label, in the form LABEL-title, which is how we save it in the
+% aux file. We strip off the -title and look up \XRLABEL-lof, which
+% has the text we're supposed to typeset here.
+%
+% Figures without xref labels will not be included in the list (since
+% they won't appear in the aux file).
+%
+\def\listoffloatsdo#1{\listoffloatsdoentry#1\finish}
+\def\listoffloatsdoentry#1-title\finish{{%
+ % Can't fully expand XR#1-lof because it can contain anything. Just
+ % pass the control sequence. On the other hand, XR#1-pg is just the
+ % page number, and we want to fully expand that so we can get a link
+ % in pdf output.
+ \toksA = \expandafter{\csname XR#1-lof\endcsname}%
+ %
+ % use the same \entry macro we use to generate the TOC and index.
+ \edef\writeentry{\noexpand\entry{\the\toksA}{\csname XR#1-pg\endcsname}}%
+ \writeentry
+}}
+
+
+\message{localization,}
+
+% For single-language documents, @documentlanguage is usually given very
+% early, just after @documentencoding. Single argument is the language
+% (de) or locale (de_DE) abbreviation.
+%
+{
+ \catcode`\_ = \active
+ \globaldefs=1
+\parseargdef\documentlanguage{\begingroup
+ \let_=\normalunderscore % normal _ character for filenames
+ \tex % read txi-??.tex file in plain TeX.
+ % Read the file by the name they passed if it exists.
+ \openin 1 txi-#1.tex
+ \ifeof 1
+ \documentlanguagetrywithoutunderscore{#1_\finish}%
+ \else
+ \globaldefs = 1 % everything in the txi-LL files needs to persist
+ \input txi-#1.tex
+ \fi
+ \closein 1
+ \endgroup % end raw TeX
+\endgroup}
+%
+% If they passed de_DE, and txi-de_DE.tex doesn't exist,
+% try txi-de.tex.
+%
+\gdef\documentlanguagetrywithoutunderscore#1_#2\finish{%
+ \openin 1 txi-#1.tex
+ \ifeof 1
+ \errhelp = \nolanghelp
+ \errmessage{Cannot read language file txi-#1.tex}%
+ \else
+ \globaldefs = 1 % everything in the txi-LL files needs to persist
+ \input txi-#1.tex
+ \fi
+ \closein 1
+}
+}% end of special _ catcode
+%
+\newhelp\nolanghelp{The given language definition file cannot be found or
+is empty. Maybe you need to install it? Putting it in the current
+directory should work if nowhere else does.}
+
+% This macro is called from txi-??.tex files; the first argument is the
+% \language name to set (without the "\lang@" prefix), the second and
+% third args are \{left,right}hyphenmin.
+%
+% The language names to pass are determined when the format is built.
+% See the etex.log file created at that time, e.g.,
+% /usr/local/texlive/2008/texmf-var/web2c/pdftex/etex.log.
+%
+% With TeX Live 2008, etex now includes hyphenation patterns for all
+% available languages. This means we can support hyphenation in
+% Texinfo, at least to some extent. (This still doesn't solve the
+% accented characters problem.)
+%
+\catcode`@=11
+\def\txisetlanguage#1#2#3{%
+ % do not set the language if the name is undefined in the current TeX.
+ \expandafter\ifx\csname lang@#1\endcsname \relax
+ \message{no patterns for #1}%
+ \else
+ \global\language = \csname lang@#1\endcsname
+ \fi
+ % but there is no harm in adjusting the hyphenmin values regardless.
+ \global\lefthyphenmin = #2\relax
+ \global\righthyphenmin = #3\relax
+}
+
+% Helpers for encodings.
+% Set the catcode of characters 128 through 255 to the specified number.
+%
+\def\setnonasciicharscatcode#1{%
+ \count255=128
+ \loop\ifnum\count255<256
+ \global\catcode\count255=#1\relax
+ \advance\count255 by 1
+ \repeat
+}
+
+\def\setnonasciicharscatcodenonglobal#1{%
+ \count255=128
+ \loop\ifnum\count255<256
+ \catcode\count255=#1\relax
+ \advance\count255 by 1
+ \repeat
+}
+
+% @documentencoding sets the definition of non-ASCII characters
+% according to the specified encoding.
+%
+\parseargdef\documentencoding{%
+ % Encoding being declared for the document.
+ \def\declaredencoding{\csname #1.enc\endcsname}%
+ %
+ % Supported encodings: names converted to tokens in order to be able
+ % to compare them with \ifx.
+ \def\ascii{\csname US-ASCII.enc\endcsname}%
+ \def\latnine{\csname ISO-8859-15.enc\endcsname}%
+ \def\latone{\csname ISO-8859-1.enc\endcsname}%
+ \def\lattwo{\csname ISO-8859-2.enc\endcsname}%
+ \def\utfeight{\csname UTF-8.enc\endcsname}%
+ %
+ \ifx \declaredencoding \ascii
+ \asciichardefs
+ %
+ \else \ifx \declaredencoding \lattwo
+ \setnonasciicharscatcode\active
+ \lattwochardefs
+ %
+ \else \ifx \declaredencoding \latone
+ \setnonasciicharscatcode\active
+ \latonechardefs
+ %
+ \else \ifx \declaredencoding \latnine
+ \setnonasciicharscatcode\active
+ \latninechardefs
+ %
+ \else \ifx \declaredencoding \utfeight
+ \setnonasciicharscatcode\active
+ \utfeightchardefs
+ %
+ \else
+ \message{Unknown document encoding #1, ignoring.}%
+ %
+ \fi % utfeight
+ \fi % latnine
+ \fi % latone
+ \fi % lattwo
+ \fi % ascii
+}
+
+% A message to be logged when using a character that isn't available
+% the default font encoding (OT1).
+%
+\def\missingcharmsg#1{\message{Character missing in OT1 encoding: #1.}}
+
+% Take account of \c (plain) vs. \, (Texinfo) difference.
+\def\cedilla#1{\ifx\c\ptexc\c{#1}\else\,{#1}\fi}
+
+% First, make active non-ASCII characters in order for them to be
+% correctly categorized when TeX reads the replacement text of
+% macros containing the character definitions.
+\setnonasciicharscatcode\active
+%
+% Latin1 (ISO-8859-1) character definitions.
+\def\latonechardefs{%
+ \gdef^^a0{~}
+ \gdef^^a1{\exclamdown}
+ \gdef^^a2{\missingcharmsg{CENT SIGN}}
+ \gdef^^a3{{\pounds}}
+ \gdef^^a4{\missingcharmsg{CURRENCY SIGN}}
+ \gdef^^a5{\missingcharmsg{YEN SIGN}}
+ \gdef^^a6{\missingcharmsg{BROKEN BAR}}
+ \gdef^^a7{\S}
+ \gdef^^a8{\"{}}
+ \gdef^^a9{\copyright}
+ \gdef^^aa{\ordf}
+ \gdef^^ab{\guillemetleft}
+ \gdef^^ac{$\lnot$}
+ \gdef^^ad{\-}
+ \gdef^^ae{\registeredsymbol}
+ \gdef^^af{\={}}
+ %
+ \gdef^^b0{\textdegree}
+ \gdef^^b1{$\pm$}
+ \gdef^^b2{$^2$}
+ \gdef^^b3{$^3$}
+ \gdef^^b4{\'{}}
+ \gdef^^b5{$\mu$}
+ \gdef^^b6{\P}
+ %
+ \gdef^^b7{$^.$}
+ \gdef^^b8{\cedilla\ }
+ \gdef^^b9{$^1$}
+ \gdef^^ba{\ordm}
+ %
+ \gdef^^bb{\guilletright}
+ \gdef^^bc{$1\over4$}
+ \gdef^^bd{$1\over2$}
+ \gdef^^be{$3\over4$}
+ \gdef^^bf{\questiondown}
+ %
+ \gdef^^c0{\`A}
+ \gdef^^c1{\'A}
+ \gdef^^c2{\^A}
+ \gdef^^c3{\~A}
+ \gdef^^c4{\"A}
+ \gdef^^c5{\ringaccent A}
+ \gdef^^c6{\AE}
+ \gdef^^c7{\cedilla C}
+ \gdef^^c8{\`E}
+ \gdef^^c9{\'E}
+ \gdef^^ca{\^E}
+ \gdef^^cb{\"E}
+ \gdef^^cc{\`I}
+ \gdef^^cd{\'I}
+ \gdef^^ce{\^I}
+ \gdef^^cf{\"I}
+ %
+ \gdef^^d0{\DH}
+ \gdef^^d1{\~N}
+ \gdef^^d2{\`O}
+ \gdef^^d3{\'O}
+ \gdef^^d4{\^O}
+ \gdef^^d5{\~O}
+ \gdef^^d6{\"O}
+ \gdef^^d7{$\times$}
+ \gdef^^d8{\O}
+ \gdef^^d9{\`U}
+ \gdef^^da{\'U}
+ \gdef^^db{\^U}
+ \gdef^^dc{\"U}
+ \gdef^^dd{\'Y}
+ \gdef^^de{\TH}
+ \gdef^^df{\ss}
+ %
+ \gdef^^e0{\`a}
+ \gdef^^e1{\'a}
+ \gdef^^e2{\^a}
+ \gdef^^e3{\~a}
+ \gdef^^e4{\"a}
+ \gdef^^e5{\ringaccent a}
+ \gdef^^e6{\ae}
+ \gdef^^e7{\cedilla c}
+ \gdef^^e8{\`e}
+ \gdef^^e9{\'e}
+ \gdef^^ea{\^e}
+ \gdef^^eb{\"e}
+ \gdef^^ec{\`{\dotless i}}
+ \gdef^^ed{\'{\dotless i}}
+ \gdef^^ee{\^{\dotless i}}
+ \gdef^^ef{\"{\dotless i}}
+ %
+ \gdef^^f0{\dh}
+ \gdef^^f1{\~n}
+ \gdef^^f2{\`o}
+ \gdef^^f3{\'o}
+ \gdef^^f4{\^o}
+ \gdef^^f5{\~o}
+ \gdef^^f6{\"o}
+ \gdef^^f7{$\div$}
+ \gdef^^f8{\o}
+ \gdef^^f9{\`u}
+ \gdef^^fa{\'u}
+ \gdef^^fb{\^u}
+ \gdef^^fc{\"u}
+ \gdef^^fd{\'y}
+ \gdef^^fe{\th}
+ \gdef^^ff{\"y}
+}
+
+% Latin9 (ISO-8859-15) encoding character definitions.
+\def\latninechardefs{%
+ % Encoding is almost identical to Latin1.
+ \latonechardefs
+ %
+ \gdef^^a4{\euro}
+ \gdef^^a6{\v S}
+ \gdef^^a8{\v s}
+ \gdef^^b4{\v Z}
+ \gdef^^b8{\v z}
+ \gdef^^bc{\OE}
+ \gdef^^bd{\oe}
+ \gdef^^be{\"Y}
+}
+
+% Latin2 (ISO-8859-2) character definitions.
+\def\lattwochardefs{%
+ \gdef^^a0{~}
+ \gdef^^a1{\ogonek{A}}
+ \gdef^^a2{\u{}}
+ \gdef^^a3{\L}
+ \gdef^^a4{\missingcharmsg{CURRENCY SIGN}}
+ \gdef^^a5{\v L}
+ \gdef^^a6{\'S}
+ \gdef^^a7{\S}
+ \gdef^^a8{\"{}}
+ \gdef^^a9{\v S}
+ \gdef^^aa{\cedilla S}
+ \gdef^^ab{\v T}
+ \gdef^^ac{\'Z}
+ \gdef^^ad{\-}
+ \gdef^^ae{\v Z}
+ \gdef^^af{\dotaccent Z}
+ %
+ \gdef^^b0{\textdegree}
+ \gdef^^b1{\ogonek{a}}
+ \gdef^^b2{\ogonek{ }}
+ \gdef^^b3{\l}
+ \gdef^^b4{\'{}}
+ \gdef^^b5{\v l}
+ \gdef^^b6{\'s}
+ \gdef^^b7{\v{}}
+ \gdef^^b8{\cedilla\ }
+ \gdef^^b9{\v s}
+ \gdef^^ba{\cedilla s}
+ \gdef^^bb{\v t}
+ \gdef^^bc{\'z}
+ \gdef^^bd{\H{}}
+ \gdef^^be{\v z}
+ \gdef^^bf{\dotaccent z}
+ %
+ \gdef^^c0{\'R}
+ \gdef^^c1{\'A}
+ \gdef^^c2{\^A}
+ \gdef^^c3{\u A}
+ \gdef^^c4{\"A}
+ \gdef^^c5{\'L}
+ \gdef^^c6{\'C}
+ \gdef^^c7{\cedilla C}
+ \gdef^^c8{\v C}
+ \gdef^^c9{\'E}
+ \gdef^^ca{\ogonek{E}}
+ \gdef^^cb{\"E}
+ \gdef^^cc{\v E}
+ \gdef^^cd{\'I}
+ \gdef^^ce{\^I}
+ \gdef^^cf{\v D}
+ %
+ \gdef^^d0{\DH}
+ \gdef^^d1{\'N}
+ \gdef^^d2{\v N}
+ \gdef^^d3{\'O}
+ \gdef^^d4{\^O}
+ \gdef^^d5{\H O}
+ \gdef^^d6{\"O}
+ \gdef^^d7{$\times$}
+ \gdef^^d8{\v R}
+ \gdef^^d9{\ringaccent U}
+ \gdef^^da{\'U}
+ \gdef^^db{\H U}
+ \gdef^^dc{\"U}
+ \gdef^^dd{\'Y}
+ \gdef^^de{\cedilla T}
+ \gdef^^df{\ss}
+ %
+ \gdef^^e0{\'r}
+ \gdef^^e1{\'a}
+ \gdef^^e2{\^a}
+ \gdef^^e3{\u a}
+ \gdef^^e4{\"a}
+ \gdef^^e5{\'l}
+ \gdef^^e6{\'c}
+ \gdef^^e7{\cedilla c}
+ \gdef^^e8{\v c}
+ \gdef^^e9{\'e}
+ \gdef^^ea{\ogonek{e}}
+ \gdef^^eb{\"e}
+ \gdef^^ec{\v e}
+ \gdef^^ed{\'\i}
+ \gdef^^ee{\^\i}
+ \gdef^^ef{\v d}
+ %
+ \gdef^^f0{\dh}
+ \gdef^^f1{\'n}
+ \gdef^^f2{\v n}
+ \gdef^^f3{\'o}
+ \gdef^^f4{\^o}
+ \gdef^^f5{\H o}
+ \gdef^^f6{\"o}
+ \gdef^^f7{$\div$}
+ \gdef^^f8{\v r}
+ \gdef^^f9{\ringaccent u}
+ \gdef^^fa{\'u}
+ \gdef^^fb{\H u}
+ \gdef^^fc{\"u}
+ \gdef^^fd{\'y}
+ \gdef^^fe{\cedilla t}
+ \gdef^^ff{\dotaccent{}}
+}
+
+% UTF-8 character definitions.
+%
+% This code to support UTF-8 is based on LaTeX's utf8.def, with some
+% changes for Texinfo conventions. It is included here under the GPL by
+% permission from Frank Mittelbach and the LaTeX team.
+%
+\newcount\countUTFx
+\newcount\countUTFy
+\newcount\countUTFz
+
+\gdef\UTFviiiTwoOctets#1#2{\expandafter
+ \UTFviiiDefined\csname u8:#1\string #2\endcsname}
+%
+\gdef\UTFviiiThreeOctets#1#2#3{\expandafter
+ \UTFviiiDefined\csname u8:#1\string #2\string #3\endcsname}
+%
+\gdef\UTFviiiFourOctets#1#2#3#4{\expandafter
+ \UTFviiiDefined\csname u8:#1\string #2\string #3\string #4\endcsname}
+
+\gdef\UTFviiiDefined#1{%
+ \ifx #1\relax
+ \message{\linenumber Unicode char \string #1 not defined for Texinfo}%
+ \else
+ \expandafter #1%
+ \fi
+}
+
+\begingroup
+ \catcode`\~13
+ \catcode`\"12
+
+ \def\UTFviiiLoop{%
+ \global\catcode\countUTFx\active
+ \uccode`\~\countUTFx
+ \uppercase\expandafter{\UTFviiiTmp}%
+ \advance\countUTFx by 1
+ \ifnum\countUTFx < \countUTFy
+ \expandafter\UTFviiiLoop
+ \fi}
+
+ \countUTFx = "C2
+ \countUTFy = "E0
+ \def\UTFviiiTmp{%
+ \xdef~{\noexpand\UTFviiiTwoOctets\string~}}
+ \UTFviiiLoop
+
+ \countUTFx = "E0
+ \countUTFy = "F0
+ \def\UTFviiiTmp{%
+ \xdef~{\noexpand\UTFviiiThreeOctets\string~}}
+ \UTFviiiLoop
+
+ \countUTFx = "F0
+ \countUTFy = "F4
+ \def\UTFviiiTmp{%
+ \xdef~{\noexpand\UTFviiiFourOctets\string~}}
+ \UTFviiiLoop
+\endgroup
+
+\begingroup
+ \catcode`\"=12
+ \catcode`\<=12
+ \catcode`\.=12
+ \catcode`\,=12
+ \catcode`\;=12
+ \catcode`\!=12
+ \catcode`\~=13
+
+ \gdef\DeclareUnicodeCharacter#1#2{%
+ \countUTFz = "#1\relax
+ \wlog{\space\space defining Unicode char U+#1 (decimal \the\countUTFz)}%
+ \begingroup
+ \parseXMLCharref
+ \def\UTFviiiTwoOctets##1##2{%
+ \csname u8:##1\string ##2\endcsname}%
+ \def\UTFviiiThreeOctets##1##2##3{%
+ \csname u8:##1\string ##2\string ##3\endcsname}%
+ \def\UTFviiiFourOctets##1##2##3##4{%
+ \csname u8:##1\string ##2\string ##3\string ##4\endcsname}%
+ \expandafter\expandafter\expandafter\expandafter
+ \expandafter\expandafter\expandafter
+ \gdef\UTFviiiTmp{#2}%
+ \endgroup}
+
+ \gdef\parseXMLCharref{%
+ \ifnum\countUTFz < "A0\relax
+ \errhelp = \EMsimple
+ \errmessage{Cannot define Unicode char value < 00A0}%
+ \else\ifnum\countUTFz < "800\relax
+ \parseUTFviiiA,%
+ \parseUTFviiiB C\UTFviiiTwoOctets.,%
+ \else\ifnum\countUTFz < "10000\relax
+ \parseUTFviiiA;%
+ \parseUTFviiiA,%
+ \parseUTFviiiB E\UTFviiiThreeOctets.{,;}%
+ \else
+ \parseUTFviiiA;%
+ \parseUTFviiiA,%
+ \parseUTFviiiA!%
+ \parseUTFviiiB F\UTFviiiFourOctets.{!,;}%
+ \fi\fi\fi
+ }
+
+ \gdef\parseUTFviiiA#1{%
+ \countUTFx = \countUTFz
+ \divide\countUTFz by 64
+ \countUTFy = \countUTFz
+ \multiply\countUTFz by 64
+ \advance\countUTFx by -\countUTFz
+ \advance\countUTFx by 128
+ \uccode `#1\countUTFx
+ \countUTFz = \countUTFy}
+
+ \gdef\parseUTFviiiB#1#2#3#4{%
+ \advance\countUTFz by "#10\relax
+ \uccode `#3\countUTFz
+ \uppercase{\gdef\UTFviiiTmp{#2#3#4}}}
+\endgroup
+
+\def\utfeightchardefs{%
+ \DeclareUnicodeCharacter{00A0}{\tie}
+ \DeclareUnicodeCharacter{00A1}{\exclamdown}
+ \DeclareUnicodeCharacter{00A3}{\pounds}
+ \DeclareUnicodeCharacter{00A8}{\"{ }}
+ \DeclareUnicodeCharacter{00A9}{\copyright}
+ \DeclareUnicodeCharacter{00AA}{\ordf}
+ \DeclareUnicodeCharacter{00AB}{\guillemetleft}
+ \DeclareUnicodeCharacter{00AD}{\-}
+ \DeclareUnicodeCharacter{00AE}{\registeredsymbol}
+ \DeclareUnicodeCharacter{00AF}{\={ }}
+
+ \DeclareUnicodeCharacter{00B0}{\ringaccent{ }}
+ \DeclareUnicodeCharacter{00B4}{\'{ }}
+ \DeclareUnicodeCharacter{00B8}{\cedilla{ }}
+ \DeclareUnicodeCharacter{00BA}{\ordm}
+ \DeclareUnicodeCharacter{00BB}{\guillemetright}
+ \DeclareUnicodeCharacter{00BF}{\questiondown}
+
+ \DeclareUnicodeCharacter{00C0}{\`A}
+ \DeclareUnicodeCharacter{00C1}{\'A}
+ \DeclareUnicodeCharacter{00C2}{\^A}
+ \DeclareUnicodeCharacter{00C3}{\~A}
+ \DeclareUnicodeCharacter{00C4}{\"A}
+ \DeclareUnicodeCharacter{00C5}{\AA}
+ \DeclareUnicodeCharacter{00C6}{\AE}
+ \DeclareUnicodeCharacter{00C7}{\cedilla{C}}
+ \DeclareUnicodeCharacter{00C8}{\`E}
+ \DeclareUnicodeCharacter{00C9}{\'E}
+ \DeclareUnicodeCharacter{00CA}{\^E}
+ \DeclareUnicodeCharacter{00CB}{\"E}
+ \DeclareUnicodeCharacter{00CC}{\`I}
+ \DeclareUnicodeCharacter{00CD}{\'I}
+ \DeclareUnicodeCharacter{00CE}{\^I}
+ \DeclareUnicodeCharacter{00CF}{\"I}
+
+ \DeclareUnicodeCharacter{00D0}{\DH}
+ \DeclareUnicodeCharacter{00D1}{\~N}
+ \DeclareUnicodeCharacter{00D2}{\`O}
+ \DeclareUnicodeCharacter{00D3}{\'O}
+ \DeclareUnicodeCharacter{00D4}{\^O}
+ \DeclareUnicodeCharacter{00D5}{\~O}
+ \DeclareUnicodeCharacter{00D6}{\"O}
+ \DeclareUnicodeCharacter{00D8}{\O}
+ \DeclareUnicodeCharacter{00D9}{\`U}
+ \DeclareUnicodeCharacter{00DA}{\'U}
+ \DeclareUnicodeCharacter{00DB}{\^U}
+ \DeclareUnicodeCharacter{00DC}{\"U}
+ \DeclareUnicodeCharacter{00DD}{\'Y}
+ \DeclareUnicodeCharacter{00DE}{\TH}
+ \DeclareUnicodeCharacter{00DF}{\ss}
+
+ \DeclareUnicodeCharacter{00E0}{\`a}
+ \DeclareUnicodeCharacter{00E1}{\'a}
+ \DeclareUnicodeCharacter{00E2}{\^a}
+ \DeclareUnicodeCharacter{00E3}{\~a}
+ \DeclareUnicodeCharacter{00E4}{\"a}
+ \DeclareUnicodeCharacter{00E5}{\aa}
+ \DeclareUnicodeCharacter{00E6}{\ae}
+ \DeclareUnicodeCharacter{00E7}{\cedilla{c}}
+ \DeclareUnicodeCharacter{00E8}{\`e}
+ \DeclareUnicodeCharacter{00E9}{\'e}
+ \DeclareUnicodeCharacter{00EA}{\^e}
+ \DeclareUnicodeCharacter{00EB}{\"e}
+ \DeclareUnicodeCharacter{00EC}{\`{\dotless{i}}}
+ \DeclareUnicodeCharacter{00ED}{\'{\dotless{i}}}
+ \DeclareUnicodeCharacter{00EE}{\^{\dotless{i}}}
+ \DeclareUnicodeCharacter{00EF}{\"{\dotless{i}}}
+
+ \DeclareUnicodeCharacter{00F0}{\dh}
+ \DeclareUnicodeCharacter{00F1}{\~n}
+ \DeclareUnicodeCharacter{00F2}{\`o}
+ \DeclareUnicodeCharacter{00F3}{\'o}
+ \DeclareUnicodeCharacter{00F4}{\^o}
+ \DeclareUnicodeCharacter{00F5}{\~o}
+ \DeclareUnicodeCharacter{00F6}{\"o}
+ \DeclareUnicodeCharacter{00F8}{\o}
+ \DeclareUnicodeCharacter{00F9}{\`u}
+ \DeclareUnicodeCharacter{00FA}{\'u}
+ \DeclareUnicodeCharacter{00FB}{\^u}
+ \DeclareUnicodeCharacter{00FC}{\"u}
+ \DeclareUnicodeCharacter{00FD}{\'y}
+ \DeclareUnicodeCharacter{00FE}{\th}
+ \DeclareUnicodeCharacter{00FF}{\"y}
+
+ \DeclareUnicodeCharacter{0100}{\=A}
+ \DeclareUnicodeCharacter{0101}{\=a}
+ \DeclareUnicodeCharacter{0102}{\u{A}}
+ \DeclareUnicodeCharacter{0103}{\u{a}}
+ \DeclareUnicodeCharacter{0104}{\ogonek{A}}
+ \DeclareUnicodeCharacter{0105}{\ogonek{a}}
+ \DeclareUnicodeCharacter{0106}{\'C}
+ \DeclareUnicodeCharacter{0107}{\'c}
+ \DeclareUnicodeCharacter{0108}{\^C}
+ \DeclareUnicodeCharacter{0109}{\^c}
+ \DeclareUnicodeCharacter{0118}{\ogonek{E}}
+ \DeclareUnicodeCharacter{0119}{\ogonek{e}}
+ \DeclareUnicodeCharacter{010A}{\dotaccent{C}}
+ \DeclareUnicodeCharacter{010B}{\dotaccent{c}}
+ \DeclareUnicodeCharacter{010C}{\v{C}}
+ \DeclareUnicodeCharacter{010D}{\v{c}}
+ \DeclareUnicodeCharacter{010E}{\v{D}}
+
+ \DeclareUnicodeCharacter{0112}{\=E}
+ \DeclareUnicodeCharacter{0113}{\=e}
+ \DeclareUnicodeCharacter{0114}{\u{E}}
+ \DeclareUnicodeCharacter{0115}{\u{e}}
+ \DeclareUnicodeCharacter{0116}{\dotaccent{E}}
+ \DeclareUnicodeCharacter{0117}{\dotaccent{e}}
+ \DeclareUnicodeCharacter{011A}{\v{E}}
+ \DeclareUnicodeCharacter{011B}{\v{e}}
+ \DeclareUnicodeCharacter{011C}{\^G}
+ \DeclareUnicodeCharacter{011D}{\^g}
+ \DeclareUnicodeCharacter{011E}{\u{G}}
+ \DeclareUnicodeCharacter{011F}{\u{g}}
+
+ \DeclareUnicodeCharacter{0120}{\dotaccent{G}}
+ \DeclareUnicodeCharacter{0121}{\dotaccent{g}}
+ \DeclareUnicodeCharacter{0124}{\^H}
+ \DeclareUnicodeCharacter{0125}{\^h}
+ \DeclareUnicodeCharacter{0128}{\~I}
+ \DeclareUnicodeCharacter{0129}{\~{\dotless{i}}}
+ \DeclareUnicodeCharacter{012A}{\=I}
+ \DeclareUnicodeCharacter{012B}{\={\dotless{i}}}
+ \DeclareUnicodeCharacter{012C}{\u{I}}
+ \DeclareUnicodeCharacter{012D}{\u{\dotless{i}}}
+
+ \DeclareUnicodeCharacter{0130}{\dotaccent{I}}
+ \DeclareUnicodeCharacter{0131}{\dotless{i}}
+ \DeclareUnicodeCharacter{0132}{IJ}
+ \DeclareUnicodeCharacter{0133}{ij}
+ \DeclareUnicodeCharacter{0134}{\^J}
+ \DeclareUnicodeCharacter{0135}{\^{\dotless{j}}}
+ \DeclareUnicodeCharacter{0139}{\'L}
+ \DeclareUnicodeCharacter{013A}{\'l}
+
+ \DeclareUnicodeCharacter{0141}{\L}
+ \DeclareUnicodeCharacter{0142}{\l}
+ \DeclareUnicodeCharacter{0143}{\'N}
+ \DeclareUnicodeCharacter{0144}{\'n}
+ \DeclareUnicodeCharacter{0147}{\v{N}}
+ \DeclareUnicodeCharacter{0148}{\v{n}}
+ \DeclareUnicodeCharacter{014C}{\=O}
+ \DeclareUnicodeCharacter{014D}{\=o}
+ \DeclareUnicodeCharacter{014E}{\u{O}}
+ \DeclareUnicodeCharacter{014F}{\u{o}}
+
+ \DeclareUnicodeCharacter{0150}{\H{O}}
+ \DeclareUnicodeCharacter{0151}{\H{o}}
+ \DeclareUnicodeCharacter{0152}{\OE}
+ \DeclareUnicodeCharacter{0153}{\oe}
+ \DeclareUnicodeCharacter{0154}{\'R}
+ \DeclareUnicodeCharacter{0155}{\'r}
+ \DeclareUnicodeCharacter{0158}{\v{R}}
+ \DeclareUnicodeCharacter{0159}{\v{r}}
+ \DeclareUnicodeCharacter{015A}{\'S}
+ \DeclareUnicodeCharacter{015B}{\'s}
+ \DeclareUnicodeCharacter{015C}{\^S}
+ \DeclareUnicodeCharacter{015D}{\^s}
+ \DeclareUnicodeCharacter{015E}{\cedilla{S}}
+ \DeclareUnicodeCharacter{015F}{\cedilla{s}}
+
+ \DeclareUnicodeCharacter{0160}{\v{S}}
+ \DeclareUnicodeCharacter{0161}{\v{s}}
+ \DeclareUnicodeCharacter{0162}{\cedilla{t}}
+ \DeclareUnicodeCharacter{0163}{\cedilla{T}}
+ \DeclareUnicodeCharacter{0164}{\v{T}}
+
+ \DeclareUnicodeCharacter{0168}{\~U}
+ \DeclareUnicodeCharacter{0169}{\~u}
+ \DeclareUnicodeCharacter{016A}{\=U}
+ \DeclareUnicodeCharacter{016B}{\=u}
+ \DeclareUnicodeCharacter{016C}{\u{U}}
+ \DeclareUnicodeCharacter{016D}{\u{u}}
+ \DeclareUnicodeCharacter{016E}{\ringaccent{U}}
+ \DeclareUnicodeCharacter{016F}{\ringaccent{u}}
+
+ \DeclareUnicodeCharacter{0170}{\H{U}}
+ \DeclareUnicodeCharacter{0171}{\H{u}}
+ \DeclareUnicodeCharacter{0174}{\^W}
+ \DeclareUnicodeCharacter{0175}{\^w}
+ \DeclareUnicodeCharacter{0176}{\^Y}
+ \DeclareUnicodeCharacter{0177}{\^y}
+ \DeclareUnicodeCharacter{0178}{\"Y}
+ \DeclareUnicodeCharacter{0179}{\'Z}
+ \DeclareUnicodeCharacter{017A}{\'z}
+ \DeclareUnicodeCharacter{017B}{\dotaccent{Z}}
+ \DeclareUnicodeCharacter{017C}{\dotaccent{z}}
+ \DeclareUnicodeCharacter{017D}{\v{Z}}
+ \DeclareUnicodeCharacter{017E}{\v{z}}
+
+ \DeclareUnicodeCharacter{01C4}{D\v{Z}}
+ \DeclareUnicodeCharacter{01C5}{D\v{z}}
+ \DeclareUnicodeCharacter{01C6}{d\v{z}}
+ \DeclareUnicodeCharacter{01C7}{LJ}
+ \DeclareUnicodeCharacter{01C8}{Lj}
+ \DeclareUnicodeCharacter{01C9}{lj}
+ \DeclareUnicodeCharacter{01CA}{NJ}
+ \DeclareUnicodeCharacter{01CB}{Nj}
+ \DeclareUnicodeCharacter{01CC}{nj}
+ \DeclareUnicodeCharacter{01CD}{\v{A}}
+ \DeclareUnicodeCharacter{01CE}{\v{a}}
+ \DeclareUnicodeCharacter{01CF}{\v{I}}
+
+ \DeclareUnicodeCharacter{01D0}{\v{\dotless{i}}}
+ \DeclareUnicodeCharacter{01D1}{\v{O}}
+ \DeclareUnicodeCharacter{01D2}{\v{o}}
+ \DeclareUnicodeCharacter{01D3}{\v{U}}
+ \DeclareUnicodeCharacter{01D4}{\v{u}}
+
+ \DeclareUnicodeCharacter{01E2}{\={\AE}}
+ \DeclareUnicodeCharacter{01E3}{\={\ae}}
+ \DeclareUnicodeCharacter{01E6}{\v{G}}
+ \DeclareUnicodeCharacter{01E7}{\v{g}}
+ \DeclareUnicodeCharacter{01E8}{\v{K}}
+ \DeclareUnicodeCharacter{01E9}{\v{k}}
+
+ \DeclareUnicodeCharacter{01F0}{\v{\dotless{j}}}
+ \DeclareUnicodeCharacter{01F1}{DZ}
+ \DeclareUnicodeCharacter{01F2}{Dz}
+ \DeclareUnicodeCharacter{01F3}{dz}
+ \DeclareUnicodeCharacter{01F4}{\'G}
+ \DeclareUnicodeCharacter{01F5}{\'g}
+ \DeclareUnicodeCharacter{01F8}{\`N}
+ \DeclareUnicodeCharacter{01F9}{\`n}
+ \DeclareUnicodeCharacter{01FC}{\'{\AE}}
+ \DeclareUnicodeCharacter{01FD}{\'{\ae}}
+ \DeclareUnicodeCharacter{01FE}{\'{\O}}
+ \DeclareUnicodeCharacter{01FF}{\'{\o}}
+
+ \DeclareUnicodeCharacter{021E}{\v{H}}
+ \DeclareUnicodeCharacter{021F}{\v{h}}
+
+ \DeclareUnicodeCharacter{0226}{\dotaccent{A}}
+ \DeclareUnicodeCharacter{0227}{\dotaccent{a}}
+ \DeclareUnicodeCharacter{0228}{\cedilla{E}}
+ \DeclareUnicodeCharacter{0229}{\cedilla{e}}
+ \DeclareUnicodeCharacter{022E}{\dotaccent{O}}
+ \DeclareUnicodeCharacter{022F}{\dotaccent{o}}
+
+ \DeclareUnicodeCharacter{0232}{\=Y}
+ \DeclareUnicodeCharacter{0233}{\=y}
+ \DeclareUnicodeCharacter{0237}{\dotless{j}}
+
+ \DeclareUnicodeCharacter{02DB}{\ogonek{ }}
+
+ \DeclareUnicodeCharacter{1E02}{\dotaccent{B}}
+ \DeclareUnicodeCharacter{1E03}{\dotaccent{b}}
+ \DeclareUnicodeCharacter{1E04}{\udotaccent{B}}
+ \DeclareUnicodeCharacter{1E05}{\udotaccent{b}}
+ \DeclareUnicodeCharacter{1E06}{\ubaraccent{B}}
+ \DeclareUnicodeCharacter{1E07}{\ubaraccent{b}}
+ \DeclareUnicodeCharacter{1E0A}{\dotaccent{D}}
+ \DeclareUnicodeCharacter{1E0B}{\dotaccent{d}}
+ \DeclareUnicodeCharacter{1E0C}{\udotaccent{D}}
+ \DeclareUnicodeCharacter{1E0D}{\udotaccent{d}}
+ \DeclareUnicodeCharacter{1E0E}{\ubaraccent{D}}
+ \DeclareUnicodeCharacter{1E0F}{\ubaraccent{d}}
+
+ \DeclareUnicodeCharacter{1E1E}{\dotaccent{F}}
+ \DeclareUnicodeCharacter{1E1F}{\dotaccent{f}}
+
+ \DeclareUnicodeCharacter{1E20}{\=G}
+ \DeclareUnicodeCharacter{1E21}{\=g}
+ \DeclareUnicodeCharacter{1E22}{\dotaccent{H}}
+ \DeclareUnicodeCharacter{1E23}{\dotaccent{h}}
+ \DeclareUnicodeCharacter{1E24}{\udotaccent{H}}
+ \DeclareUnicodeCharacter{1E25}{\udotaccent{h}}
+ \DeclareUnicodeCharacter{1E26}{\"H}
+ \DeclareUnicodeCharacter{1E27}{\"h}
+
+ \DeclareUnicodeCharacter{1E30}{\'K}
+ \DeclareUnicodeCharacter{1E31}{\'k}
+ \DeclareUnicodeCharacter{1E32}{\udotaccent{K}}
+ \DeclareUnicodeCharacter{1E33}{\udotaccent{k}}
+ \DeclareUnicodeCharacter{1E34}{\ubaraccent{K}}
+ \DeclareUnicodeCharacter{1E35}{\ubaraccent{k}}
+ \DeclareUnicodeCharacter{1E36}{\udotaccent{L}}
+ \DeclareUnicodeCharacter{1E37}{\udotaccent{l}}
+ \DeclareUnicodeCharacter{1E3A}{\ubaraccent{L}}
+ \DeclareUnicodeCharacter{1E3B}{\ubaraccent{l}}
+ \DeclareUnicodeCharacter{1E3E}{\'M}
+ \DeclareUnicodeCharacter{1E3F}{\'m}
+
+ \DeclareUnicodeCharacter{1E40}{\dotaccent{M}}
+ \DeclareUnicodeCharacter{1E41}{\dotaccent{m}}
+ \DeclareUnicodeCharacter{1E42}{\udotaccent{M}}
+ \DeclareUnicodeCharacter{1E43}{\udotaccent{m}}
+ \DeclareUnicodeCharacter{1E44}{\dotaccent{N}}
+ \DeclareUnicodeCharacter{1E45}{\dotaccent{n}}
+ \DeclareUnicodeCharacter{1E46}{\udotaccent{N}}
+ \DeclareUnicodeCharacter{1E47}{\udotaccent{n}}
+ \DeclareUnicodeCharacter{1E48}{\ubaraccent{N}}
+ \DeclareUnicodeCharacter{1E49}{\ubaraccent{n}}
+
+ \DeclareUnicodeCharacter{1E54}{\'P}
+ \DeclareUnicodeCharacter{1E55}{\'p}
+ \DeclareUnicodeCharacter{1E56}{\dotaccent{P}}
+ \DeclareUnicodeCharacter{1E57}{\dotaccent{p}}
+ \DeclareUnicodeCharacter{1E58}{\dotaccent{R}}
+ \DeclareUnicodeCharacter{1E59}{\dotaccent{r}}
+ \DeclareUnicodeCharacter{1E5A}{\udotaccent{R}}
+ \DeclareUnicodeCharacter{1E5B}{\udotaccent{r}}
+ \DeclareUnicodeCharacter{1E5E}{\ubaraccent{R}}
+ \DeclareUnicodeCharacter{1E5F}{\ubaraccent{r}}
+
+ \DeclareUnicodeCharacter{1E60}{\dotaccent{S}}
+ \DeclareUnicodeCharacter{1E61}{\dotaccent{s}}
+ \DeclareUnicodeCharacter{1E62}{\udotaccent{S}}
+ \DeclareUnicodeCharacter{1E63}{\udotaccent{s}}
+ \DeclareUnicodeCharacter{1E6A}{\dotaccent{T}}
+ \DeclareUnicodeCharacter{1E6B}{\dotaccent{t}}
+ \DeclareUnicodeCharacter{1E6C}{\udotaccent{T}}
+ \DeclareUnicodeCharacter{1E6D}{\udotaccent{t}}
+ \DeclareUnicodeCharacter{1E6E}{\ubaraccent{T}}
+ \DeclareUnicodeCharacter{1E6F}{\ubaraccent{t}}
+
+ \DeclareUnicodeCharacter{1E7C}{\~V}
+ \DeclareUnicodeCharacter{1E7D}{\~v}
+ \DeclareUnicodeCharacter{1E7E}{\udotaccent{V}}
+ \DeclareUnicodeCharacter{1E7F}{\udotaccent{v}}
+
+ \DeclareUnicodeCharacter{1E80}{\`W}
+ \DeclareUnicodeCharacter{1E81}{\`w}
+ \DeclareUnicodeCharacter{1E82}{\'W}
+ \DeclareUnicodeCharacter{1E83}{\'w}
+ \DeclareUnicodeCharacter{1E84}{\"W}
+ \DeclareUnicodeCharacter{1E85}{\"w}
+ \DeclareUnicodeCharacter{1E86}{\dotaccent{W}}
+ \DeclareUnicodeCharacter{1E87}{\dotaccent{w}}
+ \DeclareUnicodeCharacter{1E88}{\udotaccent{W}}
+ \DeclareUnicodeCharacter{1E89}{\udotaccent{w}}
+ \DeclareUnicodeCharacter{1E8A}{\dotaccent{X}}
+ \DeclareUnicodeCharacter{1E8B}{\dotaccent{x}}
+ \DeclareUnicodeCharacter{1E8C}{\"X}
+ \DeclareUnicodeCharacter{1E8D}{\"x}
+ \DeclareUnicodeCharacter{1E8E}{\dotaccent{Y}}
+ \DeclareUnicodeCharacter{1E8F}{\dotaccent{y}}
+
+ \DeclareUnicodeCharacter{1E90}{\^Z}
+ \DeclareUnicodeCharacter{1E91}{\^z}
+ \DeclareUnicodeCharacter{1E92}{\udotaccent{Z}}
+ \DeclareUnicodeCharacter{1E93}{\udotaccent{z}}
+ \DeclareUnicodeCharacter{1E94}{\ubaraccent{Z}}
+ \DeclareUnicodeCharacter{1E95}{\ubaraccent{z}}
+ \DeclareUnicodeCharacter{1E96}{\ubaraccent{h}}
+ \DeclareUnicodeCharacter{1E97}{\"t}
+ \DeclareUnicodeCharacter{1E98}{\ringaccent{w}}
+ \DeclareUnicodeCharacter{1E99}{\ringaccent{y}}
+
+ \DeclareUnicodeCharacter{1EA0}{\udotaccent{A}}
+ \DeclareUnicodeCharacter{1EA1}{\udotaccent{a}}
+
+ \DeclareUnicodeCharacter{1EB8}{\udotaccent{E}}
+ \DeclareUnicodeCharacter{1EB9}{\udotaccent{e}}
+ \DeclareUnicodeCharacter{1EBC}{\~E}
+ \DeclareUnicodeCharacter{1EBD}{\~e}
+
+ \DeclareUnicodeCharacter{1ECA}{\udotaccent{I}}
+ \DeclareUnicodeCharacter{1ECB}{\udotaccent{i}}
+ \DeclareUnicodeCharacter{1ECC}{\udotaccent{O}}
+ \DeclareUnicodeCharacter{1ECD}{\udotaccent{o}}
+
+ \DeclareUnicodeCharacter{1EE4}{\udotaccent{U}}
+ \DeclareUnicodeCharacter{1EE5}{\udotaccent{u}}
+
+ \DeclareUnicodeCharacter{1EF2}{\`Y}
+ \DeclareUnicodeCharacter{1EF3}{\`y}
+ \DeclareUnicodeCharacter{1EF4}{\udotaccent{Y}}
+
+ \DeclareUnicodeCharacter{1EF8}{\~Y}
+ \DeclareUnicodeCharacter{1EF9}{\~y}
+
+ \DeclareUnicodeCharacter{2013}{--}
+ \DeclareUnicodeCharacter{2014}{---}
+ \DeclareUnicodeCharacter{2018}{\quoteleft}
+ \DeclareUnicodeCharacter{2019}{\quoteright}
+ \DeclareUnicodeCharacter{201A}{\quotesinglbase}
+ \DeclareUnicodeCharacter{201C}{\quotedblleft}
+ \DeclareUnicodeCharacter{201D}{\quotedblright}
+ \DeclareUnicodeCharacter{201E}{\quotedblbase}
+ \DeclareUnicodeCharacter{2022}{\bullet}
+ \DeclareUnicodeCharacter{2026}{\dots}
+ \DeclareUnicodeCharacter{2039}{\guilsinglleft}
+ \DeclareUnicodeCharacter{203A}{\guilsinglright}
+ \DeclareUnicodeCharacter{20AC}{\euro}
+
+ \DeclareUnicodeCharacter{2192}{\expansion}
+ \DeclareUnicodeCharacter{21D2}{\result}
+
+ \DeclareUnicodeCharacter{2212}{\minus}
+ \DeclareUnicodeCharacter{2217}{\point}
+ \DeclareUnicodeCharacter{2261}{\equiv}
+}% end of \utfeightchardefs
+
+
+% US-ASCII character definitions.
+\def\asciichardefs{% nothing need be done
+ \relax
+}
+
+% Make non-ASCII characters printable again for compatibility with
+% existing Texinfo documents that may use them, even without declaring a
+% document encoding.
+%
+\setnonasciicharscatcode \other
+
+
+\message{formatting,}
+
+\newdimen\defaultparindent \defaultparindent = 15pt
+
+\chapheadingskip = 15pt plus 4pt minus 2pt
+\secheadingskip = 12pt plus 3pt minus 2pt
+\subsecheadingskip = 9pt plus 2pt minus 2pt
+
+% Prevent underfull vbox error messages.
+\vbadness = 10000
+
+% Don't be so finicky about underfull hboxes, either.
+\hbadness = 2000
+
+% Following George Bush, get rid of widows and orphans.
+\widowpenalty=10000
+\clubpenalty=10000
+
+% Use TeX 3.0's \emergencystretch to help line breaking, but if we're
+% using an old version of TeX, don't do anything. We want the amount of
+% stretch added to depend on the line length, hence the dependence on
+% \hsize. We call this whenever the paper size is set.
+%
+\def\setemergencystretch{%
+ \ifx\emergencystretch\thisisundefined
+ % Allow us to assign to \emergencystretch anyway.
+ \def\emergencystretch{\dimen0}%
+ \else
+ \emergencystretch = .15\hsize
+ \fi
+}
+
+% Parameters in order: 1) textheight; 2) textwidth;
+% 3) voffset; 4) hoffset; 5) binding offset; 6) topskip;
+% 7) physical page height; 8) physical page width.
+%
+% We also call \setleading{\textleading}, so the caller should define
+% \textleading. The caller should also set \parskip.
+%
+\def\internalpagesizes#1#2#3#4#5#6#7#8{%
+ \voffset = #3\relax
+ \topskip = #6\relax
+ \splittopskip = \topskip
+ %
+ \vsize = #1\relax
+ \advance\vsize by \topskip
+ \outervsize = \vsize
+ \advance\outervsize by 2\topandbottommargin
+ \pageheight = \vsize
+ %
+ \hsize = #2\relax
+ \outerhsize = \hsize
+ \advance\outerhsize by 0.5in
+ \pagewidth = \hsize
+ %
+ \normaloffset = #4\relax
+ \bindingoffset = #5\relax
+ %
+ \ifpdf
+ \pdfpageheight #7\relax
+ \pdfpagewidth #8\relax
+ % if we don't reset these, they will remain at "1 true in" of
+ % whatever layout pdftex was dumped with.
+ \pdfhorigin = 1 true in
+ \pdfvorigin = 1 true in
+ \fi
+ %
+ \setleading{\textleading}
+ %
+ \parindent = \defaultparindent
+ \setemergencystretch
+}
+
+% @letterpaper (the default).
+\def\letterpaper{{\globaldefs = 1
+ \parskip = 3pt plus 2pt minus 1pt
+ \textleading = 13.2pt
+ %
+ % If page is nothing but text, make it come out even.
+ \internalpagesizes{607.2pt}{6in}% that's 46 lines
+ {\voffset}{.25in}%
+ {\bindingoffset}{36pt}%
+ {11in}{8.5in}%
+}}
+
+% Use @smallbook to reset parameters for 7x9.25 trim size.
+\def\smallbook{{\globaldefs = 1
+ \parskip = 2pt plus 1pt
+ \textleading = 12pt
+ %
+ \internalpagesizes{7.5in}{5in}%
+ {-.2in}{0in}%
+ {\bindingoffset}{16pt}%
+ {9.25in}{7in}%
+ %
+ \lispnarrowing = 0.3in
+ \tolerance = 700
+ \hfuzz = 1pt
+ \contentsrightmargin = 0pt
+ \defbodyindent = .5cm
+}}
+
+% Use @smallerbook to reset parameters for 6x9 trim size.
+% (Just testing, parameters still in flux.)
+\def\smallerbook{{\globaldefs = 1
+ \parskip = 1.5pt plus 1pt
+ \textleading = 12pt
+ %
+ \internalpagesizes{7.4in}{4.8in}%
+ {-.2in}{-.4in}%
+ {0pt}{14pt}%
+ {9in}{6in}%
+ %
+ \lispnarrowing = 0.25in
+ \tolerance = 700
+ \hfuzz = 1pt
+ \contentsrightmargin = 0pt
+ \defbodyindent = .4cm
+}}
+
+% Use @afourpaper to print on European A4 paper.
+\def\afourpaper{{\globaldefs = 1
+ \parskip = 3pt plus 2pt minus 1pt
+ \textleading = 13.2pt
+ %
+ % Double-side printing via postscript on Laserjet 4050
+ % prints double-sided nicely when \bindingoffset=10mm and \hoffset=-6mm.
+ % To change the settings for a different printer or situation, adjust
+ % \normaloffset until the front-side and back-side texts align. Then
+ % do the same for \bindingoffset. You can set these for testing in
+ % your texinfo source file like this:
+ % @tex
+ % \global\normaloffset = -6mm
+ % \global\bindingoffset = 10mm
+ % @end tex
+ \internalpagesizes{673.2pt}{160mm}% that's 51 lines
+ {\voffset}{\hoffset}%
+ {\bindingoffset}{44pt}%
+ {297mm}{210mm}%
+ %
+ \tolerance = 700
+ \hfuzz = 1pt
+ \contentsrightmargin = 0pt
+ \defbodyindent = 5mm
+}}
+
+% Use @afivepaper to print on European A5 paper.
+% From romildo at urano.iceb.ufop.br, 2 July 2000.
+% He also recommends making @example and @lisp be small.
+\def\afivepaper{{\globaldefs = 1
+ \parskip = 2pt plus 1pt minus 0.1pt
+ \textleading = 12.5pt
+ %
+ \internalpagesizes{160mm}{120mm}%
+ {\voffset}{\hoffset}%
+ {\bindingoffset}{8pt}%
+ {210mm}{148mm}%
+ %
+ \lispnarrowing = 0.2in
+ \tolerance = 800
+ \hfuzz = 1.2pt
+ \contentsrightmargin = 0pt
+ \defbodyindent = 2mm
+ \tableindent = 12mm
+}}
+
+% A specific text layout, 24x15cm overall, intended for A4 paper.
+\def\afourlatex{{\globaldefs = 1
+ \afourpaper
+ \internalpagesizes{237mm}{150mm}%
+ {\voffset}{4.6mm}%
+ {\bindingoffset}{7mm}%
+ {297mm}{210mm}%
+ %
+ % Must explicitly reset to 0 because we call \afourpaper.
+ \globaldefs = 0
+}}
+
+% Use @afourwide to print on A4 paper in landscape format.
+\def\afourwide{{\globaldefs = 1
+ \afourpaper
+ \internalpagesizes{241mm}{165mm}%
+ {\voffset}{-2.95mm}%
+ {\bindingoffset}{7mm}%
+ {297mm}{210mm}%
+ \globaldefs = 0
+}}
+
+% @pagesizes TEXTHEIGHT[,TEXTWIDTH]
+% Perhaps we should allow setting the margins, \topskip, \parskip,
+% and/or leading, also. Or perhaps we should compute them somehow.
+%
+\parseargdef\pagesizes{\pagesizesyyy #1,,\finish}
+\def\pagesizesyyy#1,#2,#3\finish{{%
+ \setbox0 = \hbox{\ignorespaces #2}\ifdim\wd0 > 0pt \hsize=#2\relax \fi
+ \globaldefs = 1
+ %
+ \parskip = 3pt plus 2pt minus 1pt
+ \setleading{\textleading}%
+ %
+ \dimen0 = #1\relax
+ \advance\dimen0 by \voffset
+ %
+ \dimen2 = \hsize
+ \advance\dimen2 by \normaloffset
+ %
+ \internalpagesizes{#1}{\hsize}%
+ {\voffset}{\normaloffset}%
+ {\bindingoffset}{44pt}%
+ {\dimen0}{\dimen2}%
+}}
+
+% Set default to letter.
+%
+\letterpaper
+
+
+\message{and turning on texinfo input format.}
+
+% DEL is a comment character, in case @c does not suffice.
+\catcode`\^^? = 14
+
+% Define macros to output various characters with catcode for normal text.
+\catcode`\"=\other
+\catcode`\~=\other
+\catcode`\^=\other
+\catcode`\_=\other
+\catcode`\|=\other
+\catcode`\<=\other
+\catcode`\>=\other
+\catcode`\+=\other
+\catcode`\$=\other
+\def\normaldoublequote{"}
+\def\normaltilde{~}
+\def\normalcaret{^}
+\def\normalunderscore{_}
+\def\normalverticalbar{|}
+\def\normalless{<}
+\def\normalgreater{>}
+\def\normalplus{+}
+\def\normaldollar{$}%$ font-lock fix
+
+% This macro is used to make a character print one way in \tt
+% (where it can probably be output as-is), and another way in other fonts,
+% where something hairier probably needs to be done.
+%
+% #1 is what to print if we are indeed using \tt; #2 is what to print
+% otherwise. Since all the Computer Modern typewriter fonts have zero
+% interword stretch (and shrink), and it is reasonable to expect all
+% typewriter fonts to have this, we can check that font parameter.
+%
+\def\ifusingtt#1#2{\ifdim \fontdimen3\font=0pt #1\else #2\fi}
+
+% Same as above, but check for italic font. Actually this also catches
+% non-italic slanted fonts since it is impossible to distinguish them from
+% italic fonts. But since this is only used by $ and it uses \sl anyway
+% this is not a problem.
+\def\ifusingit#1#2{\ifdim \fontdimen1\font>0pt #1\else #2\fi}
+
+% Turn off all special characters except @
+% (and those which the user can use as if they were ordinary).
+% Most of these we simply print from the \tt font, but for some, we can
+% use math or other variants that look better in normal text.
+
+\catcode`\"=\active
+\def\activedoublequote{{\tt\char34}}
+\let"=\activedoublequote
+\catcode`\~=\active
+\def~{{\tt\char126}}
+\chardef\hat=`\^
+\catcode`\^=\active
+\def^{{\tt \hat}}
+
+\catcode`\_=\active
+\def_{\ifusingtt\normalunderscore\_}
+\let\realunder=_
+% Subroutine for the previous macro.
+\def\_{\leavevmode \kern.07em \vbox{\hrule width.3em height.1ex}\kern .07em }
+
+\catcode`\|=\active
+\def|{{\tt\char124}}
+\chardef \less=`\<
+\catcode`\<=\active
+\def<{{\tt \less}}
+\chardef \gtr=`\>
+\catcode`\>=\active
+\def>{{\tt \gtr}}
+\catcode`\+=\active
+\def+{{\tt \char 43}}
+\catcode`\$=\active
+\def${\ifusingit{{\sl\$}}\normaldollar}%$ font-lock fix
+
+% If a .fmt file is being used, characters that might appear in a file
+% name cannot be active until we have parsed the command line.
+% So turn them off again, and have \everyjob (or @setfilename) turn them on.
+% \otherifyactive is called near the end of this file.
+\def\otherifyactive{\catcode`+=\other \catcode`\_=\other}
+
+% Used sometimes to turn off (effectively) the active characters even after
+% parsing them.
+\def\turnoffactive{%
+ \normalturnoffactive
+ \otherbackslash
+}
+
+\catcode`\@=0
+
+% \backslashcurfont outputs one backslash character in current font,
+% as in \char`\\.
+\global\chardef\backslashcurfont=`\\
+\global\let\rawbackslashxx=\backslashcurfont % let existing .??s files work
+
+% \realbackslash is an actual character `\' with catcode other, and
+% \doublebackslash is two of them (for the pdf outlines).
+{\catcode`\\=\other @gdef at realbackslash{\} @gdef at doublebackslash{\\}}
+
+% In texinfo, backslash is an active character; it prints the backslash
+% in fixed width font.
+\catcode`\\=\active
+ at def@normalbackslash{{@tt at backslashcurfont}}
+% On startup, @fixbackslash assigns:
+% @let \ = @normalbackslash
+
+% \rawbackslash defines an active \ to do \backslashcurfont.
+% \otherbackslash defines an active \ to be a literal `\' character with
+% catcode other.
+ at gdef@rawbackslash{@let\=@backslashcurfont}
+ at gdef@otherbackslash{@let\=@realbackslash}
+
+% Same as @turnoffactive except outputs \ as {\tt\char`\\} instead of
+% the literal character `\'.
+%
+ at def@normalturnoffactive{%
+ @let\=@normalbackslash
+ @let"=@normaldoublequote
+ @let~=@normaltilde
+ @let^=@normalcaret
+ @let_=@normalunderscore
+ @let|=@normalverticalbar
+ @let<=@normalless
+ @let>=@normalgreater
+ @let+=@normalplus
+ @let$=@normaldollar %$ font-lock fix
+ @markupsetuplqdefault
+ @markupsetuprqdefault
+ @unsepspaces
+}
+
+% Make _ and + \other characters, temporarily.
+% This is canceled by @fixbackslash.
+ at otherifyactive
+
+% If a .fmt file is being used, we don't want the `\input texinfo' to show up.
+% That is what \eatinput is for; after that, the `\' should revert to printing
+% a backslash.
+%
+ at gdef@eatinput input texinfo{@fixbackslash}
+ at global@let\ = @eatinput
+
+% On the other hand, perhaps the file did not have a `\input texinfo'. Then
+% the first `\' in the file would cause an error. This macro tries to fix
+% that, assuming it is called before the first `\' could plausibly occur.
+% Also turn back on active characters that might appear in the input
+% file name, in case not using a pre-dumped format.
+%
+ at gdef@fixbackslash{%
+ @ifx\@eatinput @let\ = @normalbackslash @fi
+ @catcode`+=@active
+ @catcode`@_=@active
+}
+
+% Say @foo, not \foo, in error messages.
+ at escapechar = `@@
+
+% These look ok in all fonts, so just make them not special.
+ at catcode`@& = @other
+ at catcode`@# = @other
+ at catcode`@% = @other
+
+ at c Finally, make ` and ' active, so that txicodequoteundirected and
+ at c txicodequotebacktick work right in, e.g., @w{@code{`foo'}}. If we
+ at c don't make ` and ' active, @code will not get them as active chars.
+ at c Do this last of all since we use ` in the previous @catcode assignments.
+ at catcode`@'=@active
+ at catcode`@`=@active
+ at markupsetuplqdefault
+ at markupsetuprqdefault
+
+ at c Local variables:
+ at c eval: (add-hook 'write-file-hooks 'time-stamp)
+ at c page-delimiter: "^\\\\message"
+ at c time-stamp-start: "def\\\\texinfoversion{"
+ at c time-stamp-format: "%:y-%02m-%02d.%02H"
+ at c time-stamp-end: "}"
+ at c End:
+
+ at c vim:sw=2:
+
+ at ignore
+ arch-tag: e1b36e32-c96e-4135-a41a-0b2efa2ea115
+ at end ignore
diff --git a/src/libGkArrays/configure b/src/libGkArrays/configure
new file mode 100755
index 0000000..fb3c40f
--- /dev/null
+++ b/src/libGkArrays/configure
@@ -0,0 +1,18480 @@
+#! /bin/sh
+# From configure.ac Revision: 763 .
+# Guess values for system-dependent variables and create Makefiles.
+# Generated by GNU Autoconf 2.67 for libGkArrays 2.1.0.
+#
+# Report bugs to <crac-gkarrays at lists.gforge.inria.fr>.
+#
+#
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
+# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
+# Foundation, Inc.
+#
+#
+# This configure script is free software; the Free Software Foundation
+# gives unlimited permission to copy, distribute and modify it.
+#
+#
+# *******************************************************************************
+# * *
+# * Copyright(C) 2010-2013 --IRB/INSERM *
+# * (Institut de Recherches en Biothérapie / *
+# * Institut National de la Santé et de la Recherche *
+# * Médicale) *
+# * LIFL/INRIA *
+# * (Laboratoire d'Informatique Fondamentale de *
+# * Lille / Institut National de Recherche en *
+# * Informatique et Automatique) *
+# * LIRMM/CNRS *
+# * (Laboratoire d'Informatique, de Robotique et de *
+# * Microélectronique de Montpellier / *
+# * Centre National de la Recherche Scientifique) *
+# * LITIS *
+# * (Laboratoire d'Informatique, du Traitement de *
+# * l'Information et des Systèmes). *
+# * *
+# * Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+# * Mikaël SALSON <mikael.salson at lifl.fr> *
+# * Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+# * Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+# * Éric RIVALS <eric.rivals at lirmm.fr> *
+# * *
+# * Programmeurs *
+# * /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+# * Mikaël SALSON <mikael.salson at lifl.fr> *
+# * with additional contribution: *
+# * Alban MANCHERON <alban.mancheron at lirmm.fr> *
+# * *
+# * Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+# * *
+# * ------------------------------------------------------------------------- *
+# * *
+# * Ce fichier fait partie de la librairie Gk-arrays. *
+# * *
+# * La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+# * lectures de séquences issues du séquençage haut-débit. *
+# * *
+# * Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+# * respectant les principes de diffusion des logiciels libres. Vous pouvez *
+# * utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+# * la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+# * le site "http://www.cecill.info". *
+# * *
+# * ------------------------------------------------------------------------- *
+# * *
+# * This File is part of the Gk-arrays library. *
+# * *
+# * The Gk-arrays library aims at indexing k-factors from a huge set of *
+# * sequencing reads. *
+# * *
+# * This software is governed by the CeCILL-C license under French law and *
+# * abiding by the rules of distribution of free software. You can use, *
+# * modify and/ or redistribute the software under the terms of the CeCILL-C *
+# * license as circulated by CEA, CNRS and INRIA at the following URL *
+# * "http://www.cecill.info". *
+# * *
+# ******************************************************************************/
+#
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
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+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
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+ case $arg in #(
+ *"$as_nl"*)
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+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
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+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
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+
+# Find who we are. Look in the path if we contain no directory separator.
+case $0 in #((
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+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
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+IFS=$as_save_IFS
+
+ ;;
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+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
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+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
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+PS1='$ '
+PS2='> '
+PS4='+ '
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+# NLS nuisances.
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+export LC_ALL
+LANGUAGE=C
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+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test "x$CONFIG_SHELL" = x; then
+ as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
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+
+ if test "x$CONFIG_SHELL" != x; then :
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+ BASH_ENV=/dev/null
+ ENV=/dev/null
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+ if test x$as_have_required = xno; then :
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+ if test x${ZSH_VERSION+set} = xset ; then
+ $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should"
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+unset CLICOLOR_FORCE GREP_OPTIONS
+
+## --------------------- ##
+## M4sh Shell Functions. ##
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+ # Avoid inline document here, it may be left over
+ :
+elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' ; then
+ # Yippee, $ECHO works!
+ :
+else
+ # Restart under the correct shell.
+ exec $SHELL "$0" --no-reexec ${1+"$@"}
+fi
+
+if test "X$1" = X--fallback-echo; then
+ # used as fallback echo
+ shift
+ cat <<_LT_EOF
+$*
+_LT_EOF
+ exit 0
+fi
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test -z "$lt_ECHO"; then
+ if test "X${echo_test_string+set}" != Xset; then
+ # find a string as large as possible, as long as the shell can cope with it
+ for cmd in 'sed 50q "$0"' 'sed 20q "$0"' 'sed 10q "$0"' 'sed 2q "$0"' 'echo test'; do
+ # expected sizes: less than 2Kb, 1Kb, 512 bytes, 16 bytes, ...
+ if { echo_test_string=`eval $cmd`; } 2>/dev/null &&
+ { test "X$echo_test_string" = "X$echo_test_string"; } 2>/dev/null
+ then
+ break
+ fi
+ done
+ fi
+
+ if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ :
+ else
+ # The Solaris, AIX, and Digital Unix default echo programs unquote
+ # backslashes. This makes it impossible to quote backslashes using
+ # echo "$something" | sed 's/\\/\\\\/g'
+ #
+ # So, first we look for a working echo in the user's PATH.
+
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for dir in $PATH /usr/ucb; do
+ IFS="$lt_save_ifs"
+ if (test -f $dir/echo || test -f $dir/echo$ac_exeext) &&
+ test "X`($dir/echo '\t') 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`($dir/echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ ECHO="$dir/echo"
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+
+ if test "X$ECHO" = Xecho; then
+ # We didn't find a better echo, so look for alternatives.
+ if test "X`{ print -r '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ print -r "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ # This shell has a builtin print -r that does the trick.
+ ECHO='print -r'
+ elif { test -f /bin/ksh || test -f /bin/ksh$ac_exeext; } &&
+ test "X$CONFIG_SHELL" != X/bin/ksh; then
+ # If we have ksh, try running configure again with it.
+ ORIGINAL_CONFIG_SHELL=${CONFIG_SHELL-/bin/sh}
+ export ORIGINAL_CONFIG_SHELL
+ CONFIG_SHELL=/bin/ksh
+ export CONFIG_SHELL
+ exec $CONFIG_SHELL "$0" --no-reexec ${1+"$@"}
+ else
+ # Try using printf.
+ ECHO='printf %s\n'
+ if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ # Cool, printf works
+ :
+ elif echo_testing_string=`($ORIGINAL_CONFIG_SHELL "$0" --fallback-echo '\t') 2>/dev/null` &&
+ test "X$echo_testing_string" = 'X\t' &&
+ echo_testing_string=`($ORIGINAL_CONFIG_SHELL "$0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ CONFIG_SHELL=$ORIGINAL_CONFIG_SHELL
+ export CONFIG_SHELL
+ SHELL="$CONFIG_SHELL"
+ export SHELL
+ ECHO="$CONFIG_SHELL $0 --fallback-echo"
+ elif echo_testing_string=`($CONFIG_SHELL "$0" --fallback-echo '\t') 2>/dev/null` &&
+ test "X$echo_testing_string" = 'X\t' &&
+ echo_testing_string=`($CONFIG_SHELL "$0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ ECHO="$CONFIG_SHELL $0 --fallback-echo"
+ else
+ # maybe with a smaller string...
+ prev=:
+
+ for cmd in 'echo test' 'sed 2q "$0"' 'sed 10q "$0"' 'sed 20q "$0"' 'sed 50q "$0"'; do
+ if { test "X$echo_test_string" = "X`eval $cmd`"; } 2>/dev/null
+ then
+ break
+ fi
+ prev="$cmd"
+ done
+
+ if test "$prev" != 'sed 50q "$0"'; then
+ echo_test_string=`eval $prev`
+ export echo_test_string
+ exec ${ORIGINAL_CONFIG_SHELL-${CONFIG_SHELL-/bin/sh}} "$0" ${1+"$@"}
+ else
+ # Oops. We lost completely, so just stick with echo.
+ ECHO=echo
+ fi
+ fi
+ fi
+ fi
+ fi
+fi
+
+# Copy echo and quote the copy suitably for passing to libtool from
+# the Makefile, instead of quoting the original, which is used later.
+lt_ECHO=$ECHO
+if test "X$lt_ECHO" = "X$CONFIG_SHELL $0 --fallback-echo"; then
+ lt_ECHO="$CONFIG_SHELL \\\$\$0 --fallback-echo"
+fi
+
+
+
+
+test -n "$DJDIR" || exec 7<&0 </dev/null
+exec 6>&1
+
+# Name of the host.
+# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status,
+# so uname gets run too.
+ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
+
+#
+# Initializations.
+#
+ac_default_prefix=/usr/local
+ac_clean_files=
+ac_config_libobj_dir=.
+LIBOBJS=
+cross_compiling=no
+subdirs=
+MFLAGS=
+MAKEFLAGS=
+
+# Identity of this package.
+PACKAGE_NAME='libGkArrays'
+PACKAGE_TARNAME='libGkArrays'
+PACKAGE_VERSION='2.1.0'
+PACKAGE_STRING='libGkArrays 2.1.0'
+PACKAGE_BUGREPORT='crac-gkarrays at lists.gforge.inria.fr'
+PACKAGE_URL='http://crac.gforge.inria.fr/gkarrays'
+
+ac_unique_file="src/gkArrays.h"
+# Factoring default headers for most tests.
+ac_includes_default="\
+#include <stdio.h>
+#ifdef HAVE_SYS_TYPES_H
+# include <sys/types.h>
+#endif
+#ifdef HAVE_SYS_STAT_H
+# include <sys/stat.h>
+#endif
+#ifdef STDC_HEADERS
+# include <stdlib.h>
+# include <stddef.h>
+#else
+# ifdef HAVE_STDLIB_H
+# include <stdlib.h>
+# endif
+#endif
+#ifdef HAVE_STRING_H
+# if !defined STDC_HEADERS && defined HAVE_MEMORY_H
+# include <memory.h>
+# endif
+# include <string.h>
+#endif
+#ifdef HAVE_STRINGS_H
+# include <strings.h>
+#endif
+#ifdef HAVE_INTTYPES_H
+# include <inttypes.h>
+#endif
+#ifdef HAVE_STDINT_H
+# include <stdint.h>
+#endif
+#ifdef HAVE_UNISTD_H
+# include <unistd.h>
+#endif"
+
+enable_option_checking=no
+ac_subst_vars='am__EXEEXT_FALSE
+am__EXEEXT_TRUE
+LTLIBOBJS
+INCLUDED_PROGRESSBAR_FALSE
+INCLUDED_PROGRESSBAR_TRUE
+subdirs
+hacked_prefix
+LIBOBJS
+DEB_BUILDER
+ARCH
+ISODATE
+CXXCPP
+OTOOL64
+OTOOL
+LIPO
+NMEDIT
+DSYMUTIL
+lt_ECHO
+RANLIB
+AR
+OBJDUMP
+NM
+ac_ct_DUMPBIN
+DUMPBIN
+LD
+FGREP
+EGREP
+GREP
+SED
+host_os
+host_vendor
+host_cpu
+host
+build_os
+build_vendor
+build_cpu
+build
+LIBTOOL
+BUILD_DOC_FALSE
+BUILD_DOC_TRUE
+KPSEWHICH
+PDFTEX
+TEXI2DVI
+LN_S
+CPP
+am__fastdepCC_FALSE
+am__fastdepCC_TRUE
+CCDEPMODE
+ac_ct_CC
+CFLAGS
+CC
+am__fastdepCXX_FALSE
+am__fastdepCXX_TRUE
+CXXDEPMODE
+AMDEPBACKSLASH
+AMDEP_FALSE
+AMDEP_TRUE
+am__quote
+am__include
+DEPDIR
+OBJEXT
+EXEEXT
+ac_ct_CXX
+CPPFLAGS
+LDFLAGS
+CXXFLAGS
+CXX
+am__untar
+am__tar
+AMTAR
+am__leading_dot
+SET_MAKE
+AWK
+mkdir_p
+MKDIR_P
+INSTALL_STRIP_PROGRAM
+STRIP
+install_sh
+MAKEINFO
+AUTOHEADER
+AUTOMAKE
+AUTOCONF
+ACLOCAL
+PACKAGE
+CYGPATH_W
+am__isrc
+INSTALL_DATA
+INSTALL_SCRIPT
+INSTALL_PROGRAM
+LIB_VERSION_EXT
+LIB_VERSION
+VERSION
+PACKAGE_DESCRIPTION
+target_alias
+host_alias
+build_alias
+LIBS
+ECHO_T
+ECHO_N
+ECHO_C
+DEFS
+mandir
+localedir
+libdir
+psdir
+pdfdir
+dvidir
+htmldir
+infodir
+docdir
+oldincludedir
+includedir
+localstatedir
+sharedstatedir
+sysconfdir
+datadir
+datarootdir
+libexecdir
+sbindir
+bindir
+program_transform_name
+prefix
+exec_prefix
+PACKAGE_URL
+PACKAGE_BUGREPORT
+PACKAGE_STRING
+PACKAGE_VERSION
+PACKAGE_TARNAME
+PACKAGE_NAME
+PATH_SEPARATOR
+SHELL'
+ac_subst_files='postrm_script
+postinst_script'
+ac_user_opts='
+enable_option_checking
+enable_dependency_tracking
+enable_shared
+enable_static
+with_pic
+enable_fast_install
+with_gnu_ld
+enable_libtool_lock
+enable_debug
+enable_coverage
+with_included_ProgressBar
+with_libProgressBar_prefix
+'
+ ac_precious_vars='build_alias
+host_alias
+target_alias
+CXX
+CXXFLAGS
+LDFLAGS
+LIBS
+CPPFLAGS
+CCC
+CC
+CFLAGS
+CPP
+CXXCPP'
+ac_subdirs_all='src/libProgressBar-1.2.0'
+
+# Initialize some variables set by options.
+ac_init_help=
+ac_init_version=false
+ac_unrecognized_opts=
+ac_unrecognized_sep=
+# The variables have the same names as the options, with
+# dashes changed to underlines.
+cache_file=/dev/null
+exec_prefix=NONE
+no_create=
+no_recursion=
+prefix=NONE
+program_prefix=NONE
+program_suffix=NONE
+program_transform_name=s,x,x,
+silent=
+site=
+srcdir=
+verbose=
+x_includes=NONE
+x_libraries=NONE
+
+# Installation directory options.
+# These are left unexpanded so users can "make install exec_prefix=/foo"
+# and all the variables that are supposed to be based on exec_prefix
+# by default will actually change.
+# Use braces instead of parens because sh, perl, etc. also accept them.
+# (The list follows the same order as the GNU Coding Standards.)
+bindir='${exec_prefix}/bin'
+sbindir='${exec_prefix}/sbin'
+libexecdir='${exec_prefix}/libexec'
+datarootdir='${prefix}/share'
+datadir='${datarootdir}'
+sysconfdir='${prefix}/etc'
+sharedstatedir='${prefix}/com'
+localstatedir='${prefix}/var'
+includedir='${prefix}/include'
+oldincludedir='/usr/include'
+docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
+infodir='${datarootdir}/info'
+htmldir='${docdir}'
+dvidir='${docdir}'
+pdfdir='${docdir}'
+psdir='${docdir}'
+libdir='${exec_prefix}/lib'
+localedir='${datarootdir}/locale'
+mandir='${datarootdir}/man'
+
+ac_prev=
+ac_dashdash=
+for ac_option
+do
+ # If the previous option needs an argument, assign it.
+ if test -n "$ac_prev"; then
+ eval $ac_prev=\$ac_option
+ ac_prev=
+ continue
+ fi
+
+ case $ac_option in
+ *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
+ *=) ac_optarg= ;;
+ *) ac_optarg=yes ;;
+ esac
+
+ # Accept the important Cygnus configure options, so we can diagnose typos.
+
+ case $ac_dashdash$ac_option in
+ --)
+ ac_dashdash=yes ;;
+
+ -bindir | --bindir | --bindi | --bind | --bin | --bi)
+ ac_prev=bindir ;;
+ -bindir=* | --bindir=* | --bindi=* | --bind=* | --bin=* | --bi=*)
+ bindir=$ac_optarg ;;
+
+ -build | --build | --buil | --bui | --bu)
+ ac_prev=build_alias ;;
+ -build=* | --build=* | --buil=* | --bui=* | --bu=*)
+ build_alias=$ac_optarg ;;
+
+ -cache-file | --cache-file | --cache-fil | --cache-fi \
+ | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)
+ ac_prev=cache_file ;;
+ -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \
+ | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* | --c=*)
+ cache_file=$ac_optarg ;;
+
+ --config-cache | -C)
+ cache_file=config.cache ;;
+
+ -datadir | --datadir | --datadi | --datad)
+ ac_prev=datadir ;;
+ -datadir=* | --datadir=* | --datadi=* | --datad=*)
+ datadir=$ac_optarg ;;
+
+ -datarootdir | --datarootdir | --datarootdi | --datarootd | --dataroot \
+ | --dataroo | --dataro | --datar)
+ ac_prev=datarootdir ;;
+ -datarootdir=* | --datarootdir=* | --datarootdi=* | --datarootd=* \
+ | --dataroot=* | --dataroo=* | --dataro=* | --datar=*)
+ datarootdir=$ac_optarg ;;
+
+ -disable-* | --disable-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid feature name: $ac_useropt"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"enable_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--disable-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval enable_$ac_useropt=no ;;
+
+ -docdir | --docdir | --docdi | --doc | --do)
+ ac_prev=docdir ;;
+ -docdir=* | --docdir=* | --docdi=* | --doc=* | --do=*)
+ docdir=$ac_optarg ;;
+
+ -dvidir | --dvidir | --dvidi | --dvid | --dvi | --dv)
+ ac_prev=dvidir ;;
+ -dvidir=* | --dvidir=* | --dvidi=* | --dvid=* | --dvi=* | --dv=*)
+ dvidir=$ac_optarg ;;
+
+ -enable-* | --enable-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid feature name: $ac_useropt"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"enable_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--enable-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval enable_$ac_useropt=\$ac_optarg ;;
+
+ -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \
+ | --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \
+ | --exec | --exe | --ex)
+ ac_prev=exec_prefix ;;
+ -exec-prefix=* | --exec_prefix=* | --exec-prefix=* | --exec-prefi=* \
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+ | --exec=* | --exe=* | --ex=*)
+ exec_prefix=$ac_optarg ;;
+
+ -gas | --gas | --ga | --g)
+ # Obsolete; use --with-gas.
+ with_gas=yes ;;
+
+ -help | --help | --hel | --he | -h)
+ ac_init_help=long ;;
+ -help=r* | --help=r* | --hel=r* | --he=r* | -hr*)
+ ac_init_help=recursive ;;
+ -help=s* | --help=s* | --hel=s* | --he=s* | -hs*)
+ ac_init_help=short ;;
+
+ -host | --host | --hos | --ho)
+ ac_prev=host_alias ;;
+ -host=* | --host=* | --hos=* | --ho=*)
+ host_alias=$ac_optarg ;;
+
+ -htmldir | --htmldir | --htmldi | --htmld | --html | --htm | --ht)
+ ac_prev=htmldir ;;
+ -htmldir=* | --htmldir=* | --htmldi=* | --htmld=* | --html=* | --htm=* \
+ | --ht=*)
+ htmldir=$ac_optarg ;;
+
+ -includedir | --includedir | --includedi | --included | --include \
+ | --includ | --inclu | --incl | --inc)
+ ac_prev=includedir ;;
+ -includedir=* | --includedir=* | --includedi=* | --included=* | --include=* \
+ | --includ=* | --inclu=* | --incl=* | --inc=*)
+ includedir=$ac_optarg ;;
+
+ -infodir | --infodir | --infodi | --infod | --info | --inf)
+ ac_prev=infodir ;;
+ -infodir=* | --infodir=* | --infodi=* | --infod=* | --info=* | --inf=*)
+ infodir=$ac_optarg ;;
+
+ -libdir | --libdir | --libdi | --libd)
+ ac_prev=libdir ;;
+ -libdir=* | --libdir=* | --libdi=* | --libd=*)
+ libdir=$ac_optarg ;;
+
+ -libexecdir | --libexecdir | --libexecdi | --libexecd | --libexec \
+ | --libexe | --libex | --libe)
+ ac_prev=libexecdir ;;
+ -libexecdir=* | --libexecdir=* | --libexecdi=* | --libexecd=* | --libexec=* \
+ | --libexe=* | --libex=* | --libe=*)
+ libexecdir=$ac_optarg ;;
+
+ -localedir | --localedir | --localedi | --localed | --locale)
+ ac_prev=localedir ;;
+ -localedir=* | --localedir=* | --localedi=* | --localed=* | --locale=*)
+ localedir=$ac_optarg ;;
+
+ -localstatedir | --localstatedir | --localstatedi | --localstated \
+ | --localstate | --localstat | --localsta | --localst | --locals)
+ ac_prev=localstatedir ;;
+ -localstatedir=* | --localstatedir=* | --localstatedi=* | --localstated=* \
+ | --localstate=* | --localstat=* | --localsta=* | --localst=* | --locals=*)
+ localstatedir=$ac_optarg ;;
+
+ -mandir | --mandir | --mandi | --mand | --man | --ma | --m)
+ ac_prev=mandir ;;
+ -mandir=* | --mandir=* | --mandi=* | --mand=* | --man=* | --ma=* | --m=*)
+ mandir=$ac_optarg ;;
+
+ -nfp | --nfp | --nf)
+ # Obsolete; use --without-fp.
+ with_fp=no ;;
+
+ -no-create | --no-create | --no-creat | --no-crea | --no-cre \
+ | --no-cr | --no-c | -n)
+ no_create=yes ;;
+
+ -no-recursion | --no-recursion | --no-recursio | --no-recursi \
+ | --no-recurs | --no-recur | --no-recu | --no-rec | --no-re | --no-r)
+ no_recursion=yes ;;
+
+ -oldincludedir | --oldincludedir | --oldincludedi | --oldincluded \
+ | --oldinclude | --oldinclud | --oldinclu | --oldincl | --oldinc \
+ | --oldin | --oldi | --old | --ol | --o)
+ ac_prev=oldincludedir ;;
+ -oldincludedir=* | --oldincludedir=* | --oldincludedi=* | --oldincluded=* \
+ | --oldinclude=* | --oldinclud=* | --oldinclu=* | --oldincl=* | --oldinc=* \
+ | --oldin=* | --oldi=* | --old=* | --ol=* | --o=*)
+ oldincludedir=$ac_optarg ;;
+
+ -prefix | --prefix | --prefi | --pref | --pre | --pr | --p)
+ ac_prev=prefix ;;
+ -prefix=* | --prefix=* | --prefi=* | --pref=* | --pre=* | --pr=* | --p=*)
+ prefix=$ac_optarg ;;
+
+ -program-prefix | --program-prefix | --program-prefi | --program-pref \
+ | --program-pre | --program-pr | --program-p)
+ ac_prev=program_prefix ;;
+ -program-prefix=* | --program-prefix=* | --program-prefi=* \
+ | --program-pref=* | --program-pre=* | --program-pr=* | --program-p=*)
+ program_prefix=$ac_optarg ;;
+
+ -program-suffix | --program-suffix | --program-suffi | --program-suff \
+ | --program-suf | --program-su | --program-s)
+ ac_prev=program_suffix ;;
+ -program-suffix=* | --program-suffix=* | --program-suffi=* \
+ | --program-suff=* | --program-suf=* | --program-su=* | --program-s=*)
+ program_suffix=$ac_optarg ;;
+
+ -program-transform-name | --program-transform-name \
+ | --program-transform-nam | --program-transform-na \
+ | --program-transform-n | --program-transform- \
+ | --program-transform | --program-transfor \
+ | --program-transfo | --program-transf \
+ | --program-trans | --program-tran \
+ | --progr-tra | --program-tr | --program-t)
+ ac_prev=program_transform_name ;;
+ -program-transform-name=* | --program-transform-name=* \
+ | --program-transform-nam=* | --program-transform-na=* \
+ | --program-transform-n=* | --program-transform-=* \
+ | --program-transform=* | --program-transfor=* \
+ | --program-transfo=* | --program-transf=* \
+ | --program-trans=* | --program-tran=* \
+ | --progr-tra=* | --program-tr=* | --program-t=*)
+ program_transform_name=$ac_optarg ;;
+
+ -pdfdir | --pdfdir | --pdfdi | --pdfd | --pdf | --pd)
+ ac_prev=pdfdir ;;
+ -pdfdir=* | --pdfdir=* | --pdfdi=* | --pdfd=* | --pdf=* | --pd=*)
+ pdfdir=$ac_optarg ;;
+
+ -psdir | --psdir | --psdi | --psd | --ps)
+ ac_prev=psdir ;;
+ -psdir=* | --psdir=* | --psdi=* | --psd=* | --ps=*)
+ psdir=$ac_optarg ;;
+
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil)
+ silent=yes ;;
+
+ -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
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+libGkArrays configure 2.1.0
+generated by GNU Autoconf 2.67
+
+Copyright (C) 2010 Free Software Foundation, Inc.
+This configure script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it.
+
+
+*******************************************************************************
+* *
+* Copyright(C) 2010-2013 --IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+******************************************************************************/
+
+_ACEOF
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+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_compile
+
+# ac_fn_c_try_cpp LINENO
+# ----------------------
+# Try to preprocess conftest.$ac_ext, and return whether this succeeded.
+ac_fn_c_try_cpp ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if { { ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } > conftest.i && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_cpp
+
+# ac_fn_c_try_link LINENO
+# -----------------------
+# Try to link conftest.$ac_ext, and return whether this succeeded.
+ac_fn_c_try_link ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext conftest$ac_exeext
+ if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ # Delete the IPA/IPO (Inter Procedural Analysis/Optimization) information
+ # created by the PGI compiler (conftest_ipa8_conftest.oo), as it would
+ # interfere with the next link command; also delete a directory that is
+ # left behind by Apple's compiler. We do this before executing the actions.
+ rm -rf conftest.dSYM conftest_ipa8_conftest.oo
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_link
+
+# ac_fn_c_check_header_compile LINENO HEADER VAR INCLUDES
+# -------------------------------------------------------
+# Tests whether HEADER exists and can be compiled using the include files in
+# INCLUDES, setting the cache variable VAR accordingly.
+ac_fn_c_check_header_compile ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+#include <$2>
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ eval "$3=yes"
+else
+ eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_c_check_header_compile
+
+# ac_fn_c_try_run LINENO
+# ----------------------
+# Try to link conftest.$ac_ext, and return whether this succeeded. Assumes
+# that executables *can* be run.
+ac_fn_c_try_run ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && { ac_try='./conftest$ac_exeext'
+ { { case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=$ac_status
+fi
+ rm -rf conftest.dSYM conftest_ipa8_conftest.oo
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_run
+
+# ac_fn_c_check_func LINENO FUNC VAR
+# ----------------------------------
+# Tests whether FUNC exists, setting the cache variable VAR accordingly
+ac_fn_c_check_func ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+/* Define $2 to an innocuous variant, in case <limits.h> declares $2.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define $2 innocuous_$2
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $2 (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $2
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $2 ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_$2 || defined __stub___$2
+choke me
+#endif
+
+int
+main ()
+{
+return $2 ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ eval "$3=yes"
+else
+ eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_c_check_func
+
+# ac_fn_cxx_try_cpp LINENO
+# ------------------------
+# Try to preprocess conftest.$ac_ext, and return whether this succeeded.
+ac_fn_cxx_try_cpp ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if { { ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } > conftest.i && {
+ test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_cxx_try_cpp
+
+# ac_fn_cxx_try_link LINENO
+# -------------------------
+# Try to link conftest.$ac_ext, and return whether this succeeded.
+ac_fn_cxx_try_link ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext conftest$ac_exeext
+ if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ # Delete the IPA/IPO (Inter Procedural Analysis/Optimization) information
+ # created by the PGI compiler (conftest_ipa8_conftest.oo), as it would
+ # interfere with the next link command; also delete a directory that is
+ # left behind by Apple's compiler. We do this before executing the actions.
+ rm -rf conftest.dSYM conftest_ipa8_conftest.oo
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_cxx_try_link
+
+# ac_fn_c_check_header_mongrel LINENO HEADER VAR INCLUDES
+# -------------------------------------------------------
+# Tests whether HEADER exists, giving a warning if it cannot be compiled using
+# the include files in INCLUDES and setting the cache variable VAR
+# accordingly.
+ac_fn_c_check_header_mongrel ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if eval "test \"\${$3+set}\"" = set; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+else
+ # Is the header compilable?
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 usability" >&5
+$as_echo_n "checking $2 usability... " >&6; }
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+#include <$2>
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_header_compiler=yes
+else
+ ac_header_compiler=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_compiler" >&5
+$as_echo "$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 presence" >&5
+$as_echo_n "checking $2 presence... " >&6; }
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <$2>
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+ ac_header_preproc=yes
+else
+ ac_header_preproc=no
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_preproc" >&5
+$as_echo "$ac_header_preproc" >&6; }
+
+# So? What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in #((
+ yes:no: )
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&5
+$as_echo "$as_me: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
+ ;;
+ no:yes:* )
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: present but cannot be compiled" >&5
+$as_echo "$as_me: WARNING: $2: present but cannot be compiled" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: check for missing prerequisite headers?" >&5
+$as_echo "$as_me: WARNING: $2: check for missing prerequisite headers?" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: see the Autoconf documentation" >&5
+$as_echo "$as_me: WARNING: $2: see the Autoconf documentation" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&5
+$as_echo "$as_me: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
+( $as_echo "## -------------------------------------------------- ##
+## Report this to crac-gkarrays at lists.gforge.inria.fr ##
+## -------------------------------------------------- ##"
+ ) | sed "s/^/$as_me: WARNING: /" >&2
+ ;;
+esac
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ eval "$3=\$ac_header_compiler"
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+fi
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_c_check_header_mongrel
+
+# ac_fn_c_check_type LINENO TYPE VAR INCLUDES
+# -------------------------------------------
+# Tests whether TYPE exists after having included INCLUDES, setting cache
+# variable VAR accordingly.
+ac_fn_c_check_type ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ eval "$3=no"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+int
+main ()
+{
+if (sizeof ($2))
+ return 0;
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+int
+main ()
+{
+if (sizeof (($2)))
+ return 0;
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+
+else
+ eval "$3=yes"
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_c_check_type
+
+# ac_fn_c_find_uintX_t LINENO BITS VAR
+# ------------------------------------
+# Finds an unsigned integer type with width BITS, setting cache variable VAR
+# accordingly.
+ac_fn_c_find_uintX_t ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for uint$2_t" >&5
+$as_echo_n "checking for uint$2_t... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ eval "$3=no"
+ # Order is important - never check a type that is potentially smaller
+ # than half of the expected target width.
+ for ac_type in uint$2_t 'unsigned int' 'unsigned long int' \
+ 'unsigned long long int' 'unsigned short int' 'unsigned char'; do
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !((($ac_type) -1 >> ($2 / 2 - 1)) >> ($2 / 2 - 1) == 3)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ case $ac_type in #(
+ uint$2_t) :
+ eval "$3=yes" ;; #(
+ *) :
+ eval "$3=\$ac_type" ;;
+esac
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ if eval test \"x\$"$3"\" = x"no"; then :
+
+else
+ break
+fi
+ done
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_c_find_uintX_t
+cat >config.log <<_ACEOF
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by libGkArrays $as_me 2.1.0, which was
+generated by GNU Autoconf 2.67. Invocation command line was
+
+ $ $0 $@
+
+_ACEOF
+exec 5>>config.log
+{
+cat <<_ASUNAME
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = `(hostname || uname -n) 2>/dev/null | sed 1q`
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null || echo unknown`
+
+/bin/arch = `(/bin/arch) 2>/dev/null || echo unknown`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null || echo unknown`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown`
+/usr/bin/hostinfo = `(/usr/bin/hostinfo) 2>/dev/null || echo unknown`
+/bin/machine = `(/bin/machine) 2>/dev/null || echo unknown`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null || echo unknown`
+/bin/universe = `(/bin/universe) 2>/dev/null || echo unknown`
+
+_ASUNAME
+
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ $as_echo "PATH: $as_dir"
+ done
+IFS=$as_save_IFS
+
+} >&5
+
+cat >&5 <<_ACEOF
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+_ACEOF
+
+
+# Keep a trace of the command line.
+# Strip out --no-create and --no-recursion so they do not pile up.
+# Strip out --silent because we don't want to record it for future runs.
+# Also quote any args containing shell meta-characters.
+# Make two passes to allow for proper duplicate-argument suppression.
+ac_configure_args=
+ac_configure_args0=
+ac_configure_args1=
+ac_must_keep_next=false
+for ac_pass in 1 2
+do
+ for ac_arg
+ do
+ case $ac_arg in
+ -no-create | --no-c* | -n | -no-recursion | --no-r*) continue ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil)
+ continue ;;
+ *\'*)
+ ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ case $ac_pass in
+ 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;;
+ 2)
+ as_fn_append ac_configure_args1 " '$ac_arg'"
+ if test $ac_must_keep_next = true; then
+ ac_must_keep_next=false # Got value, back to normal.
+ else
+ case $ac_arg in
+ *=* | --config-cache | -C | -disable-* | --disable-* \
+ | -enable-* | --enable-* | -gas | --g* | -nfp | --nf* \
+ | -q | -quiet | --q* | -silent | --sil* | -v | -verb* \
+ | -with-* | --with-* | -without-* | --without-* | --x)
+ case "$ac_configure_args0 " in
+ "$ac_configure_args1"*" '$ac_arg' "* ) continue ;;
+ esac
+ ;;
+ -* ) ac_must_keep_next=true ;;
+ esac
+ fi
+ as_fn_append ac_configure_args " '$ac_arg'"
+ ;;
+ esac
+ done
+done
+{ ac_configure_args0=; unset ac_configure_args0;}
+{ ac_configure_args1=; unset ac_configure_args1;}
+
+# When interrupted or exit'd, cleanup temporary files, and complete
+# config.log. We remove comments because anyway the quotes in there
+# would cause problems or look ugly.
+# WARNING: Use '\'' to represent an apostrophe within the trap.
+# WARNING: Do not start the trap code with a newline, due to a FreeBSD 4.0 bug.
+trap 'exit_status=$?
+ # Save into config.log some information that might help in debugging.
+ {
+ echo
+
+ $as_echo "## ---------------- ##
+## Cache variables. ##
+## ---------------- ##"
+ echo
+ # The following way of writing the cache mishandles newlines in values,
+(
+ for ac_var in `(set) 2>&1 | sed -n '\''s/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'\''`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) { eval $ac_var=; unset $ac_var;} ;;
+ esac ;;
+ esac
+ done
+ (set) 2>&1 |
+ case $as_nl`(ac_space='\'' '\''; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ sed -n \
+ "s/'\''/'\''\\\\'\'''\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\''\\2'\''/p"
+ ;; #(
+ *)
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+)
+ echo
+
+ $as_echo "## ----------------- ##
+## Output variables. ##
+## ----------------- ##"
+ echo
+ for ac_var in $ac_subst_vars
+ do
+ eval ac_val=\$$ac_var
+ case $ac_val in
+ *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+ esac
+ $as_echo "$ac_var='\''$ac_val'\''"
+ done | sort
+ echo
+
+ if test -n "$ac_subst_files"; then
+ $as_echo "## ------------------- ##
+## File substitutions. ##
+## ------------------- ##"
+ echo
+ for ac_var in $ac_subst_files
+ do
+ eval ac_val=\$$ac_var
+ case $ac_val in
+ *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+ esac
+ $as_echo "$ac_var='\''$ac_val'\''"
+ done | sort
+ echo
+ fi
+
+ if test -s confdefs.h; then
+ $as_echo "## ----------- ##
+## confdefs.h. ##
+## ----------- ##"
+ echo
+ cat confdefs.h
+ echo
+ fi
+ test "$ac_signal" != 0 &&
+ $as_echo "$as_me: caught signal $ac_signal"
+ $as_echo "$as_me: exit $exit_status"
+ } >&5
+ rm -f core *.core core.conftest.* &&
+ rm -f -r conftest* confdefs* conf$$* $ac_clean_files &&
+ exit $exit_status
+' 0
+for ac_signal in 1 2 13 15; do
+ trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal
+done
+ac_signal=0
+
+# confdefs.h avoids OS command line length limits that DEFS can exceed.
+rm -f -r conftest* confdefs.h
+
+$as_echo "/* confdefs.h */" > confdefs.h
+
+# Predefined preprocessor variables.
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_NAME "$PACKAGE_NAME"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_TARNAME "$PACKAGE_TARNAME"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_VERSION "$PACKAGE_VERSION"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_STRING "$PACKAGE_STRING"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_URL "$PACKAGE_URL"
+_ACEOF
+
+
+# Let the site file select an alternate cache file if it wants to.
+# Prefer an explicitly selected file to automatically selected ones.
+ac_site_file1=NONE
+ac_site_file2=NONE
+if test -n "$CONFIG_SITE"; then
+ # We do not want a PATH search for config.site.
+ case $CONFIG_SITE in #((
+ -*) ac_site_file1=./$CONFIG_SITE;;
+ */*) ac_site_file1=$CONFIG_SITE;;
+ *) ac_site_file1=./$CONFIG_SITE;;
+ esac
+elif test "x$prefix" != xNONE; then
+ ac_site_file1=$prefix/share/config.site
+ ac_site_file2=$prefix/etc/config.site
+else
+ ac_site_file1=$ac_default_prefix/share/config.site
+ ac_site_file2=$ac_default_prefix/etc/config.site
+fi
+for ac_site_file in "$ac_site_file1" "$ac_site_file2"
+do
+ test "x$ac_site_file" = xNONE && continue
+ if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5
+$as_echo "$as_me: loading site script $ac_site_file" >&6;}
+ sed 's/^/| /' "$ac_site_file" >&5
+ . "$ac_site_file" \
+ || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "failed to load site script $ac_site_file
+See \`config.log' for more details" "$LINENO" 5 ; }
+ fi
+done
+
+if test -r "$cache_file"; then
+ # Some versions of bash will fail to source /dev/null (special files
+ # actually), so we avoid doing that. DJGPP emulates it as a regular file.
+ if test /dev/null != "$cache_file" && test -f "$cache_file"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5
+$as_echo "$as_me: loading cache $cache_file" >&6;}
+ case $cache_file in
+ [\\/]* | ?:[\\/]* ) . "$cache_file";;
+ *) . "./$cache_file";;
+ esac
+ fi
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5
+$as_echo "$as_me: creating cache $cache_file" >&6;}
+ >$cache_file
+fi
+
+# Check that the precious variables saved in the cache have kept the same
+# value.
+ac_cache_corrupted=false
+for ac_var in $ac_precious_vars; do
+ eval ac_old_set=\$ac_cv_env_${ac_var}_set
+ eval ac_new_set=\$ac_env_${ac_var}_set
+ eval ac_old_val=\$ac_cv_env_${ac_var}_value
+ eval ac_new_val=\$ac_env_${ac_var}_value
+ case $ac_old_set,$ac_new_set in
+ set,)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
+$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,set)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5
+$as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,);;
+ *)
+ if test "x$ac_old_val" != "x$ac_new_val"; then
+ # differences in whitespace do not lead to failure.
+ ac_old_val_w=`echo x $ac_old_val`
+ ac_new_val_w=`echo x $ac_new_val`
+ if test "$ac_old_val_w" != "$ac_new_val_w"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5
+$as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
+ ac_cache_corrupted=:
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5
+$as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;}
+ eval $ac_var=\$ac_old_val
+ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5
+$as_echo "$as_me: former value: \`$ac_old_val'" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5
+$as_echo "$as_me: current value: \`$ac_new_val'" >&2;}
+ fi;;
+ esac
+ # Pass precious variables to config.status.
+ if test "$ac_new_set" = set; then
+ case $ac_new_val in
+ *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
+ *) ac_arg=$ac_var=$ac_new_val ;;
+ esac
+ case " $ac_configure_args " in
+ *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy.
+ *) as_fn_append ac_configure_args " '$ac_arg'" ;;
+ esac
+ fi
+done
+if $ac_cache_corrupted; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
+$as_echo "$as_me: error: changes in the environment can compromise the build" >&2;}
+ as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
+fi
+## -------------------- ##
+## Main body of script. ##
+## -------------------- ##
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+PACKAGE_DESCRIPTION="Library for building and using GkArrays"
+
+
+
+
+
+
+
+LIB_CURRENT=2
+LIB_REVISION=0
+LIB_AGE=1
+LIB_VERSION=$LIB_CURRENT:$LIB_REVISION:$LIB_AGE
+
+
+
+LIB_VERSION_EXT="2"_"1"_"0"
+
+
+if test x"$CFLAGS" == "x"; then :
+ CFLAGS=""
+fi
+if test x"$CPPFLAGS" == "x"; then :
+ CPPFLAGS=""
+fi
+if test x"$CXXFLAGS" == "x"; then :
+ CXXFLAGS=""
+fi
+if test x"$LDFLAGS" == "x"; then :
+ LDFLAGS=""
+fi
+
+ac_aux_dir=
+for ac_dir in config "$srcdir"/config; do
+ if test -f "$ac_dir/install-sh"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install-sh -c"
+ break
+ elif test -f "$ac_dir/install.sh"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install.sh -c"
+ break
+ elif test -f "$ac_dir/shtool"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/shtool install -c"
+ break
+ fi
+done
+if test -z "$ac_aux_dir"; then
+ as_fn_error $? "cannot find install-sh, install.sh, or shtool in config \"$srcdir\"/config" "$LINENO" 5
+fi
+
+# These three variables are undocumented and unsupported,
+# and are intended to be withdrawn in a future Autoconf release.
+# They can cause serious problems if a builder's source tree is in a directory
+# whose full name contains unusual characters.
+ac_config_guess="$SHELL $ac_aux_dir/config.guess" # Please don't use this var.
+ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var.
+ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var.
+
+
+ac_config_headers="$ac_config_headers config/config.h"
+
+am__api_version='1.11'
+
+# Find a good install program. We prefer a C program (faster),
+# so one script is as good as another. But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AmigaOS /C/install, which installs bootblocks on floppy discs
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# OS/2's system install, which has a completely different semantic
+# ./install, which can be erroneously created by make from ./install.sh.
+# Reject install programs that cannot install multiple files.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5
+$as_echo_n "checking for a BSD-compatible install... " >&6; }
+if test -z "$INSTALL"; then
+if test "${ac_cv_path_install+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ # Account for people who put trailing slashes in PATH elements.
+case $as_dir/ in #((
+ ./ | .// | /[cC]/* | \
+ /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
+ ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \
+ /usr/ucb/* ) ;;
+ *)
+ # OSF1 and SCO ODT 3.0 have their own names for install.
+ # Don't use installbsd from OSF since it installs stuff as root
+ # by default.
+ for ac_prog in ginstall scoinst install; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
+ if test $ac_prog = install &&
+ grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # AIX install. It has an incompatible calling convention.
+ :
+ elif test $ac_prog = install &&
+ grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # program-specific install script used by HP pwplus--don't use.
+ :
+ else
+ rm -rf conftest.one conftest.two conftest.dir
+ echo one > conftest.one
+ echo two > conftest.two
+ mkdir conftest.dir
+ if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" &&
+ test -s conftest.one && test -s conftest.two &&
+ test -s conftest.dir/conftest.one &&
+ test -s conftest.dir/conftest.two
+ then
+ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
+ break 3
+ fi
+ fi
+ fi
+ done
+ done
+ ;;
+esac
+
+ done
+IFS=$as_save_IFS
+
+rm -rf conftest.one conftest.two conftest.dir
+
+fi
+ if test "${ac_cv_path_install+set}" = set; then
+ INSTALL=$ac_cv_path_install
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for INSTALL within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ INSTALL=$ac_install_sh
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5
+$as_echo "$INSTALL" >&6; }
+
+# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
+# It thinks the first close brace ends the variable substitution.
+test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5
+$as_echo_n "checking whether build environment is sane... " >&6; }
+# Just in case
+sleep 1
+echo timestamp > conftest.file
+# Reject unsafe characters in $srcdir or the absolute working directory
+# name. Accept space and tab only in the latter.
+am_lf='
+'
+case `pwd` in
+ *[\\\"\#\$\&\'\`$am_lf]*)
+ as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5 ;;
+esac
+case $srcdir in
+ *[\\\"\#\$\&\'\`$am_lf\ \ ]*)
+ as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5 ;;
+esac
+
+# Do `set' in a subshell so we don't clobber the current shell's
+# arguments. Must try -L first in case configure is actually a
+# symlink; some systems play weird games with the mod time of symlinks
+# (eg FreeBSD returns the mod time of the symlink's containing
+# directory).
+if (
+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
+ if test "$*" = "X"; then
+ # -L didn't work.
+ set X `ls -t "$srcdir/configure" conftest.file`
+ fi
+ rm -f conftest.file
+ if test "$*" != "X $srcdir/configure conftest.file" \
+ && test "$*" != "X conftest.file $srcdir/configure"; then
+
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ as_fn_error $? "ls -t appears to fail. Make sure there is not a broken
+alias in your environment" "$LINENO" 5
+ fi
+
+ test "$2" = conftest.file
+ )
+then
+ # Ok.
+ :
+else
+ as_fn_error $? "newly created file is older than distributed files!
+Check your system clock" "$LINENO" 5
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+test "$program_prefix" != NONE &&
+ program_transform_name="s&^&$program_prefix&;$program_transform_name"
+# Use a double $ so make ignores it.
+test "$program_suffix" != NONE &&
+ program_transform_name="s&\$&$program_suffix&;$program_transform_name"
+# Double any \ or $.
+# By default was `s,x,x', remove it if useless.
+ac_script='s/[\\$]/&&/g;s/;s,x,x,$//'
+program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`
+
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
+
+if test x"${MISSING+set}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;;
+ *)
+ MISSING="\${SHELL} $am_aux_dir/missing" ;;
+ esac
+fi
+# Use eval to expand $SHELL
+if eval "$MISSING --run true"; then
+ am_missing_run="$MISSING --run "
+else
+ am_missing_run=
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`missing' script is too old or missing" >&5
+$as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
+fi
+
+if test x"${install_sh}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
+ *)
+ install_sh="\${SHELL} $am_aux_dir/install-sh"
+ esac
+fi
+
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'. However `strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
+# will honor the `STRIP' environment variable to overrule this program.
+if test "$cross_compiling" != no; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
+set dummy ${ac_tool_prefix}strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_STRIP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$STRIP"; then
+ ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_STRIP="${ac_tool_prefix}strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+STRIP=$ac_cv_prog_STRIP
+if test -n "$STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5
+$as_echo "$STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_STRIP"; then
+ ac_ct_STRIP=$STRIP
+ # Extract the first word of "strip", so it can be a program name with args.
+set dummy strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_STRIP"; then
+ ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_STRIP="strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
+if test -n "$ac_ct_STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5
+$as_echo "$ac_ct_STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_STRIP" = x; then
+ STRIP=":"
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+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ STRIP=$ac_ct_STRIP
+ fi
+else
+ STRIP="$ac_cv_prog_STRIP"
+fi
+
+fi
+INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5
+$as_echo_n "checking for a thread-safe mkdir -p... " >&6; }
+if test -z "$MKDIR_P"; then
+ if test "${ac_cv_path_mkdir+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/opt/sfw/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in mkdir gmkdir; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue
+ case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #(
+ 'mkdir (GNU coreutils) '* | \
+ 'mkdir (coreutils) '* | \
+ 'mkdir (fileutils) '4.1*)
+ ac_cv_path_mkdir=$as_dir/$ac_prog$ac_exec_ext
+ break 3;;
+ esac
+ done
+ done
+ done
+IFS=$as_save_IFS
+
+fi
+
+ test -d ./--version && rmdir ./--version
+ if test "${ac_cv_path_mkdir+set}" = set; then
+ MKDIR_P="$ac_cv_path_mkdir -p"
+ else
+ # As a last resort, use the slow shell script. Don't cache a
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+ # break other packages using the cache if that directory is
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+ MKDIR_P="$ac_install_sh -d"
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
+$as_echo "$MKDIR_P" >&6; }
+
+mkdir_p="$MKDIR_P"
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+ */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
+esac
+
+for ac_prog in gawk mawk nawk awk
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
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+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_AWK+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$AWK"; then
+ ac_cv_prog_AWK="$AWK" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_AWK="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+AWK=$ac_cv_prog_AWK
+if test -n "$AWK"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5
+$as_echo "$AWK" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
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+
+
+ test -n "$AWK" && break
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+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
+set x ${MAKE-make}
+ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
+if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.make <<\_ACEOF
+SHELL = /bin/sh
+all:
+ @echo '@@@%%%=$(MAKE)=@@@%%%'
+_ACEOF
+# GNU make sometimes prints "make[1]: Entering ...", which would confuse us.
+case `${MAKE-make} -f conftest.make 2>/dev/null` in
+ *@@@%%%=?*=@@@%%%*)
+ eval ac_cv_prog_make_${ac_make}_set=yes;;
+ *)
+ eval ac_cv_prog_make_${ac_make}_set=no;;
+esac
+rm -f conftest.make
+fi
+if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ SET_MAKE=
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ SET_MAKE="MAKE=${MAKE-make}"
+fi
+
+rm -rf .tst 2>/dev/null
+mkdir .tst 2>/dev/null
+if test -d .tst; then
+ am__leading_dot=.
+else
+ am__leading_dot=_
+fi
+rmdir .tst 2>/dev/null
+
+if test "`cd $srcdir && pwd`" != "`pwd`"; then
+ # Use -I$(srcdir) only when $(srcdir) != ., so that make's output
+ # is not polluted with repeated "-I."
+ am__isrc=' -I$(srcdir)'
+ # test to see if srcdir already configured
+ if test -f $srcdir/config.status; then
+ as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5
+ fi
+fi
+
+# test whether we have cygpath
+if test -z "$CYGPATH_W"; then
+ if (cygpath --version) >/dev/null 2>/dev/null; then
+ CYGPATH_W='cygpath -w'
+ else
+ CYGPATH_W=echo
+ fi
+fi
+
+
+# Define the identity of the package.
+ PACKAGE='libGkArrays'
+ VERSION='2.1.0'
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE "$PACKAGE"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define VERSION "$VERSION"
+_ACEOF
+
+# Some tools Automake needs.
+
+ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"}
+
+
+AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"}
+
+
+AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"}
+
+
+AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"}
+
+
+MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
+
+# We need awk for the "check" target. The system "awk" is bad on
+# some platforms.
+# Always define AMTAR for backward compatibility.
+
+AMTAR=${AMTAR-"${am_missing_run}tar"}
+
+am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'
+
+
+
+
+
+
+
+
+# Checks for programs.
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+if test -z "$CXX"; then
+ if test -n "$CCC"; then
+ CXX=$CCC
+ else
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
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+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
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+ if test -n "$CXX"; then
+ ac_cv_prog_CXX="$CXX" # Let the user override the test.
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+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
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+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CXX=$ac_cv_prog_CXX
+if test -n "$CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5
+$as_echo "$CXX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CXX" && break
+ done
+fi
+if test -z "$CXX"; then
+ ac_ct_CXX=$CXX
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CXX"; then
+ ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CXX="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
+if test -n "$ac_ct_CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5
+$as_echo "$ac_ct_CXX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CXX" && break
+done
+
+ if test "x$ac_ct_CXX" = x; then
+ CXX="g++"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CXX=$ac_ct_CXX
+ fi
+fi
+
+ fi
+fi
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+ { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
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+ *) ac_try_echo=$ac_try;;
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+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ sed '10a\
+... rest of stderr output deleted ...
+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
+
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out"
+# Try to create an executable without -o first, disregard a.out.
+# It will help us diagnose broken compilers, and finding out an intuition
+# of exeext.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C++ compiler works" >&5
+$as_echo_n "checking whether the C++ compiler works... " >&6; }
+ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
+
+# The possible output files:
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+
+ac_rmfiles=
+for ac_file in $ac_files
+do
+ case $ac_file in
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+ * ) ac_rmfiles="$ac_rmfiles $ac_file";;
+ esac
+done
+rm -f $ac_rmfiles
+
+if { { ac_try="$ac_link_default"
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+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
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+ (eval "$ac_link_default") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ # Autoconf-2.13 could set the ac_cv_exeext variable to `no'.
+# So ignore a value of `no', otherwise this would lead to `EXEEXT = no'
+# in a Makefile. We should not override ac_cv_exeext if it was cached,
+# so that the user can short-circuit this test for compilers unknown to
+# Autoconf.
+for ac_file in $ac_files ''
+do
+ test -f "$ac_file" || continue
+ case $ac_file in
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+ ;;
+ [ab].out )
+ # We found the default executable, but exeext='' is most
+ # certainly right.
+ break;;
+ *.* )
+ if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
+ then :; else
+ ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ fi
+ # We set ac_cv_exeext here because the later test for it is not
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+ # argument, so we may need to know it at that point already.
+ # Even if this section looks crufty: it has the advantage of
+ # actually working.
+ break;;
+ * )
+ break;;
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+test "$ac_cv_exeext" = no && ac_cv_exeext=
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+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
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+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler default output file name" >&5
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+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5
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+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
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+ ac_status=$?
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+ case $ac_file in
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+ *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ break;;
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+else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
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+
+rm -f conftest.$ac_ext
+EXEEXT=$ac_cv_exeext
+ac_exeext=$EXEEXT
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdio.h>
+int
+main ()
+{
+FILE *f = fopen ("conftest.out", "w");
+ return ferror (f) || fclose (f) != 0;
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files="$ac_clean_files conftest.out"
+# Check that the compiler produces executables we can run. If not, either
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+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5
+$as_echo_n "checking whether we are cross compiling... " >&6; }
+if test "$cross_compiling" != yes; then
+ { { ac_try="$ac_link"
+case "(($ac_try" in
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+ *) ac_try_echo=$ac_try;;
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+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+ if { ac_try='./conftest$ac_cv_exeext'
+ { { case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; }; then
+ cross_compiling=no
+ else
+ if test "$cross_compiling" = maybe; then
+ cross_compiling=yes
+ else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot run C++ compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details" "$LINENO" 5 ; }
+ fi
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5
+$as_echo "$cross_compiling" >&6; }
+
+rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out
+ac_clean_files=$ac_clean_files_save
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5
+$as_echo_n "checking for suffix of object files... " >&6; }
+if test "${ac_cv_objext+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.o conftest.obj
+if { { ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compile") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ for ac_file in conftest.o conftest.obj conftest.*; do
+ test -f "$ac_file" || continue;
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;;
+ *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'`
+ break;;
+ esac
+done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot compute suffix of object files: cannot compile
+See \`config.log' for more details" "$LINENO" 5 ; }
+fi
+rm -f conftest.$ac_cv_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5
+$as_echo "$ac_cv_objext" >&6; }
+OBJEXT=$ac_cv_objext
+ac_objext=$OBJEXT
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5
+$as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; }
+if test "${ac_cv_cxx_compiler_gnu+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_compiler_gnu=yes
+else
+ ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_cxx_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5
+$as_echo "$ac_cv_cxx_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GXX=yes
+else
+ GXX=
+fi
+ac_test_CXXFLAGS=${CXXFLAGS+set}
+ac_save_CXXFLAGS=$CXXFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5
+$as_echo_n "checking whether $CXX accepts -g... " >&6; }
+if test "${ac_cv_prog_cxx_g+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_cxx_werror_flag=$ac_cxx_werror_flag
+ ac_cxx_werror_flag=yes
+ ac_cv_prog_cxx_g=no
+ CXXFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_prog_cxx_g=yes
+else
+ CXXFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+
+else
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+ CXXFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_prog_cxx_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5
+$as_echo "$ac_cv_prog_cxx_g" >&6; }
+if test "$ac_test_CXXFLAGS" = set; then
+ CXXFLAGS=$ac_save_CXXFLAGS
+elif test $ac_cv_prog_cxx_g = yes; then
+ if test "$GXX" = yes; then
+ CXXFLAGS="-g -O2"
+ else
+ CXXFLAGS="-g"
+ fi
+else
+ if test "$GXX" = yes; then
+ CXXFLAGS="-O2"
+ else
+ CXXFLAGS=
+ fi
+fi
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+DEPDIR="${am__leading_dot}deps"
+
+ac_config_commands="$ac_config_commands depfiles"
+
+
+am_make=${MAKE-make}
+cat > confinc << 'END'
+am__doit:
+ @echo this is the am__doit target
+.PHONY: am__doit
+END
+# If we don't find an include directive, just comment out the code.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5
+$as_echo_n "checking for style of include used by $am_make... " >&6; }
+am__include="#"
+am__quote=
+_am_result=none
+# First try GNU make style include.
+echo "include confinc" > confmf
+# Ignore all kinds of additional output from `make'.
+case `$am_make -s -f confmf 2> /dev/null` in #(
+*the\ am__doit\ target*)
+ am__include=include
+ am__quote=
+ _am_result=GNU
+ ;;
+esac
+# Now try BSD make style include.
+if test "$am__include" = "#"; then
+ echo '.include "confinc"' > confmf
+ case `$am_make -s -f confmf 2> /dev/null` in #(
+ *the\ am__doit\ target*)
+ am__include=.include
+ am__quote="\""
+ _am_result=BSD
+ ;;
+ esac
+fi
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5
+$as_echo "$_am_result" >&6; }
+rm -f confinc confmf
+
+# Check whether --enable-dependency-tracking was given.
+if test "${enable_dependency_tracking+set}" = set; then :
+ enableval=$enable_dependency_tracking;
+fi
+
+if test "x$enable_dependency_tracking" != xno; then
+ am_depcomp="$ac_aux_dir/depcomp"
+ AMDEPBACKSLASH='\'
+fi
+ if test "x$enable_dependency_tracking" != xno; then
+ AMDEP_TRUE=
+ AMDEP_FALSE='#'
+else
+ AMDEP_TRUE='#'
+ AMDEP_FALSE=
+fi
+
+
+
+depcc="$CXX" am_compiler_list=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CXX_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
+ case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CXX_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CXX_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CXX_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CXX_dependencies_compiler_type" >&6; }
+CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CXX_dependencies_compiler_type" = gcc3; then
+ am__fastdepCXX_TRUE=
+ am__fastdepCXX_FALSE='#'
+else
+ am__fastdepCXX_TRUE='#'
+ am__fastdepCXX_FALSE=
+fi
+
+
+for ac_prog in gawk mawk nawk awk
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_AWK+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$AWK"; then
+ ac_cv_prog_AWK="$AWK" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_AWK="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+AWK=$ac_cv_prog_AWK
+if test -n "$AWK"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5
+$as_echo "$AWK" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$AWK" && break
+done
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}gcc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="${ac_tool_prefix}gcc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_CC"; then
+ ac_ct_CC=$CC
+ # Extract the first word of "gcc", so it can be a program name with args.
+set dummy gcc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CC="gcc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+else
+ CC="$ac_cv_prog_CC"
+fi
+
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}cc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="${ac_tool_prefix}cc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ fi
+fi
+if test -z "$CC"; then
+ # Extract the first word of "cc", so it can be a program name with args.
+set dummy cc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+ ac_prog_rejected=no
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
+ ac_prog_rejected=yes
+ continue
+ fi
+ ac_cv_prog_CC="cc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+if test $ac_prog_rejected = yes; then
+ # We found a bogon in the path, so make sure we never use it.
+ set dummy $ac_cv_prog_CC
+ shift
+ if test $# != 0; then
+ # We chose a different compiler from the bogus one.
+ # However, it has the same basename, so the bogon will be chosen
+ # first if we set CC to just the basename; use the full file name.
+ shift
+ ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@"
+ fi
+fi
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in cl.exe
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CC" && break
+ done
+fi
+if test -z "$CC"; then
+ ac_ct_CC=$CC
+ for ac_prog in cl.exe
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CC="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CC" && break
+done
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+fi
+
+fi
+
+
+test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "no acceptable C compiler found in \$PATH
+See \`config.log' for more details" "$LINENO" 5 ; }
+
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+ { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ sed '10a\
+... rest of stderr output deleted ...
+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5
+$as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
+if test "${ac_cv_c_compiler_gnu+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_compiler_gnu=yes
+else
+ ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_c_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5
+$as_echo "$ac_cv_c_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GCC=yes
+else
+ GCC=
+fi
+ac_test_CFLAGS=${CFLAGS+set}
+ac_save_CFLAGS=$CFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5
+$as_echo_n "checking whether $CC accepts -g... " >&6; }
+if test "${ac_cv_prog_cc_g+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_c_werror_flag=$ac_c_werror_flag
+ ac_c_werror_flag=yes
+ ac_cv_prog_cc_g=no
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
+else
+ CFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+
+else
+ ac_c_werror_flag=$ac_save_c_werror_flag
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_c_werror_flag=$ac_save_c_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5
+$as_echo "$ac_cv_prog_cc_g" >&6; }
+if test "$ac_test_CFLAGS" = set; then
+ CFLAGS=$ac_save_CFLAGS
+elif test $ac_cv_prog_cc_g = yes; then
+ if test "$GCC" = yes; then
+ CFLAGS="-g -O2"
+ else
+ CFLAGS="-g"
+ fi
+else
+ if test "$GCC" = yes; then
+ CFLAGS="-O2"
+ else
+ CFLAGS=
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5
+$as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
+if test "${ac_cv_prog_cc_c89+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_prog_cc_c89=no
+ac_save_CC=$CC
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdarg.h>
+#include <stdio.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */
+struct buf { int x; };
+FILE * (*rcsopen) (struct buf *, struct stat *, int);
+static char *e (p, i)
+ char **p;
+ int i;
+{
+ return p[i];
+}
+static char *f (char * (*g) (char **, int), char **p, ...)
+{
+ char *s;
+ va_list v;
+ va_start (v,p);
+ s = g (p, va_arg (v,int));
+ va_end (v);
+ return s;
+}
+
+/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has
+ function prototypes and stuff, but not '\xHH' hex character constants.
+ These don't provoke an error unfortunately, instead are silently treated
+ as 'x'. The following induces an error, until -std is added to get
+ proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an
+ array size at least. It's necessary to write '\x00'==0 to get something
+ that's true only with -std. */
+int osf4_cc_array ['\x00' == 0 ? 1 : -1];
+
+/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters
+ inside strings and character constants. */
+#define FOO(x) 'x'
+int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1];
+
+int test (int i, double x);
+struct s1 {int (*f) (int a);};
+struct s2 {int (*f) (double a);};
+int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
+int argc;
+char **argv;
+int
+main ()
+{
+return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1];
+ ;
+ return 0;
+}
+_ACEOF
+for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \
+ -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
+do
+ CC="$ac_save_CC $ac_arg"
+ if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_c89=$ac_arg
+fi
+rm -f core conftest.err conftest.$ac_objext
+ test "x$ac_cv_prog_cc_c89" != "xno" && break
+done
+rm -f conftest.$ac_ext
+CC=$ac_save_CC
+
+fi
+# AC_CACHE_VAL
+case "x$ac_cv_prog_cc_c89" in
+ x)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
+$as_echo "none needed" >&6; } ;;
+ xno)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
+$as_echo "unsupported" >&6; } ;;
+ *)
+ CC="$CC $ac_cv_prog_cc_c89"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5
+$as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
+esac
+if test "x$ac_cv_prog_cc_c89" != xno; then :
+
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+depcc="$CC" am_compiler_list=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CC_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
+ case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CC_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CC_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CC_dependencies_compiler_type" >&6; }
+CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
+ am__fastdepCC_TRUE=
+ am__fastdepCC_FALSE='#'
+else
+ am__fastdepCC_TRUE='#'
+ am__fastdepCC_FALSE=
+fi
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C preprocessor" >&5
+$as_echo_n "checking how to run the C preprocessor... " >&6; }
+# On Suns, sometimes $CPP names a directory.
+if test -n "$CPP" && test -d "$CPP"; then
+ CPP=
+fi
+if test -z "$CPP"; then
+ if test "${ac_cv_prog_CPP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ # Double quotes because CPP needs to be expanded
+ for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp"
+ do
+ ac_preproc_ok=false
+for ac_c_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+
+else
+ # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+ # Broken: success on invalid input.
+continue
+else
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.i conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then :
+ break
+fi
+
+ done
+ ac_cv_prog_CPP=$CPP
+
+fi
+ CPP=$ac_cv_prog_CPP
+else
+ ac_cv_prog_CPP=$CPP
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPP" >&5
+$as_echo "$CPP" >&6; }
+ac_preproc_ok=false
+for ac_c_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+
+else
+ # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+ # Broken: success on invalid input.
+continue
+else
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.i conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then :
+
+else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details" "$LINENO" 5 ; }
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ln -s works" >&5
+$as_echo_n "checking whether ln -s works... " >&6; }
+LN_S=$as_ln_s
+if test "$LN_S" = "ln -s"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no, using $LN_S" >&5
+$as_echo "no, using $LN_S" >&6; }
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
+set x ${MAKE-make}
+ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
+if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.make <<\_ACEOF
+SHELL = /bin/sh
+all:
+ @echo '@@@%%%=$(MAKE)=@@@%%%'
+_ACEOF
+# GNU make sometimes prints "make[1]: Entering ...", which would confuse us.
+case `${MAKE-make} -f conftest.make 2>/dev/null` in
+ *@@@%%%=?*=@@@%%%*)
+ eval ac_cv_prog_make_${ac_make}_set=yes;;
+ *)
+ eval ac_cv_prog_make_${ac_make}_set=no;;
+esac
+rm -f conftest.make
+fi
+if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ SET_MAKE=
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ SET_MAKE="MAKE=${MAKE-make}"
+fi
+
+# Extract the first word of "texi2dvi", so it can be a program name with args.
+set dummy texi2dvi; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_TEXI2DVI+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$TEXI2DVI"; then
+ ac_cv_prog_TEXI2DVI="$TEXI2DVI" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_TEXI2DVI="texi2dvi"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+TEXI2DVI=$ac_cv_prog_TEXI2DVI
+if test -n "$TEXI2DVI"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $TEXI2DVI" >&5
+$as_echo "$TEXI2DVI" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+# Extract the first word of "pdftex", so it can be a program name with args.
+set dummy pdftex; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_PDFTEX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$PDFTEX"; then
+ ac_cv_prog_PDFTEX="$PDFTEX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_PDFTEX="pdftex"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+PDFTEX=$ac_cv_prog_PDFTEX
+if test -n "$PDFTEX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PDFTEX" >&5
+$as_echo "$PDFTEX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+# Extract the first word of "kpsewhich", so it can be a program name with args.
+set dummy kpsewhich; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_KPSEWHICH+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$KPSEWHICH"; then
+ ac_cv_prog_KPSEWHICH="$KPSEWHICH" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_KPSEWHICH="kpsewhich"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+KPSEWHICH=$ac_cv_prog_KPSEWHICH
+if test -n "$KPSEWHICH"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $KPSEWHICH" >&5
+$as_echo "$KPSEWHICH" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+BUILD_DOC=false
+if test "x$TEXI2DVI" != "xtexi2dvi" || test "x$PDFTEX" != "xpdftex"; then :
+ BUILD_DOC=false
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: The 'texi2dvi' or 'pdftex' program could not be found. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases." >&5
+$as_echo "$as_me: WARNING: The 'texi2dvi' or 'pdftex' program could not be found. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases." >&2;}
+fi
+
+if test "x$KPSEWHICH" != "xkpsewhich" || test "$(kpsewhich -show-path=fmt)" == "/nonesuch"; then :
+ BUILD_DOC=false
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: The 'texi2dvi' or 'pdftex' is missing a correct latex installation. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases." >&5
+$as_echo "$as_me: WARNING: The 'texi2dvi' or 'pdftex' is missing a correct latex installation. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases." >&2;}
+fi
+ if $BUILD_DOC; then
+ BUILD_DOC_TRUE=
+ BUILD_DOC_FALSE='#'
+else
+ BUILD_DOC_TRUE='#'
+ BUILD_DOC_FALSE=
+fi
+
+
+case `pwd` in
+ *\ * | *\ *)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Libtool does not cope well with whitespace in \`pwd\`" >&5
+$as_echo "$as_me: WARNING: Libtool does not cope well with whitespace in \`pwd\`" >&2;} ;;
+esac
+
+
+
+macro_version='2.2.6b'
+macro_revision='1.3017'
+
+
+
+
+
+
+
+
+
+
+
+
+
+ltmain="$ac_aux_dir/ltmain.sh"
+
+# Make sure we can run config.sub.
+$SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 ||
+ as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5
+$as_echo_n "checking build system type... " >&6; }
+if test "${ac_cv_build+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_build_alias=$build_alias
+test "x$ac_build_alias" = x &&
+ ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"`
+test "x$ac_build_alias" = x &&
+ as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5
+ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` ||
+ as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5
+$as_echo "$ac_cv_build" >&6; }
+case $ac_cv_build in
+*-*-*) ;;
+*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5 ;;
+esac
+build=$ac_cv_build
+ac_save_IFS=$IFS; IFS='-'
+set x $ac_cv_build
+shift
+build_cpu=$1
+build_vendor=$2
+shift; shift
+# Remember, the first character of IFS is used to create $*,
+# except with old shells:
+build_os=$*
+IFS=$ac_save_IFS
+case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5
+$as_echo_n "checking host system type... " >&6; }
+if test "${ac_cv_host+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "x$host_alias" = x; then
+ ac_cv_host=$ac_cv_build
+else
+ ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` ||
+ as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_host" >&5
+$as_echo "$ac_cv_host" >&6; }
+case $ac_cv_host in
+*-*-*) ;;
+*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5 ;;
+esac
+host=$ac_cv_host
+ac_save_IFS=$IFS; IFS='-'
+set x $ac_cv_host
+shift
+host_cpu=$1
+host_vendor=$2
+shift; shift
+# Remember, the first character of IFS is used to create $*,
+# except with old shells:
+host_os=$*
+IFS=$ac_save_IFS
+case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a sed that does not truncate output" >&5
+$as_echo_n "checking for a sed that does not truncate output... " >&6; }
+if test "${ac_cv_path_SED+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_script=s/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb/
+ for ac_i in 1 2 3 4 5 6 7; do
+ ac_script="$ac_script$as_nl$ac_script"
+ done
+ echo "$ac_script" 2>/dev/null | sed 99q >conftest.sed
+ { ac_script=; unset ac_script;}
+ if test -z "$SED"; then
+ ac_path_SED_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in sed gsed; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_SED="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_SED" && $as_test_x "$ac_path_SED"; } || continue
+# Check for GNU ac_path_SED and select it if it is found.
+ # Check for GNU $ac_path_SED
+case `"$ac_path_SED" --version 2>&1` in
+*GNU*)
+ ac_cv_path_SED="$ac_path_SED" ac_path_SED_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo '' >> "conftest.nl"
+ "$ac_path_SED" -f conftest.sed < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
+ if test $ac_count -gt ${ac_path_SED_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_SED="$ac_path_SED"
+ ac_path_SED_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_SED_found && break 3
+ done
+ done
+ done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_SED"; then
+ as_fn_error $? "no acceptable sed could be found in \$PATH" "$LINENO" 5
+ fi
+else
+ ac_cv_path_SED=$SED
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_SED" >&5
+$as_echo "$ac_cv_path_SED" >&6; }
+ SED="$ac_cv_path_SED"
+ rm -f conftest.sed
+
+test -z "$SED" && SED=sed
+Xsed="$SED -e 1s/^X//"
+
+
+
+
+
+
+
+
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5
+$as_echo_n "checking for grep that handles long lines and -e... " >&6; }
+if test "${ac_cv_path_GREP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$GREP"; then
+ ac_path_GREP_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in grep ggrep; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue
+# Check for GNU ac_path_GREP and select it if it is found.
+ # Check for GNU $ac_path_GREP
+case `"$ac_path_GREP" --version 2>&1` in
+*GNU*)
+ ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo 'GREP' >> "conftest.nl"
+ "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
+ if test $ac_count -gt ${ac_path_GREP_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_GREP="$ac_path_GREP"
+ ac_path_GREP_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_GREP_found && break 3
+ done
+ done
+ done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_GREP"; then
+ as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+ fi
+else
+ ac_cv_path_GREP=$GREP
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5
+$as_echo "$ac_cv_path_GREP" >&6; }
+ GREP="$ac_cv_path_GREP"
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5
+$as_echo_n "checking for egrep... " >&6; }
+if test "${ac_cv_path_EGREP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if echo a | $GREP -E '(a|b)' >/dev/null 2>&1
+ then ac_cv_path_EGREP="$GREP -E"
+ else
+ if test -z "$EGREP"; then
+ ac_path_EGREP_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in egrep; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue
+# Check for GNU ac_path_EGREP and select it if it is found.
+ # Check for GNU $ac_path_EGREP
+case `"$ac_path_EGREP" --version 2>&1` in
+*GNU*)
+ ac_cv_path_EGREP="$ac_path_EGREP" ac_path_EGREP_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo 'EGREP' >> "conftest.nl"
+ "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
+ if test $ac_count -gt ${ac_path_EGREP_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_EGREP="$ac_path_EGREP"
+ ac_path_EGREP_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_EGREP_found && break 3
+ done
+ done
+ done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_EGREP"; then
+ as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+ fi
+else
+ ac_cv_path_EGREP=$EGREP
+fi
+
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5
+$as_echo "$ac_cv_path_EGREP" >&6; }
+ EGREP="$ac_cv_path_EGREP"
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for fgrep" >&5
+$as_echo_n "checking for fgrep... " >&6; }
+if test "${ac_cv_path_FGREP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if echo 'ab*c' | $GREP -F 'ab*c' >/dev/null 2>&1
+ then ac_cv_path_FGREP="$GREP -F"
+ else
+ if test -z "$FGREP"; then
+ ac_path_FGREP_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in fgrep; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_FGREP="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_FGREP" && $as_test_x "$ac_path_FGREP"; } || continue
+# Check for GNU ac_path_FGREP and select it if it is found.
+ # Check for GNU $ac_path_FGREP
+case `"$ac_path_FGREP" --version 2>&1` in
+*GNU*)
+ ac_cv_path_FGREP="$ac_path_FGREP" ac_path_FGREP_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo 'FGREP' >> "conftest.nl"
+ "$ac_path_FGREP" FGREP < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
+ if test $ac_count -gt ${ac_path_FGREP_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_FGREP="$ac_path_FGREP"
+ ac_path_FGREP_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_FGREP_found && break 3
+ done
+ done
+ done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_FGREP"; then
+ as_fn_error $? "no acceptable fgrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+ fi
+else
+ ac_cv_path_FGREP=$FGREP
+fi
+
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_FGREP" >&5
+$as_echo "$ac_cv_path_FGREP" >&6; }
+ FGREP="$ac_cv_path_FGREP"
+
+
+test -z "$GREP" && GREP=grep
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# Check whether --with-gnu-ld was given.
+if test "${with_gnu_ld+set}" = set; then :
+ withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes
+else
+ with_gnu_ld=no
+fi
+
+ac_prog=ld
+if test "$GCC" = yes; then
+ # Check if gcc -print-prog-name=ld gives a path.
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ld used by $CC" >&5
+$as_echo_n "checking for ld used by $CC... " >&6; }
+ case $host in
+ *-*-mingw*)
+ # gcc leaves a trailing carriage return which upsets mingw
+ ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+ *)
+ ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+ esac
+ case $ac_prog in
+ # Accept absolute paths.
+ [\\/]* | ?:[\\/]*)
+ re_direlt='/[^/][^/]*/\.\./'
+ # Canonicalize the pathname of ld
+ ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'`
+ while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do
+ ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"`
+ done
+ test -z "$LD" && LD="$ac_prog"
+ ;;
+ "")
+ # If it fails, then pretend we aren't using GCC.
+ ac_prog=ld
+ ;;
+ *)
+ # If it is relative, then search for the first ld in PATH.
+ with_gnu_ld=unknown
+ ;;
+ esac
+elif test "$with_gnu_ld" = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU ld" >&5
+$as_echo_n "checking for GNU ld... " >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for non-GNU ld" >&5
+$as_echo_n "checking for non-GNU ld... " >&6; }
+fi
+if test "${lt_cv_path_LD+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$LD"; then
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+ lt_cv_path_LD="$ac_dir/$ac_prog"
+ # Check to see if the program is GNU ld. I'd rather use --version,
+ # but apparently some variants of GNU ld only accept -v.
+ # Break only if it was the GNU/non-GNU ld that we prefer.
+ case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+ *GNU* | *'with BFD'*)
+ test "$with_gnu_ld" != no && break
+ ;;
+ *)
+ test "$with_gnu_ld" != yes && break
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+else
+ lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi
+fi
+
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LD" >&5
+$as_echo "$LD" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+test -z "$LD" && as_fn_error $? "no acceptable ld found in \$PATH" "$LINENO" 5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if the linker ($LD) is GNU ld" >&5
+$as_echo_n "checking if the linker ($LD) is GNU ld... " >&6; }
+if test "${lt_cv_prog_gnu_ld+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ # I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+ lt_cv_prog_gnu_ld=yes
+ ;;
+*)
+ lt_cv_prog_gnu_ld=no
+ ;;
+esac
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_gnu_ld" >&5
+$as_echo "$lt_cv_prog_gnu_ld" >&6; }
+with_gnu_ld=$lt_cv_prog_gnu_ld
+
+
+
+
+
+
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for BSD- or MS-compatible name lister (nm)" >&5
+$as_echo_n "checking for BSD- or MS-compatible name lister (nm)... " >&6; }
+if test "${lt_cv_path_NM+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$NM"; then
+ # Let the user override the test.
+ lt_cv_path_NM="$NM"
+else
+ lt_nm_to_check="${ac_tool_prefix}nm"
+ if test -n "$ac_tool_prefix" && test "$build" = "$host"; then
+ lt_nm_to_check="$lt_nm_to_check nm"
+ fi
+ for lt_tmp_nm in $lt_nm_to_check; do
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ tmp_nm="$ac_dir/$lt_tmp_nm"
+ if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then
+ # Check to see if the nm accepts a BSD-compat flag.
+ # Adding the `sed 1q' prevents false positives on HP-UX, which says:
+ # nm: unknown option "B" ignored
+ # Tru64's nm complains that /dev/null is an invalid object file
+ case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in
+ */dev/null* | *'Invalid file or object type'*)
+ lt_cv_path_NM="$tmp_nm -B"
+ break
+ ;;
+ *)
+ case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in
+ */dev/null*)
+ lt_cv_path_NM="$tmp_nm -p"
+ break
+ ;;
+ *)
+ lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but
+ continue # so that we can try to find one that supports BSD flags
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+ done
+ : ${lt_cv_path_NM=no}
+fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_path_NM" >&5
+$as_echo "$lt_cv_path_NM" >&6; }
+if test "$lt_cv_path_NM" != "no"; then
+ NM="$lt_cv_path_NM"
+else
+ # Didn't find any BSD compatible name lister, look for dumpbin.
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in "dumpbin -symbols" "link -dump -symbols"
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_DUMPBIN+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$DUMPBIN"; then
+ ac_cv_prog_DUMPBIN="$DUMPBIN" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_DUMPBIN="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+DUMPBIN=$ac_cv_prog_DUMPBIN
+if test -n "$DUMPBIN"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DUMPBIN" >&5
+$as_echo "$DUMPBIN" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$DUMPBIN" && break
+ done
+fi
+if test -z "$DUMPBIN"; then
+ ac_ct_DUMPBIN=$DUMPBIN
+ for ac_prog in "dumpbin -symbols" "link -dump -symbols"
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_DUMPBIN+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_DUMPBIN"; then
+ ac_cv_prog_ac_ct_DUMPBIN="$ac_ct_DUMPBIN" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_DUMPBIN="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_DUMPBIN=$ac_cv_prog_ac_ct_DUMPBIN
+if test -n "$ac_ct_DUMPBIN"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DUMPBIN" >&5
+$as_echo "$ac_ct_DUMPBIN" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_DUMPBIN" && break
+done
+
+ if test "x$ac_ct_DUMPBIN" = x; then
+ DUMPBIN=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ DUMPBIN=$ac_ct_DUMPBIN
+ fi
+fi
+
+
+ if test "$DUMPBIN" != ":"; then
+ NM="$DUMPBIN"
+ fi
+fi
+test -z "$NM" && NM=nm
+
+
+
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking the name lister ($NM) interface" >&5
+$as_echo_n "checking the name lister ($NM) interface... " >&6; }
+if test "${lt_cv_nm_interface+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_nm_interface="BSD nm"
+ echo "int some_variable = 0;" > conftest.$ac_ext
+ (eval echo "\"\$as_me:5640: $ac_compile\"" >&5)
+ (eval "$ac_compile" 2>conftest.err)
+ cat conftest.err >&5
+ (eval echo "\"\$as_me:5643: $NM \\\"conftest.$ac_objext\\\"\"" >&5)
+ (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out)
+ cat conftest.err >&5
+ (eval echo "\"\$as_me:5646: output\"" >&5)
+ cat conftest.out >&5
+ if $GREP 'External.*some_variable' conftest.out > /dev/null; then
+ lt_cv_nm_interface="MS dumpbin"
+ fi
+ rm -f conftest*
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_nm_interface" >&5
+$as_echo "$lt_cv_nm_interface" >&6; }
+
+# find the maximum length of command line arguments
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking the maximum length of command line arguments" >&5
+$as_echo_n "checking the maximum length of command line arguments... " >&6; }
+if test "${lt_cv_sys_max_cmd_len+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ i=0
+ teststring="ABCD"
+
+ case $build_os in
+ msdosdjgpp*)
+ # On DJGPP, this test can blow up pretty badly due to problems in libc
+ # (any single argument exceeding 2000 bytes causes a buffer overrun
+ # during glob expansion). Even if it were fixed, the result of this
+ # check would be larger than it should be.
+ lt_cv_sys_max_cmd_len=12288; # 12K is about right
+ ;;
+
+ gnu*)
+ # Under GNU Hurd, this test is not required because there is
+ # no limit to the length of command line arguments.
+ # Libtool will interpret -1 as no limit whatsoever
+ lt_cv_sys_max_cmd_len=-1;
+ ;;
+
+ cygwin* | mingw* | cegcc*)
+ # On Win9x/ME, this test blows up -- it succeeds, but takes
+ # about 5 minutes as the teststring grows exponentially.
+ # Worse, since 9x/ME are not pre-emptively multitasking,
+ # you end up with a "frozen" computer, even though with patience
+ # the test eventually succeeds (with a max line length of 256k).
+ # Instead, let's just punt: use the minimum linelength reported by
+ # all of the supported platforms: 8192 (on NT/2K/XP).
+ lt_cv_sys_max_cmd_len=8192;
+ ;;
+
+ amigaos*)
+ # On AmigaOS with pdksh, this test takes hours, literally.
+ # So we just punt and use a minimum line length of 8192.
+ lt_cv_sys_max_cmd_len=8192;
+ ;;
+
+ netbsd* | freebsd* | openbsd* | darwin* | dragonfly*)
+ # This has been around since 386BSD, at least. Likely further.
+ if test -x /sbin/sysctl; then
+ lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax`
+ elif test -x /usr/sbin/sysctl; then
+ lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax`
+ else
+ lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs
+ fi
+ # And add a safety zone
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+ ;;
+
+ interix*)
+ # We know the value 262144 and hardcode it with a safety zone (like BSD)
+ lt_cv_sys_max_cmd_len=196608
+ ;;
+
+ osf*)
+ # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure
+ # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not
+ # nice to cause kernel panics so lets avoid the loop below.
+ # First set a reasonable default.
+ lt_cv_sys_max_cmd_len=16384
+ #
+ if test -x /sbin/sysconfig; then
+ case `/sbin/sysconfig -q proc exec_disable_arg_limit` in
+ *1*) lt_cv_sys_max_cmd_len=-1 ;;
+ esac
+ fi
+ ;;
+ sco3.2v5*)
+ lt_cv_sys_max_cmd_len=102400
+ ;;
+ sysv5* | sco5v6* | sysv4.2uw2*)
+ kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null`
+ if test -n "$kargmax"; then
+ lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[ ]//'`
+ else
+ lt_cv_sys_max_cmd_len=32768
+ fi
+ ;;
+ *)
+ lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null`
+ if test -n "$lt_cv_sys_max_cmd_len"; then
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+ else
+ # Make teststring a little bigger before we do anything with it.
+ # a 1K string should be a reasonable start.
+ for i in 1 2 3 4 5 6 7 8 ; do
+ teststring=$teststring$teststring
+ done
+ SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}}
+ # If test is not a shell built-in, we'll probably end up computing a
+ # maximum length that is only half of the actual maximum length, but
+ # we can't tell.
+ while { test "X"`$SHELL $0 --fallback-echo "X$teststring$teststring" 2>/dev/null` \
+ = "XX$teststring$teststring"; } >/dev/null 2>&1 &&
+ test $i != 17 # 1/2 MB should be enough
+ do
+ i=`expr $i + 1`
+ teststring=$teststring$teststring
+ done
+ # Only check the string length outside the loop.
+ lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1`
+ teststring=
+ # Add a significant safety factor because C++ compilers can tack on
+ # massive amounts of additional arguments before passing them to the
+ # linker. It appears as though 1/2 is a usable value.
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2`
+ fi
+ ;;
+ esac
+
+fi
+
+if test -n $lt_cv_sys_max_cmd_len ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_sys_max_cmd_len" >&5
+$as_echo "$lt_cv_sys_max_cmd_len" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: none" >&5
+$as_echo "none" >&6; }
+fi
+max_cmd_len=$lt_cv_sys_max_cmd_len
+
+
+
+
+
+
+: ${CP="cp -f"}
+: ${MV="mv -f"}
+: ${RM="rm -f"}
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the shell understands some XSI constructs" >&5
+$as_echo_n "checking whether the shell understands some XSI constructs... " >&6; }
+# Try some XSI features
+xsi_shell=no
+( _lt_dummy="a/b/c"
+ test "${_lt_dummy##*/},${_lt_dummy%/*},"${_lt_dummy%"$_lt_dummy"}, \
+ = c,a/b,, \
+ && eval 'test $(( 1 + 1 )) -eq 2 \
+ && test "${#_lt_dummy}" -eq 5' ) >/dev/null 2>&1 \
+ && xsi_shell=yes
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $xsi_shell" >&5
+$as_echo "$xsi_shell" >&6; }
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the shell understands \"+=\"" >&5
+$as_echo_n "checking whether the shell understands \"+=\"... " >&6; }
+lt_shell_append=no
+( foo=bar; set foo baz; eval "$1+=\$2" && test "$foo" = barbaz ) \
+ >/dev/null 2>&1 \
+ && lt_shell_append=yes
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_shell_append" >&5
+$as_echo "$lt_shell_append" >&6; }
+
+
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+ lt_unset=unset
+else
+ lt_unset=false
+fi
+
+
+
+
+
+# test EBCDIC or ASCII
+case `echo X|tr X '\101'` in
+ A) # ASCII based system
+ # \n is not interpreted correctly by Solaris 8 /usr/ucb/tr
+ lt_SP2NL='tr \040 \012'
+ lt_NL2SP='tr \015\012 \040\040'
+ ;;
+ *) # EBCDIC based system
+ lt_SP2NL='tr \100 \n'
+ lt_NL2SP='tr \r\n \100\100'
+ ;;
+esac
+
+
+
+
+
+
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $LD option to reload object files" >&5
+$as_echo_n "checking for $LD option to reload object files... " >&6; }
+if test "${lt_cv_ld_reload_flag+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_ld_reload_flag='-r'
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_reload_flag" >&5
+$as_echo "$lt_cv_ld_reload_flag" >&6; }
+reload_flag=$lt_cv_ld_reload_flag
+case $reload_flag in
+"" | " "*) ;;
+*) reload_flag=" $reload_flag" ;;
+esac
+reload_cmds='$LD$reload_flag -o $output$reload_objs'
+case $host_os in
+ darwin*)
+ if test "$GCC" = yes; then
+ reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs'
+ else
+ reload_cmds='$LD$reload_flag -o $output$reload_objs'
+ fi
+ ;;
+esac
+
+
+
+
+
+
+
+
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}objdump", so it can be a program name with args.
+set dummy ${ac_tool_prefix}objdump; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_OBJDUMP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$OBJDUMP"; then
+ ac_cv_prog_OBJDUMP="$OBJDUMP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_OBJDUMP="${ac_tool_prefix}objdump"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+OBJDUMP=$ac_cv_prog_OBJDUMP
+if test -n "$OBJDUMP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OBJDUMP" >&5
+$as_echo "$OBJDUMP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_OBJDUMP"; then
+ ac_ct_OBJDUMP=$OBJDUMP
+ # Extract the first word of "objdump", so it can be a program name with args.
+set dummy objdump; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_OBJDUMP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_OBJDUMP"; then
+ ac_cv_prog_ac_ct_OBJDUMP="$ac_ct_OBJDUMP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_OBJDUMP="objdump"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_OBJDUMP=$ac_cv_prog_ac_ct_OBJDUMP
+if test -n "$ac_ct_OBJDUMP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OBJDUMP" >&5
+$as_echo "$ac_ct_OBJDUMP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_OBJDUMP" = x; then
+ OBJDUMP="false"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ OBJDUMP=$ac_ct_OBJDUMP
+ fi
+else
+ OBJDUMP="$ac_cv_prog_OBJDUMP"
+fi
+
+test -z "$OBJDUMP" && OBJDUMP=objdump
+
+
+
+
+
+
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to recognize dependent libraries" >&5
+$as_echo_n "checking how to recognize dependent libraries... " >&6; }
+if test "${lt_cv_deplibs_check_method+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_file_magic_cmd='$MAGIC_CMD'
+lt_cv_file_magic_test_file=
+lt_cv_deplibs_check_method='unknown'
+# Need to set the preceding variable on all platforms that support
+# interlibrary dependencies.
+# 'none' -- dependencies not supported.
+# `unknown' -- same as none, but documents that we really don't know.
+# 'pass_all' -- all dependencies passed with no checks.
+# 'test_compile' -- check by making test program.
+# 'file_magic [[regex]]' -- check by looking for files in library path
+# which responds to the $file_magic_cmd with a given extended regex.
+# If you have `file' or equivalent on your system and you're not sure
+# whether `pass_all' will *always* work, you probably want this one.
+
+case $host_os in
+aix[4-9]*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+beos*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+bsdi[45]*)
+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib)'
+ lt_cv_file_magic_cmd='/usr/bin/file -L'
+ lt_cv_file_magic_test_file=/shlib/libc.so
+ ;;
+
+cygwin*)
+ # func_win32_libid is a shell function defined in ltmain.sh
+ lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+ lt_cv_file_magic_cmd='func_win32_libid'
+ ;;
+
+mingw* | pw32*)
+ # Base MSYS/MinGW do not provide the 'file' command needed by
+ # func_win32_libid shell function, so use a weaker test based on 'objdump',
+ # unless we find 'file', for example because we are cross-compiling.
+ if ( file / ) >/dev/null 2>&1; then
+ lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+ lt_cv_file_magic_cmd='func_win32_libid'
+ else
+ lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?'
+ lt_cv_file_magic_cmd='$OBJDUMP -f'
+ fi
+ ;;
+
+cegcc)
+ # use the weaker test based on 'objdump'. See mingw*.
+ lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?'
+ lt_cv_file_magic_cmd='$OBJDUMP -f'
+ ;;
+
+darwin* | rhapsody*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+freebsd* | dragonfly*)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
+ case $host_cpu in
+ i*86 )
+ # Not sure whether the presence of OpenBSD here was a mistake.
+ # Let's accept both of them until this is cleared up.
+ lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[3-9]86 (compact )?demand paged shared library'
+ lt_cv_file_magic_cmd=/usr/bin/file
+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*`
+ ;;
+ esac
+ else
+ lt_cv_deplibs_check_method=pass_all
+ fi
+ ;;
+
+gnu*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+hpux10.20* | hpux11*)
+ lt_cv_file_magic_cmd=/usr/bin/file
+ case $host_cpu in
+ ia64*)
+ lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - IA64'
+ lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so
+ ;;
+ hppa*64*)
+ lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]'
+ lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl
+ ;;
+ *)
+ lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|PA-RISC[0-9].[0-9]) shared library'
+ lt_cv_file_magic_test_file=/usr/lib/libc.sl
+ ;;
+ esac
+ ;;
+
+interix[3-9]*)
+ # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|\.a)$'
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $LD in
+ *-32|*"-32 ") libmagic=32-bit;;
+ *-n32|*"-n32 ") libmagic=N32;;
+ *-64|*"-64 ") libmagic=64-bit;;
+ *) libmagic=never-match;;
+ esac
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$'
+ else
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|_pic\.a)$'
+ fi
+ ;;
+
+newos6*)
+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (executable|dynamic lib)'
+ lt_cv_file_magic_cmd=/usr/bin/file
+ lt_cv_file_magic_test_file=/usr/lib/libnls.so
+ ;;
+
+*nto* | *qnx*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+openbsd*)
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|\.so|_pic\.a)$'
+ else
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$'
+ fi
+ ;;
+
+osf3* | osf4* | osf5*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+rdos*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+solaris*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+sysv4 | sysv4.3*)
+ case $host_vendor in
+ motorola)
+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib) M[0-9][0-9]* Version [0-9]'
+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*`
+ ;;
+ ncr)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ sequent)
+ lt_cv_file_magic_cmd='/bin/file'
+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [LM]SB (shared object|dynamic lib )'
+ ;;
+ sni)
+ lt_cv_file_magic_cmd='/bin/file'
+ lt_cv_deplibs_check_method="file_magic ELF [0-9][0-9]*-bit [LM]SB dynamic lib"
+ lt_cv_file_magic_test_file=/lib/libc.so
+ ;;
+ siemens)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ pc)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ esac
+ ;;
+
+tpf*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+esac
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_deplibs_check_method" >&5
+$as_echo "$lt_cv_deplibs_check_method" >&6; }
+file_magic_cmd=$lt_cv_file_magic_cmd
+deplibs_check_method=$lt_cv_deplibs_check_method
+test -z "$deplibs_check_method" && deplibs_check_method=unknown
+
+
+
+
+
+
+
+
+
+
+
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}ar", so it can be a program name with args.
+set dummy ${ac_tool_prefix}ar; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_AR+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$AR"; then
+ ac_cv_prog_AR="$AR" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_AR="${ac_tool_prefix}ar"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+AR=$ac_cv_prog_AR
+if test -n "$AR"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AR" >&5
+$as_echo "$AR" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_AR"; then
+ ac_ct_AR=$AR
+ # Extract the first word of "ar", so it can be a program name with args.
+set dummy ar; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_AR+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_AR"; then
+ ac_cv_prog_ac_ct_AR="$ac_ct_AR" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_AR="ar"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_AR=$ac_cv_prog_ac_ct_AR
+if test -n "$ac_ct_AR"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_AR" >&5
+$as_echo "$ac_ct_AR" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_AR" = x; then
+ AR="false"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ AR=$ac_ct_AR
+ fi
+else
+ AR="$ac_cv_prog_AR"
+fi
+
+test -z "$AR" && AR=ar
+test -z "$AR_FLAGS" && AR_FLAGS=cru
+
+
+
+
+
+
+
+
+
+
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
+set dummy ${ac_tool_prefix}strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_STRIP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$STRIP"; then
+ ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_STRIP="${ac_tool_prefix}strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+STRIP=$ac_cv_prog_STRIP
+if test -n "$STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5
+$as_echo "$STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_STRIP"; then
+ ac_ct_STRIP=$STRIP
+ # Extract the first word of "strip", so it can be a program name with args.
+set dummy strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_STRIP"; then
+ ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_STRIP="strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
+if test -n "$ac_ct_STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5
+$as_echo "$ac_ct_STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_STRIP" = x; then
+ STRIP=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ STRIP=$ac_ct_STRIP
+ fi
+else
+ STRIP="$ac_cv_prog_STRIP"
+fi
+
+test -z "$STRIP" && STRIP=:
+
+
+
+
+
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args.
+set dummy ${ac_tool_prefix}ranlib; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_RANLIB+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$RANLIB"; then
+ ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+RANLIB=$ac_cv_prog_RANLIB
+if test -n "$RANLIB"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $RANLIB" >&5
+$as_echo "$RANLIB" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_RANLIB"; then
+ ac_ct_RANLIB=$RANLIB
+ # Extract the first word of "ranlib", so it can be a program name with args.
+set dummy ranlib; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_RANLIB"; then
+ ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_RANLIB="ranlib"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB
+if test -n "$ac_ct_RANLIB"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_RANLIB" >&5
+$as_echo "$ac_ct_RANLIB" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_RANLIB" = x; then
+ RANLIB=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ RANLIB=$ac_ct_RANLIB
+ fi
+else
+ RANLIB="$ac_cv_prog_RANLIB"
+fi
+
+test -z "$RANLIB" && RANLIB=:
+
+
+
+
+
+
+# Determine commands to create old-style static archives.
+old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs'
+old_postinstall_cmds='chmod 644 $oldlib'
+old_postuninstall_cmds=
+
+if test -n "$RANLIB"; then
+ case $host_os in
+ openbsd*)
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib"
+ ;;
+ *)
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib"
+ ;;
+ esac
+ old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib"
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+
+# Check for command to grab the raw symbol name followed by C symbol from nm.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking command to parse $NM output from $compiler object" >&5
+$as_echo_n "checking command to parse $NM output from $compiler object... " >&6; }
+if test "${lt_cv_sys_global_symbol_pipe+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+
+# These are sane defaults that work on at least a few old systems.
+# [They come from Ultrix. What could be older than Ultrix?!! ;)]
+
+# Character class describing NM global symbol codes.
+symcode='[BCDEGRST]'
+
+# Regexp to match symbols that can be accessed directly from C.
+sympat='\([_A-Za-z][_A-Za-z0-9]*\)'
+
+# Define system-specific variables.
+case $host_os in
+aix*)
+ symcode='[BCDT]'
+ ;;
+cygwin* | mingw* | pw32* | cegcc*)
+ symcode='[ABCDGISTW]'
+ ;;
+hpux*)
+ if test "$host_cpu" = ia64; then
+ symcode='[ABCDEGRST]'
+ fi
+ ;;
+irix* | nonstopux*)
+ symcode='[BCDEGRST]'
+ ;;
+osf*)
+ symcode='[BCDEGQRST]'
+ ;;
+solaris*)
+ symcode='[BDRT]'
+ ;;
+sco3.2v5*)
+ symcode='[DT]'
+ ;;
+sysv4.2uw2*)
+ symcode='[DT]'
+ ;;
+sysv5* | sco5v6* | unixware* | OpenUNIX*)
+ symcode='[ABDT]'
+ ;;
+sysv4)
+ symcode='[DFNSTU]'
+ ;;
+esac
+
+# If we're using GNU nm, then use its standard symbol codes.
+case `$NM -V 2>&1` in
+*GNU* | *'with BFD'*)
+ symcode='[ABCDGIRSTW]' ;;
+esac
+
+# Transform an extracted symbol line into a proper C declaration.
+# Some systems (esp. on ia64) link data and code symbols differently,
+# so use this general approach.
+lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'"
+
+# Transform an extracted symbol line into symbol name and symbol address
+lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"\2\", (void *) \&\2},/p'"
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \(lib[^ ]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"lib\2\", (void *) \&\2},/p'"
+
+# Handle CRLF in mingw tool chain
+opt_cr=
+case $build_os in
+mingw*)
+ opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp
+ ;;
+esac
+
+# Try without a prefix underscore, then with it.
+for ac_symprfx in "" "_"; do
+
+ # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol.
+ symxfrm="\\1 $ac_symprfx\\2 \\2"
+
+ # Write the raw and C identifiers.
+ if test "$lt_cv_nm_interface" = "MS dumpbin"; then
+ # Fake it for dumpbin and say T for any non-static function
+ # and D for any global variable.
+ # Also find C++ and __fastcall symbols from MSVC++,
+ # which start with @ or ?.
+ lt_cv_sys_global_symbol_pipe="$AWK '"\
+" {last_section=section; section=\$ 3};"\
+" /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\
+" \$ 0!~/External *\|/{next};"\
+" / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\
+" {if(hide[section]) next};"\
+" {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\
+" {split(\$ 0, a, /\||\r/); split(a[2], s)};"\
+" s[1]~/^[@?]/{print s[1], s[1]; next};"\
+" s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\
+" ' prfx=^$ac_symprfx"
+ else
+ lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[ ]\($symcode$symcode*\)[ ][ ]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'"
+ fi
+
+ # Check to see that the pipe works correctly.
+ pipe_works=no
+
+ rm -f conftest*
+ cat > conftest.$ac_ext <<_LT_EOF
+#ifdef __cplusplus
+extern "C" {
+#endif
+char nm_test_var;
+void nm_test_func(void);
+void nm_test_func(void){}
+#ifdef __cplusplus
+}
+#endif
+int main(){nm_test_var='a';nm_test_func();return(0);}
+_LT_EOF
+
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ # Now try to grab the symbols.
+ nlist=conftest.nm
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist\""; } >&5
+ (eval $NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && test -s "$nlist"; then
+ # Try sorting and uniquifying the output.
+ if sort "$nlist" | uniq > "$nlist"T; then
+ mv -f "$nlist"T "$nlist"
+ else
+ rm -f "$nlist"T
+ fi
+
+ # Make sure that we snagged all the symbols we need.
+ if $GREP ' nm_test_var$' "$nlist" >/dev/null; then
+ if $GREP ' nm_test_func$' "$nlist" >/dev/null; then
+ cat <<_LT_EOF > conftest.$ac_ext
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+_LT_EOF
+ # Now generate the symbol file.
+ eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext'
+
+ cat <<_LT_EOF >> conftest.$ac_ext
+
+/* The mapping between symbol names and symbols. */
+const struct {
+ const char *name;
+ void *address;
+}
+lt__PROGRAM__LTX_preloaded_symbols[] =
+{
+ { "@PROGRAM@", (void *) 0 },
+_LT_EOF
+ $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext
+ cat <<\_LT_EOF >> conftest.$ac_ext
+ {0, (void *) 0}
+};
+
+/* This works around a problem in FreeBSD linker */
+#ifdef FREEBSD_WORKAROUND
+static const void *lt_preloaded_setup() {
+ return lt__PROGRAM__LTX_preloaded_symbols;
+}
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+_LT_EOF
+ # Now try linking the two files.
+ mv conftest.$ac_objext conftstm.$ac_objext
+ lt_save_LIBS="$LIBS"
+ lt_save_CFLAGS="$CFLAGS"
+ LIBS="conftstm.$ac_objext"
+ CFLAGS="$CFLAGS$lt_prog_compiler_no_builtin_flag"
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5
+ (eval $ac_link) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && test -s conftest${ac_exeext}; then
+ pipe_works=yes
+ fi
+ LIBS="$lt_save_LIBS"
+ CFLAGS="$lt_save_CFLAGS"
+ else
+ echo "cannot find nm_test_func in $nlist" >&5
+ fi
+ else
+ echo "cannot find nm_test_var in $nlist" >&5
+ fi
+ else
+ echo "cannot run $lt_cv_sys_global_symbol_pipe" >&5
+ fi
+ else
+ echo "$progname: failed program was:" >&5
+ cat conftest.$ac_ext >&5
+ fi
+ rm -rf conftest* conftst*
+
+ # Do not use the global_symbol_pipe unless it works.
+ if test "$pipe_works" = yes; then
+ break
+ else
+ lt_cv_sys_global_symbol_pipe=
+ fi
+done
+
+fi
+
+if test -z "$lt_cv_sys_global_symbol_pipe"; then
+ lt_cv_sys_global_symbol_to_cdecl=
+fi
+if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: failed" >&5
+$as_echo "failed" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: ok" >&5
+$as_echo "ok" >&6; }
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# Check whether --enable-libtool-lock was given.
+if test "${enable_libtool_lock+set}" = set; then :
+ enableval=$enable_libtool_lock;
+fi
+
+test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes
+
+# Some flags need to be propagated to the compiler or linker for good
+# libtool support.
+case $host in
+ia64-*-hpux*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *ELF-32*)
+ HPUX_IA64_MODE="32"
+ ;;
+ *ELF-64*)
+ HPUX_IA64_MODE="64"
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+*-*-irix6*)
+ # Find out which ABI we are using.
+ echo '#line 6841 "configure"' > conftest.$ac_ext
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *32-bit*)
+ LD="${LD-ld} -melf32bsmip"
+ ;;
+ *N32*)
+ LD="${LD-ld} -melf32bmipn32"
+ ;;
+ *64-bit*)
+ LD="${LD-ld} -melf64bmip"
+ ;;
+ esac
+ else
+ case `/usr/bin/file conftest.$ac_objext` in
+ *32-bit*)
+ LD="${LD-ld} -32"
+ ;;
+ *N32*)
+ LD="${LD-ld} -n32"
+ ;;
+ *64-bit*)
+ LD="${LD-ld} -64"
+ ;;
+ esac
+ fi
+ fi
+ rm -rf conftest*
+ ;;
+
+x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \
+s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ case `/usr/bin/file conftest.o` in
+ *32-bit*)
+ case $host in
+ x86_64-*kfreebsd*-gnu)
+ LD="${LD-ld} -m elf_i386_fbsd"
+ ;;
+ x86_64-*linux*)
+ LD="${LD-ld} -m elf_i386"
+ ;;
+ ppc64-*linux*|powerpc64-*linux*)
+ LD="${LD-ld} -m elf32ppclinux"
+ ;;
+ s390x-*linux*)
+ LD="${LD-ld} -m elf_s390"
+ ;;
+ sparc64-*linux*)
+ LD="${LD-ld} -m elf32_sparc"
+ ;;
+ esac
+ ;;
+ *64-bit*)
+ case $host in
+ x86_64-*kfreebsd*-gnu)
+ LD="${LD-ld} -m elf_x86_64_fbsd"
+ ;;
+ x86_64-*linux*)
+ LD="${LD-ld} -m elf_x86_64"
+ ;;
+ ppc*-*linux*|powerpc*-*linux*)
+ LD="${LD-ld} -m elf64ppc"
+ ;;
+ s390*-*linux*|s390*-*tpf*)
+ LD="${LD-ld} -m elf64_s390"
+ ;;
+ sparc*-*linux*)
+ LD="${LD-ld} -m elf64_sparc"
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+
+*-*-sco3.2v5*)
+ # On SCO OpenServer 5, we need -belf to get full-featured binaries.
+ SAVE_CFLAGS="$CFLAGS"
+ CFLAGS="$CFLAGS -belf"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler needs -belf" >&5
+$as_echo_n "checking whether the C compiler needs -belf... " >&6; }
+if test "${lt_cv_cc_needs_belf+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ lt_cv_cc_needs_belf=yes
+else
+ lt_cv_cc_needs_belf=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+ ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_cc_needs_belf" >&5
+$as_echo "$lt_cv_cc_needs_belf" >&6; }
+ if test x"$lt_cv_cc_needs_belf" != x"yes"; then
+ # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf
+ CFLAGS="$SAVE_CFLAGS"
+ fi
+ ;;
+sparc*-*solaris*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ case `/usr/bin/file conftest.o` in
+ *64-bit*)
+ case $lt_cv_prog_gnu_ld in
+ yes*) LD="${LD-ld} -m elf64_sparc" ;;
+ *)
+ if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then
+ LD="${LD-ld} -64"
+ fi
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+esac
+
+need_locks="$enable_libtool_lock"
+
+
+ case $host_os in
+ rhapsody* | darwin*)
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}dsymutil", so it can be a program name with args.
+set dummy ${ac_tool_prefix}dsymutil; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_DSYMUTIL+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$DSYMUTIL"; then
+ ac_cv_prog_DSYMUTIL="$DSYMUTIL" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_DSYMUTIL="${ac_tool_prefix}dsymutil"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+DSYMUTIL=$ac_cv_prog_DSYMUTIL
+if test -n "$DSYMUTIL"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DSYMUTIL" >&5
+$as_echo "$DSYMUTIL" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_DSYMUTIL"; then
+ ac_ct_DSYMUTIL=$DSYMUTIL
+ # Extract the first word of "dsymutil", so it can be a program name with args.
+set dummy dsymutil; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_DSYMUTIL+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_DSYMUTIL"; then
+ ac_cv_prog_ac_ct_DSYMUTIL="$ac_ct_DSYMUTIL" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_DSYMUTIL="dsymutil"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_DSYMUTIL=$ac_cv_prog_ac_ct_DSYMUTIL
+if test -n "$ac_ct_DSYMUTIL"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DSYMUTIL" >&5
+$as_echo "$ac_ct_DSYMUTIL" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_DSYMUTIL" = x; then
+ DSYMUTIL=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ DSYMUTIL=$ac_ct_DSYMUTIL
+ fi
+else
+ DSYMUTIL="$ac_cv_prog_DSYMUTIL"
+fi
+
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}nmedit", so it can be a program name with args.
+set dummy ${ac_tool_prefix}nmedit; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_NMEDIT+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$NMEDIT"; then
+ ac_cv_prog_NMEDIT="$NMEDIT" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_NMEDIT="${ac_tool_prefix}nmedit"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+NMEDIT=$ac_cv_prog_NMEDIT
+if test -n "$NMEDIT"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $NMEDIT" >&5
+$as_echo "$NMEDIT" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_NMEDIT"; then
+ ac_ct_NMEDIT=$NMEDIT
+ # Extract the first word of "nmedit", so it can be a program name with args.
+set dummy nmedit; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_NMEDIT+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_NMEDIT"; then
+ ac_cv_prog_ac_ct_NMEDIT="$ac_ct_NMEDIT" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_NMEDIT="nmedit"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_NMEDIT=$ac_cv_prog_ac_ct_NMEDIT
+if test -n "$ac_ct_NMEDIT"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_NMEDIT" >&5
+$as_echo "$ac_ct_NMEDIT" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_NMEDIT" = x; then
+ NMEDIT=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ NMEDIT=$ac_ct_NMEDIT
+ fi
+else
+ NMEDIT="$ac_cv_prog_NMEDIT"
+fi
+
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}lipo", so it can be a program name with args.
+set dummy ${ac_tool_prefix}lipo; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_LIPO+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$LIPO"; then
+ ac_cv_prog_LIPO="$LIPO" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_LIPO="${ac_tool_prefix}lipo"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+LIPO=$ac_cv_prog_LIPO
+if test -n "$LIPO"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LIPO" >&5
+$as_echo "$LIPO" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_LIPO"; then
+ ac_ct_LIPO=$LIPO
+ # Extract the first word of "lipo", so it can be a program name with args.
+set dummy lipo; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_LIPO+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_LIPO"; then
+ ac_cv_prog_ac_ct_LIPO="$ac_ct_LIPO" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_LIPO="lipo"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_LIPO=$ac_cv_prog_ac_ct_LIPO
+if test -n "$ac_ct_LIPO"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_LIPO" >&5
+$as_echo "$ac_ct_LIPO" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_LIPO" = x; then
+ LIPO=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ LIPO=$ac_ct_LIPO
+ fi
+else
+ LIPO="$ac_cv_prog_LIPO"
+fi
+
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}otool", so it can be a program name with args.
+set dummy ${ac_tool_prefix}otool; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_OTOOL+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$OTOOL"; then
+ ac_cv_prog_OTOOL="$OTOOL" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_OTOOL="${ac_tool_prefix}otool"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+OTOOL=$ac_cv_prog_OTOOL
+if test -n "$OTOOL"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL" >&5
+$as_echo "$OTOOL" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_OTOOL"; then
+ ac_ct_OTOOL=$OTOOL
+ # Extract the first word of "otool", so it can be a program name with args.
+set dummy otool; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_OTOOL+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_OTOOL"; then
+ ac_cv_prog_ac_ct_OTOOL="$ac_ct_OTOOL" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_OTOOL="otool"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_OTOOL=$ac_cv_prog_ac_ct_OTOOL
+if test -n "$ac_ct_OTOOL"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL" >&5
+$as_echo "$ac_ct_OTOOL" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_OTOOL" = x; then
+ OTOOL=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ OTOOL=$ac_ct_OTOOL
+ fi
+else
+ OTOOL="$ac_cv_prog_OTOOL"
+fi
+
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}otool64", so it can be a program name with args.
+set dummy ${ac_tool_prefix}otool64; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_OTOOL64+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$OTOOL64"; then
+ ac_cv_prog_OTOOL64="$OTOOL64" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_OTOOL64="${ac_tool_prefix}otool64"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+OTOOL64=$ac_cv_prog_OTOOL64
+if test -n "$OTOOL64"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL64" >&5
+$as_echo "$OTOOL64" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_OTOOL64"; then
+ ac_ct_OTOOL64=$OTOOL64
+ # Extract the first word of "otool64", so it can be a program name with args.
+set dummy otool64; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_OTOOL64+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_OTOOL64"; then
+ ac_cv_prog_ac_ct_OTOOL64="$ac_ct_OTOOL64" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_OTOOL64="otool64"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_OTOOL64=$ac_cv_prog_ac_ct_OTOOL64
+if test -n "$ac_ct_OTOOL64"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL64" >&5
+$as_echo "$ac_ct_OTOOL64" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_OTOOL64" = x; then
+ OTOOL64=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ OTOOL64=$ac_ct_OTOOL64
+ fi
+else
+ OTOOL64="$ac_cv_prog_OTOOL64"
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -single_module linker flag" >&5
+$as_echo_n "checking for -single_module linker flag... " >&6; }
+if test "${lt_cv_apple_cc_single_mod+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_apple_cc_single_mod=no
+ if test -z "${LT_MULTI_MODULE}"; then
+ # By default we will add the -single_module flag. You can override
+ # by either setting the environment variable LT_MULTI_MODULE
+ # non-empty at configure time, or by adding -multi_module to the
+ # link flags.
+ rm -rf libconftest.dylib*
+ echo "int foo(void){return 1;}" > conftest.c
+ echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+-dynamiclib -Wl,-single_module conftest.c" >&5
+ $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+ -dynamiclib -Wl,-single_module conftest.c 2>conftest.err
+ _lt_result=$?
+ if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then
+ lt_cv_apple_cc_single_mod=yes
+ else
+ cat conftest.err >&5
+ fi
+ rm -rf libconftest.dylib*
+ rm -f conftest.*
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_apple_cc_single_mod" >&5
+$as_echo "$lt_cv_apple_cc_single_mod" >&6; }
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -exported_symbols_list linker flag" >&5
+$as_echo_n "checking for -exported_symbols_list linker flag... " >&6; }
+if test "${lt_cv_ld_exported_symbols_list+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_ld_exported_symbols_list=no
+ save_LDFLAGS=$LDFLAGS
+ echo "_main" > conftest.sym
+ LDFLAGS="$LDFLAGS -Wl,-exported_symbols_list,conftest.sym"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ lt_cv_ld_exported_symbols_list=yes
+else
+ lt_cv_ld_exported_symbols_list=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+ LDFLAGS="$save_LDFLAGS"
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_exported_symbols_list" >&5
+$as_echo "$lt_cv_ld_exported_symbols_list" >&6; }
+ case $host_os in
+ rhapsody* | darwin1.[012])
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}suppress' ;;
+ darwin1.*)
+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+ darwin*) # darwin 5.x on
+ # if running on 10.5 or later, the deployment target defaults
+ # to the OS version, if on x86, and 10.4, the deployment
+ # target defaults to 10.4. Don't you love it?
+ case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in
+ 10.0,*86*-darwin8*|10.0,*-darwin[91]*)
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+ 10.[012]*)
+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+ 10.*)
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+ esac
+ ;;
+ esac
+ if test "$lt_cv_apple_cc_single_mod" = "yes"; then
+ _lt_dar_single_mod='$single_module'
+ fi
+ if test "$lt_cv_ld_exported_symbols_list" = "yes"; then
+ _lt_dar_export_syms=' ${wl}-exported_symbols_list,$output_objdir/${libname}-symbols.expsym'
+ else
+ _lt_dar_export_syms='~$NMEDIT -s $output_objdir/${libname}-symbols.expsym ${lib}'
+ fi
+ if test "$DSYMUTIL" != ":"; then
+ _lt_dsymutil='~$DSYMUTIL $lib || :'
+ else
+ _lt_dsymutil=
+ fi
+ ;;
+ esac
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5
+$as_echo_n "checking for ANSI C header files... " >&6; }
+if test "${ac_cv_header_stdc+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdlib.h>
+#include <stdarg.h>
+#include <string.h>
+#include <float.h>
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_header_stdc=yes
+else
+ ac_cv_header_stdc=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+
+if test $ac_cv_header_stdc = yes; then
+ # SunOS 4.x string.h does not declare mem*, contrary to ANSI.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <string.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "memchr" >/dev/null 2>&1; then :
+
+else
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdlib.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "free" >/dev/null 2>&1; then :
+
+else
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi.
+ if test "$cross_compiling" = yes; then :
+ :
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ctype.h>
+#include <stdlib.h>
+#if ((' ' & 0x0FF) == 0x020)
+# define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
+# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
+#else
+# define ISLOWER(c) \
+ (('a' <= (c) && (c) <= 'i') \
+ || ('j' <= (c) && (c) <= 'r') \
+ || ('s' <= (c) && (c) <= 'z'))
+# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c))
+#endif
+
+#define XOR(e, f) (((e) && !(f)) || (!(e) && (f)))
+int
+main ()
+{
+ int i;
+ for (i = 0; i < 256; i++)
+ if (XOR (islower (i), ISLOWER (i))
+ || toupper (i) != TOUPPER (i))
+ return 2;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_run "$LINENO"; then :
+
+else
+ ac_cv_header_stdc=no
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
+ conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+
+fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5
+$as_echo "$ac_cv_header_stdc" >&6; }
+if test $ac_cv_header_stdc = yes; then
+
+$as_echo "#define STDC_HEADERS 1" >>confdefs.h
+
+fi
+
+# On IRIX 5.3, sys/types and inttypes.h are conflicting.
+for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \
+ inttypes.h stdint.h unistd.h
+do :
+ as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default
+"
+if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+
+for ac_header in dlfcn.h
+do :
+ ac_fn_c_check_header_compile "$LINENO" "dlfcn.h" "ac_cv_header_dlfcn_h" "$ac_includes_default
+"
+if test "x$ac_cv_header_dlfcn_h" = x""yes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_DLFCN_H 1
+_ACEOF
+
+fi
+
+done
+
+
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+if test -z "$CXX"; then
+ if test -n "$CCC"; then
+ CXX=$CCC
+ else
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CXX"; then
+ ac_cv_prog_CXX="$CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CXX=$ac_cv_prog_CXX
+if test -n "$CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5
+$as_echo "$CXX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CXX" && break
+ done
+fi
+if test -z "$CXX"; then
+ ac_ct_CXX=$CXX
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CXX"; then
+ ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CXX="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
+if test -n "$ac_ct_CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5
+$as_echo "$ac_ct_CXX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CXX" && break
+done
+
+ if test "x$ac_ct_CXX" = x; then
+ CXX="g++"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CXX=$ac_ct_CXX
+ fi
+fi
+
+ fi
+fi
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+ { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ sed '10a\
+... rest of stderr output deleted ...
+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5
+$as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; }
+if test "${ac_cv_cxx_compiler_gnu+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_compiler_gnu=yes
+else
+ ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_cxx_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5
+$as_echo "$ac_cv_cxx_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GXX=yes
+else
+ GXX=
+fi
+ac_test_CXXFLAGS=${CXXFLAGS+set}
+ac_save_CXXFLAGS=$CXXFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5
+$as_echo_n "checking whether $CXX accepts -g... " >&6; }
+if test "${ac_cv_prog_cxx_g+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_cxx_werror_flag=$ac_cxx_werror_flag
+ ac_cxx_werror_flag=yes
+ ac_cv_prog_cxx_g=no
+ CXXFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_prog_cxx_g=yes
+else
+ CXXFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+
+else
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+ CXXFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_prog_cxx_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5
+$as_echo "$ac_cv_prog_cxx_g" >&6; }
+if test "$ac_test_CXXFLAGS" = set; then
+ CXXFLAGS=$ac_save_CXXFLAGS
+elif test $ac_cv_prog_cxx_g = yes; then
+ if test "$GXX" = yes; then
+ CXXFLAGS="-g -O2"
+ else
+ CXXFLAGS="-g"
+ fi
+else
+ if test "$GXX" = yes; then
+ CXXFLAGS="-O2"
+ else
+ CXXFLAGS=
+ fi
+fi
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+depcc="$CXX" am_compiler_list=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CXX_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
+ case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CXX_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CXX_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CXX_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CXX_dependencies_compiler_type" >&6; }
+CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CXX_dependencies_compiler_type" = gcc3; then
+ am__fastdepCXX_TRUE=
+ am__fastdepCXX_FALSE='#'
+else
+ am__fastdepCXX_TRUE='#'
+ am__fastdepCXX_FALSE=
+fi
+
+
+if test -n "$CXX" && ( test "X$CXX" != "Xno" &&
+ ( (test "X$CXX" = "Xg++" && `g++ -v >/dev/null 2>&1` ) ||
+ (test "X$CXX" != "Xg++"))) ; then
+ ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C++ preprocessor" >&5
+$as_echo_n "checking how to run the C++ preprocessor... " >&6; }
+if test -z "$CXXCPP"; then
+ if test "${ac_cv_prog_CXXCPP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ # Double quotes because CXXCPP needs to be expanded
+ for CXXCPP in "$CXX -E" "/lib/cpp"
+ do
+ ac_preproc_ok=false
+for ac_cxx_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if ac_fn_cxx_try_cpp "$LINENO"; then :
+
+else
+ # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if ac_fn_cxx_try_cpp "$LINENO"; then :
+ # Broken: success on invalid input.
+continue
+else
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.i conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then :
+ break
+fi
+
+ done
+ ac_cv_prog_CXXCPP=$CXXCPP
+
+fi
+ CXXCPP=$ac_cv_prog_CXXCPP
+else
+ ac_cv_prog_CXXCPP=$CXXCPP
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXXCPP" >&5
+$as_echo "$CXXCPP" >&6; }
+ac_preproc_ok=false
+for ac_cxx_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if ac_fn_cxx_try_cpp "$LINENO"; then :
+
+else
+ # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if ac_fn_cxx_try_cpp "$LINENO"; then :
+ # Broken: success on invalid input.
+continue
+else
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.i conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then :
+
+else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+_lt_caught_CXX_error=yes; }
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+else
+ _lt_caught_CXX_error=yes
+fi
+
+
+
+
+
+# Set options
+
+
+
+ enable_dlopen=no
+
+
+ enable_win32_dll=no
+
+
+ # Check whether --enable-shared was given.
+if test "${enable_shared+set}" = set; then :
+ enableval=$enable_shared; p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_shared=yes ;;
+ no) enable_shared=no ;;
+ *)
+ enable_shared=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_shared=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac
+else
+ enable_shared=yes
+fi
+
+
+
+
+
+
+
+
+
+ # Check whether --enable-static was given.
+if test "${enable_static+set}" = set; then :
+ enableval=$enable_static; p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_static=yes ;;
+ no) enable_static=no ;;
+ *)
+ enable_static=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_static=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac
+else
+ enable_static=yes
+fi
+
+
+
+
+
+
+
+
+
+
+# Check whether --with-pic was given.
+if test "${with_pic+set}" = set; then :
+ withval=$with_pic; pic_mode="$withval"
+else
+ pic_mode=default
+fi
+
+
+test -z "$pic_mode" && pic_mode=default
+
+
+
+
+
+
+
+ # Check whether --enable-fast-install was given.
+if test "${enable_fast_install+set}" = set; then :
+ enableval=$enable_fast_install; p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_fast_install=yes ;;
+ no) enable_fast_install=no ;;
+ *)
+ enable_fast_install=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_fast_install=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac
+else
+ enable_fast_install=yes
+fi
+
+
+
+
+
+
+
+
+
+
+
+# This can be used to rebuild libtool when needed
+LIBTOOL_DEPS="$ltmain"
+
+# Always use our own libtool.
+LIBTOOL='$(SHELL) $(top_builddir)/libtool'
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+test -z "$LN_S" && LN_S="ln -s"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+if test -n "${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for objdir" >&5
+$as_echo_n "checking for objdir... " >&6; }
+if test "${lt_cv_objdir+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ rm -f .libs 2>/dev/null
+mkdir .libs 2>/dev/null
+if test -d .libs; then
+ lt_cv_objdir=.libs
+else
+ # MS-DOS does not allow filenames that begin with a dot.
+ lt_cv_objdir=_libs
+fi
+rmdir .libs 2>/dev/null
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_objdir" >&5
+$as_echo "$lt_cv_objdir" >&6; }
+objdir=$lt_cv_objdir
+
+
+
+
+
+cat >>confdefs.h <<_ACEOF
+#define LT_OBJDIR "$lt_cv_objdir/"
+_ACEOF
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+case $host_os in
+aix3*)
+ # AIX sometimes has problems with the GCC collect2 program. For some
+ # reason, if we set the COLLECT_NAMES environment variable, the problems
+ # vanish in a puff of smoke.
+ if test "X${COLLECT_NAMES+set}" != Xset; then
+ COLLECT_NAMES=
+ export COLLECT_NAMES
+ fi
+ ;;
+esac
+
+# Sed substitution that helps us do robust quoting. It backslashifies
+# metacharacters that are still active within double-quoted strings.
+sed_quote_subst='s/\(["`$\\]\)/\\\1/g'
+
+# Same as above, but do not quote variable references.
+double_quote_subst='s/\(["`\\]\)/\\\1/g'
+
+# Sed substitution to delay expansion of an escaped shell variable in a
+# double_quote_subst'ed string.
+delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g'
+
+# Sed substitution to delay expansion of an escaped single quote.
+delay_single_quote_subst='s/'\''/'\'\\\\\\\'\''/g'
+
+# Sed substitution to avoid accidental globbing in evaled expressions
+no_glob_subst='s/\*/\\\*/g'
+
+# Global variables:
+ofile=libtool
+can_build_shared=yes
+
+# All known linkers require a `.a' archive for static linking (except MSVC,
+# which needs '.lib').
+libext=a
+
+with_gnu_ld="$lt_cv_prog_gnu_ld"
+
+old_CC="$CC"
+old_CFLAGS="$CFLAGS"
+
+# Set sane defaults for various variables
+test -z "$CC" && CC=cc
+test -z "$LTCC" && LTCC=$CC
+test -z "$LTCFLAGS" && LTCFLAGS=$CFLAGS
+test -z "$LD" && LD=ld
+test -z "$ac_objext" && ac_objext=o
+
+for cc_temp in $compiler""; do
+ case $cc_temp in
+ compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+ distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+ \-*) ;;
+ *) break;;
+ esac
+done
+cc_basename=`$ECHO "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+
+
+# Only perform the check for file, if the check method requires it
+test -z "$MAGIC_CMD" && MAGIC_CMD=file
+case $deplibs_check_method in
+file_magic*)
+ if test "$file_magic_cmd" = '$MAGIC_CMD'; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ${ac_tool_prefix}file" >&5
+$as_echo_n "checking for ${ac_tool_prefix}file... " >&6; }
+if test "${lt_cv_path_MAGIC_CMD+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ case $MAGIC_CMD in
+[\\/*] | ?:[\\/]*)
+ lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path.
+ ;;
+*)
+ lt_save_MAGIC_CMD="$MAGIC_CMD"
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ ac_dummy="/usr/bin$PATH_SEPARATOR$PATH"
+ for ac_dir in $ac_dummy; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f $ac_dir/${ac_tool_prefix}file; then
+ lt_cv_path_MAGIC_CMD="$ac_dir/${ac_tool_prefix}file"
+ if test -n "$file_magic_test_file"; then
+ case $deplibs_check_method in
+ "file_magic "*)
+ file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"`
+ MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+ if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null |
+ $EGREP "$file_magic_regex" > /dev/null; then
+ :
+ else
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the command libtool uses to detect shared libraries,
+*** $file_magic_cmd, produces output that libtool cannot recognize.
+*** The result is that libtool may fail to recognize shared libraries
+*** as such. This will affect the creation of libtool libraries that
+*** depend on shared libraries, but programs linked with such libtool
+*** libraries will work regardless of this problem. Nevertheless, you
+*** may want to report the problem to your system manager and/or to
+*** bug-libtool at gnu.org
+
+_LT_EOF
+ fi ;;
+ esac
+ fi
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+ MAGIC_CMD="$lt_save_MAGIC_CMD"
+ ;;
+esac
+fi
+
+MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+if test -n "$MAGIC_CMD"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MAGIC_CMD" >&5
+$as_echo "$MAGIC_CMD" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+
+
+
+if test -z "$lt_cv_path_MAGIC_CMD"; then
+ if test -n "$ac_tool_prefix"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for file" >&5
+$as_echo_n "checking for file... " >&6; }
+if test "${lt_cv_path_MAGIC_CMD+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ case $MAGIC_CMD in
+[\\/*] | ?:[\\/]*)
+ lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path.
+ ;;
+*)
+ lt_save_MAGIC_CMD="$MAGIC_CMD"
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ ac_dummy="/usr/bin$PATH_SEPARATOR$PATH"
+ for ac_dir in $ac_dummy; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f $ac_dir/file; then
+ lt_cv_path_MAGIC_CMD="$ac_dir/file"
+ if test -n "$file_magic_test_file"; then
+ case $deplibs_check_method in
+ "file_magic "*)
+ file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"`
+ MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+ if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null |
+ $EGREP "$file_magic_regex" > /dev/null; then
+ :
+ else
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the command libtool uses to detect shared libraries,
+*** $file_magic_cmd, produces output that libtool cannot recognize.
+*** The result is that libtool may fail to recognize shared libraries
+*** as such. This will affect the creation of libtool libraries that
+*** depend on shared libraries, but programs linked with such libtool
+*** libraries will work regardless of this problem. Nevertheless, you
+*** may want to report the problem to your system manager and/or to
+*** bug-libtool at gnu.org
+
+_LT_EOF
+ fi ;;
+ esac
+ fi
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+ MAGIC_CMD="$lt_save_MAGIC_CMD"
+ ;;
+esac
+fi
+
+MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+if test -n "$MAGIC_CMD"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MAGIC_CMD" >&5
+$as_echo "$MAGIC_CMD" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ else
+ MAGIC_CMD=:
+ fi
+fi
+
+ fi
+ ;;
+esac
+
+# Use C for the default configuration in the libtool script
+
+lt_save_CC="$CC"
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+# Source file extension for C test sources.
+ac_ext=c
+
+# Object file extension for compiled C test sources.
+objext=o
+objext=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="int some_variable = 0;"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='int main(){return(0);}'
+
+
+
+
+
+
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+# Save the default compiler, since it gets overwritten when the other
+# tags are being tested, and _LT_TAGVAR(compiler, []) is a NOP.
+compiler_DEFAULT=$CC
+
+# save warnings/boilerplate of simple test code
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$RM conftest*
+
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$RM -r conftest*
+
+
+if test -n "$compiler"; then
+
+lt_prog_compiler_no_builtin_flag=
+
+if test "$GCC" = yes; then
+ lt_prog_compiler_no_builtin_flag=' -fno-builtin'
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler supports -fno-rtti -fno-exceptions" >&5
+$as_echo_n "checking if $compiler supports -fno-rtti -fno-exceptions... " >&6; }
+if test "${lt_cv_prog_compiler_rtti_exceptions+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_rtti_exceptions=no
+ ac_outfile=conftest.$ac_objext
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+ lt_compiler_flag="-fno-rtti -fno-exceptions"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ # The option is referenced via a variable to avoid confusing sed.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:8756: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>conftest.err)
+ ac_status=$?
+ cat conftest.err >&5
+ echo "$as_me:8760: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s "$ac_outfile"; then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings other than the usual output.
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_rtti_exceptions=yes
+ fi
+ fi
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_rtti_exceptions" >&5
+$as_echo "$lt_cv_prog_compiler_rtti_exceptions" >&6; }
+
+if test x"$lt_cv_prog_compiler_rtti_exceptions" = xyes; then
+ lt_prog_compiler_no_builtin_flag="$lt_prog_compiler_no_builtin_flag -fno-rtti -fno-exceptions"
+else
+ :
+fi
+
+fi
+
+
+
+
+
+
+ lt_prog_compiler_wl=
+lt_prog_compiler_pic=
+lt_prog_compiler_static=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $compiler option to produce PIC" >&5
+$as_echo_n "checking for $compiler option to produce PIC... " >&6; }
+
+ if test "$GCC" = yes; then
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_static='-static'
+
+ case $host_os in
+ aix*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ lt_prog_compiler_static='-Bstatic'
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ lt_prog_compiler_pic='-fPIC'
+ ;;
+ m68k)
+ # FIXME: we need at least 68020 code to build shared libraries, but
+ # adding the `-m68020' flag to GCC prevents building anything better,
+ # like `-m68040'.
+ lt_prog_compiler_pic='-m68020 -resident32 -malways-restore-a4'
+ ;;
+ esac
+ ;;
+
+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+ # PIC is the default for these OSes.
+ ;;
+
+ mingw* | cygwin* | pw32* | os2* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ # Although the cygwin gcc ignores -fPIC, still need this for old-style
+ # (--disable-auto-import) libraries
+ lt_prog_compiler_pic='-DDLL_EXPORT'
+ ;;
+
+ darwin* | rhapsody*)
+ # PIC is the default on this platform
+ # Common symbols not allowed in MH_DYLIB files
+ lt_prog_compiler_pic='-fno-common'
+ ;;
+
+ hpux*)
+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit
+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag
+ # sets the default TLS model and affects inlining.
+ case $host_cpu in
+ hppa*64*)
+ # +Z the default
+ ;;
+ *)
+ lt_prog_compiler_pic='-fPIC'
+ ;;
+ esac
+ ;;
+
+ interix[3-9]*)
+ # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+ # Instead, we relocate shared libraries at runtime.
+ ;;
+
+ msdosdjgpp*)
+ # Just because we use GCC doesn't mean we suddenly get shared libraries
+ # on systems that don't support them.
+ lt_prog_compiler_can_build_shared=no
+ enable_shared=no
+ ;;
+
+ *nto* | *qnx*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ lt_prog_compiler_pic='-fPIC -shared'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ lt_prog_compiler_pic=-Kconform_pic
+ fi
+ ;;
+
+ *)
+ lt_prog_compiler_pic='-fPIC'
+ ;;
+ esac
+ else
+ # PORTME Check for flag to pass linker flags through the system compiler.
+ case $host_os in
+ aix*)
+ lt_prog_compiler_wl='-Wl,'
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ lt_prog_compiler_static='-Bstatic'
+ else
+ lt_prog_compiler_static='-bnso -bI:/lib/syscalls.exp'
+ fi
+ ;;
+
+ mingw* | cygwin* | pw32* | os2* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ lt_prog_compiler_pic='-DDLL_EXPORT'
+ ;;
+
+ hpux9* | hpux10* | hpux11*)
+ lt_prog_compiler_wl='-Wl,'
+ # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+ # not for PA HP-UX.
+ case $host_cpu in
+ hppa*64*|ia64*)
+ # +Z the default
+ ;;
+ *)
+ lt_prog_compiler_pic='+Z'
+ ;;
+ esac
+ # Is there a better lt_prog_compiler_static that works with the bundled CC?
+ lt_prog_compiler_static='${wl}-a ${wl}archive'
+ ;;
+
+ irix5* | irix6* | nonstopux*)
+ lt_prog_compiler_wl='-Wl,'
+ # PIC (with -KPIC) is the default.
+ lt_prog_compiler_static='-non_shared'
+ ;;
+
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ # old Intel for x86_64 which still supported -KPIC.
+ ecc*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-static'
+ ;;
+ # icc used to be incompatible with GCC.
+ # ICC 10 doesn't accept -KPIC any more.
+ icc* | ifort*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-fPIC'
+ lt_prog_compiler_static='-static'
+ ;;
+ # Lahey Fortran 8.1.
+ lf95*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='--shared'
+ lt_prog_compiler_static='--static'
+ ;;
+ pgcc* | pgf77* | pgf90* | pgf95*)
+ # Portland Group compilers (*not* the Pentium gcc compiler,
+ # which looks to be a dead project)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-fpic'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+ ccc*)
+ lt_prog_compiler_wl='-Wl,'
+ # All Alpha code is PIC.
+ lt_prog_compiler_static='-non_shared'
+ ;;
+ xl*)
+ # IBM XL C 8.0/Fortran 10.1 on PPC
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-qpic'
+ lt_prog_compiler_static='-qstaticlink'
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C 5.9
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ lt_prog_compiler_wl='-Wl,'
+ ;;
+ *Sun\ F*)
+ # Sun Fortran 8.3 passes all unrecognized flags to the linker
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ lt_prog_compiler_wl=''
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+
+ newsos6)
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ *nto* | *qnx*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ lt_prog_compiler_pic='-fPIC -shared'
+ ;;
+
+ osf3* | osf4* | osf5*)
+ lt_prog_compiler_wl='-Wl,'
+ # All OSF/1 code is PIC.
+ lt_prog_compiler_static='-non_shared'
+ ;;
+
+ rdos*)
+ lt_prog_compiler_static='-non_shared'
+ ;;
+
+ solaris*)
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ case $cc_basename in
+ f77* | f90* | f95*)
+ lt_prog_compiler_wl='-Qoption ld ';;
+ *)
+ lt_prog_compiler_wl='-Wl,';;
+ esac
+ ;;
+
+ sunos4*)
+ lt_prog_compiler_wl='-Qoption ld '
+ lt_prog_compiler_pic='-PIC'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ sysv4 | sysv4.2uw2* | sysv4.3*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec ;then
+ lt_prog_compiler_pic='-Kconform_pic'
+ lt_prog_compiler_static='-Bstatic'
+ fi
+ ;;
+
+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ unicos*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_can_build_shared=no
+ ;;
+
+ uts4*)
+ lt_prog_compiler_pic='-pic'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ *)
+ lt_prog_compiler_can_build_shared=no
+ ;;
+ esac
+ fi
+
+case $host_os in
+ # For platforms which do not support PIC, -DPIC is meaningless:
+ *djgpp*)
+ lt_prog_compiler_pic=
+ ;;
+ *)
+ lt_prog_compiler_pic="$lt_prog_compiler_pic -DPIC"
+ ;;
+esac
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_prog_compiler_pic" >&5
+$as_echo "$lt_prog_compiler_pic" >&6; }
+
+
+
+
+
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$lt_prog_compiler_pic"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler PIC flag $lt_prog_compiler_pic works" >&5
+$as_echo_n "checking if $compiler PIC flag $lt_prog_compiler_pic works... " >&6; }
+if test "${lt_cv_prog_compiler_pic_works+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_pic_works=no
+ ac_outfile=conftest.$ac_objext
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+ lt_compiler_flag="$lt_prog_compiler_pic -DPIC"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ # The option is referenced via a variable to avoid confusing sed.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:9095: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>conftest.err)
+ ac_status=$?
+ cat conftest.err >&5
+ echo "$as_me:9099: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s "$ac_outfile"; then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings other than the usual output.
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_pic_works=yes
+ fi
+ fi
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_pic_works" >&5
+$as_echo "$lt_cv_prog_compiler_pic_works" >&6; }
+
+if test x"$lt_cv_prog_compiler_pic_works" = xyes; then
+ case $lt_prog_compiler_pic in
+ "" | " "*) ;;
+ *) lt_prog_compiler_pic=" $lt_prog_compiler_pic" ;;
+ esac
+else
+ lt_prog_compiler_pic=
+ lt_prog_compiler_can_build_shared=no
+fi
+
+fi
+
+
+
+
+
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$lt_prog_compiler_wl eval lt_tmp_static_flag=\"$lt_prog_compiler_static\"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler static flag $lt_tmp_static_flag works" >&5
+$as_echo_n "checking if $compiler static flag $lt_tmp_static_flag works... " >&6; }
+if test "${lt_cv_prog_compiler_static_works+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_static_works=no
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS $lt_tmp_static_flag"
+ echo "$lt_simple_link_test_code" > conftest.$ac_ext
+ if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+ # The linker can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ if test -s conftest.err; then
+ # Append any errors to the config.log.
+ cat conftest.err 1>&5
+ $ECHO "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_static_works=yes
+ fi
+ else
+ lt_cv_prog_compiler_static_works=yes
+ fi
+ fi
+ $RM -r conftest*
+ LDFLAGS="$save_LDFLAGS"
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_static_works" >&5
+$as_echo "$lt_cv_prog_compiler_static_works" >&6; }
+
+if test x"$lt_cv_prog_compiler_static_works" = xyes; then
+ :
+else
+ lt_prog_compiler_static=
+fi
+
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler supports -c -o file.$ac_objext" >&5
+$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; }
+if test "${lt_cv_prog_compiler_c_o+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_c_o=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:9200: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&5
+ echo "$as_me:9204: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_c_o=yes
+ fi
+ fi
+ chmod u+w . 2>&5
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_c_o" >&5
+$as_echo "$lt_cv_prog_compiler_c_o" >&6; }
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler supports -c -o file.$ac_objext" >&5
+$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; }
+if test "${lt_cv_prog_compiler_c_o+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_c_o=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:9255: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&5
+ echo "$as_me:9259: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_c_o=yes
+ fi
+ fi
+ chmod u+w . 2>&5
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_c_o" >&5
+$as_echo "$lt_cv_prog_compiler_c_o" >&6; }
+
+
+
+
+hard_links="nottested"
+if test "$lt_cv_prog_compiler_c_o" = no && test "$need_locks" != no; then
+ # do not overwrite the value of need_locks provided by the user
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if we can lock with hard links" >&5
+$as_echo_n "checking if we can lock with hard links... " >&6; }
+ hard_links=yes
+ $RM conftest*
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ touch conftest.a
+ ln conftest.a conftest.b 2>&5 || hard_links=no
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $hard_links" >&5
+$as_echo "$hard_links" >&6; }
+ if test "$hard_links" = no; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&5
+$as_echo "$as_me: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&2;}
+ need_locks=warn
+ fi
+else
+ need_locks=no
+fi
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+$as_echo_n "checking whether the $compiler linker ($LD) supports shared libraries... " >&6; }
+
+ runpath_var=
+ allow_undefined_flag=
+ always_export_symbols=no
+ archive_cmds=
+ archive_expsym_cmds=
+ compiler_needs_object=no
+ enable_shared_with_static_runtimes=no
+ export_dynamic_flag_spec=
+ export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ hardcode_automatic=no
+ hardcode_direct=no
+ hardcode_direct_absolute=no
+ hardcode_libdir_flag_spec=
+ hardcode_libdir_flag_spec_ld=
+ hardcode_libdir_separator=
+ hardcode_minus_L=no
+ hardcode_shlibpath_var=unsupported
+ inherit_rpath=no
+ link_all_deplibs=unknown
+ module_cmds=
+ module_expsym_cmds=
+ old_archive_from_new_cmds=
+ old_archive_from_expsyms_cmds=
+ thread_safe_flag_spec=
+ whole_archive_flag_spec=
+ # include_expsyms should be a list of space-separated symbols to be *always*
+ # included in the symbol list
+ include_expsyms=
+ # exclude_expsyms can be an extended regexp of symbols to exclude
+ # it will be wrapped by ` (' and `)$', so one must not match beginning or
+ # end of line. Example: `a|bc|.*d.*' will exclude the symbols `a' and `bc',
+ # as well as any symbol that contains `d'.
+ exclude_expsyms='_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*'
+ # Although _GLOBAL_OFFSET_TABLE_ is a valid symbol C name, most a.out
+ # platforms (ab)use it in PIC code, but their linkers get confused if
+ # the symbol is explicitly referenced. Since portable code cannot
+ # rely on this symbol name, it's probably fine to never include it in
+ # preloaded symbol tables.
+ # Exclude shared library initialization/finalization symbols.
+ extract_expsyms_cmds=
+
+ case $host_os in
+ cygwin* | mingw* | pw32* | cegcc*)
+ # FIXME: the MSVC++ port hasn't been tested in a loooong time
+ # When not using gcc, we currently assume that we are using
+ # Microsoft Visual C++.
+ if test "$GCC" != yes; then
+ with_gnu_ld=no
+ fi
+ ;;
+ interix*)
+ # we just hope/assume this is gcc and not c89 (= MSVC++)
+ with_gnu_ld=yes
+ ;;
+ openbsd*)
+ with_gnu_ld=no
+ ;;
+ linux* | k*bsd*-gnu)
+ link_all_deplibs=no
+ ;;
+ esac
+
+ ld_shlibs=yes
+ if test "$with_gnu_ld" = yes; then
+ # If archive_cmds runs LD, not CC, wlarc should be empty
+ wlarc='${wl}'
+
+ # Set some defaults for GNU ld with shared library support. These
+ # are reset later if shared libraries are not supported. Putting them
+ # here allows them to be overridden if necessary.
+ runpath_var=LD_RUN_PATH
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ export_dynamic_flag_spec='${wl}--export-dynamic'
+ # ancient GNU ld didn't support --whole-archive et. al.
+ if $LD --help 2>&1 | $GREP 'no-whole-archive' > /dev/null; then
+ whole_archive_flag_spec="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ else
+ whole_archive_flag_spec=
+ fi
+ supports_anon_versioning=no
+ case `$LD -v 2>&1` in
+ *GNU\ gold*) supports_anon_versioning=yes ;;
+ *\ [01].* | *\ 2.[0-9].* | *\ 2.10.*) ;; # catch versions < 2.11
+ *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ...
+ *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ...
+ *\ 2.11.*) ;; # other 2.11 versions
+ *) supports_anon_versioning=yes ;;
+ esac
+
+ # See if GNU ld supports shared libraries.
+ case $host_os in
+ aix[3-9]*)
+ # On AIX/PPC, the GNU linker is very broken
+ if test "$host_cpu" != ia64; then
+ ld_shlibs=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the GNU linker, at least up to release 2.9.1, is reported
+*** to be unable to reliably create shared libraries on AIX.
+*** Therefore, libtool is disabling shared libraries support. If you
+*** really care for shared libraries, you may want to modify your PATH
+*** so that a non-GNU linker is found, and then restart.
+
+_LT_EOF
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds=''
+ ;;
+ m68k)
+ archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_minus_L=yes
+ ;;
+ esac
+ ;;
+
+ beos*)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ allow_undefined_flag=unsupported
+ # Joseph Beckenbach <jrb3 at best.com> says some releases of gcc
+ # support --undefined. This deserves some investigation. FIXME
+ archive_cmds='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # _LT_TAGVAR(hardcode_libdir_flag_spec, ) is actually meaningless,
+ # as there is no search path for DLLs.
+ hardcode_libdir_flag_spec='-L$libdir'
+ allow_undefined_flag=unsupported
+ always_export_symbols=no
+ enable_shared_with_static_runtimes=yes
+ export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1 DATA/'\'' | $SED -e '\''/^[AITW][ ]/s/.*[ ]//'\'' | sort | uniq > $export_symbols'
+
+ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ # If the export-symbols file already is a .def file (1st line
+ # is EXPORTS), use it as is; otherwise, prepend...
+ archive_expsym_cmds='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+ cp $export_symbols $output_objdir/$soname.def;
+ else
+ echo EXPORTS > $output_objdir/$soname.def;
+ cat $export_symbols >> $output_objdir/$soname.def;
+ fi~
+ $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ interix[3-9]*)
+ hardcode_direct=no
+ hardcode_shlibpath_var=no
+ hardcode_libdir_flag_spec='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec='${wl}-E'
+ # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+ # Instead, shared libraries are loaded at an image base (0x10000000 by
+ # default) and relocated if they conflict, which is a slow very memory
+ # consuming and fragmenting process. To avoid this, we pick a random,
+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+ # time. Moving up from 0x10000000 also allows more sbrk(2) space.
+ archive_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ archive_expsym_cmds='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ ;;
+
+ gnu* | linux* | tpf* | k*bsd*-gnu | kopensolaris*-gnu)
+ tmp_diet=no
+ if test "$host_os" = linux-dietlibc; then
+ case $cc_basename in
+ diet\ *) tmp_diet=yes;; # linux-dietlibc with static linking (!diet-dyn)
+ esac
+ fi
+ if $LD --help 2>&1 | $EGREP ': supported targets:.* elf' > /dev/null \
+ && test "$tmp_diet" = no
+ then
+ tmp_addflag=
+ tmp_sharedflag='-shared'
+ case $cc_basename,$host_cpu in
+ pgcc*) # Portland Group C compiler
+ whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ tmp_addflag=' $pic_flag'
+ ;;
+ pgf77* | pgf90* | pgf95*) # Portland Group f77 and f90 compilers
+ whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ tmp_addflag=' $pic_flag -Mnomain' ;;
+ ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64
+ tmp_addflag=' -i_dynamic' ;;
+ efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64
+ tmp_addflag=' -i_dynamic -nofor_main' ;;
+ ifc* | ifort*) # Intel Fortran compiler
+ tmp_addflag=' -nofor_main' ;;
+ lf95*) # Lahey Fortran 8.1
+ whole_archive_flag_spec=
+ tmp_sharedflag='--shared' ;;
+ xl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ tmp_sharedflag='-qmkshrobj'
+ tmp_addflag= ;;
+ esac
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*) # Sun C 5.9
+ whole_archive_flag_spec='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ compiler_needs_object=yes
+ tmp_sharedflag='-G' ;;
+ *Sun\ F*) # Sun Fortran 8.3
+ tmp_sharedflag='-G' ;;
+ esac
+ archive_cmds='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+
+ if test "x$supports_anon_versioning" = xyes; then
+ archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+ fi
+
+ case $cc_basename in
+ xlf*)
+ # IBM XL Fortran 10.1 on PPC cannot create shared libs itself
+ whole_archive_flag_spec='--whole-archive$convenience --no-whole-archive'
+ hardcode_libdir_flag_spec=
+ hardcode_libdir_flag_spec_ld='-rpath $libdir'
+ archive_cmds='$LD -shared $libobjs $deplibs $compiler_flags -soname $soname -o $lib'
+ if test "x$supports_anon_versioning" = xyes; then
+ archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $LD -shared $libobjs $deplibs $compiler_flags -soname $soname -version-script $output_objdir/$libname.ver -o $lib'
+ fi
+ ;;
+ esac
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ archive_cmds='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
+ wlarc=
+ else
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ fi
+ ;;
+
+ solaris*)
+ if $LD -v 2>&1 | $GREP 'BFD 2\.8' > /dev/null; then
+ ld_shlibs=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: The releases 2.8.* of the GNU linker cannot reliably
+*** create shared libraries on Solaris systems. Therefore, libtool
+*** is disabling shared libraries support. We urge you to upgrade GNU
+*** binutils to release 2.9.1 or newer. Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+ elif $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*)
+ case `$LD -v 2>&1` in
+ *\ [01].* | *\ 2.[0-9].* | *\ 2.1[0-5].*)
+ ld_shlibs=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not
+*** reliably create shared libraries on SCO systems. Therefore, libtool
+*** is disabling shared libraries support. We urge you to upgrade GNU
+*** binutils to release 2.16.91.0.3 or newer. Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+ ;;
+ *)
+ # For security reasons, it is highly recommended that you always
+ # use absolute paths for naming shared libraries, and exclude the
+ # DT_RUNPATH tag from executables and libraries. But doing so
+ # requires that you compile everything twice, which is a pain.
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+ esac
+ ;;
+
+ sunos4*)
+ archive_cmds='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ wlarc=
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ *)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+ esac
+
+ if test "$ld_shlibs" = no; then
+ runpath_var=
+ hardcode_libdir_flag_spec=
+ export_dynamic_flag_spec=
+ whole_archive_flag_spec=
+ fi
+ else
+ # PORTME fill in a description of your system's linker (not GNU ld)
+ case $host_os in
+ aix3*)
+ allow_undefined_flag=unsupported
+ always_export_symbols=yes
+ archive_expsym_cmds='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname'
+ # Note: this linker hardcodes the directories in LIBPATH if there
+ # are no directories specified by -L.
+ hardcode_minus_L=yes
+ if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then
+ # Neither direct hardcoding nor static linking is supported with a
+ # broken collect2.
+ hardcode_direct=unsupported
+ fi
+ ;;
+
+ aix[4-9]*)
+ if test "$host_cpu" = ia64; then
+ # On IA64, the linker does run time linking by default, so we don't
+ # have to do anything special.
+ aix_use_runtimelinking=no
+ exp_sym_flag='-Bexport'
+ no_entry_flag=""
+ else
+ # If we're using GNU nm, then we don't want the "-C" option.
+ # -C means demangle to AIX nm, but means don't demangle with GNU nm
+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then
+ export_symbols_cmds='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ else
+ export_symbols_cmds='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ fi
+ aix_use_runtimelinking=no
+
+ # Test if we are trying to use run time linking or normal
+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+ # need to do runtime linking.
+ case $host_os in aix4.[23]|aix4.[23].*|aix[5-9]*)
+ for ld_flag in $LDFLAGS; do
+ if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then
+ aix_use_runtimelinking=yes
+ break
+ fi
+ done
+ ;;
+ esac
+
+ exp_sym_flag='-bexport'
+ no_entry_flag='-bnoentry'
+ fi
+
+ # When large executables or shared objects are built, AIX ld can
+ # have problems creating the table of contents. If linking a library
+ # or program results in "error TOC overflow" add -mminimal-toc to
+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not
+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+ archive_cmds=''
+ hardcode_direct=yes
+ hardcode_direct_absolute=yes
+ hardcode_libdir_separator=':'
+ link_all_deplibs=yes
+ file_list_spec='${wl}-f,'
+
+ if test "$GCC" = yes; then
+ case $host_os in aix4.[012]|aix4.[012].*)
+ # We only want to do this on AIX 4.2 and lower, the check
+ # below for broken collect2 doesn't work under 4.3+
+ collect2name=`${CC} -print-prog-name=collect2`
+ if test -f "$collect2name" &&
+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null
+ then
+ # We have reworked collect2
+ :
+ else
+ # We have old collect2
+ hardcode_direct=unsupported
+ # It fails to find uninstalled libraries when the uninstalled
+ # path is not listed in the libpath. Setting hardcode_minus_L
+ # to unsupported forces relinking
+ hardcode_minus_L=yes
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_libdir_separator=
+ fi
+ ;;
+ esac
+ shared_flag='-shared'
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag="$shared_flag "'${wl}-G'
+ fi
+ link_all_deplibs=no
+ else
+ # not using gcc
+ if test "$host_cpu" = ia64; then
+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+ # chokes on -Wl,-G. The following line is correct:
+ shared_flag='-G'
+ else
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag='${wl}-G'
+ else
+ shared_flag='${wl}-bM:SRE'
+ fi
+ fi
+ fi
+
+ export_dynamic_flag_spec='${wl}-bexpall'
+ # It seems that -bexpall does not export symbols beginning with
+ # underscore (_), so it is better to generate a list of symbols to export.
+ always_export_symbols=yes
+ if test "$aix_use_runtimelinking" = yes; then
+ # Warning - without using the other runtime loading flags (-brtl),
+ # -berok will link without error, but may produce a broken library.
+ allow_undefined_flag='-berok'
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+ hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath"
+ archive_expsym_cmds='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+ else
+ if test "$host_cpu" = ia64; then
+ hardcode_libdir_flag_spec='${wl}-R $libdir:/usr/lib:/lib'
+ allow_undefined_flag="-z nodefs"
+ archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+ else
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+ hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath"
+ # Warning - without using the other run time loading flags,
+ # -berok will link without error, but may produce a broken library.
+ no_undefined_flag=' ${wl}-bernotok'
+ allow_undefined_flag=' ${wl}-berok'
+ # Exported symbols can be pulled into shared objects from archives
+ whole_archive_flag_spec='$convenience'
+ archive_cmds_need_lc=yes
+ # This is similar to how AIX traditionally builds its shared libraries.
+ archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+ fi
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds=''
+ ;;
+ m68k)
+ archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_minus_L=yes
+ ;;
+ esac
+ ;;
+
+ bsdi[45]*)
+ export_dynamic_flag_spec=-rdynamic
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # When not using gcc, we currently assume that we are using
+ # Microsoft Visual C++.
+ # hardcode_libdir_flag_spec is actually meaningless, as there is
+ # no search path for DLLs.
+ hardcode_libdir_flag_spec=' '
+ allow_undefined_flag=unsupported
+ # Tell ltmain to make .lib files, not .a files.
+ libext=lib
+ # Tell ltmain to make .dll files, not .so files.
+ shrext_cmds=".dll"
+ # FIXME: Setting linknames here is a bad hack.
+ archive_cmds='$CC -o $lib $libobjs $compiler_flags `$ECHO "X$deplibs" | $Xsed -e '\''s/ -lc$//'\''` -link -dll~linknames='
+ # The linker will automatically build a .lib file if we build a DLL.
+ old_archive_from_new_cmds='true'
+ # FIXME: Should let the user specify the lib program.
+ old_archive_cmds='lib -OUT:$oldlib$oldobjs$old_deplibs'
+ fix_srcfile_path='`cygpath -w "$srcfile"`'
+ enable_shared_with_static_runtimes=yes
+ ;;
+
+ darwin* | rhapsody*)
+
+
+ archive_cmds_need_lc=no
+ hardcode_direct=no
+ hardcode_automatic=yes
+ hardcode_shlibpath_var=unsupported
+ whole_archive_flag_spec=''
+ link_all_deplibs=yes
+ allow_undefined_flag="$_lt_dar_allow_undefined"
+ case $cc_basename in
+ ifort*) _lt_dar_can_shared=yes ;;
+ *) _lt_dar_can_shared=$GCC ;;
+ esac
+ if test "$_lt_dar_can_shared" = "yes"; then
+ output_verbose_link_cmd=echo
+ archive_cmds="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}"
+ module_cmds="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}"
+ archive_expsym_cmds="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}"
+ module_expsym_cmds="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}"
+
+ else
+ ld_shlibs=no
+ fi
+
+ ;;
+
+ dgux*)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_shlibpath_var=no
+ ;;
+
+ freebsd1*)
+ ld_shlibs=no
+ ;;
+
+ # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor
+ # support. Future versions do this automatically, but an explicit c++rt0.o
+ # does not break anything, and helps significantly (at the cost of a little
+ # extra space).
+ freebsd2.2*)
+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o'
+ hardcode_libdir_flag_spec='-R$libdir'
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ # Unfortunately, older versions of FreeBSD 2 do not have this feature.
+ freebsd2*)
+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_direct=yes
+ hardcode_minus_L=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ # FreeBSD 3 and greater uses gcc -shared to do shared libraries.
+ freebsd* | dragonfly*)
+ archive_cmds='$CC -shared -o $lib $libobjs $deplibs $compiler_flags'
+ hardcode_libdir_flag_spec='-R$libdir'
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ hpux9*)
+ if test "$GCC" = yes; then
+ archive_cmds='$RM $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ else
+ archive_cmds='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ fi
+ hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
+ hardcode_libdir_separator=:
+ hardcode_direct=yes
+
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ hardcode_minus_L=yes
+ export_dynamic_flag_spec='${wl}-E'
+ ;;
+
+ hpux10*)
+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+ archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags'
+ fi
+ if test "$with_gnu_ld" = no; then
+ hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
+ hardcode_libdir_flag_spec_ld='+b $libdir'
+ hardcode_libdir_separator=:
+ hardcode_direct=yes
+ hardcode_direct_absolute=yes
+ export_dynamic_flag_spec='${wl}-E'
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ hardcode_minus_L=yes
+ fi
+ ;;
+
+ hpux11*)
+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+ case $host_cpu in
+ hppa*64*)
+ archive_cmds='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ ia64*)
+ archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ else
+ case $host_cpu in
+ hppa*64*)
+ archive_cmds='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ ia64*)
+ archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ fi
+ if test "$with_gnu_ld" = no; then
+ hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
+ hardcode_libdir_separator=:
+
+ case $host_cpu in
+ hppa*64*|ia64*)
+ hardcode_direct=no
+ hardcode_shlibpath_var=no
+ ;;
+ *)
+ hardcode_direct=yes
+ hardcode_direct_absolute=yes
+ export_dynamic_flag_spec='${wl}-E'
+
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ hardcode_minus_L=yes
+ ;;
+ esac
+ fi
+ ;;
+
+ irix5* | irix6* | nonstopux*)
+ if test "$GCC" = yes; then
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ # Try to use the -exported_symbol ld option, if it does not
+ # work, assume that -exports_file does not work either and
+ # implicitly export all symbols.
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+int foo(void) {}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib'
+
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+ LDFLAGS="$save_LDFLAGS"
+ else
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib'
+ fi
+ archive_cmds_need_lc='no'
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator=:
+ inherit_rpath=yes
+ link_all_deplibs=yes
+ ;;
+
+ netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out
+ else
+ archive_cmds='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF
+ fi
+ hardcode_libdir_flag_spec='-R$libdir'
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ newsos6)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_direct=yes
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator=:
+ hardcode_shlibpath_var=no
+ ;;
+
+ *nto* | *qnx*)
+ ;;
+
+ openbsd*)
+ if test -f /usr/libexec/ld.so; then
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ hardcode_direct_absolute=yes
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols'
+ hardcode_libdir_flag_spec='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec='${wl}-E'
+ else
+ case $host_os in
+ openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*)
+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_libdir_flag_spec='-R$libdir'
+ ;;
+ *)
+ archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+ hardcode_libdir_flag_spec='${wl}-rpath,$libdir'
+ ;;
+ esac
+ fi
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ os2*)
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_minus_L=yes
+ allow_undefined_flag=unsupported
+ archive_cmds='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def'
+ old_archive_from_new_cmds='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def'
+ ;;
+
+ osf3*)
+ if test "$GCC" = yes; then
+ allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*'
+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ else
+ allow_undefined_flag=' -expect_unresolved \*'
+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ fi
+ archive_cmds_need_lc='no'
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator=:
+ ;;
+
+ osf4* | osf5*) # as osf3* with the addition of -msym flag
+ if test "$GCC" = yes; then
+ allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*'
+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ else
+ allow_undefined_flag=' -expect_unresolved \*'
+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ archive_expsym_cmds='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~
+ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp'
+
+ # Both c and cxx compiler support -rpath directly
+ hardcode_libdir_flag_spec='-rpath $libdir'
+ fi
+ archive_cmds_need_lc='no'
+ hardcode_libdir_separator=:
+ ;;
+
+ solaris*)
+ no_undefined_flag=' -z defs'
+ if test "$GCC" = yes; then
+ wlarc='${wl}'
+ archive_cmds='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp'
+ else
+ case `$CC -V 2>&1` in
+ *"Compilers 5.0"*)
+ wlarc=''
+ archive_cmds='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp'
+ ;;
+ *)
+ wlarc='${wl}'
+ archive_cmds='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp'
+ ;;
+ esac
+ fi
+ hardcode_libdir_flag_spec='-R$libdir'
+ hardcode_shlibpath_var=no
+ case $host_os in
+ solaris2.[0-5] | solaris2.[0-5].*) ;;
+ *)
+ # The compiler driver will combine and reorder linker options,
+ # but understands `-z linker_flag'. GCC discards it without `$wl',
+ # but is careful enough not to reorder.
+ # Supported since Solaris 2.6 (maybe 2.5.1?)
+ if test "$GCC" = yes; then
+ whole_archive_flag_spec='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract'
+ else
+ whole_archive_flag_spec='-z allextract$convenience -z defaultextract'
+ fi
+ ;;
+ esac
+ link_all_deplibs=yes
+ ;;
+
+ sunos4*)
+ if test "x$host_vendor" = xsequent; then
+ # Use $CC to link under sequent, because it throws in some extra .o
+ # files that make .init and .fini sections work.
+ archive_cmds='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ archive_cmds='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags'
+ fi
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_direct=yes
+ hardcode_minus_L=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ sysv4)
+ case $host_vendor in
+ sni)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_direct=yes # is this really true???
+ ;;
+ siemens)
+ ## LD is ld it makes a PLAMLIB
+ ## CC just makes a GrossModule.
+ archive_cmds='$LD -G -o $lib $libobjs $deplibs $linker_flags'
+ reload_cmds='$CC -r -o $output$reload_objs'
+ hardcode_direct=no
+ ;;
+ motorola)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_direct=no #Motorola manual says yes, but my tests say they lie
+ ;;
+ esac
+ runpath_var='LD_RUN_PATH'
+ hardcode_shlibpath_var=no
+ ;;
+
+ sysv4.3*)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_shlibpath_var=no
+ export_dynamic_flag_spec='-Bexport'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_shlibpath_var=no
+ runpath_var=LD_RUN_PATH
+ hardcode_runpath_var=yes
+ ld_shlibs=yes
+ fi
+ ;;
+
+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*)
+ no_undefined_flag='${wl}-z,text'
+ archive_cmds_need_lc=no
+ hardcode_shlibpath_var=no
+ runpath_var='LD_RUN_PATH'
+
+ if test "$GCC" = yes; then
+ archive_cmds='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ archive_cmds='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ fi
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6*)
+ # Note: We can NOT use -z defs as we might desire, because we do not
+ # link with -lc, and that would cause any symbols used from libc to
+ # always be unresolved, which means just about no library would
+ # ever link correctly. If we're not using GNU ld we use -z text
+ # though, which does catch some bad symbols but isn't as heavy-handed
+ # as -z defs.
+ no_undefined_flag='${wl}-z,text'
+ allow_undefined_flag='${wl}-z,nodefs'
+ archive_cmds_need_lc=no
+ hardcode_shlibpath_var=no
+ hardcode_libdir_flag_spec='${wl}-R,$libdir'
+ hardcode_libdir_separator=':'
+ link_all_deplibs=yes
+ export_dynamic_flag_spec='${wl}-Bexport'
+ runpath_var='LD_RUN_PATH'
+
+ if test "$GCC" = yes; then
+ archive_cmds='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ archive_cmds='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ fi
+ ;;
+
+ uts4*)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_shlibpath_var=no
+ ;;
+
+ *)
+ ld_shlibs=no
+ ;;
+ esac
+
+ if test x$host_vendor = xsni; then
+ case $host in
+ sysv4 | sysv4.2uw2* | sysv4.3* | sysv5*)
+ export_dynamic_flag_spec='${wl}-Blargedynsym'
+ ;;
+ esac
+ fi
+ fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ld_shlibs" >&5
+$as_echo "$ld_shlibs" >&6; }
+test "$ld_shlibs" = no && can_build_shared=no
+
+with_gnu_ld=$with_gnu_ld
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$archive_cmds_need_lc" in
+x|xyes)
+ # Assume -lc should be added
+ archive_cmds_need_lc=yes
+
+ if test "$enable_shared" = yes && test "$GCC" = yes; then
+ case $archive_cmds in
+ *'~'*)
+ # FIXME: we may have to deal with multi-command sequences.
+ ;;
+ '$CC '*)
+ # Test whether the compiler implicitly links with -lc since on some
+ # systems, -lgcc has to come before -lc. If gcc already passes -lc
+ # to ld, don't add -lc before -lgcc.
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether -lc should be explicitly linked in" >&5
+$as_echo_n "checking whether -lc should be explicitly linked in... " >&6; }
+ $RM conftest*
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } 2>conftest.err; then
+ soname=conftest
+ lib=conftest
+ libobjs=conftest.$ac_objext
+ deplibs=
+ wl=$lt_prog_compiler_wl
+ pic_flag=$lt_prog_compiler_pic
+ compiler_flags=-v
+ linker_flags=-v
+ verstring=
+ output_objdir=.
+ libname=conftest
+ lt_save_allow_undefined_flag=$allow_undefined_flag
+ allow_undefined_flag=
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$archive_cmds 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1\""; } >&5
+ (eval $archive_cmds 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+ then
+ archive_cmds_need_lc=no
+ else
+ archive_cmds_need_lc=yes
+ fi
+ allow_undefined_flag=$lt_save_allow_undefined_flag
+ else
+ cat conftest.err 1>&5
+ fi
+ $RM conftest*
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $archive_cmds_need_lc" >&5
+$as_echo "$archive_cmds_need_lc" >&6; }
+ ;;
+ esac
+ fi
+ ;;
+esac
+
+
+
+
+
+
+
+
+
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+
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+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking dynamic linker characteristics" >&5
+$as_echo_n "checking dynamic linker characteristics... " >&6; }
+
+if test "$GCC" = yes; then
+ case $host_os in
+ darwin*) lt_awk_arg="/^libraries:/,/LR/" ;;
+ *) lt_awk_arg="/^libraries:/" ;;
+ esac
+ lt_search_path_spec=`$CC -print-search-dirs | awk $lt_awk_arg | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$lt_search_path_spec" | $GREP ';' >/dev/null ; then
+ # if the path contains ";" then we assume it to be the separator
+ # otherwise default to the standard path separator (i.e. ":") - it is
+ # assumed that no part of a normal pathname contains ";" but that should
+ # okay in the real world where ";" in dirpaths is itself problematic.
+ lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ # Ok, now we have the path, separated by spaces, we can step through it
+ # and add multilib dir if necessary.
+ lt_tmp_lt_search_path_spec=
+ lt_multi_os_dir=`$CC $CPPFLAGS $CFLAGS $LDFLAGS -print-multi-os-directory 2>/dev/null`
+ for lt_sys_path in $lt_search_path_spec; do
+ if test -d "$lt_sys_path/$lt_multi_os_dir"; then
+ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path/$lt_multi_os_dir"
+ else
+ test -d "$lt_sys_path" && \
+ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path"
+ fi
+ done
+ lt_search_path_spec=`$ECHO $lt_tmp_lt_search_path_spec | awk '
+BEGIN {RS=" "; FS="/|\n";} {
+ lt_foo="";
+ lt_count=0;
+ for (lt_i = NF; lt_i > 0; lt_i--) {
+ if ($lt_i != "" && $lt_i != ".") {
+ if ($lt_i == "..") {
+ lt_count++;
+ } else {
+ if (lt_count == 0) {
+ lt_foo="/" $lt_i lt_foo;
+ } else {
+ lt_count--;
+ }
+ }
+ }
+ }
+ if (lt_foo != "") { lt_freq[lt_foo]++; }
+ if (lt_freq[lt_foo] == 1) { print lt_foo; }
+}'`
+ sys_lib_search_path_spec=`$ECHO $lt_search_path_spec`
+else
+ sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib"
+fi
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+ shlibpath_var=LIBPATH
+
+ # AIX 3 has no versioning support, so we append a major version to the name.
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+
+aix[4-9]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ hardcode_into_libs=yes
+ if test "$host_cpu" = ia64; then
+ # AIX 5 supports IA64
+ library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ else
+ # With GCC up to 2.95.x, collect2 would create an import file
+ # for dependence libraries. The import file would start with
+ # the line `#! .'. This would cause the generated library to
+ # depend on `.', always an invalid library. This was fixed in
+ # development snapshots of GCC prior to 3.0.
+ case $host_os in
+ aix4 | aix4.[01] | aix4.[01].*)
+ if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+ echo ' yes '
+ echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then
+ :
+ else
+ can_build_shared=no
+ fi
+ ;;
+ esac
+ # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+ # soname into executable. Probably we can add versioning support to
+ # collect2, so additional links can be useful in future.
+ if test "$aix_use_runtimelinking" = yes; then
+ # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+ # instead of lib<name>.a to let people know that these are not
+ # typical AIX shared libraries.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ else
+ # We preserve .a as extension for shared libraries through AIX4.2
+ # and later when we are not doing run time linking.
+ library_names_spec='${libname}${release}.a $libname.a'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ fi
+ shlibpath_var=LIBPATH
+ fi
+ ;;
+
+amigaos*)
+ case $host_cpu in
+ powerpc)
+ # Since July 2007 AmigaOS4 officially supports .so libraries.
+ # When compiling the executable, add -use-dynld -Lsobjs: to the compileline.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ ;;
+ m68k)
+ library_names_spec='$libname.ixlibrary $libname.a'
+ # Create ${libname}_ixlibrary.a entries in /sys/libs.
+ finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$ECHO "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+ ;;
+ esac
+ ;;
+
+beos*)
+ library_names_spec='${libname}${shared_ext}'
+ dynamic_linker="$host_os ld.so"
+ shlibpath_var=LIBRARY_PATH
+ ;;
+
+bsdi[45]*)
+ version_type=linux
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+ sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+ # the default ld.so.conf also contains /usr/contrib/lib and
+ # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+ # libtool to hard-code these into programs
+ ;;
+
+cygwin* | mingw* | pw32* | cegcc*)
+ version_type=windows
+ shrext_cmds=".dll"
+ need_version=no
+ need_lib_prefix=no
+
+ case $GCC,$host_os in
+ yes,cygwin* | yes,mingw* | yes,pw32* | yes,cegcc*)
+ library_names_spec='$libname.dll.a'
+ # DLL is installed to $(libdir)/../bin by postinstall_cmds
+ postinstall_cmds='base_file=`basename \${file}`~
+ dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i; echo \$dlname'\''`~
+ dldir=$destdir/`dirname \$dlpath`~
+ test -d \$dldir || mkdir -p \$dldir~
+ $install_prog $dir/$dlname \$dldir/$dlname~
+ chmod a+x \$dldir/$dlname~
+ if test -n '\''$stripme'\'' && test -n '\''$striplib'\''; then
+ eval '\''$striplib \$dldir/$dlname'\'' || exit \$?;
+ fi'
+ postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+ dlpath=$dir/\$dldll~
+ $RM \$dlpath'
+ shlibpath_overrides_runpath=yes
+
+ case $host_os in
+ cygwin*)
+ # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+ soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+ ;;
+ mingw* | cegcc*)
+ # MinGW DLLs use traditional 'lib' prefix
+ soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec=`$CC -print-search-dirs | $GREP "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$sys_lib_search_path_spec" | $GREP ';[c-zC-Z]:/' >/dev/null; then
+ # It is most probably a Windows format PATH printed by
+ # mingw gcc, but we are running on Cygwin. Gcc prints its search
+ # path with ; separators, and with drive letters. We can handle the
+ # drive letters (cygwin fileutils understands them), so leave them,
+ # especially as we might pass files found there to a mingw objdump,
+ # which wouldn't understand a cygwinified path. Ahh.
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ ;;
+ pw32*)
+ # pw32 DLLs use 'pw' prefix rather than 'lib'
+ library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ ;;
+ esac
+ ;;
+
+ *)
+ library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib'
+ ;;
+ esac
+ dynamic_linker='Win32 ld.exe'
+ # FIXME: first we should search . and the directory the executable is in
+ shlibpath_var=PATH
+ ;;
+
+darwin* | rhapsody*)
+ dynamic_linker="$host_os dyld"
+ version_type=darwin
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+ soname_spec='${libname}${release}${major}$shared_ext'
+ shlibpath_overrides_runpath=yes
+ shlibpath_var=DYLD_LIBRARY_PATH
+ shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /usr/local/lib"
+ sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+ ;;
+
+dgux*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+freebsd1*)
+ dynamic_linker=no
+ ;;
+
+freebsd* | dragonfly*)
+ # DragonFly does not have aout. When/if they implement a new
+ # versioning mechanism, adjust this.
+ if test -x /usr/bin/objformat; then
+ objformat=`/usr/bin/objformat`
+ else
+ case $host_os in
+ freebsd[123]*) objformat=aout ;;
+ *) objformat=elf ;;
+ esac
+ fi
+ version_type=freebsd-$objformat
+ case $version_type in
+ freebsd-elf*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ need_version=no
+ need_lib_prefix=no
+ ;;
+ freebsd-*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+ need_version=yes
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_os in
+ freebsd2*)
+ shlibpath_overrides_runpath=yes
+ ;;
+ freebsd3.[01]* | freebsdelf3.[01]*)
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ freebsd3.[2-9]* | freebsdelf3.[2-9]* | \
+ freebsd4.[0-5] | freebsdelf4.[0-5] | freebsd4.1.1 | freebsdelf4.1.1)
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+ *) # from 4.6 on, and DragonFly
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ esac
+ ;;
+
+gnu*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ hardcode_into_libs=yes
+ ;;
+
+hpux9* | hpux10* | hpux11*)
+ # Give a soname corresponding to the major version so that dld.sl refuses to
+ # link against other versions.
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ case $host_cpu in
+ ia64*)
+ shrext_cmds='.so'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.so"
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ if test "X$HPUX_IA64_MODE" = X32; then
+ sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+ else
+ sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+ fi
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ hppa*64*)
+ shrext_cmds='.sl'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ *)
+ shrext_cmds='.sl'
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=SHLIB_PATH
+ shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+ esac
+ # HP-UX runs *really* slowly unless shared libraries are mode 555.
+ postinstall_cmds='chmod 555 $lib'
+ ;;
+
+interix[3-9]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $host_os in
+ nonstopux*) version_type=nonstopux ;;
+ *)
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ version_type=linux
+ else
+ version_type=irix
+ fi ;;
+ esac
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+ case $host_os in
+ irix5* | nonstopux*)
+ libsuff= shlibsuff=
+ ;;
+ *)
+ case $LD in # libtool.m4 will add one of these switches to LD
+ *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+ libsuff= shlibsuff= libmagic=32-bit;;
+ *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+ libsuff=32 shlibsuff=N32 libmagic=N32;;
+ *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+ libsuff=64 shlibsuff=64 libmagic=64-bit;;
+ *) libsuff= shlibsuff= libmagic=never-match;;
+ esac
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+ sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+ hardcode_into_libs=yes
+ ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+ dynamic_linker=no
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ # Some binutils ld are patched to set DT_RUNPATH
+ save_LDFLAGS=$LDFLAGS
+ save_libdir=$libdir
+ eval "libdir=/foo; wl=\"$lt_prog_compiler_wl\"; \
+ LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec\""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then :
+ shlibpath_overrides_runpath=yes
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+ LDFLAGS=$save_LDFLAGS
+ libdir=$save_libdir
+
+ # This implies no fast_install, which is unacceptable.
+ # Some rework will be needed to allow for fast_install
+ # before this can be enabled.
+ hardcode_into_libs=yes
+
+ # Append ld.so.conf contents to the search path
+ if test -f /etc/ld.so.conf; then
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ fi
+
+ # We used to test for /lib/ld.so.1 and disable shared libraries on
+ # powerpc, because MkLinux only supported shared libraries with the
+ # GNU dynamic linker. Since this was broken with cross compilers,
+ # most powerpc-linux boxes support dynamic linking these days and
+ # people can always --disable-shared, the test was removed, and we
+ # assume the GNU/Linux dynamic linker is in use.
+ dynamic_linker='GNU/Linux ld.so'
+ ;;
+
+netbsdelf*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='NetBSD ld.elf_so'
+ ;;
+
+netbsd*)
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ dynamic_linker='NetBSD (a.out) ld.so'
+ else
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='NetBSD ld.elf_so'
+ fi
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+
+newsos6)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ ;;
+
+*nto* | *qnx*)
+ version_type=qnx
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='ldqnx.so'
+ ;;
+
+openbsd*)
+ version_type=sunos
+ sys_lib_dlsearch_path_spec="/usr/lib"
+ need_lib_prefix=no
+ # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+ case $host_os in
+ openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+ *) need_version=no ;;
+ esac
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ case $host_os in
+ openbsd2.[89] | openbsd2.[89].*)
+ shlibpath_overrides_runpath=no
+ ;;
+ *)
+ shlibpath_overrides_runpath=yes
+ ;;
+ esac
+ else
+ shlibpath_overrides_runpath=yes
+ fi
+ ;;
+
+os2*)
+ libname_spec='$name'
+ shrext_cmds=".dll"
+ need_lib_prefix=no
+ library_names_spec='$libname${shared_ext} $libname.a'
+ dynamic_linker='OS/2 ld.exe'
+ shlibpath_var=LIBPATH
+ ;;
+
+osf3* | osf4* | osf5*)
+ version_type=osf
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+ sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+ ;;
+
+rdos*)
+ dynamic_linker=no
+ ;;
+
+solaris*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ # ldd complains unless libraries are executable
+ postinstall_cmds='chmod +x $lib'
+ ;;
+
+sunos4*)
+ version_type=sunos
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ if test "$with_gnu_ld" = yes; then
+ need_lib_prefix=no
+ fi
+ need_version=yes
+ ;;
+
+sysv4 | sysv4.3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_vendor in
+ sni)
+ shlibpath_overrides_runpath=no
+ need_lib_prefix=no
+ runpath_var=LD_RUN_PATH
+ ;;
+ siemens)
+ need_lib_prefix=no
+ ;;
+ motorola)
+ need_lib_prefix=no
+ need_version=no
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+ ;;
+ esac
+ ;;
+
+sysv4*MP*)
+ if test -d /usr/nec ;then
+ version_type=linux
+ library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+ soname_spec='$libname${shared_ext}.$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ fi
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ version_type=freebsd-elf
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ if test "$with_gnu_ld" = yes; then
+ sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+ else
+ sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+ case $host_os in
+ sco3.2v5*)
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+ ;;
+ esac
+ fi
+ sys_lib_dlsearch_path_spec='/usr/lib'
+ ;;
+
+tpf*)
+ # TPF is a cross-target only. Preferred cross-host = GNU/Linux.
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+uts4*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+*)
+ dynamic_linker=no
+ ;;
+esac
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $dynamic_linker" >&5
+$as_echo "$dynamic_linker" >&6; }
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+ variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+
+if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then
+ sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec"
+fi
+if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then
+ sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec"
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to hardcode library paths into programs" >&5
+$as_echo_n "checking how to hardcode library paths into programs... " >&6; }
+hardcode_action=
+if test -n "$hardcode_libdir_flag_spec" ||
+ test -n "$runpath_var" ||
+ test "X$hardcode_automatic" = "Xyes" ; then
+
+ # We can hardcode non-existent directories.
+ if test "$hardcode_direct" != no &&
+ # If the only mechanism to avoid hardcoding is shlibpath_var, we
+ # have to relink, otherwise we might link with an installed library
+ # when we should be linking with a yet-to-be-installed one
+ ## test "$_LT_TAGVAR(hardcode_shlibpath_var, )" != no &&
+ test "$hardcode_minus_L" != no; then
+ # Linking always hardcodes the temporary library directory.
+ hardcode_action=relink
+ else
+ # We can link without hardcoding, and we can hardcode nonexisting dirs.
+ hardcode_action=immediate
+ fi
+else
+ # We cannot hardcode anything, or else we can only hardcode existing
+ # directories.
+ hardcode_action=unsupported
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $hardcode_action" >&5
+$as_echo "$hardcode_action" >&6; }
+
+if test "$hardcode_action" = relink ||
+ test "$inherit_rpath" = yes; then
+ # Fast installation is not supported
+ enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+ test "$enable_shared" = no; then
+ # Fast installation is not necessary
+ enable_fast_install=needless
+fi
+
+
+
+
+
+
+ if test "x$enable_dlopen" != xyes; then
+ enable_dlopen=unknown
+ enable_dlopen_self=unknown
+ enable_dlopen_self_static=unknown
+else
+ lt_cv_dlopen=no
+ lt_cv_dlopen_libs=
+
+ case $host_os in
+ beos*)
+ lt_cv_dlopen="load_add_on"
+ lt_cv_dlopen_libs=
+ lt_cv_dlopen_self=yes
+ ;;
+
+ mingw* | pw32* | cegcc*)
+ lt_cv_dlopen="LoadLibrary"
+ lt_cv_dlopen_libs=
+ ;;
+
+ cygwin*)
+ lt_cv_dlopen="dlopen"
+ lt_cv_dlopen_libs=
+ ;;
+
+ darwin*)
+ # if libdl is installed we need to link against it
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -ldl" >&5
+$as_echo_n "checking for dlopen in -ldl... " >&6; }
+if test "${ac_cv_lib_dl_dlopen+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldl $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+int
+main ()
+{
+return dlopen ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_dl_dlopen=yes
+else
+ ac_cv_lib_dl_dlopen=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dl_dlopen" >&5
+$as_echo "$ac_cv_lib_dl_dlopen" >&6; }
+if test "x$ac_cv_lib_dl_dlopen" = x""yes; then :
+ lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"
+else
+
+ lt_cv_dlopen="dyld"
+ lt_cv_dlopen_libs=
+ lt_cv_dlopen_self=yes
+
+fi
+
+ ;;
+
+ *)
+ ac_fn_c_check_func "$LINENO" "shl_load" "ac_cv_func_shl_load"
+if test "x$ac_cv_func_shl_load" = x""yes; then :
+ lt_cv_dlopen="shl_load"
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for shl_load in -ldld" >&5
+$as_echo_n "checking for shl_load in -ldld... " >&6; }
+if test "${ac_cv_lib_dld_shl_load+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldld $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char shl_load ();
+int
+main ()
+{
+return shl_load ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_dld_shl_load=yes
+else
+ ac_cv_lib_dld_shl_load=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dld_shl_load" >&5
+$as_echo "$ac_cv_lib_dld_shl_load" >&6; }
+if test "x$ac_cv_lib_dld_shl_load" = x""yes; then :
+ lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-ldld"
+else
+ ac_fn_c_check_func "$LINENO" "dlopen" "ac_cv_func_dlopen"
+if test "x$ac_cv_func_dlopen" = x""yes; then :
+ lt_cv_dlopen="dlopen"
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -ldl" >&5
+$as_echo_n "checking for dlopen in -ldl... " >&6; }
+if test "${ac_cv_lib_dl_dlopen+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldl $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+int
+main ()
+{
+return dlopen ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_dl_dlopen=yes
+else
+ ac_cv_lib_dl_dlopen=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dl_dlopen" >&5
+$as_echo "$ac_cv_lib_dl_dlopen" >&6; }
+if test "x$ac_cv_lib_dl_dlopen" = x""yes; then :
+ lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -lsvld" >&5
+$as_echo_n "checking for dlopen in -lsvld... " >&6; }
+if test "${ac_cv_lib_svld_dlopen+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lsvld $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+int
+main ()
+{
+return dlopen ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_svld_dlopen=yes
+else
+ ac_cv_lib_svld_dlopen=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_svld_dlopen" >&5
+$as_echo "$ac_cv_lib_svld_dlopen" >&6; }
+if test "x$ac_cv_lib_svld_dlopen" = x""yes; then :
+ lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld"
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dld_link in -ldld" >&5
+$as_echo_n "checking for dld_link in -ldld... " >&6; }
+if test "${ac_cv_lib_dld_dld_link+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldld $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dld_link ();
+int
+main ()
+{
+return dld_link ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_dld_dld_link=yes
+else
+ ac_cv_lib_dld_dld_link=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dld_dld_link" >&5
+$as_echo "$ac_cv_lib_dld_dld_link" >&6; }
+if test "x$ac_cv_lib_dld_dld_link" = x""yes; then :
+ lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-ldld"
+fi
+
+
+fi
+
+
+fi
+
+
+fi
+
+
+fi
+
+
+fi
+
+ ;;
+ esac
+
+ if test "x$lt_cv_dlopen" != xno; then
+ enable_dlopen=yes
+ else
+ enable_dlopen=no
+ fi
+
+ case $lt_cv_dlopen in
+ dlopen)
+ save_CPPFLAGS="$CPPFLAGS"
+ test "x$ac_cv_header_dlfcn_h" = xyes && CPPFLAGS="$CPPFLAGS -DHAVE_DLFCN_H"
+
+ save_LDFLAGS="$LDFLAGS"
+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\"
+
+ save_LIBS="$LIBS"
+ LIBS="$lt_cv_dlopen_libs $LIBS"
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether a program can dlopen itself" >&5
+$as_echo_n "checking whether a program can dlopen itself... " >&6; }
+if test "${lt_cv_dlopen_self+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then :
+ lt_cv_dlopen_self=cross
+else
+ lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
+ lt_status=$lt_dlunknown
+ cat > conftest.$ac_ext <<_LT_EOF
+#line 11639 "configure"
+#include "confdefs.h"
+
+#if HAVE_DLFCN_H
+#include <dlfcn.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef RTLD_GLOBAL
+# define LT_DLGLOBAL RTLD_GLOBAL
+#else
+# ifdef DL_GLOBAL
+# define LT_DLGLOBAL DL_GLOBAL
+# else
+# define LT_DLGLOBAL 0
+# endif
+#endif
+
+/* We may have to define LT_DLLAZY_OR_NOW in the command line if we
+ find out it does not work in some platform. */
+#ifndef LT_DLLAZY_OR_NOW
+# ifdef RTLD_LAZY
+# define LT_DLLAZY_OR_NOW RTLD_LAZY
+# else
+# ifdef DL_LAZY
+# define LT_DLLAZY_OR_NOW DL_LAZY
+# else
+# ifdef RTLD_NOW
+# define LT_DLLAZY_OR_NOW RTLD_NOW
+# else
+# ifdef DL_NOW
+# define LT_DLLAZY_OR_NOW DL_NOW
+# else
+# define LT_DLLAZY_OR_NOW 0
+# endif
+# endif
+# endif
+# endif
+#endif
+
+void fnord() { int i=42;}
+int main ()
+{
+ void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW);
+ int status = $lt_dlunknown;
+
+ if (self)
+ {
+ if (dlsym (self,"fnord")) status = $lt_dlno_uscore;
+ else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore;
+ /* dlclose (self); */
+ }
+ else
+ puts (dlerror ());
+
+ return status;
+}
+_LT_EOF
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5
+ (eval $ac_link) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && test -s conftest${ac_exeext} 2>/dev/null; then
+ (./conftest; exit; ) >&5 2>/dev/null
+ lt_status=$?
+ case x$lt_status in
+ x$lt_dlno_uscore) lt_cv_dlopen_self=yes ;;
+ x$lt_dlneed_uscore) lt_cv_dlopen_self=yes ;;
+ x$lt_dlunknown|x*) lt_cv_dlopen_self=no ;;
+ esac
+ else :
+ # compilation failed
+ lt_cv_dlopen_self=no
+ fi
+fi
+rm -fr conftest*
+
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_dlopen_self" >&5
+$as_echo "$lt_cv_dlopen_self" >&6; }
+
+ if test "x$lt_cv_dlopen_self" = xyes; then
+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether a statically linked program can dlopen itself" >&5
+$as_echo_n "checking whether a statically linked program can dlopen itself... " >&6; }
+if test "${lt_cv_dlopen_self_static+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then :
+ lt_cv_dlopen_self_static=cross
+else
+ lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
+ lt_status=$lt_dlunknown
+ cat > conftest.$ac_ext <<_LT_EOF
+#line 11735 "configure"
+#include "confdefs.h"
+
+#if HAVE_DLFCN_H
+#include <dlfcn.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef RTLD_GLOBAL
+# define LT_DLGLOBAL RTLD_GLOBAL
+#else
+# ifdef DL_GLOBAL
+# define LT_DLGLOBAL DL_GLOBAL
+# else
+# define LT_DLGLOBAL 0
+# endif
+#endif
+
+/* We may have to define LT_DLLAZY_OR_NOW in the command line if we
+ find out it does not work in some platform. */
+#ifndef LT_DLLAZY_OR_NOW
+# ifdef RTLD_LAZY
+# define LT_DLLAZY_OR_NOW RTLD_LAZY
+# else
+# ifdef DL_LAZY
+# define LT_DLLAZY_OR_NOW DL_LAZY
+# else
+# ifdef RTLD_NOW
+# define LT_DLLAZY_OR_NOW RTLD_NOW
+# else
+# ifdef DL_NOW
+# define LT_DLLAZY_OR_NOW DL_NOW
+# else
+# define LT_DLLAZY_OR_NOW 0
+# endif
+# endif
+# endif
+# endif
+#endif
+
+void fnord() { int i=42;}
+int main ()
+{
+ void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW);
+ int status = $lt_dlunknown;
+
+ if (self)
+ {
+ if (dlsym (self,"fnord")) status = $lt_dlno_uscore;
+ else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore;
+ /* dlclose (self); */
+ }
+ else
+ puts (dlerror ());
+
+ return status;
+}
+_LT_EOF
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5
+ (eval $ac_link) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && test -s conftest${ac_exeext} 2>/dev/null; then
+ (./conftest; exit; ) >&5 2>/dev/null
+ lt_status=$?
+ case x$lt_status in
+ x$lt_dlno_uscore) lt_cv_dlopen_self_static=yes ;;
+ x$lt_dlneed_uscore) lt_cv_dlopen_self_static=yes ;;
+ x$lt_dlunknown|x*) lt_cv_dlopen_self_static=no ;;
+ esac
+ else :
+ # compilation failed
+ lt_cv_dlopen_self_static=no
+ fi
+fi
+rm -fr conftest*
+
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_dlopen_self_static" >&5
+$as_echo "$lt_cv_dlopen_self_static" >&6; }
+ fi
+
+ CPPFLAGS="$save_CPPFLAGS"
+ LDFLAGS="$save_LDFLAGS"
+ LIBS="$save_LIBS"
+ ;;
+ esac
+
+ case $lt_cv_dlopen_self in
+ yes|no) enable_dlopen_self=$lt_cv_dlopen_self ;;
+ *) enable_dlopen_self=unknown ;;
+ esac
+
+ case $lt_cv_dlopen_self_static in
+ yes|no) enable_dlopen_self_static=$lt_cv_dlopen_self_static ;;
+ *) enable_dlopen_self_static=unknown ;;
+ esac
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+striplib=
+old_striplib=
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether stripping libraries is possible" >&5
+$as_echo_n "checking whether stripping libraries is possible... " >&6; }
+if test -n "$STRIP" && $STRIP -V 2>&1 | $GREP "GNU strip" >/dev/null; then
+ test -z "$old_striplib" && old_striplib="$STRIP --strip-debug"
+ test -z "$striplib" && striplib="$STRIP --strip-unneeded"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+else
+# FIXME - insert some real tests, host_os isn't really good enough
+ case $host_os in
+ darwin*)
+ if test -n "$STRIP" ; then
+ striplib="$STRIP -x"
+ old_striplib="$STRIP -S"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ fi
+ ;;
+ *)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ ;;
+ esac
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+ # Report which library types will actually be built
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if libtool supports shared libraries" >&5
+$as_echo_n "checking if libtool supports shared libraries... " >&6; }
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $can_build_shared" >&5
+$as_echo "$can_build_shared" >&6; }
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to build shared libraries" >&5
+$as_echo_n "checking whether to build shared libraries... " >&6; }
+ test "$can_build_shared" = "no" && enable_shared=no
+
+ # On AIX, shared libraries and static libraries use the same namespace, and
+ # are all built from PIC.
+ case $host_os in
+ aix3*)
+ test "$enable_shared" = yes && enable_static=no
+ if test -n "$RANLIB"; then
+ archive_cmds="$archive_cmds~\$RANLIB \$lib"
+ postinstall_cmds='$RANLIB $lib'
+ fi
+ ;;
+
+ aix[4-9]*)
+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+ test "$enable_shared" = yes && enable_static=no
+ fi
+ ;;
+ esac
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $enable_shared" >&5
+$as_echo "$enable_shared" >&6; }
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to build static libraries" >&5
+$as_echo_n "checking whether to build static libraries... " >&6; }
+ # Make sure either enable_shared or enable_static is yes.
+ test "$enable_shared" = yes || enable_static=yes
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $enable_static" >&5
+$as_echo "$enable_static" >&6; }
+
+
+
+
+fi
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+CC="$lt_save_CC"
+
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+archive_cmds_need_lc_CXX=no
+allow_undefined_flag_CXX=
+always_export_symbols_CXX=no
+archive_expsym_cmds_CXX=
+compiler_needs_object_CXX=no
+export_dynamic_flag_spec_CXX=
+hardcode_direct_CXX=no
+hardcode_direct_absolute_CXX=no
+hardcode_libdir_flag_spec_CXX=
+hardcode_libdir_flag_spec_ld_CXX=
+hardcode_libdir_separator_CXX=
+hardcode_minus_L_CXX=no
+hardcode_shlibpath_var_CXX=unsupported
+hardcode_automatic_CXX=no
+inherit_rpath_CXX=no
+module_cmds_CXX=
+module_expsym_cmds_CXX=
+link_all_deplibs_CXX=unknown
+old_archive_cmds_CXX=$old_archive_cmds
+no_undefined_flag_CXX=
+whole_archive_flag_spec_CXX=
+enable_shared_with_static_runtimes_CXX=no
+
+# Source file extension for C++ test sources.
+ac_ext=cpp
+
+# Object file extension for compiled C++ test sources.
+objext=o
+objext_CXX=$objext
+
+# No sense in running all these tests if we already determined that
+# the CXX compiler isn't working. Some variables (like enable_shared)
+# are currently assumed to apply to all compilers on this platform,
+# and will be corrupted by setting them based on a non-working compiler.
+if test "$_lt_caught_CXX_error" != yes; then
+ # Code to be used in simple compile tests
+ lt_simple_compile_test_code="int some_variable = 0;"
+
+ # Code to be used in simple link tests
+ lt_simple_link_test_code='int main(int, char *[]) { return(0); }'
+
+ # ltmain only uses $CC for tagged configurations so make sure $CC is set.
+
+
+
+
+
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+
+ # save warnings/boilerplate of simple test code
+ ac_outfile=conftest.$ac_objext
+echo "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$RM conftest*
+
+ ac_outfile=conftest.$ac_objext
+echo "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$RM -r conftest*
+
+
+ # Allow CC to be a program name with arguments.
+ lt_save_CC=$CC
+ lt_save_LD=$LD
+ lt_save_GCC=$GCC
+ GCC=$GXX
+ lt_save_with_gnu_ld=$with_gnu_ld
+ lt_save_path_LD=$lt_cv_path_LD
+ if test -n "${lt_cv_prog_gnu_ldcxx+set}"; then
+ lt_cv_prog_gnu_ld=$lt_cv_prog_gnu_ldcxx
+ else
+ $as_unset lt_cv_prog_gnu_ld
+ fi
+ if test -n "${lt_cv_path_LDCXX+set}"; then
+ lt_cv_path_LD=$lt_cv_path_LDCXX
+ else
+ $as_unset lt_cv_path_LD
+ fi
+ test -z "${LDCXX+set}" || LD=$LDCXX
+ CC=${CXX-"c++"}
+ compiler=$CC
+ compiler_CXX=$CC
+ for cc_temp in $compiler""; do
+ case $cc_temp in
+ compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+ distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+ \-*) ;;
+ *) break;;
+ esac
+done
+cc_basename=`$ECHO "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+
+
+ if test -n "$compiler"; then
+ # We don't want -fno-exception when compiling C++ code, so set the
+ # no_builtin_flag separately
+ if test "$GXX" = yes; then
+ lt_prog_compiler_no_builtin_flag_CXX=' -fno-builtin'
+ else
+ lt_prog_compiler_no_builtin_flag_CXX=
+ fi
+
+ if test "$GXX" = yes; then
+ # Set up default GNU C++ configuration
+
+
+
+# Check whether --with-gnu-ld was given.
+if test "${with_gnu_ld+set}" = set; then :
+ withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes
+else
+ with_gnu_ld=no
+fi
+
+ac_prog=ld
+if test "$GCC" = yes; then
+ # Check if gcc -print-prog-name=ld gives a path.
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ld used by $CC" >&5
+$as_echo_n "checking for ld used by $CC... " >&6; }
+ case $host in
+ *-*-mingw*)
+ # gcc leaves a trailing carriage return which upsets mingw
+ ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+ *)
+ ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+ esac
+ case $ac_prog in
+ # Accept absolute paths.
+ [\\/]* | ?:[\\/]*)
+ re_direlt='/[^/][^/]*/\.\./'
+ # Canonicalize the pathname of ld
+ ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'`
+ while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do
+ ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"`
+ done
+ test -z "$LD" && LD="$ac_prog"
+ ;;
+ "")
+ # If it fails, then pretend we aren't using GCC.
+ ac_prog=ld
+ ;;
+ *)
+ # If it is relative, then search for the first ld in PATH.
+ with_gnu_ld=unknown
+ ;;
+ esac
+elif test "$with_gnu_ld" = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU ld" >&5
+$as_echo_n "checking for GNU ld... " >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for non-GNU ld" >&5
+$as_echo_n "checking for non-GNU ld... " >&6; }
+fi
+if test "${lt_cv_path_LD+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$LD"; then
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+ lt_cv_path_LD="$ac_dir/$ac_prog"
+ # Check to see if the program is GNU ld. I'd rather use --version,
+ # but apparently some variants of GNU ld only accept -v.
+ # Break only if it was the GNU/non-GNU ld that we prefer.
+ case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+ *GNU* | *'with BFD'*)
+ test "$with_gnu_ld" != no && break
+ ;;
+ *)
+ test "$with_gnu_ld" != yes && break
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+else
+ lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi
+fi
+
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LD" >&5
+$as_echo "$LD" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+test -z "$LD" && as_fn_error $? "no acceptable ld found in \$PATH" "$LINENO" 5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if the linker ($LD) is GNU ld" >&5
+$as_echo_n "checking if the linker ($LD) is GNU ld... " >&6; }
+if test "${lt_cv_prog_gnu_ld+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ # I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+ lt_cv_prog_gnu_ld=yes
+ ;;
+*)
+ lt_cv_prog_gnu_ld=no
+ ;;
+esac
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_gnu_ld" >&5
+$as_echo "$lt_cv_prog_gnu_ld" >&6; }
+with_gnu_ld=$lt_cv_prog_gnu_ld
+
+
+
+
+
+
+
+ # Check if GNU C++ uses GNU ld as the underlying linker, since the
+ # archiving commands below assume that GNU ld is being used.
+ if test "$with_gnu_ld" = yes; then
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+
+ # If archive_cmds runs LD, not CC, wlarc should be empty
+ # XXX I think wlarc can be eliminated in ltcf-cxx, but I need to
+ # investigate it a little bit more. (MM)
+ wlarc='${wl}'
+
+ # ancient GNU ld didn't support --whole-archive et. al.
+ if eval "`$CC -print-prog-name=ld` --help 2>&1" |
+ $GREP 'no-whole-archive' > /dev/null; then
+ whole_archive_flag_spec_CXX="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ else
+ whole_archive_flag_spec_CXX=
+ fi
+ else
+ with_gnu_ld=no
+ wlarc=
+
+ # A generic and very simple default shared library creation
+ # command for GNU C++ for the case where it uses the native
+ # linker, instead of GNU ld. If possible, this setting should
+ # overridden to take advantage of the native linker features on
+ # the platform it is being used on.
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+ fi
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+
+ else
+ GXX=no
+ with_gnu_ld=no
+ wlarc=
+ fi
+
+ # PORTME: fill in a description of your system's C++ link characteristics
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+$as_echo_n "checking whether the $compiler linker ($LD) supports shared libraries... " >&6; }
+ ld_shlibs_CXX=yes
+ case $host_os in
+ aix3*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ aix[4-9]*)
+ if test "$host_cpu" = ia64; then
+ # On IA64, the linker does run time linking by default, so we don't
+ # have to do anything special.
+ aix_use_runtimelinking=no
+ exp_sym_flag='-Bexport'
+ no_entry_flag=""
+ else
+ aix_use_runtimelinking=no
+
+ # Test if we are trying to use run time linking or normal
+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+ # need to do runtime linking.
+ case $host_os in aix4.[23]|aix4.[23].*|aix[5-9]*)
+ for ld_flag in $LDFLAGS; do
+ case $ld_flag in
+ *-brtl*)
+ aix_use_runtimelinking=yes
+ break
+ ;;
+ esac
+ done
+ ;;
+ esac
+
+ exp_sym_flag='-bexport'
+ no_entry_flag='-bnoentry'
+ fi
+
+ # When large executables or shared objects are built, AIX ld can
+ # have problems creating the table of contents. If linking a library
+ # or program results in "error TOC overflow" add -mminimal-toc to
+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not
+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+ archive_cmds_CXX=''
+ hardcode_direct_CXX=yes
+ hardcode_direct_absolute_CXX=yes
+ hardcode_libdir_separator_CXX=':'
+ link_all_deplibs_CXX=yes
+ file_list_spec_CXX='${wl}-f,'
+
+ if test "$GXX" = yes; then
+ case $host_os in aix4.[012]|aix4.[012].*)
+ # We only want to do this on AIX 4.2 and lower, the check
+ # below for broken collect2 doesn't work under 4.3+
+ collect2name=`${CC} -print-prog-name=collect2`
+ if test -f "$collect2name" &&
+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null
+ then
+ # We have reworked collect2
+ :
+ else
+ # We have old collect2
+ hardcode_direct_CXX=unsupported
+ # It fails to find uninstalled libraries when the uninstalled
+ # path is not listed in the libpath. Setting hardcode_minus_L
+ # to unsupported forces relinking
+ hardcode_minus_L_CXX=yes
+ hardcode_libdir_flag_spec_CXX='-L$libdir'
+ hardcode_libdir_separator_CXX=
+ fi
+ esac
+ shared_flag='-shared'
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag="$shared_flag "'${wl}-G'
+ fi
+ else
+ # not using gcc
+ if test "$host_cpu" = ia64; then
+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+ # chokes on -Wl,-G. The following line is correct:
+ shared_flag='-G'
+ else
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag='${wl}-G'
+ else
+ shared_flag='${wl}-bM:SRE'
+ fi
+ fi
+ fi
+
+ export_dynamic_flag_spec_CXX='${wl}-bexpall'
+ # It seems that -bexpall does not export symbols beginning with
+ # underscore (_), so it is better to generate a list of symbols to
+ # export.
+ always_export_symbols_CXX=yes
+ if test "$aix_use_runtimelinking" = yes; then
+ # Warning - without using the other runtime loading flags (-brtl),
+ # -berok will link without error, but may produce a broken library.
+ allow_undefined_flag_CXX='-berok'
+ # Determine the default libpath from the value encoded in an empty
+ # executable.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+ hardcode_libdir_flag_spec_CXX='${wl}-blibpath:$libdir:'"$aix_libpath"
+
+ archive_expsym_cmds_CXX='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+ else
+ if test "$host_cpu" = ia64; then
+ hardcode_libdir_flag_spec_CXX='${wl}-R $libdir:/usr/lib:/lib'
+ allow_undefined_flag_CXX="-z nodefs"
+ archive_expsym_cmds_CXX="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+ else
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+ hardcode_libdir_flag_spec_CXX='${wl}-blibpath:$libdir:'"$aix_libpath"
+ # Warning - without using the other run time loading flags,
+ # -berok will link without error, but may produce a broken library.
+ no_undefined_flag_CXX=' ${wl}-bernotok'
+ allow_undefined_flag_CXX=' ${wl}-berok'
+ # Exported symbols can be pulled into shared objects from archives
+ whole_archive_flag_spec_CXX='$convenience'
+ archive_cmds_need_lc_CXX=yes
+ # This is similar to how AIX traditionally builds its shared
+ # libraries.
+ archive_expsym_cmds_CXX="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+ fi
+ fi
+ ;;
+
+ beos*)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ allow_undefined_flag_CXX=unsupported
+ # Joseph Beckenbach <jrb3 at best.com> says some releases of gcc
+ # support --undefined. This deserves some investigation. FIXME
+ archive_cmds_CXX='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ else
+ ld_shlibs_CXX=no
+ fi
+ ;;
+
+ chorus*)
+ case $cc_basename in
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # _LT_TAGVAR(hardcode_libdir_flag_spec, CXX) is actually meaningless,
+ # as there is no search path for DLLs.
+ hardcode_libdir_flag_spec_CXX='-L$libdir'
+ allow_undefined_flag_CXX=unsupported
+ always_export_symbols_CXX=no
+ enable_shared_with_static_runtimes_CXX=yes
+
+ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ # If the export-symbols file already is a .def file (1st line
+ # is EXPORTS), use it as is; otherwise, prepend...
+ archive_expsym_cmds_CXX='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+ cp $export_symbols $output_objdir/$soname.def;
+ else
+ echo EXPORTS > $output_objdir/$soname.def;
+ cat $export_symbols >> $output_objdir/$soname.def;
+ fi~
+ $CC -shared -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ else
+ ld_shlibs_CXX=no
+ fi
+ ;;
+ darwin* | rhapsody*)
+
+
+ archive_cmds_need_lc_CXX=no
+ hardcode_direct_CXX=no
+ hardcode_automatic_CXX=yes
+ hardcode_shlibpath_var_CXX=unsupported
+ whole_archive_flag_spec_CXX=''
+ link_all_deplibs_CXX=yes
+ allow_undefined_flag_CXX="$_lt_dar_allow_undefined"
+ case $cc_basename in
+ ifort*) _lt_dar_can_shared=yes ;;
+ *) _lt_dar_can_shared=$GCC ;;
+ esac
+ if test "$_lt_dar_can_shared" = "yes"; then
+ output_verbose_link_cmd=echo
+ archive_cmds_CXX="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}"
+ module_cmds_CXX="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}"
+ archive_expsym_cmds_CXX="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}"
+ module_expsym_cmds_CXX="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}"
+ if test "$lt_cv_apple_cc_single_mod" != "yes"; then
+ archive_cmds_CXX="\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dsymutil}"
+ archive_expsym_cmds_CXX="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dar_export_syms}${_lt_dsymutil}"
+ fi
+
+ else
+ ld_shlibs_CXX=no
+ fi
+
+ ;;
+
+ dgux*)
+ case $cc_basename in
+ ec++*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ ghcx*)
+ # Green Hills C++ Compiler
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ freebsd[12]*)
+ # C++ shared libraries reported to be fairly broken before
+ # switch to ELF
+ ld_shlibs_CXX=no
+ ;;
+
+ freebsd-elf*)
+ archive_cmds_need_lc_CXX=no
+ ;;
+
+ freebsd* | dragonfly*)
+ # FreeBSD 3 and later use GNU C++ and GNU ld with standard ELF
+ # conventions
+ ld_shlibs_CXX=yes
+ ;;
+
+ gnu*)
+ ;;
+
+ hpux9*)
+ hardcode_libdir_flag_spec_CXX='${wl}+b ${wl}$libdir'
+ hardcode_libdir_separator_CXX=:
+ export_dynamic_flag_spec_CXX='${wl}-E'
+ hardcode_direct_CXX=yes
+ hardcode_minus_L_CXX=yes # Not in the search PATH,
+ # but as the default
+ # location of the library.
+
+ case $cc_basename in
+ CC*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ aCC*)
+ archive_cmds_CXX='$RM $output_objdir/$soname~$CC -b ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $EGREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ archive_cmds_CXX='$RM $output_objdir/$soname~$CC -shared -nostdlib -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ else
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ fi
+ ;;
+ esac
+ ;;
+
+ hpux10*|hpux11*)
+ if test $with_gnu_ld = no; then
+ hardcode_libdir_flag_spec_CXX='${wl}+b ${wl}$libdir'
+ hardcode_libdir_separator_CXX=:
+
+ case $host_cpu in
+ hppa*64*|ia64*)
+ ;;
+ *)
+ export_dynamic_flag_spec_CXX='${wl}-E'
+ ;;
+ esac
+ fi
+ case $host_cpu in
+ hppa*64*|ia64*)
+ hardcode_direct_CXX=no
+ hardcode_shlibpath_var_CXX=no
+ ;;
+ *)
+ hardcode_direct_CXX=yes
+ hardcode_direct_absolute_CXX=yes
+ hardcode_minus_L_CXX=yes # Not in the search PATH,
+ # but as the default
+ # location of the library.
+ ;;
+ esac
+
+ case $cc_basename in
+ CC*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ aCC*)
+ case $host_cpu in
+ hppa*64*)
+ archive_cmds_CXX='$CC -b ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ ia64*)
+ archive_cmds_CXX='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ esac
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $GREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ if test $with_gnu_ld = no; then
+ case $host_cpu in
+ hppa*64*)
+ archive_cmds_CXX='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ ia64*)
+ archive_cmds_CXX='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ esac
+ fi
+ else
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ fi
+ ;;
+ esac
+ ;;
+
+ interix[3-9]*)
+ hardcode_direct_CXX=no
+ hardcode_shlibpath_var_CXX=no
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec_CXX='${wl}-E'
+ # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+ # Instead, shared libraries are loaded at an image base (0x10000000 by
+ # default) and relocated if they conflict, which is a slow very memory
+ # consuming and fragmenting process. To avoid this, we pick a random,
+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+ # time. Moving up from 0x10000000 also allows more sbrk(2) space.
+ archive_cmds_CXX='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ archive_expsym_cmds_CXX='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ ;;
+ irix5* | irix6*)
+ case $cc_basename in
+ CC*)
+ # SGI C++
+ archive_cmds_CXX='$CC -shared -all -multigot $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+
+ # Archives containing C++ object files must be created using
+ # "CC -ar", where "CC" is the IRIX C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ old_archive_cmds_CXX='$CC -ar -WR,-u -o $oldlib $oldobjs'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ if test "$with_gnu_ld" = no; then
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ else
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` -o $lib'
+ fi
+ fi
+ link_all_deplibs_CXX=yes
+ ;;
+ esac
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator_CXX=:
+ inherit_rpath_CXX=yes
+ ;;
+
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ KCC*)
+ # Kuck and Associates, Inc. (KAI) C++ Compiler
+
+ # KCC will only create a shared library if the output file
+ # ends with ".so" (or ".sl" for HP-UX), so rename the library
+ # to its proper name (with version) after linking.
+ archive_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+ archive_expsym_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib ${wl}-retain-symbols-file,$export_symbols; mv \$templib $lib'
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 | $GREP "ld"`; rm -f libconftest$shared_ext; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+
+ # Archives containing C++ object files must be created using
+ # "CC -Bstatic", where "CC" is the KAI C++ compiler.
+ old_archive_cmds_CXX='$CC -Bstatic -o $oldlib $oldobjs'
+ ;;
+ icpc* | ecpc* )
+ # Intel C++
+ with_gnu_ld=yes
+ # version 8.0 and above of icpc choke on multiply defined symbols
+ # if we add $predep_objects and $postdep_objects, however 7.1 and
+ # earlier do not add the objects themselves.
+ case `$CC -V 2>&1` in
+ *"Version 7."*)
+ archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ ;;
+ *) # Version 8.0 or newer
+ tmp_idyn=
+ case $host_cpu in
+ ia64*) tmp_idyn=' -i_dynamic';;
+ esac
+ archive_cmds_CXX='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ ;;
+ esac
+ archive_cmds_need_lc_CXX=no
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+ whole_archive_flag_spec_CXX='${wl}--whole-archive$convenience ${wl}--no-whole-archive'
+ ;;
+ pgCC* | pgcpp*)
+ # Portland Group C++ compiler
+ case `$CC -V` in
+ *pgCC\ [1-5]* | *pgcpp\ [1-5]*)
+ prelink_cmds_CXX='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $objs $libobjs $compile_deplibs~
+ compile_command="$compile_command `find $tpldir -name \*.o | $NL2SP`"'
+ old_archive_cmds_CXX='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $oldobjs$old_deplibs~
+ $AR $AR_FLAGS $oldlib$oldobjs$old_deplibs `find $tpldir -name \*.o | $NL2SP`~
+ $RANLIB $oldlib'
+ archive_cmds_CXX='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~
+ $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+ archive_expsym_cmds_CXX='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~
+ $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+ ;;
+ *) # Version 6 will use weak symbols
+ archive_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+ ;;
+ esac
+
+ hardcode_libdir_flag_spec_CXX='${wl}--rpath ${wl}$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+ whole_archive_flag_spec_CXX='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ ;;
+ cxx*)
+ # Compaq C++
+ archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib ${wl}-retain-symbols-file $wl$export_symbols'
+
+ runpath_var=LD_RUN_PATH
+ hardcode_libdir_flag_spec_CXX='-rpath $libdir'
+ hardcode_libdir_separator_CXX=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld .*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ xl*)
+ # IBM XL 8.0 on PPC, with GNU ld
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+ archive_cmds_CXX='$CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ if test "x$supports_anon_versioning" = xyes; then
+ archive_expsym_cmds_CXX='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+ fi
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+ no_undefined_flag_CXX=' -zdefs'
+ archive_cmds_CXX='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file ${wl}$export_symbols'
+ hardcode_libdir_flag_spec_CXX='-R$libdir'
+ whole_archive_flag_spec_CXX='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ compiler_needs_object_CXX=yes
+
+ # Not sure whether something based on
+ # $CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1
+ # would be better.
+ output_verbose_link_cmd='echo'
+
+ # Archives containing C++ object files must be created using
+ # "CC -xar", where "CC" is the Sun C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ old_archive_cmds_CXX='$CC -xar -o $oldlib $oldobjs'
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+
+ lynxos*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+
+ m88k*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+
+ mvs*)
+ case $cc_basename in
+ cxx*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ netbsd*)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ archive_cmds_CXX='$LD -Bshareable -o $lib $predep_objects $libobjs $deplibs $postdep_objects $linker_flags'
+ wlarc=
+ hardcode_libdir_flag_spec_CXX='-R$libdir'
+ hardcode_direct_CXX=yes
+ hardcode_shlibpath_var_CXX=no
+ fi
+ # Workaround some broken pre-1.5 toolchains
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP conftest.$objext | $SED -e "s:-lgcc -lc -lgcc::"'
+ ;;
+
+ *nto* | *qnx*)
+ ld_shlibs_CXX=yes
+ ;;
+
+ openbsd2*)
+ # C++ shared libraries are fairly broken
+ ld_shlibs_CXX=no
+ ;;
+
+ openbsd*)
+ if test -f /usr/libexec/ld.so; then
+ hardcode_direct_CXX=yes
+ hardcode_shlibpath_var_CXX=no
+ hardcode_direct_absolute_CXX=yes
+ archive_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ archive_expsym_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file,$export_symbols -o $lib'
+ export_dynamic_flag_spec_CXX='${wl}-E'
+ whole_archive_flag_spec_CXX="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ fi
+ output_verbose_link_cmd=echo
+ else
+ ld_shlibs_CXX=no
+ fi
+ ;;
+
+ osf3* | osf4* | osf5*)
+ case $cc_basename in
+ KCC*)
+ # Kuck and Associates, Inc. (KAI) C++ Compiler
+
+ # KCC will only create a shared library if the output file
+ # ends with ".so" (or ".sl" for HP-UX), so rename the library
+ # to its proper name (with version) after linking.
+ archive_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo "$lib" | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ hardcode_libdir_separator_CXX=:
+
+ # Archives containing C++ object files must be created using
+ # the KAI C++ compiler.
+ case $host in
+ osf3*) old_archive_cmds_CXX='$CC -Bstatic -o $oldlib $oldobjs' ;;
+ *) old_archive_cmds_CXX='$CC -o $oldlib $oldobjs' ;;
+ esac
+ ;;
+ RCC*)
+ # Rational C++ 2.4.1
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ cxx*)
+ case $host in
+ osf3*)
+ allow_undefined_flag_CXX=' ${wl}-expect_unresolved ${wl}\*'
+ archive_cmds_CXX='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $soname `test -n "$verstring" && $ECHO "X${wl}-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ ;;
+ *)
+ allow_undefined_flag_CXX=' -expect_unresolved \*'
+ archive_cmds_CXX='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ archive_expsym_cmds_CXX='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done~
+ echo "-hidden">> $lib.exp~
+ $CC -shared$allow_undefined_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname ${wl}-input ${wl}$lib.exp `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~
+ $RM $lib.exp'
+ hardcode_libdir_flag_spec_CXX='-rpath $libdir'
+ ;;
+ esac
+
+ hardcode_libdir_separator_CXX=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld" | $GREP -v "ld:"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld.*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+ allow_undefined_flag_CXX=' ${wl}-expect_unresolved ${wl}\*'
+ case $host in
+ osf3*)
+ archive_cmds_CXX='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ ;;
+ esac
+
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator_CXX=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+
+ else
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ fi
+ ;;
+ esac
+ ;;
+
+ psos*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+
+ sunos4*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.x
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ lcc*)
+ # Lucid
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ solaris*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.2, 5.x and Centerline C++
+ archive_cmds_need_lc_CXX=yes
+ no_undefined_flag_CXX=' -zdefs'
+ archive_cmds_CXX='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ archive_expsym_cmds_CXX='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G${allow_undefined_flag} ${wl}-M ${wl}$lib.exp -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ hardcode_libdir_flag_spec_CXX='-R$libdir'
+ hardcode_shlibpath_var_CXX=no
+ case $host_os in
+ solaris2.[0-5] | solaris2.[0-5].*) ;;
+ *)
+ # The compiler driver will combine and reorder linker options,
+ # but understands `-z linker_flag'.
+ # Supported since Solaris 2.6 (maybe 2.5.1?)
+ whole_archive_flag_spec_CXX='-z allextract$convenience -z defaultextract'
+ ;;
+ esac
+ link_all_deplibs_CXX=yes
+
+ output_verbose_link_cmd='echo'
+
+ # Archives containing C++ object files must be created using
+ # "CC -xar", where "CC" is the Sun C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ old_archive_cmds_CXX='$CC -xar -o $oldlib $oldobjs'
+ ;;
+ gcx*)
+ # Green Hills C++ Compiler
+ archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+
+ # The C++ compiler must be used to create the archive.
+ old_archive_cmds_CXX='$CC $LDFLAGS -archive -o $oldlib $oldobjs'
+ ;;
+ *)
+ # GNU C++ compiler with Solaris linker
+ if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+ no_undefined_flag_CXX=' ${wl}-z ${wl}defs'
+ if $CC --version | $GREP -v '^2\.7' > /dev/null; then
+ archive_cmds_CXX='$CC -shared -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -shared -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+ else
+ # g++ 2.7 appears to require `-G' NOT `-shared' on this
+ # platform.
+ archive_cmds_CXX='$CC -G -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -G $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+ fi
+
+ hardcode_libdir_flag_spec_CXX='${wl}-R $wl$libdir'
+ case $host_os in
+ solaris2.[0-5] | solaris2.[0-5].*) ;;
+ *)
+ whole_archive_flag_spec_CXX='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract'
+ ;;
+ esac
+ fi
+ ;;
+ esac
+ ;;
+
+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*)
+ no_undefined_flag_CXX='${wl}-z,text'
+ archive_cmds_need_lc_CXX=no
+ hardcode_shlibpath_var_CXX=no
+ runpath_var='LD_RUN_PATH'
+
+ case $cc_basename in
+ CC*)
+ archive_cmds_CXX='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6*)
+ # Note: We can NOT use -z defs as we might desire, because we do not
+ # link with -lc, and that would cause any symbols used from libc to
+ # always be unresolved, which means just about no library would
+ # ever link correctly. If we're not using GNU ld we use -z text
+ # though, which does catch some bad symbols but isn't as heavy-handed
+ # as -z defs.
+ no_undefined_flag_CXX='${wl}-z,text'
+ allow_undefined_flag_CXX='${wl}-z,nodefs'
+ archive_cmds_need_lc_CXX=no
+ hardcode_shlibpath_var_CXX=no
+ hardcode_libdir_flag_spec_CXX='${wl}-R,$libdir'
+ hardcode_libdir_separator_CXX=':'
+ link_all_deplibs_CXX=yes
+ export_dynamic_flag_spec_CXX='${wl}-Bexport'
+ runpath_var='LD_RUN_PATH'
+
+ case $cc_basename in
+ CC*)
+ archive_cmds_CXX='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ ;;
+
+ tandem*)
+ case $cc_basename in
+ NCC*)
+ # NonStop-UX NCC 3.20
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ vxworks*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ld_shlibs_CXX" >&5
+$as_echo "$ld_shlibs_CXX" >&6; }
+ test "$ld_shlibs_CXX" = no && can_build_shared=no
+
+ GCC_CXX="$GXX"
+ LD_CXX="$LD"
+
+ ## CAVEAT EMPTOR:
+ ## There is no encapsulation within the following macros, do not change
+ ## the running order or otherwise move them around unless you know exactly
+ ## what you are doing...
+ # Dependencies to place before and after the object being linked:
+predep_objects_CXX=
+postdep_objects_CXX=
+predeps_CXX=
+postdeps_CXX=
+compiler_lib_search_path_CXX=
+
+cat > conftest.$ac_ext <<_LT_EOF
+class Foo
+{
+public:
+ Foo (void) { a = 0; }
+private:
+ int a;
+};
+_LT_EOF
+
+if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ # Parse the compiler output and extract the necessary
+ # objects, libraries and library flags.
+
+ # Sentinel used to keep track of whether or not we are before
+ # the conftest object file.
+ pre_test_object_deps_done=no
+
+ for p in `eval "$output_verbose_link_cmd"`; do
+ case $p in
+
+ -L* | -R* | -l*)
+ # Some compilers place space between "-{L,R}" and the path.
+ # Remove the space.
+ if test $p = "-L" ||
+ test $p = "-R"; then
+ prev=$p
+ continue
+ else
+ prev=
+ fi
+
+ if test "$pre_test_object_deps_done" = no; then
+ case $p in
+ -L* | -R*)
+ # Internal compiler library paths should come after those
+ # provided the user. The postdeps already come after the
+ # user supplied libs so there is no need to process them.
+ if test -z "$compiler_lib_search_path_CXX"; then
+ compiler_lib_search_path_CXX="${prev}${p}"
+ else
+ compiler_lib_search_path_CXX="${compiler_lib_search_path_CXX} ${prev}${p}"
+ fi
+ ;;
+ # The "-l" case would never come before the object being
+ # linked, so don't bother handling this case.
+ esac
+ else
+ if test -z "$postdeps_CXX"; then
+ postdeps_CXX="${prev}${p}"
+ else
+ postdeps_CXX="${postdeps_CXX} ${prev}${p}"
+ fi
+ fi
+ ;;
+
+ *.$objext)
+ # This assumes that the test object file only shows up
+ # once in the compiler output.
+ if test "$p" = "conftest.$objext"; then
+ pre_test_object_deps_done=yes
+ continue
+ fi
+
+ if test "$pre_test_object_deps_done" = no; then
+ if test -z "$predep_objects_CXX"; then
+ predep_objects_CXX="$p"
+ else
+ predep_objects_CXX="$predep_objects_CXX $p"
+ fi
+ else
+ if test -z "$postdep_objects_CXX"; then
+ postdep_objects_CXX="$p"
+ else
+ postdep_objects_CXX="$postdep_objects_CXX $p"
+ fi
+ fi
+ ;;
+
+ *) ;; # Ignore the rest.
+
+ esac
+ done
+
+ # Clean up.
+ rm -f a.out a.exe
+else
+ echo "libtool.m4: error: problem compiling CXX test program"
+fi
+
+$RM -f confest.$objext
+
+# PORTME: override above test on systems where it is broken
+case $host_os in
+interix[3-9]*)
+ # Interix 3.5 installs completely hosed .la files for C++, so rather than
+ # hack all around it, let's just trust "g++" to DTRT.
+ predep_objects_CXX=
+ postdep_objects_CXX=
+ postdeps_CXX=
+ ;;
+
+linux*)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+
+ # The more standards-conforming stlport4 library is
+ # incompatible with the Cstd library. Avoid specifying
+ # it if it's in CXXFLAGS. Ignore libCrun as
+ # -library=stlport4 depends on it.
+ case " $CXX $CXXFLAGS " in
+ *" -library=stlport4 "*)
+ solaris_use_stlport4=yes
+ ;;
+ esac
+
+ if test "$solaris_use_stlport4" != yes; then
+ postdeps_CXX='-library=Cstd -library=Crun'
+ fi
+ ;;
+ esac
+ ;;
+
+solaris*)
+ case $cc_basename in
+ CC*)
+ # The more standards-conforming stlport4 library is
+ # incompatible with the Cstd library. Avoid specifying
+ # it if it's in CXXFLAGS. Ignore libCrun as
+ # -library=stlport4 depends on it.
+ case " $CXX $CXXFLAGS " in
+ *" -library=stlport4 "*)
+ solaris_use_stlport4=yes
+ ;;
+ esac
+
+ # Adding this requires a known-good setup of shared libraries for
+ # Sun compiler versions before 5.6, else PIC objects from an old
+ # archive will be linked into the output, leading to subtle bugs.
+ if test "$solaris_use_stlport4" != yes; then
+ postdeps_CXX='-library=Cstd -library=Crun'
+ fi
+ ;;
+ esac
+ ;;
+esac
+
+
+case " $postdeps_CXX " in
+*" -lc "*) archive_cmds_need_lc_CXX=no ;;
+esac
+ compiler_lib_search_dirs_CXX=
+if test -n "${compiler_lib_search_path_CXX}"; then
+ compiler_lib_search_dirs_CXX=`echo " ${compiler_lib_search_path_CXX}" | ${SED} -e 's! -L! !g' -e 's!^ !!'`
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ lt_prog_compiler_wl_CXX=
+lt_prog_compiler_pic_CXX=
+lt_prog_compiler_static_CXX=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $compiler option to produce PIC" >&5
+$as_echo_n "checking for $compiler option to produce PIC... " >&6; }
+
+ # C++ specific cases for pic, static, wl, etc.
+ if test "$GXX" = yes; then
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_static_CXX='-static'
+
+ case $host_os in
+ aix*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ lt_prog_compiler_static_CXX='-Bstatic'
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ lt_prog_compiler_pic_CXX='-fPIC'
+ ;;
+ m68k)
+ # FIXME: we need at least 68020 code to build shared libraries, but
+ # adding the `-m68020' flag to GCC prevents building anything better,
+ # like `-m68040'.
+ lt_prog_compiler_pic_CXX='-m68020 -resident32 -malways-restore-a4'
+ ;;
+ esac
+ ;;
+
+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+ # PIC is the default for these OSes.
+ ;;
+ mingw* | cygwin* | os2* | pw32* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ # Although the cygwin gcc ignores -fPIC, still need this for old-style
+ # (--disable-auto-import) libraries
+ lt_prog_compiler_pic_CXX='-DDLL_EXPORT'
+ ;;
+ darwin* | rhapsody*)
+ # PIC is the default on this platform
+ # Common symbols not allowed in MH_DYLIB files
+ lt_prog_compiler_pic_CXX='-fno-common'
+ ;;
+ *djgpp*)
+ # DJGPP does not support shared libraries at all
+ lt_prog_compiler_pic_CXX=
+ ;;
+ interix[3-9]*)
+ # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+ # Instead, we relocate shared libraries at runtime.
+ ;;
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ lt_prog_compiler_pic_CXX=-Kconform_pic
+ fi
+ ;;
+ hpux*)
+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit
+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag
+ # sets the default TLS model and affects inlining.
+ case $host_cpu in
+ hppa*64*)
+ ;;
+ *)
+ lt_prog_compiler_pic_CXX='-fPIC'
+ ;;
+ esac
+ ;;
+ *qnx* | *nto*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ lt_prog_compiler_pic_CXX='-fPIC -shared'
+ ;;
+ *)
+ lt_prog_compiler_pic_CXX='-fPIC'
+ ;;
+ esac
+ else
+ case $host_os in
+ aix[4-9]*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ lt_prog_compiler_static_CXX='-Bstatic'
+ else
+ lt_prog_compiler_static_CXX='-bnso -bI:/lib/syscalls.exp'
+ fi
+ ;;
+ chorus*)
+ case $cc_basename in
+ cxch68*)
+ # Green Hills C++ Compiler
+ # _LT_TAGVAR(lt_prog_compiler_static, CXX)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a"
+ ;;
+ esac
+ ;;
+ dgux*)
+ case $cc_basename in
+ ec++*)
+ lt_prog_compiler_pic_CXX='-KPIC'
+ ;;
+ ghcx*)
+ # Green Hills C++ Compiler
+ lt_prog_compiler_pic_CXX='-pic'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ freebsd* | dragonfly*)
+ # FreeBSD uses GNU C++
+ ;;
+ hpux9* | hpux10* | hpux11*)
+ case $cc_basename in
+ CC*)
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_static_CXX='${wl}-a ${wl}archive'
+ if test "$host_cpu" != ia64; then
+ lt_prog_compiler_pic_CXX='+Z'
+ fi
+ ;;
+ aCC*)
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_static_CXX='${wl}-a ${wl}archive'
+ case $host_cpu in
+ hppa*64*|ia64*)
+ # +Z the default
+ ;;
+ *)
+ lt_prog_compiler_pic_CXX='+Z'
+ ;;
+ esac
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ interix*)
+ # This is c89, which is MS Visual C++ (no shared libs)
+ # Anyone wants to do a port?
+ ;;
+ irix5* | irix6* | nonstopux*)
+ case $cc_basename in
+ CC*)
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_static_CXX='-non_shared'
+ # CC pic flag -KPIC is the default.
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ KCC*)
+ # KAI C++ Compiler
+ lt_prog_compiler_wl_CXX='--backend -Wl,'
+ lt_prog_compiler_pic_CXX='-fPIC'
+ ;;
+ ecpc* )
+ # old Intel C++ for x86_64 which still supported -KPIC.
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-KPIC'
+ lt_prog_compiler_static_CXX='-static'
+ ;;
+ icpc* )
+ # Intel C++, used to be incompatible with GCC.
+ # ICC 10 doesn't accept -KPIC any more.
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-fPIC'
+ lt_prog_compiler_static_CXX='-static'
+ ;;
+ pgCC* | pgcpp*)
+ # Portland Group C++ compiler
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-fpic'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ ;;
+ cxx*)
+ # Compaq C++
+ # Make sure the PIC flag is empty. It appears that all Alpha
+ # Linux and Compaq Tru64 Unix objects are PIC.
+ lt_prog_compiler_pic_CXX=
+ lt_prog_compiler_static_CXX='-non_shared'
+ ;;
+ xlc* | xlC*)
+ # IBM XL 8.0 on PPC
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-qpic'
+ lt_prog_compiler_static_CXX='-qstaticlink'
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+ lt_prog_compiler_pic_CXX='-KPIC'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ lt_prog_compiler_wl_CXX='-Qoption ld '
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+ lynxos*)
+ ;;
+ m88k*)
+ ;;
+ mvs*)
+ case $cc_basename in
+ cxx*)
+ lt_prog_compiler_pic_CXX='-W c,exportall'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ netbsd* | netbsdelf*-gnu)
+ ;;
+ *qnx* | *nto*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ lt_prog_compiler_pic_CXX='-fPIC -shared'
+ ;;
+ osf3* | osf4* | osf5*)
+ case $cc_basename in
+ KCC*)
+ lt_prog_compiler_wl_CXX='--backend -Wl,'
+ ;;
+ RCC*)
+ # Rational C++ 2.4.1
+ lt_prog_compiler_pic_CXX='-pic'
+ ;;
+ cxx*)
+ # Digital/Compaq C++
+ lt_prog_compiler_wl_CXX='-Wl,'
+ # Make sure the PIC flag is empty. It appears that all Alpha
+ # Linux and Compaq Tru64 Unix objects are PIC.
+ lt_prog_compiler_pic_CXX=
+ lt_prog_compiler_static_CXX='-non_shared'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ psos*)
+ ;;
+ solaris*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.2, 5.x and Centerline C++
+ lt_prog_compiler_pic_CXX='-KPIC'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ lt_prog_compiler_wl_CXX='-Qoption ld '
+ ;;
+ gcx*)
+ # Green Hills C++ Compiler
+ lt_prog_compiler_pic_CXX='-PIC'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ sunos4*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.x
+ lt_prog_compiler_pic_CXX='-pic'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ ;;
+ lcc*)
+ # Lucid
+ lt_prog_compiler_pic_CXX='-pic'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+ case $cc_basename in
+ CC*)
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-KPIC'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ ;;
+ esac
+ ;;
+ tandem*)
+ case $cc_basename in
+ NCC*)
+ # NonStop-UX NCC 3.20
+ lt_prog_compiler_pic_CXX='-KPIC'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ vxworks*)
+ ;;
+ *)
+ lt_prog_compiler_can_build_shared_CXX=no
+ ;;
+ esac
+ fi
+
+case $host_os in
+ # For platforms which do not support PIC, -DPIC is meaningless:
+ *djgpp*)
+ lt_prog_compiler_pic_CXX=
+ ;;
+ *)
+ lt_prog_compiler_pic_CXX="$lt_prog_compiler_pic_CXX -DPIC"
+ ;;
+esac
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_prog_compiler_pic_CXX" >&5
+$as_echo "$lt_prog_compiler_pic_CXX" >&6; }
+
+
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$lt_prog_compiler_pic_CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler PIC flag $lt_prog_compiler_pic_CXX works" >&5
+$as_echo_n "checking if $compiler PIC flag $lt_prog_compiler_pic_CXX works... " >&6; }
+if test "${lt_cv_prog_compiler_pic_works_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_pic_works_CXX=no
+ ac_outfile=conftest.$ac_objext
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+ lt_compiler_flag="$lt_prog_compiler_pic_CXX -DPIC"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ # The option is referenced via a variable to avoid confusing sed.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:13691: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>conftest.err)
+ ac_status=$?
+ cat conftest.err >&5
+ echo "$as_me:13695: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s "$ac_outfile"; then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings other than the usual output.
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_pic_works_CXX=yes
+ fi
+ fi
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_pic_works_CXX" >&5
+$as_echo "$lt_cv_prog_compiler_pic_works_CXX" >&6; }
+
+if test x"$lt_cv_prog_compiler_pic_works_CXX" = xyes; then
+ case $lt_prog_compiler_pic_CXX in
+ "" | " "*) ;;
+ *) lt_prog_compiler_pic_CXX=" $lt_prog_compiler_pic_CXX" ;;
+ esac
+else
+ lt_prog_compiler_pic_CXX=
+ lt_prog_compiler_can_build_shared_CXX=no
+fi
+
+fi
+
+
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$lt_prog_compiler_wl_CXX eval lt_tmp_static_flag=\"$lt_prog_compiler_static_CXX\"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler static flag $lt_tmp_static_flag works" >&5
+$as_echo_n "checking if $compiler static flag $lt_tmp_static_flag works... " >&6; }
+if test "${lt_cv_prog_compiler_static_works_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_static_works_CXX=no
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS $lt_tmp_static_flag"
+ echo "$lt_simple_link_test_code" > conftest.$ac_ext
+ if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+ # The linker can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ if test -s conftest.err; then
+ # Append any errors to the config.log.
+ cat conftest.err 1>&5
+ $ECHO "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_static_works_CXX=yes
+ fi
+ else
+ lt_cv_prog_compiler_static_works_CXX=yes
+ fi
+ fi
+ $RM -r conftest*
+ LDFLAGS="$save_LDFLAGS"
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_static_works_CXX" >&5
+$as_echo "$lt_cv_prog_compiler_static_works_CXX" >&6; }
+
+if test x"$lt_cv_prog_compiler_static_works_CXX" = xyes; then
+ :
+else
+ lt_prog_compiler_static_CXX=
+fi
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler supports -c -o file.$ac_objext" >&5
+$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; }
+if test "${lt_cv_prog_compiler_c_o_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_c_o_CXX=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:13790: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&5
+ echo "$as_me:13794: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_c_o_CXX=yes
+ fi
+ fi
+ chmod u+w . 2>&5
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_c_o_CXX" >&5
+$as_echo "$lt_cv_prog_compiler_c_o_CXX" >&6; }
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler supports -c -o file.$ac_objext" >&5
+$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; }
+if test "${lt_cv_prog_compiler_c_o_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_c_o_CXX=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:13842: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&5
+ echo "$as_me:13846: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_c_o_CXX=yes
+ fi
+ fi
+ chmod u+w . 2>&5
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_c_o_CXX" >&5
+$as_echo "$lt_cv_prog_compiler_c_o_CXX" >&6; }
+
+
+
+
+hard_links="nottested"
+if test "$lt_cv_prog_compiler_c_o_CXX" = no && test "$need_locks" != no; then
+ # do not overwrite the value of need_locks provided by the user
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if we can lock with hard links" >&5
+$as_echo_n "checking if we can lock with hard links... " >&6; }
+ hard_links=yes
+ $RM conftest*
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ touch conftest.a
+ ln conftest.a conftest.b 2>&5 || hard_links=no
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $hard_links" >&5
+$as_echo "$hard_links" >&6; }
+ if test "$hard_links" = no; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&5
+$as_echo "$as_me: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&2;}
+ need_locks=warn
+ fi
+else
+ need_locks=no
+fi
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+$as_echo_n "checking whether the $compiler linker ($LD) supports shared libraries... " >&6; }
+
+ export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ case $host_os in
+ aix[4-9]*)
+ # If we're using GNU nm, then we don't want the "-C" option.
+ # -C means demangle to AIX nm, but means don't demangle with GNU nm
+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then
+ export_symbols_cmds_CXX='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ else
+ export_symbols_cmds_CXX='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ fi
+ ;;
+ pw32*)
+ export_symbols_cmds_CXX="$ltdll_cmds"
+ ;;
+ cygwin* | mingw* | cegcc*)
+ export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1 DATA/;/^.*[ ]__nm__/s/^.*[ ]__nm__\([^ ]*\)[ ][^ ]*/\1 DATA/;/^I[ ]/d;/^[AITW][ ]/s/.* //'\'' | sort | uniq > $export_symbols'
+ ;;
+ linux* | k*bsd*-gnu)
+ link_all_deplibs_CXX=no
+ ;;
+ *)
+ export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ ;;
+ esac
+ exclude_expsyms_CXX='_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*'
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ld_shlibs_CXX" >&5
+$as_echo "$ld_shlibs_CXX" >&6; }
+test "$ld_shlibs_CXX" = no && can_build_shared=no
+
+with_gnu_ld_CXX=$with_gnu_ld
+
+
+
+
+
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$archive_cmds_need_lc_CXX" in
+x|xyes)
+ # Assume -lc should be added
+ archive_cmds_need_lc_CXX=yes
+
+ if test "$enable_shared" = yes && test "$GCC" = yes; then
+ case $archive_cmds_CXX in
+ *'~'*)
+ # FIXME: we may have to deal with multi-command sequences.
+ ;;
+ '$CC '*)
+ # Test whether the compiler implicitly links with -lc since on some
+ # systems, -lgcc has to come before -lc. If gcc already passes -lc
+ # to ld, don't add -lc before -lgcc.
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether -lc should be explicitly linked in" >&5
+$as_echo_n "checking whether -lc should be explicitly linked in... " >&6; }
+ $RM conftest*
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } 2>conftest.err; then
+ soname=conftest
+ lib=conftest
+ libobjs=conftest.$ac_objext
+ deplibs=
+ wl=$lt_prog_compiler_wl_CXX
+ pic_flag=$lt_prog_compiler_pic_CXX
+ compiler_flags=-v
+ linker_flags=-v
+ verstring=
+ output_objdir=.
+ libname=conftest
+ lt_save_allow_undefined_flag=$allow_undefined_flag_CXX
+ allow_undefined_flag_CXX=
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$archive_cmds_CXX 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1\""; } >&5
+ (eval $archive_cmds_CXX 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+ then
+ archive_cmds_need_lc_CXX=no
+ else
+ archive_cmds_need_lc_CXX=yes
+ fi
+ allow_undefined_flag_CXX=$lt_save_allow_undefined_flag
+ else
+ cat conftest.err 1>&5
+ fi
+ $RM conftest*
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $archive_cmds_need_lc_CXX" >&5
+$as_echo "$archive_cmds_need_lc_CXX" >&6; }
+ ;;
+ esac
+ fi
+ ;;
+esac
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking dynamic linker characteristics" >&5
+$as_echo_n "checking dynamic linker characteristics... " >&6; }
+
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+ shlibpath_var=LIBPATH
+
+ # AIX 3 has no versioning support, so we append a major version to the name.
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+
+aix[4-9]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ hardcode_into_libs=yes
+ if test "$host_cpu" = ia64; then
+ # AIX 5 supports IA64
+ library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ else
+ # With GCC up to 2.95.x, collect2 would create an import file
+ # for dependence libraries. The import file would start with
+ # the line `#! .'. This would cause the generated library to
+ # depend on `.', always an invalid library. This was fixed in
+ # development snapshots of GCC prior to 3.0.
+ case $host_os in
+ aix4 | aix4.[01] | aix4.[01].*)
+ if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+ echo ' yes '
+ echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then
+ :
+ else
+ can_build_shared=no
+ fi
+ ;;
+ esac
+ # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+ # soname into executable. Probably we can add versioning support to
+ # collect2, so additional links can be useful in future.
+ if test "$aix_use_runtimelinking" = yes; then
+ # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+ # instead of lib<name>.a to let people know that these are not
+ # typical AIX shared libraries.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ else
+ # We preserve .a as extension for shared libraries through AIX4.2
+ # and later when we are not doing run time linking.
+ library_names_spec='${libname}${release}.a $libname.a'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ fi
+ shlibpath_var=LIBPATH
+ fi
+ ;;
+
+amigaos*)
+ case $host_cpu in
+ powerpc)
+ # Since July 2007 AmigaOS4 officially supports .so libraries.
+ # When compiling the executable, add -use-dynld -Lsobjs: to the compileline.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ ;;
+ m68k)
+ library_names_spec='$libname.ixlibrary $libname.a'
+ # Create ${libname}_ixlibrary.a entries in /sys/libs.
+ finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$ECHO "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+ ;;
+ esac
+ ;;
+
+beos*)
+ library_names_spec='${libname}${shared_ext}'
+ dynamic_linker="$host_os ld.so"
+ shlibpath_var=LIBRARY_PATH
+ ;;
+
+bsdi[45]*)
+ version_type=linux
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+ sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+ # the default ld.so.conf also contains /usr/contrib/lib and
+ # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+ # libtool to hard-code these into programs
+ ;;
+
+cygwin* | mingw* | pw32* | cegcc*)
+ version_type=windows
+ shrext_cmds=".dll"
+ need_version=no
+ need_lib_prefix=no
+
+ case $GCC,$host_os in
+ yes,cygwin* | yes,mingw* | yes,pw32* | yes,cegcc*)
+ library_names_spec='$libname.dll.a'
+ # DLL is installed to $(libdir)/../bin by postinstall_cmds
+ postinstall_cmds='base_file=`basename \${file}`~
+ dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i; echo \$dlname'\''`~
+ dldir=$destdir/`dirname \$dlpath`~
+ test -d \$dldir || mkdir -p \$dldir~
+ $install_prog $dir/$dlname \$dldir/$dlname~
+ chmod a+x \$dldir/$dlname~
+ if test -n '\''$stripme'\'' && test -n '\''$striplib'\''; then
+ eval '\''$striplib \$dldir/$dlname'\'' || exit \$?;
+ fi'
+ postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+ dlpath=$dir/\$dldll~
+ $RM \$dlpath'
+ shlibpath_overrides_runpath=yes
+
+ case $host_os in
+ cygwin*)
+ # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+ soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+ ;;
+ mingw* | cegcc*)
+ # MinGW DLLs use traditional 'lib' prefix
+ soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec=`$CC -print-search-dirs | $GREP "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$sys_lib_search_path_spec" | $GREP ';[c-zC-Z]:/' >/dev/null; then
+ # It is most probably a Windows format PATH printed by
+ # mingw gcc, but we are running on Cygwin. Gcc prints its search
+ # path with ; separators, and with drive letters. We can handle the
+ # drive letters (cygwin fileutils understands them), so leave them,
+ # especially as we might pass files found there to a mingw objdump,
+ # which wouldn't understand a cygwinified path. Ahh.
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ ;;
+ pw32*)
+ # pw32 DLLs use 'pw' prefix rather than 'lib'
+ library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ ;;
+ esac
+ ;;
+
+ *)
+ library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib'
+ ;;
+ esac
+ dynamic_linker='Win32 ld.exe'
+ # FIXME: first we should search . and the directory the executable is in
+ shlibpath_var=PATH
+ ;;
+
+darwin* | rhapsody*)
+ dynamic_linker="$host_os dyld"
+ version_type=darwin
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+ soname_spec='${libname}${release}${major}$shared_ext'
+ shlibpath_overrides_runpath=yes
+ shlibpath_var=DYLD_LIBRARY_PATH
+ shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+
+ sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+ ;;
+
+dgux*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+freebsd1*)
+ dynamic_linker=no
+ ;;
+
+freebsd* | dragonfly*)
+ # DragonFly does not have aout. When/if they implement a new
+ # versioning mechanism, adjust this.
+ if test -x /usr/bin/objformat; then
+ objformat=`/usr/bin/objformat`
+ else
+ case $host_os in
+ freebsd[123]*) objformat=aout ;;
+ *) objformat=elf ;;
+ esac
+ fi
+ version_type=freebsd-$objformat
+ case $version_type in
+ freebsd-elf*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ need_version=no
+ need_lib_prefix=no
+ ;;
+ freebsd-*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+ need_version=yes
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_os in
+ freebsd2*)
+ shlibpath_overrides_runpath=yes
+ ;;
+ freebsd3.[01]* | freebsdelf3.[01]*)
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ freebsd3.[2-9]* | freebsdelf3.[2-9]* | \
+ freebsd4.[0-5] | freebsdelf4.[0-5] | freebsd4.1.1 | freebsdelf4.1.1)
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+ *) # from 4.6 on, and DragonFly
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ esac
+ ;;
+
+gnu*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ hardcode_into_libs=yes
+ ;;
+
+hpux9* | hpux10* | hpux11*)
+ # Give a soname corresponding to the major version so that dld.sl refuses to
+ # link against other versions.
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ case $host_cpu in
+ ia64*)
+ shrext_cmds='.so'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.so"
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ if test "X$HPUX_IA64_MODE" = X32; then
+ sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+ else
+ sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+ fi
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ hppa*64*)
+ shrext_cmds='.sl'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ *)
+ shrext_cmds='.sl'
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=SHLIB_PATH
+ shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+ esac
+ # HP-UX runs *really* slowly unless shared libraries are mode 555.
+ postinstall_cmds='chmod 555 $lib'
+ ;;
+
+interix[3-9]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $host_os in
+ nonstopux*) version_type=nonstopux ;;
+ *)
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ version_type=linux
+ else
+ version_type=irix
+ fi ;;
+ esac
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+ case $host_os in
+ irix5* | nonstopux*)
+ libsuff= shlibsuff=
+ ;;
+ *)
+ case $LD in # libtool.m4 will add one of these switches to LD
+ *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+ libsuff= shlibsuff= libmagic=32-bit;;
+ *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+ libsuff=32 shlibsuff=N32 libmagic=N32;;
+ *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+ libsuff=64 shlibsuff=64 libmagic=64-bit;;
+ *) libsuff= shlibsuff= libmagic=never-match;;
+ esac
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+ sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+ hardcode_into_libs=yes
+ ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+ dynamic_linker=no
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ # Some binutils ld are patched to set DT_RUNPATH
+ save_LDFLAGS=$LDFLAGS
+ save_libdir=$libdir
+ eval "libdir=/foo; wl=\"$lt_prog_compiler_wl_CXX\"; \
+ LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec_CXX\""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+ if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then :
+ shlibpath_overrides_runpath=yes
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+ LDFLAGS=$save_LDFLAGS
+ libdir=$save_libdir
+
+ # This implies no fast_install, which is unacceptable.
+ # Some rework will be needed to allow for fast_install
+ # before this can be enabled.
+ hardcode_into_libs=yes
+
+ # Append ld.so.conf contents to the search path
+ if test -f /etc/ld.so.conf; then
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ fi
+
+ # We used to test for /lib/ld.so.1 and disable shared libraries on
+ # powerpc, because MkLinux only supported shared libraries with the
+ # GNU dynamic linker. Since this was broken with cross compilers,
+ # most powerpc-linux boxes support dynamic linking these days and
+ # people can always --disable-shared, the test was removed, and we
+ # assume the GNU/Linux dynamic linker is in use.
+ dynamic_linker='GNU/Linux ld.so'
+ ;;
+
+netbsdelf*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='NetBSD ld.elf_so'
+ ;;
+
+netbsd*)
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ dynamic_linker='NetBSD (a.out) ld.so'
+ else
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='NetBSD ld.elf_so'
+ fi
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+
+newsos6)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ ;;
+
+*nto* | *qnx*)
+ version_type=qnx
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='ldqnx.so'
+ ;;
+
+openbsd*)
+ version_type=sunos
+ sys_lib_dlsearch_path_spec="/usr/lib"
+ need_lib_prefix=no
+ # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+ case $host_os in
+ openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+ *) need_version=no ;;
+ esac
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ case $host_os in
+ openbsd2.[89] | openbsd2.[89].*)
+ shlibpath_overrides_runpath=no
+ ;;
+ *)
+ shlibpath_overrides_runpath=yes
+ ;;
+ esac
+ else
+ shlibpath_overrides_runpath=yes
+ fi
+ ;;
+
+os2*)
+ libname_spec='$name'
+ shrext_cmds=".dll"
+ need_lib_prefix=no
+ library_names_spec='$libname${shared_ext} $libname.a'
+ dynamic_linker='OS/2 ld.exe'
+ shlibpath_var=LIBPATH
+ ;;
+
+osf3* | osf4* | osf5*)
+ version_type=osf
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+ sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+ ;;
+
+rdos*)
+ dynamic_linker=no
+ ;;
+
+solaris*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ # ldd complains unless libraries are executable
+ postinstall_cmds='chmod +x $lib'
+ ;;
+
+sunos4*)
+ version_type=sunos
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ if test "$with_gnu_ld" = yes; then
+ need_lib_prefix=no
+ fi
+ need_version=yes
+ ;;
+
+sysv4 | sysv4.3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_vendor in
+ sni)
+ shlibpath_overrides_runpath=no
+ need_lib_prefix=no
+ runpath_var=LD_RUN_PATH
+ ;;
+ siemens)
+ need_lib_prefix=no
+ ;;
+ motorola)
+ need_lib_prefix=no
+ need_version=no
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+ ;;
+ esac
+ ;;
+
+sysv4*MP*)
+ if test -d /usr/nec ;then
+ version_type=linux
+ library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+ soname_spec='$libname${shared_ext}.$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ fi
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ version_type=freebsd-elf
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ if test "$with_gnu_ld" = yes; then
+ sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+ else
+ sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+ case $host_os in
+ sco3.2v5*)
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+ ;;
+ esac
+ fi
+ sys_lib_dlsearch_path_spec='/usr/lib'
+ ;;
+
+tpf*)
+ # TPF is a cross-target only. Preferred cross-host = GNU/Linux.
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+uts4*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+*)
+ dynamic_linker=no
+ ;;
+esac
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $dynamic_linker" >&5
+$as_echo "$dynamic_linker" >&6; }
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+ variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+
+if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then
+ sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec"
+fi
+if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then
+ sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec"
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to hardcode library paths into programs" >&5
+$as_echo_n "checking how to hardcode library paths into programs... " >&6; }
+hardcode_action_CXX=
+if test -n "$hardcode_libdir_flag_spec_CXX" ||
+ test -n "$runpath_var_CXX" ||
+ test "X$hardcode_automatic_CXX" = "Xyes" ; then
+
+ # We can hardcode non-existent directories.
+ if test "$hardcode_direct_CXX" != no &&
+ # If the only mechanism to avoid hardcoding is shlibpath_var, we
+ # have to relink, otherwise we might link with an installed library
+ # when we should be linking with a yet-to-be-installed one
+ ## test "$_LT_TAGVAR(hardcode_shlibpath_var, CXX)" != no &&
+ test "$hardcode_minus_L_CXX" != no; then
+ # Linking always hardcodes the temporary library directory.
+ hardcode_action_CXX=relink
+ else
+ # We can link without hardcoding, and we can hardcode nonexisting dirs.
+ hardcode_action_CXX=immediate
+ fi
+else
+ # We cannot hardcode anything, or else we can only hardcode existing
+ # directories.
+ hardcode_action_CXX=unsupported
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $hardcode_action_CXX" >&5
+$as_echo "$hardcode_action_CXX" >&6; }
+
+if test "$hardcode_action_CXX" = relink ||
+ test "$inherit_rpath_CXX" = yes; then
+ # Fast installation is not supported
+ enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+ test "$enable_shared" = no; then
+ # Fast installation is not necessary
+ enable_fast_install=needless
+fi
+
+
+
+
+
+
+
+ fi # test -n "$compiler"
+
+ CC=$lt_save_CC
+ LDCXX=$LD
+ LD=$lt_save_LD
+ GCC=$lt_save_GCC
+ with_gnu_ld=$lt_save_with_gnu_ld
+ lt_cv_path_LDCXX=$lt_cv_path_LD
+ lt_cv_path_LD=$lt_save_path_LD
+ lt_cv_prog_gnu_ldcxx=$lt_cv_prog_gnu_ld
+ lt_cv_prog_gnu_ld=$lt_save_with_gnu_ld
+fi # test "$_lt_caught_CXX_error" != yes
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ac_config_commands="$ac_config_commands libtool"
+
+
+
+
+# Only expand once:
+
+
+
+
+# Check whether --with-gnu-ld was given.
+if test "${with_gnu_ld+set}" = set; then :
+ withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes
+else
+ with_gnu_ld=no
+fi
+
+ac_prog=ld
+if test "$GCC" = yes; then
+ # Check if gcc -print-prog-name=ld gives a path.
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ld used by $CC" >&5
+$as_echo_n "checking for ld used by $CC... " >&6; }
+ case $host in
+ *-*-mingw*)
+ # gcc leaves a trailing carriage return which upsets mingw
+ ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+ *)
+ ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+ esac
+ case $ac_prog in
+ # Accept absolute paths.
+ [\\/]* | ?:[\\/]*)
+ re_direlt='/[^/][^/]*/\.\./'
+ # Canonicalize the pathname of ld
+ ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'`
+ while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do
+ ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"`
+ done
+ test -z "$LD" && LD="$ac_prog"
+ ;;
+ "")
+ # If it fails, then pretend we aren't using GCC.
+ ac_prog=ld
+ ;;
+ *)
+ # If it is relative, then search for the first ld in PATH.
+ with_gnu_ld=unknown
+ ;;
+ esac
+elif test "$with_gnu_ld" = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU ld" >&5
+$as_echo_n "checking for GNU ld... " >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for non-GNU ld" >&5
+$as_echo_n "checking for non-GNU ld... " >&6; }
+fi
+if test "${lt_cv_path_LD+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$LD"; then
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+ lt_cv_path_LD="$ac_dir/$ac_prog"
+ # Check to see if the program is GNU ld. I'd rather use --version,
+ # but apparently some variants of GNU ld only accept -v.
+ # Break only if it was the GNU/non-GNU ld that we prefer.
+ case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+ *GNU* | *'with BFD'*)
+ test "$with_gnu_ld" != no && break
+ ;;
+ *)
+ test "$with_gnu_ld" != yes && break
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+else
+ lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi
+fi
+
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LD" >&5
+$as_echo "$LD" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+test -z "$LD" && as_fn_error $? "no acceptable ld found in \$PATH" "$LINENO" 5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if the linker ($LD) is GNU ld" >&5
+$as_echo_n "checking if the linker ($LD) is GNU ld... " >&6; }
+if test "${lt_cv_prog_gnu_ld+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ # I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+ lt_cv_prog_gnu_ld=yes
+ ;;
+*)
+ lt_cv_prog_gnu_ld=no
+ ;;
+esac
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_gnu_ld" >&5
+$as_echo "$lt_cv_prog_gnu_ld" >&6; }
+with_gnu_ld=$lt_cv_prog_gnu_ld
+
+
+
+
+
+
+
+ISODATE=`date +%Y-%m-%d`
+
+
+ARCH=`uname -m | sed s/i.86/i386/ | sed s/x86_64/amd64/`
+
+
+# Extract the first word of "dpkg", so it can be a program name with args.
+set dummy dpkg; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_path_DEB_BUILDER+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ case $DEB_BUILDER in
+ [\\/]* | ?:[\\/]*)
+ ac_cv_path_DEB_BUILDER="$DEB_BUILDER" # Let the user override the test with a path.
+ ;;
+ *)
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_path_DEB_BUILDER="$as_dir/$ac_word$ac_exec_ext"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+fi
+DEB_BUILDER=$ac_cv_path_DEB_BUILDER
+if test -n "$DEB_BUILDER"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DEB_BUILDER" >&5
+$as_echo "$DEB_BUILDER" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+
+for ac_header in stdint.h stdlib.h string.h sys/time.h
+do :
+ as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+ac_fn_c_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default"
+if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+
+# Checks for library functions.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for inline" >&5
+$as_echo_n "checking for inline... " >&6; }
+if test "${ac_cv_c_inline+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_c_inline=no
+for ac_kw in inline __inline__ __inline; do
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifndef __cplusplus
+typedef int foo_t;
+static $ac_kw foo_t static_foo () {return 0; }
+$ac_kw foo_t foo () {return 0; }
+#endif
+
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_c_inline=$ac_kw
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ test "$ac_cv_c_inline" != no && break
+done
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_inline" >&5
+$as_echo "$ac_cv_c_inline" >&6; }
+
+case $ac_cv_c_inline in
+ inline | yes) ;;
+ *)
+ case $ac_cv_c_inline in
+ no) ac_val=;;
+ *) ac_val=$ac_cv_c_inline;;
+ esac
+ cat >>confdefs.h <<_ACEOF
+#ifndef __cplusplus
+#define inline $ac_val
+#endif
+_ACEOF
+ ;;
+esac
+
+for ac_header in stdlib.h
+do :
+ ac_fn_c_check_header_mongrel "$LINENO" "stdlib.h" "ac_cv_header_stdlib_h" "$ac_includes_default"
+if test "x$ac_cv_header_stdlib_h" = x""yes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_STDLIB_H 1
+_ACEOF
+
+fi
+
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU libc compatible malloc" >&5
+$as_echo_n "checking for GNU libc compatible malloc... " >&6; }
+if test "${ac_cv_func_malloc_0_nonnull+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then :
+ ac_cv_func_malloc_0_nonnull=no
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#if defined STDC_HEADERS || defined HAVE_STDLIB_H
+# include <stdlib.h>
+#else
+char *malloc ();
+#endif
+
+int
+main ()
+{
+return ! malloc (0);
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_run "$LINENO"; then :
+ ac_cv_func_malloc_0_nonnull=yes
+else
+ ac_cv_func_malloc_0_nonnull=no
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
+ conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_malloc_0_nonnull" >&5
+$as_echo "$ac_cv_func_malloc_0_nonnull" >&6; }
+if test $ac_cv_func_malloc_0_nonnull = yes; then :
+
+$as_echo "#define HAVE_MALLOC 1" >>confdefs.h
+
+else
+ $as_echo "#define HAVE_MALLOC 0" >>confdefs.h
+
+ case " $LIBOBJS " in
+ *" malloc.$ac_objext "* ) ;;
+ *) LIBOBJS="$LIBOBJS malloc.$ac_objext"
+ ;;
+esac
+
+
+$as_echo "#define malloc rpl_malloc" >>confdefs.h
+
+fi
+
+
+for ac_header in stdlib.h
+do :
+ ac_fn_c_check_header_mongrel "$LINENO" "stdlib.h" "ac_cv_header_stdlib_h" "$ac_includes_default"
+if test "x$ac_cv_header_stdlib_h" = x""yes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_STDLIB_H 1
+_ACEOF
+
+fi
+
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU libc compatible realloc" >&5
+$as_echo_n "checking for GNU libc compatible realloc... " >&6; }
+if test "${ac_cv_func_realloc_0_nonnull+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then :
+ ac_cv_func_realloc_0_nonnull=no
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#if defined STDC_HEADERS || defined HAVE_STDLIB_H
+# include <stdlib.h>
+#else
+char *realloc ();
+#endif
+
+int
+main ()
+{
+return ! realloc (0, 0);
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_run "$LINENO"; then :
+ ac_cv_func_realloc_0_nonnull=yes
+else
+ ac_cv_func_realloc_0_nonnull=no
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
+ conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_realloc_0_nonnull" >&5
+$as_echo "$ac_cv_func_realloc_0_nonnull" >&6; }
+if test $ac_cv_func_realloc_0_nonnull = yes; then :
+
+$as_echo "#define HAVE_REALLOC 1" >>confdefs.h
+
+else
+ $as_echo "#define HAVE_REALLOC 0" >>confdefs.h
+
+ case " $LIBOBJS " in
+ *" realloc.$ac_objext "* ) ;;
+ *) LIBOBJS="$LIBOBJS realloc.$ac_objext"
+ ;;
+esac
+
+
+$as_echo "#define realloc rpl_realloc" >>confdefs.h
+
+fi
+
+
+for ac_func in gettimeofday memset select
+do :
+ as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
+if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for stdbool.h that conforms to C99" >&5
+$as_echo_n "checking for stdbool.h that conforms to C99... " >&6; }
+if test "${ac_cv_header_stdbool_h+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+#include <stdbool.h>
+#ifndef bool
+ "error: bool is not defined"
+#endif
+#ifndef false
+ "error: false is not defined"
+#endif
+#if false
+ "error: false is not 0"
+#endif
+#ifndef true
+ "error: true is not defined"
+#endif
+#if true != 1
+ "error: true is not 1"
+#endif
+#ifndef __bool_true_false_are_defined
+ "error: __bool_true_false_are_defined is not defined"
+#endif
+
+ struct s { _Bool s: 1; _Bool t; } s;
+
+ char a[true == 1 ? 1 : -1];
+ char b[false == 0 ? 1 : -1];
+ char c[__bool_true_false_are_defined == 1 ? 1 : -1];
+ char d[(bool) 0.5 == true ? 1 : -1];
+ bool e = &s;
+ char f[(_Bool) 0.0 == false ? 1 : -1];
+ char g[true];
+ char h[sizeof (_Bool)];
+ char i[sizeof s.t];
+ enum { j = false, k = true, l = false * true, m = true * 256 };
+ /* The following fails for
+ HP aC++/ANSI C B3910B A.05.55 [Dec 04 2003]. */
+ _Bool n[m];
+ char o[sizeof n == m * sizeof n[0] ? 1 : -1];
+ char p[-1 - (_Bool) 0 < 0 && -1 - (bool) 0 < 0 ? 1 : -1];
+# if defined __xlc__ || defined __GNUC__
+ /* Catch a bug in IBM AIX xlc compiler version 6.0.0.0
+ reported by James Lemley on 2005-10-05; see
+ http://lists.gnu.org/archive/html/bug-coreutils/2005-10/msg00086.html
+ This test is not quite right, since xlc is allowed to
+ reject this program, as the initializer for xlcbug is
+ not one of the forms that C requires support for.
+ However, doing the test right would require a runtime
+ test, and that would make cross-compilation harder.
+ Let us hope that IBM fixes the xlc bug, and also adds
+ support for this kind of constant expression. In the
+ meantime, this test will reject xlc, which is OK, since
+ our stdbool.h substitute should suffice. We also test
+ this with GCC, where it should work, to detect more
+ quickly whether someone messes up the test in the
+ future. */
+ char digs[] = "0123456789";
+ int xlcbug = 1 / (&(digs + 5)[-2 + (bool) 1] == &digs[4] ? 1 : -1);
+# endif
+ /* Catch a bug in an HP-UX C compiler. See
+ http://gcc.gnu.org/ml/gcc-patches/2003-12/msg02303.html
+ http://lists.gnu.org/archive/html/bug-coreutils/2005-11/msg00161.html
+ */
+ _Bool q = true;
+ _Bool *pq = &q;
+
+int
+main ()
+{
+
+ *pq |= q;
+ *pq |= ! q;
+ /* Refer to every declared value, to avoid compiler optimizations. */
+ return (!a + !b + !c + !d + !e + !f + !g + !h + !i + !!j + !k + !!l
+ + !m + !n + !o + !p + !q + !pq);
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_header_stdbool_h=yes
+else
+ ac_cv_header_stdbool_h=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdbool_h" >&5
+$as_echo "$ac_cv_header_stdbool_h" >&6; }
+ac_fn_c_check_type "$LINENO" "_Bool" "ac_cv_type__Bool" "$ac_includes_default"
+if test "x$ac_cv_type__Bool" = x""yes; then :
+
+cat >>confdefs.h <<_ACEOF
+#define HAVE__BOOL 1
+_ACEOF
+
+
+fi
+
+if test $ac_cv_header_stdbool_h = yes; then
+
+$as_echo "#define HAVE_STDBOOL_H 1" >>confdefs.h
+
+fi
+
+ac_fn_c_check_type "$LINENO" "size_t" "ac_cv_type_size_t" "$ac_includes_default"
+if test "x$ac_cv_type_size_t" = x""yes; then :
+
+else
+
+cat >>confdefs.h <<_ACEOF
+#define size_t unsigned int
+_ACEOF
+
+fi
+
+ac_fn_c_find_uintX_t "$LINENO" "8" "ac_cv_c_uint8_t"
+case $ac_cv_c_uint8_t in #(
+ no|yes) ;; #(
+ *)
+
+$as_echo "#define _UINT8_T 1" >>confdefs.h
+
+
+cat >>confdefs.h <<_ACEOF
+#define uint8_t $ac_cv_c_uint8_t
+_ACEOF
+;;
+ esac
+
+ac_fn_c_find_uintX_t "$LINENO" "32" "ac_cv_c_uint32_t"
+case $ac_cv_c_uint32_t in #(
+ no|yes) ;; #(
+ *)
+
+$as_echo "#define _UINT32_T 1" >>confdefs.h
+
+
+cat >>confdefs.h <<_ACEOF
+#define uint32_t $ac_cv_c_uint32_t
+_ACEOF
+;;
+ esac
+
+ac_fn_c_find_uintX_t "$LINENO" "64" "ac_cv_c_uint64_t"
+case $ac_cv_c_uint64_t in #(
+ no|yes) ;; #(
+ *)
+
+$as_echo "#define _UINT64_T 1" >>confdefs.h
+
+
+cat >>confdefs.h <<_ACEOF
+#define uint64_t $ac_cv_c_uint64_t
+_ACEOF
+;;
+ esac
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for unsigned long long int" >&5
+$as_echo_n "checking for unsigned long long int... " >&6; }
+if test "${ac_cv_type_unsigned_long_long_int+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+ /* For now, do not test the preprocessor; as of 2007 there are too many
+ implementations with broken preprocessors. Perhaps this can
+ be revisited in 2012. In the meantime, code should not expect
+ #if to work with literals wider than 32 bits. */
+ /* Test literals. */
+ long long int ll = 9223372036854775807ll;
+ long long int nll = -9223372036854775807LL;
+ unsigned long long int ull = 18446744073709551615ULL;
+ /* Test constant expressions. */
+ typedef int a[((-9223372036854775807LL < 0 && 0 < 9223372036854775807ll)
+ ? 1 : -1)];
+ typedef int b[(18446744073709551615ULL <= (unsigned long long int) -1
+ ? 1 : -1)];
+ int i = 63;
+int
+main ()
+{
+/* Test availability of runtime routines for shift and division. */
+ long long int llmax = 9223372036854775807ll;
+ unsigned long long int ullmax = 18446744073709551615ull;
+ return ((ll << 63) | (ll >> 63) | (ll < i) | (ll > i)
+ | (llmax / ll) | (llmax % ll)
+ | (ull << 63) | (ull >> 63) | (ull << i) | (ull >> i)
+ | (ullmax / ull) | (ullmax % ull));
+ ;
+ return 0;
+}
+
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_type_unsigned_long_long_int=yes
+else
+ ac_cv_type_unsigned_long_long_int=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_type_unsigned_long_long_int" >&5
+$as_echo "$ac_cv_type_unsigned_long_long_int" >&6; }
+ if test $ac_cv_type_unsigned_long_long_int = yes; then
+
+$as_echo "#define HAVE_UNSIGNED_LONG_LONG_INT 1" >>confdefs.h
+
+ fi
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for gzread in -lz" >&5
+$as_echo_n "checking for gzread in -lz... " >&6; }
+if test "${ac_cv_lib_z_gzread+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lz $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char gzread ();
+int
+main ()
+{
+return gzread ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_z_gzread=yes
+else
+ ac_cv_lib_z_gzread=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_z_gzread" >&5
+$as_echo "$ac_cv_lib_z_gzread" >&6; }
+if test "x$ac_cv_lib_z_gzread" = x""yes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBZ 1
+_ACEOF
+
+ LIBS="-lz $LIBS"
+
+else
+ as_fn_error $? "zlib not found, see http://www.zlib.net" "$LINENO" 5
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for pthread_create in -lpthread" >&5
+$as_echo_n "checking for pthread_create in -lpthread... " >&6; }
+if test "${ac_cv_lib_pthread_pthread_create+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lpthread $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char pthread_create ();
+int
+main ()
+{
+return pthread_create ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_pthread_pthread_create=yes
+else
+ ac_cv_lib_pthread_pthread_create=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_pthread_pthread_create" >&5
+$as_echo "$ac_cv_lib_pthread_pthread_create" >&6; }
+if test "x$ac_cv_lib_pthread_pthread_create" = x""yes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBPTHREAD 1
+_ACEOF
+
+ LIBS="-lpthread $LIBS"
+
+else
+ as_fn_error $? "pthread library not found" "$LINENO" 5
+fi
+
+
+
+CPPFLAGS="$CPPFLAGS -Wall -ansi -funroll-loops"
+
+hacked_prefix="${HACKED_PREFIX:-$prefix}"
+if test "x$hacked_prefix" == "xNONE"; then
+ hacked_prefix=$ac_default_prefix
+fi
+
+
+
+postrm_script=$srcdir/postrm
+
+postinst_script=$srcdir/postinst
+
+# Check whether --enable-debug was given.
+if test "${enable_debug+set}" = set; then :
+ enableval=$enable_debug; DEBUG=1
+
+$as_echo "#define OUTPUT_NB_OCC_FACTORS 1" >>confdefs.h
+
+else
+ DEBUG=0
+fi
+
+
+# Check whether --enable-coverage was given.
+if test "${enable_coverage+set}" = set; then :
+ enableval=$enable_coverage; COVERAGE=1
+else
+ COVERAGE=0
+fi
+
+
+
+# Check whether --with-included-ProgressBar was given.
+if test "${with_included_ProgressBar+set}" = set; then :
+ withval=$with_included_ProgressBar;
+else
+ with_included_ProgressBar="check"
+fi
+
+
+
+# Check whether --with-libProgressBar-prefix was given.
+if test "${with_libProgressBar_prefix+set}" = set; then :
+ withval=$with_libProgressBar_prefix; LDFLAGS="$LDFLAGS -L$with_libProgressBar_prefix/lib"
+ CPPFLAGS="$CPPFLAGS -I$with_libProgressBar_prefix/include/libProgressBar"
+else
+ with_libProgressBar_prefix=""
+fi
+
+
+PB_OK=0
+if test "x$with_included_ProgressBar" == "xcheck"; then :
+ if test "x$with_libProgressBar_prefix" != "x"; then :
+ with_included_ProgressBar="no"
+else
+ with_included_ProgressBar="yes"
+fi
+fi
+
+
+
+if test "x$with_included_ProgressBar" == "xyes"; then :
+ if test "x$with_libProgressBar_prefix" != "x"; then :
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "You can't use both --with-included-ProgressBar and --with-libProgressBar-prefix options
+See \`config.log' for more details" "$LINENO" 5 ; }
+else
+ subdirs="$subdirs src/libProgressBar-1.2.0"
+
+ PB_OK=1
+fi
+else
+ if test "x$with_libProgressBar_prefix" != "x"; then :
+ PB_OK=1
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for libProgressBarVersion in -lProgressBar" >&5
+$as_echo_n "checking for libProgressBarVersion in -lProgressBar... " >&6; }
+if test "${ac_cv_lib_ProgressBar_libProgressBarVersion+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lProgressBar $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char libProgressBarVersion ();
+int
+main ()
+{
+return libProgressBarVersion ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_ProgressBar_libProgressBarVersion=yes
+else
+ ac_cv_lib_ProgressBar_libProgressBarVersion=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_ProgressBar_libProgressBarVersion" >&5
+$as_echo "$ac_cv_lib_ProgressBar_libProgressBarVersion" >&6; }
+if test "x$ac_cv_lib_ProgressBar_libProgressBarVersion" = x""yes; then :
+ PB_OK=1
+ ProgressBar_LIBS=-lProgressBar
+fi
+
+fi
+fi
+if test "$PB_OK" == "1"; then :
+
+$as_echo "#define HAVE_LIBPROGRESSBAR 1" >>confdefs.h
+
+fi
+
+ if test "x$with_included_ProgressBar" == xyes; then
+ INCLUDED_PROGRESSBAR_TRUE=
+ INCLUDED_PROGRESSBAR_FALSE='#'
+else
+ INCLUDED_PROGRESSBAR_TRUE='#'
+ INCLUDED_PROGRESSBAR_FALSE=
+fi
+
+
+if test $COVERAGE -eq 1 || test $DEBUG -eq 1; then
+ CPPFLAGS="$CPPFLAGS -g -O0"
+ if test $COVERAGE -eq 1; then
+ CPPFLAGS="$CPPFLAGS -fprofile-arcs -ftest-coverage"
+ LDFLAGS="-fprofile-arcs -lgcov"
+ fi
+else
+ CPPFLAGS="$CPPFLAGS -O4 -DNDEBUG"
+fi
+
+LDFLAGS="$LDFLAGS $ProgressBar_LIBS"
+CPPFLAGS="$CPPFLAGS $ProgressBar_CFLAGS"
+
+ac_config_files="$ac_config_files postinst prerm control libGkArrays.pc Makefile src/Makefile tests/Makefile src/sux/Makefile src/kseq/Makefile doc/Makefile doc/libGkArrays.3 doc/package.texi"
+
+cat >confcache <<\_ACEOF
+# This file is a shell script that caches the results of configure
+# tests run on this system so they can be shared between configure
+# scripts and configure runs, see configure's option --config-cache.
+# It is not useful on other systems. If it contains results you don't
+# want to keep, you may remove or edit it.
+#
+# config.status only pays attention to the cache file if you give it
+# the --recheck option to rerun configure.
+#
+# `ac_cv_env_foo' variables (set or unset) will be overridden when
+# loading this file, other *unset* `ac_cv_foo' will be assigned the
+# following values.
+
+_ACEOF
+
+# The following way of writing the cache mishandles newlines in values,
+# but we know of no workaround that is simple, portable, and efficient.
+# So, we kill variables containing newlines.
+# Ultrix sh set writes to stderr and can't be redirected directly,
+# and sets the high bit in the cache file unless we assign to the vars.
+(
+ for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) { eval $ac_var=; unset $ac_var;} ;;
+ esac ;;
+ esac
+ done
+
+ (set) 2>&1 |
+ case $as_nl`(ac_space=' '; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ # `set' does not quote correctly, so add quotes: double-quote
+ # substitution turns \\\\ into \\, and sed turns \\ into \.
+ sed -n \
+ "s/'/'\\\\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
+ ;; #(
+ *)
+ # `set' quotes correctly as required by POSIX, so do not add quotes.
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+) |
+ sed '
+ /^ac_cv_env_/b end
+ t clear
+ :clear
+ s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/
+ t end
+ s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/
+ :end' >>confcache
+if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
+ if test -w "$cache_file"; then
+ test "x$cache_file" != "x/dev/null" &&
+ { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
+$as_echo "$as_me: updating cache $cache_file" >&6;}
+ cat confcache >$cache_file
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
+$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
+ fi
+fi
+rm -f confcache
+
+test "x$prefix" = xNONE && prefix=$ac_default_prefix
+# Let make expand exec_prefix.
+test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
+
+DEFS=-DHAVE_CONFIG_H
+
+ac_libobjs=
+ac_ltlibobjs=
+U=
+for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
+ # 1. Remove the extension, and $U if already installed.
+ ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
+ ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
+ # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
+ # will be set to the directory where LIBOBJS objects are built.
+ as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext"
+ as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo'
+done
+LIBOBJS=$ac_libobjs
+
+LTLIBOBJS=$ac_ltlibobjs
+
+
+ if test -n "$EXEEXT"; then
+ am__EXEEXT_TRUE=
+ am__EXEEXT_FALSE='#'
+else
+ am__EXEEXT_TRUE='#'
+ am__EXEEXT_FALSE=
+fi
+
+if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
+ as_fn_error $? "conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
+ as_fn_error $? "conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
+ as_fn_error $? "conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${BUILD_DOC_TRUE}" && test -z "${BUILD_DOC_FALSE}"; then
+ as_fn_error $? "conditional \"BUILD_DOC\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
+ as_fn_error $? "conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${INCLUDED_PROGRESSBAR_TRUE}" && test -z "${INCLUDED_PROGRESSBAR_FALSE}"; then
+ as_fn_error $? "conditional \"INCLUDED_PROGRESSBAR\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+
+: ${CONFIG_STATUS=./config.status}
+ac_write_fail=0
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files $CONFIG_STATUS"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5
+$as_echo "$as_me: creating $CONFIG_STATUS" >&6;}
+as_write_fail=0
+cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
+#! $SHELL
+# Generated by $as_me.
+# Run this file to recreate the current configuration.
+# Compiler output produced by configure, useful for debugging
+# configure, is in config.log if it exists.
+
+debug=false
+ac_cs_recheck=false
+ac_cs_silent=false
+
+SHELL=\${CONFIG_SHELL-$SHELL}
+export SHELL
+_ASEOF
+cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in #(
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+case $0 in #((
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
+# ----------------------------------------
+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+# script with STATUS, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ $as_echo "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} # as_fn_error
+
+
+# as_fn_set_status STATUS
+# -----------------------
+# Set $? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} # as_fn_set_status
+
+# as_fn_exit STATUS
+# -----------------
+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} # as_fn_exit
+
+# as_fn_unset VAR
+# ---------------
+# Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+# as_fn_append VAR VALUE
+# ----------------------
+# Append the text in VALUE to the end of the definition contained in VAR. Take
+# advantage of any shell optimizations that allow amortized linear growth over
+# repeated appends, instead of the typical quadratic growth present in naive
+# implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+# as_fn_arith ARG...
+# ------------------
+# Perform arithmetic evaluation on the ARGs, and store the result in the
+# global $as_val. Take advantage of shells that can avoid forks. The arguments
+# must be portable across $(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in #(((((
+-n*)
+ case `echo 'xy\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -p'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -p'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -p'
+ fi
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+
+# as_fn_mkdir_p
+# -------------
+# Create "$as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
+
+
+} # as_fn_mkdir_p
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p='mkdir -p "$as_dir"'
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+if test -x / >/dev/null 2>&1; then
+ as_test_x='test -x'
+else
+ if ls -dL / >/dev/null 2>&1; then
+ as_ls_L_option=L
+ else
+ as_ls_L_option=
+ fi
+ as_test_x='
+ eval sh -c '\''
+ if test -d "$1"; then
+ test -d "$1/.";
+ else
+ case $1 in #(
+ -*)set "./$1";;
+ esac;
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
+ ???[sx]*):;;*)false;;esac;fi
+ '\'' sh
+ '
+fi
+as_executable_p=$as_test_x
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+exec 6>&1
+## ----------------------------------- ##
+## Main body of $CONFIG_STATUS script. ##
+## ----------------------------------- ##
+_ASEOF
+test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# Save the log message, to keep $0 and so on meaningful, and to
+# report actual input values of CONFIG_FILES etc. instead of their
+# values after options handling.
+ac_log="
+This file was extended by libGkArrays $as_me 2.1.0, which was
+generated by GNU Autoconf 2.67. Invocation command line was
+
+ CONFIG_FILES = $CONFIG_FILES
+ CONFIG_HEADERS = $CONFIG_HEADERS
+ CONFIG_LINKS = $CONFIG_LINKS
+ CONFIG_COMMANDS = $CONFIG_COMMANDS
+ $ $0 $@
+
+on `(hostname || uname -n) 2>/dev/null | sed 1q`
+"
+
+_ACEOF
+
+case $ac_config_files in *"
+"*) set x $ac_config_files; shift; ac_config_files=$*;;
+esac
+
+case $ac_config_headers in *"
+"*) set x $ac_config_headers; shift; ac_config_headers=$*;;
+esac
+
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+# Files that config.status was made for.
+config_files="$ac_config_files"
+config_headers="$ac_config_headers"
+config_commands="$ac_config_commands"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+ac_cs_usage="\
+\`$as_me' instantiates files and other configuration actions
+from templates according to the current configuration. Unless the files
+and actions are specified as TAGs, all are instantiated by default.
+
+Usage: $0 [OPTION]... [TAG]...
+
+ -h, --help print this help, then exit
+ -V, --version print version number and configuration settings, then exit
+ --config print configuration, then exit
+ -q, --quiet, --silent
+ do not print progress messages
+ -d, --debug don't remove temporary files
+ --recheck update $as_me by reconfiguring in the same conditions
+ --file=FILE[:TEMPLATE]
+ instantiate the configuration file FILE
+ --header=FILE[:TEMPLATE]
+ instantiate the configuration header FILE
+
+Configuration files:
+$config_files
+
+Configuration headers:
+$config_headers
+
+Configuration commands:
+$config_commands
+
+Report bugs to <crac-gkarrays at lists.gforge.inria.fr>.
+libGkArrays home page: <http://crac.gforge.inria.fr/gkarrays>."
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
+ac_cs_version="\\
+libGkArrays config.status 2.1.0
+configured by $0, generated by GNU Autoconf 2.67,
+ with options \\"\$ac_cs_config\\"
+
+Copyright (C) 2010 Free Software Foundation, Inc.
+This config.status script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it."
+
+ac_pwd='$ac_pwd'
+srcdir='$srcdir'
+INSTALL='$INSTALL'
+MKDIR_P='$MKDIR_P'
+AWK='$AWK'
+test -n "\$AWK" || AWK=awk
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# The default lists apply if the user does not specify any file.
+ac_need_defaults=:
+while test $# != 0
+do
+ case $1 in
+ --*=?*)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
+ ac_shift=:
+ ;;
+ --*=)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=
+ ac_shift=:
+ ;;
+ *)
+ ac_option=$1
+ ac_optarg=$2
+ ac_shift=shift
+ ;;
+ esac
+
+ case $ac_option in
+ # Handling of the options.
+ -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
+ ac_cs_recheck=: ;;
+ --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
+ $as_echo "$ac_cs_version"; exit ;;
+ --config | --confi | --conf | --con | --co | --c )
+ $as_echo "$ac_cs_config"; exit ;;
+ --debug | --debu | --deb | --de | --d | -d )
+ debug=: ;;
+ --file | --fil | --fi | --f )
+ $ac_shift
+ case $ac_optarg in
+ *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ '') as_fn_error $? "missing file argument" ;;
+ esac
+ as_fn_append CONFIG_FILES " '$ac_optarg'"
+ ac_need_defaults=false;;
+ --header | --heade | --head | --hea )
+ $ac_shift
+ case $ac_optarg in
+ *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ as_fn_append CONFIG_HEADERS " '$ac_optarg'"
+ ac_need_defaults=false;;
+ --he | --h)
+ # Conflict between --help and --header
+ as_fn_error $? "ambiguous option: \`$1'
+Try \`$0 --help' for more information.";;
+ --help | --hel | -h )
+ $as_echo "$ac_cs_usage"; exit ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil | --si | --s)
+ ac_cs_silent=: ;;
+
+ # This is an error.
+ -*) as_fn_error $? "unrecognized option: \`$1'
+Try \`$0 --help' for more information." ;;
+
+ *) as_fn_append ac_config_targets " $1"
+ ac_need_defaults=false ;;
+
+ esac
+ shift
+done
+
+ac_configure_extra_args=
+
+if $ac_cs_silent; then
+ exec 6>/dev/null
+ ac_configure_extra_args="$ac_configure_extra_args --silent"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+if \$ac_cs_recheck; then
+ set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
+ shift
+ \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6
+ CONFIG_SHELL='$SHELL'
+ export CONFIG_SHELL
+ exec "\$@"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+exec 5>>config.log
+{
+ echo
+ sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX
+## Running $as_me. ##
+_ASBOX
+ $as_echo "$ac_log"
+} >&5
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+#
+# INIT-COMMANDS
+#
+AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"
+
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+sed_quote_subst='$sed_quote_subst'
+double_quote_subst='$double_quote_subst'
+delay_variable_subst='$delay_variable_subst'
+macro_version='`$ECHO "X$macro_version" | $Xsed -e "$delay_single_quote_subst"`'
+macro_revision='`$ECHO "X$macro_revision" | $Xsed -e "$delay_single_quote_subst"`'
+enable_shared='`$ECHO "X$enable_shared" | $Xsed -e "$delay_single_quote_subst"`'
+enable_static='`$ECHO "X$enable_static" | $Xsed -e "$delay_single_quote_subst"`'
+pic_mode='`$ECHO "X$pic_mode" | $Xsed -e "$delay_single_quote_subst"`'
+enable_fast_install='`$ECHO "X$enable_fast_install" | $Xsed -e "$delay_single_quote_subst"`'
+host_alias='`$ECHO "X$host_alias" | $Xsed -e "$delay_single_quote_subst"`'
+host='`$ECHO "X$host" | $Xsed -e "$delay_single_quote_subst"`'
+host_os='`$ECHO "X$host_os" | $Xsed -e "$delay_single_quote_subst"`'
+build_alias='`$ECHO "X$build_alias" | $Xsed -e "$delay_single_quote_subst"`'
+build='`$ECHO "X$build" | $Xsed -e "$delay_single_quote_subst"`'
+build_os='`$ECHO "X$build_os" | $Xsed -e "$delay_single_quote_subst"`'
+SED='`$ECHO "X$SED" | $Xsed -e "$delay_single_quote_subst"`'
+Xsed='`$ECHO "X$Xsed" | $Xsed -e "$delay_single_quote_subst"`'
+GREP='`$ECHO "X$GREP" | $Xsed -e "$delay_single_quote_subst"`'
+EGREP='`$ECHO "X$EGREP" | $Xsed -e "$delay_single_quote_subst"`'
+FGREP='`$ECHO "X$FGREP" | $Xsed -e "$delay_single_quote_subst"`'
+LD='`$ECHO "X$LD" | $Xsed -e "$delay_single_quote_subst"`'
+NM='`$ECHO "X$NM" | $Xsed -e "$delay_single_quote_subst"`'
+LN_S='`$ECHO "X$LN_S" | $Xsed -e "$delay_single_quote_subst"`'
+max_cmd_len='`$ECHO "X$max_cmd_len" | $Xsed -e "$delay_single_quote_subst"`'
+ac_objext='`$ECHO "X$ac_objext" | $Xsed -e "$delay_single_quote_subst"`'
+exeext='`$ECHO "X$exeext" | $Xsed -e "$delay_single_quote_subst"`'
+lt_unset='`$ECHO "X$lt_unset" | $Xsed -e "$delay_single_quote_subst"`'
+lt_SP2NL='`$ECHO "X$lt_SP2NL" | $Xsed -e "$delay_single_quote_subst"`'
+lt_NL2SP='`$ECHO "X$lt_NL2SP" | $Xsed -e "$delay_single_quote_subst"`'
+reload_flag='`$ECHO "X$reload_flag" | $Xsed -e "$delay_single_quote_subst"`'
+reload_cmds='`$ECHO "X$reload_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+OBJDUMP='`$ECHO "X$OBJDUMP" | $Xsed -e "$delay_single_quote_subst"`'
+deplibs_check_method='`$ECHO "X$deplibs_check_method" | $Xsed -e "$delay_single_quote_subst"`'
+file_magic_cmd='`$ECHO "X$file_magic_cmd" | $Xsed -e "$delay_single_quote_subst"`'
+AR='`$ECHO "X$AR" | $Xsed -e "$delay_single_quote_subst"`'
+AR_FLAGS='`$ECHO "X$AR_FLAGS" | $Xsed -e "$delay_single_quote_subst"`'
+STRIP='`$ECHO "X$STRIP" | $Xsed -e "$delay_single_quote_subst"`'
+RANLIB='`$ECHO "X$RANLIB" | $Xsed -e "$delay_single_quote_subst"`'
+old_postinstall_cmds='`$ECHO "X$old_postinstall_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+old_postuninstall_cmds='`$ECHO "X$old_postuninstall_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_cmds='`$ECHO "X$old_archive_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+CC='`$ECHO "X$CC" | $Xsed -e "$delay_single_quote_subst"`'
+CFLAGS='`$ECHO "X$CFLAGS" | $Xsed -e "$delay_single_quote_subst"`'
+compiler='`$ECHO "X$compiler" | $Xsed -e "$delay_single_quote_subst"`'
+GCC='`$ECHO "X$GCC" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_pipe='`$ECHO "X$lt_cv_sys_global_symbol_pipe" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_to_cdecl='`$ECHO "X$lt_cv_sys_global_symbol_to_cdecl" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_to_c_name_address='`$ECHO "X$lt_cv_sys_global_symbol_to_c_name_address" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='`$ECHO "X$lt_cv_sys_global_symbol_to_c_name_address_lib_prefix" | $Xsed -e "$delay_single_quote_subst"`'
+objdir='`$ECHO "X$objdir" | $Xsed -e "$delay_single_quote_subst"`'
+SHELL='`$ECHO "X$SHELL" | $Xsed -e "$delay_single_quote_subst"`'
+ECHO='`$ECHO "X$ECHO" | $Xsed -e "$delay_single_quote_subst"`'
+MAGIC_CMD='`$ECHO "X$MAGIC_CMD" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_no_builtin_flag='`$ECHO "X$lt_prog_compiler_no_builtin_flag" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_wl='`$ECHO "X$lt_prog_compiler_wl" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_pic='`$ECHO "X$lt_prog_compiler_pic" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_static='`$ECHO "X$lt_prog_compiler_static" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_prog_compiler_c_o='`$ECHO "X$lt_cv_prog_compiler_c_o" | $Xsed -e "$delay_single_quote_subst"`'
+need_locks='`$ECHO "X$need_locks" | $Xsed -e "$delay_single_quote_subst"`'
+DSYMUTIL='`$ECHO "X$DSYMUTIL" | $Xsed -e "$delay_single_quote_subst"`'
+NMEDIT='`$ECHO "X$NMEDIT" | $Xsed -e "$delay_single_quote_subst"`'
+LIPO='`$ECHO "X$LIPO" | $Xsed -e "$delay_single_quote_subst"`'
+OTOOL='`$ECHO "X$OTOOL" | $Xsed -e "$delay_single_quote_subst"`'
+OTOOL64='`$ECHO "X$OTOOL64" | $Xsed -e "$delay_single_quote_subst"`'
+libext='`$ECHO "X$libext" | $Xsed -e "$delay_single_quote_subst"`'
+shrext_cmds='`$ECHO "X$shrext_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+extract_expsyms_cmds='`$ECHO "X$extract_expsyms_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+archive_cmds_need_lc='`$ECHO "X$archive_cmds_need_lc" | $Xsed -e "$delay_single_quote_subst"`'
+enable_shared_with_static_runtimes='`$ECHO "X$enable_shared_with_static_runtimes" | $Xsed -e "$delay_single_quote_subst"`'
+export_dynamic_flag_spec='`$ECHO "X$export_dynamic_flag_spec" | $Xsed -e "$delay_single_quote_subst"`'
+whole_archive_flag_spec='`$ECHO "X$whole_archive_flag_spec" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_needs_object='`$ECHO "X$compiler_needs_object" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_from_new_cmds='`$ECHO "X$old_archive_from_new_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_from_expsyms_cmds='`$ECHO "X$old_archive_from_expsyms_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+archive_cmds='`$ECHO "X$archive_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+archive_expsym_cmds='`$ECHO "X$archive_expsym_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+module_cmds='`$ECHO "X$module_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+module_expsym_cmds='`$ECHO "X$module_expsym_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+with_gnu_ld='`$ECHO "X$with_gnu_ld" | $Xsed -e "$delay_single_quote_subst"`'
+allow_undefined_flag='`$ECHO "X$allow_undefined_flag" | $Xsed -e "$delay_single_quote_subst"`'
+no_undefined_flag='`$ECHO "X$no_undefined_flag" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_flag_spec='`$ECHO "X$hardcode_libdir_flag_spec" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_flag_spec_ld='`$ECHO "X$hardcode_libdir_flag_spec_ld" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_separator='`$ECHO "X$hardcode_libdir_separator" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_direct='`$ECHO "X$hardcode_direct" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_direct_absolute='`$ECHO "X$hardcode_direct_absolute" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_minus_L='`$ECHO "X$hardcode_minus_L" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_shlibpath_var='`$ECHO "X$hardcode_shlibpath_var" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_automatic='`$ECHO "X$hardcode_automatic" | $Xsed -e "$delay_single_quote_subst"`'
+inherit_rpath='`$ECHO "X$inherit_rpath" | $Xsed -e "$delay_single_quote_subst"`'
+link_all_deplibs='`$ECHO "X$link_all_deplibs" | $Xsed -e "$delay_single_quote_subst"`'
+fix_srcfile_path='`$ECHO "X$fix_srcfile_path" | $Xsed -e "$delay_single_quote_subst"`'
+always_export_symbols='`$ECHO "X$always_export_symbols" | $Xsed -e "$delay_single_quote_subst"`'
+export_symbols_cmds='`$ECHO "X$export_symbols_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+exclude_expsyms='`$ECHO "X$exclude_expsyms" | $Xsed -e "$delay_single_quote_subst"`'
+include_expsyms='`$ECHO "X$include_expsyms" | $Xsed -e "$delay_single_quote_subst"`'
+prelink_cmds='`$ECHO "X$prelink_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+file_list_spec='`$ECHO "X$file_list_spec" | $Xsed -e "$delay_single_quote_subst"`'
+variables_saved_for_relink='`$ECHO "X$variables_saved_for_relink" | $Xsed -e "$delay_single_quote_subst"`'
+need_lib_prefix='`$ECHO "X$need_lib_prefix" | $Xsed -e "$delay_single_quote_subst"`'
+need_version='`$ECHO "X$need_version" | $Xsed -e "$delay_single_quote_subst"`'
+version_type='`$ECHO "X$version_type" | $Xsed -e "$delay_single_quote_subst"`'
+runpath_var='`$ECHO "X$runpath_var" | $Xsed -e "$delay_single_quote_subst"`'
+shlibpath_var='`$ECHO "X$shlibpath_var" | $Xsed -e "$delay_single_quote_subst"`'
+shlibpath_overrides_runpath='`$ECHO "X$shlibpath_overrides_runpath" | $Xsed -e "$delay_single_quote_subst"`'
+libname_spec='`$ECHO "X$libname_spec" | $Xsed -e "$delay_single_quote_subst"`'
+library_names_spec='`$ECHO "X$library_names_spec" | $Xsed -e "$delay_single_quote_subst"`'
+soname_spec='`$ECHO "X$soname_spec" | $Xsed -e "$delay_single_quote_subst"`'
+postinstall_cmds='`$ECHO "X$postinstall_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+postuninstall_cmds='`$ECHO "X$postuninstall_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+finish_cmds='`$ECHO "X$finish_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+finish_eval='`$ECHO "X$finish_eval" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_into_libs='`$ECHO "X$hardcode_into_libs" | $Xsed -e "$delay_single_quote_subst"`'
+sys_lib_search_path_spec='`$ECHO "X$sys_lib_search_path_spec" | $Xsed -e "$delay_single_quote_subst"`'
+sys_lib_dlsearch_path_spec='`$ECHO "X$sys_lib_dlsearch_path_spec" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_action='`$ECHO "X$hardcode_action" | $Xsed -e "$delay_single_quote_subst"`'
+enable_dlopen='`$ECHO "X$enable_dlopen" | $Xsed -e "$delay_single_quote_subst"`'
+enable_dlopen_self='`$ECHO "X$enable_dlopen_self" | $Xsed -e "$delay_single_quote_subst"`'
+enable_dlopen_self_static='`$ECHO "X$enable_dlopen_self_static" | $Xsed -e "$delay_single_quote_subst"`'
+old_striplib='`$ECHO "X$old_striplib" | $Xsed -e "$delay_single_quote_subst"`'
+striplib='`$ECHO "X$striplib" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_lib_search_dirs='`$ECHO "X$compiler_lib_search_dirs" | $Xsed -e "$delay_single_quote_subst"`'
+predep_objects='`$ECHO "X$predep_objects" | $Xsed -e "$delay_single_quote_subst"`'
+postdep_objects='`$ECHO "X$postdep_objects" | $Xsed -e "$delay_single_quote_subst"`'
+predeps='`$ECHO "X$predeps" | $Xsed -e "$delay_single_quote_subst"`'
+postdeps='`$ECHO "X$postdeps" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_lib_search_path='`$ECHO "X$compiler_lib_search_path" | $Xsed -e "$delay_single_quote_subst"`'
+LD_CXX='`$ECHO "X$LD_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_cmds_CXX='`$ECHO "X$old_archive_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_CXX='`$ECHO "X$compiler_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+GCC_CXX='`$ECHO "X$GCC_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_no_builtin_flag_CXX='`$ECHO "X$lt_prog_compiler_no_builtin_flag_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_wl_CXX='`$ECHO "X$lt_prog_compiler_wl_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_pic_CXX='`$ECHO "X$lt_prog_compiler_pic_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_static_CXX='`$ECHO "X$lt_prog_compiler_static_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_prog_compiler_c_o_CXX='`$ECHO "X$lt_cv_prog_compiler_c_o_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+archive_cmds_need_lc_CXX='`$ECHO "X$archive_cmds_need_lc_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+enable_shared_with_static_runtimes_CXX='`$ECHO "X$enable_shared_with_static_runtimes_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+export_dynamic_flag_spec_CXX='`$ECHO "X$export_dynamic_flag_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+whole_archive_flag_spec_CXX='`$ECHO "X$whole_archive_flag_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_needs_object_CXX='`$ECHO "X$compiler_needs_object_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_from_new_cmds_CXX='`$ECHO "X$old_archive_from_new_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_from_expsyms_cmds_CXX='`$ECHO "X$old_archive_from_expsyms_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+archive_cmds_CXX='`$ECHO "X$archive_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+archive_expsym_cmds_CXX='`$ECHO "X$archive_expsym_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+module_cmds_CXX='`$ECHO "X$module_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+module_expsym_cmds_CXX='`$ECHO "X$module_expsym_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+with_gnu_ld_CXX='`$ECHO "X$with_gnu_ld_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+allow_undefined_flag_CXX='`$ECHO "X$allow_undefined_flag_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+no_undefined_flag_CXX='`$ECHO "X$no_undefined_flag_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_flag_spec_CXX='`$ECHO "X$hardcode_libdir_flag_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_flag_spec_ld_CXX='`$ECHO "X$hardcode_libdir_flag_spec_ld_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_separator_CXX='`$ECHO "X$hardcode_libdir_separator_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_direct_CXX='`$ECHO "X$hardcode_direct_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_direct_absolute_CXX='`$ECHO "X$hardcode_direct_absolute_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_minus_L_CXX='`$ECHO "X$hardcode_minus_L_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_shlibpath_var_CXX='`$ECHO "X$hardcode_shlibpath_var_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_automatic_CXX='`$ECHO "X$hardcode_automatic_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+inherit_rpath_CXX='`$ECHO "X$inherit_rpath_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+link_all_deplibs_CXX='`$ECHO "X$link_all_deplibs_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+fix_srcfile_path_CXX='`$ECHO "X$fix_srcfile_path_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+always_export_symbols_CXX='`$ECHO "X$always_export_symbols_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+export_symbols_cmds_CXX='`$ECHO "X$export_symbols_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+exclude_expsyms_CXX='`$ECHO "X$exclude_expsyms_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+include_expsyms_CXX='`$ECHO "X$include_expsyms_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+prelink_cmds_CXX='`$ECHO "X$prelink_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+file_list_spec_CXX='`$ECHO "X$file_list_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_action_CXX='`$ECHO "X$hardcode_action_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_lib_search_dirs_CXX='`$ECHO "X$compiler_lib_search_dirs_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+predep_objects_CXX='`$ECHO "X$predep_objects_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+postdep_objects_CXX='`$ECHO "X$postdep_objects_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+predeps_CXX='`$ECHO "X$predeps_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+postdeps_CXX='`$ECHO "X$postdeps_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_lib_search_path_CXX='`$ECHO "X$compiler_lib_search_path_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+
+LTCC='$LTCC'
+LTCFLAGS='$LTCFLAGS'
+compiler='$compiler_DEFAULT'
+
+# Quote evaled strings.
+for var in SED \
+GREP \
+EGREP \
+FGREP \
+LD \
+NM \
+LN_S \
+lt_SP2NL \
+lt_NL2SP \
+reload_flag \
+OBJDUMP \
+deplibs_check_method \
+file_magic_cmd \
+AR \
+AR_FLAGS \
+STRIP \
+RANLIB \
+CC \
+CFLAGS \
+compiler \
+lt_cv_sys_global_symbol_pipe \
+lt_cv_sys_global_symbol_to_cdecl \
+lt_cv_sys_global_symbol_to_c_name_address \
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix \
+SHELL \
+ECHO \
+lt_prog_compiler_no_builtin_flag \
+lt_prog_compiler_wl \
+lt_prog_compiler_pic \
+lt_prog_compiler_static \
+lt_cv_prog_compiler_c_o \
+need_locks \
+DSYMUTIL \
+NMEDIT \
+LIPO \
+OTOOL \
+OTOOL64 \
+shrext_cmds \
+export_dynamic_flag_spec \
+whole_archive_flag_spec \
+compiler_needs_object \
+with_gnu_ld \
+allow_undefined_flag \
+no_undefined_flag \
+hardcode_libdir_flag_spec \
+hardcode_libdir_flag_spec_ld \
+hardcode_libdir_separator \
+fix_srcfile_path \
+exclude_expsyms \
+include_expsyms \
+file_list_spec \
+variables_saved_for_relink \
+libname_spec \
+library_names_spec \
+soname_spec \
+finish_eval \
+old_striplib \
+striplib \
+compiler_lib_search_dirs \
+predep_objects \
+postdep_objects \
+predeps \
+postdeps \
+compiler_lib_search_path \
+LD_CXX \
+compiler_CXX \
+lt_prog_compiler_no_builtin_flag_CXX \
+lt_prog_compiler_wl_CXX \
+lt_prog_compiler_pic_CXX \
+lt_prog_compiler_static_CXX \
+lt_cv_prog_compiler_c_o_CXX \
+export_dynamic_flag_spec_CXX \
+whole_archive_flag_spec_CXX \
+compiler_needs_object_CXX \
+with_gnu_ld_CXX \
+allow_undefined_flag_CXX \
+no_undefined_flag_CXX \
+hardcode_libdir_flag_spec_CXX \
+hardcode_libdir_flag_spec_ld_CXX \
+hardcode_libdir_separator_CXX \
+fix_srcfile_path_CXX \
+exclude_expsyms_CXX \
+include_expsyms_CXX \
+file_list_spec_CXX \
+compiler_lib_search_dirs_CXX \
+predep_objects_CXX \
+postdep_objects_CXX \
+predeps_CXX \
+postdeps_CXX \
+compiler_lib_search_path_CXX; do
+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in
+ *[\\\\\\\`\\"\\\$]*)
+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$sed_quote_subst\\"\\\`\\\\\\""
+ ;;
+ *)
+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\""
+ ;;
+ esac
+done
+
+# Double-quote double-evaled strings.
+for var in reload_cmds \
+old_postinstall_cmds \
+old_postuninstall_cmds \
+old_archive_cmds \
+extract_expsyms_cmds \
+old_archive_from_new_cmds \
+old_archive_from_expsyms_cmds \
+archive_cmds \
+archive_expsym_cmds \
+module_cmds \
+module_expsym_cmds \
+export_symbols_cmds \
+prelink_cmds \
+postinstall_cmds \
+postuninstall_cmds \
+finish_cmds \
+sys_lib_search_path_spec \
+sys_lib_dlsearch_path_spec \
+old_archive_cmds_CXX \
+old_archive_from_new_cmds_CXX \
+old_archive_from_expsyms_cmds_CXX \
+archive_cmds_CXX \
+archive_expsym_cmds_CXX \
+module_cmds_CXX \
+module_expsym_cmds_CXX \
+export_symbols_cmds_CXX \
+prelink_cmds_CXX; do
+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in
+ *[\\\\\\\`\\"\\\$]*)
+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$double_quote_subst\\" -e \\"\\\$sed_quote_subst\\" -e \\"\\\$delay_variable_subst\\"\\\`\\\\\\""
+ ;;
+ *)
+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\""
+ ;;
+ esac
+done
+
+# Fix-up fallback echo if it was mangled by the above quoting rules.
+case \$lt_ECHO in
+*'\\\$0 --fallback-echo"') lt_ECHO=\`\$ECHO "X\$lt_ECHO" | \$Xsed -e 's/\\\\\\\\\\\\\\\$0 --fallback-echo"\$/\$0 --fallback-echo"/'\`
+ ;;
+esac
+
+ac_aux_dir='$ac_aux_dir'
+xsi_shell='$xsi_shell'
+lt_shell_append='$lt_shell_append'
+
+# See if we are running on zsh, and set the options which allow our
+# commands through without removal of \ escapes INIT.
+if test -n "\${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+fi
+
+
+ PACKAGE='$PACKAGE'
+ VERSION='$VERSION'
+ TIMESTAMP='$TIMESTAMP'
+ RM='$RM'
+ ofile='$ofile'
+
+
+
+
+
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+
+# Handling of arguments.
+for ac_config_target in $ac_config_targets
+do
+ case $ac_config_target in
+ "config/config.h") CONFIG_HEADERS="$CONFIG_HEADERS config/config.h" ;;
+ "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+ "libtool") CONFIG_COMMANDS="$CONFIG_COMMANDS libtool" ;;
+ "postinst") CONFIG_FILES="$CONFIG_FILES postinst" ;;
+ "prerm") CONFIG_FILES="$CONFIG_FILES prerm" ;;
+ "control") CONFIG_FILES="$CONFIG_FILES control" ;;
+ "libGkArrays.pc") CONFIG_FILES="$CONFIG_FILES libGkArrays.pc" ;;
+ "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
+ "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
+ "tests/Makefile") CONFIG_FILES="$CONFIG_FILES tests/Makefile" ;;
+ "src/sux/Makefile") CONFIG_FILES="$CONFIG_FILES src/sux/Makefile" ;;
+ "src/kseq/Makefile") CONFIG_FILES="$CONFIG_FILES src/kseq/Makefile" ;;
+ "doc/Makefile") CONFIG_FILES="$CONFIG_FILES doc/Makefile" ;;
+ "doc/libGkArrays.3") CONFIG_FILES="$CONFIG_FILES doc/libGkArrays.3" ;;
+ "doc/package.texi") CONFIG_FILES="$CONFIG_FILES doc/package.texi" ;;
+
+ *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5 ;;
+ esac
+done
+
+
+# If the user did not use the arguments to specify the items to instantiate,
+# then the envvar interface is used. Set only those that are not.
+# We use the long form for the default assignment because of an extremely
+# bizarre bug on SunOS 4.1.3.
+if $ac_need_defaults; then
+ test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
+ test "${CONFIG_HEADERS+set}" = set || CONFIG_HEADERS=$config_headers
+ test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands
+fi
+
+# Have a temporary directory for convenience. Make it in the build tree
+# simply because there is no reason against having it here, and in addition,
+# creating and moving files from /tmp can sometimes cause problems.
+# Hook for its removal unless debugging.
+# Note that there is a small window in which the directory will not be cleaned:
+# after its creation but before its name has been assigned to `$tmp'.
+$debug ||
+{
+ tmp=
+ trap 'exit_status=$?
+ { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status
+' 0
+ trap 'as_fn_exit 1' 1 2 13 15
+}
+# Create a (secure) tmp directory for tmp files.
+
+{
+ tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
+ test -n "$tmp" && test -d "$tmp"
+} ||
+{
+ tmp=./conf$$-$RANDOM
+ (umask 077 && mkdir "$tmp")
+} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
+
+# Set up the scripts for CONFIG_FILES section.
+# No need to generate them if there are no CONFIG_FILES.
+# This happens for instance with `./config.status config.h'.
+if test -n "$CONFIG_FILES"; then
+
+if $AWK 'BEGIN { getline <"/dev/null" }' </dev/null 2>/dev/null; then
+ ac_cs_awk_getline=:
+ ac_cs_awk_pipe_init=
+ ac_cs_awk_read_file='
+ while ((getline aline < (F[key])) > 0)
+ print(aline)
+ close(F[key])'
+ ac_cs_awk_pipe_fini=
+else
+ ac_cs_awk_getline=false
+ ac_cs_awk_pipe_init="print \"cat <<'|#_!!_#|' &&\""
+ ac_cs_awk_read_file='
+ print "|#_!!_#|"
+ print "cat " F[key] " &&"
+ '$ac_cs_awk_pipe_init
+ # The final `:' finishes the AND list.
+ ac_cs_awk_pipe_fini='END { print "|#_!!_#|"; print ":" }'
+fi
+ac_cr=`echo X | tr X '\015'`
+# On cygwin, bash can eat \r inside `` if the user requested igncr.
+# But we know of no other shell where ac_cr would be empty at this
+# point, so we can use a bashism as a fallback.
+if test "x$ac_cr" = x; then
+ eval ac_cr=\$\'\\r\'
+fi
+ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
+if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
+ ac_cs_awk_cr='\\r'
+else
+ ac_cs_awk_cr=$ac_cr
+fi
+
+echo 'BEGIN {' >"$tmp/subs1.awk" &&
+_ACEOF
+
+# Create commands to substitute file output variables.
+{
+ echo "cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1" &&
+ echo 'cat >>"\$tmp/subs1.awk" <<\\_ACAWK &&' &&
+ echo "$ac_subst_files" | sed 's/.*/F["&"]="$&"/' &&
+ echo "_ACAWK" &&
+ echo "_ACEOF"
+} >conf$$files.sh &&
+. ./conf$$files.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+rm -f conf$$files.sh
+
+{
+ echo "cat >conf$$subs.awk <<_ACEOF" &&
+ echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
+ echo "_ACEOF"
+} >conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'`
+ac_delim='%!_!# '
+for ac_last_try in false false false false false :; do
+ . ./conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+
+ ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
+ if test $ac_delim_n = $ac_delim_num; then
+ break
+ elif $ac_last_try; then
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ else
+ ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+ fi
+done
+rm -f conf$$subs.sh
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+cat >>"\$tmp/subs1.awk" <<\\_ACAWK &&
+_ACEOF
+sed -n '
+h
+s/^/S["/; s/!.*/"]=/
+p
+g
+s/^[^!]*!//
+:repl
+t repl
+s/'"$ac_delim"'$//
+t delim
+:nl
+h
+s/\(.\{148\}\)..*/\1/
+t more1
+s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/
+p
+n
+b repl
+:more1
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t nl
+:delim
+h
+s/\(.\{148\}\)..*/\1/
+t more2
+s/["\\]/\\&/g; s/^/"/; s/$/"/
+p
+b
+:more2
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t delim
+' <conf$$subs.awk | sed '
+/^[^""]/{
+ N
+ s/\n//
+}
+' >>$CONFIG_STATUS || ac_write_fail=1
+rm -f conf$$subs.awk
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+_ACAWK
+cat >>"\$tmp/subs1.awk" <<_ACAWK &&
+ for (key in S) S_is_set[key] = 1
+ FS = ""
+ \$ac_cs_awk_pipe_init
+}
+{
+ line = $ 0
+ nfields = split(line, field, "@")
+ substed = 0
+ len = length(field[1])
+ for (i = 2; i < nfields; i++) {
+ key = field[i]
+ keylen = length(key)
+ if (S_is_set[key]) {
+ value = S[key]
+ line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3)
+ len += length(value) + length(field[++i])
+ substed = 1
+ } else
+ len += 1 + keylen
+ }
+ if (nfields == 3 && !substed) {
+ key = field[2]
+ if (F[key] != "" && line ~ /^[ ]*@.*@[ ]*$/) {
+ \$ac_cs_awk_read_file
+ next
+ }
+ }
+ print line
+}
+\$ac_cs_awk_pipe_fini
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
+ sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g"
+else
+ cat
+fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \
+ || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
+_ACEOF
+
+# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
+# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
+# trailing colons and then remove the whole line if VPATH becomes empty
+# (actually we leave an empty line to preserve line numbers).
+if test "x$srcdir" = x.; then
+ ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{
+h
+s///
+s/^/:/
+s/[ ]*$/:/
+s/:\$(srcdir):/:/g
+s/:\${srcdir}:/:/g
+s/:@srcdir@:/:/g
+s/^:*//
+s/:*$//
+x
+s/\(=[ ]*\).*/\1/
+G
+s/\n//
+s/^[^=]*=[ ]*$//
+}'
+fi
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+fi # test -n "$CONFIG_FILES"
+
+# Set up the scripts for CONFIG_HEADERS section.
+# No need to generate them if there are no CONFIG_HEADERS.
+# This happens for instance with `./config.status Makefile'.
+if test -n "$CONFIG_HEADERS"; then
+cat >"$tmp/defines.awk" <<\_ACAWK ||
+BEGIN {
+_ACEOF
+
+# Transform confdefs.h into an awk script `defines.awk', embedded as
+# here-document in config.status, that substitutes the proper values into
+# config.h.in to produce config.h.
+
+# Create a delimiter string that does not exist in confdefs.h, to ease
+# handling of long lines.
+ac_delim='%!_!# '
+for ac_last_try in false false :; do
+ ac_t=`sed -n "/$ac_delim/p" confdefs.h`
+ if test -z "$ac_t"; then
+ break
+ elif $ac_last_try; then
+ as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5
+ else
+ ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+ fi
+done
+
+# For the awk script, D is an array of macro values keyed by name,
+# likewise P contains macro parameters if any. Preserve backslash
+# newline sequences.
+
+ac_word_re=[_$as_cr_Letters][_$as_cr_alnum]*
+sed -n '
+s/.\{148\}/&'"$ac_delim"'/g
+t rset
+:rset
+s/^[ ]*#[ ]*define[ ][ ]*/ /
+t def
+d
+:def
+s/\\$//
+t bsnl
+s/["\\]/\\&/g
+s/^ \('"$ac_word_re"'\)\(([^()]*)\)[ ]*\(.*\)/P["\1"]="\2"\
+D["\1"]=" \3"/p
+s/^ \('"$ac_word_re"'\)[ ]*\(.*\)/D["\1"]=" \2"/p
+d
+:bsnl
+s/["\\]/\\&/g
+s/^ \('"$ac_word_re"'\)\(([^()]*)\)[ ]*\(.*\)/P["\1"]="\2"\
+D["\1"]=" \3\\\\\\n"\\/p
+t cont
+s/^ \('"$ac_word_re"'\)[ ]*\(.*\)/D["\1"]=" \2\\\\\\n"\\/p
+t cont
+d
+:cont
+n
+s/.\{148\}/&'"$ac_delim"'/g
+t clear
+:clear
+s/\\$//
+t bsnlc
+s/["\\]/\\&/g; s/^/"/; s/$/"/p
+d
+:bsnlc
+s/["\\]/\\&/g; s/^/"/; s/$/\\\\\\n"\\/p
+b cont
+' <confdefs.h | sed '
+s/'"$ac_delim"'/"\\\
+"/g' >>$CONFIG_STATUS || ac_write_fail=1
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ for (key in D) D_is_set[key] = 1
+ FS = ""
+}
+/^[\t ]*#[\t ]*(define|undef)[\t ]+$ac_word_re([\t (]|\$)/ {
+ line = \$ 0
+ split(line, arg, " ")
+ if (arg[1] == "#") {
+ defundef = arg[2]
+ mac1 = arg[3]
+ } else {
+ defundef = substr(arg[1], 2)
+ mac1 = arg[2]
+ }
+ split(mac1, mac2, "(") #)
+ macro = mac2[1]
+ prefix = substr(line, 1, index(line, defundef) - 1)
+ if (D_is_set[macro]) {
+ # Preserve the white space surrounding the "#".
+ print prefix "define", macro P[macro] D[macro]
+ next
+ } else {
+ # Replace #undef with comments. This is necessary, for example,
+ # in the case of _POSIX_SOURCE, which is predefined and required
+ # on some systems where configure will not decide to define it.
+ if (defundef == "undef") {
+ print "/*", prefix defundef, macro, "*/"
+ next
+ }
+ }
+}
+{ print }
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+ as_fn_error $? "could not setup config headers machinery" "$LINENO" 5
+fi # test -n "$CONFIG_HEADERS"
+
+
+eval set X " :F $CONFIG_FILES :H $CONFIG_HEADERS :C $CONFIG_COMMANDS"
+shift
+for ac_tag
+do
+ case $ac_tag in
+ :[FHLC]) ac_mode=$ac_tag; continue;;
+ esac
+ case $ac_mode$ac_tag in
+ :[FHL]*:*);;
+ :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5 ;;
+ :[FH]-) ac_tag=-:-;;
+ :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
+ esac
+ ac_save_IFS=$IFS
+ IFS=:
+ set x $ac_tag
+ IFS=$ac_save_IFS
+ shift
+ ac_file=$1
+ shift
+
+ case $ac_mode in
+ :L) ac_source=$1;;
+ :[FH])
+ ac_file_inputs=
+ for ac_f
+ do
+ case $ac_f in
+ -) ac_f="$tmp/stdin";;
+ *) # Look for the file first in the build tree, then in the source tree
+ # (if the path is not absolute). The absolute path cannot be DOS-style,
+ # because $ac_f cannot contain `:'.
+ test -f "$ac_f" ||
+ case $ac_f in
+ [\\/$]*) false;;
+ *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
+ esac ||
+ as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5 ;;
+ esac
+ case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
+ as_fn_append ac_file_inputs " '$ac_f'"
+ done
+
+ # Let's still pretend it is `configure' which instantiates (i.e., don't
+ # use $as_me), people would be surprised to read:
+ # /* config.h. Generated by config.status. */
+ configure_input='Generated from '`
+ $as_echo "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g'
+ `' by configure.'
+ if test x"$ac_file" != x-; then
+ configure_input="$ac_file. $configure_input"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5
+$as_echo "$as_me: creating $ac_file" >&6;}
+ fi
+ # Neutralize special characters interpreted by sed in replacement strings.
+ case $configure_input in #(
+ *\&* | *\|* | *\\* )
+ ac_sed_conf_input=`$as_echo "$configure_input" |
+ sed 's/[\\\\&|]/\\\\&/g'`;; #(
+ *) ac_sed_conf_input=$configure_input;;
+ esac
+
+ case $ac_tag in
+ *:-:* | *:-) cat >"$tmp/stdin" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;;
+ esac
+ ;;
+ esac
+
+ ac_dir=`$as_dirname -- "$ac_file" ||
+$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$ac_file" : 'X\(//\)[^/]' \| \
+ X"$ac_file" : 'X\(//\)$' \| \
+ X"$ac_file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$ac_file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir="$ac_dir"; as_fn_mkdir_p
+ ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+ ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
+ # A ".." for each directory in $ac_dir_suffix.
+ ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
+ case $ac_top_builddir_sub in
+ "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+ *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+ esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+ .) # We are building in place.
+ ac_srcdir=.
+ ac_top_srcdir=$ac_top_builddir_sub
+ ac_abs_top_srcdir=$ac_pwd ;;
+ [\\/]* | ?:[\\/]* ) # Absolute name.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir
+ ac_abs_top_srcdir=$srcdir ;;
+ *) # Relative name.
+ ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_build_prefix$srcdir
+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+
+ case $ac_mode in
+ :F)
+ #
+ # CONFIG_FILE
+ #
+
+ case $INSTALL in
+ [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;;
+ *) ac_INSTALL=$ac_top_build_prefix$INSTALL ;;
+ esac
+ ac_MKDIR_P=$MKDIR_P
+ case $MKDIR_P in
+ [\\/$]* | ?:[\\/]* ) ;;
+ */*) ac_MKDIR_P=$ac_top_build_prefix$MKDIR_P ;;
+ esac
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# If the template does not know about datarootdir, expand it.
+# FIXME: This hack should be removed a few years after 2.60.
+ac_datarootdir_hack=; ac_datarootdir_seen=
+ac_sed_dataroot='
+/datarootdir/ {
+ p
+ q
+}
+/@datadir@/p
+/@docdir@/p
+/@infodir@/p
+/@localedir@/p
+/@mandir@/p'
+case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
+*datarootdir*) ac_datarootdir_seen=yes;;
+*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
+$as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ ac_datarootdir_hack='
+ s&@datadir@&$datadir&g
+ s&@docdir@&$docdir&g
+ s&@infodir@&$infodir&g
+ s&@localedir@&$localedir&g
+ s&@mandir@&$mandir&g
+ s&\\\${datarootdir}&$datarootdir&g' ;;
+esac
+_ACEOF
+
+# Neutralize VPATH when `$srcdir' = `.'.
+# Shell code in configure.ac might set extrasub.
+# FIXME: do we really want to maintain this feature?
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_sed_extra="$ac_vpsub
+$extrasub
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+:t
+/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
+s|@configure_input@|$ac_sed_conf_input|;t t
+s&@top_builddir@&$ac_top_builddir_sub&;t t
+s&@top_build_prefix@&$ac_top_build_prefix&;t t
+s&@srcdir@&$ac_srcdir&;t t
+s&@abs_srcdir@&$ac_abs_srcdir&;t t
+s&@top_srcdir@&$ac_top_srcdir&;t t
+s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t
+s&@builddir@&$ac_builddir&;t t
+s&@abs_builddir@&$ac_abs_builddir&;t t
+s&@abs_top_builddir@&$ac_abs_top_builddir&;t t
+s&@INSTALL@&$ac_INSTALL&;t t
+s&@MKDIR_P@&$ac_MKDIR_P&;t t
+$ac_datarootdir_hack
+"
+eval sed \"\$ac_sed_extra\" "$ac_file_inputs" |
+if $ac_cs_awk_getline; then
+ $AWK -f "$tmp/subs.awk"
+else
+ $AWK -f "$tmp/subs.awk" | $SHELL
+fi >$tmp/out \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+
+test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
+ { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } &&
+ { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } &&
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&5
+$as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&2;}
+
+ rm -f "$tmp/stdin"
+ case $ac_file in
+ -) cat "$tmp/out" && rm -f "$tmp/out";;
+ *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";;
+ esac \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ ;;
+ :H)
+ #
+ # CONFIG_HEADER
+ #
+ if test x"$ac_file" != x-; then
+ {
+ $as_echo "/* $configure_input */" \
+ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs"
+ } >"$tmp/config.h" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5
+$as_echo "$as_me: $ac_file is unchanged" >&6;}
+ else
+ rm -f "$ac_file"
+ mv "$tmp/config.h" "$ac_file" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ fi
+ else
+ $as_echo "/* $configure_input */" \
+ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \
+ || as_fn_error $? "could not create -" "$LINENO" 5
+ fi
+# Compute "$ac_file"'s index in $config_headers.
+_am_arg="$ac_file"
+_am_stamp_count=1
+for _am_header in $config_headers :; do
+ case $_am_header in
+ $_am_arg | $_am_arg:* )
+ break ;;
+ * )
+ _am_stamp_count=`expr $_am_stamp_count + 1` ;;
+ esac
+done
+echo "timestamp for $_am_arg" >`$as_dirname -- "$_am_arg" ||
+$as_expr X"$_am_arg" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$_am_arg" : 'X\(//\)[^/]' \| \
+ X"$_am_arg" : 'X\(//\)$' \| \
+ X"$_am_arg" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$_am_arg" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`/stamp-h$_am_stamp_count
+ ;;
+
+ :C) { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5
+$as_echo "$as_me: executing $ac_file commands" >&6;}
+ ;;
+ esac
+
+
+ case $ac_file$ac_mode in
+ "depfiles":C) test x"$AMDEP_TRUE" != x"" || {
+ # Autoconf 2.62 quotes --file arguments for eval, but not when files
+ # are listed without --file. Let's play safe and only enable the eval
+ # if we detect the quoting.
+ case $CONFIG_FILES in
+ *\'*) eval set x "$CONFIG_FILES" ;;
+ *) set x $CONFIG_FILES ;;
+ esac
+ shift
+ for mf
+ do
+ # Strip MF so we end up with the name of the file.
+ mf=`echo "$mf" | sed -e 's/:.*$//'`
+ # Check whether this is an Automake generated Makefile or not.
+ # We used to match only the files named `Makefile.in', but
+ # some people rename them; so instead we look at the file content.
+ # Grep'ing the first line is not enough: some people post-process
+ # each Makefile.in and add a new line on top of each file to say so.
+ # Grep'ing the whole file is not good either: AIX grep has a line
+ # limit of 2048, but all sed's we know have understand at least 4000.
+ if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
+ dirpart=`$as_dirname -- "$mf" ||
+$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$mf" : 'X\(//\)[^/]' \| \
+ X"$mf" : 'X\(//\)$' \| \
+ X"$mf" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$mf" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ else
+ continue
+ fi
+ # Extract the definition of DEPDIR, am__include, and am__quote
+ # from the Makefile without running `make'.
+ DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+ test -z "$DEPDIR" && continue
+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
+ test -z "am__include" && continue
+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # When using ansi2knr, U may be empty or an underscore; expand it
+ U=`sed -n 's/^U = //p' < "$mf"`
+ # Find all dependency output files, they are included files with
+ # $(DEPDIR) in their names. We invoke sed twice because it is the
+ # simplest approach to changing $(DEPDIR) to its actual value in the
+ # expansion.
+ for file in `sed -n "
+ s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+ # Make sure the directory exists.
+ test -f "$dirpart/$file" && continue
+ fdir=`$as_dirname -- "$file" ||
+$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$file" : 'X\(//\)[^/]' \| \
+ X"$file" : 'X\(//\)$' \| \
+ X"$file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir=$dirpart/$fdir; as_fn_mkdir_p
+ # echo "creating $dirpart/$file"
+ echo '# dummy' > "$dirpart/$file"
+ done
+ done
+}
+ ;;
+ "libtool":C)
+
+ # See if we are running on zsh, and set the options which allow our
+ # commands through without removal of \ escapes.
+ if test -n "${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+ fi
+
+ cfgfile="${ofile}T"
+ trap "$RM \"$cfgfile\"; exit 1" 1 2 15
+ $RM "$cfgfile"
+
+ cat <<_LT_EOF >> "$cfgfile"
+#! $SHELL
+
+# `$ECHO "$ofile" | sed 's%^.*/%%'` - Provide generalized library-building support services.
+# Generated automatically by $as_me ($PACKAGE$TIMESTAMP) $VERSION
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+# NOTE: Changes made to this file will be lost: look at ltmain.sh.
+#
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
+# 2006, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gordon Matzigkeit, 1996
+#
+# This file is part of GNU Libtool.
+#
+# GNU Libtool is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License as
+# published by the Free Software Foundation; either version 2 of
+# the License, or (at your option) any later version.
+#
+# As a special exception to the GNU General Public License,
+# if you distribute this file as part of a program or library that
+# is built using GNU Libtool, you may include this file under the
+# same distribution terms that you use for the rest of that program.
+#
+# GNU Libtool is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GNU Libtool; see the file COPYING. If not, a copy
+# can be downloaded from http://www.gnu.org/licenses/gpl.html, or
+# obtained by writing to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+
+# The names of the tagged configurations supported by this script.
+available_tags="CXX "
+
+# ### BEGIN LIBTOOL CONFIG
+
+# Which release of libtool.m4 was used?
+macro_version=$macro_version
+macro_revision=$macro_revision
+
+# Whether or not to build shared libraries.
+build_libtool_libs=$enable_shared
+
+# Whether or not to build static libraries.
+build_old_libs=$enable_static
+
+# What type of objects to build.
+pic_mode=$pic_mode
+
+# Whether or not to optimize for fast installation.
+fast_install=$enable_fast_install
+
+# The host system.
+host_alias=$host_alias
+host=$host
+host_os=$host_os
+
+# The build system.
+build_alias=$build_alias
+build=$build
+build_os=$build_os
+
+# A sed program that does not truncate output.
+SED=$lt_SED
+
+# Sed that helps us avoid accidentally triggering echo(1) options like -n.
+Xsed="\$SED -e 1s/^X//"
+
+# A grep program that handles long lines.
+GREP=$lt_GREP
+
+# An ERE matcher.
+EGREP=$lt_EGREP
+
+# A literal string matcher.
+FGREP=$lt_FGREP
+
+# A BSD- or MS-compatible name lister.
+NM=$lt_NM
+
+# Whether we need soft or hard links.
+LN_S=$lt_LN_S
+
+# What is the maximum length of a command?
+max_cmd_len=$max_cmd_len
+
+# Object file suffix (normally "o").
+objext=$ac_objext
+
+# Executable file suffix (normally "").
+exeext=$exeext
+
+# whether the shell understands "unset".
+lt_unset=$lt_unset
+
+# turn spaces into newlines.
+SP2NL=$lt_lt_SP2NL
+
+# turn newlines into spaces.
+NL2SP=$lt_lt_NL2SP
+
+# How to create reloadable object files.
+reload_flag=$lt_reload_flag
+reload_cmds=$lt_reload_cmds
+
+# An object symbol dumper.
+OBJDUMP=$lt_OBJDUMP
+
+# Method to check whether dependent libraries are shared objects.
+deplibs_check_method=$lt_deplibs_check_method
+
+# Command to use when deplibs_check_method == "file_magic".
+file_magic_cmd=$lt_file_magic_cmd
+
+# The archiver.
+AR=$lt_AR
+AR_FLAGS=$lt_AR_FLAGS
+
+# A symbol stripping program.
+STRIP=$lt_STRIP
+
+# Commands used to install an old-style archive.
+RANLIB=$lt_RANLIB
+old_postinstall_cmds=$lt_old_postinstall_cmds
+old_postuninstall_cmds=$lt_old_postuninstall_cmds
+
+# A C compiler.
+LTCC=$lt_CC
+
+# LTCC compiler flags.
+LTCFLAGS=$lt_CFLAGS
+
+# Take the output of nm and produce a listing of raw symbols and C names.
+global_symbol_pipe=$lt_lt_cv_sys_global_symbol_pipe
+
+# Transform the output of nm in a proper C declaration.
+global_symbol_to_cdecl=$lt_lt_cv_sys_global_symbol_to_cdecl
+
+# Transform the output of nm in a C name address pair.
+global_symbol_to_c_name_address=$lt_lt_cv_sys_global_symbol_to_c_name_address
+
+# Transform the output of nm in a C name address pair when lib prefix is needed.
+global_symbol_to_c_name_address_lib_prefix=$lt_lt_cv_sys_global_symbol_to_c_name_address_lib_prefix
+
+# The name of the directory that contains temporary libtool files.
+objdir=$objdir
+
+# Shell to use when invoking shell scripts.
+SHELL=$lt_SHELL
+
+# An echo program that does not interpret backslashes.
+ECHO=$lt_ECHO
+
+# Used to examine libraries when file_magic_cmd begins with "file".
+MAGIC_CMD=$MAGIC_CMD
+
+# Must we lock files when doing compilation?
+need_locks=$lt_need_locks
+
+# Tool to manipulate archived DWARF debug symbol files on Mac OS X.
+DSYMUTIL=$lt_DSYMUTIL
+
+# Tool to change global to local symbols on Mac OS X.
+NMEDIT=$lt_NMEDIT
+
+# Tool to manipulate fat objects and archives on Mac OS X.
+LIPO=$lt_LIPO
+
+# ldd/readelf like tool for Mach-O binaries on Mac OS X.
+OTOOL=$lt_OTOOL
+
+# ldd/readelf like tool for 64 bit Mach-O binaries on Mac OS X 10.4.
+OTOOL64=$lt_OTOOL64
+
+# Old archive suffix (normally "a").
+libext=$libext
+
+# Shared library suffix (normally ".so").
+shrext_cmds=$lt_shrext_cmds
+
+# The commands to extract the exported symbol list from a shared archive.
+extract_expsyms_cmds=$lt_extract_expsyms_cmds
+
+# Variables whose values should be saved in libtool wrapper scripts and
+# restored at link time.
+variables_saved_for_relink=$lt_variables_saved_for_relink
+
+# Do we need the "lib" prefix for modules?
+need_lib_prefix=$need_lib_prefix
+
+# Do we need a version for libraries?
+need_version=$need_version
+
+# Library versioning type.
+version_type=$version_type
+
+# Shared library runtime path variable.
+runpath_var=$runpath_var
+
+# Shared library path variable.
+shlibpath_var=$shlibpath_var
+
+# Is shlibpath searched before the hard-coded library search path?
+shlibpath_overrides_runpath=$shlibpath_overrides_runpath
+
+# Format of library name prefix.
+libname_spec=$lt_libname_spec
+
+# List of archive names. First name is the real one, the rest are links.
+# The last name is the one that the linker finds with -lNAME
+library_names_spec=$lt_library_names_spec
+
+# The coded name of the library, if different from the real name.
+soname_spec=$lt_soname_spec
+
+# Command to use after installation of a shared archive.
+postinstall_cmds=$lt_postinstall_cmds
+
+# Command to use after uninstallation of a shared archive.
+postuninstall_cmds=$lt_postuninstall_cmds
+
+# Commands used to finish a libtool library installation in a directory.
+finish_cmds=$lt_finish_cmds
+
+# As "finish_cmds", except a single script fragment to be evaled but
+# not shown.
+finish_eval=$lt_finish_eval
+
+# Whether we should hardcode library paths into libraries.
+hardcode_into_libs=$hardcode_into_libs
+
+# Compile-time system search path for libraries.
+sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+
+# Run-time system search path for libraries.
+sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec
+
+# Whether dlopen is supported.
+dlopen_support=$enable_dlopen
+
+# Whether dlopen of programs is supported.
+dlopen_self=$enable_dlopen_self
+
+# Whether dlopen of statically linked programs is supported.
+dlopen_self_static=$enable_dlopen_self_static
+
+# Commands to strip libraries.
+old_striplib=$lt_old_striplib
+striplib=$lt_striplib
+
+
+# The linker used to build libraries.
+LD=$lt_LD
+
+# Commands used to build an old-style archive.
+old_archive_cmds=$lt_old_archive_cmds
+
+# A language specific compiler.
+CC=$lt_compiler
+
+# Is the compiler the GNU compiler?
+with_gcc=$GCC
+
+# Compiler flag to turn off builtin functions.
+no_builtin_flag=$lt_lt_prog_compiler_no_builtin_flag
+
+# How to pass a linker flag through the compiler.
+wl=$lt_lt_prog_compiler_wl
+
+# Additional compiler flags for building library objects.
+pic_flag=$lt_lt_prog_compiler_pic
+
+# Compiler flag to prevent dynamic linking.
+link_static_flag=$lt_lt_prog_compiler_static
+
+# Does compiler simultaneously support -c and -o options?
+compiler_c_o=$lt_lt_cv_prog_compiler_c_o
+
+# Whether or not to add -lc for building shared libraries.
+build_libtool_need_lc=$archive_cmds_need_lc
+
+# Whether or not to disallow shared libs when runtime libs are static.
+allow_libtool_libs_with_static_runtimes=$enable_shared_with_static_runtimes
+
+# Compiler flag to allow reflexive dlopens.
+export_dynamic_flag_spec=$lt_export_dynamic_flag_spec
+
+# Compiler flag to generate shared objects directly from archives.
+whole_archive_flag_spec=$lt_whole_archive_flag_spec
+
+# Whether the compiler copes with passing no objects directly.
+compiler_needs_object=$lt_compiler_needs_object
+
+# Create an old-style archive from a shared archive.
+old_archive_from_new_cmds=$lt_old_archive_from_new_cmds
+
+# Create a temporary old-style archive to link instead of a shared archive.
+old_archive_from_expsyms_cmds=$lt_old_archive_from_expsyms_cmds
+
+# Commands used to build a shared archive.
+archive_cmds=$lt_archive_cmds
+archive_expsym_cmds=$lt_archive_expsym_cmds
+
+# Commands used to build a loadable module if different from building
+# a shared archive.
+module_cmds=$lt_module_cmds
+module_expsym_cmds=$lt_module_expsym_cmds
+
+# Whether we are building with GNU ld or not.
+with_gnu_ld=$lt_with_gnu_ld
+
+# Flag that allows shared libraries with undefined symbols to be built.
+allow_undefined_flag=$lt_allow_undefined_flag
+
+# Flag that enforces no undefined symbols.
+no_undefined_flag=$lt_no_undefined_flag
+
+# Flag to hardcode \$libdir into a binary during linking.
+# This must work even if \$libdir does not exist
+hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec
+
+# If ld is used when linking, flag to hardcode \$libdir into a binary
+# during linking. This must work even if \$libdir does not exist.
+hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld
+
+# Whether we need a single "-rpath" flag with a separated argument.
+hardcode_libdir_separator=$lt_hardcode_libdir_separator
+
+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes
+# DIR into the resulting binary.
+hardcode_direct=$hardcode_direct
+
+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes
+# DIR into the resulting binary and the resulting library dependency is
+# "absolute",i.e impossible to change by setting \${shlibpath_var} if the
+# library is relocated.
+hardcode_direct_absolute=$hardcode_direct_absolute
+
+# Set to "yes" if using the -LDIR flag during linking hardcodes DIR
+# into the resulting binary.
+hardcode_minus_L=$hardcode_minus_L
+
+# Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR
+# into the resulting binary.
+hardcode_shlibpath_var=$hardcode_shlibpath_var
+
+# Set to "yes" if building a shared library automatically hardcodes DIR
+# into the library and all subsequent libraries and executables linked
+# against it.
+hardcode_automatic=$hardcode_automatic
+
+# Set to yes if linker adds runtime paths of dependent libraries
+# to runtime path list.
+inherit_rpath=$inherit_rpath
+
+# Whether libtool must link a program against all its dependency libraries.
+link_all_deplibs=$link_all_deplibs
+
+# Fix the shell variable \$srcfile for the compiler.
+fix_srcfile_path=$lt_fix_srcfile_path
+
+# Set to "yes" if exported symbols are required.
+always_export_symbols=$always_export_symbols
+
+# The commands to list exported symbols.
+export_symbols_cmds=$lt_export_symbols_cmds
+
+# Symbols that should not be listed in the preloaded symbols.
+exclude_expsyms=$lt_exclude_expsyms
+
+# Symbols that must always be exported.
+include_expsyms=$lt_include_expsyms
+
+# Commands necessary for linking programs (against libraries) with templates.
+prelink_cmds=$lt_prelink_cmds
+
+# Specify filename containing input files.
+file_list_spec=$lt_file_list_spec
+
+# How to hardcode a shared library path into an executable.
+hardcode_action=$hardcode_action
+
+# The directories searched by this compiler when creating a shared library.
+compiler_lib_search_dirs=$lt_compiler_lib_search_dirs
+
+# Dependencies to place before and after the objects being linked to
+# create a shared library.
+predep_objects=$lt_predep_objects
+postdep_objects=$lt_postdep_objects
+predeps=$lt_predeps
+postdeps=$lt_postdeps
+
+# The library search path used internally by the compiler when linking
+# a shared library.
+compiler_lib_search_path=$lt_compiler_lib_search_path
+
+# ### END LIBTOOL CONFIG
+
+_LT_EOF
+
+ case $host_os in
+ aix3*)
+ cat <<\_LT_EOF >> "$cfgfile"
+# AIX sometimes has problems with the GCC collect2 program. For some
+# reason, if we set the COLLECT_NAMES environment variable, the problems
+# vanish in a puff of smoke.
+if test "X${COLLECT_NAMES+set}" != Xset; then
+ COLLECT_NAMES=
+ export COLLECT_NAMES
+fi
+_LT_EOF
+ ;;
+ esac
+
+
+ltmain="$ac_aux_dir/ltmain.sh"
+
+
+ # We use sed instead of cat because bash on DJGPP gets confused if
+ # if finds mixed CR/LF and LF-only lines. Since sed operates in
+ # text mode, it properly converts lines to CR/LF. This bash problem
+ # is reportedly fixed, but why not run on old versions too?
+ sed '/^# Generated shell functions inserted here/q' "$ltmain" >> "$cfgfile" \
+ || (rm -f "$cfgfile"; exit 1)
+
+ case $xsi_shell in
+ yes)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_dirname file append nondir_replacement
+# Compute the dirname of FILE. If nonempty, add APPEND to the result,
+# otherwise set result to NONDIR_REPLACEMENT.
+func_dirname ()
+{
+ case ${1} in
+ */*) func_dirname_result="${1%/*}${2}" ;;
+ * ) func_dirname_result="${3}" ;;
+ esac
+}
+
+# func_basename file
+func_basename ()
+{
+ func_basename_result="${1##*/}"
+}
+
+# func_dirname_and_basename file append nondir_replacement
+# perform func_basename and func_dirname in a single function
+# call:
+# dirname: Compute the dirname of FILE. If nonempty,
+# add APPEND to the result, otherwise set result
+# to NONDIR_REPLACEMENT.
+# value returned in "$func_dirname_result"
+# basename: Compute filename of FILE.
+# value retuned in "$func_basename_result"
+# Implementation must be kept synchronized with func_dirname
+# and func_basename. For efficiency, we do not delegate to
+# those functions but instead duplicate the functionality here.
+func_dirname_and_basename ()
+{
+ case ${1} in
+ */*) func_dirname_result="${1%/*}${2}" ;;
+ * ) func_dirname_result="${3}" ;;
+ esac
+ func_basename_result="${1##*/}"
+}
+
+# func_stripname prefix suffix name
+# strip PREFIX and SUFFIX off of NAME.
+# PREFIX and SUFFIX must not contain globbing or regex special
+# characters, hashes, percent signs, but SUFFIX may contain a leading
+# dot (in which case that matches only a dot).
+func_stripname ()
+{
+ # pdksh 5.2.14 does not do ${X%$Y} correctly if both X and Y are
+ # positional parameters, so assign one to ordinary parameter first.
+ func_stripname_result=${3}
+ func_stripname_result=${func_stripname_result#"${1}"}
+ func_stripname_result=${func_stripname_result%"${2}"}
+}
+
+# func_opt_split
+func_opt_split ()
+{
+ func_opt_split_opt=${1%%=*}
+ func_opt_split_arg=${1#*=}
+}
+
+# func_lo2o object
+func_lo2o ()
+{
+ case ${1} in
+ *.lo) func_lo2o_result=${1%.lo}.${objext} ;;
+ *) func_lo2o_result=${1} ;;
+ esac
+}
+
+# func_xform libobj-or-source
+func_xform ()
+{
+ func_xform_result=${1%.*}.lo
+}
+
+# func_arith arithmetic-term...
+func_arith ()
+{
+ func_arith_result=$(( $* ))
+}
+
+# func_len string
+# STRING may not start with a hyphen.
+func_len ()
+{
+ func_len_result=${#1}
+}
+
+_LT_EOF
+ ;;
+ *) # Bourne compatible functions.
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_dirname file append nondir_replacement
+# Compute the dirname of FILE. If nonempty, add APPEND to the result,
+# otherwise set result to NONDIR_REPLACEMENT.
+func_dirname ()
+{
+ # Extract subdirectory from the argument.
+ func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"`
+ if test "X$func_dirname_result" = "X${1}"; then
+ func_dirname_result="${3}"
+ else
+ func_dirname_result="$func_dirname_result${2}"
+ fi
+}
+
+# func_basename file
+func_basename ()
+{
+ func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"`
+}
+
+
+# func_stripname prefix suffix name
+# strip PREFIX and SUFFIX off of NAME.
+# PREFIX and SUFFIX must not contain globbing or regex special
+# characters, hashes, percent signs, but SUFFIX may contain a leading
+# dot (in which case that matches only a dot).
+# func_strip_suffix prefix name
+func_stripname ()
+{
+ case ${2} in
+ .*) func_stripname_result=`$ECHO "X${3}" \
+ | $Xsed -e "s%^${1}%%" -e "s%\\\\${2}\$%%"`;;
+ *) func_stripname_result=`$ECHO "X${3}" \
+ | $Xsed -e "s%^${1}%%" -e "s%${2}\$%%"`;;
+ esac
+}
+
+# sed scripts:
+my_sed_long_opt='1s/^\(-[^=]*\)=.*/\1/;q'
+my_sed_long_arg='1s/^-[^=]*=//'
+
+# func_opt_split
+func_opt_split ()
+{
+ func_opt_split_opt=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_opt"`
+ func_opt_split_arg=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_arg"`
+}
+
+# func_lo2o object
+func_lo2o ()
+{
+ func_lo2o_result=`$ECHO "X${1}" | $Xsed -e "$lo2o"`
+}
+
+# func_xform libobj-or-source
+func_xform ()
+{
+ func_xform_result=`$ECHO "X${1}" | $Xsed -e 's/\.[^.]*$/.lo/'`
+}
+
+# func_arith arithmetic-term...
+func_arith ()
+{
+ func_arith_result=`expr "$@"`
+}
+
+# func_len string
+# STRING may not start with a hyphen.
+func_len ()
+{
+ func_len_result=`expr "$1" : ".*" 2>/dev/null || echo $max_cmd_len`
+}
+
+_LT_EOF
+esac
+
+case $lt_shell_append in
+ yes)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$1+=\$2"
+}
+_LT_EOF
+ ;;
+ *)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$1=\$$1\$2"
+}
+
+_LT_EOF
+ ;;
+ esac
+
+
+ sed -n '/^# Generated shell functions inserted here/,$p' "$ltmain" >> "$cfgfile" \
+ || (rm -f "$cfgfile"; exit 1)
+
+ mv -f "$cfgfile" "$ofile" ||
+ (rm -f "$ofile" && cp "$cfgfile" "$ofile" && rm -f "$cfgfile")
+ chmod +x "$ofile"
+
+
+ cat <<_LT_EOF >> "$ofile"
+
+# ### BEGIN LIBTOOL TAG CONFIG: CXX
+
+# The linker used to build libraries.
+LD=$lt_LD_CXX
+
+# Commands used to build an old-style archive.
+old_archive_cmds=$lt_old_archive_cmds_CXX
+
+# A language specific compiler.
+CC=$lt_compiler_CXX
+
+# Is the compiler the GNU compiler?
+with_gcc=$GCC_CXX
+
+# Compiler flag to turn off builtin functions.
+no_builtin_flag=$lt_lt_prog_compiler_no_builtin_flag_CXX
+
+# How to pass a linker flag through the compiler.
+wl=$lt_lt_prog_compiler_wl_CXX
+
+# Additional compiler flags for building library objects.
+pic_flag=$lt_lt_prog_compiler_pic_CXX
+
+# Compiler flag to prevent dynamic linking.
+link_static_flag=$lt_lt_prog_compiler_static_CXX
+
+# Does compiler simultaneously support -c and -o options?
+compiler_c_o=$lt_lt_cv_prog_compiler_c_o_CXX
+
+# Whether or not to add -lc for building shared libraries.
+build_libtool_need_lc=$archive_cmds_need_lc_CXX
+
+# Whether or not to disallow shared libs when runtime libs are static.
+allow_libtool_libs_with_static_runtimes=$enable_shared_with_static_runtimes_CXX
+
+# Compiler flag to allow reflexive dlopens.
+export_dynamic_flag_spec=$lt_export_dynamic_flag_spec_CXX
+
+# Compiler flag to generate shared objects directly from archives.
+whole_archive_flag_spec=$lt_whole_archive_flag_spec_CXX
+
+# Whether the compiler copes with passing no objects directly.
+compiler_needs_object=$lt_compiler_needs_object_CXX
+
+# Create an old-style archive from a shared archive.
+old_archive_from_new_cmds=$lt_old_archive_from_new_cmds_CXX
+
+# Create a temporary old-style archive to link instead of a shared archive.
+old_archive_from_expsyms_cmds=$lt_old_archive_from_expsyms_cmds_CXX
+
+# Commands used to build a shared archive.
+archive_cmds=$lt_archive_cmds_CXX
+archive_expsym_cmds=$lt_archive_expsym_cmds_CXX
+
+# Commands used to build a loadable module if different from building
+# a shared archive.
+module_cmds=$lt_module_cmds_CXX
+module_expsym_cmds=$lt_module_expsym_cmds_CXX
+
+# Whether we are building with GNU ld or not.
+with_gnu_ld=$lt_with_gnu_ld_CXX
+
+# Flag that allows shared libraries with undefined symbols to be built.
+allow_undefined_flag=$lt_allow_undefined_flag_CXX
+
+# Flag that enforces no undefined symbols.
+no_undefined_flag=$lt_no_undefined_flag_CXX
+
+# Flag to hardcode \$libdir into a binary during linking.
+# This must work even if \$libdir does not exist
+hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec_CXX
+
+# If ld is used when linking, flag to hardcode \$libdir into a binary
+# during linking. This must work even if \$libdir does not exist.
+hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld_CXX
+
+# Whether we need a single "-rpath" flag with a separated argument.
+hardcode_libdir_separator=$lt_hardcode_libdir_separator_CXX
+
+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes
+# DIR into the resulting binary.
+hardcode_direct=$hardcode_direct_CXX
+
+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes
+# DIR into the resulting binary and the resulting library dependency is
+# "absolute",i.e impossible to change by setting \${shlibpath_var} if the
+# library is relocated.
+hardcode_direct_absolute=$hardcode_direct_absolute_CXX
+
+# Set to "yes" if using the -LDIR flag during linking hardcodes DIR
+# into the resulting binary.
+hardcode_minus_L=$hardcode_minus_L_CXX
+
+# Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR
+# into the resulting binary.
+hardcode_shlibpath_var=$hardcode_shlibpath_var_CXX
+
+# Set to "yes" if building a shared library automatically hardcodes DIR
+# into the library and all subsequent libraries and executables linked
+# against it.
+hardcode_automatic=$hardcode_automatic_CXX
+
+# Set to yes if linker adds runtime paths of dependent libraries
+# to runtime path list.
+inherit_rpath=$inherit_rpath_CXX
+
+# Whether libtool must link a program against all its dependency libraries.
+link_all_deplibs=$link_all_deplibs_CXX
+
+# Fix the shell variable \$srcfile for the compiler.
+fix_srcfile_path=$lt_fix_srcfile_path_CXX
+
+# Set to "yes" if exported symbols are required.
+always_export_symbols=$always_export_symbols_CXX
+
+# The commands to list exported symbols.
+export_symbols_cmds=$lt_export_symbols_cmds_CXX
+
+# Symbols that should not be listed in the preloaded symbols.
+exclude_expsyms=$lt_exclude_expsyms_CXX
+
+# Symbols that must always be exported.
+include_expsyms=$lt_include_expsyms_CXX
+
+# Commands necessary for linking programs (against libraries) with templates.
+prelink_cmds=$lt_prelink_cmds_CXX
+
+# Specify filename containing input files.
+file_list_spec=$lt_file_list_spec_CXX
+
+# How to hardcode a shared library path into an executable.
+hardcode_action=$hardcode_action_CXX
+
+# The directories searched by this compiler when creating a shared library.
+compiler_lib_search_dirs=$lt_compiler_lib_search_dirs_CXX
+
+# Dependencies to place before and after the objects being linked to
+# create a shared library.
+predep_objects=$lt_predep_objects_CXX
+postdep_objects=$lt_postdep_objects_CXX
+predeps=$lt_predeps_CXX
+postdeps=$lt_postdeps_CXX
+
+# The library search path used internally by the compiler when linking
+# a shared library.
+compiler_lib_search_path=$lt_compiler_lib_search_path_CXX
+
+# ### END LIBTOOL TAG CONFIG: CXX
+_LT_EOF
+
+ ;;
+ "postinst":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "prerm":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "control":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "libGkArrays.pc":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "Makefile":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "src/Makefile":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "tests/Makefile":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "src/sux/Makefile":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "src/kseq/Makefile":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "doc/Makefile":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "doc/libGkArrays.3":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "doc/package.texi":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+
+ esac
+done # for ac_tag
+
+
+as_fn_exit 0
+_ACEOF
+ac_clean_files=$ac_clean_files_save
+
+test $ac_write_fail = 0 ||
+ as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5
+
+
+# configure is writing to config.log, and then calls config.status.
+# config.status does its own redirection, appending to config.log.
+# Unfortunately, on DOS this fails, as config.log is still kept open
+# by configure, so config.status won't be able to write to it; its
+# output is simply discarded. So we exec the FD to /dev/null,
+# effectively closing config.log, so it can be properly (re)opened and
+# appended to by config.status. When coming back to configure, we
+# need to make the FD available again.
+if test "$no_create" != yes; then
+ ac_cs_success=:
+ ac_config_status_args=
+ test "$silent" = yes &&
+ ac_config_status_args="$ac_config_status_args --quiet"
+ exec 5>/dev/null
+ $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
+ exec 5>>config.log
+ # Use ||, not &&, to avoid exiting from the if with $? = 1, which
+ # would make configure fail if this is the last instruction.
+ $ac_cs_success || as_fn_exit 1
+fi
+
+#
+# CONFIG_SUBDIRS section.
+#
+if test "$no_recursion" != yes; then
+
+ # Remove --cache-file, --srcdir, and --disable-option-checking arguments
+ # so they do not pile up.
+ ac_sub_configure_args=
+ ac_prev=
+ eval "set x $ac_configure_args"
+ shift
+ for ac_arg
+ do
+ if test -n "$ac_prev"; then
+ ac_prev=
+ continue
+ fi
+ case $ac_arg in
+ -cache-file | --cache-file | --cache-fil | --cache-fi \
+ | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)
+ ac_prev=cache_file ;;
+ -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \
+ | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* \
+ | --c=*)
+ ;;
+ --config-cache | -C)
+ ;;
+ -srcdir | --srcdir | --srcdi | --srcd | --src | --sr)
+ ac_prev=srcdir ;;
+ -srcdir=* | --srcdir=* | --srcdi=* | --srcd=* | --src=* | --sr=*)
+ ;;
+ -prefix | --prefix | --prefi | --pref | --pre | --pr | --p)
+ ac_prev=prefix ;;
+ -prefix=* | --prefix=* | --prefi=* | --pref=* | --pre=* | --pr=* | --p=*)
+ ;;
+ --disable-option-checking)
+ ;;
+ *)
+ case $ac_arg in
+ *\'*) ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ as_fn_append ac_sub_configure_args " '$ac_arg'" ;;
+ esac
+ done
+
+ # Always prepend --prefix to ensure using the same prefix
+ # in subdir configurations.
+ ac_arg="--prefix=$prefix"
+ case $ac_arg in
+ *\'*) ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ ac_sub_configure_args="'$ac_arg' $ac_sub_configure_args"
+
+ # Pass --silent
+ if test "$silent" = yes; then
+ ac_sub_configure_args="--silent $ac_sub_configure_args"
+ fi
+
+ # Always prepend --disable-option-checking to silence warnings, since
+ # different subdirs can have different --enable and --with options.
+ ac_sub_configure_args="--disable-option-checking $ac_sub_configure_args"
+
+ ac_popdir=`pwd`
+ for ac_dir in : $subdirs; do test "x$ac_dir" = x: && continue
+
+ # Do not complain, so a configure script can configure whichever
+ # parts of a large source tree are present.
+ test -d "$srcdir/$ac_dir" || continue
+
+ ac_msg="=== configuring in $ac_dir (`pwd`/$ac_dir)"
+ $as_echo "$as_me:${as_lineno-$LINENO}: $ac_msg" >&5
+ $as_echo "$ac_msg" >&6
+ as_dir="$ac_dir"; as_fn_mkdir_p
+ ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+ ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
+ # A ".." for each directory in $ac_dir_suffix.
+ ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
+ case $ac_top_builddir_sub in
+ "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+ *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+ esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+ .) # We are building in place.
+ ac_srcdir=.
+ ac_top_srcdir=$ac_top_builddir_sub
+ ac_abs_top_srcdir=$ac_pwd ;;
+ [\\/]* | ?:[\\/]* ) # Absolute name.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir
+ ac_abs_top_srcdir=$srcdir ;;
+ *) # Relative name.
+ ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_build_prefix$srcdir
+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+
+ cd "$ac_dir"
+
+ # Check for guested configure; otherwise get Cygnus style configure.
+ if test -f "$ac_srcdir/configure.gnu"; then
+ ac_sub_configure=$ac_srcdir/configure.gnu
+ elif test -f "$ac_srcdir/configure"; then
+ ac_sub_configure=$ac_srcdir/configure
+ elif test -f "$ac_srcdir/configure.in"; then
+ # This should be Cygnus configure.
+ ac_sub_configure=$ac_aux_dir/configure
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: no configuration information is in $ac_dir" >&5
+$as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2;}
+ ac_sub_configure=
+ fi
+
+ # The recursion is here.
+ if test -n "$ac_sub_configure"; then
+ # Make the cache file name correct relative to the subdirectory.
+ case $cache_file in
+ [\\/]* | ?:[\\/]* ) ac_sub_cache_file=$cache_file ;;
+ *) # Relative name.
+ ac_sub_cache_file=$ac_top_build_prefix$cache_file ;;
+ esac
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: running $SHELL $ac_sub_configure $ac_sub_configure_args --cache-file=$ac_sub_cache_file --srcdir=$ac_srcdir" >&5
+$as_echo "$as_me: running $SHELL $ac_sub_configure $ac_sub_configure_args --cache-file=$ac_sub_cache_file --srcdir=$ac_srcdir" >&6;}
+ # The eval makes quoting arguments work.
+ eval "\$SHELL \"\$ac_sub_configure\" $ac_sub_configure_args \
+ --cache-file=\"\$ac_sub_cache_file\" --srcdir=\"\$ac_srcdir\"" ||
+ as_fn_error $? "$ac_sub_configure failed for $ac_dir" "$LINENO" 5
+ fi
+
+ cd "$ac_popdir"
+ done
+fi
+if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
+$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
+fi
+
diff --git a/src/libGkArrays/configure.ac b/src/libGkArrays/configure.ac
new file mode 100644
index 0000000..8354f35
--- /dev/null
+++ b/src/libGkArrays/configure.ac
@@ -0,0 +1,356 @@
+dnl Process this file with autoconf to produce a configure script.
+
+dnl Copyright © 2010-2013 -- IRB/INSERM
+dnl (Institut de Recherches en Biothérapie /
+dnl Institut National de la Santé et de la Recherche
+dnl Médicale)
+dnl LIFL/INRIA
+dnl (Laboratoire d'Informatique Fondamentale de
+dnl Lille / Institut National de Recherche en
+dnl Informatique et Automatique)
+dnl LIRMM/CNRS
+dnl (Laboratoire d'Informatique, de Robotique et de
+dnl Microélectronique de Montpellier /
+dnl Centre National de la Recherche Scientifique)
+dnl LITIS
+dnl (Laboratoire d'Informatique, du Traitement de
+dnl l'Information et des Systèmes).
+dnl
+dnl Auteurs/Authors:
+dnl Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+dnl Mikaël SALSON <mikael.salson at lifl.fr>
+dnl Thierry LECROQ <thierry.lecroq at univ-rouen.fr>
+dnl Martine LÉONARD <Martine.Leonard at univ-rouen.fr>
+dnl Éric RIVALS <eric.rivals at lirmm.fr>
+dnl
+dnl Programmeurs
+dnl /Progammers:
+dnl Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+dnl Mikaël SALSON <mikael.salson at lifl.fr>
+dnl with additional contribution for the packaging of:
+dnl Alban MANCHERON <alban.mancheron at lirmm.fr>
+dnl
+dnl Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr>
+dnl -------------------------------------------------------------------------
+dnl
+dnl Ce fichier fait partie de la librairie Gk-arrays.
+dnl
+dnl La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de
+dnl lectures de séquences issues du séquençage haut-débit.
+dnl
+dnl Ce logiciel est régi par la licence CeCILL-C soumise au droit français et
+dnl respectant les principes de diffusion des logiciels libres. Vous pouvez
+dnl utiliser, modifier et/ou redistribuer ce programme sous les conditions de
+dnl la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur
+dnl le site "http://www.cecill.info".
+dnl
+dnl En contrepartie de l'accessibilité au code source et des droits de copie,
+dnl de modification et de redistribution accordés par cette licence, il n'est
+dnl offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons,
+dnl seule une responsabilité restreinte pèse sur l'auteur du programme, le
+dnl titulaire des droits patrimoniaux et les concédants successifs.
+dnl
+dnl À cet égard l'attention de l'utilisateur est attirée sur les risques
+dnl associés au chargement, à l'utilisation, à la modification et/ou au
+dnl développement et à la reproduction du logiciel par l'utilisateur étant
+dnl donné sa spécificité de logiciel libre, qui peut le rendre complexe à
+dnl manipuler et qui le réserve donc à des développeurs et des professionnels
+dnl avertis possédant des connaissances informatiques approfondies. Les
+dnl utilisateurs sont donc invités à charger et tester l'adéquation du
+dnl logiciel à leurs besoins dans des conditions permettant d'assurer la
+dnl sécurité de leurs systêmes et ou de leurs données et, plus généralement,
+dnl à l'utiliser et l'exploiter dans les mêmes conditions de sécurité.
+dnl
+dnl Le fait que vous puissiez accéder à cet en-tête signifie que vous avez
+dnl pris connaissance de la licence CeCILL-C, et que vous en avez accepté les
+dnl termes.
+dnl
+dnl -------------------------------------------------------------------------
+dnl
+dnl This File is part of the Gk-arrays library.
+dnl
+dnl The Gk-arrays library aims at indexing k-factors from a huge set of
+dnl sequencing reads
+dnl
+dnl This software is governed by the CeCILL-C license under French law and
+dnl abiding by the rules of distribution of free software. You can use,
+dnl modify and/ or redistribute the software under the terms of the CeCILL-C
+dnl license as circulated by CEA, CNRS and INRIA at the following URL
+dnl "http://www.cecill.info".
+dnl
+dnl As a counterpart to the access to the source code and rights to copy,
+dnl modify and redistribute granted by the license, users are provided only
+dnl with a limited warranty and the software's author, the holder of the
+dnl economic rights, and the successive licensors have only limited
+dnl liability.
+dnl
+dnl In this respect, the user's attention is drawn to the risks associated
+dnl with loading, using, modifying and/or developing or reproducing the
+dnl software by the user in light of its specific status of free software,
+dnl that may mean that it is complicated to manipulate, and that also
+dnl therefore means that it is reserved for developers and experienced
+dnl professionals having in-depth computer knowledge. Users are therefore
+dnl encouraged to load and test the software's suitability as regards their
+dnl requirements in conditions enabling the security of their systems and/or
+dnl data to be ensured and, more generally, to use and operate it in the same
+dnl conditions as regards security.
+dnl
+dnl The fact that you are presently reading this means that you have had
+dnl knowledge of the CeCILL-C license and that you accept its terms.
+
+dnl $Id: configure.ac 763 2011-07-10 20:48:29Z salson $
+
+AC_PREREQ(2.64)
+
+m4_define([VERSION_MAJOR], [2])
+m4_define([VERSION_MINOR], [1])
+m4_define([VERSION_MICRO], [0])
+
+AC_INIT([libGkArrays],
+ [VERSION_MAJOR.VERSION_MINOR.VERSION_MICRO],
+ [crac-gkarrays at lists.gforge.inria.fr],
+ [libGkArrays],
+ [http://crac.gforge.inria.fr/gkarrays])
+PACKAGE_DESCRIPTION="Library for building and using GkArrays"
+AC_SUBST([PACKAGE_DESCRIPTION])
+
+AC_CONFIG_SRCDIR([src/gkArrays.h])
+AC_REVISION([$Revision: 763 $])
+AC_COPYRIGHT([
+*******************************************************************************
+* *
+* Copyright(C) 2010-2013 --IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+******************************************************************************/
+])
+
+
+dnl The most recent interface number that this library implements.
+LIB_CURRENT=2
+dnl The implementation number of the current interface.
+LIB_REVISION=0
+dnl The difference between the newest and oldest interfaces that this library implements.
+LIB_AGE=1
+dnl LIB_VERSION is not the release number.
+dnl Please read libtool documentation about versionning
+LIB_VERSION=$LIB_CURRENT:$LIB_REVISION:$LIB_AGE
+dnl Ending numbers of library will be $((LIB_CURRENT-LIB_AGE)).$LIB_AGE.$LIB_REVISION
+
+AC_SUBST([VERSION])
+AC_SUBST([LIB_VERSION])
+AC_SUBST([LIB_VERSION_EXT], ["VERSION_MAJOR"_"VERSION_MINOR"_"VERSION_MICRO"])
+
+AS_IF([test x"$CFLAGS" == "x"], [CFLAGS=""])
+AS_IF([test x"$CPPFLAGS" == "x"], [CPPFLAGS=""])
+AS_IF([test x"$CXXFLAGS" == "x"], [CXXFLAGS=""])
+AS_IF([test x"$LDFLAGS" == "x"], [LDFLAGS=""])
+
+AC_CONFIG_AUX_DIR([config])
+dnl create a config.h file (Automake will add -DHAVE_CONFIG_H)
+AC_CONFIG_HEADERS([config/config.h])
+dnl Every other copy of the package version number gets its value from here
+AM_INIT_AUTOMAKE
+
+AC_CONFIG_MACRO_DIR([config/m4])
+
+# Checks for programs.
+AC_PROG_CXX
+AC_PROG_AWK
+AC_PROG_CC
+AC_PROG_CPP
+AC_PROG_INSTALL
+AC_PROG_LN_S
+AC_PROG_MAKE_SET
+AC_CHECK_PROG([TEXI2DVI], [texi2dvi], [texi2dvi])
+AC_CHECK_PROG([PDFTEX], [pdftex], [pdftex])
+AC_CHECK_PROG([KPSEWHICH], [kpsewhich], [kpsewhich])
+BUILD_DOC=false
+AS_IF([test "x$TEXI2DVI" != "xtexi2dvi" || test "x$PDFTEX" != "xpdftex"],
+ [BUILD_DOC=false
+ AC_MSG_WARN([The 'texi2dvi' or 'pdftex' program could not be found. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases.])])
+
+AS_IF([test "x$KPSEWHICH" != "xkpsewhich" || test "$(kpsewhich -show-path=fmt)" == "/nonesuch"],
+ [BUILD_DOC=false
+ AC_MSG_WARN([The 'texi2dvi' or 'pdftex' is missing a correct latex installation. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases.])])
+AM_CONDITIONAL([BUILD_DOC], [$BUILD_DOC])
+
+LT_INIT
+LT_PATH_LD
+
+ISODATE=`date +%Y-%m-%d`
+AC_SUBST([ISODATE])
+
+ARCH=`uname -m | sed s/i.86/i386/ | sed s/x86_64/amd64/`
+AC_SUBST([ARCH])
+
+AC_PATH_PROG([DEB_BUILDER], [dpkg])
+
+dnl Checks for header files.
+AC_CHECK_HEADERS([stdint.h stdlib.h string.h sys/time.h])
+
+# Checks for library functions.
+AC_C_INLINE
+AC_FUNC_MALLOC
+AC_FUNC_REALLOC
+AC_CHECK_FUNCS([gettimeofday memset select])
+AC_HEADER_STDBOOL
+AC_TYPE_SIZE_T
+AC_TYPE_UINT8_T
+AC_TYPE_UINT32_T
+AC_TYPE_UINT64_T
+AC_TYPE_UNSIGNED_LONG_LONG_INT
+dnl AC_CHECK_TYPE([uint],
+dnl [],
+dnl [AC_DEFINE_UNQUOTED([uint], [unsigned int],
+dnl [Define to `unsigned int' if <sys/types.h> does not define.])])
+
+AC_CHECK_LIB([z], [gzread], ,
+ [AC_MSG_ERROR([zlib not found, see http://www.zlib.net])])
+AC_CHECK_LIB([pthread], [pthread_create], ,
+ [AC_MSG_ERROR([pthread library not found])])
+
+
+CPPFLAGS="$CPPFLAGS -Wall -ansi -funroll-loops"
+
+hacked_prefix="${HACKED_PREFIX:-$prefix}"
+if test "x$hacked_prefix" == "xNONE"; then
+ hacked_prefix=$ac_default_prefix
+fi
+AC_SUBST([hacked_prefix])
+
+dnl Additional Scripts for debian packages
+AC_SUBST_FILE([postrm_script])
+postrm_script=$srcdir/postrm
+AC_SUBST_FILE([postinst_script])
+postinst_script=$srcdir/postinst
+
+dnl Add option --enable-debug (default to --disable-debug)
+AC_ARG_ENABLE([debug],
+ [AS_HELP_STRING([--enable-debug],
+ [enable debugging informations])],
+ [DEBUG=1
+ AC_DEFINE([OUTPUT_NB_OCC_FACTORS],[1],[Output the factors' number of occurences])],
+ [DEBUG=0])
+
+AC_ARG_ENABLE([coverage],
+ [AS_HELP_STRING([--enable-coverage],
+ [enable coverage information])],
+ [COVERAGE=1],
+ [COVERAGE=0])
+
+dnl Add option --without-included-ProgressBar (default --with-included-ProgressBar=check)
+AC_ARG_WITH([included-ProgressBar],
+ [AS_HELP_STRING([--without-included-ProgressBar],
+ [don't use the ProgressBar library included here])],
+ [],
+ [with_included_ProgressBar="check"])
+
+dnl Add option --with-libProgressBar-prefix=PATH (default --without-libProgressBar-prefix)
+AC_ARG_WITH([libProgressBar-prefix],
+ [AS_HELP_STRING([--with-libProgressBar-prefix=DIR],
+ [search for libProgressBar in DIR/include/libProgressBar and DIR/lib])],
+ [LDFLAGS="$LDFLAGS -L$with_libProgressBar_prefix/lib"
+ CPPFLAGS="$CPPFLAGS -I$with_libProgressBar_prefix/include/libProgressBar"],
+ [with_libProgressBar_prefix=""])
+
+dnl Check if we need included ProgressBar library.
+PB_OK=0
+AS_IF([test "x$with_included_ProgressBar" == "xcheck"],
+ [AS_IF([test "x$with_libProgressBar_prefix" != "x"],
+ [with_included_ProgressBar="no"],
+ [with_included_ProgressBar="yes"])])
+
+AS_IF([test "x$with_included_ProgressBar" == "xyes"],
+ [AS_IF([test "x$with_libProgressBar_prefix" != "x"],
+ [AC_MSG_FAILURE([You can't use both --with-included-ProgressBar and --with-libProgressBar-prefix options])],
+ [AC_CONFIG_SUBDIRS([src/libProgressBar-1.2.0])
+ PB_OK=1])],
+ [AS_IF([test "x$with_libProgressBar_prefix" != "x"],
+ [PB_OK=1],
+ [AC_CHECK_LIB([ProgressBar],
+ [libProgressBarVersion],
+ [PB_OK=1
+ ProgressBar_LIBS=-lProgressBar])])]) dnl Override the default behavior of AC_CHECK_LIB (we don't want -lProgressBar in LIBS).
+
+AS_IF([test "$PB_OK" == "1"], [AC_DEFINE([HAVE_LIBPROGRESSBAR], [1], [Define to 1 in order to Use libProgressBar])])
+
+dnl Set INCLUDED_PROGRESSBAR conditionnal for automake
+AM_CONDITIONAL([INCLUDED_PROGRESSBAR], [test "x$with_included_ProgressBar" == xyes])
+
+if test $COVERAGE -eq 1 || test $DEBUG -eq 1; then
+ CPPFLAGS="$CPPFLAGS -g -O0"
+ if test $COVERAGE -eq 1; then
+ CPPFLAGS="$CPPFLAGS -fprofile-arcs -ftest-coverage"
+ LDFLAGS="-fprofile-arcs -lgcov"
+ fi
+else
+ CPPFLAGS="$CPPFLAGS -O4 -DNDEBUG"
+fi
+
+LDFLAGS="$LDFLAGS $ProgressBar_LIBS"
+CPPFLAGS="$CPPFLAGS $ProgressBar_CFLAGS"
+
+dnl Output files and make debian scripts executable
+AC_CONFIG_FILES([\
+ postinst prerm control libGkArrays.pc \
+ Makefile src/Makefile tests/Makefile \
+ src/sux/Makefile src/kseq/Makefile \
+ doc/Makefile doc/libGkArrays.3 doc/package.texi \
+], [ \
+ chmod 755 postinst && chmod 755 prerm \
+])
+AC_OUTPUT
diff --git a/src/libGkArrays/control.in b/src/libGkArrays/control.in
new file mode 100644
index 0000000..e7d8b5e
--- /dev/null
+++ b/src/libGkArrays/control.in
@@ -0,0 +1,29 @@
+Package: @PACKAGE@
+Version: @PACKAGE_VERSION@
+Section: libs
+Priority: optional
+Architecture: @ARCH@
+Essential: no
+Depends:
+Recommends:
+Suggests:
+Conflicts:
+Installed-Size: @INSTALLED_SIZE@
+Maintainer: DoccY <@PACKAGE_BUGREPORT@>
+Provides: @PACKAGE@
+Description: libGkArrays is a C++ library to build GkArrays.
+ .
+ GkArrays are a set of arrays that indexes all k-factors of given collection
+ of q reads of length m.
+ .
+ This structure provides constant access to:
+ - the number of occurences of a given k-factor ;
+ - the number of occurences of a k-factor in at a given position in some read.
+ This structure provides linear in the number of occurences access to:
+ - the positions of each occurences of a given k-factor ;
+ - the number of reads sharing a given k-factor.
+ .
+ The construction of GkArrays requires O(q x m x k) time and O(q x m) space.
+ More peculiarly, if K is the number of distinct k-factors in the given set of
+ reads, GkArrays use 2 x (q x (m-k+1)) + K memory words.
+ .
diff --git a/src/libGkArrays/doc/CeCILL-C.texi b/src/libGkArrays/doc/CeCILL-C.texi
new file mode 100644
index 0000000..2b14994
--- /dev/null
+++ b/src/libGkArrays/doc/CeCILL-C.texi
@@ -0,0 +1,587 @@
+ at setfilename CeCILL-C.info
+ at documentencoding UTF-8
+
+ at unnumbered CeCILL-C FREE SOFTWARE LICENSE AGREEMENT
+
+ at copying
+CeCILL-C FREE SOFTWARE LICENSE AGREEMENT Version 1.0 dated 2006-09-05.
+
+Copyright @copyright{} 2006,
+
+ at itemize
+ at item
+Commissariat @`a l'@'Energie Atomique - @sc{c@'ea}, a public scientific, technical
+and industrial research establishment, having its principal place of
+business at 25 rue Leblanc, immeuble Le Ponant D, 75015 @sc{Paris}, France.
+
+ at item
+Centre National de la Recherche Scientifique - @sc{cnrs}, a public scientific
+and technological establishment, having its principal place of business
+at 3 rue Michel-Ange, 75794 @sc{Paris} @sc{cedex} 16, France.
+
+ at item
+Institut National de Recherche en Informatique et en Automatique -
+ at sc{inria}, a public scientific and technological establishment, having its
+principal place of business at Domaine de Voluceau, @sc{Rocquencourt},
+ at sc{bp} 105, 78153 @sc{Le Chesnay} @sc{cedex}, France.
+
+ at end itemize
+
+ at quotation
+Everyone is permitted to copy and distribute verbatim copies
+of this license document, but changing it is not allowed.
+ at end quotation
+
+ at end copying
+ at ifnotinfo
+ at insertcopying
+ at end ifnotinfo
+ at unnumberedsec Notice
+
+This Agreement is a Free Software license agreement that is the result
+of discussions between its authors in order to ensure compliance with
+the two main principles guiding its drafting:
+
+ at itemize
+ at item
+firstly, compliance with the principles governing the distribution
+of Free Software: access to source code, broad rights granted to
+users,
+ at item
+secondly, the election of a governing law, French law, with which
+it is conformant, both as regards the law of torts and
+intellectual property law, and the protection that it offers to
+both authors and holders of the economic rights over software.
+ at end itemize
+
+The authors of the @sc{c}@'e at sc{cill}- at sc{c} (for C@'e[a] C[nrs] I[nria] L[ogiciel] L[ibre])
+license are:
+
+Commissariat @`a l'@'Energie Atomique - @sc{c@'ea}, a public scientific, technical
+and industrial research establishment, having its principal place of
+business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
+
+Centre National de la Recherche Scientifique - @sc{cnrs}, a public scientific
+and technological establishment, having its principal place of business
+at 3 rue Michel-Ange, 75794 @sc{Paris} @sc{cedex} 16, France.
+
+Institut National de Recherche en Informatique et en Automatique -
+ at sc{inria}, a public scientific and technological establishment, having its
+principal place of business at Domaine de Voluceau, @sc{Rocquencourt},
+ at sc{bp} 105, 78153 @sc{Le Chesnay} @sc{cedex}, France.
+
+ at unnumberedsec Preamble
+
+The purpose of this Free Software license agreement is to grant users
+the right to modify and re-use the software governed by this license.
+
+The exercising of this right is conditional upon the obligation to make
+available to the community the modifications made to the source code of
+the software so as to contribute to its evolution.
+
+In consideration of access to the source code and the rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors only have limited liability.
+
+In this respect, the risks associated with loading, using, modifying
+and/or developing or reproducing the software by the user are brought to
+the user's attention, given its Free Software status, which may make it
+complicated to use, with the result that its use is reserved for
+developers and experienced professionals having in-depth computer
+knowledge. Users are therefore encouraged to load and test the
+suitability of the software as regards their requirements in conditions
+enabling the security of their systems and/or data to be ensured and,
+more generally, to use and operate it in the same conditions of
+security. This Agreement may be freely reproduced and published,
+provided it is not altered, and that no provisions are either added or
+removed herefrom.
+
+This Agreement may apply to any or all software for which the holder of
+the economic rights decides to submit the use thereof to its provisions.
+
+
+ at unnumberedsec Article 1 - DEFINITIONS
+
+For the purpose of this Agreement, when the following expressions
+commence with a capital letter, they shall have the following meaning:
+
+ at strong{Agreement:} means this license agreement, and its possible
+subsequent versions and annexes.
+
+ at strong{Software:} means the software in its Object Code and/or Source Code form
+and, where applicable, its documentation, "as is" when the Licensee
+accepts the Agreement.
+
+ at strong{Initial Software:} means the Software in its Source Code and possibly its
+Object Code form and, where applicable, its documentation, "as is" when
+it is first distributed under the terms and conditions of the Agreement.
+
+ at strong{Modified Software:} means the Software modified by at least one
+Integrated Contribution.
+
+ at strong{Source Code:} means all the Software's instructions and program lines to
+which access is required so as to modify the Software.
+
+ at strong{Object Code:} means the binary files originating from the compilation of
+the Source Code.
+
+ at strong{Holder:} means the holder(s) of the economic rights over the Initial
+Software.
+
+ at strong{Licensee:} means the Software user(s) having accepted the Agreement.
+
+ at strong{Contributor:} means a Licensee having made at least one Integrated
+Contribution.
+
+ at strong{Licensor:} means the Holder, or any other individual or legal entity, who
+distributes the Software under the Agreement.
+
+ at strong{Integrated Contribution:} means any or all modifications, corrections,
+translations, adaptations and/or new functions integrated into the
+Source Code by any or all Contributors.
+
+ at strong{Related Module:} means a set of sources files including their
+documentation that, without modification to the Source Code, enables
+supplementary functions or services in addition to those offered
+by the Software.
+
+ at strong{Derivative Software:} means any combination of the Software, modified or
+not, and of a Related Module.
+
+ at strong{Parties:} mean both the Licensee and the Licensor.
+
+These expressions may be used both in singular and plural form.
+
+
+ at unnumberedsec Article 2 - PURPOSE
+
+The purpose of the Agreement is the grant by the Licensor to the
+Licensee of a non-exclusive, transferable and worldwide license for the
+Software as set forth in Article 5 hereinafter for the whole term of the
+protection granted by the rights over said Software.
+
+
+ at unnumberedsec Article 3 - ACCEPTANCE
+
+ at subheading 3.1
+The Licensee shall be deemed as having accepted the terms and
+conditions of this Agreement upon the occurrence of the first of the
+following events:
+
+ at itemize @w{}
+ at item (i)
+loading the Software by any or all means, notably, by
+downloading from a remote server, or by loading from a physical
+medium;
+
+ at item (ii)
+the first time the Licensee exercises any of the rights
+granted hereunder.
+ at end itemize
+
+ at subheading 3.2
+One copy of the Agreement, containing a notice relating to the
+characteristics of the Software, to the limited warranty, and to the
+fact that its use is restricted to experienced users has been provided
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+understood it.
+
+ at unnumberedsec Article 4 - EFFECTIVE DATE AND TERM
+
+ at subheading 4.1 EFFECTIVE DATE
+
+The Agreement shall become effective on the date when it is accepted by
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+
+ at subheading 4.2 TERM
+
+The Agreement shall remain in force for the entire legal term of
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+
+ at unnumberedsec Article 5 - SCOPE OF RIGHTS GRANTED
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+
+ at subheading 5.1 RIGHT OF USE
+
+The Licensee is authorized to use the Software, without any limitation
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+ at subsubheading 5.1.3
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+
+ at subheading 5.2 RIGHT OF MODIFICATION
+
+The right of modification includes the right to translate, adapt,
+arrange, or make any or all modifications to the Software, and the right
+to reproduce the resulting software. It includes, in particular, the
+right to create a Derivative Software.
+
+The Licensee is authorized to make any or all modification to the
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+ at subheading 5.3 RIGHT OF DISTRIBUTION
+
+In particular, the right of distribution includes the right to publish,
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+
+The Licensee is further authorized to distribute copies of the modified
+or unmodified Software to third parties according to the terms and
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+
+
+ at subsubheading 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+
+The Licensee is authorized to distribute true copies of the Software in
+Source Code or Object Code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ at enumerate
+ at item
+a copy of the Agreement,
+
+ at item
+a notice relating to the limitation of both the Licensor's
+warranty and liability as set forth in Articles 8 and 9,
+ at end enumerate
+
+and that, in the event that only the Object Code of the Software is
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+Code of the Software at a minimum during the entire period of its
+distribution of the Software, it being understood that the additional
+cost of acquiring the Source Code shall not exceed the cost of
+transferring the data.
+
+
+ at subsubheading 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
+
+
+When the Licensee makes an Integrated Contribution to the Software, the
+terms and conditions for the distribution of the resulting Modified
+Software become subject to all the provisions of this Agreement.
+
+The Licensee is authorized to distribute the Modified Software, in
+source code or object code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied
+by:
+
+ at enumerate
+ at item
+a copy of the Agreement,
+
+ at item
+a notice relating to the limitation of both the Licensor's
+warranty and liability as set forth in Articles 8 and 9,
+ at end enumerate
+
+and that, in the event that only the object code of the Modified
+Software is redistributed, the Licensee allows effective access to the
+full source code of the Modified Software at a minimum during the entire
+period of its distribution of the Modified Software, it being understood
+that the additional cost of acquiring the source code shall not exceed
+the cost of transferring the data.
+
+ at subsubheading 5.3.3 DISTRIBUTION OF DERIVATIVE SOFTWARE
+
+When the Licensee creates Derivative Software, this Derivative Software
+may be distributed under a license agreement other than this Agreement,
+subject to compliance with the requirement to include a notice
+concerning the rights over the Software as defined in Article 6.4.
+In the event the creation of the Derivative Software required modification
+of the Source Code, the Licensee undertakes that:
+
+ at enumerate
+ at item
+the resulting Modified Software will be governed by this Agreement,
+
+ at item
+the Integrated Contributions in the resulting Modified Software
+will be clearly identified and documented,
+
+ at item
+the Licensee will allow effective access to the source code of the
+Modified Software, at a minimum during the entire period of
+distribution of the Derivative Software, such that such
+modifications may be carried over in a subsequent version of the
+Software; it being understood that the additional cost of
+purchasing the source code of the Modified Software shall not
+exceed the cost of transferring the data.
+ at end enumerate
+
+ at subsubheading 5.3.4 COMPATIBILITY WITH THE CeCILL LICENSE
+
+When a Modified Software contains an Integrated Contribution subject to
+the @sc{c}@'e at sc{cill} license agreement, or when a Derivative Software contains a
+Related Module subject to the @sc{c}@'e at sc{cill} license agreement, the provisions
+set forth in the third item of Article 6.4 are optional.
+
+ at unnumberedsec Article 6 - INTELLECTUAL PROPERTY
+
+
+ at subheading 6.1 OVER THE INITIAL SOFTWARE
+
+The Holder owns the economic rights over the Initial Software. Any or
+all use of the Initial Software is subject to compliance with the terms
+and conditions under which the Holder has elected to distribute its work
+and no one shall be entitled to modify the terms and conditions for the
+distribution of said Initial Software.
+
+The Holder undertakes that the Initial Software will remain ruled at
+least by this Agreement, for the duration set forth in Article 4.2.
+
+
+ at subheading 6.2 OVER THE INTEGRATED CONTRIBUTIONS
+
+The Licensee who develops an Integrated Contribution is the owner of the
+intellectual property rights over this Contribution as defined by
+applicable law.
+
+
+ at subheading 6.3 OVER THE RELATED MODULES
+
+The Licensee who develops an Related Module is the owner of the
+intellectual property rights over this Related Module as defined by
+applicable law and is free to choose the type of agreement that shall
+govern its distribution under the conditions defined in Article 5.3.3.
+
+ at subheading 6.4 NOTICE OF RIGHTS.
+
+The Licensee expressly undertakes:
+
+ at enumerate
+ at item
+not to remove, or modify, in any manner, the intellectual property
+notices attached to the Software;
+
+ at item
+to reproduce said notices, in an identical manner, in the copies
+of the Software modified or not;
+
+ at item
+to ensure that use of the Software, its intellectual property
+notices and the fact that it is governed by the Agreement is
+indicated in a text that is easily accessible, specifically from
+the interface of any Derivative Software.
+ at end enumerate
+
+The Licensee undertakes not to directly or indirectly infringe the
+intellectual property rights of the Holder and/or Contributors on the
+Software and to take, where applicable, vis-@`a-vis its staff, any and all
+measures required to ensure respect of said intellectual property rights
+of the Holder and/or Contributors.
+
+
+ at unnumberedsec Article 7 - RELATED SERVICES
+
+ at subheading 7.1
+Under no circumstances shall the Agreement oblige the Licensor to
+provide technical assistance or maintenance services for the Software.
+
+However, the Licensor is entitled to offer this type of services. The
+terms and conditions of such technical assistance, and/or such
+maintenance, shall be set forth in a separate instrument. Only the
+Licensor offering said maintenance and/or technical assistance services
+shall incur liability therefor.
+
+ at subheading 7.2
+Similarly, any Licensor is entitled to offer to its licensees, under
+its sole responsibility, a warranty, that shall only be binding upon
+itself, for the redistribution of the Software and/or the Modified
+Software, under terms and conditions that it is free to decide. Said
+warranty, and the financial terms and conditions of its application,
+shall be subject of a separate instrument executed between the Licensor
+and the Licensee.
+
+ at unnumberedsec Article 8 - LIABILITY
+
+ at subheading 8.1
+Subject to the provisions of Article 8.2, the Licensee shall be
+entitled to claim compensation for any direct loss it may have suffered
+from the Software as a result of a fault on the part of the relevant
+Licensor, subject to providing evidence thereof.
+
+ at subheading 8.2
+The Licensor's liability is limited to the commitments made under
+this Agreement and shall not be incurred as a result of in particular:
+(i) loss due the Licensee's total or partial failure to fulfill its
+obligations, (ii) direct or consequential loss that is suffered by the
+Licensee due to the use or performance of the Software, and (iii) more
+generally, any consequential loss. In particular the Parties expressly
+agree that any or all pecuniary or business loss (i.e. loss of data,
+loss of profits, operating loss, loss of customers or orders,
+opportunity cost, any disturbance to business activities) or any or all
+legal proceedings instituted against the Licensee by a third party,
+shall constitute consequential loss and shall not provide entitlement to
+any or all compensation from the Licensor.
+
+ at unnumberedsec Article 9 - WARRANTY
+
+ at subheading 9.1
+The Licensee acknowledges that the scientific and technical
+state-of-the-art when the Software was distributed did not enable all
+possible uses to be tested and verified, nor for the presence of
+possible defects to be detected. In this respect, the Licensee's
+attention has been drawn to the risks associated with loading, using,
+modifying and/or developing and reproducing the Software which are
+reserved for experienced users.
+
+The Licensee shall be responsible for verifying, by any or all means,
+the suitability of the product for its requirements, its good working
+order, and for ensuring that it shall not cause damage to either persons
+or properties.
+
+ at subheading 9.2
+The Licensor hereby represents, in good faith, that it is entitled
+to grant all the rights over the Software (including in particular the
+rights set forth in Article 5).
+
+ at subheading 9.3
+The Licensee acknowledges that the Software is supplied "as is" by
+the Licensor without any other express or tacit warranty, other than
+that provided for in Article 9.2 and, in particular, without any warranty
+as to its commercial value, its secured, safe, innovative or relevant
+nature.
+
+Specifically, the Licensor does not warrant that the Software is free
+from any error, that it will operate without interruption, that it will
+be compatible with the Licensee's own equipment and software
+configuration, nor that it will meet the Licensee's requirements.
+
+ at subheading 9.4
+The Licensor does not either expressly or tacitly warrant that the
+Software does not infringe any third party intellectual property right
+relating to a patent, software or any other property right. Therefore,
+the Licensor disclaims any and all liability towards the Licensee
+arising out of any or all proceedings for infringement that may be
+instituted in respect of the use, modification and redistribution of the
+Software. Nevertheless, should such proceedings be instituted against
+the Licensee, the Licensor shall provide it with technical and legal
+assistance for its defense. Such technical and legal assistance shall be
+decided on a case-by-case basis between the relevant Licensor and the
+Licensee pursuant to a memorandum of understanding. The Licensor
+disclaims any and all liability as regards the Licensee's use of the
+name of the Software. No warranty is given as regards the existence of
+prior rights over the name of the Software or as regards the existence
+of a trademark.
+
+ at unnumberedsec Article 10 - TERMINATION
+
+ at subheading 10.1
+In the event of a breach by the Licensee of its obligations
+hereunder, the Licensor may automatically terminate this Agreement
+thirty (30) days after notice has been sent to the Licensee and has
+remained ineffective.
+
+ at subheading 10.2
+A Licensee whose Agreement is terminated shall no longer be
+authorized to use, modify or distribute the Software. However, any
+licenses that it may have granted prior to termination of the Agreement
+shall remain valid subject to their having been granted in compliance
+with the terms and conditions hereof.
+
+ at unnumberedsec Article 11 - MISCELLANEOUS
+
+
+ at subheading 11.1 EXCUSABLE EVENTS
+
+Neither Party shall be liable for any or all delay, or failure to
+perform the Agreement, that may be attributable to an event of force
+majeure, an act of God or an outside cause, such as defective
+functioning or interruptions of the electricity or telecommunications
+networks, network paralysis following a virus attack, intervention by
+government authorities, natural disasters, water damage, earthquakes,
+fire, explosions, strikes and labor unrest, war, etc.
+
+ at subheading 11.2
+Any failure by either Party, on one or more occasions, to invoke
+one or more of the provisions hereof, shall under no circumstances be
+interpreted as being a waiver by the interested Party of its right to
+invoke said provision(s) subsequently.
+
+ at subheading 11.3
+The Agreement cancels and replaces any or all previous agreements,
+whether written or oral, between the Parties and having the same
+purpose, and constitutes the entirety of the agreement between said
+Parties concerning said purpose. No supplement or modification to the
+terms and conditions hereof shall be effective as between the Parties
+unless it is made in writing and signed by their duly authorized
+representatives.
+
+ at subheading 11.4
+In the event that one or more of the provisions hereof were to
+conflict with a current or future applicable act or legislative text,
+said act or legislative text shall prevail, and the Parties shall make
+the necessary amendments so as to comply with said act or legislative
+text. All other provisions shall remain effective. Similarly, invalidity
+of a provision of the Agreement, for any reason whatsoever, shall not
+cause the Agreement as a whole to be invalid.
+
+ at subheading 11.5 LANGUAGE
+
+The Agreement is drafted in both French and English and both versions
+are deemed authentic.
+
+
+ at unnumberedsec Article 12 - NEW VERSIONS OF THE AGREEMENT
+
+ at subheading 12.1
+Any person is authorized to duplicate and distribute copies of this
+Agreement.
+
+ at subheading 12.2
+So as to ensure coherence, the wording of this Agreement is
+protected and may only be modified by the authors of the License, who
+reserve the right to periodically publish updates or new versions of the
+Agreement, each with a separate number. These subsequent versions may
+address new issues encountered by Free Software.
+
+ at subheading 12.3
+Any Software distributed under a given version of the Agreement may
+only be subsequently distributed under the same version of the Agreement
+or a subsequent version.
+
+ at unnumberedsec Article 13 - GOVERNING LAW AND JURISDICTION
+
+ at subheading 13.1
+The Agreement is governed by French law. The Parties agree to
+endeavor to seek an amicable solution to any disagreements or disputes
+that may arise during the performance of the Agreement.
+
+ at subheading 13.2
+Failing an amicable solution within two (2) months as from their
+occurrence, and unless emergency proceedings are necessary, the
+disagreements or disputes shall be referred to the Paris Courts having
+jurisdiction, by the more diligent Party.
diff --git a/src/libGkArrays/doc/Makefile.am b/src/libGkArrays/doc/Makefile.am
new file mode 100644
index 0000000..a7e00da
--- /dev/null
+++ b/src/libGkArrays/doc/Makefile.am
@@ -0,0 +1,129 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thierry LECROQ <thierry.lecroq at univ-rouen.fr> #
+# Martine LÉONARD <Martine.Leonard at univ-rouen.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie de la librairie Gk-arrays. #
+# #
+# La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de #
+# lectures de séquences issues du séquençage haut-débit. #
+# #
+# Ce logiciel est régi par la licence CeCILL-C soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL-C, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the Gk-arrays library. #
+# #
+# The Gk-arrays library aims at indexing k-factors from a huge set of #
+# sequencing reads. #
+# #
+# This software is governed by the CeCILL-C license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL-C #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL-C license and that you accept its terms. #
+# #
+###############################################################################
+#
+# $Id: Makefile.am 195 2011-02-10 09:41:41Z mancheron $
+#
+###############################################################################
+
+# build and install the .info pages
+info_TEXINFOS = libGkArrays.texi
+libGkArrays_TEXINFOS = CeCILL-C.texi
+nodist_libGkArrays_TEXINFOS = package.texi
+libGkArrays.info: libGkArrays.texi $(libGkArrays_TEXINFOS) $(nodist_libGkArrays_TEXINFOS)
+libGkArrays.dvi: libGkArrays.texi $(libGkArrays_TEXINFOS) $(nodist_libGkArrays_TEXINFOS)
+libGkArrays.pdf: libGkArrays.texi $(libGkArrays_TEXINFOS) $(nodist_libGkArrays_TEXINFOS)
+libGkArrays.html: libGkArrays.texi $(libGkArrays_TEXINFOS) $(nodist_libGkArrays_TEXINFOS)
+
+# Install the man page, but do not include it in
+# the distributed source since it is generated from template.
+nodist_man_MANS = libGkArrays.3
+
+# Extra files to add in distributed sources
+EXTRA_DIST = libGkArrays.3.in package.texi.in
+
+all-local: info pdf html
+
+install-data-local: install-html install-pdf
+
+MOSTLYCLEANFILES=$(nodist_man_MANS) *~
+CLEANFILES=*~
+DISTCLEANFILES=*~
+MAINTAINERCLEANFILES=*~
diff --git a/src/libGkArrays/doc/Makefile.in b/src/libGkArrays/doc/Makefile.in
new file mode 100644
index 0000000..b8d4834
--- /dev/null
+++ b/src/libGkArrays/doc/Makefile.in
@@ -0,0 +1,829 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thierry LECROQ <thierry.lecroq at univ-rouen.fr> #
+# Martine LÉONARD <Martine.Leonard at univ-rouen.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie de la librairie Gk-arrays. #
+# #
+# La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de #
+# lectures de séquences issues du séquençage haut-débit. #
+# #
+# Ce logiciel est régi par la licence CeCILL-C soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL-C, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the Gk-arrays library. #
+# #
+# The Gk-arrays library aims at indexing k-factors from a huge set of #
+# sequencing reads. #
+# #
+# This software is governed by the CeCILL-C license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL-C #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL-C license and that you accept its terms. #
+# #
+###############################################################################
+#
+# $Id: Makefile.am 195 2011-02-10 09:41:41Z mancheron $
+#
+###############################################################################
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+
+install-html: install-html-am
+
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+
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+ $(srcdir)/*) file=`echo "$$file" | sed "s|^$$srcdirstrip/||"`;; \
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+ $(INSTALL_DATA) $$files "$(DESTDIR)$(infodir)" || exit $$?; done
+ @$(POST_INSTALL)
+ @if (install-info --version && \
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+ echo " install-info --info-dir='$(DESTDIR)$(infodir)' '$(DESTDIR)$(infodir)/$$relfile'";\
+ install-info --info-dir="$(DESTDIR)$(infodir)" "$(DESTDIR)$(infodir)/$$relfile" || :;\
+ done; \
+ else : ; fi
+install-man: install-man3
+
+install-pdf: install-pdf-am
+
+install-pdf-am: $(PDFS)
+ @$(NORMAL_INSTALL)
+ test -z "$(pdfdir)" || $(MKDIR_P) "$(DESTDIR)$(pdfdir)"
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+ while read files; do \
+ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(pdfdir)'"; \
+ $(INSTALL_DATA) $$files "$(DESTDIR)$(pdfdir)" || exit $$?; done
+install-ps: install-ps-am
+
+install-ps-am: $(PSS)
+ @$(NORMAL_INSTALL)
+ test -z "$(psdir)" || $(MKDIR_P) "$(DESTDIR)$(psdir)"
+ @list='$(PSS)'; test -n "$(psdir)" || list=; \
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+ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+ echo "$$d$$p"; \
+ done | $(am__base_list) | \
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+ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(psdir)'"; \
+ $(INSTALL_DATA) $$files "$(DESTDIR)$(psdir)" || exit $$?; done
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-aminfo \
+ maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-aminfo mostlyclean-generic \
+ mostlyclean-libtool
+
+pdf: pdf-am
+
+pdf-am: $(PDFS)
+
+ps: ps-am
+
+ps-am: $(PSS)
+
+uninstall-am: uninstall-dvi-am uninstall-html-am uninstall-info-am \
+ uninstall-man uninstall-pdf-am uninstall-ps-am
+
+uninstall-man: uninstall-man3
+
+.MAKE: install-am install-strip
+
+.PHONY: all all-am all-local check check-am clean clean-aminfo \
+ clean-generic clean-libtool dist-info distclean \
+ distclean-generic distclean-libtool distdir dvi dvi-am html \
+ html-am info info-am install install-am install-data \
+ install-data-am install-data-local install-dvi install-dvi-am \
+ install-exec install-exec-am install-html install-html-am \
+ install-info install-info-am install-man install-man3 \
+ install-pdf install-pdf-am install-ps install-ps-am \
+ install-strip installcheck installcheck-am installdirs \
+ maintainer-clean maintainer-clean-aminfo \
+ maintainer-clean-generic mostlyclean mostlyclean-aminfo \
+ mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
+ uninstall uninstall-am uninstall-dvi-am uninstall-html-am \
+ uninstall-info-am uninstall-man uninstall-man3 \
+ uninstall-pdf-am uninstall-ps-am
+
+libGkArrays.info: libGkArrays.texi $(libGkArrays_TEXINFOS) $(nodist_libGkArrays_TEXINFOS)
+libGkArrays.dvi: libGkArrays.texi $(libGkArrays_TEXINFOS) $(nodist_libGkArrays_TEXINFOS)
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+libGkArrays.html: libGkArrays.texi $(libGkArrays_TEXINFOS) $(nodist_libGkArrays_TEXINFOS)
+
+all-local: info pdf html
+
+install-data-local: install-html install-pdf
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/src/libGkArrays/doc/libGkArrays.3.in b/src/libGkArrays/doc/libGkArrays.3.in
new file mode 100644
index 0000000..3b946ac
--- /dev/null
+++ b/src/libGkArrays/doc/libGkArrays.3.in
@@ -0,0 +1,184 @@
+.\" hey, Emacs: -*- nroff -*-
+.\"
+.\" Copyright © 2010-2012 -- LIRMM/CNRS
+.\" (Laboratoire d'Informatique, de Robotique et de
+.\" Microélectronique de Montpellier /
+.\" Centre National de la Recherche Scientifique).
+.\" LIFL/INRIA
+.\" (Laboratoire d'Informatique Fondamentale de
+.\" Lille / Institut National de Recherche en
+.\" Informatique et Automatique)
+.\" LITIS
+.\" (Laboratoire d'Informatique, du Traitement de
+.\" l'Information et des Systèmes)
+.\"
+.\" Auteurs/Authors: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr>
+.\" Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+.\" Mikaël SALSON <mikael.salson at lifl.fr>
+.\" Thierry LECROQ <thierry.lecroq at univ-rouen.fr>
+.\" Martine LÉONARD <Martine.Leonard at univ-rouen.fr>
+.\" Éric RIVALS <eric.rivals at lirmm.fr>
+.\" Alban MANCHERON <alban.mancheron at lirmm.fr>
+.\"
+.\" -------------------------------------------------------------------------
+.\"
+.\" Ce fichier fait partie de la librairie Gk-arrays.
+.\"
+.\" La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de
+.\" lectures de séquences issues du séquençage haut-débit.
+.\"
+.\" La librairie GkArrays permet l'indexation des k-facteurs présents dans un
+.\" ensemble de textes.
+.\"
+.\" Ce logiciel est régi par la licence CeCILL-C soumise au droit français et
+.\" respectant les principes de diffusion des logiciels libres. Vous pouvez
+.\" utiliser, modifier et/ou redistribuer ce programme sous les conditions de
+.\" la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur
+.\" le site "http://www.cecill.info".
+.\"
+.\" En contrepartie de l'accessibilité au code source et des droits de copie,
+.\" de modification et de redistribution accordés par cette licence, il n'est
+.\" offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons,
+.\" seule une responsabilité restreinte pèse sur l'auteur du programme, le
+.\" titulaire des droits patrimoniaux et les concédants successifs.
+.\"
+.\" À cet égard l'attention de l'utilisateur est attirée sur les risques
+.\" associés au chargement, à l'utilisation, à la modification et/ou au
+.\" développement et à la reproduction du logiciel par l'utilisateur étant
+.\" donné sa spécificité de logiciel libre, qui peut le rendre complexe à
+.\" manipuler et qui le réserve donc à des développeurs et des professionnels
+.\" avertis possédant des connaissances informatiques approfondies. Les
+.\" utilisateurs sont donc invités à charger et tester l'adéquation du
+.\" logiciel à leurs besoins dans des conditions permettant d'assurer la
+.\" sécurité de leurs systêmes et ou de leurs données et, plus généralement,
+.\" à l'utiliser et l'exploiter dans les mêmes conditions de sécurité.
+.\"
+.\" Le fait que vous puissiez accéder à cet en-tête signifie que vous avez
+.\" pris connaissance de la licence CeCILL-C, et que vous en avez accepté les
+.\" termes.
+.\"
+.\" -------------------------------------------------------------------------
+.\"
+.\" This File is part of the Gk-arrays library.
+.\"
+.\" The Gk-arrays library aims at indexing k-factors from a huge set of
+.\" sequencing reads.
+.\"
+.\" This software is governed by the CeCILL-C license under French law and
+.\" abiding by the rules of distribution of free software. You can use,
+.\" modify and/ or redistribute the software under the terms of the CeCILL-C
+.\" license as circulated by CEA, CNRS and INRIA at the following URL
+.\" "http://www.cecill.info".
+.\"
+.\" As a counterpart to the access to the source code and rights to copy,
+.\" modify and redistribute granted by the license, users are provided only
+.\" with a limited warranty and the software's author, the holder of the
+.\" economic rights, and the successive licensors have only limited
+.\" liability.
+.\"
+.\" In this respect, the user's attention is drawn to the risks associated
+.\" with loading, using, modifying and/or developing or reproducing the
+.\" software by the user in light of its specific status of free software,
+.\" that may mean that it is complicated to manipulate, and that also
+.\" therefore means that it is reserved for developers and experienced
+.\" professionals having in-depth computer knowledge. Users are therefore
+.\" encouraged to load and test the software's suitability as regards their
+.\" requirements in conditions enabling the security of their systems and/or
+.\" data to be ensured and, more generally, to use and operate it in the same
+.\" conditions as regards security.
+.\"
+.\" The fact that you are presently reading this means that you have had
+.\" knowledge of the CeCILL-C license and that you accept its terms.
+.\"
+.\" $Id: libGkArrays.3.in 195 2011-02-10 09:41:41Z mancheron $
+
+.TH @PACKAGE@ 3 "@ISODATE@" "@PACKAGE@ version @VERSION@" "C++"
+
+.\" Please update the above date whenever this man page is modified.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins (default)
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+
+
+.\"
+.\" SECTION "NAME"
+.\"
+.SH "NAME"
+
+.ce 3
+.SB @PACKAGE@
+
+The GkArrays library allows to index all k-factors of a set of texts.
+.ce 0
+
+.\"
+.\" SECTION "SEE ALSO"
+.\"
+.SH "SEE ALSO"
+
+The full documentation for
+.B @PACKAGE@
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B @PACKAGE@
+programs are properly installed at your site, the command
+.IP
+.B info @PACKAGE@
+.PP
+should give you access to the complete manual.
+.PP
+You can also find the pdf versions of this manual in /usr/local/share/@PACKAGE@/.
+
+.\"
+.\" SECTION "COPYRIGHT"
+.\"
+.SH "COPYRIGHT"
+
+Copyright © 2010-2012 -- LIRMM/CNRS
+ (Laboratoire d'Informatique, de Robotique et de
+ Microélectronique de Montpellier /
+ Centre National de la Recherche Scientifique).
+ LIFL/INRIA
+ (Laboratoire d'Informatique Fondamentale de
+ Lille / Institut National de Recherche en
+ Informatique et Automatique)
+ LITIS
+ (Laboratoire d'Informatique, du Traitement de
+ l'Information et des Systèmes)
+.PP
+ at PACKAGE@ comes with ABSOLUTELY NO WARRANTY.
+.PP
+This is free library, and you are welcome to redistribute it under certain conditions.
+.PP
+See the CeCILL-C License for more details.
+
+.\"
+.\" SECTION "BUGS"
+.\"
+.SH "BUGS"
+
+We thank you for reporting bugs to:
+.RS
+<@PACKAGE_BUGREPORT@>
+
+
+.\"
+.\" SECTION "AUTHOR"
+.\"
+.SH "AUTHOR"
+
+Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>,
+Mikaël SALSON <mikael.salson at lifl.fr>,
+Thierry LECROQ <thierry.lecroq at univ-rouen.fr>,
+Martine LÉONARD <Martine.Leonard at univ-rouen.fr>
+Éric RIVALS <eric.rivals at lirmm.fr>,
+Alban MANCHERON <alban.mancheron at lirmm.fr>
diff --git a/src/libGkArrays/doc/libGkArrays.info b/src/libGkArrays/doc/libGkArrays.info
new file mode 100644
index 0000000..2d83d28
--- /dev/null
+++ b/src/libGkArrays/doc/libGkArrays.info
@@ -0,0 +1,899 @@
+This is libGkArrays.info, produced by makeinfo version 4.13 from
+libGkArrays.texi.
+
+This file documents the Gk-Arrays library.
+
+ Copyright (C) 2010-2013 - IRB/INSERM
+(Institut de Recherches en Biothe'rapie /
+Institut National de la Sante' et de la Recherche
+ Médicale), LIFL/INRIA
+(Laboratoire d'Informatique Fondamentale de
+Lille / Institut National de Recherche en
+Informatique et Automatique), LIRMM/CNRS
+ (Laboratoire d'Informatique, de Robotique et de
+ Microe'lectronique de Montpellier /
+ Centre National de la Recherche Scientifique),
+ LITIS (Laboratoire d'Informatique, du
+Traitement de l'Information et des Syste`mes).
+
+ Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>, Mikae"l
+SALSON <mikael.salson at lifl.fr>, Thierry LECROQ
+<thierry.lecroq at univ-rouen.fr>, Martine LE'ONARD
+<Martine.Leonard at univ-rouen.fr>, Eric RIVALS <eric.rivals at lirmm.fr>
+
+ Permission is granted to make and distribute verbatim copies of this
+manual provided the copyright notice and this permission notice are
+preserved on all copies.
+
+ Permission is granted to copy and distribute modified versions of
+this manual under the conditions for verbatim copying, provided that
+the entire resulting derived work is distributed under the terms of a
+permission notice identical to this one.
+
+ Permission is granted to copy and distribute translations of this
+manual into another language, under the above conditions for modified
+versions, except that this permission notice may be stated in a
+translation as circulated by CE'A, CNRS and INRIA at the following URL
+`http://www.cecill.info'.
+
+
+File: libGkArrays.info, Node: Top, Next: Instructions, Prev: (dir), Up: (dir)
+
+The Gk-arrays library aims at indexing k-factors from a huge set of sequencing reads.
+*************************************************************************************
+
+ Documentation for the version 2.1.0 of the Gk-Arrays library.
+
+* Menu:
+
+* Instructions:: How to Read This Manual
+* Developing:: How to develop using the Gk-Arrays library
+* Copying:: How you can copy and share the Gk-Arrays library
+* Problems:: Reporting Bugs
+* Concept Index:: Concept Index
+
+
+File: libGkArrays.info, Node: Instructions, Next: Developing, Prev: Top, Up: Top
+
+1 How to Read This Manual
+*************************
+
+ * In the Developing section, we explain how to use the Gk-arrays
+ library in your code.
+
+ * You will find in the Copying section the CeCILL-C License.
+
+
+File: libGkArrays.info, Node: Developing, Next: Copying, Prev: Instructions, Up: Top
+
+2 Developing
+************
+
+ The Gk-arrays library is dedicated to indexing millions of reads from
+high-throughput sequencing experiments. This library can index
+variable-length (as produced by Roche 454) or fixed-length reads. It
+provides several functions to find reads or occurrences in reads of
+k-mers where k is specified at index creation.
+
+If you use Gk-arrays, please don't forget to cite:
+N. Philippe, M. Salson, T. Lecroq, M. Le'onard, T. Commes, E'. Rivals.
+Querying large read collections in main memory: a versatile data
+structure. In BMC Bioinformatics, 2011, doi:10.1186/1471-2105-12-242.
+
+2.1 Installing Gk-arrays
+========================
+
+2.1.1 Installation from the source code
+---------------------------------------
+
+ 1. Unpack the archive
+
+ 2. Enter the directory libGkArrays-version-number
+
+ 3. Type ./configure
+
+ 4. If everything went fine, run make
+
+ 5. To install the library on your machine, type make install as an
+ administrator
+
+ 6. Afterwards, you may want to run ldconfig as an administrator
+
+ You can specify parameters to the configure script. For instance
+you can choose to build a static version (quicker) of the library
+rather than a shared version. Typing ./configure -help will provide you
+the list of available options.
+
+2.1.2 Installation from the deb package
+---------------------------------------
+
+ You just need to install the package using a dedicated program on
+your distribution or by typing dpkg -i package-name This will install
+the library and source file headers.
+
+2.2 Using Gk-arrays in your code
+================================
+
+ First, you need to include the header file that defines all the
+functions in the Gk-arrays:
+#include <libGkArrays/gkArrays.h>
+
+ The Gk-arrays consist of a C++ class. To build an index on a new
+collection of reads, you first need to build a new object from that
+class. The class is called gkArrays in the namespace gkarrays.
+
+ The constructor of that class has two compulsory parameters and one
+optional:
+ 1. The name of the file containing the reads in raw, FASTA, FASTQ
+ format. The file can also be gunzipped.
+
+ 2. The length of the k-mer you want to use, ie the value of k.
+
+ 3. (optional) The length of the reads. The length of the reads is
+ automatically detected but you may want to specify a shorter
+ length (cannot be larger than the actual length).
+ Hence, if filename holds the name of a file and 10 is the
+desired value of k, a valid index creation would be:
+gkarrays::gkArrays *reads = new gkarrays::gkArrays(filename, 10);
+
+ Then the main methods are (but you can report to the full
+documentation in the docs/documentation directory of the project or to
+the online documentation `http://crac.gforge.inria.fr/gkarrays/doc'):
+
+Method Purpose
+--------------------------------------------------------------------------
+getNbTags() Number of reads indexed
+getTag(i) Return a char* containing the read itself
+getTagNumWithFactor(r, l) Read numbers (indexed from 0) containing
+ the same k-mer as in read r at position l.
+getTagsWithFactor(r, l) Same as above but return the occurrences
+ as a pair (read number, position in the
+ read).
+getNbTagsWithFactor(r, l, m) Return the number of occurrences returned
+ by getTagsWithFactor(r, l) (if m is true)
+ or by getTagNumWithFactor(r, l) (if m is
+ false).
+
+2.3 Compiling your code
+=======================
+
+ At compilation time, you need to specify that you are using the
+Gk-arrays library. This can be done by specifying -lGkArrays during
+the linking. You may have to specify where the library is installed
+using the -L flag if you didn't install the library in the default
+library directory.
+
+2.4 Example
+===========
+
+#include <iostream>
+#include <cstdlib>
+#include <libGkArrays/gkArrays.h>
+#include <cstdio>
+
+int main(int argc, char **argv) {
+
+ if (argc < 2) {
+ std::cerr << "Usage: " << argv[0] << " filename" << std::endl;
+ exit(1);
+ }
+
+ // Default k-mer length
+ int k = 5;
+ // Building the index
+ gkarrays::gkArrays *reads = new gkarrays::gkArrays(argv[1], k);
+ // Retrieving the first k-mer of the first read
+ char *kmer = reads->getTagFactor(0, 0, k);
+
+ // Displaying the number of indexed reads
+ printf("%d reads in the collection\n", reads->getNbTags());
+
+ // Displaying the number of reads with a given k-mer
+ printf("%d read(s) share the k-mer %s\n",
+ reads->getNbTagsWithFactor(0, 0, false),
+ kmer);
+
+ // Displaying the read numbers that contain that specific k-mer
+ printf("Read containing the occurrences:\n");
+ uint *read_occurrences = reads->getTagNumWithFactor(0, 0);
+ for (uint i = 0; i < reads->getNbTagsWithFactor(0, 0, false); i++)
+ printf("%d\t", read_occurrences[i]);
+ printf("\n");
+
+ // Displaying the occurrences (read number, position in the read)
+ // for that specific k-mer.
+ printf("All the occurrences:\n");
+ std::pair<uint, uint> *occurrences = reads->getTagsWithFactor(0, 0);
+ for (uint i = 0; i < reads->getNbTagsWithFactor(0, 0, true); i++) {
+ printf("(%d,%d)\t", occurrences[i].first, occurrences[i].second);
+ }
+ printf("\n");
+
+ // Free-ing memory.
+ free(read_occurrences);
+ delete [] occurrences;
+ delete reads;
+ delete [] kmer;
+ exit(0);
+}
+
+ If you store this example in a file called test.cpp, you can compile
+it with g++ -Wall -pedantic -O3 test4.cpp -o test4 -lGkArrays. Note
+that a more complete example is given in the src directory in the file
+buildTables.cpp.
+
+
+File: libGkArrays.info, Node: Copying, Next: Problems, Prev: Developing, Up: Top
+
+CeCILL-C FREE SOFTWARE LICENSE AGREEMENT
+****************************************
+
+ CeCILL-C FREE SOFTWARE LICENSE AGREEMENT Version 1.0 dated
+2006-09-05.
+
+ Copyright (C) 2006,
+
+ * Commissariat à l'Énergie Atomique - CéA, a public scientific,
+ technical and industrial research establishment, having its
+ principal place of business at 25 rue Leblanc, immeuble Le Ponant
+ D, 75015 PARIS, France.
+
+ * Centre National de la Recherche Scientifique - CNRS, a public
+ scientific and technological establishment, having its principal
+ place of business at 3 rue Michel-Ange, 75794 PARIS CEDEX 16,
+ France.
+
+ * Institut National de Recherche en Informatique et en Automatique -
+ INRIA, a public scientific and technological establishment, having
+ its principal place of business at Domaine de Voluceau,
+ ROCQUENCOURT, BP 105, 78153 LE CHESNAY CEDEX, France.
+
+
+ Everyone is permitted to copy and distribute verbatim copies of
+ this license document, but changing it is not allowed.
+
+Notice
+======
+
+ This Agreement is a Free Software license agreement that is the
+result of discussions between its authors in order to ensure compliance
+with the two main principles guiding its drafting:
+
+ * firstly, compliance with the principles governing the distribution
+ of Free Software: access to source code, broad rights granted to
+ users,
+
+ * secondly, the election of a governing law, French law, with which
+ it is conformant, both as regards the law of torts and
+ intellectual property law, and the protection that it offers to
+ both authors and holders of the economic rights over software.
+
+ The authors of the CéCILL-C (for Cé[a] C[nrs] I[nria] L[ogiciel]
+L[ibre]) license are:
+
+ Commissariat à l'Énergie Atomique - CéA, a public scientific,
+technical and industrial research establishment, having its principal
+place of business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris,
+France.
+
+ Centre National de la Recherche Scientifique - CNRS, a public
+scientific and technological establishment, having its principal place
+of business at 3 rue Michel-Ange, 75794 PARIS CEDEX 16, France.
+
+ Institut National de Recherche en Informatique et en Automatique -
+INRIA, a public scientific and technological establishment, having its
+principal place of business at Domaine de Voluceau, ROCQUENCOURT, BP
+105, 78153 LE CHESNAY CEDEX, France.
+
+Preamble
+========
+
+ The purpose of this Free Software license agreement is to grant users
+the right to modify and re-use the software governed by this license.
+
+ The exercising of this right is conditional upon the obligation to
+make available to the community the modifications made to the source
+code of the software so as to contribute to its evolution.
+
+ In consideration of access to the source code and the rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors only have limited
+liability.
+
+ In this respect, the risks associated with loading, using, modifying
+and/or developing or reproducing the software by the user are brought to
+the user's attention, given its Free Software status, which may make it
+complicated to use, with the result that its use is reserved for
+developers and experienced professionals having in-depth computer
+knowledge. Users are therefore encouraged to load and test the
+suitability of the software as regards their requirements in conditions
+enabling the security of their systems and/or data to be ensured and,
+more generally, to use and operate it in the same conditions of
+security. This Agreement may be freely reproduced and published,
+provided it is not altered, and that no provisions are either added or
+removed herefrom.
+
+ This Agreement may apply to any or all software for which the holder
+of the economic rights decides to submit the use thereof to its
+provisions.
+
+Article 1 - DEFINITIONS
+=======================
+
+ For the purpose of this Agreement, when the following expressions
+commence with a capital letter, they shall have the following meaning:
+
+ *Agreement:* means this license agreement, and its possible
+subsequent versions and annexes.
+
+ *Software:* means the software in its Object Code and/or Source Code
+form and, where applicable, its documentation, "as is" when the Licensee
+accepts the Agreement.
+
+ *Initial Software:* means the Software in its Source Code and
+possibly its Object Code form and, where applicable, its documentation,
+"as is" when it is first distributed under the terms and conditions of
+the Agreement.
+
+ *Modified Software:* means the Software modified by at least one
+Integrated Contribution.
+
+ *Source Code:* means all the Software's instructions and program
+lines to which access is required so as to modify the Software.
+
+ *Object Code:* means the binary files originating from the
+compilation of the Source Code.
+
+ *Holder:* means the holder(s) of the economic rights over the Initial
+Software.
+
+ *Licensee:* means the Software user(s) having accepted the Agreement.
+
+ *Contributor:* means a Licensee having made at least one Integrated
+Contribution.
+
+ *Licensor:* means the Holder, or any other individual or legal
+entity, who distributes the Software under the Agreement.
+
+ *Integrated Contribution:* means any or all modifications,
+corrections, translations, adaptations and/or new functions integrated
+into the Source Code by any or all Contributors.
+
+ *Related Module:* means a set of sources files including their
+documentation that, without modification to the Source Code, enables
+supplementary functions or services in addition to those offered by the
+Software.
+
+ *Derivative Software:* means any combination of the Software,
+modified or not, and of a Related Module.
+
+ *Parties:* mean both the Licensee and the Licensor.
+
+ These expressions may be used both in singular and plural form.
+
+Article 2 - PURPOSE
+===================
+
+ The purpose of the Agreement is the grant by the Licensor to the
+Licensee of a non-exclusive, transferable and worldwide license for the
+Software as set forth in Article 5 hereinafter for the whole term of the
+protection granted by the rights over said Software.
+
+Article 3 - ACCEPTANCE
+======================
+
+3.1
+---
+
+ The Licensee shall be deemed as having accepted the terms and
+conditions of this Agreement upon the occurrence of the first of the
+following events:
+
+ (i) loading the Software by any or all means, notably, by
+ downloading from a remote server, or by loading from a physical
+ medium;
+
+ (ii) the first time the Licensee exercises any of the rights
+ granted hereunder.
+
+3.2
+---
+
+ One copy of the Agreement, containing a notice relating to the
+characteristics of the Software, to the limited warranty, and to the
+fact that its use is restricted to experienced users has been provided
+to the Licensee prior to its acceptance as set forth in Article 3.1
+hereinabove, and the Licensee hereby acknowledges that it has read and
+understood it.
+
+Article 4 - EFFECTIVE DATE AND TERM
+===================================
+
+4.1 EFFECTIVE DATE
+------------------
+
+ The Agreement shall become effective on the date when it is accepted
+by the Licensee as set forth in Article 3.1.
+
+4.2 TERM
+--------
+
+ The Agreement shall remain in force for the entire legal term of
+protection of the economic rights over the Software.
+
+Article 5 - SCOPE OF RIGHTS GRANTED
+===================================
+
+ The Licensor hereby grants to the Licensee, who accepts, the
+following rights over the Software for any or all use, and for the term
+of the Agreement, on the basis of the terms and conditions set forth
+hereinafter.
+
+ Besides, if the Licensor owns or comes to own one or more patents
+protecting all or part of the functions of the Software or of its
+components, the Licensor undertakes not to enforce the rights granted by
+these patents against successive Licensees using, exploiting or
+modifying the Software. If these patents are transferred, the Licensor
+undertakes to have the transferees subscribe to the obligations set
+forth in this paragraph.
+
+5.1 RIGHT OF USE
+----------------
+
+ The Licensee is authorized to use the Software, without any
+limitation as to its fields of application, with it being hereinafter
+specified that this comprises:
+
+5.1.1
+.....
+
+ permanent or temporary reproduction of all or part of the Software
+by any or all means and in any or all form.
+
+5.1.2
+.....
+
+ loading, displaying, running, or storing the Software on any or all
+medium.
+
+5.1.3
+.....
+
+ entitlement to observe, study or test its operation so as to
+determine the ideas and principles behind any or all constituent
+elements of said Software. This shall apply when the Licensee carries
+out any or all loading, displaying, running, transmission or storage
+operation as regards the Software, that it is entitled to carry out
+hereunder.
+
+5.2 RIGHT OF MODIFICATION
+-------------------------
+
+ The right of modification includes the right to translate, adapt,
+arrange, or make any or all modifications to the Software, and the right
+to reproduce the resulting software. It includes, in particular, the
+right to create a Derivative Software.
+
+ The Licensee is authorized to make any or all modification to the
+Software provided that it includes an explicit notice that it is the
+author of said modification and indicates the date of the creation
+thereof.
+
+5.3 RIGHT OF DISTRIBUTION
+-------------------------
+
+ In particular, the right of distribution includes the right to
+publish, transmit and communicate the Software to the general public on
+any or all medium, and by any or all means, and the right to market,
+either in consideration of a fee, or free of charge, one or more copies
+of the Software by any means.
+
+ The Licensee is further authorized to distribute copies of the
+modified or unmodified Software to third parties according to the terms
+and conditions set forth hereinafter.
+
+5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+...................................................
+
+ The Licensee is authorized to distribute true copies of the Software
+in Source Code or Object Code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ 1. a copy of the Agreement,
+
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+
+ and that, in the event that only the Object Code of the Software is
+redistributed, the Licensee allows effective access to the full Source
+Code of the Software at a minimum during the entire period of its
+distribution of the Software, it being understood that the additional
+cost of acquiring the Source Code shall not exceed the cost of
+transferring the data.
+
+5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
+.......................................
+
+ When the Licensee makes an Integrated Contribution to the Software,
+the terms and conditions for the distribution of the resulting Modified
+Software become subject to all the provisions of this Agreement.
+
+ The Licensee is authorized to distribute the Modified Software, in
+source code or object code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ 1. a copy of the Agreement,
+
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+
+ and that, in the event that only the object code of the Modified
+Software is redistributed, the Licensee allows effective access to the
+full source code of the Modified Software at a minimum during the entire
+period of its distribution of the Modified Software, it being understood
+that the additional cost of acquiring the source code shall not exceed
+the cost of transferring the data.
+
+5.3.3 DISTRIBUTION OF DERIVATIVE SOFTWARE
+.........................................
+
+ When the Licensee creates Derivative Software, this Derivative
+Software may be distributed under a license agreement other than this
+Agreement, subject to compliance with the requirement to include a
+notice concerning the rights over the Software as defined in Article
+6.4. In the event the creation of the Derivative Software required
+modification of the Source Code, the Licensee undertakes that:
+
+ 1. the resulting Modified Software will be governed by this Agreement,
+
+ 2. the Integrated Contributions in the resulting Modified Software
+ will be clearly identified and documented,
+
+ 3. the Licensee will allow effective access to the source code of the
+ Modified Software, at a minimum during the entire period of
+ distribution of the Derivative Software, such that such
+ modifications may be carried over in a subsequent version of the
+ Software; it being understood that the additional cost of
+ purchasing the source code of the Modified Software shall not
+ exceed the cost of transferring the data.
+
+5.3.4 COMPATIBILITY WITH THE CeCILL LICENSE
+...........................................
+
+ When a Modified Software contains an Integrated Contribution subject
+to the CéCILL license agreement, or when a Derivative Software contains
+a Related Module subject to the CéCILL license agreement, the provisions
+set forth in the third item of Article 6.4 are optional.
+
+Article 6 - INTELLECTUAL PROPERTY
+=================================
+
+6.1 OVER THE INITIAL SOFTWARE
+-----------------------------
+
+ The Holder owns the economic rights over the Initial Software. Any or
+all use of the Initial Software is subject to compliance with the terms
+and conditions under which the Holder has elected to distribute its work
+and no one shall be entitled to modify the terms and conditions for the
+distribution of said Initial Software.
+
+ The Holder undertakes that the Initial Software will remain ruled at
+least by this Agreement, for the duration set forth in Article 4.2.
+
+6.2 OVER THE INTEGRATED CONTRIBUTIONS
+-------------------------------------
+
+ The Licensee who develops an Integrated Contribution is the owner of
+the intellectual property rights over this Contribution as defined by
+applicable law.
+
+6.3 OVER THE RELATED MODULES
+----------------------------
+
+ The Licensee who develops an Related Module is the owner of the
+intellectual property rights over this Related Module as defined by
+applicable law and is free to choose the type of agreement that shall
+govern its distribution under the conditions defined in Article 5.3.3.
+
+6.4 NOTICE OF RIGHTS.
+---------------------
+
+ The Licensee expressly undertakes:
+
+ 1. not to remove, or modify, in any manner, the intellectual property
+ notices attached to the Software;
+
+ 2. to reproduce said notices, in an identical manner, in the copies
+ of the Software modified or not;
+
+ 3. to ensure that use of the Software, its intellectual property
+ notices and the fact that it is governed by the Agreement is
+ indicated in a text that is easily accessible, specifically from
+ the interface of any Derivative Software.
+
+ The Licensee undertakes not to directly or indirectly infringe the
+intellectual property rights of the Holder and/or Contributors on the
+Software and to take, where applicable, vis-à-vis its staff, any and all
+measures required to ensure respect of said intellectual property rights
+of the Holder and/or Contributors.
+
+Article 7 - RELATED SERVICES
+============================
+
+7.1
+---
+
+ Under no circumstances shall the Agreement oblige the Licensor to
+provide technical assistance or maintenance services for the Software.
+
+ However, the Licensor is entitled to offer this type of services. The
+terms and conditions of such technical assistance, and/or such
+maintenance, shall be set forth in a separate instrument. Only the
+Licensor offering said maintenance and/or technical assistance services
+shall incur liability therefor.
+
+7.2
+---
+
+ Similarly, any Licensor is entitled to offer to its licensees, under
+its sole responsibility, a warranty, that shall only be binding upon
+itself, for the redistribution of the Software and/or the Modified
+Software, under terms and conditions that it is free to decide. Said
+warranty, and the financial terms and conditions of its application,
+shall be subject of a separate instrument executed between the Licensor
+and the Licensee.
+
+Article 8 - LIABILITY
+=====================
+
+8.1
+---
+
+ Subject to the provisions of Article 8.2, the Licensee shall be
+entitled to claim compensation for any direct loss it may have suffered
+from the Software as a result of a fault on the part of the relevant
+Licensor, subject to providing evidence thereof.
+
+8.2
+---
+
+ The Licensor's liability is limited to the commitments made under
+this Agreement and shall not be incurred as a result of in particular:
+(i) loss due the Licensee's total or partial failure to fulfill its
+obligations, (ii) direct or consequential loss that is suffered by the
+Licensee due to the use or performance of the Software, and (iii) more
+generally, any consequential loss. In particular the Parties expressly
+agree that any or all pecuniary or business loss (i.e. loss of data,
+loss of profits, operating loss, loss of customers or orders,
+opportunity cost, any disturbance to business activities) or any or all
+legal proceedings instituted against the Licensee by a third party,
+shall constitute consequential loss and shall not provide entitlement to
+any or all compensation from the Licensor.
+
+Article 9 - WARRANTY
+====================
+
+9.1
+---
+
+ The Licensee acknowledges that the scientific and technical
+state-of-the-art when the Software was distributed did not enable all
+possible uses to be tested and verified, nor for the presence of
+possible defects to be detected. In this respect, the Licensee's
+attention has been drawn to the risks associated with loading, using,
+modifying and/or developing and reproducing the Software which are
+reserved for experienced users.
+
+ The Licensee shall be responsible for verifying, by any or all means,
+the suitability of the product for its requirements, its good working
+order, and for ensuring that it shall not cause damage to either persons
+or properties.
+
+9.2
+---
+
+ The Licensor hereby represents, in good faith, that it is entitled
+to grant all the rights over the Software (including in particular the
+rights set forth in Article 5).
+
+9.3
+---
+
+ The Licensee acknowledges that the Software is supplied "as is" by
+the Licensor without any other express or tacit warranty, other than
+that provided for in Article 9.2 and, in particular, without any
+warranty as to its commercial value, its secured, safe, innovative or
+relevant nature.
+
+ Specifically, the Licensor does not warrant that the Software is free
+from any error, that it will operate without interruption, that it will
+be compatible with the Licensee's own equipment and software
+configuration, nor that it will meet the Licensee's requirements.
+
+9.4
+---
+
+ The Licensor does not either expressly or tacitly warrant that the
+Software does not infringe any third party intellectual property right
+relating to a patent, software or any other property right. Therefore,
+the Licensor disclaims any and all liability towards the Licensee
+arising out of any or all proceedings for infringement that may be
+instituted in respect of the use, modification and redistribution of the
+Software. Nevertheless, should such proceedings be instituted against
+the Licensee, the Licensor shall provide it with technical and legal
+assistance for its defense. Such technical and legal assistance shall be
+decided on a case-by-case basis between the relevant Licensor and the
+Licensee pursuant to a memorandum of understanding. The Licensor
+disclaims any and all liability as regards the Licensee's use of the
+name of the Software. No warranty is given as regards the existence of
+prior rights over the name of the Software or as regards the existence
+of a trademark.
+
+Article 10 - TERMINATION
+========================
+
+10.1
+----
+
+ In the event of a breach by the Licensee of its obligations
+hereunder, the Licensor may automatically terminate this Agreement
+thirty (30) days after notice has been sent to the Licensee and has
+remained ineffective.
+
+10.2
+----
+
+ A Licensee whose Agreement is terminated shall no longer be
+authorized to use, modify or distribute the Software. However, any
+licenses that it may have granted prior to termination of the Agreement
+shall remain valid subject to their having been granted in compliance
+with the terms and conditions hereof.
+
+Article 11 - MISCELLANEOUS
+==========================
+
+11.1 EXCUSABLE EVENTS
+---------------------
+
+ Neither Party shall be liable for any or all delay, or failure to
+perform the Agreement, that may be attributable to an event of force
+majeure, an act of God or an outside cause, such as defective
+functioning or interruptions of the electricity or telecommunications
+networks, network paralysis following a virus attack, intervention by
+government authorities, natural disasters, water damage, earthquakes,
+fire, explosions, strikes and labor unrest, war, etc.
+
+11.2
+----
+
+ Any failure by either Party, on one or more occasions, to invoke one
+or more of the provisions hereof, shall under no circumstances be
+interpreted as being a waiver by the interested Party of its right to
+invoke said provision(s) subsequently.
+
+11.3
+----
+
+ The Agreement cancels and replaces any or all previous agreements,
+whether written or oral, between the Parties and having the same
+purpose, and constitutes the entirety of the agreement between said
+Parties concerning said purpose. No supplement or modification to the
+terms and conditions hereof shall be effective as between the Parties
+unless it is made in writing and signed by their duly authorized
+representatives.
+
+11.4
+----
+
+ In the event that one or more of the provisions hereof were to
+conflict with a current or future applicable act or legislative text,
+said act or legislative text shall prevail, and the Parties shall make
+the necessary amendments so as to comply with said act or legislative
+text. All other provisions shall remain effective. Similarly, invalidity
+of a provision of the Agreement, for any reason whatsoever, shall not
+cause the Agreement as a whole to be invalid.
+
+11.5 LANGUAGE
+-------------
+
+ The Agreement is drafted in both French and English and both versions
+are deemed authentic.
+
+Article 12 - NEW VERSIONS OF THE AGREEMENT
+==========================================
+
+12.1
+----
+
+ Any person is authorized to duplicate and distribute copies of this
+Agreement.
+
+12.2
+----
+
+ So as to ensure coherence, the wording of this Agreement is
+protected and may only be modified by the authors of the License, who
+reserve the right to periodically publish updates or new versions of the
+Agreement, each with a separate number. These subsequent versions may
+address new issues encountered by Free Software.
+
+12.3
+----
+
+ Any Software distributed under a given version of the Agreement may
+only be subsequently distributed under the same version of the Agreement
+or a subsequent version.
+
+Article 13 - GOVERNING LAW AND JURISDICTION
+===========================================
+
+13.1
+----
+
+ The Agreement is governed by French law. The Parties agree to
+endeavor to seek an amicable solution to any disagreements or disputes
+that may arise during the performance of the Agreement.
+
+13.2
+----
+
+ Failing an amicable solution within two (2) months as from their
+occurrence, and unless emergency proceedings are necessary, the
+disagreements or disputes shall be referred to the Paris Courts having
+jurisdiction, by the more diligent Party.
+
+
+File: libGkArrays.info, Node: Problems, Next: Concept Index, Prev: Copying, Up: Top
+
+3 Reporting Bugs
+****************
+
+ If you find a bug in Gk-arrays library, please send electronic mail
+to <crac-gkarrays at lists.gforge.inria.fr>. Include the version number.
+Also include in your message the output that the program produced and
+the output you expected.
+
+ If you have other questions, comments or suggestions about the
+GkArrays library, contact the authors via electronic mail to
+<crac-gkarrays at lists.gforge.inria.fr>. The authors will try to help
+you out, although they may not have time to fix your problems.
+
+
+File: libGkArrays.info, Node: Concept Index, Prev: Problems, Up: Top
+
+Concept Index
+*************
+
+ [index ]
+* Menu:
+
+* bugs: Problems. (line 6)
+* class: Developing. (line 6)
+* code: Developing. (line 6)
+* compilation: Developing. (line 6)
+* development: Developing. (line 6)
+* how to read: Instructions. (line 6)
+* library: Developing. (line 6)
+* manual, how to read: Instructions. (line 6)
+* method: Developing. (line 6)
+* problems: Problems. (line 6)
+* reading: Instructions. (line 6)
+* tail recursion: Concept Index. (line 6)
+
+
+
+Tag Table:
+Node: Top1713
+Node: Instructions2352
+Node: Developing2654
+Node: Copying8448
+Node: Problems32324
+Node: Concept Index32948
+
+End Tag Table
+
+
+Local Variables:
+coding: utf-8
+End:
diff --git a/src/libGkArrays/doc/libGkArrays.texi b/src/libGkArrays/doc/libGkArrays.texi
new file mode 100644
index 0000000..4e01524
--- /dev/null
+++ b/src/libGkArrays/doc/libGkArrays.texi
@@ -0,0 +1,400 @@
+\input texinfo @c -*-texinfo-*-
+ at documentlanguage en
+ at documentencoding UTF-8
+ at c This file uses the @command command introduced in Texinfo 4.0.
+ at c %**start of header
+ at setfilename libGkArrays.info
+ at settitle The Gk-arrays library aims at indexing k-factors from a huge set of sequencing reads.
+ at finalout
+ at setchapternewpage odd
+ at iftex
+ at afourpaper
+ at afourwide
+ at end iftex
+ at ifinfo
+ at firstparagraphindent insert
+ at end ifinfo
+ at setcontentsaftertitlepage
+ at c %**end of header
+
+ at include package.texi
+
+ at set mails @email{nicolas.philippe@@lirmm.fr}, @email{mikael.salson@@lifl.fr}, @email{thierry.lecroq@@univ-rouen.fr}, @email{Martine.Leonard@@univ-rouen.fr}, @email{eric.rivals@@lirmm.fr}
+ at set authormails Nicolas @sc{Philippe} @email{nicolas.philippe@@lirmm.fr}, Mika@"el @sc{Salson} @email{mikael.salson@@lifl.fr}, Thierry @sc{Lecroq} @email{thierry.lecroq@@univ-rouen.fr}, Martine @sc{L@'eonard} @email{Martine.Leonard@@univ-rouen.fr}, Eric @sc{Rivals} @email{eric.rivals@@lirmm.fr}
+ at set BUGREPORT @email{crac-gkarrays@@lists.gforge.inria.fr}
+ at iftex
+ at clear mails
+ at clear authormails
+ at clear BUGREPORT
+ at set mails <@email{nicolas.philippe@@lirmm.fr}>, <@email{mikael.salson@@lifl.fr}>, <@email{thierry.lecroq@@univ-rouen.fr}>, <@email{Martine.Leonard@@univ-rouen.fr}>, <@email{eric.rivals@@lirmm.fr}>
+ at set authormails Nicolas @sc{Philippe} <@email{nicolas.philippe@@lirmm.fr}>, Mika@"el @sc{Salson} <@email{mikael.salson@@lifl.fr}>, Thierry @sc{Lecroq} <@email{thierry.lecroq@@univ-rouen.fr}>, Martine @sc{L@'eonard} <@email{Martine.Leonard@@univ-rouen.fr}>, Eric @sc{Rivals} <@email{eric.rivals@@lirmm.fr}>
+ at set BUGREPORT <@email{crac-gkarrays@@lists.gforge.inria.fr}>
+ at end iftex
+
+ at ifinfo
+This file documents the Gk-Arrays library.
+
+Copyright @copyright{} 2010-2013 -- @sc{IRB}/@sc{INSERM}
+ (Institut de Recherches en Bioth@'erapie /
+ Institut National de la Sant@'e et de la Recherche
+ Médicale),
+ @sc{lifl}/@sc{inria}
+ (Laboratoire d'Informatique Fondamentale de
+ Lille / Institut National de Recherche en
+ Informatique et Automatique),
+ @sc{lirmm}/@sc{cnrs}
+ (Laboratoire d'Informatique, de Robotique et de
+ Micro@'electronique de Montpellier /
+ Centre National de la Recherche Scientifique),
+ @sc{litis}
+ (Laboratoire d'Informatique, du Traitement de
+ l'Information et des Syst@`emes).
+
+Authors: @value{authormails}
+
+Permission is granted to make and distribute verbatim copies of
+this manual provided the copyright notice and this permission notice
+are preserved on all copies.
+
+ at ignore
+Permission is granted to process this file through TeX and print the
+results, provided the printed document carries copying permission
+notice identical to this one except for the removal of this paragraph
+(this paragraph not being relevant to the printed manual).
+
+ at end ignore
+Permission is granted to copy and distribute modified versions of this
+manual under the conditions for verbatim copying, provided that the entire
+resulting derived work is distributed under the terms of a permission
+notice identical to this one.
+
+Permission is granted to copy and distribute translations of this
+manual into another language, under the above conditions for modified
+versions, except that this permission notice may be stated in a
+translation as circulated by @sc{c@'ea}, @sc{cnrs} and @sc{inria} at the
+following @sc{url} @url{http://www.cecill.info}.
+ at end ifinfo
+
+ at titlepage
+ at title The Gk-arrays library
+ at subtitle The Gk-arrays library aims at indexing k-factors from a huge set of sequencing reads.
+ at author Nicolas @sc{Philippe}
+ at author Mika@"el @sc{Salson}
+ at author Thierry @sc{Lecroq}
+ at author Martine @sc{L@'eonard}
+ at author Eric @sc{Rivals}
+
+ at page
+ at vskip 0pt plus 1filll
+Copyright @copyright{} 2010-2013 -- @sc{IRB}/@sc{INSERM}
+ (Institut de Recherches en Bioth@'erapie /
+ Institut National de la Sant@'e et de la Recherche
+ Médicale),
+ @sc{lifl}/@sc{inria}
+ (Laboratoire d'Informatique Fondamentale de
+ Lille / Institut National de Recherche en
+ Informatique et Automatique),
+ @sc{lirmm}/@sc{cnrs}
+ (Laboratoire d'Informatique, de Robotique et de
+ Micro@'electronique de Montpellier /
+ Centre National de la Recherche Scientifique),
+ @sc{litis}
+ (Laboratoire d'Informatique, du Traitement de
+ l'Information et des Syst@`emes).
+
+Authors: @value{authormails}
+
+Permission is granted to make and distribute verbatim copies of
+this manual provided the copyright notice and this permission notice
+are preserved on all copies.
+
+Permission is granted to copy and distribute modified versions of this
+manual under the conditions for verbatim copying, provided that the entire
+resulting derived work is distributed under the terms of a permission
+notice identical to this one.
+
+Permission is granted to copy and distribute translations of this
+manual into another language, under the above conditions for modified
+versions, except that this permission notice may be stated in a
+translation as circulated by @sc{c@'ea}, @sc{cnrs} and @sc{inria} at the
+following @sc{url} @url{http://www.cecill.info}.
+ at end titlepage
+ at headings on
+
+ at c Before using the EMACS texinfo-every-node-update (C-c C-u C-e)
+ at c and texinfo-all-menus-update (C-c C-u C-a) commands, follow these
+ at c instructions:
+ at c - Go to the node Copying and uncomment its @chapter line.
+ at c - Go to the node Table of contents and uncomment its @unnumbered
+ at c line.
+ at c - Do the update
+ at c - Go to the node Copying and comment again its @chapter line.
+ at c - Go to the node Table of contents and comment again its
+ at c @unnumbered line.
+ at c - Remove the inserted menu (a few lines below):
+ at c @menu
+ at c * Instructions::
+ at c * Copying::
+ at c ...
+ at c * Table of contents::
+ at c @end menu
+ at c - Replace the line (just below):
+ at c '@node Top, Top, (dir), (dir)' by
+ at c '@node Top, Instructions'.
+ at c - Replace the line (near the end):
+ at c '@node Problems, Table of contents, Copying, Top' by
+ at c '@node Problems, Concept Index, Copying, Top'.
+ at c - Replace the line in the @ifinfo block (near the end):
+ at c '@node Concept Index, Table of contents, Problems, Top' by
+ at c '@node Concept Index, , Problems, Top'.
+ at c - Replace the line (near the end):
+ at c '@node Table of contents, , Problems, Top' by
+ at c '@node Table of contents, , Concept Index, Top'.
+
+ at c All the nodes can be updated using the EMACS command
+ at c texinfo-every-node-update, which is normally bound to C-c C-u C-e.
+ at ifnotinfo
+ at node Top, Instructions
+ at end ifnotinfo
+
+ at ifinfo
+ at node Top, Instructions, (dir), (dir)
+ at end ifinfo
+
+ at ifhtml
+ at top Documentation of the Gk-Arrays library version @value{VERSION}
+ at end ifhtml
+ at ifnottex
+ at ifnothtml
+ at top
+
+Documentation for the version @value{VERSION} of the Gk-Arrays library.
+ at end ifnothtml
+ at end ifnottex
+
+ at c All the menus can be updated with the EMACS command
+ at c texinfo-all-menus-update, which is normally bound to C-c C-u C-a.
+ at c * Table of Contents:: Contents of this manual.
+ at menu
+* Instructions:: How to Read This Manual
+* Developing:: How to develop using the Gk-Arrays library
+* Copying:: How you can copy and share the Gk-Arrays library
+* Problems:: Reporting Bugs
+* Concept Index:: Concept Index
+ at ifnotinfo
+* Table of contents:: Table of Contents
+ at end ifnotinfo
+ at end menu
+
+ at node Instructions, Developing, Top, Top
+ at chapter How to Read This Manual
+
+ at cindex reading
+ at cindex manual, how to read
+ at cindex how to read
+ at itemize
+ at item
+In the Developing section, we explain how to use the Gk-arrays library in
+your code.
+ at item
+You will find in the Copying section the CeCILL-C License.
+ at end itemize
+
+ at node Developing, Copying, Instructions, Top
+ at chapter Developing
+
+ at cindex library
+ at cindex development
+ at cindex code
+ at cindex class
+ at cindex method
+ at cindex compilation
+The Gk-arrays library is dedicated to indexing millions of reads from
+high-throughput sequencing experiments.
+This library can index variable-length (as produced by Roche 454) or
+fixed-length reads.
+It provides several functions to find reads or occurrences in reads of
+ at math{k}-mers where @math{k} is specified at index creation.
+
+ at noindent If you use Gk-arrays, please don't forget to cite:@*
+N. Philippe, M. Salson, T. Lecroq, M. L@'eonard, T. Commes, @'E. Rivals. Querying large read collections in main memory: a versatile data structure. In @i{BMC Bioinformatics}, 2011, doi:10.1186/1471-2105-12-242.
+
+ at section Installing Gk-arrays
+ at subsection Installation from the source code
+ at enumerate
+ at item
+Unpack the archive
+ at item
+Enter the directory libGkArrays- at i{version-number}
+ at item
+Type @t{./configure}
+ at item
+If everything went fine, run @t{make}
+ at item
+To install the library on your machine, type @t{make install} as an administrator
+ at item
+Afterwards, you may want to run @t{ldconfig} as an administrator
+ at end enumerate
+
+You can specify parameters to the configure script.
+For instance you can choose to build a static version (quicker) of the library
+rather than a shared version. Typing @t{./configure --help} will
+provide you the list of available options.
+
+ at subsection Installation from the @t{deb} package
+You just need to install the package using a dedicated program on your
+distribution or by typing @t{dpkg -i @i{package-name}}
+This will install the library and source file headers.
+
+ at section Using Gk-arrays in your code
+
+First, you need to include the header file that defines all the functions
+in the Gk-arrays:
+ at verbatim
+#include <libGkArrays/gkArrays.h>
+ at end verbatim
+
+The Gk-arrays consist of a @t{C++} class. To build an index
+on a new collection of reads, you first need to build a new object from
+that class.
+The class is called @t{gkArrays} in the namespace @t{gkarrays}.
+
+The constructor of that class has two compulsory parameters and one optional:
+ at enumerate
+ at item
+The name of the file containing the reads in raw, FASTA, FASTQ format.
+The file can also be gunzipped.
+ at item
+The length of the @math{k}-mer you want to use, @i{ie} the value of @math{k}.
+ at item
+(optional) The length of the reads. The length of the reads is automatically
+detected but you may want to specify a shorter length (cannot be larger than
+the actual length).
+ at end enumerate
+Hence, if filename holds the name of a file and 10 is the desired value of @math{k}, a valid index creation would be:
+ at verbatim
+gkarrays::gkArrays *reads = new gkarrays::gkArrays(filename, 10);
+ at end verbatim
+
+Then the main methods are (but you can report to the full documentation in
+the @t{docs/documentation} directory of the project or to the online
+documentation @url{http://crac.gforge.inria.fr/gkarrays/doc}):
+
+ at multitable @columnfractions .4 .6
+ at headitem Method @tab Purpose
+ at item @t{getNbTags()} @tab Number of reads indexed
+ at item @t{getTag(i)} @tab Return a @t{char*} containing the read itself
+ at item @t{getTagNumWithFactor(r, l)} @tab Read numbers (indexed from 0) containing the same @math{k}-mer as in read @t{r} at position @t{l}.
+ at item @t{getTagsWithFactor(r, l)} @tab Same as above but return the occurrences
+as a pair (read number, position in the read).
+ at item @t{getNbTagsWithFactor(r, l, m)} @tab Return the number of occurrences
+returned by @t{getTagsWithFactor(r, l)} (if @t{m} is @t{true}) or by
+ at t{getTagNumWithFactor(r, l)} (if @t{m} is @t{false}).
+ at end multitable
+
+
+ at section Compiling your code
+
+At compilation time, you need to specify that you are using the
+Gk-arrays library.
+This can be done by specifying @t{-lGkArrays} during the linking.
+You may have to specify where the library is installed using the @t{-L} flag
+if you didn't install the library in the default library directory.
+
+
+ at section Example
+
+ at verbatim
+#include <iostream>
+#include <cstdlib>
+#include <libGkArrays/gkArrays.h>
+#include <cstdio>
+
+int main(int argc, char **argv) {
+
+ if (argc < 2) {
+ std::cerr << "Usage: " << argv[0] << " filename" << std::endl;
+ exit(1);
+ }
+
+ // Default k-mer length
+ int k = 5;
+ // Building the index
+ gkarrays::gkArrays *reads = new gkarrays::gkArrays(argv[1], k);
+ // Retrieving the first k-mer of the first read
+ char *kmer = reads->getTagFactor(0, 0, k);
+
+ // Displaying the number of indexed reads
+ printf("%d reads in the collection\n", reads->getNbTags());
+
+ // Displaying the number of reads with a given k-mer
+ printf("%d read(s) share the k-mer %s\n",
+ reads->getNbTagsWithFactor(0, 0, false),
+ kmer);
+
+ // Displaying the read numbers that contain that specific k-mer
+ printf("Read containing the occurrences:\n");
+ uint *read_occurrences = reads->getTagNumWithFactor(0, 0);
+ for (uint i = 0; i < reads->getNbTagsWithFactor(0, 0, false); i++)
+ printf("%d\t", read_occurrences[i]);
+ printf("\n");
+
+ // Displaying the occurrences (read number, position in the read)
+ // for that specific k-mer.
+ printf("All the occurrences:\n");
+ std::pair<uint, uint> *occurrences = reads->getTagsWithFactor(0, 0);
+ for (uint i = 0; i < reads->getNbTagsWithFactor(0, 0, true); i++) {
+ printf("(%d,%d)\t", occurrences[i].first, occurrences[i].second);
+ }
+ printf("\n");
+
+ // Free-ing memory.
+ free(read_occurrences);
+ delete [] occurrences;
+ delete reads;
+ delete [] kmer;
+ exit(0);
+}
+ at end verbatim
+
+If you store this example in a file called @t{test.cpp}, you can compile it
+with @t{g++ -Wall -pedantic -O3 test4.cpp -o test4 -lGkArrays}.
+Note that a more complete example is given in the @t{src} directory in the
+file @t{buildTables.cpp}.
+
+ at node Copying, Problems, Developing, Top
+ at c @chapter How you can copy and share the Gk-arrays library.
+ at include CeCILL-C.texi
+
+ at node Problems, Concept Index, Copying, Top
+ at chapter Reporting Bugs
+ at cindex bugs
+ at cindex problems
+
+If you find a bug in Gk-arrays library, please send
+electronic mail to @value{BUGREPORT}. Include the version
+number. Also include in your message the output that the program
+produced and the output you expected. at refill
+
+If you have other questions, comments or suggestions about the
+GkArrays library, contact the authors via electronic mail to
+ at value{BUGREPORT}. The authors will try to help you out, although
+they may not have time to fix your problems.
+
+ at ifinfo
+ at node Concept Index, , Problems, Top
+ at end ifinfo
+ at ifnotinfo
+ at node Concept Index, Table of contents, Problems, Top
+ at end ifnotinfo
+ at unnumbered Concept Index
+
+ at cindex tail recursion
+ at printindex cp
+
+ at ifnotinfo
+ at node Table of contents, , Concept Index, Top
+ at c @unnumbered Table of contents
+ at contents
+ at end ifnotinfo
+ at bye
diff --git a/src/libGkArrays/doc/package.texi.in b/src/libGkArrays/doc/package.texi.in
new file mode 100644
index 0000000..c53f183
--- /dev/null
+++ b/src/libGkArrays/doc/package.texi.in
@@ -0,0 +1,2 @@
+ at set VERSION @PACKAGE_VERSION@
+ at set PACKAGE @PACKAGE@
diff --git a/src/libGkArrays/doc/texinfo.tex b/src/libGkArrays/doc/texinfo.tex
new file mode 100644
index 0000000..0d3ba16
--- /dev/null
+++ b/src/libGkArrays/doc/texinfo.tex
@@ -0,0 +1,9291 @@
+% texinfo.tex -- TeX macros to handle Texinfo files.
+%
+% Load plain if necessary, i.e., if running under initex.
+\expandafter\ifx\csname fmtname\endcsname\relax\input plain\fi
+%
+\def\texinfoversion{2009-05-16.16}
+%
+% Copyright 1985, 1986, 1988, 1990, 1991, 1992, 1993, 1994, 1995,
+% 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006,
+% 2007, 2008, 2009 Free Software Foundation, Inc.
+%
+% This texinfo.tex file is free software: you can redistribute it and/or
+% modify it under the terms of the GNU General Public License as
+% published by the Free Software Foundation, either version 3 of the
+% License, or (at your option) any later version.
+%
+% This texinfo.tex file is distributed in the hope that it will be
+% useful, but WITHOUT ANY WARRANTY; without even the implied warranty
+% of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program. If not, see <http://www.gnu.org/licenses/>.
+%
+% As a special exception, when this file is read by TeX when processing
+% a Texinfo source document, you may use the result without
+% restriction. (This has been our intent since Texinfo was invented.)
+%
+% Please try the latest version of texinfo.tex before submitting bug
+% reports; you can get the latest version from:
+% http://www.gnu.org/software/texinfo/ (the Texinfo home page), or
+% ftp://tug.org/tex/texinfo.tex
+% (and all CTAN mirrors, see http://www.ctan.org).
+% The texinfo.tex in any given distribution could well be out
+% of date, so if that's what you're using, please check.
+%
+% Send bug reports to bug-texinfo at gnu.org. Please include including a
+% complete document in each bug report with which we can reproduce the
+% problem. Patches are, of course, greatly appreciated.
+%
+% To process a Texinfo manual with TeX, it's most reliable to use the
+% texi2dvi shell script that comes with the distribution. For a simple
+% manual foo.texi, however, you can get away with this:
+% tex foo.texi
+% texindex foo.??
+% tex foo.texi
+% tex foo.texi
+% dvips foo.dvi -o # or whatever; this makes foo.ps.
+% The extra TeX runs get the cross-reference information correct.
+% Sometimes one run after texindex suffices, and sometimes you need more
+% than two; texi2dvi does it as many times as necessary.
+%
+% It is possible to adapt texinfo.tex for other languages, to some
+% extent. You can get the existing language-specific files from the
+% full Texinfo distribution.
+%
+% The GNU Texinfo home page is http://www.gnu.org/software/texinfo.
+
+
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+
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+
+% sometimes characters are active, so we need control sequences.
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+% The following is used inside several \edef's.
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+
+% Hyphenation fixes.
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+ Flor-i-da Ghost-script Ghost-view Mac-OS Post-Script
+ ap-pen-dix bit-map bit-maps
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+
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+% that the text looks ok even though it passes the margin).
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+
+% @| inserts a changebar to the left of the current line. It should
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+% change spans more than two lines of output. To handle that, we would
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+% vertical list for the beginning and end of each change).
+%
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+ % Append this vertical mode material after the current line in the output.
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+ %
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+ %
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+ \hskip 12pt
+ }%
+ }%
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+
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+% and nothing on the terminal. We don't just call \tracingall here,
+% since that produces some useless output on the terminal. We also make
+% some effort to order the tracing commands to reduce output in the log
+% file; cf. trace.sty in LaTeX.
+%
+\def\gloggingall{\begingroup \globaldefs = 1 \loggingall \endgroup}%
+\def\loggingall{%
+ \tracingstats2
+ \tracingpages1
+ \tracinglostchars2 % 2 gives us more in etex
+ \tracingparagraphs1
+ \tracingoutput1
+ \tracingmacros2
+ \tracingrestores1
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+ \tracingifs1
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+ \tracingcommands3 % 3 gives us more in etex
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+%
+% A mark contains a subexpression of the \ifcase ... \fi construct.
+% \get*marks macros below extract the needed part using \ifcase.
+%
+% Another complication is to let the user choose whether \thischapter
+% (\thissection) refers to the chapter (section) in effect at the top
+% of a page, or that at the bottom of a page. The solution is
+% described on page 260 of The TeXbook. It involves outputting two
+% marks for the sectioning macros, one before the section break, and
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+ \mark{%
+ \the\toks0 \the\toks2
+ \noexpand\or \the\toks4 \the\toks6
+ \noexpand\else \the\toks8
+ }%
+}
+% \topmark doesn't work for the very first chapter (after the title
+% page or the contents), so we use \firstmark there -- this gets us
+% the mark with the chapter defs, unless the user sneaks in, e.g.,
+% @setcolor (or @url, or @link, etc.) between @contents and the very
+% first @chapter.
+\def\gettopheadingmarks{%
+ \ifcase0\topmark\fi
+ \ifx\thischapter\empty \ifcase0\firstmark\fi \fi
+}
+\def\getbottomheadingmarks{\ifcase1\botmark\fi}
+\def\getcolormarks{\ifcase2\topmark\fi}
+
+% Avoid "undefined control sequence" errors.
+\def\lastchapterdefs{}
+\def\lastsectiondefs{}
+\def\prevchapterdefs{}
+\def\prevsectiondefs{}
+\def\lastcolordefs{}
+
+% Main output routine.
+\chardef\PAGE = 255
+\output = {\onepageout{\pagecontents\PAGE}}
+
+\newbox\headlinebox
+\newbox\footlinebox
+
+% \onepageout takes a vbox as an argument. Note that \pagecontents
+% does insertions, but you have to call it yourself.
+\def\onepageout#1{%
+ \ifcropmarks \hoffset=0pt \else \hoffset=\normaloffset \fi
+ %
+ \ifodd\pageno \advance\hoffset by \bindingoffset
+ \else \advance\hoffset by -\bindingoffset\fi
+ %
+ % Do this outside of the \shipout so @code etc. will be expanded in
+ % the headline as they should be, not taken literally (outputting ''code).
+ \ifodd\pageno \getoddheadingmarks \else \getevenheadingmarks \fi
+ \setbox\headlinebox = \vbox{\let\hsize=\pagewidth \makeheadline}%
+ \ifodd\pageno \getoddfootingmarks \else \getevenfootingmarks \fi
+ \setbox\footlinebox = \vbox{\let\hsize=\pagewidth \makefootline}%
+ %
+ {%
+ % Have to do this stuff outside the \shipout because we want it to
+ % take effect in \write's, yet the group defined by the \vbox ends
+ % before the \shipout runs.
+ %
+ \indexdummies % don't expand commands in the output.
+ \normalturnoffactive % \ in index entries must not stay \, e.g., if
+ % the page break happens to be in the middle of an example.
+ % We don't want .vr (or whatever) entries like this:
+ % \entry{{\tt \indexbackslash }acronym}{32}{\code {\acronym}}
+ % "\acronym" won't work when it's read back in;
+ % it needs to be
+ % {\code {{\tt \backslashcurfont }acronym}
+ \shipout\vbox{%
+ % Do this early so pdf references go to the beginning of the page.
+ \ifpdfmakepagedest \pdfdest name{\the\pageno} xyz\fi
+ %
+ \ifcropmarks \vbox to \outervsize\bgroup
+ \hsize = \outerhsize
+ \vskip-\topandbottommargin
+ \vtop to0pt{%
+ \line{\ewtop\hfil\ewtop}%
+ \nointerlineskip
+ \line{%
+ \vbox{\moveleft\cornerthick\nstop}%
+ \hfill
+ \vbox{\moveright\cornerthick\nstop}%
+ }%
+ \vss}%
+ \vskip\topandbottommargin
+ \line\bgroup
+ \hfil % center the page within the outer (page) hsize.
+ \ifodd\pageno\hskip\bindingoffset\fi
+ \vbox\bgroup
+ \fi
+ %
+ \unvbox\headlinebox
+ \pagebody{#1}%
+ \ifdim\ht\footlinebox > 0pt
+ % Only leave this space if the footline is nonempty.
+ % (We lessened \vsize for it in \oddfootingyyy.)
+ % The \baselineskip=24pt in plain's \makefootline has no effect.
+ \vskip 24pt
+ \unvbox\footlinebox
+ \fi
+ %
+ \ifcropmarks
+ \egroup % end of \vbox\bgroup
+ \hfil\egroup % end of (centering) \line\bgroup
+ \vskip\topandbottommargin plus1fill minus1fill
+ \boxmaxdepth = \cornerthick
+ \vbox to0pt{\vss
+ \line{%
+ \vbox{\moveleft\cornerthick\nsbot}%
+ \hfill
+ \vbox{\moveright\cornerthick\nsbot}%
+ }%
+ \nointerlineskip
+ \line{\ewbot\hfil\ewbot}%
+ }%
+ \egroup % \vbox from first cropmarks clause
+ \fi
+ }% end of \shipout\vbox
+ }% end of group with \indexdummies
+ \advancepageno
+ \ifnum\outputpenalty>-20000 \else\dosupereject\fi
+}
+
+\newinsert\margin \dimen\margin=\maxdimen
+
+\def\pagebody#1{\vbox to\pageheight{\boxmaxdepth=\maxdepth #1}}
+{\catcode`\@ =11
+\gdef\pagecontents#1{\ifvoid\topins\else\unvbox\topins\fi
+% marginal hacks, juha at viisa.uucp (Juha Takala)
+\ifvoid\margin\else % marginal info is present
+ \rlap{\kern\hsize\vbox to\z@{\kern1pt\box\margin \vss}}\fi
+\dimen@=\dp#1\relax \unvbox#1\relax
+\ifvoid\footins\else\vskip\skip\footins\footnoterule \unvbox\footins\fi
+\ifr at ggedbottom \kern-\dimen@ \vfil \fi}
+}
+
+% Here are the rules for the cropmarks. Note that they are
+% offset so that the space between them is truly \outerhsize or \outervsize
+% (P. A. MacKay, 12 November, 1986)
+%
+\def\ewtop{\vrule height\cornerthick depth0pt width\cornerlong}
+\def\nstop{\vbox
+ {\hrule height\cornerthick depth\cornerlong width\cornerthick}}
+\def\ewbot{\vrule height0pt depth\cornerthick width\cornerlong}
+\def\nsbot{\vbox
+ {\hrule height\cornerlong depth\cornerthick width\cornerthick}}
+
+% Parse an argument, then pass it to #1. The argument is the rest of
+% the input line (except we remove a trailing comment). #1 should be a
+% macro which expects an ordinary undelimited TeX argument.
+%
+\def\parsearg{\parseargusing{}}
+\def\parseargusing#1#2{%
+ \def\argtorun{#2}%
+ \begingroup
+ \obeylines
+ \spaceisspace
+ #1%
+ \parseargline\empty% Insert the \empty token, see \finishparsearg below.
+}
+
+{\obeylines %
+ \gdef\parseargline#1^^M{%
+ \endgroup % End of the group started in \parsearg.
+ \argremovecomment #1\comment\ArgTerm%
+ }%
+}
+
+% First remove any @comment, then any @c comment.
+\def\argremovecomment#1\comment#2\ArgTerm{\argremovec #1\c\ArgTerm}
+\def\argremovec#1\c#2\ArgTerm{\argcheckspaces#1\^^M\ArgTerm}
+
+% Each occurrence of `\^^M' or `<space>\^^M' is replaced by a single space.
+%
+% \argremovec might leave us with trailing space, e.g.,
+% @end itemize @c foo
+% This space token undergoes the same procedure and is eventually removed
+% by \finishparsearg.
+%
+\def\argcheckspaces#1\^^M{\argcheckspacesX#1\^^M \^^M}
+\def\argcheckspacesX#1 \^^M{\argcheckspacesY#1\^^M}
+\def\argcheckspacesY#1\^^M#2\^^M#3\ArgTerm{%
+ \def\temp{#3}%
+ \ifx\temp\empty
+ % Do not use \next, perhaps the caller of \parsearg uses it; reuse \temp:
+ \let\temp\finishparsearg
+ \else
+ \let\temp\argcheckspaces
+ \fi
+ % Put the space token in:
+ \temp#1 #3\ArgTerm
+}
+
+% If a _delimited_ argument is enclosed in braces, they get stripped; so
+% to get _exactly_ the rest of the line, we had to prevent such situation.
+% We prepended an \empty token at the very beginning and we expand it now,
+% just before passing the control to \argtorun.
+% (Similarly, we have to think about #3 of \argcheckspacesY above: it is
+% either the null string, or it ends with \^^M---thus there is no danger
+% that a pair of braces would be stripped.
+%
+% But first, we have to remove the trailing space token.
+%
+\def\finishparsearg#1 \ArgTerm{\expandafter\argtorun\expandafter{#1}}
+
+% \parseargdef\foo{...}
+% is roughly equivalent to
+% \def\foo{\parsearg\Xfoo}
+% \def\Xfoo#1{...}
+%
+% Actually, I use \csname\string\foo\endcsname, ie. \\foo, as it is my
+% favourite TeX trick. --kasal, 16nov03
+
+\def\parseargdef#1{%
+ \expandafter \doparseargdef \csname\string#1\endcsname #1%
+}
+\def\doparseargdef#1#2{%
+ \def#2{\parsearg#1}%
+ \def#1##1%
+}
+
+% Several utility definitions with active space:
+{
+ \obeyspaces
+ \gdef\obeyedspace{ }
+
+ % Make each space character in the input produce a normal interword
+ % space in the output. Don't allow a line break at this space, as this
+ % is used only in environments like @example, where each line of input
+ % should produce a line of output anyway.
+ %
+ \gdef\sepspaces{\obeyspaces\let =\tie}
+
+ % If an index command is used in an @example environment, any spaces
+ % therein should become regular spaces in the raw index file, not the
+ % expansion of \tie (\leavevmode \penalty \@M \ ).
+ \gdef\unsepspaces{\let =\space}
+}
+
+
+\def\flushcr{\ifx\par\lisppar \def\next##1{}\else \let\next=\relax \fi \next}
+
+% Define the framework for environments in texinfo.tex. It's used like this:
+%
+% \envdef\foo{...}
+% \def\Efoo{...}
+%
+% It's the responsibility of \envdef to insert \begingroup before the
+% actual body; @end closes the group after calling \Efoo. \envdef also
+% defines \thisenv, so the current environment is known; @end checks
+% whether the environment name matches. The \checkenv macro can also be
+% used to check whether the current environment is the one expected.
+%
+% Non-false conditionals (@iftex, @ifset) don't fit into this, so they
+% are not treated as environments; they don't open a group. (The
+% implementation of @end takes care not to call \endgroup in this
+% special case.)
+
+
+% At run-time, environments start with this:
+\def\startenvironment#1{\begingroup\def\thisenv{#1}}
+% initialize
+\let\thisenv\empty
+
+% ... but they get defined via ``\envdef\foo{...}'':
+\long\def\envdef#1#2{\def#1{\startenvironment#1#2}}
+\def\envparseargdef#1#2{\parseargdef#1{\startenvironment#1#2}}
+
+% Check whether we're in the right environment:
+\def\checkenv#1{%
+ \def\temp{#1}%
+ \ifx\thisenv\temp
+ \else
+ \badenverr
+ \fi
+}
+
+% Environment mismatch, #1 expected:
+\def\badenverr{%
+ \errhelp = \EMsimple
+ \errmessage{This command can appear only \inenvironment\temp,
+ not \inenvironment\thisenv}%
+}
+\def\inenvironment#1{%
+ \ifx#1\empty
+ out of any environment%
+ \else
+ in environment \expandafter\string#1%
+ \fi
+}
+
+% @end foo executes the definition of \Efoo.
+% But first, it executes a specialized version of \checkenv
+%
+\parseargdef\end{%
+ \if 1\csname iscond.#1\endcsname
+ \else
+ % The general wording of \badenverr may not be ideal, but... --kasal, 06nov03
+ \expandafter\checkenv\csname#1\endcsname
+ \csname E#1\endcsname
+ \endgroup
+ \fi
+}
+
+\newhelp\EMsimple{Press RETURN to continue.}
+
+
+%% Simple single-character @ commands
+
+% @@ prints an @
+% Kludge this until the fonts are right (grr).
+\def\@{{\tt\char64}}
+
+% This is turned off because it was never documented
+% and you can use @w{...} around a quote to suppress ligatures.
+%% Define @` and @' to be the same as ` and '
+%% but suppressing ligatures.
+%\def\`{{`}}
+%\def\'{{'}}
+
+% Used to generate quoted braces.
+\def\mylbrace {{\tt\char123}}
+\def\myrbrace {{\tt\char125}}
+\let\{=\mylbrace
+\let\}=\myrbrace
+\begingroup
+ % Definitions to produce \{ and \} commands for indices,
+ % and @{ and @} for the aux/toc files.
+ \catcode`\{ = \other \catcode`\} = \other
+ \catcode`\[ = 1 \catcode`\] = 2
+ \catcode`\! = 0 \catcode`\\ = \other
+ !gdef!lbracecmd[\{]%
+ !gdef!rbracecmd[\}]%
+ !gdef!lbraceatcmd[@{]%
+ !gdef!rbraceatcmd[@}]%
+!endgroup
+
+% @comma{} to avoid , parsing problems.
+\let\comma = ,
+
+% Accents: @, @dotaccent @ringaccent @ubaraccent @udotaccent
+% Others are defined by plain TeX: @` @' @" @^ @~ @= @u @v @H.
+\let\, = \c
+\let\dotaccent = \.
+\def\ringaccent#1{{\accent23 #1}}
+\let\tieaccent = \t
+\let\ubaraccent = \b
+\let\udotaccent = \d
+
+% Other special characters: @questiondown @exclamdown @ordf @ordm
+% Plain TeX defines: @AA @AE @O @OE @L (plus lowercase versions) @ss.
+\def\questiondown{?`}
+\def\exclamdown{!`}
+\def\ordf{\leavevmode\raise1ex\hbox{\selectfonts\lllsize \underbar{a}}}
+\def\ordm{\leavevmode\raise1ex\hbox{\selectfonts\lllsize \underbar{o}}}
+
+% Dotless i and dotless j, used for accents.
+\def\imacro{i}
+\def\jmacro{j}
+\def\dotless#1{%
+ \def\temp{#1}%
+ \ifx\temp\imacro \ifmmode\imath \else\ptexi \fi
+ \else\ifx\temp\jmacro \ifmmode\jmath \else\j \fi
+ \else \errmessage{@dotless can be used only with i or j}%
+ \fi\fi
+}
+
+% The \TeX{} logo, as in plain, but resetting the spacing so that a
+% period following counts as ending a sentence. (Idea found in latex.)
+%
+\edef\TeX{\TeX \spacefactor=1000 }
+
+% @LaTeX{} logo. Not quite the same results as the definition in
+% latex.ltx, since we use a different font for the raised A; it's most
+% convenient for us to use an explicitly smaller font, rather than using
+% the \scriptstyle font (since we don't reset \scriptstyle and
+% \scriptscriptstyle).
+%
+\def\LaTeX{%
+ L\kern-.36em
+ {\setbox0=\hbox{T}%
+ \vbox to \ht0{\hbox{\selectfonts\lllsize A}\vss}}%
+ \kern-.15em
+ \TeX
+}
+
+% Be sure we're in horizontal mode when doing a tie, since we make space
+% equivalent to this in @example-like environments. Otherwise, a space
+% at the beginning of a line will start with \penalty -- and
+% since \penalty is valid in vertical mode, we'd end up putting the
+% penalty on the vertical list instead of in the new paragraph.
+{\catcode`@ = 11
+ % Avoid using \@M directly, because that causes trouble
+ % if the definition is written into an index file.
+ \global\let\tiepenalty = \@M
+ \gdef\tie{\leavevmode\penalty\tiepenalty\ }
+}
+
+% @: forces normal size whitespace following.
+\def\:{\spacefactor=1000 }
+
+% @* forces a line break.
+\def\*{\hfil\break\hbox{}\ignorespaces}
+
+% @/ allows a line break.
+\let\/=\allowbreak
+
+% @. is an end-of-sentence period.
+\def\.{.\spacefactor=\endofsentencespacefactor\space}
+
+% @! is an end-of-sentence bang.
+\def\!{!\spacefactor=\endofsentencespacefactor\space}
+
+% @? is an end-of-sentence query.
+\def\?{?\spacefactor=\endofsentencespacefactor\space}
+
+% @frenchspacing on|off says whether to put extra space after punctuation.
+%
+\def\onword{on}
+\def\offword{off}
+%
+\parseargdef\frenchspacing{%
+ \def\temp{#1}%
+ \ifx\temp\onword \plainfrenchspacing
+ \else\ifx\temp\offword \plainnonfrenchspacing
+ \else
+ \errhelp = \EMsimple
+ \errmessage{Unknown @frenchspacing option `\temp', must be on/off}%
+ \fi\fi
+}
+
+% @w prevents a word break. Without the \leavevmode, @w at the
+% beginning of a paragraph, when TeX is still in vertical mode, would
+% produce a whole line of output instead of starting the paragraph.
+\def\w#1{\leavevmode\hbox{#1}}
+
+% @group ... @end group forces ... to be all on one page, by enclosing
+% it in a TeX vbox. We use \vtop instead of \vbox to construct the box
+% to keep its height that of a normal line. According to the rules for
+% \topskip (p.114 of the TeXbook), the glue inserted is
+% max (\topskip - \ht (first item), 0). If that height is large,
+% therefore, no glue is inserted, and the space between the headline and
+% the text is small, which looks bad.
+%
+% Another complication is that the group might be very large. This can
+% cause the glue on the previous page to be unduly stretched, because it
+% does not have much material. In this case, it's better to add an
+% explicit \vfill so that the extra space is at the bottom. The
+% threshold for doing this is if the group is more than \vfilllimit
+% percent of a page (\vfilllimit can be changed inside of @tex).
+%
+\newbox\groupbox
+\def\vfilllimit{0.7}
+%
+\envdef\group{%
+ \ifnum\catcode`\^^M=\active \else
+ \errhelp = \groupinvalidhelp
+ \errmessage{@group invalid in context where filling is enabled}%
+ \fi
+ \startsavinginserts
+ %
+ \setbox\groupbox = \vtop\bgroup
+ % Do @comment since we are called inside an environment such as
+ % @example, where each end-of-line in the input causes an
+ % end-of-line in the output. We don't want the end-of-line after
+ % the `@group' to put extra space in the output. Since @group
+ % should appear on a line by itself (according to the Texinfo
+ % manual), we don't worry about eating any user text.
+ \comment
+}
+%
+% The \vtop produces a box with normal height and large depth; thus, TeX puts
+% \baselineskip glue before it, and (when the next line of text is done)
+% \lineskip glue after it. Thus, space below is not quite equal to space
+% above. But it's pretty close.
+\def\Egroup{%
+ % To get correct interline space between the last line of the group
+ % and the first line afterwards, we have to propagate \prevdepth.
+ \endgraf % Not \par, as it may have been set to \lisppar.
+ \global\dimen1 = \prevdepth
+ \egroup % End the \vtop.
+ % \dimen0 is the vertical size of the group's box.
+ \dimen0 = \ht\groupbox \advance\dimen0 by \dp\groupbox
+ % \dimen2 is how much space is left on the page (more or less).
+ \dimen2 = \pageheight \advance\dimen2 by -\pagetotal
+ % if the group doesn't fit on the current page, and it's a big big
+ % group, force a page break.
+ \ifdim \dimen0 > \dimen2
+ \ifdim \pagetotal < \vfilllimit\pageheight
+ \page
+ \fi
+ \fi
+ \box\groupbox
+ \prevdepth = \dimen1
+ \checkinserts
+}
+%
+% TeX puts in an \escapechar (i.e., `@') at the beginning of the help
+% message, so this ends up printing `@group can only ...'.
+%
+\newhelp\groupinvalidhelp{%
+group can only be used in environments such as @example,^^J%
+where each line of input produces a line of output.}
+
+% @need space-in-mils
+% forces a page break if there is not space-in-mils remaining.
+
+\newdimen\mil \mil=0.001in
+
+% Old definition--didn't work.
+%\parseargdef\need{\par %
+%% This method tries to make TeX break the page naturally
+%% if the depth of the box does not fit.
+%{\baselineskip=0pt%
+%\vtop to #1\mil{\vfil}\kern -#1\mil\nobreak
+%\prevdepth=-1000pt
+%}}
+
+\parseargdef\need{%
+ % Ensure vertical mode, so we don't make a big box in the middle of a
+ % paragraph.
+ \par
+ %
+ % If the @need value is less than one line space, it's useless.
+ \dimen0 = #1\mil
+ \dimen2 = \ht\strutbox
+ \advance\dimen2 by \dp\strutbox
+ \ifdim\dimen0 > \dimen2
+ %
+ % Do a \strut just to make the height of this box be normal, so the
+ % normal leading is inserted relative to the preceding line.
+ % And a page break here is fine.
+ \vtop to #1\mil{\strut\vfil}%
+ %
+ % TeX does not even consider page breaks if a penalty added to the
+ % main vertical list is 10000 or more. But in order to see if the
+ % empty box we just added fits on the page, we must make it consider
+ % page breaks. On the other hand, we don't want to actually break the
+ % page after the empty box. So we use a penalty of 9999.
+ %
+ % There is an extremely small chance that TeX will actually break the
+ % page at this \penalty, if there are no other feasible breakpoints in
+ % sight. (If the user is using lots of big @group commands, which
+ % almost-but-not-quite fill up a page, TeX will have a hard time doing
+ % good page breaking, for example.) However, I could not construct an
+ % example where a page broke at this \penalty; if it happens in a real
+ % document, then we can reconsider our strategy.
+ \penalty9999
+ %
+ % Back up by the size of the box, whether we did a page break or not.
+ \kern -#1\mil
+ %
+ % Do not allow a page break right after this kern.
+ \nobreak
+ \fi
+}
+
+% @br forces paragraph break (and is undocumented).
+
+\let\br = \par
+
+% @page forces the start of a new page.
+%
+\def\page{\par\vfill\supereject}
+
+% @exdent text....
+% outputs text on separate line in roman font, starting at standard page margin
+
+% This records the amount of indent in the innermost environment.
+% That's how much \exdent should take out.
+\newskip\exdentamount
+
+% This defn is used inside fill environments such as @defun.
+\parseargdef\exdent{\hfil\break\hbox{\kern -\exdentamount{\rm#1}}\hfil\break}
+
+% This defn is used inside nofill environments such as @example.
+\parseargdef\nofillexdent{{\advance \leftskip by -\exdentamount
+ \leftline{\hskip\leftskip{\rm#1}}}}
+
+% @inmargin{WHICH}{TEXT} puts TEXT in the WHICH margin next to the current
+% paragraph. For more general purposes, use the \margin insertion
+% class. WHICH is `l' or `r'.
+%
+\newskip\inmarginspacing \inmarginspacing=1cm
+\def\strutdepth{\dp\strutbox}
+%
+\def\doinmargin#1#2{\strut\vadjust{%
+ \nobreak
+ \kern-\strutdepth
+ \vtop to \strutdepth{%
+ \baselineskip=\strutdepth
+ \vss
+ % if you have multiple lines of stuff to put here, you'll need to
+ % make the vbox yourself of the appropriate size.
+ \ifx#1l%
+ \llap{\ignorespaces #2\hskip\inmarginspacing}%
+ \else
+ \rlap{\hskip\hsize \hskip\inmarginspacing \ignorespaces #2}%
+ \fi
+ \null
+ }%
+}}
+\def\inleftmargin{\doinmargin l}
+\def\inrightmargin{\doinmargin r}
+%
+% @inmargin{TEXT [, RIGHT-TEXT]}
+% (if RIGHT-TEXT is given, use TEXT for left page, RIGHT-TEXT for right;
+% else use TEXT for both).
+%
+\def\inmargin#1{\parseinmargin #1,,\finish}
+\def\parseinmargin#1,#2,#3\finish{% not perfect, but better than nothing.
+ \setbox0 = \hbox{\ignorespaces #2}%
+ \ifdim\wd0 > 0pt
+ \def\lefttext{#1}% have both texts
+ \def\righttext{#2}%
+ \else
+ \def\lefttext{#1}% have only one text
+ \def\righttext{#1}%
+ \fi
+ %
+ \ifodd\pageno
+ \def\temp{\inrightmargin\righttext}% odd page -> outside is right margin
+ \else
+ \def\temp{\inleftmargin\lefttext}%
+ \fi
+ \temp
+}
+
+% @include FILE -- \input text of FILE.
+%
+\def\include{\parseargusing\filenamecatcodes\includezzz}
+\def\includezzz#1{%
+ \pushthisfilestack
+ \def\thisfile{#1}%
+ {%
+ \makevalueexpandable % we want to expand any @value in FILE.
+ \turnoffactive % and allow special characters in the expansion
+ \indexnofonts % Allow `@@' and other weird things in file names.
+ \edef\temp{\noexpand\input #1 }%
+ %
+ % This trickery is to read FILE outside of a group, in case it makes
+ % definitions, etc.
+ \expandafter
+ }\temp
+ \popthisfilestack
+}
+\def\filenamecatcodes{%
+ \catcode`\\=\other
+ \catcode`~=\other
+ \catcode`^=\other
+ \catcode`_=\other
+ \catcode`|=\other
+ \catcode`<=\other
+ \catcode`>=\other
+ \catcode`+=\other
+ \catcode`-=\other
+ \catcode`\`=\other
+ \catcode`\'=\other
+}
+
+\def\pushthisfilestack{%
+ \expandafter\pushthisfilestackX\popthisfilestack\StackTerm
+}
+\def\pushthisfilestackX{%
+ \expandafter\pushthisfilestackY\thisfile\StackTerm
+}
+\def\pushthisfilestackY #1\StackTerm #2\StackTerm {%
+ \gdef\popthisfilestack{\gdef\thisfile{#1}\gdef\popthisfilestack{#2}}%
+}
+
+\def\popthisfilestack{\errthisfilestackempty}
+\def\errthisfilestackempty{\errmessage{Internal error:
+ the stack of filenames is empty.}}
+
+\def\thisfile{}
+
+% @center line
+% outputs that line, centered.
+%
+\parseargdef\center{%
+ \ifhmode
+ \let\next\centerH
+ \else
+ \let\next\centerV
+ \fi
+ \next{\hfil \ignorespaces#1\unskip \hfil}%
+}
+\def\centerH#1{%
+ {%
+ \hfil\break
+ \advance\hsize by -\leftskip
+ \advance\hsize by -\rightskip
+ \line{#1}%
+ \break
+ }%
+}
+\def\centerV#1{\line{\kern\leftskip #1\kern\rightskip}}
+
+% @sp n outputs n lines of vertical space
+
+\parseargdef\sp{\vskip #1\baselineskip}
+
+% @comment ...line which is ignored...
+% @c is the same as @comment
+% @ignore ... @end ignore is another way to write a comment
+
+\def\comment{\begingroup \catcode`\^^M=\other%
+\catcode`\@=\other \catcode`\{=\other \catcode`\}=\other%
+\commentxxx}
+{\catcode`\^^M=\other \gdef\commentxxx#1^^M{\endgroup}}
+
+\let\c=\comment
+
+% @paragraphindent NCHARS
+% We'll use ems for NCHARS, close enough.
+% NCHARS can also be the word `asis' or `none'.
+% We cannot feasibly implement @paragraphindent asis, though.
+%
+\def\asisword{asis} % no translation, these are keywords
+\def\noneword{none}
+%
+\parseargdef\paragraphindent{%
+ \def\temp{#1}%
+ \ifx\temp\asisword
+ \else
+ \ifx\temp\noneword
+ \defaultparindent = 0pt
+ \else
+ \defaultparindent = #1em
+ \fi
+ \fi
+ \parindent = \defaultparindent
+}
+
+% @exampleindent NCHARS
+% We'll use ems for NCHARS like @paragraphindent.
+% It seems @exampleindent asis isn't necessary, but
+% I preserve it to make it similar to @paragraphindent.
+\parseargdef\exampleindent{%
+ \def\temp{#1}%
+ \ifx\temp\asisword
+ \else
+ \ifx\temp\noneword
+ \lispnarrowing = 0pt
+ \else
+ \lispnarrowing = #1em
+ \fi
+ \fi
+}
+
+% @firstparagraphindent WORD
+% If WORD is `none', then suppress indentation of the first paragraph
+% after a section heading. If WORD is `insert', then do indent at such
+% paragraphs.
+%
+% The paragraph indentation is suppressed or not by calling
+% \suppressfirstparagraphindent, which the sectioning commands do.
+% We switch the definition of this back and forth according to WORD.
+% By default, we suppress indentation.
+%
+\def\suppressfirstparagraphindent{\dosuppressfirstparagraphindent}
+\def\insertword{insert}
+%
+\parseargdef\firstparagraphindent{%
+ \def\temp{#1}%
+ \ifx\temp\noneword
+ \let\suppressfirstparagraphindent = \dosuppressfirstparagraphindent
+ \else\ifx\temp\insertword
+ \let\suppressfirstparagraphindent = \relax
+ \else
+ \errhelp = \EMsimple
+ \errmessage{Unknown @firstparagraphindent option `\temp'}%
+ \fi\fi
+}
+
+% Here is how we actually suppress indentation. Redefine \everypar to
+% \kern backwards by \parindent, and then reset itself to empty.
+%
+% We also make \indent itself not actually do anything until the next
+% paragraph.
+%
+\gdef\dosuppressfirstparagraphindent{%
+ \gdef\indent{%
+ \restorefirstparagraphindent
+ \indent
+ }%
+ \gdef\noindent{%
+ \restorefirstparagraphindent
+ \noindent
+ }%
+ \global\everypar = {%
+ \kern -\parindent
+ \restorefirstparagraphindent
+ }%
+}
+
+\gdef\restorefirstparagraphindent{%
+ \global \let \indent = \ptexindent
+ \global \let \noindent = \ptexnoindent
+ \global \everypar = {}%
+}
+
+
+% @asis just yields its argument. Used with @table, for example.
+%
+\def\asis#1{#1}
+
+% @math outputs its argument in math mode.
+%
+% One complication: _ usually means subscripts, but it could also mean
+% an actual _ character, as in @math{@var{some_variable} + 1}. So make
+% _ active, and distinguish by seeing if the current family is \slfam,
+% which is what @var uses.
+{
+ \catcode`\_ = \active
+ \gdef\mathunderscore{%
+ \catcode`\_=\active
+ \def_{\ifnum\fam=\slfam \_\else\sb\fi}%
+ }
+}
+% Another complication: we want \\ (and @\) to output a \ character.
+% FYI, plain.tex uses \\ as a temporary control sequence (why?), but
+% this is not advertised and we don't care. Texinfo does not
+% otherwise define @\.
+%
+% The \mathchar is class=0=ordinary, family=7=ttfam, position=5C=\.
+\def\mathbackslash{\ifnum\fam=\ttfam \mathchar"075C \else\backslash \fi}
+%
+\def\math{%
+ \tex
+ \mathunderscore
+ \let\\ = \mathbackslash
+ \mathactive
+ % make the texinfo accent commands work in math mode
+ \let\"=\ddot
+ \let\'=\acute
+ \let\==\bar
+ \let\^=\hat
+ \let\`=\grave
+ \let\u=\breve
+ \let\v=\check
+ \let\~=\tilde
+ \let\dotaccent=\dot
+ $\finishmath
+}
+\def\finishmath#1{#1$\endgroup} % Close the group opened by \tex.
+
+% Some active characters (such as <) are spaced differently in math.
+% We have to reset their definitions in case the @math was an argument
+% to a command which sets the catcodes (such as @item or @section).
+%
+{
+ \catcode`^ = \active
+ \catcode`< = \active
+ \catcode`> = \active
+ \catcode`+ = \active
+ \catcode`' = \active
+ \gdef\mathactive{%
+ \let^ = \ptexhat
+ \let< = \ptexless
+ \let> = \ptexgtr
+ \let+ = \ptexplus
+ \let' = \ptexquoteright
+ }
+}
+
+% Some math mode symbols.
+\def\bullet{$\ptexbullet$}
+\def\geq{\ifmmode \ge\else $\ge$\fi}
+\def\leq{\ifmmode \le\else $\le$\fi}
+\def\minus{\ifmmode -\else $-$\fi}
+
+% @dots{} outputs an ellipsis using the current font.
+% We do .5em per period so that it has the same spacing in the cm
+% typewriter fonts as three actual period characters; on the other hand,
+% in other typewriter fonts three periods are wider than 1.5em. So do
+% whichever is larger.
+%
+\def\dots{%
+ \leavevmode
+ \setbox0=\hbox{...}% get width of three periods
+ \ifdim\wd0 > 1.5em
+ \dimen0 = \wd0
+ \else
+ \dimen0 = 1.5em
+ \fi
+ \hbox to \dimen0{%
+ \hskip 0pt plus.25fil
+ .\hskip 0pt plus1fil
+ .\hskip 0pt plus1fil
+ .\hskip 0pt plus.5fil
+ }%
+}
+
+% @enddots{} is an end-of-sentence ellipsis.
+%
+\def\enddots{%
+ \dots
+ \spacefactor=\endofsentencespacefactor
+}
+
+% @comma{} is so commas can be inserted into text without messing up
+% Texinfo's parsing.
+%
+\let\comma = ,
+
+% @refill is a no-op.
+\let\refill=\relax
+
+% If working on a large document in chapters, it is convenient to
+% be able to disable indexing, cross-referencing, and contents, for test runs.
+% This is done with @novalidate (before @setfilename).
+%
+\newif\iflinks \linkstrue % by default we want the aux files.
+\let\novalidate = \linksfalse
+
+% @setfilename is done at the beginning of every texinfo file.
+% So open here the files we need to have open while reading the input.
+% This makes it possible to make a .fmt file for texinfo.
+\def\setfilename{%
+ \fixbackslash % Turn off hack to swallow `\input texinfo'.
+ \iflinks
+ \tryauxfile
+ % Open the new aux file. TeX will close it automatically at exit.
+ \immediate\openout\auxfile=\jobname.aux
+ \fi % \openindices needs to do some work in any case.
+ \openindices
+ \let\setfilename=\comment % Ignore extra @setfilename cmds.
+ %
+ % If texinfo.cnf is present on the system, read it.
+ % Useful for site-wide @afourpaper, etc.
+ \openin 1 texinfo.cnf
+ \ifeof 1 \else \input texinfo.cnf \fi
+ \closein 1
+ %
+ \comment % Ignore the actual filename.
+}
+
+% Called from \setfilename.
+%
+\def\openindices{%
+ \newindex{cp}%
+ \newcodeindex{fn}%
+ \newcodeindex{vr}%
+ \newcodeindex{tp}%
+ \newcodeindex{ky}%
+ \newcodeindex{pg}%
+}
+
+% @bye.
+\outer\def\bye{\pagealignmacro\tracingstats=1\ptexend}
+
+
+\message{pdf,}
+% adobe `portable' document format
+\newcount\tempnum
+\newcount\lnkcount
+\newtoks\filename
+\newcount\filenamelength
+\newcount\pgn
+\newtoks\toksA
+\newtoks\toksB
+\newtoks\toksC
+\newtoks\toksD
+\newbox\boxA
+\newcount\countA
+\newif\ifpdf
+\newif\ifpdfmakepagedest
+
+% when pdftex is run in dvi mode, \pdfoutput is defined (so \pdfoutput=1
+% can be set). So we test for \relax and 0 as well as \undefined,
+% borrowed from ifpdf.sty.
+\ifx\pdfoutput\undefined
+\else
+ \ifx\pdfoutput\relax
+ \else
+ \ifcase\pdfoutput
+ \else
+ \pdftrue
+ \fi
+ \fi
+\fi
+
+% PDF uses PostScript string constants for the names of xref targets,
+% for display in the outlines, and in other places. Thus, we have to
+% double any backslashes. Otherwise, a name like "\node" will be
+% interpreted as a newline (\n), followed by o, d, e. Not good.
+% http://www.ntg.nl/pipermail/ntg-pdftex/2004-July/000654.html
+% (and related messages, the final outcome is that it is up to the TeX
+% user to double the backslashes and otherwise make the string valid, so
+% that's what we do).
+
+% double active backslashes.
+%
+{\catcode`\@=0 \catcode`\\=\active
+ @gdef at activebackslashdouble{%
+ @catcode`@\=@active
+ @let\=@doublebackslash}
+}
+
+% To handle parens, we must adopt a different approach, since parens are
+% not active characters. hyperref.dtx (which has the same problem as
+% us) handles it with this amazing macro to replace tokens, with minor
+% changes for Texinfo. It is included here under the GPL by permission
+% from the author, Heiko Oberdiek.
+%
+% #1 is the tokens to replace.
+% #2 is the replacement.
+% #3 is the control sequence with the string.
+%
+\def\HyPsdSubst#1#2#3{%
+ \def\HyPsdReplace##1#1##2\END{%
+ ##1%
+ \ifx\\##2\\%
+ \else
+ #2%
+ \HyReturnAfterFi{%
+ \HyPsdReplace##2\END
+ }%
+ \fi
+ }%
+ \xdef#3{\expandafter\HyPsdReplace#3#1\END}%
+}
+\long\def\HyReturnAfterFi#1\fi{\fi#1}
+
+% #1 is a control sequence in which to do the replacements.
+\def\backslashparens#1{%
+ \xdef#1{#1}% redefine it as its expansion; the definition is simply
+ % \lastnode when called from \setref -> \pdfmkdest.
+ \HyPsdSubst{(}{\realbackslash(}{#1}%
+ \HyPsdSubst{)}{\realbackslash)}{#1}%
+}
+
+\newhelp\nopdfimagehelp{Texinfo supports .png, .jpg, .jpeg, and .pdf images
+with PDF output, and none of those formats could be found. (.eps cannot
+be supported due to the design of the PDF format; use regular TeX (DVI
+output) for that.)}
+
+\ifpdf
+ %
+ % Color manipulation macros based on pdfcolor.tex.
+ \def\cmykDarkRed{0.28 1 1 0.35}
+ \def\cmykBlack{0 0 0 1}
+ %
+ % k sets the color for filling (usual text, etc.);
+ % K sets the color for stroking (thin rules, e.g., normal _'s).
+ \def\pdfsetcolor#1{\pdfliteral{#1 k #1 K}}
+ %
+ % Set color, and create a mark which defines \thiscolor accordingly,
+ % so that \makeheadline knows which color to restore.
+ \def\setcolor#1{%
+ \xdef\lastcolordefs{\gdef\noexpand\thiscolor{#1}}%
+ \domark
+ \pdfsetcolor{#1}%
+ }
+ %
+ \def\maincolor{\cmykBlack}
+ \pdfsetcolor{\maincolor}
+ \edef\thiscolor{\maincolor}
+ \def\lastcolordefs{}
+ %
+ \def\makefootline{%
+ \baselineskip24pt
+ \line{\pdfsetcolor{\maincolor}\the\footline}%
+ }
+ %
+ \def\makeheadline{%
+ \vbox to 0pt{%
+ \vskip-22.5pt
+ \line{%
+ \vbox to8.5pt{}%
+ % Extract \thiscolor definition from the marks.
+ \getcolormarks
+ % Typeset the headline with \maincolor, then restore the color.
+ \pdfsetcolor{\maincolor}\the\headline\pdfsetcolor{\thiscolor}%
+ }%
+ \vss
+ }%
+ \nointerlineskip
+ }
+ %
+ %
+ \pdfcatalog{/PageMode /UseOutlines}
+ %
+ % #1 is image name, #2 width (might be empty/whitespace), #3 height (ditto).
+ \def\dopdfimage#1#2#3{%
+ \def\imagewidth{#2}\setbox0 = \hbox{\ignorespaces #2}%
+ \def\imageheight{#3}\setbox2 = \hbox{\ignorespaces #3}%
+ %
+ % pdftex (and the PDF format) support .png, .jpg, .pdf (among
+ % others). Let's try in that order.
+ \let\pdfimgext=\empty
+ \begingroup
+ \openin 1 #1.png \ifeof 1
+ \openin 1 #1.jpg \ifeof 1
+ \openin 1 #1.jpeg \ifeof 1
+ \openin 1 #1.JPG \ifeof 1
+ \openin 1 #1.pdf \ifeof 1
+ \openin 1 #1.PDF \ifeof 1
+ \errhelp = \nopdfimagehelp
+ \errmessage{Could not find image file #1 for pdf}%
+ \else \gdef\pdfimgext{PDF}%
+ \fi
+ \else \gdef\pdfimgext{pdf}%
+ \fi
+ \else \gdef\pdfimgext{JPG}%
+ \fi
+ \else \gdef\pdfimgext{jpeg}%
+ \fi
+ \else \gdef\pdfimgext{jpg}%
+ \fi
+ \else \gdef\pdfimgext{png}%
+ \fi
+ \closein 1
+ \endgroup
+ %
+ % without \immediate, ancient pdftex seg faults when the same image is
+ % included twice. (Version 3.14159-pre-1.0-unofficial-20010704.)
+ \ifnum\pdftexversion < 14
+ \immediate\pdfimage
+ \else
+ \immediate\pdfximage
+ \fi
+ \ifdim \wd0 >0pt width \imagewidth \fi
+ \ifdim \wd2 >0pt height \imageheight \fi
+ \ifnum\pdftexversion<13
+ #1.\pdfimgext
+ \else
+ {#1.\pdfimgext}%
+ \fi
+ \ifnum\pdftexversion < 14 \else
+ \pdfrefximage \pdflastximage
+ \fi}
+ %
+ \def\pdfmkdest#1{{%
+ % We have to set dummies so commands such as @code, and characters
+ % such as \, aren't expanded when present in a section title.
+ \indexnofonts
+ \turnoffactive
+ \activebackslashdouble
+ \makevalueexpandable
+ \def\pdfdestname{#1}%
+ \backslashparens\pdfdestname
+ \safewhatsit{\pdfdest name{\pdfdestname} xyz}%
+ }}
+ %
+ % used to mark target names; must be expandable.
+ \def\pdfmkpgn#1{#1}
+ %
+ % by default, use a color that is dark enough to print on paper as
+ % nearly black, but still distinguishable for online viewing.
+ \def\urlcolor{\cmykDarkRed}
+ \def\linkcolor{\cmykDarkRed}
+ \def\endlink{\setcolor{\maincolor}\pdfendlink}
+ %
+ % Adding outlines to PDF; macros for calculating structure of outlines
+ % come from Petr Olsak
+ \def\expnumber#1{\expandafter\ifx\csname#1\endcsname\relax 0%
+ \else \csname#1\endcsname \fi}
+ \def\advancenumber#1{\tempnum=\expnumber{#1}\relax
+ \advance\tempnum by 1
+ \expandafter\xdef\csname#1\endcsname{\the\tempnum}}
+ %
+ % #1 is the section text, which is what will be displayed in the
+ % outline by the pdf viewer. #2 is the pdf expression for the number
+ % of subentries (or empty, for subsubsections). #3 is the node text,
+ % which might be empty if this toc entry had no corresponding node.
+ % #4 is the page number
+ %
+ \def\dopdfoutline#1#2#3#4{%
+ % Generate a link to the node text if that exists; else, use the
+ % page number. We could generate a destination for the section
+ % text in the case where a section has no node, but it doesn't
+ % seem worth the trouble, since most documents are normally structured.
+ \def\pdfoutlinedest{#3}%
+ \ifx\pdfoutlinedest\empty
+ \def\pdfoutlinedest{#4}%
+ \else
+ % Doubled backslashes in the name.
+ {\activebackslashdouble \xdef\pdfoutlinedest{#3}%
+ \backslashparens\pdfoutlinedest}%
+ \fi
+ %
+ % Also double the backslashes in the display string.
+ {\activebackslashdouble \xdef\pdfoutlinetext{#1}%
+ \backslashparens\pdfoutlinetext}%
+ %
+ \pdfoutline goto name{\pdfmkpgn{\pdfoutlinedest}}#2{\pdfoutlinetext}%
+ }
+ %
+ \def\pdfmakeoutlines{%
+ \begingroup
+ % Thanh's hack / proper braces in bookmarks
+ \edef\mylbrace{\iftrue \string{\else}\fi}\let\{=\mylbrace
+ \edef\myrbrace{\iffalse{\else\string}\fi}\let\}=\myrbrace
+ %
+ % Read toc silently, to get counts of subentries for \pdfoutline.
+ \def\numchapentry##1##2##3##4{%
+ \def\thischapnum{##2}%
+ \def\thissecnum{0}%
+ \def\thissubsecnum{0}%
+ }%
+ \def\numsecentry##1##2##3##4{%
+ \advancenumber{chap\thischapnum}%
+ \def\thissecnum{##2}%
+ \def\thissubsecnum{0}%
+ }%
+ \def\numsubsecentry##1##2##3##4{%
+ \advancenumber{sec\thissecnum}%
+ \def\thissubsecnum{##2}%
+ }%
+ \def\numsubsubsecentry##1##2##3##4{%
+ \advancenumber{subsec\thissubsecnum}%
+ }%
+ \def\thischapnum{0}%
+ \def\thissecnum{0}%
+ \def\thissubsecnum{0}%
+ %
+ % use \def rather than \let here because we redefine \chapentry et
+ % al. a second time, below.
+ \def\appentry{\numchapentry}%
+ \def\appsecentry{\numsecentry}%
+ \def\appsubsecentry{\numsubsecentry}%
+ \def\appsubsubsecentry{\numsubsubsecentry}%
+ \def\unnchapentry{\numchapentry}%
+ \def\unnsecentry{\numsecentry}%
+ \def\unnsubsecentry{\numsubsecentry}%
+ \def\unnsubsubsecentry{\numsubsubsecentry}%
+ \readdatafile{toc}%
+ %
+ % Read toc second time, this time actually producing the outlines.
+ % The `-' means take the \expnumber as the absolute number of
+ % subentries, which we calculated on our first read of the .toc above.
+ %
+ % We use the node names as the destinations.
+ \def\numchapentry##1##2##3##4{%
+ \dopdfoutline{##1}{count-\expnumber{chap##2}}{##3}{##4}}%
+ \def\numsecentry##1##2##3##4{%
+ \dopdfoutline{##1}{count-\expnumber{sec##2}}{##3}{##4}}%
+ \def\numsubsecentry##1##2##3##4{%
+ \dopdfoutline{##1}{count-\expnumber{subsec##2}}{##3}{##4}}%
+ \def\numsubsubsecentry##1##2##3##4{% count is always zero
+ \dopdfoutline{##1}{}{##3}{##4}}%
+ %
+ % PDF outlines are displayed using system fonts, instead of
+ % document fonts. Therefore we cannot use special characters,
+ % since the encoding is unknown. For example, the eogonek from
+ % Latin 2 (0xea) gets translated to a | character. Info from
+ % Staszek Wawrykiewicz, 19 Jan 2004 04:09:24 +0100.
+ %
+ % xx to do this right, we have to translate 8-bit characters to
+ % their "best" equivalent, based on the @documentencoding. Right
+ % now, I guess we'll just let the pdf reader have its way.
+ \indexnofonts
+ \setupdatafile
+ \catcode`\\=\active \otherbackslash
+ \input \tocreadfilename
+ \endgroup
+ }
+ %
+ \def\skipspaces#1{\def\PP{#1}\def\D{|}%
+ \ifx\PP\D\let\nextsp\relax
+ \else\let\nextsp\skipspaces
+ \ifx\p\space\else\addtokens{\filename}{\PP}%
+ \advance\filenamelength by 1
+ \fi
+ \fi
+ \nextsp}
+ \def\getfilename#1{\filenamelength=0\expandafter\skipspaces#1|\relax}
+ \ifnum\pdftexversion < 14
+ \let \startlink \pdfannotlink
+ \else
+ \let \startlink \pdfstartlink
+ \fi
+ % make a live url in pdf output.
+ \def\pdfurl#1{%
+ \begingroup
+ % it seems we really need yet another set of dummies; have not
+ % tried to figure out what each command should do in the context
+ % of @url. for now, just make @/ a no-op, that's the only one
+ % people have actually reported a problem with.
+ %
+ \normalturnoffactive
+ \def\@{@}%
+ \let\/=\empty
+ \makevalueexpandable
+ % do we want to go so far as to use \indexnofonts instead of just
+ % special-casing \var here?
+ \def\var##1{##1}%
+ %
+ \leavevmode\setcolor{\urlcolor}%
+ \startlink attr{/Border [0 0 0]}%
+ user{/Subtype /Link /A << /S /URI /URI (#1) >>}%
+ \endgroup}
+ \def\pdfgettoks#1.{\setbox\boxA=\hbox{\toksA={#1.}\toksB={}\maketoks}}
+ \def\addtokens#1#2{\edef\addtoks{\noexpand#1={\the#1#2}}\addtoks}
+ \def\adn#1{\addtokens{\toksC}{#1}\global\countA=1\let\next=\maketoks}
+ \def\poptoks#1#2|ENDTOKS|{\let\first=#1\toksD={#1}\toksA={#2}}
+ \def\maketoks{%
+ \expandafter\poptoks\the\toksA|ENDTOKS|\relax
+ \ifx\first0\adn0
+ \else\ifx\first1\adn1 \else\ifx\first2\adn2 \else\ifx\first3\adn3
+ \else\ifx\first4\adn4 \else\ifx\first5\adn5 \else\ifx\first6\adn6
+ \else\ifx\first7\adn7 \else\ifx\first8\adn8 \else\ifx\first9\adn9
+ \else
+ \ifnum0=\countA\else\makelink\fi
+ \ifx\first.\let\next=\done\else
+ \let\next=\maketoks
+ \addtokens{\toksB}{\the\toksD}
+ \ifx\first,\addtokens{\toksB}{\space}\fi
+ \fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \next}
+ \def\makelink{\addtokens{\toksB}%
+ {\noexpand\pdflink{\the\toksC}}\toksC={}\global\countA=0}
+ \def\pdflink#1{%
+ \startlink attr{/Border [0 0 0]} goto name{\pdfmkpgn{#1}}
+ \setcolor{\linkcolor}#1\endlink}
+ \def\done{\edef\st{\global\noexpand\toksA={\the\toksB}}\st}
+\else
+ % non-pdf mode
+ \let\pdfmkdest = \gobble
+ \let\pdfurl = \gobble
+ \let\endlink = \relax
+ \let\setcolor = \gobble
+ \let\pdfsetcolor = \gobble
+ \let\pdfmakeoutlines = \relax
+\fi % \ifx\pdfoutput
+
+
+\message{fonts,}
+
+% Change the current font style to #1, remembering it in \curfontstyle.
+% For now, we do not accumulate font styles: @b{@i{foo}} prints foo in
+% italics, not bold italics.
+%
+\def\setfontstyle#1{%
+ \def\curfontstyle{#1}% not as a control sequence, because we are \edef'd.
+ \csname ten#1\endcsname % change the current font
+}
+
+% Select #1 fonts with the current style.
+%
+\def\selectfonts#1{\csname #1fonts\endcsname \csname\curfontstyle\endcsname}
+
+\def\rm{\fam=0 \setfontstyle{rm}}
+\def\it{\fam=\itfam \setfontstyle{it}}
+\def\sl{\fam=\slfam \setfontstyle{sl}}
+\def\bf{\fam=\bffam \setfontstyle{bf}}\def\bfstylename{bf}
+\def\tt{\fam=\ttfam \setfontstyle{tt}}
+
+% Unfortunately, we have to override this for titles and the like, since
+% in those cases "rm" is bold. Sigh.
+\def\rmisbold{\rm\def\curfontstyle{bf}}
+
+% Texinfo sort of supports the sans serif font style, which plain TeX does not.
+% So we set up a \sf.
+\newfam\sffam
+\def\sf{\fam=\sffam \setfontstyle{sf}}
+\let\li = \sf % Sometimes we call it \li, not \sf.
+
+% We don't need math for this font style.
+\def\ttsl{\setfontstyle{ttsl}}
+
+
+% Default leading.
+\newdimen\textleading \textleading = 13.2pt
+
+% Set the baselineskip to #1, and the lineskip and strut size
+% correspondingly. There is no deep meaning behind these magic numbers
+% used as factors; they just match (closely enough) what Knuth defined.
+%
+\def\lineskipfactor{.08333}
+\def\strutheightpercent{.70833}
+\def\strutdepthpercent {.29167}
+%
+% can get a sort of poor man's double spacing by redefining this.
+\def\baselinefactor{1}
+%
+\def\setleading#1{%
+ \dimen0 = #1\relax
+ \normalbaselineskip = \baselinefactor\dimen0
+ \normallineskip = \lineskipfactor\normalbaselineskip
+ \normalbaselines
+ \setbox\strutbox =\hbox{%
+ \vrule width0pt height\strutheightpercent\baselineskip
+ depth \strutdepthpercent \baselineskip
+ }%
+}
+
+% PDF CMaps. See also LaTeX's t1.cmap.
+%
+% do nothing with this by default.
+\expandafter\let\csname cmapOT1\endcsname\gobble
+\expandafter\let\csname cmapOT1IT\endcsname\gobble
+\expandafter\let\csname cmapOT1TT\endcsname\gobble
+
+% if we are producing pdf, and we have \pdffontattr, then define cmaps.
+% (\pdffontattr was introduced many years ago, but people still run
+% older pdftex's; it's easy to conditionalize, so we do.)
+\ifpdf \ifx\pdffontattr\undefined \else
+ \begingroup
+ \catcode`\^^M=\active \def^^M{^^J}% Output line endings as the ^^J char.
+ \catcode`\%=12 \immediate\pdfobj stream {%!PS-Adobe-3.0 Resource-CMap
+%%DocumentNeededResources: ProcSet (CIDInit)
+%%IncludeResource: ProcSet (CIDInit)
+%%BeginResource: CMap (TeX-OT1-0)
+%%Title: (TeX-OT1-0 TeX OT1 0)
+%%Version: 1.000
+%%EndComments
+/CIDInit /ProcSet findresource begin
+12 dict begin
+begincmap
+/CIDSystemInfo
+<< /Registry (TeX)
+/Ordering (OT1)
+/Supplement 0
+>> def
+/CMapName /TeX-OT1-0 def
+/CMapType 2 def
+1 begincodespacerange
+<00> <7F>
+endcodespacerange
+8 beginbfrange
+<00> <01> <0393>
+<09> <0A> <03A8>
+<23> <26> <0023>
+<28> <3B> <0028>
+<3F> <5B> <003F>
+<5D> <5E> <005D>
+<61> <7A> <0061>
+<7B> <7C> <2013>
+endbfrange
+40 beginbfchar
+<02> <0398>
+<03> <039B>
+<04> <039E>
+<05> <03A0>
+<06> <03A3>
+<07> <03D2>
+<08> <03A6>
+<0B> <00660066>
+<0C> <00660069>
+<0D> <0066006C>
+<0E> <006600660069>
+<0F> <00660066006C>
+<10> <0131>
+<11> <0237>
+<12> <0060>
+<13> <00B4>
+<14> <02C7>
+<15> <02D8>
+<16> <00AF>
+<17> <02DA>
+<18> <00B8>
+<19> <00DF>
+<1A> <00E6>
+<1B> <0153>
+<1C> <00F8>
+<1D> <00C6>
+<1E> <0152>
+<1F> <00D8>
+<21> <0021>
+<22> <201D>
+<27> <2019>
+<3C> <00A1>
+<3D> <003D>
+<3E> <00BF>
+<5C> <201C>
+<5F> <02D9>
+<60> <2018>
+<7D> <02DD>
+<7E> <007E>
+<7F> <00A8>
+endbfchar
+endcmap
+CMapName currentdict /CMap defineresource pop
+end
+end
+%%EndResource
+%%EOF
+ }\endgroup
+ \expandafter\edef\csname cmapOT1\endcsname#1{%
+ \pdffontattr#1{/ToUnicode \the\pdflastobj\space 0 R}%
+ }%
+%
+% \cmapOT1IT
+ \begingroup
+ \catcode`\^^M=\active \def^^M{^^J}% Output line endings as the ^^J char.
+ \catcode`\%=12 \immediate\pdfobj stream {%!PS-Adobe-3.0 Resource-CMap
+%%DocumentNeededResources: ProcSet (CIDInit)
+%%IncludeResource: ProcSet (CIDInit)
+%%BeginResource: CMap (TeX-OT1IT-0)
+%%Title: (TeX-OT1IT-0 TeX OT1IT 0)
+%%Version: 1.000
+%%EndComments
+/CIDInit /ProcSet findresource begin
+12 dict begin
+begincmap
+/CIDSystemInfo
+<< /Registry (TeX)
+/Ordering (OT1IT)
+/Supplement 0
+>> def
+/CMapName /TeX-OT1IT-0 def
+/CMapType 2 def
+1 begincodespacerange
+<00> <7F>
+endcodespacerange
+8 beginbfrange
+<00> <01> <0393>
+<09> <0A> <03A8>
+<25> <26> <0025>
+<28> <3B> <0028>
+<3F> <5B> <003F>
+<5D> <5E> <005D>
+<61> <7A> <0061>
+<7B> <7C> <2013>
+endbfrange
+42 beginbfchar
+<02> <0398>
+<03> <039B>
+<04> <039E>
+<05> <03A0>
+<06> <03A3>
+<07> <03D2>
+<08> <03A6>
+<0B> <00660066>
+<0C> <00660069>
+<0D> <0066006C>
+<0E> <006600660069>
+<0F> <00660066006C>
+<10> <0131>
+<11> <0237>
+<12> <0060>
+<13> <00B4>
+<14> <02C7>
+<15> <02D8>
+<16> <00AF>
+<17> <02DA>
+<18> <00B8>
+<19> <00DF>
+<1A> <00E6>
+<1B> <0153>
+<1C> <00F8>
+<1D> <00C6>
+<1E> <0152>
+<1F> <00D8>
+<21> <0021>
+<22> <201D>
+<23> <0023>
+<24> <00A3>
+<27> <2019>
+<3C> <00A1>
+<3D> <003D>
+<3E> <00BF>
+<5C> <201C>
+<5F> <02D9>
+<60> <2018>
+<7D> <02DD>
+<7E> <007E>
+<7F> <00A8>
+endbfchar
+endcmap
+CMapName currentdict /CMap defineresource pop
+end
+end
+%%EndResource
+%%EOF
+ }\endgroup
+ \expandafter\edef\csname cmapOT1IT\endcsname#1{%
+ \pdffontattr#1{/ToUnicode \the\pdflastobj\space 0 R}%
+ }%
+%
+% \cmapOT1TT
+ \begingroup
+ \catcode`\^^M=\active \def^^M{^^J}% Output line endings as the ^^J char.
+ \catcode`\%=12 \immediate\pdfobj stream {%!PS-Adobe-3.0 Resource-CMap
+%%DocumentNeededResources: ProcSet (CIDInit)
+%%IncludeResource: ProcSet (CIDInit)
+%%BeginResource: CMap (TeX-OT1TT-0)
+%%Title: (TeX-OT1TT-0 TeX OT1TT 0)
+%%Version: 1.000
+%%EndComments
+/CIDInit /ProcSet findresource begin
+12 dict begin
+begincmap
+/CIDSystemInfo
+<< /Registry (TeX)
+/Ordering (OT1TT)
+/Supplement 0
+>> def
+/CMapName /TeX-OT1TT-0 def
+/CMapType 2 def
+1 begincodespacerange
+<00> <7F>
+endcodespacerange
+5 beginbfrange
+<00> <01> <0393>
+<09> <0A> <03A8>
+<21> <26> <0021>
+<28> <5F> <0028>
+<61> <7E> <0061>
+endbfrange
+32 beginbfchar
+<02> <0398>
+<03> <039B>
+<04> <039E>
+<05> <03A0>
+<06> <03A3>
+<07> <03D2>
+<08> <03A6>
+<0B> <2191>
+<0C> <2193>
+<0D> <0027>
+<0E> <00A1>
+<0F> <00BF>
+<10> <0131>
+<11> <0237>
+<12> <0060>
+<13> <00B4>
+<14> <02C7>
+<15> <02D8>
+<16> <00AF>
+<17> <02DA>
+<18> <00B8>
+<19> <00DF>
+<1A> <00E6>
+<1B> <0153>
+<1C> <00F8>
+<1D> <00C6>
+<1E> <0152>
+<1F> <00D8>
+<20> <2423>
+<27> <2019>
+<60> <2018>
+<7F> <00A8>
+endbfchar
+endcmap
+CMapName currentdict /CMap defineresource pop
+end
+end
+%%EndResource
+%%EOF
+ }\endgroup
+ \expandafter\edef\csname cmapOT1TT\endcsname#1{%
+ \pdffontattr#1{/ToUnicode \the\pdflastobj\space 0 R}%
+ }%
+\fi\fi
+
+
+% Set the font macro #1 to the font named #2, adding on the
+% specified font prefix (normally `cm').
+% #3 is the font's design size, #4 is a scale factor, #5 is the CMap
+% encoding (currently only OT1, OT1IT and OT1TT are allowed, pass
+% empty to omit).
+\def\setfont#1#2#3#4#5{%
+ \font#1=\fontprefix#2#3 scaled #4
+ \csname cmap#5\endcsname#1%
+}
+% This is what gets called when #5 of \setfont is empty.
+\let\cmap\gobble
+% emacs-page end of cmaps
+
+% Use cm as the default font prefix.
+% To specify the font prefix, you must define \fontprefix
+% before you read in texinfo.tex.
+\ifx\fontprefix\undefined
+\def\fontprefix{cm}
+\fi
+% Support font families that don't use the same naming scheme as CM.
+\def\rmshape{r}
+\def\rmbshape{bx} %where the normal face is bold
+\def\bfshape{b}
+\def\bxshape{bx}
+\def\ttshape{tt}
+\def\ttbshape{tt}
+\def\ttslshape{sltt}
+\def\itshape{ti}
+\def\itbshape{bxti}
+\def\slshape{sl}
+\def\slbshape{bxsl}
+\def\sfshape{ss}
+\def\sfbshape{ss}
+\def\scshape{csc}
+\def\scbshape{csc}
+
+% Definitions for a main text size of 11pt. This is the default in
+% Texinfo.
+%
+\def\definetextfontsizexi{%
+% Text fonts (11.2pt, magstep1).
+\def\textnominalsize{11pt}
+\edef\mainmagstep{\magstephalf}
+\setfont\textrm\rmshape{10}{\mainmagstep}{OT1}
+\setfont\texttt\ttshape{10}{\mainmagstep}{OT1TT}
+\setfont\textbf\bfshape{10}{\mainmagstep}{OT1}
+\setfont\textit\itshape{10}{\mainmagstep}{OT1IT}
+\setfont\textsl\slshape{10}{\mainmagstep}{OT1}
+\setfont\textsf\sfshape{10}{\mainmagstep}{OT1}
+\setfont\textsc\scshape{10}{\mainmagstep}{OT1}
+\setfont\textttsl\ttslshape{10}{\mainmagstep}{OT1TT}
+\font\texti=cmmi10 scaled \mainmagstep
+\font\textsy=cmsy10 scaled \mainmagstep
+\def\textecsize{1095}
+
+% A few fonts for @defun names and args.
+\setfont\defbf\bfshape{10}{\magstep1}{OT1}
+\setfont\deftt\ttshape{10}{\magstep1}{OT1TT}
+\setfont\defttsl\ttslshape{10}{\magstep1}{OT1TT}
+\def\df{\let\tentt=\deftt \let\tenbf = \defbf \let\tenttsl=\defttsl \bf}
+
+% Fonts for indices, footnotes, small examples (9pt).
+\def\smallnominalsize{9pt}
+\setfont\smallrm\rmshape{9}{1000}{OT1}
+\setfont\smalltt\ttshape{9}{1000}{OT1TT}
+\setfont\smallbf\bfshape{10}{900}{OT1}
+\setfont\smallit\itshape{9}{1000}{OT1IT}
+\setfont\smallsl\slshape{9}{1000}{OT1}
+\setfont\smallsf\sfshape{9}{1000}{OT1}
+\setfont\smallsc\scshape{10}{900}{OT1}
+\setfont\smallttsl\ttslshape{10}{900}{OT1TT}
+\font\smalli=cmmi9
+\font\smallsy=cmsy9
+\def\smallecsize{0900}
+
+% Fonts for small examples (8pt).
+\def\smallernominalsize{8pt}
+\setfont\smallerrm\rmshape{8}{1000}{OT1}
+\setfont\smallertt\ttshape{8}{1000}{OT1TT}
+\setfont\smallerbf\bfshape{10}{800}{OT1}
+\setfont\smallerit\itshape{8}{1000}{OT1IT}
+\setfont\smallersl\slshape{8}{1000}{OT1}
+\setfont\smallersf\sfshape{8}{1000}{OT1}
+\setfont\smallersc\scshape{10}{800}{OT1}
+\setfont\smallerttsl\ttslshape{10}{800}{OT1TT}
+\font\smalleri=cmmi8
+\font\smallersy=cmsy8
+\def\smallerecsize{0800}
+
+% Fonts for title page (20.4pt):
+\def\titlenominalsize{20pt}
+\setfont\titlerm\rmbshape{12}{\magstep3}{OT1}
+\setfont\titleit\itbshape{10}{\magstep4}{OT1IT}
+\setfont\titlesl\slbshape{10}{\magstep4}{OT1}
+\setfont\titlett\ttbshape{12}{\magstep3}{OT1TT}
+\setfont\titlettsl\ttslshape{10}{\magstep4}{OT1TT}
+\setfont\titlesf\sfbshape{17}{\magstep1}{OT1}
+\let\titlebf=\titlerm
+\setfont\titlesc\scbshape{10}{\magstep4}{OT1}
+\font\titlei=cmmi12 scaled \magstep3
+\font\titlesy=cmsy10 scaled \magstep4
+\def\titleecsize{2074}
+
+% Chapter (and unnumbered) fonts (17.28pt).
+\def\chapnominalsize{17pt}
+\setfont\chaprm\rmbshape{12}{\magstep2}{OT1}
+\setfont\chapit\itbshape{10}{\magstep3}{OT1IT}
+\setfont\chapsl\slbshape{10}{\magstep3}{OT1}
+\setfont\chaptt\ttbshape{12}{\magstep2}{OT1TT}
+\setfont\chapttsl\ttslshape{10}{\magstep3}{OT1TT}
+\setfont\chapsf\sfbshape{17}{1000}{OT1}
+\let\chapbf=\chaprm
+\setfont\chapsc\scbshape{10}{\magstep3}{OT1}
+\font\chapi=cmmi12 scaled \magstep2
+\font\chapsy=cmsy10 scaled \magstep3
+\def\chapecsize{1728}
+
+% Section fonts (14.4pt).
+\def\secnominalsize{14pt}
+\setfont\secrm\rmbshape{12}{\magstep1}{OT1}
+\setfont\secit\itbshape{10}{\magstep2}{OT1IT}
+\setfont\secsl\slbshape{10}{\magstep2}{OT1}
+\setfont\sectt\ttbshape{12}{\magstep1}{OT1TT}
+\setfont\secttsl\ttslshape{10}{\magstep2}{OT1TT}
+\setfont\secsf\sfbshape{12}{\magstep1}{OT1}
+\let\secbf\secrm
+\setfont\secsc\scbshape{10}{\magstep2}{OT1}
+\font\seci=cmmi12 scaled \magstep1
+\font\secsy=cmsy10 scaled \magstep2
+\def\sececsize{1440}
+
+% Subsection fonts (13.15pt).
+\def\ssecnominalsize{13pt}
+\setfont\ssecrm\rmbshape{12}{\magstephalf}{OT1}
+\setfont\ssecit\itbshape{10}{1315}{OT1IT}
+\setfont\ssecsl\slbshape{10}{1315}{OT1}
+\setfont\ssectt\ttbshape{12}{\magstephalf}{OT1TT}
+\setfont\ssecttsl\ttslshape{10}{1315}{OT1TT}
+\setfont\ssecsf\sfbshape{12}{\magstephalf}{OT1}
+\let\ssecbf\ssecrm
+\setfont\ssecsc\scbshape{10}{1315}{OT1}
+\font\sseci=cmmi12 scaled \magstephalf
+\font\ssecsy=cmsy10 scaled 1315
+\def\ssececsize{1200}
+
+% Reduced fonts for @acro in text (10pt).
+\def\reducednominalsize{10pt}
+\setfont\reducedrm\rmshape{10}{1000}{OT1}
+\setfont\reducedtt\ttshape{10}{1000}{OT1TT}
+\setfont\reducedbf\bfshape{10}{1000}{OT1}
+\setfont\reducedit\itshape{10}{1000}{OT1IT}
+\setfont\reducedsl\slshape{10}{1000}{OT1}
+\setfont\reducedsf\sfshape{10}{1000}{OT1}
+\setfont\reducedsc\scshape{10}{1000}{OT1}
+\setfont\reducedttsl\ttslshape{10}{1000}{OT1TT}
+\font\reducedi=cmmi10
+\font\reducedsy=cmsy10
+\def\reducedecsize{1000}
+
+% reset the current fonts
+\textfonts
+\rm
+} % end of 11pt text font size definitions
+
+
+% Definitions to make the main text be 10pt Computer Modern, with
+% section, chapter, etc., sizes following suit. This is for the GNU
+% Press printing of the Emacs 22 manual. Maybe other manuals in the
+% future. Used with @smallbook, which sets the leading to 12pt.
+%
+\def\definetextfontsizex{%
+% Text fonts (10pt).
+\def\textnominalsize{10pt}
+\edef\mainmagstep{1000}
+\setfont\textrm\rmshape{10}{\mainmagstep}{OT1}
+\setfont\texttt\ttshape{10}{\mainmagstep}{OT1TT}
+\setfont\textbf\bfshape{10}{\mainmagstep}{OT1}
+\setfont\textit\itshape{10}{\mainmagstep}{OT1IT}
+\setfont\textsl\slshape{10}{\mainmagstep}{OT1}
+\setfont\textsf\sfshape{10}{\mainmagstep}{OT1}
+\setfont\textsc\scshape{10}{\mainmagstep}{OT1}
+\setfont\textttsl\ttslshape{10}{\mainmagstep}{OT1TT}
+\font\texti=cmmi10 scaled \mainmagstep
+\font\textsy=cmsy10 scaled \mainmagstep
+\def\textecsize{1000}
+
+% A few fonts for @defun names and args.
+\setfont\defbf\bfshape{10}{\magstephalf}{OT1}
+\setfont\deftt\ttshape{10}{\magstephalf}{OT1TT}
+\setfont\defttsl\ttslshape{10}{\magstephalf}{OT1TT}
+\def\df{\let\tentt=\deftt \let\tenbf = \defbf \let\tenttsl=\defttsl \bf}
+
+% Fonts for indices, footnotes, small examples (9pt).
+\def\smallnominalsize{9pt}
+\setfont\smallrm\rmshape{9}{1000}{OT1}
+\setfont\smalltt\ttshape{9}{1000}{OT1TT}
+\setfont\smallbf\bfshape{10}{900}{OT1}
+\setfont\smallit\itshape{9}{1000}{OT1IT}
+\setfont\smallsl\slshape{9}{1000}{OT1}
+\setfont\smallsf\sfshape{9}{1000}{OT1}
+\setfont\smallsc\scshape{10}{900}{OT1}
+\setfont\smallttsl\ttslshape{10}{900}{OT1TT}
+\font\smalli=cmmi9
+\font\smallsy=cmsy9
+\def\smallecsize{0900}
+
+% Fonts for small examples (8pt).
+\def\smallernominalsize{8pt}
+\setfont\smallerrm\rmshape{8}{1000}{OT1}
+\setfont\smallertt\ttshape{8}{1000}{OT1TT}
+\setfont\smallerbf\bfshape{10}{800}{OT1}
+\setfont\smallerit\itshape{8}{1000}{OT1IT}
+\setfont\smallersl\slshape{8}{1000}{OT1}
+\setfont\smallersf\sfshape{8}{1000}{OT1}
+\setfont\smallersc\scshape{10}{800}{OT1}
+\setfont\smallerttsl\ttslshape{10}{800}{OT1TT}
+\font\smalleri=cmmi8
+\font\smallersy=cmsy8
+\def\smallerecsize{0800}
+
+% Fonts for title page (20.4pt):
+\def\titlenominalsize{20pt}
+\setfont\titlerm\rmbshape{12}{\magstep3}{OT1}
+\setfont\titleit\itbshape{10}{\magstep4}{OT1IT}
+\setfont\titlesl\slbshape{10}{\magstep4}{OT1}
+\setfont\titlett\ttbshape{12}{\magstep3}{OT1TT}
+\setfont\titlettsl\ttslshape{10}{\magstep4}{OT1TT}
+\setfont\titlesf\sfbshape{17}{\magstep1}{OT1}
+\let\titlebf=\titlerm
+\setfont\titlesc\scbshape{10}{\magstep4}{OT1}
+\font\titlei=cmmi12 scaled \magstep3
+\font\titlesy=cmsy10 scaled \magstep4
+\def\titleecsize{2074}
+
+% Chapter fonts (14.4pt).
+\def\chapnominalsize{14pt}
+\setfont\chaprm\rmbshape{12}{\magstep1}{OT1}
+\setfont\chapit\itbshape{10}{\magstep2}{OT1IT}
+\setfont\chapsl\slbshape{10}{\magstep2}{OT1}
+\setfont\chaptt\ttbshape{12}{\magstep1}{OT1TT}
+\setfont\chapttsl\ttslshape{10}{\magstep2}{OT1TT}
+\setfont\chapsf\sfbshape{12}{\magstep1}{OT1}
+\let\chapbf\chaprm
+\setfont\chapsc\scbshape{10}{\magstep2}{OT1}
+\font\chapi=cmmi12 scaled \magstep1
+\font\chapsy=cmsy10 scaled \magstep2
+\def\chapecsize{1440}
+
+% Section fonts (12pt).
+\def\secnominalsize{12pt}
+\setfont\secrm\rmbshape{12}{1000}{OT1}
+\setfont\secit\itbshape{10}{\magstep1}{OT1IT}
+\setfont\secsl\slbshape{10}{\magstep1}{OT1}
+\setfont\sectt\ttbshape{12}{1000}{OT1TT}
+\setfont\secttsl\ttslshape{10}{\magstep1}{OT1TT}
+\setfont\secsf\sfbshape{12}{1000}{OT1}
+\let\secbf\secrm
+\setfont\secsc\scbshape{10}{\magstep1}{OT1}
+\font\seci=cmmi12
+\font\secsy=cmsy10 scaled \magstep1
+\def\sececsize{1200}
+
+% Subsection fonts (10pt).
+\def\ssecnominalsize{10pt}
+\setfont\ssecrm\rmbshape{10}{1000}{OT1}
+\setfont\ssecit\itbshape{10}{1000}{OT1IT}
+\setfont\ssecsl\slbshape{10}{1000}{OT1}
+\setfont\ssectt\ttbshape{10}{1000}{OT1TT}
+\setfont\ssecttsl\ttslshape{10}{1000}{OT1TT}
+\setfont\ssecsf\sfbshape{10}{1000}{OT1}
+\let\ssecbf\ssecrm
+\setfont\ssecsc\scbshape{10}{1000}{OT1}
+\font\sseci=cmmi10
+\font\ssecsy=cmsy10
+\def\ssececsize{1000}
+
+% Reduced fonts for @acro in text (9pt).
+\def\reducednominalsize{9pt}
+\setfont\reducedrm\rmshape{9}{1000}{OT1}
+\setfont\reducedtt\ttshape{9}{1000}{OT1TT}
+\setfont\reducedbf\bfshape{10}{900}{OT1}
+\setfont\reducedit\itshape{9}{1000}{OT1IT}
+\setfont\reducedsl\slshape{9}{1000}{OT1}
+\setfont\reducedsf\sfshape{9}{1000}{OT1}
+\setfont\reducedsc\scshape{10}{900}{OT1}
+\setfont\reducedttsl\ttslshape{10}{900}{OT1TT}
+\font\reducedi=cmmi9
+\font\reducedsy=cmsy9
+\def\reducedecsize{0900}
+
+% reduce space between paragraphs
+\divide\parskip by 2
+
+% reset the current fonts
+\textfonts
+\rm
+} % end of 10pt text font size definitions
+
+
+% We provide the user-level command
+% @fonttextsize 10
+% (or 11) to redefine the text font size. pt is assumed.
+%
+\def\xword{10}
+\def\xiword{11}
+%
+\parseargdef\fonttextsize{%
+ \def\textsizearg{#1}%
+ \wlog{doing @fonttextsize \textsizearg}%
+ %
+ % Set \globaldefs so that documents can use this inside @tex, since
+ % makeinfo 4.8 does not support it, but we need it nonetheless.
+ %
+ \begingroup \globaldefs=1
+ \ifx\textsizearg\xword \definetextfontsizex
+ \else \ifx\textsizearg\xiword \definetextfontsizexi
+ \else
+ \errhelp=\EMsimple
+ \errmessage{@fonttextsize only supports `10' or `11', not `\textsizearg'}
+ \fi\fi
+ \endgroup
+}
+
+
+% In order for the font changes to affect most math symbols and letters,
+% we have to define the \textfont of the standard families. Since
+% texinfo doesn't allow for producing subscripts and superscripts except
+% in the main text, we don't bother to reset \scriptfont and
+% \scriptscriptfont (which would also require loading a lot more fonts).
+%
+\def\resetmathfonts{%
+ \textfont0=\tenrm \textfont1=\teni \textfont2=\tensy
+ \textfont\itfam=\tenit \textfont\slfam=\tensl \textfont\bffam=\tenbf
+ \textfont\ttfam=\tentt \textfont\sffam=\tensf
+}
+
+% The font-changing commands redefine the meanings of \tenSTYLE, instead
+% of just \STYLE. We do this because \STYLE needs to also set the
+% current \fam for math mode. Our \STYLE (e.g., \rm) commands hardwire
+% \tenSTYLE to set the current font.
+%
+% Each font-changing command also sets the names \lsize (one size lower)
+% and \lllsize (three sizes lower). These relative commands are used in
+% the LaTeX logo and acronyms.
+%
+% This all needs generalizing, badly.
+%
+\def\textfonts{%
+ \let\tenrm=\textrm \let\tenit=\textit \let\tensl=\textsl
+ \let\tenbf=\textbf \let\tentt=\texttt \let\smallcaps=\textsc
+ \let\tensf=\textsf \let\teni=\texti \let\tensy=\textsy
+ \let\tenttsl=\textttsl
+ \def\curfontsize{text}%
+ \def\lsize{reduced}\def\lllsize{smaller}%
+ \resetmathfonts \setleading{\textleading}}
+\def\titlefonts{%
+ \let\tenrm=\titlerm \let\tenit=\titleit \let\tensl=\titlesl
+ \let\tenbf=\titlebf \let\tentt=\titlett \let\smallcaps=\titlesc
+ \let\tensf=\titlesf \let\teni=\titlei \let\tensy=\titlesy
+ \let\tenttsl=\titlettsl
+ \def\curfontsize{title}%
+ \def\lsize{chap}\def\lllsize{subsec}%
+ \resetmathfonts \setleading{25pt}}
+\def\titlefont#1{{\titlefonts\rmisbold #1}}
+\def\chapfonts{%
+ \let\tenrm=\chaprm \let\tenit=\chapit \let\tensl=\chapsl
+ \let\tenbf=\chapbf \let\tentt=\chaptt \let\smallcaps=\chapsc
+ \let\tensf=\chapsf \let\teni=\chapi \let\tensy=\chapsy
+ \let\tenttsl=\chapttsl
+ \def\curfontsize{chap}%
+ \def\lsize{sec}\def\lllsize{text}%
+ \resetmathfonts \setleading{19pt}}
+\def\secfonts{%
+ \let\tenrm=\secrm \let\tenit=\secit \let\tensl=\secsl
+ \let\tenbf=\secbf \let\tentt=\sectt \let\smallcaps=\secsc
+ \let\tensf=\secsf \let\teni=\seci \let\tensy=\secsy
+ \let\tenttsl=\secttsl
+ \def\curfontsize{sec}%
+ \def\lsize{subsec}\def\lllsize{reduced}%
+ \resetmathfonts \setleading{16pt}}
+\def\subsecfonts{%
+ \let\tenrm=\ssecrm \let\tenit=\ssecit \let\tensl=\ssecsl
+ \let\tenbf=\ssecbf \let\tentt=\ssectt \let\smallcaps=\ssecsc
+ \let\tensf=\ssecsf \let\teni=\sseci \let\tensy=\ssecsy
+ \let\tenttsl=\ssecttsl
+ \def\curfontsize{ssec}%
+ \def\lsize{text}\def\lllsize{small}%
+ \resetmathfonts \setleading{15pt}}
+\let\subsubsecfonts = \subsecfonts
+\def\reducedfonts{%
+ \let\tenrm=\reducedrm \let\tenit=\reducedit \let\tensl=\reducedsl
+ \let\tenbf=\reducedbf \let\tentt=\reducedtt \let\reducedcaps=\reducedsc
+ \let\tensf=\reducedsf \let\teni=\reducedi \let\tensy=\reducedsy
+ \let\tenttsl=\reducedttsl
+ \def\curfontsize{reduced}%
+ \def\lsize{small}\def\lllsize{smaller}%
+ \resetmathfonts \setleading{10.5pt}}
+\def\smallfonts{%
+ \let\tenrm=\smallrm \let\tenit=\smallit \let\tensl=\smallsl
+ \let\tenbf=\smallbf \let\tentt=\smalltt \let\smallcaps=\smallsc
+ \let\tensf=\smallsf \let\teni=\smalli \let\tensy=\smallsy
+ \let\tenttsl=\smallttsl
+ \def\curfontsize{small}%
+ \def\lsize{smaller}\def\lllsize{smaller}%
+ \resetmathfonts \setleading{10.5pt}}
+\def\smallerfonts{%
+ \let\tenrm=\smallerrm \let\tenit=\smallerit \let\tensl=\smallersl
+ \let\tenbf=\smallerbf \let\tentt=\smallertt \let\smallcaps=\smallersc
+ \let\tensf=\smallersf \let\teni=\smalleri \let\tensy=\smallersy
+ \let\tenttsl=\smallerttsl
+ \def\curfontsize{smaller}%
+ \def\lsize{smaller}\def\lllsize{smaller}%
+ \resetmathfonts \setleading{9.5pt}}
+
+% Fonts for short table of contents.
+\setfont\shortcontrm\rmshape{12}{1000}{OT1}
+\setfont\shortcontbf\bfshape{10}{\magstep1}{OT1} % no cmb12
+\setfont\shortcontsl\slshape{12}{1000}{OT1}
+\setfont\shortconttt\ttshape{12}{1000}{OT1TT}
+
+% Define these just so they can be easily changed for other fonts.
+\def\angleleft{$\langle$}
+\def\angleright{$\rangle$}
+
+% Set the fonts to use with the @small... environments.
+\let\smallexamplefonts = \smallfonts
+
+% About \smallexamplefonts. If we use \smallfonts (9pt), @smallexample
+% can fit this many characters:
+% 8.5x11=86 smallbook=72 a4=90 a5=69
+% If we use \scriptfonts (8pt), then we can fit this many characters:
+% 8.5x11=90+ smallbook=80 a4=90+ a5=77
+% For me, subjectively, the few extra characters that fit aren't worth
+% the additional smallness of 8pt. So I'm making the default 9pt.
+%
+% By the way, for comparison, here's what fits with @example (10pt):
+% 8.5x11=71 smallbook=60 a4=75 a5=58
+% --karl, 24jan03.
+
+% Set up the default fonts, so we can use them for creating boxes.
+%
+\definetextfontsizexi
+
+
+\message{markup,}
+
+% Check if we are currently using a typewriter font. Since all the
+% Computer Modern typewriter fonts have zero interword stretch (and
+% shrink), and it is reasonable to expect all typewriter fonts to have
+% this property, we can check that font parameter.
+%
+\def\ifmonospace{\ifdim\fontdimen3\font=0pt }
+
+% Markup style infrastructure. \defmarkupstylesetup\INITMACRO will
+% define and register \INITMACRO to be called on markup style changes.
+% \INITMACRO can check \currentmarkupstyle for the innermost
+% style and the set of \ifmarkupSTYLE switches for all styles
+% currently in effect.
+\newif\ifmarkupvar
+\newif\ifmarkupsamp
+\newif\ifmarkupkey
+%\newif\ifmarkupfile % @file == @samp.
+%\newif\ifmarkupoption % @option == @samp.
+\newif\ifmarkupcode
+\newif\ifmarkupkbd
+%\newif\ifmarkupenv % @env == @code.
+%\newif\ifmarkupcommand % @command == @code.
+\newif\ifmarkuptex % @tex (and part of @math, for now).
+\newif\ifmarkupexample
+\newif\ifmarkupverb
+\newif\ifmarkupverbatim
+
+\let\currentmarkupstyle\empty
+
+\def\setupmarkupstyle#1{%
+ \csname markup#1true\endcsname
+ \def\currentmarkupstyle{#1}%
+ \markupstylesetup
+}
+
+\let\markupstylesetup\empty
+
+\def\defmarkupstylesetup#1{%
+ \expandafter\def\expandafter\markupstylesetup
+ \expandafter{\markupstylesetup #1}%
+ \def#1%
+}
+
+% Markup style setup for left and right quotes.
+\defmarkupstylesetup\markupsetuplq{%
+ \expandafter\let\expandafter \temp \csname markupsetuplq\currentmarkupstyle\endcsname
+ \ifx\temp\relax \markupsetuplqdefault \else \temp \fi
+}
+
+\defmarkupstylesetup\markupsetuprq{%
+ \expandafter\let\expandafter \temp \csname markupsetuprq\currentmarkupstyle\endcsname
+ \ifx\temp\relax \markupsetuprqdefault \else \temp \fi
+}
+
+{
+\catcode`\'=\active
+\catcode`\`=\active
+
+\gdef\markupsetuplqdefault{\let`\lq}
+\gdef\markupsetuprqdefault{\let'\rq}
+
+\gdef\markupsetcodequoteleft{\let`\codequoteleft}
+\gdef\markupsetcodequoteright{\let'\codequoteright}
+
+\gdef\markupsetnoligaturesquoteleft{\let`\noligaturesquoteleft}
+}
+
+\let\markupsetuplqcode \markupsetcodequoteleft
+\let\markupsetuprqcode \markupsetcodequoteright
+\let\markupsetuplqexample \markupsetcodequoteleft
+\let\markupsetuprqexample \markupsetcodequoteright
+\let\markupsetuplqverb \markupsetcodequoteleft
+\let\markupsetuprqverb \markupsetcodequoteright
+\let\markupsetuplqverbatim \markupsetcodequoteleft
+\let\markupsetuprqverbatim \markupsetcodequoteright
+
+\let\markupsetuplqsamp \markupsetnoligaturesquoteleft
+\let\markupsetuplqkbd \markupsetnoligaturesquoteleft
+
+% Allow an option to not replace quotes with a regular directed right
+% quote/apostrophe (char 0x27), but instead use the undirected quote
+% from cmtt (char 0x0d). The undirected quote is ugly, so don't make it
+% the default, but it works for pasting with more pdf viewers (at least
+% evince), the lilypond developers report. xpdf does work with the
+% regular 0x27.
+%
+\def\codequoteright{%
+ \expandafter\ifx\csname SETtxicodequoteundirected\endcsname\relax
+ \expandafter\ifx\csname SETcodequoteundirected\endcsname\relax
+ '%
+ \else \char'15 \fi
+ \else \char'15 \fi
+}
+%
+% and a similar option for the left quote char vs. a grave accent.
+% Modern fonts display ASCII 0x60 as a grave accent, so some people like
+% the code environments to do likewise.
+%
+\def\codequoteleft{%
+ \expandafter\ifx\csname SETtxicodequotebacktick\endcsname\relax
+ \expandafter\ifx\csname SETcodequotebacktick\endcsname\relax
+ % [Knuth] pp. 380,381,391
+ % \relax disables Spanish ligatures ?` and !` of \tt font.
+ \relax`%
+ \else \char'22 \fi
+ \else \char'22 \fi
+}
+
+% [Knuth] pp. 380,381,391, disable Spanish ligatures ?` and !` of \tt font.
+\def\noligaturesquoteleft{\relax\lq}
+
+% Count depth in font-changes, for error checks
+\newcount\fontdepth \fontdepth=0
+
+%% Add scribe-like font environments, plus @l for inline lisp (usually sans
+%% serif) and @ii for TeX italic
+
+% \smartitalic{ARG} outputs arg in italics, followed by an italic correction
+% unless the following character is such as not to need one.
+\def\smartitalicx{\ifx\next,\else\ifx\next-\else\ifx\next.\else
+ \ptexslash\fi\fi\fi}
+\def\smartslanted#1{{\ifusingtt\ttsl\sl #1}\futurelet\next\smartitalicx}
+\def\smartitalic#1{{\ifusingtt\ttsl\it #1}\futurelet\next\smartitalicx}
+
+% like \smartslanted except unconditionally uses \ttsl.
+% @var is set to this for defun arguments.
+\def\ttslanted#1{{\ttsl #1}\futurelet\next\smartitalicx}
+
+% @cite is like \smartslanted except unconditionally use \sl. We never want
+% ttsl for book titles, do we?
+\def\cite#1{{\sl #1}\futurelet\next\smartitalicx}
+
+\let\i=\smartitalic
+\let\slanted=\smartslanted
+\def\var#1{{\setupmarkupstyle{var}\smartslanted{#1}}}
+\let\dfn=\smartslanted
+\let\emph=\smartitalic
+
+% Explicit font changes: @r, @sc, undocumented @ii.
+\def\r#1{{\rm #1}} % roman font
+\def\sc#1{{\smallcaps#1}} % smallcaps font
+\def\ii#1{{\it #1}} % italic font
+
+% @b, explicit bold. Also @strong.
+\def\b#1{{\bf #1}}
+\let\strong=\b
+
+% @sansserif, explicit sans.
+\def\sansserif#1{{\sf #1}}
+
+% We can't just use \exhyphenpenalty, because that only has effect at
+% the end of a paragraph. Restore normal hyphenation at the end of the
+% group within which \nohyphenation is presumably called.
+%
+\def\nohyphenation{\hyphenchar\font = -1 \aftergroup\restorehyphenation}
+\def\restorehyphenation{\hyphenchar\font = `- }
+
+% Set sfcode to normal for the chars that usually have another value.
+% Can't use plain's \frenchspacing because it uses the `\x notation, and
+% sometimes \x has an active definition that messes things up.
+%
+\catcode`@=11
+ \def\plainfrenchspacing{%
+ \sfcode\dotChar =\@m \sfcode\questChar=\@m \sfcode\exclamChar=\@m
+ \sfcode\colonChar=\@m \sfcode\semiChar =\@m \sfcode\commaChar =\@m
+ \def\endofsentencespacefactor{1000}% for @. and friends
+ }
+ \def\plainnonfrenchspacing{%
+ \sfcode`\.3000\sfcode`\?3000\sfcode`\!3000
+ \sfcode`\:2000\sfcode`\;1500\sfcode`\,1250
+ \def\endofsentencespacefactor{3000}% for @. and friends
+ }
+\catcode`@=\other
+\def\endofsentencespacefactor{3000}% default
+
+% @t, explicit typewriter.
+\def\t#1{%
+ {\tt \rawbackslash \plainfrenchspacing #1}%
+ \null
+}
+
+% @samp.
+\def\samp#1{{\setupmarkupstyle{samp}\lq\tclose{#1}\rq\null}}
+
+% definition of @key that produces a lozenge. Doesn't adjust to text size.
+%\setfont\keyrm\rmshape{8}{1000}{OT1}
+%\font\keysy=cmsy9
+%\def\key#1{{\keyrm\textfont2=\keysy \leavevmode\hbox{%
+% \raise0.4pt\hbox{\angleleft}\kern-.08em\vtop{%
+% \vbox{\hrule\kern-0.4pt
+% \hbox{\raise0.4pt\hbox{\vphantom{\angleleft}}#1}}%
+% \kern-0.4pt\hrule}%
+% \kern-.06em\raise0.4pt\hbox{\angleright}}}}
+
+% definition of @key with no lozenge. If the current font is already
+% monospace, don't change it; that way, we respect @kbdinputstyle. But
+% if it isn't monospace, then use \tt.
+%
+\def\key#1{{\setupmarkupstyle{key}%
+ \nohyphenation
+ \ifmonospace\else\tt\fi
+ #1}\null}
+
+% ctrl is no longer a Texinfo command.
+\def\ctrl #1{{\tt \rawbackslash \hat}#1}
+
+% @file, @option are the same as @samp.
+\let\file=\samp
+\let\option=\samp
+
+% @code is a modification of @t,
+% which makes spaces the same size as normal in the surrounding text.
+\def\tclose#1{%
+ {%
+ % Change normal interword space to be same as for the current font.
+ \spaceskip = \fontdimen2\font
+ %
+ % Switch to typewriter.
+ \tt
+ %
+ % But `\ ' produces the large typewriter interword space.
+ \def\ {{\spaceskip = 0pt{} }}%
+ %
+ % Turn off hyphenation.
+ \nohyphenation
+ %
+ \rawbackslash
+ \plainfrenchspacing
+ #1%
+ }%
+ \null
+}
+
+% We *must* turn on hyphenation at `-' and `_' in @code.
+% Otherwise, it is too hard to avoid overfull hboxes
+% in the Emacs manual, the Library manual, etc.
+
+% Unfortunately, TeX uses one parameter (\hyphenchar) to control
+% both hyphenation at - and hyphenation within words.
+% We must therefore turn them both off (\tclose does that)
+% and arrange explicitly to hyphenate at a dash.
+% -- rms.
+{
+ \catcode`\-=\active \catcode`\_=\active
+ \catcode`\'=\active \catcode`\`=\active
+ \global\let'=\rq \global\let`=\lq % default definitions
+ %
+ \global\def\code{\begingroup
+ \setupmarkupstyle{code}%
+ % The following should really be moved into \setupmarkupstyle handlers.
+ \catcode\dashChar=\active \catcode\underChar=\active
+ \ifallowcodebreaks
+ \let-\codedash
+ \let_\codeunder
+ \else
+ \let-\realdash
+ \let_\realunder
+ \fi
+ \codex
+ }
+}
+
+\def\realdash{-}
+\def\codedash{-\discretionary{}{}{}}
+\def\codeunder{%
+ % this is all so @math{@code{var_name}+1} can work. In math mode, _
+ % is "active" (mathcode"8000) and \normalunderscore (or \char95, etc.)
+ % will therefore expand the active definition of _, which is us
+ % (inside @code that is), therefore an endless loop.
+ \ifusingtt{\ifmmode
+ \mathchar"075F % class 0=ordinary, family 7=ttfam, pos 0x5F=_.
+ \else\normalunderscore \fi
+ \discretionary{}{}{}}%
+ {\_}%
+}
+\def\codex #1{\tclose{#1}\endgroup}
+
+% An additional complication: the above will allow breaks after, e.g.,
+% each of the four underscores in __typeof__. This is undesirable in
+% some manuals, especially if they don't have long identifiers in
+% general. @allowcodebreaks provides a way to control this.
+%
+\newif\ifallowcodebreaks \allowcodebreakstrue
+
+\def\keywordtrue{true}
+\def\keywordfalse{false}
+
+\parseargdef\allowcodebreaks{%
+ \def\txiarg{#1}%
+ \ifx\txiarg\keywordtrue
+ \allowcodebreakstrue
+ \else\ifx\txiarg\keywordfalse
+ \allowcodebreaksfalse
+ \else
+ \errhelp = \EMsimple
+ \errmessage{Unknown @allowcodebreaks option `\txiarg'}%
+ \fi\fi
+}
+
+% @kbd is like @code, except that if the argument is just one @key command,
+% then @kbd has no effect.
+\def\kbd#1{{\setupmarkupstyle{kbd}\def\look{#1}\expandafter\kbdfoo\look??\par}}
+
+% @kbdinputstyle -- arg is `distinct' (@kbd uses slanted tty font always),
+% `example' (@kbd uses ttsl only inside of @example and friends),
+% or `code' (@kbd uses normal tty font always).
+\parseargdef\kbdinputstyle{%
+ \def\txiarg{#1}%
+ \ifx\txiarg\worddistinct
+ \gdef\kbdexamplefont{\ttsl}\gdef\kbdfont{\ttsl}%
+ \else\ifx\txiarg\wordexample
+ \gdef\kbdexamplefont{\ttsl}\gdef\kbdfont{\tt}%
+ \else\ifx\txiarg\wordcode
+ \gdef\kbdexamplefont{\tt}\gdef\kbdfont{\tt}%
+ \else
+ \errhelp = \EMsimple
+ \errmessage{Unknown @kbdinputstyle option `\txiarg'}%
+ \fi\fi\fi
+}
+\def\worddistinct{distinct}
+\def\wordexample{example}
+\def\wordcode{code}
+
+% Default is `distinct'.
+\kbdinputstyle distinct
+
+\def\xkey{\key}
+\def\kbdfoo#1#2#3\par{\def\one{#1}\def\three{#3}\def\threex{??}%
+\ifx\one\xkey\ifx\threex\three \key{#2}%
+\else{\tclose{\kbdfont\setupmarkupstyle{kbd}\look}}\fi
+\else{\tclose{\kbdfont\setupmarkupstyle{kbd}\look}}\fi}
+
+% For @indicateurl, @env, @command quotes seem unnecessary, so use \code.
+\let\indicateurl=\code
+\let\env=\code
+\let\command=\code
+
+% @clicksequence{File @click{} Open ...}
+\def\clicksequence#1{\begingroup #1\endgroup}
+
+% @clickstyle @arrow (by default)
+\parseargdef\clickstyle{\def\click{#1}}
+\def\click{\arrow}
+
+% @uref (abbreviation for `urlref') takes an optional (comma-separated)
+% second argument specifying the text to display and an optional third
+% arg as text to display instead of (rather than in addition to) the url
+% itself. First (mandatory) arg is the url. Perhaps eventually put in
+% a hypertex \special here.
+%
+\def\uref#1{\douref #1,,,\finish}
+\def\douref#1,#2,#3,#4\finish{\begingroup
+ \unsepspaces
+ \pdfurl{#1}%
+ \setbox0 = \hbox{\ignorespaces #3}%
+ \ifdim\wd0 > 0pt
+ \unhbox0 % third arg given, show only that
+ \else
+ \setbox0 = \hbox{\ignorespaces #2}%
+ \ifdim\wd0 > 0pt
+ \ifpdf
+ \unhbox0 % PDF: 2nd arg given, show only it
+ \else
+ \unhbox0\ (\code{#1})% DVI: 2nd arg given, show both it and url
+ \fi
+ \else
+ \code{#1}% only url given, so show it
+ \fi
+ \fi
+ \endlink
+\endgroup}
+
+% @url synonym for @uref, since that's how everyone uses it.
+%
+\let\url=\uref
+
+% rms does not like angle brackets --karl, 17may97.
+% So now @email is just like @uref, unless we are pdf.
+%
+%\def\email#1{\angleleft{\tt #1}\angleright}
+\ifpdf
+ \def\email#1{\doemail#1,,\finish}
+ \def\doemail#1,#2,#3\finish{\begingroup
+ \unsepspaces
+ \pdfurl{mailto:#1}%
+ \setbox0 = \hbox{\ignorespaces #2}%
+ \ifdim\wd0>0pt\unhbox0\else\code{#1}\fi
+ \endlink
+ \endgroup}
+\else
+ \let\email=\uref
+\fi
+
+% Typeset a dimension, e.g., `in' or `pt'. The only reason for the
+% argument is to make the input look right: @dmn{pt} instead of @dmn{}pt.
+%
+\def\dmn#1{\thinspace #1}
+
+% @l was never documented to mean ``switch to the Lisp font'',
+% and it is not used as such in any manual I can find. We need it for
+% Polish suppressed-l. --karl, 22sep96.
+%\def\l#1{{\li #1}\null}
+
+% @acronym for "FBI", "NATO", and the like.
+% We print this one point size smaller, since it's intended for
+% all-uppercase.
+%
+\def\acronym#1{\doacronym #1,,\finish}
+\def\doacronym#1,#2,#3\finish{%
+ {\selectfonts\lsize #1}%
+ \def\temp{#2}%
+ \ifx\temp\empty \else
+ \space ({\unsepspaces \ignorespaces \temp \unskip})%
+ \fi
+}
+
+% @abbr for "Comput. J." and the like.
+% No font change, but don't do end-of-sentence spacing.
+%
+\def\abbr#1{\doabbr #1,,\finish}
+\def\doabbr#1,#2,#3\finish{%
+ {\plainfrenchspacing #1}%
+ \def\temp{#2}%
+ \ifx\temp\empty \else
+ \space ({\unsepspaces \ignorespaces \temp \unskip})%
+ \fi
+}
+
+
+\message{glyphs,}
+
+% @point{}, @result{}, @expansion{}, @print{}, @equiv{}.
+%
+% Since these characters are used in examples, they should be an even number of
+% \tt widths. Each \tt character is 1en, so two makes it 1em.
+%
+\def\point{$\star$}
+\def\arrow{\leavevmode\raise.05ex\hbox to 1em{\hfil$\rightarrow$\hfil}}
+\def\result{\leavevmode\raise.05ex\hbox to 1em{\hfil$\Rightarrow$\hfil}}
+\def\expansion{\leavevmode\hbox to 1em{\hfil$\mapsto$\hfil}}
+\def\print{\leavevmode\lower.1ex\hbox to 1em{\hfil$\dashv$\hfil}}
+\def\equiv{\leavevmode\hbox to 1em{\hfil$\ptexequiv$\hfil}}
+
+% The @error{} command.
+% Adapted from the TeXbook's \boxit.
+%
+\newbox\errorbox
+%
+{\tentt \global\dimen0 = 3em}% Width of the box.
+\dimen2 = .55pt % Thickness of rules
+% The text. (`r' is open on the right, `e' somewhat less so on the left.)
+\setbox0 = \hbox{\kern-.75pt \reducedsf error\kern-1.5pt}
+%
+\setbox\errorbox=\hbox to \dimen0{\hfil
+ \hsize = \dimen0 \advance\hsize by -5.8pt % Space to left+right.
+ \advance\hsize by -2\dimen2 % Rules.
+ \vbox{%
+ \hrule height\dimen2
+ \hbox{\vrule width\dimen2 \kern3pt % Space to left of text.
+ \vtop{\kern2.4pt \box0 \kern2.4pt}% Space above/below.
+ \kern3pt\vrule width\dimen2}% Space to right.
+ \hrule height\dimen2}
+ \hfil}
+%
+\def\error{\leavevmode\lower.7ex\copy\errorbox}
+
+% @pounds{} is a sterling sign, which Knuth put in the CM italic font.
+%
+\def\pounds{{\it\$}}
+
+% @euro{} comes from a separate font, depending on the current style.
+% We use the free feym* fonts from the eurosym package by Henrik
+% Theiling, which support regular, slanted, bold and bold slanted (and
+% "outlined" (blackboard board, sort of) versions, which we don't need).
+% It is available from http://www.ctan.org/tex-archive/fonts/eurosym.
+%
+% Although only regular is the truly official Euro symbol, we ignore
+% that. The Euro is designed to be slightly taller than the regular
+% font height.
+%
+% feymr - regular
+% feymo - slanted
+% feybr - bold
+% feybo - bold slanted
+%
+% There is no good (free) typewriter version, to my knowledge.
+% A feymr10 euro is ~7.3pt wide, while a normal cmtt10 char is ~5.25pt wide.
+% Hmm.
+%
+% Also doesn't work in math. Do we need to do math with euro symbols?
+% Hope not.
+%
+%
+\def\euro{{\eurofont e}}
+\def\eurofont{%
+ % We set the font at each command, rather than predefining it in
+ % \textfonts and the other font-switching commands, so that
+ % installations which never need the symbol don't have to have the
+ % font installed.
+ %
+ % There is only one designed size (nominal 10pt), so we always scale
+ % that to the current nominal size.
+ %
+ % By the way, simply using "at 1em" works for cmr10 and the like, but
+ % does not work for cmbx10 and other extended/shrunken fonts.
+ %
+ \def\eurosize{\csname\curfontsize nominalsize\endcsname}%
+ %
+ \ifx\curfontstyle\bfstylename
+ % bold:
+ \font\thiseurofont = \ifusingit{feybo10}{feybr10} at \eurosize
+ \else
+ % regular:
+ \font\thiseurofont = \ifusingit{feymo10}{feymr10} at \eurosize
+ \fi
+ \thiseurofont
+}
+
+% Glyphs from the EC fonts. We don't use \let for the aliases, because
+% sometimes we redefine the original macro, and the alias should reflect
+% the redefinition.
+%
+% Use LaTeX names for the Icelandic letters.
+\def\DH{{\ecfont \char"D0}} % Eth
+\def\dh{{\ecfont \char"F0}} % eth
+\def\TH{{\ecfont \char"DE}} % Thorn
+\def\th{{\ecfont \char"FE}} % thorn
+%
+\def\guillemetleft{{\ecfont \char"13}}
+\def\guillemotleft{\guillemetleft}
+\def\guillemetright{{\ecfont \char"14}}
+\def\guillemotright{\guillemetright}
+\def\guilsinglleft{{\ecfont \char"0E}}
+\def\guilsinglright{{\ecfont \char"0F}}
+\def\quotedblbase{{\ecfont \char"12}}
+\def\quotesinglbase{{\ecfont \char"0D}}
+%
+% This positioning is not perfect (see the ogonek LaTeX package), but
+% we have the precomposed glyphs for the most common cases. We put the
+% tests to use those glyphs in the single \ogonek macro so we have fewer
+% dummy definitions to worry about for index entries, etc.
+%
+% ogonek is also used with other letters in Lithuanian (IOU), but using
+% the precomposed glyphs for those is not so easy since they aren't in
+% the same EC font.
+\def\ogonek#1{{%
+ \def\temp{#1}%
+ \ifx\temp\macrocharA\Aogonek
+ \else\ifx\temp\macrochara\aogonek
+ \else\ifx\temp\macrocharE\Eogonek
+ \else\ifx\temp\macrochare\eogonek
+ \else
+ \ecfont \setbox0=\hbox{#1}%
+ \ifdim\ht0=1ex\accent"0C #1%
+ \else\ooalign{\unhbox0\crcr\hidewidth\char"0C \hidewidth}%
+ \fi
+ \fi\fi\fi\fi
+ }%
+}
+\def\Aogonek{{\ecfont \char"81}}\def\macrocharA{A}
+\def\aogonek{{\ecfont \char"A1}}\def\macrochara{a}
+\def\Eogonek{{\ecfont \char"86}}\def\macrocharE{E}
+\def\eogonek{{\ecfont \char"A6}}\def\macrochare{e}
+%
+% Use the ec* fonts (cm-super in outline format) for non-CM glyphs.
+\def\ecfont{%
+ % We can't distinguish serif/sans and italic/slanted, but this
+ % is used for crude hacks anyway (like adding French and German
+ % quotes to documents typeset with CM, where we lose kerning), so
+ % hopefully nobody will notice/care.
+ \edef\ecsize{\csname\curfontsize ecsize\endcsname}%
+ \edef\nominalsize{\csname\curfontsize nominalsize\endcsname}%
+ \ifx\curfontstyle\bfstylename
+ % bold:
+ \font\thisecfont = ecb\ifusingit{i}{x}\ecsize \space at \nominalsize
+ \else
+ % regular:
+ \font\thisecfont = ec\ifusingit{ti}{rm}\ecsize \space at \nominalsize
+ \fi
+ \thisecfont
+}
+
+% @registeredsymbol - R in a circle. The font for the R should really
+% be smaller yet, but lllsize is the best we can do for now.
+% Adapted from the plain.tex definition of \copyright.
+%
+\def\registeredsymbol{%
+ $^{{\ooalign{\hfil\raise.07ex\hbox{\selectfonts\lllsize R}%
+ \hfil\crcr\Orb}}%
+ }$%
+}
+
+% @textdegree - the normal degrees sign.
+%
+\def\textdegree{$^\circ$}
+
+% Laurent Siebenmann reports \Orb undefined with:
+% Textures 1.7.7 (preloaded format=plain 93.10.14) (68K) 16 APR 2004 02:38
+% so we'll define it if necessary.
+%
+\ifx\Orb\undefined
+\def\Orb{\mathhexbox20D}
+\fi
+
+% Quotes.
+\chardef\quotedblleft="5C
+\chardef\quotedblright=`\"
+\chardef\quoteleft=`\`
+\chardef\quoteright=`\'
+
+
+\message{page headings,}
+
+\newskip\titlepagetopglue \titlepagetopglue = 1.5in
+\newskip\titlepagebottomglue \titlepagebottomglue = 2pc
+
+% First the title page. Must do @settitle before @titlepage.
+\newif\ifseenauthor
+\newif\iffinishedtitlepage
+
+% Do an implicit @contents or @shortcontents after @end titlepage if the
+% user says @setcontentsaftertitlepage or @setshortcontentsaftertitlepage.
+%
+\newif\ifsetcontentsaftertitlepage
+ \let\setcontentsaftertitlepage = \setcontentsaftertitlepagetrue
+\newif\ifsetshortcontentsaftertitlepage
+ \let\setshortcontentsaftertitlepage = \setshortcontentsaftertitlepagetrue
+
+\parseargdef\shorttitlepage{\begingroup\hbox{}\vskip 1.5in \chaprm \centerline{#1}%
+ \endgroup\page\hbox{}\page}
+
+\envdef\titlepage{%
+ % Open one extra group, as we want to close it in the middle of \Etitlepage.
+ \begingroup
+ \parindent=0pt \textfonts
+ % Leave some space at the very top of the page.
+ \vglue\titlepagetopglue
+ % No rule at page bottom unless we print one at the top with @title.
+ \finishedtitlepagetrue
+ %
+ % Most title ``pages'' are actually two pages long, with space
+ % at the top of the second. We don't want the ragged left on the second.
+ \let\oldpage = \page
+ \def\page{%
+ \iffinishedtitlepage\else
+ \finishtitlepage
+ \fi
+ \let\page = \oldpage
+ \page
+ \null
+ }%
+}
+
+\def\Etitlepage{%
+ \iffinishedtitlepage\else
+ \finishtitlepage
+ \fi
+ % It is important to do the page break before ending the group,
+ % because the headline and footline are only empty inside the group.
+ % If we use the new definition of \page, we always get a blank page
+ % after the title page, which we certainly don't want.
+ \oldpage
+ \endgroup
+ %
+ % Need this before the \...aftertitlepage checks so that if they are
+ % in effect the toc pages will come out with page numbers.
+ \HEADINGSon
+ %
+ % If they want short, they certainly want long too.
+ \ifsetshortcontentsaftertitlepage
+ \shortcontents
+ \contents
+ \global\let\shortcontents = \relax
+ \global\let\contents = \relax
+ \fi
+ %
+ \ifsetcontentsaftertitlepage
+ \contents
+ \global\let\contents = \relax
+ \global\let\shortcontents = \relax
+ \fi
+}
+
+\def\finishtitlepage{%
+ \vskip4pt \hrule height 2pt width \hsize
+ \vskip\titlepagebottomglue
+ \finishedtitlepagetrue
+}
+
+%%% Macros to be used within @titlepage:
+
+\let\subtitlerm=\tenrm
+\def\subtitlefont{\subtitlerm \normalbaselineskip = 13pt \normalbaselines}
+
+\parseargdef\title{%
+ \checkenv\titlepage
+ \leftline{\titlefonts\rmisbold #1}
+ % print a rule at the page bottom also.
+ \finishedtitlepagefalse
+ \vskip4pt \hrule height 4pt width \hsize \vskip4pt
+}
+
+\parseargdef\subtitle{%
+ \checkenv\titlepage
+ {\subtitlefont \rightline{#1}}%
+}
+
+% @author should come last, but may come many times.
+% It can also be used inside @quotation.
+%
+\parseargdef\author{%
+ \def\temp{\quotation}%
+ \ifx\thisenv\temp
+ \def\quotationauthor{#1}% printed in \Equotation.
+ \else
+ \checkenv\titlepage
+ \ifseenauthor\else \vskip 0pt plus 1filll \seenauthortrue \fi
+ {\secfonts\rmisbold \leftline{#1}}%
+ \fi
+}
+
+
+%%% Set up page headings and footings.
+
+\let\thispage=\folio
+
+\newtoks\evenheadline % headline on even pages
+\newtoks\oddheadline % headline on odd pages
+\newtoks\evenfootline % footline on even pages
+\newtoks\oddfootline % footline on odd pages
+
+% Now make TeX use those variables
+\headline={{\textfonts\rm \ifodd\pageno \the\oddheadline
+ \else \the\evenheadline \fi}}
+\footline={{\textfonts\rm \ifodd\pageno \the\oddfootline
+ \else \the\evenfootline \fi}\HEADINGShook}
+\let\HEADINGShook=\relax
+
+% Commands to set those variables.
+% For example, this is what @headings on does
+% @evenheading @thistitle|@thispage|@thischapter
+% @oddheading @thischapter|@thispage|@thistitle
+% @evenfooting @thisfile||
+% @oddfooting ||@thisfile
+
+
+\def\evenheading{\parsearg\evenheadingxxx}
+\def\evenheadingxxx #1{\evenheadingyyy #1\|\|\|\|\finish}
+\def\evenheadingyyy #1\|#2\|#3\|#4\finish{%
+\global\evenheadline={\rlap{\centerline{#2}}\line{#1\hfil#3}}}
+
+\def\oddheading{\parsearg\oddheadingxxx}
+\def\oddheadingxxx #1{\oddheadingyyy #1\|\|\|\|\finish}
+\def\oddheadingyyy #1\|#2\|#3\|#4\finish{%
+\global\oddheadline={\rlap{\centerline{#2}}\line{#1\hfil#3}}}
+
+\parseargdef\everyheading{\oddheadingxxx{#1}\evenheadingxxx{#1}}%
+
+\def\evenfooting{\parsearg\evenfootingxxx}
+\def\evenfootingxxx #1{\evenfootingyyy #1\|\|\|\|\finish}
+\def\evenfootingyyy #1\|#2\|#3\|#4\finish{%
+\global\evenfootline={\rlap{\centerline{#2}}\line{#1\hfil#3}}}
+
+\def\oddfooting{\parsearg\oddfootingxxx}
+\def\oddfootingxxx #1{\oddfootingyyy #1\|\|\|\|\finish}
+\def\oddfootingyyy #1\|#2\|#3\|#4\finish{%
+ \global\oddfootline = {\rlap{\centerline{#2}}\line{#1\hfil#3}}%
+ %
+ % Leave some space for the footline. Hopefully ok to assume
+ % @evenfooting will not be used by itself.
+ \global\advance\pageheight by -12pt
+ \global\advance\vsize by -12pt
+}
+
+\parseargdef\everyfooting{\oddfootingxxx{#1}\evenfootingxxx{#1}}
+
+% @evenheadingmarks top \thischapter <- chapter at the top of a page
+% @evenheadingmarks bottom \thischapter <- chapter at the bottom of a page
+%
+% The same set of arguments for:
+%
+% @oddheadingmarks
+% @evenfootingmarks
+% @oddfootingmarks
+% @everyheadingmarks
+% @everyfootingmarks
+
+\def\evenheadingmarks{\headingmarks{even}{heading}}
+\def\oddheadingmarks{\headingmarks{odd}{heading}}
+\def\evenfootingmarks{\headingmarks{even}{footing}}
+\def\oddfootingmarks{\headingmarks{odd}{footing}}
+\def\everyheadingmarks#1 {\headingmarks{even}{heading}{#1}
+ \headingmarks{odd}{heading}{#1} }
+\def\everyfootingmarks#1 {\headingmarks{even}{footing}{#1}
+ \headingmarks{odd}{footing}{#1} }
+% #1 = even/odd, #2 = heading/footing, #3 = top/bottom.
+\def\headingmarks#1#2#3 {%
+ \expandafter\let\expandafter\temp \csname get#3headingmarks\endcsname
+ \global\expandafter\let\csname get#1#2marks\endcsname \temp
+}
+
+\everyheadingmarks bottom
+\everyfootingmarks bottom
+
+% @headings double turns headings on for double-sided printing.
+% @headings single turns headings on for single-sided printing.
+% @headings off turns them off.
+% @headings on same as @headings double, retained for compatibility.
+% @headings after turns on double-sided headings after this page.
+% @headings doubleafter turns on double-sided headings after this page.
+% @headings singleafter turns on single-sided headings after this page.
+% By default, they are off at the start of a document,
+% and turned `on' after @end titlepage.
+
+\def\headings #1 {\csname HEADINGS#1\endcsname}
+
+\def\HEADINGSoff{%
+\global\evenheadline={\hfil} \global\evenfootline={\hfil}
+\global\oddheadline={\hfil} \global\oddfootline={\hfil}}
+\HEADINGSoff
+% When we turn headings on, set the page number to 1.
+% For double-sided printing, put current file name in lower left corner,
+% chapter name on inside top of right hand pages, document
+% title on inside top of left hand pages, and page numbers on outside top
+% edge of all pages.
+\def\HEADINGSdouble{%
+\global\pageno=1
+\global\evenfootline={\hfil}
+\global\oddfootline={\hfil}
+\global\evenheadline={\line{\folio\hfil\thistitle}}
+\global\oddheadline={\line{\thischapter\hfil\folio}}
+\global\let\contentsalignmacro = \chapoddpage
+}
+\let\contentsalignmacro = \chappager
+
+% For single-sided printing, chapter title goes across top left of page,
+% page number on top right.
+\def\HEADINGSsingle{%
+\global\pageno=1
+\global\evenfootline={\hfil}
+\global\oddfootline={\hfil}
+\global\evenheadline={\line{\thischapter\hfil\folio}}
+\global\oddheadline={\line{\thischapter\hfil\folio}}
+\global\let\contentsalignmacro = \chappager
+}
+\def\HEADINGSon{\HEADINGSdouble}
+
+\def\HEADINGSafter{\let\HEADINGShook=\HEADINGSdoublex}
+\let\HEADINGSdoubleafter=\HEADINGSafter
+\def\HEADINGSdoublex{%
+\global\evenfootline={\hfil}
+\global\oddfootline={\hfil}
+\global\evenheadline={\line{\folio\hfil\thistitle}}
+\global\oddheadline={\line{\thischapter\hfil\folio}}
+\global\let\contentsalignmacro = \chapoddpage
+}
+
+\def\HEADINGSsingleafter{\let\HEADINGShook=\HEADINGSsinglex}
+\def\HEADINGSsinglex{%
+\global\evenfootline={\hfil}
+\global\oddfootline={\hfil}
+\global\evenheadline={\line{\thischapter\hfil\folio}}
+\global\oddheadline={\line{\thischapter\hfil\folio}}
+\global\let\contentsalignmacro = \chappager
+}
+
+% Subroutines used in generating headings
+% This produces Day Month Year style of output.
+% Only define if not already defined, in case a txi-??.tex file has set
+% up a different format (e.g., txi-cs.tex does this).
+\ifx\today\undefined
+\def\today{%
+ \number\day\space
+ \ifcase\month
+ \or\putwordMJan\or\putwordMFeb\or\putwordMMar\or\putwordMApr
+ \or\putwordMMay\or\putwordMJun\or\putwordMJul\or\putwordMAug
+ \or\putwordMSep\or\putwordMOct\or\putwordMNov\or\putwordMDec
+ \fi
+ \space\number\year}
+\fi
+
+% @settitle line... specifies the title of the document, for headings.
+% It generates no output of its own.
+\def\thistitle{\putwordNoTitle}
+\def\settitle{\parsearg{\gdef\thistitle}}
+
+
+\message{tables,}
+% Tables -- @table, @ftable, @vtable, @item(x).
+
+% default indentation of table text
+\newdimen\tableindent \tableindent=.8in
+% default indentation of @itemize and @enumerate text
+\newdimen\itemindent \itemindent=.3in
+% margin between end of table item and start of table text.
+\newdimen\itemmargin \itemmargin=.1in
+
+% used internally for \itemindent minus \itemmargin
+\newdimen\itemmax
+
+% Note @table, @ftable, and @vtable define @item, @itemx, etc., with
+% these defs.
+% They also define \itemindex
+% to index the item name in whatever manner is desired (perhaps none).
+
+\newif\ifitemxneedsnegativevskip
+
+\def\itemxpar{\par\ifitemxneedsnegativevskip\nobreak\vskip-\parskip\nobreak\fi}
+
+\def\internalBitem{\smallbreak \parsearg\itemzzz}
+\def\internalBitemx{\itemxpar \parsearg\itemzzz}
+
+\def\itemzzz #1{\begingroup %
+ \advance\hsize by -\rightskip
+ \advance\hsize by -\tableindent
+ \setbox0=\hbox{\itemindicate{#1}}%
+ \itemindex{#1}%
+ \nobreak % This prevents a break before @itemx.
+ %
+ % If the item text does not fit in the space we have, put it on a line
+ % by itself, and do not allow a page break either before or after that
+ % line. We do not start a paragraph here because then if the next
+ % command is, e.g., @kindex, the whatsit would get put into the
+ % horizontal list on a line by itself, resulting in extra blank space.
+ \ifdim \wd0>\itemmax
+ %
+ % Make this a paragraph so we get the \parskip glue and wrapping,
+ % but leave it ragged-right.
+ \begingroup
+ \advance\leftskip by-\tableindent
+ \advance\hsize by\tableindent
+ \advance\rightskip by0pt plus1fil
+ \leavevmode\unhbox0\par
+ \endgroup
+ %
+ % We're going to be starting a paragraph, but we don't want the
+ % \parskip glue -- logically it's part of the @item we just started.
+ \nobreak \vskip-\parskip
+ %
+ % Stop a page break at the \parskip glue coming up. However, if
+ % what follows is an environment such as @example, there will be no
+ % \parskip glue; then the negative vskip we just inserted would
+ % cause the example and the item to crash together. So we use this
+ % bizarre value of 10001 as a signal to \aboveenvbreak to insert
+ % \parskip glue after all. Section titles are handled this way also.
+ %
+ \penalty 10001
+ \endgroup
+ \itemxneedsnegativevskipfalse
+ \else
+ % The item text fits into the space. Start a paragraph, so that the
+ % following text (if any) will end up on the same line.
+ \noindent
+ % Do this with kerns and \unhbox so that if there is a footnote in
+ % the item text, it can migrate to the main vertical list and
+ % eventually be printed.
+ \nobreak\kern-\tableindent
+ \dimen0 = \itemmax \advance\dimen0 by \itemmargin \advance\dimen0 by -\wd0
+ \unhbox0
+ \nobreak\kern\dimen0
+ \endgroup
+ \itemxneedsnegativevskiptrue
+ \fi
+}
+
+\def\item{\errmessage{@item while not in a list environment}}
+\def\itemx{\errmessage{@itemx while not in a list environment}}
+
+% @table, @ftable, @vtable.
+\envdef\table{%
+ \let\itemindex\gobble
+ \tablecheck{table}%
+}
+\envdef\ftable{%
+ \def\itemindex ##1{\doind {fn}{\code{##1}}}%
+ \tablecheck{ftable}%
+}
+\envdef\vtable{%
+ \def\itemindex ##1{\doind {vr}{\code{##1}}}%
+ \tablecheck{vtable}%
+}
+\def\tablecheck#1{%
+ \ifnum \the\catcode`\^^M=\active
+ \endgroup
+ \errmessage{This command won't work in this context; perhaps the problem is
+ that we are \inenvironment\thisenv}%
+ \def\next{\doignore{#1}}%
+ \else
+ \let\next\tablex
+ \fi
+ \next
+}
+\def\tablex#1{%
+ \def\itemindicate{#1}%
+ \parsearg\tabley
+}
+\def\tabley#1{%
+ {%
+ \makevalueexpandable
+ \edef\temp{\noexpand\tablez #1\space\space\space}%
+ \expandafter
+ }\temp \endtablez
+}
+\def\tablez #1 #2 #3 #4\endtablez{%
+ \aboveenvbreak
+ \ifnum 0#1>0 \advance \leftskip by #1\mil \fi
+ \ifnum 0#2>0 \tableindent=#2\mil \fi
+ \ifnum 0#3>0 \advance \rightskip by #3\mil \fi
+ \itemmax=\tableindent
+ \advance \itemmax by -\itemmargin
+ \advance \leftskip by \tableindent
+ \exdentamount=\tableindent
+ \parindent = 0pt
+ \parskip = \smallskipamount
+ \ifdim \parskip=0pt \parskip=2pt \fi
+ \let\item = \internalBitem
+ \let\itemx = \internalBitemx
+}
+\def\Etable{\endgraf\afterenvbreak}
+\let\Eftable\Etable
+\let\Evtable\Etable
+\let\Eitemize\Etable
+\let\Eenumerate\Etable
+
+% This is the counter used by @enumerate, which is really @itemize
+
+\newcount \itemno
+
+\envdef\itemize{\parsearg\doitemize}
+
+\def\doitemize#1{%
+ \aboveenvbreak
+ \itemmax=\itemindent
+ \advance\itemmax by -\itemmargin
+ \advance\leftskip by \itemindent
+ \exdentamount=\itemindent
+ \parindent=0pt
+ \parskip=\smallskipamount
+ \ifdim\parskip=0pt \parskip=2pt \fi
+ %
+ % Try typesetting the item mark that if the document erroneously says
+ % something like @itemize @samp (intending @table), there's an error
+ % right away at the @itemize. It's not the best error message in the
+ % world, but it's better than leaving it to the @item. This means if
+ % the user wants an empty mark, they have to say @w{} not just @w.
+ \def\itemcontents{#1}%
+ \setbox0 = \hbox{\itemcontents}%
+ %
+ % @itemize with no arg is equivalent to @itemize @bullet.
+ \ifx\itemcontents\empty\def\itemcontents{\bullet}\fi
+ %
+ \let\item=\itemizeitem
+}
+
+% Definition of @item while inside @itemize and @enumerate.
+%
+\def\itemizeitem{%
+ \advance\itemno by 1 % for enumerations
+ {\let\par=\endgraf \smallbreak}% reasonable place to break
+ {%
+ % If the document has an @itemize directly after a section title, a
+ % \nobreak will be last on the list, and \sectionheading will have
+ % done a \vskip-\parskip. In that case, we don't want to zero
+ % parskip, or the item text will crash with the heading. On the
+ % other hand, when there is normal text preceding the item (as there
+ % usually is), we do want to zero parskip, or there would be too much
+ % space. In that case, we won't have a \nobreak before. At least
+ % that's the theory.
+ \ifnum\lastpenalty<10000 \parskip=0in \fi
+ \noindent
+ \hbox to 0pt{\hss \itemcontents \kern\itemmargin}%
+ %
+ \vadjust{\penalty 1200}}% not good to break after first line of item.
+ \flushcr
+}
+
+% \splitoff TOKENS\endmark defines \first to be the first token in
+% TOKENS, and \rest to be the remainder.
+%
+\def\splitoff#1#2\endmark{\def\first{#1}\def\rest{#2}}%
+
+% Allow an optional argument of an uppercase letter, lowercase letter,
+% or number, to specify the first label in the enumerated list. No
+% argument is the same as `1'.
+%
+\envparseargdef\enumerate{\enumeratey #1 \endenumeratey}
+\def\enumeratey #1 #2\endenumeratey{%
+ % If we were given no argument, pretend we were given `1'.
+ \def\thearg{#1}%
+ \ifx\thearg\empty \def\thearg{1}\fi
+ %
+ % Detect if the argument is a single token. If so, it might be a
+ % letter. Otherwise, the only valid thing it can be is a number.
+ % (We will always have one token, because of the test we just made.
+ % This is a good thing, since \splitoff doesn't work given nothing at
+ % all -- the first parameter is undelimited.)
+ \expandafter\splitoff\thearg\endmark
+ \ifx\rest\empty
+ % Only one token in the argument. It could still be anything.
+ % A ``lowercase letter'' is one whose \lccode is nonzero.
+ % An ``uppercase letter'' is one whose \lccode is both nonzero, and
+ % not equal to itself.
+ % Otherwise, we assume it's a number.
+ %
+ % We need the \relax at the end of the \ifnum lines to stop TeX from
+ % continuing to look for a <number>.
+ %
+ \ifnum\lccode\expandafter`\thearg=0\relax
+ \numericenumerate % a number (we hope)
+ \else
+ % It's a letter.
+ \ifnum\lccode\expandafter`\thearg=\expandafter`\thearg\relax
+ \lowercaseenumerate % lowercase letter
+ \else
+ \uppercaseenumerate % uppercase letter
+ \fi
+ \fi
+ \else
+ % Multiple tokens in the argument. We hope it's a number.
+ \numericenumerate
+ \fi
+}
+
+% An @enumerate whose labels are integers. The starting integer is
+% given in \thearg.
+%
+\def\numericenumerate{%
+ \itemno = \thearg
+ \startenumeration{\the\itemno}%
+}
+
+% The starting (lowercase) letter is in \thearg.
+\def\lowercaseenumerate{%
+ \itemno = \expandafter`\thearg
+ \startenumeration{%
+ % Be sure we're not beyond the end of the alphabet.
+ \ifnum\itemno=0
+ \errmessage{No more lowercase letters in @enumerate; get a bigger
+ alphabet}%
+ \fi
+ \char\lccode\itemno
+ }%
+}
+
+% The starting (uppercase) letter is in \thearg.
+\def\uppercaseenumerate{%
+ \itemno = \expandafter`\thearg
+ \startenumeration{%
+ % Be sure we're not beyond the end of the alphabet.
+ \ifnum\itemno=0
+ \errmessage{No more uppercase letters in @enumerate; get a bigger
+ alphabet}
+ \fi
+ \char\uccode\itemno
+ }%
+}
+
+% Call \doitemize, adding a period to the first argument and supplying the
+% common last two arguments. Also subtract one from the initial value in
+% \itemno, since @item increments \itemno.
+%
+\def\startenumeration#1{%
+ \advance\itemno by -1
+ \doitemize{#1.}\flushcr
+}
+
+% @alphaenumerate and @capsenumerate are abbreviations for giving an arg
+% to @enumerate.
+%
+\def\alphaenumerate{\enumerate{a}}
+\def\capsenumerate{\enumerate{A}}
+\def\Ealphaenumerate{\Eenumerate}
+\def\Ecapsenumerate{\Eenumerate}
+
+
+% @multitable macros
+% Amy Hendrickson, 8/18/94, 3/6/96
+%
+% @multitable ... @end multitable will make as many columns as desired.
+% Contents of each column will wrap at width given in preamble. Width
+% can be specified either with sample text given in a template line,
+% or in percent of \hsize, the current width of text on page.
+
+% Table can continue over pages but will only break between lines.
+
+% To make preamble:
+%
+% Either define widths of columns in terms of percent of \hsize:
+% @multitable @columnfractions .25 .3 .45
+% @item ...
+%
+% Numbers following @columnfractions are the percent of the total
+% current hsize to be used for each column. You may use as many
+% columns as desired.
+
+
+% Or use a template:
+% @multitable {Column 1 template} {Column 2 template} {Column 3 template}
+% @item ...
+% using the widest term desired in each column.
+
+% Each new table line starts with @item, each subsequent new column
+% starts with @tab. Empty columns may be produced by supplying @tab's
+% with nothing between them for as many times as empty columns are needed,
+% ie, @tab at tab@tab will produce two empty columns.
+
+% @item, @tab do not need to be on their own lines, but it will not hurt
+% if they are.
+
+% Sample multitable:
+
+% @multitable {Column 1 template} {Column 2 template} {Column 3 template}
+% @item first col stuff @tab second col stuff @tab third col
+% @item
+% first col stuff
+% @tab
+% second col stuff
+% @tab
+% third col
+% @item first col stuff @tab second col stuff
+% @tab Many paragraphs of text may be used in any column.
+%
+% They will wrap at the width determined by the template.
+% @item at tab@tab This will be in third column.
+% @end multitable
+
+% Default dimensions may be reset by user.
+% @multitableparskip is vertical space between paragraphs in table.
+% @multitableparindent is paragraph indent in table.
+% @multitablecolmargin is horizontal space to be left between columns.
+% @multitablelinespace is space to leave between table items, baseline
+% to baseline.
+% 0pt means it depends on current normal line spacing.
+%
+\newskip\multitableparskip
+\newskip\multitableparindent
+\newdimen\multitablecolspace
+\newskip\multitablelinespace
+\multitableparskip=0pt
+\multitableparindent=6pt
+\multitablecolspace=12pt
+\multitablelinespace=0pt
+
+% Macros used to set up halign preamble:
+%
+\let\endsetuptable\relax
+\def\xendsetuptable{\endsetuptable}
+\let\columnfractions\relax
+\def\xcolumnfractions{\columnfractions}
+\newif\ifsetpercent
+
+% #1 is the @columnfraction, usually a decimal number like .5, but might
+% be just 1. We just use it, whatever it is.
+%
+\def\pickupwholefraction#1 {%
+ \global\advance\colcount by 1
+ \expandafter\xdef\csname col\the\colcount\endcsname{#1\hsize}%
+ \setuptable
+}
+
+\newcount\colcount
+\def\setuptable#1{%
+ \def\firstarg{#1}%
+ \ifx\firstarg\xendsetuptable
+ \let\go = \relax
+ \else
+ \ifx\firstarg\xcolumnfractions
+ \global\setpercenttrue
+ \else
+ \ifsetpercent
+ \let\go\pickupwholefraction
+ \else
+ \global\advance\colcount by 1
+ \setbox0=\hbox{#1\unskip\space}% Add a normal word space as a
+ % separator; typically that is always in the input, anyway.
+ \expandafter\xdef\csname col\the\colcount\endcsname{\the\wd0}%
+ \fi
+ \fi
+ \ifx\go\pickupwholefraction
+ % Put the argument back for the \pickupwholefraction call, so
+ % we'll always have a period there to be parsed.
+ \def\go{\pickupwholefraction#1}%
+ \else
+ \let\go = \setuptable
+ \fi%
+ \fi
+ \go
+}
+
+% multitable-only commands.
+%
+% @headitem starts a heading row, which we typeset in bold.
+% Assignments have to be global since we are inside the implicit group
+% of an alignment entry. \everycr resets \everytab so we don't have to
+% undo it ourselves.
+\def\headitemfont{\b}% for people to use in the template row; not changeable
+\def\headitem{%
+ \checkenv\multitable
+ \crcr
+ \global\everytab={\bf}% can't use \headitemfont since the parsing differs
+ \the\everytab % for the first item
+}%
+%
+% A \tab used to include \hskip1sp. But then the space in a template
+% line is not enough. That is bad. So let's go back to just `&' until
+% we again encounter the problem the 1sp was intended to solve.
+% --karl, nathan at acm.org, 20apr99.
+\def\tab{\checkenv\multitable &\the\everytab}%
+
+% @multitable ... @end multitable definitions:
+%
+\newtoks\everytab % insert after every tab.
+%
+\envdef\multitable{%
+ \vskip\parskip
+ \startsavinginserts
+ %
+ % @item within a multitable starts a normal row.
+ % We use \def instead of \let so that if one of the multitable entries
+ % contains an @itemize, we don't choke on the \item (seen as \crcr aka
+ % \endtemplate) expanding \doitemize.
+ \def\item{\crcr}%
+ %
+ \tolerance=9500
+ \hbadness=9500
+ \setmultitablespacing
+ \parskip=\multitableparskip
+ \parindent=\multitableparindent
+ \overfullrule=0pt
+ \global\colcount=0
+ %
+ \everycr = {%
+ \noalign{%
+ \global\everytab={}%
+ \global\colcount=0 % Reset the column counter.
+ % Check for saved footnotes, etc.
+ \checkinserts
+ % Keeps underfull box messages off when table breaks over pages.
+ %\filbreak
+ % Maybe so, but it also creates really weird page breaks when the
+ % table breaks over pages. Wouldn't \vfil be better? Wait until the
+ % problem manifests itself, so it can be fixed for real --karl.
+ }%
+ }%
+ %
+ \parsearg\domultitable
+}
+\def\domultitable#1{%
+ % To parse everything between @multitable and @item:
+ \setuptable#1 \endsetuptable
+ %
+ % This preamble sets up a generic column definition, which will
+ % be used as many times as user calls for columns.
+ % \vtop will set a single line and will also let text wrap and
+ % continue for many paragraphs if desired.
+ \halign\bgroup &%
+ \global\advance\colcount by 1
+ \multistrut
+ \vtop{%
+ % Use the current \colcount to find the correct column width:
+ \hsize=\expandafter\csname col\the\colcount\endcsname
+ %
+ % In order to keep entries from bumping into each other
+ % we will add a \leftskip of \multitablecolspace to all columns after
+ % the first one.
+ %
+ % If a template has been used, we will add \multitablecolspace
+ % to the width of each template entry.
+ %
+ % If the user has set preamble in terms of percent of \hsize we will
+ % use that dimension as the width of the column, and the \leftskip
+ % will keep entries from bumping into each other. Table will start at
+ % left margin and final column will justify at right margin.
+ %
+ % Make sure we don't inherit \rightskip from the outer environment.
+ \rightskip=0pt
+ \ifnum\colcount=1
+ % The first column will be indented with the surrounding text.
+ \advance\hsize by\leftskip
+ \else
+ \ifsetpercent \else
+ % If user has not set preamble in terms of percent of \hsize
+ % we will advance \hsize by \multitablecolspace.
+ \advance\hsize by \multitablecolspace
+ \fi
+ % In either case we will make \leftskip=\multitablecolspace:
+ \leftskip=\multitablecolspace
+ \fi
+ % Ignoring space at the beginning and end avoids an occasional spurious
+ % blank line, when TeX decides to break the line at the space before the
+ % box from the multistrut, so the strut ends up on a line by itself.
+ % For example:
+ % @multitable @columnfractions .11 .89
+ % @item @code{#}
+ % @tab Legal holiday which is valid in major parts of the whole country.
+ % Is automatically provided with highlighting sequences respectively
+ % marking characters.
+ \noindent\ignorespaces##\unskip\multistrut
+ }\cr
+}
+\def\Emultitable{%
+ \crcr
+ \egroup % end the \halign
+ \global\setpercentfalse
+}
+
+\def\setmultitablespacing{%
+ \def\multistrut{\strut}% just use the standard line spacing
+ %
+ % Compute \multitablelinespace (if not defined by user) for use in
+ % \multitableparskip calculation. We used define \multistrut based on
+ % this, but (ironically) that caused the spacing to be off.
+ % See bug-texinfo report from Werner Lemberg, 31 Oct 2004 12:52:20 +0100.
+\ifdim\multitablelinespace=0pt
+\setbox0=\vbox{X}\global\multitablelinespace=\the\baselineskip
+\global\advance\multitablelinespace by-\ht0
+\fi
+%% Test to see if parskip is larger than space between lines of
+%% table. If not, do nothing.
+%% If so, set to same dimension as multitablelinespace.
+\ifdim\multitableparskip>\multitablelinespace
+\global\multitableparskip=\multitablelinespace
+\global\advance\multitableparskip-7pt %% to keep parskip somewhat smaller
+ %% than skip between lines in the table.
+\fi%
+\ifdim\multitableparskip=0pt
+\global\multitableparskip=\multitablelinespace
+\global\advance\multitableparskip-7pt %% to keep parskip somewhat smaller
+ %% than skip between lines in the table.
+\fi}
+
+
+\message{conditionals,}
+
+% @iftex, @ifnotdocbook, @ifnothtml, @ifnotinfo, @ifnotplaintext,
+% @ifnotxml always succeed. They currently do nothing; we don't
+% attempt to check whether the conditionals are properly nested. But we
+% have to remember that they are conditionals, so that @end doesn't
+% attempt to close an environment group.
+%
+\def\makecond#1{%
+ \expandafter\let\csname #1\endcsname = \relax
+ \expandafter\let\csname iscond.#1\endcsname = 1
+}
+\makecond{iftex}
+\makecond{ifnotdocbook}
+\makecond{ifnothtml}
+\makecond{ifnotinfo}
+\makecond{ifnotplaintext}
+\makecond{ifnotxml}
+
+% Ignore @ignore, @ifhtml, @ifinfo, and the like.
+%
+\def\direntry{\doignore{direntry}}
+\def\documentdescription{\doignore{documentdescription}}
+\def\docbook{\doignore{docbook}}
+\def\html{\doignore{html}}
+\def\ifdocbook{\doignore{ifdocbook}}
+\def\ifhtml{\doignore{ifhtml}}
+\def\ifinfo{\doignore{ifinfo}}
+\def\ifnottex{\doignore{ifnottex}}
+\def\ifplaintext{\doignore{ifplaintext}}
+\def\ifxml{\doignore{ifxml}}
+\def\ignore{\doignore{ignore}}
+\def\menu{\doignore{menu}}
+\def\xml{\doignore{xml}}
+
+% Ignore text until a line `@end #1', keeping track of nested conditionals.
+%
+% A count to remember the depth of nesting.
+\newcount\doignorecount
+
+\def\doignore#1{\begingroup
+ % Scan in ``verbatim'' mode:
+ \obeylines
+ \catcode`\@ = \other
+ \catcode`\{ = \other
+ \catcode`\} = \other
+ %
+ % Make sure that spaces turn into tokens that match what \doignoretext wants.
+ \spaceisspace
+ %
+ % Count number of #1's that we've seen.
+ \doignorecount = 0
+ %
+ % Swallow text until we reach the matching `@end #1'.
+ \dodoignore{#1}%
+}
+
+{ \catcode`_=11 % We want to use \_STOP_ which cannot appear in texinfo source.
+ \obeylines %
+ %
+ \gdef\dodoignore#1{%
+ % #1 contains the command name as a string, e.g., `ifinfo'.
+ %
+ % Define a command to find the next `@end #1'.
+ \long\def\doignoretext##1^^M at end #1{%
+ \doignoretextyyy##1^^M@#1\_STOP_}%
+ %
+ % And this command to find another #1 command, at the beginning of a
+ % line. (Otherwise, we would consider a line `@c @ifset', for
+ % example, to count as an @ifset for nesting.)
+ \long\def\doignoretextyyy##1^^M@#1##2\_STOP_{\doignoreyyy{##2}\_STOP_}%
+ %
+ % And now expand that command.
+ \doignoretext ^^M%
+ }%
+}
+
+\def\doignoreyyy#1{%
+ \def\temp{#1}%
+ \ifx\temp\empty % Nothing found.
+ \let\next\doignoretextzzz
+ \else % Found a nested condition, ...
+ \advance\doignorecount by 1
+ \let\next\doignoretextyyy % ..., look for another.
+ % If we're here, #1 ends with ^^M\ifinfo (for example).
+ \fi
+ \next #1% the token \_STOP_ is present just after this macro.
+}
+
+% We have to swallow the remaining "\_STOP_".
+%
+\def\doignoretextzzz#1{%
+ \ifnum\doignorecount = 0 % We have just found the outermost @end.
+ \let\next\enddoignore
+ \else % Still inside a nested condition.
+ \advance\doignorecount by -1
+ \let\next\doignoretext % Look for the next @end.
+ \fi
+ \next
+}
+
+% Finish off ignored text.
+{ \obeylines%
+ % Ignore anything after the last `@end #1'; this matters in verbatim
+ % environments, where otherwise the newline after an ignored conditional
+ % would result in a blank line in the output.
+ \gdef\enddoignore#1^^M{\endgroup\ignorespaces}%
+}
+
+
+% @set VAR sets the variable VAR to an empty value.
+% @set VAR REST-OF-LINE sets VAR to the value REST-OF-LINE.
+%
+% Since we want to separate VAR from REST-OF-LINE (which might be
+% empty), we can't just use \parsearg; we have to insert a space of our
+% own to delimit the rest of the line, and then take it out again if we
+% didn't need it.
+% We rely on the fact that \parsearg sets \catcode`\ =10.
+%
+\parseargdef\set{\setyyy#1 \endsetyyy}
+\def\setyyy#1 #2\endsetyyy{%
+ {%
+ \makevalueexpandable
+ \def\temp{#2}%
+ \edef\next{\gdef\makecsname{SET#1}}%
+ \ifx\temp\empty
+ \next{}%
+ \else
+ \setzzz#2\endsetzzz
+ \fi
+ }%
+}
+% Remove the trailing space \setxxx inserted.
+\def\setzzz#1 \endsetzzz{\next{#1}}
+
+% @clear VAR clears (i.e., unsets) the variable VAR.
+%
+\parseargdef\clear{%
+ {%
+ \makevalueexpandable
+ \global\expandafter\let\csname SET#1\endcsname=\relax
+ }%
+}
+
+% @value{foo} gets the text saved in variable foo.
+\def\value{\begingroup\makevalueexpandable\valuexxx}
+\def\valuexxx#1{\expandablevalue{#1}\endgroup}
+{
+ \catcode`\- = \active \catcode`\_ = \active
+ %
+ \gdef\makevalueexpandable{%
+ \let\value = \expandablevalue
+ % We don't want these characters active, ...
+ \catcode`\-=\other \catcode`\_=\other
+ % ..., but we might end up with active ones in the argument if
+ % we're called from @code, as @code{@value{foo-bar_}}, though.
+ % So \let them to their normal equivalents.
+ \let-\realdash \let_\normalunderscore
+ }
+}
+
+% We have this subroutine so that we can handle at least some @value's
+% properly in indexes (we call \makevalueexpandable in \indexdummies).
+% The command has to be fully expandable (if the variable is set), since
+% the result winds up in the index file. This means that if the
+% variable's value contains other Texinfo commands, it's almost certain
+% it will fail (although perhaps we could fix that with sufficient work
+% to do a one-level expansion on the result, instead of complete).
+%
+\def\expandablevalue#1{%
+ \expandafter\ifx\csname SET#1\endcsname\relax
+ {[No value for ``#1'']}%
+ \message{Variable `#1', used in @value, is not set.}%
+ \else
+ \csname SET#1\endcsname
+ \fi
+}
+
+% @ifset VAR ... @end ifset reads the `...' iff VAR has been defined
+% with @set.
+%
+% To get special treatment of `@end ifset,' call \makeond and the redefine.
+%
+\makecond{ifset}
+\def\ifset{\parsearg{\doifset{\let\next=\ifsetfail}}}
+\def\doifset#1#2{%
+ {%
+ \makevalueexpandable
+ \let\next=\empty
+ \expandafter\ifx\csname SET#2\endcsname\relax
+ #1% If not set, redefine \next.
+ \fi
+ \expandafter
+ }\next
+}
+\def\ifsetfail{\doignore{ifset}}
+
+% @ifclear VAR ... @end ifclear reads the `...' iff VAR has never been
+% defined with @set, or has been undefined with @clear.
+%
+% The `\else' inside the `\doifset' parameter is a trick to reuse the
+% above code: if the variable is not set, do nothing, if it is set,
+% then redefine \next to \ifclearfail.
+%
+\makecond{ifclear}
+\def\ifclear{\parsearg{\doifset{\else \let\next=\ifclearfail}}}
+\def\ifclearfail{\doignore{ifclear}}
+
+% @dircategory CATEGORY -- specify a category of the dir file
+% which this file should belong to. Ignore this in TeX.
+\let\dircategory=\comment
+
+% @defininfoenclose.
+\let\definfoenclose=\comment
+
+
+\message{indexing,}
+% Index generation facilities
+
+% Define \newwrite to be identical to plain tex's \newwrite
+% except not \outer, so it can be used within macros and \if's.
+\edef\newwrite{\makecsname{ptexnewwrite}}
+
+% \newindex {foo} defines an index named foo.
+% It automatically defines \fooindex such that
+% \fooindex ...rest of line... puts an entry in the index foo.
+% It also defines \fooindfile to be the number of the output channel for
+% the file that accumulates this index. The file's extension is foo.
+% The name of an index should be no more than 2 characters long
+% for the sake of vms.
+%
+\def\newindex#1{%
+ \iflinks
+ \expandafter\newwrite \csname#1indfile\endcsname
+ \openout \csname#1indfile\endcsname \jobname.#1 % Open the file
+ \fi
+ \expandafter\xdef\csname#1index\endcsname{% % Define @#1index
+ \noexpand\doindex{#1}}
+}
+
+% @defindex foo == \newindex{foo}
+%
+\def\defindex{\parsearg\newindex}
+
+% Define @defcodeindex, like @defindex except put all entries in @code.
+%
+\def\defcodeindex{\parsearg\newcodeindex}
+%
+\def\newcodeindex#1{%
+ \iflinks
+ \expandafter\newwrite \csname#1indfile\endcsname
+ \openout \csname#1indfile\endcsname \jobname.#1
+ \fi
+ \expandafter\xdef\csname#1index\endcsname{%
+ \noexpand\docodeindex{#1}}%
+}
+
+
+% @synindex foo bar makes index foo feed into index bar.
+% Do this instead of @defindex foo if you don't want it as a separate index.
+%
+% @syncodeindex foo bar similar, but put all entries made for index foo
+% inside @code.
+%
+\def\synindex#1 #2 {\dosynindex\doindex{#1}{#2}}
+\def\syncodeindex#1 #2 {\dosynindex\docodeindex{#1}{#2}}
+
+% #1 is \doindex or \docodeindex, #2 the index getting redefined (foo),
+% #3 the target index (bar).
+\def\dosynindex#1#2#3{%
+ % Only do \closeout if we haven't already done it, else we'll end up
+ % closing the target index.
+ \expandafter \ifx\csname donesynindex#2\endcsname \relax
+ % The \closeout helps reduce unnecessary open files; the limit on the
+ % Acorn RISC OS is a mere 16 files.
+ \expandafter\closeout\csname#2indfile\endcsname
+ \expandafter\let\csname donesynindex#2\endcsname = 1
+ \fi
+ % redefine \fooindfile:
+ \expandafter\let\expandafter\temp\expandafter=\csname#3indfile\endcsname
+ \expandafter\let\csname#2indfile\endcsname=\temp
+ % redefine \fooindex:
+ \expandafter\xdef\csname#2index\endcsname{\noexpand#1{#3}}%
+}
+
+% Define \doindex, the driver for all \fooindex macros.
+% Argument #1 is generated by the calling \fooindex macro,
+% and it is "foo", the name of the index.
+
+% \doindex just uses \parsearg; it calls \doind for the actual work.
+% This is because \doind is more useful to call from other macros.
+
+% There is also \dosubind {index}{topic}{subtopic}
+% which makes an entry in a two-level index such as the operation index.
+
+\def\doindex#1{\edef\indexname{#1}\parsearg\singleindexer}
+\def\singleindexer #1{\doind{\indexname}{#1}}
+
+% like the previous two, but they put @code around the argument.
+\def\docodeindex#1{\edef\indexname{#1}\parsearg\singlecodeindexer}
+\def\singlecodeindexer #1{\doind{\indexname}{\code{#1}}}
+
+% Take care of Texinfo commands that can appear in an index entry.
+% Since there are some commands we want to expand, and others we don't,
+% we have to laboriously prevent expansion for those that we don't.
+%
+\def\indexdummies{%
+ \escapechar = `\\ % use backslash in output files.
+ \def\@{@}% change to @@ when we switch to @ as escape char in index files.
+ \def\ {\realbackslash\space }%
+ %
+ % Need these in case \tex is in effect and \{ is a \delimiter again.
+ % But can't use \lbracecmd and \rbracecmd because texindex assumes
+ % braces and backslashes are used only as delimiters.
+ \let\{ = \mylbrace
+ \let\} = \myrbrace
+ %
+ % I don't entirely understand this, but when an index entry is
+ % generated from a macro call, the \endinput which \scanmacro inserts
+ % causes processing to be prematurely terminated. This is,
+ % apparently, because \indexsorttmp is fully expanded, and \endinput
+ % is an expandable command. The redefinition below makes \endinput
+ % disappear altogether for that purpose -- although logging shows that
+ % processing continues to some further point. On the other hand, it
+ % seems \endinput does not hurt in the printed index arg, since that
+ % is still getting written without apparent harm.
+ %
+ % Sample source (mac-idx3.tex, reported by Graham Percival to
+ % help-texinfo, 22may06):
+ % @macro funindex {WORD}
+ % @findex xyz
+ % @end macro
+ % ...
+ % @funindex commtest
+ %
+ % The above is not enough to reproduce the bug, but it gives the flavor.
+ %
+ % Sample whatsit resulting:
+ % . at write3{\entry{xyz}{@folio }{@code {xyz at endinput }}}
+ %
+ % So:
+ \let\endinput = \empty
+ %
+ % Do the redefinitions.
+ \commondummies
+}
+
+% For the aux and toc files, @ is the escape character. So we want to
+% redefine everything using @ as the escape character (instead of
+% \realbackslash, still used for index files). When everything uses @,
+% this will be simpler.
+%
+\def\atdummies{%
+ \def\@{@@}%
+ \def\ {@ }%
+ \let\{ = \lbraceatcmd
+ \let\} = \rbraceatcmd
+ %
+ % Do the redefinitions.
+ \commondummies
+ \otherbackslash
+}
+
+% Called from \indexdummies and \atdummies.
+%
+\def\commondummies{%
+ %
+ % \definedummyword defines \#1 as \string\#1\space, thus effectively
+ % preventing its expansion. This is used only for control% words,
+ % not control letters, because the \space would be incorrect for
+ % control characters, but is needed to separate the control word
+ % from whatever follows.
+ %
+ % For control letters, we have \definedummyletter, which omits the
+ % space.
+ %
+ % These can be used both for control words that take an argument and
+ % those that do not. If it is followed by {arg} in the input, then
+ % that will dutifully get written to the index (or wherever).
+ %
+ \def\definedummyword ##1{\def##1{\string##1\space}}%
+ \def\definedummyletter##1{\def##1{\string##1}}%
+ \let\definedummyaccent\definedummyletter
+ %
+ \commondummiesnofonts
+ %
+ \definedummyletter\_%
+ %
+ % Non-English letters.
+ \definedummyword\AA
+ \definedummyword\AE
+ \definedummyword\DH
+ \definedummyword\L
+ \definedummyword\O
+ \definedummyword\OE
+ \definedummyword\TH
+ \definedummyword\aa
+ \definedummyword\ae
+ \definedummyword\dh
+ \definedummyword\exclamdown
+ \definedummyword\l
+ \definedummyword\o
+ \definedummyword\oe
+ \definedummyword\ordf
+ \definedummyword\ordm
+ \definedummyword\questiondown
+ \definedummyword\ss
+ \definedummyword\th
+ %
+ % Although these internal commands shouldn't show up, sometimes they do.
+ \definedummyword\bf
+ \definedummyword\gtr
+ \definedummyword\hat
+ \definedummyword\less
+ \definedummyword\sf
+ \definedummyword\sl
+ \definedummyword\tclose
+ \definedummyword\tt
+ %
+ \definedummyword\LaTeX
+ \definedummyword\TeX
+ %
+ % Assorted special characters.
+ \definedummyword\bullet
+ \definedummyword\comma
+ \definedummyword\copyright
+ \definedummyword\registeredsymbol
+ \definedummyword\dots
+ \definedummyword\enddots
+ \definedummyword\equiv
+ \definedummyword\error
+ \definedummyword\euro
+ \definedummyword\guillemetleft
+ \definedummyword\guillemetright
+ \definedummyword\guilsinglleft
+ \definedummyword\guilsinglright
+ \definedummyword\expansion
+ \definedummyword\minus
+ \definedummyword\ogonek
+ \definedummyword\pounds
+ \definedummyword\point
+ \definedummyword\print
+ \definedummyword\quotedblbase
+ \definedummyword\quotedblleft
+ \definedummyword\quotedblright
+ \definedummyword\quoteleft
+ \definedummyword\quoteright
+ \definedummyword\quotesinglbase
+ \definedummyword\result
+ \definedummyword\textdegree
+ %
+ % We want to disable all macros so that they are not expanded by \write.
+ \macrolist
+ %
+ \normalturnoffactive
+ %
+ % Handle some cases of @value -- where it does not contain any
+ % (non-fully-expandable) commands.
+ \makevalueexpandable
+}
+
+% \commondummiesnofonts: common to \commondummies and \indexnofonts.
+%
+\def\commondummiesnofonts{%
+ % Control letters and accents.
+ \definedummyletter\!%
+ \definedummyaccent\"%
+ \definedummyaccent\'%
+ \definedummyletter\*%
+ \definedummyaccent\,%
+ \definedummyletter\.%
+ \definedummyletter\/%
+ \definedummyletter\:%
+ \definedummyaccent\=%
+ \definedummyletter\?%
+ \definedummyaccent\^%
+ \definedummyaccent\`%
+ \definedummyaccent\~%
+ \definedummyword\u
+ \definedummyword\v
+ \definedummyword\H
+ \definedummyword\dotaccent
+ \definedummyword\ogonek
+ \definedummyword\ringaccent
+ \definedummyword\tieaccent
+ \definedummyword\ubaraccent
+ \definedummyword\udotaccent
+ \definedummyword\dotless
+ %
+ % Texinfo font commands.
+ \definedummyword\b
+ \definedummyword\i
+ \definedummyword\r
+ \definedummyword\sc
+ \definedummyword\t
+ %
+ % Commands that take arguments.
+ \definedummyword\acronym
+ \definedummyword\cite
+ \definedummyword\code
+ \definedummyword\command
+ \definedummyword\dfn
+ \definedummyword\emph
+ \definedummyword\env
+ \definedummyword\file
+ \definedummyword\kbd
+ \definedummyword\key
+ \definedummyword\math
+ \definedummyword\option
+ \definedummyword\pxref
+ \definedummyword\ref
+ \definedummyword\samp
+ \definedummyword\strong
+ \definedummyword\tie
+ \definedummyword\uref
+ \definedummyword\url
+ \definedummyword\var
+ \definedummyword\verb
+ \definedummyword\w
+ \definedummyword\xref
+}
+
+% \indexnofonts is used when outputting the strings to sort the index
+% by, and when constructing control sequence names. It eliminates all
+% control sequences and just writes whatever the best ASCII sort string
+% would be for a given command (usually its argument).
+%
+\def\indexnofonts{%
+ % Accent commands should become @asis.
+ \def\definedummyaccent##1{\let##1\asis}%
+ % We can just ignore other control letters.
+ \def\definedummyletter##1{\let##1\empty}%
+ % Hopefully, all control words can become @asis.
+ \let\definedummyword\definedummyaccent
+ %
+ \commondummiesnofonts
+ %
+ % Don't no-op \tt, since it isn't a user-level command
+ % and is used in the definitions of the active chars like <, >, |, etc.
+ % Likewise with the other plain tex font commands.
+ %\let\tt=\asis
+ %
+ \def\ { }%
+ \def\@{@}%
+ % how to handle braces?
+ \def\_{\normalunderscore}%
+ %
+ % Non-English letters.
+ \def\AA{AA}%
+ \def\AE{AE}%
+ \def\DH{DZZ}%
+ \def\L{L}%
+ \def\OE{OE}%
+ \def\O{O}%
+ \def\TH{ZZZ}%
+ \def\aa{aa}%
+ \def\ae{ae}%
+ \def\dh{dzz}%
+ \def\exclamdown{!}%
+ \def\l{l}%
+ \def\oe{oe}%
+ \def\ordf{a}%
+ \def\ordm{o}%
+ \def\o{o}%
+ \def\questiondown{?}%
+ \def\ss{ss}%
+ \def\th{zzz}%
+ %
+ \def\LaTeX{LaTeX}%
+ \def\TeX{TeX}%
+ %
+ % Assorted special characters.
+ % (The following {} will end up in the sort string, but that's ok.)
+ \def\bullet{bullet}%
+ \def\comma{,}%
+ \def\copyright{copyright}%
+ \def\dots{...}%
+ \def\enddots{...}%
+ \def\equiv{==}%
+ \def\error{error}%
+ \def\euro{euro}%
+ \def\expansion{==>}%
+ \def\guillemetleft{<<}%
+ \def\guillemetright{>>}%
+ \def\guilsinglleft{<}%
+ \def\guilsinglright{>}%
+ \def\minus{-}%
+ \def\point{.}%
+ \def\pounds{pounds}%
+ \def\print{-|}%
+ \def\quotedblbase{"}%
+ \def\quotedblleft{"}%
+ \def\quotedblright{"}%
+ \def\quoteleft{`}%
+ \def\quoteright{'}%
+ \def\quotesinglbase{,}%
+ \def\registeredsymbol{R}%
+ \def\result{=>}%
+ \def\textdegree{o}%
+ %
+ % We need to get rid of all macros, leaving only the arguments (if present).
+ % Of course this is not nearly correct, but it is the best we can do for now.
+ % makeinfo does not expand macros in the argument to @deffn, which ends up
+ % writing an index entry, and texindex isn't prepared for an index sort entry
+ % that starts with \.
+ %
+ % Since macro invocations are followed by braces, we can just redefine them
+ % to take a single TeX argument. The case of a macro invocation that
+ % goes to end-of-line is not handled.
+ %
+ \macrolist
+}
+
+\let\indexbackslash=0 %overridden during \printindex.
+\let\SETmarginindex=\relax % put index entries in margin (undocumented)?
+
+% Most index entries go through here, but \dosubind is the general case.
+% #1 is the index name, #2 is the entry text.
+\def\doind#1#2{\dosubind{#1}{#2}{}}
+
+% Workhorse for all \fooindexes.
+% #1 is name of index, #2 is stuff to put there, #3 is subentry --
+% empty if called from \doind, as we usually are (the main exception
+% is with most defuns, which call us directly).
+%
+\def\dosubind#1#2#3{%
+ \iflinks
+ {%
+ % Store the main index entry text (including the third arg).
+ \toks0 = {#2}%
+ % If third arg is present, precede it with a space.
+ \def\thirdarg{#3}%
+ \ifx\thirdarg\empty \else
+ \toks0 = \expandafter{\the\toks0 \space #3}%
+ \fi
+ %
+ \edef\writeto{\csname#1indfile\endcsname}%
+ %
+ \safewhatsit\dosubindwrite
+ }%
+ \fi
+}
+
+% Write the entry in \toks0 to the index file:
+%
+\def\dosubindwrite{%
+ % Put the index entry in the margin if desired.
+ \ifx\SETmarginindex\relax\else
+ \insert\margin{\hbox{\vrule height8pt depth3pt width0pt \the\toks0}}%
+ \fi
+ %
+ % Remember, we are within a group.
+ \indexdummies % Must do this here, since \bf, etc expand at this stage
+ \def\backslashcurfont{\indexbackslash}% \indexbackslash isn't defined now
+ % so it will be output as is; and it will print as backslash.
+ %
+ % Process the index entry with all font commands turned off, to
+ % get the string to sort by.
+ {\indexnofonts
+ \edef\temp{\the\toks0}% need full expansion
+ \xdef\indexsorttmp{\temp}%
+ }%
+ %
+ % Set up the complete index entry, with both the sort key and
+ % the original text, including any font commands. We write
+ % three arguments to \entry to the .?? file (four in the
+ % subentry case), texindex reduces to two when writing the .??s
+ % sorted result.
+ \edef\temp{%
+ \write\writeto{%
+ \string\entry{\indexsorttmp}{\noexpand\folio}{\the\toks0}}%
+ }%
+ \temp
+}
+
+% Take care of unwanted page breaks/skips around a whatsit:
+%
+% If a skip is the last thing on the list now, preserve it
+% by backing up by \lastskip, doing the \write, then inserting
+% the skip again. Otherwise, the whatsit generated by the
+% \write or \pdfdest will make \lastskip zero. The result is that
+% sequences like this:
+% @end defun
+% @tindex whatever
+% @defun ...
+% will have extra space inserted, because the \medbreak in the
+% start of the @defun won't see the skip inserted by the @end of
+% the previous defun.
+%
+% But don't do any of this if we're not in vertical mode. We
+% don't want to do a \vskip and prematurely end a paragraph.
+%
+% Avoid page breaks due to these extra skips, too.
+%
+% But wait, there is a catch there:
+% We'll have to check whether \lastskip is zero skip. \ifdim is not
+% sufficient for this purpose, as it ignores stretch and shrink parts
+% of the skip. The only way seems to be to check the textual
+% representation of the skip.
+%
+% The following is almost like \def\zeroskipmacro{0.0pt} except that
+% the ``p'' and ``t'' characters have catcode \other, not 11 (letter).
+%
+\edef\zeroskipmacro{\expandafter\the\csname z at skip\endcsname}
+%
+\newskip\whatsitskip
+\newcount\whatsitpenalty
+%
+% ..., ready, GO:
+%
+\def\safewhatsit#1{%
+\ifhmode
+ #1%
+\else
+ % \lastskip and \lastpenalty cannot both be nonzero simultaneously.
+ \whatsitskip = \lastskip
+ \edef\lastskipmacro{\the\lastskip}%
+ \whatsitpenalty = \lastpenalty
+ %
+ % If \lastskip is nonzero, that means the last item was a
+ % skip. And since a skip is discardable, that means this
+ % -\whatsitskip glue we're inserting is preceded by a
+ % non-discardable item, therefore it is not a potential
+ % breakpoint, therefore no \nobreak needed.
+ \ifx\lastskipmacro\zeroskipmacro
+ \else
+ \vskip-\whatsitskip
+ \fi
+ %
+ #1%
+ %
+ \ifx\lastskipmacro\zeroskipmacro
+ % If \lastskip was zero, perhaps the last item was a penalty, and
+ % perhaps it was >=10000, e.g., a \nobreak. In that case, we want
+ % to re-insert the same penalty (values >10000 are used for various
+ % signals); since we just inserted a non-discardable item, any
+ % following glue (such as a \parskip) would be a breakpoint. For example:
+ %
+ % @deffn deffn-whatever
+ % @vindex index-whatever
+ % Description.
+ % would allow a break between the index-whatever whatsit
+ % and the "Description." paragraph.
+ \ifnum\whatsitpenalty>9999 \penalty\whatsitpenalty \fi
+ \else
+ % On the other hand, if we had a nonzero \lastskip,
+ % this make-up glue would be preceded by a non-discardable item
+ % (the whatsit from the \write), so we must insert a \nobreak.
+ \nobreak\vskip\whatsitskip
+ \fi
+\fi
+}
+
+% The index entry written in the file actually looks like
+% \entry {sortstring}{page}{topic}
+% or
+% \entry {sortstring}{page}{topic}{subtopic}
+% The texindex program reads in these files and writes files
+% containing these kinds of lines:
+% \initial {c}
+% before the first topic whose initial is c
+% \entry {topic}{pagelist}
+% for a topic that is used without subtopics
+% \primary {topic}
+% for the beginning of a topic that is used with subtopics
+% \secondary {subtopic}{pagelist}
+% for each subtopic.
+
+% Define the user-accessible indexing commands
+% @findex, @vindex, @kindex, @cindex.
+
+\def\findex {\fnindex}
+\def\kindex {\kyindex}
+\def\cindex {\cpindex}
+\def\vindex {\vrindex}
+\def\tindex {\tpindex}
+\def\pindex {\pgindex}
+
+\def\cindexsub {\begingroup\obeylines\cindexsub}
+{\obeylines %
+\gdef\cindexsub "#1" #2^^M{\endgroup %
+\dosubind{cp}{#2}{#1}}}
+
+% Define the macros used in formatting output of the sorted index material.
+
+% @printindex causes a particular index (the ??s file) to get printed.
+% It does not print any chapter heading (usually an @unnumbered).
+%
+\parseargdef\printindex{\begingroup
+ \dobreak \chapheadingskip{10000}%
+ %
+ \smallfonts \rm
+ \tolerance = 9500
+ \plainfrenchspacing
+ \everypar = {}% don't want the \kern\-parindent from indentation suppression.
+ %
+ % See if the index file exists and is nonempty.
+ % Change catcode of @ here so that if the index file contains
+ % \initial {@}
+ % as its first line, TeX doesn't complain about mismatched braces
+ % (because it thinks @} is a control sequence).
+ \catcode`\@ = 11
+ \openin 1 \jobname.#1s
+ \ifeof 1
+ % \enddoublecolumns gets confused if there is no text in the index,
+ % and it loses the chapter title and the aux file entries for the
+ % index. The easiest way to prevent this problem is to make sure
+ % there is some text.
+ \putwordIndexNonexistent
+ \else
+ %
+ % If the index file exists but is empty, then \openin leaves \ifeof
+ % false. We have to make TeX try to read something from the file, so
+ % it can discover if there is anything in it.
+ \read 1 to \temp
+ \ifeof 1
+ \putwordIndexIsEmpty
+ \else
+ % Index files are almost Texinfo source, but we use \ as the escape
+ % character. It would be better to use @, but that's too big a change
+ % to make right now.
+ \def\indexbackslash{\backslashcurfont}%
+ \catcode`\\ = 0
+ \escapechar = `\\
+ \begindoublecolumns
+ \input \jobname.#1s
+ \enddoublecolumns
+ \fi
+ \fi
+ \closein 1
+\endgroup}
+
+% These macros are used by the sorted index file itself.
+% Change them to control the appearance of the index.
+
+\def\initial#1{{%
+ % Some minor font changes for the special characters.
+ \let\tentt=\sectt \let\tt=\sectt \let\sf=\sectt
+ %
+ % Remove any glue we may have, we'll be inserting our own.
+ \removelastskip
+ %
+ % We like breaks before the index initials, so insert a bonus.
+ \nobreak
+ \vskip 0pt plus 3\baselineskip
+ \penalty 0
+ \vskip 0pt plus -3\baselineskip
+ %
+ % Typeset the initial. Making this add up to a whole number of
+ % baselineskips increases the chance of the dots lining up from column
+ % to column. It still won't often be perfect, because of the stretch
+ % we need before each entry, but it's better.
+ %
+ % No shrink because it confuses \balancecolumns.
+ \vskip 1.67\baselineskip plus .5\baselineskip
+ \leftline{\secbf #1}%
+ % Do our best not to break after the initial.
+ \nobreak
+ \vskip .33\baselineskip plus .1\baselineskip
+}}
+
+% \entry typesets a paragraph consisting of the text (#1), dot leaders, and
+% then page number (#2) flushed to the right margin. It is used for index
+% and table of contents entries. The paragraph is indented by \leftskip.
+%
+% A straightforward implementation would start like this:
+% \def\entry#1#2{...
+% But this freezes the catcodes in the argument, and can cause problems to
+% @code, which sets - active. This problem was fixed by a kludge---
+% ``-'' was active throughout whole index, but this isn't really right.
+%
+% The right solution is to prevent \entry from swallowing the whole text.
+% --kasal, 21nov03
+\def\entry{%
+ \begingroup
+ %
+ % Start a new paragraph if necessary, so our assignments below can't
+ % affect previous text.
+ \par
+ %
+ % Do not fill out the last line with white space.
+ \parfillskip = 0in
+ %
+ % No extra space above this paragraph.
+ \parskip = 0in
+ %
+ % Do not prefer a separate line ending with a hyphen to fewer lines.
+ \finalhyphendemerits = 0
+ %
+ % \hangindent is only relevant when the entry text and page number
+ % don't both fit on one line. In that case, bob suggests starting the
+ % dots pretty far over on the line. Unfortunately, a large
+ % indentation looks wrong when the entry text itself is broken across
+ % lines. So we use a small indentation and put up with long leaders.
+ %
+ % \hangafter is reset to 1 (which is the value we want) at the start
+ % of each paragraph, so we need not do anything with that.
+ \hangindent = 2em
+ %
+ % When the entry text needs to be broken, just fill out the first line
+ % with blank space.
+ \rightskip = 0pt plus1fil
+ %
+ % A bit of stretch before each entry for the benefit of balancing
+ % columns.
+ \vskip 0pt plus1pt
+ %
+ % Swallow the left brace of the text (first parameter):
+ \afterassignment\doentry
+ \let\temp =
+}
+\def\doentry{%
+ \bgroup % Instead of the swallowed brace.
+ \noindent
+ \aftergroup\finishentry
+ % And now comes the text of the entry.
+}
+\def\finishentry#1{%
+ % #1 is the page number.
+ %
+ % The following is kludged to not output a line of dots in the index if
+ % there are no page numbers. The next person who breaks this will be
+ % cursed by a Unix daemon.
+ \setbox\boxA = \hbox{#1}%
+ \ifdim\wd\boxA = 0pt
+ \ %
+ \else
+ %
+ % If we must, put the page number on a line of its own, and fill out
+ % this line with blank space. (The \hfil is overwhelmed with the
+ % fill leaders glue in \indexdotfill if the page number does fit.)
+ \hfil\penalty50
+ \null\nobreak\indexdotfill % Have leaders before the page number.
+ %
+ % The `\ ' here is removed by the implicit \unskip that TeX does as
+ % part of (the primitive) \par. Without it, a spurious underfull
+ % \hbox ensues.
+ \ifpdf
+ \pdfgettoks#1.%
+ \ \the\toksA
+ \else
+ \ #1%
+ \fi
+ \fi
+ \par
+ \endgroup
+}
+
+% Like plain.tex's \dotfill, except uses up at least 1 em.
+\def\indexdotfill{\cleaders
+ \hbox{$\mathsurround=0pt \mkern1.5mu.\mkern1.5mu$}\hskip 1em plus 1fill}
+
+\def\primary #1{\line{#1\hfil}}
+
+\newskip\secondaryindent \secondaryindent=0.5cm
+\def\secondary#1#2{{%
+ \parfillskip=0in
+ \parskip=0in
+ \hangindent=1in
+ \hangafter=1
+ \noindent\hskip\secondaryindent\hbox{#1}\indexdotfill
+ \ifpdf
+ \pdfgettoks#2.\ \the\toksA % The page number ends the paragraph.
+ \else
+ #2
+ \fi
+ \par
+}}
+
+% Define two-column mode, which we use to typeset indexes.
+% Adapted from the TeXbook, page 416, which is to say,
+% the manmac.tex format used to print the TeXbook itself.
+\catcode`\@=11
+
+\newbox\partialpage
+\newdimen\doublecolumnhsize
+
+\def\begindoublecolumns{\begingroup % ended by \enddoublecolumns
+ % Grab any single-column material above us.
+ \output = {%
+ %
+ % Here is a possibility not foreseen in manmac: if we accumulate a
+ % whole lot of material, we might end up calling this \output
+ % routine twice in a row (see the doublecol-lose test, which is
+ % essentially a couple of indexes with @setchapternewpage off). In
+ % that case we just ship out what is in \partialpage with the normal
+ % output routine. Generally, \partialpage will be empty when this
+ % runs and this will be a no-op. See the indexspread.tex test case.
+ \ifvoid\partialpage \else
+ \onepageout{\pagecontents\partialpage}%
+ \fi
+ %
+ \global\setbox\partialpage = \vbox{%
+ % Unvbox the main output page.
+ \unvbox\PAGE
+ \kern-\topskip \kern\baselineskip
+ }%
+ }%
+ \eject % run that output routine to set \partialpage
+ %
+ % Use the double-column output routine for subsequent pages.
+ \output = {\doublecolumnout}%
+ %
+ % Change the page size parameters. We could do this once outside this
+ % routine, in each of @smallbook, @afourpaper, and the default 8.5x11
+ % format, but then we repeat the same computation. Repeating a couple
+ % of assignments once per index is clearly meaningless for the
+ % execution time, so we may as well do it in one place.
+ %
+ % First we halve the line length, less a little for the gutter between
+ % the columns. We compute the gutter based on the line length, so it
+ % changes automatically with the paper format. The magic constant
+ % below is chosen so that the gutter has the same value (well, +-<1pt)
+ % as it did when we hard-coded it.
+ %
+ % We put the result in a separate register, \doublecolumhsize, so we
+ % can restore it in \pagesofar, after \hsize itself has (potentially)
+ % been clobbered.
+ %
+ \doublecolumnhsize = \hsize
+ \advance\doublecolumnhsize by -.04154\hsize
+ \divide\doublecolumnhsize by 2
+ \hsize = \doublecolumnhsize
+ %
+ % Double the \vsize as well. (We don't need a separate register here,
+ % since nobody clobbers \vsize.)
+ \vsize = 2\vsize
+}
+
+% The double-column output routine for all double-column pages except
+% the last.
+%
+\def\doublecolumnout{%
+ \splittopskip=\topskip \splitmaxdepth=\maxdepth
+ % Get the available space for the double columns -- the normal
+ % (undoubled) page height minus any material left over from the
+ % previous page.
+ \dimen@ = \vsize
+ \divide\dimen@ by 2
+ \advance\dimen@ by -\ht\partialpage
+ %
+ % box0 will be the left-hand column, box2 the right.
+ \setbox0=\vsplit255 to\dimen@ \setbox2=\vsplit255 to\dimen@
+ \onepageout\pagesofar
+ \unvbox255
+ \penalty\outputpenalty
+}
+%
+% Re-output the contents of the output page -- any previous material,
+% followed by the two boxes we just split, in box0 and box2.
+\def\pagesofar{%
+ \unvbox\partialpage
+ %
+ \hsize = \doublecolumnhsize
+ \wd0=\hsize \wd2=\hsize
+ \hbox to\pagewidth{\box0\hfil\box2}%
+}
+%
+% All done with double columns.
+\def\enddoublecolumns{%
+ % The following penalty ensures that the page builder is exercised
+ % _before_ we change the output routine. This is necessary in the
+ % following situation:
+ %
+ % The last section of the index consists only of a single entry.
+ % Before this section, \pagetotal is less than \pagegoal, so no
+ % break occurs before the last section starts. However, the last
+ % section, consisting of \initial and the single \entry, does not
+ % fit on the page and has to be broken off. Without the following
+ % penalty the page builder will not be exercised until \eject
+ % below, and by that time we'll already have changed the output
+ % routine to the \balancecolumns version, so the next-to-last
+ % double-column page will be processed with \balancecolumns, which
+ % is wrong: The two columns will go to the main vertical list, with
+ % the broken-off section in the recent contributions. As soon as
+ % the output routine finishes, TeX starts reconsidering the page
+ % break. The two columns and the broken-off section both fit on the
+ % page, because the two columns now take up only half of the page
+ % goal. When TeX sees \eject from below which follows the final
+ % section, it invokes the new output routine that we've set after
+ % \balancecolumns below; \onepageout will try to fit the two columns
+ % and the final section into the vbox of \pageheight (see
+ % \pagebody), causing an overfull box.
+ %
+ % Note that glue won't work here, because glue does not exercise the
+ % page builder, unlike penalties (see The TeXbook, pp. 280-281).
+ \penalty0
+ %
+ \output = {%
+ % Split the last of the double-column material. Leave it on the
+ % current page, no automatic page break.
+ \balancecolumns
+ %
+ % If we end up splitting too much material for the current page,
+ % though, there will be another page break right after this \output
+ % invocation ends. Having called \balancecolumns once, we do not
+ % want to call it again. Therefore, reset \output to its normal
+ % definition right away. (We hope \balancecolumns will never be
+ % called on to balance too much material, but if it is, this makes
+ % the output somewhat more palatable.)
+ \global\output = {\onepageout{\pagecontents\PAGE}}%
+ }%
+ \eject
+ \endgroup % started in \begindoublecolumns
+ %
+ % \pagegoal was set to the doubled \vsize above, since we restarted
+ % the current page. We're now back to normal single-column
+ % typesetting, so reset \pagegoal to the normal \vsize (after the
+ % \endgroup where \vsize got restored).
+ \pagegoal = \vsize
+}
+%
+% Called at the end of the double column material.
+\def\balancecolumns{%
+ \setbox0 = \vbox{\unvbox255}% like \box255 but more efficient, see p.120.
+ \dimen@ = \ht0
+ \advance\dimen@ by \topskip
+ \advance\dimen@ by-\baselineskip
+ \divide\dimen@ by 2 % target to split to
+ %debug\message{final 2-column material height=\the\ht0, target=\the\dimen at .}%
+ \splittopskip = \topskip
+ % Loop until we get a decent breakpoint.
+ {%
+ \vbadness = 10000
+ \loop
+ \global\setbox3 = \copy0
+ \global\setbox1 = \vsplit3 to \dimen@
+ \ifdim\ht3>\dimen@
+ \global\advance\dimen@ by 1pt
+ \repeat
+ }%
+ %debug\message{split to \the\dimen@, column heights: \the\ht1, \the\ht3.}%
+ \setbox0=\vbox to\dimen@{\unvbox1}%
+ \setbox2=\vbox to\dimen@{\unvbox3}%
+ %
+ \pagesofar
+}
+\catcode`\@ = \other
+
+
+\message{sectioning,}
+% Chapters, sections, etc.
+
+% \unnumberedno is an oxymoron, of course. But we count the unnumbered
+% sections so that we can refer to them unambiguously in the pdf
+% outlines by their "section number". We avoid collisions with chapter
+% numbers by starting them at 10000. (If a document ever has 10000
+% chapters, we're in trouble anyway, I'm sure.)
+\newcount\unnumberedno \unnumberedno = 10000
+\newcount\chapno
+\newcount\secno \secno=0
+\newcount\subsecno \subsecno=0
+\newcount\subsubsecno \subsubsecno=0
+
+% This counter is funny since it counts through charcodes of letters A, B, ...
+\newcount\appendixno \appendixno = `\@
+%
+% \def\appendixletter{\char\the\appendixno}
+% We do the following ugly conditional instead of the above simple
+% construct for the sake of pdftex, which needs the actual
+% letter in the expansion, not just typeset.
+%
+\def\appendixletter{%
+ \ifnum\appendixno=`A A%
+ \else\ifnum\appendixno=`B B%
+ \else\ifnum\appendixno=`C C%
+ \else\ifnum\appendixno=`D D%
+ \else\ifnum\appendixno=`E E%
+ \else\ifnum\appendixno=`F F%
+ \else\ifnum\appendixno=`G G%
+ \else\ifnum\appendixno=`H H%
+ \else\ifnum\appendixno=`I I%
+ \else\ifnum\appendixno=`J J%
+ \else\ifnum\appendixno=`K K%
+ \else\ifnum\appendixno=`L L%
+ \else\ifnum\appendixno=`M M%
+ \else\ifnum\appendixno=`N N%
+ \else\ifnum\appendixno=`O O%
+ \else\ifnum\appendixno=`P P%
+ \else\ifnum\appendixno=`Q Q%
+ \else\ifnum\appendixno=`R R%
+ \else\ifnum\appendixno=`S S%
+ \else\ifnum\appendixno=`T T%
+ \else\ifnum\appendixno=`U U%
+ \else\ifnum\appendixno=`V V%
+ \else\ifnum\appendixno=`W W%
+ \else\ifnum\appendixno=`X X%
+ \else\ifnum\appendixno=`Y Y%
+ \else\ifnum\appendixno=`Z Z%
+ % The \the is necessary, despite appearances, because \appendixletter is
+ % expanded while writing the .toc file. \char\appendixno is not
+ % expandable, thus it is written literally, thus all appendixes come out
+ % with the same letter (or @) in the toc without it.
+ \else\char\the\appendixno
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi}
+
+% Each @chapter defines these (using marks) as the number+name, number
+% and name of the chapter. Page headings and footings can use
+% these. @section does likewise.
+\def\thischapter{}
+\def\thischapternum{}
+\def\thischaptername{}
+\def\thissection{}
+\def\thissectionnum{}
+\def\thissectionname{}
+
+\newcount\absseclevel % used to calculate proper heading level
+\newcount\secbase\secbase=0 % @raisesections/@lowersections modify this count
+
+% @raisesections: treat @section as chapter, @subsection as section, etc.
+\def\raisesections{\global\advance\secbase by -1}
+\let\up=\raisesections % original BFox name
+
+% @lowersections: treat @chapter as section, @section as subsection, etc.
+\def\lowersections{\global\advance\secbase by 1}
+\let\down=\lowersections % original BFox name
+
+% we only have subsub.
+\chardef\maxseclevel = 3
+%
+% A numbered section within an unnumbered changes to unnumbered too.
+% To achive this, remember the "biggest" unnum. sec. we are currently in:
+\chardef\unmlevel = \maxseclevel
+%
+% Trace whether the current chapter is an appendix or not:
+% \chapheadtype is "N" or "A", unnumbered chapters are ignored.
+\def\chapheadtype{N}
+
+% Choose a heading macro
+% #1 is heading type
+% #2 is heading level
+% #3 is text for heading
+\def\genhead#1#2#3{%
+ % Compute the abs. sec. level:
+ \absseclevel=#2
+ \advance\absseclevel by \secbase
+ % Make sure \absseclevel doesn't fall outside the range:
+ \ifnum \absseclevel < 0
+ \absseclevel = 0
+ \else
+ \ifnum \absseclevel > 3
+ \absseclevel = 3
+ \fi
+ \fi
+ % The heading type:
+ \def\headtype{#1}%
+ \if \headtype U%
+ \ifnum \absseclevel < \unmlevel
+ \chardef\unmlevel = \absseclevel
+ \fi
+ \else
+ % Check for appendix sections:
+ \ifnum \absseclevel = 0
+ \edef\chapheadtype{\headtype}%
+ \else
+ \if \headtype A\if \chapheadtype N%
+ \errmessage{@appendix... within a non-appendix chapter}%
+ \fi\fi
+ \fi
+ % Check for numbered within unnumbered:
+ \ifnum \absseclevel > \unmlevel
+ \def\headtype{U}%
+ \else
+ \chardef\unmlevel = 3
+ \fi
+ \fi
+ % Now print the heading:
+ \if \headtype U%
+ \ifcase\absseclevel
+ \unnumberedzzz{#3}%
+ \or \unnumberedseczzz{#3}%
+ \or \unnumberedsubseczzz{#3}%
+ \or \unnumberedsubsubseczzz{#3}%
+ \fi
+ \else
+ \if \headtype A%
+ \ifcase\absseclevel
+ \appendixzzz{#3}%
+ \or \appendixsectionzzz{#3}%
+ \or \appendixsubseczzz{#3}%
+ \or \appendixsubsubseczzz{#3}%
+ \fi
+ \else
+ \ifcase\absseclevel
+ \chapterzzz{#3}%
+ \or \seczzz{#3}%
+ \or \numberedsubseczzz{#3}%
+ \or \numberedsubsubseczzz{#3}%
+ \fi
+ \fi
+ \fi
+ \suppressfirstparagraphindent
+}
+
+% an interface:
+\def\numhead{\genhead N}
+\def\apphead{\genhead A}
+\def\unnmhead{\genhead U}
+
+% @chapter, @appendix, @unnumbered. Increment top-level counter, reset
+% all lower-level sectioning counters to zero.
+%
+% Also set \chaplevelprefix, which we prepend to @float sequence numbers
+% (e.g., figures), q.v. By default (before any chapter), that is empty.
+\let\chaplevelprefix = \empty
+%
+\outer\parseargdef\chapter{\numhead0{#1}} % normally numhead0 calls chapterzzz
+\def\chapterzzz#1{%
+ % section resetting is \global in case the chapter is in a group, such
+ % as an @include file.
+ \global\secno=0 \global\subsecno=0 \global\subsubsecno=0
+ \global\advance\chapno by 1
+ %
+ % Used for \float.
+ \gdef\chaplevelprefix{\the\chapno.}%
+ \resetallfloatnos
+ %
+ % \putwordChapter can contain complex things in translations.
+ \toks0=\expandafter{\putwordChapter}%
+ \message{\the\toks0 \space \the\chapno}%
+ %
+ % Write the actual heading.
+ \chapmacro{#1}{Ynumbered}{\the\chapno}%
+ %
+ % So @section and the like are numbered underneath this chapter.
+ \global\let\section = \numberedsec
+ \global\let\subsection = \numberedsubsec
+ \global\let\subsubsection = \numberedsubsubsec
+}
+
+\outer\parseargdef\appendix{\apphead0{#1}} % normally calls appendixzzz
+%
+\def\appendixzzz#1{%
+ \global\secno=0 \global\subsecno=0 \global\subsubsecno=0
+ \global\advance\appendixno by 1
+ \gdef\chaplevelprefix{\appendixletter.}%
+ \resetallfloatnos
+ %
+ % \putwordAppendix can contain complex things in translations.
+ \toks0=\expandafter{\putwordAppendix}%
+ \message{\the\toks0 \space \appendixletter}%
+ %
+ \chapmacro{#1}{Yappendix}{\appendixletter}%
+ %
+ \global\let\section = \appendixsec
+ \global\let\subsection = \appendixsubsec
+ \global\let\subsubsection = \appendixsubsubsec
+}
+
+\outer\parseargdef\unnumbered{\unnmhead0{#1}} % normally unnmhead0 calls unnumberedzzz
+\def\unnumberedzzz#1{%
+ \global\secno=0 \global\subsecno=0 \global\subsubsecno=0
+ \global\advance\unnumberedno by 1
+ %
+ % Since an unnumbered has no number, no prefix for figures.
+ \global\let\chaplevelprefix = \empty
+ \resetallfloatnos
+ %
+ % This used to be simply \message{#1}, but TeX fully expands the
+ % argument to \message. Therefore, if #1 contained @-commands, TeX
+ % expanded them. For example, in `@unnumbered The @cite{Book}', TeX
+ % expanded @cite (which turns out to cause errors because \cite is meant
+ % to be executed, not expanded).
+ %
+ % Anyway, we don't want the fully-expanded definition of @cite to appear
+ % as a result of the \message, we just want `@cite' itself. We use
+ % \the<toks register> to achieve this: TeX expands \the<toks> only once,
+ % simply yielding the contents of <toks register>. (We also do this for
+ % the toc entries.)
+ \toks0 = {#1}%
+ \message{(\the\toks0)}%
+ %
+ \chapmacro{#1}{Ynothing}{\the\unnumberedno}%
+ %
+ \global\let\section = \unnumberedsec
+ \global\let\subsection = \unnumberedsubsec
+ \global\let\subsubsection = \unnumberedsubsubsec
+}
+
+% @centerchap is like @unnumbered, but the heading is centered.
+\outer\parseargdef\centerchap{%
+ % Well, we could do the following in a group, but that would break
+ % an assumption that \chapmacro is called at the outermost level.
+ % Thus we are safer this way: --kasal, 24feb04
+ \let\centerparametersmaybe = \centerparameters
+ \unnmhead0{#1}%
+ \let\centerparametersmaybe = \relax
+}
+
+% @top is like @unnumbered.
+\let\top\unnumbered
+
+% Sections.
+\outer\parseargdef\numberedsec{\numhead1{#1}} % normally calls seczzz
+\def\seczzz#1{%
+ \global\subsecno=0 \global\subsubsecno=0 \global\advance\secno by 1
+ \sectionheading{#1}{sec}{Ynumbered}{\the\chapno.\the\secno}%
+}
+
+\outer\parseargdef\appendixsection{\apphead1{#1}} % normally calls appendixsectionzzz
+\def\appendixsectionzzz#1{%
+ \global\subsecno=0 \global\subsubsecno=0 \global\advance\secno by 1
+ \sectionheading{#1}{sec}{Yappendix}{\appendixletter.\the\secno}%
+}
+\let\appendixsec\appendixsection
+
+\outer\parseargdef\unnumberedsec{\unnmhead1{#1}} % normally calls unnumberedseczzz
+\def\unnumberedseczzz#1{%
+ \global\subsecno=0 \global\subsubsecno=0 \global\advance\secno by 1
+ \sectionheading{#1}{sec}{Ynothing}{\the\unnumberedno.\the\secno}%
+}
+
+% Subsections.
+\outer\parseargdef\numberedsubsec{\numhead2{#1}} % normally calls numberedsubseczzz
+\def\numberedsubseczzz#1{%
+ \global\subsubsecno=0 \global\advance\subsecno by 1
+ \sectionheading{#1}{subsec}{Ynumbered}{\the\chapno.\the\secno.\the\subsecno}%
+}
+
+\outer\parseargdef\appendixsubsec{\apphead2{#1}} % normally calls appendixsubseczzz
+\def\appendixsubseczzz#1{%
+ \global\subsubsecno=0 \global\advance\subsecno by 1
+ \sectionheading{#1}{subsec}{Yappendix}%
+ {\appendixletter.\the\secno.\the\subsecno}%
+}
+
+\outer\parseargdef\unnumberedsubsec{\unnmhead2{#1}} %normally calls unnumberedsubseczzz
+\def\unnumberedsubseczzz#1{%
+ \global\subsubsecno=0 \global\advance\subsecno by 1
+ \sectionheading{#1}{subsec}{Ynothing}%
+ {\the\unnumberedno.\the\secno.\the\subsecno}%
+}
+
+% Subsubsections.
+\outer\parseargdef\numberedsubsubsec{\numhead3{#1}} % normally numberedsubsubseczzz
+\def\numberedsubsubseczzz#1{%
+ \global\advance\subsubsecno by 1
+ \sectionheading{#1}{subsubsec}{Ynumbered}%
+ {\the\chapno.\the\secno.\the\subsecno.\the\subsubsecno}%
+}
+
+\outer\parseargdef\appendixsubsubsec{\apphead3{#1}} % normally appendixsubsubseczzz
+\def\appendixsubsubseczzz#1{%
+ \global\advance\subsubsecno by 1
+ \sectionheading{#1}{subsubsec}{Yappendix}%
+ {\appendixletter.\the\secno.\the\subsecno.\the\subsubsecno}%
+}
+
+\outer\parseargdef\unnumberedsubsubsec{\unnmhead3{#1}} %normally unnumberedsubsubseczzz
+\def\unnumberedsubsubseczzz#1{%
+ \global\advance\subsubsecno by 1
+ \sectionheading{#1}{subsubsec}{Ynothing}%
+ {\the\unnumberedno.\the\secno.\the\subsecno.\the\subsubsecno}%
+}
+
+% These macros control what the section commands do, according
+% to what kind of chapter we are in (ordinary, appendix, or unnumbered).
+% Define them by default for a numbered chapter.
+\let\section = \numberedsec
+\let\subsection = \numberedsubsec
+\let\subsubsection = \numberedsubsubsec
+
+% Define @majorheading, @heading and @subheading
+
+% NOTE on use of \vbox for chapter headings, section headings, and such:
+% 1) We use \vbox rather than the earlier \line to permit
+% overlong headings to fold.
+% 2) \hyphenpenalty is set to 10000 because hyphenation in a
+% heading is obnoxious; this forbids it.
+% 3) Likewise, headings look best if no \parindent is used, and
+% if justification is not attempted. Hence \raggedright.
+
+\def\majorheading{%
+ {\advance\chapheadingskip by 10pt \chapbreak }%
+ \parsearg\chapheadingzzz
+}
+
+\def\chapheading{\chapbreak \parsearg\chapheadingzzz}
+\def\chapheadingzzz#1{%
+ {\chapfonts \vbox{\hyphenpenalty=10000\tolerance=5000
+ \parindent=0pt\ptexraggedright
+ \rmisbold #1\hfill}}%
+ \bigskip \par\penalty 200\relax
+ \suppressfirstparagraphindent
+}
+
+% @heading, @subheading, @subsubheading.
+\parseargdef\heading{\sectionheading{#1}{sec}{Yomitfromtoc}{}
+ \suppressfirstparagraphindent}
+\parseargdef\subheading{\sectionheading{#1}{subsec}{Yomitfromtoc}{}
+ \suppressfirstparagraphindent}
+\parseargdef\subsubheading{\sectionheading{#1}{subsubsec}{Yomitfromtoc}{}
+ \suppressfirstparagraphindent}
+
+% These macros generate a chapter, section, etc. heading only
+% (including whitespace, linebreaking, etc. around it),
+% given all the information in convenient, parsed form.
+
+%%% Args are the skip and penalty (usually negative)
+\def\dobreak#1#2{\par\ifdim\lastskip<#1\removelastskip\penalty#2\vskip#1\fi}
+
+%%% Define plain chapter starts, and page on/off switching for it
+% Parameter controlling skip before chapter headings (if needed)
+
+\newskip\chapheadingskip
+
+\def\chapbreak{\dobreak \chapheadingskip {-4000}}
+\def\chappager{\par\vfill\supereject}
+% Because \domark is called before \chapoddpage, the filler page will
+% get the headings for the next chapter, which is wrong. But we don't
+% care -- we just disable all headings on the filler page.
+\def\chapoddpage{%
+ \chappager
+ \ifodd\pageno \else
+ \begingroup
+ \evenheadline={\hfil}\evenfootline={\hfil}%
+ \oddheadline={\hfil}\oddfootline={\hfil}%
+ \hbox to 0pt{}%
+ \chappager
+ \endgroup
+ \fi
+}
+
+\def\setchapternewpage #1 {\csname CHAPPAG#1\endcsname}
+
+\def\CHAPPAGoff{%
+\global\let\contentsalignmacro = \chappager
+\global\let\pchapsepmacro=\chapbreak
+\global\let\pagealignmacro=\chappager}
+
+\def\CHAPPAGon{%
+\global\let\contentsalignmacro = \chappager
+\global\let\pchapsepmacro=\chappager
+\global\let\pagealignmacro=\chappager
+\global\def\HEADINGSon{\HEADINGSsingle}}
+
+\def\CHAPPAGodd{%
+\global\let\contentsalignmacro = \chapoddpage
+\global\let\pchapsepmacro=\chapoddpage
+\global\let\pagealignmacro=\chapoddpage
+\global\def\HEADINGSon{\HEADINGSdouble}}
+
+\CHAPPAGon
+
+% Chapter opening.
+%
+% #1 is the text, #2 is the section type (Ynumbered, Ynothing,
+% Yappendix, Yomitfromtoc), #3 the chapter number.
+%
+% To test against our argument.
+\def\Ynothingkeyword{Ynothing}
+\def\Yomitfromtockeyword{Yomitfromtoc}
+\def\Yappendixkeyword{Yappendix}
+%
+\def\chapmacro#1#2#3{%
+ % Insert the first mark before the heading break (see notes for \domark).
+ \let\prevchapterdefs=\lastchapterdefs
+ \let\prevsectiondefs=\lastsectiondefs
+ \gdef\lastsectiondefs{\gdef\thissectionname{}\gdef\thissectionnum{}%
+ \gdef\thissection{}}%
+ %
+ \def\temptype{#2}%
+ \ifx\temptype\Ynothingkeyword
+ \gdef\lastchapterdefs{\gdef\thischaptername{#1}\gdef\thischapternum{}%
+ \gdef\thischapter{\thischaptername}}%
+ \else\ifx\temptype\Yomitfromtockeyword
+ \gdef\lastchapterdefs{\gdef\thischaptername{#1}\gdef\thischapternum{}%
+ \gdef\thischapter{}}%
+ \else\ifx\temptype\Yappendixkeyword
+ \toks0={#1}%
+ \xdef\lastchapterdefs{%
+ \gdef\noexpand\thischaptername{\the\toks0}%
+ \gdef\noexpand\thischapternum{\appendixletter}%
+ % \noexpand\putwordAppendix avoids expanding indigestible
+ % commands in some of the translations.
+ \gdef\noexpand\thischapter{\noexpand\putwordAppendix{}
+ \noexpand\thischapternum:
+ \noexpand\thischaptername}%
+ }%
+ \else
+ \toks0={#1}%
+ \xdef\lastchapterdefs{%
+ \gdef\noexpand\thischaptername{\the\toks0}%
+ \gdef\noexpand\thischapternum{\the\chapno}%
+ % \noexpand\putwordChapter avoids expanding indigestible
+ % commands in some of the translations.
+ \gdef\noexpand\thischapter{\noexpand\putwordChapter{}
+ \noexpand\thischapternum:
+ \noexpand\thischaptername}%
+ }%
+ \fi\fi\fi
+ %
+ % Output the mark. Pass it through \safewhatsit, to take care of
+ % the preceding space.
+ \safewhatsit\domark
+ %
+ % Insert the chapter heading break.
+ \pchapsepmacro
+ %
+ % Now the second mark, after the heading break. No break points
+ % between here and the heading.
+ \let\prevchapterdefs=\lastchapterdefs
+ \let\prevsectiondefs=\lastsectiondefs
+ \domark
+ %
+ {%
+ \chapfonts \rmisbold
+ %
+ % Have to define \lastsection before calling \donoderef, because the
+ % xref code eventually uses it. On the other hand, it has to be called
+ % after \pchapsepmacro, or the headline will change too soon.
+ \gdef\lastsection{#1}%
+ %
+ % Only insert the separating space if we have a chapter/appendix
+ % number, and don't print the unnumbered ``number''.
+ \ifx\temptype\Ynothingkeyword
+ \setbox0 = \hbox{}%
+ \def\toctype{unnchap}%
+ \else\ifx\temptype\Yomitfromtockeyword
+ \setbox0 = \hbox{}% contents like unnumbered, but no toc entry
+ \def\toctype{omit}%
+ \else\ifx\temptype\Yappendixkeyword
+ \setbox0 = \hbox{\putwordAppendix{} #3\enspace}%
+ \def\toctype{app}%
+ \else
+ \setbox0 = \hbox{#3\enspace}%
+ \def\toctype{numchap}%
+ \fi\fi\fi
+ %
+ % Write the toc entry for this chapter. Must come before the
+ % \donoderef, because we include the current node name in the toc
+ % entry, and \donoderef resets it to empty.
+ \writetocentry{\toctype}{#1}{#3}%
+ %
+ % For pdftex, we have to write out the node definition (aka, make
+ % the pdfdest) after any page break, but before the actual text has
+ % been typeset. If the destination for the pdf outline is after the
+ % text, then jumping from the outline may wind up with the text not
+ % being visible, for instance under high magnification.
+ \donoderef{#2}%
+ %
+ % Typeset the actual heading.
+ \nobreak % Avoid page breaks at the interline glue.
+ \vbox{\hyphenpenalty=10000 \tolerance=5000 \parindent=0pt \ptexraggedright
+ \hangindent=\wd0 \centerparametersmaybe
+ \unhbox0 #1\par}%
+ }%
+ \nobreak\bigskip % no page break after a chapter title
+ \nobreak
+}
+
+% @centerchap -- centered and unnumbered.
+\let\centerparametersmaybe = \relax
+\def\centerparameters{%
+ \advance\rightskip by 3\rightskip
+ \leftskip = \rightskip
+ \parfillskip = 0pt
+}
+
+
+% I don't think this chapter style is supported any more, so I'm not
+% updating it with the new noderef stuff. We'll see. --karl, 11aug03.
+%
+\def\setchapterstyle #1 {\csname CHAPF#1\endcsname}
+%
+\def\unnchfopen #1{%
+\chapoddpage {\chapfonts \vbox{\hyphenpenalty=10000\tolerance=5000
+ \parindent=0pt\ptexraggedright
+ \rmisbold #1\hfill}}\bigskip \par\nobreak
+}
+\def\chfopen #1#2{\chapoddpage {\chapfonts
+\vbox to 3in{\vfil \hbox to\hsize{\hfil #2} \hbox to\hsize{\hfil #1} \vfil}}%
+\par\penalty 5000 %
+}
+\def\centerchfopen #1{%
+\chapoddpage {\chapfonts \vbox{\hyphenpenalty=10000\tolerance=5000
+ \parindent=0pt
+ \hfill {\rmisbold #1}\hfill}}\bigskip \par\nobreak
+}
+\def\CHAPFopen{%
+ \global\let\chapmacro=\chfopen
+ \global\let\centerchapmacro=\centerchfopen}
+
+
+% Section titles. These macros combine the section number parts and
+% call the generic \sectionheading to do the printing.
+%
+\newskip\secheadingskip
+\def\secheadingbreak{\dobreak \secheadingskip{-1000}}
+
+% Subsection titles.
+\newskip\subsecheadingskip
+\def\subsecheadingbreak{\dobreak \subsecheadingskip{-500}}
+
+% Subsubsection titles.
+\def\subsubsecheadingskip{\subsecheadingskip}
+\def\subsubsecheadingbreak{\subsecheadingbreak}
+
+
+% Print any size, any type, section title.
+%
+% #1 is the text, #2 is the section level (sec/subsec/subsubsec), #3 is
+% the section type for xrefs (Ynumbered, Ynothing, Yappendix), #4 is the
+% section number.
+%
+\def\seckeyword{sec}
+%
+\def\sectionheading#1#2#3#4{%
+ {%
+ % Switch to the right set of fonts.
+ \csname #2fonts\endcsname \rmisbold
+ %
+ \def\sectionlevel{#2}%
+ \def\temptype{#3}%
+ %
+ % Insert first mark before the heading break (see notes for \domark).
+ \let\prevsectiondefs=\lastsectiondefs
+ \ifx\temptype\Ynothingkeyword
+ \ifx\sectionlevel\seckeyword
+ \gdef\lastsectiondefs{\gdef\thissectionname{#1}\gdef\thissectionnum{}%
+ \gdef\thissection{\thissectionname}}%
+ \fi
+ \else\ifx\temptype\Yomitfromtockeyword
+ % Don't redefine \thissection.
+ \else\ifx\temptype\Yappendixkeyword
+ \ifx\sectionlevel\seckeyword
+ \toks0={#1}%
+ \xdef\lastsectiondefs{%
+ \gdef\noexpand\thissectionname{\the\toks0}%
+ \gdef\noexpand\thissectionnum{#4}%
+ % \noexpand\putwordSection avoids expanding indigestible
+ % commands in some of the translations.
+ \gdef\noexpand\thissection{\noexpand\putwordSection{}
+ \noexpand\thissectionnum:
+ \noexpand\thissectionname}%
+ }%
+ \fi
+ \else
+ \ifx\sectionlevel\seckeyword
+ \toks0={#1}%
+ \xdef\lastsectiondefs{%
+ \gdef\noexpand\thissectionname{\the\toks0}%
+ \gdef\noexpand\thissectionnum{#4}%
+ % \noexpand\putwordSection avoids expanding indigestible
+ % commands in some of the translations.
+ \gdef\noexpand\thissection{\noexpand\putwordSection{}
+ \noexpand\thissectionnum:
+ \noexpand\thissectionname}%
+ }%
+ \fi
+ \fi\fi\fi
+ %
+ % Go into vertical mode. Usually we'll already be there, but we
+ % don't want the following whatsit to end up in a preceding paragraph
+ % if the document didn't happen to have a blank line.
+ \par
+ %
+ % Output the mark. Pass it through \safewhatsit, to take care of
+ % the preceding space.
+ \safewhatsit\domark
+ %
+ % Insert space above the heading.
+ \csname #2headingbreak\endcsname
+ %
+ % Now the second mark, after the heading break. No break points
+ % between here and the heading.
+ \let\prevsectiondefs=\lastsectiondefs
+ \domark
+ %
+ % Only insert the space after the number if we have a section number.
+ \ifx\temptype\Ynothingkeyword
+ \setbox0 = \hbox{}%
+ \def\toctype{unn}%
+ \gdef\lastsection{#1}%
+ \else\ifx\temptype\Yomitfromtockeyword
+ % for @headings -- no section number, don't include in toc,
+ % and don't redefine \lastsection.
+ \setbox0 = \hbox{}%
+ \def\toctype{omit}%
+ \let\sectionlevel=\empty
+ \else\ifx\temptype\Yappendixkeyword
+ \setbox0 = \hbox{#4\enspace}%
+ \def\toctype{app}%
+ \gdef\lastsection{#1}%
+ \else
+ \setbox0 = \hbox{#4\enspace}%
+ \def\toctype{num}%
+ \gdef\lastsection{#1}%
+ \fi\fi\fi
+ %
+ % Write the toc entry (before \donoderef). See comments in \chapmacro.
+ \writetocentry{\toctype\sectionlevel}{#1}{#4}%
+ %
+ % Write the node reference (= pdf destination for pdftex).
+ % Again, see comments in \chapmacro.
+ \donoderef{#3}%
+ %
+ % Interline glue will be inserted when the vbox is completed.
+ % That glue will be a valid breakpoint for the page, since it'll be
+ % preceded by a whatsit (usually from the \donoderef, or from the
+ % \writetocentry if there was no node). We don't want to allow that
+ % break, since then the whatsits could end up on page n while the
+ % section is on page n+1, thus toc/etc. are wrong. Debian bug 276000.
+ \nobreak
+ %
+ % Output the actual section heading.
+ \vbox{\hyphenpenalty=10000 \tolerance=5000 \parindent=0pt \ptexraggedright
+ \hangindent=\wd0 % zero if no section number
+ \unhbox0 #1}%
+ }%
+ % Add extra space after the heading -- half of whatever came above it.
+ % Don't allow stretch, though.
+ \kern .5 \csname #2headingskip\endcsname
+ %
+ % Do not let the kern be a potential breakpoint, as it would be if it
+ % was followed by glue.
+ \nobreak
+ %
+ % We'll almost certainly start a paragraph next, so don't let that
+ % glue accumulate. (Not a breakpoint because it's preceded by a
+ % discardable item.)
+ \vskip-\parskip
+ %
+ % This is purely so the last item on the list is a known \penalty >
+ % 10000. This is so \startdefun can avoid allowing breakpoints after
+ % section headings. Otherwise, it would insert a valid breakpoint between:
+ %
+ % @section sec-whatever
+ % @deffn def-whatever
+ \penalty 10001
+}
+
+
+\message{toc,}
+% Table of contents.
+\newwrite\tocfile
+
+% Write an entry to the toc file, opening it if necessary.
+% Called from @chapter, etc.
+%
+% Example usage: \writetocentry{sec}{Section Name}{\the\chapno.\the\secno}
+% We append the current node name (if any) and page number as additional
+% arguments for the \{chap,sec,...}entry macros which will eventually
+% read this. The node name is used in the pdf outlines as the
+% destination to jump to.
+%
+% We open the .toc file for writing here instead of at @setfilename (or
+% any other fixed time) so that @contents can be anywhere in the document.
+% But if #1 is `omit', then we don't do anything. This is used for the
+% table of contents chapter openings themselves.
+%
+\newif\iftocfileopened
+\def\omitkeyword{omit}%
+%
+\def\writetocentry#1#2#3{%
+ \edef\writetoctype{#1}%
+ \ifx\writetoctype\omitkeyword \else
+ \iftocfileopened\else
+ \immediate\openout\tocfile = \jobname.toc
+ \global\tocfileopenedtrue
+ \fi
+ %
+ \iflinks
+ {\atdummies
+ \edef\temp{%
+ \write\tocfile{@#1entry{#2}{#3}{\lastnode}{\noexpand\folio}}}%
+ \temp
+ }%
+ \fi
+ \fi
+ %
+ % Tell \shipout to create a pdf destination on each page, if we're
+ % writing pdf. These are used in the table of contents. We can't
+ % just write one on every page because the title pages are numbered
+ % 1 and 2 (the page numbers aren't printed), and so are the first
+ % two pages of the document. Thus, we'd have two destinations named
+ % `1', and two named `2'.
+ \ifpdf \global\pdfmakepagedesttrue \fi
+}
+
+
+% These characters do not print properly in the Computer Modern roman
+% fonts, so we must take special care. This is more or less redundant
+% with the Texinfo input format setup at the end of this file.
+%
+\def\activecatcodes{%
+ \catcode`\"=\active
+ \catcode`\$=\active
+ \catcode`\<=\active
+ \catcode`\>=\active
+ \catcode`\\=\active
+ \catcode`\^=\active
+ \catcode`\_=\active
+ \catcode`\|=\active
+ \catcode`\~=\active
+}
+
+
+% Read the toc file, which is essentially Texinfo input.
+\def\readtocfile{%
+ \setupdatafile
+ \activecatcodes
+ \input \tocreadfilename
+}
+
+\newskip\contentsrightmargin \contentsrightmargin=1in
+\newcount\savepageno
+\newcount\lastnegativepageno \lastnegativepageno = -1
+
+% Prepare to read what we've written to \tocfile.
+%
+\def\startcontents#1{%
+ % If @setchapternewpage on, and @headings double, the contents should
+ % start on an odd page, unlike chapters. Thus, we maintain
+ % \contentsalignmacro in parallel with \pagealignmacro.
+ % From: Torbjorn Granlund <tege at matematik.su.se>
+ \contentsalignmacro
+ \immediate\closeout\tocfile
+ %
+ % Don't need to put `Contents' or `Short Contents' in the headline.
+ % It is abundantly clear what they are.
+ \chapmacro{#1}{Yomitfromtoc}{}%
+ %
+ \savepageno = \pageno
+ \begingroup % Set up to handle contents files properly.
+ \raggedbottom % Worry more about breakpoints than the bottom.
+ \advance\hsize by -\contentsrightmargin % Don't use the full line length.
+ %
+ % Roman numerals for page numbers.
+ \ifnum \pageno>0 \global\pageno = \lastnegativepageno \fi
+}
+
+% redefined for the two-volume lispref. We always output on
+% \jobname.toc even if this is redefined.
+%
+\def\tocreadfilename{\jobname.toc}
+
+% Normal (long) toc.
+%
+\def\contents{%
+ \startcontents{\putwordTOC}%
+ \openin 1 \tocreadfilename\space
+ \ifeof 1 \else
+ \readtocfile
+ \fi
+ \vfill \eject
+ \contentsalignmacro % in case @setchapternewpage odd is in effect
+ \ifeof 1 \else
+ \pdfmakeoutlines
+ \fi
+ \closein 1
+ \endgroup
+ \lastnegativepageno = \pageno
+ \global\pageno = \savepageno
+}
+
+% And just the chapters.
+\def\summarycontents{%
+ \startcontents{\putwordShortTOC}%
+ %
+ \let\numchapentry = \shortchapentry
+ \let\appentry = \shortchapentry
+ \let\unnchapentry = \shortunnchapentry
+ % We want a true roman here for the page numbers.
+ \secfonts
+ \let\rm=\shortcontrm \let\bf=\shortcontbf
+ \let\sl=\shortcontsl \let\tt=\shortconttt
+ \rm
+ \hyphenpenalty = 10000
+ \advance\baselineskip by 1pt % Open it up a little.
+ \def\numsecentry##1##2##3##4{}
+ \let\appsecentry = \numsecentry
+ \let\unnsecentry = \numsecentry
+ \let\numsubsecentry = \numsecentry
+ \let\appsubsecentry = \numsecentry
+ \let\unnsubsecentry = \numsecentry
+ \let\numsubsubsecentry = \numsecentry
+ \let\appsubsubsecentry = \numsecentry
+ \let\unnsubsubsecentry = \numsecentry
+ \openin 1 \tocreadfilename\space
+ \ifeof 1 \else
+ \readtocfile
+ \fi
+ \closein 1
+ \vfill \eject
+ \contentsalignmacro % in case @setchapternewpage odd is in effect
+ \endgroup
+ \lastnegativepageno = \pageno
+ \global\pageno = \savepageno
+}
+\let\shortcontents = \summarycontents
+
+% Typeset the label for a chapter or appendix for the short contents.
+% The arg is, e.g., `A' for an appendix, or `3' for a chapter.
+%
+\def\shortchaplabel#1{%
+ % This space should be enough, since a single number is .5em, and the
+ % widest letter (M) is 1em, at least in the Computer Modern fonts.
+ % But use \hss just in case.
+ % (This space doesn't include the extra space that gets added after
+ % the label; that gets put in by \shortchapentry above.)
+ %
+ % We'd like to right-justify chapter numbers, but that looks strange
+ % with appendix letters. And right-justifying numbers and
+ % left-justifying letters looks strange when there is less than 10
+ % chapters. Have to read the whole toc once to know how many chapters
+ % there are before deciding ...
+ \hbox to 1em{#1\hss}%
+}
+
+% These macros generate individual entries in the table of contents.
+% The first argument is the chapter or section name.
+% The last argument is the page number.
+% The arguments in between are the chapter number, section number, ...
+
+% Chapters, in the main contents.
+\def\numchapentry#1#2#3#4{\dochapentry{#2\labelspace#1}{#4}}
+%
+% Chapters, in the short toc.
+% See comments in \dochapentry re vbox and related settings.
+\def\shortchapentry#1#2#3#4{%
+ \tocentry{\shortchaplabel{#2}\labelspace #1}{\doshortpageno\bgroup#4\egroup}%
+}
+
+% Appendices, in the main contents.
+% Need the word Appendix, and a fixed-size box.
+%
+\def\appendixbox#1{%
+ % We use M since it's probably the widest letter.
+ \setbox0 = \hbox{\putwordAppendix{} M}%
+ \hbox to \wd0{\putwordAppendix{} #1\hss}}
+%
+\def\appentry#1#2#3#4{\dochapentry{\appendixbox{#2}\labelspace#1}{#4}}
+
+% Unnumbered chapters.
+\def\unnchapentry#1#2#3#4{\dochapentry{#1}{#4}}
+\def\shortunnchapentry#1#2#3#4{\tocentry{#1}{\doshortpageno\bgroup#4\egroup}}
+
+% Sections.
+\def\numsecentry#1#2#3#4{\dosecentry{#2\labelspace#1}{#4}}
+\let\appsecentry=\numsecentry
+\def\unnsecentry#1#2#3#4{\dosecentry{#1}{#4}}
+
+% Subsections.
+\def\numsubsecentry#1#2#3#4{\dosubsecentry{#2\labelspace#1}{#4}}
+\let\appsubsecentry=\numsubsecentry
+\def\unnsubsecentry#1#2#3#4{\dosubsecentry{#1}{#4}}
+
+% And subsubsections.
+\def\numsubsubsecentry#1#2#3#4{\dosubsubsecentry{#2\labelspace#1}{#4}}
+\let\appsubsubsecentry=\numsubsubsecentry
+\def\unnsubsubsecentry#1#2#3#4{\dosubsubsecentry{#1}{#4}}
+
+% This parameter controls the indentation of the various levels.
+% Same as \defaultparindent.
+\newdimen\tocindent \tocindent = 15pt
+
+% Now for the actual typesetting. In all these, #1 is the text and #2 is the
+% page number.
+%
+% If the toc has to be broken over pages, we want it to be at chapters
+% if at all possible; hence the \penalty.
+\def\dochapentry#1#2{%
+ \penalty-300 \vskip1\baselineskip plus.33\baselineskip minus.25\baselineskip
+ \begingroup
+ \chapentryfonts
+ \tocentry{#1}{\dopageno\bgroup#2\egroup}%
+ \endgroup
+ \nobreak\vskip .25\baselineskip plus.1\baselineskip
+}
+
+\def\dosecentry#1#2{\begingroup
+ \secentryfonts \leftskip=\tocindent
+ \tocentry{#1}{\dopageno\bgroup#2\egroup}%
+\endgroup}
+
+\def\dosubsecentry#1#2{\begingroup
+ \subsecentryfonts \leftskip=2\tocindent
+ \tocentry{#1}{\dopageno\bgroup#2\egroup}%
+\endgroup}
+
+\def\dosubsubsecentry#1#2{\begingroup
+ \subsubsecentryfonts \leftskip=3\tocindent
+ \tocentry{#1}{\dopageno\bgroup#2\egroup}%
+\endgroup}
+
+% We use the same \entry macro as for the index entries.
+\let\tocentry = \entry
+
+% Space between chapter (or whatever) number and the title.
+\def\labelspace{\hskip1em \relax}
+
+\def\dopageno#1{{\rm #1}}
+\def\doshortpageno#1{{\rm #1}}
+
+\def\chapentryfonts{\secfonts \rm}
+\def\secentryfonts{\textfonts}
+\def\subsecentryfonts{\textfonts}
+\def\subsubsecentryfonts{\textfonts}
+
+
+\message{environments,}
+% @foo ... @end foo.
+
+% @tex ... @end tex escapes into raw Tex temporarily.
+% One exception: @ is still an escape character, so that @end tex works.
+% But \@ or @@ will get a plain tex @ character.
+
+\envdef\tex{%
+ \setupmarkupstyle{tex}%
+ \catcode `\\=0 \catcode `\{=1 \catcode `\}=2
+ \catcode `\$=3 \catcode `\&=4 \catcode `\#=6
+ \catcode `\^=7 \catcode `\_=8 \catcode `\~=\active \let~=\tie
+ \catcode `\%=14
+ \catcode `\+=\other
+ \catcode `\"=\other
+ \catcode `\|=\other
+ \catcode `\<=\other
+ \catcode `\>=\other
+ \catcode`\`=\other
+ \catcode`\'=\other
+ \escapechar=`\\
+ %
+ \let\b=\ptexb
+ \let\bullet=\ptexbullet
+ \let\c=\ptexc
+ \let\,=\ptexcomma
+ \let\.=\ptexdot
+ \let\dots=\ptexdots
+ \let\equiv=\ptexequiv
+ \let\!=\ptexexclam
+ \let\i=\ptexi
+ \let\indent=\ptexindent
+ \let\noindent=\ptexnoindent
+ \let\{=\ptexlbrace
+ \let\+=\tabalign
+ \let\}=\ptexrbrace
+ \let\/=\ptexslash
+ \let\*=\ptexstar
+ \let\t=\ptext
+ \expandafter \let\csname top\endcsname=\ptextop % outer
+ \let\frenchspacing=\plainfrenchspacing
+ %
+ \def\endldots{\mathinner{\ldots\ldots\ldots\ldots}}%
+ \def\enddots{\relax\ifmmode\endldots\else$\mathsurround=0pt \endldots\,$\fi}%
+ \def\@{@}%
+}
+% There is no need to define \Etex.
+
+% Define @lisp ... @end lisp.
+% @lisp environment forms a group so it can rebind things,
+% including the definition of @end lisp (which normally is erroneous).
+
+% Amount to narrow the margins by for @lisp.
+\newskip\lispnarrowing \lispnarrowing=0.4in
+
+% This is the definition that ^^M gets inside @lisp, @example, and other
+% such environments. \null is better than a space, since it doesn't
+% have any width.
+\def\lisppar{\null\endgraf}
+
+% This space is always present above and below environments.
+\newskip\envskipamount \envskipamount = 0pt
+
+% Make spacing and below environment symmetrical. We use \parskip here
+% to help in doing that, since in @example-like environments \parskip
+% is reset to zero; thus the \afterenvbreak inserts no space -- but the
+% start of the next paragraph will insert \parskip.
+%
+\def\aboveenvbreak{{%
+ % =10000 instead of <10000 because of a special case in \itemzzz and
+ % \sectionheading, q.v.
+ \ifnum \lastpenalty=10000 \else
+ \advance\envskipamount by \parskip
+ \endgraf
+ \ifdim\lastskip<\envskipamount
+ \removelastskip
+ % it's not a good place to break if the last penalty was \nobreak
+ % or better ...
+ \ifnum\lastpenalty<10000 \penalty-50 \fi
+ \vskip\envskipamount
+ \fi
+ \fi
+}}
+
+\let\afterenvbreak = \aboveenvbreak
+
+% \nonarrowing is a flag. If "set", @lisp etc don't narrow margins; it will
+% also clear it, so that its embedded environments do the narrowing again.
+\let\nonarrowing=\relax
+
+% @cartouche ... @end cartouche: draw rectangle w/rounded corners around
+% environment contents.
+\font\circle=lcircle10
+\newdimen\circthick
+\newdimen\cartouter\newdimen\cartinner
+\newskip\normbskip\newskip\normpskip\newskip\normlskip
+\circthick=\fontdimen8\circle
+%
+\def\ctl{{\circle\char'013\hskip -6pt}}% 6pt from pl file: 1/2charwidth
+\def\ctr{{\hskip 6pt\circle\char'010}}
+\def\cbl{{\circle\char'012\hskip -6pt}}
+\def\cbr{{\hskip 6pt\circle\char'011}}
+\def\carttop{\hbox to \cartouter{\hskip\lskip
+ \ctl\leaders\hrule height\circthick\hfil\ctr
+ \hskip\rskip}}
+\def\cartbot{\hbox to \cartouter{\hskip\lskip
+ \cbl\leaders\hrule height\circthick\hfil\cbr
+ \hskip\rskip}}
+%
+\newskip\lskip\newskip\rskip
+
+\envdef\cartouche{%
+ \ifhmode\par\fi % can't be in the midst of a paragraph.
+ \startsavinginserts
+ \lskip=\leftskip \rskip=\rightskip
+ \leftskip=0pt\rightskip=0pt % we want these *outside*.
+ \cartinner=\hsize \advance\cartinner by-\lskip
+ \advance\cartinner by-\rskip
+ \cartouter=\hsize
+ \advance\cartouter by 18.4pt % allow for 3pt kerns on either
+ % side, and for 6pt waste from
+ % each corner char, and rule thickness
+ \normbskip=\baselineskip \normpskip=\parskip \normlskip=\lineskip
+ % Flag to tell @lisp, etc., not to narrow margin.
+ \let\nonarrowing = t%
+ \vbox\bgroup
+ \baselineskip=0pt\parskip=0pt\lineskip=0pt
+ \carttop
+ \hbox\bgroup
+ \hskip\lskip
+ \vrule\kern3pt
+ \vbox\bgroup
+ \kern3pt
+ \hsize=\cartinner
+ \baselineskip=\normbskip
+ \lineskip=\normlskip
+ \parskip=\normpskip
+ \vskip -\parskip
+ \comment % For explanation, see the end of \def\group.
+}
+\def\Ecartouche{%
+ \ifhmode\par\fi
+ \kern3pt
+ \egroup
+ \kern3pt\vrule
+ \hskip\rskip
+ \egroup
+ \cartbot
+ \egroup
+ \checkinserts
+}
+
+
+% This macro is called at the beginning of all the @example variants,
+% inside a group.
+\newdimen\nonfillparindent
+\def\nonfillstart{%
+ \aboveenvbreak
+ \hfuzz = 12pt % Don't be fussy
+ \sepspaces % Make spaces be word-separators rather than space tokens.
+ \let\par = \lisppar % don't ignore blank lines
+ \obeylines % each line of input is a line of output
+ \parskip = 0pt
+ % Turn off paragraph indentation but redefine \indent to emulate
+ % the normal \indent.
+ \nonfillparindent=\parindent
+ \parindent = 0pt
+ \let\indent\nonfillindent
+ %
+ \emergencystretch = 0pt % don't try to avoid overfull boxes
+ \ifx\nonarrowing\relax
+ \advance \leftskip by \lispnarrowing
+ \exdentamount=\lispnarrowing
+ \else
+ \let\nonarrowing = \relax
+ \fi
+ \let\exdent=\nofillexdent
+}
+
+\begingroup
+\obeyspaces
+% We want to swallow spaces (but not other tokens) after the fake
+% @indent in our nonfill-environments, where spaces are normally
+% active and set to @tie, resulting in them not being ignored after
+% @indent.
+\gdef\nonfillindent{\futurelet\temp\nonfillindentcheck}%
+\gdef\nonfillindentcheck{%
+\ifx\temp %
+\expandafter\nonfillindentgobble%
+\else%
+\leavevmode\nonfillindentbox%
+\fi%
+}%
+\endgroup
+\def\nonfillindentgobble#1{\nonfillindent}
+\def\nonfillindentbox{\hbox to \nonfillparindent{\hss}}
+
+% If you want all examples etc. small: @set dispenvsize small.
+% If you want even small examples the full size: @set dispenvsize nosmall.
+% This affects the following displayed environments:
+% @example, @display, @format, @lisp
+%
+\def\smallword{small}
+\def\nosmallword{nosmall}
+\let\SETdispenvsize\relax
+\def\setnormaldispenv{%
+ \ifx\SETdispenvsize\smallword
+ % end paragraph for sake of leading, in case document has no blank
+ % line. This is redundant with what happens in \aboveenvbreak, but
+ % we need to do it before changing the fonts, and it's inconvenient
+ % to change the fonts afterward.
+ \ifnum \lastpenalty=10000 \else \endgraf \fi
+ \smallexamplefonts \rm
+ \fi
+}
+\def\setsmalldispenv{%
+ \ifx\SETdispenvsize\nosmallword
+ \else
+ \ifnum \lastpenalty=10000 \else \endgraf \fi
+ \smallexamplefonts \rm
+ \fi
+}
+
+% We often define two environments, @foo and @smallfoo.
+% Let's do it by one command:
+\def\makedispenv #1#2{
+ \expandafter\envdef\csname#1\endcsname {\setnormaldispenv #2}
+ \expandafter\envdef\csname small#1\endcsname {\setsmalldispenv #2}
+ \expandafter\let\csname E#1\endcsname \afterenvbreak
+ \expandafter\let\csname Esmall#1\endcsname \afterenvbreak
+}
+
+% Define two synonyms:
+\def\maketwodispenvs #1#2#3{
+ \makedispenv{#1}{#3}
+ \makedispenv{#2}{#3}
+}
+
+% @lisp: indented, narrowed, typewriter font; @example: same as @lisp.
+%
+% @smallexample and @smalllisp: use smaller fonts.
+% Originally contributed by Pavel at xerox.
+%
+\maketwodispenvs {lisp}{example}{%
+ \nonfillstart
+ \tt\setupmarkupstyle{example}%
+ \let\kbdfont = \kbdexamplefont % Allow @kbd to do something special.
+ \gobble % eat return
+}
+% @display/@smalldisplay: same as @lisp except keep current font.
+%
+\makedispenv {display}{%
+ \nonfillstart
+ \gobble
+}
+
+% @format/@smallformat: same as @display except don't narrow margins.
+%
+\makedispenv{format}{%
+ \let\nonarrowing = t%
+ \nonfillstart
+ \gobble
+}
+
+% @flushleft: same as @format, but doesn't obey \SETdispenvsize.
+\envdef\flushleft{%
+ \let\nonarrowing = t%
+ \nonfillstart
+ \gobble
+}
+\let\Eflushleft = \afterenvbreak
+
+% @flushright.
+%
+\envdef\flushright{%
+ \let\nonarrowing = t%
+ \nonfillstart
+ \advance\leftskip by 0pt plus 1fill
+ \gobble
+}
+\let\Eflushright = \afterenvbreak
+
+
+% @raggedright does more-or-less normal line breaking but no right
+% justification. From plain.tex.
+\envdef\raggedright{%
+ \rightskip0pt plus2em \spaceskip.3333em \xspaceskip.5em\relax
+}
+\let\Eraggedright\par
+
+\envdef\raggedleft{%
+ \parindent=0pt \leftskip0pt plus2em
+ \spaceskip.3333em \xspaceskip.5em \parfillskip=0pt
+ \hbadness=10000 % Last line will usually be underfull, so turn off
+ % badness reporting.
+}
+\let\Eraggedleft\par
+
+\envdef\raggedcenter{%
+ \parindent=0pt \rightskip0pt plus1em \leftskip0pt plus1em
+ \spaceskip.3333em \xspaceskip.5em \parfillskip=0pt
+ \hbadness=10000 % Last line will usually be underfull, so turn off
+ % badness reporting.
+}
+\let\Eraggedcenter\par
+
+
+% @quotation does normal linebreaking (hence we can't use \nonfillstart)
+% and narrows the margins. We keep \parskip nonzero in general, since
+% we're doing normal filling. So, when using \aboveenvbreak and
+% \afterenvbreak, temporarily make \parskip 0.
+%
+\def\quotationstart{%
+ {\parskip=0pt \aboveenvbreak}% because \aboveenvbreak inserts \parskip
+ \parindent=0pt
+ %
+ % @cartouche defines \nonarrowing to inhibit narrowing at next level down.
+ \ifx\nonarrowing\relax
+ \advance\leftskip by \lispnarrowing
+ \advance\rightskip by \lispnarrowing
+ \exdentamount = \lispnarrowing
+ \else
+ \let\nonarrowing = \relax
+ \fi
+ \parsearg\quotationlabel
+}
+
+\envdef\quotation{%
+ \setnormaldispenv
+ \quotationstart
+}
+
+\envdef\smallquotation{%
+ \setsmalldispenv
+ \quotationstart
+}
+\let\Esmallquotation = \Equotation
+
+% We have retained a nonzero parskip for the environment, since we're
+% doing normal filling.
+%
+\def\Equotation{%
+ \par
+ \ifx\quotationauthor\undefined\else
+ % indent a bit.
+ \leftline{\kern 2\leftskip \sl ---\quotationauthor}%
+ \fi
+ {\parskip=0pt \afterenvbreak}%
+}
+
+% If we're given an argument, typeset it in bold with a colon after.
+\def\quotationlabel#1{%
+ \def\temp{#1}%
+ \ifx\temp\empty \else
+ {\bf #1: }%
+ \fi
+}
+
+
+% LaTeX-like @verbatim... at end verbatim and @verb{<char>...<char>}
+% If we want to allow any <char> as delimiter,
+% we need the curly braces so that makeinfo sees the @verb command, eg:
+% `@verbx...x' would look like the '@verbx' command. --janneke at gnu.org
+%
+% [Knuth]: Donald Ervin Knuth, 1996. The TeXbook.
+%
+% [Knuth] p.344; only we need to do the other characters Texinfo sets
+% active too. Otherwise, they get lost as the first character on a
+% verbatim line.
+\def\dospecials{%
+ \do\ \do\\\do\{\do\}\do\$\do\&%
+ \do\#\do\^\do\^^K\do\_\do\^^A\do\%\do\~%
+ \do\<\do\>\do\|\do\@\do+\do\"%
+ % Don't do the quotes -- if we do, @set txicodequoteundirected and
+ % @set txicodequotebacktick will not have effect on @verb and
+ % @verbatim, and ?` and !` ligatures won't get disabled.
+ %\do\`\do\'%
+}
+%
+% [Knuth] p. 380
+\def\uncatcodespecials{%
+ \def\do##1{\catcode`##1=\other}\dospecials}
+%
+% Setup for the @verb command.
+%
+% Eight spaces for a tab
+\begingroup
+ \catcode`\^^I=\active
+ \gdef\tabeightspaces{\catcode`\^^I=\active\def^^I{\ \ \ \ \ \ \ \ }}
+\endgroup
+%
+\def\setupverb{%
+ \tt % easiest (and conventionally used) font for verbatim
+ \def\par{\leavevmode\endgraf}%
+ \setupmarkupstyle{verb}%
+ \tabeightspaces
+ % Respect line breaks,
+ % print special symbols as themselves, and
+ % make each space count
+ % must do in this order:
+ \obeylines \uncatcodespecials \sepspaces
+}
+
+% Setup for the @verbatim environment
+%
+% Real tab expansion
+\newdimen\tabw \setbox0=\hbox{\tt\space} \tabw=8\wd0 % tab amount
+%
+\def\starttabbox{\setbox0=\hbox\bgroup}
+%
+\begingroup
+ \catcode`\^^I=\active
+ \gdef\tabexpand{%
+ \catcode`\^^I=\active
+ \def^^I{\leavevmode\egroup
+ \dimen0=\wd0 % the width so far, or since the previous tab
+ \divide\dimen0 by\tabw
+ \multiply\dimen0 by\tabw % compute previous multiple of \tabw
+ \advance\dimen0 by\tabw % advance to next multiple of \tabw
+ \wd0=\dimen0 \box0 \starttabbox
+ }%
+ }
+\endgroup
+
+% start the verbatim environment.
+\def\setupverbatim{%
+ \let\nonarrowing = t%
+ \nonfillstart
+ % Easiest (and conventionally used) font for verbatim
+ \tt
+ \def\par{\leavevmode\egroup\box0\endgraf}%
+ \tabexpand
+ \setupmarkupstyle{verbatim}%
+ % Respect line breaks,
+ % print special symbols as themselves, and
+ % make each space count
+ % must do in this order:
+ \obeylines \uncatcodespecials \sepspaces
+ \everypar{\starttabbox}%
+}
+
+% Do the @verb magic: verbatim text is quoted by unique
+% delimiter characters. Before first delimiter expect a
+% right brace, after last delimiter expect closing brace:
+%
+% \def\doverb'{'<char>#1<char>'}'{#1}
+%
+% [Knuth] p. 382; only eat outer {}
+\begingroup
+ \catcode`[=1\catcode`]=2\catcode`\{=\other\catcode`\}=\other
+ \gdef\doverb{#1[\def\next##1#1}[##1\endgroup]\next]
+\endgroup
+%
+\def\verb{\begingroup\setupverb\doverb}
+%
+%
+% Do the @verbatim magic: define the macro \doverbatim so that
+% the (first) argument ends when '@end verbatim' is reached, ie:
+%
+% \def\doverbatim#1 at end verbatim{#1}
+%
+% For Texinfo it's a lot easier than for LaTeX,
+% because texinfo's \verbatim doesn't stop at '\end{verbatim}':
+% we need not redefine '\', '{' and '}'.
+%
+% Inspired by LaTeX's verbatim command set [latex.ltx]
+%
+\begingroup
+ \catcode`\ =\active
+ \obeylines %
+ % ignore everything up to the first ^^M, that's the newline at the end
+ % of the @verbatim input line itself. Otherwise we get an extra blank
+ % line in the output.
+ \xdef\doverbatim#1^^M#2 at end verbatim{#2\noexpand\end\gobble verbatim}%
+ % We really want {...\end verbatim} in the body of the macro, but
+ % without the active space; thus we have to use \xdef and \gobble.
+\endgroup
+%
+\envdef\verbatim{%
+ \setupverbatim\doverbatim
+}
+\let\Everbatim = \afterenvbreak
+
+
+% @verbatiminclude FILE - insert text of file in verbatim environment.
+%
+\def\verbatiminclude{\parseargusing\filenamecatcodes\doverbatiminclude}
+%
+\def\doverbatiminclude#1{%
+ {%
+ \makevalueexpandable
+ \setupverbatim
+ \indexnofonts % Allow `@@' and other weird things in file names.
+ \input #1
+ \afterenvbreak
+ }%
+}
+
+% @copying ... @end copying.
+% Save the text away for @insertcopying later.
+%
+% We save the uninterpreted tokens, rather than creating a box.
+% Saving the text in a box would be much easier, but then all the
+% typesetting commands (@smallbook, font changes, etc.) have to be done
+% beforehand -- and a) we want @copying to be done first in the source
+% file; b) letting users define the frontmatter in as flexible order as
+% possible is very desirable.
+%
+\def\copying{\checkenv{}\begingroup\scanargctxt\docopying}
+\def\docopying#1 at end copying{\endgroup\def\copyingtext{#1}}
+%
+\def\insertcopying{%
+ \begingroup
+ \parindent = 0pt % paragraph indentation looks wrong on title page
+ \scanexp\copyingtext
+ \endgroup
+}
+
+
+\message{defuns,}
+% @defun etc.
+
+\newskip\defbodyindent \defbodyindent=.4in
+\newskip\defargsindent \defargsindent=50pt
+\newskip\deflastargmargin \deflastargmargin=18pt
+\newcount\defunpenalty
+
+% Start the processing of @deffn:
+\def\startdefun{%
+ \ifnum\lastpenalty<10000
+ \medbreak
+ \defunpenalty=10003 % Will keep this @deffn together with the
+ % following @def command, see below.
+ \else
+ % If there are two @def commands in a row, we'll have a \nobreak,
+ % which is there to keep the function description together with its
+ % header. But if there's nothing but headers, we need to allow a
+ % break somewhere. Check specifically for penalty 10002, inserted
+ % by \printdefunline, instead of 10000, since the sectioning
+ % commands also insert a nobreak penalty, and we don't want to allow
+ % a break between a section heading and a defun.
+ %
+ % As a minor refinement, we avoid "club" headers by signalling
+ % with penalty of 10003 after the very first @deffn in the
+ % sequence (see above), and penalty of 10002 after any following
+ % @def command.
+ \ifnum\lastpenalty=10002 \penalty2000 \else \defunpenalty=10002 \fi
+ %
+ % Similarly, after a section heading, do not allow a break.
+ % But do insert the glue.
+ \medskip % preceded by discardable penalty, so not a breakpoint
+ \fi
+ %
+ \parindent=0in
+ \advance\leftskip by \defbodyindent
+ \exdentamount=\defbodyindent
+}
+
+\def\dodefunx#1{%
+ % First, check whether we are in the right environment:
+ \checkenv#1%
+ %
+ % As above, allow line break if we have multiple x headers in a row.
+ % It's not a great place, though.
+ \ifnum\lastpenalty=10002 \penalty3000 \else \defunpenalty=10002 \fi
+ %
+ % And now, it's time to reuse the body of the original defun:
+ \expandafter\gobbledefun#1%
+}
+\def\gobbledefun#1\startdefun{}
+
+% \printdefunline \deffnheader{text}
+%
+\def\printdefunline#1#2{%
+ \begingroup
+ % call \deffnheader:
+ #1#2 \endheader
+ % common ending:
+ \interlinepenalty = 10000
+ \advance\rightskip by 0pt plus 1fil
+ \endgraf
+ \nobreak\vskip -\parskip
+ \penalty\defunpenalty % signal to \startdefun and \dodefunx
+ % Some of the @defun-type tags do not enable magic parentheses,
+ % rendering the following check redundant. But we don't optimize.
+ \checkparencounts
+ \endgroup
+}
+
+\def\Edefun{\endgraf\medbreak}
+
+% \makedefun{deffn} creates \deffn, \deffnx and \Edeffn;
+% the only thing remaining is to define \deffnheader.
+%
+\def\makedefun#1{%
+ \expandafter\let\csname E#1\endcsname = \Edefun
+ \edef\temp{\noexpand\domakedefun
+ \makecsname{#1}\makecsname{#1x}\makecsname{#1header}}%
+ \temp
+}
+
+% \domakedefun \deffn \deffnx \deffnheader
+%
+% Define \deffn and \deffnx, without parameters.
+% \deffnheader has to be defined explicitly.
+%
+\def\domakedefun#1#2#3{%
+ \envdef#1{%
+ \startdefun
+ \parseargusing\activeparens{\printdefunline#3}%
+ }%
+ \def#2{\dodefunx#1}%
+ \def#3%
+}
+
+%%% Untyped functions:
+
+% @deffn category name args
+\makedefun{deffn}{\deffngeneral{}}
+
+% @deffn category class name args
+\makedefun{defop}#1 {\defopon{#1\ \putwordon}}
+
+% \defopon {category on}class name args
+\def\defopon#1#2 {\deffngeneral{\putwordon\ \code{#2}}{#1\ \code{#2}} }
+
+% \deffngeneral {subind}category name args
+%
+\def\deffngeneral#1#2 #3 #4\endheader{%
+ % Remember that \dosubind{fn}{foo}{} is equivalent to \doind{fn}{foo}.
+ \dosubind{fn}{\code{#3}}{#1}%
+ \defname{#2}{}{#3}\magicamp\defunargs{#4\unskip}%
+}
+
+%%% Typed functions:
+
+% @deftypefn category type name args
+\makedefun{deftypefn}{\deftypefngeneral{}}
+
+% @deftypeop category class type name args
+\makedefun{deftypeop}#1 {\deftypeopon{#1\ \putwordon}}
+
+% \deftypeopon {category on}class type name args
+\def\deftypeopon#1#2 {\deftypefngeneral{\putwordon\ \code{#2}}{#1\ \code{#2}} }
+
+% \deftypefngeneral {subind}category type name args
+%
+\def\deftypefngeneral#1#2 #3 #4 #5\endheader{%
+ \dosubind{fn}{\code{#4}}{#1}%
+ \defname{#2}{#3}{#4}\defunargs{#5\unskip}%
+}
+
+%%% Typed variables:
+
+% @deftypevr category type var args
+\makedefun{deftypevr}{\deftypecvgeneral{}}
+
+% @deftypecv category class type var args
+\makedefun{deftypecv}#1 {\deftypecvof{#1\ \putwordof}}
+
+% \deftypecvof {category of}class type var args
+\def\deftypecvof#1#2 {\deftypecvgeneral{\putwordof\ \code{#2}}{#1\ \code{#2}} }
+
+% \deftypecvgeneral {subind}category type var args
+%
+\def\deftypecvgeneral#1#2 #3 #4 #5\endheader{%
+ \dosubind{vr}{\code{#4}}{#1}%
+ \defname{#2}{#3}{#4}\defunargs{#5\unskip}%
+}
+
+%%% Untyped variables:
+
+% @defvr category var args
+\makedefun{defvr}#1 {\deftypevrheader{#1} {} }
+
+% @defcv category class var args
+\makedefun{defcv}#1 {\defcvof{#1\ \putwordof}}
+
+% \defcvof {category of}class var args
+\def\defcvof#1#2 {\deftypecvof{#1}#2 {} }
+
+%%% Type:
+% @deftp category name args
+\makedefun{deftp}#1 #2 #3\endheader{%
+ \doind{tp}{\code{#2}}%
+ \defname{#1}{}{#2}\defunargs{#3\unskip}%
+}
+
+% Remaining @defun-like shortcuts:
+\makedefun{defun}{\deffnheader{\putwordDeffunc} }
+\makedefun{defmac}{\deffnheader{\putwordDefmac} }
+\makedefun{defspec}{\deffnheader{\putwordDefspec} }
+\makedefun{deftypefun}{\deftypefnheader{\putwordDeffunc} }
+\makedefun{defvar}{\defvrheader{\putwordDefvar} }
+\makedefun{defopt}{\defvrheader{\putwordDefopt} }
+\makedefun{deftypevar}{\deftypevrheader{\putwordDefvar} }
+\makedefun{defmethod}{\defopon\putwordMethodon}
+\makedefun{deftypemethod}{\deftypeopon\putwordMethodon}
+\makedefun{defivar}{\defcvof\putwordInstanceVariableof}
+\makedefun{deftypeivar}{\deftypecvof\putwordInstanceVariableof}
+
+% \defname, which formats the name of the @def (not the args).
+% #1 is the category, such as "Function".
+% #2 is the return type, if any.
+% #3 is the function name.
+%
+% We are followed by (but not passed) the arguments, if any.
+%
+\def\defname#1#2#3{%
+ % Get the values of \leftskip and \rightskip as they were outside the @def...
+ \advance\leftskip by -\defbodyindent
+ %
+ % How we'll format the type name. Putting it in brackets helps
+ % distinguish it from the body text that may end up on the next line
+ % just below it.
+ \def\temp{#1}%
+ \setbox0=\hbox{\kern\deflastargmargin \ifx\temp\empty\else [\rm\temp]\fi}
+ %
+ % Figure out line sizes for the paragraph shape.
+ % The first line needs space for \box0; but if \rightskip is nonzero,
+ % we need only space for the part of \box0 which exceeds it:
+ \dimen0=\hsize \advance\dimen0 by -\wd0 \advance\dimen0 by \rightskip
+ % The continuations:
+ \dimen2=\hsize \advance\dimen2 by -\defargsindent
+ % (plain.tex says that \dimen1 should be used only as global.)
+ \parshape 2 0in \dimen0 \defargsindent \dimen2
+ %
+ % Put the type name to the right margin.
+ \noindent
+ \hbox to 0pt{%
+ \hfil\box0 \kern-\hsize
+ % \hsize has to be shortened this way:
+ \kern\leftskip
+ % Intentionally do not respect \rightskip, since we need the space.
+ }%
+ %
+ % Allow all lines to be underfull without complaint:
+ \tolerance=10000 \hbadness=10000
+ \exdentamount=\defbodyindent
+ {%
+ % defun fonts. We use typewriter by default (used to be bold) because:
+ % . we're printing identifiers, they should be in tt in principle.
+ % . in languages with many accents, such as Czech or French, it's
+ % common to leave accents off identifiers. The result looks ok in
+ % tt, but exceedingly strange in rm.
+ % . we don't want -- and --- to be treated as ligatures.
+ % . this still does not fix the ?` and !` ligatures, but so far no
+ % one has made identifiers using them :).
+ \df \tt
+ \def\temp{#2}% return value type
+ \ifx\temp\empty\else \tclose{\temp} \fi
+ #3% output function name
+ }%
+ {\rm\enskip}% hskip 0.5 em of \tenrm
+ %
+ \boldbrax
+ % arguments will be output next, if any.
+}
+
+% Print arguments in slanted roman (not ttsl), inconsistently with using
+% tt for the name. This is because literal text is sometimes needed in
+% the argument list (groff manual), and ttsl and tt are not very
+% distinguishable. Prevent hyphenation at `-' chars.
+%
+\def\defunargs#1{%
+ % use sl by default (not ttsl),
+ % tt for the names.
+ \df \sl \hyphenchar\font=0
+ %
+ % On the other hand, if an argument has two dashes (for instance), we
+ % want a way to get ttsl. Let's try @var for that.
+ \def\var##1{{\setupmarkupstyle{var}\ttslanted{##1}}}%
+ #1%
+ \sl\hyphenchar\font=45
+}
+
+% We want ()&[] to print specially on the defun line.
+%
+\def\activeparens{%
+ \catcode`\(=\active \catcode`\)=\active
+ \catcode`\[=\active \catcode`\]=\active
+ \catcode`\&=\active
+}
+
+% Make control sequences which act like normal parenthesis chars.
+\let\lparen = ( \let\rparen = )
+
+% Be sure that we always have a definition for `(', etc. For example,
+% if the fn name has parens in it, \boldbrax will not be in effect yet,
+% so TeX would otherwise complain about undefined control sequence.
+{
+ \activeparens
+ \global\let(=\lparen \global\let)=\rparen
+ \global\let[=\lbrack \global\let]=\rbrack
+ \global\let& = \&
+
+ \gdef\boldbrax{\let(=\opnr\let)=\clnr\let[=\lbrb\let]=\rbrb}
+ \gdef\magicamp{\let&=\amprm}
+}
+
+\newcount\parencount
+
+% If we encounter &foo, then turn on ()-hacking afterwards
+\newif\ifampseen
+\def\amprm#1 {\ampseentrue{\bf\ }}
+
+\def\parenfont{%
+ \ifampseen
+ % At the first level, print parens in roman,
+ % otherwise use the default font.
+ \ifnum \parencount=1 \rm \fi
+ \else
+ % The \sf parens (in \boldbrax) actually are a little bolder than
+ % the contained text. This is especially needed for [ and ] .
+ \sf
+ \fi
+}
+\def\infirstlevel#1{%
+ \ifampseen
+ \ifnum\parencount=1
+ #1%
+ \fi
+ \fi
+}
+\def\bfafterword#1 {#1 \bf}
+
+\def\opnr{%
+ \global\advance\parencount by 1
+ {\parenfont(}%
+ \infirstlevel \bfafterword
+}
+\def\clnr{%
+ {\parenfont)}%
+ \infirstlevel \sl
+ \global\advance\parencount by -1
+}
+
+\newcount\brackcount
+\def\lbrb{%
+ \global\advance\brackcount by 1
+ {\bf[}%
+}
+\def\rbrb{%
+ {\bf]}%
+ \global\advance\brackcount by -1
+}
+
+\def\checkparencounts{%
+ \ifnum\parencount=0 \else \badparencount \fi
+ \ifnum\brackcount=0 \else \badbrackcount \fi
+}
+% these should not use \errmessage; the glibc manual, at least, actually
+% has such constructs (when documenting function pointers).
+\def\badparencount{%
+ \message{Warning: unbalanced parentheses in @def...}%
+ \global\parencount=0
+}
+\def\badbrackcount{%
+ \message{Warning: unbalanced square brackets in @def...}%
+ \global\brackcount=0
+}
+
+
+\message{macros,}
+% @macro.
+
+% To do this right we need a feature of e-TeX, \scantokens,
+% which we arrange to emulate with a temporary file in ordinary TeX.
+\ifx\eTeXversion\undefined
+ \newwrite\macscribble
+ \def\scantokens#1{%
+ \toks0={#1}%
+ \immediate\openout\macscribble=\jobname.tmp
+ \immediate\write\macscribble{\the\toks0}%
+ \immediate\closeout\macscribble
+ \input \jobname.tmp
+ }
+\fi
+
+\def\scanmacro#1{%
+ \begingroup
+ \newlinechar`\^^M
+ \let\xeatspaces\eatspaces
+ % Undo catcode changes of \startcontents and \doprintindex
+ % When called from @insertcopying or (short)caption, we need active
+ % backslash to get it printed correctly. Previously, we had
+ % \catcode`\\=\other instead. We'll see whether a problem appears
+ % with macro expansion. --kasal, 19aug04
+ \catcode`\@=0 \catcode`\\=\active \escapechar=`\@
+ % ... and \example
+ \spaceisspace
+ %
+ % Append \endinput to make sure that TeX does not see the ending newline.
+ % I've verified that it is necessary both for e-TeX and for ordinary TeX
+ % --kasal, 29nov03
+ \scantokens{#1\endinput}%
+ \endgroup
+}
+
+\def\scanexp#1{%
+ \edef\temp{\noexpand\scanmacro{#1}}%
+ \temp
+}
+
+\newcount\paramno % Count of parameters
+\newtoks\macname % Macro name
+\newif\ifrecursive % Is it recursive?
+
+% List of all defined macros in the form
+% \definedummyword\macro1\definedummyword\macro2...
+% Currently is also contains all @aliases; the list can be split
+% if there is a need.
+\def\macrolist{}
+
+% Add the macro to \macrolist
+\def\addtomacrolist#1{\expandafter \addtomacrolistxxx \csname#1\endcsname}
+\def\addtomacrolistxxx#1{%
+ \toks0 = \expandafter{\macrolist\definedummyword#1}%
+ \xdef\macrolist{\the\toks0}%
+}
+
+% Utility routines.
+% This does \let #1 = #2, with \csnames; that is,
+% \let \csname#1\endcsname = \csname#2\endcsname
+% (except of course we have to play expansion games).
+%
+\def\cslet#1#2{%
+ \expandafter\let
+ \csname#1\expandafter\endcsname
+ \csname#2\endcsname
+}
+
+% Trim leading and trailing spaces off a string.
+% Concepts from aro-bend problem 15 (see CTAN).
+{\catcode`\@=11
+\gdef\eatspaces #1{\expandafter\trim@\expandafter{#1 }}
+\gdef\trim@ #1{\trim@@ @#1 @ #1 @ @@}
+\gdef\trim@@ #1@ #2@ #3@@{\trim@@@\empty #2 @}
+\def\unbrace#1{#1}
+\unbrace{\gdef\trim@@@ #1 } #2@{#1}
+}
+
+% Trim a single trailing ^^M off a string.
+{\catcode`\^^M=\other \catcode`\Q=3%
+\gdef\eatcr #1{\eatcra #1Q^^MQ}%
+\gdef\eatcra#1^^MQ{\eatcrb#1Q}%
+\gdef\eatcrb#1Q#2Q{#1}%
+}
+
+% Macro bodies are absorbed as an argument in a context where
+% all characters are catcode 10, 11 or 12, except \ which is active
+% (as in normal texinfo). It is necessary to change the definition of \.
+
+% Non-ASCII encodings make 8-bit characters active, so un-activate
+% them to avoid their expansion. Must do this non-globally, to
+% confine the change to the current group.
+
+% It's necessary to have hard CRs when the macro is executed. This is
+% done by making ^^M (\endlinechar) catcode 12 when reading the macro
+% body, and then making it the \newlinechar in \scanmacro.
+
+\def\scanctxt{%
+ \catcode`\"=\other
+ \catcode`\+=\other
+ \catcode`\<=\other
+ \catcode`\>=\other
+ \catcode`\@=\other
+ \catcode`\^=\other
+ \catcode`\_=\other
+ \catcode`\|=\other
+ \catcode`\~=\other
+ \ifx\declaredencoding\ascii \else \setnonasciicharscatcodenonglobal\other \fi
+}
+
+\def\scanargctxt{%
+ \scanctxt
+ \catcode`\\=\other
+ \catcode`\^^M=\other
+}
+
+\def\macrobodyctxt{%
+ \scanctxt
+ \catcode`\{=\other
+ \catcode`\}=\other
+ \catcode`\^^M=\other
+ \usembodybackslash
+}
+
+\def\macroargctxt{%
+ \scanctxt
+ \catcode`\\=\other
+}
+
+% \mbodybackslash is the definition of \ in @macro bodies.
+% It maps \foo\ => \csname macarg.foo\endcsname => #N
+% where N is the macro parameter number.
+% We define \csname macarg.\endcsname to be \realbackslash, so
+% \\ in macro replacement text gets you a backslash.
+
+{\catcode`@=0 @catcode`@\=@active
+ @gdef at usembodybackslash{@let\=@mbodybackslash}
+ @gdef at mbodybackslash#1\{@csname macarg.#1 at endcsname}
+}
+\expandafter\def\csname macarg.\endcsname{\realbackslash}
+
+\def\macro{\recursivefalse\parsearg\macroxxx}
+\def\rmacro{\recursivetrue\parsearg\macroxxx}
+
+\def\macroxxx#1{%
+ \getargs{#1}% now \macname is the macname and \argl the arglist
+ \ifx\argl\empty % no arguments
+ \paramno=0%
+ \else
+ \expandafter\parsemargdef \argl;%
+ \fi
+ \if1\csname ismacro.\the\macname\endcsname
+ \message{Warning: redefining \the\macname}%
+ \else
+ \expandafter\ifx\csname \the\macname\endcsname \relax
+ \else \errmessage{Macro name \the\macname\space already defined}\fi
+ \global\cslet{macsave.\the\macname}{\the\macname}%
+ \global\expandafter\let\csname ismacro.\the\macname\endcsname=1%
+ \addtomacrolist{\the\macname}%
+ \fi
+ \begingroup \macrobodyctxt
+ \ifrecursive \expandafter\parsermacbody
+ \else \expandafter\parsemacbody
+ \fi}
+
+\parseargdef\unmacro{%
+ \if1\csname ismacro.#1\endcsname
+ \global\cslet{#1}{macsave.#1}%
+ \global\expandafter\let \csname ismacro.#1\endcsname=0%
+ % Remove the macro name from \macrolist:
+ \begingroup
+ \expandafter\let\csname#1\endcsname \relax
+ \let\definedummyword\unmacrodo
+ \xdef\macrolist{\macrolist}%
+ \endgroup
+ \else
+ \errmessage{Macro #1 not defined}%
+ \fi
+}
+
+% Called by \do from \dounmacro on each macro. The idea is to omit any
+% macro definitions that have been changed to \relax.
+%
+\def\unmacrodo#1{%
+ \ifx #1\relax
+ % remove this
+ \else
+ \noexpand\definedummyword \noexpand#1%
+ \fi
+}
+
+% This makes use of the obscure feature that if the last token of a
+% <parameter list> is #, then the preceding argument is delimited by
+% an opening brace, and that opening brace is not consumed.
+\def\getargs#1{\getargsxxx#1{}}
+\def\getargsxxx#1#{\getmacname #1 \relax\getmacargs}
+\def\getmacname #1 #2\relax{\macname={#1}}
+\def\getmacargs#1{\def\argl{#1}}
+
+% Parse the optional {params} list. Set up \paramno and \paramlist
+% so \defmacro knows what to do. Define \macarg.blah for each blah
+% in the params list, to be ##N where N is the position in that list.
+% That gets used by \mbodybackslash (above).
+
+% We need to get `macro parameter char #' into several definitions.
+% The technique used is stolen from LaTeX: let \hash be something
+% unexpandable, insert that wherever you need a #, and then redefine
+% it to # just before using the token list produced.
+%
+% The same technique is used to protect \eatspaces till just before
+% the macro is used.
+
+\def\parsemargdef#1;{\paramno=0\def\paramlist{}%
+ \let\hash\relax\let\xeatspaces\relax\parsemargdefxxx#1,;,}
+\def\parsemargdefxxx#1,{%
+ \if#1;\let\next=\relax
+ \else \let\next=\parsemargdefxxx
+ \advance\paramno by 1%
+ \expandafter\edef\csname macarg.\eatspaces{#1}\endcsname
+ {\xeatspaces{\hash\the\paramno}}%
+ \edef\paramlist{\paramlist\hash\the\paramno,}%
+ \fi\next}
+
+% These two commands read recursive and nonrecursive macro bodies.
+% (They're different since rec and nonrec macros end differently.)
+
+\long\def\parsemacbody#1 at end macro%
+{\xdef\temp{\eatcr{#1}}\endgroup\defmacro}%
+\long\def\parsermacbody#1 at end rmacro%
+{\xdef\temp{\eatcr{#1}}\endgroup\defmacro}%
+
+% This defines the macro itself. There are six cases: recursive and
+% nonrecursive macros of zero, one, and many arguments.
+% Much magic with \expandafter here.
+% \xdef is used so that macro definitions will survive the file
+% they're defined in; @include reads the file inside a group.
+\def\defmacro{%
+ \let\hash=##% convert placeholders to macro parameter chars
+ \ifrecursive
+ \ifcase\paramno
+ % 0
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \noexpand\scanmacro{\temp}}%
+ \or % 1
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \bgroup\noexpand\macroargctxt
+ \noexpand\braceorline
+ \expandafter\noexpand\csname\the\macname xxx\endcsname}%
+ \expandafter\xdef\csname\the\macname xxx\endcsname##1{%
+ \egroup\noexpand\scanmacro{\temp}}%
+ \else % many
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \bgroup\noexpand\macroargctxt
+ \noexpand\csname\the\macname xx\endcsname}%
+ \expandafter\xdef\csname\the\macname xx\endcsname##1{%
+ \expandafter\noexpand\csname\the\macname xxx\endcsname ##1,}%
+ \expandafter\expandafter
+ \expandafter\xdef
+ \expandafter\expandafter
+ \csname\the\macname xxx\endcsname
+ \paramlist{\egroup\noexpand\scanmacro{\temp}}%
+ \fi
+ \else
+ \ifcase\paramno
+ % 0
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \noexpand\norecurse{\the\macname}%
+ \noexpand\scanmacro{\temp}\egroup}%
+ \or % 1
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \bgroup\noexpand\macroargctxt
+ \noexpand\braceorline
+ \expandafter\noexpand\csname\the\macname xxx\endcsname}%
+ \expandafter\xdef\csname\the\macname xxx\endcsname##1{%
+ \egroup
+ \noexpand\norecurse{\the\macname}%
+ \noexpand\scanmacro{\temp}\egroup}%
+ \else % many
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \bgroup\noexpand\macroargctxt
+ \expandafter\noexpand\csname\the\macname xx\endcsname}%
+ \expandafter\xdef\csname\the\macname xx\endcsname##1{%
+ \expandafter\noexpand\csname\the\macname xxx\endcsname ##1,}%
+ \expandafter\expandafter
+ \expandafter\xdef
+ \expandafter\expandafter
+ \csname\the\macname xxx\endcsname
+ \paramlist{%
+ \egroup
+ \noexpand\norecurse{\the\macname}%
+ \noexpand\scanmacro{\temp}\egroup}%
+ \fi
+ \fi}
+
+\def\norecurse#1{\bgroup\cslet{#1}{macsave.#1}}
+
+% \braceorline decides whether the next nonwhitespace character is a
+% {. If so it reads up to the closing }, if not, it reads the whole
+% line. Whatever was read is then fed to the next control sequence
+% as an argument (by \parsebrace or \parsearg)
+\def\braceorline#1{\let\macnamexxx=#1\futurelet\nchar\braceorlinexxx}
+\def\braceorlinexxx{%
+ \ifx\nchar\bgroup\else
+ \expandafter\parsearg
+ \fi \macnamexxx}
+
+
+% @alias.
+% We need some trickery to remove the optional spaces around the equal
+% sign. Just make them active and then expand them all to nothing.
+\def\alias{\parseargusing\obeyspaces\aliasxxx}
+\def\aliasxxx #1{\aliasyyy#1\relax}
+\def\aliasyyy #1=#2\relax{%
+ {%
+ \expandafter\let\obeyedspace=\empty
+ \addtomacrolist{#1}%
+ \xdef\next{\global\let\makecsname{#1}=\makecsname{#2}}%
+ }%
+ \next
+}
+
+
+\message{cross references,}
+
+\newwrite\auxfile
+\newif\ifhavexrefs % True if xref values are known.
+\newif\ifwarnedxrefs % True if we warned once that they aren't known.
+
+% @inforef is relatively simple.
+\def\inforef #1{\inforefzzz #1,,,,**}
+\def\inforefzzz #1,#2,#3,#4**{\putwordSee{} \putwordInfo{} \putwordfile{} \file{\ignorespaces #3{}},
+ node \samp{\ignorespaces#1{}}}
+
+% @node's only job in TeX is to define \lastnode, which is used in
+% cross-references. The @node line might or might not have commas, and
+% might or might not have spaces before the first comma, like:
+% @node foo , bar , ...
+% We don't want such trailing spaces in the node name.
+%
+\parseargdef\node{\checkenv{}\donode #1 ,\finishnodeparse}
+%
+% also remove a trailing comma, in case of something like this:
+% @node Help-Cross, , , Cross-refs
+\def\donode#1 ,#2\finishnodeparse{\dodonode #1,\finishnodeparse}
+\def\dodonode#1,#2\finishnodeparse{\gdef\lastnode{#1}}
+
+\let\nwnode=\node
+\let\lastnode=\empty
+
+% Write a cross-reference definition for the current node. #1 is the
+% type (Ynumbered, Yappendix, Ynothing).
+%
+\def\donoderef#1{%
+ \ifx\lastnode\empty\else
+ \setref{\lastnode}{#1}%
+ \global\let\lastnode=\empty
+ \fi
+}
+
+% @anchor{NAME} -- define xref target at arbitrary point.
+%
+\newcount\savesfregister
+%
+\def\savesf{\relax \ifhmode \savesfregister=\spacefactor \fi}
+\def\restoresf{\relax \ifhmode \spacefactor=\savesfregister \fi}
+\def\anchor#1{\savesf \setref{#1}{Ynothing}\restoresf \ignorespaces}
+
+% \setref{NAME}{SNT} defines a cross-reference point NAME (a node or an
+% anchor), which consists of three parts:
+% 1) NAME-title - the current sectioning name taken from \lastsection,
+% or the anchor name.
+% 2) NAME-snt - section number and type, passed as the SNT arg, or
+% empty for anchors.
+% 3) NAME-pg - the page number.
+%
+% This is called from \donoderef, \anchor, and \dofloat. In the case of
+% floats, there is an additional part, which is not written here:
+% 4) NAME-lof - the text as it should appear in a @listoffloats.
+%
+\def\setref#1#2{%
+ \pdfmkdest{#1}%
+ \iflinks
+ {%
+ \atdummies % preserve commands, but don't expand them
+ \edef\writexrdef##1##2{%
+ \write\auxfile{@xrdef{#1-% #1 of \setref, expanded by the \edef
+ ##1}{##2}}% these are parameters of \writexrdef
+ }%
+ \toks0 = \expandafter{\lastsection}%
+ \immediate \writexrdef{title}{\the\toks0 }%
+ \immediate \writexrdef{snt}{\csname #2\endcsname}% \Ynumbered etc.
+ \safewhatsit{\writexrdef{pg}{\folio}}% will be written later, during \shipout
+ }%
+ \fi
+}
+
+% @xref, @pxref, and @ref generate cross-references. For \xrefX, #1 is
+% the node name, #2 the name of the Info cross-reference, #3 the printed
+% node name, #4 the name of the Info file, #5 the name of the printed
+% manual. All but the node name can be omitted.
+%
+\def\pxref#1{\putwordsee{} \xrefX[#1,,,,,,,]}
+\def\xref#1{\putwordSee{} \xrefX[#1,,,,,,,]}
+\def\ref#1{\xrefX[#1,,,,,,,]}
+\def\xrefX[#1,#2,#3,#4,#5,#6]{\begingroup
+ \unsepspaces
+ \def\printedmanual{\ignorespaces #5}%
+ \def\printedrefname{\ignorespaces #3}%
+ \setbox1=\hbox{\printedmanual\unskip}%
+ \setbox0=\hbox{\printedrefname\unskip}%
+ \ifdim \wd0 = 0pt
+ % No printed node name was explicitly given.
+ \expandafter\ifx\csname SETxref-automatic-section-title\endcsname\relax
+ % Use the node name inside the square brackets.
+ \def\printedrefname{\ignorespaces #1}%
+ \else
+ % Use the actual chapter/section title appear inside
+ % the square brackets. Use the real section title if we have it.
+ \ifdim \wd1 > 0pt
+ % It is in another manual, so we don't have it.
+ \def\printedrefname{\ignorespaces #1}%
+ \else
+ \ifhavexrefs
+ % We know the real title if we have the xref values.
+ \def\printedrefname{\refx{#1-title}{}}%
+ \else
+ % Otherwise just copy the Info node name.
+ \def\printedrefname{\ignorespaces #1}%
+ \fi%
+ \fi
+ \fi
+ \fi
+ %
+ % Make link in pdf output.
+ \ifpdf
+ {\indexnofonts
+ \turnoffactive
+ % This expands tokens, so do it after making catcode changes, so _
+ % etc. don't get their TeX definitions.
+ \getfilename{#4}%
+ %
+ % See comments at \activebackslashdouble.
+ {\activebackslashdouble \xdef\pdfxrefdest{#1}%
+ \backslashparens\pdfxrefdest}%
+ %
+ \leavevmode
+ \startlink attr{/Border [0 0 0]}%
+ \ifnum\filenamelength>0
+ goto file{\the\filename.pdf} name{\pdfxrefdest}%
+ \else
+ goto name{\pdfmkpgn{\pdfxrefdest}}%
+ \fi
+ }%
+ \setcolor{\linkcolor}%
+ \fi
+ %
+ % Float references are printed completely differently: "Figure 1.2"
+ % instead of "[somenode], p.3". We distinguish them by the
+ % LABEL-title being set to a magic string.
+ {%
+ % Have to otherify everything special to allow the \csname to
+ % include an _ in the xref name, etc.
+ \indexnofonts
+ \turnoffactive
+ \expandafter\global\expandafter\let\expandafter\Xthisreftitle
+ \csname XR#1-title\endcsname
+ }%
+ \iffloat\Xthisreftitle
+ % If the user specified the print name (third arg) to the ref,
+ % print it instead of our usual "Figure 1.2".
+ \ifdim\wd0 = 0pt
+ \refx{#1-snt}{}%
+ \else
+ \printedrefname
+ \fi
+ %
+ % if the user also gave the printed manual name (fifth arg), append
+ % "in MANUALNAME".
+ \ifdim \wd1 > 0pt
+ \space \putwordin{} \cite{\printedmanual}%
+ \fi
+ \else
+ % node/anchor (non-float) references.
+ %
+ % If we use \unhbox0 and \unhbox1 to print the node names, TeX does not
+ % insert empty discretionaries after hyphens, which means that it will
+ % not find a line break at a hyphen in a node names. Since some manuals
+ % are best written with fairly long node names, containing hyphens, this
+ % is a loss. Therefore, we give the text of the node name again, so it
+ % is as if TeX is seeing it for the first time.
+ \ifdim \wd1 > 0pt
+ \putwordSection{} ``\printedrefname'' \putwordin{} \cite{\printedmanual}%
+ \else
+ % _ (for example) has to be the character _ for the purposes of the
+ % control sequence corresponding to the node, but it has to expand
+ % into the usual \leavevmode...\vrule stuff for purposes of
+ % printing. So we \turnoffactive for the \refx-snt, back on for the
+ % printing, back off for the \refx-pg.
+ {\turnoffactive
+ % Only output a following space if the -snt ref is nonempty; for
+ % @unnumbered and @anchor, it won't be.
+ \setbox2 = \hbox{\ignorespaces \refx{#1-snt}{}}%
+ \ifdim \wd2 > 0pt \refx{#1-snt}\space\fi
+ }%
+ % output the `[mynode]' via a macro so it can be overridden.
+ \xrefprintnodename\printedrefname
+ %
+ % But we always want a comma and a space:
+ ,\space
+ %
+ % output the `page 3'.
+ \turnoffactive \putwordpage\tie\refx{#1-pg}{}%
+ \fi
+ \fi
+ \endlink
+\endgroup}
+
+% This macro is called from \xrefX for the `[nodename]' part of xref
+% output. It's a separate macro only so it can be changed more easily,
+% since square brackets don't work well in some documents. Particularly
+% one that Bob is working on :).
+%
+\def\xrefprintnodename#1{[#1]}
+
+% Things referred to by \setref.
+%
+\def\Ynothing{}
+\def\Yomitfromtoc{}
+\def\Ynumbered{%
+ \ifnum\secno=0
+ \putwordChapter at tie \the\chapno
+ \else \ifnum\subsecno=0
+ \putwordSection at tie \the\chapno.\the\secno
+ \else \ifnum\subsubsecno=0
+ \putwordSection at tie \the\chapno.\the\secno.\the\subsecno
+ \else
+ \putwordSection at tie \the\chapno.\the\secno.\the\subsecno.\the\subsubsecno
+ \fi\fi\fi
+}
+\def\Yappendix{%
+ \ifnum\secno=0
+ \putwordAppendix at tie @char\the\appendixno{}%
+ \else \ifnum\subsecno=0
+ \putwordSection at tie @char\the\appendixno.\the\secno
+ \else \ifnum\subsubsecno=0
+ \putwordSection at tie @char\the\appendixno.\the\secno.\the\subsecno
+ \else
+ \putwordSection at tie
+ @char\the\appendixno.\the\secno.\the\subsecno.\the\subsubsecno
+ \fi\fi\fi
+}
+
+% Define \refx{NAME}{SUFFIX} to reference a cross-reference string named NAME.
+% If its value is nonempty, SUFFIX is output afterward.
+%
+\def\refx#1#2{%
+ {%
+ \indexnofonts
+ \otherbackslash
+ \expandafter\global\expandafter\let\expandafter\thisrefX
+ \csname XR#1\endcsname
+ }%
+ \ifx\thisrefX\relax
+ % If not defined, say something at least.
+ \angleleft un\-de\-fined\angleright
+ \iflinks
+ \ifhavexrefs
+ \message{\linenumber Undefined cross reference `#1'.}%
+ \else
+ \ifwarnedxrefs\else
+ \global\warnedxrefstrue
+ \message{Cross reference values unknown; you must run TeX again.}%
+ \fi
+ \fi
+ \fi
+ \else
+ % It's defined, so just use it.
+ \thisrefX
+ \fi
+ #2% Output the suffix in any case.
+}
+
+% This is the macro invoked by entries in the aux file. Usually it's
+% just a \def (we prepend XR to the control sequence name to avoid
+% collisions). But if this is a float type, we have more work to do.
+%
+\def\xrdef#1#2{%
+ {% The node name might contain 8-bit characters, which in our current
+ % implementation are changed to commands like @'e. Don't let these
+ % mess up the control sequence name.
+ \indexnofonts
+ \turnoffactive
+ \xdef\safexrefname{#1}%
+ }%
+ %
+ \expandafter\gdef\csname XR\safexrefname\endcsname{#2}% remember this xref
+ %
+ % Was that xref control sequence that we just defined for a float?
+ \expandafter\iffloat\csname XR\safexrefname\endcsname
+ % it was a float, and we have the (safe) float type in \iffloattype.
+ \expandafter\let\expandafter\floatlist
+ \csname floatlist\iffloattype\endcsname
+ %
+ % Is this the first time we've seen this float type?
+ \expandafter\ifx\floatlist\relax
+ \toks0 = {\do}% yes, so just \do
+ \else
+ % had it before, so preserve previous elements in list.
+ \toks0 = \expandafter{\floatlist\do}%
+ \fi
+ %
+ % Remember this xref in the control sequence \floatlistFLOATTYPE,
+ % for later use in \listoffloats.
+ \expandafter\xdef\csname floatlist\iffloattype\endcsname{\the\toks0
+ {\safexrefname}}%
+ \fi
+}
+
+% Read the last existing aux file, if any. No error if none exists.
+%
+\def\tryauxfile{%
+ \openin 1 \jobname.aux
+ \ifeof 1 \else
+ \readdatafile{aux}%
+ \global\havexrefstrue
+ \fi
+ \closein 1
+}
+
+\def\setupdatafile{%
+ \catcode`\^^@=\other
+ \catcode`\^^A=\other
+ \catcode`\^^B=\other
+ \catcode`\^^C=\other
+ \catcode`\^^D=\other
+ \catcode`\^^E=\other
+ \catcode`\^^F=\other
+ \catcode`\^^G=\other
+ \catcode`\^^H=\other
+ \catcode`\^^K=\other
+ \catcode`\^^L=\other
+ \catcode`\^^N=\other
+ \catcode`\^^P=\other
+ \catcode`\^^Q=\other
+ \catcode`\^^R=\other
+ \catcode`\^^S=\other
+ \catcode`\^^T=\other
+ \catcode`\^^U=\other
+ \catcode`\^^V=\other
+ \catcode`\^^W=\other
+ \catcode`\^^X=\other
+ \catcode`\^^Z=\other
+ \catcode`\^^[=\other
+ \catcode`\^^\=\other
+ \catcode`\^^]=\other
+ \catcode`\^^^=\other
+ \catcode`\^^_=\other
+ % It was suggested to set the catcode of ^ to 7, which would allow ^^e4 etc.
+ % in xref tags, i.e., node names. But since ^^e4 notation isn't
+ % supported in the main text, it doesn't seem desirable. Furthermore,
+ % that is not enough: for node names that actually contain a ^
+ % character, we would end up writing a line like this: 'xrdef {'hat
+ % b-title}{'hat b} and \xrdef does a \csname...\endcsname on the first
+ % argument, and \hat is not an expandable control sequence. It could
+ % all be worked out, but why? Either we support ^^ or we don't.
+ %
+ % The other change necessary for this was to define \auxhat:
+ % \def\auxhat{\def^{'hat }}% extra space so ok if followed by letter
+ % and then to call \auxhat in \setq.
+ %
+ \catcode`\^=\other
+ %
+ % Special characters. Should be turned off anyway, but...
+ \catcode`\~=\other
+ \catcode`\[=\other
+ \catcode`\]=\other
+ \catcode`\"=\other
+ \catcode`\_=\other
+ \catcode`\|=\other
+ \catcode`\<=\other
+ \catcode`\>=\other
+ \catcode`\$=\other
+ \catcode`\#=\other
+ \catcode`\&=\other
+ \catcode`\%=\other
+ \catcode`+=\other % avoid \+ for paranoia even though we've turned it off
+ %
+ % This is to support \ in node names and titles, since the \
+ % characters end up in a \csname. It's easier than
+ % leaving it active and making its active definition an actual \
+ % character. What I don't understand is why it works in the *value*
+ % of the xrdef. Seems like it should be a catcode12 \, and that
+ % should not typeset properly. But it works, so I'm moving on for
+ % now. --karl, 15jan04.
+ \catcode`\\=\other
+ %
+ % Make the characters 128-255 be printing characters.
+ {%
+ \count1=128
+ \def\loop{%
+ \catcode\count1=\other
+ \advance\count1 by 1
+ \ifnum \count1<256 \loop \fi
+ }%
+ }%
+ %
+ % @ is our escape character in .aux files, and we need braces.
+ \catcode`\{=1
+ \catcode`\}=2
+ \catcode`\@=0
+}
+
+\def\readdatafile#1{%
+\begingroup
+ \setupdatafile
+ \input\jobname.#1
+\endgroup}
+
+
+\message{insertions,}
+% including footnotes.
+
+\newcount \footnoteno
+
+% The trailing space in the following definition for supereject is
+% vital for proper filling; pages come out unaligned when you do a
+% pagealignmacro call if that space before the closing brace is
+% removed. (Generally, numeric constants should always be followed by a
+% space to prevent strange expansion errors.)
+\def\supereject{\par\penalty -20000\footnoteno =0 }
+
+% @footnotestyle is meaningful for info output only.
+\let\footnotestyle=\comment
+
+{\catcode `\@=11
+%
+% Auto-number footnotes. Otherwise like plain.
+\gdef\footnote{%
+ \let\indent=\ptexindent
+ \let\noindent=\ptexnoindent
+ \global\advance\footnoteno by \@ne
+ \edef\thisfootno{$^{\the\footnoteno}$}%
+ %
+ % In case the footnote comes at the end of a sentence, preserve the
+ % extra spacing after we do the footnote number.
+ \let\@sf\empty
+ \ifhmode\edef\@sf{\spacefactor\the\spacefactor}\ptexslash\fi
+ %
+ % Remove inadvertent blank space before typesetting the footnote number.
+ \unskip
+ \thisfootno\@sf
+ \dofootnote
+}%
+
+% Don't bother with the trickery in plain.tex to not require the
+% footnote text as a parameter. Our footnotes don't need to be so general.
+%
+% Oh yes, they do; otherwise, @ifset (and anything else that uses
+% \parseargline) fails inside footnotes because the tokens are fixed when
+% the footnote is read. --karl, 16nov96.
+%
+\gdef\dofootnote{%
+ \insert\footins\bgroup
+ % We want to typeset this text as a normal paragraph, even if the
+ % footnote reference occurs in (for example) a display environment.
+ % So reset some parameters.
+ \hsize=\pagewidth
+ \interlinepenalty\interfootnotelinepenalty
+ \splittopskip\ht\strutbox % top baseline for broken footnotes
+ \splitmaxdepth\dp\strutbox
+ \floatingpenalty\@MM
+ \leftskip\z at skip
+ \rightskip\z at skip
+ \spaceskip\z at skip
+ \xspaceskip\z at skip
+ \parindent\defaultparindent
+ %
+ \smallfonts \rm
+ %
+ % Because we use hanging indentation in footnotes, a @noindent appears
+ % to exdent this text, so make it be a no-op. makeinfo does not use
+ % hanging indentation so @noindent can still be needed within footnote
+ % text after an @example or the like (not that this is good style).
+ \let\noindent = \relax
+ %
+ % Hang the footnote text off the number. Use \everypar in case the
+ % footnote extends for more than one paragraph.
+ \everypar = {\hang}%
+ \textindent{\thisfootno}%
+ %
+ % Don't crash into the line above the footnote text. Since this
+ % expands into a box, it must come within the paragraph, lest it
+ % provide a place where TeX can split the footnote.
+ \footstrut
+ \futurelet\next\fo at t
+}
+}%end \catcode `\@=11
+
+% In case a @footnote appears in a vbox, save the footnote text and create
+% the real \insert just after the vbox finished. Otherwise, the insertion
+% would be lost.
+% Similarly, if a @footnote appears inside an alignment, save the footnote
+% text to a box and make the \insert when a row of the table is finished.
+% And the same can be done for other insert classes. --kasal, 16nov03.
+
+% Replace the \insert primitive by a cheating macro.
+% Deeper inside, just make sure that the saved insertions are not spilled
+% out prematurely.
+%
+\def\startsavinginserts{%
+ \ifx \insert\ptexinsert
+ \let\insert\saveinsert
+ \else
+ \let\checkinserts\relax
+ \fi
+}
+
+% This \insert replacement works for both \insert\footins{foo} and
+% \insert\footins\bgroup foo\egroup, but it doesn't work for \insert27{foo}.
+%
+\def\saveinsert#1{%
+ \edef\next{\noexpand\savetobox \makeSAVEname#1}%
+ \afterassignment\next
+ % swallow the left brace
+ \let\temp =
+}
+\def\makeSAVEname#1{\makecsname{SAVE\expandafter\gobble\string#1}}
+\def\savetobox#1{\global\setbox#1 = \vbox\bgroup \unvbox#1}
+
+\def\checksaveins#1{\ifvoid#1\else \placesaveins#1\fi}
+
+\def\placesaveins#1{%
+ \ptexinsert \csname\expandafter\gobblesave\string#1\endcsname
+ {\box#1}%
+}
+
+% eat @SAVE -- beware, all of them have catcode \other:
+{
+ \def\dospecials{\do S\do A\do V\do E} \uncatcodespecials % ;-)
+ \gdef\gobblesave @SAVE{}
+}
+
+% initialization:
+\def\newsaveins #1{%
+ \edef\next{\noexpand\newsaveinsX \makeSAVEname#1}%
+ \next
+}
+\def\newsaveinsX #1{%
+ \csname newbox\endcsname #1%
+ \expandafter\def\expandafter\checkinserts\expandafter{\checkinserts
+ \checksaveins #1}%
+}
+
+% initialize:
+\let\checkinserts\empty
+\newsaveins\footins
+\newsaveins\margin
+
+
+% @image. We use the macros from epsf.tex to support this.
+% If epsf.tex is not installed and @image is used, we complain.
+%
+% Check for and read epsf.tex up front. If we read it only at @image
+% time, we might be inside a group, and then its definitions would get
+% undone and the next image would fail.
+\openin 1 = epsf.tex
+\ifeof 1 \else
+ % Do not bother showing banner with epsf.tex v2.7k (available in
+ % doc/epsf.tex and on ctan).
+ \def\epsfannounce{\toks0 = }%
+ \input epsf.tex
+\fi
+\closein 1
+%
+% We will only complain once about lack of epsf.tex.
+\newif\ifwarnednoepsf
+\newhelp\noepsfhelp{epsf.tex must be installed for images to
+ work. It is also included in the Texinfo distribution, or you can get
+ it from ftp://tug.org/tex/epsf.tex.}
+%
+\def\image#1{%
+ \ifx\epsfbox\undefined
+ \ifwarnednoepsf \else
+ \errhelp = \noepsfhelp
+ \errmessage{epsf.tex not found, images will be ignored}%
+ \global\warnednoepsftrue
+ \fi
+ \else
+ \imagexxx #1,,,,,\finish
+ \fi
+}
+%
+% Arguments to @image:
+% #1 is (mandatory) image filename; we tack on .eps extension.
+% #2 is (optional) width, #3 is (optional) height.
+% #4 is (ignored optional) html alt text.
+% #5 is (ignored optional) extension.
+% #6 is just the usual extra ignored arg for parsing this stuff.
+\newif\ifimagevmode
+\def\imagexxx#1,#2,#3,#4,#5,#6\finish{\begingroup
+ \catcode`\^^M = 5 % in case we're inside an example
+ \normalturnoffactive % allow _ et al. in names
+ % If the image is by itself, center it.
+ \ifvmode
+ \imagevmodetrue
+ \nobreak\medskip
+ % Usually we'll have text after the image which will insert
+ % \parskip glue, so insert it here too to equalize the space
+ % above and below.
+ \nobreak\vskip\parskip
+ \nobreak
+ \fi
+ %
+ % Leave vertical mode so that indentation from an enclosing
+ % environment such as @quotation is respected. On the other hand, if
+ % it's at the top level, we don't want the normal paragraph indentation.
+ \noindent
+ %
+ % Output the image.
+ \ifpdf
+ \dopdfimage{#1}{#2}{#3}%
+ \else
+ % \epsfbox itself resets \epsf?size at each figure.
+ \setbox0 = \hbox{\ignorespaces #2}\ifdim\wd0 > 0pt \epsfxsize=#2\relax \fi
+ \setbox0 = \hbox{\ignorespaces #3}\ifdim\wd0 > 0pt \epsfysize=#3\relax \fi
+ \epsfbox{#1.eps}%
+ \fi
+ %
+ \ifimagevmode \medskip \fi % space after the standalone image
+\endgroup}
+
+
+% @float FLOATTYPE,LABEL,LOC ... @end float for displayed figures, tables,
+% etc. We don't actually implement floating yet, we always include the
+% float "here". But it seemed the best name for the future.
+%
+\envparseargdef\float{\eatcommaspace\eatcommaspace\dofloat#1, , ,\finish}
+
+% There may be a space before second and/or third parameter; delete it.
+\def\eatcommaspace#1, {#1,}
+
+% #1 is the optional FLOATTYPE, the text label for this float, typically
+% "Figure", "Table", "Example", etc. Can't contain commas. If omitted,
+% this float will not be numbered and cannot be referred to.
+%
+% #2 is the optional xref label. Also must be present for the float to
+% be referable.
+%
+% #3 is the optional positioning argument; for now, it is ignored. It
+% will somehow specify the positions allowed to float to (here, top, bottom).
+%
+% We keep a separate counter for each FLOATTYPE, which we reset at each
+% chapter-level command.
+\let\resetallfloatnos=\empty
+%
+\def\dofloat#1,#2,#3,#4\finish{%
+ \let\thiscaption=\empty
+ \let\thisshortcaption=\empty
+ %
+ % don't lose footnotes inside @float.
+ %
+ % BEWARE: when the floats start float, we have to issue warning whenever an
+ % insert appears inside a float which could possibly float. --kasal, 26may04
+ %
+ \startsavinginserts
+ %
+ % We can't be used inside a paragraph.
+ \par
+ %
+ \vtop\bgroup
+ \def\floattype{#1}%
+ \def\floatlabel{#2}%
+ \def\floatloc{#3}% we do nothing with this yet.
+ %
+ \ifx\floattype\empty
+ \let\safefloattype=\empty
+ \else
+ {%
+ % the floattype might have accents or other special characters,
+ % but we need to use it in a control sequence name.
+ \indexnofonts
+ \turnoffactive
+ \xdef\safefloattype{\floattype}%
+ }%
+ \fi
+ %
+ % If label is given but no type, we handle that as the empty type.
+ \ifx\floatlabel\empty \else
+ % We want each FLOATTYPE to be numbered separately (Figure 1,
+ % Table 1, Figure 2, ...). (And if no label, no number.)
+ %
+ \expandafter\getfloatno\csname\safefloattype floatno\endcsname
+ \global\advance\floatno by 1
+ %
+ {%
+ % This magic value for \lastsection is output by \setref as the
+ % XREFLABEL-title value. \xrefX uses it to distinguish float
+ % labels (which have a completely different output format) from
+ % node and anchor labels. And \xrdef uses it to construct the
+ % lists of floats.
+ %
+ \edef\lastsection{\floatmagic=\safefloattype}%
+ \setref{\floatlabel}{Yfloat}%
+ }%
+ \fi
+ %
+ % start with \parskip glue, I guess.
+ \vskip\parskip
+ %
+ % Don't suppress indentation if a float happens to start a section.
+ \restorefirstparagraphindent
+}
+
+% we have these possibilities:
+% @float Foo,lbl & @caption{Cap}: Foo 1.1: Cap
+% @float Foo,lbl & no caption: Foo 1.1
+% @float Foo & @caption{Cap}: Foo: Cap
+% @float Foo & no caption: Foo
+% @float ,lbl & Caption{Cap}: 1.1: Cap
+% @float ,lbl & no caption: 1.1
+% @float & @caption{Cap}: Cap
+% @float & no caption:
+%
+\def\Efloat{%
+ \let\floatident = \empty
+ %
+ % In all cases, if we have a float type, it comes first.
+ \ifx\floattype\empty \else \def\floatident{\floattype}\fi
+ %
+ % If we have an xref label, the number comes next.
+ \ifx\floatlabel\empty \else
+ \ifx\floattype\empty \else % if also had float type, need tie first.
+ \appendtomacro\floatident{\tie}%
+ \fi
+ % the number.
+ \appendtomacro\floatident{\chaplevelprefix\the\floatno}%
+ \fi
+ %
+ % Start the printed caption with what we've constructed in
+ % \floatident, but keep it separate; we need \floatident again.
+ \let\captionline = \floatident
+ %
+ \ifx\thiscaption\empty \else
+ \ifx\floatident\empty \else
+ \appendtomacro\captionline{: }% had ident, so need a colon between
+ \fi
+ %
+ % caption text.
+ \appendtomacro\captionline{\scanexp\thiscaption}%
+ \fi
+ %
+ % If we have anything to print, print it, with space before.
+ % Eventually this needs to become an \insert.
+ \ifx\captionline\empty \else
+ \vskip.5\parskip
+ \captionline
+ %
+ % Space below caption.
+ \vskip\parskip
+ \fi
+ %
+ % If have an xref label, write the list of floats info. Do this
+ % after the caption, to avoid chance of it being a breakpoint.
+ \ifx\floatlabel\empty \else
+ % Write the text that goes in the lof to the aux file as
+ % \floatlabel-lof. Besides \floatident, we include the short
+ % caption if specified, else the full caption if specified, else nothing.
+ {%
+ \atdummies
+ %
+ % since we read the caption text in the macro world, where ^^M
+ % is turned into a normal character, we have to scan it back, so
+ % we don't write the literal three characters "^^M" into the aux file.
+ \scanexp{%
+ \xdef\noexpand\gtemp{%
+ \ifx\thisshortcaption\empty
+ \thiscaption
+ \else
+ \thisshortcaption
+ \fi
+ }%
+ }%
+ \immediate\write\auxfile{@xrdef{\floatlabel-lof}{\floatident
+ \ifx\gtemp\empty \else : \gtemp \fi}}%
+ }%
+ \fi
+ \egroup % end of \vtop
+ %
+ % place the captured inserts
+ %
+ % BEWARE: when the floats start floating, we have to issue warning
+ % whenever an insert appears inside a float which could possibly
+ % float. --kasal, 26may04
+ %
+ \checkinserts
+}
+
+% Append the tokens #2 to the definition of macro #1, not expanding either.
+%
+\def\appendtomacro#1#2{%
+ \expandafter\def\expandafter#1\expandafter{#1#2}%
+}
+
+% @caption, @shortcaption
+%
+\def\caption{\docaption\thiscaption}
+\def\shortcaption{\docaption\thisshortcaption}
+\def\docaption{\checkenv\float \bgroup\scanargctxt\defcaption}
+\def\defcaption#1#2{\egroup \def#1{#2}}
+
+% The parameter is the control sequence identifying the counter we are
+% going to use. Create it if it doesn't exist and assign it to \floatno.
+\def\getfloatno#1{%
+ \ifx#1\relax
+ % Haven't seen this figure type before.
+ \csname newcount\endcsname #1%
+ %
+ % Remember to reset this floatno at the next chap.
+ \expandafter\gdef\expandafter\resetallfloatnos
+ \expandafter{\resetallfloatnos #1=0 }%
+ \fi
+ \let\floatno#1%
+}
+
+% \setref calls this to get the XREFLABEL-snt value. We want an @xref
+% to the FLOATLABEL to expand to "Figure 3.1". We call \setref when we
+% first read the @float command.
+%
+\def\Yfloat{\floattype at tie \chaplevelprefix\the\floatno}%
+
+% Magic string used for the XREFLABEL-title value, so \xrefX can
+% distinguish floats from other xref types.
+\def\floatmagic{!!float!!}
+
+% #1 is the control sequence we are passed; we expand into a conditional
+% which is true if #1 represents a float ref. That is, the magic
+% \lastsection value which we \setref above.
+%
+\def\iffloat#1{\expandafter\doiffloat#1==\finish}
+%
+% #1 is (maybe) the \floatmagic string. If so, #2 will be the
+% (safe) float type for this float. We set \iffloattype to #2.
+%
+\def\doiffloat#1=#2=#3\finish{%
+ \def\temp{#1}%
+ \def\iffloattype{#2}%
+ \ifx\temp\floatmagic
+}
+
+% @listoffloats FLOATTYPE - print a list of floats like a table of contents.
+%
+\parseargdef\listoffloats{%
+ \def\floattype{#1}% floattype
+ {%
+ % the floattype might have accents or other special characters,
+ % but we need to use it in a control sequence name.
+ \indexnofonts
+ \turnoffactive
+ \xdef\safefloattype{\floattype}%
+ }%
+ %
+ % \xrdef saves the floats as a \do-list in \floatlistSAFEFLOATTYPE.
+ \expandafter\ifx\csname floatlist\safefloattype\endcsname \relax
+ \ifhavexrefs
+ % if the user said @listoffloats foo but never @float foo.
+ \message{\linenumber No `\safefloattype' floats to list.}%
+ \fi
+ \else
+ \begingroup
+ \leftskip=\tocindent % indent these entries like a toc
+ \let\do=\listoffloatsdo
+ \csname floatlist\safefloattype\endcsname
+ \endgroup
+ \fi
+}
+
+% This is called on each entry in a list of floats. We're passed the
+% xref label, in the form LABEL-title, which is how we save it in the
+% aux file. We strip off the -title and look up \XRLABEL-lof, which
+% has the text we're supposed to typeset here.
+%
+% Figures without xref labels will not be included in the list (since
+% they won't appear in the aux file).
+%
+\def\listoffloatsdo#1{\listoffloatsdoentry#1\finish}
+\def\listoffloatsdoentry#1-title\finish{{%
+ % Can't fully expand XR#1-lof because it can contain anything. Just
+ % pass the control sequence. On the other hand, XR#1-pg is just the
+ % page number, and we want to fully expand that so we can get a link
+ % in pdf output.
+ \toksA = \expandafter{\csname XR#1-lof\endcsname}%
+ %
+ % use the same \entry macro we use to generate the TOC and index.
+ \edef\writeentry{\noexpand\entry{\the\toksA}{\csname XR#1-pg\endcsname}}%
+ \writeentry
+}}
+
+
+\message{localization,}
+
+% For single-language documents, @documentlanguage is usually given very
+% early, just after @documentencoding. Single argument is the language
+% (de) or locale (de_DE) abbreviation.
+%
+{
+ \catcode`\_ = \active
+ \globaldefs=1
+\parseargdef\documentlanguage{\begingroup
+ \let_=\normalunderscore % normal _ character for filenames
+ \tex % read txi-??.tex file in plain TeX.
+ % Read the file by the name they passed if it exists.
+ \openin 1 txi-#1.tex
+ \ifeof 1
+ \documentlanguagetrywithoutunderscore{#1_\finish}%
+ \else
+ \globaldefs = 1 % everything in the txi-LL files needs to persist
+ \input txi-#1.tex
+ \fi
+ \closein 1
+ \endgroup % end raw TeX
+\endgroup}
+%
+% If they passed de_DE, and txi-de_DE.tex doesn't exist,
+% try txi-de.tex.
+%
+\gdef\documentlanguagetrywithoutunderscore#1_#2\finish{%
+ \openin 1 txi-#1.tex
+ \ifeof 1
+ \errhelp = \nolanghelp
+ \errmessage{Cannot read language file txi-#1.tex}%
+ \else
+ \globaldefs = 1 % everything in the txi-LL files needs to persist
+ \input txi-#1.tex
+ \fi
+ \closein 1
+}
+}% end of special _ catcode
+%
+\newhelp\nolanghelp{The given language definition file cannot be found or
+is empty. Maybe you need to install it? Putting it in the current
+directory should work if nowhere else does.}
+
+% This macro is called from txi-??.tex files; the first argument is the
+% \language name to set (without the "\lang@" prefix), the second and
+% third args are \{left,right}hyphenmin.
+%
+% The language names to pass are determined when the format is built.
+% See the etex.log file created at that time, e.g.,
+% /usr/local/texlive/2008/texmf-var/web2c/pdftex/etex.log.
+%
+% With TeX Live 2008, etex now includes hyphenation patterns for all
+% available languages. This means we can support hyphenation in
+% Texinfo, at least to some extent. (This still doesn't solve the
+% accented characters problem.)
+%
+\catcode`@=11
+\def\txisetlanguage#1#2#3{%
+ % do not set the language if the name is undefined in the current TeX.
+ \expandafter\ifx\csname lang@#1\endcsname \relax
+ \message{no patterns for #1}%
+ \else
+ \global\language = \csname lang@#1\endcsname
+ \fi
+ % but there is no harm in adjusting the hyphenmin values regardless.
+ \global\lefthyphenmin = #2\relax
+ \global\righthyphenmin = #3\relax
+}
+
+% Helpers for encodings.
+% Set the catcode of characters 128 through 255 to the specified number.
+%
+\def\setnonasciicharscatcode#1{%
+ \count255=128
+ \loop\ifnum\count255<256
+ \global\catcode\count255=#1\relax
+ \advance\count255 by 1
+ \repeat
+}
+
+\def\setnonasciicharscatcodenonglobal#1{%
+ \count255=128
+ \loop\ifnum\count255<256
+ \catcode\count255=#1\relax
+ \advance\count255 by 1
+ \repeat
+}
+
+% @documentencoding sets the definition of non-ASCII characters
+% according to the specified encoding.
+%
+\parseargdef\documentencoding{%
+ % Encoding being declared for the document.
+ \def\declaredencoding{\csname #1.enc\endcsname}%
+ %
+ % Supported encodings: names converted to tokens in order to be able
+ % to compare them with \ifx.
+ \def\ascii{\csname US-ASCII.enc\endcsname}%
+ \def\latnine{\csname ISO-8859-15.enc\endcsname}%
+ \def\latone{\csname ISO-8859-1.enc\endcsname}%
+ \def\lattwo{\csname ISO-8859-2.enc\endcsname}%
+ \def\utfeight{\csname UTF-8.enc\endcsname}%
+ %
+ \ifx \declaredencoding \ascii
+ \asciichardefs
+ %
+ \else \ifx \declaredencoding \lattwo
+ \setnonasciicharscatcode\active
+ \lattwochardefs
+ %
+ \else \ifx \declaredencoding \latone
+ \setnonasciicharscatcode\active
+ \latonechardefs
+ %
+ \else \ifx \declaredencoding \latnine
+ \setnonasciicharscatcode\active
+ \latninechardefs
+ %
+ \else \ifx \declaredencoding \utfeight
+ \setnonasciicharscatcode\active
+ \utfeightchardefs
+ %
+ \else
+ \message{Unknown document encoding #1, ignoring.}%
+ %
+ \fi % utfeight
+ \fi % latnine
+ \fi % latone
+ \fi % lattwo
+ \fi % ascii
+}
+
+% A message to be logged when using a character that isn't available
+% the default font encoding (OT1).
+%
+\def\missingcharmsg#1{\message{Character missing in OT1 encoding: #1.}}
+
+% Take account of \c (plain) vs. \, (Texinfo) difference.
+\def\cedilla#1{\ifx\c\ptexc\c{#1}\else\,{#1}\fi}
+
+% First, make active non-ASCII characters in order for them to be
+% correctly categorized when TeX reads the replacement text of
+% macros containing the character definitions.
+\setnonasciicharscatcode\active
+%
+% Latin1 (ISO-8859-1) character definitions.
+\def\latonechardefs{%
+ \gdef^^a0{~}
+ \gdef^^a1{\exclamdown}
+ \gdef^^a2{\missingcharmsg{CENT SIGN}}
+ \gdef^^a3{{\pounds}}
+ \gdef^^a4{\missingcharmsg{CURRENCY SIGN}}
+ \gdef^^a5{\missingcharmsg{YEN SIGN}}
+ \gdef^^a6{\missingcharmsg{BROKEN BAR}}
+ \gdef^^a7{\S}
+ \gdef^^a8{\"{}}
+ \gdef^^a9{\copyright}
+ \gdef^^aa{\ordf}
+ \gdef^^ab{\guillemetleft}
+ \gdef^^ac{$\lnot$}
+ \gdef^^ad{\-}
+ \gdef^^ae{\registeredsymbol}
+ \gdef^^af{\={}}
+ %
+ \gdef^^b0{\textdegree}
+ \gdef^^b1{$\pm$}
+ \gdef^^b2{$^2$}
+ \gdef^^b3{$^3$}
+ \gdef^^b4{\'{}}
+ \gdef^^b5{$\mu$}
+ \gdef^^b6{\P}
+ %
+ \gdef^^b7{$^.$}
+ \gdef^^b8{\cedilla\ }
+ \gdef^^b9{$^1$}
+ \gdef^^ba{\ordm}
+ %
+ \gdef^^bb{\guilletright}
+ \gdef^^bc{$1\over4$}
+ \gdef^^bd{$1\over2$}
+ \gdef^^be{$3\over4$}
+ \gdef^^bf{\questiondown}
+ %
+ \gdef^^c0{\`A}
+ \gdef^^c1{\'A}
+ \gdef^^c2{\^A}
+ \gdef^^c3{\~A}
+ \gdef^^c4{\"A}
+ \gdef^^c5{\ringaccent A}
+ \gdef^^c6{\AE}
+ \gdef^^c7{\cedilla C}
+ \gdef^^c8{\`E}
+ \gdef^^c9{\'E}
+ \gdef^^ca{\^E}
+ \gdef^^cb{\"E}
+ \gdef^^cc{\`I}
+ \gdef^^cd{\'I}
+ \gdef^^ce{\^I}
+ \gdef^^cf{\"I}
+ %
+ \gdef^^d0{\DH}
+ \gdef^^d1{\~N}
+ \gdef^^d2{\`O}
+ \gdef^^d3{\'O}
+ \gdef^^d4{\^O}
+ \gdef^^d5{\~O}
+ \gdef^^d6{\"O}
+ \gdef^^d7{$\times$}
+ \gdef^^d8{\O}
+ \gdef^^d9{\`U}
+ \gdef^^da{\'U}
+ \gdef^^db{\^U}
+ \gdef^^dc{\"U}
+ \gdef^^dd{\'Y}
+ \gdef^^de{\TH}
+ \gdef^^df{\ss}
+ %
+ \gdef^^e0{\`a}
+ \gdef^^e1{\'a}
+ \gdef^^e2{\^a}
+ \gdef^^e3{\~a}
+ \gdef^^e4{\"a}
+ \gdef^^e5{\ringaccent a}
+ \gdef^^e6{\ae}
+ \gdef^^e7{\cedilla c}
+ \gdef^^e8{\`e}
+ \gdef^^e9{\'e}
+ \gdef^^ea{\^e}
+ \gdef^^eb{\"e}
+ \gdef^^ec{\`{\dotless i}}
+ \gdef^^ed{\'{\dotless i}}
+ \gdef^^ee{\^{\dotless i}}
+ \gdef^^ef{\"{\dotless i}}
+ %
+ \gdef^^f0{\dh}
+ \gdef^^f1{\~n}
+ \gdef^^f2{\`o}
+ \gdef^^f3{\'o}
+ \gdef^^f4{\^o}
+ \gdef^^f5{\~o}
+ \gdef^^f6{\"o}
+ \gdef^^f7{$\div$}
+ \gdef^^f8{\o}
+ \gdef^^f9{\`u}
+ \gdef^^fa{\'u}
+ \gdef^^fb{\^u}
+ \gdef^^fc{\"u}
+ \gdef^^fd{\'y}
+ \gdef^^fe{\th}
+ \gdef^^ff{\"y}
+}
+
+% Latin9 (ISO-8859-15) encoding character definitions.
+\def\latninechardefs{%
+ % Encoding is almost identical to Latin1.
+ \latonechardefs
+ %
+ \gdef^^a4{\euro}
+ \gdef^^a6{\v S}
+ \gdef^^a8{\v s}
+ \gdef^^b4{\v Z}
+ \gdef^^b8{\v z}
+ \gdef^^bc{\OE}
+ \gdef^^bd{\oe}
+ \gdef^^be{\"Y}
+}
+
+% Latin2 (ISO-8859-2) character definitions.
+\def\lattwochardefs{%
+ \gdef^^a0{~}
+ \gdef^^a1{\ogonek{A}}
+ \gdef^^a2{\u{}}
+ \gdef^^a3{\L}
+ \gdef^^a4{\missingcharmsg{CURRENCY SIGN}}
+ \gdef^^a5{\v L}
+ \gdef^^a6{\'S}
+ \gdef^^a7{\S}
+ \gdef^^a8{\"{}}
+ \gdef^^a9{\v S}
+ \gdef^^aa{\cedilla S}
+ \gdef^^ab{\v T}
+ \gdef^^ac{\'Z}
+ \gdef^^ad{\-}
+ \gdef^^ae{\v Z}
+ \gdef^^af{\dotaccent Z}
+ %
+ \gdef^^b0{\textdegree}
+ \gdef^^b1{\ogonek{a}}
+ \gdef^^b2{\ogonek{ }}
+ \gdef^^b3{\l}
+ \gdef^^b4{\'{}}
+ \gdef^^b5{\v l}
+ \gdef^^b6{\'s}
+ \gdef^^b7{\v{}}
+ \gdef^^b8{\cedilla\ }
+ \gdef^^b9{\v s}
+ \gdef^^ba{\cedilla s}
+ \gdef^^bb{\v t}
+ \gdef^^bc{\'z}
+ \gdef^^bd{\H{}}
+ \gdef^^be{\v z}
+ \gdef^^bf{\dotaccent z}
+ %
+ \gdef^^c0{\'R}
+ \gdef^^c1{\'A}
+ \gdef^^c2{\^A}
+ \gdef^^c3{\u A}
+ \gdef^^c4{\"A}
+ \gdef^^c5{\'L}
+ \gdef^^c6{\'C}
+ \gdef^^c7{\cedilla C}
+ \gdef^^c8{\v C}
+ \gdef^^c9{\'E}
+ \gdef^^ca{\ogonek{E}}
+ \gdef^^cb{\"E}
+ \gdef^^cc{\v E}
+ \gdef^^cd{\'I}
+ \gdef^^ce{\^I}
+ \gdef^^cf{\v D}
+ %
+ \gdef^^d0{\DH}
+ \gdef^^d1{\'N}
+ \gdef^^d2{\v N}
+ \gdef^^d3{\'O}
+ \gdef^^d4{\^O}
+ \gdef^^d5{\H O}
+ \gdef^^d6{\"O}
+ \gdef^^d7{$\times$}
+ \gdef^^d8{\v R}
+ \gdef^^d9{\ringaccent U}
+ \gdef^^da{\'U}
+ \gdef^^db{\H U}
+ \gdef^^dc{\"U}
+ \gdef^^dd{\'Y}
+ \gdef^^de{\cedilla T}
+ \gdef^^df{\ss}
+ %
+ \gdef^^e0{\'r}
+ \gdef^^e1{\'a}
+ \gdef^^e2{\^a}
+ \gdef^^e3{\u a}
+ \gdef^^e4{\"a}
+ \gdef^^e5{\'l}
+ \gdef^^e6{\'c}
+ \gdef^^e7{\cedilla c}
+ \gdef^^e8{\v c}
+ \gdef^^e9{\'e}
+ \gdef^^ea{\ogonek{e}}
+ \gdef^^eb{\"e}
+ \gdef^^ec{\v e}
+ \gdef^^ed{\'\i}
+ \gdef^^ee{\^\i}
+ \gdef^^ef{\v d}
+ %
+ \gdef^^f0{\dh}
+ \gdef^^f1{\'n}
+ \gdef^^f2{\v n}
+ \gdef^^f3{\'o}
+ \gdef^^f4{\^o}
+ \gdef^^f5{\H o}
+ \gdef^^f6{\"o}
+ \gdef^^f7{$\div$}
+ \gdef^^f8{\v r}
+ \gdef^^f9{\ringaccent u}
+ \gdef^^fa{\'u}
+ \gdef^^fb{\H u}
+ \gdef^^fc{\"u}
+ \gdef^^fd{\'y}
+ \gdef^^fe{\cedilla t}
+ \gdef^^ff{\dotaccent{}}
+}
+
+% UTF-8 character definitions.
+%
+% This code to support UTF-8 is based on LaTeX's utf8.def, with some
+% changes for Texinfo conventions. It is included here under the GPL by
+% permission from Frank Mittelbach and the LaTeX team.
+%
+\newcount\countUTFx
+\newcount\countUTFy
+\newcount\countUTFz
+
+\gdef\UTFviiiTwoOctets#1#2{\expandafter
+ \UTFviiiDefined\csname u8:#1\string #2\endcsname}
+%
+\gdef\UTFviiiThreeOctets#1#2#3{\expandafter
+ \UTFviiiDefined\csname u8:#1\string #2\string #3\endcsname}
+%
+\gdef\UTFviiiFourOctets#1#2#3#4{\expandafter
+ \UTFviiiDefined\csname u8:#1\string #2\string #3\string #4\endcsname}
+
+\gdef\UTFviiiDefined#1{%
+ \ifx #1\relax
+ \message{\linenumber Unicode char \string #1 not defined for Texinfo}%
+ \else
+ \expandafter #1%
+ \fi
+}
+
+\begingroup
+ \catcode`\~13
+ \catcode`\"12
+
+ \def\UTFviiiLoop{%
+ \global\catcode\countUTFx\active
+ \uccode`\~\countUTFx
+ \uppercase\expandafter{\UTFviiiTmp}%
+ \advance\countUTFx by 1
+ \ifnum\countUTFx < \countUTFy
+ \expandafter\UTFviiiLoop
+ \fi}
+
+ \countUTFx = "C2
+ \countUTFy = "E0
+ \def\UTFviiiTmp{%
+ \xdef~{\noexpand\UTFviiiTwoOctets\string~}}
+ \UTFviiiLoop
+
+ \countUTFx = "E0
+ \countUTFy = "F0
+ \def\UTFviiiTmp{%
+ \xdef~{\noexpand\UTFviiiThreeOctets\string~}}
+ \UTFviiiLoop
+
+ \countUTFx = "F0
+ \countUTFy = "F4
+ \def\UTFviiiTmp{%
+ \xdef~{\noexpand\UTFviiiFourOctets\string~}}
+ \UTFviiiLoop
+\endgroup
+
+\begingroup
+ \catcode`\"=12
+ \catcode`\<=12
+ \catcode`\.=12
+ \catcode`\,=12
+ \catcode`\;=12
+ \catcode`\!=12
+ \catcode`\~=13
+
+ \gdef\DeclareUnicodeCharacter#1#2{%
+ \countUTFz = "#1\relax
+ \wlog{\space\space defining Unicode char U+#1 (decimal \the\countUTFz)}%
+ \begingroup
+ \parseXMLCharref
+ \def\UTFviiiTwoOctets##1##2{%
+ \csname u8:##1\string ##2\endcsname}%
+ \def\UTFviiiThreeOctets##1##2##3{%
+ \csname u8:##1\string ##2\string ##3\endcsname}%
+ \def\UTFviiiFourOctets##1##2##3##4{%
+ \csname u8:##1\string ##2\string ##3\string ##4\endcsname}%
+ \expandafter\expandafter\expandafter\expandafter
+ \expandafter\expandafter\expandafter
+ \gdef\UTFviiiTmp{#2}%
+ \endgroup}
+
+ \gdef\parseXMLCharref{%
+ \ifnum\countUTFz < "A0\relax
+ \errhelp = \EMsimple
+ \errmessage{Cannot define Unicode char value < 00A0}%
+ \else\ifnum\countUTFz < "800\relax
+ \parseUTFviiiA,%
+ \parseUTFviiiB C\UTFviiiTwoOctets.,%
+ \else\ifnum\countUTFz < "10000\relax
+ \parseUTFviiiA;%
+ \parseUTFviiiA,%
+ \parseUTFviiiB E\UTFviiiThreeOctets.{,;}%
+ \else
+ \parseUTFviiiA;%
+ \parseUTFviiiA,%
+ \parseUTFviiiA!%
+ \parseUTFviiiB F\UTFviiiFourOctets.{!,;}%
+ \fi\fi\fi
+ }
+
+ \gdef\parseUTFviiiA#1{%
+ \countUTFx = \countUTFz
+ \divide\countUTFz by 64
+ \countUTFy = \countUTFz
+ \multiply\countUTFz by 64
+ \advance\countUTFx by -\countUTFz
+ \advance\countUTFx by 128
+ \uccode `#1\countUTFx
+ \countUTFz = \countUTFy}
+
+ \gdef\parseUTFviiiB#1#2#3#4{%
+ \advance\countUTFz by "#10\relax
+ \uccode `#3\countUTFz
+ \uppercase{\gdef\UTFviiiTmp{#2#3#4}}}
+\endgroup
+
+\def\utfeightchardefs{%
+ \DeclareUnicodeCharacter{00A0}{\tie}
+ \DeclareUnicodeCharacter{00A1}{\exclamdown}
+ \DeclareUnicodeCharacter{00A3}{\pounds}
+ \DeclareUnicodeCharacter{00A8}{\"{ }}
+ \DeclareUnicodeCharacter{00A9}{\copyright}
+ \DeclareUnicodeCharacter{00AA}{\ordf}
+ \DeclareUnicodeCharacter{00AB}{\guillemetleft}
+ \DeclareUnicodeCharacter{00AD}{\-}
+ \DeclareUnicodeCharacter{00AE}{\registeredsymbol}
+ \DeclareUnicodeCharacter{00AF}{\={ }}
+
+ \DeclareUnicodeCharacter{00B0}{\ringaccent{ }}
+ \DeclareUnicodeCharacter{00B4}{\'{ }}
+ \DeclareUnicodeCharacter{00B8}{\cedilla{ }}
+ \DeclareUnicodeCharacter{00BA}{\ordm}
+ \DeclareUnicodeCharacter{00BB}{\guillemetright}
+ \DeclareUnicodeCharacter{00BF}{\questiondown}
+
+ \DeclareUnicodeCharacter{00C0}{\`A}
+ \DeclareUnicodeCharacter{00C1}{\'A}
+ \DeclareUnicodeCharacter{00C2}{\^A}
+ \DeclareUnicodeCharacter{00C3}{\~A}
+ \DeclareUnicodeCharacter{00C4}{\"A}
+ \DeclareUnicodeCharacter{00C5}{\AA}
+ \DeclareUnicodeCharacter{00C6}{\AE}
+ \DeclareUnicodeCharacter{00C7}{\cedilla{C}}
+ \DeclareUnicodeCharacter{00C8}{\`E}
+ \DeclareUnicodeCharacter{00C9}{\'E}
+ \DeclareUnicodeCharacter{00CA}{\^E}
+ \DeclareUnicodeCharacter{00CB}{\"E}
+ \DeclareUnicodeCharacter{00CC}{\`I}
+ \DeclareUnicodeCharacter{00CD}{\'I}
+ \DeclareUnicodeCharacter{00CE}{\^I}
+ \DeclareUnicodeCharacter{00CF}{\"I}
+
+ \DeclareUnicodeCharacter{00D0}{\DH}
+ \DeclareUnicodeCharacter{00D1}{\~N}
+ \DeclareUnicodeCharacter{00D2}{\`O}
+ \DeclareUnicodeCharacter{00D3}{\'O}
+ \DeclareUnicodeCharacter{00D4}{\^O}
+ \DeclareUnicodeCharacter{00D5}{\~O}
+ \DeclareUnicodeCharacter{00D6}{\"O}
+ \DeclareUnicodeCharacter{00D8}{\O}
+ \DeclareUnicodeCharacter{00D9}{\`U}
+ \DeclareUnicodeCharacter{00DA}{\'U}
+ \DeclareUnicodeCharacter{00DB}{\^U}
+ \DeclareUnicodeCharacter{00DC}{\"U}
+ \DeclareUnicodeCharacter{00DD}{\'Y}
+ \DeclareUnicodeCharacter{00DE}{\TH}
+ \DeclareUnicodeCharacter{00DF}{\ss}
+
+ \DeclareUnicodeCharacter{00E0}{\`a}
+ \DeclareUnicodeCharacter{00E1}{\'a}
+ \DeclareUnicodeCharacter{00E2}{\^a}
+ \DeclareUnicodeCharacter{00E3}{\~a}
+ \DeclareUnicodeCharacter{00E4}{\"a}
+ \DeclareUnicodeCharacter{00E5}{\aa}
+ \DeclareUnicodeCharacter{00E6}{\ae}
+ \DeclareUnicodeCharacter{00E7}{\cedilla{c}}
+ \DeclareUnicodeCharacter{00E8}{\`e}
+ \DeclareUnicodeCharacter{00E9}{\'e}
+ \DeclareUnicodeCharacter{00EA}{\^e}
+ \DeclareUnicodeCharacter{00EB}{\"e}
+ \DeclareUnicodeCharacter{00EC}{\`{\dotless{i}}}
+ \DeclareUnicodeCharacter{00ED}{\'{\dotless{i}}}
+ \DeclareUnicodeCharacter{00EE}{\^{\dotless{i}}}
+ \DeclareUnicodeCharacter{00EF}{\"{\dotless{i}}}
+
+ \DeclareUnicodeCharacter{00F0}{\dh}
+ \DeclareUnicodeCharacter{00F1}{\~n}
+ \DeclareUnicodeCharacter{00F2}{\`o}
+ \DeclareUnicodeCharacter{00F3}{\'o}
+ \DeclareUnicodeCharacter{00F4}{\^o}
+ \DeclareUnicodeCharacter{00F5}{\~o}
+ \DeclareUnicodeCharacter{00F6}{\"o}
+ \DeclareUnicodeCharacter{00F8}{\o}
+ \DeclareUnicodeCharacter{00F9}{\`u}
+ \DeclareUnicodeCharacter{00FA}{\'u}
+ \DeclareUnicodeCharacter{00FB}{\^u}
+ \DeclareUnicodeCharacter{00FC}{\"u}
+ \DeclareUnicodeCharacter{00FD}{\'y}
+ \DeclareUnicodeCharacter{00FE}{\th}
+ \DeclareUnicodeCharacter{00FF}{\"y}
+
+ \DeclareUnicodeCharacter{0100}{\=A}
+ \DeclareUnicodeCharacter{0101}{\=a}
+ \DeclareUnicodeCharacter{0102}{\u{A}}
+ \DeclareUnicodeCharacter{0103}{\u{a}}
+ \DeclareUnicodeCharacter{0104}{\ogonek{A}}
+ \DeclareUnicodeCharacter{0105}{\ogonek{a}}
+ \DeclareUnicodeCharacter{0106}{\'C}
+ \DeclareUnicodeCharacter{0107}{\'c}
+ \DeclareUnicodeCharacter{0108}{\^C}
+ \DeclareUnicodeCharacter{0109}{\^c}
+ \DeclareUnicodeCharacter{0118}{\ogonek{E}}
+ \DeclareUnicodeCharacter{0119}{\ogonek{e}}
+ \DeclareUnicodeCharacter{010A}{\dotaccent{C}}
+ \DeclareUnicodeCharacter{010B}{\dotaccent{c}}
+ \DeclareUnicodeCharacter{010C}{\v{C}}
+ \DeclareUnicodeCharacter{010D}{\v{c}}
+ \DeclareUnicodeCharacter{010E}{\v{D}}
+
+ \DeclareUnicodeCharacter{0112}{\=E}
+ \DeclareUnicodeCharacter{0113}{\=e}
+ \DeclareUnicodeCharacter{0114}{\u{E}}
+ \DeclareUnicodeCharacter{0115}{\u{e}}
+ \DeclareUnicodeCharacter{0116}{\dotaccent{E}}
+ \DeclareUnicodeCharacter{0117}{\dotaccent{e}}
+ \DeclareUnicodeCharacter{011A}{\v{E}}
+ \DeclareUnicodeCharacter{011B}{\v{e}}
+ \DeclareUnicodeCharacter{011C}{\^G}
+ \DeclareUnicodeCharacter{011D}{\^g}
+ \DeclareUnicodeCharacter{011E}{\u{G}}
+ \DeclareUnicodeCharacter{011F}{\u{g}}
+
+ \DeclareUnicodeCharacter{0120}{\dotaccent{G}}
+ \DeclareUnicodeCharacter{0121}{\dotaccent{g}}
+ \DeclareUnicodeCharacter{0124}{\^H}
+ \DeclareUnicodeCharacter{0125}{\^h}
+ \DeclareUnicodeCharacter{0128}{\~I}
+ \DeclareUnicodeCharacter{0129}{\~{\dotless{i}}}
+ \DeclareUnicodeCharacter{012A}{\=I}
+ \DeclareUnicodeCharacter{012B}{\={\dotless{i}}}
+ \DeclareUnicodeCharacter{012C}{\u{I}}
+ \DeclareUnicodeCharacter{012D}{\u{\dotless{i}}}
+
+ \DeclareUnicodeCharacter{0130}{\dotaccent{I}}
+ \DeclareUnicodeCharacter{0131}{\dotless{i}}
+ \DeclareUnicodeCharacter{0132}{IJ}
+ \DeclareUnicodeCharacter{0133}{ij}
+ \DeclareUnicodeCharacter{0134}{\^J}
+ \DeclareUnicodeCharacter{0135}{\^{\dotless{j}}}
+ \DeclareUnicodeCharacter{0139}{\'L}
+ \DeclareUnicodeCharacter{013A}{\'l}
+
+ \DeclareUnicodeCharacter{0141}{\L}
+ \DeclareUnicodeCharacter{0142}{\l}
+ \DeclareUnicodeCharacter{0143}{\'N}
+ \DeclareUnicodeCharacter{0144}{\'n}
+ \DeclareUnicodeCharacter{0147}{\v{N}}
+ \DeclareUnicodeCharacter{0148}{\v{n}}
+ \DeclareUnicodeCharacter{014C}{\=O}
+ \DeclareUnicodeCharacter{014D}{\=o}
+ \DeclareUnicodeCharacter{014E}{\u{O}}
+ \DeclareUnicodeCharacter{014F}{\u{o}}
+
+ \DeclareUnicodeCharacter{0150}{\H{O}}
+ \DeclareUnicodeCharacter{0151}{\H{o}}
+ \DeclareUnicodeCharacter{0152}{\OE}
+ \DeclareUnicodeCharacter{0153}{\oe}
+ \DeclareUnicodeCharacter{0154}{\'R}
+ \DeclareUnicodeCharacter{0155}{\'r}
+ \DeclareUnicodeCharacter{0158}{\v{R}}
+ \DeclareUnicodeCharacter{0159}{\v{r}}
+ \DeclareUnicodeCharacter{015A}{\'S}
+ \DeclareUnicodeCharacter{015B}{\'s}
+ \DeclareUnicodeCharacter{015C}{\^S}
+ \DeclareUnicodeCharacter{015D}{\^s}
+ \DeclareUnicodeCharacter{015E}{\cedilla{S}}
+ \DeclareUnicodeCharacter{015F}{\cedilla{s}}
+
+ \DeclareUnicodeCharacter{0160}{\v{S}}
+ \DeclareUnicodeCharacter{0161}{\v{s}}
+ \DeclareUnicodeCharacter{0162}{\cedilla{t}}
+ \DeclareUnicodeCharacter{0163}{\cedilla{T}}
+ \DeclareUnicodeCharacter{0164}{\v{T}}
+
+ \DeclareUnicodeCharacter{0168}{\~U}
+ \DeclareUnicodeCharacter{0169}{\~u}
+ \DeclareUnicodeCharacter{016A}{\=U}
+ \DeclareUnicodeCharacter{016B}{\=u}
+ \DeclareUnicodeCharacter{016C}{\u{U}}
+ \DeclareUnicodeCharacter{016D}{\u{u}}
+ \DeclareUnicodeCharacter{016E}{\ringaccent{U}}
+ \DeclareUnicodeCharacter{016F}{\ringaccent{u}}
+
+ \DeclareUnicodeCharacter{0170}{\H{U}}
+ \DeclareUnicodeCharacter{0171}{\H{u}}
+ \DeclareUnicodeCharacter{0174}{\^W}
+ \DeclareUnicodeCharacter{0175}{\^w}
+ \DeclareUnicodeCharacter{0176}{\^Y}
+ \DeclareUnicodeCharacter{0177}{\^y}
+ \DeclareUnicodeCharacter{0178}{\"Y}
+ \DeclareUnicodeCharacter{0179}{\'Z}
+ \DeclareUnicodeCharacter{017A}{\'z}
+ \DeclareUnicodeCharacter{017B}{\dotaccent{Z}}
+ \DeclareUnicodeCharacter{017C}{\dotaccent{z}}
+ \DeclareUnicodeCharacter{017D}{\v{Z}}
+ \DeclareUnicodeCharacter{017E}{\v{z}}
+
+ \DeclareUnicodeCharacter{01C4}{D\v{Z}}
+ \DeclareUnicodeCharacter{01C5}{D\v{z}}
+ \DeclareUnicodeCharacter{01C6}{d\v{z}}
+ \DeclareUnicodeCharacter{01C7}{LJ}
+ \DeclareUnicodeCharacter{01C8}{Lj}
+ \DeclareUnicodeCharacter{01C9}{lj}
+ \DeclareUnicodeCharacter{01CA}{NJ}
+ \DeclareUnicodeCharacter{01CB}{Nj}
+ \DeclareUnicodeCharacter{01CC}{nj}
+ \DeclareUnicodeCharacter{01CD}{\v{A}}
+ \DeclareUnicodeCharacter{01CE}{\v{a}}
+ \DeclareUnicodeCharacter{01CF}{\v{I}}
+
+ \DeclareUnicodeCharacter{01D0}{\v{\dotless{i}}}
+ \DeclareUnicodeCharacter{01D1}{\v{O}}
+ \DeclareUnicodeCharacter{01D2}{\v{o}}
+ \DeclareUnicodeCharacter{01D3}{\v{U}}
+ \DeclareUnicodeCharacter{01D4}{\v{u}}
+
+ \DeclareUnicodeCharacter{01E2}{\={\AE}}
+ \DeclareUnicodeCharacter{01E3}{\={\ae}}
+ \DeclareUnicodeCharacter{01E6}{\v{G}}
+ \DeclareUnicodeCharacter{01E7}{\v{g}}
+ \DeclareUnicodeCharacter{01E8}{\v{K}}
+ \DeclareUnicodeCharacter{01E9}{\v{k}}
+
+ \DeclareUnicodeCharacter{01F0}{\v{\dotless{j}}}
+ \DeclareUnicodeCharacter{01F1}{DZ}
+ \DeclareUnicodeCharacter{01F2}{Dz}
+ \DeclareUnicodeCharacter{01F3}{dz}
+ \DeclareUnicodeCharacter{01F4}{\'G}
+ \DeclareUnicodeCharacter{01F5}{\'g}
+ \DeclareUnicodeCharacter{01F8}{\`N}
+ \DeclareUnicodeCharacter{01F9}{\`n}
+ \DeclareUnicodeCharacter{01FC}{\'{\AE}}
+ \DeclareUnicodeCharacter{01FD}{\'{\ae}}
+ \DeclareUnicodeCharacter{01FE}{\'{\O}}
+ \DeclareUnicodeCharacter{01FF}{\'{\o}}
+
+ \DeclareUnicodeCharacter{021E}{\v{H}}
+ \DeclareUnicodeCharacter{021F}{\v{h}}
+
+ \DeclareUnicodeCharacter{0226}{\dotaccent{A}}
+ \DeclareUnicodeCharacter{0227}{\dotaccent{a}}
+ \DeclareUnicodeCharacter{0228}{\cedilla{E}}
+ \DeclareUnicodeCharacter{0229}{\cedilla{e}}
+ \DeclareUnicodeCharacter{022E}{\dotaccent{O}}
+ \DeclareUnicodeCharacter{022F}{\dotaccent{o}}
+
+ \DeclareUnicodeCharacter{0232}{\=Y}
+ \DeclareUnicodeCharacter{0233}{\=y}
+ \DeclareUnicodeCharacter{0237}{\dotless{j}}
+
+ \DeclareUnicodeCharacter{02DB}{\ogonek{ }}
+
+ \DeclareUnicodeCharacter{1E02}{\dotaccent{B}}
+ \DeclareUnicodeCharacter{1E03}{\dotaccent{b}}
+ \DeclareUnicodeCharacter{1E04}{\udotaccent{B}}
+ \DeclareUnicodeCharacter{1E05}{\udotaccent{b}}
+ \DeclareUnicodeCharacter{1E06}{\ubaraccent{B}}
+ \DeclareUnicodeCharacter{1E07}{\ubaraccent{b}}
+ \DeclareUnicodeCharacter{1E0A}{\dotaccent{D}}
+ \DeclareUnicodeCharacter{1E0B}{\dotaccent{d}}
+ \DeclareUnicodeCharacter{1E0C}{\udotaccent{D}}
+ \DeclareUnicodeCharacter{1E0D}{\udotaccent{d}}
+ \DeclareUnicodeCharacter{1E0E}{\ubaraccent{D}}
+ \DeclareUnicodeCharacter{1E0F}{\ubaraccent{d}}
+
+ \DeclareUnicodeCharacter{1E1E}{\dotaccent{F}}
+ \DeclareUnicodeCharacter{1E1F}{\dotaccent{f}}
+
+ \DeclareUnicodeCharacter{1E20}{\=G}
+ \DeclareUnicodeCharacter{1E21}{\=g}
+ \DeclareUnicodeCharacter{1E22}{\dotaccent{H}}
+ \DeclareUnicodeCharacter{1E23}{\dotaccent{h}}
+ \DeclareUnicodeCharacter{1E24}{\udotaccent{H}}
+ \DeclareUnicodeCharacter{1E25}{\udotaccent{h}}
+ \DeclareUnicodeCharacter{1E26}{\"H}
+ \DeclareUnicodeCharacter{1E27}{\"h}
+
+ \DeclareUnicodeCharacter{1E30}{\'K}
+ \DeclareUnicodeCharacter{1E31}{\'k}
+ \DeclareUnicodeCharacter{1E32}{\udotaccent{K}}
+ \DeclareUnicodeCharacter{1E33}{\udotaccent{k}}
+ \DeclareUnicodeCharacter{1E34}{\ubaraccent{K}}
+ \DeclareUnicodeCharacter{1E35}{\ubaraccent{k}}
+ \DeclareUnicodeCharacter{1E36}{\udotaccent{L}}
+ \DeclareUnicodeCharacter{1E37}{\udotaccent{l}}
+ \DeclareUnicodeCharacter{1E3A}{\ubaraccent{L}}
+ \DeclareUnicodeCharacter{1E3B}{\ubaraccent{l}}
+ \DeclareUnicodeCharacter{1E3E}{\'M}
+ \DeclareUnicodeCharacter{1E3F}{\'m}
+
+ \DeclareUnicodeCharacter{1E40}{\dotaccent{M}}
+ \DeclareUnicodeCharacter{1E41}{\dotaccent{m}}
+ \DeclareUnicodeCharacter{1E42}{\udotaccent{M}}
+ \DeclareUnicodeCharacter{1E43}{\udotaccent{m}}
+ \DeclareUnicodeCharacter{1E44}{\dotaccent{N}}
+ \DeclareUnicodeCharacter{1E45}{\dotaccent{n}}
+ \DeclareUnicodeCharacter{1E46}{\udotaccent{N}}
+ \DeclareUnicodeCharacter{1E47}{\udotaccent{n}}
+ \DeclareUnicodeCharacter{1E48}{\ubaraccent{N}}
+ \DeclareUnicodeCharacter{1E49}{\ubaraccent{n}}
+
+ \DeclareUnicodeCharacter{1E54}{\'P}
+ \DeclareUnicodeCharacter{1E55}{\'p}
+ \DeclareUnicodeCharacter{1E56}{\dotaccent{P}}
+ \DeclareUnicodeCharacter{1E57}{\dotaccent{p}}
+ \DeclareUnicodeCharacter{1E58}{\dotaccent{R}}
+ \DeclareUnicodeCharacter{1E59}{\dotaccent{r}}
+ \DeclareUnicodeCharacter{1E5A}{\udotaccent{R}}
+ \DeclareUnicodeCharacter{1E5B}{\udotaccent{r}}
+ \DeclareUnicodeCharacter{1E5E}{\ubaraccent{R}}
+ \DeclareUnicodeCharacter{1E5F}{\ubaraccent{r}}
+
+ \DeclareUnicodeCharacter{1E60}{\dotaccent{S}}
+ \DeclareUnicodeCharacter{1E61}{\dotaccent{s}}
+ \DeclareUnicodeCharacter{1E62}{\udotaccent{S}}
+ \DeclareUnicodeCharacter{1E63}{\udotaccent{s}}
+ \DeclareUnicodeCharacter{1E6A}{\dotaccent{T}}
+ \DeclareUnicodeCharacter{1E6B}{\dotaccent{t}}
+ \DeclareUnicodeCharacter{1E6C}{\udotaccent{T}}
+ \DeclareUnicodeCharacter{1E6D}{\udotaccent{t}}
+ \DeclareUnicodeCharacter{1E6E}{\ubaraccent{T}}
+ \DeclareUnicodeCharacter{1E6F}{\ubaraccent{t}}
+
+ \DeclareUnicodeCharacter{1E7C}{\~V}
+ \DeclareUnicodeCharacter{1E7D}{\~v}
+ \DeclareUnicodeCharacter{1E7E}{\udotaccent{V}}
+ \DeclareUnicodeCharacter{1E7F}{\udotaccent{v}}
+
+ \DeclareUnicodeCharacter{1E80}{\`W}
+ \DeclareUnicodeCharacter{1E81}{\`w}
+ \DeclareUnicodeCharacter{1E82}{\'W}
+ \DeclareUnicodeCharacter{1E83}{\'w}
+ \DeclareUnicodeCharacter{1E84}{\"W}
+ \DeclareUnicodeCharacter{1E85}{\"w}
+ \DeclareUnicodeCharacter{1E86}{\dotaccent{W}}
+ \DeclareUnicodeCharacter{1E87}{\dotaccent{w}}
+ \DeclareUnicodeCharacter{1E88}{\udotaccent{W}}
+ \DeclareUnicodeCharacter{1E89}{\udotaccent{w}}
+ \DeclareUnicodeCharacter{1E8A}{\dotaccent{X}}
+ \DeclareUnicodeCharacter{1E8B}{\dotaccent{x}}
+ \DeclareUnicodeCharacter{1E8C}{\"X}
+ \DeclareUnicodeCharacter{1E8D}{\"x}
+ \DeclareUnicodeCharacter{1E8E}{\dotaccent{Y}}
+ \DeclareUnicodeCharacter{1E8F}{\dotaccent{y}}
+
+ \DeclareUnicodeCharacter{1E90}{\^Z}
+ \DeclareUnicodeCharacter{1E91}{\^z}
+ \DeclareUnicodeCharacter{1E92}{\udotaccent{Z}}
+ \DeclareUnicodeCharacter{1E93}{\udotaccent{z}}
+ \DeclareUnicodeCharacter{1E94}{\ubaraccent{Z}}
+ \DeclareUnicodeCharacter{1E95}{\ubaraccent{z}}
+ \DeclareUnicodeCharacter{1E96}{\ubaraccent{h}}
+ \DeclareUnicodeCharacter{1E97}{\"t}
+ \DeclareUnicodeCharacter{1E98}{\ringaccent{w}}
+ \DeclareUnicodeCharacter{1E99}{\ringaccent{y}}
+
+ \DeclareUnicodeCharacter{1EA0}{\udotaccent{A}}
+ \DeclareUnicodeCharacter{1EA1}{\udotaccent{a}}
+
+ \DeclareUnicodeCharacter{1EB8}{\udotaccent{E}}
+ \DeclareUnicodeCharacter{1EB9}{\udotaccent{e}}
+ \DeclareUnicodeCharacter{1EBC}{\~E}
+ \DeclareUnicodeCharacter{1EBD}{\~e}
+
+ \DeclareUnicodeCharacter{1ECA}{\udotaccent{I}}
+ \DeclareUnicodeCharacter{1ECB}{\udotaccent{i}}
+ \DeclareUnicodeCharacter{1ECC}{\udotaccent{O}}
+ \DeclareUnicodeCharacter{1ECD}{\udotaccent{o}}
+
+ \DeclareUnicodeCharacter{1EE4}{\udotaccent{U}}
+ \DeclareUnicodeCharacter{1EE5}{\udotaccent{u}}
+
+ \DeclareUnicodeCharacter{1EF2}{\`Y}
+ \DeclareUnicodeCharacter{1EF3}{\`y}
+ \DeclareUnicodeCharacter{1EF4}{\udotaccent{Y}}
+
+ \DeclareUnicodeCharacter{1EF8}{\~Y}
+ \DeclareUnicodeCharacter{1EF9}{\~y}
+
+ \DeclareUnicodeCharacter{2013}{--}
+ \DeclareUnicodeCharacter{2014}{---}
+ \DeclareUnicodeCharacter{2018}{\quoteleft}
+ \DeclareUnicodeCharacter{2019}{\quoteright}
+ \DeclareUnicodeCharacter{201A}{\quotesinglbase}
+ \DeclareUnicodeCharacter{201C}{\quotedblleft}
+ \DeclareUnicodeCharacter{201D}{\quotedblright}
+ \DeclareUnicodeCharacter{201E}{\quotedblbase}
+ \DeclareUnicodeCharacter{2022}{\bullet}
+ \DeclareUnicodeCharacter{2026}{\dots}
+ \DeclareUnicodeCharacter{2039}{\guilsinglleft}
+ \DeclareUnicodeCharacter{203A}{\guilsinglright}
+ \DeclareUnicodeCharacter{20AC}{\euro}
+
+ \DeclareUnicodeCharacter{2192}{\expansion}
+ \DeclareUnicodeCharacter{21D2}{\result}
+
+ \DeclareUnicodeCharacter{2212}{\minus}
+ \DeclareUnicodeCharacter{2217}{\point}
+ \DeclareUnicodeCharacter{2261}{\equiv}
+}% end of \utfeightchardefs
+
+
+% US-ASCII character definitions.
+\def\asciichardefs{% nothing need be done
+ \relax
+}
+
+% Make non-ASCII characters printable again for compatibility with
+% existing Texinfo documents that may use them, even without declaring a
+% document encoding.
+%
+\setnonasciicharscatcode \other
+
+
+\message{formatting,}
+
+\newdimen\defaultparindent \defaultparindent = 15pt
+
+\chapheadingskip = 15pt plus 4pt minus 2pt
+\secheadingskip = 12pt plus 3pt minus 2pt
+\subsecheadingskip = 9pt plus 2pt minus 2pt
+
+% Prevent underfull vbox error messages.
+\vbadness = 10000
+
+% Don't be so finicky about underfull hboxes, either.
+\hbadness = 2000
+
+% Following George Bush, get rid of widows and orphans.
+\widowpenalty=10000
+\clubpenalty=10000
+
+% Use TeX 3.0's \emergencystretch to help line breaking, but if we're
+% using an old version of TeX, don't do anything. We want the amount of
+% stretch added to depend on the line length, hence the dependence on
+% \hsize. We call this whenever the paper size is set.
+%
+\def\setemergencystretch{%
+ \ifx\emergencystretch\thisisundefined
+ % Allow us to assign to \emergencystretch anyway.
+ \def\emergencystretch{\dimen0}%
+ \else
+ \emergencystretch = .15\hsize
+ \fi
+}
+
+% Parameters in order: 1) textheight; 2) textwidth;
+% 3) voffset; 4) hoffset; 5) binding offset; 6) topskip;
+% 7) physical page height; 8) physical page width.
+%
+% We also call \setleading{\textleading}, so the caller should define
+% \textleading. The caller should also set \parskip.
+%
+\def\internalpagesizes#1#2#3#4#5#6#7#8{%
+ \voffset = #3\relax
+ \topskip = #6\relax
+ \splittopskip = \topskip
+ %
+ \vsize = #1\relax
+ \advance\vsize by \topskip
+ \outervsize = \vsize
+ \advance\outervsize by 2\topandbottommargin
+ \pageheight = \vsize
+ %
+ \hsize = #2\relax
+ \outerhsize = \hsize
+ \advance\outerhsize by 0.5in
+ \pagewidth = \hsize
+ %
+ \normaloffset = #4\relax
+ \bindingoffset = #5\relax
+ %
+ \ifpdf
+ \pdfpageheight #7\relax
+ \pdfpagewidth #8\relax
+ % if we don't reset these, they will remain at "1 true in" of
+ % whatever layout pdftex was dumped with.
+ \pdfhorigin = 1 true in
+ \pdfvorigin = 1 true in
+ \fi
+ %
+ \setleading{\textleading}
+ %
+ \parindent = \defaultparindent
+ \setemergencystretch
+}
+
+% @letterpaper (the default).
+\def\letterpaper{{\globaldefs = 1
+ \parskip = 3pt plus 2pt minus 1pt
+ \textleading = 13.2pt
+ %
+ % If page is nothing but text, make it come out even.
+ \internalpagesizes{607.2pt}{6in}% that's 46 lines
+ {\voffset}{.25in}%
+ {\bindingoffset}{36pt}%
+ {11in}{8.5in}%
+}}
+
+% Use @smallbook to reset parameters for 7x9.25 trim size.
+\def\smallbook{{\globaldefs = 1
+ \parskip = 2pt plus 1pt
+ \textleading = 12pt
+ %
+ \internalpagesizes{7.5in}{5in}%
+ {-.2in}{0in}%
+ {\bindingoffset}{16pt}%
+ {9.25in}{7in}%
+ %
+ \lispnarrowing = 0.3in
+ \tolerance = 700
+ \hfuzz = 1pt
+ \contentsrightmargin = 0pt
+ \defbodyindent = .5cm
+}}
+
+% Use @smallerbook to reset parameters for 6x9 trim size.
+% (Just testing, parameters still in flux.)
+\def\smallerbook{{\globaldefs = 1
+ \parskip = 1.5pt plus 1pt
+ \textleading = 12pt
+ %
+ \internalpagesizes{7.4in}{4.8in}%
+ {-.2in}{-.4in}%
+ {0pt}{14pt}%
+ {9in}{6in}%
+ %
+ \lispnarrowing = 0.25in
+ \tolerance = 700
+ \hfuzz = 1pt
+ \contentsrightmargin = 0pt
+ \defbodyindent = .4cm
+}}
+
+% Use @afourpaper to print on European A4 paper.
+\def\afourpaper{{\globaldefs = 1
+ \parskip = 3pt plus 2pt minus 1pt
+ \textleading = 13.2pt
+ %
+ % Double-side printing via postscript on Laserjet 4050
+ % prints double-sided nicely when \bindingoffset=10mm and \hoffset=-6mm.
+ % To change the settings for a different printer or situation, adjust
+ % \normaloffset until the front-side and back-side texts align. Then
+ % do the same for \bindingoffset. You can set these for testing in
+ % your texinfo source file like this:
+ % @tex
+ % \global\normaloffset = -6mm
+ % \global\bindingoffset = 10mm
+ % @end tex
+ \internalpagesizes{673.2pt}{160mm}% that's 51 lines
+ {\voffset}{\hoffset}%
+ {\bindingoffset}{44pt}%
+ {297mm}{210mm}%
+ %
+ \tolerance = 700
+ \hfuzz = 1pt
+ \contentsrightmargin = 0pt
+ \defbodyindent = 5mm
+}}
+
+% Use @afivepaper to print on European A5 paper.
+% From romildo at urano.iceb.ufop.br, 2 July 2000.
+% He also recommends making @example and @lisp be small.
+\def\afivepaper{{\globaldefs = 1
+ \parskip = 2pt plus 1pt minus 0.1pt
+ \textleading = 12.5pt
+ %
+ \internalpagesizes{160mm}{120mm}%
+ {\voffset}{\hoffset}%
+ {\bindingoffset}{8pt}%
+ {210mm}{148mm}%
+ %
+ \lispnarrowing = 0.2in
+ \tolerance = 800
+ \hfuzz = 1.2pt
+ \contentsrightmargin = 0pt
+ \defbodyindent = 2mm
+ \tableindent = 12mm
+}}
+
+% A specific text layout, 24x15cm overall, intended for A4 paper.
+\def\afourlatex{{\globaldefs = 1
+ \afourpaper
+ \internalpagesizes{237mm}{150mm}%
+ {\voffset}{4.6mm}%
+ {\bindingoffset}{7mm}%
+ {297mm}{210mm}%
+ %
+ % Must explicitly reset to 0 because we call \afourpaper.
+ \globaldefs = 0
+}}
+
+% Use @afourwide to print on A4 paper in landscape format.
+\def\afourwide{{\globaldefs = 1
+ \afourpaper
+ \internalpagesizes{241mm}{165mm}%
+ {\voffset}{-2.95mm}%
+ {\bindingoffset}{7mm}%
+ {297mm}{210mm}%
+ \globaldefs = 0
+}}
+
+% @pagesizes TEXTHEIGHT[,TEXTWIDTH]
+% Perhaps we should allow setting the margins, \topskip, \parskip,
+% and/or leading, also. Or perhaps we should compute them somehow.
+%
+\parseargdef\pagesizes{\pagesizesyyy #1,,\finish}
+\def\pagesizesyyy#1,#2,#3\finish{{%
+ \setbox0 = \hbox{\ignorespaces #2}\ifdim\wd0 > 0pt \hsize=#2\relax \fi
+ \globaldefs = 1
+ %
+ \parskip = 3pt plus 2pt minus 1pt
+ \setleading{\textleading}%
+ %
+ \dimen0 = #1\relax
+ \advance\dimen0 by \voffset
+ %
+ \dimen2 = \hsize
+ \advance\dimen2 by \normaloffset
+ %
+ \internalpagesizes{#1}{\hsize}%
+ {\voffset}{\normaloffset}%
+ {\bindingoffset}{44pt}%
+ {\dimen0}{\dimen2}%
+}}
+
+% Set default to letter.
+%
+\letterpaper
+
+
+\message{and turning on texinfo input format.}
+
+% DEL is a comment character, in case @c does not suffice.
+\catcode`\^^? = 14
+
+% Define macros to output various characters with catcode for normal text.
+\catcode`\"=\other
+\catcode`\~=\other
+\catcode`\^=\other
+\catcode`\_=\other
+\catcode`\|=\other
+\catcode`\<=\other
+\catcode`\>=\other
+\catcode`\+=\other
+\catcode`\$=\other
+\def\normaldoublequote{"}
+\def\normaltilde{~}
+\def\normalcaret{^}
+\def\normalunderscore{_}
+\def\normalverticalbar{|}
+\def\normalless{<}
+\def\normalgreater{>}
+\def\normalplus{+}
+\def\normaldollar{$}%$ font-lock fix
+
+% This macro is used to make a character print one way in \tt
+% (where it can probably be output as-is), and another way in other fonts,
+% where something hairier probably needs to be done.
+%
+% #1 is what to print if we are indeed using \tt; #2 is what to print
+% otherwise. Since all the Computer Modern typewriter fonts have zero
+% interword stretch (and shrink), and it is reasonable to expect all
+% typewriter fonts to have this, we can check that font parameter.
+%
+\def\ifusingtt#1#2{\ifdim \fontdimen3\font=0pt #1\else #2\fi}
+
+% Same as above, but check for italic font. Actually this also catches
+% non-italic slanted fonts since it is impossible to distinguish them from
+% italic fonts. But since this is only used by $ and it uses \sl anyway
+% this is not a problem.
+\def\ifusingit#1#2{\ifdim \fontdimen1\font>0pt #1\else #2\fi}
+
+% Turn off all special characters except @
+% (and those which the user can use as if they were ordinary).
+% Most of these we simply print from the \tt font, but for some, we can
+% use math or other variants that look better in normal text.
+
+\catcode`\"=\active
+\def\activedoublequote{{\tt\char34}}
+\let"=\activedoublequote
+\catcode`\~=\active
+\def~{{\tt\char126}}
+\chardef\hat=`\^
+\catcode`\^=\active
+\def^{{\tt \hat}}
+
+\catcode`\_=\active
+\def_{\ifusingtt\normalunderscore\_}
+\let\realunder=_
+% Subroutine for the previous macro.
+\def\_{\leavevmode \kern.07em \vbox{\hrule width.3em height.1ex}\kern .07em }
+
+\catcode`\|=\active
+\def|{{\tt\char124}}
+\chardef \less=`\<
+\catcode`\<=\active
+\def<{{\tt \less}}
+\chardef \gtr=`\>
+\catcode`\>=\active
+\def>{{\tt \gtr}}
+\catcode`\+=\active
+\def+{{\tt \char 43}}
+\catcode`\$=\active
+\def${\ifusingit{{\sl\$}}\normaldollar}%$ font-lock fix
+
+% If a .fmt file is being used, characters that might appear in a file
+% name cannot be active until we have parsed the command line.
+% So turn them off again, and have \everyjob (or @setfilename) turn them on.
+% \otherifyactive is called near the end of this file.
+\def\otherifyactive{\catcode`+=\other \catcode`\_=\other}
+
+% Used sometimes to turn off (effectively) the active characters even after
+% parsing them.
+\def\turnoffactive{%
+ \normalturnoffactive
+ \otherbackslash
+}
+
+\catcode`\@=0
+
+% \backslashcurfont outputs one backslash character in current font,
+% as in \char`\\.
+\global\chardef\backslashcurfont=`\\
+\global\let\rawbackslashxx=\backslashcurfont % let existing .??s files work
+
+% \realbackslash is an actual character `\' with catcode other, and
+% \doublebackslash is two of them (for the pdf outlines).
+{\catcode`\\=\other @gdef at realbackslash{\} @gdef at doublebackslash{\\}}
+
+% In texinfo, backslash is an active character; it prints the backslash
+% in fixed width font.
+\catcode`\\=\active
+ at def@normalbackslash{{@tt at backslashcurfont}}
+% On startup, @fixbackslash assigns:
+% @let \ = @normalbackslash
+
+% \rawbackslash defines an active \ to do \backslashcurfont.
+% \otherbackslash defines an active \ to be a literal `\' character with
+% catcode other.
+ at gdef@rawbackslash{@let\=@backslashcurfont}
+ at gdef@otherbackslash{@let\=@realbackslash}
+
+% Same as @turnoffactive except outputs \ as {\tt\char`\\} instead of
+% the literal character `\'.
+%
+ at def@normalturnoffactive{%
+ @let\=@normalbackslash
+ @let"=@normaldoublequote
+ @let~=@normaltilde
+ @let^=@normalcaret
+ @let_=@normalunderscore
+ @let|=@normalverticalbar
+ @let<=@normalless
+ @let>=@normalgreater
+ @let+=@normalplus
+ @let$=@normaldollar %$ font-lock fix
+ @markupsetuplqdefault
+ @markupsetuprqdefault
+ @unsepspaces
+}
+
+% Make _ and + \other characters, temporarily.
+% This is canceled by @fixbackslash.
+ at otherifyactive
+
+% If a .fmt file is being used, we don't want the `\input texinfo' to show up.
+% That is what \eatinput is for; after that, the `\' should revert to printing
+% a backslash.
+%
+ at gdef@eatinput input texinfo{@fixbackslash}
+ at global@let\ = @eatinput
+
+% On the other hand, perhaps the file did not have a `\input texinfo'. Then
+% the first `\' in the file would cause an error. This macro tries to fix
+% that, assuming it is called before the first `\' could plausibly occur.
+% Also turn back on active characters that might appear in the input
+% file name, in case not using a pre-dumped format.
+%
+ at gdef@fixbackslash{%
+ @ifx\@eatinput @let\ = @normalbackslash @fi
+ @catcode`+=@active
+ @catcode`@_=@active
+}
+
+% Say @foo, not \foo, in error messages.
+ at escapechar = `@@
+
+% These look ok in all fonts, so just make them not special.
+ at catcode`@& = @other
+ at catcode`@# = @other
+ at catcode`@% = @other
+
+ at c Finally, make ` and ' active, so that txicodequoteundirected and
+ at c txicodequotebacktick work right in, e.g., @w{@code{`foo'}}. If we
+ at c don't make ` and ' active, @code will not get them as active chars.
+ at c Do this last of all since we use ` in the previous @catcode assignments.
+ at catcode`@'=@active
+ at catcode`@`=@active
+ at markupsetuplqdefault
+ at markupsetuprqdefault
+
+ at c Gnulib now utterly and painfully insists on no trailing whitespace.
+ at c So we have to nuke it.
+
+ at c Local variables:
+ at c eval: (add-hook 'write-file-hooks 'time-stamp)
+ at c eval: (add-hook 'write-file-hooks 'nuke-trailing-whitespace)
+ at c page-delimiter: "^\\\\message"
+ at c time-stamp-start: "def\\\\texinfoversion{"
+ at c time-stamp-format: "%:y-%02m-%02d.%02H"
+ at c time-stamp-end: "}"
+ at c End:
+
+ at c vim:sw=2:
+
+ at ignore
+ arch-tag: e1b36e32-c96e-4135-a41a-0b2efa2ea115
+ at end ignore
diff --git a/src/libGkArrays/libGkArrays.pc.in b/src/libGkArrays/libGkArrays.pc.in
new file mode 100644
index 0000000..5f282af
--- /dev/null
+++ b/src/libGkArrays/libGkArrays.pc.in
@@ -0,0 +1,10 @@
+prefix=@hacked_prefix@
+exec_prefix=@exec_prefix@
+libdir=@libdir@
+includedir=@includedir@
+
+Name: libGkArrays
+Description: C++ library to build GkArrays.
+Version: @VERSION@
+Libs: -L${libdir} -l at PACKAGE@- at VERSION@
+Cflags: -I${includedir}/@PACKAGE at -@VERSION@ -I${libdir}/@PACKAGE at -@VERSION@/include
diff --git a/src/libGkArrays/postinst.in b/src/libGkArrays/postinst.in
new file mode 100644
index 0000000..6ad36a2
--- /dev/null
+++ b/src/libGkArrays/postinst.in
@@ -0,0 +1,108 @@
+#!/bin/sh
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thierry LECROQ <thierry.lecroq at univ-rouen.fr> #
+# Martine LÉONARD <Martine.Leonard at univ-rouen.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie de la librairie Gk-arrays. #
+# #
+# La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de #
+# lectures de séquences issues du séquençage haut-débit. #
+# #
+# Ce logiciel est régi par la licence CeCILL-C soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL-C, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the Gk-arrays library. #
+# #
+# The Gk-arrays library aims at indexing k-factors from a huge set of #
+# sequencing reads. #
+# #
+# This software is governed by the CeCILL-C license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL-C #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL-C license and that you accept its terms. #
+# #
+###############################################################################
+#
+# $Id: postinst.in 195 2011-02-10 09:41:41Z mancheron $
+#
+###############################################################################
+set -e
+echo "@hacked_prefix@/lib" > /etc/ld.so.conf.d/@PACKAGE at -@VERSION at .conf
+ldconfig
diff --git a/src/libGkArrays/prerm.in b/src/libGkArrays/prerm.in
new file mode 100644
index 0000000..71a7d5b
--- /dev/null
+++ b/src/libGkArrays/prerm.in
@@ -0,0 +1,108 @@
+#!/bin/sh
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thierry LECROQ <thierry.lecroq at univ-rouen.fr> #
+# Martine LÉONARD <Martine.Leonard at univ-rouen.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie de la librairie Gk-arrays. #
+# #
+# La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de #
+# lectures de séquences issues du séquençage haut-débit. #
+# #
+# Ce logiciel est régi par la licence CeCILL-C soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL-C, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the Gk-arrays library. #
+# #
+# The Gk-arrays library aims at indexing k-factors from a huge set of #
+# sequencing reads. #
+# #
+# This software is governed by the CeCILL-C license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL-C #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL-C license and that you accept its terms. #
+# #
+###############################################################################
+#
+# $Id: prerm.in 195 2011-02-10 09:41:41Z mancheron $
+#
+###############################################################################
+set -e
+rm /etc/ld.so.conf.d/@PACKAGE at -@VERSION at .conf
+ldconfig
diff --git a/src/libGkArrays/src/Makefile.am b/src/libGkArrays/src/Makefile.am
new file mode 100644
index 0000000..5c9b933
--- /dev/null
+++ b/src/libGkArrays/src/Makefile.am
@@ -0,0 +1,163 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thierry LECROQ <thierry.lecroq at univ-rouen.fr> #
+# Martine LÉONARD <Martine.Leonard at univ-rouen.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie de la librairie Gk-arrays. #
+# #
+# La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de #
+# lectures de séquences issues du séquençage haut-débit. #
+# #
+# Ce logiciel est régi par la licence CeCILL-C soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL-C, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the Gk-arrays library. #
+# #
+# The Gk-arrays library aims at indexing k-factors from a huge set of #
+# sequencing reads. #
+# #
+# This software is governed by the CeCILL-C license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL-C #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL-C license and that you accept its terms. #
+# #
+###############################################################################
+#
+# $Id: Makefile.am 763 2011-07-10 20:48:29Z salson $
+#
+###############################################################################
+
+SUBDIRS = kseq sux
+
+if INCLUDED_PROGRESSBAR
+ SUBDIRS += libProgressBar-1.2.0
+endif
+
+KSEQ_DIR=kseq
+KSEQ_HDRS=$(KSEQ_DIR)/kseq.h
+
+SUX_DIR=sux
+SUX_SRCS=$(SUX_DIR)/rank9b.cpp
+SUX_HDRS=\
+ $(SUX_DIR)/macros.h \
+ $(SUX_DIR)/popcount.h \
+ $(SUX_DIR)/rank9b.h
+
+AM_LDFLAGS = -lpthread
+AM_CPPFLAGS = -I at abs_top_srcdir@
+# if INCLUDED_DIVSUFSORT
+# AM_LDFLAGS += -L at abs_top_builddir@/libdivsufsort/lib/.libs
+# AM_CPPFLAGS += -I at abs_top_builddir@/libdivsufsort/include
+# endif
+
+
+includedir = @includedir@/@PACKAGE at -@VERSION@
+libdir=@libdir@
+include_HEADERS = gkArrays.h solArray.h gkArraysTypes.h gkArraysBuilder.h gkSABuilder.h gkCFPSBuilder.h gkIFABuilder.h readsReader.h bitvector.hxx largebinvect.hxx bitvector.cxx largebinvect.cxx binvect.hxx
+noinst_HEADERS = utils.h basic.h const.h $(KSEQ_HDRS) $(SUX_HDRS)
+
+lib_LTLIBRARIES = libGkArrays.la
+libGkArrays_ladir = @abs_srcdir@
+libGkArrays_la_SOURCES = gkArrays.cpp solArray.cpp utils.cpp gkArraysBuilder.cpp gkSABuilder.cpp gkCFPSBuilder.cpp gkIFABuilder.cpp readsReader.cpp largebinvect.cxx bitvector.cxx $(SUX_SRCS)
+libGkArrays_la_configdir = @libdir@/@PACKAGE at -@VERSION@/include
+libGkArrays_la_config_DATA = @abs_top_builddir@/config/config.h
+libGkArrays_la_LDFLAGS = -version-info @LIB_VERSION@ -release @VERSION@ $(AM_LDFLAGS) # @LIBDIVSUFSORT@
+
+if INCLUDED_PROGRESSBAR
+ AM_LDFLAGS += -L at abs_builddir@/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar
+ AM_CPPFLAGS += -I at abs_srcdir@/libProgressBar-1.2.0/
+endif
+
+noinst_PROGRAMS = buildTables
+buildTables_SOURCES = buildTables.cpp
+buildTables_LDADD=libGkArrays.la
+buildTables_LDFLAGS = -lGkArrays $(AM_LDFLAGS)
+
+install-data-hook:
+ $(LN_S) -f @PACKAGE at -@VERSION@ $(DESTDIR)@includedir@/@PACKAGE@
+
+uninstall-hook:
+ test "`readlink $(DESTDIR)@includedir@/@PACKAGE@`" != @PACKAGE at -@VERSION@ \
+ || $(RM) -f $(DESTDIR)@includedir@/@PACKAGE@
+
+MOSTLYCLEANFILES=*~
+CLEANFILES=*~ *.gcda *.gcno
+DISTCLEANFILES=*~
+MAINTAINERCLEANFILES=*~
diff --git a/src/libGkArrays/src/Makefile.in b/src/libGkArrays/src/Makefile.in
new file mode 100644
index 0000000..da16e87
--- /dev/null
+++ b/src/libGkArrays/src/Makefile.in
@@ -0,0 +1,951 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thierry LECROQ <thierry.lecroq at univ-rouen.fr> #
+# Martine LÉONARD <Martine.Leonard at univ-rouen.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie de la librairie Gk-arrays. #
+# #
+# La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de #
+# lectures de séquences issues du séquençage haut-débit. #
+# #
+# Ce logiciel est régi par la licence CeCILL-C soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL-C, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the Gk-arrays library. #
+# #
+# The Gk-arrays library aims at indexing k-factors from a huge set of #
+# sequencing reads. #
+# #
+# This software is governed by the CeCILL-C license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL-C #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL-C license and that you accept its terms. #
+# #
+###############################################################################
+#
+# $Id: Makefile.am 763 2011-07-10 20:48:29Z salson $
+#
+###############################################################################
+
+
+
+
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+ at INCLUDED_PROGRESSBAR_TRUE@am__append_1 = libProgressBar-1.2.0
+ at INCLUDED_PROGRESSBAR_TRUE@am__append_2 = -L at abs_builddir@/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar
+ at INCLUDED_PROGRESSBAR_TRUE@am__append_3 = -I at abs_srcdir@/libProgressBar-1.2.0/
+noinst_PROGRAMS = buildTables$(EXEEXT)
+subdir = src
+DIST_COMMON = $(include_HEADERS) $(noinst_HEADERS) \
+ $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+ $(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/config/config.h
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+ $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
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diff --git a/src/libGkArrays/src/basic.h b/src/libGkArrays/src/basic.h
new file mode 100755
index 0000000..901be9b
--- /dev/null
+++ b/src/libGkArrays/src/basic.h
@@ -0,0 +1,64 @@
+/* basics.h
+
+ Code mostly inspired from original file written by Rodrigo Gonzalez.
+
+ Copyright (C) 2005, Rodrigo Gonzalez, all rights reserved.
+
+ Some preliminary stuff
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+*/
+
+
+#ifndef BASICSINCLUDED
+#define BASICSINCLUDED
+
+#include <limits>
+#ifdef HAVE_CONFIG_H
+# include <config.h>
+#endif
+
+/*number of bits of a machine word */
+const size_t W = std::numeric_limits<u_int64_t>::digits;
+
+/* reads bit p from e */
+template <class T>
+bool bitget(const T * const e, const u_int64_t p) {
+ return ((e[p/W] >> (p % W)) & u_int64_t(1));
+}
+
+/* sets bit p in e */
+template <class T>
+void bitset(T * const e, const u_int64_t p) {
+ e[p/W] |= u_int64_t(1) << (p % W);
+}
+
+/* cleans bit p in e */
+template <class T>
+void bitclean(T * const e, const u_int64_t p) {
+ e[p/W] &= ~(u_int64_t(1) << (p % W));
+}
+
+/* number of machine words requiered to represents e elements of length n */
+inline u_int64_t nb_digits(const u_int64_t &e, const u_int64_t &n) {
+ return (e * n) / W + ((e * n) % W > 0);
+}
+
+#endif
+
+// Local Variables:
+// mode:c++
+// End:
diff --git a/src/libGkArrays/src/binvect.hxx b/src/libGkArrays/src/binvect.hxx
new file mode 100644
index 0000000..a6361db
--- /dev/null
+++ b/src/libGkArrays/src/binvect.hxx
@@ -0,0 +1,119 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef __BINVECT_HXX__
+#define __BINVECT_HXX__
+
+#include <iostream>
+#include <sstream>
+#include <cstring>
+#include <cstdlib>
+#include <cassert>
+#include <exception>
+#include <stdexcept>
+#include <new>
+
+class BinVectOverflow: public std::exception {
+public:
+ BinVectOverflow() throw() {}
+};
+
+
+#endif
diff --git a/src/libGkArrays/src/bitvector.cxx b/src/libGkArrays/src/bitvector.cxx
new file mode 100644
index 0000000..3c736dc
--- /dev/null
+++ b/src/libGkArrays/src/bitvector.cxx
@@ -0,0 +1,465 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef __BITVECTOR_CXX__
+#define __BITVECTOR_CXX__
+
+#include "bitvector.hxx"
+
+#define BV BitVector<CountWordSize, InnerWordSize>
+#define NO_TYPE
+#define tpl(ret_type, fct) \
+template <typename CountWordSize, typename InnerWordSize> \
+ret_type BV::fct
+
+tpl(NO_TYPE, BitVector(const CountWordSize length, const InnerWordSize nb_bits)):nb_bits(nb_bits), data(length*nb_bits, 0) {
+ assert((((unsigned long int)length)*nb_bits) <= (unsigned long int)(InnerWordSize(~0)));
+}
+
+tpl(NO_TYPE, BitVector(const BitVector &v)): nb_bits(v.nb_bits), data(v.data) {
+}
+
+tpl(NO_TYPE, ~BitVector()) {
+}
+
+tpl(BV &,operator=(const BitVector &v)) {
+ if (this != &v) {
+ nb_bits = v.nb_bits;
+ data = v.data;
+ }
+ return *this;
+}
+
+tpl(inline LargeBinVect<InnerWordSize>, operator[](const CountWordSize i) const) {
+ return data(i*nb_bits, nb_bits);
+}
+
+tpl(unsigned long int, GetValue(const CountWordSize i) const) {
+ return data.GetValue(i*nb_bits, nb_bits);
+}
+
+
+// Set value at position i (>= 0, < length) to value
+tpl(BV &, OldSetValue(const CountWordSize i, const InnerWordSize value)) {
+ InnerWordSize v = value;
+ for (InnerWordSize j = nb_bits; j > 0; j--) {
+ data.SetBit(i * nb_bits + j - 1, 1&v);
+ v >>= 1;
+ }
+ return *this;
+}
+
+// Set value at position i (>= 0, < length) to value
+tpl(BV &, SetValue(const CountWordSize i, const InnerWordSize value)) {
+ data.SetBitRange(i * nb_bits, (i + 1) * nb_bits - 1, value);
+ return *this;
+}
+
+tpl(BV &, Clear()) {
+ data.Clear(0);
+ return *this;
+}
+
+tpl(BV &, Resize(const CountWordSize length)) {
+ data.Resize(length*nb_bits);
+ return *this;
+}
+
+tpl(BV &, CompleteResize(const CountWordSize length, const InnerWordSize nb_bits)) {
+ this->nb_bits = nb_bits;
+ data.Resize(length*nb_bits);
+ return *this;
+}
+
+tpl(CountWordSize, GetLength() const) {
+ return data.GetLength()/nb_bits;
+}
+
+tpl(InnerWordSize, GetBitLength() const) {
+ return data.GetLength();
+}
+
+tpl(InnerWordSize, GetMinimalBit(InnerWordSize w)) {
+ for(InnerWordSize i = (sizeof(InnerWordSize) * 8)-1 ; i > 0 ; i--) {
+ if(w>>i) {
+ return i+1;
+ }
+ }
+ return 1;
+}
+
+
+#ifdef TEST_BITVECTOR
+// Compile this test program with the following command line:
+// g++ bitvector.cxx -DTEST_BITVECTOR -o test_bitvector -Wall -ansi -pedantic -O4
+
+#include <sys/time.h>
+#include <sys/resource.h>
+#include <vector>
+
+
+using std::cout;
+using std::endl;
+
+template <typename CountWordSize, typename InnerWordSize>
+void TestBitVectors(char *cws, char *iws, CountWordSize default_size) {
+ cout << "Testing class BitVector<" << cws << ", " << iws << ">" << endl;
+ cout << "SizeOf(" << cws << ") = "
+ << sizeof(CountWordSize) << "Bytes (= "
+ << 8*sizeof(CountWordSize) << "bits)" << endl;
+ cout << "SizeOf(" << iws << ") = "
+ << sizeof(InnerWordSize) << "Bytes (= "
+ << 8*sizeof(InnerWordSize) << "bits)" << endl << endl;
+ cout << endl;
+
+ cout << "Testing constructor without arguments" << endl;
+ BV *bv = new BV();
+ cout << "It gives a vector of size " << (long unsigned int) bv->GetLength() << endl;
+ cout << "having " << (long unsigned int) bv->GetBitLength() << " bits" << endl;
+ cout << "Destroying the bitvector" << endl;
+ delete bv;
+
+ cout << "Testing constructor with first argument = " << (unsigned long int) default_size << endl;
+ bv = new BV(default_size);
+ cout << "It gives a vector of size " << (long unsigned int) bv->GetLength() << endl;
+ cout << "having " << (long unsigned int) bv->GetBitLength() << " bits" << endl;
+ cout << "Destroying the bitvector" << endl;
+ delete bv;
+
+ cout << "Testing constructor with first argument = " << (unsigned long int) default_size << " and second argument 3" << endl;
+ bv = new BV(default_size, 3);
+ cout << "It gives a vector of size " << (long unsigned int) bv->GetLength() << endl;
+ cout << "having " << (long unsigned int) bv->GetBitLength() << " bits" << endl;
+
+ cout << "Testing copy constructor" << endl;
+ BV v(*bv);
+ cout << "It gives a vector of size " << (long unsigned int) v.GetLength() << endl;
+ cout << "having " << (long unsigned int) v.GetBitLength() << " bits" << endl;
+
+ cout << "Testing assignment operator" << endl;
+ *bv = v;
+ cout << "It gives a vector of size " << (long unsigned int) bv->GetLength() << endl;
+ cout << "having " << (long unsigned int) bv->GetBitLength() << " bits" << endl;
+ cout << "Destroying the bitvector" << endl;
+ delete bv;
+
+ cout << "Accessing value at position " << (unsigned long int) (default_size - 3) << endl;
+ cout << "v[" << (unsigned long int) (default_size - 3) << "] = "
+ << (long unsigned int) v[default_size - 3] << endl;
+ cout << "v.GetValue(" << (unsigned long int) (default_size - 3) << ") = "
+ << (long unsigned int) v.GetValue(default_size - 3) << endl;
+
+ cout << "Setting value 5 at position " << (unsigned long int) (default_size - 3) << endl;
+ v.SetValue(default_size - 3, 5);
+
+ cout << "v.GetValue(" << (unsigned long int) (default_size - 3) << ") = "
+ << (long unsigned int) v.GetValue(default_size - 3) << endl;
+
+ cout << "Setting value 5 from position 0 to 3" << endl;
+ for (CountWordSize i = 0; i < 4; i++) {
+ v.SetValue(i, 5);
+ }
+ for (CountWordSize i = 0; i < 10; i++) {
+ cout << "v.GetValue(" << (long unsigned int) i << ") = " << (long unsigned int) v.GetValue(i) << endl;
+ }
+
+ cout << "Clearing the vector" << endl;
+ v.Clear();
+ for (CountWordSize i = 0; i < 5; i++) {
+ cout << "v.GetValue(" << (long unsigned int) i << ") = " << (long unsigned int) v.GetValue(i) << endl;
+ }
+ cout << "..." << endl;
+ for (CountWordSize i = v.GetLength() - 3; i < v.GetLength(); i++) {
+ cout << "v.GetValue(" << (long unsigned int) i << ") = " << (long unsigned int) v.GetValue(i) << endl;
+ }
+
+ cout << "Setting value 5 from position 0 to 3" << endl;
+ for (CountWordSize i = 0; i < 4; i++) {
+ v.SetValue(i, 5);
+ }
+ for (CountWordSize i = 0; i < 5; i++) {
+ cout << "v.GetValue(" << (long unsigned int) i << ") = " << (long unsigned int) v.GetValue(i) << endl;
+ }
+ cout << "..." << endl;
+ for (CountWordSize i = v.GetLength() - 3; i < v.GetLength(); i++) {
+ cout << "v.GetValue(" << (long unsigned int) i << ") = " << (long unsigned int) v.GetValue(i) << endl;
+ }
+
+ cout << "Resize the vector to 3" << endl;
+ v.Resize(3);
+ cout << "It gives a vector of size " << (long unsigned int) v.GetLength() << endl;
+ cout << "having " << (long unsigned int) v.GetBitLength() << " bits" << endl;
+ for (CountWordSize i = 0; i < v.GetLength(); i++) {
+ cout << "v.GetValue(" << (long unsigned int) i << ") = " << (long unsigned int) v.GetValue(i) << endl;
+ }
+
+ cout << "Resize the vector to 10" << endl;
+ v.Resize(10);
+ cout << "It gives a vector of size " << (long unsigned int) v.GetLength();
+ cout << " having " << (long unsigned int) v.GetBitLength() << " bits" << endl;
+ for (CountWordSize i = 0; i < v.GetLength(); i++) {
+ cout << "v.GetValue(" << (long unsigned int) i << ") = " << (long unsigned int) v.GetValue(i) << endl;
+ }
+ cout << "===" << endl << endl;
+
+}
+
+#define TestBV(type1, type2, v) TestBitVectors<type1, type2>((char*) #type1, (char*) #type2, v)
+
+#define GetRUsage(fct, name) \
+ getrusage(RUSAGE_SELF, &usage); \
+ elapsed_utime = usage.ru_utime; \
+ elapsed_stime = usage.ru_stime; \
+ fct; \
+ getrusage(RUSAGE_SELF, &usage); \
+ elapsed_utime.tv_sec = usage.ru_utime.tv_sec - elapsed_utime.tv_sec; \
+ if (usage.ru_utime.tv_usec > elapsed_utime.tv_usec) { \
+ elapsed_utime.tv_usec = usage.ru_utime.tv_usec - elapsed_utime.tv_usec; \
+ } else { \
+ elapsed_utime.tv_sec--; \
+ elapsed_utime.tv_usec = 1000000 - elapsed_utime.tv_usec + usage.ru_utime.tv_usec; \
+ } \
+ elapsed_stime.tv_sec = usage.ru_stime.tv_sec - elapsed_stime.tv_sec; \
+ if (usage.ru_stime.tv_usec > elapsed_stime.tv_usec) { \
+ elapsed_stime.tv_usec = usage.ru_stime.tv_usec - elapsed_stime.tv_usec; \
+ } else { \
+ elapsed_stime.tv_sec--; \
+ elapsed_stime.tv_usec = 1000000 - elapsed_stime.tv_usec + usage.ru_stime.tv_usec; \
+ } \
+ cout << "- " #name ": " << endl; \
+ cout << " - User time: "; \
+ cout << "~ " << (elapsed_utime.tv_sec*1e9 + elapsed_utime.tv_usec*1e3)/nb_tests << " nanosecond by function call" << endl; \
+ cout << " - System time: "; \
+ cout << "~ " << (elapsed_stime.tv_sec*1e9 + elapsed_stime.tv_usec*1e3)/nb_tests << " nanosecond by function call" << endl
+
+int main(int argc, char** argv) {
+ // TestBV(<any>, unsigned char, 2^8/8-1);
+ TestBV(unsigned char, unsigned char, 31);
+ // TestBV(<unsigned short int or more>, unsigned short int, 2^16/16-1);
+ TestBV(unsigned short int, unsigned short int, 4095);
+ // TestBV(<unsigned int or more>, unsigned int, 2^32/32-1);
+ // TestBV(unsigned long int, unsigned long int, 2^64/64-1);
+
+ // TestBV(unsigned char, <unsigned short int or more>, 2^8-1);
+ TestBV(unsigned char, unsigned short int, 255);
+ // TestBV(unsigned short int, <unsigned int or more>, 2^16-1);
+ TestBV(unsigned short int, unsigned long int, 65535);
+ // TestBV(unsigned int, unsigned long int, 2^32-1);
+
+ cout << "Creating a vector of size 1000000000 x 20 bits" << endl;
+ BitVector<unsigned int, unsigned long int> bv(1000000000, 20);
+ cout << "It gives a vector of size " << (long unsigned int) bv.GetLength() << endl;
+ double l = (unsigned long int)bv.GetBitLength();
+ cout << "having " << (unsigned long int) l << " bits";
+ char u = 0;
+ l/=8;
+ while (l/1024 > 1) {
+ l /= 1024;
+ u++;
+ }
+ char unit[] = "?B";
+ switch (u) {
+ case 0:
+ cout << endl;
+ return 0;
+ case 1:
+ unit[0] = 'K';
+ break;
+ case 2:
+ unit[0] = 'M';
+ break;
+ case 3:
+ unit[0] = 'G';
+ break;
+ case 4:
+ unit[0] = 'T';
+ break;
+ default:
+ break;
+ }
+ cout.setf(std::ios::fixed,std::ios::floatfield);
+ cout.precision(1);
+ cout << " (=" << l << unit << ")" << endl;
+
+
+ cout << "Finally comparing performances of OldSetValue and SetValue " << endl;
+
+ const unsigned int nb_tests = 10000000;
+ struct rusage usage;
+ struct timeval elapsed_utime, elapsed_stime;
+ cout << "Statistics (computed on " << nb_tests << " tests / this may take some time):" << endl;
+ unsigned int x;
+ cout.precision(3);
+
+ x = 0;
+ GetRUsage(
+ while (x++ < nb_tests) {
+ unsigned int i = lrand48() % 1000000000;
+ long unsigned int v = lrand48();
+ bv.OldSetValue(i, v);
+ }, OldSetValue);
+
+ x = 0;
+ GetRUsage(
+ while (x++ < nb_tests) {
+ unsigned int i = lrand48() % 1000000000;
+ long unsigned int v = lrand48();
+ bv.SetValue(i, v);
+ }, SetValue);
+
+ x = 0;
+ GetRUsage(
+ while (x++ < nb_tests) {
+ unsigned int i = lrand48() % 1000000000;
+ bv.GetValue(i);
+ }, GetValue);
+
+ cout << "Resize the vector to size 20000 x 13 bits" << endl;
+ bv.CompleteResize(20000, 13);
+ cout << "It gives a vector of size " << (long unsigned int) bv.GetLength() << endl;
+ l = (unsigned long int)bv.GetBitLength();
+ cout << "having " << (unsigned long int) l << " bits";
+ u = 0;
+ l/=8;
+ while (l/1024 > 1) {
+ l /= 1024;
+ u++;
+ }
+ unit[0] = '?';
+ switch (u) {
+ case 0:
+ cout << endl;
+ return 0;
+ case 1:
+ unit[0] = 'K';
+ break;
+ case 2:
+ unit[0] = 'M';
+ break;
+ case 3:
+ unit[0] = 'G';
+ break;
+ case 4:
+ unit[0] = 'T';
+ break;
+ default:
+ break;
+ }
+ cout.setf(std::ios::fixed,std::ios::floatfield);
+ cout.precision(1);
+ cout << " (=" << l << unit << ")" << endl;
+
+ // bv.Clear();
+ for (unsigned int i = 0; i < bv.GetLength(); i++) {
+ unsigned long int n = rand()%8000;
+ bv.OldSetValue(i, n);
+ if (bv.GetValue(i) != n) {
+ cout << "ERROR at bv.GetValue(" << i << ") = " << bv.GetValue(i) << " <> n = " << n<< endl;
+ }
+ bv.SetValue(i, n);
+ if (bv.GetValue(i) != n) {
+ cout << "ERROR at bv.SetValue(" << i << ", " << n <<") = " << bv.GetValue(i) << " <> n = " << n<< endl;
+ }
+ }
+
+ return 0;
+}
+#endif
+#endif
diff --git a/src/libGkArrays/src/bitvector.hxx b/src/libGkArrays/src/bitvector.hxx
new file mode 100644
index 0000000..89a257e
--- /dev/null
+++ b/src/libGkArrays/src/bitvector.hxx
@@ -0,0 +1,159 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef __BITVECTOR_HXX__
+#define __BITVECTOR_HXX__
+
+#include "largebinvect.hxx"
+
+template <typename CountWordSize = unsigned char, typename InnerWordSize = unsigned char>
+class BitVector {
+private:
+ InnerWordSize nb_bits;
+ LargeBinVect<InnerWordSize> data;
+
+public:
+ // Constructors
+ BitVector(const CountWordSize length = 0, const InnerWordSize nb_bits = sizeof(InnerWordSize)*8);
+ BitVector(const BitVector &v);
+
+ // Destructors
+ ~BitVector();
+
+ // Operators
+ inline BitVector &operator=(const BitVector &v);
+
+ // [ReadOnly] Access bit at position i (>= 0, < length)
+ // LargeBinVect<InnerWordSize> operator[](const CountWordSize i) const;
+ inline LargeBinVect<InnerWordSize> operator[](const CountWordSize i) const;
+
+ // mostly equivalent of cast of to operator[]
+ inline unsigned long int GetValue(const CountWordSize i) const;
+
+ // Set value at position i (>= 0, < length) to value (bit-to-bit version)
+ inline BitVector &OldSetValue(const CountWordSize i, const InnerWordSize value);
+
+ // Set value at position i (>= 0, < length) to value
+ inline BitVector &SetValue(const CountWordSize i, const InnerWordSize value);
+
+ // Clear the vector
+ inline BitVector &Clear();
+
+ // Resize the vector according to length and set all new elements to 0 (if any)
+ inline BitVector &Resize(const CountWordSize length);
+
+ // Resize the vector according to length and nb_bits (doesn't clear the values)
+ inline BitVector &CompleteResize(const CountWordSize length, const InnerWordSize nb_bits);
+
+ // Get vector length.
+ inline CountWordSize GetLength() const;
+
+ // Get vector length in bits.
+ inline InnerWordSize GetBitLength() const;
+
+ /**
+ * @param w: the maximal value to be inserted
+ * @return the minimal number of bits to represent w
+ */
+ static InnerWordSize GetMinimalBit(InnerWordSize w);
+};
+
+#include "bitvector.cxx"
+#endif
diff --git a/src/libGkArrays/src/buildTables.cpp b/src/libGkArrays/src/buildTables.cpp
new file mode 100644
index 0000000..512abf5
--- /dev/null
+++ b/src/libGkArrays/src/buildTables.cpp
@@ -0,0 +1,269 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at etud.univ-montp2.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <iostream>
+#include <cstdlib>
+#include <ctime>
+#include <cstring>
+#ifdef HAVE_CONFIG_H
+# include <config.h>
+#endif
+#include <gkArrays.h>
+#include <sys/time.h>
+
+#ifndef ullong
+#define ullong unsigned long long
+#endif
+
+using namespace std;
+using namespace gkarrays;
+
+ullong getChrono() {
+ struct timeval time;
+ time_t sec;
+ suseconds_t usec;
+
+ if (gettimeofday(&time,NULL) != -1) {
+ sec = time.tv_sec;
+ usec = time.tv_usec;
+ return (ullong)sec*1000000+usec;
+ }
+ return 0;
+}
+
+int main(int argc, char **argv) {
+ uint nb_queries = 100;
+ time_t seed = 0;
+ uint nb_threads = 1;
+ bool pairedEnd = false;
+ int param;
+ gkArrays *tags;
+ uint read_length;
+ uint k;
+ bool use_bitvector;
+ bool is_stranded;
+
+
+
+ if (argc < 4) {
+ cerr << "Usage: " << argv[0] << " <file> [-p <paired_end_file>] <read_length> <k> <use_bitvector> <is_stranded> [nb_threads] [nb_queries] [seed]" << endl
+ << " <file> : text file containing the reads in FASTA/FASTQ format. " << endl
+ << " -p <file> : second text file containing the reads in FASTA/FASTQ format for paired-end reads. " << endl
+ << " <read_length> : integer giving the length of the reads." << endl
+ << " <k> : integer setting the length of indexed k-mers." << endl
+ << " <use_bitvector> : specify if we should store the data structures using" << endl
+ << " bit vectors rather than conventionnal arrays" << endl
+ << " (more space efficient, and more time consuming)." << endl
+ << " <is_stranded> : specify if reads are oriented or not." << endl;
+ exit(1);
+ }
+
+ // If -p option we have paired-end reads
+ if(strcmp(argv[2],"-p") == 0) {
+ pairedEnd = true;
+ param = 4;
+ } else {
+ param = 2;
+ }
+ read_length = atoi(argv[param++]);
+ k = atol(argv[param++]);
+ use_bitvector = atol(argv[param++]);
+ is_stranded = atol(argv[param++]);
+ if (argc >= param+1)
+ nb_threads = atol(argv[param++]);
+ if (argc >= param+1)
+ nb_queries = atol(argv[param++]);
+ if (argc >= param+1)
+ seed = atol(argv[param++]);
+
+ ullong start = getChrono();
+ if(pairedEnd) {
+ tags = new gkArrays(argv[1],argv[3], k, use_bitvector, read_length,
+ is_stranded, nb_threads);
+ } else {
+ tags = new gkArrays(argv[1], k, use_bitvector, read_length,
+ is_stranded, nb_threads);
+ }
+ cout << "Creation: " << (getChrono()-start)/1000000. << " s" << endl;
+
+ if (seed == 0)
+ seed = time(NULL);
+
+ srand(seed);
+// srand(seed = time(NULL));
+
+ cout << "Pseudo-randomly choosing "<< nb_queries << " k-mers for the queries" <<endl;
+ cout << "I.e., pseudo-randomly choosing "<< nb_queries << " tag numbers and tag_positions" <<endl;
+ uint *tag_numbers = new uint[nb_queries];
+ uint *tag_positions = new uint[nb_queries];
+ uint nb_tags = tags->getNbTags();
+ for (uint i=0; i < nb_queries; i++) {
+ tag_numbers[i] = rand() % nb_tags;
+ tag_positions[i] = rand() % (tags->getTagLength(tag_numbers[i]) - k + 1);
+ }
+
+ cout << "We have " << tags->getGkCFALength() << " distinct k-mers in the dataset." << endl
+ << endl;
+
+ cout << "Running "<< nb_queries << " queries of type Q1, Q2, Q3, Q4 with a k-mer f." <<endl;
+ cout << "Query 1: what are the reads where f occurs?" << endl;
+
+ start = getChrono();
+ for (uint i=0; i < nb_queries; i++) {
+ uint *matched_tags = tags->getTagNumWithFactor(tag_numbers[i],
+ tag_positions[i]);
+ free(matched_tags);
+ }
+ cout << "Query 1: " << (getChrono()-start)*1./nb_queries << " us" << endl;
+
+ cout << "Query 2: In how many reads does f occur?" << endl;
+
+ start = getChrono();
+ ullong total = 0;
+ for (uint i=0; i < nb_queries; i++) {
+ total += tags->getNbTagsWithFactor(tag_numbers[i],
+ tag_positions[i]);
+ }
+ cout << "Query 2: " << (getChrono()-start)*1./nb_queries << " us" << endl;
+ cout << " (total: " << total << " tags)" << endl;
+
+ cout << "Query 3: What are the occurrence positions of f in the reads?" << endl;
+
+ start = getChrono();
+ for (uint i=0; i < nb_queries; i++) {
+ pair<uint,uint> *matched_tags = tags->getTagsWithFactor(tag_numbers[i],
+ tag_positions[i]);
+ delete [] matched_tags;
+ }
+ cout << "Query 3: " << (getChrono()-start)*1./nb_queries << " us" << endl;
+
+ cout << "Query 4: What is the number of occurrences of f in the reads?" << endl;
+
+ start = getChrono();
+ total = 0;
+ for (uint i=0; i < nb_queries; i++) {
+ total += tags->getNbTagsWithFactor(tag_numbers[i],
+ tag_positions[i],
+ true);
+ }
+ cout << "Query 4: " << (getChrono()-start)*1./nb_queries << " us" << endl;
+ cout << " (total: " << total << " tags)" << endl;
+
+ char *tagFactor = tags->getTagFactor(tag_numbers[0],tag_positions[0],k);
+ cout << tags->getNbTagsWithFactor(tag_numbers[0], tag_positions[0])
+ << " tags share the factor "
+ << tagFactor << " (read " << tag_numbers[0] << ", position "
+ << " " << tag_positions[0] << ")"
+ << " and occurs " << tags->getNbTagsWithFactor(tag_numbers[0],
+ tag_positions[0],
+ true)
+ << " times in total" << endl;
+
+ delete [] tagFactor;
+
+ cout << "Seed used from pseudo-random generation: " << seed << endl;
+
+ delete [] tag_positions;
+ delete [] tag_numbers;
+ delete tags;
+}
diff --git a/src/libGkArrays/src/const.h b/src/libGkArrays/src/const.h
new file mode 100644
index 0000000..c1d71be
--- /dev/null
+++ b/src/libGkArrays/src/const.h
@@ -0,0 +1,119 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef CONST_H
+#define CONST_H
+
+#ifndef THRESHOLD_TO_SORT_BY_INSERTION
+#define THRESHOLD_TO_SORT_BY_INSERTION 50 /* choose sort by insertion instead quick sort for short array of elements */
+#endif
+
+#ifndef MIN_SIZE_FOR_THREAD_CALL
+/**
+ * The minimal range size to enable a recursive call to another thread.
+ * We determine a minimal range size so that we avoid too many calls to
+ * recursive functions
+ */
+#define MIN_SIZE_FOR_THREAD_CALL 8192
+#endif
+
+#endif
diff --git a/src/libGkArrays/src/gkArrays.cpp b/src/libGkArrays/src/gkArrays.cpp
new file mode 100644
index 0000000..4672b34
--- /dev/null
+++ b/src/libGkArrays/src/gkArrays.cpp
@@ -0,0 +1,635 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at etud.univ-montp2.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <algorithm>
+#include <iostream>
+#include <fstream>
+#include <cstdlib>
+#include <cstdio>
+#include <cstring>
+#include <stdexcept>
+#include "basic.h"
+#include "utils.h"
+#include "gkArrays.h"
+#include "gkArraysBuilder.h"
+#include "const.h"
+#include <sys/ioctl.h>
+#ifdef HAVE_LIBPROGRESSBAR
+#include <libProgressBar/progressBar.h>
+#endif
+
+// extern "C" {
+// #include <divsufsort.h>
+// #include <divsufsort64.h>
+// }
+
+
+using namespace std;
+
+namespace gkarrays {
+
+ extern "C" {
+ char *libGkArraysVersion() {
+ return (char*)PACKAGE_VERSION;
+ }
+ }
+
+ ////////////////////////////////////////////////////////////
+
+ bool gkArrays::show_progressbar = false;
+ unsigned int gkArrays::GetNbColumns() {
+ return nb_cols;
+ }
+
+ unsigned int gkArrays::nb_cols = 80;
+ bool gkArrays::ShowProgressBar() {
+ return show_progressbar;
+ }
+
+ ////////////////////////////////////////////////////////////
+
+ bool gkArrays::isDiscarded(uint actual_length, uint theoretical_length, uint k) {
+ return (actual_length < theoretical_length || actual_length < k);
+ }
+
+ gkArrays::gkArrays(char *tags_file, uint threshold, bool use_bitvector,
+ uint tag_length, bool stranded, uint nb_threads,
+ bool show_progressbar)
+ :threshold(threshold), use_bitvector(use_bitvector), tag_length(tag_length),
+ is_stranded(stranded), nb_threads(nb_threads)
+ {
+ gkArrays::show_progressbar = show_progressbar;
+ reads = new readsReader(tags_file,threshold,tag_length);
+ init();
+ }
+
+ gkArrays::gkArrays(char *tags_file1, char *tags_file2, uint threshold, bool use_bitvector,
+ uint tag_length, bool stranded, uint nb_threads,
+ bool show_progressbar)
+ :threshold(threshold), use_bitvector(use_bitvector), tag_length(tag_length),
+ is_stranded(stranded), nb_threads(nb_threads)
+ {
+ gkArrays::show_progressbar = show_progressbar;
+ reads = new readsReader(tags_file1,tags_file2,threshold,tag_length);
+ init();
+ }
+
+ void gkArrays::init() {
+ if (threshold > tag_length && tag_length){
+ cerr << "k-mer length is greater than read length" << endl;
+ exit(9);
+ }
+ uintSA totalLength = 0;
+ is_large = false;
+ nb_tags = 0;
+
+ // Reading reads to know the total length we have.
+ readIterator *it = reads->begin(true);
+ while (!it->isFinished()) {
+ totalLength += (tag_length > 0 ? tag_length : it->getLength());
+ nb_tags++;
+ ++(*it);
+ }
+
+ delete it;
+
+ this->tag_length = tag_length;
+
+ // Initialise the mask which stores the read lengths
+ if (!tag_length){
+ read_lengths = (uint64_t*)Calloc<uint64_t>(nb_digits(totalLength+2, 1));
+ // Add an extra 1 at the beginning
+ bitset(read_lengths,0);
+ // And we also have an extra 0 at the end.
+ }
+
+ if (nb_tags == 0) {
+ cerr << "There is no read in the input file!" << endl;
+ exit(12);
+ }
+
+ alltags = Calloc<uchar>(totalLength + 1);
+ uintSA currentPos = 0;
+ it = reads->begin();
+
+#ifdef HAVE_LIBPROGRESSBAR
+ DoccY::ProgressBar *PB = NULL;
+ unsigned int pb_step = 0;
+ unsigned int pb_refresh = 0;
+ if (show_progressbar) {
+#ifdef TIOCGSIZE
+ struct ttysize ts;
+ nb_cols = ioctl(STDIN_FILENO, TIOCGSIZE, &ts) ? 80 : ts.ts_cols;
+#elif defined(TIOCGWINSZ)
+ struct winsize ts;
+ nb_cols = ioctl(STDIN_FILENO, TIOCGWINSZ, &ts) ? 80 : ts.ws_col;
+#endif /* TIOCGSIZE */
+
+ PB = new DoccY::ProgressBar ("Scanning Reads ", nb_tags, nb_cols, cerr, false);
+ PB->ShowPercent();
+ PB->ShowTime();
+ PB->update();
+ pb_refresh = nb_tags / (nb_cols ? nb_cols : 100);
+ pb_refresh = pb_refresh > 0 ? pb_refresh : 1;
+ }
+#endif
+ // strore each tags in the char array alltags[]
+ while (!it->isFinished()) {
+ if (tag_length) {
+ if (it->getLength() >= tag_length) {
+ strncpy((char *) &(alltags[currentPos]), it->getSequence(),
+ tag_length);
+ currentPos += tag_length;
+ }
+ } else {
+ if (threshold <= it->getLength()) {
+ strncpy((char *) &(alltags[currentPos]), it->getSequence(),
+ it->getLength());
+ currentPos += it->getLength();
+ bitset(read_lengths, currentPos);
+ // read_lengths[currentPos] = 1;
+ }
+ }
+ ++(*it);
+
+#ifdef HAVE_LIBPROGRESSBAR
+ if (show_progressbar) {
+ PB->Step(!(++pb_step % pb_refresh));
+ }
+#endif
+ }
+#ifdef HAVE_LIBPROGRESSBAR
+ if (show_progressbar) {
+ PB->update(false);
+ delete PB;
+ }
+#endif
+
+ delete it;
+ dnaFiltration((char *)alltags, totalLength);
+
+ if (!tag_length){
+ // Create the rank and select structure on the bit vector
+ read_lengths_rank = new rank9b(read_lengths, totalLength+2);
+ read_lengths_select = read_lengths_rank;
+ }
+
+
+ // CR with DNA 2 bits coding
+ for (uintSA i=0; i < totalLength/4; i+=1) {
+ alltags[i] = (uchar)DNAtoInt((char *)&alltags[i*4],4);
+ }
+
+ alltags[totalLength/4] = (uchar)(DNAtoInt((char *)&alltags[(totalLength/4)*4],
+ (totalLength)%4)
+ << (8 - 2*(totalLength%4)));
+
+ alltags = Realloc<uchar>(alltags, totalLength/4+1);
+
+ // Determine what type of arrays we are going to store
+ is_large = (totalLength >= (uint) numeric_limits<uint>::max());
+ array_type type_to_build = (is_large ? LARGE_ARRAY : SMALL_ARRAY);
+ if (use_bitvector)
+ type_to_build = OPTIMAL_ARRAY;
+
+ // Creates the structure
+ GkArraysBuilder gkBuild(alltags,totalLength,threshold,this,type_to_build,nb_threads);
+
+ gkSA = gkBuild.getGkSA();
+ gkISA = gkBuild.getGkIFA();
+ gkCFPS = gkBuild.getGkCFPS();
+ }
+
+ gkArrays::~gkArrays() {
+ free(alltags);
+ if (!tag_length){
+ delete read_lengths_select;
+ // delete read_lengths_rank;
+ free(read_lengths);
+ }
+ delete gkSA;
+ delete gkISA;
+ delete gkCFPS;
+ delete reads;
+ }
+
+ uintSA gkArrays::getEndPosOfTagNum(uint tag_num) {
+ return getStartPosOfTagNum(tag_num) + getTagLength(tag_num) - 1;
+ }
+
+ uintSA gkArrays::getGkCFA(uintSA i) {
+ return (*gkCFPS)[i+1] - (*gkCFPS)[i];
+ }
+
+ uintSA gkArrays::getGkCFALength() {
+ return gkCFPS->length()-1;
+ }
+
+ uintSA gkArrays::getGkISA(uintSA i) {
+ return (*gkISA)[i];
+ }
+
+ uintSA gkArrays::getGkSA(uintSA i) {
+ return (*gkSA)[i];
+ }
+
+ uintSA gkArrays::getGkSALength() {
+ return gkSA->length();
+ }
+
+ uintSA gkArrays::getNbPposition(uintSA nb_reads){
+ return getStartQPosOfTagNum(nb_reads-1)+getTagLength(nb_reads-1)-getThreshold()+1;
+ }
+
+ uint gkArrays::getNbTags(){
+ return nb_tags;
+ }
+
+ uint gkArrays::getNbTagsWithFactor(uint tag_num, uint pos_factor,
+ bool multiplicity){
+ uintSA pos_in_common = getPosInCommon(tag_num,pos_factor);
+ uint nb;
+ nb =(*gkCFPS)[pos_in_common+1] - (*gkCFPS)[pos_in_common];
+ if (multiplicity || nb==1) {
+ return nb;
+ } else {
+ nb = 1;
+ for (uintSA i=(*gkCFPS)[pos_in_common]+1;
+ i < (*gkCFPS)[pos_in_common+1]; i++) {
+ // Do the two positions belong to the same read?
+ if (getTagNum((*gkSA)[i]) != getTagNum((*gkSA)[i-1]))
+ nb++;
+ }
+ }
+ return nb;
+ }
+
+ uint gkArrays::getPair(uint i){
+ if(reads->isPairedEnd()){
+ if(i%2 == 0) return i+1;
+ else return i-1;
+ } else {
+ return -1;
+ }
+ }
+
+ bool gkArrays::isTheFirstMemberOfPair(uint i){
+ if(reads->isPairedEnd()){
+ if(i%2 == 0) return true;
+ else return false;
+ } else {
+ cerr << "Ask for a paired-end function using non-paired-end reads" << endl;
+ return false;
+ }
+ }
+
+ readsReader *gkArrays::getReads() {
+ return reads;
+ }
+
+ uintSA gkArrays::getStartPosOfTagNum(uint tag_num) {
+ if (tag_length){
+ return (uintSA) tag_num * tag_length;
+ }else{
+ // +1 when starting at 1
+ return read_lengths_select->select(tag_num);
+ }
+ }
+
+ uintSA gkArrays::getStartQPosOfTagNum(uint tag_num) {
+ if (tag_length){
+ return (uintSA)tag_num * tag_length - tag_num * (threshold - 1);
+ }else{
+ // tag_num+1 when starting at 1
+ return read_lengths_select->select(tag_num) - tag_num * (threshold - 1);
+ }
+ }
+
+ char *gkArrays::getTag(uint i) {
+ uint this_tag_length = getTagLength(i);
+ uint length_char = this_tag_length+1;
+ char dna[5];
+ char *final_dna = new char[length_char];
+ uint previous_length;
+ uintSA readPos = getStartPosOfTagNum(i);
+ uintSA nextReadPos = readPos + getTagLength(i);
+ dna[4]=0;
+ final_dna[length_char-1] = 0;
+ intToDNA(alltags[readPos/4],4,dna);
+ previous_length = 4-(readPos%4);
+ strncpy(final_dna, &dna[readPos%4], previous_length);
+
+ uint j;
+ for (j=1 ; previous_length+4 <= this_tag_length ; j++) {
+ intToDNA(alltags[readPos/4+j],4,dna);
+ strncpy(&final_dna[previous_length], dna, 4);
+ previous_length+=4;
+ }
+ if (nextReadPos%4 > 0) {
+ intToDNA(alltags[nextReadPos/4], 4, dna);
+ strncpy(&final_dna[previous_length], dna, nextReadPos%4);
+ }
+ return final_dna;
+ }
+
+ char *gkArrays::getTagFactor(uint i, uint p, uint fact_length) {
+ uint length_char = fact_length+1;
+ char dna[5];
+ char *final_dna = new char[length_char];
+ uint previous_length = 0;
+ uintSA readPos = getStartPosOfTagNum(i);
+ dna[4]=0;
+ final_dna[length_char-1] = 0;
+
+ // Retrieving text factors that end a compacted int
+ intToDNA(alltags[(p+readPos)/4],4,dna);
+ // Either we go to the end of the int or we stop before if we want to retrieve a short factor
+ previous_length = (fact_length < 4-((p+readPos)%4) ? fact_length : 4-((p+readPos)%4));
+ strncpy(final_dna, &dna[(p+readPos)%4], previous_length);
+
+ // Retrieving text factors that are fully contained in a compacted int
+ uint j = 0;
+ for (j=1 ; previous_length+4 <= fact_length ; j++) {
+ intToDNA(alltags[(p+readPos)/4+j],4,dna);
+ strncpy(&final_dna[previous_length], dna, 4);
+ previous_length+=4;
+ }
+ // Retrieving factors that are prefix in a compacted int
+ if ((p+fact_length+readPos)%4 > 0 && previous_length < fact_length) {
+ intToDNA(alltags[(p+readPos)/4+j], 4, dna);
+ strncpy(&final_dna[previous_length], dna, (p+fact_length+readPos)%4);
+ }
+ return final_dna;
+ }
+
+ uint gkArrays::getTagNum(uintSA pos) {
+ if (tag_length){
+ return pos/tag_length;
+ }else{
+ return read_lengths_rank->rank(pos+1) - 1;
+ }
+ }
+
+ std::pair<uint, uint> gkArrays::getTagNumAndPosFromAbsolutePos(uintSA pos) {
+ std::pair<uint, uint> result;
+ result.first = getTagNum(pos);
+ result.second = pos - getStartPosOfTagNum(result.first);
+ return result;
+ }
+
+ uint *gkArrays::getTagNumWithFactor(uint tag_num, uint pos_factor) {
+ uintSA pos_in_common = getPosInCommon(tag_num,pos_factor);
+ uintSA nb_init;
+ uint *result;
+ uint nb = 1;
+
+ nb_init = (*gkCFPS)[pos_in_common+1] - (*gkCFPS)[pos_in_common];
+ result = Calloc<uint>(nb_init);
+ result[0] = getTagNum((*gkSA)[(*gkCFPS)[pos_in_common]]);
+ for (uintSA i=(*gkCFPS)[pos_in_common]+1;
+ i < (*gkCFPS)[pos_in_common+1]; i++) {
+ uint tag_num = getTagNum((*gkSA)[i]);
+ if (tag_num != result[nb-1]) {
+ result[nb] = tag_num;
+ nb++;
+ }
+ }
+ if (nb != nb_init) {
+ return Realloc(result, nb);
+ }
+ return result;
+ }
+
+ pair <uint, uint> *gkArrays::getTagsWithFactor(uint tag_num, uint pos_factor){
+ uintSA pos_in_common = getPosInCommon(tag_num,pos_factor);
+ uint nb_fact = getNbTagsWithFactor(tag_num,pos_factor, true);
+ pair <uint, uint> *tagsAndPos = new pair<uint,uint>[nb_fact];
+ uintSA nbc = (*gkCFPS)[pos_in_common];
+ for (uint i = 0 ; i < nb_fact ; i++){
+ if (tag_length){
+ tagsAndPos[i] = pair<uint,uint>((*gkSA)[nbc+i]/tag_length,
+ (*gkSA)[nbc+i]%tag_length);
+ }else{
+ tagsAndPos[i] = getTagNumAndPosFromAbsolutePos((*gkSA)[nbc+i]);
+ }
+ }
+ return tagsAndPos;
+ }
+
+ pair <uint, uint> *gkArrays::getTagsWithFactor(char *factor, uint factor_length
+ , uint &nb_fact) {
+ // Binary search over the suffix array to find the occurrences
+ // Code from Gonzalez and Makinen
+ uintSA left=0;
+ uintSA right = gkSA->length()-1;
+ uintSA currentIndex=(left+right)/2;
+ uintSA min=0;
+ uintSA max=0;
+ char *text_factor;
+ /* Search for the left boundary */
+ while (left < right-1) {
+ text_factor = getTextFactor((*gkSA)[currentIndex], factor_length);
+ if (strcmp(text_factor, factor) >= 0) {
+ right = currentIndex;
+ } else {
+ left = currentIndex;
+ }
+ currentIndex = (right+left)/2;
+ delete [] text_factor;
+ }
+ min=right;
+
+ /* Search for the right boundary */
+ left=min-1;
+ right=gkSA->length()-1;
+ currentIndex=(left+right)/2;
+ while (left < right-1) {
+ text_factor = getTextFactor((*gkSA)[currentIndex], factor_length);
+ if (strcmp(text_factor, factor) <= 0) {
+ left = currentIndex;
+ } else {
+ right = currentIndex;
+ }
+ currentIndex = (right+left)/2;
+ delete [] text_factor;
+ }
+ max=left;
+
+ nb_fact = max-min+1;
+ pair<uint, uint> *occurrences = new pair<uint, uint>[nb_fact];
+ for (uint i=0; i < nb_fact; i++) {
+ occurrences[i] = getTagNumAndPosFromAbsolutePos((*gkSA)[min+i]);
+ }
+
+ return occurrences;
+ }
+
+ uint *gkArrays::getSupport(uint i) {
+ uint this_tag_length = getTagLength(i);
+ uint posMax_tag = this_tag_length-threshold+1;
+ uint *support = new uint[posMax_tag];
+ uintSA startPos_tag = getStartQPosOfTagNum(i);
+ for (uint j=0; j < posMax_tag; j++) {
+ support[j] = (*gkCFPS)[(*gkISA)[j+startPos_tag]+1]
+ - (*gkCFPS)[(*gkISA)[j+startPos_tag]];
+ }
+
+ return support;
+ }
+
+ uint gkArrays::getTagLength(uint i){
+ if (tag_length){
+ return tag_length;
+ }else{
+ // i+2 and i+1 when starting at 1
+ return read_lengths_select->select(i+1)
+ - read_lengths_select->select(i);
+ }
+ }
+
+ char *gkArrays::getTextFactor(uintSA pos, uint length) {
+ std::pair<uint,uint> infos = getTagNumAndPosFromAbsolutePos(pos);
+ return getTagFactor(infos.first,infos.second, length);
+ }
+
+ uint gkArrays::getThreshold(){
+ return threshold;
+ }
+
+ uint gkArrays::getSupportLength(uint i) {
+ return getTagLength(i) - threshold +1;
+ }
+
+ array_type gkArrays::getType(){
+ return gkSA->getType();
+ }
+
+ bool gkArrays::isLarge(){
+ return is_large;
+ }
+
+ bool gkArrays::isPposition(uintSA pos) {
+ if (tag_length){
+ return pos % tag_length <= tag_length - threshold;
+ }else{
+ uint tag_num = getTagNum(pos);
+ // tag_num+2 when starting at 1
+ uintSA end_read = read_lengths_select->select(tag_num + 1);
+ return end_read - pos >= threshold;
+ }
+ }
+
+ bool gkArrays::isStranded(){
+ return is_stranded;
+ }
+
+ uintSA gkArrays::convertPposToQpos(uintSA i) {
+ return i - getTagNum(i) * (threshold - 1);
+ }
+
+ uintSA gkArrays::getPosInCommon(uint tag_num, uint pos_factor){
+ uintSA start_pos = getStartQPosOfTagNum(tag_num);
+ return (*gkISA)[start_pos + pos_factor];
+ }
+}
+
diff --git a/src/libGkArrays/src/gkArrays.h b/src/libGkArrays/src/gkArrays.h
new file mode 100644
index 0000000..fa0d617
--- /dev/null
+++ b/src/libGkArrays/src/gkArrays.h
@@ -0,0 +1,477 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at etud.univ-montp2.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef GKARRAYS_H
+#define GKARRAYS_H
+
+#include <utility>
+#ifdef HAVE_CONFIG_H
+# include <config.h>
+#endif
+#include "gkArraysTypes.h"
+#include "solArray.h"
+
+#include "sux/rank9b.h"
+#include "readsReader.h"
+
+namespace gkarrays {
+
+ extern "C" {
+ /* One can use this function to test the library availability */
+ char *libGkArraysVersion();
+ }
+
+ class gkArrays {
+ private:
+ uchar *alltags;
+ uintSA nb_tags;
+ SolArray *gkSA;
+ SolArray *gkISA;
+ SolArray *gkCFPS;
+
+ uint threshold;
+ bool use_bitvector;
+ uint tag_length;
+ uint64_t *read_lengths;
+ rank9b *read_lengths_select;
+ rank9b *read_lengths_rank;
+
+ readsReader *reads;
+
+ bool is_large;
+ bool is_stranded;
+ uint nb_threads;
+
+ /**
+ * A static variable to control whether progress bar should be displayed or not...
+ */
+ static bool show_progressbar;
+
+ /**
+ * A static variable to store the number of columns for displkay the progress bar...
+ */
+ static unsigned int nb_cols;
+
+ public:
+ /**
+ * Construct the read index
+ *
+ * @param tags_file Name of the file containg the reads
+ * @param threshold length of k-mers we have to use
+ * @param use_bitvector: true iff we must store the array using a bit vector
+ * (slower but more space efficient)
+ * @param tag_length length of the reads. If a shorter read is found,
+ * it raises
+ * an error. If a longer read is found, only the prefix
+ * of tag_length characters is kept.
+ * If tag_length == 0 (default), just gess what the read length
+ * is.
+ * @param stranded: true iff we know which strand has been sequenced and,
+ * therefore, (for instance) AACG must not be considered as equal
+ * to its revcomp (CGTT).
+ * @param nb_threads allows to build GkSA on a multi-thread architecture
+ * @param show_progressbar display a progress bar when building the index
+ */
+ gkArrays(char *tags_file, uint threshold, bool use_bitvector=false, uint tag_length=0, bool stranded=false,uint nb_threads=1, bool show_progressbar = false);
+
+ /**
+ * Alternative to construct the read index with paired-end reads
+ *
+ * @param tags_file1 Name of the file containing the reads of the first pair
+ * @param tags_file2 Name of the file containing the reads of the second pair
+ * @param threshold length of k-mers we have to use
+ * @param use_bitvector: true iff we must store the array using a bit vector
+ * (slower but more space efficient)
+ * @param tag_length length of the reads. If a shorter read is found,
+ * it raises
+ * an error. If a longer read is found, only the prefix
+ * of tag_length characters is kept.
+ * If tag_length == 0 (default), just gess what the read length
+ * is.
+ * @param stranded: true iff we know which strand has been sequenced and,
+ * therefore, (for instance) AACG must not be considered as equal
+ * to its revcomp (CGTT).
+ * @param nb_threads allows to build GkSA on a multi-thread architecture
+ * @param show_progressbar display a progress bar when building the index
+ */
+ gkArrays(char *tags_file1, char *tags_file2, uint threshold, bool use_bitvector=false, uint tag_length=0, bool stranded=false,uint nb_threads=1, bool show_progressbar = false);
+
+ ~gkArrays();
+
+ /**
+ * @return true iff the read is not suitable ie. if it is shorter than
+ * the specified length (if any) or shorter than the specified
+ * k-mer length.
+ */
+ static bool isDiscarded(uint actual_length, uint theoretical_length=0, uint k=0);
+
+ /**
+ * Convert a position from P-position to Q-position
+ * (if you do not understand this, please read our article!).
+ * That converts a position as in the concatenation of reads
+ * to the position in GkIFA (for example).
+ * In the article, values of GkSA are also renumbered to Q-position
+ * but we do not renumber them in practice (it is quite useless).
+ * @param i: a P-position
+ * @return a Q-position
+ */
+ uintSA convertPposToQpos(uintSA i);
+
+ /**
+ * Gives the end position of a given read in the concatenation of reads.
+ * @param tag_num: tag number
+ * @return the end position of the read #tag_num in C_R (the concatenation
+ * of reads)
+ */
+ uintSA getEndPosOfTagNum(uint tag_num);
+
+ /**
+ * @param i the index position in the array (starting at 0).
+ * @return the value of GkCFA at the given index ie. the number of k-factors
+ * of rank i, where i is the requested index.
+ */
+ uintSA getGkCFA(uintSA i);
+
+ /**
+ * @return the number of elements in the GkCFA array. In other terms it
+ * corresponds to the number of distinct k-mers in the input.
+ */
+ uintSA getGkCFALength();
+
+ /**
+ * @param i the index position in the array (starting at 0).
+ * @return the value of GkISA at the given index ie. the rank of the k-factor
+ * at position P-position i.
+ */
+ uintSA getGkISA(uintSA i);
+ /**
+ * @param i the index position in the array (starting at 0).
+ * @return the value of GkSA at the given index ie. the P-position of the
+ * k-factor whose rank is i
+ */
+ uintSA getGkSA(uintSA i);
+
+ /**
+ * @return the number of entries in gkSA (ie. the number of P-positions)
+ */
+ uintSA getGkSALength();
+
+ /**
+ * @return the number of P-positions in Cr from a number of reads (fixed length or not)
+ * This function is available before the construction of gkSA.
+ */
+ uintSA getNbPposition(uintSA nb_reads);
+
+ /**
+ * @return the number of tags (or reads) indexed in the Gk Arrays
+ */
+ uint getNbTags();
+
+ /**
+ * @param tag_num The number of the tag in the index
+ * @param pos_factor Position of the factor in the tag
+ * @param multiplicity Counts (if false) only once a tag
+ * that contains the factor many times
+ * @return Return the number of tags sharing the factor
+ * starting at position pos_factor in the tag
+ * tag_num.
+ * This is the number of elements returned
+ * by the function getTagsWithFactor(.)
+ */
+ uint getNbTagsWithFactor(uint tag_num, uint pos_factor, bool multiplicity=0);
+
+ /**
+ * @return the number of threads the GkArrays have been told to use.
+ * The threads can be used for the construction.
+ */
+ uint getNbThreads();
+
+ /**
+ * @param i The number of the tag in the index
+ * @return the tag number of the paired-end read associated with i
+ * or -1 if reads are not paired-end.
+ */
+ uint getPair(uint i);
+
+ /**
+ * @return the rank of the P-k factor starting at position pos_factor in the
+ * read number tag_num.
+ */
+ uintSA getPosInCommon(uint tag_num,uint pos_factor);
+
+ /**
+ * @return the object that allows to get a readIterator
+ */
+ readsReader *getReads();
+
+ /**
+ * Gives the start position of a given read in the concatenation of reads.
+ * @param tag_num: tag number
+ * @return the start position of the read #tag_num in C_R (the concatenation
+ * of reads)
+ */
+ uintSA getStartPosOfTagNum(uint tag_num);
+
+ /**
+ * Gives the start Q-position of a given read in the ISA array
+ * @param tag_num: tag number
+ * @return the start Q-position of the read #tag_num in GkISA.
+ */
+ uintSA getStartQPosOfTagNum(uint tag_num);
+
+ /**
+ * @param i Tag number
+ * @return an array whose length is getSupportLength(i)
+ * and where the value at position k is the number of occurrences
+ * of the k-factor starting at position k in the reads
+ * among all the Pk-factors.
+ */
+ uint *getSupport(uint i);
+
+ /**
+ * Return the length of the support.
+ * @return getTagLength(i) - getThreshold()+1
+ */
+ uint getSupportLength(uint i=0);
+
+ /**
+ * @param i the read number to be retrieved
+ * @return the read number i.
+ */
+ char *getTag(uint i);
+
+ /**
+ * @param i Tag number (if the length is not constant)
+ * @return the length of the read.
+ */
+ uint getTagLength(uint i=0);
+
+ /**
+ * @param i The number of the tag in the index
+ * @param p Position of the factor in the tag
+ * @param l The length of the factor
+ * @return the factor at the position p in the tag number i
+ */
+ char *getTagFactor(uint i, uint p, uint l);
+
+ /**
+ * Gives the number of a read
+ * @param pos a position in SA or in the concatenated
+ * sequence of reads
+ * @return the read number where this position lies
+ */
+ uint getTagNum(uintSA pos);
+
+ /**
+ * Return the number of tag and the relative position in that tag
+ * corresponding to a given position in the concatenation of reads
+ * @param pos position in the concatenation of reads
+ * @return a pair whose fist element is the tag number and the second
+ * element is the position in the tag.
+ */
+ std::pair<uint, uint> getTagNumAndPosFromAbsolutePos(uintSA pos);
+
+ /**
+ * @param tag_num The number of the tag in the index
+ * @param pos_factor Position of the factor in the tag
+ * @return Return an array that contains each tag number
+ * where the factors matches.
+ * @post The array is sorted
+ */
+ uint *getTagNumWithFactor(uint tag_num, uint pos_factor);
+
+ /**
+ * @param tag_num The number of the tag in the index
+ * @param pos_factor Position of the factor in the tag
+ * @return Return an array composed of pairs
+ * (tag, pos) corresponding to all the Pk-factors
+ * equal to the Pk-factor
+ * starting at position pos_factor in the tag
+ * tag_num.
+ * @post The array is sorted according to read number and read position
+ */
+ std::pair <uint, uint> *getTagsWithFactor(uint tag_num, uint pos_factor);
+
+ /**
+ * @param factor the pattern to be searched.
+ * @param factor_length the length of the factor, should be <= getThreshold()
+ * @param nb_fact nb_fact is used to give the number of occurrences
+ * in the array.
+ * @return Return an array composed of pairs
+ * (tag, pos) corresponding to all the Pk-factors
+ * equal to the k-factor factor
+ */
+ std::pair <uint, uint> *getTagsWithFactor(char *factor, uint factor_length,
+ uint &nb_fact);
+
+ /**
+ * @param pos The position from where we want to retrieve a text subtring.
+ * The position must be given in the original text (not the filtered one).
+ * @param length the length of the substring to be retrieved.
+ * @return text factor at position pos of length length.
+ * The returned string is NULL-terminated.
+ */
+ char *getTextFactor(uintSA pos, uint length);
+
+ /**
+ * @return return the length of the k-factors (ie. return k).
+ */
+ uint getThreshold();
+
+ /**
+ *@return the array type used for building GkSA and GkISA (either
+ * SMALL_ARRAY, LARGE_ARRAY or OPTIMAL_ARRAY).
+ */
+ array_type getType();
+
+ /**
+ *@return true if the nbPposition > 2^32
+ */
+ bool isLarge();
+
+ /**
+ * @return true iff the position does not lie in the threshold - 1
+ * last characters of a read, ie. if it is a P-position.
+ */
+ bool isPposition(uintSA pos);
+
+ /**
+ * @return true iff the GkArrays have been built as a strand-dependant
+ * index. Therefore a k-mer and its revcomp won't be considered
+ * as equal.
+ */
+ bool isStranded();
+
+ /**
+ * @param i the number of the tag in the index
+ * @return true if the tag is the first member of is pair
+ * in case of paired-end files. False either
+ */
+ bool isTheFirstMemberOfPair(uint i);
+
+ /**
+ * This static method return the value of the static show_progressbar boolean value.
+ */
+ static bool ShowProgressBar();
+
+ /**
+ * This static method return the value of the static nb_cols.
+ */
+ static unsigned int GetNbColumns();
+
+ private:
+
+ /**
+ * The function init is called at the end of each constructor
+ * Init() build the gKarrays and related structures
+ */
+ void init();
+
+ };
+
+}
+#endif
+
+// Local Variables:
+// mode:c++
+// End:
diff --git a/src/libGkArrays/src/gkArraysBuilder.cpp b/src/libGkArrays/src/gkArraysBuilder.cpp
new file mode 100644
index 0000000..dd4d22b
--- /dev/null
+++ b/src/libGkArrays/src/gkArraysBuilder.cpp
@@ -0,0 +1,160 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "gkArraysBuilder.h"
+#include "basic.h"
+#include "utils.h"
+#include "solArray.h"
+#include "const.h"
+#include <cstdlib>
+#include <cstring>
+#include <gkSABuilder.h>
+#include <gkCFPSBuilder.h>
+#include <gkIFABuilder.h>
+
+using namespace std;
+
+namespace gkarrays {
+
+ //When nb_kmers < threshold_sorting by insertion is more efficient and quicksort is more efficient otherwise
+ GkArraysBuilder::GkArraysBuilder(unsigned char *cr, uintSA cr_length, int k, gkArrays *gk, array_type type, uint nb_threads){
+
+ uintSA nb_reads=gk->getNbTags();
+ uintSA nb_kmers=gk->getNbPposition(nb_reads);
+ // We allocate nb_kmers+1 just in case the number of kmers
+ // equals the number of distinct buckets (when creating GkCFPS, later)
+ SolArray* values= new SolArray(nb_kmers+1, LARGE_ARRAY);
+
+ // Building GkSA
+ GkSABuilder SAbuild;
+ SAbuild.build(values, cr, cr_length, k, gk, THRESHOLD_TO_SORT_BY_INSERTION, type, nb_threads);
+ gkSA = SAbuild.getGkSA();
+
+
+ // Building GkCFPS
+ GkCFPSBuilder CFPSbuild;
+ // values is realloc-ed by gkCFPS and therefore values doesn't need be
+ // deleted at the end of the function.
+ CFPSbuild.build(values, nb_kmers, type, nb_threads);
+ gkCFPS = CFPSbuild.getGkCFPS();
+
+ // Building GkIFA
+ GkIFABuilder IFAbuild;
+ IFAbuild.build(gk, gkSA, gkCFPS, type, nb_threads);
+ gkIFA = IFAbuild.getGkIFA();
+ }
+
+ GkArraysBuilder::~GkArraysBuilder() {}
+
+ SolArray *GkArraysBuilder::getGkCFPS(){
+ return gkCFPS;
+ }
+
+ SolArray *GkArraysBuilder::getGkIFA(){
+ return gkIFA;
+ }
+
+ SolArray *GkArraysBuilder::getGkSA(){
+ return gkSA;
+ }
+
+}
diff --git a/src/libGkArrays/src/gkArraysBuilder.h b/src/libGkArrays/src/gkArraysBuilder.h
new file mode 100644
index 0000000..bb1d66b
--- /dev/null
+++ b/src/libGkArrays/src/gkArraysBuilder.h
@@ -0,0 +1,141 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef GKARRAYSBUILDER_H
+#define GKARRAYSBUILDER_H
+
+#include "gkArraysTypes.h"
+#include "gkArrays.h"
+#include "solArray.h"
+
+using namespace std;
+
+namespace gkarrays {
+
+class GkArraysBuilder {
+
+ private:
+ SolArray *gkSA;
+ SolArray *gkCFPS;
+ SolArray *gkIFA;
+
+ public:
+ /**
+ * Build the tables of the GkArrays for the input data.
+ * @param cr: the concatenation of reads
+ * @param length: length of the read concatenation
+ * @param k: length of the k-mers
+ * @param gk: gkArrays to be used for computing gkIFA
+ * @param type: the type of array to build
+ * @param nb_threads: the number of threads that can be used
+ */
+ GkArraysBuilder(unsigned char* cr, uintSA length, int k, gkArrays *gk, array_type type, uint nb_threads);
+
+ ~GkArraysBuilder();
+
+
+ SolArray *getGkCFPS();
+ SolArray *getGkIFA();
+ SolArray *getGkSA();
+
+};
+
+}
+#endif
diff --git a/src/libGkArrays/src/gkArraysTypes.h b/src/libGkArrays/src/gkArraysTypes.h
new file mode 100644
index 0000000..87ef4d3
--- /dev/null
+++ b/src/libGkArrays/src/gkArraysTypes.h
@@ -0,0 +1,139 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+/*
+ * =============================================
+ *
+ * $Id: gkArraysTypes.h 736 2011-07-07 15:14:30Z salson $
+ *
+ * =============================================
+ */
+
+#ifndef GKARRAYS_TYPES_H
+#define GKARRAYS_TYPES_H
+
+#include <sys/types.h>
+#ifdef HAVE_CONFIG_H
+# include <config.h>
+#endif
+
+typedef u_int64_t uintSA;
+
+#ifndef __USE_MISC
+typedef u_int32_t uint;
+#endif
+
+#ifndef ulong
+#define ulong uint
+#endif
+
+typedef u_int64_t uint64;
+
+typedef int64_t longint;
+
+typedef u_int8_t byte;
+
+typedef unsigned char uchar;
+
+#endif
+
+// Local Variables:
+// mode:c++
+// End:
diff --git a/src/libGkArrays/src/gkCFPSBuilder.cpp b/src/libGkArrays/src/gkCFPSBuilder.cpp
new file mode 100644
index 0000000..09b42d7
--- /dev/null
+++ b/src/libGkArrays/src/gkCFPSBuilder.cpp
@@ -0,0 +1,180 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <cstdlib>
+#include <pthread.h>
+#include <gkCFPSBuilder.h>
+#include "basic.h"
+#include "utils.h"
+#include "solArray.h"
+#include <iostream>
+#include "gkArrays.h"
+#ifdef HAVE_LIBPROGRESSBAR
+#include <libProgressBar/progressBar.h>
+#endif
+using namespace std;
+
+namespace gkarrays {
+
+ GkCFPSBuilder::GkCFPSBuilder():gkCFPS(NULL) {}
+ GkCFPSBuilder::~GkCFPSBuilder() {}
+
+ void GkCFPSBuilder::build(SolArray *values, uintSA length, array_type t,
+ uint nb_threads){
+
+ // Building GkCFPS
+ gkCFPS = values;
+
+ // It is so quick that we don't need to bother with multithread construction.
+ monothreadConstruction(values, length);
+ }
+
+ SolArray *GkCFPSBuilder::getGkCFPS(){
+ return gkCFPS;
+ }
+
+ void GkCFPSBuilder::monothreadConstruction(SolArray *values, uintSA length) {
+ uintSA bucket_id = ~0;
+ uintSA nb_buckets = 0;
+ uintSA pos_gkCFPS = 0;
+
+#ifdef HAVE_LIBPROGRESSBAR
+ DoccY::ProgressBar *PB = NULL;
+ unsigned int maxval = 0;
+ unsigned int reset_cpt = 0;
+ unsigned int cpt = 0;
+ if (gkArrays::ShowProgressBar()) {
+ maxval = gkArrays::GetNbColumns() ? gkArrays::GetNbColumns() : 100;
+ reset_cpt = length / maxval;
+ PB = new DoccY::ProgressBar ("Building gkCFPS ", maxval, gkArrays::GetNbColumns(), cerr, false);
+ PB->ShowPercent();
+ PB->ShowTime();
+ PB->update();
+ }
+#endif
+
+ for (uintSA i = 0; i < length; i++) {
+ if (values->get(i) != bucket_id) {
+ bucket_id = values->get(i);
+ gkCFPS->set(pos_gkCFPS, nb_buckets);
+ pos_gkCFPS++;
+ }
+ nb_buckets++;
+#ifdef HAVE_LIBPROGRESSBAR
+ if ((cpt++ == reset_cpt) && gkArrays::ShowProgressBar()) {
+ PB->Step();
+ cpt = 0;
+ }
+#endif
+ }
+ gkCFPS->set(pos_gkCFPS, nb_buckets);
+ gkCFPS->realloc(pos_gkCFPS+1);
+#ifdef HAVE_LIBPROGRESSBAR
+ if (gkArrays::ShowProgressBar()) {
+ PB->SetVal(maxval);
+ PB->update(false);
+ cerr << endl;
+ delete PB;
+ }
+#endif
+ }
+}
diff --git a/src/libGkArrays/src/gkCFPSBuilder.h b/src/libGkArrays/src/gkCFPSBuilder.h
new file mode 100644
index 0000000..3ecfefc
--- /dev/null
+++ b/src/libGkArrays/src/gkCFPSBuilder.h
@@ -0,0 +1,146 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef GKCFPS_BUILDER_H
+#define GKCFPS_BUILDER_H
+
+#include "basic.h"
+#include "utils.h"
+#include "solArray.h"
+#include <cstdlib>
+#include <pthread.h>
+
+using namespace std;
+
+namespace gkarrays {
+
+ class GkCFPSBuilder {
+ private:
+ SolArray *gkCFPS;
+
+ void monothreadConstruction(SolArray *values, uintSA length);
+
+ public :
+
+ GkCFPSBuilder() ;
+ ~GkCFPSBuilder() ;
+
+ /**
+ * Build a GkCFPS
+ * @param values: a sorted array containing k-mer integer values
+ * @param length: length of the array values (number of elements)
+ * @param t: the type of array to build
+ * @param nb_threads: the number of threads that can be used
+ */
+ void build(SolArray *values, uintSA length, array_type t,
+ uint nb_threads=1);
+
+ /**
+ * @return the last GkCFPS that has been built
+ */
+ SolArray *getGkCFPS();
+
+ };
+
+}
+
+#endif
diff --git a/src/libGkArrays/src/gkIFABuilder.cpp b/src/libGkArrays/src/gkIFABuilder.cpp
new file mode 100644
index 0000000..740dade
--- /dev/null
+++ b/src/libGkArrays/src/gkIFABuilder.cpp
@@ -0,0 +1,202 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <cstdlib>
+#include <pthread.h>
+#include <gkIFABuilder.h>
+#include "basic.h"
+#include "utils.h"
+#include "solArray.h"
+#ifdef HAVE_LIBPROGRESSBAR
+#include <libProgressBar/progressBar.h>
+#endif
+
+using namespace std;
+
+namespace gkarrays {
+
+ GkIFABuilder::GkIFABuilder():gkIFA(NULL) {}
+ GkIFABuilder::~GkIFABuilder() {}
+
+ void GkIFABuilder::build(gkArrays *gk, SolArray *gkSA, SolArray *gkCFPS,
+ array_type t, uint nb_threads){
+ uintSA nb_kmers = gkSA->length();
+ struct ifa_builder_thread ibt[nb_threads];
+ pthread_t threads[nb_threads];
+ // Building GkIFA
+ gkIFA = new SolArray(nb_kmers, t);
+
+ // Monothread and multithread are equivalent
+ for (uint i = 0; i < nb_threads; i++) {
+ ibt[i].gk = gk;
+ ibt[i].gkSA = gkSA;
+ ibt[i].gkCFPS = gkCFPS;
+ ibt[i].gkIFA = gkIFA;
+ ibt[i].thread_id = i;
+ ibt[i].nb_threads = nb_threads;
+
+ pthread_create(&threads[i], NULL, thread_work_ifa, (void *)&ibt[i]);
+ }
+
+ for (uint i = 0; i < nb_threads; i++) {
+ pthread_join(threads[i], NULL);
+ }
+ }
+
+ SolArray *GkIFABuilder::getGkIFA(){
+ return gkIFA;
+ }
+
+ void *thread_work_ifa(void *data) {
+ struct ifa_builder_thread *ibt = (struct ifa_builder_thread *)data;
+ gkArrays *gk = ibt->gk;
+ SolArray *gkSA = ibt->gkSA;
+ SolArray *gkCFPS = ibt->gkCFPS;
+ SolArray *gkIFA = ibt->gkIFA;
+ uintSA len_gkCFPS = gkCFPS->length();
+ uintSA pos_gkCFPS = 1 + ibt->thread_id * (len_gkCFPS / ibt->nb_threads);
+ uintSA end = pos_gkCFPS + len_gkCFPS / ibt->nb_threads;
+ uintSA i = gkCFPS->get(pos_gkCFPS - 1);
+
+ if (ibt->thread_id == ibt->nb_threads - 1)
+ end = len_gkCFPS;
+
+#ifdef HAVE_LIBPROGRESSBAR
+ DoccY::ProgressBar *PB = NULL;
+ unsigned int maxval = 0;
+ unsigned int reset_cpt = 0;
+ unsigned int cpt = 0;
+ bool show_pb = !ibt->thread_id && gkArrays::ShowProgressBar();
+ if (show_pb) {
+ maxval = gkArrays::GetNbColumns() ? gkArrays::GetNbColumns() : 100;
+ reset_cpt = (end - pos_gkCFPS) / maxval;
+ PB = new DoccY::ProgressBar ("Building IFA ", maxval, gkArrays::GetNbColumns(), cerr, false);
+ PB->ShowPercent();
+ PB->ShowTime();
+ PB->update();
+ }
+#endif
+ while (pos_gkCFPS < end) {
+ uintSA nb_in_bucket = gkCFPS->get(pos_gkCFPS) - gkCFPS->get(pos_gkCFPS-1);
+ for (uintSA j = 0; j < nb_in_bucket; j++) {
+ gkIFA->set(gk->convertPposToQpos(gkSA->get(i+j)), pos_gkCFPS - 1);
+ }
+ pos_gkCFPS++;
+ i += nb_in_bucket;
+#ifdef HAVE_LIBPROGRESSBAR
+ if ((cpt++ == reset_cpt) && show_pb) {
+ PB->Step();
+ cpt = 0;
+ }
+#endif
+ }
+
+#ifdef HAVE_LIBPROGRESSBAR
+ if (show_pb) {
+ PB->SetVal(maxval);
+ PB->update(false);
+ delete PB;
+ }
+#endif
+ return NULL;
+ }
+}
diff --git a/src/libGkArrays/src/gkIFABuilder.h b/src/libGkArrays/src/gkIFABuilder.h
new file mode 100644
index 0000000..96d1f53
--- /dev/null
+++ b/src/libGkArrays/src/gkIFABuilder.h
@@ -0,0 +1,154 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef GKIFA_BUILDER_H
+#define GKIFA_BUILDER_H
+
+#include "solArray.h"
+#include <gkArrays.h>
+
+namespace gkarrays {
+
+ struct ifa_builder_thread {
+ gkArrays *gk;
+ SolArray *gkSA;
+ SolArray *gkCFPS;
+ SolArray *gkIFA;
+ uint thread_id; /* ID of the thread (start at 0) */
+ uint nb_threads; /* Number of working threads */
+ };
+
+ class GkIFABuilder {
+ private:
+ SolArray *gkIFA;
+
+ public :
+
+ GkIFABuilder() ;
+ ~GkIFABuilder() ;
+
+ /**
+ * Build a GkIFA
+ * @param gk: gkArrays to be used for computing gkIFA
+ * @param gkSA: gkSA to be used for computing gkIFA
+ * @param gkCFPS: gkCFPS to be used for computing gkIFA
+ * @param t: the type of array to build
+ * @param nb_threads: the number of threads that can be used
+ */
+ void build(gkArrays *gk, SolArray *gkSA, SolArray *gkCFPS, array_type t,
+ uint nb_threads=1);
+
+ /**
+ * @return the last GkIFA that has been built
+ */
+ SolArray *getGkIFA();
+
+ };
+
+ /**
+ * Work done by a thread: the computation of a range in GkIFA
+ */
+ void *thread_work_ifa(void *data);
+
+}
+
+#endif
diff --git a/src/libGkArrays/src/gkSABuilder.cpp b/src/libGkArrays/src/gkSABuilder.cpp
new file mode 100644
index 0000000..ed8e5f1
--- /dev/null
+++ b/src/libGkArrays/src/gkSABuilder.cpp
@@ -0,0 +1,486 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at etud.univ-montp2.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <gkSABuilder.h>
+#include "basic.h"
+#include "utils.h"
+#include "solArray.h"
+#include <cstdlib>
+#include <cstdio>
+#include <cstring>
+#include <iostream>
+#include <stdexcept>
+#include <pthread.h>
+#include <errno.h>
+#include <gkCFPSBuilder.h>
+#include <gkIFABuilder.h>
+#include <const.h>
+#ifdef HAVE_LIBPROGRESSBAR
+#include <libProgressBar/progressBar.h>
+uintSA PB_thread_master_start_pos = 0;
+#endif
+
+using namespace std;
+
+namespace gkarrays {
+
+ GkSABuilder::GkSABuilder():gkSA(NULL){}
+
+ //When nb_kmers < threshold_sorting by insertion is more efficient and
+ //quicksort is more efficient otherwise
+ void GkSABuilder::build(SolArray *values, unsigned char *cr, uintSA cr_length,
+ int k, gkArrays *gk, int threshold_sort, array_type type, uint nb_threads){
+
+ uintSA nb_reads=gk->getNbTags();
+ uintSA nb_kmers=gk->getNbPposition(nb_reads);
+
+ // Creates the structure
+ gkSA = new SolArray(nb_kmers, cr_length, type);
+
+ // Building GkSA
+ // gkSA is divided by nb_threads
+ pthread_t T[nb_threads];
+ uintSA start=0;
+ uintSA step=nb_reads/nb_threads;
+ subGkSA sgkSA[nb_threads];
+ void *fus;
+
+ // We just initialize SA with an increasing sequence of numbers (ie. after
+ // that gkSA[i] == i) and values with the corresponding values. After
+ // that, values[i] == the integer value of the k-mer starting at
+ // P-position i
+ for(uintSA i=0;i<nb_threads-1;i++){
+ sgkSA[i].cr = cr;
+ sgkSA[i].gkSA = gkSA;
+ sgkSA[i].values = values;
+ sgkSA[i].k = k;
+ sgkSA[i].gk = gk;
+ sgkSA[i].start = gk->getStartPosOfTagNum(start);
+ sgkSA[i].end = gk->getEndPosOfTagNum(start+step);
+ sgkSA[i].offset = gk->getStartQPosOfTagNum(i*step);
+ pthread_create(&T[i], NULL, calc_gkSASubPart, (void *)&sgkSA[i]);
+ start=start+step;
+ }
+
+ // Plus the final one.
+ subGkSA s;
+ s.cr = cr;
+ s.gkSA = gkSA;
+ s.values = values;
+ s.k = k;
+ s.gk = gk;
+ s.start = gk->getStartPosOfTagNum(start);
+ s.end = cr_length-1;
+ s.offset = gk->getStartQPosOfTagNum((nb_threads-1)*step);
+ pthread_create(&T[nb_threads-1], NULL, calc_gkSASubPart, (void*)&s);
+
+ // Wait for them to finish their job
+ for(uint i=0;i<nb_threads;i++){
+ pthread_join(T[i], &fus);
+ }
+
+ sem_t thread_semaphore; // Semaphore used for counting the number of
+ // threads launched and for avoiding launching
+ // more threads than needed.
+ if (sem_init(&thread_semaphore, 0, nb_threads-1) == -1) {
+ perror("Semaphore initialization for multi-threading\n");
+ exit(2);
+ }
+
+#ifdef HAVE_LIBPROGRESSBAR
+ clock_t start_sort = clock();
+ int width = (gkArrays::GetNbColumns() ? gkArrays::GetNbColumns() : 100);
+ if (gkArrays::ShowProgressBar()) {
+ cerr << "Sorting SA [This may take a while"
+ << setw(width - 54)
+ << setfill('.') << "]"
+ << setw(width - 1) << setfill('\b') << '\b' << flush;
+ }
+#endif
+ quickSort(gkSA,values,0,nb_kmers-1,threshold_sort,&thread_semaphore, true);
+ // The current thread is going to wait, so we say that we have another
+ // thread free for computations
+ sem_post(&thread_semaphore);
+
+ int val = 0;
+ useconds_t delay = 1000;
+ // Wait for all the threads to finish
+ while (val < (int)nb_threads) {
+ sem_getvalue(&thread_semaphore, &val);
+ usleep(delay);
+ if (delay < 100000)
+ delay *= 2;
+ }
+#ifdef HAVE_LIBPROGRESSBAR
+ if (gkArrays::ShowProgressBar()) {
+ double temps = (clock() - start_sort)/double(CLOCKS_PER_SEC);
+ stringstream tps;
+ tps << " 100 % (";
+ if (temps < 60.0) {
+ tps.precision((temps < 10.0)?2:1);
+ tps.setf(stringstream::fixed,stringstream::floatfield);
+ tps << temps << "s";
+ } else {
+ tps.precision(0);
+ if (temps < 3600.0) {
+ tps << int(temps)/60 << "m"
+ << setfill('0') << setw(2) << int(temps)%60;
+ } else {
+ if (temps < 86400.0) {
+ tps << int(temps)/3600 << "h"
+ << setfill('0') << setw(2) << int(temps)%3600/60;
+ } else {
+ tps << int(temps)/86400 << "d"
+ << setfill('0') << setw(2) << int(temps)%86400/3600;
+ }
+ }
+ }
+ tps << ")";
+ cerr << "Sorting SA ["
+ << setw(width - 19 - tps.str().length())
+ << setfill('=') << "]" << tps.str() << endl;
+ }
+#endif
+
+ }
+
+ GkSABuilder::~GkSABuilder() {}
+
+ SolArray *GkSABuilder::getGkSA(){
+ return gkSA;
+ }
+
+ //PRIVATE
+
+ //tri rapide f est le seuil pour lancer le tri par insertion, r est le nombre de thread deja lancés et t est le nombre de thread max
+ void quickSort(SolArray *sa, SolArray *values, int64_t start, int64_t end,
+ int threshold_sort, sem_t *s_threads, bool is_threaded){
+ if(start>=end){
+ return;
+ }
+ if((end-start)<threshold_sort){
+ insertion_sort(sa,values,start,end);
+ return;
+ }
+ // Choose the pivot
+ uintSA pivot=start + (rand() % (end - start + 1));
+ // Partition the array.
+ int64_t m=partition(sa,values,start,end,pivot);
+
+ pthread_t thread, thread2;
+ qs *valeur = (qs*)malloc(sizeof(qs)), *valeur2 = (qs*)malloc(sizeof(qs)),
+ *biggest, *smallest, *remaining;
+ init_qs_ptr(valeur, sa, values, m+1, end, threshold_sort, s_threads);
+ init_qs_ptr(valeur2, sa, values, start, m-1, threshold_sort, s_threads);
+
+ // In which part do we have more work?
+ if (end - m > m - start) {
+ biggest = valeur;
+ smallest = valeur2;
+ } else {
+ biggest = valeur2;
+ smallest = valeur;
+ }
+
+ if (smallest->end - smallest->start < MIN_SIZE_FOR_THREAD_CALL ||
+ sem_trywait(s_threads) == -1) {
+ quickSort(sa, values, smallest->start, smallest->end, threshold_sort,
+ s_threads);
+ remaining = biggest;
+ free(smallest);
+ } else {
+ pthread_create(&thread, NULL, quickSortT, (void*)biggest);
+ // Let the thread go, we won't join it, otherwise that poses
+ // some difficult challenges to wait for the threads while not
+ // counting a resource (a thread) for that task (waiting).
+ pthread_detach(thread);
+ remaining = smallest;
+ }
+
+ if (remaining->end - remaining->start < MIN_SIZE_FOR_THREAD_CALL ||
+ sem_trywait(s_threads) == -1) {
+ quickSort(sa, values, remaining->start, remaining->end, threshold_sort,
+ s_threads);
+ free(remaining);
+ } else {
+ pthread_create(&thread2, NULL, quickSortT, (void*)remaining);
+ pthread_detach(thread2);
+ }
+
+ }
+
+ void* quickSortT(void* data){
+ qs *dat=(qs *)data;
+ quickSort(dat->gkSA,dat->values, dat->start, dat->end,dat->threshold_sort,dat->s_threads, true);
+ // If we launched that quicksort in a new thread, we can tell that
+ // it is done. Indeed, we have nothing else to do!
+ sem_post(dat->s_threads);
+ free(dat);
+ return 0;
+ }
+
+
+
+ //partitionne le tableau et renvoie la position du pivot
+ int64_t partition(SolArray *sa,SolArray *values,uintSA start, uintSA end,uintSA p){
+ uintSA i = start;
+ uintSA j = end+1;
+ uintSA pivotv=values->get(p);
+ uintSA pivotp=sa->get(p);
+ uintSA tmp;
+ swap(sa,values,p,start);
+ while(true)
+ {do{
+ j--;
+ }
+ while(((j >= start) && (pivotv < values->get(j))) || ((pivotv==values->get(j)) && (pivotp<sa->get(j))));
+ do{
+ i++;
+ }
+ while(i <= end && values->get(i) < pivotv||((pivotv==values->get(i)) &&(pivotp>sa->get(i))));
+ if(i<j)
+ {
+ tmp = values->get(i);
+ values->set(i, values->get(j));
+ values->set(j,tmp);
+ tmp = sa->get(i);
+ sa->set(i,sa->get(j));
+ sa->set(j,tmp);
+ }
+ else{
+ swap(sa,values,j,start);
+ return j;
+ }
+ }
+ return 0;
+ }
+
+
+ void insertion_sort(SolArray *sa , SolArray *values, int64_t &start, int64_t &end){
+ int64_t i, j;
+ for (i = start; i <= end; ++i) {
+ uintSA elem2=sa->get(i);
+ uintSA elem = values->get(i);
+ for (j = i; j > 0 && (values->get(j-1) > elem||(values->get(j-1)==elem&&sa->get(j-1)>elem2)); j--){
+ values->set(j,values->get(j-1));
+ sa->set(j,sa->get(j-1));
+ }
+ values->set(j,elem);
+ sa->set(j,elem2);
+ }
+ }
+
+ //return the value at pos p on the strand forward
+ uintSA vals(uintSA p,unsigned char dna[],int k,int64_t *last,uintSA *valfwd, uintSA *valrev){
+ int e=p-*last;
+ if(e!=1){
+ *last=p;
+ *valfwd = factorsToInt(p, dna, k);
+ }else{
+ // Compute the new value from the previous one.
+ uintSA np=(p+k-1)/4;
+ int rp=(p+k-1)%4;
+ uintSA m=1;
+ *valfwd%=m<<(2*k-2);
+ *valfwd<<=2;
+ int i=dna[np]%(1<<(8-2*rp));
+ i/=(1<<(6-2*rp));
+ *valfwd+=i;
+ *last=p;
+ }
+ return *valfwd;
+ }
+
+ //return the minumum value of the k-mer at pos p between strand rev and stran fwd
+ uintSA valns(uintSA p, unsigned char dna[],int k,int64_t *last,uintSA *valfwd,uintSA *valrev){
+ int e=p-*last;
+ if(e!=1){
+ *last=p;
+ *valfwd=factorsToInt(p, dna, k);
+ *valrev=intRevcomp(*valfwd, k);
+ }else{
+ // Compute the new value from the previous one.
+ uintSA np=(p+k-1)/4;
+ int rp=(p+k-1)%4;
+ uintSA m=1;
+ *valfwd%=m<<(2*k-2);
+ *valfwd<<=2;
+ int i=dna[np]%(1<<(8-2*rp));
+ i/=(1<<(6-2*rp));
+ *valfwd+=i;
+ *last=p;
+ *valrev/=1<<(2);
+ *valrev+=complementaryNuc(i)<<(2*k-2);
+ }
+ return min(*valfwd,*valrev);
+ }
+
+
+ //compute gkSA values on a subpart depending on a function given as parameter
+ void *calc_gkSASubPart(void *data) {
+ subGkSA sgkSA=*(subGkSA *)data;
+ uintSA gkSA_pos = sgkSA.offset;
+ uintSA valrev,valfwd;
+ int64_t last(-3);
+ bool isPairedEnd = sgkSA.gk->getReads()->isPairedEnd();
+ bool isStranded = sgkSA.gk->isStranded();
+
+#ifdef HAVE_LIBPROGRESSBAR
+ bool show_pb = (gkSA_pos == PB_thread_master_start_pos) && gkArrays::ShowProgressBar();
+ DoccY::ProgressBar *PB = NULL;
+ unsigned int maxval = 0;
+ unsigned int reset_cpt = 0;
+ unsigned int cpt = 0;
+ if (show_pb) {
+ maxval = gkArrays::GetNbColumns() ? gkArrays::GetNbColumns() : 100;
+ reset_cpt = (sgkSA.end - sgkSA.start) / maxval;
+ PB = new DoccY::ProgressBar ("Building SA ", maxval, gkArrays::GetNbColumns(), cerr, false);
+ PB->ShowPercent();
+ PB->ShowTime();
+ PB->update();
+ }
+#endif
+
+ for(uintSA i=sgkSA.start;i<sgkSA.end;i++){
+ if(sgkSA.gk->isPposition(i)){
+ if(isStranded) {
+ if(isPairedEnd && sgkSA.gk->isTheFirstMemberOfPair(sgkSA.gk->getTagNum(i))) {
+ valns(i,sgkSA.cr, sgkSA.k, &last,&valfwd,&valrev);
+ sgkSA.values->set(gkSA_pos,valrev);
+ } else {
+ sgkSA.values->set(gkSA_pos,vals(i,sgkSA.cr, sgkSA.k, &last,&valfwd,&valrev));
+ }
+ } else {
+ sgkSA.values->set(gkSA_pos,valns(i,sgkSA.cr, sgkSA.k, &last,&valfwd,&valrev));
+ }
+ sgkSA.gkSA->set(gkSA_pos,i);
+ gkSA_pos++;
+ }
+#ifdef HAVE_LIBPROGRESSBAR
+ if ((cpt++ == reset_cpt) && show_pb) {
+ PB->Step();
+ cpt = 0;
+ }
+#endif
+ }
+
+#ifdef HAVE_LIBPROGRESSBAR
+ if (show_pb) {
+ PB->SetVal(maxval);
+ PB->update(false);
+ delete PB;
+ }
+#endif
+ return 0;
+ }
+
+ void init_qs_ptr(struct qs *data, SolArray *sa, SolArray *val, int64_t start,
+ int64_t end, int threshold_sort, sem_t *s_threads) {
+ data->gkSA = sa;
+ data->values = val;
+ data->start = start;
+ data->end = end;
+ data->threshold_sort = threshold_sort;
+ data->s_threads = s_threads;
+ }
+}
diff --git a/src/libGkArrays/src/gkSABuilder.h b/src/libGkArrays/src/gkSABuilder.h
new file mode 100644
index 0000000..e0d2728
--- /dev/null
+++ b/src/libGkArrays/src/gkSABuilder.h
@@ -0,0 +1,242 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at etud.univ-montp2.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef GKSABUILDER_H
+#define GKSABUILDER_H
+
+#include "gkArraysTypes.h"
+#include "gkArrays.h"
+#include "solArray.h"
+#include <semaphore.h>
+
+using namespace std;
+
+namespace gkarrays {
+
+struct qs
+{
+ SolArray *gkSA;
+ SolArray *values;
+ int64_t start;
+ int64_t end;
+ int threshold_sort;
+ sem_t *s_threads;
+};
+
+/**
+ * Initializes a pointer to a qs data structure.
+ */
+ void init_qs_ptr(struct qs *data, SolArray *sa, SolArray *val, int64_t start,
+ int64_t end, int threshold_sort, sem_t *s_threads);
+
+struct subGkSA
+{
+ //general features
+ unsigned char *cr;
+ SolArray *gkSA;
+ SolArray *values;
+ int m;
+ int k;
+ gkArrays *gk;
+ //subGkSA features
+ uintSA start;
+ uintSA end;
+ uintSA offset;
+};
+
+class GkSABuilder {
+
+ private:
+ SolArray *gkSA;
+
+ public:
+
+ GkSABuilder();
+ ~GkSABuilder();
+
+ /**
+ * Build a GkSA
+ * @param values: array storing the integer values of the k-mers
+ * @param cr: the concatenation of reads
+ * @param length: length of the read concatenation
+ * @param k: length of the k-mers
+ * @param gk: gkArrays to be used for computing gkIFA
+ * @param threshold_sort: threshold below which an insertion sort is performed
+ * rather than a quicksort
+ * @param type: the type of SolArray to build
+ * @param nb_threads: the number of threads that can be used
+ */
+ void build(SolArray *values, unsigned char* cr, uintSA length, int k,
+ gkArrays *gk, int threshold_sort,
+ array_type type, uint nb_threads);
+
+ /**
+ * @return the last GkSA that has been built.
+ */
+ SolArray *getGkSA();
+
+};
+
+/**
+ * Sort the elements in sa according to the values stored in values. Both arrays are sorted at the same time
+ * (actually the operations performed on values are also performed on sa).
+ * @param sa: the array to be sorted, its values are not used for sorting
+ * @param values: the array whose values are used for sorting
+ * @param start: where to start the sort in the input arrays.
+ * @param end: where the sort should end in the input arrays.
+ * @param threshold_sort: Threshold below which an insertion sort is used rather than a quicksort.
+ * Insertion sort is quicker for small arrays. TODO: replace insertion sort by heapsort.
+ * @param s_threads: the semaphore for the threads
+ */
+ void quickSort(SolArray *sa, SolArray values[], int64_t start, int64_t end,int threshold_sort,sem_t *s_threads, bool is_threaded=false);
+
+/**
+ * The function called by each thread when they're created.
+ * This function then direcly calls the function quickSort with the values
+ * stored in the data parameter.
+ * @return NULL
+ */
+void* quickSortT(void* data);
+
+/**
+ * Partition step in quicksort algorithm
+ * @param sa: the arrays to be sorted, but its values are not considered for sorting
+ * @param values: the arrays to be sorted, the exact same operations are performed on sa
+ * @param start: start pos.
+ * @param end: end pos.
+ * @param p: Pivot value.
+ * @return the pivot's position in the array values.
+ */
+int64_t partition(SolArray *sa,SolArray *values,uintSA start, uintSA end,uintSA p);
+
+/**
+ * Performs an insertion sort on the given arrays, at the given start and end
+ * positions
+ */
+void insertion_sort(SolArray *sa , SolArray *values, int64_t &start, int64_t &end);
+
+//return the value at pos p on the strand forward
+//the last parameter is just for the compatibility with valns
+uintSA vals(uintSA p,unsigned char dna[],int k,int64_t *last,uintSA *valfwd, uintSA *val=NULL);
+
+ //return the minumum value of the k-mer at pos p between strand rev and stran fwd
+uintSA valns(uintSA p, unsigned char dna[],int k,int64_t *last,uintSA *valfwd,uintSA *valrev);
+
+// It is a function that is common to calcs and calcns
+// It performs all the computations for putting the values in GkSA, and dedicates
+// the GkSA value calculation to the function given in parameter
+ void *calc_gkSASubPart(void *data);
+
+ inline void swap(SolArray *sa,SolArray *values, uintSA &a, uintSA &b){
+ if(a!=b){
+ uintSA temp = values->get(a);
+ uintSA temp2= sa->get(a);
+ values->set(a, values->get(b));
+ values->set(b, temp);
+ sa->set(a,sa->get(b));
+ sa->set(b,temp2);
+ }
+ }
+
+}
+#endif
diff --git a/src/libGkArrays/src/kseq/Makefile.am b/src/libGkArrays/src/kseq/Makefile.am
new file mode 100644
index 0000000..a4de908
--- /dev/null
+++ b/src/libGkArrays/src/kseq/Makefile.am
@@ -0,0 +1,113 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thierry LECROQ <thierry.lecroq at univ-rouen.fr> #
+# Martine LÉONARD <Martine.Leonard at univ-rouen.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie de la librairie Gk-arrays. #
+# #
+# La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de #
+# lectures de séquences issues du séquençage haut-débit. #
+# #
+# Ce logiciel est régi par la licence CeCILL-C soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL-C, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the Gk-arrays library. #
+# #
+# The Gk-arrays library aims at indexing k-factors from a huge set of #
+# sequencing reads. #
+# #
+# This software is governed by the CeCILL-C license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL-C #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL-C license and that you accept its terms. #
+# #
+###############################################################################
+#
+# $Id: Makefile.am 215 2011-02-14 14:39:11Z salson $
+#
+###############################################################################
+
+kseqdir = $(includedir)/@PACKAGE at -@VERSION@/kseq
+kseq_HEADERS = kseq.h
+# EXTRA_DIST=kseq.h
+
+MOSTLYCLEANFILES=*~
+CLEANFILES=*~
+DISTCLEANFILES=*~
+MAINTAINERCLEANFILES=*~
diff --git a/src/libGkArrays/src/kseq/Makefile.in b/src/libGkArrays/src/kseq/Makefile.in
new file mode 100644
index 0000000..4399b8e
--- /dev/null
+++ b/src/libGkArrays/src/kseq/Makefile.in
@@ -0,0 +1,577 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thierry LECROQ <thierry.lecroq at univ-rouen.fr> #
+# Martine LÉONARD <Martine.Leonard at univ-rouen.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie de la librairie Gk-arrays. #
+# #
+# La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de #
+# lectures de séquences issues du séquençage haut-débit. #
+# #
+# Ce logiciel est régi par la licence CeCILL-C soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL-C, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the Gk-arrays library. #
+# #
+# The Gk-arrays library aims at indexing k-factors from a huge set of #
+# sequencing reads. #
+# #
+# This software is governed by the CeCILL-C license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL-C #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL-C license and that you accept its terms. #
+# #
+###############################################################################
+#
+# $Id: Makefile.am 215 2011-02-14 14:39:11Z salson $
+#
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+ mostlyclean-libtool pdf pdf-am ps ps-am tags uninstall \
+ uninstall-am uninstall-kseqHEADERS
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/src/libGkArrays/src/kseq/kseq.h b/src/libGkArrays/src/kseq/kseq.h
new file mode 100644
index 0000000..a8565e0
--- /dev/null
+++ b/src/libGkArrays/src/kseq/kseq.h
@@ -0,0 +1,229 @@
+/* The MIT License
+
+ Copyright (c) 2008, by Heng Li <lh3 at sanger.ac.uk>
+ 2011, by Mikael Salson <mikael.salson at lifl.fr>
+ (added the ability to read raw files)
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+#ifndef AC_KSEQ_H
+#define AC_KSEQ_H
+
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+
+#define __KS_TYPE(type_t) \
+ typedef struct __kstream_t { \
+ char *buf; \
+ int begin, end, is_eof; \
+ type_t f; \
+ char type; \
+ } kstream_t;
+
+#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
+#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
+
+#define __KS_BASIC(type_t, __bufsize) \
+ static inline kstream_t *ks_init(type_t f) \
+ { \
+ kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
+ ks->f = f; \
+ ks->buf = (char*)malloc(__bufsize); \
+ return ks; \
+ } \
+ static inline void ks_destroy(kstream_t *ks) \
+ { \
+ if (ks) { \
+ free(ks->buf); \
+ free(ks); \
+ } \
+ }
+
+#define __KS_GETC(__read, __bufsize) \
+ static inline int ks_getc(kstream_t *ks) \
+ { \
+ if (ks->is_eof && ks->begin >= ks->end) return -1; \
+ if (ks->begin >= ks->end) { \
+ ks->begin = 0; \
+ ks->end = __read(ks->f, ks->buf, __bufsize); \
+ if (ks->end < __bufsize) ks->is_eof = 1; \
+ if (ks->end == 0) return -1; \
+ } \
+ return (int)ks->buf[ks->begin++]; \
+ }
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+ size_t l, m;
+ char *s;
+} kstring_t;
+#endif
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#define __KS_GETUNTIL(__read, __bufsize) \
+ static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
+ { \
+ if (dret) *dret = 0; \
+ str->l = 0; \
+ if (ks->begin >= ks->end && ks->is_eof) return -1; \
+ for (;;) { \
+ int i; \
+ if (ks->begin >= ks->end) { \
+ if (!ks->is_eof) { \
+ ks->begin = 0; \
+ ks->end = __read(ks->f, ks->buf, __bufsize); \
+ if (ks->end < __bufsize) ks->is_eof = 1; \
+ if (ks->end == 0) break; \
+ } else break; \
+ } \
+ if (delimiter) { \
+ for (i = ks->begin; i < ks->end; ++i) \
+ if (ks->buf[i] == delimiter) break; \
+ } else { \
+ for (i = ks->begin; i < ks->end; ++i) \
+ if (isspace(ks->buf[i])) break; \
+ } \
+ if (((int) (str->m - str->l)) < i - ks->begin + 1) { \
+ str->m = str->l + (i - ks->begin) + 1; \
+ kroundup32(str->m); \
+ str->s = (char*)realloc(str->s, str->m); \
+ } \
+ memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
+ str->l = str->l + (i - ks->begin); \
+ ks->begin = i + 1; \
+ if (i < ks->end) { \
+ if (dret) *dret = ks->buf[i]; \
+ break; \
+ } \
+ } \
+ str->s[str->l] = '\0'; \
+ return str->l; \
+ }
+
+#define KSTREAM_INIT(type_t, __read, __bufsize) \
+ __KS_TYPE(type_t) \
+ __KS_BASIC(type_t, __bufsize) \
+ __KS_GETC(__read, __bufsize) \
+ __KS_GETUNTIL(__read, __bufsize)
+
+#define __KSEQ_BASIC(type_t) \
+ static inline kseq_t *kseq_init(type_t fd) \
+ { \
+ kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \
+ s->f = ks_init(fd); \
+ return s; \
+ } \
+ static inline void kseq_rewind(kseq_t *ks) \
+ { \
+ ks->last_char = 0; \
+ ks->f->is_eof = ks->f->begin = ks->f->end = 0; \
+ } \
+ static inline void kseq_destroy(kseq_t *ks) \
+ { \
+ if (!ks) return; \
+ free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \
+ ks_destroy(ks->f); \
+ free(ks); \
+ }
+
+/* Return value:
+ >=0 length of the sequence (normal)
+ -1 end-of-file
+ -2 truncated quality string
+*/
+#define __KSEQ_READ \
+ static void kseq_set_type(kstream_t *ks) { \
+ int c = ks_getc(ks); \
+ while (c != -1 && (c == '\r' || c == '\n' || c == ' ' || c == '\t')) \
+ c = ks_getc(ks); \
+ if ((c >= 'A' && c <= 'Z') || (c >= 'a' && c <= 'z')) { \
+ ks->type = 'r'; \
+ } else \
+ ks->type = 'f'; \
+ ks->begin--; \
+ } \
+ static int kseq_read(kseq_t *seq) \
+ { \
+ int c; \
+ kstream_t *ks = seq->f; \
+ if (! ks->type) { \
+ kseq_set_type(ks); \
+ } \
+ if (seq->last_char == 0 && ks->type == 'f') { /* then jump to the next header line */ \
+ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
+ if (c == -1) return -1; /* end of file */ \
+ seq->last_char = c; \
+ } /* the first header char has been read */ \
+ seq->comment.l = seq->seq.l = seq->qual.l = 0; \
+ if (ks->type == 'f') { \
+ if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; \
+ if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0); \
+ } \
+ while ((c = ks_getc(ks)) != -1 \
+ && ((ks->type == 'f' && c != '>' && c != '+' && c != '@') \
+ || (ks->type == 'r' && c != '\n'))) { \
+ if (isgraph(c)) { /* printable non-space character */ \
+ if (seq->seq.l + 1 >= seq->seq.m) { /* double the memory */ \
+ seq->seq.m = seq->seq.l + 2; \
+ kroundup32(seq->seq.m); /* rounded to next closest 2^k */ \
+ seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
+ } \
+ seq->seq.s[seq->seq.l++] = (char)c; \
+ } \
+ } \
+ if (ks->type == 'r' && c==-1) return -1; \
+ if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
+ seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
+ if (c != '+' || ks->type == 'r') return seq->seq.l; /* FASTA or raw */ \
+ if (seq->qual.m < seq->seq.m) { /* allocate enough memory */ \
+ seq->qual.m = seq->seq.m; \
+ seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
+ } \
+ while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
+ if (c == -1) return -2; /* we should not stop here */ \
+ while ((c = ks_getc(ks)) != -1 && seq->qual.l < seq->seq.l) \
+ if (c >= 33 && c <= 127) seq->qual.s[seq->qual.l++] = (unsigned char)c; \
+ seq->qual.s[seq->qual.l] = 0; /* null terminated string */ \
+ seq->last_char = 0; /* we have not come to the next header line */ \
+ if (seq->seq.l != seq->qual.l) return -2; /* qual string is shorter than seq string */ \
+ return seq->seq.l; \
+ }
+
+#define __KSEQ_TYPE(type_t) \
+ typedef struct { \
+ kstring_t name, comment, seq, qual; \
+ int last_char; \
+ kstream_t *f; \
+ } kseq_t;
+
+#define KSEQ_INIT(type_t, __read) \
+ KSTREAM_INIT(type_t, __read, 4096) \
+ __KSEQ_TYPE(type_t) \
+ __KSEQ_BASIC(type_t) \
+ __KSEQ_READ
+
+#endif
diff --git a/src/libGkArrays/src/largebinvect.cxx b/src/libGkArrays/src/largebinvect.cxx
new file mode 100644
index 0000000..f40b9c2
--- /dev/null
+++ b/src/libGkArrays/src/largebinvect.cxx
@@ -0,0 +1,1259 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef __LARGEBINVECT_CXX__
+#define __LARGEBINVECT_CXX__
+
+#include "largebinvect.hxx"
+
+using std::ostream;
+
+template <typename CountWordSize>
+CountWordSize LargeBinVect<CountWordSize>::GetDataArrayLength() const {
+ CountWordSize w = length/8 + ((length % 8) > 0);
+ return w;
+}
+
+template <typename CountWordSize>
+unsigned char LargeBinVect<CountWordSize>::GetDataArrayEndingMask() const {
+ unsigned char mask = (length % 8 ? 255 << (8 - (length % 8)) : 255);
+ return mask;
+}
+
+template <typename CountWordSize>
+unsigned char *MyCalloc(const CountWordSize w, const int value = -1) throw (std::bad_alloc) {
+ unsigned char *array;
+ if (!w) {
+ return NULL;
+ }
+ if ((array = (unsigned char *) malloc(w*sizeof(unsigned char))) == NULL) {
+ throw std::bad_alloc();
+ }
+ if (value >= 0) {
+ memset(array, value, w*sizeof(unsigned char));
+ }
+ return array;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize>::LargeBinVect(const CountWordSize length, const bool value) throw (std::bad_alloc)
+ : length(length) {
+ CountWordSize w = GetDataArrayLength();
+ unsigned char mask = GetDataArrayEndingMask();
+ data = MyCalloc(w, (value ? 255 : 0));
+ if (w) {
+ data[w - 1] |= ~mask;
+ }
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize>::LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc) {
+ length = strlen(binary_string);
+ if (length != (long unsigned int) length) {
+ throw BinVectOverflow();
+ }
+ CountWordSize w = GetDataArrayLength();
+ unsigned char mask = GetDataArrayEndingMask();
+ data = MyCalloc(w, 0);
+ for (CountWordSize i = 0; i < length; i++) {
+ if (binary_string[i] == '1') {
+ unsigned char m = 1 << (7 - (i%8));
+ data[i/8] |= m;
+ }
+ }
+ if (w) {
+ data[w - 1] |= ~mask;
+ }
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize>::LargeBinVect(const LargeBinVect<CountWordSize> &v) throw (std::bad_alloc)
+ : length(v.length) {
+ CountWordSize w = v.GetDataArrayLength();
+ data = MyCalloc(w);
+ for (CountWordSize i = 0; i < w; i++) {
+ data[i] = v.data[i];
+ }
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize>::~LargeBinVect() {
+ if (data) {
+ free(data);
+ }
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator=(const LargeBinVect<CountWordSize> &v) throw (std::bad_alloc) {
+ if (this != &v) {
+ if (data) {
+ free(data);
+ }
+ length = v.length;
+ CountWordSize w = v.GetDataArrayLength();
+ data = MyCalloc(w);
+ for (CountWordSize i = 0; i < w; i++) {
+ data[i] = v.data[i];
+ }
+ }
+ return *this;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator~() const {
+ LargeBinVect<CountWordSize> bv(*this);
+ CountWordSize w = bv.GetDataArrayLength();
+ for (CountWordSize i = 0; i < w; i++) {
+ bv.data[i] ^= 255;
+ }
+ unsigned char mask = GetDataArrayEndingMask();
+ if (w) {
+ bv.data[w - 1] |= ~mask;
+ }
+ return bv;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator^(const LargeBinVect<CountWordSize> &v) const {
+ assert(v.length == length);
+ LargeBinVect<CountWordSize> bv(*this);
+ CountWordSize w = bv.GetDataArrayLength();
+ for (CountWordSize i = 0; i < w; i++) {
+ bv.data[i] ^= v.data[i];
+ }
+ unsigned char mask = GetDataArrayEndingMask();
+ if (w) {
+ bv.data[w - 1] |= ~mask;
+ }
+ return bv;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator|(const LargeBinVect<CountWordSize> &v) const {
+ assert(v.length == length);
+ LargeBinVect<CountWordSize> bv(*this);
+ CountWordSize w = bv.GetDataArrayLength();
+ for (CountWordSize i = 0; i < w; i++) {
+ bv.data[i] |= v.data[i];
+ }
+ return bv;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator&(const LargeBinVect<CountWordSize> &v) const {
+ assert(v.length == length);
+ LargeBinVect<CountWordSize> bv(*this);
+ CountWordSize w = bv.GetDataArrayLength();
+ for (CountWordSize i = 0; i < w; i++) {
+ bv.data[i] &= v.data[i];
+ }
+ return bv;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator<<(const CountWordSize s) const {
+ LargeBinVect<CountWordSize> v(*this);
+ v<<=s;
+ return v;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator>>(const CountWordSize s) const {
+ LargeBinVect<CountWordSize> v(*this);
+ v>>=s;
+ return v;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator^=(const LargeBinVect<CountWordSize> &v) {
+ assert(v.length == length);
+ CountWordSize w = GetDataArrayLength();
+ unsigned char mask = GetDataArrayEndingMask();
+ for (CountWordSize i = 0; i < w; i++) {
+ data[i] ^= v.data[i];
+ }
+ if (w) {
+ data[w - 1] |= ~mask;
+ }
+ return *this;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator|=(const LargeBinVect<CountWordSize> &v) {
+ assert(v.length == length);
+ CountWordSize w = GetDataArrayLength();
+ for (CountWordSize i = 0; i < w; i++) {
+ data[i] |= v.data[i];
+ }
+ return *this;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator&=(const LargeBinVect<CountWordSize> &v) {
+ assert(v.length == length);
+ CountWordSize w = GetDataArrayLength();
+ for (CountWordSize i = 0; i < w; i++) {
+ data[i] &= v.data[i];
+ }
+ return *this;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator<<=(const CountWordSize s) {
+ CountWordSize w = GetDataArrayLength();
+ unsigned char m = ~(255>>s);
+ unsigned char mask = GetDataArrayEndingMask();
+ for (CountWordSize i = 0; i < w - 1; i++) {
+ if (i) {
+ data[i - 1] |= (data[i] & m) >> (8-s);
+ }
+ data[i] <<= s;
+ }
+ if (w) {
+ if (w - 1) {
+ data[w - 2] |= (data[w - 1] & m & mask) >> (8-s);
+ }
+ data[w - 1] &= mask;
+ data[w - 1] <<= s;
+ data[w - 1] |= ~mask;
+ }
+ return *this;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator>>=(const CountWordSize s) {
+ CountWordSize w = GetDataArrayLength();
+ unsigned char m = ~(255<<s);
+ unsigned char mask = GetDataArrayEndingMask();
+ if (!w) {
+ return *this;
+ }
+ data[w - 1] &= mask;
+ data[w - 1] >>= s;
+ for (CountWordSize i = w - 2; (i >= 0) && (i < w - 1); i--) {
+ data[i + 1] |= (data[i] & m) << (8-s);
+ data[i] >>= s;
+ }
+ data[w - 1] |= ~mask;
+ return *this;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator()(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) {
+ if ((b < 0) || (b > length)) {
+ std::stringstream msg;
+ msg << __FILE__ << ":"
+ << __PRETTY_FUNCTION__ << ":"
+ << __LINE__ << ":"
+ << "b=" << (unsigned long int) b
+ << " should be >= 0 and <= " << (unsigned long int) length;
+ throw std::out_of_range(msg.str());
+ }
+ CountWordSize l = (lg > length ? length : lg);
+ if (b+l > length) {
+ l = length - b;
+ }
+ assert(l <= length || l == 0);
+ LargeBinVect<CountWordSize> bv(l);
+ for (CountWordSize i = 0; i < l; i++) {
+ bv.SetBit(i, GetBit(i+b));
+ }
+ return bv;
+}
+
+
+template <typename CountWordSize>
+unsigned long int LargeBinVect<CountWordSize>::GetValue(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) {
+ if ((b < 0) || (b > length)) {
+ std::stringstream msg;
+ msg << __FILE__ << ":"
+ << __PRETTY_FUNCTION__ << ":"
+ << __LINE__ << ":"
+ << "b=" << (unsigned long int) b
+ << " should be >= 0 and <= " << (unsigned long int) length;
+ throw std::out_of_range(msg.str());
+ }
+ unsigned long int r = 0;
+ CountWordSize l = b + (lg > sizeof(unsigned long int)*8 ? sizeof(unsigned long int)*8 : lg);
+// std::cerr << "1: b = " << (unsigned int) b
+// << ", l = " << (unsigned int) l
+// << std::endl;
+ if ((l > length) || (l < b)) {
+ l = length;
+ }
+// std::cerr << "2: b = " << (unsigned int) b
+// << ", l = " << (unsigned int) l
+// << std::endl;
+ assert(l <= length || l == 0);
+ for (CountWordSize i = b; i < l; i++) {
+ r <<= 1;
+ r |= GetBit(i);
+// std::cerr << "i = " << (unsigned int) i
+// << ", GetBit(i) = " << GetBit(i)
+// << ", r = " << r
+// << std::endl;
+ }
+ return r;
+}
+
+template <typename CountWordSize>
+bool LargeBinVect<CountWordSize>::operator[](const CountWordSize i) const throw (std::out_of_range) {
+ if ((i < 0) || (i >= length)) {
+ std::stringstream msg;
+ msg << __FILE__ << ":"
+ << __PRETTY_FUNCTION__ << ":"
+ << __LINE__ << ":"
+ << "i=" << (unsigned long int) i
+ << " should be >= 0 and < " << (unsigned long int) length;
+ throw std::out_of_range(msg.str());
+ }
+ return (128&(data[i/8]<<(i%8)));
+}
+
+template <typename CountWordSize>
+bool LargeBinVect<CountWordSize>::operator==(const LargeBinVect<CountWordSize> &v) const {
+ if (length != v.length) {
+ return false;
+ }
+ const CountWordSize w = GetDataArrayLength();
+ for (CountWordSize i = 0; i < w; i++) {
+ if (data[i] ^ v.data[i]) { // True if they differ by at least one bit
+ return false;
+ }
+ }
+ return true;
+}
+
+template <typename CountWordSize>
+bool LargeBinVect<CountWordSize>::operator!=(const LargeBinVect<CountWordSize> &v) const {
+ return !(*this == v);
+}
+
+template <typename CountWordSize>
+bool LargeBinVect<CountWordSize>::operator<(const LargeBinVect<CountWordSize> &v) const {
+ const CountWordSize &lg = (length > v.length ? v.length : length);
+ const CountWordSize w = lg/8;
+ CountWordSize i;
+ for (i = 0; i < w; i++) {
+ if (data[i] ^ v.data[i]) { // True if they differ by at least one bit
+ return (data[i] < v.data[i]);
+ }
+ }
+ if (lg%8) {
+ unsigned char mask = (length > v.length ? v.GetDataArrayEndingMask() : GetDataArrayEndingMask());
+ if ((data[i]&mask) ^ (v.data[i]&mask)) { // True if they differ by at least one bit
+ return ((data[i]&mask) < (v.data[i]&mask));
+ }
+ }
+ return (length < v.length);
+}
+
+template <typename CountWordSize>
+bool LargeBinVect<CountWordSize>::operator>(const LargeBinVect<CountWordSize> &v) const {
+ return v < *this;
+}
+
+template <typename CountWordSize>
+bool LargeBinVect<CountWordSize>::operator<=(const LargeBinVect<CountWordSize> &v) const {
+ const CountWordSize &lg = (length > v.length ? v.length : length);
+ const CountWordSize w = lg/8;
+ CountWordSize i;
+ for (i = 0; i < w; i++) {
+ if (data[i] ^ v.data[i]) { // True if they differ by at least one bit
+ return (data[i] < v.data[i]);
+ }
+ }
+ if (lg%8) {
+ unsigned char mask = (length > v.length ? v.GetDataArrayEndingMask() : GetDataArrayEndingMask());
+ if ((data[i]&mask) ^ (v.data[i]&mask)) { // True if they differ by at least one bit
+ return ((data[i]&mask) < (v.data[i]&mask));
+ }
+ }
+ return (length <= v.length);
+}
+
+template <typename CountWordSize>
+bool LargeBinVect<CountWordSize>::operator>=(const LargeBinVect<CountWordSize> &v) const {
+ return v <= *this;
+}
+
+template <typename CountWordSize>
+bool LargeBinVect<CountWordSize>::GetBit(const CountWordSize i) const throw (std::out_of_range) {
+ if ((i < 0) || (i >= length)) {
+ std::stringstream msg;
+ msg << __FILE__ << ":"
+ << __PRETTY_FUNCTION__ << ":"
+ << __LINE__ << ":"
+ << "i=" << (unsigned long int) i
+ << " should be >= 0 and < " << (unsigned long int) length;
+ throw std::out_of_range(msg.str());
+ }
+ return (data[i/8] & (1 << (7-(i%8))));
+}
+
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::SetBit(const CountWordSize i, const bool value) throw (std::out_of_range) {
+ if ((i < 0) || (i >= length)) {
+ std::stringstream msg;
+ msg << __FILE__ << ":"
+ << __PRETTY_FUNCTION__ << ":"
+ << __LINE__ << ":"
+ << "i=" << (unsigned long int) i
+ << " should be >= 0 and < " << (unsigned long int) length;
+ throw std::out_of_range(msg.str());
+ }
+ if (value) {
+ data[i/8] |= (1 << (7-(i%8)));
+ } else {
+ data[i/8] &= ~(1 << (7-(i%8)));
+ }
+ return *this;
+}
+
+// Set Bits between positions i and j (>= 0, < length) to value
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range) {
+ if ((i < 0) || (i >= length)) {
+ std::stringstream msg;
+ msg << __FILE__ << ":"
+ << __PRETTY_FUNCTION__ << ":"
+ << __LINE__ << ":"
+ << "i=" << (unsigned long int) i
+ << " should be >= 0 and < " << (unsigned long int) length;
+ throw std::out_of_range(msg.str());
+ }
+ if ((j < i) || (j >= length)) {
+ std::stringstream msg;
+ msg << __FILE__ << ":"
+ << __PRETTY_FUNCTION__ << ":"
+ << __LINE__ << ":"
+ << "j=" << (unsigned long int) j
+ << " should be >= " << i << " and < " << (unsigned long int) length;
+ throw std::out_of_range(msg.str());
+ }
+ long unsigned int v = value;
+// cerr << "i / 8 = " << (unsigned int) i <<" / 8 = " << i / 8 << " et i % 8 = " << i % 8 << endl;
+// cerr << "j / 8 = " << (unsigned int) j <<" / 8 = " << j / 8 << " et j % 8 = " << j % 8 << endl;
+ if ((j / 8) > (i / 8)) {
+// cerr << "cas 1" << endl;
+ if ((j + 1) % 8) {
+// cerr << "cas 1A" << endl;
+ unsigned char mask = ~(255 << (j % 8 + 1));
+ unsigned char clear_mask = ~(255 << (7 - (j % 8)));
+// cerr << "clearing mask = " << bitset<8>(clear_mask) << ", setting mask = " << bitset<8>(mask) << endl;
+// cerr << "data["<<(unsigned int) j<<" / 8] = " << bitset<8>(data[j / 8]) << endl;
+ data[j / 8] &= clear_mask;
+// cerr << "clearing => " << bitset<8>(data[j / 8]) << endl;
+ data[j / 8] |= ((char) v & mask) << (7 - (j % 8));
+// cerr << "setting with " << bitset<8>(((char) v & mask)) << "<<" << 7 - (j % 8) << " => " << bitset<8>(data[j / 8]) << endl;
+ v >>= (j % 8 + 1);
+// cerr << "shifting value by " << j % 8 + 1 << " bits => " << bitset<8>(v) << endl;
+ }
+ for (CountWordSize x = j / 8 - ((j + 1) % 8 != 0); x > i / 8; x--) {
+// cerr << "cas 1B for data[x = " << (unsigned int) x << "]" << endl;
+ data[x] = (char) v & 255;
+ v >>= 8;
+// cerr << "shifting value by 8 bits => " << bitset<8>(v) << endl;
+ }
+// cerr << "cas 1C" << endl;
+ unsigned char mask = 255 << (8 - (i % 8));
+// cerr << "clearing mask = " << bitset<8>(mask) << ", setting mask = " << bitset<8>(~mask) << endl;
+// cerr << "data[" << (unsigned int) i <<" / 8] = " << bitset<8>(data[i / 8]) << endl;
+ data[i / 8] &= mask;
+// cerr << "clearing => " << bitset<8>(data[i / 8]) << endl;
+ data[i / 8] |= (char) v & ~mask;
+// cerr << "setting => " << bitset<8>(data[i / 8]) << endl;
+ } else {
+// cerr << "cas 2" << endl;
+ if (i / 8 == length / 8) {
+// cerr << "cas 2A" << endl;
+ unsigned char mask = ~(255 << (j - i + 1));
+ unsigned char clear_mask = ~(mask << (8 - (length % 8)));
+// cerr << "clearing mask is " << bitset<8>(clear_mask) << endl;
+ data[i / 8] &= clear_mask;
+// cerr << "clearing => " << bitset<8>(data[i / 8]) << endl;
+// cerr << "value setting mask = " << bitset<8>(mask) << endl;
+// cerr << "result of masking will be shifted by " << (8 - (length % 8)) << " positions" << endl;
+ data[i / 8] |= (v & mask) << (8 - (length % 8));
+// cerr << "setting => " << bitset<8>(data[i / 8]) << endl;
+ } else {
+// cerr << "cas 2B" << endl;
+ unsigned char clearing_mask = ~((255 >> (i % 8)) & (255 << (7 - (j % 8))));
+ unsigned char setting_mask = ~(255 << (j - i + 1));
+// cerr << "clearing mask = " << bitset<8>(clearing_mask) << ", setting mask = " << bitset<8>(setting_mask) << endl;
+// cerr << "data[" << (unsigned int) i <<" / 8] = " << bitset<8>(data[i / 8]) << endl;
+ data[i / 8] &= clearing_mask;
+// cerr << "clearing => " << bitset<8>(data[i / 8]) << endl;
+ data[i / 8] |= ((char) v & setting_mask) << (7 - (j % 8));
+// cerr << "setting => " << bitset<8>(data[i / 8]) << endl;
+ }
+ }
+ return *this;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::Clear(const bool value) {
+ unsigned char mask = GetDataArrayEndingMask();
+ CountWordSize w = GetDataArrayLength();
+ if (w) {
+ memset(data, (value ? 255 : 0), w*sizeof(unsigned char));
+ data[w - 1] |= ~mask;
+ }
+ return *this;
+}
+
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::RandomInit() {
+ unsigned char mask = GetDataArrayEndingMask();
+ CountWordSize w = GetDataArrayLength();
+ if (w) {
+ for (CountWordSize i = 0; i < w; i++) {
+ data[i] = (unsigned char) random();
+ }
+ data[w - 1] |= ~mask;
+ }
+ return *this;
+}
+
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::Resize(const CountWordSize length, const bool value) throw (std::bad_alloc) {
+ CountWordSize old_w = GetDataArrayLength();
+ unsigned char mask = GetDataArrayEndingMask();
+ this->length = length;
+ CountWordSize w = GetDataArrayLength();
+
+ if (!w) { // If length is 0 ;-)
+ free(data);
+ data = NULL;
+ return *this;
+ }
+
+ if (old_w) {
+ if (value) {
+ data[old_w - 1] |= ~mask;
+ } else {
+ data[old_w - 1] &= mask;
+ }
+ }
+
+ if ((data = (unsigned char *) realloc(data, w*sizeof(unsigned char))) == NULL) {
+ throw std::bad_alloc();
+ }
+ if (w > old_w) {
+ memset(data+old_w, (value ? 255 : 0), (w-old_w)*sizeof(unsigned char));
+ }
+ mask = GetDataArrayEndingMask();
+ data[w - 1] |= ~mask;
+
+ return *this;
+
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::Append(const bool value) throw (BinVectOverflow, std::bad_alloc) {
+ if (length == CountWordSize(~0)) {
+ throw BinVectOverflow();
+ }
+ return Resize(length+1, value);
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc) {
+ if (length == CountWordSize(~0)) {
+ throw BinVectOverflow();
+ }
+ Resize(length+1) >>= 1;
+ if (value) {
+ data[0] |= 128;
+ }
+ return *this;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator+=(const LargeBinVect<CountWordSize> &v) throw (BinVectOverflow, std::bad_alloc) {
+ if ((length + v.length < length) || (length + v.length < v.length)) {
+ throw BinVectOverflow();
+ }
+ if (!v.length) {
+ return *this;
+ }
+ CountWordSize old_w = GetDataArrayLength();
+ unsigned char mask = GetDataArrayEndingMask();
+ CountWordSize app_w = v.GetDataArrayLength();
+ unsigned int shift = (length%8);
+ Resize(length + v.length);
+ if (shift) {
+ assert(old_w);
+ assert(app_w);
+ old_w--;
+ data[old_w] &= mask;
+ mask = v.GetDataArrayEndingMask();
+ v.data[app_w - 1] &= mask;
+ for (CountWordSize i = 0; i < app_w - 1; i++) {
+ data[old_w + i] |= v.data[i] >> shift;
+ data[old_w + i + 1] |= v.data[i] << (8 - shift);
+ }
+ data[old_w + app_w - 1] |= v.data[app_w - 1] >> shift;
+ if (old_w + app_w == GetDataArrayLength() - 1) {
+ data[old_w + app_w] |= v.data[app_w - 1] << (8 - shift);
+ }
+ } else {
+ for (CountWordSize i = 0; i < app_w; i++) {
+ data[old_w + i] = v.data[i];
+ }
+ mask = GetDataArrayEndingMask();
+ data[old_w + app_w - 1] |= ~mask;
+ }
+ return *this;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator++() throw (BinVectOverflow, std::bad_alloc) {
+ CountWordSize w = GetDataArrayLength();
+ unsigned char mask = ~GetDataArrayEndingMask();
+ ++mask;
+ while (mask && w--) {
+ unsigned char old = data[w];
+ data[w] += mask;
+ mask = (data[w] < old);
+ }
+ if (mask) {
+ Prepend(true);
+ }
+ return *this;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator++(int) throw (BinVectOverflow, std::bad_alloc) {
+ LargeBinVect<CountWordSize> ret(*this);
+ ++(*this);
+ return ret;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator--() throw (BinVectOverflow) {
+ CountWordSize w = GetDataArrayLength();
+ unsigned char mask = ~GetDataArrayEndingMask();
+ ++mask;
+ while (mask && w--) {
+ unsigned char old = data[w];
+ data[w] -= mask;
+ mask = (data[w] > old);
+ }
+ if (mask) {
+ throw BinVectOverflow();
+ }
+ return *this;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator--(int) throw (BinVectOverflow, std::bad_alloc) {
+ LargeBinVect<CountWordSize> ret(*this);
+ --(*this);
+ return ret;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc) {
+ if ((i < 0) || (i > length)) {
+ std::stringstream msg;
+ msg << __FILE__ << ":"
+ << __PRETTY_FUNCTION__ << ":"
+ << __LINE__ << ":"
+ << "i=" << (unsigned long int) i
+ << " should be >= 0 and < " << (unsigned long int) length;
+ throw std::out_of_range(msg.str());
+ }
+ if (i == length) {
+ return LargeBinVect<CountWordSize>();
+ } else {
+ LargeBinVect<CountWordSize> bv = (*this)(i, length - i);
+ Resize(i);
+ return bv;
+ }
+}
+
+template <typename CountWordSize>
+CountWordSize LargeBinVect<CountWordSize>::GetLonguestCommonPrefix(const LargeBinVect<CountWordSize> &v) const {
+ const CountWordSize &lg = (length > v.length ? v.length : length);
+ const CountWordSize w = lg/8;
+ CountWordSize i;
+ for (i = 0; i < w; i++) {
+ unsigned char m = data[i] ^ v.data[i];
+ CountWordSize p;
+ if (m) { // True if they differ by at least one bit
+ for (p = i*8; !(128 & m); p++) {
+ m <<= 1;
+ }
+ return p;
+ }
+ }
+ if (lg%8) {
+ unsigned char mask = (length > v.length ? v.GetDataArrayEndingMask() : GetDataArrayEndingMask());
+ unsigned char m = (data[i] & mask) ^ (v.data[i] & mask);
+ CountWordSize p;
+ if (m) { // True if they differ by at least one bit
+ for (p = i*8; !(128 & m); p++) {
+ m <<= 1;
+ }
+ return p;
+ }
+ }
+ return lg;
+}
+
+template <typename CountWordSize>
+CountWordSize LargeBinVect<CountWordSize>::GetLonguestCommonSuffix(const LargeBinVect<CountWordSize> &v) const {
+ if (length > v.length) {
+ return v.GetLonguestCommonSuffix(*this);
+ } else { // length <= v.length
+ const CountWordSize delta = v.length - length;
+ for (CountWordSize i = length - 1; (i >= 0) && (i < length); i--) {
+ if (GetBit(i) != v.GetBit(i+delta)) {
+ return length - i - 1;
+ }
+ }
+ return length;
+ }
+}
+
+template <typename CountWordSize>
+char * LargeBinVect<CountWordSize>::ToString() const {
+ char* tmp;
+ tmp = new char [length + 1];
+ const CountWordSize w = length / 8;
+ unsigned char m;
+ for (CountWordSize i = 0; i < w; i++) {
+ m = data[i];
+ for (unsigned char b = 0; b < 8; b++) {
+ tmp[i*8+b] = ((128 & m) ? '1' : '0');
+ m<<=1;
+ }
+ }
+ if (length % 8) {
+ m = data[w];
+ for (unsigned char b = 0; b < length % 8; b++) {
+ tmp[w*8+b] = ((128 & m) ? '1' : '0');
+ m<<=1;
+ }
+ }
+ tmp[length]=0;
+ return tmp;
+}
+
+template <typename CountWordSize>
+CountWordSize LargeBinVect<CountWordSize>::GetLength() const {
+ return length;
+}
+
+// Cast operators
+template <typename CountWordSize, typename target_type>
+target_type cast(const LargeBinVect<CountWordSize> &v) {
+ target_type r = 0;
+ CountWordSize i = sizeof(target_type)*8;
+ if (i > v.GetLength()) {
+ i = v.GetLength();
+ }
+ for (; i > 0; i--) {
+ r <<= 1;
+ r |= v.GetBit(v.GetLength() - i);
+ }
+ return r;
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize>::operator char() const {
+ return cast<CountWordSize, char>(*this);
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize>::operator unsigned char() const {
+ return cast<CountWordSize, unsigned char>(*this);
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize>::operator short int() const {
+ return cast<CountWordSize, short int>(*this);
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize>::operator unsigned short int() const {
+ return cast<CountWordSize, unsigned short int>(*this);
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize>::operator int() const {
+ return cast<CountWordSize, int>(*this);
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize>::operator unsigned int() const {
+ return cast<CountWordSize, unsigned int>(*this);
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize>::operator long int() const {
+ return cast<CountWordSize, long int>(*this);
+}
+
+template <typename CountWordSize>
+LargeBinVect<CountWordSize>::operator unsigned long int() const {
+ return cast<CountWordSize, unsigned long int>(*this);
+}
+
+template <typename CountWordSize>
+std::ostream &operator<<(std::ostream &os, const LargeBinVect<CountWordSize> &v) {
+ char *tmp = v.ToString();
+ os << tmp;
+ delete [] tmp;
+ return os;
+}
+
+#ifdef TEST_LARGEBINVECT
+// Compile this test program with the following command line:
+// g++ largebinvect.cxx -DTEST_LARGEBINVECT -o test_largebinvect -Wall -ansi -pedantic -O4
+
+using std::cout;
+using std::endl;
+#include <bitset>
+
+template <typename CountWordSize>
+void TestLargeBinVectors(char *title, CountWordSize max_test_length) {
+ cout << "Testing class LargeBinVect<" << title << ">" << endl;
+ cout << "SizeOf(" << title << ") = "
+ << sizeof(CountWordSize) << "Bytes (= "
+ << 8*sizeof(CountWordSize) << "bits)" << endl << endl;
+ const char *binary_string1 = "1001010111010001011110100010101";
+ const char *binary_string2 = "10010101110100010101";
+ cout << "Building a short binvect from string '" << binary_string1 << "'" << endl;
+ LargeBinVect<CountWordSize> * v1 = new LargeBinVect<CountWordSize>(binary_string1);
+ cout << "=> '" << *v1 << "' of length " << (unsigned long int) v1->GetLength() << endl;
+ LargeBinVect<CountWordSize> * v2 = new LargeBinVect<CountWordSize>(binary_string2);
+ cout << "=> '" << *v2 << "' of length " << (unsigned long int) v2->GetLength() << endl;
+ cout << "Compute the longuest common prefix (size 18) between" << endl;
+ cout << "bv1='" << *v1 << "'" << endl;
+ cout << "bv2='" << *v2 << "'" << endl;
+ cout << "It returns " << (unsigned long int)v1->GetLonguestCommonPrefix(*v2);
+ cout << " which should also be " << (unsigned long int)v2->GetLonguestCommonPrefix(*v1) << endl;
+
+ cout << "Compute the longuest common suffix (size 13) between" << endl;
+ cout << "bv1='" << *v1 << "'" << endl;
+ cout << "bv2='" << *v2 << "'" << endl;
+ cout << "It returns " << (unsigned long int)v1->GetLonguestCommonSuffix(*v2);
+ cout << " which should also be " << (unsigned long int)v2->GetLonguestCommonSuffix(*v1) << endl;
+ cout << endl;
+
+ cout << "Resizing bv1 to 78 bits (filling with 0)" << endl;
+ cout << "bv1 was ='" << *v1 << "'" << endl;
+ v1->Resize(78);
+ cout << "bv1 is ='" << *v1 << "'" << endl;
+ cout << "Resizing bv2 to 35 bits (filling with 1)" << endl;
+ cout << "bv2 was ='" << *v2 << "'" << endl;
+ v2->Resize(35, 1);
+ cout << "bv2 is ='" << *v2 << "'" << endl;
+ cout << "Resizing bv1 to 35 bits ([not] filling with 1)" << endl;
+ cout << "bv1 was ='" << *v1 << "'" << endl;
+ v1->Resize(35, 1);
+ cout << "bv1 is ='" << *v1 << "'" << endl;
+ cout << "Resizing bv2 to 13 bits ([not] filling with 0)" << endl;
+ cout << "bv2 was ='" << *v2 << "'" << endl;
+ v2->Resize(13);
+ cout << "bv2 is ='" << *v2 << "'" << endl;
+ cout << "Resizing bv2 to 20 bits (filling with 0)" << endl;
+ cout << "bv2 was ='" << *v2 << "'" << endl;
+ v2->Resize(20);
+ cout << "bv2 is ='" << *v2 << "'" << endl;
+ cout << endl;
+
+ *v2 = LargeBinVect<CountWordSize>("1000000010000000100000001000000010000000100000001000000010000000");
+
+ cout << "Testing cast operators" << endl;
+ cout << "casting " << *v2 << " to char:" << (int) ((char) *v2)
+ << ", which should be -128" << endl;
+ cout << "casting " << *v2 << " to unsigned char:" << (unsigned int) (unsigned char) *v2
+ << ", which should be 128" << endl;
+ cout << "casting " << *v2 << " to short:" << (short int) *v2
+ << ", which should be -32640" << endl;
+ cout << "casting " << *v2 << " to unsigned short:" << (unsigned short int) *v2
+ << ", which should be 32896" << endl;
+ cout << "casting " << *v2 << " to int:" << (int) *v2
+ << ", which should be -2139062144" << endl;
+ cout << "casting " << *v2 << " to unsigned int:" << (unsigned int) *v2
+ << ", which should be 2155905152" << endl;
+ cout << "casting " << *v2 << " to long:" << (long int) *v2
+ << ", which should be -9187201950435737472" << endl;
+ cout << "casting " << *v2 << " to unsigned long:" << (unsigned long int) *v2
+ << ", which should be 9259542123273814144" << endl;
+ cout << endl;
+
+ cout << "Deleting the binvectors" << endl;
+ delete v1;
+ delete v2;
+
+ cout << endl;
+ cout << "Creating empty binvector" << endl;
+ v1 = new LargeBinVect<CountWordSize>();
+ cout << "LargeBinVect is '" << *v1 << "'" << endl;
+ cout << "Preincrementing '" << *v1 << "'" << endl;
+ cout << "=> '" << ++(*v1) << "'" << endl;
+ cout << "Postincrementing '" << (*v1)++ << "'" << endl;
+ cout << "=> '" << *v1 << "'" << "'" << endl;
+ cout << "Incrementing '" << *v1 << "'" << endl;
+ cout << "=> '" << ++(*v1) << "'" << endl;
+ cout << "Incrementing '" << *v1 << "'" << endl;
+ cout << "=> '" << ++(*v1) << "'" << endl;
+ cout << "Appending '111111111111111' to '" << *v1 << "'" << endl;
+ *v1 += LargeBinVect<CountWordSize>("111111111111111");
+ cout << "=> '" << *v1 << "'" << endl;
+ cout << "Incrementing '" << *v1 << "'" << endl;
+ cout << "=> '" << ++(*v1) << "'" << endl;
+
+ cout << "Predecrementing '" << *v1 << "'" << endl;
+ cout << "=> '" << --(*v1) << "'" << endl;
+ cout << "Postdecrementing '" << (*v1)-- << "'" << endl;
+ cout << "=> '" << *v1 << "'" << endl;
+ cout << "Decrementing '" << *v1 << "'" << endl;
+ cout << "=> '" << --(*v1) << "'" << endl;
+ cout << "Decrementing '" << *v1 << "'" << endl;
+ cout << "=> '" << --(*v1) << "'" << endl;
+ cout << "Decrementing '" << *v1 << "'" << endl;
+ cout << "=> '" << --(*v1) << "'" << endl;
+ cout << "Resizing '" << *v1 << "' to 3 bits" << endl;
+ v1->Resize(3);
+ cout << "Decrementing '" << *v1 << "'" << endl;
+ cout << "=> '" << --(*v1) << "'" << endl;
+ cout << "Decrementing '" << *v1 << "'" << endl;
+ cout << "=> '" << --(*v1) << "'" << endl;
+ cout << "Decrementing '" << *v1 << "'" << endl;
+ cout << "=> '" << --(*v1) << "'" << endl;
+ cout << "Decrementing '" << *v1 << "'" << endl;
+ cout << "=> '" << --(*v1) << "'" << endl;
+ cout << endl;
+ cout << "Deleting the binvector" << endl;
+ delete v1;
+
+ cout << "===" << endl;
+ for (CountWordSize i = 1; i < max_test_length; i*=2) {
+ cout << endl;
+ cout << "Make 0-filled binvect of length " << (unsigned long int) i << endl;
+ LargeBinVect<CountWordSize> bv(i);
+ cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
+
+ cout << "Overwrite (operator=) the binvect with a 1-filled one of same length" << endl;
+ bv = LargeBinVect<CountWordSize>(i, 1);
+ cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
+
+ cout << "Clearing the binvect with 0" << endl;
+ bv.Clear();
+ cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
+
+ cout << "Clearing the binvect with 1" << endl;
+ bv.Clear(1);
+ cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
+
+ long unsigned int r = rand();
+ cout << "Setting the bit range from " << i / 3
+ << " to " << 3 * i / 4
+ << " with the value " << std::bitset<20>(r) << endl;
+ bv.SetBitRange(i / 3, 3 * i / 4, r);
+ cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
+
+ cout << "Setting even bits to 0" << endl;
+ cout << "was '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
+ for (CountWordSize b = 0; b < i; b+=2) {
+ bv.SetBit(b, 0);
+ }
+ cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
+
+ cout << "Left Shifting (Self assignment) binvect by 3" << endl;
+ cout << "was '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
+ bv <<= 3;
+ cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
+
+ cout << "Right Shifting (Self assignment) binvect by 4" << endl;
+ cout << "was '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
+ bv >>= 4;
+ cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
+
+ cout << "Assigning its inversed bit values" << endl;
+ cout << "was '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
+ bv = ~bv;
+ cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
+
+ cout << endl;
+ cout << "Generating a random bitvector having same length" << endl;
+ LargeBinVect<CountWordSize> rbv(i);
+ rbv.RandomInit();
+ cout << "=> '" << rbv << "' of length " << (unsigned long int) rbv.GetLength() << endl;
+
+ cout << "Performing XOR between bv and rbv" << endl;
+ LargeBinVect<CountWordSize> res = (bv ^ rbv);
+ cout << "bv ='" << bv << "'" << endl;
+ cout << "rbv='" << rbv << "'" << endl;
+ cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
+
+ cout << "Performing OR between bv and rbv" << endl;
+ res = (bv | rbv);
+ cout << "bv ='" << bv << "'" << endl;
+ cout << "rbv='" << rbv << "'" << endl;
+ cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
+
+ cout << "Performing AND between bv and rbv" << endl;
+ res = (bv & rbv);
+ cout << "bv ='" << bv << "'" << endl;
+ cout << "rbv='" << rbv << "'" << endl;
+ cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
+
+ cout << "Using the copy constructor" << endl;
+ v1 = new LargeBinVect<CountWordSize>(res);
+ cout << "res='" << res << "'" << endl;
+ cout << "=> '" << *v1 << "' of length " << (unsigned long int) v1->GetLength() << endl;
+ delete v1;
+
+ cout << "Performing Self Assignment XOR between copy of bv and rbv" << endl;
+ res = bv;
+ res ^= rbv;
+ cout << "bv ='" << bv << "'" << endl;
+ cout << "rbv='" << rbv << "'" << endl;
+ cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
+
+ cout << "Performing Self Assignment OR between copy of bv and rbv" << endl;
+ res = bv;
+ res |= rbv;
+ cout << "bv ='" << bv << "'" << endl;
+ cout << "rbv='" << rbv << "'" << endl;
+ cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
+
+ cout << "Performing Self Assignment AND between copy of bv and rbv" << endl;
+ res = bv;
+ res &= rbv;
+ cout << "bv ='" << bv << "'" << endl;
+ cout << "rbv='" << rbv << "'" << endl;
+ cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
+
+ cout << "Build prefix of rbv of length " << (unsigned long int) rbv.GetLength()/3 << endl;
+ res = rbv(0, rbv.GetLength()/3);
+ cout << "rbv='" << rbv << "'" << endl;
+ cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
+
+ cout << endl;
+ cout << "res='" << res << "'" << endl;
+ cout << "rbv='" << rbv << "'" << endl;
+ cout << "Testing between rbv < res" << endl;
+ cout << "=> " << (rbv < res ? "true" : "false") << endl;
+ cout << "Testing between rbv <= res" << endl;
+ cout << "=> " << (rbv <= res ? "true" : "false") << endl;
+ cout << "Testing between rbv > res" << endl;
+ cout << "=> " << (rbv > res ? "true" : "false") << endl;
+ cout << "Testing between rbv >= res" << endl;
+ cout << "=> " << (rbv >= res ? "true" : "false") << endl;
+ cout << "Testing between rbv == res" << endl;
+ cout << "=> " << (rbv == res ? "true" : "false") << endl;
+ cout << "Testing between rbv != res" << endl;
+ cout << "=> " << (rbv != res ? "true" : "false") << endl;
+
+ CountWordSize p = 0;
+ if (res.GetLength()) {
+ p = rand() % res.GetLength();
+ cout << "Spin bit at position " << (unsigned long int) p << " in res (using GetBit, SetBit and operator[])" << endl;
+ cout << "res["<<(unsigned long int) p<<"] was " << res[p];
+ res.SetBit(p, !res.GetBit(p));
+ cout << " and now is " << res[p]<<endl;
+ cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
+ }
+
+ cout << endl;
+ cout << "Computing the longuest common prefix between res and rbv should give " << (res.GetLength() ? (unsigned long int) p : 0) << endl;
+ cout << "res='" << res << "'" << endl;
+ cout << "rbv='" << rbv << "'" << endl;
+ cout << "It returns " << (unsigned long int)res.GetLonguestCommonPrefix(rbv);
+ cout << " which should also be " << (unsigned long int)rbv.GetLonguestCommonPrefix(res) << endl;
+
+ cout << endl;
+ cout << "Build suffix of rbv of length " << (unsigned long int) rbv.GetLength()/3 << endl;
+ res = rbv(rbv.GetLength() - rbv.GetLength()/3 - 1, rbv.GetLength()/3);
+ cout << "rbv='" << rbv << "'" << endl;
+ cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
+
+ if (res.GetLength()) {
+ p = rand() % res.GetLength();
+ cout << "Spin bit at position " << (unsigned long int) p << " in res (using GetBit, SetBit and operator[])" << endl;
+ cout << "res["<<(unsigned long int) p<<"] was " << res[p];
+ res.SetBit(p, !res.GetBit(p));
+ cout << " and now is " << res[p]<<endl;
+ cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
+ }
+
+ cout << endl;
+ cout << "Computing the longuest common suffix between res and rbv" << endl;
+ cout << "res='" << res << "'" << endl;
+ cout << "rbv='" << rbv << "'" << endl;
+ cout << "It returns " << (unsigned long int)res.GetLonguestCommonSuffix(rbv);
+ cout << " which should also be " << (unsigned long int)rbv.GetLonguestCommonSuffix(res) << endl;
+
+ cout << endl;
+ cout << "Build centered factor of rbv of length " << (unsigned long int) rbv.GetLength()/3 << endl;
+ res = rbv(rbv.GetLength()/3, rbv.GetLength()/3);
+ cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
+
+ cout << "Compute the longuest common prefix between res and rbv." << endl;
+ cout << "res='" << res << "'" << endl;
+ cout << "rbv='" << rbv << "'" << endl;
+ cout << "It returns " << (unsigned long int)res.GetLonguestCommonPrefix(rbv);
+ cout << " which should also be " << (unsigned long int)rbv.GetLonguestCommonPrefix(res) << endl;
+
+ cout << "Compute the longuest common suffix between res and rbv." << endl;
+ cout << "res='" << res << "'" << endl;
+ cout << "rbv='" << rbv << "'" << endl;
+ cout << "It returns " << (unsigned long int)res.GetLonguestCommonSuffix(rbv);
+ cout << " which should also be " << (unsigned long int)rbv.GetLonguestCommonSuffix(res) << endl;
+ cout << "===" << endl;
+
+ cout << "Append longuest common prefix between res and rbv to the longuest common suffix between res and rbv." << endl;
+ cout << "res='" << res << "'" << endl;
+ cout << "rbv='" << rbv << "'" << endl;
+ cout << "* res.GetLength() = " << (unsigned long int)res.GetLength() << endl;
+ cout << "* res.GetLonguestCommonSuffix(rbv) = " << (unsigned long int) res.GetLonguestCommonSuffix(rbv) << endl;
+ cout << "* res.GetLength() - res.GetLonguestCommonSuffix(rbv) = " << (unsigned long int)(res.GetLength() - res.GetLonguestCommonSuffix(rbv)) << endl;
+ bv = res(res.GetLength() - res.GetLonguestCommonSuffix(rbv));
+ res = res(0, res.GetLonguestCommonPrefix(rbv));
+ cout << "longuest common prefix is '" << res << "'" << endl;
+ cout << "longuest common suffix is '" << bv << "'" << endl;
+ res += bv;
+ cout << "res is ='" << res << "'" << endl;
+ cout << "===" << endl;
+
+ res = rbv;
+ cout << "Append a 0 to res." << endl;
+ cout << "res='" << res << "'" << endl;
+ cout << "now='" << res.Append(0) << "'" << endl;
+
+ cout << "Append a 1 to res." << endl;
+ cout << "res='" << res << "'" << endl;
+ cout << "now='" << res.Append(1) << "'" << endl;
+
+ cout << "Prepend a 0 to res." << endl;
+ cout << "res='" << res << "'" << endl;
+ cout << "now='" << res.Prepend(0) << "'" << endl;
+
+ cout << "Prepend a 1 to res." << endl;
+ cout << "res='" << res << "'" << endl;
+ cout << "now='" << res.Prepend(1) << "'" << endl;
+
+ cout << "Split res at position " << (unsigned long int) i/3 << "." << endl;
+ cout << "res='" << res << "'" << endl;
+ rbv = res.Split(i/3);
+ cout << "now='" << res << "'" << endl;
+ cout << "suf='" << rbv << "'" << endl;
+ }
+}
+int main(int argc, char** argv) {
+
+ TestLargeBinVectors<unsigned char>((char *)"unsigned char", 128);
+ TestLargeBinVectors<unsigned int>((char *)"unsigned int", 1000000);
+ TestLargeBinVectors<long unsigned int>((char *)"long unsigned int", 1000000);
+
+ return 0;
+}
+#endif
+#endif
diff --git a/src/libGkArrays/src/largebinvect.hxx b/src/libGkArrays/src/largebinvect.hxx
new file mode 100644
index 0000000..fc6b2c8
--- /dev/null
+++ b/src/libGkArrays/src/largebinvect.hxx
@@ -0,0 +1,242 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef __LARGEBINVECT_HXX__
+#define __LARGEBINVECT_HXX__
+
+#include "binvect.hxx"
+
+template <typename CountWordSize = unsigned char>
+class LargeBinVect {
+private:
+ unsigned char *data;
+ CountWordSize length;
+
+ // Get the data internal array length
+ CountWordSize GetDataArrayLength() const;
+ // Get the last unsigned char mask for the internal array
+ unsigned char GetDataArrayEndingMask() const;
+
+public:
+ // Constructors
+ LargeBinVect(const CountWordSize length = 0, const bool value = 0) throw (std::bad_alloc);
+ LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc);
+ LargeBinVect(const LargeBinVect<CountWordSize> &v) throw (std::bad_alloc);
+
+ // Destructors
+ ~LargeBinVect();
+
+ // Operators
+ inline LargeBinVect<CountWordSize> &operator=(const LargeBinVect<CountWordSize> &v) throw (std::bad_alloc);
+
+ // Bitwise NOT
+ inline LargeBinVect<CountWordSize> operator~() const;
+ // Bitwise XOR
+ inline LargeBinVect<CountWordSize> operator^(const LargeBinVect<CountWordSize> &v) const;
+ // Bitwise OR
+ inline LargeBinVect<CountWordSize> operator|(const LargeBinVect<CountWordSize> &v) const;
+ // Bitwise AND
+ inline LargeBinVect<CountWordSize> operator&(const LargeBinVect<CountWordSize> &v) const;
+ // Right to Left shift by 's' bits
+ inline LargeBinVect<CountWordSize> operator<<(const CountWordSize s) const;
+ // Left to Right shift by 's' bits
+ inline LargeBinVect<CountWordSize> operator>>(const CountWordSize s) const;
+
+ // Bitwise XOR with self assignment
+ inline LargeBinVect<CountWordSize> &operator^=(const LargeBinVect<CountWordSize> &v);
+ // Bitwise OR with self assignment
+ inline LargeBinVect<CountWordSize> &operator|=(const LargeBinVect<CountWordSize> &v);
+ // Bitwise AND with self assignment
+ inline LargeBinVect<CountWordSize> &operator&=(const LargeBinVect<CountWordSize> &v);
+ // Right to Left shift by 's' bits with self assignment
+ inline LargeBinVect<CountWordSize> &operator<<=(const CountWordSize s);
+ // Left to Right shift by 's' bits with self assignment
+ inline LargeBinVect<CountWordSize> &operator>>=(const CountWordSize s);
+
+ // Sub-LargeBinVector starting at position b (>= 0) and
+ // of length lg (or to the end)
+ inline LargeBinVect<CountWordSize> operator()(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range);
+
+ // Optimized already casted version
+ inline unsigned long int GetValue(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range);
+
+ // [ReadOnly] Access bit at position i (>= 0, < length)
+ inline bool operator[](const CountWordSize i) const throw (std::out_of_range);
+
+ // Bitwise equality. False if *this and v doesn't have the same length.
+ inline bool operator==(const LargeBinVect<CountWordSize> &v) const;
+ // Bitwise inequality. True if *this and v doesn't have the same length.
+ inline bool operator!=(const LargeBinVect<CountWordSize> &v) const;
+ // less than lexicographic operator
+ inline bool operator<(const LargeBinVect<CountWordSize> &v) const;
+ // greater than lexicographic operator
+ inline bool operator>(const LargeBinVect<CountWordSize> &v) const;
+ // less than or equal to lexicographic operator
+ inline bool operator<=(const LargeBinVect<CountWordSize> &v) const;
+ // greater than or equal to lexicographic operator
+ inline bool operator>=(const LargeBinVect<CountWordSize> &v) const;
+
+ // equivalent to operator[]
+ inline bool GetBit(const CountWordSize i) const throw (std::out_of_range);
+ // Set Bit at position i (>= 0, < length) to value
+ inline LargeBinVect<CountWordSize> &SetBit(const CountWordSize i, const bool value) throw (std::out_of_range);
+
+ // Set Bits between positions i and j (>= 0, < length) to value
+ inline LargeBinVect<CountWordSize> &SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range);
+
+ // Clear the bit vector and set all bits to value
+ inline LargeBinVect<CountWordSize> &Clear(const bool value = 0);
+
+ // set each bit of the vector to a random value
+ inline LargeBinVect<CountWordSize> &RandomInit();
+
+ // Resize the bit vector according to length and set all extra bits to value (if any)
+ inline LargeBinVect<CountWordSize> &Resize(const CountWordSize length, const bool value = 0) throw (std::bad_alloc);
+
+ // Append a bit to the vector and set its value to value
+ inline LargeBinVect<CountWordSize> &Append(const bool value) throw (BinVectOverflow, std::bad_alloc);
+
+ // Prepend a bit to the vector and set its value to value
+ inline LargeBinVect<CountWordSize> &Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc);
+
+ // Concatenate v to the current binary vector
+ inline LargeBinVect<CountWordSize> &operator+=(const LargeBinVect<CountWordSize> &v) throw (BinVectOverflow, std::bad_alloc);
+
+ // Pre-Increment the current binary vector by 1
+ inline LargeBinVect<CountWordSize> &operator++() throw (BinVectOverflow, std::bad_alloc);
+ // Post-Increment the current binary vector by 1
+ inline LargeBinVect<CountWordSize> operator++(int) throw (BinVectOverflow, std::bad_alloc);
+
+ // Pre-Decrement the current binary vector by 1
+ inline LargeBinVect<CountWordSize> &operator--() throw (BinVectOverflow);
+ // Post-Decrement the current binary vector by 1
+ inline LargeBinVect<CountWordSize> operator--(int) throw (BinVectOverflow, std::bad_alloc);
+
+ // Split the bit vector at position i.
+ // Current object is set to the prefix of length i and the remaining suffix is returned.
+ inline LargeBinVect<CountWordSize> Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc);
+
+ // Get longuest common prefix length.
+ inline CountWordSize GetLonguestCommonPrefix(const LargeBinVect<CountWordSize> &v) const;
+ // Get longuest common suffix length.
+ inline CountWordSize GetLonguestCommonSuffix(const LargeBinVect<CountWordSize> &v) const;
+
+ // Get bit vector length.
+ inline CountWordSize GetLength() const;
+
+ // Convert to ascii
+ inline char *ToString() const;
+
+ // Cast operators
+ inline operator char() const;
+ inline operator unsigned char() const;
+ inline operator short int() const;
+ inline operator unsigned short int() const;
+ inline operator int() const;
+ inline operator unsigned int() const;
+ inline operator long int() const;
+ inline operator unsigned long int() const;
+};
+
+template <typename CountWordSize>
+std::ostream &operator<<(std::ostream &os, const LargeBinVect<CountWordSize> &v);
+
+#include "largebinvect.cxx"
+#endif
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/AUTHORS b/src/libGkArrays/src/libProgressBar-1.2.0/AUTHORS
new file mode 100644
index 0000000..09dbb8f
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/AUTHORS
@@ -0,0 +1,2 @@
+libProgressBar is a part of my research stuff:
+ DoccY <alban.mancheron at inria.fr>
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/COPYING b/src/libGkArrays/src/libProgressBar-1.2.0/COPYING
new file mode 100644
index 0000000..eb685a5
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/COPYING
@@ -0,0 +1,481 @@
+ GNU LIBRARY GENERAL PUBLIC LICENSE
+ Version 2, June 1991
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diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/ChangeLog b/src/libGkArrays/src/libProgressBar-1.2.0/ChangeLog
new file mode 100644
index 0000000..c75bed9
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/ChangeLog
@@ -0,0 +1,118 @@
+2013-11-29 Friday tag Release_1_2_0
+
+2013-11-29 Friday DoccY <alban at mancheron.infos.st>
+
+ * configure.in (1.9), Makefile.am (1.7),
+ libProgressBar/progressBar.cpp (1.4),
+ libProgressBar/progressBar.h (1.4), libProgressBar/testPB.cpp
+ (1.3), configure (1.9), Makefile.in (1.5), doc/Makefile.in (1.3),
+ libProgressBar/Makefile.in (1.4):
+
+ Update:
+ - Time display enhancement.
+ - Allows systems without tex distribution to install the library (doc is just not built).
+ - Add a method/constructor option to add/set an initial a value to the timer.
+ - Add a 'C' function to get version number.
+
+2013-11-22 Friday DoccY <alban at mancheron.infos.st>
+
+ * INSTALL (1.2), Makefile.am (1.6), Makefile.in (1.4), aclocal.m4
+ (1.2), config.guess (1.2), config.sub (1.2), configure (1.7),
+ configure.in (1.8), depcomp (1.2), install-sh (1.2),
+ libProgressBar-1.1.pc.in (1.2), libProgressBar.pc.in (1.1),
+ ltmain.sh (1.2), missing (1.2), mkinstalldirs (1.2),
+ doc/Makefile.am (1.2), doc/Makefile.in (1.2),
+ doc/libProgressBar.1.in (1.3), doc/libProgressBar.3.in (1.1),
+ doc/texinfo.tex (1.2), libProgressBar/Makefile.am (1.4),
+ libProgressBar/Makefile.in (1.3), libProgressBar/config.h.in
+ (1.2), m4/libtool.m4 (1.1), m4/ltoptions.m4 (1.1), m4/ltsugar.m4
+ (1.1), m4/ltversion.m4 (1.1), m4/lt~obsolete.m4 (1.1), configure
+ (1.8):
+
+ Update:
+ - autotools automatic update.
+
+ BugFix:
+ - pkg-config configuration was erroneous.
+ - man page was in wrong section
+
+2007-10-17 Wednesday DoccY <alban.mancheron at lirmm.fr>
+
+ * configure.in (1.7), configure (1.6):
+
+ Changement de x86_64 amd64 pour les paquets 'deb'.
+
+2007-09-27 Thursday DoccY <alban.mancheron at lirmm.fr>
+
+ * AUTHORS (1.2), README (1.2), configure.in (1.6),
+ libProgressBar.spec.in (1.3), doc/libProgressBar.1.in (1.2),
+ doc/libProgressBar.texinfo (1.2):
+
+ Mise � jour des mentions l�gales et de mon adresse mail.
+
+2007-09-27 Thursday DoccY <alban.mancheron at lirmm.fr>
+
+ * configure.in (1.5), libProgressBar-1.0.pc.in (1.3),
+ libProgressBar-1.1.pc.in (1.1), libProgressBar/Makefile.am (1.3),
+ libProgressBar/progressBar.cpp (1.3),
+ libProgressBar/progressBar.h (1.3), libProgressBar/testPB.cpp
+ (1.2), libProgressBar/Makefile.in (1.2):
+
+ Ajout de la m�thode GetTime() qui permet de r�cup�rer le temps
+ �coul� (en s.) depuis le d�but du processus en progr�s.
+
+2007-09-10 Monday DoccY <alban.mancheron at lirmm.fr>
+
+ * Makefile.am (1.5), Makefile.in (1.2):
+
+ Coquille dans la g�n�ration du paquet debian.
+
+2007-09-10 Monday DoccY <alban.mancheron at lirmm.fr>
+
+ * Makefile.in (1.1), libProgressBar/testPB.cpp (1.1),
+ libProgressBar/Makefile.in (1.1), doc/Makefile.in (1.1):
+
+ Fichiers manquant pour l'import/export.
+
+2007-09-09 Sunday DoccY <alban.mancheron at lirmm.fr>
+
+ * Makefile.am (1.4), configure.in (1.4), postrm.in (1.3), prerm.in
+ (1.1), configure (1.4):
+
+ Bonne correction du bug sur le script de suppression pour le paquet
+ debian!!!
+
+2007-09-09 Sunday DoccY <alban.mancheron at lirmm.fr>
+
+ * postrm.in (1.2):
+
+ Correction de ce qui semble �tre un bug dans le fichier de
+ post suppression du paquet debian...
+
+2007-09-09 Sunday DoccY <alban.mancheron at lirmm.fr>
+
+ * libProgressBar/Makefile.am (1.2), libProgressBar/progressBar.cpp
+ (1.2), libProgressBar/progressBar.h (1.2):
+
+ Modulation de l'affichage (avec ou sans temps/pourcentage).
+
+2007-08-16 Thursday DoccY <alban.mancheron at lirmm.fr>
+
+ * postinst.in (1.2):
+
+ Bug dans le script de post-installation.
+
+2007-08-16 Thursday DoccY <alban.mancheron at lirmm.fr>
+
+ * Makefile.am (1.3), configure.in (1.3), libProgressBar.spec.in
+ (1.2), postinst.in (1.1), postrm.in (1.1), configure (1.3):
+
+ Ajout des scripts de mise � jour pour la liaison dynamque.
+
+2007-08-15 Wednesday DoccY <alban.mancheron at lirmm.fr>
+
+ * Makefile.am (1.2), configure.in (1.2), libProgressBar-1.0.pc.in
+ (1.2), configure (1.2):
+
+ Petit bug pour pkg-config.
+
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/INSTALL b/src/libGkArrays/src/libProgressBar-1.2.0/INSTALL
new file mode 100644
index 0000000..7d1c323
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/INSTALL
@@ -0,0 +1,365 @@
+Installation Instructions
+*************************
+
+Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005,
+2006, 2007, 2008, 2009 Free Software Foundation, Inc.
+
+ Copying and distribution of this file, with or without modification,
+are permitted in any medium without royalty provided the copyright
+notice and this notice are preserved. This file is offered as-is,
+without warranty of any kind.
+
+Basic Installation
+==================
+
+ Briefly, the shell commands `./configure; make; make install' should
+configure, build, and install this package. The following
+more-detailed instructions are generic; see the `README' file for
+instructions specific to this package. Some packages provide this
+`INSTALL' file but do not implement all of the features documented
+below. The lack of an optional feature in a given package is not
+necessarily a bug. More recommendations for GNU packages can be found
+in *note Makefile Conventions: (standards)Makefile Conventions.
+
+ The `configure' shell script attempts to guess correct values for
+various system-dependent variables used during compilation. It uses
+those values to create a `Makefile' in each directory of the package.
+It may also create one or more `.h' files containing system-dependent
+definitions. Finally, it creates a shell script `config.status' that
+you can run in the future to recreate the current configuration, and a
+file `config.log' containing compiler output (useful mainly for
+debugging `configure').
+
+ It can also use an optional file (typically called `config.cache'
+and enabled with `--cache-file=config.cache' or simply `-C') that saves
+the results of its tests to speed up reconfiguring. Caching is
+disabled by default to prevent problems with accidental use of stale
+cache files.
+
+ If you need to do unusual things to compile the package, please try
+to figure out how `configure' could check whether to do them, and mail
+diffs or instructions to the address given in the `README' so they can
+be considered for the next release. If you are using the cache, and at
+some point `config.cache' contains results you don't want to keep, you
+may remove or edit it.
+
+ The file `configure.ac' (or `configure.in') is used to create
+`configure' by a program called `autoconf'. You need `configure.ac' if
+you want to change it or regenerate `configure' using a newer version
+of `autoconf'.
+
+ The simplest way to compile this package is:
+
+ 1. `cd' to the directory containing the package's source code and type
+ `./configure' to configure the package for your system.
+
+ Running `configure' might take a while. While running, it prints
+ some messages telling which features it is checking for.
+
+ 2. Type `make' to compile the package.
+
+ 3. Optionally, type `make check' to run any self-tests that come with
+ the package, generally using the just-built uninstalled binaries.
+
+ 4. Type `make install' to install the programs and any data files and
+ documentation. When installing into a prefix owned by root, it is
+ recommended that the package be configured and built as a regular
+ user, and only the `make install' phase executed with root
+ privileges.
+
+ 5. Optionally, type `make installcheck' to repeat any self-tests, but
+ this time using the binaries in their final installed location.
+ This target does not install anything. Running this target as a
+ regular user, particularly if the prior `make install' required
+ root privileges, verifies that the installation completed
+ correctly.
+
+ 6. You can remove the program binaries and object files from the
+ source code directory by typing `make clean'. To also remove the
+ files that `configure' created (so you can compile the package for
+ a different kind of computer), type `make distclean'. There is
+ also a `make maintainer-clean' target, but that is intended mainly
+ for the package's developers. If you use it, you may have to get
+ all sorts of other programs in order to regenerate files that came
+ with the distribution.
+
+ 7. Often, you can also type `make uninstall' to remove the installed
+ files again. In practice, not all packages have tested that
+ uninstallation works correctly, even though it is required by the
+ GNU Coding Standards.
+
+ 8. Some packages, particularly those that use Automake, provide `make
+ distcheck', which can by used by developers to test that all other
+ targets like `make install' and `make uninstall' work correctly.
+ This target is generally not run by end users.
+
+Compilers and Options
+=====================
+
+ Some systems require unusual options for compilation or linking that
+the `configure' script does not know about. Run `./configure --help'
+for details on some of the pertinent environment variables.
+
+ You can give `configure' initial values for configuration parameters
+by setting variables in the command line or in the environment. Here
+is an example:
+
+ ./configure CC=c99 CFLAGS=-g LIBS=-lposix
+
+ *Note Defining Variables::, for more details.
+
+Compiling For Multiple Architectures
+====================================
+
+ You can compile the package for more than one kind of computer at the
+same time, by placing the object files for each architecture in their
+own directory. To do this, you can use GNU `make'. `cd' to the
+directory where you want the object files and executables to go and run
+the `configure' script. `configure' automatically checks for the
+source code in the directory that `configure' is in and in `..'. This
+is known as a "VPATH" build.
+
+ With a non-GNU `make', it is safer to compile the package for one
+architecture at a time in the source code directory. After you have
+installed the package for one architecture, use `make distclean' before
+reconfiguring for another architecture.
+
+ On MacOS X 10.5 and later systems, you can create libraries and
+executables that work on multiple system types--known as "fat" or
+"universal" binaries--by specifying multiple `-arch' options to the
+compiler but only a single `-arch' option to the preprocessor. Like
+this:
+
+ ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+ CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+ CPP="gcc -E" CXXCPP="g++ -E"
+
+ This is not guaranteed to produce working output in all cases, you
+may have to build one architecture at a time and combine the results
+using the `lipo' tool if you have problems.
+
+Installation Names
+==================
+
+ By default, `make install' installs the package's commands under
+`/usr/local/bin', include files under `/usr/local/include', etc. You
+can specify an installation prefix other than `/usr/local' by giving
+`configure' the option `--prefix=PREFIX', where PREFIX must be an
+absolute file name.
+
+ You can specify separate installation prefixes for
+architecture-specific files and architecture-independent files. If you
+pass the option `--exec-prefix=PREFIX' to `configure', the package uses
+PREFIX as the prefix for installing programs and libraries.
+Documentation and other data files still use the regular prefix.
+
+ In addition, if you use an unusual directory layout you can give
+options like `--bindir=DIR' to specify different values for particular
+kinds of files. Run `configure --help' for a list of the directories
+you can set and what kinds of files go in them. In general, the
+default for these options is expressed in terms of `${prefix}', so that
+specifying just `--prefix' will affect all of the other directory
+specifications that were not explicitly provided.
+
+ The most portable way to affect installation locations is to pass the
+correct locations to `configure'; however, many packages provide one or
+both of the following shortcuts of passing variable assignments to the
+`make install' command line to change installation locations without
+having to reconfigure or recompile.
+
+ The first method involves providing an override variable for each
+affected directory. For example, `make install
+prefix=/alternate/directory' will choose an alternate location for all
+directory configuration variables that were expressed in terms of
+`${prefix}'. Any directories that were specified during `configure',
+but not in terms of `${prefix}', must each be overridden at install
+time for the entire installation to be relocated. The approach of
+makefile variable overrides for each directory variable is required by
+the GNU Coding Standards, and ideally causes no recompilation.
+However, some platforms have known limitations with the semantics of
+shared libraries that end up requiring recompilation when using this
+method, particularly noticeable in packages that use GNU Libtool.
+
+ The second method involves providing the `DESTDIR' variable. For
+example, `make install DESTDIR=/alternate/directory' will prepend
+`/alternate/directory' before all installation names. The approach of
+`DESTDIR' overrides is not required by the GNU Coding Standards, and
+does not work on platforms that have drive letters. On the other hand,
+it does better at avoiding recompilation issues, and works well even
+when some directory options were not specified in terms of `${prefix}'
+at `configure' time.
+
+Optional Features
+=================
+
+ If the package supports it, you can cause programs to be installed
+with an extra prefix or suffix on their names by giving `configure' the
+option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
+
+ Some packages pay attention to `--enable-FEATURE' options to
+`configure', where FEATURE indicates an optional part of the package.
+They may also pay attention to `--with-PACKAGE' options, where PACKAGE
+is something like `gnu-as' or `x' (for the X Window System). The
+`README' should mention any `--enable-' and `--with-' options that the
+package recognizes.
+
+ For packages that use the X Window System, `configure' can usually
+find the X include and library files automatically, but if it doesn't,
+you can use the `configure' options `--x-includes=DIR' and
+`--x-libraries=DIR' to specify their locations.
+
+ Some packages offer the ability to configure how verbose the
+execution of `make' will be. For these packages, running `./configure
+--enable-silent-rules' sets the default to minimal output, which can be
+overridden with `make V=1'; while running `./configure
+--disable-silent-rules' sets the default to verbose, which can be
+overridden with `make V=0'.
+
+Particular systems
+==================
+
+ On HP-UX, the default C compiler is not ANSI C compatible. If GNU
+CC is not installed, it is recommended to use the following options in
+order to use an ANSI C compiler:
+
+ ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
+
+and if that doesn't work, install pre-built binaries of GCC for HP-UX.
+
+ On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
+parse its `<wchar.h>' header file. The option `-nodtk' can be used as
+a workaround. If GNU CC is not installed, it is therefore recommended
+to try
+
+ ./configure CC="cc"
+
+and if that doesn't work, try
+
+ ./configure CC="cc -nodtk"
+
+ On Solaris, don't put `/usr/ucb' early in your `PATH'. This
+directory contains several dysfunctional programs; working variants of
+these programs are available in `/usr/bin'. So, if you need `/usr/ucb'
+in your `PATH', put it _after_ `/usr/bin'.
+
+ On Haiku, software installed for all users goes in `/boot/common',
+not `/usr/local'. It is recommended to use the following options:
+
+ ./configure --prefix=/boot/common
+
+Specifying the System Type
+==========================
+
+ There may be some features `configure' cannot figure out
+automatically, but needs to determine by the type of machine the package
+will run on. Usually, assuming the package is built to be run on the
+_same_ architectures, `configure' can figure that out, but if it prints
+a message saying it cannot guess the machine type, give it the
+`--build=TYPE' option. TYPE can either be a short name for the system
+type, such as `sun4', or a canonical name which has the form:
+
+ CPU-COMPANY-SYSTEM
+
+where SYSTEM can have one of these forms:
+
+ OS
+ KERNEL-OS
+
+ See the file `config.sub' for the possible values of each field. If
+`config.sub' isn't included in this package, then this package doesn't
+need to know the machine type.
+
+ If you are _building_ compiler tools for cross-compiling, you should
+use the option `--target=TYPE' to select the type of system they will
+produce code for.
+
+ If you want to _use_ a cross compiler, that generates code for a
+platform different from the build platform, you should specify the
+"host" platform (i.e., that on which the generated programs will
+eventually be run) with `--host=TYPE'.
+
+Sharing Defaults
+================
+
+ If you want to set default values for `configure' scripts to share,
+you can create a site shell script called `config.site' that gives
+default values for variables like `CC', `cache_file', and `prefix'.
+`configure' looks for `PREFIX/share/config.site' if it exists, then
+`PREFIX/etc/config.site' if it exists. Or, you can set the
+`CONFIG_SITE' environment variable to the location of the site script.
+A warning: not all `configure' scripts look for a site script.
+
+Defining Variables
+==================
+
+ Variables not defined in a site shell script can be set in the
+environment passed to `configure'. However, some packages may run
+configure again during the build, and the customized values of these
+variables may be lost. In order to avoid this problem, you should set
+them in the `configure' command line, using `VAR=value'. For example:
+
+ ./configure CC=/usr/local2/bin/gcc
+
+causes the specified `gcc' to be used as the C compiler (unless it is
+overridden in the site shell script).
+
+Unfortunately, this technique does not work for `CONFIG_SHELL' due to
+an Autoconf bug. Until the bug is fixed you can use this workaround:
+
+ CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash
+
+`configure' Invocation
+======================
+
+ `configure' recognizes the following options to control how it
+operates.
+
+`--help'
+`-h'
+ Print a summary of all of the options to `configure', and exit.
+
+`--help=short'
+`--help=recursive'
+ Print a summary of the options unique to this package's
+ `configure', and exit. The `short' variant lists options used
+ only in the top level, while the `recursive' variant lists options
+ also present in any nested packages.
+
+`--version'
+`-V'
+ Print the version of Autoconf used to generate the `configure'
+ script, and exit.
+
+`--cache-file=FILE'
+ Enable the cache: use and save the results of the tests in FILE,
+ traditionally `config.cache'. FILE defaults to `/dev/null' to
+ disable caching.
+
+`--config-cache'
+`-C'
+ Alias for `--cache-file=config.cache'.
+
+`--quiet'
+`--silent'
+`-q'
+ Do not print messages saying which checks are being made. To
+ suppress all normal output, redirect it to `/dev/null' (any error
+ messages will still be shown).
+
+`--srcdir=DIR'
+ Look for the package's source code in directory DIR. Usually
+ `configure' can determine that directory automatically.
+
+`--prefix=DIR'
+ Use DIR as the installation prefix. *note Installation Names::
+ for more details, including other options available for fine-tuning
+ the installation locations.
+
+`--no-create'
+`-n'
+ Run the configure checks, but stop before creating any output
+ files.
+
+`configure' also accepts some other, not widely useful, options. Run
+`configure --help' for more details.
+
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/Makefile.am b/src/libGkArrays/src/libProgressBar-1.2.0/Makefile.am
new file mode 100644
index 0000000..49853cd
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/Makefile.am
@@ -0,0 +1,124 @@
+SUBDIRS = $(PACKAGE)
+
+if BUILD_DOC
+ SUBDIRS += doc
+endif
+
+DISTSUBDIRS = $(PACKAGE)
+EXTRA_DIST=$(PACKAGE).lsm.in $(PACKAGE).spec.in control.in AUTHORS COPYING ChangeLog INSTALL NEWS README
+
+pkgconfigdir = $(libdir)/pkgconfig
+pkgconfig_DATA = @PACKAGE at -@PACKAGE_VERSION at .pc
+
+ at PACKAGE@- at PACKAGE_VERSION@.pc: @PACKAGE at .pc
+ cp "$^" "$@"
+
+deb: @PACKAGE at _@PACKAGE_VERSION at _@ARCH at .deb
+
+rpm: rpm-bin rpm-src
+rpm-bin: @PACKAGE at -@PACKAGE_VERSION at -1.@ARCH at .rpm
+rpm-src: @PACKAGE at -@PACKAGE_VERSION at -1.src.rpm
+
+ACLOCAL_AMFLAGS=-I m4
+
+ at PACKAGE@_ at PACKAGE_VERSION@_ at ARCH@.deb:
+ @if [ "@DEB_BUILDER@" == "" ]; then \
+ echo "You need to install a debian package builder and to reconfigure this package.";\
+ exit 1;\
+ fi
+ make dist
+ $(am__remove_distdir)
+ GZIP=$(GZIP_ENV) gunzip -c $(distdir).tar.gz | $(AMTAR) xf -
+ mkdir $(distdir)/_build
+ mkdir -p $(distdir)/_inst/_deb/$(prefix)
+ chmod a-w $(distdir)
+ dc_install_base=`$(am__cd) $(distdir)/_inst/_deb/$(prefix) && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
+ && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
+ && cd $(distdir)/_build \
+ && localedir=$(datadir)/locale \
+ && HACKED_PREFIX=$(prefix) ../configure --srcdir=.. --prefix="$$dc_install_base" \
+ $(DISTCHECK_CONFIGURE_FLAGS) \
+ && $(MAKE) $(AM_MAKEFLAGS) localedir=$$localedir \
+ && $(MAKE) $(AM_MAKEFLAGS) dvi \
+ && $(MAKE) $(AM_MAKEFLAGS) check \
+ && $(MAKE) $(AM_MAKEFLAGS) install \
+ && $(MAKE) $(AM_MAKEFLAGS) installcheck \
+ && cd ../_inst/_deb \
+ && find . -type f -exec md5sum {} \; | sed "s,\.\/,,g" > ../md5sums \
+ && mkdir DEBIAN \
+ && mv ../md5sums DEBIAN/ \
+ && cp ../../_build/control DEBIAN/ \
+ && cp ../../_build/postinst DEBIAN/ \
+ && cp ../../_build/prerm DEBIAN/ \
+ && sed "s/@INSTALLED_SIZE@/`du -ck . | tail -1 | cut -f1`/" ../../_build/control > DEBIAN/control \
+ && cd ../ \
+ && dpkg -b _deb $@ \
+ && mv $@ ../../ \
+ && rm -f "$$dc_install_base/DEBIAN/control" \
+ && rm -f "$$dc_install_base/DEBIAN/prerm" \
+ && rm -f "$$dc_install_base/DEBIAN/postinst" \
+ && cd ../_build \
+ && $(MAKE) $(AM_MAKEFLAGS) uninstall \
+ && $(MAKE) $(AM_MAKEFLAGS) distuninstallcheck_dir="$$dc_install_base" \
+ distuninstallcheck \
+ && chmod -R a-w "$$dc_install_base" \
+ && ({ \
+ (cd ../.. && $(mkinstalldirs) "$$dc_destdir") \
+ && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" install \
+ && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" uninstall \
+ && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" \
+ distuninstallcheck_dir="$$dc_destdir" distuninstallcheck; \
+ } || { rm -rf "$$dc_destdir"; exit 1; }) \
+ && rm -rf "$$dc_destdir" \
+ && $(MAKE) $(AM_MAKEFLAGS) distcleancheck
+ $(am__remove_distdir)
+ @echo "$@ is ready for distribution" | \
+ sed 'h;s/./=/g;p;x;p;x'
+
+rpm-all:
+ @if [ "@RPM_BUILDER@" == "" ]; then \
+ echo "You need to install a rpm package builder and to reconfigure this package.";\
+ exit 1;\
+ fi
+ make dist
+ $(am__remove_distdir)
+ mkdir $(distdir)
+ mkdir -p $(distdir)/BUILD
+ mkdir -p $(distdir)/RPMS
+ mkdir -p $(distdir)/SOURCES
+ mkdir -p $(distdir)/SPECS
+ mkdir -p $(distdir)/SRPMS
+ cp $(distdir).tar.gz $(distdir)/SOURCES
+
+ at PACKAGE@- at VERSION@-1. at ARCH@.rpm : @PACKAGE at .spec
+ make rpm-all
+ @RPM_BUILDER@ --clean -bb --sign --quiet $<
+ mv $(distdir)/RPMS/@ARCH@/$@ .
+ $(am__remove_distdir)
+ @echo "$@ is ready for distribution" | \
+ sed 'h;s/./=/g;p;x;p;x'
+
+ at PACKAGE@- at VERSION@-1.src.rpm : @PACKAGE at .spec
+ make rpm-all
+ @RPM_BUILDER@ --clean -bs --sign --quiet $<
+ mv $(distdir)/SRPMS/$@ .
+ $(am__remove_distdir)
+ @echo "$@ is ready for distribution" | \
+ sed 'h;s/./=/g;p;x;p;x'
+
+
+install-data-hook:
+ $(LN_S) -f @PACKAGE at -@VERSION at .pc $(DESTDIR)@libdir@/pkgconfig/@PACKAGE at .pc
+
+uninstall-hook:
+ test "`readlink $(DESTDIR)@libdir@/pkgconfig/@PACKAGE at .pc`" != @PACKAGE at -@VERSION at .pc \
+ || $(RM) $(DESTDIR)@libdir@/pkgconfig/@PACKAGE at .pc
+
+MOSTLYCLEANFILES=*~
+CLEANFILES=*~
+DISTCLEANFILES=*~ control $(distdir).tar.gz
+DISTCLEANFILES+=@PACKAGE@*- at PACKAGE_VERSION@.pc
+DISTCLEANFILES+=@PACKAGE at _@PACKAGE_VERSION at _@ARCH at .deb
+DISTCLEANFILES+=@PACKAGE at -@PACKAGE_VERSION at -1.@ARCH at .rpm
+DISTCLEANFILES+=@PACKAGE at -@PACKAGE_VERSION at -1.src.rpm
+MAINTAINERCLEANFILES=*~
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/Makefile.in b/src/libGkArrays/src/libProgressBar-1.2.0/Makefile.in
new file mode 100644
index 0000000..3370f0a
--- /dev/null
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+
+maintainer-clean-generic:
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+ @echo "it deletes files that may require special tools to rebuild."
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diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/NEWS b/src/libGkArrays/src/libProgressBar-1.2.0/NEWS
new file mode 100644
index 0000000..e69de29
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/README b/src/libGkArrays/src/libProgressBar-1.2.0/README
new file mode 100644
index 0000000..c2003dc
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/README
@@ -0,0 +1,29 @@
+ libProgressBar is a C++ library to manage... Progress bars!!!
+
+ Copyright � 2007 -- Universit� de Antilles et de la Guyane
+ Copyright � 2007 -- Institut National de Recherche en Informatique et en Automatique
+
+ Author: DoccY <alban.mancheron at inria.fr>
+
+ This File initially comes from StatiSTARS.
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Library General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or (at your
+ option) any later version.
+
+ This library is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public
+ License for more details.
+
+ You should have received a copy of the GNU Library General Public License
+ along with this library; if not, write:
+
+ the Free Software Foundation, Inc.,
+ 59 Temple Place - Suite 330,
+ Boston, MA 02111-1307, USA.
+
+Comments are welcome.
+
+ - DoccY <alban.mancheron at inria.fr>
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/acinclude.m4 b/src/libGkArrays/src/libProgressBar-1.2.0/acinclude.m4
new file mode 100644
index 0000000..6fceaec
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/acinclude.m4
@@ -0,0 +1,40 @@
+#serial 3
+
+dnl From Jim Meyering
+
+dnl Define HAVE_STRUCT_UTIMBUF if `struct utimbuf' is declared --
+dnl usually in <utime.h>.
+dnl Some systems have utime.h but don't declare the struct anywhere.
+
+AC_DEFUN([jm_CHECK_TYPE_STRUCT_UTIMBUF],
+[
+ AC_CHECK_HEADERS(utime.h)
+ AC_REQUIRE([AC_HEADER_TIME])
+ AC_CACHE_CHECK([for struct utimbuf], fu_cv_sys_struct_utimbuf,
+ [AC_TRY_COMPILE(
+ [
+#ifdef TIME_WITH_SYS_TIME
+# include <sys/time.h>
+# include <time.h>
+#else
+# ifdef HAVE_SYS_TIME_H
+# include <sys/time.h>
+# else
+# include <time.h>
+# endif
+#endif
+#ifdef HAVE_UTIME_H
+# include <utime.h>
+#endif
+ ],
+ [static struct utimbuf x; x.actime = x.modtime;],
+ fu_cv_sys_struct_utimbuf=yes,
+ fu_cv_sys_struct_utimbuf=no)
+ ])
+
+ if test $fu_cv_sys_struct_utimbuf = yes; then
+ AC_DEFINE_UNQUOTED(HAVE_STRUCT_UTIMBUF, 1,
+[Define if struct utimbuf is declared -- usually in <utime.h>.
+ Some systems have utime.h but don't declare the struct anywhere. ])
+ fi
+])
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/aclocal.m4 b/src/libGkArrays/src/libProgressBar-1.2.0/aclocal.m4
new file mode 100644
index 0000000..c8f002a
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/aclocal.m4
@@ -0,0 +1,8918 @@
+# generated automatically by aclocal 1.11.1 -*- Autoconf -*-
+
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
+# 2005, 2006, 2007, 2008, 2009 Free Software Foundation, Inc.
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+m4_ifndef([AC_AUTOCONF_VERSION],
+ [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
+m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.67],,
+[m4_warning([this file was generated for autoconf 2.67.
+You have another version of autoconf. It may work, but is not guaranteed to.
+If you have problems, you may need to regenerate the build system entirely.
+To do so, use the procedure documented by the package, typically `autoreconf'.])])
+
+# libtool.m4 - Configure libtool for the host system. -*-Autoconf-*-
+#
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
+# 2006, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gordon Matzigkeit, 1996
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+m4_define([_LT_COPYING], [dnl
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
+# 2006, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gordon Matzigkeit, 1996
+#
+# This file is part of GNU Libtool.
+#
+# GNU Libtool is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License as
+# published by the Free Software Foundation; either version 2 of
+# the License, or (at your option) any later version.
+#
+# As a special exception to the GNU General Public License,
+# if you distribute this file as part of a program or library that
+# is built using GNU Libtool, you may include this file under the
+# same distribution terms that you use for the rest of that program.
+#
+# GNU Libtool is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GNU Libtool; see the file COPYING. If not, a copy
+# can be downloaded from http://www.gnu.org/licenses/gpl.html, or
+# obtained by writing to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+])
+
+# serial 56 LT_INIT
+
+
+# LT_PREREQ(VERSION)
+# ------------------
+# Complain and exit if this libtool version is less that VERSION.
+m4_defun([LT_PREREQ],
+[m4_if(m4_version_compare(m4_defn([LT_PACKAGE_VERSION]), [$1]), -1,
+ [m4_default([$3],
+ [m4_fatal([Libtool version $1 or higher is required],
+ 63)])],
+ [$2])])
+
+
+# _LT_CHECK_BUILDDIR
+# ------------------
+# Complain if the absolute build directory name contains unusual characters
+m4_defun([_LT_CHECK_BUILDDIR],
+[case `pwd` in
+ *\ * | *\ *)
+ AC_MSG_WARN([Libtool does not cope well with whitespace in `pwd`]) ;;
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+])
+
+
+# LT_INIT([OPTIONS])
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+AC_BEFORE([$0], [LT_LANG])dnl
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+m4_require([_LT_PROG_LTMAIN])dnl
+
+dnl Parse OPTIONS
+_LT_SET_OPTIONS([$0], [$1])
+
+# This can be used to rebuild libtool when needed
+LIBTOOL_DEPS="$ltmain"
+
+# Always use our own libtool.
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+AC_SUBST(LIBTOOL)dnl
+
+_LT_SETUP
+
+# Only expand once:
+m4_define([LT_INIT])
+])# LT_INIT
+
+# Old names:
+AU_ALIAS([AC_PROG_LIBTOOL], [LT_INIT])
+AU_ALIAS([AM_PROG_LIBTOOL], [LT_INIT])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_PROG_LIBTOOL], [])
+dnl AC_DEFUN([AM_PROG_LIBTOOL], [])
+
+
+# _LT_CC_BASENAME(CC)
+# -------------------
+# Calculate cc_basename. Skip known compiler wrappers and cross-prefix.
+m4_defun([_LT_CC_BASENAME],
+[for cc_temp in $1""; do
+ case $cc_temp in
+ compile | *[[\\/]]compile | ccache | *[[\\/]]ccache ) ;;
+ distcc | *[[\\/]]distcc | purify | *[[\\/]]purify ) ;;
+ \-*) ;;
+ *) break;;
+ esac
+done
+cc_basename=`$ECHO "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+])
+
+
+# _LT_FILEUTILS_DEFAULTS
+# ----------------------
+# It is okay to use these file commands and assume they have been set
+# sensibly after `m4_require([_LT_FILEUTILS_DEFAULTS])'.
+m4_defun([_LT_FILEUTILS_DEFAULTS],
+[: ${CP="cp -f"}
+: ${MV="mv -f"}
+: ${RM="rm -f"}
+])# _LT_FILEUTILS_DEFAULTS
+
+
+# _LT_SETUP
+# ---------
+m4_defun([_LT_SETUP],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+AC_REQUIRE([AC_CANONICAL_BUILD])dnl
+_LT_DECL([], [host_alias], [0], [The host system])dnl
+_LT_DECL([], [host], [0])dnl
+_LT_DECL([], [host_os], [0])dnl
+dnl
+_LT_DECL([], [build_alias], [0], [The build system])dnl
+_LT_DECL([], [build], [0])dnl
+_LT_DECL([], [build_os], [0])dnl
+dnl
+AC_REQUIRE([AC_PROG_CC])dnl
+AC_REQUIRE([LT_PATH_LD])dnl
+AC_REQUIRE([LT_PATH_NM])dnl
+dnl
+AC_REQUIRE([AC_PROG_LN_S])dnl
+test -z "$LN_S" && LN_S="ln -s"
+_LT_DECL([], [LN_S], [1], [Whether we need soft or hard links])dnl
+dnl
+AC_REQUIRE([LT_CMD_MAX_LEN])dnl
+_LT_DECL([objext], [ac_objext], [0], [Object file suffix (normally "o")])dnl
+_LT_DECL([], [exeext], [0], [Executable file suffix (normally "")])dnl
+dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_CHECK_SHELL_FEATURES])dnl
+m4_require([_LT_CMD_RELOAD])dnl
+m4_require([_LT_CHECK_MAGIC_METHOD])dnl
+m4_require([_LT_CMD_OLD_ARCHIVE])dnl
+m4_require([_LT_CMD_GLOBAL_SYMBOLS])dnl
+
+_LT_CONFIG_LIBTOOL_INIT([
+# See if we are running on zsh, and set the options which allow our
+# commands through without removal of \ escapes INIT.
+if test -n "\${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+fi
+])
+if test -n "${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+fi
+
+_LT_CHECK_OBJDIR
+
+m4_require([_LT_TAG_COMPILER])dnl
+_LT_PROG_ECHO_BACKSLASH
+
+case $host_os in
+aix3*)
+ # AIX sometimes has problems with the GCC collect2 program. For some
+ # reason, if we set the COLLECT_NAMES environment variable, the problems
+ # vanish in a puff of smoke.
+ if test "X${COLLECT_NAMES+set}" != Xset; then
+ COLLECT_NAMES=
+ export COLLECT_NAMES
+ fi
+ ;;
+esac
+
+# Sed substitution that helps us do robust quoting. It backslashifies
+# metacharacters that are still active within double-quoted strings.
+sed_quote_subst='s/\([["`$\\]]\)/\\\1/g'
+
+# Same as above, but do not quote variable references.
+double_quote_subst='s/\([["`\\]]\)/\\\1/g'
+
+# Sed substitution to delay expansion of an escaped shell variable in a
+# double_quote_subst'ed string.
+delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g'
+
+# Sed substitution to delay expansion of an escaped single quote.
+delay_single_quote_subst='s/'\''/'\'\\\\\\\'\''/g'
+
+# Sed substitution to avoid accidental globbing in evaled expressions
+no_glob_subst='s/\*/\\\*/g'
+
+# Global variables:
+ofile=libtool
+can_build_shared=yes
+
+# All known linkers require a `.a' archive for static linking (except MSVC,
+# which needs '.lib').
+libext=a
+
+with_gnu_ld="$lt_cv_prog_gnu_ld"
+
+old_CC="$CC"
+old_CFLAGS="$CFLAGS"
+
+# Set sane defaults for various variables
+test -z "$CC" && CC=cc
+test -z "$LTCC" && LTCC=$CC
+test -z "$LTCFLAGS" && LTCFLAGS=$CFLAGS
+test -z "$LD" && LD=ld
+test -z "$ac_objext" && ac_objext=o
+
+_LT_CC_BASENAME([$compiler])
+
+# Only perform the check for file, if the check method requires it
+test -z "$MAGIC_CMD" && MAGIC_CMD=file
+case $deplibs_check_method in
+file_magic*)
+ if test "$file_magic_cmd" = '$MAGIC_CMD'; then
+ _LT_PATH_MAGIC
+ fi
+ ;;
+esac
+
+# Use C for the default configuration in the libtool script
+LT_SUPPORTED_TAG([CC])
+_LT_LANG_C_CONFIG
+_LT_LANG_DEFAULT_CONFIG
+_LT_CONFIG_COMMANDS
+])# _LT_SETUP
+
+
+# _LT_PROG_LTMAIN
+# ---------------
+# Note that this code is called both from `configure', and `config.status'
+# now that we use AC_CONFIG_COMMANDS to generate libtool. Notably,
+# `config.status' has no value for ac_aux_dir unless we are using Automake,
+# so we pass a copy along to make sure it has a sensible value anyway.
+m4_defun([_LT_PROG_LTMAIN],
+[m4_ifdef([AC_REQUIRE_AUX_FILE], [AC_REQUIRE_AUX_FILE([ltmain.sh])])dnl
+_LT_CONFIG_LIBTOOL_INIT([ac_aux_dir='$ac_aux_dir'])
+ltmain="$ac_aux_dir/ltmain.sh"
+])# _LT_PROG_LTMAIN
+
+
+
+# So that we can recreate a full libtool script including additional
+# tags, we accumulate the chunks of code to send to AC_CONFIG_COMMANDS
+# in macros and then make a single call at the end using the `libtool'
+# label.
+
+
+# _LT_CONFIG_LIBTOOL_INIT([INIT-COMMANDS])
+# ----------------------------------------
+# Register INIT-COMMANDS to be passed to AC_CONFIG_COMMANDS later.
+m4_define([_LT_CONFIG_LIBTOOL_INIT],
+[m4_ifval([$1],
+ [m4_append([_LT_OUTPUT_LIBTOOL_INIT],
+ [$1
+])])])
+
+# Initialize.
+m4_define([_LT_OUTPUT_LIBTOOL_INIT])
+
+
+# _LT_CONFIG_LIBTOOL([COMMANDS])
+# ------------------------------
+# Register COMMANDS to be passed to AC_CONFIG_COMMANDS later.
+m4_define([_LT_CONFIG_LIBTOOL],
+[m4_ifval([$1],
+ [m4_append([_LT_OUTPUT_LIBTOOL_COMMANDS],
+ [$1
+])])])
+
+# Initialize.
+m4_define([_LT_OUTPUT_LIBTOOL_COMMANDS])
+
+
+# _LT_CONFIG_SAVE_COMMANDS([COMMANDS], [INIT_COMMANDS])
+# -----------------------------------------------------
+m4_defun([_LT_CONFIG_SAVE_COMMANDS],
+[_LT_CONFIG_LIBTOOL([$1])
+_LT_CONFIG_LIBTOOL_INIT([$2])
+])
+
+
+# _LT_FORMAT_COMMENT([COMMENT])
+# -----------------------------
+# Add leading comment marks to the start of each line, and a trailing
+# full-stop to the whole comment if one is not present already.
+m4_define([_LT_FORMAT_COMMENT],
+[m4_ifval([$1], [
+m4_bpatsubst([m4_bpatsubst([$1], [^ *], [# ])],
+ [['`$\]], [\\\&])]m4_bmatch([$1], [[!?.]$], [], [.])
+)])
+
+
+
+
+
+# _LT_DECL([CONFIGNAME], VARNAME, VALUE, [DESCRIPTION], [IS-TAGGED?])
+# -------------------------------------------------------------------
+# CONFIGNAME is the name given to the value in the libtool script.
+# VARNAME is the (base) name used in the configure script.
+# VALUE may be 0, 1 or 2 for a computed quote escaped value based on
+# VARNAME. Any other value will be used directly.
+m4_define([_LT_DECL],
+[lt_if_append_uniq([lt_decl_varnames], [$2], [, ],
+ [lt_dict_add_subkey([lt_decl_dict], [$2], [libtool_name],
+ [m4_ifval([$1], [$1], [$2])])
+ lt_dict_add_subkey([lt_decl_dict], [$2], [value], [$3])
+ m4_ifval([$4],
+ [lt_dict_add_subkey([lt_decl_dict], [$2], [description], [$4])])
+ lt_dict_add_subkey([lt_decl_dict], [$2],
+ [tagged?], [m4_ifval([$5], [yes], [no])])])
+])
+
+
+# _LT_TAGDECL([CONFIGNAME], VARNAME, VALUE, [DESCRIPTION])
+# --------------------------------------------------------
+m4_define([_LT_TAGDECL], [_LT_DECL([$1], [$2], [$3], [$4], [yes])])
+
+
+# lt_decl_tag_varnames([SEPARATOR], [VARNAME1...])
+# ------------------------------------------------
+m4_define([lt_decl_tag_varnames],
+[_lt_decl_filter([tagged?], [yes], $@)])
+
+
+# _lt_decl_filter(SUBKEY, VALUE, [SEPARATOR], [VARNAME1..])
+# ---------------------------------------------------------
+m4_define([_lt_decl_filter],
+[m4_case([$#],
+ [0], [m4_fatal([$0: too few arguments: $#])],
+ [1], [m4_fatal([$0: too few arguments: $#: $1])],
+ [2], [lt_dict_filter([lt_decl_dict], [$1], [$2], [], lt_decl_varnames)],
+ [3], [lt_dict_filter([lt_decl_dict], [$1], [$2], [$3], lt_decl_varnames)],
+ [lt_dict_filter([lt_decl_dict], $@)])[]dnl
+])
+
+
+# lt_decl_quote_varnames([SEPARATOR], [VARNAME1...])
+# --------------------------------------------------
+m4_define([lt_decl_quote_varnames],
+[_lt_decl_filter([value], [1], $@)])
+
+
+# lt_decl_dquote_varnames([SEPARATOR], [VARNAME1...])
+# ---------------------------------------------------
+m4_define([lt_decl_dquote_varnames],
+[_lt_decl_filter([value], [2], $@)])
+
+
+# lt_decl_varnames_tagged([SEPARATOR], [VARNAME1...])
+# ---------------------------------------------------
+m4_define([lt_decl_varnames_tagged],
+[m4_assert([$# <= 2])dnl
+_$0(m4_quote(m4_default([$1], [[, ]])),
+ m4_ifval([$2], [[$2]], [m4_dquote(lt_decl_tag_varnames)]),
+ m4_split(m4_normalize(m4_quote(_LT_TAGS)), [ ]))])
+m4_define([_lt_decl_varnames_tagged],
+[m4_ifval([$3], [lt_combine([$1], [$2], [_], $3)])])
+
+
+# lt_decl_all_varnames([SEPARATOR], [VARNAME1...])
+# ------------------------------------------------
+m4_define([lt_decl_all_varnames],
+[_$0(m4_quote(m4_default([$1], [[, ]])),
+ m4_if([$2], [],
+ m4_quote(lt_decl_varnames),
+ m4_quote(m4_shift($@))))[]dnl
+])
+m4_define([_lt_decl_all_varnames],
+[lt_join($@, lt_decl_varnames_tagged([$1],
+ lt_decl_tag_varnames([[, ]], m4_shift($@))))dnl
+])
+
+
+# _LT_CONFIG_STATUS_DECLARE([VARNAME])
+# ------------------------------------
+# Quote a variable value, and forward it to `config.status' so that its
+# declaration there will have the same value as in `configure'. VARNAME
+# must have a single quote delimited value for this to work.
+m4_define([_LT_CONFIG_STATUS_DECLARE],
+[$1='`$ECHO "X$][$1" | $Xsed -e "$delay_single_quote_subst"`'])
+
+
+# _LT_CONFIG_STATUS_DECLARATIONS
+# ------------------------------
+# We delimit libtool config variables with single quotes, so when
+# we write them to config.status, we have to be sure to quote all
+# embedded single quotes properly. In configure, this macro expands
+# each variable declared with _LT_DECL (and _LT_TAGDECL) into:
+#
+# <var>='`$ECHO "X$<var>" | $Xsed -e "$delay_single_quote_subst"`'
+m4_defun([_LT_CONFIG_STATUS_DECLARATIONS],
+[m4_foreach([_lt_var], m4_quote(lt_decl_all_varnames),
+ [m4_n([_LT_CONFIG_STATUS_DECLARE(_lt_var)])])])
+
+
+# _LT_LIBTOOL_TAGS
+# ----------------
+# Output comment and list of tags supported by the script
+m4_defun([_LT_LIBTOOL_TAGS],
+[_LT_FORMAT_COMMENT([The names of the tagged configurations supported by this script])dnl
+available_tags="_LT_TAGS"dnl
+])
+
+
+# _LT_LIBTOOL_DECLARE(VARNAME, [TAG])
+# -----------------------------------
+# Extract the dictionary values for VARNAME (optionally with TAG) and
+# expand to a commented shell variable setting:
+#
+# # Some comment about what VAR is for.
+# visible_name=$lt_internal_name
+m4_define([_LT_LIBTOOL_DECLARE],
+[_LT_FORMAT_COMMENT(m4_quote(lt_dict_fetch([lt_decl_dict], [$1],
+ [description])))[]dnl
+m4_pushdef([_libtool_name],
+ m4_quote(lt_dict_fetch([lt_decl_dict], [$1], [libtool_name])))[]dnl
+m4_case(m4_quote(lt_dict_fetch([lt_decl_dict], [$1], [value])),
+ [0], [_libtool_name=[$]$1],
+ [1], [_libtool_name=$lt_[]$1],
+ [2], [_libtool_name=$lt_[]$1],
+ [_libtool_name=lt_dict_fetch([lt_decl_dict], [$1], [value])])[]dnl
+m4_ifval([$2], [_$2])[]m4_popdef([_libtool_name])[]dnl
+])
+
+
+# _LT_LIBTOOL_CONFIG_VARS
+# -----------------------
+# Produce commented declarations of non-tagged libtool config variables
+# suitable for insertion in the LIBTOOL CONFIG section of the `libtool'
+# script. Tagged libtool config variables (even for the LIBTOOL CONFIG
+# section) are produced by _LT_LIBTOOL_TAG_VARS.
+m4_defun([_LT_LIBTOOL_CONFIG_VARS],
+[m4_foreach([_lt_var],
+ m4_quote(_lt_decl_filter([tagged?], [no], [], lt_decl_varnames)),
+ [m4_n([_LT_LIBTOOL_DECLARE(_lt_var)])])])
+
+
+# _LT_LIBTOOL_TAG_VARS(TAG)
+# -------------------------
+m4_define([_LT_LIBTOOL_TAG_VARS],
+[m4_foreach([_lt_var], m4_quote(lt_decl_tag_varnames),
+ [m4_n([_LT_LIBTOOL_DECLARE(_lt_var, [$1])])])])
+
+
+# _LT_TAGVAR(VARNAME, [TAGNAME])
+# ------------------------------
+m4_define([_LT_TAGVAR], [m4_ifval([$2], [$1_$2], [$1])])
+
+
+# _LT_CONFIG_COMMANDS
+# -------------------
+# Send accumulated output to $CONFIG_STATUS. Thanks to the lists of
+# variables for single and double quote escaping we saved from calls
+# to _LT_DECL, we can put quote escaped variables declarations
+# into `config.status', and then the shell code to quote escape them in
+# for loops in `config.status'. Finally, any additional code accumulated
+# from calls to _LT_CONFIG_LIBTOOL_INIT is expanded.
+m4_defun([_LT_CONFIG_COMMANDS],
+[AC_PROVIDE_IFELSE([LT_OUTPUT],
+ dnl If the libtool generation code has been placed in $CONFIG_LT,
+ dnl instead of duplicating it all over again into config.status,
+ dnl then we will have config.status run $CONFIG_LT later, so it
+ dnl needs to know what name is stored there:
+ [AC_CONFIG_COMMANDS([libtool],
+ [$SHELL $CONFIG_LT || AS_EXIT(1)], [CONFIG_LT='$CONFIG_LT'])],
+ dnl If the libtool generation code is destined for config.status,
+ dnl expand the accumulated commands and init code now:
+ [AC_CONFIG_COMMANDS([libtool],
+ [_LT_OUTPUT_LIBTOOL_COMMANDS], [_LT_OUTPUT_LIBTOOL_COMMANDS_INIT])])
+])#_LT_CONFIG_COMMANDS
+
+
+# Initialize.
+m4_define([_LT_OUTPUT_LIBTOOL_COMMANDS_INIT],
+[
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+sed_quote_subst='$sed_quote_subst'
+double_quote_subst='$double_quote_subst'
+delay_variable_subst='$delay_variable_subst'
+_LT_CONFIG_STATUS_DECLARATIONS
+LTCC='$LTCC'
+LTCFLAGS='$LTCFLAGS'
+compiler='$compiler_DEFAULT'
+
+# Quote evaled strings.
+for var in lt_decl_all_varnames([[ \
+]], lt_decl_quote_varnames); do
+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in
+ *[[\\\\\\\`\\"\\\$]]*)
+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$sed_quote_subst\\"\\\`\\\\\\""
+ ;;
+ *)
+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\""
+ ;;
+ esac
+done
+
+# Double-quote double-evaled strings.
+for var in lt_decl_all_varnames([[ \
+]], lt_decl_dquote_varnames); do
+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in
+ *[[\\\\\\\`\\"\\\$]]*)
+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$double_quote_subst\\" -e \\"\\\$sed_quote_subst\\" -e \\"\\\$delay_variable_subst\\"\\\`\\\\\\""
+ ;;
+ *)
+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\""
+ ;;
+ esac
+done
+
+# Fix-up fallback echo if it was mangled by the above quoting rules.
+case \$lt_ECHO in
+*'\\\[$]0 --fallback-echo"')dnl "
+ lt_ECHO=\`\$ECHO "X\$lt_ECHO" | \$Xsed -e 's/\\\\\\\\\\\\\\\[$]0 --fallback-echo"\[$]/\[$]0 --fallback-echo"/'\`
+ ;;
+esac
+
+_LT_OUTPUT_LIBTOOL_INIT
+])
+
+
+# LT_OUTPUT
+# ---------
+# This macro allows early generation of the libtool script (before
+# AC_OUTPUT is called), incase it is used in configure for compilation
+# tests.
+AC_DEFUN([LT_OUTPUT],
+[: ${CONFIG_LT=./config.lt}
+AC_MSG_NOTICE([creating $CONFIG_LT])
+cat >"$CONFIG_LT" <<_LTEOF
+#! $SHELL
+# Generated by $as_me.
+# Run this file to recreate a libtool stub with the current configuration.
+
+lt_cl_silent=false
+SHELL=\${CONFIG_SHELL-$SHELL}
+_LTEOF
+
+cat >>"$CONFIG_LT" <<\_LTEOF
+AS_SHELL_SANITIZE
+_AS_PREPARE
+
+exec AS_MESSAGE_FD>&1
+exec AS_MESSAGE_LOG_FD>>config.log
+{
+ echo
+ AS_BOX([Running $as_me.])
+} >&AS_MESSAGE_LOG_FD
+
+lt_cl_help="\
+\`$as_me' creates a local libtool stub from the current configuration,
+for use in further configure time tests before the real libtool is
+generated.
+
+Usage: $[0] [[OPTIONS]]
+
+ -h, --help print this help, then exit
+ -V, --version print version number, then exit
+ -q, --quiet do not print progress messages
+ -d, --debug don't remove temporary files
+
+Report bugs to <bug-libtool at gnu.org>."
+
+lt_cl_version="\
+m4_ifset([AC_PACKAGE_NAME], [AC_PACKAGE_NAME ])config.lt[]dnl
+m4_ifset([AC_PACKAGE_VERSION], [ AC_PACKAGE_VERSION])
+configured by $[0], generated by m4_PACKAGE_STRING.
+
+Copyright (C) 2008 Free Software Foundation, Inc.
+This config.lt script is free software; the Free Software Foundation
+gives unlimited permision to copy, distribute and modify it."
+
+while test $[#] != 0
+do
+ case $[1] in
+ --version | --v* | -V )
+ echo "$lt_cl_version"; exit 0 ;;
+ --help | --h* | -h )
+ echo "$lt_cl_help"; exit 0 ;;
+ --debug | --d* | -d )
+ debug=: ;;
+ --quiet | --q* | --silent | --s* | -q )
+ lt_cl_silent=: ;;
+
+ -*) AC_MSG_ERROR([unrecognized option: $[1]
+Try \`$[0] --help' for more information.]) ;;
+
+ *) AC_MSG_ERROR([unrecognized argument: $[1]
+Try \`$[0] --help' for more information.]) ;;
+ esac
+ shift
+done
+
+if $lt_cl_silent; then
+ exec AS_MESSAGE_FD>/dev/null
+fi
+_LTEOF
+
+cat >>"$CONFIG_LT" <<_LTEOF
+_LT_OUTPUT_LIBTOOL_COMMANDS_INIT
+_LTEOF
+
+cat >>"$CONFIG_LT" <<\_LTEOF
+AC_MSG_NOTICE([creating $ofile])
+_LT_OUTPUT_LIBTOOL_COMMANDS
+AS_EXIT(0)
+_LTEOF
+chmod +x "$CONFIG_LT"
+
+# configure is writing to config.log, but config.lt does its own redirection,
+# appending to config.log, which fails on DOS, as config.log is still kept
+# open by configure. Here we exec the FD to /dev/null, effectively closing
+# config.log, so it can be properly (re)opened and appended to by config.lt.
+if test "$no_create" != yes; then
+ lt_cl_success=:
+ test "$silent" = yes &&
+ lt_config_lt_args="$lt_config_lt_args --quiet"
+ exec AS_MESSAGE_LOG_FD>/dev/null
+ $SHELL "$CONFIG_LT" $lt_config_lt_args || lt_cl_success=false
+ exec AS_MESSAGE_LOG_FD>>config.log
+ $lt_cl_success || AS_EXIT(1)
+fi
+])# LT_OUTPUT
+
+
+# _LT_CONFIG(TAG)
+# ---------------
+# If TAG is the built-in tag, create an initial libtool script with a
+# default configuration from the untagged config vars. Otherwise add code
+# to config.status for appending the configuration named by TAG from the
+# matching tagged config vars.
+m4_defun([_LT_CONFIG],
+[m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+_LT_CONFIG_SAVE_COMMANDS([
+ m4_define([_LT_TAG], m4_if([$1], [], [C], [$1]))dnl
+ m4_if(_LT_TAG, [C], [
+ # See if we are running on zsh, and set the options which allow our
+ # commands through without removal of \ escapes.
+ if test -n "${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+ fi
+
+ cfgfile="${ofile}T"
+ trap "$RM \"$cfgfile\"; exit 1" 1 2 15
+ $RM "$cfgfile"
+
+ cat <<_LT_EOF >> "$cfgfile"
+#! $SHELL
+
+# `$ECHO "$ofile" | sed 's%^.*/%%'` - Provide generalized library-building support services.
+# Generated automatically by $as_me ($PACKAGE$TIMESTAMP) $VERSION
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+# NOTE: Changes made to this file will be lost: look at ltmain.sh.
+#
+_LT_COPYING
+_LT_LIBTOOL_TAGS
+
+# ### BEGIN LIBTOOL CONFIG
+_LT_LIBTOOL_CONFIG_VARS
+_LT_LIBTOOL_TAG_VARS
+# ### END LIBTOOL CONFIG
+
+_LT_EOF
+
+ case $host_os in
+ aix3*)
+ cat <<\_LT_EOF >> "$cfgfile"
+# AIX sometimes has problems with the GCC collect2 program. For some
+# reason, if we set the COLLECT_NAMES environment variable, the problems
+# vanish in a puff of smoke.
+if test "X${COLLECT_NAMES+set}" != Xset; then
+ COLLECT_NAMES=
+ export COLLECT_NAMES
+fi
+_LT_EOF
+ ;;
+ esac
+
+ _LT_PROG_LTMAIN
+
+ # We use sed instead of cat because bash on DJGPP gets confused if
+ # if finds mixed CR/LF and LF-only lines. Since sed operates in
+ # text mode, it properly converts lines to CR/LF. This bash problem
+ # is reportedly fixed, but why not run on old versions too?
+ sed '/^# Generated shell functions inserted here/q' "$ltmain" >> "$cfgfile" \
+ || (rm -f "$cfgfile"; exit 1)
+
+ _LT_PROG_XSI_SHELLFNS
+
+ sed -n '/^# Generated shell functions inserted here/,$p' "$ltmain" >> "$cfgfile" \
+ || (rm -f "$cfgfile"; exit 1)
+
+ mv -f "$cfgfile" "$ofile" ||
+ (rm -f "$ofile" && cp "$cfgfile" "$ofile" && rm -f "$cfgfile")
+ chmod +x "$ofile"
+],
+[cat <<_LT_EOF >> "$ofile"
+
+dnl Unfortunately we have to use $1 here, since _LT_TAG is not expanded
+dnl in a comment (ie after a #).
+# ### BEGIN LIBTOOL TAG CONFIG: $1
+_LT_LIBTOOL_TAG_VARS(_LT_TAG)
+# ### END LIBTOOL TAG CONFIG: $1
+_LT_EOF
+])dnl /m4_if
+],
+[m4_if([$1], [], [
+ PACKAGE='$PACKAGE'
+ VERSION='$VERSION'
+ TIMESTAMP='$TIMESTAMP'
+ RM='$RM'
+ ofile='$ofile'], [])
+])dnl /_LT_CONFIG_SAVE_COMMANDS
+])# _LT_CONFIG
+
+
+# LT_SUPPORTED_TAG(TAG)
+# ---------------------
+# Trace this macro to discover what tags are supported by the libtool
+# --tag option, using:
+# autoconf --trace 'LT_SUPPORTED_TAG:$1'
+AC_DEFUN([LT_SUPPORTED_TAG], [])
+
+
+# C support is built-in for now
+m4_define([_LT_LANG_C_enabled], [])
+m4_define([_LT_TAGS], [])
+
+
+# LT_LANG(LANG)
+# -------------
+# Enable libtool support for the given language if not already enabled.
+AC_DEFUN([LT_LANG],
+[AC_BEFORE([$0], [LT_OUTPUT])dnl
+m4_case([$1],
+ [C], [_LT_LANG(C)],
+ [C++], [_LT_LANG(CXX)],
+ [Java], [_LT_LANG(GCJ)],
+ [Fortran 77], [_LT_LANG(F77)],
+ [Fortran], [_LT_LANG(FC)],
+ [Windows Resource], [_LT_LANG(RC)],
+ [m4_ifdef([_LT_LANG_]$1[_CONFIG],
+ [_LT_LANG($1)],
+ [m4_fatal([$0: unsupported language: "$1"])])])dnl
+])# LT_LANG
+
+
+# _LT_LANG(LANGNAME)
+# ------------------
+m4_defun([_LT_LANG],
+[m4_ifdef([_LT_LANG_]$1[_enabled], [],
+ [LT_SUPPORTED_TAG([$1])dnl
+ m4_append([_LT_TAGS], [$1 ])dnl
+ m4_define([_LT_LANG_]$1[_enabled], [])dnl
+ _LT_LANG_$1_CONFIG($1)])dnl
+])# _LT_LANG
+
+
+# _LT_LANG_DEFAULT_CONFIG
+# -----------------------
+m4_defun([_LT_LANG_DEFAULT_CONFIG],
+[AC_PROVIDE_IFELSE([AC_PROG_CXX],
+ [LT_LANG(CXX)],
+ [m4_define([AC_PROG_CXX], defn([AC_PROG_CXX])[LT_LANG(CXX)])])
+
+AC_PROVIDE_IFELSE([AC_PROG_F77],
+ [LT_LANG(F77)],
+ [m4_define([AC_PROG_F77], defn([AC_PROG_F77])[LT_LANG(F77)])])
+
+AC_PROVIDE_IFELSE([AC_PROG_FC],
+ [LT_LANG(FC)],
+ [m4_define([AC_PROG_FC], defn([AC_PROG_FC])[LT_LANG(FC)])])
+
+dnl The call to [A][M_PROG_GCJ] is quoted like that to stop aclocal
+dnl pulling things in needlessly.
+AC_PROVIDE_IFELSE([AC_PROG_GCJ],
+ [LT_LANG(GCJ)],
+ [AC_PROVIDE_IFELSE([A][M_PROG_GCJ],
+ [LT_LANG(GCJ)],
+ [AC_PROVIDE_IFELSE([LT_PROG_GCJ],
+ [LT_LANG(GCJ)],
+ [m4_ifdef([AC_PROG_GCJ],
+ [m4_define([AC_PROG_GCJ], defn([AC_PROG_GCJ])[LT_LANG(GCJ)])])
+ m4_ifdef([A][M_PROG_GCJ],
+ [m4_define([A][M_PROG_GCJ], defn([A][M_PROG_GCJ])[LT_LANG(GCJ)])])
+ m4_ifdef([LT_PROG_GCJ],
+ [m4_define([LT_PROG_GCJ], defn([LT_PROG_GCJ])[LT_LANG(GCJ)])])])])])
+
+AC_PROVIDE_IFELSE([LT_PROG_RC],
+ [LT_LANG(RC)],
+ [m4_define([LT_PROG_RC], defn([LT_PROG_RC])[LT_LANG(RC)])])
+])# _LT_LANG_DEFAULT_CONFIG
+
+# Obsolete macros:
+AU_DEFUN([AC_LIBTOOL_CXX], [LT_LANG(C++)])
+AU_DEFUN([AC_LIBTOOL_F77], [LT_LANG(Fortran 77)])
+AU_DEFUN([AC_LIBTOOL_FC], [LT_LANG(Fortran)])
+AU_DEFUN([AC_LIBTOOL_GCJ], [LT_LANG(Java)])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_CXX], [])
+dnl AC_DEFUN([AC_LIBTOOL_F77], [])
+dnl AC_DEFUN([AC_LIBTOOL_FC], [])
+dnl AC_DEFUN([AC_LIBTOOL_GCJ], [])
+
+
+# _LT_TAG_COMPILER
+# ----------------
+m4_defun([_LT_TAG_COMPILER],
+[AC_REQUIRE([AC_PROG_CC])dnl
+
+_LT_DECL([LTCC], [CC], [1], [A C compiler])dnl
+_LT_DECL([LTCFLAGS], [CFLAGS], [1], [LTCC compiler flags])dnl
+_LT_TAGDECL([CC], [compiler], [1], [A language specific compiler])dnl
+_LT_TAGDECL([with_gcc], [GCC], [0], [Is the compiler the GNU compiler?])dnl
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+])# _LT_TAG_COMPILER
+
+
+# _LT_COMPILER_BOILERPLATE
+# ------------------------
+# Check for compiler boilerplate output or warnings with
+# the simple compiler test code.
+m4_defun([_LT_COMPILER_BOILERPLATE],
+[m4_require([_LT_DECL_SED])dnl
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$RM conftest*
+])# _LT_COMPILER_BOILERPLATE
+
+
+# _LT_LINKER_BOILERPLATE
+# ----------------------
+# Check for linker boilerplate output or warnings with
+# the simple link test code.
+m4_defun([_LT_LINKER_BOILERPLATE],
+[m4_require([_LT_DECL_SED])dnl
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$RM -r conftest*
+])# _LT_LINKER_BOILERPLATE
+
+# _LT_REQUIRED_DARWIN_CHECKS
+# -------------------------
+m4_defun_once([_LT_REQUIRED_DARWIN_CHECKS],[
+ case $host_os in
+ rhapsody* | darwin*)
+ AC_CHECK_TOOL([DSYMUTIL], [dsymutil], [:])
+ AC_CHECK_TOOL([NMEDIT], [nmedit], [:])
+ AC_CHECK_TOOL([LIPO], [lipo], [:])
+ AC_CHECK_TOOL([OTOOL], [otool], [:])
+ AC_CHECK_TOOL([OTOOL64], [otool64], [:])
+ _LT_DECL([], [DSYMUTIL], [1],
+ [Tool to manipulate archived DWARF debug symbol files on Mac OS X])
+ _LT_DECL([], [NMEDIT], [1],
+ [Tool to change global to local symbols on Mac OS X])
+ _LT_DECL([], [LIPO], [1],
+ [Tool to manipulate fat objects and archives on Mac OS X])
+ _LT_DECL([], [OTOOL], [1],
+ [ldd/readelf like tool for Mach-O binaries on Mac OS X])
+ _LT_DECL([], [OTOOL64], [1],
+ [ldd/readelf like tool for 64 bit Mach-O binaries on Mac OS X 10.4])
+
+ AC_CACHE_CHECK([for -single_module linker flag],[lt_cv_apple_cc_single_mod],
+ [lt_cv_apple_cc_single_mod=no
+ if test -z "${LT_MULTI_MODULE}"; then
+ # By default we will add the -single_module flag. You can override
+ # by either setting the environment variable LT_MULTI_MODULE
+ # non-empty at configure time, or by adding -multi_module to the
+ # link flags.
+ rm -rf libconftest.dylib*
+ echo "int foo(void){return 1;}" > conftest.c
+ echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+-dynamiclib -Wl,-single_module conftest.c" >&AS_MESSAGE_LOG_FD
+ $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+ -dynamiclib -Wl,-single_module conftest.c 2>conftest.err
+ _lt_result=$?
+ if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then
+ lt_cv_apple_cc_single_mod=yes
+ else
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ fi
+ rm -rf libconftest.dylib*
+ rm -f conftest.*
+ fi])
+ AC_CACHE_CHECK([for -exported_symbols_list linker flag],
+ [lt_cv_ld_exported_symbols_list],
+ [lt_cv_ld_exported_symbols_list=no
+ save_LDFLAGS=$LDFLAGS
+ echo "_main" > conftest.sym
+ LDFLAGS="$LDFLAGS -Wl,-exported_symbols_list,conftest.sym"
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([],[])],
+ [lt_cv_ld_exported_symbols_list=yes],
+ [lt_cv_ld_exported_symbols_list=no])
+ LDFLAGS="$save_LDFLAGS"
+ ])
+ case $host_os in
+ rhapsody* | darwin1.[[012]])
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}suppress' ;;
+ darwin1.*)
+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+ darwin*) # darwin 5.x on
+ # if running on 10.5 or later, the deployment target defaults
+ # to the OS version, if on x86, and 10.4, the deployment
+ # target defaults to 10.4. Don't you love it?
+ case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in
+ 10.0,*86*-darwin8*|10.0,*-darwin[[91]]*)
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+ 10.[[012]]*)
+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+ 10.*)
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+ esac
+ ;;
+ esac
+ if test "$lt_cv_apple_cc_single_mod" = "yes"; then
+ _lt_dar_single_mod='$single_module'
+ fi
+ if test "$lt_cv_ld_exported_symbols_list" = "yes"; then
+ _lt_dar_export_syms=' ${wl}-exported_symbols_list,$output_objdir/${libname}-symbols.expsym'
+ else
+ _lt_dar_export_syms='~$NMEDIT -s $output_objdir/${libname}-symbols.expsym ${lib}'
+ fi
+ if test "$DSYMUTIL" != ":"; then
+ _lt_dsymutil='~$DSYMUTIL $lib || :'
+ else
+ _lt_dsymutil=
+ fi
+ ;;
+ esac
+])
+
+
+# _LT_DARWIN_LINKER_FEATURES
+# --------------------------
+# Checks for linker and compiler features on darwin
+m4_defun([_LT_DARWIN_LINKER_FEATURES],
+[
+ m4_require([_LT_REQUIRED_DARWIN_CHECKS])
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_automatic, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=''
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(allow_undefined_flag, $1)="$_lt_dar_allow_undefined"
+ case $cc_basename in
+ ifort*) _lt_dar_can_shared=yes ;;
+ *) _lt_dar_can_shared=$GCC ;;
+ esac
+ if test "$_lt_dar_can_shared" = "yes"; then
+ output_verbose_link_cmd=echo
+ _LT_TAGVAR(archive_cmds, $1)="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}"
+ _LT_TAGVAR(module_cmds, $1)="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}"
+ _LT_TAGVAR(archive_expsym_cmds, $1)="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}"
+ _LT_TAGVAR(module_expsym_cmds, $1)="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}"
+ m4_if([$1], [CXX],
+[ if test "$lt_cv_apple_cc_single_mod" != "yes"; then
+ _LT_TAGVAR(archive_cmds, $1)="\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dsymutil}"
+ _LT_TAGVAR(archive_expsym_cmds, $1)="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dar_export_syms}${_lt_dsymutil}"
+ fi
+],[])
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+])
+
+# _LT_SYS_MODULE_PATH_AIX
+# -----------------------
+# Links a minimal program and checks the executable
+# for the system default hardcoded library path. In most cases,
+# this is /usr/lib:/lib, but when the MPI compilers are used
+# the location of the communication and MPI libs are included too.
+# If we don't find anything, use the default library path according
+# to the aix ld manual.
+m4_defun([_LT_SYS_MODULE_PATH_AIX],
+[m4_require([_LT_DECL_SED])dnl
+AC_LINK_IFELSE(AC_LANG_PROGRAM,[
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi],[])
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+])# _LT_SYS_MODULE_PATH_AIX
+
+
+# _LT_SHELL_INIT(ARG)
+# -------------------
+m4_define([_LT_SHELL_INIT],
+[ifdef([AC_DIVERSION_NOTICE],
+ [AC_DIVERT_PUSH(AC_DIVERSION_NOTICE)],
+ [AC_DIVERT_PUSH(NOTICE)])
+$1
+AC_DIVERT_POP
+])# _LT_SHELL_INIT
+
+
+# _LT_PROG_ECHO_BACKSLASH
+# -----------------------
+# Add some code to the start of the generated configure script which
+# will find an echo command which doesn't interpret backslashes.
+m4_defun([_LT_PROG_ECHO_BACKSLASH],
+[_LT_SHELL_INIT([
+# Check that we are running under the correct shell.
+SHELL=${CONFIG_SHELL-/bin/sh}
+
+case X$lt_ECHO in
+X*--fallback-echo)
+ # Remove one level of quotation (which was required for Make).
+ ECHO=`echo "$lt_ECHO" | sed 's,\\\\\[$]\\[$]0,'[$]0','`
+ ;;
+esac
+
+ECHO=${lt_ECHO-echo}
+if test "X[$]1" = X--no-reexec; then
+ # Discard the --no-reexec flag, and continue.
+ shift
+elif test "X[$]1" = X--fallback-echo; then
+ # Avoid inline document here, it may be left over
+ :
+elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' ; then
+ # Yippee, $ECHO works!
+ :
+else
+ # Restart under the correct shell.
+ exec $SHELL "[$]0" --no-reexec ${1+"[$]@"}
+fi
+
+if test "X[$]1" = X--fallback-echo; then
+ # used as fallback echo
+ shift
+ cat <<_LT_EOF
+[$]*
+_LT_EOF
+ exit 0
+fi
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test -z "$lt_ECHO"; then
+ if test "X${echo_test_string+set}" != Xset; then
+ # find a string as large as possible, as long as the shell can cope with it
+ for cmd in 'sed 50q "[$]0"' 'sed 20q "[$]0"' 'sed 10q "[$]0"' 'sed 2q "[$]0"' 'echo test'; do
+ # expected sizes: less than 2Kb, 1Kb, 512 bytes, 16 bytes, ...
+ if { echo_test_string=`eval $cmd`; } 2>/dev/null &&
+ { test "X$echo_test_string" = "X$echo_test_string"; } 2>/dev/null
+ then
+ break
+ fi
+ done
+ fi
+
+ if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ :
+ else
+ # The Solaris, AIX, and Digital Unix default echo programs unquote
+ # backslashes. This makes it impossible to quote backslashes using
+ # echo "$something" | sed 's/\\/\\\\/g'
+ #
+ # So, first we look for a working echo in the user's PATH.
+
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for dir in $PATH /usr/ucb; do
+ IFS="$lt_save_ifs"
+ if (test -f $dir/echo || test -f $dir/echo$ac_exeext) &&
+ test "X`($dir/echo '\t') 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`($dir/echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ ECHO="$dir/echo"
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+
+ if test "X$ECHO" = Xecho; then
+ # We didn't find a better echo, so look for alternatives.
+ if test "X`{ print -r '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ print -r "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ # This shell has a builtin print -r that does the trick.
+ ECHO='print -r'
+ elif { test -f /bin/ksh || test -f /bin/ksh$ac_exeext; } &&
+ test "X$CONFIG_SHELL" != X/bin/ksh; then
+ # If we have ksh, try running configure again with it.
+ ORIGINAL_CONFIG_SHELL=${CONFIG_SHELL-/bin/sh}
+ export ORIGINAL_CONFIG_SHELL
+ CONFIG_SHELL=/bin/ksh
+ export CONFIG_SHELL
+ exec $CONFIG_SHELL "[$]0" --no-reexec ${1+"[$]@"}
+ else
+ # Try using printf.
+ ECHO='printf %s\n'
+ if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ # Cool, printf works
+ :
+ elif echo_testing_string=`($ORIGINAL_CONFIG_SHELL "[$]0" --fallback-echo '\t') 2>/dev/null` &&
+ test "X$echo_testing_string" = 'X\t' &&
+ echo_testing_string=`($ORIGINAL_CONFIG_SHELL "[$]0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ CONFIG_SHELL=$ORIGINAL_CONFIG_SHELL
+ export CONFIG_SHELL
+ SHELL="$CONFIG_SHELL"
+ export SHELL
+ ECHO="$CONFIG_SHELL [$]0 --fallback-echo"
+ elif echo_testing_string=`($CONFIG_SHELL "[$]0" --fallback-echo '\t') 2>/dev/null` &&
+ test "X$echo_testing_string" = 'X\t' &&
+ echo_testing_string=`($CONFIG_SHELL "[$]0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ ECHO="$CONFIG_SHELL [$]0 --fallback-echo"
+ else
+ # maybe with a smaller string...
+ prev=:
+
+ for cmd in 'echo test' 'sed 2q "[$]0"' 'sed 10q "[$]0"' 'sed 20q "[$]0"' 'sed 50q "[$]0"'; do
+ if { test "X$echo_test_string" = "X`eval $cmd`"; } 2>/dev/null
+ then
+ break
+ fi
+ prev="$cmd"
+ done
+
+ if test "$prev" != 'sed 50q "[$]0"'; then
+ echo_test_string=`eval $prev`
+ export echo_test_string
+ exec ${ORIGINAL_CONFIG_SHELL-${CONFIG_SHELL-/bin/sh}} "[$]0" ${1+"[$]@"}
+ else
+ # Oops. We lost completely, so just stick with echo.
+ ECHO=echo
+ fi
+ fi
+ fi
+ fi
+ fi
+fi
+
+# Copy echo and quote the copy suitably for passing to libtool from
+# the Makefile, instead of quoting the original, which is used later.
+lt_ECHO=$ECHO
+if test "X$lt_ECHO" = "X$CONFIG_SHELL [$]0 --fallback-echo"; then
+ lt_ECHO="$CONFIG_SHELL \\\$\[$]0 --fallback-echo"
+fi
+
+AC_SUBST(lt_ECHO)
+])
+_LT_DECL([], [SHELL], [1], [Shell to use when invoking shell scripts])
+_LT_DECL([], [ECHO], [1],
+ [An echo program that does not interpret backslashes])
+])# _LT_PROG_ECHO_BACKSLASH
+
+
+# _LT_ENABLE_LOCK
+# ---------------
+m4_defun([_LT_ENABLE_LOCK],
+[AC_ARG_ENABLE([libtool-lock],
+ [AS_HELP_STRING([--disable-libtool-lock],
+ [avoid locking (might break parallel builds)])])
+test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes
+
+# Some flags need to be propagated to the compiler or linker for good
+# libtool support.
+case $host in
+ia64-*-hpux*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *ELF-32*)
+ HPUX_IA64_MODE="32"
+ ;;
+ *ELF-64*)
+ HPUX_IA64_MODE="64"
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+*-*-irix6*)
+ # Find out which ABI we are using.
+ echo '[#]line __oline__ "configure"' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *32-bit*)
+ LD="${LD-ld} -melf32bsmip"
+ ;;
+ *N32*)
+ LD="${LD-ld} -melf32bmipn32"
+ ;;
+ *64-bit*)
+ LD="${LD-ld} -melf64bmip"
+ ;;
+ esac
+ else
+ case `/usr/bin/file conftest.$ac_objext` in
+ *32-bit*)
+ LD="${LD-ld} -32"
+ ;;
+ *N32*)
+ LD="${LD-ld} -n32"
+ ;;
+ *64-bit*)
+ LD="${LD-ld} -64"
+ ;;
+ esac
+ fi
+ fi
+ rm -rf conftest*
+ ;;
+
+x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \
+s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ case `/usr/bin/file conftest.o` in
+ *32-bit*)
+ case $host in
+ x86_64-*kfreebsd*-gnu)
+ LD="${LD-ld} -m elf_i386_fbsd"
+ ;;
+ x86_64-*linux*)
+ LD="${LD-ld} -m elf_i386"
+ ;;
+ ppc64-*linux*|powerpc64-*linux*)
+ LD="${LD-ld} -m elf32ppclinux"
+ ;;
+ s390x-*linux*)
+ LD="${LD-ld} -m elf_s390"
+ ;;
+ sparc64-*linux*)
+ LD="${LD-ld} -m elf32_sparc"
+ ;;
+ esac
+ ;;
+ *64-bit*)
+ case $host in
+ x86_64-*kfreebsd*-gnu)
+ LD="${LD-ld} -m elf_x86_64_fbsd"
+ ;;
+ x86_64-*linux*)
+ LD="${LD-ld} -m elf_x86_64"
+ ;;
+ ppc*-*linux*|powerpc*-*linux*)
+ LD="${LD-ld} -m elf64ppc"
+ ;;
+ s390*-*linux*|s390*-*tpf*)
+ LD="${LD-ld} -m elf64_s390"
+ ;;
+ sparc*-*linux*)
+ LD="${LD-ld} -m elf64_sparc"
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+
+*-*-sco3.2v5*)
+ # On SCO OpenServer 5, we need -belf to get full-featured binaries.
+ SAVE_CFLAGS="$CFLAGS"
+ CFLAGS="$CFLAGS -belf"
+ AC_CACHE_CHECK([whether the C compiler needs -belf], lt_cv_cc_needs_belf,
+ [AC_LANG_PUSH(C)
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[]],[[]])],[lt_cv_cc_needs_belf=yes],[lt_cv_cc_needs_belf=no])
+ AC_LANG_POP])
+ if test x"$lt_cv_cc_needs_belf" != x"yes"; then
+ # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf
+ CFLAGS="$SAVE_CFLAGS"
+ fi
+ ;;
+sparc*-*solaris*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ case `/usr/bin/file conftest.o` in
+ *64-bit*)
+ case $lt_cv_prog_gnu_ld in
+ yes*) LD="${LD-ld} -m elf64_sparc" ;;
+ *)
+ if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then
+ LD="${LD-ld} -64"
+ fi
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+esac
+
+need_locks="$enable_libtool_lock"
+])# _LT_ENABLE_LOCK
+
+
+# _LT_CMD_OLD_ARCHIVE
+# -------------------
+m4_defun([_LT_CMD_OLD_ARCHIVE],
+[AC_CHECK_TOOL(AR, ar, false)
+test -z "$AR" && AR=ar
+test -z "$AR_FLAGS" && AR_FLAGS=cru
+_LT_DECL([], [AR], [1], [The archiver])
+_LT_DECL([], [AR_FLAGS], [1])
+
+AC_CHECK_TOOL(STRIP, strip, :)
+test -z "$STRIP" && STRIP=:
+_LT_DECL([], [STRIP], [1], [A symbol stripping program])
+
+AC_CHECK_TOOL(RANLIB, ranlib, :)
+test -z "$RANLIB" && RANLIB=:
+_LT_DECL([], [RANLIB], [1],
+ [Commands used to install an old-style archive])
+
+# Determine commands to create old-style static archives.
+old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs'
+old_postinstall_cmds='chmod 644 $oldlib'
+old_postuninstall_cmds=
+
+if test -n "$RANLIB"; then
+ case $host_os in
+ openbsd*)
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib"
+ ;;
+ *)
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib"
+ ;;
+ esac
+ old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib"
+fi
+_LT_DECL([], [old_postinstall_cmds], [2])
+_LT_DECL([], [old_postuninstall_cmds], [2])
+_LT_TAGDECL([], [old_archive_cmds], [2],
+ [Commands used to build an old-style archive])
+])# _LT_CMD_OLD_ARCHIVE
+
+
+# _LT_COMPILER_OPTION(MESSAGE, VARIABLE-NAME, FLAGS,
+# [OUTPUT-FILE], [ACTION-SUCCESS], [ACTION-FAILURE])
+# ----------------------------------------------------------------
+# Check whether the given compiler option works
+AC_DEFUN([_LT_COMPILER_OPTION],
+[m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_SED])dnl
+AC_CACHE_CHECK([$1], [$2],
+ [$2=no
+ m4_if([$4], , [ac_outfile=conftest.$ac_objext], [ac_outfile=$4])
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+ lt_compiler_flag="$3"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ # The option is referenced via a variable to avoid confusing sed.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [[^ ]]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:__oline__: $lt_compile\"" >&AS_MESSAGE_LOG_FD)
+ (eval "$lt_compile" 2>conftest.err)
+ ac_status=$?
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ echo "$as_me:__oline__: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
+ if (exit $ac_status) && test -s "$ac_outfile"; then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings other than the usual output.
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+ $2=yes
+ fi
+ fi
+ $RM conftest*
+])
+
+if test x"[$]$2" = xyes; then
+ m4_if([$5], , :, [$5])
+else
+ m4_if([$6], , :, [$6])
+fi
+])# _LT_COMPILER_OPTION
+
+# Old name:
+AU_ALIAS([AC_LIBTOOL_COMPILER_OPTION], [_LT_COMPILER_OPTION])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_COMPILER_OPTION], [])
+
+
+# _LT_LINKER_OPTION(MESSAGE, VARIABLE-NAME, FLAGS,
+# [ACTION-SUCCESS], [ACTION-FAILURE])
+# ----------------------------------------------------
+# Check whether the given linker option works
+AC_DEFUN([_LT_LINKER_OPTION],
+[m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_SED])dnl
+AC_CACHE_CHECK([$1], [$2],
+ [$2=no
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS $3"
+ echo "$lt_simple_link_test_code" > conftest.$ac_ext
+ if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+ # The linker can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ if test -s conftest.err; then
+ # Append any errors to the config.log.
+ cat conftest.err 1>&AS_MESSAGE_LOG_FD
+ $ECHO "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if diff conftest.exp conftest.er2 >/dev/null; then
+ $2=yes
+ fi
+ else
+ $2=yes
+ fi
+ fi
+ $RM -r conftest*
+ LDFLAGS="$save_LDFLAGS"
+])
+
+if test x"[$]$2" = xyes; then
+ m4_if([$4], , :, [$4])
+else
+ m4_if([$5], , :, [$5])
+fi
+])# _LT_LINKER_OPTION
+
+# Old name:
+AU_ALIAS([AC_LIBTOOL_LINKER_OPTION], [_LT_LINKER_OPTION])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_LINKER_OPTION], [])
+
+
+# LT_CMD_MAX_LEN
+#---------------
+AC_DEFUN([LT_CMD_MAX_LEN],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+# find the maximum length of command line arguments
+AC_MSG_CHECKING([the maximum length of command line arguments])
+AC_CACHE_VAL([lt_cv_sys_max_cmd_len], [dnl
+ i=0
+ teststring="ABCD"
+
+ case $build_os in
+ msdosdjgpp*)
+ # On DJGPP, this test can blow up pretty badly due to problems in libc
+ # (any single argument exceeding 2000 bytes causes a buffer overrun
+ # during glob expansion). Even if it were fixed, the result of this
+ # check would be larger than it should be.
+ lt_cv_sys_max_cmd_len=12288; # 12K is about right
+ ;;
+
+ gnu*)
+ # Under GNU Hurd, this test is not required because there is
+ # no limit to the length of command line arguments.
+ # Libtool will interpret -1 as no limit whatsoever
+ lt_cv_sys_max_cmd_len=-1;
+ ;;
+
+ cygwin* | mingw* | cegcc*)
+ # On Win9x/ME, this test blows up -- it succeeds, but takes
+ # about 5 minutes as the teststring grows exponentially.
+ # Worse, since 9x/ME are not pre-emptively multitasking,
+ # you end up with a "frozen" computer, even though with patience
+ # the test eventually succeeds (with a max line length of 256k).
+ # Instead, let's just punt: use the minimum linelength reported by
+ # all of the supported platforms: 8192 (on NT/2K/XP).
+ lt_cv_sys_max_cmd_len=8192;
+ ;;
+
+ amigaos*)
+ # On AmigaOS with pdksh, this test takes hours, literally.
+ # So we just punt and use a minimum line length of 8192.
+ lt_cv_sys_max_cmd_len=8192;
+ ;;
+
+ netbsd* | freebsd* | openbsd* | darwin* | dragonfly*)
+ # This has been around since 386BSD, at least. Likely further.
+ if test -x /sbin/sysctl; then
+ lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax`
+ elif test -x /usr/sbin/sysctl; then
+ lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax`
+ else
+ lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs
+ fi
+ # And add a safety zone
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+ ;;
+
+ interix*)
+ # We know the value 262144 and hardcode it with a safety zone (like BSD)
+ lt_cv_sys_max_cmd_len=196608
+ ;;
+
+ osf*)
+ # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure
+ # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not
+ # nice to cause kernel panics so lets avoid the loop below.
+ # First set a reasonable default.
+ lt_cv_sys_max_cmd_len=16384
+ #
+ if test -x /sbin/sysconfig; then
+ case `/sbin/sysconfig -q proc exec_disable_arg_limit` in
+ *1*) lt_cv_sys_max_cmd_len=-1 ;;
+ esac
+ fi
+ ;;
+ sco3.2v5*)
+ lt_cv_sys_max_cmd_len=102400
+ ;;
+ sysv5* | sco5v6* | sysv4.2uw2*)
+ kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null`
+ if test -n "$kargmax"; then
+ lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[[ ]]//'`
+ else
+ lt_cv_sys_max_cmd_len=32768
+ fi
+ ;;
+ *)
+ lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null`
+ if test -n "$lt_cv_sys_max_cmd_len"; then
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+ else
+ # Make teststring a little bigger before we do anything with it.
+ # a 1K string should be a reasonable start.
+ for i in 1 2 3 4 5 6 7 8 ; do
+ teststring=$teststring$teststring
+ done
+ SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}}
+ # If test is not a shell built-in, we'll probably end up computing a
+ # maximum length that is only half of the actual maximum length, but
+ # we can't tell.
+ while { test "X"`$SHELL [$]0 --fallback-echo "X$teststring$teststring" 2>/dev/null` \
+ = "XX$teststring$teststring"; } >/dev/null 2>&1 &&
+ test $i != 17 # 1/2 MB should be enough
+ do
+ i=`expr $i + 1`
+ teststring=$teststring$teststring
+ done
+ # Only check the string length outside the loop.
+ lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1`
+ teststring=
+ # Add a significant safety factor because C++ compilers can tack on
+ # massive amounts of additional arguments before passing them to the
+ # linker. It appears as though 1/2 is a usable value.
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2`
+ fi
+ ;;
+ esac
+])
+if test -n $lt_cv_sys_max_cmd_len ; then
+ AC_MSG_RESULT($lt_cv_sys_max_cmd_len)
+else
+ AC_MSG_RESULT(none)
+fi
+max_cmd_len=$lt_cv_sys_max_cmd_len
+_LT_DECL([], [max_cmd_len], [0],
+ [What is the maximum length of a command?])
+])# LT_CMD_MAX_LEN
+
+# Old name:
+AU_ALIAS([AC_LIBTOOL_SYS_MAX_CMD_LEN], [LT_CMD_MAX_LEN])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_SYS_MAX_CMD_LEN], [])
+
+
+# _LT_HEADER_DLFCN
+# ----------------
+m4_defun([_LT_HEADER_DLFCN],
+[AC_CHECK_HEADERS([dlfcn.h], [], [], [AC_INCLUDES_DEFAULT])dnl
+])# _LT_HEADER_DLFCN
+
+
+# _LT_TRY_DLOPEN_SELF (ACTION-IF-TRUE, ACTION-IF-TRUE-W-USCORE,
+# ACTION-IF-FALSE, ACTION-IF-CROSS-COMPILING)
+# ----------------------------------------------------------------
+m4_defun([_LT_TRY_DLOPEN_SELF],
+[m4_require([_LT_HEADER_DLFCN])dnl
+if test "$cross_compiling" = yes; then :
+ [$4]
+else
+ lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
+ lt_status=$lt_dlunknown
+ cat > conftest.$ac_ext <<_LT_EOF
+[#line __oline__ "configure"
+#include "confdefs.h"
+
+#if HAVE_DLFCN_H
+#include <dlfcn.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef RTLD_GLOBAL
+# define LT_DLGLOBAL RTLD_GLOBAL
+#else
+# ifdef DL_GLOBAL
+# define LT_DLGLOBAL DL_GLOBAL
+# else
+# define LT_DLGLOBAL 0
+# endif
+#endif
+
+/* We may have to define LT_DLLAZY_OR_NOW in the command line if we
+ find out it does not work in some platform. */
+#ifndef LT_DLLAZY_OR_NOW
+# ifdef RTLD_LAZY
+# define LT_DLLAZY_OR_NOW RTLD_LAZY
+# else
+# ifdef DL_LAZY
+# define LT_DLLAZY_OR_NOW DL_LAZY
+# else
+# ifdef RTLD_NOW
+# define LT_DLLAZY_OR_NOW RTLD_NOW
+# else
+# ifdef DL_NOW
+# define LT_DLLAZY_OR_NOW DL_NOW
+# else
+# define LT_DLLAZY_OR_NOW 0
+# endif
+# endif
+# endif
+# endif
+#endif
+
+void fnord() { int i=42;}
+int main ()
+{
+ void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW);
+ int status = $lt_dlunknown;
+
+ if (self)
+ {
+ if (dlsym (self,"fnord")) status = $lt_dlno_uscore;
+ else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore;
+ /* dlclose (self); */
+ }
+ else
+ puts (dlerror ());
+
+ return status;
+}]
+_LT_EOF
+ if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext} 2>/dev/null; then
+ (./conftest; exit; ) >&AS_MESSAGE_LOG_FD 2>/dev/null
+ lt_status=$?
+ case x$lt_status in
+ x$lt_dlno_uscore) $1 ;;
+ x$lt_dlneed_uscore) $2 ;;
+ x$lt_dlunknown|x*) $3 ;;
+ esac
+ else :
+ # compilation failed
+ $3
+ fi
+fi
+rm -fr conftest*
+])# _LT_TRY_DLOPEN_SELF
+
+
+# LT_SYS_DLOPEN_SELF
+# ------------------
+AC_DEFUN([LT_SYS_DLOPEN_SELF],
+[m4_require([_LT_HEADER_DLFCN])dnl
+if test "x$enable_dlopen" != xyes; then
+ enable_dlopen=unknown
+ enable_dlopen_self=unknown
+ enable_dlopen_self_static=unknown
+else
+ lt_cv_dlopen=no
+ lt_cv_dlopen_libs=
+
+ case $host_os in
+ beos*)
+ lt_cv_dlopen="load_add_on"
+ lt_cv_dlopen_libs=
+ lt_cv_dlopen_self=yes
+ ;;
+
+ mingw* | pw32* | cegcc*)
+ lt_cv_dlopen="LoadLibrary"
+ lt_cv_dlopen_libs=
+ ;;
+
+ cygwin*)
+ lt_cv_dlopen="dlopen"
+ lt_cv_dlopen_libs=
+ ;;
+
+ darwin*)
+ # if libdl is installed we need to link against it
+ AC_CHECK_LIB([dl], [dlopen],
+ [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"],[
+ lt_cv_dlopen="dyld"
+ lt_cv_dlopen_libs=
+ lt_cv_dlopen_self=yes
+ ])
+ ;;
+
+ *)
+ AC_CHECK_FUNC([shl_load],
+ [lt_cv_dlopen="shl_load"],
+ [AC_CHECK_LIB([dld], [shl_load],
+ [lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-ldld"],
+ [AC_CHECK_FUNC([dlopen],
+ [lt_cv_dlopen="dlopen"],
+ [AC_CHECK_LIB([dl], [dlopen],
+ [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"],
+ [AC_CHECK_LIB([svld], [dlopen],
+ [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld"],
+ [AC_CHECK_LIB([dld], [dld_link],
+ [lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-ldld"])
+ ])
+ ])
+ ])
+ ])
+ ])
+ ;;
+ esac
+
+ if test "x$lt_cv_dlopen" != xno; then
+ enable_dlopen=yes
+ else
+ enable_dlopen=no
+ fi
+
+ case $lt_cv_dlopen in
+ dlopen)
+ save_CPPFLAGS="$CPPFLAGS"
+ test "x$ac_cv_header_dlfcn_h" = xyes && CPPFLAGS="$CPPFLAGS -DHAVE_DLFCN_H"
+
+ save_LDFLAGS="$LDFLAGS"
+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\"
+
+ save_LIBS="$LIBS"
+ LIBS="$lt_cv_dlopen_libs $LIBS"
+
+ AC_CACHE_CHECK([whether a program can dlopen itself],
+ lt_cv_dlopen_self, [dnl
+ _LT_TRY_DLOPEN_SELF(
+ lt_cv_dlopen_self=yes, lt_cv_dlopen_self=yes,
+ lt_cv_dlopen_self=no, lt_cv_dlopen_self=cross)
+ ])
+
+ if test "x$lt_cv_dlopen_self" = xyes; then
+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\"
+ AC_CACHE_CHECK([whether a statically linked program can dlopen itself],
+ lt_cv_dlopen_self_static, [dnl
+ _LT_TRY_DLOPEN_SELF(
+ lt_cv_dlopen_self_static=yes, lt_cv_dlopen_self_static=yes,
+ lt_cv_dlopen_self_static=no, lt_cv_dlopen_self_static=cross)
+ ])
+ fi
+
+ CPPFLAGS="$save_CPPFLAGS"
+ LDFLAGS="$save_LDFLAGS"
+ LIBS="$save_LIBS"
+ ;;
+ esac
+
+ case $lt_cv_dlopen_self in
+ yes|no) enable_dlopen_self=$lt_cv_dlopen_self ;;
+ *) enable_dlopen_self=unknown ;;
+ esac
+
+ case $lt_cv_dlopen_self_static in
+ yes|no) enable_dlopen_self_static=$lt_cv_dlopen_self_static ;;
+ *) enable_dlopen_self_static=unknown ;;
+ esac
+fi
+_LT_DECL([dlopen_support], [enable_dlopen], [0],
+ [Whether dlopen is supported])
+_LT_DECL([dlopen_self], [enable_dlopen_self], [0],
+ [Whether dlopen of programs is supported])
+_LT_DECL([dlopen_self_static], [enable_dlopen_self_static], [0],
+ [Whether dlopen of statically linked programs is supported])
+])# LT_SYS_DLOPEN_SELF
+
+# Old name:
+AU_ALIAS([AC_LIBTOOL_DLOPEN_SELF], [LT_SYS_DLOPEN_SELF])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_DLOPEN_SELF], [])
+
+
+# _LT_COMPILER_C_O([TAGNAME])
+# ---------------------------
+# Check to see if options -c and -o are simultaneously supported by compiler.
+# This macro does not hard code the compiler like AC_PROG_CC_C_O.
+m4_defun([_LT_COMPILER_C_O],
+[m4_require([_LT_DECL_SED])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_TAG_COMPILER])dnl
+AC_CACHE_CHECK([if $compiler supports -c -o file.$ac_objext],
+ [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)],
+ [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [[^ ]]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:__oline__: $lt_compile\"" >&AS_MESSAGE_LOG_FD)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&AS_MESSAGE_LOG_FD
+ echo "$as_me:__oline__: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ _LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=yes
+ fi
+ fi
+ chmod u+w . 2>&AS_MESSAGE_LOG_FD
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+])
+_LT_TAGDECL([compiler_c_o], [lt_cv_prog_compiler_c_o], [1],
+ [Does compiler simultaneously support -c and -o options?])
+])# _LT_COMPILER_C_O
+
+
+# _LT_COMPILER_FILE_LOCKS([TAGNAME])
+# ----------------------------------
+# Check to see if we can do hard links to lock some files if needed
+m4_defun([_LT_COMPILER_FILE_LOCKS],
+[m4_require([_LT_ENABLE_LOCK])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+_LT_COMPILER_C_O([$1])
+
+hard_links="nottested"
+if test "$_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)" = no && test "$need_locks" != no; then
+ # do not overwrite the value of need_locks provided by the user
+ AC_MSG_CHECKING([if we can lock with hard links])
+ hard_links=yes
+ $RM conftest*
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ touch conftest.a
+ ln conftest.a conftest.b 2>&5 || hard_links=no
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ AC_MSG_RESULT([$hard_links])
+ if test "$hard_links" = no; then
+ AC_MSG_WARN([`$CC' does not support `-c -o', so `make -j' may be unsafe])
+ need_locks=warn
+ fi
+else
+ need_locks=no
+fi
+_LT_DECL([], [need_locks], [1], [Must we lock files when doing compilation?])
+])# _LT_COMPILER_FILE_LOCKS
+
+
+# _LT_CHECK_OBJDIR
+# ----------------
+m4_defun([_LT_CHECK_OBJDIR],
+[AC_CACHE_CHECK([for objdir], [lt_cv_objdir],
+[rm -f .libs 2>/dev/null
+mkdir .libs 2>/dev/null
+if test -d .libs; then
+ lt_cv_objdir=.libs
+else
+ # MS-DOS does not allow filenames that begin with a dot.
+ lt_cv_objdir=_libs
+fi
+rmdir .libs 2>/dev/null])
+objdir=$lt_cv_objdir
+_LT_DECL([], [objdir], [0],
+ [The name of the directory that contains temporary libtool files])dnl
+m4_pattern_allow([LT_OBJDIR])dnl
+AC_DEFINE_UNQUOTED(LT_OBJDIR, "$lt_cv_objdir/",
+ [Define to the sub-directory in which libtool stores uninstalled libraries.])
+])# _LT_CHECK_OBJDIR
+
+
+# _LT_LINKER_HARDCODE_LIBPATH([TAGNAME])
+# --------------------------------------
+# Check hardcoding attributes.
+m4_defun([_LT_LINKER_HARDCODE_LIBPATH],
+[AC_MSG_CHECKING([how to hardcode library paths into programs])
+_LT_TAGVAR(hardcode_action, $1)=
+if test -n "$_LT_TAGVAR(hardcode_libdir_flag_spec, $1)" ||
+ test -n "$_LT_TAGVAR(runpath_var, $1)" ||
+ test "X$_LT_TAGVAR(hardcode_automatic, $1)" = "Xyes" ; then
+
+ # We can hardcode non-existent directories.
+ if test "$_LT_TAGVAR(hardcode_direct, $1)" != no &&
+ # If the only mechanism to avoid hardcoding is shlibpath_var, we
+ # have to relink, otherwise we might link with an installed library
+ # when we should be linking with a yet-to-be-installed one
+ ## test "$_LT_TAGVAR(hardcode_shlibpath_var, $1)" != no &&
+ test "$_LT_TAGVAR(hardcode_minus_L, $1)" != no; then
+ # Linking always hardcodes the temporary library directory.
+ _LT_TAGVAR(hardcode_action, $1)=relink
+ else
+ # We can link without hardcoding, and we can hardcode nonexisting dirs.
+ _LT_TAGVAR(hardcode_action, $1)=immediate
+ fi
+else
+ # We cannot hardcode anything, or else we can only hardcode existing
+ # directories.
+ _LT_TAGVAR(hardcode_action, $1)=unsupported
+fi
+AC_MSG_RESULT([$_LT_TAGVAR(hardcode_action, $1)])
+
+if test "$_LT_TAGVAR(hardcode_action, $1)" = relink ||
+ test "$_LT_TAGVAR(inherit_rpath, $1)" = yes; then
+ # Fast installation is not supported
+ enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+ test "$enable_shared" = no; then
+ # Fast installation is not necessary
+ enable_fast_install=needless
+fi
+_LT_TAGDECL([], [hardcode_action], [0],
+ [How to hardcode a shared library path into an executable])
+])# _LT_LINKER_HARDCODE_LIBPATH
+
+
+# _LT_CMD_STRIPLIB
+# ----------------
+m4_defun([_LT_CMD_STRIPLIB],
+[m4_require([_LT_DECL_EGREP])
+striplib=
+old_striplib=
+AC_MSG_CHECKING([whether stripping libraries is possible])
+if test -n "$STRIP" && $STRIP -V 2>&1 | $GREP "GNU strip" >/dev/null; then
+ test -z "$old_striplib" && old_striplib="$STRIP --strip-debug"
+ test -z "$striplib" && striplib="$STRIP --strip-unneeded"
+ AC_MSG_RESULT([yes])
+else
+# FIXME - insert some real tests, host_os isn't really good enough
+ case $host_os in
+ darwin*)
+ if test -n "$STRIP" ; then
+ striplib="$STRIP -x"
+ old_striplib="$STRIP -S"
+ AC_MSG_RESULT([yes])
+ else
+ AC_MSG_RESULT([no])
+ fi
+ ;;
+ *)
+ AC_MSG_RESULT([no])
+ ;;
+ esac
+fi
+_LT_DECL([], [old_striplib], [1], [Commands to strip libraries])
+_LT_DECL([], [striplib], [1])
+])# _LT_CMD_STRIPLIB
+
+
+# _LT_SYS_DYNAMIC_LINKER([TAG])
+# -----------------------------
+# PORTME Fill in your ld.so characteristics
+m4_defun([_LT_SYS_DYNAMIC_LINKER],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+m4_require([_LT_DECL_EGREP])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_OBJDUMP])dnl
+m4_require([_LT_DECL_SED])dnl
+AC_MSG_CHECKING([dynamic linker characteristics])
+m4_if([$1],
+ [], [
+if test "$GCC" = yes; then
+ case $host_os in
+ darwin*) lt_awk_arg="/^libraries:/,/LR/" ;;
+ *) lt_awk_arg="/^libraries:/" ;;
+ esac
+ lt_search_path_spec=`$CC -print-search-dirs | awk $lt_awk_arg | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$lt_search_path_spec" | $GREP ';' >/dev/null ; then
+ # if the path contains ";" then we assume it to be the separator
+ # otherwise default to the standard path separator (i.e. ":") - it is
+ # assumed that no part of a normal pathname contains ";" but that should
+ # okay in the real world where ";" in dirpaths is itself problematic.
+ lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ # Ok, now we have the path, separated by spaces, we can step through it
+ # and add multilib dir if necessary.
+ lt_tmp_lt_search_path_spec=
+ lt_multi_os_dir=`$CC $CPPFLAGS $CFLAGS $LDFLAGS -print-multi-os-directory 2>/dev/null`
+ for lt_sys_path in $lt_search_path_spec; do
+ if test -d "$lt_sys_path/$lt_multi_os_dir"; then
+ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path/$lt_multi_os_dir"
+ else
+ test -d "$lt_sys_path" && \
+ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path"
+ fi
+ done
+ lt_search_path_spec=`$ECHO $lt_tmp_lt_search_path_spec | awk '
+BEGIN {RS=" "; FS="/|\n";} {
+ lt_foo="";
+ lt_count=0;
+ for (lt_i = NF; lt_i > 0; lt_i--) {
+ if ($lt_i != "" && $lt_i != ".") {
+ if ($lt_i == "..") {
+ lt_count++;
+ } else {
+ if (lt_count == 0) {
+ lt_foo="/" $lt_i lt_foo;
+ } else {
+ lt_count--;
+ }
+ }
+ }
+ }
+ if (lt_foo != "") { lt_freq[[lt_foo]]++; }
+ if (lt_freq[[lt_foo]] == 1) { print lt_foo; }
+}'`
+ sys_lib_search_path_spec=`$ECHO $lt_search_path_spec`
+else
+ sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib"
+fi])
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+ shlibpath_var=LIBPATH
+
+ # AIX 3 has no versioning support, so we append a major version to the name.
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+
+aix[[4-9]]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ hardcode_into_libs=yes
+ if test "$host_cpu" = ia64; then
+ # AIX 5 supports IA64
+ library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ else
+ # With GCC up to 2.95.x, collect2 would create an import file
+ # for dependence libraries. The import file would start with
+ # the line `#! .'. This would cause the generated library to
+ # depend on `.', always an invalid library. This was fixed in
+ # development snapshots of GCC prior to 3.0.
+ case $host_os in
+ aix4 | aix4.[[01]] | aix4.[[01]].*)
+ if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+ echo ' yes '
+ echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then
+ :
+ else
+ can_build_shared=no
+ fi
+ ;;
+ esac
+ # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+ # soname into executable. Probably we can add versioning support to
+ # collect2, so additional links can be useful in future.
+ if test "$aix_use_runtimelinking" = yes; then
+ # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+ # instead of lib<name>.a to let people know that these are not
+ # typical AIX shared libraries.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ else
+ # We preserve .a as extension for shared libraries through AIX4.2
+ # and later when we are not doing run time linking.
+ library_names_spec='${libname}${release}.a $libname.a'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ fi
+ shlibpath_var=LIBPATH
+ fi
+ ;;
+
+amigaos*)
+ case $host_cpu in
+ powerpc)
+ # Since July 2007 AmigaOS4 officially supports .so libraries.
+ # When compiling the executable, add -use-dynld -Lsobjs: to the compileline.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ ;;
+ m68k)
+ library_names_spec='$libname.ixlibrary $libname.a'
+ # Create ${libname}_ixlibrary.a entries in /sys/libs.
+ finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$ECHO "X$lib" | $Xsed -e '\''s%^.*/\([[^/]]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+ ;;
+ esac
+ ;;
+
+beos*)
+ library_names_spec='${libname}${shared_ext}'
+ dynamic_linker="$host_os ld.so"
+ shlibpath_var=LIBRARY_PATH
+ ;;
+
+bsdi[[45]]*)
+ version_type=linux
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+ sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+ # the default ld.so.conf also contains /usr/contrib/lib and
+ # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+ # libtool to hard-code these into programs
+ ;;
+
+cygwin* | mingw* | pw32* | cegcc*)
+ version_type=windows
+ shrext_cmds=".dll"
+ need_version=no
+ need_lib_prefix=no
+
+ case $GCC,$host_os in
+ yes,cygwin* | yes,mingw* | yes,pw32* | yes,cegcc*)
+ library_names_spec='$libname.dll.a'
+ # DLL is installed to $(libdir)/../bin by postinstall_cmds
+ postinstall_cmds='base_file=`basename \${file}`~
+ dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i; echo \$dlname'\''`~
+ dldir=$destdir/`dirname \$dlpath`~
+ test -d \$dldir || mkdir -p \$dldir~
+ $install_prog $dir/$dlname \$dldir/$dlname~
+ chmod a+x \$dldir/$dlname~
+ if test -n '\''$stripme'\'' && test -n '\''$striplib'\''; then
+ eval '\''$striplib \$dldir/$dlname'\'' || exit \$?;
+ fi'
+ postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+ dlpath=$dir/\$dldll~
+ $RM \$dlpath'
+ shlibpath_overrides_runpath=yes
+
+ case $host_os in
+ cygwin*)
+ # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+ soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+ ;;
+ mingw* | cegcc*)
+ # MinGW DLLs use traditional 'lib' prefix
+ soname_spec='${libname}`echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec=`$CC -print-search-dirs | $GREP "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$sys_lib_search_path_spec" | [$GREP ';[c-zC-Z]:/' >/dev/null]; then
+ # It is most probably a Windows format PATH printed by
+ # mingw gcc, but we are running on Cygwin. Gcc prints its search
+ # path with ; separators, and with drive letters. We can handle the
+ # drive letters (cygwin fileutils understands them), so leave them,
+ # especially as we might pass files found there to a mingw objdump,
+ # which wouldn't understand a cygwinified path. Ahh.
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ ;;
+ pw32*)
+ # pw32 DLLs use 'pw' prefix rather than 'lib'
+ library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}'
+ ;;
+ esac
+ ;;
+
+ *)
+ library_names_spec='${libname}`echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext} $libname.lib'
+ ;;
+ esac
+ dynamic_linker='Win32 ld.exe'
+ # FIXME: first we should search . and the directory the executable is in
+ shlibpath_var=PATH
+ ;;
+
+darwin* | rhapsody*)
+ dynamic_linker="$host_os dyld"
+ version_type=darwin
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+ soname_spec='${libname}${release}${major}$shared_ext'
+ shlibpath_overrides_runpath=yes
+ shlibpath_var=DYLD_LIBRARY_PATH
+ shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+m4_if([$1], [],[
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /usr/local/lib"])
+ sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+ ;;
+
+dgux*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+freebsd1*)
+ dynamic_linker=no
+ ;;
+
+freebsd* | dragonfly*)
+ # DragonFly does not have aout. When/if they implement a new
+ # versioning mechanism, adjust this.
+ if test -x /usr/bin/objformat; then
+ objformat=`/usr/bin/objformat`
+ else
+ case $host_os in
+ freebsd[[123]]*) objformat=aout ;;
+ *) objformat=elf ;;
+ esac
+ fi
+ version_type=freebsd-$objformat
+ case $version_type in
+ freebsd-elf*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ need_version=no
+ need_lib_prefix=no
+ ;;
+ freebsd-*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+ need_version=yes
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_os in
+ freebsd2*)
+ shlibpath_overrides_runpath=yes
+ ;;
+ freebsd3.[[01]]* | freebsdelf3.[[01]]*)
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ freebsd3.[[2-9]]* | freebsdelf3.[[2-9]]* | \
+ freebsd4.[[0-5]] | freebsdelf4.[[0-5]] | freebsd4.1.1 | freebsdelf4.1.1)
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+ *) # from 4.6 on, and DragonFly
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ esac
+ ;;
+
+gnu*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ hardcode_into_libs=yes
+ ;;
+
+hpux9* | hpux10* | hpux11*)
+ # Give a soname corresponding to the major version so that dld.sl refuses to
+ # link against other versions.
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ case $host_cpu in
+ ia64*)
+ shrext_cmds='.so'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.so"
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ if test "X$HPUX_IA64_MODE" = X32; then
+ sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+ else
+ sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+ fi
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ hppa*64*)
+ shrext_cmds='.sl'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ *)
+ shrext_cmds='.sl'
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=SHLIB_PATH
+ shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+ esac
+ # HP-UX runs *really* slowly unless shared libraries are mode 555.
+ postinstall_cmds='chmod 555 $lib'
+ ;;
+
+interix[[3-9]]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $host_os in
+ nonstopux*) version_type=nonstopux ;;
+ *)
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ version_type=linux
+ else
+ version_type=irix
+ fi ;;
+ esac
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+ case $host_os in
+ irix5* | nonstopux*)
+ libsuff= shlibsuff=
+ ;;
+ *)
+ case $LD in # libtool.m4 will add one of these switches to LD
+ *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+ libsuff= shlibsuff= libmagic=32-bit;;
+ *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+ libsuff=32 shlibsuff=N32 libmagic=N32;;
+ *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+ libsuff=64 shlibsuff=64 libmagic=64-bit;;
+ *) libsuff= shlibsuff= libmagic=never-match;;
+ esac
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+ sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+ hardcode_into_libs=yes
+ ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+ dynamic_linker=no
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ # Some binutils ld are patched to set DT_RUNPATH
+ save_LDFLAGS=$LDFLAGS
+ save_libdir=$libdir
+ eval "libdir=/foo; wl=\"$_LT_TAGVAR(lt_prog_compiler_wl, $1)\"; \
+ LDFLAGS=\"\$LDFLAGS $_LT_TAGVAR(hardcode_libdir_flag_spec, $1)\""
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([],[])],
+ [AS_IF([ ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null],
+ [shlibpath_overrides_runpath=yes])])
+ LDFLAGS=$save_LDFLAGS
+ libdir=$save_libdir
+
+ # This implies no fast_install, which is unacceptable.
+ # Some rework will be needed to allow for fast_install
+ # before this can be enabled.
+ hardcode_into_libs=yes
+
+ # Append ld.so.conf contents to the search path
+ if test -f /etc/ld.so.conf; then
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \[$]2)); skip = 1; } { if (!skip) print \[$]0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ fi
+
+ # We used to test for /lib/ld.so.1 and disable shared libraries on
+ # powerpc, because MkLinux only supported shared libraries with the
+ # GNU dynamic linker. Since this was broken with cross compilers,
+ # most powerpc-linux boxes support dynamic linking these days and
+ # people can always --disable-shared, the test was removed, and we
+ # assume the GNU/Linux dynamic linker is in use.
+ dynamic_linker='GNU/Linux ld.so'
+ ;;
+
+netbsdelf*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='NetBSD ld.elf_so'
+ ;;
+
+netbsd*)
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ dynamic_linker='NetBSD (a.out) ld.so'
+ else
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='NetBSD ld.elf_so'
+ fi
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+
+newsos6)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ ;;
+
+*nto* | *qnx*)
+ version_type=qnx
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='ldqnx.so'
+ ;;
+
+openbsd*)
+ version_type=sunos
+ sys_lib_dlsearch_path_spec="/usr/lib"
+ need_lib_prefix=no
+ # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+ case $host_os in
+ openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+ *) need_version=no ;;
+ esac
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ case $host_os in
+ openbsd2.[[89]] | openbsd2.[[89]].*)
+ shlibpath_overrides_runpath=no
+ ;;
+ *)
+ shlibpath_overrides_runpath=yes
+ ;;
+ esac
+ else
+ shlibpath_overrides_runpath=yes
+ fi
+ ;;
+
+os2*)
+ libname_spec='$name'
+ shrext_cmds=".dll"
+ need_lib_prefix=no
+ library_names_spec='$libname${shared_ext} $libname.a'
+ dynamic_linker='OS/2 ld.exe'
+ shlibpath_var=LIBPATH
+ ;;
+
+osf3* | osf4* | osf5*)
+ version_type=osf
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+ sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+ ;;
+
+rdos*)
+ dynamic_linker=no
+ ;;
+
+solaris*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ # ldd complains unless libraries are executable
+ postinstall_cmds='chmod +x $lib'
+ ;;
+
+sunos4*)
+ version_type=sunos
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ if test "$with_gnu_ld" = yes; then
+ need_lib_prefix=no
+ fi
+ need_version=yes
+ ;;
+
+sysv4 | sysv4.3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_vendor in
+ sni)
+ shlibpath_overrides_runpath=no
+ need_lib_prefix=no
+ runpath_var=LD_RUN_PATH
+ ;;
+ siemens)
+ need_lib_prefix=no
+ ;;
+ motorola)
+ need_lib_prefix=no
+ need_version=no
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+ ;;
+ esac
+ ;;
+
+sysv4*MP*)
+ if test -d /usr/nec ;then
+ version_type=linux
+ library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+ soname_spec='$libname${shared_ext}.$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ fi
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ version_type=freebsd-elf
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ if test "$with_gnu_ld" = yes; then
+ sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+ else
+ sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+ case $host_os in
+ sco3.2v5*)
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+ ;;
+ esac
+ fi
+ sys_lib_dlsearch_path_spec='/usr/lib'
+ ;;
+
+tpf*)
+ # TPF is a cross-target only. Preferred cross-host = GNU/Linux.
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+uts4*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+*)
+ dynamic_linker=no
+ ;;
+esac
+AC_MSG_RESULT([$dynamic_linker])
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+ variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+
+if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then
+ sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec"
+fi
+if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then
+ sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec"
+fi
+
+_LT_DECL([], [variables_saved_for_relink], [1],
+ [Variables whose values should be saved in libtool wrapper scripts and
+ restored at link time])
+_LT_DECL([], [need_lib_prefix], [0],
+ [Do we need the "lib" prefix for modules?])
+_LT_DECL([], [need_version], [0], [Do we need a version for libraries?])
+_LT_DECL([], [version_type], [0], [Library versioning type])
+_LT_DECL([], [runpath_var], [0], [Shared library runtime path variable])
+_LT_DECL([], [shlibpath_var], [0],[Shared library path variable])
+_LT_DECL([], [shlibpath_overrides_runpath], [0],
+ [Is shlibpath searched before the hard-coded library search path?])
+_LT_DECL([], [libname_spec], [1], [Format of library name prefix])
+_LT_DECL([], [library_names_spec], [1],
+ [[List of archive names. First name is the real one, the rest are links.
+ The last name is the one that the linker finds with -lNAME]])
+_LT_DECL([], [soname_spec], [1],
+ [[The coded name of the library, if different from the real name]])
+_LT_DECL([], [postinstall_cmds], [2],
+ [Command to use after installation of a shared archive])
+_LT_DECL([], [postuninstall_cmds], [2],
+ [Command to use after uninstallation of a shared archive])
+_LT_DECL([], [finish_cmds], [2],
+ [Commands used to finish a libtool library installation in a directory])
+_LT_DECL([], [finish_eval], [1],
+ [[As "finish_cmds", except a single script fragment to be evaled but
+ not shown]])
+_LT_DECL([], [hardcode_into_libs], [0],
+ [Whether we should hardcode library paths into libraries])
+_LT_DECL([], [sys_lib_search_path_spec], [2],
+ [Compile-time system search path for libraries])
+_LT_DECL([], [sys_lib_dlsearch_path_spec], [2],
+ [Run-time system search path for libraries])
+])# _LT_SYS_DYNAMIC_LINKER
+
+
+# _LT_PATH_TOOL_PREFIX(TOOL)
+# --------------------------
+# find a file program which can recognize shared library
+AC_DEFUN([_LT_PATH_TOOL_PREFIX],
+[m4_require([_LT_DECL_EGREP])dnl
+AC_MSG_CHECKING([for $1])
+AC_CACHE_VAL(lt_cv_path_MAGIC_CMD,
+[case $MAGIC_CMD in
+[[\\/*] | ?:[\\/]*])
+ lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path.
+ ;;
+*)
+ lt_save_MAGIC_CMD="$MAGIC_CMD"
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+dnl $ac_dummy forces splitting on constant user-supplied paths.
+dnl POSIX.2 word splitting is done only on the output of word expansions,
+dnl not every word. This closes a longstanding sh security hole.
+ ac_dummy="m4_if([$2], , $PATH, [$2])"
+ for ac_dir in $ac_dummy; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f $ac_dir/$1; then
+ lt_cv_path_MAGIC_CMD="$ac_dir/$1"
+ if test -n "$file_magic_test_file"; then
+ case $deplibs_check_method in
+ "file_magic "*)
+ file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"`
+ MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+ if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null |
+ $EGREP "$file_magic_regex" > /dev/null; then
+ :
+ else
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the command libtool uses to detect shared libraries,
+*** $file_magic_cmd, produces output that libtool cannot recognize.
+*** The result is that libtool may fail to recognize shared libraries
+*** as such. This will affect the creation of libtool libraries that
+*** depend on shared libraries, but programs linked with such libtool
+*** libraries will work regardless of this problem. Nevertheless, you
+*** may want to report the problem to your system manager and/or to
+*** bug-libtool at gnu.org
+
+_LT_EOF
+ fi ;;
+ esac
+ fi
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+ MAGIC_CMD="$lt_save_MAGIC_CMD"
+ ;;
+esac])
+MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+if test -n "$MAGIC_CMD"; then
+ AC_MSG_RESULT($MAGIC_CMD)
+else
+ AC_MSG_RESULT(no)
+fi
+_LT_DECL([], [MAGIC_CMD], [0],
+ [Used to examine libraries when file_magic_cmd begins with "file"])dnl
+])# _LT_PATH_TOOL_PREFIX
+
+# Old name:
+AU_ALIAS([AC_PATH_TOOL_PREFIX], [_LT_PATH_TOOL_PREFIX])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_PATH_TOOL_PREFIX], [])
+
+
+# _LT_PATH_MAGIC
+# --------------
+# find a file program which can recognize a shared library
+m4_defun([_LT_PATH_MAGIC],
+[_LT_PATH_TOOL_PREFIX(${ac_tool_prefix}file, /usr/bin$PATH_SEPARATOR$PATH)
+if test -z "$lt_cv_path_MAGIC_CMD"; then
+ if test -n "$ac_tool_prefix"; then
+ _LT_PATH_TOOL_PREFIX(file, /usr/bin$PATH_SEPARATOR$PATH)
+ else
+ MAGIC_CMD=:
+ fi
+fi
+])# _LT_PATH_MAGIC
+
+
+# LT_PATH_LD
+# ----------
+# find the pathname to the GNU or non-GNU linker
+AC_DEFUN([LT_PATH_LD],
+[AC_REQUIRE([AC_PROG_CC])dnl
+AC_REQUIRE([AC_CANONICAL_HOST])dnl
+AC_REQUIRE([AC_CANONICAL_BUILD])dnl
+m4_require([_LT_DECL_SED])dnl
+m4_require([_LT_DECL_EGREP])dnl
+
+AC_ARG_WITH([gnu-ld],
+ [AS_HELP_STRING([--with-gnu-ld],
+ [assume the C compiler uses GNU ld @<:@default=no@:>@])],
+ [test "$withval" = no || with_gnu_ld=yes],
+ [with_gnu_ld=no])dnl
+
+ac_prog=ld
+if test "$GCC" = yes; then
+ # Check if gcc -print-prog-name=ld gives a path.
+ AC_MSG_CHECKING([for ld used by $CC])
+ case $host in
+ *-*-mingw*)
+ # gcc leaves a trailing carriage return which upsets mingw
+ ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+ *)
+ ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+ esac
+ case $ac_prog in
+ # Accept absolute paths.
+ [[\\/]]* | ?:[[\\/]]*)
+ re_direlt='/[[^/]][[^/]]*/\.\./'
+ # Canonicalize the pathname of ld
+ ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'`
+ while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do
+ ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"`
+ done
+ test -z "$LD" && LD="$ac_prog"
+ ;;
+ "")
+ # If it fails, then pretend we aren't using GCC.
+ ac_prog=ld
+ ;;
+ *)
+ # If it is relative, then search for the first ld in PATH.
+ with_gnu_ld=unknown
+ ;;
+ esac
+elif test "$with_gnu_ld" = yes; then
+ AC_MSG_CHECKING([for GNU ld])
+else
+ AC_MSG_CHECKING([for non-GNU ld])
+fi
+AC_CACHE_VAL(lt_cv_path_LD,
+[if test -z "$LD"; then
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+ lt_cv_path_LD="$ac_dir/$ac_prog"
+ # Check to see if the program is GNU ld. I'd rather use --version,
+ # but apparently some variants of GNU ld only accept -v.
+ # Break only if it was the GNU/non-GNU ld that we prefer.
+ case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+ *GNU* | *'with BFD'*)
+ test "$with_gnu_ld" != no && break
+ ;;
+ *)
+ test "$with_gnu_ld" != yes && break
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+else
+ lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi])
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+ AC_MSG_RESULT($LD)
+else
+ AC_MSG_RESULT(no)
+fi
+test -z "$LD" && AC_MSG_ERROR([no acceptable ld found in \$PATH])
+_LT_PATH_LD_GNU
+AC_SUBST([LD])
+
+_LT_TAGDECL([], [LD], [1], [The linker used to build libraries])
+])# LT_PATH_LD
+
+# Old names:
+AU_ALIAS([AM_PROG_LD], [LT_PATH_LD])
+AU_ALIAS([AC_PROG_LD], [LT_PATH_LD])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AM_PROG_LD], [])
+dnl AC_DEFUN([AC_PROG_LD], [])
+
+
+# _LT_PATH_LD_GNU
+#- --------------
+m4_defun([_LT_PATH_LD_GNU],
+[AC_CACHE_CHECK([if the linker ($LD) is GNU ld], lt_cv_prog_gnu_ld,
+[# I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+ lt_cv_prog_gnu_ld=yes
+ ;;
+*)
+ lt_cv_prog_gnu_ld=no
+ ;;
+esac])
+with_gnu_ld=$lt_cv_prog_gnu_ld
+])# _LT_PATH_LD_GNU
+
+
+# _LT_CMD_RELOAD
+# --------------
+# find reload flag for linker
+# -- PORTME Some linkers may need a different reload flag.
+m4_defun([_LT_CMD_RELOAD],
+[AC_CACHE_CHECK([for $LD option to reload object files],
+ lt_cv_ld_reload_flag,
+ [lt_cv_ld_reload_flag='-r'])
+reload_flag=$lt_cv_ld_reload_flag
+case $reload_flag in
+"" | " "*) ;;
+*) reload_flag=" $reload_flag" ;;
+esac
+reload_cmds='$LD$reload_flag -o $output$reload_objs'
+case $host_os in
+ darwin*)
+ if test "$GCC" = yes; then
+ reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs'
+ else
+ reload_cmds='$LD$reload_flag -o $output$reload_objs'
+ fi
+ ;;
+esac
+_LT_DECL([], [reload_flag], [1], [How to create reloadable object files])dnl
+_LT_DECL([], [reload_cmds], [2])dnl
+])# _LT_CMD_RELOAD
+
+
+# _LT_CHECK_MAGIC_METHOD
+# ----------------------
+# how to check for library dependencies
+# -- PORTME fill in with the dynamic library characteristics
+m4_defun([_LT_CHECK_MAGIC_METHOD],
+[m4_require([_LT_DECL_EGREP])
+m4_require([_LT_DECL_OBJDUMP])
+AC_CACHE_CHECK([how to recognize dependent libraries],
+lt_cv_deplibs_check_method,
+[lt_cv_file_magic_cmd='$MAGIC_CMD'
+lt_cv_file_magic_test_file=
+lt_cv_deplibs_check_method='unknown'
+# Need to set the preceding variable on all platforms that support
+# interlibrary dependencies.
+# 'none' -- dependencies not supported.
+# `unknown' -- same as none, but documents that we really don't know.
+# 'pass_all' -- all dependencies passed with no checks.
+# 'test_compile' -- check by making test program.
+# 'file_magic [[regex]]' -- check by looking for files in library path
+# which responds to the $file_magic_cmd with a given extended regex.
+# If you have `file' or equivalent on your system and you're not sure
+# whether `pass_all' will *always* work, you probably want this one.
+
+case $host_os in
+aix[[4-9]]*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+beos*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+bsdi[[45]]*)
+ lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (shared object|dynamic lib)'
+ lt_cv_file_magic_cmd='/usr/bin/file -L'
+ lt_cv_file_magic_test_file=/shlib/libc.so
+ ;;
+
+cygwin*)
+ # func_win32_libid is a shell function defined in ltmain.sh
+ lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+ lt_cv_file_magic_cmd='func_win32_libid'
+ ;;
+
+mingw* | pw32*)
+ # Base MSYS/MinGW do not provide the 'file' command needed by
+ # func_win32_libid shell function, so use a weaker test based on 'objdump',
+ # unless we find 'file', for example because we are cross-compiling.
+ if ( file / ) >/dev/null 2>&1; then
+ lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+ lt_cv_file_magic_cmd='func_win32_libid'
+ else
+ lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?'
+ lt_cv_file_magic_cmd='$OBJDUMP -f'
+ fi
+ ;;
+
+cegcc)
+ # use the weaker test based on 'objdump'. See mingw*.
+ lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?'
+ lt_cv_file_magic_cmd='$OBJDUMP -f'
+ ;;
+
+darwin* | rhapsody*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+freebsd* | dragonfly*)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
+ case $host_cpu in
+ i*86 )
+ # Not sure whether the presence of OpenBSD here was a mistake.
+ # Let's accept both of them until this is cleared up.
+ lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[[3-9]]86 (compact )?demand paged shared library'
+ lt_cv_file_magic_cmd=/usr/bin/file
+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*`
+ ;;
+ esac
+ else
+ lt_cv_deplibs_check_method=pass_all
+ fi
+ ;;
+
+gnu*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+hpux10.20* | hpux11*)
+ lt_cv_file_magic_cmd=/usr/bin/file
+ case $host_cpu in
+ ia64*)
+ lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|ELF-[[0-9]][[0-9]]) shared object file - IA64'
+ lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so
+ ;;
+ hppa*64*)
+ [lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]']
+ lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl
+ ;;
+ *)
+ lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|PA-RISC[[0-9]].[[0-9]]) shared library'
+ lt_cv_file_magic_test_file=/usr/lib/libc.sl
+ ;;
+ esac
+ ;;
+
+interix[[3-9]]*)
+ # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|\.a)$'
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $LD in
+ *-32|*"-32 ") libmagic=32-bit;;
+ *-n32|*"-n32 ") libmagic=N32;;
+ *-64|*"-64 ") libmagic=64-bit;;
+ *) libmagic=never-match;;
+ esac
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$'
+ else
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|_pic\.a)$'
+ fi
+ ;;
+
+newos6*)
+ lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (executable|dynamic lib)'
+ lt_cv_file_magic_cmd=/usr/bin/file
+ lt_cv_file_magic_test_file=/usr/lib/libnls.so
+ ;;
+
+*nto* | *qnx*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+openbsd*)
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|\.so|_pic\.a)$'
+ else
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$'
+ fi
+ ;;
+
+osf3* | osf4* | osf5*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+rdos*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+solaris*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+sysv4 | sysv4.3*)
+ case $host_vendor in
+ motorola)
+ lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (shared object|dynamic lib) M[[0-9]][[0-9]]* Version [[0-9]]'
+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*`
+ ;;
+ ncr)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ sequent)
+ lt_cv_file_magic_cmd='/bin/file'
+ lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB (shared object|dynamic lib )'
+ ;;
+ sni)
+ lt_cv_file_magic_cmd='/bin/file'
+ lt_cv_deplibs_check_method="file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB dynamic lib"
+ lt_cv_file_magic_test_file=/lib/libc.so
+ ;;
+ siemens)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ pc)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ esac
+ ;;
+
+tpf*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+esac
+])
+file_magic_cmd=$lt_cv_file_magic_cmd
+deplibs_check_method=$lt_cv_deplibs_check_method
+test -z "$deplibs_check_method" && deplibs_check_method=unknown
+
+_LT_DECL([], [deplibs_check_method], [1],
+ [Method to check whether dependent libraries are shared objects])
+_LT_DECL([], [file_magic_cmd], [1],
+ [Command to use when deplibs_check_method == "file_magic"])
+])# _LT_CHECK_MAGIC_METHOD
+
+
+# LT_PATH_NM
+# ----------
+# find the pathname to a BSD- or MS-compatible name lister
+AC_DEFUN([LT_PATH_NM],
+[AC_REQUIRE([AC_PROG_CC])dnl
+AC_CACHE_CHECK([for BSD- or MS-compatible name lister (nm)], lt_cv_path_NM,
+[if test -n "$NM"; then
+ # Let the user override the test.
+ lt_cv_path_NM="$NM"
+else
+ lt_nm_to_check="${ac_tool_prefix}nm"
+ if test -n "$ac_tool_prefix" && test "$build" = "$host"; then
+ lt_nm_to_check="$lt_nm_to_check nm"
+ fi
+ for lt_tmp_nm in $lt_nm_to_check; do
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ tmp_nm="$ac_dir/$lt_tmp_nm"
+ if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then
+ # Check to see if the nm accepts a BSD-compat flag.
+ # Adding the `sed 1q' prevents false positives on HP-UX, which says:
+ # nm: unknown option "B" ignored
+ # Tru64's nm complains that /dev/null is an invalid object file
+ case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in
+ */dev/null* | *'Invalid file or object type'*)
+ lt_cv_path_NM="$tmp_nm -B"
+ break
+ ;;
+ *)
+ case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in
+ */dev/null*)
+ lt_cv_path_NM="$tmp_nm -p"
+ break
+ ;;
+ *)
+ lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but
+ continue # so that we can try to find one that supports BSD flags
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+ done
+ : ${lt_cv_path_NM=no}
+fi])
+if test "$lt_cv_path_NM" != "no"; then
+ NM="$lt_cv_path_NM"
+else
+ # Didn't find any BSD compatible name lister, look for dumpbin.
+ AC_CHECK_TOOLS(DUMPBIN, ["dumpbin -symbols" "link -dump -symbols"], :)
+ AC_SUBST([DUMPBIN])
+ if test "$DUMPBIN" != ":"; then
+ NM="$DUMPBIN"
+ fi
+fi
+test -z "$NM" && NM=nm
+AC_SUBST([NM])
+_LT_DECL([], [NM], [1], [A BSD- or MS-compatible name lister])dnl
+
+AC_CACHE_CHECK([the name lister ($NM) interface], [lt_cv_nm_interface],
+ [lt_cv_nm_interface="BSD nm"
+ echo "int some_variable = 0;" > conftest.$ac_ext
+ (eval echo "\"\$as_me:__oline__: $ac_compile\"" >&AS_MESSAGE_LOG_FD)
+ (eval "$ac_compile" 2>conftest.err)
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ (eval echo "\"\$as_me:__oline__: $NM \\\"conftest.$ac_objext\\\"\"" >&AS_MESSAGE_LOG_FD)
+ (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out)
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ (eval echo "\"\$as_me:__oline__: output\"" >&AS_MESSAGE_LOG_FD)
+ cat conftest.out >&AS_MESSAGE_LOG_FD
+ if $GREP 'External.*some_variable' conftest.out > /dev/null; then
+ lt_cv_nm_interface="MS dumpbin"
+ fi
+ rm -f conftest*])
+])# LT_PATH_NM
+
+# Old names:
+AU_ALIAS([AM_PROG_NM], [LT_PATH_NM])
+AU_ALIAS([AC_PROG_NM], [LT_PATH_NM])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AM_PROG_NM], [])
+dnl AC_DEFUN([AC_PROG_NM], [])
+
+
+# LT_LIB_M
+# --------
+# check for math library
+AC_DEFUN([LT_LIB_M],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+LIBM=
+case $host in
+*-*-beos* | *-*-cygwin* | *-*-pw32* | *-*-darwin*)
+ # These system don't have libm, or don't need it
+ ;;
+*-ncr-sysv4.3*)
+ AC_CHECK_LIB(mw, _mwvalidcheckl, LIBM="-lmw")
+ AC_CHECK_LIB(m, cos, LIBM="$LIBM -lm")
+ ;;
+*)
+ AC_CHECK_LIB(m, cos, LIBM="-lm")
+ ;;
+esac
+AC_SUBST([LIBM])
+])# LT_LIB_M
+
+# Old name:
+AU_ALIAS([AC_CHECK_LIBM], [LT_LIB_M])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_CHECK_LIBM], [])
+
+
+# _LT_COMPILER_NO_RTTI([TAGNAME])
+# -------------------------------
+m4_defun([_LT_COMPILER_NO_RTTI],
+[m4_require([_LT_TAG_COMPILER])dnl
+
+_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=
+
+if test "$GCC" = yes; then
+ _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin'
+
+ _LT_COMPILER_OPTION([if $compiler supports -fno-rtti -fno-exceptions],
+ lt_cv_prog_compiler_rtti_exceptions,
+ [-fno-rtti -fno-exceptions], [],
+ [_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)="$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1) -fno-rtti -fno-exceptions"])
+fi
+_LT_TAGDECL([no_builtin_flag], [lt_prog_compiler_no_builtin_flag], [1],
+ [Compiler flag to turn off builtin functions])
+])# _LT_COMPILER_NO_RTTI
+
+
+# _LT_CMD_GLOBAL_SYMBOLS
+# ----------------------
+m4_defun([_LT_CMD_GLOBAL_SYMBOLS],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+AC_REQUIRE([AC_PROG_CC])dnl
+AC_REQUIRE([LT_PATH_NM])dnl
+AC_REQUIRE([LT_PATH_LD])dnl
+m4_require([_LT_DECL_SED])dnl
+m4_require([_LT_DECL_EGREP])dnl
+m4_require([_LT_TAG_COMPILER])dnl
+
+# Check for command to grab the raw symbol name followed by C symbol from nm.
+AC_MSG_CHECKING([command to parse $NM output from $compiler object])
+AC_CACHE_VAL([lt_cv_sys_global_symbol_pipe],
+[
+# These are sane defaults that work on at least a few old systems.
+# [They come from Ultrix. What could be older than Ultrix?!! ;)]
+
+# Character class describing NM global symbol codes.
+symcode='[[BCDEGRST]]'
+
+# Regexp to match symbols that can be accessed directly from C.
+sympat='\([[_A-Za-z]][[_A-Za-z0-9]]*\)'
+
+# Define system-specific variables.
+case $host_os in
+aix*)
+ symcode='[[BCDT]]'
+ ;;
+cygwin* | mingw* | pw32* | cegcc*)
+ symcode='[[ABCDGISTW]]'
+ ;;
+hpux*)
+ if test "$host_cpu" = ia64; then
+ symcode='[[ABCDEGRST]]'
+ fi
+ ;;
+irix* | nonstopux*)
+ symcode='[[BCDEGRST]]'
+ ;;
+osf*)
+ symcode='[[BCDEGQRST]]'
+ ;;
+solaris*)
+ symcode='[[BDRT]]'
+ ;;
+sco3.2v5*)
+ symcode='[[DT]]'
+ ;;
+sysv4.2uw2*)
+ symcode='[[DT]]'
+ ;;
+sysv5* | sco5v6* | unixware* | OpenUNIX*)
+ symcode='[[ABDT]]'
+ ;;
+sysv4)
+ symcode='[[DFNSTU]]'
+ ;;
+esac
+
+# If we're using GNU nm, then use its standard symbol codes.
+case `$NM -V 2>&1` in
+*GNU* | *'with BFD'*)
+ symcode='[[ABCDGIRSTW]]' ;;
+esac
+
+# Transform an extracted symbol line into a proper C declaration.
+# Some systems (esp. on ia64) link data and code symbols differently,
+# so use this general approach.
+lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'"
+
+# Transform an extracted symbol line into symbol name and symbol address
+lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p'"
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \(lib[[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"lib\2\", (void *) \&\2},/p'"
+
+# Handle CRLF in mingw tool chain
+opt_cr=
+case $build_os in
+mingw*)
+ opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp
+ ;;
+esac
+
+# Try without a prefix underscore, then with it.
+for ac_symprfx in "" "_"; do
+
+ # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol.
+ symxfrm="\\1 $ac_symprfx\\2 \\2"
+
+ # Write the raw and C identifiers.
+ if test "$lt_cv_nm_interface" = "MS dumpbin"; then
+ # Fake it for dumpbin and say T for any non-static function
+ # and D for any global variable.
+ # Also find C++ and __fastcall symbols from MSVC++,
+ # which start with @ or ?.
+ lt_cv_sys_global_symbol_pipe="$AWK ['"\
+" {last_section=section; section=\$ 3};"\
+" /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\
+" \$ 0!~/External *\|/{next};"\
+" / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\
+" {if(hide[section]) next};"\
+" {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\
+" {split(\$ 0, a, /\||\r/); split(a[2], s)};"\
+" s[1]~/^[@?]/{print s[1], s[1]; next};"\
+" s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\
+" ' prfx=^$ac_symprfx]"
+ else
+ lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[[ ]]\($symcode$symcode*\)[[ ]][[ ]]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'"
+ fi
+
+ # Check to see that the pipe works correctly.
+ pipe_works=no
+
+ rm -f conftest*
+ cat > conftest.$ac_ext <<_LT_EOF
+#ifdef __cplusplus
+extern "C" {
+#endif
+char nm_test_var;
+void nm_test_func(void);
+void nm_test_func(void){}
+#ifdef __cplusplus
+}
+#endif
+int main(){nm_test_var='a';nm_test_func();return(0);}
+_LT_EOF
+
+ if AC_TRY_EVAL(ac_compile); then
+ # Now try to grab the symbols.
+ nlist=conftest.nm
+ if AC_TRY_EVAL(NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) && test -s "$nlist"; then
+ # Try sorting and uniquifying the output.
+ if sort "$nlist" | uniq > "$nlist"T; then
+ mv -f "$nlist"T "$nlist"
+ else
+ rm -f "$nlist"T
+ fi
+
+ # Make sure that we snagged all the symbols we need.
+ if $GREP ' nm_test_var$' "$nlist" >/dev/null; then
+ if $GREP ' nm_test_func$' "$nlist" >/dev/null; then
+ cat <<_LT_EOF > conftest.$ac_ext
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+_LT_EOF
+ # Now generate the symbol file.
+ eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext'
+
+ cat <<_LT_EOF >> conftest.$ac_ext
+
+/* The mapping between symbol names and symbols. */
+const struct {
+ const char *name;
+ void *address;
+}
+lt__PROGRAM__LTX_preloaded_symbols[[]] =
+{
+ { "@PROGRAM@", (void *) 0 },
+_LT_EOF
+ $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext
+ cat <<\_LT_EOF >> conftest.$ac_ext
+ {0, (void *) 0}
+};
+
+/* This works around a problem in FreeBSD linker */
+#ifdef FREEBSD_WORKAROUND
+static const void *lt_preloaded_setup() {
+ return lt__PROGRAM__LTX_preloaded_symbols;
+}
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+_LT_EOF
+ # Now try linking the two files.
+ mv conftest.$ac_objext conftstm.$ac_objext
+ lt_save_LIBS="$LIBS"
+ lt_save_CFLAGS="$CFLAGS"
+ LIBS="conftstm.$ac_objext"
+ CFLAGS="$CFLAGS$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)"
+ if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext}; then
+ pipe_works=yes
+ fi
+ LIBS="$lt_save_LIBS"
+ CFLAGS="$lt_save_CFLAGS"
+ else
+ echo "cannot find nm_test_func in $nlist" >&AS_MESSAGE_LOG_FD
+ fi
+ else
+ echo "cannot find nm_test_var in $nlist" >&AS_MESSAGE_LOG_FD
+ fi
+ else
+ echo "cannot run $lt_cv_sys_global_symbol_pipe" >&AS_MESSAGE_LOG_FD
+ fi
+ else
+ echo "$progname: failed program was:" >&AS_MESSAGE_LOG_FD
+ cat conftest.$ac_ext >&5
+ fi
+ rm -rf conftest* conftst*
+
+ # Do not use the global_symbol_pipe unless it works.
+ if test "$pipe_works" = yes; then
+ break
+ else
+ lt_cv_sys_global_symbol_pipe=
+ fi
+done
+])
+if test -z "$lt_cv_sys_global_symbol_pipe"; then
+ lt_cv_sys_global_symbol_to_cdecl=
+fi
+if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then
+ AC_MSG_RESULT(failed)
+else
+ AC_MSG_RESULT(ok)
+fi
+
+_LT_DECL([global_symbol_pipe], [lt_cv_sys_global_symbol_pipe], [1],
+ [Take the output of nm and produce a listing of raw symbols and C names])
+_LT_DECL([global_symbol_to_cdecl], [lt_cv_sys_global_symbol_to_cdecl], [1],
+ [Transform the output of nm in a proper C declaration])
+_LT_DECL([global_symbol_to_c_name_address],
+ [lt_cv_sys_global_symbol_to_c_name_address], [1],
+ [Transform the output of nm in a C name address pair])
+_LT_DECL([global_symbol_to_c_name_address_lib_prefix],
+ [lt_cv_sys_global_symbol_to_c_name_address_lib_prefix], [1],
+ [Transform the output of nm in a C name address pair when lib prefix is needed])
+]) # _LT_CMD_GLOBAL_SYMBOLS
+
+
+# _LT_COMPILER_PIC([TAGNAME])
+# ---------------------------
+m4_defun([_LT_COMPILER_PIC],
+[m4_require([_LT_TAG_COMPILER])dnl
+_LT_TAGVAR(lt_prog_compiler_wl, $1)=
+_LT_TAGVAR(lt_prog_compiler_pic, $1)=
+_LT_TAGVAR(lt_prog_compiler_static, $1)=
+
+AC_MSG_CHECKING([for $compiler option to produce PIC])
+m4_if([$1], [CXX], [
+ # C++ specific cases for pic, static, wl, etc.
+ if test "$GXX" = yes; then
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+
+ case $host_os in
+ aix*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ m68k)
+ # FIXME: we need at least 68020 code to build shared libraries, but
+ # adding the `-m68020' flag to GCC prevents building anything better,
+ # like `-m68040'.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4'
+ ;;
+ esac
+ ;;
+
+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+ # PIC is the default for these OSes.
+ ;;
+ mingw* | cygwin* | os2* | pw32* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ # Although the cygwin gcc ignores -fPIC, still need this for old-style
+ # (--disable-auto-import) libraries
+ m4_if([$1], [GCJ], [],
+ [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT'])
+ ;;
+ darwin* | rhapsody*)
+ # PIC is the default on this platform
+ # Common symbols not allowed in MH_DYLIB files
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common'
+ ;;
+ *djgpp*)
+ # DJGPP does not support shared libraries at all
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ ;;
+ interix[[3-9]]*)
+ # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+ # Instead, we relocate shared libraries at runtime.
+ ;;
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic
+ fi
+ ;;
+ hpux*)
+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit
+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag
+ # sets the default TLS model and affects inlining.
+ case $host_cpu in
+ hppa*64*)
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ esac
+ ;;
+ *qnx* | *nto*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared'
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ esac
+ else
+ case $host_os in
+ aix[[4-9]]*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ else
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp'
+ fi
+ ;;
+ chorus*)
+ case $cc_basename in
+ cxch68*)
+ # Green Hills C++ Compiler
+ # _LT_TAGVAR(lt_prog_compiler_static, $1)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a"
+ ;;
+ esac
+ ;;
+ dgux*)
+ case $cc_basename in
+ ec++*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ ;;
+ ghcx*)
+ # Green Hills C++ Compiler
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ freebsd* | dragonfly*)
+ # FreeBSD uses GNU C++
+ ;;
+ hpux9* | hpux10* | hpux11*)
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive'
+ if test "$host_cpu" != ia64; then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z'
+ fi
+ ;;
+ aCC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive'
+ case $host_cpu in
+ hppa*64*|ia64*)
+ # +Z the default
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z'
+ ;;
+ esac
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ interix*)
+ # This is c89, which is MS Visual C++ (no shared libs)
+ # Anyone wants to do a port?
+ ;;
+ irix5* | irix6* | nonstopux*)
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ # CC pic flag -KPIC is the default.
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ KCC*)
+ # KAI C++ Compiler
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ ecpc* )
+ # old Intel C++ for x86_64 which still supported -KPIC.
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ icpc* )
+ # Intel C++, used to be incompatible with GCC.
+ # ICC 10 doesn't accept -KPIC any more.
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ pgCC* | pgcpp*)
+ # Portland Group C++ compiler
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+ cxx*)
+ # Compaq C++
+ # Make sure the PIC flag is empty. It appears that all Alpha
+ # Linux and Compaq Tru64 Unix objects are PIC.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+ xlc* | xlC*)
+ # IBM XL 8.0 on PPC
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink'
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld '
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+ lynxos*)
+ ;;
+ m88k*)
+ ;;
+ mvs*)
+ case $cc_basename in
+ cxx*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-W c,exportall'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ netbsd* | netbsdelf*-gnu)
+ ;;
+ *qnx* | *nto*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared'
+ ;;
+ osf3* | osf4* | osf5*)
+ case $cc_basename in
+ KCC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,'
+ ;;
+ RCC*)
+ # Rational C++ 2.4.1
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ ;;
+ cxx*)
+ # Digital/Compaq C++
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # Make sure the PIC flag is empty. It appears that all Alpha
+ # Linux and Compaq Tru64 Unix objects are PIC.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ psos*)
+ ;;
+ solaris*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.2, 5.x and Centerline C++
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld '
+ ;;
+ gcx*)
+ # Green Hills C++ Compiler
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ sunos4*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.x
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+ lcc*)
+ # Lucid
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+ esac
+ ;;
+ tandem*)
+ case $cc_basename in
+ NCC*)
+ # NonStop-UX NCC 3.20
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ vxworks*)
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+ ;;
+ esac
+ fi
+],
+[
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+
+ case $host_os in
+ aix*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ m68k)
+ # FIXME: we need at least 68020 code to build shared libraries, but
+ # adding the `-m68020' flag to GCC prevents building anything better,
+ # like `-m68040'.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4'
+ ;;
+ esac
+ ;;
+
+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+ # PIC is the default for these OSes.
+ ;;
+
+ mingw* | cygwin* | pw32* | os2* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ # Although the cygwin gcc ignores -fPIC, still need this for old-style
+ # (--disable-auto-import) libraries
+ m4_if([$1], [GCJ], [],
+ [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT'])
+ ;;
+
+ darwin* | rhapsody*)
+ # PIC is the default on this platform
+ # Common symbols not allowed in MH_DYLIB files
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common'
+ ;;
+
+ hpux*)
+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit
+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag
+ # sets the default TLS model and affects inlining.
+ case $host_cpu in
+ hppa*64*)
+ # +Z the default
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ esac
+ ;;
+
+ interix[[3-9]]*)
+ # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+ # Instead, we relocate shared libraries at runtime.
+ ;;
+
+ msdosdjgpp*)
+ # Just because we use GCC doesn't mean we suddenly get shared libraries
+ # on systems that don't support them.
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+ enable_shared=no
+ ;;
+
+ *nto* | *qnx*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic
+ fi
+ ;;
+
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ esac
+ else
+ # PORTME Check for flag to pass linker flags through the system compiler.
+ case $host_os in
+ aix*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ else
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp'
+ fi
+ ;;
+
+ mingw* | cygwin* | pw32* | os2* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ m4_if([$1], [GCJ], [],
+ [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT'])
+ ;;
+
+ hpux9* | hpux10* | hpux11*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+ # not for PA HP-UX.
+ case $host_cpu in
+ hppa*64*|ia64*)
+ # +Z the default
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z'
+ ;;
+ esac
+ # Is there a better lt_prog_compiler_static that works with the bundled CC?
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive'
+ ;;
+
+ irix5* | irix6* | nonstopux*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # PIC (with -KPIC) is the default.
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ # old Intel for x86_64 which still supported -KPIC.
+ ecc*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ # icc used to be incompatible with GCC.
+ # ICC 10 doesn't accept -KPIC any more.
+ icc* | ifort*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ # Lahey Fortran 8.1.
+ lf95*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='--shared'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='--static'
+ ;;
+ pgcc* | pgf77* | pgf90* | pgf95*)
+ # Portland Group compilers (*not* the Pentium gcc compiler,
+ # which looks to be a dead project)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+ ccc*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # All Alpha code is PIC.
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+ xl*)
+ # IBM XL C 8.0/Fortran 10.1 on PPC
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink'
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C 5.9
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ ;;
+ *Sun\ F*)
+ # Sun Fortran 8.3 passes all unrecognized flags to the linker
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)=''
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+
+ newsos6)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ *nto* | *qnx*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared'
+ ;;
+
+ osf3* | osf4* | osf5*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # All OSF/1 code is PIC.
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+
+ rdos*)
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+
+ solaris*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ case $cc_basename in
+ f77* | f90* | f95*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ';;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,';;
+ esac
+ ;;
+
+ sunos4*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld '
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ sysv4 | sysv4.2uw2* | sysv4.3*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec ;then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-Kconform_pic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ fi
+ ;;
+
+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ unicos*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+ ;;
+
+ uts4*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ *)
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+ ;;
+ esac
+ fi
+])
+case $host_os in
+ # For platforms which do not support PIC, -DPIC is meaningless:
+ *djgpp*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)="$_LT_TAGVAR(lt_prog_compiler_pic, $1)@&t at m4_if([$1],[],[ -DPIC],[m4_if([$1],[CXX],[ -DPIC],[])])"
+ ;;
+esac
+AC_MSG_RESULT([$_LT_TAGVAR(lt_prog_compiler_pic, $1)])
+_LT_TAGDECL([wl], [lt_prog_compiler_wl], [1],
+ [How to pass a linker flag through the compiler])
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$_LT_TAGVAR(lt_prog_compiler_pic, $1)"; then
+ _LT_COMPILER_OPTION([if $compiler PIC flag $_LT_TAGVAR(lt_prog_compiler_pic, $1) works],
+ [_LT_TAGVAR(lt_cv_prog_compiler_pic_works, $1)],
+ [$_LT_TAGVAR(lt_prog_compiler_pic, $1)@&t at m4_if([$1],[],[ -DPIC],[m4_if([$1],[CXX],[ -DPIC],[])])], [],
+ [case $_LT_TAGVAR(lt_prog_compiler_pic, $1) in
+ "" | " "*) ;;
+ *) _LT_TAGVAR(lt_prog_compiler_pic, $1)=" $_LT_TAGVAR(lt_prog_compiler_pic, $1)" ;;
+ esac],
+ [_LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no])
+fi
+_LT_TAGDECL([pic_flag], [lt_prog_compiler_pic], [1],
+ [Additional compiler flags for building library objects])
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$_LT_TAGVAR(lt_prog_compiler_wl, $1) eval lt_tmp_static_flag=\"$_LT_TAGVAR(lt_prog_compiler_static, $1)\"
+_LT_LINKER_OPTION([if $compiler static flag $lt_tmp_static_flag works],
+ _LT_TAGVAR(lt_cv_prog_compiler_static_works, $1),
+ $lt_tmp_static_flag,
+ [],
+ [_LT_TAGVAR(lt_prog_compiler_static, $1)=])
+_LT_TAGDECL([link_static_flag], [lt_prog_compiler_static], [1],
+ [Compiler flag to prevent dynamic linking])
+])# _LT_COMPILER_PIC
+
+
+# _LT_LINKER_SHLIBS([TAGNAME])
+# ----------------------------
+# See if the linker supports building shared libraries.
+m4_defun([_LT_LINKER_SHLIBS],
+[AC_REQUIRE([LT_PATH_LD])dnl
+AC_REQUIRE([LT_PATH_NM])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_EGREP])dnl
+m4_require([_LT_DECL_SED])dnl
+m4_require([_LT_CMD_GLOBAL_SYMBOLS])dnl
+m4_require([_LT_TAG_COMPILER])dnl
+AC_MSG_CHECKING([whether the $compiler linker ($LD) supports shared libraries])
+m4_if([$1], [CXX], [
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ case $host_os in
+ aix[[4-9]]*)
+ # If we're using GNU nm, then we don't want the "-C" option.
+ # -C means demangle to AIX nm, but means don't demangle with GNU nm
+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ else
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ fi
+ ;;
+ pw32*)
+ _LT_TAGVAR(export_symbols_cmds, $1)="$ltdll_cmds"
+ ;;
+ cygwin* | mingw* | cegcc*)
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]][[ ]]/s/.*[[ ]]\([[^ ]]*\)/\1 DATA/;/^.*[[ ]]__nm__/s/^.*[[ ]]__nm__\([[^ ]]*\)[[ ]][[^ ]]*/\1 DATA/;/^I[[ ]]/d;/^[[AITW]][[ ]]/s/.* //'\'' | sort | uniq > $export_symbols'
+ ;;
+ linux* | k*bsd*-gnu)
+ _LT_TAGVAR(link_all_deplibs, $1)=no
+ ;;
+ *)
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ ;;
+ esac
+ _LT_TAGVAR(exclude_expsyms, $1)=['_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*']
+], [
+ runpath_var=
+ _LT_TAGVAR(allow_undefined_flag, $1)=
+ _LT_TAGVAR(always_export_symbols, $1)=no
+ _LT_TAGVAR(archive_cmds, $1)=
+ _LT_TAGVAR(archive_expsym_cmds, $1)=
+ _LT_TAGVAR(compiler_needs_object, $1)=no
+ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)=
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ _LT_TAGVAR(hardcode_automatic, $1)=no
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+ _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=
+ _LT_TAGVAR(hardcode_minus_L, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
+ _LT_TAGVAR(inherit_rpath, $1)=no
+ _LT_TAGVAR(link_all_deplibs, $1)=unknown
+ _LT_TAGVAR(module_cmds, $1)=
+ _LT_TAGVAR(module_expsym_cmds, $1)=
+ _LT_TAGVAR(old_archive_from_new_cmds, $1)=
+ _LT_TAGVAR(old_archive_from_expsyms_cmds, $1)=
+ _LT_TAGVAR(thread_safe_flag_spec, $1)=
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ # include_expsyms should be a list of space-separated symbols to be *always*
+ # included in the symbol list
+ _LT_TAGVAR(include_expsyms, $1)=
+ # exclude_expsyms can be an extended regexp of symbols to exclude
+ # it will be wrapped by ` (' and `)$', so one must not match beginning or
+ # end of line. Example: `a|bc|.*d.*' will exclude the symbols `a' and `bc',
+ # as well as any symbol that contains `d'.
+ _LT_TAGVAR(exclude_expsyms, $1)=['_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*']
+ # Although _GLOBAL_OFFSET_TABLE_ is a valid symbol C name, most a.out
+ # platforms (ab)use it in PIC code, but their linkers get confused if
+ # the symbol is explicitly referenced. Since portable code cannot
+ # rely on this symbol name, it's probably fine to never include it in
+ # preloaded symbol tables.
+ # Exclude shared library initialization/finalization symbols.
+dnl Note also adjust exclude_expsyms for C++ above.
+ extract_expsyms_cmds=
+
+ case $host_os in
+ cygwin* | mingw* | pw32* | cegcc*)
+ # FIXME: the MSVC++ port hasn't been tested in a loooong time
+ # When not using gcc, we currently assume that we are using
+ # Microsoft Visual C++.
+ if test "$GCC" != yes; then
+ with_gnu_ld=no
+ fi
+ ;;
+ interix*)
+ # we just hope/assume this is gcc and not c89 (= MSVC++)
+ with_gnu_ld=yes
+ ;;
+ openbsd*)
+ with_gnu_ld=no
+ ;;
+ linux* | k*bsd*-gnu)
+ _LT_TAGVAR(link_all_deplibs, $1)=no
+ ;;
+ esac
+
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ if test "$with_gnu_ld" = yes; then
+ # If archive_cmds runs LD, not CC, wlarc should be empty
+ wlarc='${wl}'
+
+ # Set some defaults for GNU ld with shared library support. These
+ # are reset later if shared libraries are not supported. Putting them
+ # here allows them to be overridden if necessary.
+ runpath_var=LD_RUN_PATH
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+ # ancient GNU ld didn't support --whole-archive et. al.
+ if $LD --help 2>&1 | $GREP 'no-whole-archive' > /dev/null; then
+ _LT_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ else
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ fi
+ supports_anon_versioning=no
+ case `$LD -v 2>&1` in
+ *GNU\ gold*) supports_anon_versioning=yes ;;
+ *\ [[01]].* | *\ 2.[[0-9]].* | *\ 2.10.*) ;; # catch versions < 2.11
+ *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ...
+ *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ...
+ *\ 2.11.*) ;; # other 2.11 versions
+ *) supports_anon_versioning=yes ;;
+ esac
+
+ # See if GNU ld supports shared libraries.
+ case $host_os in
+ aix[[3-9]]*)
+ # On AIX/PPC, the GNU linker is very broken
+ if test "$host_cpu" != ia64; then
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the GNU linker, at least up to release 2.9.1, is reported
+*** to be unable to reliably create shared libraries on AIX.
+*** Therefore, libtool is disabling shared libraries support. If you
+*** really care for shared libraries, you may want to modify your PATH
+*** so that a non-GNU linker is found, and then restart.
+
+_LT_EOF
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)=''
+ ;;
+ m68k)
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ ;;
+ esac
+ ;;
+
+ beos*)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ # Joseph Beckenbach <jrb3 at best.com> says some releases of gcc
+ # support --undefined. This deserves some investigation. FIXME
+ _LT_TAGVAR(archive_cmds, $1)='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # _LT_TAGVAR(hardcode_libdir_flag_spec, $1) is actually meaningless,
+ # as there is no search path for DLLs.
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ _LT_TAGVAR(always_export_symbols, $1)=no
+ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]][[ ]]/s/.*[[ ]]\([[^ ]]*\)/\1 DATA/'\'' | $SED -e '\''/^[[AITW]][[ ]]/s/.*[[ ]]//'\'' | sort | uniq > $export_symbols'
+
+ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ # If the export-symbols file already is a .def file (1st line
+ # is EXPORTS), use it as is; otherwise, prepend...
+ _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+ cp $export_symbols $output_objdir/$soname.def;
+ else
+ echo EXPORTS > $output_objdir/$soname.def;
+ cat $export_symbols >> $output_objdir/$soname.def;
+ fi~
+ $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ interix[[3-9]]*)
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+ # Instead, shared libraries are loaded at an image base (0x10000000 by
+ # default) and relocated if they conflict, which is a slow very memory
+ # consuming and fragmenting process. To avoid this, we pick a random,
+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+ # time. Moving up from 0x10000000 also allows more sbrk(2) space.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ ;;
+
+ gnu* | linux* | tpf* | k*bsd*-gnu | kopensolaris*-gnu)
+ tmp_diet=no
+ if test "$host_os" = linux-dietlibc; then
+ case $cc_basename in
+ diet\ *) tmp_diet=yes;; # linux-dietlibc with static linking (!diet-dyn)
+ esac
+ fi
+ if $LD --help 2>&1 | $EGREP ': supported targets:.* elf' > /dev/null \
+ && test "$tmp_diet" = no
+ then
+ tmp_addflag=
+ tmp_sharedflag='-shared'
+ case $cc_basename,$host_cpu in
+ pgcc*) # Portland Group C compiler
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ tmp_addflag=' $pic_flag'
+ ;;
+ pgf77* | pgf90* | pgf95*) # Portland Group f77 and f90 compilers
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ tmp_addflag=' $pic_flag -Mnomain' ;;
+ ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64
+ tmp_addflag=' -i_dynamic' ;;
+ efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64
+ tmp_addflag=' -i_dynamic -nofor_main' ;;
+ ifc* | ifort*) # Intel Fortran compiler
+ tmp_addflag=' -nofor_main' ;;
+ lf95*) # Lahey Fortran 8.1
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ tmp_sharedflag='--shared' ;;
+ xl[[cC]]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ tmp_sharedflag='-qmkshrobj'
+ tmp_addflag= ;;
+ esac
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*) # Sun C 5.9
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ _LT_TAGVAR(compiler_needs_object, $1)=yes
+ tmp_sharedflag='-G' ;;
+ *Sun\ F*) # Sun Fortran 8.3
+ tmp_sharedflag='-G' ;;
+ esac
+ _LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+
+ if test "x$supports_anon_versioning" = xyes; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+ fi
+
+ case $cc_basename in
+ xlf*)
+ # IBM XL Fortran 10.1 on PPC cannot create shared libs itself
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='--whole-archive$convenience --no-whole-archive'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+ _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='-rpath $libdir'
+ _LT_TAGVAR(archive_cmds, $1)='$LD -shared $libobjs $deplibs $compiler_flags -soname $soname -o $lib'
+ if test "x$supports_anon_versioning" = xyes; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $LD -shared $libobjs $deplibs $compiler_flags -soname $soname -version-script $output_objdir/$libname.ver -o $lib'
+ fi
+ ;;
+ esac
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
+ wlarc=
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ fi
+ ;;
+
+ solaris*)
+ if $LD -v 2>&1 | $GREP 'BFD 2\.8' > /dev/null; then
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: The releases 2.8.* of the GNU linker cannot reliably
+*** create shared libraries on Solaris systems. Therefore, libtool
+*** is disabling shared libraries support. We urge you to upgrade GNU
+*** binutils to release 2.9.1 or newer. Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+ elif $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*)
+ case `$LD -v 2>&1` in
+ *\ [[01]].* | *\ 2.[[0-9]].* | *\ 2.1[[0-5]].*)
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not
+*** reliably create shared libraries on SCO systems. Therefore, libtool
+*** is disabling shared libraries support. We urge you to upgrade GNU
+*** binutils to release 2.16.91.0.3 or newer. Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+ ;;
+ *)
+ # For security reasons, it is highly recommended that you always
+ # use absolute paths for naming shared libraries, and exclude the
+ # DT_RUNPATH tag from executables and libraries. But doing so
+ # requires that you compile everything twice, which is a pain.
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+ ;;
+
+ sunos4*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ wlarc=
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ *)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+
+ if test "$_LT_TAGVAR(ld_shlibs, $1)" = no; then
+ runpath_var=
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)=
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ fi
+ else
+ # PORTME fill in a description of your system's linker (not GNU ld)
+ case $host_os in
+ aix3*)
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ _LT_TAGVAR(always_export_symbols, $1)=yes
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname'
+ # Note: this linker hardcodes the directories in LIBPATH if there
+ # are no directories specified by -L.
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then
+ # Neither direct hardcoding nor static linking is supported with a
+ # broken collect2.
+ _LT_TAGVAR(hardcode_direct, $1)=unsupported
+ fi
+ ;;
+
+ aix[[4-9]]*)
+ if test "$host_cpu" = ia64; then
+ # On IA64, the linker does run time linking by default, so we don't
+ # have to do anything special.
+ aix_use_runtimelinking=no
+ exp_sym_flag='-Bexport'
+ no_entry_flag=""
+ else
+ # If we're using GNU nm, then we don't want the "-C" option.
+ # -C means demangle to AIX nm, but means don't demangle with GNU nm
+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ else
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ fi
+ aix_use_runtimelinking=no
+
+ # Test if we are trying to use run time linking or normal
+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+ # need to do runtime linking.
+ case $host_os in aix4.[[23]]|aix4.[[23]].*|aix[[5-9]]*)
+ for ld_flag in $LDFLAGS; do
+ if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then
+ aix_use_runtimelinking=yes
+ break
+ fi
+ done
+ ;;
+ esac
+
+ exp_sym_flag='-bexport'
+ no_entry_flag='-bnoentry'
+ fi
+
+ # When large executables or shared objects are built, AIX ld can
+ # have problems creating the table of contents. If linking a library
+ # or program results in "error TOC overflow" add -mminimal-toc to
+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not
+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+ _LT_TAGVAR(archive_cmds, $1)=''
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=':'
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(file_list_spec, $1)='${wl}-f,'
+
+ if test "$GCC" = yes; then
+ case $host_os in aix4.[[012]]|aix4.[[012]].*)
+ # We only want to do this on AIX 4.2 and lower, the check
+ # below for broken collect2 doesn't work under 4.3+
+ collect2name=`${CC} -print-prog-name=collect2`
+ if test -f "$collect2name" &&
+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null
+ then
+ # We have reworked collect2
+ :
+ else
+ # We have old collect2
+ _LT_TAGVAR(hardcode_direct, $1)=unsupported
+ # It fails to find uninstalled libraries when the uninstalled
+ # path is not listed in the libpath. Setting hardcode_minus_L
+ # to unsupported forces relinking
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=
+ fi
+ ;;
+ esac
+ shared_flag='-shared'
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag="$shared_flag "'${wl}-G'
+ fi
+ _LT_TAGVAR(link_all_deplibs, $1)=no
+ else
+ # not using gcc
+ if test "$host_cpu" = ia64; then
+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+ # chokes on -Wl,-G. The following line is correct:
+ shared_flag='-G'
+ else
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag='${wl}-G'
+ else
+ shared_flag='${wl}-bM:SRE'
+ fi
+ fi
+ fi
+
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-bexpall'
+ # It seems that -bexpall does not export symbols beginning with
+ # underscore (_), so it is better to generate a list of symbols to export.
+ _LT_TAGVAR(always_export_symbols, $1)=yes
+ if test "$aix_use_runtimelinking" = yes; then
+ # Warning - without using the other runtime loading flags (-brtl),
+ # -berok will link without error, but may produce a broken library.
+ _LT_TAGVAR(allow_undefined_flag, $1)='-berok'
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ _LT_SYS_MODULE_PATH_AIX
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+ else
+ if test "$host_cpu" = ia64; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $libdir:/usr/lib:/lib'
+ _LT_TAGVAR(allow_undefined_flag, $1)="-z nodefs"
+ _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+ else
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ _LT_SYS_MODULE_PATH_AIX
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+ # Warning - without using the other run time loading flags,
+ # -berok will link without error, but may produce a broken library.
+ _LT_TAGVAR(no_undefined_flag, $1)=' ${wl}-bernotok'
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-berok'
+ # Exported symbols can be pulled into shared objects from archives
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='$convenience'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=yes
+ # This is similar to how AIX traditionally builds its shared libraries.
+ _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+ fi
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)=''
+ ;;
+ m68k)
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ ;;
+ esac
+ ;;
+
+ bsdi[[45]]*)
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)=-rdynamic
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # When not using gcc, we currently assume that we are using
+ # Microsoft Visual C++.
+ # hardcode_libdir_flag_spec is actually meaningless, as there is
+ # no search path for DLLs.
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=' '
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ # Tell ltmain to make .lib files, not .a files.
+ libext=lib
+ # Tell ltmain to make .dll files, not .so files.
+ shrext_cmds=".dll"
+ # FIXME: Setting linknames here is a bad hack.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -o $lib $libobjs $compiler_flags `$ECHO "X$deplibs" | $Xsed -e '\''s/ -lc$//'\''` -link -dll~linknames='
+ # The linker will automatically build a .lib file if we build a DLL.
+ _LT_TAGVAR(old_archive_from_new_cmds, $1)='true'
+ # FIXME: Should let the user specify the lib program.
+ _LT_TAGVAR(old_archive_cmds, $1)='lib -OUT:$oldlib$oldobjs$old_deplibs'
+ _LT_TAGVAR(fix_srcfile_path, $1)='`cygpath -w "$srcfile"`'
+ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+ ;;
+
+ darwin* | rhapsody*)
+ _LT_DARWIN_LINKER_FEATURES($1)
+ ;;
+
+ dgux*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ freebsd1*)
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor
+ # support. Future versions do this automatically, but an explicit c++rt0.o
+ # does not break anything, and helps significantly (at the cost of a little
+ # extra space).
+ freebsd2.2*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ # Unfortunately, older versions of FreeBSD 2 do not have this feature.
+ freebsd2*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ # FreeBSD 3 and greater uses gcc -shared to do shared libraries.
+ freebsd* | dragonfly*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ hpux9*)
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ fi
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ ;;
+
+ hpux10*)
+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags'
+ fi
+ if test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='+b $libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ fi
+ ;;
+
+ hpux11*)
+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+ case $host_cpu in
+ hppa*64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ ia64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ else
+ case $host_cpu in
+ hppa*64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ ia64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ fi
+ if test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ case $host_cpu in
+ hppa*64*|ia64*)
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+ *)
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ ;;
+ esac
+ fi
+ ;;
+
+ irix5* | irix6* | nonstopux*)
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ # Try to use the -exported_symbol ld option, if it does not
+ # work, assume that -exports_file does not work either and
+ # implicitly export all symbols.
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null"
+ AC_LINK_IFELSE(int foo(void) {},
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib'
+ )
+ LDFLAGS="$save_LDFLAGS"
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib'
+ fi
+ _LT_TAGVAR(archive_cmds_need_lc, $1)='no'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(inherit_rpath, $1)=yes
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ ;;
+
+ netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF
+ fi
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ newsos6)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ *nto* | *qnx*)
+ ;;
+
+ openbsd*)
+ if test -f /usr/libexec/ld.so; then
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ else
+ case $host_os in
+ openbsd[[01]].* | openbsd2.[[0-7]] | openbsd2.[[0-7]].*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ ;;
+ esac
+ fi
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ os2*)
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ _LT_TAGVAR(archive_cmds, $1)='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def'
+ _LT_TAGVAR(old_archive_from_new_cmds, $1)='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def'
+ ;;
+
+ osf3*)
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ else
+ _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ fi
+ _LT_TAGVAR(archive_cmds_need_lc, $1)='no'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ ;;
+
+ osf4* | osf5*) # as osf3* with the addition of -msym flag
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ else
+ _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~
+ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp'
+
+ # Both c and cxx compiler support -rpath directly
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir'
+ fi
+ _LT_TAGVAR(archive_cmds_need_lc, $1)='no'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ ;;
+
+ solaris*)
+ _LT_TAGVAR(no_undefined_flag, $1)=' -z defs'
+ if test "$GCC" = yes; then
+ wlarc='${wl}'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp'
+ else
+ case `$CC -V 2>&1` in
+ *"Compilers 5.0"*)
+ wlarc=''
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp'
+ ;;
+ *)
+ wlarc='${wl}'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp'
+ ;;
+ esac
+ fi
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ case $host_os in
+ solaris2.[[0-5]] | solaris2.[[0-5]].*) ;;
+ *)
+ # The compiler driver will combine and reorder linker options,
+ # but understands `-z linker_flag'. GCC discards it without `$wl',
+ # but is careful enough not to reorder.
+ # Supported since Solaris 2.6 (maybe 2.5.1?)
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract'
+ else
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='-z allextract$convenience -z defaultextract'
+ fi
+ ;;
+ esac
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ ;;
+
+ sunos4*)
+ if test "x$host_vendor" = xsequent; then
+ # Use $CC to link under sequent, because it throws in some extra .o
+ # files that make .init and .fini sections work.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags'
+ fi
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ sysv4)
+ case $host_vendor in
+ sni)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_direct, $1)=yes # is this really true???
+ ;;
+ siemens)
+ ## LD is ld it makes a PLAMLIB
+ ## CC just makes a GrossModule.
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(reload_cmds, $1)='$CC -r -o $output$reload_objs'
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ ;;
+ motorola)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_direct, $1)=no #Motorola manual says yes, but my tests say they lie
+ ;;
+ esac
+ runpath_var='LD_RUN_PATH'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ sysv4.3*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='-Bexport'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ runpath_var=LD_RUN_PATH
+ hardcode_runpath_var=yes
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ fi
+ ;;
+
+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[[01]].[[10]]* | unixware7* | sco3.2v5.0.[[024]]*)
+ _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ runpath_var='LD_RUN_PATH'
+
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ fi
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6*)
+ # Note: We can NOT use -z defs as we might desire, because we do not
+ # link with -lc, and that would cause any symbols used from libc to
+ # always be unresolved, which means just about no library would
+ # ever link correctly. If we're not using GNU ld we use -z text
+ # though, which does catch some bad symbols but isn't as heavy-handed
+ # as -z defs.
+ _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+ _LT_TAGVAR(allow_undefined_flag, $1)='${wl}-z,nodefs'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R,$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=':'
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Bexport'
+ runpath_var='LD_RUN_PATH'
+
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ fi
+ ;;
+
+ uts4*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ *)
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+
+ if test x$host_vendor = xsni; then
+ case $host in
+ sysv4 | sysv4.2uw2* | sysv4.3* | sysv5*)
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Blargedynsym'
+ ;;
+ esac
+ fi
+ fi
+])
+AC_MSG_RESULT([$_LT_TAGVAR(ld_shlibs, $1)])
+test "$_LT_TAGVAR(ld_shlibs, $1)" = no && can_build_shared=no
+
+_LT_TAGVAR(with_gnu_ld, $1)=$with_gnu_ld
+
+_LT_DECL([], [libext], [0], [Old archive suffix (normally "a")])dnl
+_LT_DECL([], [shrext_cmds], [1], [Shared library suffix (normally ".so")])dnl
+_LT_DECL([], [extract_expsyms_cmds], [2],
+ [The commands to extract the exported symbol list from a shared archive])
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$_LT_TAGVAR(archive_cmds_need_lc, $1)" in
+x|xyes)
+ # Assume -lc should be added
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=yes
+
+ if test "$enable_shared" = yes && test "$GCC" = yes; then
+ case $_LT_TAGVAR(archive_cmds, $1) in
+ *'~'*)
+ # FIXME: we may have to deal with multi-command sequences.
+ ;;
+ '$CC '*)
+ # Test whether the compiler implicitly links with -lc since on some
+ # systems, -lgcc has to come before -lc. If gcc already passes -lc
+ # to ld, don't add -lc before -lgcc.
+ AC_MSG_CHECKING([whether -lc should be explicitly linked in])
+ $RM conftest*
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ if AC_TRY_EVAL(ac_compile) 2>conftest.err; then
+ soname=conftest
+ lib=conftest
+ libobjs=conftest.$ac_objext
+ deplibs=
+ wl=$_LT_TAGVAR(lt_prog_compiler_wl, $1)
+ pic_flag=$_LT_TAGVAR(lt_prog_compiler_pic, $1)
+ compiler_flags=-v
+ linker_flags=-v
+ verstring=
+ output_objdir=.
+ libname=conftest
+ lt_save_allow_undefined_flag=$_LT_TAGVAR(allow_undefined_flag, $1)
+ _LT_TAGVAR(allow_undefined_flag, $1)=
+ if AC_TRY_EVAL(_LT_TAGVAR(archive_cmds, $1) 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1)
+ then
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ else
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=yes
+ fi
+ _LT_TAGVAR(allow_undefined_flag, $1)=$lt_save_allow_undefined_flag
+ else
+ cat conftest.err 1>&5
+ fi
+ $RM conftest*
+ AC_MSG_RESULT([$_LT_TAGVAR(archive_cmds_need_lc, $1)])
+ ;;
+ esac
+ fi
+ ;;
+esac
+
+_LT_TAGDECL([build_libtool_need_lc], [archive_cmds_need_lc], [0],
+ [Whether or not to add -lc for building shared libraries])
+_LT_TAGDECL([allow_libtool_libs_with_static_runtimes],
+ [enable_shared_with_static_runtimes], [0],
+ [Whether or not to disallow shared libs when runtime libs are static])
+_LT_TAGDECL([], [export_dynamic_flag_spec], [1],
+ [Compiler flag to allow reflexive dlopens])
+_LT_TAGDECL([], [whole_archive_flag_spec], [1],
+ [Compiler flag to generate shared objects directly from archives])
+_LT_TAGDECL([], [compiler_needs_object], [1],
+ [Whether the compiler copes with passing no objects directly])
+_LT_TAGDECL([], [old_archive_from_new_cmds], [2],
+ [Create an old-style archive from a shared archive])
+_LT_TAGDECL([], [old_archive_from_expsyms_cmds], [2],
+ [Create a temporary old-style archive to link instead of a shared archive])
+_LT_TAGDECL([], [archive_cmds], [2], [Commands used to build a shared archive])
+_LT_TAGDECL([], [archive_expsym_cmds], [2])
+_LT_TAGDECL([], [module_cmds], [2],
+ [Commands used to build a loadable module if different from building
+ a shared archive.])
+_LT_TAGDECL([], [module_expsym_cmds], [2])
+_LT_TAGDECL([], [with_gnu_ld], [1],
+ [Whether we are building with GNU ld or not])
+_LT_TAGDECL([], [allow_undefined_flag], [1],
+ [Flag that allows shared libraries with undefined symbols to be built])
+_LT_TAGDECL([], [no_undefined_flag], [1],
+ [Flag that enforces no undefined symbols])
+_LT_TAGDECL([], [hardcode_libdir_flag_spec], [1],
+ [Flag to hardcode $libdir into a binary during linking.
+ This must work even if $libdir does not exist])
+_LT_TAGDECL([], [hardcode_libdir_flag_spec_ld], [1],
+ [[If ld is used when linking, flag to hardcode $libdir into a binary
+ during linking. This must work even if $libdir does not exist]])
+_LT_TAGDECL([], [hardcode_libdir_separator], [1],
+ [Whether we need a single "-rpath" flag with a separated argument])
+_LT_TAGDECL([], [hardcode_direct], [0],
+ [Set to "yes" if using DIR/libNAME${shared_ext} during linking hardcodes
+ DIR into the resulting binary])
+_LT_TAGDECL([], [hardcode_direct_absolute], [0],
+ [Set to "yes" if using DIR/libNAME${shared_ext} during linking hardcodes
+ DIR into the resulting binary and the resulting library dependency is
+ "absolute", i.e impossible to change by setting ${shlibpath_var} if the
+ library is relocated])
+_LT_TAGDECL([], [hardcode_minus_L], [0],
+ [Set to "yes" if using the -LDIR flag during linking hardcodes DIR
+ into the resulting binary])
+_LT_TAGDECL([], [hardcode_shlibpath_var], [0],
+ [Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR
+ into the resulting binary])
+_LT_TAGDECL([], [hardcode_automatic], [0],
+ [Set to "yes" if building a shared library automatically hardcodes DIR
+ into the library and all subsequent libraries and executables linked
+ against it])
+_LT_TAGDECL([], [inherit_rpath], [0],
+ [Set to yes if linker adds runtime paths of dependent libraries
+ to runtime path list])
+_LT_TAGDECL([], [link_all_deplibs], [0],
+ [Whether libtool must link a program against all its dependency libraries])
+_LT_TAGDECL([], [fix_srcfile_path], [1],
+ [Fix the shell variable $srcfile for the compiler])
+_LT_TAGDECL([], [always_export_symbols], [0],
+ [Set to "yes" if exported symbols are required])
+_LT_TAGDECL([], [export_symbols_cmds], [2],
+ [The commands to list exported symbols])
+_LT_TAGDECL([], [exclude_expsyms], [1],
+ [Symbols that should not be listed in the preloaded symbols])
+_LT_TAGDECL([], [include_expsyms], [1],
+ [Symbols that must always be exported])
+_LT_TAGDECL([], [prelink_cmds], [2],
+ [Commands necessary for linking programs (against libraries) with templates])
+_LT_TAGDECL([], [file_list_spec], [1],
+ [Specify filename containing input files])
+dnl FIXME: Not yet implemented
+dnl _LT_TAGDECL([], [thread_safe_flag_spec], [1],
+dnl [Compiler flag to generate thread safe objects])
+])# _LT_LINKER_SHLIBS
+
+
+# _LT_LANG_C_CONFIG([TAG])
+# ------------------------
+# Ensure that the configuration variables for a C compiler are suitably
+# defined. These variables are subsequently used by _LT_CONFIG to write
+# the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_C_CONFIG],
+[m4_require([_LT_DECL_EGREP])dnl
+lt_save_CC="$CC"
+AC_LANG_PUSH(C)
+
+# Source file extension for C test sources.
+ac_ext=c
+
+# Object file extension for compiled C test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="int some_variable = 0;"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='int main(){return(0);}'
+
+_LT_TAG_COMPILER
+# Save the default compiler, since it gets overwritten when the other
+# tags are being tested, and _LT_TAGVAR(compiler, []) is a NOP.
+compiler_DEFAULT=$CC
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+if test -n "$compiler"; then
+ _LT_COMPILER_NO_RTTI($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_SYS_DYNAMIC_LINKER($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+ LT_SYS_DLOPEN_SELF
+ _LT_CMD_STRIPLIB
+
+ # Report which library types will actually be built
+ AC_MSG_CHECKING([if libtool supports shared libraries])
+ AC_MSG_RESULT([$can_build_shared])
+
+ AC_MSG_CHECKING([whether to build shared libraries])
+ test "$can_build_shared" = "no" && enable_shared=no
+
+ # On AIX, shared libraries and static libraries use the same namespace, and
+ # are all built from PIC.
+ case $host_os in
+ aix3*)
+ test "$enable_shared" = yes && enable_static=no
+ if test -n "$RANLIB"; then
+ archive_cmds="$archive_cmds~\$RANLIB \$lib"
+ postinstall_cmds='$RANLIB $lib'
+ fi
+ ;;
+
+ aix[[4-9]]*)
+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+ test "$enable_shared" = yes && enable_static=no
+ fi
+ ;;
+ esac
+ AC_MSG_RESULT([$enable_shared])
+
+ AC_MSG_CHECKING([whether to build static libraries])
+ # Make sure either enable_shared or enable_static is yes.
+ test "$enable_shared" = yes || enable_static=yes
+ AC_MSG_RESULT([$enable_static])
+
+ _LT_CONFIG($1)
+fi
+AC_LANG_POP
+CC="$lt_save_CC"
+])# _LT_LANG_C_CONFIG
+
+
+# _LT_PROG_CXX
+# ------------
+# Since AC_PROG_CXX is broken, in that it returns g++ if there is no c++
+# compiler, we have our own version here.
+m4_defun([_LT_PROG_CXX],
+[
+pushdef([AC_MSG_ERROR], [_lt_caught_CXX_error=yes])
+AC_PROG_CXX
+if test -n "$CXX" && ( test "X$CXX" != "Xno" &&
+ ( (test "X$CXX" = "Xg++" && `g++ -v >/dev/null 2>&1` ) ||
+ (test "X$CXX" != "Xg++"))) ; then
+ AC_PROG_CXXCPP
+else
+ _lt_caught_CXX_error=yes
+fi
+popdef([AC_MSG_ERROR])
+])# _LT_PROG_CXX
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([_LT_PROG_CXX], [])
+
+
+# _LT_LANG_CXX_CONFIG([TAG])
+# --------------------------
+# Ensure that the configuration variables for a C++ compiler are suitably
+# defined. These variables are subsequently used by _LT_CONFIG to write
+# the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_CXX_CONFIG],
+[AC_REQUIRE([_LT_PROG_CXX])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_EGREP])dnl
+
+AC_LANG_PUSH(C++)
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+_LT_TAGVAR(allow_undefined_flag, $1)=
+_LT_TAGVAR(always_export_symbols, $1)=no
+_LT_TAGVAR(archive_expsym_cmds, $1)=
+_LT_TAGVAR(compiler_needs_object, $1)=no
+_LT_TAGVAR(export_dynamic_flag_spec, $1)=
+_LT_TAGVAR(hardcode_direct, $1)=no
+_LT_TAGVAR(hardcode_direct_absolute, $1)=no
+_LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+_LT_TAGVAR(hardcode_libdir_separator, $1)=
+_LT_TAGVAR(hardcode_minus_L, $1)=no
+_LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
+_LT_TAGVAR(hardcode_automatic, $1)=no
+_LT_TAGVAR(inherit_rpath, $1)=no
+_LT_TAGVAR(module_cmds, $1)=
+_LT_TAGVAR(module_expsym_cmds, $1)=
+_LT_TAGVAR(link_all_deplibs, $1)=unknown
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+_LT_TAGVAR(no_undefined_flag, $1)=
+_LT_TAGVAR(whole_archive_flag_spec, $1)=
+_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+
+# Source file extension for C++ test sources.
+ac_ext=cpp
+
+# Object file extension for compiled C++ test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# No sense in running all these tests if we already determined that
+# the CXX compiler isn't working. Some variables (like enable_shared)
+# are currently assumed to apply to all compilers on this platform,
+# and will be corrupted by setting them based on a non-working compiler.
+if test "$_lt_caught_CXX_error" != yes; then
+ # Code to be used in simple compile tests
+ lt_simple_compile_test_code="int some_variable = 0;"
+
+ # Code to be used in simple link tests
+ lt_simple_link_test_code='int main(int, char *[[]]) { return(0); }'
+
+ # ltmain only uses $CC for tagged configurations so make sure $CC is set.
+ _LT_TAG_COMPILER
+
+ # save warnings/boilerplate of simple test code
+ _LT_COMPILER_BOILERPLATE
+ _LT_LINKER_BOILERPLATE
+
+ # Allow CC to be a program name with arguments.
+ lt_save_CC=$CC
+ lt_save_LD=$LD
+ lt_save_GCC=$GCC
+ GCC=$GXX
+ lt_save_with_gnu_ld=$with_gnu_ld
+ lt_save_path_LD=$lt_cv_path_LD
+ if test -n "${lt_cv_prog_gnu_ldcxx+set}"; then
+ lt_cv_prog_gnu_ld=$lt_cv_prog_gnu_ldcxx
+ else
+ $as_unset lt_cv_prog_gnu_ld
+ fi
+ if test -n "${lt_cv_path_LDCXX+set}"; then
+ lt_cv_path_LD=$lt_cv_path_LDCXX
+ else
+ $as_unset lt_cv_path_LD
+ fi
+ test -z "${LDCXX+set}" || LD=$LDCXX
+ CC=${CXX-"c++"}
+ compiler=$CC
+ _LT_TAGVAR(compiler, $1)=$CC
+ _LT_CC_BASENAME([$compiler])
+
+ if test -n "$compiler"; then
+ # We don't want -fno-exception when compiling C++ code, so set the
+ # no_builtin_flag separately
+ if test "$GXX" = yes; then
+ _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin'
+ else
+ _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=
+ fi
+
+ if test "$GXX" = yes; then
+ # Set up default GNU C++ configuration
+
+ LT_PATH_LD
+
+ # Check if GNU C++ uses GNU ld as the underlying linker, since the
+ # archiving commands below assume that GNU ld is being used.
+ if test "$with_gnu_ld" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+
+ # If archive_cmds runs LD, not CC, wlarc should be empty
+ # XXX I think wlarc can be eliminated in ltcf-cxx, but I need to
+ # investigate it a little bit more. (MM)
+ wlarc='${wl}'
+
+ # ancient GNU ld didn't support --whole-archive et. al.
+ if eval "`$CC -print-prog-name=ld` --help 2>&1" |
+ $GREP 'no-whole-archive' > /dev/null; then
+ _LT_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ else
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ fi
+ else
+ with_gnu_ld=no
+ wlarc=
+
+ # A generic and very simple default shared library creation
+ # command for GNU C++ for the case where it uses the native
+ # linker, instead of GNU ld. If possible, this setting should
+ # overridden to take advantage of the native linker features on
+ # the platform it is being used on.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+ fi
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+
+ else
+ GXX=no
+ with_gnu_ld=no
+ wlarc=
+ fi
+
+ # PORTME: fill in a description of your system's C++ link characteristics
+ AC_MSG_CHECKING([whether the $compiler linker ($LD) supports shared libraries])
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ case $host_os in
+ aix3*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ aix[[4-9]]*)
+ if test "$host_cpu" = ia64; then
+ # On IA64, the linker does run time linking by default, so we don't
+ # have to do anything special.
+ aix_use_runtimelinking=no
+ exp_sym_flag='-Bexport'
+ no_entry_flag=""
+ else
+ aix_use_runtimelinking=no
+
+ # Test if we are trying to use run time linking or normal
+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+ # need to do runtime linking.
+ case $host_os in aix4.[[23]]|aix4.[[23]].*|aix[[5-9]]*)
+ for ld_flag in $LDFLAGS; do
+ case $ld_flag in
+ *-brtl*)
+ aix_use_runtimelinking=yes
+ break
+ ;;
+ esac
+ done
+ ;;
+ esac
+
+ exp_sym_flag='-bexport'
+ no_entry_flag='-bnoentry'
+ fi
+
+ # When large executables or shared objects are built, AIX ld can
+ # have problems creating the table of contents. If linking a library
+ # or program results in "error TOC overflow" add -mminimal-toc to
+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not
+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+ _LT_TAGVAR(archive_cmds, $1)=''
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=':'
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(file_list_spec, $1)='${wl}-f,'
+
+ if test "$GXX" = yes; then
+ case $host_os in aix4.[[012]]|aix4.[[012]].*)
+ # We only want to do this on AIX 4.2 and lower, the check
+ # below for broken collect2 doesn't work under 4.3+
+ collect2name=`${CC} -print-prog-name=collect2`
+ if test -f "$collect2name" &&
+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null
+ then
+ # We have reworked collect2
+ :
+ else
+ # We have old collect2
+ _LT_TAGVAR(hardcode_direct, $1)=unsupported
+ # It fails to find uninstalled libraries when the uninstalled
+ # path is not listed in the libpath. Setting hardcode_minus_L
+ # to unsupported forces relinking
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=
+ fi
+ esac
+ shared_flag='-shared'
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag="$shared_flag "'${wl}-G'
+ fi
+ else
+ # not using gcc
+ if test "$host_cpu" = ia64; then
+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+ # chokes on -Wl,-G. The following line is correct:
+ shared_flag='-G'
+ else
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag='${wl}-G'
+ else
+ shared_flag='${wl}-bM:SRE'
+ fi
+ fi
+ fi
+
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-bexpall'
+ # It seems that -bexpall does not export symbols beginning with
+ # underscore (_), so it is better to generate a list of symbols to
+ # export.
+ _LT_TAGVAR(always_export_symbols, $1)=yes
+ if test "$aix_use_runtimelinking" = yes; then
+ # Warning - without using the other runtime loading flags (-brtl),
+ # -berok will link without error, but may produce a broken library.
+ _LT_TAGVAR(allow_undefined_flag, $1)='-berok'
+ # Determine the default libpath from the value encoded in an empty
+ # executable.
+ _LT_SYS_MODULE_PATH_AIX
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+ else
+ if test "$host_cpu" = ia64; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $libdir:/usr/lib:/lib'
+ _LT_TAGVAR(allow_undefined_flag, $1)="-z nodefs"
+ _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+ else
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ _LT_SYS_MODULE_PATH_AIX
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+ # Warning - without using the other run time loading flags,
+ # -berok will link without error, but may produce a broken library.
+ _LT_TAGVAR(no_undefined_flag, $1)=' ${wl}-bernotok'
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-berok'
+ # Exported symbols can be pulled into shared objects from archives
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='$convenience'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=yes
+ # This is similar to how AIX traditionally builds its shared
+ # libraries.
+ _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+ fi
+ fi
+ ;;
+
+ beos*)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ # Joseph Beckenbach <jrb3 at best.com> says some releases of gcc
+ # support --undefined. This deserves some investigation. FIXME
+ _LT_TAGVAR(archive_cmds, $1)='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ chorus*)
+ case $cc_basename in
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # _LT_TAGVAR(hardcode_libdir_flag_spec, $1) is actually meaningless,
+ # as there is no search path for DLLs.
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ _LT_TAGVAR(always_export_symbols, $1)=no
+ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+
+ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ # If the export-symbols file already is a .def file (1st line
+ # is EXPORTS), use it as is; otherwise, prepend...
+ _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+ cp $export_symbols $output_objdir/$soname.def;
+ else
+ echo EXPORTS > $output_objdir/$soname.def;
+ cat $export_symbols >> $output_objdir/$soname.def;
+ fi~
+ $CC -shared -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ darwin* | rhapsody*)
+ _LT_DARWIN_LINKER_FEATURES($1)
+ ;;
+
+ dgux*)
+ case $cc_basename in
+ ec++*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ ghcx*)
+ # Green Hills C++ Compiler
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ freebsd[[12]]*)
+ # C++ shared libraries reported to be fairly broken before
+ # switch to ELF
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ freebsd-elf*)
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ ;;
+
+ freebsd* | dragonfly*)
+ # FreeBSD 3 and later use GNU C++ and GNU ld with standard ELF
+ # conventions
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ ;;
+
+ gnu*)
+ ;;
+
+ hpux9*)
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes # Not in the search PATH,
+ # but as the default
+ # location of the library.
+
+ case $cc_basename in
+ CC*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ aCC*)
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -b ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $EGREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -shared -nostdlib -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ else
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+ ;;
+
+ hpux10*|hpux11*)
+ if test $with_gnu_ld = no; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ case $host_cpu in
+ hppa*64*|ia64*)
+ ;;
+ *)
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ ;;
+ esac
+ fi
+ case $host_cpu in
+ hppa*64*|ia64*)
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+ *)
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes # Not in the search PATH,
+ # but as the default
+ # location of the library.
+ ;;
+ esac
+
+ case $cc_basename in
+ CC*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ aCC*)
+ case $host_cpu in
+ hppa*64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ ia64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ esac
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $GREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ if test $with_gnu_ld = no; then
+ case $host_cpu in
+ hppa*64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ ia64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ esac
+ fi
+ else
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+ ;;
+
+ interix[[3-9]]*)
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+ # Instead, shared libraries are loaded at an image base (0x10000000 by
+ # default) and relocated if they conflict, which is a slow very memory
+ # consuming and fragmenting process. To avoid this, we pick a random,
+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+ # time. Moving up from 0x10000000 also allows more sbrk(2) space.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ ;;
+ irix5* | irix6*)
+ case $cc_basename in
+ CC*)
+ # SGI C++
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -all -multigot $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+
+ # Archives containing C++ object files must be created using
+ # "CC -ar", where "CC" is the IRIX C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC -ar -WR,-u -o $oldlib $oldobjs'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ if test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` -o $lib'
+ fi
+ fi
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ ;;
+ esac
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(inherit_rpath, $1)=yes
+ ;;
+
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ KCC*)
+ # Kuck and Associates, Inc. (KAI) C++ Compiler
+
+ # KCC will only create a shared library if the output file
+ # ends with ".so" (or ".sl" for HP-UX), so rename the library
+ # to its proper name (with version) after linking.
+ _LT_TAGVAR(archive_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib ${wl}-retain-symbols-file,$export_symbols; mv \$templib $lib'
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 | $GREP "ld"`; rm -f libconftest$shared_ext; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+
+ # Archives containing C++ object files must be created using
+ # "CC -Bstatic", where "CC" is the KAI C++ compiler.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC -Bstatic -o $oldlib $oldobjs'
+ ;;
+ icpc* | ecpc* )
+ # Intel C++
+ with_gnu_ld=yes
+ # version 8.0 and above of icpc choke on multiply defined symbols
+ # if we add $predep_objects and $postdep_objects, however 7.1 and
+ # earlier do not add the objects themselves.
+ case `$CC -V 2>&1` in
+ *"Version 7."*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ ;;
+ *) # Version 8.0 or newer
+ tmp_idyn=
+ case $host_cpu in
+ ia64*) tmp_idyn=' -i_dynamic';;
+ esac
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ ;;
+ esac
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive$convenience ${wl}--no-whole-archive'
+ ;;
+ pgCC* | pgcpp*)
+ # Portland Group C++ compiler
+ case `$CC -V` in
+ *pgCC\ [[1-5]]* | *pgcpp\ [[1-5]]*)
+ _LT_TAGVAR(prelink_cmds, $1)='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $objs $libobjs $compile_deplibs~
+ compile_command="$compile_command `find $tpldir -name \*.o | $NL2SP`"'
+ _LT_TAGVAR(old_archive_cmds, $1)='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $oldobjs$old_deplibs~
+ $AR $AR_FLAGS $oldlib$oldobjs$old_deplibs `find $tpldir -name \*.o | $NL2SP`~
+ $RANLIB $oldlib'
+ _LT_TAGVAR(archive_cmds, $1)='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~
+ $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~
+ $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+ ;;
+ *) # Version 6 will use weak symbols
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+ ;;
+ esac
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}--rpath ${wl}$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ ;;
+ cxx*)
+ # Compaq C++
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib ${wl}-retain-symbols-file $wl$export_symbols'
+
+ runpath_var=LD_RUN_PATH
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld .*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ xl*)
+ # IBM XL 8.0 on PPC, with GNU ld
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ if test "x$supports_anon_versioning" = xyes; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+ fi
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+ _LT_TAGVAR(no_undefined_flag, $1)=' -zdefs'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file ${wl}$export_symbols'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ _LT_TAGVAR(compiler_needs_object, $1)=yes
+
+ # Not sure whether something based on
+ # $CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1
+ # would be better.
+ output_verbose_link_cmd='echo'
+
+ # Archives containing C++ object files must be created using
+ # "CC -xar", where "CC" is the Sun C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC -xar -o $oldlib $oldobjs'
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+
+ lynxos*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ m88k*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ mvs*)
+ case $cc_basename in
+ cxx*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ netbsd*)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $predep_objects $libobjs $deplibs $postdep_objects $linker_flags'
+ wlarc=
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ fi
+ # Workaround some broken pre-1.5 toolchains
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP conftest.$objext | $SED -e "s:-lgcc -lc -lgcc::"'
+ ;;
+
+ *nto* | *qnx*)
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ ;;
+
+ openbsd2*)
+ # C++ shared libraries are fairly broken
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ openbsd*)
+ if test -f /usr/libexec/ld.so; then
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file,$export_symbols -o $lib'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ _LT_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ fi
+ output_verbose_link_cmd=echo
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ osf3* | osf4* | osf5*)
+ case $cc_basename in
+ KCC*)
+ # Kuck and Associates, Inc. (KAI) C++ Compiler
+
+ # KCC will only create a shared library if the output file
+ # ends with ".so" (or ".sl" for HP-UX), so rename the library
+ # to its proper name (with version) after linking.
+ _LT_TAGVAR(archive_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo "$lib" | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ # Archives containing C++ object files must be created using
+ # the KAI C++ compiler.
+ case $host in
+ osf3*) _LT_TAGVAR(old_archive_cmds, $1)='$CC -Bstatic -o $oldlib $oldobjs' ;;
+ *) _LT_TAGVAR(old_archive_cmds, $1)='$CC -o $oldlib $oldobjs' ;;
+ esac
+ ;;
+ RCC*)
+ # Rational C++ 2.4.1
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ cxx*)
+ case $host in
+ osf3*)
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $soname `test -n "$verstring" && $ECHO "X${wl}-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ ;;
+ *)
+ _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done~
+ echo "-hidden">> $lib.exp~
+ $CC -shared$allow_undefined_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname ${wl}-input ${wl}$lib.exp `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~
+ $RM $lib.exp'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir'
+ ;;
+ esac
+
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld" | $GREP -v "ld:"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld.*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+ case $host in
+ osf3*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ ;;
+ esac
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+
+ else
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+ ;;
+
+ psos*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ sunos4*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.x
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ lcc*)
+ # Lucid
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ solaris*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.2, 5.x and Centerline C++
+ _LT_TAGVAR(archive_cmds_need_lc,$1)=yes
+ _LT_TAGVAR(no_undefined_flag, $1)=' -zdefs'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G${allow_undefined_flag} ${wl}-M ${wl}$lib.exp -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ case $host_os in
+ solaris2.[[0-5]] | solaris2.[[0-5]].*) ;;
+ *)
+ # The compiler driver will combine and reorder linker options,
+ # but understands `-z linker_flag'.
+ # Supported since Solaris 2.6 (maybe 2.5.1?)
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='-z allextract$convenience -z defaultextract'
+ ;;
+ esac
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+
+ output_verbose_link_cmd='echo'
+
+ # Archives containing C++ object files must be created using
+ # "CC -xar", where "CC" is the Sun C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC -xar -o $oldlib $oldobjs'
+ ;;
+ gcx*)
+ # Green Hills C++ Compiler
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+
+ # The C++ compiler must be used to create the archive.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC $LDFLAGS -archive -o $oldlib $oldobjs'
+ ;;
+ *)
+ # GNU C++ compiler with Solaris linker
+ if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(no_undefined_flag, $1)=' ${wl}-z ${wl}defs'
+ if $CC --version | $GREP -v '^2\.7' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -shared -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+ else
+ # g++ 2.7 appears to require `-G' NOT `-shared' on this
+ # platform.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -G $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+ fi
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $wl$libdir'
+ case $host_os in
+ solaris2.[[0-5]] | solaris2.[[0-5]].*) ;;
+ *)
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract'
+ ;;
+ esac
+ fi
+ ;;
+ esac
+ ;;
+
+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[[01]].[[10]]* | unixware7* | sco3.2v5.0.[[024]]*)
+ _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ runpath_var='LD_RUN_PATH'
+
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6*)
+ # Note: We can NOT use -z defs as we might desire, because we do not
+ # link with -lc, and that would cause any symbols used from libc to
+ # always be unresolved, which means just about no library would
+ # ever link correctly. If we're not using GNU ld we use -z text
+ # though, which does catch some bad symbols but isn't as heavy-handed
+ # as -z defs.
+ _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+ _LT_TAGVAR(allow_undefined_flag, $1)='${wl}-z,nodefs'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R,$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=':'
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Bexport'
+ runpath_var='LD_RUN_PATH'
+
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ ;;
+
+ tandem*)
+ case $cc_basename in
+ NCC*)
+ # NonStop-UX NCC 3.20
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ vxworks*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+
+ AC_MSG_RESULT([$_LT_TAGVAR(ld_shlibs, $1)])
+ test "$_LT_TAGVAR(ld_shlibs, $1)" = no && can_build_shared=no
+
+ _LT_TAGVAR(GCC, $1)="$GXX"
+ _LT_TAGVAR(LD, $1)="$LD"
+
+ ## CAVEAT EMPTOR:
+ ## There is no encapsulation within the following macros, do not change
+ ## the running order or otherwise move them around unless you know exactly
+ ## what you are doing...
+ _LT_SYS_HIDDEN_LIBDEPS($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_SYS_DYNAMIC_LINKER($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+ fi # test -n "$compiler"
+
+ CC=$lt_save_CC
+ LDCXX=$LD
+ LD=$lt_save_LD
+ GCC=$lt_save_GCC
+ with_gnu_ld=$lt_save_with_gnu_ld
+ lt_cv_path_LDCXX=$lt_cv_path_LD
+ lt_cv_path_LD=$lt_save_path_LD
+ lt_cv_prog_gnu_ldcxx=$lt_cv_prog_gnu_ld
+ lt_cv_prog_gnu_ld=$lt_save_with_gnu_ld
+fi # test "$_lt_caught_CXX_error" != yes
+
+AC_LANG_POP
+])# _LT_LANG_CXX_CONFIG
+
+
+# _LT_SYS_HIDDEN_LIBDEPS([TAGNAME])
+# ---------------------------------
+# Figure out "hidden" library dependencies from verbose
+# compiler output when linking a shared library.
+# Parse the compiler output and extract the necessary
+# objects, libraries and library flags.
+m4_defun([_LT_SYS_HIDDEN_LIBDEPS],
+[m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+# Dependencies to place before and after the object being linked:
+_LT_TAGVAR(predep_objects, $1)=
+_LT_TAGVAR(postdep_objects, $1)=
+_LT_TAGVAR(predeps, $1)=
+_LT_TAGVAR(postdeps, $1)=
+_LT_TAGVAR(compiler_lib_search_path, $1)=
+
+dnl we can't use the lt_simple_compile_test_code here,
+dnl because it contains code intended for an executable,
+dnl not a library. It's possible we should let each
+dnl tag define a new lt_????_link_test_code variable,
+dnl but it's only used here...
+m4_if([$1], [], [cat > conftest.$ac_ext <<_LT_EOF
+int a;
+void foo (void) { a = 0; }
+_LT_EOF
+], [$1], [CXX], [cat > conftest.$ac_ext <<_LT_EOF
+class Foo
+{
+public:
+ Foo (void) { a = 0; }
+private:
+ int a;
+};
+_LT_EOF
+], [$1], [F77], [cat > conftest.$ac_ext <<_LT_EOF
+ subroutine foo
+ implicit none
+ integer*4 a
+ a=0
+ return
+ end
+_LT_EOF
+], [$1], [FC], [cat > conftest.$ac_ext <<_LT_EOF
+ subroutine foo
+ implicit none
+ integer a
+ a=0
+ return
+ end
+_LT_EOF
+], [$1], [GCJ], [cat > conftest.$ac_ext <<_LT_EOF
+public class foo {
+ private int a;
+ public void bar (void) {
+ a = 0;
+ }
+};
+_LT_EOF
+])
+dnl Parse the compiler output and extract the necessary
+dnl objects, libraries and library flags.
+if AC_TRY_EVAL(ac_compile); then
+ # Parse the compiler output and extract the necessary
+ # objects, libraries and library flags.
+
+ # Sentinel used to keep track of whether or not we are before
+ # the conftest object file.
+ pre_test_object_deps_done=no
+
+ for p in `eval "$output_verbose_link_cmd"`; do
+ case $p in
+
+ -L* | -R* | -l*)
+ # Some compilers place space between "-{L,R}" and the path.
+ # Remove the space.
+ if test $p = "-L" ||
+ test $p = "-R"; then
+ prev=$p
+ continue
+ else
+ prev=
+ fi
+
+ if test "$pre_test_object_deps_done" = no; then
+ case $p in
+ -L* | -R*)
+ # Internal compiler library paths should come after those
+ # provided the user. The postdeps already come after the
+ # user supplied libs so there is no need to process them.
+ if test -z "$_LT_TAGVAR(compiler_lib_search_path, $1)"; then
+ _LT_TAGVAR(compiler_lib_search_path, $1)="${prev}${p}"
+ else
+ _LT_TAGVAR(compiler_lib_search_path, $1)="${_LT_TAGVAR(compiler_lib_search_path, $1)} ${prev}${p}"
+ fi
+ ;;
+ # The "-l" case would never come before the object being
+ # linked, so don't bother handling this case.
+ esac
+ else
+ if test -z "$_LT_TAGVAR(postdeps, $1)"; then
+ _LT_TAGVAR(postdeps, $1)="${prev}${p}"
+ else
+ _LT_TAGVAR(postdeps, $1)="${_LT_TAGVAR(postdeps, $1)} ${prev}${p}"
+ fi
+ fi
+ ;;
+
+ *.$objext)
+ # This assumes that the test object file only shows up
+ # once in the compiler output.
+ if test "$p" = "conftest.$objext"; then
+ pre_test_object_deps_done=yes
+ continue
+ fi
+
+ if test "$pre_test_object_deps_done" = no; then
+ if test -z "$_LT_TAGVAR(predep_objects, $1)"; then
+ _LT_TAGVAR(predep_objects, $1)="$p"
+ else
+ _LT_TAGVAR(predep_objects, $1)="$_LT_TAGVAR(predep_objects, $1) $p"
+ fi
+ else
+ if test -z "$_LT_TAGVAR(postdep_objects, $1)"; then
+ _LT_TAGVAR(postdep_objects, $1)="$p"
+ else
+ _LT_TAGVAR(postdep_objects, $1)="$_LT_TAGVAR(postdep_objects, $1) $p"
+ fi
+ fi
+ ;;
+
+ *) ;; # Ignore the rest.
+
+ esac
+ done
+
+ # Clean up.
+ rm -f a.out a.exe
+else
+ echo "libtool.m4: error: problem compiling $1 test program"
+fi
+
+$RM -f confest.$objext
+
+# PORTME: override above test on systems where it is broken
+m4_if([$1], [CXX],
+[case $host_os in
+interix[[3-9]]*)
+ # Interix 3.5 installs completely hosed .la files for C++, so rather than
+ # hack all around it, let's just trust "g++" to DTRT.
+ _LT_TAGVAR(predep_objects,$1)=
+ _LT_TAGVAR(postdep_objects,$1)=
+ _LT_TAGVAR(postdeps,$1)=
+ ;;
+
+linux*)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+
+ # The more standards-conforming stlport4 library is
+ # incompatible with the Cstd library. Avoid specifying
+ # it if it's in CXXFLAGS. Ignore libCrun as
+ # -library=stlport4 depends on it.
+ case " $CXX $CXXFLAGS " in
+ *" -library=stlport4 "*)
+ solaris_use_stlport4=yes
+ ;;
+ esac
+
+ if test "$solaris_use_stlport4" != yes; then
+ _LT_TAGVAR(postdeps,$1)='-library=Cstd -library=Crun'
+ fi
+ ;;
+ esac
+ ;;
+
+solaris*)
+ case $cc_basename in
+ CC*)
+ # The more standards-conforming stlport4 library is
+ # incompatible with the Cstd library. Avoid specifying
+ # it if it's in CXXFLAGS. Ignore libCrun as
+ # -library=stlport4 depends on it.
+ case " $CXX $CXXFLAGS " in
+ *" -library=stlport4 "*)
+ solaris_use_stlport4=yes
+ ;;
+ esac
+
+ # Adding this requires a known-good setup of shared libraries for
+ # Sun compiler versions before 5.6, else PIC objects from an old
+ # archive will be linked into the output, leading to subtle bugs.
+ if test "$solaris_use_stlport4" != yes; then
+ _LT_TAGVAR(postdeps,$1)='-library=Cstd -library=Crun'
+ fi
+ ;;
+ esac
+ ;;
+esac
+])
+
+case " $_LT_TAGVAR(postdeps, $1) " in
+*" -lc "*) _LT_TAGVAR(archive_cmds_need_lc, $1)=no ;;
+esac
+ _LT_TAGVAR(compiler_lib_search_dirs, $1)=
+if test -n "${_LT_TAGVAR(compiler_lib_search_path, $1)}"; then
+ _LT_TAGVAR(compiler_lib_search_dirs, $1)=`echo " ${_LT_TAGVAR(compiler_lib_search_path, $1)}" | ${SED} -e 's! -L! !g' -e 's!^ !!'`
+fi
+_LT_TAGDECL([], [compiler_lib_search_dirs], [1],
+ [The directories searched by this compiler when creating a shared library])
+_LT_TAGDECL([], [predep_objects], [1],
+ [Dependencies to place before and after the objects being linked to
+ create a shared library])
+_LT_TAGDECL([], [postdep_objects], [1])
+_LT_TAGDECL([], [predeps], [1])
+_LT_TAGDECL([], [postdeps], [1])
+_LT_TAGDECL([], [compiler_lib_search_path], [1],
+ [The library search path used internally by the compiler when linking
+ a shared library])
+])# _LT_SYS_HIDDEN_LIBDEPS
+
+
+# _LT_PROG_F77
+# ------------
+# Since AC_PROG_F77 is broken, in that it returns the empty string
+# if there is no fortran compiler, we have our own version here.
+m4_defun([_LT_PROG_F77],
+[
+pushdef([AC_MSG_ERROR], [_lt_disable_F77=yes])
+AC_PROG_F77
+if test -z "$F77" || test "X$F77" = "Xno"; then
+ _lt_disable_F77=yes
+fi
+popdef([AC_MSG_ERROR])
+])# _LT_PROG_F77
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([_LT_PROG_F77], [])
+
+
+# _LT_LANG_F77_CONFIG([TAG])
+# --------------------------
+# Ensure that the configuration variables for a Fortran 77 compiler are
+# suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_F77_CONFIG],
+[AC_REQUIRE([_LT_PROG_F77])dnl
+AC_LANG_PUSH(Fortran 77)
+
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+_LT_TAGVAR(allow_undefined_flag, $1)=
+_LT_TAGVAR(always_export_symbols, $1)=no
+_LT_TAGVAR(archive_expsym_cmds, $1)=
+_LT_TAGVAR(export_dynamic_flag_spec, $1)=
+_LT_TAGVAR(hardcode_direct, $1)=no
+_LT_TAGVAR(hardcode_direct_absolute, $1)=no
+_LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+_LT_TAGVAR(hardcode_libdir_separator, $1)=
+_LT_TAGVAR(hardcode_minus_L, $1)=no
+_LT_TAGVAR(hardcode_automatic, $1)=no
+_LT_TAGVAR(inherit_rpath, $1)=no
+_LT_TAGVAR(module_cmds, $1)=
+_LT_TAGVAR(module_expsym_cmds, $1)=
+_LT_TAGVAR(link_all_deplibs, $1)=unknown
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+_LT_TAGVAR(no_undefined_flag, $1)=
+_LT_TAGVAR(whole_archive_flag_spec, $1)=
+_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+
+# Source file extension for f77 test sources.
+ac_ext=f
+
+# Object file extension for compiled f77 test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# No sense in running all these tests if we already determined that
+# the F77 compiler isn't working. Some variables (like enable_shared)
+# are currently assumed to apply to all compilers on this platform,
+# and will be corrupted by setting them based on a non-working compiler.
+if test "$_lt_disable_F77" != yes; then
+ # Code to be used in simple compile tests
+ lt_simple_compile_test_code="\
+ subroutine t
+ return
+ end
+"
+
+ # Code to be used in simple link tests
+ lt_simple_link_test_code="\
+ program t
+ end
+"
+
+ # ltmain only uses $CC for tagged configurations so make sure $CC is set.
+ _LT_TAG_COMPILER
+
+ # save warnings/boilerplate of simple test code
+ _LT_COMPILER_BOILERPLATE
+ _LT_LINKER_BOILERPLATE
+
+ # Allow CC to be a program name with arguments.
+ lt_save_CC="$CC"
+ lt_save_GCC=$GCC
+ CC=${F77-"f77"}
+ compiler=$CC
+ _LT_TAGVAR(compiler, $1)=$CC
+ _LT_CC_BASENAME([$compiler])
+ GCC=$G77
+ if test -n "$compiler"; then
+ AC_MSG_CHECKING([if libtool supports shared libraries])
+ AC_MSG_RESULT([$can_build_shared])
+
+ AC_MSG_CHECKING([whether to build shared libraries])
+ test "$can_build_shared" = "no" && enable_shared=no
+
+ # On AIX, shared libraries and static libraries use the same namespace, and
+ # are all built from PIC.
+ case $host_os in
+ aix3*)
+ test "$enable_shared" = yes && enable_static=no
+ if test -n "$RANLIB"; then
+ archive_cmds="$archive_cmds~\$RANLIB \$lib"
+ postinstall_cmds='$RANLIB $lib'
+ fi
+ ;;
+ aix[[4-9]]*)
+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+ test "$enable_shared" = yes && enable_static=no
+ fi
+ ;;
+ esac
+ AC_MSG_RESULT([$enable_shared])
+
+ AC_MSG_CHECKING([whether to build static libraries])
+ # Make sure either enable_shared or enable_static is yes.
+ test "$enable_shared" = yes || enable_static=yes
+ AC_MSG_RESULT([$enable_static])
+
+ _LT_TAGVAR(GCC, $1)="$G77"
+ _LT_TAGVAR(LD, $1)="$LD"
+
+ ## CAVEAT EMPTOR:
+ ## There is no encapsulation within the following macros, do not change
+ ## the running order or otherwise move them around unless you know exactly
+ ## what you are doing...
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_SYS_DYNAMIC_LINKER($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+ fi # test -n "$compiler"
+
+ GCC=$lt_save_GCC
+ CC="$lt_save_CC"
+fi # test "$_lt_disable_F77" != yes
+
+AC_LANG_POP
+])# _LT_LANG_F77_CONFIG
+
+
+# _LT_PROG_FC
+# -----------
+# Since AC_PROG_FC is broken, in that it returns the empty string
+# if there is no fortran compiler, we have our own version here.
+m4_defun([_LT_PROG_FC],
+[
+pushdef([AC_MSG_ERROR], [_lt_disable_FC=yes])
+AC_PROG_FC
+if test -z "$FC" || test "X$FC" = "Xno"; then
+ _lt_disable_FC=yes
+fi
+popdef([AC_MSG_ERROR])
+])# _LT_PROG_FC
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([_LT_PROG_FC], [])
+
+
+# _LT_LANG_FC_CONFIG([TAG])
+# -------------------------
+# Ensure that the configuration variables for a Fortran compiler are
+# suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_FC_CONFIG],
+[AC_REQUIRE([_LT_PROG_FC])dnl
+AC_LANG_PUSH(Fortran)
+
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+_LT_TAGVAR(allow_undefined_flag, $1)=
+_LT_TAGVAR(always_export_symbols, $1)=no
+_LT_TAGVAR(archive_expsym_cmds, $1)=
+_LT_TAGVAR(export_dynamic_flag_spec, $1)=
+_LT_TAGVAR(hardcode_direct, $1)=no
+_LT_TAGVAR(hardcode_direct_absolute, $1)=no
+_LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+_LT_TAGVAR(hardcode_libdir_separator, $1)=
+_LT_TAGVAR(hardcode_minus_L, $1)=no
+_LT_TAGVAR(hardcode_automatic, $1)=no
+_LT_TAGVAR(inherit_rpath, $1)=no
+_LT_TAGVAR(module_cmds, $1)=
+_LT_TAGVAR(module_expsym_cmds, $1)=
+_LT_TAGVAR(link_all_deplibs, $1)=unknown
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+_LT_TAGVAR(no_undefined_flag, $1)=
+_LT_TAGVAR(whole_archive_flag_spec, $1)=
+_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+
+# Source file extension for fc test sources.
+ac_ext=${ac_fc_srcext-f}
+
+# Object file extension for compiled fc test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# No sense in running all these tests if we already determined that
+# the FC compiler isn't working. Some variables (like enable_shared)
+# are currently assumed to apply to all compilers on this platform,
+# and will be corrupted by setting them based on a non-working compiler.
+if test "$_lt_disable_FC" != yes; then
+ # Code to be used in simple compile tests
+ lt_simple_compile_test_code="\
+ subroutine t
+ return
+ end
+"
+
+ # Code to be used in simple link tests
+ lt_simple_link_test_code="\
+ program t
+ end
+"
+
+ # ltmain only uses $CC for tagged configurations so make sure $CC is set.
+ _LT_TAG_COMPILER
+
+ # save warnings/boilerplate of simple test code
+ _LT_COMPILER_BOILERPLATE
+ _LT_LINKER_BOILERPLATE
+
+ # Allow CC to be a program name with arguments.
+ lt_save_CC="$CC"
+ lt_save_GCC=$GCC
+ CC=${FC-"f95"}
+ compiler=$CC
+ GCC=$ac_cv_fc_compiler_gnu
+
+ _LT_TAGVAR(compiler, $1)=$CC
+ _LT_CC_BASENAME([$compiler])
+
+ if test -n "$compiler"; then
+ AC_MSG_CHECKING([if libtool supports shared libraries])
+ AC_MSG_RESULT([$can_build_shared])
+
+ AC_MSG_CHECKING([whether to build shared libraries])
+ test "$can_build_shared" = "no" && enable_shared=no
+
+ # On AIX, shared libraries and static libraries use the same namespace, and
+ # are all built from PIC.
+ case $host_os in
+ aix3*)
+ test "$enable_shared" = yes && enable_static=no
+ if test -n "$RANLIB"; then
+ archive_cmds="$archive_cmds~\$RANLIB \$lib"
+ postinstall_cmds='$RANLIB $lib'
+ fi
+ ;;
+ aix[[4-9]]*)
+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+ test "$enable_shared" = yes && enable_static=no
+ fi
+ ;;
+ esac
+ AC_MSG_RESULT([$enable_shared])
+
+ AC_MSG_CHECKING([whether to build static libraries])
+ # Make sure either enable_shared or enable_static is yes.
+ test "$enable_shared" = yes || enable_static=yes
+ AC_MSG_RESULT([$enable_static])
+
+ _LT_TAGVAR(GCC, $1)="$ac_cv_fc_compiler_gnu"
+ _LT_TAGVAR(LD, $1)="$LD"
+
+ ## CAVEAT EMPTOR:
+ ## There is no encapsulation within the following macros, do not change
+ ## the running order or otherwise move them around unless you know exactly
+ ## what you are doing...
+ _LT_SYS_HIDDEN_LIBDEPS($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_SYS_DYNAMIC_LINKER($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+ fi # test -n "$compiler"
+
+ GCC=$lt_save_GCC
+ CC="$lt_save_CC"
+fi # test "$_lt_disable_FC" != yes
+
+AC_LANG_POP
+])# _LT_LANG_FC_CONFIG
+
+
+# _LT_LANG_GCJ_CONFIG([TAG])
+# --------------------------
+# Ensure that the configuration variables for the GNU Java Compiler compiler
+# are suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_GCJ_CONFIG],
+[AC_REQUIRE([LT_PROG_GCJ])dnl
+AC_LANG_SAVE
+
+# Source file extension for Java test sources.
+ac_ext=java
+
+# Object file extension for compiled Java test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="class foo {}"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='public class conftest { public static void main(String[[]] argv) {}; }'
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+_LT_TAG_COMPILER
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+# Allow CC to be a program name with arguments.
+lt_save_CC="$CC"
+lt_save_GCC=$GCC
+GCC=yes
+CC=${GCJ-"gcj"}
+compiler=$CC
+_LT_TAGVAR(compiler, $1)=$CC
+_LT_TAGVAR(LD, $1)="$LD"
+_LT_CC_BASENAME([$compiler])
+
+# GCJ did not exist at the time GCC didn't implicitly link libc in.
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+
+if test -n "$compiler"; then
+ _LT_COMPILER_NO_RTTI($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+fi
+
+AC_LANG_RESTORE
+
+GCC=$lt_save_GCC
+CC="$lt_save_CC"
+])# _LT_LANG_GCJ_CONFIG
+
+
+# _LT_LANG_RC_CONFIG([TAG])
+# -------------------------
+# Ensure that the configuration variables for the Windows resource compiler
+# are suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_RC_CONFIG],
+[AC_REQUIRE([LT_PROG_RC])dnl
+AC_LANG_SAVE
+
+# Source file extension for RC test sources.
+ac_ext=rc
+
+# Object file extension for compiled RC test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code='sample MENU { MENUITEM "&Soup", 100, CHECKED }'
+
+# Code to be used in simple link tests
+lt_simple_link_test_code="$lt_simple_compile_test_code"
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+_LT_TAG_COMPILER
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+# Allow CC to be a program name with arguments.
+lt_save_CC="$CC"
+lt_save_GCC=$GCC
+GCC=
+CC=${RC-"windres"}
+compiler=$CC
+_LT_TAGVAR(compiler, $1)=$CC
+_LT_CC_BASENAME([$compiler])
+_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=yes
+
+if test -n "$compiler"; then
+ :
+ _LT_CONFIG($1)
+fi
+
+GCC=$lt_save_GCC
+AC_LANG_RESTORE
+CC="$lt_save_CC"
+])# _LT_LANG_RC_CONFIG
+
+
+# LT_PROG_GCJ
+# -----------
+AC_DEFUN([LT_PROG_GCJ],
+[m4_ifdef([AC_PROG_GCJ], [AC_PROG_GCJ],
+ [m4_ifdef([A][M_PROG_GCJ], [A][M_PROG_GCJ],
+ [AC_CHECK_TOOL(GCJ, gcj,)
+ test "x${GCJFLAGS+set}" = xset || GCJFLAGS="-g -O2"
+ AC_SUBST(GCJFLAGS)])])[]dnl
+])
+
+# Old name:
+AU_ALIAS([LT_AC_PROG_GCJ], [LT_PROG_GCJ])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([LT_AC_PROG_GCJ], [])
+
+
+# LT_PROG_RC
+# ----------
+AC_DEFUN([LT_PROG_RC],
+[AC_CHECK_TOOL(RC, windres,)
+])
+
+# Old name:
+AU_ALIAS([LT_AC_PROG_RC], [LT_PROG_RC])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([LT_AC_PROG_RC], [])
+
+
+# _LT_DECL_EGREP
+# --------------
+# If we don't have a new enough Autoconf to choose the best grep
+# available, choose the one first in the user's PATH.
+m4_defun([_LT_DECL_EGREP],
+[AC_REQUIRE([AC_PROG_EGREP])dnl
+AC_REQUIRE([AC_PROG_FGREP])dnl
+test -z "$GREP" && GREP=grep
+_LT_DECL([], [GREP], [1], [A grep program that handles long lines])
+_LT_DECL([], [EGREP], [1], [An ERE matcher])
+_LT_DECL([], [FGREP], [1], [A literal string matcher])
+dnl Non-bleeding-edge autoconf doesn't subst GREP, so do it here too
+AC_SUBST([GREP])
+])
+
+
+# _LT_DECL_OBJDUMP
+# --------------
+# If we don't have a new enough Autoconf to choose the best objdump
+# available, choose the one first in the user's PATH.
+m4_defun([_LT_DECL_OBJDUMP],
+[AC_CHECK_TOOL(OBJDUMP, objdump, false)
+test -z "$OBJDUMP" && OBJDUMP=objdump
+_LT_DECL([], [OBJDUMP], [1], [An object symbol dumper])
+AC_SUBST([OBJDUMP])
+])
+
+
+# _LT_DECL_SED
+# ------------
+# Check for a fully-functional sed program, that truncates
+# as few characters as possible. Prefer GNU sed if found.
+m4_defun([_LT_DECL_SED],
+[AC_PROG_SED
+test -z "$SED" && SED=sed
+Xsed="$SED -e 1s/^X//"
+_LT_DECL([], [SED], [1], [A sed program that does not truncate output])
+_LT_DECL([], [Xsed], ["\$SED -e 1s/^X//"],
+ [Sed that helps us avoid accidentally triggering echo(1) options like -n])
+])# _LT_DECL_SED
+
+m4_ifndef([AC_PROG_SED], [
+# NOTE: This macro has been submitted for inclusion into #
+# GNU Autoconf as AC_PROG_SED. When it is available in #
+# a released version of Autoconf we should remove this #
+# macro and use it instead. #
+
+m4_defun([AC_PROG_SED],
+[AC_MSG_CHECKING([for a sed that does not truncate output])
+AC_CACHE_VAL(lt_cv_path_SED,
+[# Loop through the user's path and test for sed and gsed.
+# Then use that list of sed's as ones to test for truncation.
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for lt_ac_prog in sed gsed; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$lt_ac_prog$ac_exec_ext"; then
+ lt_ac_sed_list="$lt_ac_sed_list $as_dir/$lt_ac_prog$ac_exec_ext"
+ fi
+ done
+ done
+done
+IFS=$as_save_IFS
+lt_ac_max=0
+lt_ac_count=0
+# Add /usr/xpg4/bin/sed as it is typically found on Solaris
+# along with /bin/sed that truncates output.
+for lt_ac_sed in $lt_ac_sed_list /usr/xpg4/bin/sed; do
+ test ! -f $lt_ac_sed && continue
+ cat /dev/null > conftest.in
+ lt_ac_count=0
+ echo $ECHO_N "0123456789$ECHO_C" >conftest.in
+ # Check for GNU sed and select it if it is found.
+ if "$lt_ac_sed" --version 2>&1 < /dev/null | grep 'GNU' > /dev/null; then
+ lt_cv_path_SED=$lt_ac_sed
+ break
+ fi
+ while true; do
+ cat conftest.in conftest.in >conftest.tmp
+ mv conftest.tmp conftest.in
+ cp conftest.in conftest.nl
+ echo >>conftest.nl
+ $lt_ac_sed -e 's/a$//' < conftest.nl >conftest.out || break
+ cmp -s conftest.out conftest.nl || break
+ # 10000 chars as input seems more than enough
+ test $lt_ac_count -gt 10 && break
+ lt_ac_count=`expr $lt_ac_count + 1`
+ if test $lt_ac_count -gt $lt_ac_max; then
+ lt_ac_max=$lt_ac_count
+ lt_cv_path_SED=$lt_ac_sed
+ fi
+ done
+done
+])
+SED=$lt_cv_path_SED
+AC_SUBST([SED])
+AC_MSG_RESULT([$SED])
+])#AC_PROG_SED
+])#m4_ifndef
+
+# Old name:
+AU_ALIAS([LT_AC_PROG_SED], [AC_PROG_SED])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([LT_AC_PROG_SED], [])
+
+
+# _LT_CHECK_SHELL_FEATURES
+# ------------------------
+# Find out whether the shell is Bourne or XSI compatible,
+# or has some other useful features.
+m4_defun([_LT_CHECK_SHELL_FEATURES],
+[AC_MSG_CHECKING([whether the shell understands some XSI constructs])
+# Try some XSI features
+xsi_shell=no
+( _lt_dummy="a/b/c"
+ test "${_lt_dummy##*/},${_lt_dummy%/*},"${_lt_dummy%"$_lt_dummy"}, \
+ = c,a/b,, \
+ && eval 'test $(( 1 + 1 )) -eq 2 \
+ && test "${#_lt_dummy}" -eq 5' ) >/dev/null 2>&1 \
+ && xsi_shell=yes
+AC_MSG_RESULT([$xsi_shell])
+_LT_CONFIG_LIBTOOL_INIT([xsi_shell='$xsi_shell'])
+
+AC_MSG_CHECKING([whether the shell understands "+="])
+lt_shell_append=no
+( foo=bar; set foo baz; eval "$[1]+=\$[2]" && test "$foo" = barbaz ) \
+ >/dev/null 2>&1 \
+ && lt_shell_append=yes
+AC_MSG_RESULT([$lt_shell_append])
+_LT_CONFIG_LIBTOOL_INIT([lt_shell_append='$lt_shell_append'])
+
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+ lt_unset=unset
+else
+ lt_unset=false
+fi
+_LT_DECL([], [lt_unset], [0], [whether the shell understands "unset"])dnl
+
+# test EBCDIC or ASCII
+case `echo X|tr X '\101'` in
+ A) # ASCII based system
+ # \n is not interpreted correctly by Solaris 8 /usr/ucb/tr
+ lt_SP2NL='tr \040 \012'
+ lt_NL2SP='tr \015\012 \040\040'
+ ;;
+ *) # EBCDIC based system
+ lt_SP2NL='tr \100 \n'
+ lt_NL2SP='tr \r\n \100\100'
+ ;;
+esac
+_LT_DECL([SP2NL], [lt_SP2NL], [1], [turn spaces into newlines])dnl
+_LT_DECL([NL2SP], [lt_NL2SP], [1], [turn newlines into spaces])dnl
+])# _LT_CHECK_SHELL_FEATURES
+
+
+# _LT_PROG_XSI_SHELLFNS
+# ---------------------
+# Bourne and XSI compatible variants of some useful shell functions.
+m4_defun([_LT_PROG_XSI_SHELLFNS],
+[case $xsi_shell in
+ yes)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_dirname file append nondir_replacement
+# Compute the dirname of FILE. If nonempty, add APPEND to the result,
+# otherwise set result to NONDIR_REPLACEMENT.
+func_dirname ()
+{
+ case ${1} in
+ */*) func_dirname_result="${1%/*}${2}" ;;
+ * ) func_dirname_result="${3}" ;;
+ esac
+}
+
+# func_basename file
+func_basename ()
+{
+ func_basename_result="${1##*/}"
+}
+
+# func_dirname_and_basename file append nondir_replacement
+# perform func_basename and func_dirname in a single function
+# call:
+# dirname: Compute the dirname of FILE. If nonempty,
+# add APPEND to the result, otherwise set result
+# to NONDIR_REPLACEMENT.
+# value returned in "$func_dirname_result"
+# basename: Compute filename of FILE.
+# value retuned in "$func_basename_result"
+# Implementation must be kept synchronized with func_dirname
+# and func_basename. For efficiency, we do not delegate to
+# those functions but instead duplicate the functionality here.
+func_dirname_and_basename ()
+{
+ case ${1} in
+ */*) func_dirname_result="${1%/*}${2}" ;;
+ * ) func_dirname_result="${3}" ;;
+ esac
+ func_basename_result="${1##*/}"
+}
+
+# func_stripname prefix suffix name
+# strip PREFIX and SUFFIX off of NAME.
+# PREFIX and SUFFIX must not contain globbing or regex special
+# characters, hashes, percent signs, but SUFFIX may contain a leading
+# dot (in which case that matches only a dot).
+func_stripname ()
+{
+ # pdksh 5.2.14 does not do ${X%$Y} correctly if both X and Y are
+ # positional parameters, so assign one to ordinary parameter first.
+ func_stripname_result=${3}
+ func_stripname_result=${func_stripname_result#"${1}"}
+ func_stripname_result=${func_stripname_result%"${2}"}
+}
+
+# func_opt_split
+func_opt_split ()
+{
+ func_opt_split_opt=${1%%=*}
+ func_opt_split_arg=${1#*=}
+}
+
+# func_lo2o object
+func_lo2o ()
+{
+ case ${1} in
+ *.lo) func_lo2o_result=${1%.lo}.${objext} ;;
+ *) func_lo2o_result=${1} ;;
+ esac
+}
+
+# func_xform libobj-or-source
+func_xform ()
+{
+ func_xform_result=${1%.*}.lo
+}
+
+# func_arith arithmetic-term...
+func_arith ()
+{
+ func_arith_result=$(( $[*] ))
+}
+
+# func_len string
+# STRING may not start with a hyphen.
+func_len ()
+{
+ func_len_result=${#1}
+}
+
+_LT_EOF
+ ;;
+ *) # Bourne compatible functions.
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_dirname file append nondir_replacement
+# Compute the dirname of FILE. If nonempty, add APPEND to the result,
+# otherwise set result to NONDIR_REPLACEMENT.
+func_dirname ()
+{
+ # Extract subdirectory from the argument.
+ func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"`
+ if test "X$func_dirname_result" = "X${1}"; then
+ func_dirname_result="${3}"
+ else
+ func_dirname_result="$func_dirname_result${2}"
+ fi
+}
+
+# func_basename file
+func_basename ()
+{
+ func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"`
+}
+
+dnl func_dirname_and_basename
+dnl A portable version of this function is already defined in general.m4sh
+dnl so there is no need for it here.
+
+# func_stripname prefix suffix name
+# strip PREFIX and SUFFIX off of NAME.
+# PREFIX and SUFFIX must not contain globbing or regex special
+# characters, hashes, percent signs, but SUFFIX may contain a leading
+# dot (in which case that matches only a dot).
+# func_strip_suffix prefix name
+func_stripname ()
+{
+ case ${2} in
+ .*) func_stripname_result=`$ECHO "X${3}" \
+ | $Xsed -e "s%^${1}%%" -e "s%\\\\${2}\$%%"`;;
+ *) func_stripname_result=`$ECHO "X${3}" \
+ | $Xsed -e "s%^${1}%%" -e "s%${2}\$%%"`;;
+ esac
+}
+
+# sed scripts:
+my_sed_long_opt='1s/^\(-[[^=]]*\)=.*/\1/;q'
+my_sed_long_arg='1s/^-[[^=]]*=//'
+
+# func_opt_split
+func_opt_split ()
+{
+ func_opt_split_opt=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_opt"`
+ func_opt_split_arg=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_arg"`
+}
+
+# func_lo2o object
+func_lo2o ()
+{
+ func_lo2o_result=`$ECHO "X${1}" | $Xsed -e "$lo2o"`
+}
+
+# func_xform libobj-or-source
+func_xform ()
+{
+ func_xform_result=`$ECHO "X${1}" | $Xsed -e 's/\.[[^.]]*$/.lo/'`
+}
+
+# func_arith arithmetic-term...
+func_arith ()
+{
+ func_arith_result=`expr "$[@]"`
+}
+
+# func_len string
+# STRING may not start with a hyphen.
+func_len ()
+{
+ func_len_result=`expr "$[1]" : ".*" 2>/dev/null || echo $max_cmd_len`
+}
+
+_LT_EOF
+esac
+
+case $lt_shell_append in
+ yes)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$[1]+=\$[2]"
+}
+_LT_EOF
+ ;;
+ *)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$[1]=\$$[1]\$[2]"
+}
+
+_LT_EOF
+ ;;
+ esac
+])
+
+# Helper functions for option handling. -*- Autoconf -*-
+#
+# Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gary V. Vaughan, 2004
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+# serial 6 ltoptions.m4
+
+# This is to help aclocal find these macros, as it can't see m4_define.
+AC_DEFUN([LTOPTIONS_VERSION], [m4_if([1])])
+
+
+# _LT_MANGLE_OPTION(MACRO-NAME, OPTION-NAME)
+# ------------------------------------------
+m4_define([_LT_MANGLE_OPTION],
+[[_LT_OPTION_]m4_bpatsubst($1__$2, [[^a-zA-Z0-9_]], [_])])
+
+
+# _LT_SET_OPTION(MACRO-NAME, OPTION-NAME)
+# ---------------------------------------
+# Set option OPTION-NAME for macro MACRO-NAME, and if there is a
+# matching handler defined, dispatch to it. Other OPTION-NAMEs are
+# saved as a flag.
+m4_define([_LT_SET_OPTION],
+[m4_define(_LT_MANGLE_OPTION([$1], [$2]))dnl
+m4_ifdef(_LT_MANGLE_DEFUN([$1], [$2]),
+ _LT_MANGLE_DEFUN([$1], [$2]),
+ [m4_warning([Unknown $1 option `$2'])])[]dnl
+])
+
+
+# _LT_IF_OPTION(MACRO-NAME, OPTION-NAME, IF-SET, [IF-NOT-SET])
+# ------------------------------------------------------------
+# Execute IF-SET if OPTION is set, IF-NOT-SET otherwise.
+m4_define([_LT_IF_OPTION],
+[m4_ifdef(_LT_MANGLE_OPTION([$1], [$2]), [$3], [$4])])
+
+
+# _LT_UNLESS_OPTIONS(MACRO-NAME, OPTION-LIST, IF-NOT-SET)
+# -------------------------------------------------------
+# Execute IF-NOT-SET unless all options in OPTION-LIST for MACRO-NAME
+# are set.
+m4_define([_LT_UNLESS_OPTIONS],
+[m4_foreach([_LT_Option], m4_split(m4_normalize([$2])),
+ [m4_ifdef(_LT_MANGLE_OPTION([$1], _LT_Option),
+ [m4_define([$0_found])])])[]dnl
+m4_ifdef([$0_found], [m4_undefine([$0_found])], [$3
+])[]dnl
+])
+
+
+# _LT_SET_OPTIONS(MACRO-NAME, OPTION-LIST)
+# ----------------------------------------
+# OPTION-LIST is a space-separated list of Libtool options associated
+# with MACRO-NAME. If any OPTION has a matching handler declared with
+# LT_OPTION_DEFINE, dispatch to that macro; otherwise complain about
+# the unknown option and exit.
+m4_defun([_LT_SET_OPTIONS],
+[# Set options
+m4_foreach([_LT_Option], m4_split(m4_normalize([$2])),
+ [_LT_SET_OPTION([$1], _LT_Option)])
+
+m4_if([$1],[LT_INIT],[
+ dnl
+ dnl Simply set some default values (i.e off) if boolean options were not
+ dnl specified:
+ _LT_UNLESS_OPTIONS([LT_INIT], [dlopen], [enable_dlopen=no
+ ])
+ _LT_UNLESS_OPTIONS([LT_INIT], [win32-dll], [enable_win32_dll=no
+ ])
+ dnl
+ dnl If no reference was made to various pairs of opposing options, then
+ dnl we run the default mode handler for the pair. For example, if neither
+ dnl `shared' nor `disable-shared' was passed, we enable building of shared
+ dnl archives by default:
+ _LT_UNLESS_OPTIONS([LT_INIT], [shared disable-shared], [_LT_ENABLE_SHARED])
+ _LT_UNLESS_OPTIONS([LT_INIT], [static disable-static], [_LT_ENABLE_STATIC])
+ _LT_UNLESS_OPTIONS([LT_INIT], [pic-only no-pic], [_LT_WITH_PIC])
+ _LT_UNLESS_OPTIONS([LT_INIT], [fast-install disable-fast-install],
+ [_LT_ENABLE_FAST_INSTALL])
+ ])
+])# _LT_SET_OPTIONS
+
+
+
+# _LT_MANGLE_DEFUN(MACRO-NAME, OPTION-NAME)
+# -----------------------------------------
+m4_define([_LT_MANGLE_DEFUN],
+[[_LT_OPTION_DEFUN_]m4_bpatsubst(m4_toupper([$1__$2]), [[^A-Z0-9_]], [_])])
+
+
+# LT_OPTION_DEFINE(MACRO-NAME, OPTION-NAME, CODE)
+# -----------------------------------------------
+m4_define([LT_OPTION_DEFINE],
+[m4_define(_LT_MANGLE_DEFUN([$1], [$2]), [$3])[]dnl
+])# LT_OPTION_DEFINE
+
+
+# dlopen
+# ------
+LT_OPTION_DEFINE([LT_INIT], [dlopen], [enable_dlopen=yes
+])
+
+AU_DEFUN([AC_LIBTOOL_DLOPEN],
+[_LT_SET_OPTION([LT_INIT], [dlopen])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you
+put the `dlopen' option into LT_INIT's first parameter.])
+])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_DLOPEN], [])
+
+
+# win32-dll
+# ---------
+# Declare package support for building win32 dll's.
+LT_OPTION_DEFINE([LT_INIT], [win32-dll],
+[enable_win32_dll=yes
+
+case $host in
+*-*-cygwin* | *-*-mingw* | *-*-pw32* | *-cegcc*)
+ AC_CHECK_TOOL(AS, as, false)
+ AC_CHECK_TOOL(DLLTOOL, dlltool, false)
+ AC_CHECK_TOOL(OBJDUMP, objdump, false)
+ ;;
+esac
+
+test -z "$AS" && AS=as
+_LT_DECL([], [AS], [0], [Assembler program])dnl
+
+test -z "$DLLTOOL" && DLLTOOL=dlltool
+_LT_DECL([], [DLLTOOL], [0], [DLL creation program])dnl
+
+test -z "$OBJDUMP" && OBJDUMP=objdump
+_LT_DECL([], [OBJDUMP], [0], [Object dumper program])dnl
+])# win32-dll
+
+AU_DEFUN([AC_LIBTOOL_WIN32_DLL],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+_LT_SET_OPTION([LT_INIT], [win32-dll])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you
+put the `win32-dll' option into LT_INIT's first parameter.])
+])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_WIN32_DLL], [])
+
+
+# _LT_ENABLE_SHARED([DEFAULT])
+# ----------------------------
+# implement the --enable-shared flag, and supports the `shared' and
+# `disable-shared' LT_INIT options.
+# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'.
+m4_define([_LT_ENABLE_SHARED],
+[m4_define([_LT_ENABLE_SHARED_DEFAULT], [m4_if($1, no, no, yes)])dnl
+AC_ARG_ENABLE([shared],
+ [AS_HELP_STRING([--enable-shared@<:@=PKGS@:>@],
+ [build shared libraries @<:@default=]_LT_ENABLE_SHARED_DEFAULT[@:>@])],
+ [p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_shared=yes ;;
+ no) enable_shared=no ;;
+ *)
+ enable_shared=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_shared=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac],
+ [enable_shared=]_LT_ENABLE_SHARED_DEFAULT)
+
+ _LT_DECL([build_libtool_libs], [enable_shared], [0],
+ [Whether or not to build shared libraries])
+])# _LT_ENABLE_SHARED
+
+LT_OPTION_DEFINE([LT_INIT], [shared], [_LT_ENABLE_SHARED([yes])])
+LT_OPTION_DEFINE([LT_INIT], [disable-shared], [_LT_ENABLE_SHARED([no])])
+
+# Old names:
+AC_DEFUN([AC_ENABLE_SHARED],
+[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[shared])
+])
+
+AC_DEFUN([AC_DISABLE_SHARED],
+[_LT_SET_OPTION([LT_INIT], [disable-shared])
+])
+
+AU_DEFUN([AM_ENABLE_SHARED], [AC_ENABLE_SHARED($@)])
+AU_DEFUN([AM_DISABLE_SHARED], [AC_DISABLE_SHARED($@)])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AM_ENABLE_SHARED], [])
+dnl AC_DEFUN([AM_DISABLE_SHARED], [])
+
+
+
+# _LT_ENABLE_STATIC([DEFAULT])
+# ----------------------------
+# implement the --enable-static flag, and support the `static' and
+# `disable-static' LT_INIT options.
+# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'.
+m4_define([_LT_ENABLE_STATIC],
+[m4_define([_LT_ENABLE_STATIC_DEFAULT], [m4_if($1, no, no, yes)])dnl
+AC_ARG_ENABLE([static],
+ [AS_HELP_STRING([--enable-static@<:@=PKGS@:>@],
+ [build static libraries @<:@default=]_LT_ENABLE_STATIC_DEFAULT[@:>@])],
+ [p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_static=yes ;;
+ no) enable_static=no ;;
+ *)
+ enable_static=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_static=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac],
+ [enable_static=]_LT_ENABLE_STATIC_DEFAULT)
+
+ _LT_DECL([build_old_libs], [enable_static], [0],
+ [Whether or not to build static libraries])
+])# _LT_ENABLE_STATIC
+
+LT_OPTION_DEFINE([LT_INIT], [static], [_LT_ENABLE_STATIC([yes])])
+LT_OPTION_DEFINE([LT_INIT], [disable-static], [_LT_ENABLE_STATIC([no])])
+
+# Old names:
+AC_DEFUN([AC_ENABLE_STATIC],
+[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[static])
+])
+
+AC_DEFUN([AC_DISABLE_STATIC],
+[_LT_SET_OPTION([LT_INIT], [disable-static])
+])
+
+AU_DEFUN([AM_ENABLE_STATIC], [AC_ENABLE_STATIC($@)])
+AU_DEFUN([AM_DISABLE_STATIC], [AC_DISABLE_STATIC($@)])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AM_ENABLE_STATIC], [])
+dnl AC_DEFUN([AM_DISABLE_STATIC], [])
+
+
+
+# _LT_ENABLE_FAST_INSTALL([DEFAULT])
+# ----------------------------------
+# implement the --enable-fast-install flag, and support the `fast-install'
+# and `disable-fast-install' LT_INIT options.
+# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'.
+m4_define([_LT_ENABLE_FAST_INSTALL],
+[m4_define([_LT_ENABLE_FAST_INSTALL_DEFAULT], [m4_if($1, no, no, yes)])dnl
+AC_ARG_ENABLE([fast-install],
+ [AS_HELP_STRING([--enable-fast-install@<:@=PKGS@:>@],
+ [optimize for fast installation @<:@default=]_LT_ENABLE_FAST_INSTALL_DEFAULT[@:>@])],
+ [p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_fast_install=yes ;;
+ no) enable_fast_install=no ;;
+ *)
+ enable_fast_install=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_fast_install=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac],
+ [enable_fast_install=]_LT_ENABLE_FAST_INSTALL_DEFAULT)
+
+_LT_DECL([fast_install], [enable_fast_install], [0],
+ [Whether or not to optimize for fast installation])dnl
+])# _LT_ENABLE_FAST_INSTALL
+
+LT_OPTION_DEFINE([LT_INIT], [fast-install], [_LT_ENABLE_FAST_INSTALL([yes])])
+LT_OPTION_DEFINE([LT_INIT], [disable-fast-install], [_LT_ENABLE_FAST_INSTALL([no])])
+
+# Old names:
+AU_DEFUN([AC_ENABLE_FAST_INSTALL],
+[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[fast-install])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you put
+the `fast-install' option into LT_INIT's first parameter.])
+])
+
+AU_DEFUN([AC_DISABLE_FAST_INSTALL],
+[_LT_SET_OPTION([LT_INIT], [disable-fast-install])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you put
+the `disable-fast-install' option into LT_INIT's first parameter.])
+])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_ENABLE_FAST_INSTALL], [])
+dnl AC_DEFUN([AM_DISABLE_FAST_INSTALL], [])
+
+
+# _LT_WITH_PIC([MODE])
+# --------------------
+# implement the --with-pic flag, and support the `pic-only' and `no-pic'
+# LT_INIT options.
+# MODE is either `yes' or `no'. If omitted, it defaults to `both'.
+m4_define([_LT_WITH_PIC],
+[AC_ARG_WITH([pic],
+ [AS_HELP_STRING([--with-pic],
+ [try to use only PIC/non-PIC objects @<:@default=use both@:>@])],
+ [pic_mode="$withval"],
+ [pic_mode=default])
+
+test -z "$pic_mode" && pic_mode=m4_default([$1], [default])
+
+_LT_DECL([], [pic_mode], [0], [What type of objects to build])dnl
+])# _LT_WITH_PIC
+
+LT_OPTION_DEFINE([LT_INIT], [pic-only], [_LT_WITH_PIC([yes])])
+LT_OPTION_DEFINE([LT_INIT], [no-pic], [_LT_WITH_PIC([no])])
+
+# Old name:
+AU_DEFUN([AC_LIBTOOL_PICMODE],
+[_LT_SET_OPTION([LT_INIT], [pic-only])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you
+put the `pic-only' option into LT_INIT's first parameter.])
+])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_PICMODE], [])
+
+
+m4_define([_LTDL_MODE], [])
+LT_OPTION_DEFINE([LTDL_INIT], [nonrecursive],
+ [m4_define([_LTDL_MODE], [nonrecursive])])
+LT_OPTION_DEFINE([LTDL_INIT], [recursive],
+ [m4_define([_LTDL_MODE], [recursive])])
+LT_OPTION_DEFINE([LTDL_INIT], [subproject],
+ [m4_define([_LTDL_MODE], [subproject])])
+
+m4_define([_LTDL_TYPE], [])
+LT_OPTION_DEFINE([LTDL_INIT], [installable],
+ [m4_define([_LTDL_TYPE], [installable])])
+LT_OPTION_DEFINE([LTDL_INIT], [convenience],
+ [m4_define([_LTDL_TYPE], [convenience])])
+
+# ltsugar.m4 -- libtool m4 base layer. -*-Autoconf-*-
+#
+# Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gary V. Vaughan, 2004
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+# serial 6 ltsugar.m4
+
+# This is to help aclocal find these macros, as it can't see m4_define.
+AC_DEFUN([LTSUGAR_VERSION], [m4_if([0.1])])
+
+
+# lt_join(SEP, ARG1, [ARG2...])
+# -----------------------------
+# Produce ARG1SEPARG2...SEPARGn, omitting [] arguments and their
+# associated separator.
+# Needed until we can rely on m4_join from Autoconf 2.62, since all earlier
+# versions in m4sugar had bugs.
+m4_define([lt_join],
+[m4_if([$#], [1], [],
+ [$#], [2], [[$2]],
+ [m4_if([$2], [], [], [[$2]_])$0([$1], m4_shift(m4_shift($@)))])])
+m4_define([_lt_join],
+[m4_if([$#$2], [2], [],
+ [m4_if([$2], [], [], [[$1$2]])$0([$1], m4_shift(m4_shift($@)))])])
+
+
+# lt_car(LIST)
+# lt_cdr(LIST)
+# ------------
+# Manipulate m4 lists.
+# These macros are necessary as long as will still need to support
+# Autoconf-2.59 which quotes differently.
+m4_define([lt_car], [[$1]])
+m4_define([lt_cdr],
+[m4_if([$#], 0, [m4_fatal([$0: cannot be called without arguments])],
+ [$#], 1, [],
+ [m4_dquote(m4_shift($@))])])
+m4_define([lt_unquote], $1)
+
+
+# lt_append(MACRO-NAME, STRING, [SEPARATOR])
+# ------------------------------------------
+# Redefine MACRO-NAME to hold its former content plus `SEPARATOR'`STRING'.
+# Note that neither SEPARATOR nor STRING are expanded; they are appended
+# to MACRO-NAME as is (leaving the expansion for when MACRO-NAME is invoked).
+# No SEPARATOR is output if MACRO-NAME was previously undefined (different
+# than defined and empty).
+#
+# This macro is needed until we can rely on Autoconf 2.62, since earlier
+# versions of m4sugar mistakenly expanded SEPARATOR but not STRING.
+m4_define([lt_append],
+[m4_define([$1],
+ m4_ifdef([$1], [m4_defn([$1])[$3]])[$2])])
+
+
+
+# lt_combine(SEP, PREFIX-LIST, INFIX, SUFFIX1, [SUFFIX2...])
+# ----------------------------------------------------------
+# Produce a SEP delimited list of all paired combinations of elements of
+# PREFIX-LIST with SUFFIX1 through SUFFIXn. Each element of the list
+# has the form PREFIXmINFIXSUFFIXn.
+# Needed until we can rely on m4_combine added in Autoconf 2.62.
+m4_define([lt_combine],
+[m4_if(m4_eval([$# > 3]), [1],
+ [m4_pushdef([_Lt_sep], [m4_define([_Lt_sep], m4_defn([lt_car]))])]]dnl
+[[m4_foreach([_Lt_prefix], [$2],
+ [m4_foreach([_Lt_suffix],
+ ]m4_dquote(m4_dquote(m4_shift(m4_shift(m4_shift($@)))))[,
+ [_Lt_sep([$1])[]m4_defn([_Lt_prefix])[$3]m4_defn([_Lt_suffix])])])])])
+
+
+# lt_if_append_uniq(MACRO-NAME, VARNAME, [SEPARATOR], [UNIQ], [NOT-UNIQ])
+# -----------------------------------------------------------------------
+# Iff MACRO-NAME does not yet contain VARNAME, then append it (delimited
+# by SEPARATOR if supplied) and expand UNIQ, else NOT-UNIQ.
+m4_define([lt_if_append_uniq],
+[m4_ifdef([$1],
+ [m4_if(m4_index([$3]m4_defn([$1])[$3], [$3$2$3]), [-1],
+ [lt_append([$1], [$2], [$3])$4],
+ [$5])],
+ [lt_append([$1], [$2], [$3])$4])])
+
+
+# lt_dict_add(DICT, KEY, VALUE)
+# -----------------------------
+m4_define([lt_dict_add],
+[m4_define([$1($2)], [$3])])
+
+
+# lt_dict_add_subkey(DICT, KEY, SUBKEY, VALUE)
+# --------------------------------------------
+m4_define([lt_dict_add_subkey],
+[m4_define([$1($2:$3)], [$4])])
+
+
+# lt_dict_fetch(DICT, KEY, [SUBKEY])
+# ----------------------------------
+m4_define([lt_dict_fetch],
+[m4_ifval([$3],
+ m4_ifdef([$1($2:$3)], [m4_defn([$1($2:$3)])]),
+ m4_ifdef([$1($2)], [m4_defn([$1($2)])]))])
+
+
+# lt_if_dict_fetch(DICT, KEY, [SUBKEY], VALUE, IF-TRUE, [IF-FALSE])
+# -----------------------------------------------------------------
+m4_define([lt_if_dict_fetch],
+[m4_if(lt_dict_fetch([$1], [$2], [$3]), [$4],
+ [$5],
+ [$6])])
+
+
+# lt_dict_filter(DICT, [SUBKEY], VALUE, [SEPARATOR], KEY, [...])
+# --------------------------------------------------------------
+m4_define([lt_dict_filter],
+[m4_if([$5], [], [],
+ [lt_join(m4_quote(m4_default([$4], [[, ]])),
+ lt_unquote(m4_split(m4_normalize(m4_foreach(_Lt_key, lt_car([m4_shiftn(4, $@)]),
+ [lt_if_dict_fetch([$1], _Lt_key, [$2], [$3], [_Lt_key ])])))))])[]dnl
+])
+
+# ltversion.m4 -- version numbers -*- Autoconf -*-
+#
+# Copyright (C) 2004 Free Software Foundation, Inc.
+# Written by Scott James Remnant, 2004
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+# Generated from ltversion.in.
+
+# serial 3017 ltversion.m4
+# This file is part of GNU Libtool
+
+m4_define([LT_PACKAGE_VERSION], [2.2.6b])
+m4_define([LT_PACKAGE_REVISION], [1.3017])
+
+AC_DEFUN([LTVERSION_VERSION],
+[macro_version='2.2.6b'
+macro_revision='1.3017'
+_LT_DECL(, macro_version, 0, [Which release of libtool.m4 was used?])
+_LT_DECL(, macro_revision, 0)
+])
+
+# lt~obsolete.m4 -- aclocal satisfying obsolete definitions. -*-Autoconf-*-
+#
+# Copyright (C) 2004, 2005, 2007 Free Software Foundation, Inc.
+# Written by Scott James Remnant, 2004.
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+# serial 4 lt~obsolete.m4
+
+# These exist entirely to fool aclocal when bootstrapping libtool.
+#
+# In the past libtool.m4 has provided macros via AC_DEFUN (or AU_DEFUN)
+# which have later been changed to m4_define as they aren't part of the
+# exported API, or moved to Autoconf or Automake where they belong.
+#
+# The trouble is, aclocal is a bit thick. It'll see the old AC_DEFUN
+# in /usr/share/aclocal/libtool.m4 and remember it, then when it sees us
+# using a macro with the same name in our local m4/libtool.m4 it'll
+# pull the old libtool.m4 in (it doesn't see our shiny new m4_define
+# and doesn't know about Autoconf macros at all.)
+#
+# So we provide this file, which has a silly filename so it's always
+# included after everything else. This provides aclocal with the
+# AC_DEFUNs it wants, but when m4 processes it, it doesn't do anything
+# because those macros already exist, or will be overwritten later.
+# We use AC_DEFUN over AU_DEFUN for compatibility with aclocal-1.6.
+#
+# Anytime we withdraw an AC_DEFUN or AU_DEFUN, remember to add it here.
+# Yes, that means every name once taken will need to remain here until
+# we give up compatibility with versions before 1.7, at which point
+# we need to keep only those names which we still refer to.
+
+# This is to help aclocal find these macros, as it can't see m4_define.
+AC_DEFUN([LTOBSOLETE_VERSION], [m4_if([1])])
+
+m4_ifndef([AC_LIBTOOL_LINKER_OPTION], [AC_DEFUN([AC_LIBTOOL_LINKER_OPTION])])
+m4_ifndef([AC_PROG_EGREP], [AC_DEFUN([AC_PROG_EGREP])])
+m4_ifndef([_LT_AC_PROG_ECHO_BACKSLASH], [AC_DEFUN([_LT_AC_PROG_ECHO_BACKSLASH])])
+m4_ifndef([_LT_AC_SHELL_INIT], [AC_DEFUN([_LT_AC_SHELL_INIT])])
+m4_ifndef([_LT_AC_SYS_LIBPATH_AIX], [AC_DEFUN([_LT_AC_SYS_LIBPATH_AIX])])
+m4_ifndef([_LT_PROG_LTMAIN], [AC_DEFUN([_LT_PROG_LTMAIN])])
+m4_ifndef([_LT_AC_TAGVAR], [AC_DEFUN([_LT_AC_TAGVAR])])
+m4_ifndef([AC_LTDL_ENABLE_INSTALL], [AC_DEFUN([AC_LTDL_ENABLE_INSTALL])])
+m4_ifndef([AC_LTDL_PREOPEN], [AC_DEFUN([AC_LTDL_PREOPEN])])
+m4_ifndef([_LT_AC_SYS_COMPILER], [AC_DEFUN([_LT_AC_SYS_COMPILER])])
+m4_ifndef([_LT_AC_LOCK], [AC_DEFUN([_LT_AC_LOCK])])
+m4_ifndef([AC_LIBTOOL_SYS_OLD_ARCHIVE], [AC_DEFUN([AC_LIBTOOL_SYS_OLD_ARCHIVE])])
+m4_ifndef([_LT_AC_TRY_DLOPEN_SELF], [AC_DEFUN([_LT_AC_TRY_DLOPEN_SELF])])
+m4_ifndef([AC_LIBTOOL_PROG_CC_C_O], [AC_DEFUN([AC_LIBTOOL_PROG_CC_C_O])])
+m4_ifndef([AC_LIBTOOL_SYS_HARD_LINK_LOCKS], [AC_DEFUN([AC_LIBTOOL_SYS_HARD_LINK_LOCKS])])
+m4_ifndef([AC_LIBTOOL_OBJDIR], [AC_DEFUN([AC_LIBTOOL_OBJDIR])])
+m4_ifndef([AC_LTDL_OBJDIR], [AC_DEFUN([AC_LTDL_OBJDIR])])
+m4_ifndef([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH], [AC_DEFUN([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH])])
+m4_ifndef([AC_LIBTOOL_SYS_LIB_STRIP], [AC_DEFUN([AC_LIBTOOL_SYS_LIB_STRIP])])
+m4_ifndef([AC_PATH_MAGIC], [AC_DEFUN([AC_PATH_MAGIC])])
+m4_ifndef([AC_PROG_LD_GNU], [AC_DEFUN([AC_PROG_LD_GNU])])
+m4_ifndef([AC_PROG_LD_RELOAD_FLAG], [AC_DEFUN([AC_PROG_LD_RELOAD_FLAG])])
+m4_ifndef([AC_DEPLIBS_CHECK_METHOD], [AC_DEFUN([AC_DEPLIBS_CHECK_METHOD])])
+m4_ifndef([AC_LIBTOOL_PROG_COMPILER_NO_RTTI], [AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_NO_RTTI])])
+m4_ifndef([AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE], [AC_DEFUN([AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE])])
+m4_ifndef([AC_LIBTOOL_PROG_COMPILER_PIC], [AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_PIC])])
+m4_ifndef([AC_LIBTOOL_PROG_LD_SHLIBS], [AC_DEFUN([AC_LIBTOOL_PROG_LD_SHLIBS])])
+m4_ifndef([AC_LIBTOOL_POSTDEP_PREDEP], [AC_DEFUN([AC_LIBTOOL_POSTDEP_PREDEP])])
+m4_ifndef([LT_AC_PROG_EGREP], [AC_DEFUN([LT_AC_PROG_EGREP])])
+m4_ifndef([LT_AC_PROG_SED], [AC_DEFUN([LT_AC_PROG_SED])])
+m4_ifndef([_LT_CC_BASENAME], [AC_DEFUN([_LT_CC_BASENAME])])
+m4_ifndef([_LT_COMPILER_BOILERPLATE], [AC_DEFUN([_LT_COMPILER_BOILERPLATE])])
+m4_ifndef([_LT_LINKER_BOILERPLATE], [AC_DEFUN([_LT_LINKER_BOILERPLATE])])
+m4_ifndef([_AC_PROG_LIBTOOL], [AC_DEFUN([_AC_PROG_LIBTOOL])])
+m4_ifndef([AC_LIBTOOL_SETUP], [AC_DEFUN([AC_LIBTOOL_SETUP])])
+m4_ifndef([_LT_AC_CHECK_DLFCN], [AC_DEFUN([_LT_AC_CHECK_DLFCN])])
+m4_ifndef([AC_LIBTOOL_SYS_DYNAMIC_LINKER], [AC_DEFUN([AC_LIBTOOL_SYS_DYNAMIC_LINKER])])
+m4_ifndef([_LT_AC_TAGCONFIG], [AC_DEFUN([_LT_AC_TAGCONFIG])])
+m4_ifndef([AC_DISABLE_FAST_INSTALL], [AC_DEFUN([AC_DISABLE_FAST_INSTALL])])
+m4_ifndef([_LT_AC_LANG_CXX], [AC_DEFUN([_LT_AC_LANG_CXX])])
+m4_ifndef([_LT_AC_LANG_F77], [AC_DEFUN([_LT_AC_LANG_F77])])
+m4_ifndef([_LT_AC_LANG_GCJ], [AC_DEFUN([_LT_AC_LANG_GCJ])])
+m4_ifndef([AC_LIBTOOL_RC], [AC_DEFUN([AC_LIBTOOL_RC])])
+m4_ifndef([AC_LIBTOOL_LANG_C_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_C_CONFIG])])
+m4_ifndef([_LT_AC_LANG_C_CONFIG], [AC_DEFUN([_LT_AC_LANG_C_CONFIG])])
+m4_ifndef([AC_LIBTOOL_LANG_CXX_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_CXX_CONFIG])])
+m4_ifndef([_LT_AC_LANG_CXX_CONFIG], [AC_DEFUN([_LT_AC_LANG_CXX_CONFIG])])
+m4_ifndef([AC_LIBTOOL_LANG_F77_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_F77_CONFIG])])
+m4_ifndef([_LT_AC_LANG_F77_CONFIG], [AC_DEFUN([_LT_AC_LANG_F77_CONFIG])])
+m4_ifndef([AC_LIBTOOL_LANG_GCJ_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_GCJ_CONFIG])])
+m4_ifndef([_LT_AC_LANG_GCJ_CONFIG], [AC_DEFUN([_LT_AC_LANG_GCJ_CONFIG])])
+m4_ifndef([AC_LIBTOOL_LANG_RC_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_RC_CONFIG])])
+m4_ifndef([_LT_AC_LANG_RC_CONFIG], [AC_DEFUN([_LT_AC_LANG_RC_CONFIG])])
+m4_ifndef([AC_LIBTOOL_CONFIG], [AC_DEFUN([AC_LIBTOOL_CONFIG])])
+m4_ifndef([_LT_AC_FILE_LTDLL_C], [AC_DEFUN([_LT_AC_FILE_LTDLL_C])])
+
+# Copyright (C) 2002, 2003, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_AUTOMAKE_VERSION(VERSION)
+# ----------------------------
+# Automake X.Y traces this macro to ensure aclocal.m4 has been
+# generated from the m4 files accompanying Automake X.Y.
+# (This private macro should not be called outside this file.)
+AC_DEFUN([AM_AUTOMAKE_VERSION],
+[am__api_version='1.11'
+dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
+dnl require some minimum version. Point them to the right macro.
+m4_if([$1], [1.11.1], [],
+ [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
+])
+
+# _AM_AUTOCONF_VERSION(VERSION)
+# -----------------------------
+# aclocal traces this macro to find the Autoconf version.
+# This is a private macro too. Using m4_define simplifies
+# the logic in aclocal, which can simply ignore this definition.
+m4_define([_AM_AUTOCONF_VERSION], [])
+
+# AM_SET_CURRENT_AUTOMAKE_VERSION
+# -------------------------------
+# Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
+# This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
+AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
+[AM_AUTOMAKE_VERSION([1.11.1])dnl
+m4_ifndef([AC_AUTOCONF_VERSION],
+ [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
+_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
+
+# AM_AUX_DIR_EXPAND -*- Autoconf -*-
+
+# Copyright (C) 2001, 2003, 2005 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# For projects using AC_CONFIG_AUX_DIR([foo]), Autoconf sets
+# $ac_aux_dir to `$srcdir/foo'. In other projects, it is set to
+# `$srcdir', `$srcdir/..', or `$srcdir/../..'.
+#
+# Of course, Automake must honor this variable whenever it calls a
+# tool from the auxiliary directory. The problem is that $srcdir (and
+# therefore $ac_aux_dir as well) can be either absolute or relative,
+# depending on how configure is run. This is pretty annoying, since
+# it makes $ac_aux_dir quite unusable in subdirectories: in the top
+# source directory, any form will work fine, but in subdirectories a
+# relative path needs to be adjusted first.
+#
+# $ac_aux_dir/missing
+# fails when called from a subdirectory if $ac_aux_dir is relative
+# $top_srcdir/$ac_aux_dir/missing
+# fails if $ac_aux_dir is absolute,
+# fails when called from a subdirectory in a VPATH build with
+# a relative $ac_aux_dir
+#
+# The reason of the latter failure is that $top_srcdir and $ac_aux_dir
+# are both prefixed by $srcdir. In an in-source build this is usually
+# harmless because $srcdir is `.', but things will broke when you
+# start a VPATH build or use an absolute $srcdir.
+#
+# So we could use something similar to $top_srcdir/$ac_aux_dir/missing,
+# iff we strip the leading $srcdir from $ac_aux_dir. That would be:
+# am_aux_dir='\$(top_srcdir)/'`expr "$ac_aux_dir" : "$srcdir//*\(.*\)"`
+# and then we would define $MISSING as
+# MISSING="\${SHELL} $am_aux_dir/missing"
+# This will work as long as MISSING is not called from configure, because
+# unfortunately $(top_srcdir) has no meaning in configure.
+# However there are other variables, like CC, which are often used in
+# configure, and could therefore not use this "fixed" $ac_aux_dir.
+#
+# Another solution, used here, is to always expand $ac_aux_dir to an
+# absolute PATH. The drawback is that using absolute paths prevent a
+# configured tree to be moved without reconfiguration.
+
+AC_DEFUN([AM_AUX_DIR_EXPAND],
+[dnl Rely on autoconf to set up CDPATH properly.
+AC_PREREQ([2.50])dnl
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
+])
+
+# AM_CONDITIONAL -*- Autoconf -*-
+
+# Copyright (C) 1997, 2000, 2001, 2003, 2004, 2005, 2006, 2008
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 9
+
+# AM_CONDITIONAL(NAME, SHELL-CONDITION)
+# -------------------------------------
+# Define a conditional.
+AC_DEFUN([AM_CONDITIONAL],
+[AC_PREREQ(2.52)dnl
+ ifelse([$1], [TRUE], [AC_FATAL([$0: invalid condition: $1])],
+ [$1], [FALSE], [AC_FATAL([$0: invalid condition: $1])])dnl
+AC_SUBST([$1_TRUE])dnl
+AC_SUBST([$1_FALSE])dnl
+_AM_SUBST_NOTMAKE([$1_TRUE])dnl
+_AM_SUBST_NOTMAKE([$1_FALSE])dnl
+m4_define([_AM_COND_VALUE_$1], [$2])dnl
+if $2; then
+ $1_TRUE=
+ $1_FALSE='#'
+else
+ $1_TRUE='#'
+ $1_FALSE=
+fi
+AC_CONFIG_COMMANDS_PRE(
+[if test -z "${$1_TRUE}" && test -z "${$1_FALSE}"; then
+ AC_MSG_ERROR([[conditional "$1" was never defined.
+Usually this means the macro was only invoked conditionally.]])
+fi])])
+
+# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2009
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 10
+
+# There are a few dirty hacks below to avoid letting `AC_PROG_CC' be
+# written in clear, in which case automake, when reading aclocal.m4,
+# will think it sees a *use*, and therefore will trigger all it's
+# C support machinery. Also note that it means that autoscan, seeing
+# CC etc. in the Makefile, will ask for an AC_PROG_CC use...
+
+
+# _AM_DEPENDENCIES(NAME)
+# ----------------------
+# See how the compiler implements dependency checking.
+# NAME is "CC", "CXX", "GCJ", or "OBJC".
+# We try a few techniques and use that to set a single cache variable.
+#
+# We don't AC_REQUIRE the corresponding AC_PROG_CC since the latter was
+# modified to invoke _AM_DEPENDENCIES(CC); we would have a circular
+# dependency, and given that the user is not expected to run this macro,
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+ # side effect of compilation, but ICC will put the dependencies in
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+ if test "$am_compiler_list" = ""; then
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+ for depmode in $am_compiler_list; do
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+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
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+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
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+ continue
+ else
+ break
+ fi
+ ;;
+ msvisualcpp | msvcmsys)
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+ # so weak that their functioning should not be impacted.
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+ am__minus_obj=
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+ none) break ;;
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+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
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+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
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+ # The diagnosis changed in icc 8.0:
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+])
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+AM_CONDITIONAL([am__fastdep$1], [
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+# Generate code to set up dependency tracking. -*- Autoconf -*-
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+# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2008
+# Free Software Foundation, Inc.
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+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
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+}
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+
+# AM_OUTPUT_DEPENDENCY_COMMANDS
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+# Do all the work for Automake. -*- Autoconf -*-
+
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
+# 2005, 2006, 2008, 2009 Free Software Foundation, Inc.
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+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
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+# This macro actually does too much. Some checks are only needed if
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+# Copyright (C) 2001, 2003, 2005, 2008 Free Software Foundation, Inc.
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+# AM_PROG_INSTALL_SH
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+# Copyright (C) 2003, 2005 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
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+# with or without modifications, as long as this notice is preserved.
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+# Check to see how 'make' treats includes. -*- Autoconf -*-
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+# Copyright (C) 2001, 2002, 2003, 2005, 2009 Free Software Foundation, Inc.
+#
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+# with or without modifications, as long as this notice is preserved.
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+# serial 4
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+# AM_MAKE_INCLUDE()
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+# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
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+# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2004, 2005, 2008
+# Free Software Foundation, Inc.
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+# gives unlimited permission to copy and/or distribute it,
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+# Helper functions for option handling. -*- Autoconf -*-
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+# Copyright (C) 2001, 2002, 2003, 2005, 2008 Free Software Foundation, Inc.
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+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 2
+
+# _AM_SUBST_NOTMAKE(VARIABLE)
+# ---------------------------
+# Prevent Automake from outputting VARIABLE = @VARIABLE@ in Makefile.in.
+# This macro is traced by Automake.
+AC_DEFUN([_AM_SUBST_NOTMAKE])
+
+# AM_SUBST_NOTMAKE(VARIABLE)
+# ---------------------------
+# Public sister of _AM_SUBST_NOTMAKE.
+AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
+
+# Check how to create a tarball. -*- Autoconf -*-
+
+# Copyright (C) 2004, 2005 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 2
+
+# _AM_PROG_TAR(FORMAT)
+# --------------------
+# Check how to create a tarball in format FORMAT.
+# FORMAT should be one of `v7', `ustar', or `pax'.
+#
+# Substitute a variable $(am__tar) that is a command
+# writing to stdout a FORMAT-tarball containing the directory
+# $tardir.
+# tardir=directory && $(am__tar) > result.tar
+#
+# Substitute a variable $(am__untar) that extract such
+# a tarball read from stdin.
+# $(am__untar) < result.tar
+AC_DEFUN([_AM_PROG_TAR],
+[# Always define AMTAR for backward compatibility.
+AM_MISSING_PROG([AMTAR], [tar])
+m4_if([$1], [v7],
+ [am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'],
+ [m4_case([$1], [ustar],, [pax],,
+ [m4_fatal([Unknown tar format])])
+AC_MSG_CHECKING([how to create a $1 tar archive])
+# Loop over all known methods to create a tar archive until one works.
+_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
+_am_tools=${am_cv_prog_tar_$1-$_am_tools}
+# Do not fold the above two line into one, because Tru64 sh and
+# Solaris sh will not grok spaces in the rhs of `-'.
+for _am_tool in $_am_tools
+do
+ case $_am_tool in
+ gnutar)
+ for _am_tar in tar gnutar gtar;
+ do
+ AM_RUN_LOG([$_am_tar --version]) && break
+ done
+ am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
+ am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
+ am__untar="$_am_tar -xf -"
+ ;;
+ plaintar)
+ # Must skip GNU tar: if it does not support --format= it doesn't create
+ # ustar tarball either.
+ (tar --version) >/dev/null 2>&1 && continue
+ am__tar='tar chf - "$$tardir"'
+ am__tar_='tar chf - "$tardir"'
+ am__untar='tar xf -'
+ ;;
+ pax)
+ am__tar='pax -L -x $1 -w "$$tardir"'
+ am__tar_='pax -L -x $1 -w "$tardir"'
+ am__untar='pax -r'
+ ;;
+ cpio)
+ am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
+ am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
+ am__untar='cpio -i -H $1 -d'
+ ;;
+ none)
+ am__tar=false
+ am__tar_=false
+ am__untar=false
+ ;;
+ esac
+
+ # If the value was cached, stop now. We just wanted to have am__tar
+ # and am__untar set.
+ test -n "${am_cv_prog_tar_$1}" && break
+
+ # tar/untar a dummy directory, and stop if the command works
+ rm -rf conftest.dir
+ mkdir conftest.dir
+ echo GrepMe > conftest.dir/file
+ AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
+ rm -rf conftest.dir
+ if test -s conftest.tar; then
+ AM_RUN_LOG([$am__untar <conftest.tar])
+ grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
+ fi
+done
+rm -rf conftest.dir
+
+AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
+AC_MSG_RESULT([$am_cv_prog_tar_$1])])
+AC_SUBST([am__tar])
+AC_SUBST([am__untar])
+]) # _AM_PROG_TAR
+
+m4_include([acinclude.m4])
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/config.guess b/src/libGkArrays/src/libProgressBar-1.2.0/config.guess
new file mode 100755
index 0000000..40eaed4
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/config.guess
@@ -0,0 +1,1517 @@
+#! /bin/sh
+# Attempt to guess a canonical system name.
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
+# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,
+# 2011 Free Software Foundation, Inc.
+
+timestamp='2011-05-11'
+
+# This file is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
+# 02110-1301, USA.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+
+# Originally written by Per Bothner. Please send patches (context
+# diff format) to <config-patches at gnu.org> and include a ChangeLog
+# entry.
+#
+# This script attempts to guess a canonical system name similar to
+# config.sub. If it succeeds, it prints the system name on stdout, and
+# exits with 0. Otherwise, it exits with 1.
+#
+# You can get the latest version of this script from:
+# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
+
+me=`echo "$0" | sed -e 's,.*/,,'`
+
+usage="\
+Usage: $0 [OPTION]
+
+Output the configuration name of the system \`$me' is run on.
+
+Operation modes:
+ -h, --help print this help, then exit
+ -t, --time-stamp print date of last modification, then exit
+ -v, --version print version number, then exit
+
+Report bugs and patches to <config-patches at gnu.org>."
+
+version="\
+GNU config.guess ($timestamp)
+
+Originally written by Per Bothner.
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000,
+2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free
+Software Foundation, Inc.
+
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+
+help="
+Try \`$me --help' for more information."
+
+# Parse command line
+while test $# -gt 0 ; do
+ case $1 in
+ --time-stamp | --time* | -t )
+ echo "$timestamp" ; exit ;;
+ --version | -v )
+ echo "$version" ; exit ;;
+ --help | --h* | -h )
+ echo "$usage"; exit ;;
+ -- ) # Stop option processing
+ shift; break ;;
+ - ) # Use stdin as input.
+ break ;;
+ -* )
+ echo "$me: invalid option $1$help" >&2
+ exit 1 ;;
+ * )
+ break ;;
+ esac
+done
+
+if test $# != 0; then
+ echo "$me: too many arguments$help" >&2
+ exit 1
+fi
+
+trap 'exit 1' 1 2 15
+
+# CC_FOR_BUILD -- compiler used by this script. Note that the use of a
+# compiler to aid in system detection is discouraged as it requires
+# temporary files to be created and, as you can see below, it is a
+# headache to deal with in a portable fashion.
+
+# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still
+# use `HOST_CC' if defined, but it is deprecated.
+
+# Portable tmp directory creation inspired by the Autoconf team.
+
+set_cc_for_build='
+trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ;
+trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ;
+: ${TMPDIR=/tmp} ;
+ { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
+ { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||
+ { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } ||
+ { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ;
+dummy=$tmp/dummy ;
+tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ;
+case $CC_FOR_BUILD,$HOST_CC,$CC in
+ ,,) echo "int x;" > $dummy.c ;
+ for c in cc gcc c89 c99 ; do
+ if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then
+ CC_FOR_BUILD="$c"; break ;
+ fi ;
+ done ;
+ if test x"$CC_FOR_BUILD" = x ; then
+ CC_FOR_BUILD=no_compiler_found ;
+ fi
+ ;;
+ ,,*) CC_FOR_BUILD=$CC ;;
+ ,*,*) CC_FOR_BUILD=$HOST_CC ;;
+esac ; set_cc_for_build= ;'
+
+# This is needed to find uname on a Pyramid OSx when run in the BSD universe.
+# (ghazi at noc.rutgers.edu 1994-08-24)
+if (test -f /.attbin/uname) >/dev/null 2>&1 ; then
+ PATH=$PATH:/.attbin ; export PATH
+fi
+
+UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown
+UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
+UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown
+UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
+
+# Note: order is significant - the case branches are not exclusive.
+
+case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
+ *:NetBSD:*:*)
+ # NetBSD (nbsd) targets should (where applicable) match one or
+ # more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*,
+ # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently
+ # switched to ELF, *-*-netbsd* would select the old
+ # object file format. This provides both forward
+ # compatibility and a consistent mechanism for selecting the
+ # object file format.
+ #
+ # Note: NetBSD doesn't particularly care about the vendor
+ # portion of the name. We always set it to "unknown".
+ sysctl="sysctl -n hw.machine_arch"
+ UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \
+ /usr/sbin/$sysctl 2>/dev/null || echo unknown)`
+ case "${UNAME_MACHINE_ARCH}" in
+ armeb) machine=armeb-unknown ;;
+ arm*) machine=arm-unknown ;;
+ sh3el) machine=shl-unknown ;;
+ sh3eb) machine=sh-unknown ;;
+ sh5el) machine=sh5le-unknown ;;
+ *) machine=${UNAME_MACHINE_ARCH}-unknown ;;
+ esac
+ # The Operating System including object format, if it has switched
+ # to ELF recently, or will in the future.
+ case "${UNAME_MACHINE_ARCH}" in
+ arm*|i386|m68k|ns32k|sh3*|sparc|vax)
+ eval $set_cc_for_build
+ if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep -q __ELF__
+ then
+ # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout).
+ # Return netbsd for either. FIX?
+ os=netbsd
+ else
+ os=netbsdelf
+ fi
+ ;;
+ *)
+ os=netbsd
+ ;;
+ esac
+ # The OS release
+ # Debian GNU/NetBSD machines have a different userland, and
+ # thus, need a distinct triplet. However, they do not need
+ # kernel version information, so it can be replaced with a
+ # suitable tag, in the style of linux-gnu.
+ case "${UNAME_VERSION}" in
+ Debian*)
+ release='-gnu'
+ ;;
+ *)
+ release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'`
+ ;;
+ esac
+ # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM:
+ # contains redundant information, the shorter form:
+ # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used.
+ echo "${machine}-${os}${release}"
+ exit ;;
+ *:OpenBSD:*:*)
+ UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'`
+ echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE}
+ exit ;;
+ *:ekkoBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE}
+ exit ;;
+ *:SolidBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-solidbsd${UNAME_RELEASE}
+ exit ;;
+ macppc:MirBSD:*:*)
+ echo powerpc-unknown-mirbsd${UNAME_RELEASE}
+ exit ;;
+ *:MirBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE}
+ exit ;;
+ alpha:OSF1:*:*)
+ case $UNAME_RELEASE in
+ *4.0)
+ UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
+ ;;
+ *5.*)
+ UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
+ ;;
+ esac
+ # According to Compaq, /usr/sbin/psrinfo has been available on
+ # OSF/1 and Tru64 systems produced since 1995. I hope that
+ # covers most systems running today. This code pipes the CPU
+ # types through head -n 1, so we only detect the type of CPU 0.
+ ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
+ case "$ALPHA_CPU_TYPE" in
+ "EV4 (21064)")
+ UNAME_MACHINE="alpha" ;;
+ "EV4.5 (21064)")
+ UNAME_MACHINE="alpha" ;;
+ "LCA4 (21066/21068)")
+ UNAME_MACHINE="alpha" ;;
+ "EV5 (21164)")
+ UNAME_MACHINE="alphaev5" ;;
+ "EV5.6 (21164A)")
+ UNAME_MACHINE="alphaev56" ;;
+ "EV5.6 (21164PC)")
+ UNAME_MACHINE="alphapca56" ;;
+ "EV5.7 (21164PC)")
+ UNAME_MACHINE="alphapca57" ;;
+ "EV6 (21264)")
+ UNAME_MACHINE="alphaev6" ;;
+ "EV6.7 (21264A)")
+ UNAME_MACHINE="alphaev67" ;;
+ "EV6.8CB (21264C)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.8AL (21264B)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.8CX (21264D)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.9A (21264/EV69A)")
+ UNAME_MACHINE="alphaev69" ;;
+ "EV7 (21364)")
+ UNAME_MACHINE="alphaev7" ;;
+ "EV7.9 (21364A)")
+ UNAME_MACHINE="alphaev79" ;;
+ esac
+ # A Pn.n version is a patched version.
+ # A Vn.n version is a released version.
+ # A Tn.n version is a released field test version.
+ # A Xn.n version is an unreleased experimental baselevel.
+ # 1.2 uses "1.2" for uname -r.
+ echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
+ # Reset EXIT trap before exiting to avoid spurious non-zero exit code.
+ exitcode=$?
+ trap '' 0
+ exit $exitcode ;;
+ Alpha\ *:Windows_NT*:*)
+ # How do we know it's Interix rather than the generic POSIX subsystem?
+ # Should we change UNAME_MACHINE based on the output of uname instead
+ # of the specific Alpha model?
+ echo alpha-pc-interix
+ exit ;;
+ 21064:Windows_NT:50:3)
+ echo alpha-dec-winnt3.5
+ exit ;;
+ Amiga*:UNIX_System_V:4.0:*)
+ echo m68k-unknown-sysv4
+ exit ;;
+ *:[Aa]miga[Oo][Ss]:*:*)
+ echo ${UNAME_MACHINE}-unknown-amigaos
+ exit ;;
+ *:[Mm]orph[Oo][Ss]:*:*)
+ echo ${UNAME_MACHINE}-unknown-morphos
+ exit ;;
+ *:OS/390:*:*)
+ echo i370-ibm-openedition
+ exit ;;
+ *:z/VM:*:*)
+ echo s390-ibm-zvmoe
+ exit ;;
+ *:OS400:*:*)
+ echo powerpc-ibm-os400
+ exit ;;
+ arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
+ echo arm-acorn-riscix${UNAME_RELEASE}
+ exit ;;
+ arm:riscos:*:*|arm:RISCOS:*:*)
+ echo arm-unknown-riscos
+ exit ;;
+ SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*)
+ echo hppa1.1-hitachi-hiuxmpp
+ exit ;;
+ Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*)
+ # akee at wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE.
+ if test "`(/bin/universe) 2>/dev/null`" = att ; then
+ echo pyramid-pyramid-sysv3
+ else
+ echo pyramid-pyramid-bsd
+ fi
+ exit ;;
+ NILE*:*:*:dcosx)
+ echo pyramid-pyramid-svr4
+ exit ;;
+ DRS?6000:unix:4.0:6*)
+ echo sparc-icl-nx6
+ exit ;;
+ DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*)
+ case `/usr/bin/uname -p` in
+ sparc) echo sparc-icl-nx7; exit ;;
+ esac ;;
+ s390x:SunOS:*:*)
+ echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4H:SunOS:5.*:*)
+ echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
+ echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*)
+ echo i386-pc-auroraux${UNAME_RELEASE}
+ exit ;;
+ i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*)
+ eval $set_cc_for_build
+ SUN_ARCH="i386"
+ # If there is a compiler, see if it is configured for 64-bit objects.
+ # Note that the Sun cc does not turn __LP64__ into 1 like gcc does.
+ # This test works for both compilers.
+ if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
+ if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \
+ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_64BIT_ARCH >/dev/null
+ then
+ SUN_ARCH="x86_64"
+ fi
+ fi
+ echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4*:SunOS:6*:*)
+ # According to config.sub, this is the proper way to canonicalize
+ # SunOS6. Hard to guess exactly what SunOS6 will be like, but
+ # it's likely to be more like Solaris than SunOS4.
+ echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4*:SunOS:*:*)
+ case "`/usr/bin/arch -k`" in
+ Series*|S4*)
+ UNAME_RELEASE=`uname -v`
+ ;;
+ esac
+ # Japanese Language versions have a version number like `4.1.3-JL'.
+ echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'`
+ exit ;;
+ sun3*:SunOS:*:*)
+ echo m68k-sun-sunos${UNAME_RELEASE}
+ exit ;;
+ sun*:*:4.2BSD:*)
+ UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
+ test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3
+ case "`/bin/arch`" in
+ sun3)
+ echo m68k-sun-sunos${UNAME_RELEASE}
+ ;;
+ sun4)
+ echo sparc-sun-sunos${UNAME_RELEASE}
+ ;;
+ esac
+ exit ;;
+ aushp:SunOS:*:*)
+ echo sparc-auspex-sunos${UNAME_RELEASE}
+ exit ;;
+ # The situation for MiNT is a little confusing. The machine name
+ # can be virtually everything (everything which is not
+ # "atarist" or "atariste" at least should have a processor
+ # > m68000). The system name ranges from "MiNT" over "FreeMiNT"
+ # to the lowercase version "mint" (or "freemint"). Finally
+ # the system name "TOS" denotes a system which is actually not
+ # MiNT. But MiNT is downward compatible to TOS, so this should
+ # be no problem.
+ atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit ;;
+ atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit ;;
+ *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit ;;
+ milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
+ echo m68k-milan-mint${UNAME_RELEASE}
+ exit ;;
+ hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
+ echo m68k-hades-mint${UNAME_RELEASE}
+ exit ;;
+ *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
+ echo m68k-unknown-mint${UNAME_RELEASE}
+ exit ;;
+ m68k:machten:*:*)
+ echo m68k-apple-machten${UNAME_RELEASE}
+ exit ;;
+ powerpc:machten:*:*)
+ echo powerpc-apple-machten${UNAME_RELEASE}
+ exit ;;
+ RISC*:Mach:*:*)
+ echo mips-dec-mach_bsd4.3
+ exit ;;
+ RISC*:ULTRIX:*:*)
+ echo mips-dec-ultrix${UNAME_RELEASE}
+ exit ;;
+ VAX*:ULTRIX*:*:*)
+ echo vax-dec-ultrix${UNAME_RELEASE}
+ exit ;;
+ 2020:CLIX:*:* | 2430:CLIX:*:*)
+ echo clipper-intergraph-clix${UNAME_RELEASE}
+ exit ;;
+ mips:*:*:UMIPS | mips:*:*:RISCos)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+#ifdef __cplusplus
+#include <stdio.h> /* for printf() prototype */
+ int main (int argc, char *argv[]) {
+#else
+ int main (argc, argv) int argc; char *argv[]; {
+#endif
+ #if defined (host_mips) && defined (MIPSEB)
+ #if defined (SYSTYPE_SYSV)
+ printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0);
+ #endif
+ #if defined (SYSTYPE_SVR4)
+ printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0);
+ #endif
+ #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD)
+ printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0);
+ #endif
+ #endif
+ exit (-1);
+ }
+EOF
+ $CC_FOR_BUILD -o $dummy $dummy.c &&
+ dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` &&
+ SYSTEM_NAME=`$dummy $dummyarg` &&
+ { echo "$SYSTEM_NAME"; exit; }
+ echo mips-mips-riscos${UNAME_RELEASE}
+ exit ;;
+ Motorola:PowerMAX_OS:*:*)
+ echo powerpc-motorola-powermax
+ exit ;;
+ Motorola:*:4.3:PL8-*)
+ echo powerpc-harris-powermax
+ exit ;;
+ Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*)
+ echo powerpc-harris-powermax
+ exit ;;
+ Night_Hawk:Power_UNIX:*:*)
+ echo powerpc-harris-powerunix
+ exit ;;
+ m88k:CX/UX:7*:*)
+ echo m88k-harris-cxux7
+ exit ;;
+ m88k:*:4*:R4*)
+ echo m88k-motorola-sysv4
+ exit ;;
+ m88k:*:3*:R3*)
+ echo m88k-motorola-sysv3
+ exit ;;
+ AViiON:dgux:*:*)
+ # DG/UX returns AViiON for all architectures
+ UNAME_PROCESSOR=`/usr/bin/uname -p`
+ if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ]
+ then
+ if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \
+ [ ${TARGET_BINARY_INTERFACE}x = x ]
+ then
+ echo m88k-dg-dgux${UNAME_RELEASE}
+ else
+ echo m88k-dg-dguxbcs${UNAME_RELEASE}
+ fi
+ else
+ echo i586-dg-dgux${UNAME_RELEASE}
+ fi
+ exit ;;
+ M88*:DolphinOS:*:*) # DolphinOS (SVR3)
+ echo m88k-dolphin-sysv3
+ exit ;;
+ M88*:*:R3*:*)
+ # Delta 88k system running SVR3
+ echo m88k-motorola-sysv3
+ exit ;;
+ XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3)
+ echo m88k-tektronix-sysv3
+ exit ;;
+ Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD)
+ echo m68k-tektronix-bsd
+ exit ;;
+ *:IRIX*:*:*)
+ echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'`
+ exit ;;
+ ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX.
+ echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id
+ exit ;; # Note that: echo "'`uname -s`'" gives 'AIX '
+ i*86:AIX:*:*)
+ echo i386-ibm-aix
+ exit ;;
+ ia64:AIX:*:*)
+ if [ -x /usr/bin/oslevel ] ; then
+ IBM_REV=`/usr/bin/oslevel`
+ else
+ IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
+ fi
+ echo ${UNAME_MACHINE}-ibm-aix${IBM_REV}
+ exit ;;
+ *:AIX:2:3)
+ if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #include <sys/systemcfg.h>
+
+ main()
+ {
+ if (!__power_pc())
+ exit(1);
+ puts("powerpc-ibm-aix3.2.5");
+ exit(0);
+ }
+EOF
+ if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy`
+ then
+ echo "$SYSTEM_NAME"
+ else
+ echo rs6000-ibm-aix3.2.5
+ fi
+ elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then
+ echo rs6000-ibm-aix3.2.4
+ else
+ echo rs6000-ibm-aix3.2
+ fi
+ exit ;;
+ *:AIX:*:[4567])
+ IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
+ if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
+ IBM_ARCH=rs6000
+ else
+ IBM_ARCH=powerpc
+ fi
+ if [ -x /usr/bin/oslevel ] ; then
+ IBM_REV=`/usr/bin/oslevel`
+ else
+ IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
+ fi
+ echo ${IBM_ARCH}-ibm-aix${IBM_REV}
+ exit ;;
+ *:AIX:*:*)
+ echo rs6000-ibm-aix
+ exit ;;
+ ibmrt:4.4BSD:*|romp-ibm:BSD:*)
+ echo romp-ibm-bsd4.4
+ exit ;;
+ ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and
+ echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to
+ exit ;; # report: romp-ibm BSD 4.3
+ *:BOSX:*:*)
+ echo rs6000-bull-bosx
+ exit ;;
+ DPX/2?00:B.O.S.:*:*)
+ echo m68k-bull-sysv3
+ exit ;;
+ 9000/[34]??:4.3bsd:1.*:*)
+ echo m68k-hp-bsd
+ exit ;;
+ hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*)
+ echo m68k-hp-bsd4.4
+ exit ;;
+ 9000/[34678]??:HP-UX:*:*)
+ HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
+ case "${UNAME_MACHINE}" in
+ 9000/31? ) HP_ARCH=m68000 ;;
+ 9000/[34]?? ) HP_ARCH=m68k ;;
+ 9000/[678][0-9][0-9])
+ if [ -x /usr/bin/getconf ]; then
+ sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
+ sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
+ case "${sc_cpu_version}" in
+ 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
+ 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
+ 532) # CPU_PA_RISC2_0
+ case "${sc_kernel_bits}" in
+ 32) HP_ARCH="hppa2.0n" ;;
+ 64) HP_ARCH="hppa2.0w" ;;
+ '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20
+ esac ;;
+ esac
+ fi
+ if [ "${HP_ARCH}" = "" ]; then
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+
+ #define _HPUX_SOURCE
+ #include <stdlib.h>
+ #include <unistd.h>
+
+ int main ()
+ {
+ #if defined(_SC_KERNEL_BITS)
+ long bits = sysconf(_SC_KERNEL_BITS);
+ #endif
+ long cpu = sysconf (_SC_CPU_VERSION);
+
+ switch (cpu)
+ {
+ case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
+ case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
+ case CPU_PA_RISC2_0:
+ #if defined(_SC_KERNEL_BITS)
+ switch (bits)
+ {
+ case 64: puts ("hppa2.0w"); break;
+ case 32: puts ("hppa2.0n"); break;
+ default: puts ("hppa2.0"); break;
+ } break;
+ #else /* !defined(_SC_KERNEL_BITS) */
+ puts ("hppa2.0"); break;
+ #endif
+ default: puts ("hppa1.0"); break;
+ }
+ exit (0);
+ }
+EOF
+ (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
+ test -z "$HP_ARCH" && HP_ARCH=hppa
+ fi ;;
+ esac
+ if [ ${HP_ARCH} = "hppa2.0w" ]
+ then
+ eval $set_cc_for_build
+
+ # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating
+ # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler
+ # generating 64-bit code. GNU and HP use different nomenclature:
+ #
+ # $ CC_FOR_BUILD=cc ./config.guess
+ # => hppa2.0w-hp-hpux11.23
+ # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess
+ # => hppa64-hp-hpux11.23
+
+ if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) |
+ grep -q __LP64__
+ then
+ HP_ARCH="hppa2.0w"
+ else
+ HP_ARCH="hppa64"
+ fi
+ fi
+ echo ${HP_ARCH}-hp-hpux${HPUX_REV}
+ exit ;;
+ ia64:HP-UX:*:*)
+ HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
+ echo ia64-hp-hpux${HPUX_REV}
+ exit ;;
+ 3050*:HI-UX:*:*)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #include <unistd.h>
+ int
+ main ()
+ {
+ long cpu = sysconf (_SC_CPU_VERSION);
+ /* The order matters, because CPU_IS_HP_MC68K erroneously returns
+ true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct
+ results, however. */
+ if (CPU_IS_PA_RISC (cpu))
+ {
+ switch (cpu)
+ {
+ case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break;
+ case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break;
+ case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break;
+ default: puts ("hppa-hitachi-hiuxwe2"); break;
+ }
+ }
+ else if (CPU_IS_HP_MC68K (cpu))
+ puts ("m68k-hitachi-hiuxwe2");
+ else puts ("unknown-hitachi-hiuxwe2");
+ exit (0);
+ }
+EOF
+ $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` &&
+ { echo "$SYSTEM_NAME"; exit; }
+ echo unknown-hitachi-hiuxwe2
+ exit ;;
+ 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* )
+ echo hppa1.1-hp-bsd
+ exit ;;
+ 9000/8??:4.3bsd:*:*)
+ echo hppa1.0-hp-bsd
+ exit ;;
+ *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*)
+ echo hppa1.0-hp-mpeix
+ exit ;;
+ hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* )
+ echo hppa1.1-hp-osf
+ exit ;;
+ hp8??:OSF1:*:*)
+ echo hppa1.0-hp-osf
+ exit ;;
+ i*86:OSF1:*:*)
+ if [ -x /usr/sbin/sysversion ] ; then
+ echo ${UNAME_MACHINE}-unknown-osf1mk
+ else
+ echo ${UNAME_MACHINE}-unknown-osf1
+ fi
+ exit ;;
+ parisc*:Lites*:*:*)
+ echo hppa1.1-hp-lites
+ exit ;;
+ C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*)
+ echo c1-convex-bsd
+ exit ;;
+ C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*)
+ if getsysinfo -f scalar_acc
+ then echo c32-convex-bsd
+ else echo c2-convex-bsd
+ fi
+ exit ;;
+ C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*)
+ echo c34-convex-bsd
+ exit ;;
+ C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*)
+ echo c38-convex-bsd
+ exit ;;
+ C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*)
+ echo c4-convex-bsd
+ exit ;;
+ CRAY*Y-MP:*:*:*)
+ echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*[A-Z]90:*:*:*)
+ echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \
+ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \
+ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \
+ -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*TS:*:*:*)
+ echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*T3E:*:*:*)
+ echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*SV1:*:*:*)
+ echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ *:UNICOS/mp:*:*)
+ echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
+ FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
+ FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
+ echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+ exit ;;
+ 5000:UNIX_System_V:4.*:*)
+ FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
+ echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+ exit ;;
+ i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
+ echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE}
+ exit ;;
+ sparc*:BSD/OS:*:*)
+ echo sparc-unknown-bsdi${UNAME_RELEASE}
+ exit ;;
+ *:BSD/OS:*:*)
+ echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE}
+ exit ;;
+ *:FreeBSD:*:*)
+ case ${UNAME_MACHINE} in
+ pc98)
+ echo i386-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+ amd64)
+ echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+ *)
+ echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+ esac
+ exit ;;
+ i*:CYGWIN*:*)
+ echo ${UNAME_MACHINE}-pc-cygwin
+ exit ;;
+ *:MINGW*:*)
+ echo ${UNAME_MACHINE}-pc-mingw32
+ exit ;;
+ i*:windows32*:*)
+ # uname -m includes "-pc" on this system.
+ echo ${UNAME_MACHINE}-mingw32
+ exit ;;
+ i*:PW*:*)
+ echo ${UNAME_MACHINE}-pc-pw32
+ exit ;;
+ *:Interix*:*)
+ case ${UNAME_MACHINE} in
+ x86)
+ echo i586-pc-interix${UNAME_RELEASE}
+ exit ;;
+ authenticamd | genuineintel | EM64T)
+ echo x86_64-unknown-interix${UNAME_RELEASE}
+ exit ;;
+ IA64)
+ echo ia64-unknown-interix${UNAME_RELEASE}
+ exit ;;
+ esac ;;
+ [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*)
+ echo i${UNAME_MACHINE}-pc-mks
+ exit ;;
+ 8664:Windows_NT:*)
+ echo x86_64-pc-mks
+ exit ;;
+ i*:Windows_NT*:* | Pentium*:Windows_NT*:*)
+ # How do we know it's Interix rather than the generic POSIX subsystem?
+ # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we
+ # UNAME_MACHINE based on the output of uname instead of i386?
+ echo i586-pc-interix
+ exit ;;
+ i*:UWIN*:*)
+ echo ${UNAME_MACHINE}-pc-uwin
+ exit ;;
+ amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*)
+ echo x86_64-unknown-cygwin
+ exit ;;
+ p*:CYGWIN*:*)
+ echo powerpcle-unknown-cygwin
+ exit ;;
+ prep*:SunOS:5.*:*)
+ echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ *:GNU:*:*)
+ # the GNU system
+ echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
+ exit ;;
+ *:GNU/*:*:*)
+ # other systems with GNU libc and userland
+ echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu
+ exit ;;
+ i*86:Minix:*:*)
+ echo ${UNAME_MACHINE}-pc-minix
+ exit ;;
+ alpha:Linux:*:*)
+ case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
+ EV5) UNAME_MACHINE=alphaev5 ;;
+ EV56) UNAME_MACHINE=alphaev56 ;;
+ PCA56) UNAME_MACHINE=alphapca56 ;;
+ PCA57) UNAME_MACHINE=alphapca56 ;;
+ EV6) UNAME_MACHINE=alphaev6 ;;
+ EV67) UNAME_MACHINE=alphaev67 ;;
+ EV68*) UNAME_MACHINE=alphaev68 ;;
+ esac
+ objdump --private-headers /bin/sh | grep -q ld.so.1
+ if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi
+ echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC}
+ exit ;;
+ arm*:Linux:*:*)
+ eval $set_cc_for_build
+ if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep -q __ARM_EABI__
+ then
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ else
+ if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep -q __ARM_PCS_VFP
+ then
+ echo ${UNAME_MACHINE}-unknown-linux-gnueabi
+ else
+ echo ${UNAME_MACHINE}-unknown-linux-gnueabihf
+ fi
+ fi
+ exit ;;
+ avr32*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ cris:Linux:*:*)
+ echo cris-axis-linux-gnu
+ exit ;;
+ crisv32:Linux:*:*)
+ echo crisv32-axis-linux-gnu
+ exit ;;
+ frv:Linux:*:*)
+ echo frv-unknown-linux-gnu
+ exit ;;
+ i*86:Linux:*:*)
+ LIBC=gnu
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #ifdef __dietlibc__
+ LIBC=dietlibc
+ #endif
+EOF
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'`
+ echo "${UNAME_MACHINE}-pc-linux-${LIBC}"
+ exit ;;
+ ia64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ m32r*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ m68*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ mips:Linux:*:* | mips64:Linux:*:*)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #undef CPU
+ #undef ${UNAME_MACHINE}
+ #undef ${UNAME_MACHINE}el
+ #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
+ CPU=${UNAME_MACHINE}el
+ #else
+ #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
+ CPU=${UNAME_MACHINE}
+ #else
+ CPU=
+ #endif
+ #endif
+EOF
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'`
+ test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
+ ;;
+ or32:Linux:*:*)
+ echo or32-unknown-linux-gnu
+ exit ;;
+ padre:Linux:*:*)
+ echo sparc-unknown-linux-gnu
+ exit ;;
+ parisc64:Linux:*:* | hppa64:Linux:*:*)
+ echo hppa64-unknown-linux-gnu
+ exit ;;
+ parisc:Linux:*:* | hppa:Linux:*:*)
+ # Look for CPU level
+ case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
+ PA7*) echo hppa1.1-unknown-linux-gnu ;;
+ PA8*) echo hppa2.0-unknown-linux-gnu ;;
+ *) echo hppa-unknown-linux-gnu ;;
+ esac
+ exit ;;
+ ppc64:Linux:*:*)
+ echo powerpc64-unknown-linux-gnu
+ exit ;;
+ ppc:Linux:*:*)
+ echo powerpc-unknown-linux-gnu
+ exit ;;
+ s390:Linux:*:* | s390x:Linux:*:*)
+ echo ${UNAME_MACHINE}-ibm-linux
+ exit ;;
+ sh64*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ sh*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ sparc:Linux:*:* | sparc64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ tile*:Linux:*:*)
+ echo ${UNAME_MACHINE}-tilera-linux-gnu
+ exit ;;
+ vax:Linux:*:*)
+ echo ${UNAME_MACHINE}-dec-linux-gnu
+ exit ;;
+ x86_64:Linux:*:*)
+ echo x86_64-unknown-linux-gnu
+ exit ;;
+ xtensa*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ i*86:DYNIX/ptx:4*:*)
+ # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
+ # earlier versions are messed up and put the nodename in both
+ # sysname and nodename.
+ echo i386-sequent-sysv4
+ exit ;;
+ i*86:UNIX_SV:4.2MP:2.*)
+ # Unixware is an offshoot of SVR4, but it has its own version
+ # number series starting with 2...
+ # I am not positive that other SVR4 systems won't match this,
+ # I just have to hope. -- rms.
+ # Use sysv4.2uw... so that sysv4* matches it.
+ echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION}
+ exit ;;
+ i*86:OS/2:*:*)
+ # If we were able to find `uname', then EMX Unix compatibility
+ # is probably installed.
+ echo ${UNAME_MACHINE}-pc-os2-emx
+ exit ;;
+ i*86:XTS-300:*:STOP)
+ echo ${UNAME_MACHINE}-unknown-stop
+ exit ;;
+ i*86:atheos:*:*)
+ echo ${UNAME_MACHINE}-unknown-atheos
+ exit ;;
+ i*86:syllable:*:*)
+ echo ${UNAME_MACHINE}-pc-syllable
+ exit ;;
+ i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*)
+ echo i386-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ i*86:*DOS:*:*)
+ echo ${UNAME_MACHINE}-pc-msdosdjgpp
+ exit ;;
+ i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*)
+ UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'`
+ if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
+ echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL}
+ else
+ echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL}
+ fi
+ exit ;;
+ i*86:*:5:[678]*)
+ # UnixWare 7.x, OpenUNIX and OpenServer 6.
+ case `/bin/uname -X | grep "^Machine"` in
+ *486*) UNAME_MACHINE=i486 ;;
+ *Pentium) UNAME_MACHINE=i586 ;;
+ *Pent*|*Celeron) UNAME_MACHINE=i686 ;;
+ esac
+ echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}
+ exit ;;
+ i*86:*:3.2:*)
+ if test -f /usr/options/cb.name; then
+ UNAME_REL=`sed -n 's/.*Version //p' </usr/options/cb.name`
+ echo ${UNAME_MACHINE}-pc-isc$UNAME_REL
+ elif /bin/uname -X 2>/dev/null >/dev/null ; then
+ UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')`
+ (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486
+ (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \
+ && UNAME_MACHINE=i586
+ (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \
+ && UNAME_MACHINE=i686
+ (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \
+ && UNAME_MACHINE=i686
+ echo ${UNAME_MACHINE}-pc-sco$UNAME_REL
+ else
+ echo ${UNAME_MACHINE}-pc-sysv32
+ fi
+ exit ;;
+ pc:*:*:*)
+ # Left here for compatibility:
+ # uname -m prints for DJGPP always 'pc', but it prints nothing about
+ # the processor, so we play safe by assuming i586.
+ # Note: whatever this is, it MUST be the same as what config.sub
+ # prints for the "djgpp" host, or else GDB configury will decide that
+ # this is a cross-build.
+ echo i586-pc-msdosdjgpp
+ exit ;;
+ Intel:Mach:3*:*)
+ echo i386-pc-mach3
+ exit ;;
+ paragon:*:*:*)
+ echo i860-intel-osf1
+ exit ;;
+ i860:*:4.*:*) # i860-SVR4
+ if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then
+ echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4
+ else # Add other i860-SVR4 vendors below as they are discovered.
+ echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4
+ fi
+ exit ;;
+ mini*:CTIX:SYS*5:*)
+ # "miniframe"
+ echo m68010-convergent-sysv
+ exit ;;
+ mc68k:UNIX:SYSTEM5:3.51m)
+ echo m68k-convergent-sysv
+ exit ;;
+ M680?0:D-NIX:5.3:*)
+ echo m68k-diab-dnix
+ exit ;;
+ M68*:*:R3V[5678]*:*)
+ test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;;
+ 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0)
+ OS_REL=''
+ test -r /etc/.relid \
+ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
+ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
+ 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4; exit; } ;;
+ NCR*:*:4.2:* | MPRAS*:*:4.2:*)
+ OS_REL='.3'
+ test -r /etc/.relid \
+ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
+ && { echo i586-ncr-sysv4.3${OS_REL}; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \
+ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
+ m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
+ echo m68k-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ mc68030:UNIX_System_V:4.*:*)
+ echo m68k-atari-sysv4
+ exit ;;
+ TSUNAMI:LynxOS:2.*:*)
+ echo sparc-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ rs6000:LynxOS:2.*:*)
+ echo rs6000-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*)
+ echo powerpc-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ SM[BE]S:UNIX_SV:*:*)
+ echo mips-dde-sysv${UNAME_RELEASE}
+ exit ;;
+ RM*:ReliantUNIX-*:*:*)
+ echo mips-sni-sysv4
+ exit ;;
+ RM*:SINIX-*:*:*)
+ echo mips-sni-sysv4
+ exit ;;
+ *:SINIX-*:*:*)
+ if uname -p 2>/dev/null >/dev/null ; then
+ UNAME_MACHINE=`(uname -p) 2>/dev/null`
+ echo ${UNAME_MACHINE}-sni-sysv4
+ else
+ echo ns32k-sni-sysv
+ fi
+ exit ;;
+ PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
+ # says <Richard.M.Bartel at ccMail.Census.GOV>
+ echo i586-unisys-sysv4
+ exit ;;
+ *:UNIX_System_V:4*:FTX*)
+ # From Gerald Hewes <hewes at openmarket.com>.
+ # How about differentiating between stratus architectures? -djm
+ echo hppa1.1-stratus-sysv4
+ exit ;;
+ *:*:*:FTX*)
+ # From seanf at swdc.stratus.com.
+ echo i860-stratus-sysv4
+ exit ;;
+ i*86:VOS:*:*)
+ # From Paul.Green at stratus.com.
+ echo ${UNAME_MACHINE}-stratus-vos
+ exit ;;
+ *:VOS:*:*)
+ # From Paul.Green at stratus.com.
+ echo hppa1.1-stratus-vos
+ exit ;;
+ mc68*:A/UX:*:*)
+ echo m68k-apple-aux${UNAME_RELEASE}
+ exit ;;
+ news*:NEWS-OS:6*:*)
+ echo mips-sony-newsos6
+ exit ;;
+ R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
+ if [ -d /usr/nec ]; then
+ echo mips-nec-sysv${UNAME_RELEASE}
+ else
+ echo mips-unknown-sysv${UNAME_RELEASE}
+ fi
+ exit ;;
+ BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only.
+ echo powerpc-be-beos
+ exit ;;
+ BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only.
+ echo powerpc-apple-beos
+ exit ;;
+ BePC:BeOS:*:*) # BeOS running on Intel PC compatible.
+ echo i586-pc-beos
+ exit ;;
+ BePC:Haiku:*:*) # Haiku running on Intel PC compatible.
+ echo i586-pc-haiku
+ exit ;;
+ SX-4:SUPER-UX:*:*)
+ echo sx4-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-5:SUPER-UX:*:*)
+ echo sx5-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-6:SUPER-UX:*:*)
+ echo sx6-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-7:SUPER-UX:*:*)
+ echo sx7-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-8:SUPER-UX:*:*)
+ echo sx8-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-8R:SUPER-UX:*:*)
+ echo sx8r-nec-superux${UNAME_RELEASE}
+ exit ;;
+ Power*:Rhapsody:*:*)
+ echo powerpc-apple-rhapsody${UNAME_RELEASE}
+ exit ;;
+ *:Rhapsody:*:*)
+ echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE}
+ exit ;;
+ *:Darwin:*:*)
+ UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown
+ case $UNAME_PROCESSOR in
+ i386)
+ eval $set_cc_for_build
+ if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
+ if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
+ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_64BIT_ARCH >/dev/null
+ then
+ UNAME_PROCESSOR="x86_64"
+ fi
+ fi ;;
+ unknown) UNAME_PROCESSOR=powerpc ;;
+ esac
+ echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
+ exit ;;
+ *:procnto*:*:* | *:QNX:[0123456789]*:*)
+ UNAME_PROCESSOR=`uname -p`
+ if test "$UNAME_PROCESSOR" = "x86"; then
+ UNAME_PROCESSOR=i386
+ UNAME_MACHINE=pc
+ fi
+ echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE}
+ exit ;;
+ *:QNX:*:4*)
+ echo i386-pc-qnx
+ exit ;;
+ NEO-?:NONSTOP_KERNEL:*:*)
+ echo neo-tandem-nsk${UNAME_RELEASE}
+ exit ;;
+ NSE-?:NONSTOP_KERNEL:*:*)
+ echo nse-tandem-nsk${UNAME_RELEASE}
+ exit ;;
+ NSR-?:NONSTOP_KERNEL:*:*)
+ echo nsr-tandem-nsk${UNAME_RELEASE}
+ exit ;;
+ *:NonStop-UX:*:*)
+ echo mips-compaq-nonstopux
+ exit ;;
+ BS2000:POSIX*:*:*)
+ echo bs2000-siemens-sysv
+ exit ;;
+ DS/*:UNIX_System_V:*:*)
+ echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE}
+ exit ;;
+ *:Plan9:*:*)
+ # "uname -m" is not consistent, so use $cputype instead. 386
+ # is converted to i386 for consistency with other x86
+ # operating systems.
+ if test "$cputype" = "386"; then
+ UNAME_MACHINE=i386
+ else
+ UNAME_MACHINE="$cputype"
+ fi
+ echo ${UNAME_MACHINE}-unknown-plan9
+ exit ;;
+ *:TOPS-10:*:*)
+ echo pdp10-unknown-tops10
+ exit ;;
+ *:TENEX:*:*)
+ echo pdp10-unknown-tenex
+ exit ;;
+ KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*)
+ echo pdp10-dec-tops20
+ exit ;;
+ XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*)
+ echo pdp10-xkl-tops20
+ exit ;;
+ *:TOPS-20:*:*)
+ echo pdp10-unknown-tops20
+ exit ;;
+ *:ITS:*:*)
+ echo pdp10-unknown-its
+ exit ;;
+ SEI:*:*:SEIUX)
+ echo mips-sei-seiux${UNAME_RELEASE}
+ exit ;;
+ *:DragonFly:*:*)
+ echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
+ exit ;;
+ *:*VMS:*:*)
+ UNAME_MACHINE=`(uname -p) 2>/dev/null`
+ case "${UNAME_MACHINE}" in
+ A*) echo alpha-dec-vms ; exit ;;
+ I*) echo ia64-dec-vms ; exit ;;
+ V*) echo vax-dec-vms ; exit ;;
+ esac ;;
+ *:XENIX:*:SysV)
+ echo i386-pc-xenix
+ exit ;;
+ i*86:skyos:*:*)
+ echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//'
+ exit ;;
+ i*86:rdos:*:*)
+ echo ${UNAME_MACHINE}-pc-rdos
+ exit ;;
+ i*86:AROS:*:*)
+ echo ${UNAME_MACHINE}-pc-aros
+ exit ;;
+esac
+
+#echo '(No uname command or uname output not recognized.)' 1>&2
+#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2
+
+eval $set_cc_for_build
+cat >$dummy.c <<EOF
+#ifdef _SEQUENT_
+# include <sys/types.h>
+# include <sys/utsname.h>
+#endif
+main ()
+{
+#if defined (sony)
+#if defined (MIPSEB)
+ /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed,
+ I don't know.... */
+ printf ("mips-sony-bsd\n"); exit (0);
+#else
+#include <sys/param.h>
+ printf ("m68k-sony-newsos%s\n",
+#ifdef NEWSOS4
+ "4"
+#else
+ ""
+#endif
+ ); exit (0);
+#endif
+#endif
+
+#if defined (__arm) && defined (__acorn) && defined (__unix)
+ printf ("arm-acorn-riscix\n"); exit (0);
+#endif
+
+#if defined (hp300) && !defined (hpux)
+ printf ("m68k-hp-bsd\n"); exit (0);
+#endif
+
+#if defined (NeXT)
+#if !defined (__ARCHITECTURE__)
+#define __ARCHITECTURE__ "m68k"
+#endif
+ int version;
+ version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`;
+ if (version < 4)
+ printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version);
+ else
+ printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version);
+ exit (0);
+#endif
+
+#if defined (MULTIMAX) || defined (n16)
+#if defined (UMAXV)
+ printf ("ns32k-encore-sysv\n"); exit (0);
+#else
+#if defined (CMU)
+ printf ("ns32k-encore-mach\n"); exit (0);
+#else
+ printf ("ns32k-encore-bsd\n"); exit (0);
+#endif
+#endif
+#endif
+
+#if defined (__386BSD__)
+ printf ("i386-pc-bsd\n"); exit (0);
+#endif
+
+#if defined (sequent)
+#if defined (i386)
+ printf ("i386-sequent-dynix\n"); exit (0);
+#endif
+#if defined (ns32000)
+ printf ("ns32k-sequent-dynix\n"); exit (0);
+#endif
+#endif
+
+#if defined (_SEQUENT_)
+ struct utsname un;
+
+ uname(&un);
+
+ if (strncmp(un.version, "V2", 2) == 0) {
+ printf ("i386-sequent-ptx2\n"); exit (0);
+ }
+ if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */
+ printf ("i386-sequent-ptx1\n"); exit (0);
+ }
+ printf ("i386-sequent-ptx\n"); exit (0);
+
+#endif
+
+#if defined (vax)
+# if !defined (ultrix)
+# include <sys/param.h>
+# if defined (BSD)
+# if BSD == 43
+ printf ("vax-dec-bsd4.3\n"); exit (0);
+# else
+# if BSD == 199006
+ printf ("vax-dec-bsd4.3reno\n"); exit (0);
+# else
+ printf ("vax-dec-bsd\n"); exit (0);
+# endif
+# endif
+# else
+ printf ("vax-dec-bsd\n"); exit (0);
+# endif
+# else
+ printf ("vax-dec-ultrix\n"); exit (0);
+# endif
+#endif
+
+#if defined (alliant) && defined (i860)
+ printf ("i860-alliant-bsd\n"); exit (0);
+#endif
+
+ exit (1);
+}
+EOF
+
+$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` &&
+ { echo "$SYSTEM_NAME"; exit; }
+
+# Apollos put the system type in the environment.
+
+test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; }
+
+# Convex versions that predate uname can use getsysinfo(1)
+
+if [ -x /usr/convex/getsysinfo ]
+then
+ case `getsysinfo -f cpu_type` in
+ c1*)
+ echo c1-convex-bsd
+ exit ;;
+ c2*)
+ if getsysinfo -f scalar_acc
+ then echo c32-convex-bsd
+ else echo c2-convex-bsd
+ fi
+ exit ;;
+ c34*)
+ echo c34-convex-bsd
+ exit ;;
+ c38*)
+ echo c38-convex-bsd
+ exit ;;
+ c4*)
+ echo c4-convex-bsd
+ exit ;;
+ esac
+fi
+
+cat >&2 <<EOF
+$0: unable to guess system type
+
+This script, last modified $timestamp, has failed to recognize
+the operating system you are using. It is advised that you
+download the most up to date version of the config scripts from
+
+ http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
+and
+ http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
+
+If the version you run ($0) is already up to date, please
+send the following data and any information you think might be
+pertinent to <config-patches at gnu.org> in order to provide the needed
+information to handle your system.
+
+config.guess timestamp = $timestamp
+
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null`
+
+hostinfo = `(hostinfo) 2>/dev/null`
+/bin/universe = `(/bin/universe) 2>/dev/null`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null`
+/bin/arch = `(/bin/arch) 2>/dev/null`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null`
+
+UNAME_MACHINE = ${UNAME_MACHINE}
+UNAME_RELEASE = ${UNAME_RELEASE}
+UNAME_SYSTEM = ${UNAME_SYSTEM}
+UNAME_VERSION = ${UNAME_VERSION}
+EOF
+
+exit 1
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "timestamp='"
+# time-stamp-format: "%:y-%02m-%02d"
+# time-stamp-end: "'"
+# End:
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/config.sub b/src/libGkArrays/src/libProgressBar-1.2.0/config.sub
new file mode 100755
index 0000000..30fdca8
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/config.sub
@@ -0,0 +1,1760 @@
+#! /bin/sh
+# Configuration validation subroutine script.
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
+# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,
+# 2011 Free Software Foundation, Inc.
+
+timestamp='2011-03-23'
+
+# This file is (in principle) common to ALL GNU software.
+# The presence of a machine in this file suggests that SOME GNU software
+# can handle that machine. It does not imply ALL GNU software can.
+#
+# This file is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
+# 02110-1301, USA.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+
+# Please send patches to <config-patches at gnu.org>. Submit a context
+# diff and a properly formatted GNU ChangeLog entry.
+#
+# Configuration subroutine to validate and canonicalize a configuration type.
+# Supply the specified configuration type as an argument.
+# If it is invalid, we print an error message on stderr and exit with code 1.
+# Otherwise, we print the canonical config type on stdout and succeed.
+
+# You can get the latest version of this script from:
+# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
+
+# This file is supposed to be the same for all GNU packages
+# and recognize all the CPU types, system types and aliases
+# that are meaningful with *any* GNU software.
+# Each package is responsible for reporting which valid configurations
+# it does not support. The user should be able to distinguish
+# a failure to support a valid configuration from a meaningless
+# configuration.
+
+# The goal of this file is to map all the various variations of a given
+# machine specification into a single specification in the form:
+# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM
+# or in some cases, the newer four-part form:
+# CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM
+# It is wrong to echo any other type of specification.
+
+me=`echo "$0" | sed -e 's,.*/,,'`
+
+usage="\
+Usage: $0 [OPTION] CPU-MFR-OPSYS
+ $0 [OPTION] ALIAS
+
+Canonicalize a configuration name.
+
+Operation modes:
+ -h, --help print this help, then exit
+ -t, --time-stamp print date of last modification, then exit
+ -v, --version print version number, then exit
+
+Report bugs and patches to <config-patches at gnu.org>."
+
+version="\
+GNU config.sub ($timestamp)
+
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000,
+2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free
+Software Foundation, Inc.
+
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+
+help="
+Try \`$me --help' for more information."
+
+# Parse command line
+while test $# -gt 0 ; do
+ case $1 in
+ --time-stamp | --time* | -t )
+ echo "$timestamp" ; exit ;;
+ --version | -v )
+ echo "$version" ; exit ;;
+ --help | --h* | -h )
+ echo "$usage"; exit ;;
+ -- ) # Stop option processing
+ shift; break ;;
+ - ) # Use stdin as input.
+ break ;;
+ -* )
+ echo "$me: invalid option $1$help"
+ exit 1 ;;
+
+ *local*)
+ # First pass through any local machine types.
+ echo $1
+ exit ;;
+
+ * )
+ break ;;
+ esac
+done
+
+case $# in
+ 0) echo "$me: missing argument$help" >&2
+ exit 1;;
+ 1) ;;
+ *) echo "$me: too many arguments$help" >&2
+ exit 1;;
+esac
+
+# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any).
+# Here we must recognize all the valid KERNEL-OS combinations.
+maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
+case $maybe_os in
+ nto-qnx* | linux-gnu* | linux-android* | linux-dietlibc | linux-newlib* | \
+ linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | \
+ knetbsd*-gnu* | netbsd*-gnu* | \
+ kopensolaris*-gnu* | \
+ storm-chaos* | os2-emx* | rtmk-nova*)
+ os=-$maybe_os
+ basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
+ ;;
+ *)
+ basic_machine=`echo $1 | sed 's/-[^-]*$//'`
+ if [ $basic_machine != $1 ]
+ then os=`echo $1 | sed 's/.*-/-/'`
+ else os=; fi
+ ;;
+esac
+
+### Let's recognize common machines as not being operating systems so
+### that things like config.sub decstation-3100 work. We also
+### recognize some manufacturers as not being operating systems, so we
+### can provide default operating systems below.
+case $os in
+ -sun*os*)
+ # Prevent following clause from handling this invalid input.
+ ;;
+ -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \
+ -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \
+ -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \
+ -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
+ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
+ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
+ -apple | -axis | -knuth | -cray | -microblaze)
+ os=
+ basic_machine=$1
+ ;;
+ -bluegene*)
+ os=-cnk
+ ;;
+ -sim | -cisco | -oki | -wec | -winbond)
+ os=
+ basic_machine=$1
+ ;;
+ -scout)
+ ;;
+ -wrs)
+ os=-vxworks
+ basic_machine=$1
+ ;;
+ -chorusos*)
+ os=-chorusos
+ basic_machine=$1
+ ;;
+ -chorusrdb)
+ os=-chorusrdb
+ basic_machine=$1
+ ;;
+ -hiux*)
+ os=-hiuxwe2
+ ;;
+ -sco6)
+ os=-sco5v6
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco5)
+ os=-sco3.2v5
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco4)
+ os=-sco3.2v4
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco3.2.[4-9]*)
+ os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco3.2v[4-9]*)
+ # Don't forget version if it is 3.2v4 or newer.
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco5v6*)
+ # Don't forget version if it is 3.2v4 or newer.
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco*)
+ os=-sco3.2v2
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -udk*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -isc)
+ os=-isc2.2
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -clix*)
+ basic_machine=clipper-intergraph
+ ;;
+ -isc*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -lynx*)
+ os=-lynxos
+ ;;
+ -ptx*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'`
+ ;;
+ -windowsnt*)
+ os=`echo $os | sed -e 's/windowsnt/winnt/'`
+ ;;
+ -psos*)
+ os=-psos
+ ;;
+ -mint | -mint[0-9]*)
+ basic_machine=m68k-atari
+ os=-mint
+ ;;
+esac
+
+# Decode aliases for certain CPU-COMPANY combinations.
+case $basic_machine in
+ # Recognize the basic CPU types without company name.
+ # Some are omitted here because they have special meanings below.
+ 1750a | 580 \
+ | a29k \
+ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \
+ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \
+ | am33_2.0 \
+ | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \
+ | bfin \
+ | c4x | clipper \
+ | d10v | d30v | dlx | dsp16xx \
+ | fido | fr30 | frv \
+ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
+ | i370 | i860 | i960 | ia64 \
+ | ip2k | iq2000 \
+ | lm32 \
+ | m32c | m32r | m32rle | m68000 | m68k | m88k \
+ | maxq | mb | microblaze | mcore | mep | metag \
+ | mips | mipsbe | mipseb | mipsel | mipsle \
+ | mips16 \
+ | mips64 | mips64el \
+ | mips64octeon | mips64octeonel \
+ | mips64orion | mips64orionel \
+ | mips64r5900 | mips64r5900el \
+ | mips64vr | mips64vrel \
+ | mips64vr4100 | mips64vr4100el \
+ | mips64vr4300 | mips64vr4300el \
+ | mips64vr5000 | mips64vr5000el \
+ | mips64vr5900 | mips64vr5900el \
+ | mipsisa32 | mipsisa32el \
+ | mipsisa32r2 | mipsisa32r2el \
+ | mipsisa64 | mipsisa64el \
+ | mipsisa64r2 | mipsisa64r2el \
+ | mipsisa64sb1 | mipsisa64sb1el \
+ | mipsisa64sr71k | mipsisa64sr71kel \
+ | mipstx39 | mipstx39el \
+ | mn10200 | mn10300 \
+ | moxie \
+ | mt \
+ | msp430 \
+ | nds32 | nds32le | nds32be \
+ | nios | nios2 \
+ | ns16k | ns32k \
+ | open8 \
+ | or32 \
+ | pdp10 | pdp11 | pj | pjl \
+ | powerpc | powerpc64 | powerpc64le | powerpcle \
+ | pyramid \
+ | rx \
+ | score \
+ | sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
+ | sh64 | sh64le \
+ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \
+ | sparcv8 | sparcv9 | sparcv9b | sparcv9v \
+ | spu \
+ | tahoe | tic4x | tic54x | tic55x | tic6x | tic80 | tron \
+ | ubicom32 \
+ | v850 | v850e \
+ | we32k \
+ | x86 | xc16x | xstormy16 | xtensa \
+ | z8k | z80)
+ basic_machine=$basic_machine-unknown
+ ;;
+ c54x)
+ basic_machine=tic54x-unknown
+ ;;
+ c55x)
+ basic_machine=tic55x-unknown
+ ;;
+ c6x)
+ basic_machine=tic6x-unknown
+ ;;
+ m6811 | m68hc11 | m6812 | m68hc12 | picochip)
+ # Motorola 68HC11/12.
+ basic_machine=$basic_machine-unknown
+ os=-none
+ ;;
+ m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k)
+ ;;
+ ms1)
+ basic_machine=mt-unknown
+ ;;
+
+ strongarm | thumb | xscale)
+ basic_machine=arm-unknown
+ ;;
+
+ xscaleeb)
+ basic_machine=armeb-unknown
+ ;;
+
+ xscaleel)
+ basic_machine=armel-unknown
+ ;;
+
+ # We use `pc' rather than `unknown'
+ # because (1) that's what they normally are, and
+ # (2) the word "unknown" tends to confuse beginning users.
+ i*86 | x86_64)
+ basic_machine=$basic_machine-pc
+ ;;
+ # Object if more than one company name word.
+ *-*-*)
+ echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
+ exit 1
+ ;;
+ # Recognize the basic CPU types with company name.
+ 580-* \
+ | a29k-* \
+ | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \
+ | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \
+ | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \
+ | arm-* | armbe-* | armle-* | armeb-* | armv*-* \
+ | avr-* | avr32-* \
+ | bfin-* | bs2000-* \
+ | c[123]* | c30-* | [cjt]90-* | c4x-* \
+ | clipper-* | craynv-* | cydra-* \
+ | d10v-* | d30v-* | dlx-* \
+ | elxsi-* \
+ | f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \
+ | h8300-* | h8500-* \
+ | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
+ | i*86-* | i860-* | i960-* | ia64-* \
+ | ip2k-* | iq2000-* \
+ | lm32-* \
+ | m32c-* | m32r-* | m32rle-* \
+ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
+ | m88110-* | m88k-* | maxq-* | mcore-* | metag-* | microblaze-* \
+ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
+ | mips16-* \
+ | mips64-* | mips64el-* \
+ | mips64octeon-* | mips64octeonel-* \
+ | mips64orion-* | mips64orionel-* \
+ | mips64r5900-* | mips64r5900el-* \
+ | mips64vr-* | mips64vrel-* \
+ | mips64vr4100-* | mips64vr4100el-* \
+ | mips64vr4300-* | mips64vr4300el-* \
+ | mips64vr5000-* | mips64vr5000el-* \
+ | mips64vr5900-* | mips64vr5900el-* \
+ | mipsisa32-* | mipsisa32el-* \
+ | mipsisa32r2-* | mipsisa32r2el-* \
+ | mipsisa64-* | mipsisa64el-* \
+ | mipsisa64r2-* | mipsisa64r2el-* \
+ | mipsisa64sb1-* | mipsisa64sb1el-* \
+ | mipsisa64sr71k-* | mipsisa64sr71kel-* \
+ | mipstx39-* | mipstx39el-* \
+ | mmix-* \
+ | mt-* \
+ | msp430-* \
+ | nds32-* | nds32le-* | nds32be-* \
+ | nios-* | nios2-* \
+ | none-* | np1-* | ns16k-* | ns32k-* \
+ | open8-* \
+ | orion-* \
+ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
+ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* \
+ | pyramid-* \
+ | romp-* | rs6000-* | rx-* \
+ | sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \
+ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \
+ | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \
+ | sparclite-* \
+ | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | sv1-* | sx?-* \
+ | tahoe-* \
+ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
+ | tile-* | tilegx-* \
+ | tron-* \
+ | ubicom32-* \
+ | v850-* | v850e-* | vax-* \
+ | we32k-* \
+ | x86-* | x86_64-* | xc16x-* | xps100-* \
+ | xstormy16-* | xtensa*-* \
+ | ymp-* \
+ | z8k-* | z80-*)
+ ;;
+ # Recognize the basic CPU types without company name, with glob match.
+ xtensa*)
+ basic_machine=$basic_machine-unknown
+ ;;
+ # Recognize the various machine names and aliases which stand
+ # for a CPU type and a company and sometimes even an OS.
+ 386bsd)
+ basic_machine=i386-unknown
+ os=-bsd
+ ;;
+ 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc)
+ basic_machine=m68000-att
+ ;;
+ 3b*)
+ basic_machine=we32k-att
+ ;;
+ a29khif)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ abacus)
+ basic_machine=abacus-unknown
+ ;;
+ adobe68k)
+ basic_machine=m68010-adobe
+ os=-scout
+ ;;
+ alliant | fx80)
+ basic_machine=fx80-alliant
+ ;;
+ altos | altos3068)
+ basic_machine=m68k-altos
+ ;;
+ am29k)
+ basic_machine=a29k-none
+ os=-bsd
+ ;;
+ amd64)
+ basic_machine=x86_64-pc
+ ;;
+ amd64-*)
+ basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ amdahl)
+ basic_machine=580-amdahl
+ os=-sysv
+ ;;
+ amiga | amiga-*)
+ basic_machine=m68k-unknown
+ ;;
+ amigaos | amigados)
+ basic_machine=m68k-unknown
+ os=-amigaos
+ ;;
+ amigaunix | amix)
+ basic_machine=m68k-unknown
+ os=-sysv4
+ ;;
+ apollo68)
+ basic_machine=m68k-apollo
+ os=-sysv
+ ;;
+ apollo68bsd)
+ basic_machine=m68k-apollo
+ os=-bsd
+ ;;
+ aros)
+ basic_machine=i386-pc
+ os=-aros
+ ;;
+ aux)
+ basic_machine=m68k-apple
+ os=-aux
+ ;;
+ balance)
+ basic_machine=ns32k-sequent
+ os=-dynix
+ ;;
+ blackfin)
+ basic_machine=bfin-unknown
+ os=-linux
+ ;;
+ blackfin-*)
+ basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'`
+ os=-linux
+ ;;
+ bluegene*)
+ basic_machine=powerpc-ibm
+ os=-cnk
+ ;;
+ c54x-*)
+ basic_machine=tic54x-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ c55x-*)
+ basic_machine=tic55x-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ c6x-*)
+ basic_machine=tic6x-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ c90)
+ basic_machine=c90-cray
+ os=-unicos
+ ;;
+ cegcc)
+ basic_machine=arm-unknown
+ os=-cegcc
+ ;;
+ convex-c1)
+ basic_machine=c1-convex
+ os=-bsd
+ ;;
+ convex-c2)
+ basic_machine=c2-convex
+ os=-bsd
+ ;;
+ convex-c32)
+ basic_machine=c32-convex
+ os=-bsd
+ ;;
+ convex-c34)
+ basic_machine=c34-convex
+ os=-bsd
+ ;;
+ convex-c38)
+ basic_machine=c38-convex
+ os=-bsd
+ ;;
+ cray | j90)
+ basic_machine=j90-cray
+ os=-unicos
+ ;;
+ craynv)
+ basic_machine=craynv-cray
+ os=-unicosmp
+ ;;
+ cr16 | cr16-*)
+ basic_machine=cr16-unknown
+ os=-elf
+ ;;
+ crds | unos)
+ basic_machine=m68k-crds
+ ;;
+ crisv32 | crisv32-* | etraxfs*)
+ basic_machine=crisv32-axis
+ ;;
+ cris | cris-* | etrax*)
+ basic_machine=cris-axis
+ ;;
+ crx)
+ basic_machine=crx-unknown
+ os=-elf
+ ;;
+ da30 | da30-*)
+ basic_machine=m68k-da30
+ ;;
+ decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn)
+ basic_machine=mips-dec
+ ;;
+ decsystem10* | dec10*)
+ basic_machine=pdp10-dec
+ os=-tops10
+ ;;
+ decsystem20* | dec20*)
+ basic_machine=pdp10-dec
+ os=-tops20
+ ;;
+ delta | 3300 | motorola-3300 | motorola-delta \
+ | 3300-motorola | delta-motorola)
+ basic_machine=m68k-motorola
+ ;;
+ delta88)
+ basic_machine=m88k-motorola
+ os=-sysv3
+ ;;
+ dicos)
+ basic_machine=i686-pc
+ os=-dicos
+ ;;
+ djgpp)
+ basic_machine=i586-pc
+ os=-msdosdjgpp
+ ;;
+ dpx20 | dpx20-*)
+ basic_machine=rs6000-bull
+ os=-bosx
+ ;;
+ dpx2* | dpx2*-bull)
+ basic_machine=m68k-bull
+ os=-sysv3
+ ;;
+ ebmon29k)
+ basic_machine=a29k-amd
+ os=-ebmon
+ ;;
+ elxsi)
+ basic_machine=elxsi-elxsi
+ os=-bsd
+ ;;
+ encore | umax | mmax)
+ basic_machine=ns32k-encore
+ ;;
+ es1800 | OSE68k | ose68k | ose | OSE)
+ basic_machine=m68k-ericsson
+ os=-ose
+ ;;
+ fx2800)
+ basic_machine=i860-alliant
+ ;;
+ genix)
+ basic_machine=ns32k-ns
+ ;;
+ gmicro)
+ basic_machine=tron-gmicro
+ os=-sysv
+ ;;
+ go32)
+ basic_machine=i386-pc
+ os=-go32
+ ;;
+ h3050r* | hiux*)
+ basic_machine=hppa1.1-hitachi
+ os=-hiuxwe2
+ ;;
+ h8300hms)
+ basic_machine=h8300-hitachi
+ os=-hms
+ ;;
+ h8300xray)
+ basic_machine=h8300-hitachi
+ os=-xray
+ ;;
+ h8500hms)
+ basic_machine=h8500-hitachi
+ os=-hms
+ ;;
+ harris)
+ basic_machine=m88k-harris
+ os=-sysv3
+ ;;
+ hp300-*)
+ basic_machine=m68k-hp
+ ;;
+ hp300bsd)
+ basic_machine=m68k-hp
+ os=-bsd
+ ;;
+ hp300hpux)
+ basic_machine=m68k-hp
+ os=-hpux
+ ;;
+ hp3k9[0-9][0-9] | hp9[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hp9k2[0-9][0-9] | hp9k31[0-9])
+ basic_machine=m68000-hp
+ ;;
+ hp9k3[2-9][0-9])
+ basic_machine=m68k-hp
+ ;;
+ hp9k6[0-9][0-9] | hp6[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hp9k7[0-79][0-9] | hp7[0-79][0-9])
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k78[0-9] | hp78[0-9])
+ # FIXME: really hppa2.0-hp
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893)
+ # FIXME: really hppa2.0-hp
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[0-9][13679] | hp8[0-9][13679])
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[0-9][0-9] | hp8[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hppa-next)
+ os=-nextstep3
+ ;;
+ hppaosf)
+ basic_machine=hppa1.1-hp
+ os=-osf
+ ;;
+ hppro)
+ basic_machine=hppa1.1-hp
+ os=-proelf
+ ;;
+ i370-ibm* | ibm*)
+ basic_machine=i370-ibm
+ ;;
+# I'm not sure what "Sysv32" means. Should this be sysv3.2?
+ i*86v32)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv32
+ ;;
+ i*86v4*)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv4
+ ;;
+ i*86v)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv
+ ;;
+ i*86sol2)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-solaris2
+ ;;
+ i386mach)
+ basic_machine=i386-mach
+ os=-mach
+ ;;
+ i386-vsta | vsta)
+ basic_machine=i386-unknown
+ os=-vsta
+ ;;
+ iris | iris4d)
+ basic_machine=mips-sgi
+ case $os in
+ -irix*)
+ ;;
+ *)
+ os=-irix4
+ ;;
+ esac
+ ;;
+ isi68 | isi)
+ basic_machine=m68k-isi
+ os=-sysv
+ ;;
+ m68knommu)
+ basic_machine=m68k-unknown
+ os=-linux
+ ;;
+ m68knommu-*)
+ basic_machine=m68k-`echo $basic_machine | sed 's/^[^-]*-//'`
+ os=-linux
+ ;;
+ m88k-omron*)
+ basic_machine=m88k-omron
+ ;;
+ magnum | m3230)
+ basic_machine=mips-mips
+ os=-sysv
+ ;;
+ merlin)
+ basic_machine=ns32k-utek
+ os=-sysv
+ ;;
+ microblaze)
+ basic_machine=microblaze-xilinx
+ ;;
+ mingw32)
+ basic_machine=i386-pc
+ os=-mingw32
+ ;;
+ mingw32ce)
+ basic_machine=arm-unknown
+ os=-mingw32ce
+ ;;
+ miniframe)
+ basic_machine=m68000-convergent
+ ;;
+ *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*)
+ basic_machine=m68k-atari
+ os=-mint
+ ;;
+ mips3*-*)
+ basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`
+ ;;
+ mips3*)
+ basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown
+ ;;
+ monitor)
+ basic_machine=m68k-rom68k
+ os=-coff
+ ;;
+ morphos)
+ basic_machine=powerpc-unknown
+ os=-morphos
+ ;;
+ msdos)
+ basic_machine=i386-pc
+ os=-msdos
+ ;;
+ ms1-*)
+ basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'`
+ ;;
+ mvs)
+ basic_machine=i370-ibm
+ os=-mvs
+ ;;
+ ncr3000)
+ basic_machine=i486-ncr
+ os=-sysv4
+ ;;
+ netbsd386)
+ basic_machine=i386-unknown
+ os=-netbsd
+ ;;
+ netwinder)
+ basic_machine=armv4l-rebel
+ os=-linux
+ ;;
+ news | news700 | news800 | news900)
+ basic_machine=m68k-sony
+ os=-newsos
+ ;;
+ news1000)
+ basic_machine=m68030-sony
+ os=-newsos
+ ;;
+ news-3600 | risc-news)
+ basic_machine=mips-sony
+ os=-newsos
+ ;;
+ necv70)
+ basic_machine=v70-nec
+ os=-sysv
+ ;;
+ next | m*-next )
+ basic_machine=m68k-next
+ case $os in
+ -nextstep* )
+ ;;
+ -ns2*)
+ os=-nextstep2
+ ;;
+ *)
+ os=-nextstep3
+ ;;
+ esac
+ ;;
+ nh3000)
+ basic_machine=m68k-harris
+ os=-cxux
+ ;;
+ nh[45]000)
+ basic_machine=m88k-harris
+ os=-cxux
+ ;;
+ nindy960)
+ basic_machine=i960-intel
+ os=-nindy
+ ;;
+ mon960)
+ basic_machine=i960-intel
+ os=-mon960
+ ;;
+ nonstopux)
+ basic_machine=mips-compaq
+ os=-nonstopux
+ ;;
+ np1)
+ basic_machine=np1-gould
+ ;;
+ neo-tandem)
+ basic_machine=neo-tandem
+ ;;
+ nse-tandem)
+ basic_machine=nse-tandem
+ ;;
+ nsr-tandem)
+ basic_machine=nsr-tandem
+ ;;
+ op50n-* | op60c-*)
+ basic_machine=hppa1.1-oki
+ os=-proelf
+ ;;
+ openrisc | openrisc-*)
+ basic_machine=or32-unknown
+ ;;
+ os400)
+ basic_machine=powerpc-ibm
+ os=-os400
+ ;;
+ OSE68000 | ose68000)
+ basic_machine=m68000-ericsson
+ os=-ose
+ ;;
+ os68k)
+ basic_machine=m68k-none
+ os=-os68k
+ ;;
+ pa-hitachi)
+ basic_machine=hppa1.1-hitachi
+ os=-hiuxwe2
+ ;;
+ paragon)
+ basic_machine=i860-intel
+ os=-osf
+ ;;
+ parisc)
+ basic_machine=hppa-unknown
+ os=-linux
+ ;;
+ parisc-*)
+ basic_machine=hppa-`echo $basic_machine | sed 's/^[^-]*-//'`
+ os=-linux
+ ;;
+ pbd)
+ basic_machine=sparc-tti
+ ;;
+ pbb)
+ basic_machine=m68k-tti
+ ;;
+ pc532 | pc532-*)
+ basic_machine=ns32k-pc532
+ ;;
+ pc98)
+ basic_machine=i386-pc
+ ;;
+ pc98-*)
+ basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentium | p5 | k5 | k6 | nexgen | viac3)
+ basic_machine=i586-pc
+ ;;
+ pentiumpro | p6 | 6x86 | athlon | athlon_*)
+ basic_machine=i686-pc
+ ;;
+ pentiumii | pentium2 | pentiumiii | pentium3)
+ basic_machine=i686-pc
+ ;;
+ pentium4)
+ basic_machine=i786-pc
+ ;;
+ pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
+ basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentiumpro-* | p6-* | 6x86-* | athlon-*)
+ basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
+ basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentium4-*)
+ basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pn)
+ basic_machine=pn-gould
+ ;;
+ power) basic_machine=power-ibm
+ ;;
+ ppc | ppcbe) basic_machine=powerpc-unknown
+ ;;
+ ppc-* | ppcbe-*)
+ basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppcle | powerpclittle | ppc-le | powerpc-little)
+ basic_machine=powerpcle-unknown
+ ;;
+ ppcle-* | powerpclittle-*)
+ basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppc64) basic_machine=powerpc64-unknown
+ ;;
+ ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppc64le | powerpc64little | ppc64-le | powerpc64-little)
+ basic_machine=powerpc64le-unknown
+ ;;
+ ppc64le-* | powerpc64little-*)
+ basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ps2)
+ basic_machine=i386-ibm
+ ;;
+ pw32)
+ basic_machine=i586-unknown
+ os=-pw32
+ ;;
+ rdos)
+ basic_machine=i386-pc
+ os=-rdos
+ ;;
+ rom68k)
+ basic_machine=m68k-rom68k
+ os=-coff
+ ;;
+ rm[46]00)
+ basic_machine=mips-siemens
+ ;;
+ rtpc | rtpc-*)
+ basic_machine=romp-ibm
+ ;;
+ s390 | s390-*)
+ basic_machine=s390-ibm
+ ;;
+ s390x | s390x-*)
+ basic_machine=s390x-ibm
+ ;;
+ sa29200)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ sb1)
+ basic_machine=mipsisa64sb1-unknown
+ ;;
+ sb1el)
+ basic_machine=mipsisa64sb1el-unknown
+ ;;
+ sde)
+ basic_machine=mipsisa32-sde
+ os=-elf
+ ;;
+ sei)
+ basic_machine=mips-sei
+ os=-seiux
+ ;;
+ sequent)
+ basic_machine=i386-sequent
+ ;;
+ sh)
+ basic_machine=sh-hitachi
+ os=-hms
+ ;;
+ sh5el)
+ basic_machine=sh5le-unknown
+ ;;
+ sh64)
+ basic_machine=sh64-unknown
+ ;;
+ sparclite-wrs | simso-wrs)
+ basic_machine=sparclite-wrs
+ os=-vxworks
+ ;;
+ sps7)
+ basic_machine=m68k-bull
+ os=-sysv2
+ ;;
+ spur)
+ basic_machine=spur-unknown
+ ;;
+ st2000)
+ basic_machine=m68k-tandem
+ ;;
+ stratus)
+ basic_machine=i860-stratus
+ os=-sysv4
+ ;;
+ strongarm-* | thumb-*)
+ basic_machine=arm-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ sun2)
+ basic_machine=m68000-sun
+ ;;
+ sun2os3)
+ basic_machine=m68000-sun
+ os=-sunos3
+ ;;
+ sun2os4)
+ basic_machine=m68000-sun
+ os=-sunos4
+ ;;
+ sun3os3)
+ basic_machine=m68k-sun
+ os=-sunos3
+ ;;
+ sun3os4)
+ basic_machine=m68k-sun
+ os=-sunos4
+ ;;
+ sun4os3)
+ basic_machine=sparc-sun
+ os=-sunos3
+ ;;
+ sun4os4)
+ basic_machine=sparc-sun
+ os=-sunos4
+ ;;
+ sun4sol2)
+ basic_machine=sparc-sun
+ os=-solaris2
+ ;;
+ sun3 | sun3-*)
+ basic_machine=m68k-sun
+ ;;
+ sun4)
+ basic_machine=sparc-sun
+ ;;
+ sun386 | sun386i | roadrunner)
+ basic_machine=i386-sun
+ ;;
+ sv1)
+ basic_machine=sv1-cray
+ os=-unicos
+ ;;
+ symmetry)
+ basic_machine=i386-sequent
+ os=-dynix
+ ;;
+ t3e)
+ basic_machine=alphaev5-cray
+ os=-unicos
+ ;;
+ t90)
+ basic_machine=t90-cray
+ os=-unicos
+ ;;
+ # This must be matched before tile*.
+ tilegx*)
+ basic_machine=tilegx-unknown
+ os=-linux-gnu
+ ;;
+ tile*)
+ basic_machine=tile-unknown
+ os=-linux-gnu
+ ;;
+ tx39)
+ basic_machine=mipstx39-unknown
+ ;;
+ tx39el)
+ basic_machine=mipstx39el-unknown
+ ;;
+ toad1)
+ basic_machine=pdp10-xkl
+ os=-tops20
+ ;;
+ tower | tower-32)
+ basic_machine=m68k-ncr
+ ;;
+ tpf)
+ basic_machine=s390x-ibm
+ os=-tpf
+ ;;
+ udi29k)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ ultra3)
+ basic_machine=a29k-nyu
+ os=-sym1
+ ;;
+ v810 | necv810)
+ basic_machine=v810-nec
+ os=-none
+ ;;
+ vaxv)
+ basic_machine=vax-dec
+ os=-sysv
+ ;;
+ vms)
+ basic_machine=vax-dec
+ os=-vms
+ ;;
+ vpp*|vx|vx-*)
+ basic_machine=f301-fujitsu
+ ;;
+ vxworks960)
+ basic_machine=i960-wrs
+ os=-vxworks
+ ;;
+ vxworks68)
+ basic_machine=m68k-wrs
+ os=-vxworks
+ ;;
+ vxworks29k)
+ basic_machine=a29k-wrs
+ os=-vxworks
+ ;;
+ w65*)
+ basic_machine=w65-wdc
+ os=-none
+ ;;
+ w89k-*)
+ basic_machine=hppa1.1-winbond
+ os=-proelf
+ ;;
+ xbox)
+ basic_machine=i686-pc
+ os=-mingw32
+ ;;
+ xps | xps100)
+ basic_machine=xps100-honeywell
+ ;;
+ xscale-* | xscalee[bl]-*)
+ basic_machine=`echo $basic_machine | sed 's/^xscale/arm/'`
+ ;;
+ ymp)
+ basic_machine=ymp-cray
+ os=-unicos
+ ;;
+ z8k-*-coff)
+ basic_machine=z8k-unknown
+ os=-sim
+ ;;
+ z80-*-coff)
+ basic_machine=z80-unknown
+ os=-sim
+ ;;
+ none)
+ basic_machine=none-none
+ os=-none
+ ;;
+
+# Here we handle the default manufacturer of certain CPU types. It is in
+# some cases the only manufacturer, in others, it is the most popular.
+ w89k)
+ basic_machine=hppa1.1-winbond
+ ;;
+ op50n)
+ basic_machine=hppa1.1-oki
+ ;;
+ op60c)
+ basic_machine=hppa1.1-oki
+ ;;
+ romp)
+ basic_machine=romp-ibm
+ ;;
+ mmix)
+ basic_machine=mmix-knuth
+ ;;
+ rs6000)
+ basic_machine=rs6000-ibm
+ ;;
+ vax)
+ basic_machine=vax-dec
+ ;;
+ pdp10)
+ # there are many clones, so DEC is not a safe bet
+ basic_machine=pdp10-unknown
+ ;;
+ pdp11)
+ basic_machine=pdp11-dec
+ ;;
+ we32k)
+ basic_machine=we32k-att
+ ;;
+ sh[1234] | sh[24]a | sh[24]aeb | sh[34]eb | sh[1234]le | sh[23]ele)
+ basic_machine=sh-unknown
+ ;;
+ sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v)
+ basic_machine=sparc-sun
+ ;;
+ cydra)
+ basic_machine=cydra-cydrome
+ ;;
+ orion)
+ basic_machine=orion-highlevel
+ ;;
+ orion105)
+ basic_machine=clipper-highlevel
+ ;;
+ mac | mpw | mac-mpw)
+ basic_machine=m68k-apple
+ ;;
+ pmac | pmac-mpw)
+ basic_machine=powerpc-apple
+ ;;
+ *-unknown)
+ # Make sure to match an already-canonicalized machine name.
+ ;;
+ *)
+ echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
+ exit 1
+ ;;
+esac
+
+# Here we canonicalize certain aliases for manufacturers.
+case $basic_machine in
+ *-digital*)
+ basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'`
+ ;;
+ *-commodore*)
+ basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'`
+ ;;
+ *)
+ ;;
+esac
+
+# Decode manufacturer-specific aliases for certain operating systems.
+
+if [ x"$os" != x"" ]
+then
+case $os in
+ # First match some system type aliases
+ # that might get confused with valid system types.
+ # -solaris* is a basic system type, with this one exception.
+ -auroraux)
+ os=-auroraux
+ ;;
+ -solaris1 | -solaris1.*)
+ os=`echo $os | sed -e 's|solaris1|sunos4|'`
+ ;;
+ -solaris)
+ os=-solaris2
+ ;;
+ -svr4*)
+ os=-sysv4
+ ;;
+ -unixware*)
+ os=-sysv4.2uw
+ ;;
+ -gnu/linux*)
+ os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
+ ;;
+ # First accept the basic system types.
+ # The portable systems comes first.
+ # Each alternative MUST END IN A *, to match a version number.
+ # -sysv* is not here because it comes later, after sysvr4.
+ -gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
+ | -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\
+ | -hpux* | -unos* | -osf* | -luna* | -dgux* | -auroraux* | -solaris* \
+ | -sym* | -kopensolaris* \
+ | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
+ | -aos* | -aros* \
+ | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
+ | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
+ | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \
+ | -openbsd* | -solidbsd* \
+ | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \
+ | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
+ | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
+ | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
+ | -chorusos* | -chorusrdb* | -cegcc* \
+ | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
+ | -mingw32* | -linux-gnu* | -linux-android* \
+ | -linux-newlib* | -linux-uclibc* \
+ | -uxpv* | -beos* | -mpeix* | -udk* \
+ | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \
+ | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \
+ | -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \
+ | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
+ | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
+ | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
+ | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es*)
+ # Remember, each alternative MUST END IN *, to match a version number.
+ ;;
+ -qnx*)
+ case $basic_machine in
+ x86-* | i*86-*)
+ ;;
+ *)
+ os=-nto$os
+ ;;
+ esac
+ ;;
+ -nto-qnx*)
+ ;;
+ -nto*)
+ os=`echo $os | sed -e 's|nto|nto-qnx|'`
+ ;;
+ -sim | -es1800* | -hms* | -xray | -os68k* | -none* | -v88r* \
+ | -windows* | -osx | -abug | -netware* | -os9* | -beos* | -haiku* \
+ | -macos* | -mpw* | -magic* | -mmixware* | -mon960* | -lnews*)
+ ;;
+ -mac*)
+ os=`echo $os | sed -e 's|mac|macos|'`
+ ;;
+ -linux-dietlibc)
+ os=-linux-dietlibc
+ ;;
+ -linux*)
+ os=`echo $os | sed -e 's|linux|linux-gnu|'`
+ ;;
+ -sunos5*)
+ os=`echo $os | sed -e 's|sunos5|solaris2|'`
+ ;;
+ -sunos6*)
+ os=`echo $os | sed -e 's|sunos6|solaris3|'`
+ ;;
+ -opened*)
+ os=-openedition
+ ;;
+ -os400*)
+ os=-os400
+ ;;
+ -wince*)
+ os=-wince
+ ;;
+ -osfrose*)
+ os=-osfrose
+ ;;
+ -osf*)
+ os=-osf
+ ;;
+ -utek*)
+ os=-bsd
+ ;;
+ -dynix*)
+ os=-bsd
+ ;;
+ -acis*)
+ os=-aos
+ ;;
+ -atheos*)
+ os=-atheos
+ ;;
+ -syllable*)
+ os=-syllable
+ ;;
+ -386bsd)
+ os=-bsd
+ ;;
+ -ctix* | -uts*)
+ os=-sysv
+ ;;
+ -nova*)
+ os=-rtmk-nova
+ ;;
+ -ns2 )
+ os=-nextstep2
+ ;;
+ -nsk*)
+ os=-nsk
+ ;;
+ # Preserve the version number of sinix5.
+ -sinix5.*)
+ os=`echo $os | sed -e 's|sinix|sysv|'`
+ ;;
+ -sinix*)
+ os=-sysv4
+ ;;
+ -tpf*)
+ os=-tpf
+ ;;
+ -triton*)
+ os=-sysv3
+ ;;
+ -oss*)
+ os=-sysv3
+ ;;
+ -svr4)
+ os=-sysv4
+ ;;
+ -svr3)
+ os=-sysv3
+ ;;
+ -sysvr4)
+ os=-sysv4
+ ;;
+ # This must come after -sysvr4.
+ -sysv*)
+ ;;
+ -ose*)
+ os=-ose
+ ;;
+ -es1800*)
+ os=-ose
+ ;;
+ -xenix)
+ os=-xenix
+ ;;
+ -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
+ os=-mint
+ ;;
+ -aros*)
+ os=-aros
+ ;;
+ -kaos*)
+ os=-kaos
+ ;;
+ -zvmoe)
+ os=-zvmoe
+ ;;
+ -dicos*)
+ os=-dicos
+ ;;
+ -nacl*)
+ ;;
+ -none)
+ ;;
+ *)
+ # Get rid of the `-' at the beginning of $os.
+ os=`echo $os | sed 's/[^-]*-//'`
+ echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2
+ exit 1
+ ;;
+esac
+else
+
+# Here we handle the default operating systems that come with various machines.
+# The value should be what the vendor currently ships out the door with their
+# machine or put another way, the most popular os provided with the machine.
+
+# Note that if you're going to try to match "-MANUFACTURER" here (say,
+# "-sun"), then you have to tell the case statement up towards the top
+# that MANUFACTURER isn't an operating system. Otherwise, code above
+# will signal an error saying that MANUFACTURER isn't an operating
+# system, and we'll never get to this point.
+
+case $basic_machine in
+ score-*)
+ os=-elf
+ ;;
+ spu-*)
+ os=-elf
+ ;;
+ *-acorn)
+ os=-riscix1.2
+ ;;
+ arm*-rebel)
+ os=-linux
+ ;;
+ arm*-semi)
+ os=-aout
+ ;;
+ c4x-* | tic4x-*)
+ os=-coff
+ ;;
+ tic54x-*)
+ os=-coff
+ ;;
+ tic55x-*)
+ os=-coff
+ ;;
+ tic6x-*)
+ os=-coff
+ ;;
+ # This must come before the *-dec entry.
+ pdp10-*)
+ os=-tops20
+ ;;
+ pdp11-*)
+ os=-none
+ ;;
+ *-dec | vax-*)
+ os=-ultrix4.2
+ ;;
+ m68*-apollo)
+ os=-domain
+ ;;
+ i386-sun)
+ os=-sunos4.0.2
+ ;;
+ m68000-sun)
+ os=-sunos3
+ # This also exists in the configure program, but was not the
+ # default.
+ # os=-sunos4
+ ;;
+ m68*-cisco)
+ os=-aout
+ ;;
+ mep-*)
+ os=-elf
+ ;;
+ mips*-cisco)
+ os=-elf
+ ;;
+ mips*-*)
+ os=-elf
+ ;;
+ or32-*)
+ os=-coff
+ ;;
+ *-tti) # must be before sparc entry or we get the wrong os.
+ os=-sysv3
+ ;;
+ sparc-* | *-sun)
+ os=-sunos4.1.1
+ ;;
+ *-be)
+ os=-beos
+ ;;
+ *-haiku)
+ os=-haiku
+ ;;
+ *-ibm)
+ os=-aix
+ ;;
+ *-knuth)
+ os=-mmixware
+ ;;
+ *-wec)
+ os=-proelf
+ ;;
+ *-winbond)
+ os=-proelf
+ ;;
+ *-oki)
+ os=-proelf
+ ;;
+ *-hp)
+ os=-hpux
+ ;;
+ *-hitachi)
+ os=-hiux
+ ;;
+ i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent)
+ os=-sysv
+ ;;
+ *-cbm)
+ os=-amigaos
+ ;;
+ *-dg)
+ os=-dgux
+ ;;
+ *-dolphin)
+ os=-sysv3
+ ;;
+ m68k-ccur)
+ os=-rtu
+ ;;
+ m88k-omron*)
+ os=-luna
+ ;;
+ *-next )
+ os=-nextstep
+ ;;
+ *-sequent)
+ os=-ptx
+ ;;
+ *-crds)
+ os=-unos
+ ;;
+ *-ns)
+ os=-genix
+ ;;
+ i370-*)
+ os=-mvs
+ ;;
+ *-next)
+ os=-nextstep3
+ ;;
+ *-gould)
+ os=-sysv
+ ;;
+ *-highlevel)
+ os=-bsd
+ ;;
+ *-encore)
+ os=-bsd
+ ;;
+ *-sgi)
+ os=-irix
+ ;;
+ *-siemens)
+ os=-sysv4
+ ;;
+ *-masscomp)
+ os=-rtu
+ ;;
+ f30[01]-fujitsu | f700-fujitsu)
+ os=-uxpv
+ ;;
+ *-rom68k)
+ os=-coff
+ ;;
+ *-*bug)
+ os=-coff
+ ;;
+ *-apple)
+ os=-macos
+ ;;
+ *-atari*)
+ os=-mint
+ ;;
+ *)
+ os=-none
+ ;;
+esac
+fi
+
+# Here we handle the case where we know the os, and the CPU type, but not the
+# manufacturer. We pick the logical manufacturer.
+vendor=unknown
+case $basic_machine in
+ *-unknown)
+ case $os in
+ -riscix*)
+ vendor=acorn
+ ;;
+ -sunos*)
+ vendor=sun
+ ;;
+ -cnk*|-aix*)
+ vendor=ibm
+ ;;
+ -beos*)
+ vendor=be
+ ;;
+ -hpux*)
+ vendor=hp
+ ;;
+ -mpeix*)
+ vendor=hp
+ ;;
+ -hiux*)
+ vendor=hitachi
+ ;;
+ -unos*)
+ vendor=crds
+ ;;
+ -dgux*)
+ vendor=dg
+ ;;
+ -luna*)
+ vendor=omron
+ ;;
+ -genix*)
+ vendor=ns
+ ;;
+ -mvs* | -opened*)
+ vendor=ibm
+ ;;
+ -os400*)
+ vendor=ibm
+ ;;
+ -ptx*)
+ vendor=sequent
+ ;;
+ -tpf*)
+ vendor=ibm
+ ;;
+ -vxsim* | -vxworks* | -windiss*)
+ vendor=wrs
+ ;;
+ -aux*)
+ vendor=apple
+ ;;
+ -hms*)
+ vendor=hitachi
+ ;;
+ -mpw* | -macos*)
+ vendor=apple
+ ;;
+ -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
+ vendor=atari
+ ;;
+ -vos*)
+ vendor=stratus
+ ;;
+ esac
+ basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"`
+ ;;
+esac
+
+echo $basic_machine$os
+exit
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "timestamp='"
+# time-stamp-format: "%:y-%02m-%02d"
+# time-stamp-end: "'"
+# End:
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/configure b/src/libGkArrays/src/libProgressBar-1.2.0/configure
new file mode 100755
index 0000000..33a4d0e
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/configure
@@ -0,0 +1,18361 @@
+#! /bin/sh
+# From configure.in Revision: 1.9 .
+# Guess values for system-dependent variables and create Makefiles.
+# Generated by GNU Autoconf 2.67 for Library for manage progress bars 1.2.0.
+#
+# Report bugs to <alban.mancheron at inria.fr>.
+#
+#
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
+# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
+# Foundation, Inc.
+#
+#
+# This configure script is free software; the Free Software Foundation
+# gives unlimited permission to copy, distribute and modify it.
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in #(
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+case $0 in #((
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test "x$CONFIG_SHELL" = x; then
+ as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '\${1+\"\$@\"}'='\"\$@\"'
+ setopt NO_GLOB_SUBST
+else
+ case \`(set -o) 2>/dev/null\` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+"
+ as_required="as_fn_return () { (exit \$1); }
+as_fn_success () { as_fn_return 0; }
+as_fn_failure () { as_fn_return 1; }
+as_fn_ret_success () { return 0; }
+as_fn_ret_failure () { return 1; }
+
+exitcode=0
+as_fn_success || { exitcode=1; echo as_fn_success failed.; }
+as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; }
+as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; }
+as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; }
+if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then :
+
+else
+ exitcode=1; echo positional parameters were not saved.
+fi
+test x\$exitcode = x0 || exit 1"
+ as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
+ as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
+ eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
+ test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1
+test \$(( 1 + 1 )) = 2 || exit 1"
+ if (eval "$as_required") 2>/dev/null; then :
+ as_have_required=yes
+else
+ as_have_required=no
+fi
+ if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then :
+
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+as_found=false
+for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ as_found=:
+ case $as_dir in #(
+ /*)
+ for as_base in sh bash ksh sh5; do
+ # Try only shells that exist, to save several forks.
+ as_shell=$as_dir/$as_base
+ if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ CONFIG_SHELL=$as_shell as_have_required=yes
+ if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ break 2
+fi
+fi
+ done;;
+ esac
+ as_found=false
+done
+$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then :
+ CONFIG_SHELL=$SHELL as_have_required=yes
+fi; }
+IFS=$as_save_IFS
+
+
+ if test "x$CONFIG_SHELL" != x; then :
+ # We cannot yet assume a decent shell, so we have to provide a
+ # neutralization value for shells without unset; and this also
+ # works around shells that cannot unset nonexistent variables.
+ BASH_ENV=/dev/null
+ ENV=/dev/null
+ (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
+ export CONFIG_SHELL
+ exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"}
+fi
+
+ if test x$as_have_required = xno; then :
+ $as_echo "$0: This script requires a shell more modern than all"
+ $as_echo "$0: the shells that I found on your system."
+ if test x${ZSH_VERSION+set} = xset ; then
+ $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should"
+ $as_echo "$0: be upgraded to zsh 4.3.4 or later."
+ else
+ $as_echo "$0: Please tell bug-autoconf at gnu.org and
+$0: alban.mancheron at inria.fr about your system, including
+$0: any error possibly output before this message. Then
+$0: install a modern shell, or manually run the script
+$0: under such a shell if you do have one."
+ fi
+ exit 1
+fi
+fi
+fi
+SHELL=${CONFIG_SHELL-/bin/sh}
+export SHELL
+# Unset more variables known to interfere with behavior of common tools.
+CLICOLOR_FORCE= GREP_OPTIONS=
+unset CLICOLOR_FORCE GREP_OPTIONS
+
+## --------------------- ##
+## M4sh Shell Functions. ##
+## --------------------- ##
+# as_fn_unset VAR
+# ---------------
+# Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+
+# as_fn_set_status STATUS
+# -----------------------
+# Set $? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} # as_fn_set_status
+
+# as_fn_exit STATUS
+# -----------------
+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} # as_fn_exit
+
+# as_fn_mkdir_p
+# -------------
+# Create "$as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
+
+
+} # as_fn_mkdir_p
+# as_fn_append VAR VALUE
+# ----------------------
+# Append the text in VALUE to the end of the definition contained in VAR. Take
+# advantage of any shell optimizations that allow amortized linear growth over
+# repeated appends, instead of the typical quadratic growth present in naive
+# implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+# as_fn_arith ARG...
+# ------------------
+# Perform arithmetic evaluation on the ARGs, and store the result in the
+# global $as_val. Take advantage of shells that can avoid forks. The arguments
+# must be portable across $(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
+# ----------------------------------------
+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+# script with STATUS, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ $as_echo "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} # as_fn_error
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+
+ as_lineno_1=$LINENO as_lineno_1a=$LINENO
+ as_lineno_2=$LINENO as_lineno_2a=$LINENO
+ eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" &&
+ test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || {
+ # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-)
+ sed -n '
+ p
+ /[$]LINENO/=
+ ' <$as_myself |
+ sed '
+ s/[$]LINENO.*/&-/
+ t lineno
+ b
+ :lineno
+ N
+ :loop
+ s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
+ t loop
+ s/-\n.*//
+ ' >$as_me.lineno &&
+ chmod +x "$as_me.lineno" ||
+ { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
+
+ # Don't try to exec as it changes $[0], causing all sort of problems
+ # (the dirname of $[0] is not the place where we might find the
+ # original and so on. Autoconf is especially sensitive to this).
+ . "./$as_me.lineno"
+ # Exit status is that of the last command.
+ exit
+}
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in #(((((
+-n*)
+ case `echo 'xy\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -p'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -p'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -p'
+ fi
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p='mkdir -p "$as_dir"'
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+if test -x / >/dev/null 2>&1; then
+ as_test_x='test -x'
+else
+ if ls -dL / >/dev/null 2>&1; then
+ as_ls_L_option=L
+ else
+ as_ls_L_option=
+ fi
+ as_test_x='
+ eval sh -c '\''
+ if test -d "$1"; then
+ test -d "$1/.";
+ else
+ case $1 in #(
+ -*)set "./$1";;
+ esac;
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
+ ???[sx]*):;;*)false;;esac;fi
+ '\'' sh
+ '
+fi
+as_executable_p=$as_test_x
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+
+# Check that we are running under the correct shell.
+SHELL=${CONFIG_SHELL-/bin/sh}
+
+case X$lt_ECHO in
+X*--fallback-echo)
+ # Remove one level of quotation (which was required for Make).
+ ECHO=`echo "$lt_ECHO" | sed 's,\\\\\$\\$0,'$0','`
+ ;;
+esac
+
+ECHO=${lt_ECHO-echo}
+if test "X$1" = X--no-reexec; then
+ # Discard the --no-reexec flag, and continue.
+ shift
+elif test "X$1" = X--fallback-echo; then
+ # Avoid inline document here, it may be left over
+ :
+elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' ; then
+ # Yippee, $ECHO works!
+ :
+else
+ # Restart under the correct shell.
+ exec $SHELL "$0" --no-reexec ${1+"$@"}
+fi
+
+if test "X$1" = X--fallback-echo; then
+ # used as fallback echo
+ shift
+ cat <<_LT_EOF
+$*
+_LT_EOF
+ exit 0
+fi
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test -z "$lt_ECHO"; then
+ if test "X${echo_test_string+set}" != Xset; then
+ # find a string as large as possible, as long as the shell can cope with it
+ for cmd in 'sed 50q "$0"' 'sed 20q "$0"' 'sed 10q "$0"' 'sed 2q "$0"' 'echo test'; do
+ # expected sizes: less than 2Kb, 1Kb, 512 bytes, 16 bytes, ...
+ if { echo_test_string=`eval $cmd`; } 2>/dev/null &&
+ { test "X$echo_test_string" = "X$echo_test_string"; } 2>/dev/null
+ then
+ break
+ fi
+ done
+ fi
+
+ if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ :
+ else
+ # The Solaris, AIX, and Digital Unix default echo programs unquote
+ # backslashes. This makes it impossible to quote backslashes using
+ # echo "$something" | sed 's/\\/\\\\/g'
+ #
+ # So, first we look for a working echo in the user's PATH.
+
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for dir in $PATH /usr/ucb; do
+ IFS="$lt_save_ifs"
+ if (test -f $dir/echo || test -f $dir/echo$ac_exeext) &&
+ test "X`($dir/echo '\t') 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`($dir/echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ ECHO="$dir/echo"
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+
+ if test "X$ECHO" = Xecho; then
+ # We didn't find a better echo, so look for alternatives.
+ if test "X`{ print -r '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ print -r "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ # This shell has a builtin print -r that does the trick.
+ ECHO='print -r'
+ elif { test -f /bin/ksh || test -f /bin/ksh$ac_exeext; } &&
+ test "X$CONFIG_SHELL" != X/bin/ksh; then
+ # If we have ksh, try running configure again with it.
+ ORIGINAL_CONFIG_SHELL=${CONFIG_SHELL-/bin/sh}
+ export ORIGINAL_CONFIG_SHELL
+ CONFIG_SHELL=/bin/ksh
+ export CONFIG_SHELL
+ exec $CONFIG_SHELL "$0" --no-reexec ${1+"$@"}
+ else
+ # Try using printf.
+ ECHO='printf %s\n'
+ if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ # Cool, printf works
+ :
+ elif echo_testing_string=`($ORIGINAL_CONFIG_SHELL "$0" --fallback-echo '\t') 2>/dev/null` &&
+ test "X$echo_testing_string" = 'X\t' &&
+ echo_testing_string=`($ORIGINAL_CONFIG_SHELL "$0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ CONFIG_SHELL=$ORIGINAL_CONFIG_SHELL
+ export CONFIG_SHELL
+ SHELL="$CONFIG_SHELL"
+ export SHELL
+ ECHO="$CONFIG_SHELL $0 --fallback-echo"
+ elif echo_testing_string=`($CONFIG_SHELL "$0" --fallback-echo '\t') 2>/dev/null` &&
+ test "X$echo_testing_string" = 'X\t' &&
+ echo_testing_string=`($CONFIG_SHELL "$0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ ECHO="$CONFIG_SHELL $0 --fallback-echo"
+ else
+ # maybe with a smaller string...
+ prev=:
+
+ for cmd in 'echo test' 'sed 2q "$0"' 'sed 10q "$0"' 'sed 20q "$0"' 'sed 50q "$0"'; do
+ if { test "X$echo_test_string" = "X`eval $cmd`"; } 2>/dev/null
+ then
+ break
+ fi
+ prev="$cmd"
+ done
+
+ if test "$prev" != 'sed 50q "$0"'; then
+ echo_test_string=`eval $prev`
+ export echo_test_string
+ exec ${ORIGINAL_CONFIG_SHELL-${CONFIG_SHELL-/bin/sh}} "$0" ${1+"$@"}
+ else
+ # Oops. We lost completely, so just stick with echo.
+ ECHO=echo
+ fi
+ fi
+ fi
+ fi
+ fi
+fi
+
+# Copy echo and quote the copy suitably for passing to libtool from
+# the Makefile, instead of quoting the original, which is used later.
+lt_ECHO=$ECHO
+if test "X$lt_ECHO" = "X$CONFIG_SHELL $0 --fallback-echo"; then
+ lt_ECHO="$CONFIG_SHELL \\\$\$0 --fallback-echo"
+fi
+
+
+
+
+test -n "$DJDIR" || exec 7<&0 </dev/null
+exec 6>&1
+
+# Name of the host.
+# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status,
+# so uname gets run too.
+ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
+
+#
+# Initializations.
+#
+ac_default_prefix=/usr/local
+ac_clean_files=
+ac_config_libobj_dir=.
+LIBOBJS=
+cross_compiling=no
+subdirs=
+MFLAGS=
+MAKEFLAGS=
+
+# Identity of this package.
+PACKAGE_NAME='Library for manage progress bars'
+PACKAGE_TARNAME='libProgressBar'
+PACKAGE_VERSION='1.2.0'
+PACKAGE_STRING='Library for manage progress bars 1.2.0'
+PACKAGE_BUGREPORT='alban.mancheron at inria.fr'
+PACKAGE_URL=''
+
+ac_unique_file="libProgressBar/progressBar.cpp"
+# Factoring default headers for most tests.
+ac_includes_default="\
+#include <stdio.h>
+#ifdef HAVE_SYS_TYPES_H
+# include <sys/types.h>
+#endif
+#ifdef HAVE_SYS_STAT_H
+# include <sys/stat.h>
+#endif
+#ifdef STDC_HEADERS
+# include <stdlib.h>
+# include <stddef.h>
+#else
+# ifdef HAVE_STDLIB_H
+# include <stdlib.h>
+# endif
+#endif
+#ifdef HAVE_STRING_H
+# if !defined STDC_HEADERS && defined HAVE_MEMORY_H
+# include <memory.h>
+# endif
+# include <string.h>
+#endif
+#ifdef HAVE_STRINGS_H
+# include <strings.h>
+#endif
+#ifdef HAVE_INTTYPES_H
+# include <inttypes.h>
+#endif
+#ifdef HAVE_STDINT_H
+# include <stdint.h>
+#endif
+#ifdef HAVE_UNISTD_H
+# include <unistd.h>
+#endif"
+
+ac_subst_vars='am__EXEEXT_FALSE
+am__EXEEXT_TRUE
+LTLIBOBJS
+hacked_prefix
+LIBOBJS
+ALLOCA
+BUILD_DOC_FALSE
+BUILD_DOC_TRUE
+KPSEWHICH
+PDFTEX
+TEXI2DVI
+RPM_BUILDER
+DEB_BUILDER
+ARCH
+ISODATE
+CXXCPP
+am__fastdepCXX_FALSE
+am__fastdepCXX_TRUE
+CXXDEPMODE
+ac_ct_CXX
+CXXFLAGS
+CXX
+CPP
+OTOOL64
+OTOOL
+LIPO
+NMEDIT
+DSYMUTIL
+lt_ECHO
+RANLIB
+AR
+OBJDUMP
+LN_S
+NM
+ac_ct_DUMPBIN
+DUMPBIN
+LD
+FGREP
+EGREP
+GREP
+SED
+am__fastdepCC_FALSE
+am__fastdepCC_TRUE
+CCDEPMODE
+AMDEPBACKSLASH
+AMDEP_FALSE
+AMDEP_TRUE
+am__quote
+am__include
+DEPDIR
+OBJEXT
+EXEEXT
+ac_ct_CC
+CPPFLAGS
+LDFLAGS
+CFLAGS
+CC
+host_os
+host_vendor
+host_cpu
+host
+build_os
+build_vendor
+build_cpu
+build
+LIBTOOL
+am__untar
+am__tar
+AMTAR
+am__leading_dot
+SET_MAKE
+AWK
+mkdir_p
+MKDIR_P
+INSTALL_STRIP_PROGRAM
+STRIP
+install_sh
+MAKEINFO
+AUTOHEADER
+AUTOMAKE
+AUTOCONF
+ACLOCAL
+PACKAGE
+CYGPATH_W
+am__isrc
+INSTALL_DATA
+INSTALL_SCRIPT
+INSTALL_PROGRAM
+LIB_VERSION_EXT
+LIB_VERSION
+VERSION
+target_alias
+host_alias
+build_alias
+LIBS
+ECHO_T
+ECHO_N
+ECHO_C
+DEFS
+mandir
+localedir
+libdir
+psdir
+pdfdir
+dvidir
+htmldir
+infodir
+docdir
+oldincludedir
+includedir
+localstatedir
+sharedstatedir
+sysconfdir
+datadir
+datarootdir
+libexecdir
+sbindir
+bindir
+program_transform_name
+prefix
+exec_prefix
+PACKAGE_URL
+PACKAGE_BUGREPORT
+PACKAGE_STRING
+PACKAGE_VERSION
+PACKAGE_TARNAME
+PACKAGE_NAME
+PATH_SEPARATOR
+SHELL'
+ac_subst_files='postrm_script
+postinst_script'
+ac_user_opts='
+enable_option_checking
+enable_shared
+enable_static
+with_pic
+enable_fast_install
+enable_dependency_tracking
+with_gnu_ld
+enable_libtool_lock
+'
+ ac_precious_vars='build_alias
+host_alias
+target_alias
+CC
+CFLAGS
+LDFLAGS
+LIBS
+CPPFLAGS
+CPP
+CXX
+CXXFLAGS
+CCC
+CXXCPP'
+
+
+# Initialize some variables set by options.
+ac_init_help=
+ac_init_version=false
+ac_unrecognized_opts=
+ac_unrecognized_sep=
+# The variables have the same names as the options, with
+# dashes changed to underlines.
+cache_file=/dev/null
+exec_prefix=NONE
+no_create=
+no_recursion=
+prefix=NONE
+program_prefix=NONE
+program_suffix=NONE
+program_transform_name=s,x,x,
+silent=
+site=
+srcdir=
+verbose=
+x_includes=NONE
+x_libraries=NONE
+
+# Installation directory options.
+# These are left unexpanded so users can "make install exec_prefix=/foo"
+# and all the variables that are supposed to be based on exec_prefix
+# by default will actually change.
+# Use braces instead of parens because sh, perl, etc. also accept them.
+# (The list follows the same order as the GNU Coding Standards.)
+bindir='${exec_prefix}/bin'
+sbindir='${exec_prefix}/sbin'
+libexecdir='${exec_prefix}/libexec'
+datarootdir='${prefix}/share'
+datadir='${datarootdir}'
+sysconfdir='${prefix}/etc'
+sharedstatedir='${prefix}/com'
+localstatedir='${prefix}/var'
+includedir='${prefix}/include'
+oldincludedir='/usr/include'
+docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
+infodir='${datarootdir}/info'
+htmldir='${docdir}'
+dvidir='${docdir}'
+pdfdir='${docdir}'
+psdir='${docdir}'
+libdir='${exec_prefix}/lib'
+localedir='${datarootdir}/locale'
+mandir='${datarootdir}/man'
+
+ac_prev=
+ac_dashdash=
+for ac_option
+do
+ # If the previous option needs an argument, assign it.
+ if test -n "$ac_prev"; then
+ eval $ac_prev=\$ac_option
+ ac_prev=
+ continue
+ fi
+
+ case $ac_option in
+ *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
+ *=) ac_optarg= ;;
+ *) ac_optarg=yes ;;
+ esac
+
+ # Accept the important Cygnus configure options, so we can diagnose typos.
+
+ case $ac_dashdash$ac_option in
+ --)
+ ac_dashdash=yes ;;
+
+ -bindir | --bindir | --bindi | --bind | --bin | --bi)
+ ac_prev=bindir ;;
+ -bindir=* | --bindir=* | --bindi=* | --bind=* | --bin=* | --bi=*)
+ bindir=$ac_optarg ;;
+
+ -build | --build | --buil | --bui | --bu)
+ ac_prev=build_alias ;;
+ -build=* | --build=* | --buil=* | --bui=* | --bu=*)
+ build_alias=$ac_optarg ;;
+
+ -cache-file | --cache-file | --cache-fil | --cache-fi \
+ | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)
+ ac_prev=cache_file ;;
+ -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \
+ | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* | --c=*)
+ cache_file=$ac_optarg ;;
+
+ --config-cache | -C)
+ cache_file=config.cache ;;
+
+ -datadir | --datadir | --datadi | --datad)
+ ac_prev=datadir ;;
+ -datadir=* | --datadir=* | --datadi=* | --datad=*)
+ datadir=$ac_optarg ;;
+
+ -datarootdir | --datarootdir | --datarootdi | --datarootd | --dataroot \
+ | --dataroo | --dataro | --datar)
+ ac_prev=datarootdir ;;
+ -datarootdir=* | --datarootdir=* | --datarootdi=* | --datarootd=* \
+ | --dataroot=* | --dataroo=* | --dataro=* | --datar=*)
+ datarootdir=$ac_optarg ;;
+
+ -disable-* | --disable-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid feature name: $ac_useropt"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"enable_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--disable-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval enable_$ac_useropt=no ;;
+
+ -docdir | --docdir | --docdi | --doc | --do)
+ ac_prev=docdir ;;
+ -docdir=* | --docdir=* | --docdi=* | --doc=* | --do=*)
+ docdir=$ac_optarg ;;
+
+ -dvidir | --dvidir | --dvidi | --dvid | --dvi | --dv)
+ ac_prev=dvidir ;;
+ -dvidir=* | --dvidir=* | --dvidi=* | --dvid=* | --dvi=* | --dv=*)
+ dvidir=$ac_optarg ;;
+
+ -enable-* | --enable-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid feature name: $ac_useropt"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"enable_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--enable-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval enable_$ac_useropt=\$ac_optarg ;;
+
+ -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \
+ | --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \
+ | --exec | --exe | --ex)
+ ac_prev=exec_prefix ;;
+ -exec-prefix=* | --exec_prefix=* | --exec-prefix=* | --exec-prefi=* \
+ | --exec-pref=* | --exec-pre=* | --exec-pr=* | --exec-p=* | --exec-=* \
+ | --exec=* | --exe=* | --ex=*)
+ exec_prefix=$ac_optarg ;;
+
+ -gas | --gas | --ga | --g)
+ # Obsolete; use --with-gas.
+ with_gas=yes ;;
+
+ -help | --help | --hel | --he | -h)
+ ac_init_help=long ;;
+ -help=r* | --help=r* | --hel=r* | --he=r* | -hr*)
+ ac_init_help=recursive ;;
+ -help=s* | --help=s* | --hel=s* | --he=s* | -hs*)
+ ac_init_help=short ;;
+
+ -host | --host | --hos | --ho)
+ ac_prev=host_alias ;;
+ -host=* | --host=* | --hos=* | --ho=*)
+ host_alias=$ac_optarg ;;
+
+ -htmldir | --htmldir | --htmldi | --htmld | --html | --htm | --ht)
+ ac_prev=htmldir ;;
+ -htmldir=* | --htmldir=* | --htmldi=* | --htmld=* | --html=* | --htm=* \
+ | --ht=*)
+ htmldir=$ac_optarg ;;
+
+ -includedir | --includedir | --includedi | --included | --include \
+ | --includ | --inclu | --incl | --inc)
+ ac_prev=includedir ;;
+ -includedir=* | --includedir=* | --includedi=* | --included=* | --include=* \
+ | --includ=* | --inclu=* | --incl=* | --inc=*)
+ includedir=$ac_optarg ;;
+
+ -infodir | --infodir | --infodi | --infod | --info | --inf)
+ ac_prev=infodir ;;
+ -infodir=* | --infodir=* | --infodi=* | --infod=* | --info=* | --inf=*)
+ infodir=$ac_optarg ;;
+
+ -libdir | --libdir | --libdi | --libd)
+ ac_prev=libdir ;;
+ -libdir=* | --libdir=* | --libdi=* | --libd=*)
+ libdir=$ac_optarg ;;
+
+ -libexecdir | --libexecdir | --libexecdi | --libexecd | --libexec \
+ | --libexe | --libex | --libe)
+ ac_prev=libexecdir ;;
+ -libexecdir=* | --libexecdir=* | --libexecdi=* | --libexecd=* | --libexec=* \
+ | --libexe=* | --libex=* | --libe=*)
+ libexecdir=$ac_optarg ;;
+
+ -localedir | --localedir | --localedi | --localed | --locale)
+ ac_prev=localedir ;;
+ -localedir=* | --localedir=* | --localedi=* | --localed=* | --locale=*)
+ localedir=$ac_optarg ;;
+
+ -localstatedir | --localstatedir | --localstatedi | --localstated \
+ | --localstate | --localstat | --localsta | --localst | --locals)
+ ac_prev=localstatedir ;;
+ -localstatedir=* | --localstatedir=* | --localstatedi=* | --localstated=* \
+ | --localstate=* | --localstat=* | --localsta=* | --localst=* | --locals=*)
+ localstatedir=$ac_optarg ;;
+
+ -mandir | --mandir | --mandi | --mand | --man | --ma | --m)
+ ac_prev=mandir ;;
+ -mandir=* | --mandir=* | --mandi=* | --mand=* | --man=* | --ma=* | --m=*)
+ mandir=$ac_optarg ;;
+
+ -nfp | --nfp | --nf)
+ # Obsolete; use --without-fp.
+ with_fp=no ;;
+
+ -no-create | --no-create | --no-creat | --no-crea | --no-cre \
+ | --no-cr | --no-c | -n)
+ no_create=yes ;;
+
+ -no-recursion | --no-recursion | --no-recursio | --no-recursi \
+ | --no-recurs | --no-recur | --no-recu | --no-rec | --no-re | --no-r)
+ no_recursion=yes ;;
+
+ -oldincludedir | --oldincludedir | --oldincludedi | --oldincluded \
+ | --oldinclude | --oldinclud | --oldinclu | --oldincl | --oldinc \
+ | --oldin | --oldi | --old | --ol | --o)
+ ac_prev=oldincludedir ;;
+ -oldincludedir=* | --oldincludedir=* | --oldincludedi=* | --oldincluded=* \
+ | --oldinclude=* | --oldinclud=* | --oldinclu=* | --oldincl=* | --oldinc=* \
+ | --oldin=* | --oldi=* | --old=* | --ol=* | --o=*)
+ oldincludedir=$ac_optarg ;;
+
+ -prefix | --prefix | --prefi | --pref | --pre | --pr | --p)
+ ac_prev=prefix ;;
+ -prefix=* | --prefix=* | --prefi=* | --pref=* | --pre=* | --pr=* | --p=*)
+ prefix=$ac_optarg ;;
+
+ -program-prefix | --program-prefix | --program-prefi | --program-pref \
+ | --program-pre | --program-pr | --program-p)
+ ac_prev=program_prefix ;;
+ -program-prefix=* | --program-prefix=* | --program-prefi=* \
+ | --program-pref=* | --program-pre=* | --program-pr=* | --program-p=*)
+ program_prefix=$ac_optarg ;;
+
+ -program-suffix | --program-suffix | --program-suffi | --program-suff \
+ | --program-suf | --program-su | --program-s)
+ ac_prev=program_suffix ;;
+ -program-suffix=* | --program-suffix=* | --program-suffi=* \
+ | --program-suff=* | --program-suf=* | --program-su=* | --program-s=*)
+ program_suffix=$ac_optarg ;;
+
+ -program-transform-name | --program-transform-name \
+ | --program-transform-nam | --program-transform-na \
+ | --program-transform-n | --program-transform- \
+ | --program-transform | --program-transfor \
+ | --program-transfo | --program-transf \
+ | --program-trans | --program-tran \
+ | --progr-tra | --program-tr | --program-t)
+ ac_prev=program_transform_name ;;
+ -program-transform-name=* | --program-transform-name=* \
+ | --program-transform-nam=* | --program-transform-na=* \
+ | --program-transform-n=* | --program-transform-=* \
+ | --program-transform=* | --program-transfor=* \
+ | --program-transfo=* | --program-transf=* \
+ | --program-trans=* | --program-tran=* \
+ | --progr-tra=* | --program-tr=* | --program-t=*)
+ program_transform_name=$ac_optarg ;;
+
+ -pdfdir | --pdfdir | --pdfdi | --pdfd | --pdf | --pd)
+ ac_prev=pdfdir ;;
+ -pdfdir=* | --pdfdir=* | --pdfdi=* | --pdfd=* | --pdf=* | --pd=*)
+ pdfdir=$ac_optarg ;;
+
+ -psdir | --psdir | --psdi | --psd | --ps)
+ ac_prev=psdir ;;
+ -psdir=* | --psdir=* | --psdi=* | --psd=* | --ps=*)
+ psdir=$ac_optarg ;;
+
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil)
+ silent=yes ;;
+
+ -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
+ ac_prev=sbindir ;;
+ -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
+ | --sbi=* | --sb=*)
+ sbindir=$ac_optarg ;;
+
+ -sharedstatedir | --sharedstatedir | --sharedstatedi \
+ | --sharedstated | --sharedstate | --sharedstat | --sharedsta \
+ | --sharedst | --shareds | --shared | --share | --shar \
+ | --sha | --sh)
+ ac_prev=sharedstatedir ;;
+ -sharedstatedir=* | --sharedstatedir=* | --sharedstatedi=* \
+ | --sharedstated=* | --sharedstate=* | --sharedstat=* | --sharedsta=* \
+ | --sharedst=* | --shareds=* | --shared=* | --share=* | --shar=* \
+ | --sha=* | --sh=*)
+ sharedstatedir=$ac_optarg ;;
+
+ -site | --site | --sit)
+ ac_prev=site ;;
+ -site=* | --site=* | --sit=*)
+ site=$ac_optarg ;;
+
+ -srcdir | --srcdir | --srcdi | --srcd | --src | --sr)
+ ac_prev=srcdir ;;
+ -srcdir=* | --srcdir=* | --srcdi=* | --srcd=* | --src=* | --sr=*)
+ srcdir=$ac_optarg ;;
+
+ -sysconfdir | --sysconfdir | --sysconfdi | --sysconfd | --sysconf \
+ | --syscon | --sysco | --sysc | --sys | --sy)
+ ac_prev=sysconfdir ;;
+ -sysconfdir=* | --sysconfdir=* | --sysconfdi=* | --sysconfd=* | --sysconf=* \
+ | --syscon=* | --sysco=* | --sysc=* | --sys=* | --sy=*)
+ sysconfdir=$ac_optarg ;;
+
+ -target | --target | --targe | --targ | --tar | --ta | --t)
+ ac_prev=target_alias ;;
+ -target=* | --target=* | --targe=* | --targ=* | --tar=* | --ta=* | --t=*)
+ target_alias=$ac_optarg ;;
+
+ -v | -verbose | --verbose | --verbos | --verbo | --verb)
+ verbose=yes ;;
+
+ -version | --version | --versio | --versi | --vers | -V)
+ ac_init_version=: ;;
+
+ -with-* | --with-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid package name: $ac_useropt"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"with_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--with-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval with_$ac_useropt=\$ac_optarg ;;
+
+ -without-* | --without-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid package name: $ac_useropt"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"with_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--without-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval with_$ac_useropt=no ;;
+
+ --x)
+ # Obsolete; use --with-x.
+ with_x=yes ;;
+
+ -x-includes | --x-includes | --x-include | --x-includ | --x-inclu \
+ | --x-incl | --x-inc | --x-in | --x-i)
+ ac_prev=x_includes ;;
+ -x-includes=* | --x-includes=* | --x-include=* | --x-includ=* | --x-inclu=* \
+ | --x-incl=* | --x-inc=* | --x-in=* | --x-i=*)
+ x_includes=$ac_optarg ;;
+
+ -x-libraries | --x-libraries | --x-librarie | --x-librari \
+ | --x-librar | --x-libra | --x-libr | --x-lib | --x-li | --x-l)
+ ac_prev=x_libraries ;;
+ -x-libraries=* | --x-libraries=* | --x-librarie=* | --x-librari=* \
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+for ac_var in $ac_precious_vars; do
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+ eval ac_cv_env_${ac_var}_value=\$${ac_var}
+done
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+#
+if test "$ac_init_help" = "long"; then
+ # Omit some internal or obsolete options to make the list less imposing.
+ # This message is too long to be a string in the A/UX 3.1 sh.
+ cat <<_ACEOF
+\`configure' configures Library for manage progress bars 1.2.0 to adapt to many kinds of systems.
+
+Usage: $0 [OPTION]... [VAR=VALUE]...
+
+To assign environment variables (e.g., CC, CFLAGS...), specify them as
+VAR=VALUE. See below for descriptions of some of the useful variables.
+
+Defaults for the options are specified in brackets.
+
+Configuration:
+ -h, --help display this help and exit
+ --help=short display options specific to this package
+ --help=recursive display the short help of all the included packages
+ -V, --version display version information and exit
+ -q, --quiet, --silent do not print \`checking ...' messages
+ --cache-file=FILE cache test results in FILE [disabled]
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+ -n, --no-create do not create output files
+ --srcdir=DIR find the sources in DIR [configure dir or \`..']
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+Installation directories:
+ --prefix=PREFIX install architecture-independent files in PREFIX
+ [$ac_default_prefix]
+ --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX
+ [PREFIX]
+
+By default, \`make install' will install all the files in
+\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify
+an installation prefix other than \`$ac_default_prefix' using \`--prefix',
+for instance \`--prefix=\$HOME'.
+
+For better control, use the options below.
+
+Fine tuning of the installation directories:
+ --bindir=DIR user executables [EPREFIX/bin]
+ --sbindir=DIR system admin executables [EPREFIX/sbin]
+ --libexecdir=DIR program executables [EPREFIX/libexec]
+ --sysconfdir=DIR read-only single-machine data [PREFIX/etc]
+ --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com]
+ --localstatedir=DIR modifiable single-machine data [PREFIX/var]
+ --libdir=DIR object code libraries [EPREFIX/lib]
+ --includedir=DIR C header files [PREFIX/include]
+ --oldincludedir=DIR C header files for non-gcc [/usr/include]
+ --datarootdir=DIR read-only arch.-independent data root [PREFIX/share]
+ --datadir=DIR read-only architecture-independent data [DATAROOTDIR]
+ --infodir=DIR info documentation [DATAROOTDIR/info]
+ --localedir=DIR locale-dependent data [DATAROOTDIR/locale]
+ --mandir=DIR man documentation [DATAROOTDIR/man]
+ --docdir=DIR documentation root [DATAROOTDIR/doc/libProgressBar]
+ --htmldir=DIR html documentation [DOCDIR]
+ --dvidir=DIR dvi documentation [DOCDIR]
+ --pdfdir=DIR pdf documentation [DOCDIR]
+ --psdir=DIR ps documentation [DOCDIR]
+_ACEOF
+
+ cat <<\_ACEOF
+
+Program names:
+ --program-prefix=PREFIX prepend PREFIX to installed program names
+ --program-suffix=SUFFIX append SUFFIX to installed program names
+ --program-transform-name=PROGRAM run sed PROGRAM on installed program names
+
+System types:
+ --build=BUILD configure for building on BUILD [guessed]
+ --host=HOST cross-compile to build programs to run on HOST [BUILD]
+_ACEOF
+fi
+
+if test -n "$ac_init_help"; then
+ case $ac_init_help in
+ short | recursive ) echo "Configuration of Library for manage progress bars 1.2.0:";;
+ esac
+ cat <<\_ACEOF
+
+Optional Features:
+ --disable-option-checking ignore unrecognized --enable/--with options
+ --disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
+ --enable-FEATURE[=ARG] include FEATURE [ARG=yes]
+ --enable-shared[=PKGS] build shared libraries [default=yes]
+ --enable-static[=PKGS] build static libraries [default=yes]
+ --enable-fast-install[=PKGS]
+ optimize for fast installation [default=yes]
+ --disable-dependency-tracking speeds up one-time build
+ --enable-dependency-tracking do not reject slow dependency extractors
+ --disable-libtool-lock avoid locking (might break parallel builds)
+
+Optional Packages:
+ --with-PACKAGE[=ARG] use PACKAGE [ARG=yes]
+ --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no)
+ --with-pic try to use only PIC/non-PIC objects [default=use
+ both]
+ --with-gnu-ld assume the C compiler uses GNU ld [default=no]
+
+Some influential environment variables:
+ CC C compiler command
+ CFLAGS C compiler flags
+ LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
+ nonstandard directory <lib dir>
+ LIBS libraries to pass to the linker, e.g. -l<library>
+ CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
+ you have headers in a nonstandard directory <include dir>
+ CPP C preprocessor
+ CXX C++ compiler command
+ CXXFLAGS C++ compiler flags
+ CXXCPP C++ preprocessor
+
+Use these variables to override the choices made by `configure' or to help
+it to find libraries and programs with nonstandard names/locations.
+
+Report bugs to <alban.mancheron at inria.fr>.
+_ACEOF
+ac_status=$?
+fi
+
+if test "$ac_init_help" = "recursive"; then
+ # If there are subdirs, report their specific --help.
+ for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue
+ test -d "$ac_dir" ||
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+case "$ac_dir" in
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+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
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+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+ cd "$ac_dir" || { ac_status=$?; continue; }
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+
+test -n "$ac_init_help" && exit $ac_status
+if $ac_init_version; then
+ cat <<\_ACEOF
+Library for manage progress bars configure 1.2.0
+generated by GNU Autoconf 2.67
+
+Copyright (C) 2010 Free Software Foundation, Inc.
+This configure script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it.
+_ACEOF
+ exit
+fi
+
+## ------------------------ ##
+## Autoconf initialization. ##
+## ------------------------ ##
+
+# ac_fn_c_try_compile LINENO
+# --------------------------
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+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
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+ ac_status=$?
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+} # ac_fn_c_try_compile
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+# ac_fn_c_try_link LINENO
+# -----------------------
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+ # Delete the IPA/IPO (Inter Procedural Analysis/Optimization) information
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+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_link
+
+# ac_fn_c_check_header_compile LINENO HEADER VAR INCLUDES
+# -------------------------------------------------------
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+ $as_echo_n "(cached) " >&6
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+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+#include <$2>
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
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+eval ac_res=\$$3
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+} # ac_fn_c_check_header_compile
+
+# ac_fn_c_try_cpp LINENO
+# ----------------------
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+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_cpp
+
+# ac_fn_c_try_run LINENO
+# ----------------------
+# Try to link conftest.$ac_ext, and return whether this succeeded. Assumes
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+{
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+ { { case "(($ac_try" in
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+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; }; then :
+ ac_retval=0
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+ $as_echo "$as_me: program exited with status $ac_status" >&5
+ $as_echo "$as_me: failed program was:" >&5
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+ ac_retval=$ac_status
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+ rm -rf conftest.dSYM conftest_ipa8_conftest.oo
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
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+
+# ac_fn_c_check_func LINENO FUNC VAR
+# ----------------------------------
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+ac_fn_c_check_func ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
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+ $as_echo_n "(cached) " >&6
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+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+/* Define $2 to an innocuous variant, in case <limits.h> declares $2.
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+#define $2 innocuous_$2
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $2 (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
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+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
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+#undef $2
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $2 ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_$2 || defined __stub___$2
+choke me
+#endif
+
+int
+main ()
+{
+return $2 ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ eval "$3=yes"
+else
+ eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_c_check_func
+
+# ac_fn_cxx_try_compile LINENO
+# ----------------------------
+# Try to compile conftest.$ac_ext, and return whether this succeeded.
+ac_fn_cxx_try_compile ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext
+ if { { ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compile") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_cxx_try_compile
+
+# ac_fn_cxx_try_cpp LINENO
+# ------------------------
+# Try to preprocess conftest.$ac_ext, and return whether this succeeded.
+ac_fn_cxx_try_cpp ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if { { ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } > conftest.i && {
+ test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_cxx_try_cpp
+
+# ac_fn_cxx_try_link LINENO
+# -------------------------
+# Try to link conftest.$ac_ext, and return whether this succeeded.
+ac_fn_cxx_try_link ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext conftest$ac_exeext
+ if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ # Delete the IPA/IPO (Inter Procedural Analysis/Optimization) information
+ # created by the PGI compiler (conftest_ipa8_conftest.oo), as it would
+ # interfere with the next link command; also delete a directory that is
+ # left behind by Apple's compiler. We do this before executing the actions.
+ rm -rf conftest.dSYM conftest_ipa8_conftest.oo
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_cxx_try_link
+
+# ac_fn_c_check_header_mongrel LINENO HEADER VAR INCLUDES
+# -------------------------------------------------------
+# Tests whether HEADER exists, giving a warning if it cannot be compiled using
+# the include files in INCLUDES and setting the cache variable VAR
+# accordingly.
+ac_fn_c_check_header_mongrel ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if eval "test \"\${$3+set}\"" = set; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+else
+ # Is the header compilable?
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 usability" >&5
+$as_echo_n "checking $2 usability... " >&6; }
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+#include <$2>
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_header_compiler=yes
+else
+ ac_header_compiler=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_compiler" >&5
+$as_echo "$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 presence" >&5
+$as_echo_n "checking $2 presence... " >&6; }
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <$2>
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+ ac_header_preproc=yes
+else
+ ac_header_preproc=no
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_preproc" >&5
+$as_echo "$ac_header_preproc" >&6; }
+
+# So? What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in #((
+ yes:no: )
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&5
+$as_echo "$as_me: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
+ ;;
+ no:yes:* )
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: present but cannot be compiled" >&5
+$as_echo "$as_me: WARNING: $2: present but cannot be compiled" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: check for missing prerequisite headers?" >&5
+$as_echo "$as_me: WARNING: $2: check for missing prerequisite headers?" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: see the Autoconf documentation" >&5
+$as_echo "$as_me: WARNING: $2: see the Autoconf documentation" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&5
+$as_echo "$as_me: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
+( $as_echo "## --------------------------------------- ##
+## Report this to alban.mancheron at inria.fr ##
+## --------------------------------------- ##"
+ ) | sed "s/^/$as_me: WARNING: /" >&2
+ ;;
+esac
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ eval "$3=\$ac_header_compiler"
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+fi
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_c_check_header_mongrel
+
+# ac_fn_c_check_member LINENO AGGR MEMBER VAR INCLUDES
+# ----------------------------------------------------
+# Tries to find if the field MEMBER exists in type AGGR, after including
+# INCLUDES, setting cache variable VAR accordingly.
+ac_fn_c_check_member ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2.$3" >&5
+$as_echo_n "checking for $2.$3... " >&6; }
+if eval "test \"\${$4+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$5
+int
+main ()
+{
+static $2 ac_aggr;
+if (ac_aggr.$3)
+return 0;
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ eval "$4=yes"
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$5
+int
+main ()
+{
+static $2 ac_aggr;
+if (sizeof ac_aggr.$3)
+return 0;
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ eval "$4=yes"
+else
+ eval "$4=no"
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+eval ac_res=\$$4
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_c_check_member
+cat >config.log <<_ACEOF
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by Library for manage progress bars $as_me 1.2.0, which was
+generated by GNU Autoconf 2.67. Invocation command line was
+
+ $ $0 $@
+
+_ACEOF
+exec 5>>config.log
+{
+cat <<_ASUNAME
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = `(hostname || uname -n) 2>/dev/null | sed 1q`
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null || echo unknown`
+
+/bin/arch = `(/bin/arch) 2>/dev/null || echo unknown`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null || echo unknown`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown`
+/usr/bin/hostinfo = `(/usr/bin/hostinfo) 2>/dev/null || echo unknown`
+/bin/machine = `(/bin/machine) 2>/dev/null || echo unknown`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null || echo unknown`
+/bin/universe = `(/bin/universe) 2>/dev/null || echo unknown`
+
+_ASUNAME
+
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ $as_echo "PATH: $as_dir"
+ done
+IFS=$as_save_IFS
+
+} >&5
+
+cat >&5 <<_ACEOF
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+_ACEOF
+
+
+# Keep a trace of the command line.
+# Strip out --no-create and --no-recursion so they do not pile up.
+# Strip out --silent because we don't want to record it for future runs.
+# Also quote any args containing shell meta-characters.
+# Make two passes to allow for proper duplicate-argument suppression.
+ac_configure_args=
+ac_configure_args0=
+ac_configure_args1=
+ac_must_keep_next=false
+for ac_pass in 1 2
+do
+ for ac_arg
+ do
+ case $ac_arg in
+ -no-create | --no-c* | -n | -no-recursion | --no-r*) continue ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil)
+ continue ;;
+ *\'*)
+ ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ case $ac_pass in
+ 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;;
+ 2)
+ as_fn_append ac_configure_args1 " '$ac_arg'"
+ if test $ac_must_keep_next = true; then
+ ac_must_keep_next=false # Got value, back to normal.
+ else
+ case $ac_arg in
+ *=* | --config-cache | -C | -disable-* | --disable-* \
+ | -enable-* | --enable-* | -gas | --g* | -nfp | --nf* \
+ | -q | -quiet | --q* | -silent | --sil* | -v | -verb* \
+ | -with-* | --with-* | -without-* | --without-* | --x)
+ case "$ac_configure_args0 " in
+ "$ac_configure_args1"*" '$ac_arg' "* ) continue ;;
+ esac
+ ;;
+ -* ) ac_must_keep_next=true ;;
+ esac
+ fi
+ as_fn_append ac_configure_args " '$ac_arg'"
+ ;;
+ esac
+ done
+done
+{ ac_configure_args0=; unset ac_configure_args0;}
+{ ac_configure_args1=; unset ac_configure_args1;}
+
+# When interrupted or exit'd, cleanup temporary files, and complete
+# config.log. We remove comments because anyway the quotes in there
+# would cause problems or look ugly.
+# WARNING: Use '\'' to represent an apostrophe within the trap.
+# WARNING: Do not start the trap code with a newline, due to a FreeBSD 4.0 bug.
+trap 'exit_status=$?
+ # Save into config.log some information that might help in debugging.
+ {
+ echo
+
+ $as_echo "## ---------------- ##
+## Cache variables. ##
+## ---------------- ##"
+ echo
+ # The following way of writing the cache mishandles newlines in values,
+(
+ for ac_var in `(set) 2>&1 | sed -n '\''s/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'\''`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) { eval $ac_var=; unset $ac_var;} ;;
+ esac ;;
+ esac
+ done
+ (set) 2>&1 |
+ case $as_nl`(ac_space='\'' '\''; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ sed -n \
+ "s/'\''/'\''\\\\'\'''\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\''\\2'\''/p"
+ ;; #(
+ *)
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+)
+ echo
+
+ $as_echo "## ----------------- ##
+## Output variables. ##
+## ----------------- ##"
+ echo
+ for ac_var in $ac_subst_vars
+ do
+ eval ac_val=\$$ac_var
+ case $ac_val in
+ *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+ esac
+ $as_echo "$ac_var='\''$ac_val'\''"
+ done | sort
+ echo
+
+ if test -n "$ac_subst_files"; then
+ $as_echo "## ------------------- ##
+## File substitutions. ##
+## ------------------- ##"
+ echo
+ for ac_var in $ac_subst_files
+ do
+ eval ac_val=\$$ac_var
+ case $ac_val in
+ *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+ esac
+ $as_echo "$ac_var='\''$ac_val'\''"
+ done | sort
+ echo
+ fi
+
+ if test -s confdefs.h; then
+ $as_echo "## ----------- ##
+## confdefs.h. ##
+## ----------- ##"
+ echo
+ cat confdefs.h
+ echo
+ fi
+ test "$ac_signal" != 0 &&
+ $as_echo "$as_me: caught signal $ac_signal"
+ $as_echo "$as_me: exit $exit_status"
+ } >&5
+ rm -f core *.core core.conftest.* &&
+ rm -f -r conftest* confdefs* conf$$* $ac_clean_files &&
+ exit $exit_status
+' 0
+for ac_signal in 1 2 13 15; do
+ trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal
+done
+ac_signal=0
+
+# confdefs.h avoids OS command line length limits that DEFS can exceed.
+rm -f -r conftest* confdefs.h
+
+$as_echo "/* confdefs.h */" > confdefs.h
+
+# Predefined preprocessor variables.
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_NAME "$PACKAGE_NAME"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_TARNAME "$PACKAGE_TARNAME"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_VERSION "$PACKAGE_VERSION"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_STRING "$PACKAGE_STRING"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT"
+_ACEOF
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_URL "$PACKAGE_URL"
+_ACEOF
+
+
+# Let the site file select an alternate cache file if it wants to.
+# Prefer an explicitly selected file to automatically selected ones.
+ac_site_file1=NONE
+ac_site_file2=NONE
+if test -n "$CONFIG_SITE"; then
+ # We do not want a PATH search for config.site.
+ case $CONFIG_SITE in #((
+ -*) ac_site_file1=./$CONFIG_SITE;;
+ */*) ac_site_file1=$CONFIG_SITE;;
+ *) ac_site_file1=./$CONFIG_SITE;;
+ esac
+elif test "x$prefix" != xNONE; then
+ ac_site_file1=$prefix/share/config.site
+ ac_site_file2=$prefix/etc/config.site
+else
+ ac_site_file1=$ac_default_prefix/share/config.site
+ ac_site_file2=$ac_default_prefix/etc/config.site
+fi
+for ac_site_file in "$ac_site_file1" "$ac_site_file2"
+do
+ test "x$ac_site_file" = xNONE && continue
+ if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5
+$as_echo "$as_me: loading site script $ac_site_file" >&6;}
+ sed 's/^/| /' "$ac_site_file" >&5
+ . "$ac_site_file" \
+ || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "failed to load site script $ac_site_file
+See \`config.log' for more details" "$LINENO" 5 ; }
+ fi
+done
+
+if test -r "$cache_file"; then
+ # Some versions of bash will fail to source /dev/null (special files
+ # actually), so we avoid doing that. DJGPP emulates it as a regular file.
+ if test /dev/null != "$cache_file" && test -f "$cache_file"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5
+$as_echo "$as_me: loading cache $cache_file" >&6;}
+ case $cache_file in
+ [\\/]* | ?:[\\/]* ) . "$cache_file";;
+ *) . "./$cache_file";;
+ esac
+ fi
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5
+$as_echo "$as_me: creating cache $cache_file" >&6;}
+ >$cache_file
+fi
+
+# Check that the precious variables saved in the cache have kept the same
+# value.
+ac_cache_corrupted=false
+for ac_var in $ac_precious_vars; do
+ eval ac_old_set=\$ac_cv_env_${ac_var}_set
+ eval ac_new_set=\$ac_env_${ac_var}_set
+ eval ac_old_val=\$ac_cv_env_${ac_var}_value
+ eval ac_new_val=\$ac_env_${ac_var}_value
+ case $ac_old_set,$ac_new_set in
+ set,)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
+$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,set)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5
+$as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,);;
+ *)
+ if test "x$ac_old_val" != "x$ac_new_val"; then
+ # differences in whitespace do not lead to failure.
+ ac_old_val_w=`echo x $ac_old_val`
+ ac_new_val_w=`echo x $ac_new_val`
+ if test "$ac_old_val_w" != "$ac_new_val_w"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5
+$as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
+ ac_cache_corrupted=:
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5
+$as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;}
+ eval $ac_var=\$ac_old_val
+ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5
+$as_echo "$as_me: former value: \`$ac_old_val'" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5
+$as_echo "$as_me: current value: \`$ac_new_val'" >&2;}
+ fi;;
+ esac
+ # Pass precious variables to config.status.
+ if test "$ac_new_set" = set; then
+ case $ac_new_val in
+ *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
+ *) ac_arg=$ac_var=$ac_new_val ;;
+ esac
+ case " $ac_configure_args " in
+ *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy.
+ *) as_fn_append ac_configure_args " '$ac_arg'" ;;
+ esac
+ fi
+done
+if $ac_cache_corrupted; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
+$as_echo "$as_me: error: changes in the environment can compromise the build" >&2;}
+ as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
+fi
+## -------------------- ##
+## Main body of script. ##
+## -------------------- ##
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+
+
+
+LIB_CURRENT=1
+LIB_REVISION=2
+LIB_AGE=1
+LIB_VERSION=$LIB_CURRENT:$LIB_REVISION:$LIB_AGE
+
+
+
+LIB_VERSION_EXT="1"_"2"_"0"
+
+
+am__api_version='1.11'
+
+ac_aux_dir=
+for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
+ if test -f "$ac_dir/install-sh"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install-sh -c"
+ break
+ elif test -f "$ac_dir/install.sh"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install.sh -c"
+ break
+ elif test -f "$ac_dir/shtool"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/shtool install -c"
+ break
+ fi
+done
+if test -z "$ac_aux_dir"; then
+ as_fn_error $? "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5
+fi
+
+# These three variables are undocumented and unsupported,
+# and are intended to be withdrawn in a future Autoconf release.
+# They can cause serious problems if a builder's source tree is in a directory
+# whose full name contains unusual characters.
+ac_config_guess="$SHELL $ac_aux_dir/config.guess" # Please don't use this var.
+ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var.
+ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var.
+
+
+# Find a good install program. We prefer a C program (faster),
+# so one script is as good as another. But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AmigaOS /C/install, which installs bootblocks on floppy discs
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# OS/2's system install, which has a completely different semantic
+# ./install, which can be erroneously created by make from ./install.sh.
+# Reject install programs that cannot install multiple files.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5
+$as_echo_n "checking for a BSD-compatible install... " >&6; }
+if test -z "$INSTALL"; then
+if test "${ac_cv_path_install+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ # Account for people who put trailing slashes in PATH elements.
+case $as_dir/ in #((
+ ./ | .// | /[cC]/* | \
+ /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
+ ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \
+ /usr/ucb/* ) ;;
+ *)
+ # OSF1 and SCO ODT 3.0 have their own names for install.
+ # Don't use installbsd from OSF since it installs stuff as root
+ # by default.
+ for ac_prog in ginstall scoinst install; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
+ if test $ac_prog = install &&
+ grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # AIX install. It has an incompatible calling convention.
+ :
+ elif test $ac_prog = install &&
+ grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # program-specific install script used by HP pwplus--don't use.
+ :
+ else
+ rm -rf conftest.one conftest.two conftest.dir
+ echo one > conftest.one
+ echo two > conftest.two
+ mkdir conftest.dir
+ if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" &&
+ test -s conftest.one && test -s conftest.two &&
+ test -s conftest.dir/conftest.one &&
+ test -s conftest.dir/conftest.two
+ then
+ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
+ break 3
+ fi
+ fi
+ fi
+ done
+ done
+ ;;
+esac
+
+ done
+IFS=$as_save_IFS
+
+rm -rf conftest.one conftest.two conftest.dir
+
+fi
+ if test "${ac_cv_path_install+set}" = set; then
+ INSTALL=$ac_cv_path_install
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for INSTALL within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ INSTALL=$ac_install_sh
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5
+$as_echo "$INSTALL" >&6; }
+
+# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
+# It thinks the first close brace ends the variable substitution.
+test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5
+$as_echo_n "checking whether build environment is sane... " >&6; }
+# Just in case
+sleep 1
+echo timestamp > conftest.file
+# Reject unsafe characters in $srcdir or the absolute working directory
+# name. Accept space and tab only in the latter.
+am_lf='
+'
+case `pwd` in
+ *[\\\"\#\$\&\'\`$am_lf]*)
+ as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5 ;;
+esac
+case $srcdir in
+ *[\\\"\#\$\&\'\`$am_lf\ \ ]*)
+ as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5 ;;
+esac
+
+# Do `set' in a subshell so we don't clobber the current shell's
+# arguments. Must try -L first in case configure is actually a
+# symlink; some systems play weird games with the mod time of symlinks
+# (eg FreeBSD returns the mod time of the symlink's containing
+# directory).
+if (
+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
+ if test "$*" = "X"; then
+ # -L didn't work.
+ set X `ls -t "$srcdir/configure" conftest.file`
+ fi
+ rm -f conftest.file
+ if test "$*" != "X $srcdir/configure conftest.file" \
+ && test "$*" != "X conftest.file $srcdir/configure"; then
+
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ as_fn_error $? "ls -t appears to fail. Make sure there is not a broken
+alias in your environment" "$LINENO" 5
+ fi
+
+ test "$2" = conftest.file
+ )
+then
+ # Ok.
+ :
+else
+ as_fn_error $? "newly created file is older than distributed files!
+Check your system clock" "$LINENO" 5
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+test "$program_prefix" != NONE &&
+ program_transform_name="s&^&$program_prefix&;$program_transform_name"
+# Use a double $ so make ignores it.
+test "$program_suffix" != NONE &&
+ program_transform_name="s&\$&$program_suffix&;$program_transform_name"
+# Double any \ or $.
+# By default was `s,x,x', remove it if useless.
+ac_script='s/[\\$]/&&/g;s/;s,x,x,$//'
+program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`
+
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
+
+if test x"${MISSING+set}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;;
+ *)
+ MISSING="\${SHELL} $am_aux_dir/missing" ;;
+ esac
+fi
+# Use eval to expand $SHELL
+if eval "$MISSING --run true"; then
+ am_missing_run="$MISSING --run "
+else
+ am_missing_run=
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`missing' script is too old or missing" >&5
+$as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
+fi
+
+if test x"${install_sh}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
+ *)
+ install_sh="\${SHELL} $am_aux_dir/install-sh"
+ esac
+fi
+
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'. However `strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
+# will honor the `STRIP' environment variable to overrule this program.
+if test "$cross_compiling" != no; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
+set dummy ${ac_tool_prefix}strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_STRIP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$STRIP"; then
+ ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_STRIP="${ac_tool_prefix}strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+STRIP=$ac_cv_prog_STRIP
+if test -n "$STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5
+$as_echo "$STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_STRIP"; then
+ ac_ct_STRIP=$STRIP
+ # Extract the first word of "strip", so it can be a program name with args.
+set dummy strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_STRIP"; then
+ ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_STRIP="strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
+if test -n "$ac_ct_STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5
+$as_echo "$ac_ct_STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_STRIP" = x; then
+ STRIP=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ STRIP=$ac_ct_STRIP
+ fi
+else
+ STRIP="$ac_cv_prog_STRIP"
+fi
+
+fi
+INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5
+$as_echo_n "checking for a thread-safe mkdir -p... " >&6; }
+if test -z "$MKDIR_P"; then
+ if test "${ac_cv_path_mkdir+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/opt/sfw/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in mkdir gmkdir; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue
+ case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #(
+ 'mkdir (GNU coreutils) '* | \
+ 'mkdir (coreutils) '* | \
+ 'mkdir (fileutils) '4.1*)
+ ac_cv_path_mkdir=$as_dir/$ac_prog$ac_exec_ext
+ break 3;;
+ esac
+ done
+ done
+ done
+IFS=$as_save_IFS
+
+fi
+
+ test -d ./--version && rmdir ./--version
+ if test "${ac_cv_path_mkdir+set}" = set; then
+ MKDIR_P="$ac_cv_path_mkdir -p"
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for MKDIR_P within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ MKDIR_P="$ac_install_sh -d"
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
+$as_echo "$MKDIR_P" >&6; }
+
+mkdir_p="$MKDIR_P"
+case $mkdir_p in
+ [\\/$]* | ?:[\\/]*) ;;
+ */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
+esac
+
+for ac_prog in gawk mawk nawk awk
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_AWK+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$AWK"; then
+ ac_cv_prog_AWK="$AWK" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_AWK="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+AWK=$ac_cv_prog_AWK
+if test -n "$AWK"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5
+$as_echo "$AWK" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$AWK" && break
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
+set x ${MAKE-make}
+ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
+if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.make <<\_ACEOF
+SHELL = /bin/sh
+all:
+ @echo '@@@%%%=$(MAKE)=@@@%%%'
+_ACEOF
+# GNU make sometimes prints "make[1]: Entering ...", which would confuse us.
+case `${MAKE-make} -f conftest.make 2>/dev/null` in
+ *@@@%%%=?*=@@@%%%*)
+ eval ac_cv_prog_make_${ac_make}_set=yes;;
+ *)
+ eval ac_cv_prog_make_${ac_make}_set=no;;
+esac
+rm -f conftest.make
+fi
+if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ SET_MAKE=
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ SET_MAKE="MAKE=${MAKE-make}"
+fi
+
+rm -rf .tst 2>/dev/null
+mkdir .tst 2>/dev/null
+if test -d .tst; then
+ am__leading_dot=.
+else
+ am__leading_dot=_
+fi
+rmdir .tst 2>/dev/null
+
+if test "`cd $srcdir && pwd`" != "`pwd`"; then
+ # Use -I$(srcdir) only when $(srcdir) != ., so that make's output
+ # is not polluted with repeated "-I."
+ am__isrc=' -I$(srcdir)'
+ # test to see if srcdir already configured
+ if test -f $srcdir/config.status; then
+ as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5
+ fi
+fi
+
+# test whether we have cygpath
+if test -z "$CYGPATH_W"; then
+ if (cygpath --version) >/dev/null 2>/dev/null; then
+ CYGPATH_W='cygpath -w'
+ else
+ CYGPATH_W=echo
+ fi
+fi
+
+
+# Define the identity of the package.
+ PACKAGE='libProgressBar'
+ VERSION='1.2.0'
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE "$PACKAGE"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define VERSION "$VERSION"
+_ACEOF
+
+# Some tools Automake needs.
+
+ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"}
+
+
+AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"}
+
+
+AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"}
+
+
+AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"}
+
+
+MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
+
+# We need awk for the "check" target. The system "awk" is bad on
+# some platforms.
+# Always define AMTAR for backward compatibility.
+
+AMTAR=${AMTAR-"${am_missing_run}tar"}
+
+am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'
+
+
+
+
+
+case `pwd` in
+ *\ * | *\ *)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Libtool does not cope well with whitespace in \`pwd\`" >&5
+$as_echo "$as_me: WARNING: Libtool does not cope well with whitespace in \`pwd\`" >&2;} ;;
+esac
+
+
+
+macro_version='2.2.6b'
+macro_revision='1.3017'
+
+
+
+
+
+
+
+
+
+
+
+
+
+ltmain="$ac_aux_dir/ltmain.sh"
+
+# Make sure we can run config.sub.
+$SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 ||
+ as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5
+$as_echo_n "checking build system type... " >&6; }
+if test "${ac_cv_build+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_build_alias=$build_alias
+test "x$ac_build_alias" = x &&
+ ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"`
+test "x$ac_build_alias" = x &&
+ as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5
+ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` ||
+ as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5
+$as_echo "$ac_cv_build" >&6; }
+case $ac_cv_build in
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+*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5 ;;
+esac
+build=$ac_cv_build
+ac_save_IFS=$IFS; IFS='-'
+set x $ac_cv_build
+shift
+build_cpu=$1
+build_vendor=$2
+shift; shift
+# Remember, the first character of IFS is used to create $*,
+# except with old shells:
+build_os=$*
+IFS=$ac_save_IFS
+case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5
+$as_echo_n "checking host system type... " >&6; }
+if test "${ac_cv_host+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "x$host_alias" = x; then
+ ac_cv_host=$ac_cv_build
+else
+ ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` ||
+ as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_host" >&5
+$as_echo "$ac_cv_host" >&6; }
+case $ac_cv_host in
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+*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5 ;;
+esac
+host=$ac_cv_host
+ac_save_IFS=$IFS; IFS='-'
+set x $ac_cv_host
+shift
+host_cpu=$1
+host_vendor=$2
+shift; shift
+# Remember, the first character of IFS is used to create $*,
+# except with old shells:
+host_os=$*
+IFS=$ac_save_IFS
+case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac
+
+
+DEPDIR="${am__leading_dot}deps"
+
+ac_config_commands="$ac_config_commands depfiles"
+
+
+am_make=${MAKE-make}
+cat > confinc << 'END'
+am__doit:
+ @echo this is the am__doit target
+.PHONY: am__doit
+END
+# If we don't find an include directive, just comment out the code.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5
+$as_echo_n "checking for style of include used by $am_make... " >&6; }
+am__include="#"
+am__quote=
+_am_result=none
+# First try GNU make style include.
+echo "include confinc" > confmf
+# Ignore all kinds of additional output from `make'.
+case `$am_make -s -f confmf 2> /dev/null` in #(
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+ am__include=include
+ am__quote=
+ _am_result=GNU
+ ;;
+esac
+# Now try BSD make style include.
+if test "$am__include" = "#"; then
+ echo '.include "confinc"' > confmf
+ case `$am_make -s -f confmf 2> /dev/null` in #(
+ *the\ am__doit\ target*)
+ am__include=.include
+ am__quote="\""
+ _am_result=BSD
+ ;;
+ esac
+fi
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5
+$as_echo "$_am_result" >&6; }
+rm -f confinc confmf
+
+# Check whether --enable-dependency-tracking was given.
+if test "${enable_dependency_tracking+set}" = set; then :
+ enableval=$enable_dependency_tracking;
+fi
+
+if test "x$enable_dependency_tracking" != xno; then
+ am_depcomp="$ac_aux_dir/depcomp"
+ AMDEPBACKSLASH='\'
+fi
+ if test "x$enable_dependency_tracking" != xno; then
+ AMDEP_TRUE=
+ AMDEP_FALSE='#'
+else
+ AMDEP_TRUE='#'
+ AMDEP_FALSE=
+fi
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}gcc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="${ac_tool_prefix}gcc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_CC"; then
+ ac_ct_CC=$CC
+ # Extract the first word of "gcc", so it can be a program name with args.
+set dummy gcc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CC="gcc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+else
+ CC="$ac_cv_prog_CC"
+fi
+
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}cc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="${ac_tool_prefix}cc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ fi
+fi
+if test -z "$CC"; then
+ # Extract the first word of "cc", so it can be a program name with args.
+set dummy cc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+ ac_prog_rejected=no
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
+ ac_prog_rejected=yes
+ continue
+ fi
+ ac_cv_prog_CC="cc"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+if test $ac_prog_rejected = yes; then
+ # We found a bogon in the path, so make sure we never use it.
+ set dummy $ac_cv_prog_CC
+ shift
+ if test $# != 0; then
+ # We chose a different compiler from the bogus one.
+ # However, it has the same basename, so the bogon will be chosen
+ # first if we set CC to just the basename; use the full file name.
+ shift
+ ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@"
+ fi
+fi
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in cl.exe
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CC" && break
+ done
+fi
+if test -z "$CC"; then
+ ac_ct_CC=$CC
+ for ac_prog in cl.exe
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CC="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CC" && break
+done
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+fi
+
+fi
+
+
+test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "no acceptable C compiler found in \$PATH
+See \`config.log' for more details" "$LINENO" 5 ; }
+
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+ { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ sed '10a\
+... rest of stderr output deleted ...
+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
+
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out"
+# Try to create an executable without -o first, disregard a.out.
+# It will help us diagnose broken compilers, and finding out an intuition
+# of exeext.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler works" >&5
+$as_echo_n "checking whether the C compiler works... " >&6; }
+ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
+
+# The possible output files:
+ac_files="a.out conftest.exe conftest a.exe a_out.exe b.out conftest.*"
+
+ac_rmfiles=
+for ac_file in $ac_files
+do
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
+ * ) ac_rmfiles="$ac_rmfiles $ac_file";;
+ esac
+done
+rm -f $ac_rmfiles
+
+if { { ac_try="$ac_link_default"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link_default") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ # Autoconf-2.13 could set the ac_cv_exeext variable to `no'.
+# So ignore a value of `no', otherwise this would lead to `EXEEXT = no'
+# in a Makefile. We should not override ac_cv_exeext if it was cached,
+# so that the user can short-circuit this test for compilers unknown to
+# Autoconf.
+for ac_file in $ac_files ''
+do
+ test -f "$ac_file" || continue
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj )
+ ;;
+ [ab].out )
+ # We found the default executable, but exeext='' is most
+ # certainly right.
+ break;;
+ *.* )
+ if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
+ then :; else
+ ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ fi
+ # We set ac_cv_exeext here because the later test for it is not
+ # safe: cross compilers may not add the suffix if given an `-o'
+ # argument, so we may need to know it at that point already.
+ # Even if this section looks crufty: it has the advantage of
+ # actually working.
+ break;;
+ * )
+ break;;
+ esac
+done
+test "$ac_cv_exeext" = no && ac_cv_exeext=
+
+else
+ ac_file=''
+fi
+if test -z "$ac_file"; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error 77 "C compiler cannot create executables
+See \`config.log' for more details" "$LINENO" 5 ; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler default output file name" >&5
+$as_echo_n "checking for C compiler default output file name... " >&6; }
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5
+$as_echo "$ac_file" >&6; }
+ac_exeext=$ac_cv_exeext
+
+rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out
+ac_clean_files=$ac_clean_files_save
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5
+$as_echo_n "checking for suffix of executables... " >&6; }
+if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ # If both `conftest.exe' and `conftest' are `present' (well, observable)
+# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will
+# work properly (i.e., refer to `conftest.exe'), while it won't with
+# `rm'.
+for ac_file in conftest.exe conftest conftest.*; do
+ test -f "$ac_file" || continue
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
+ *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ break;;
+ * ) break;;
+ esac
+done
+else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details" "$LINENO" 5 ; }
+fi
+rm -f conftest conftest$ac_cv_exeext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5
+$as_echo "$ac_cv_exeext" >&6; }
+
+rm -f conftest.$ac_ext
+EXEEXT=$ac_cv_exeext
+ac_exeext=$EXEEXT
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdio.h>
+int
+main ()
+{
+FILE *f = fopen ("conftest.out", "w");
+ return ferror (f) || fclose (f) != 0;
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files="$ac_clean_files conftest.out"
+# Check that the compiler produces executables we can run. If not, either
+# the compiler is broken, or we cross compile.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5
+$as_echo_n "checking whether we are cross compiling... " >&6; }
+if test "$cross_compiling" != yes; then
+ { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+ if { ac_try='./conftest$ac_cv_exeext'
+ { { case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; }; then
+ cross_compiling=no
+ else
+ if test "$cross_compiling" = maybe; then
+ cross_compiling=yes
+ else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot run C compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details" "$LINENO" 5 ; }
+ fi
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5
+$as_echo "$cross_compiling" >&6; }
+
+rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out
+ac_clean_files=$ac_clean_files_save
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5
+$as_echo_n "checking for suffix of object files... " >&6; }
+if test "${ac_cv_objext+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.o conftest.obj
+if { { ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compile") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
+ for ac_file in conftest.o conftest.obj conftest.*; do
+ test -f "$ac_file" || continue;
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;;
+ *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'`
+ break;;
+ esac
+done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot compute suffix of object files: cannot compile
+See \`config.log' for more details" "$LINENO" 5 ; }
+fi
+rm -f conftest.$ac_cv_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5
+$as_echo "$ac_cv_objext" >&6; }
+OBJEXT=$ac_cv_objext
+ac_objext=$OBJEXT
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5
+$as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
+if test "${ac_cv_c_compiler_gnu+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_compiler_gnu=yes
+else
+ ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_c_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5
+$as_echo "$ac_cv_c_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GCC=yes
+else
+ GCC=
+fi
+ac_test_CFLAGS=${CFLAGS+set}
+ac_save_CFLAGS=$CFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5
+$as_echo_n "checking whether $CC accepts -g... " >&6; }
+if test "${ac_cv_prog_cc_g+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_c_werror_flag=$ac_c_werror_flag
+ ac_c_werror_flag=yes
+ ac_cv_prog_cc_g=no
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
+else
+ CFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+
+else
+ ac_c_werror_flag=$ac_save_c_werror_flag
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_c_werror_flag=$ac_save_c_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5
+$as_echo "$ac_cv_prog_cc_g" >&6; }
+if test "$ac_test_CFLAGS" = set; then
+ CFLAGS=$ac_save_CFLAGS
+elif test $ac_cv_prog_cc_g = yes; then
+ if test "$GCC" = yes; then
+ CFLAGS="-g -O2"
+ else
+ CFLAGS="-g"
+ fi
+else
+ if test "$GCC" = yes; then
+ CFLAGS="-O2"
+ else
+ CFLAGS=
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5
+$as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
+if test "${ac_cv_prog_cc_c89+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_prog_cc_c89=no
+ac_save_CC=$CC
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdarg.h>
+#include <stdio.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */
+struct buf { int x; };
+FILE * (*rcsopen) (struct buf *, struct stat *, int);
+static char *e (p, i)
+ char **p;
+ int i;
+{
+ return p[i];
+}
+static char *f (char * (*g) (char **, int), char **p, ...)
+{
+ char *s;
+ va_list v;
+ va_start (v,p);
+ s = g (p, va_arg (v,int));
+ va_end (v);
+ return s;
+}
+
+/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has
+ function prototypes and stuff, but not '\xHH' hex character constants.
+ These don't provoke an error unfortunately, instead are silently treated
+ as 'x'. The following induces an error, until -std is added to get
+ proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an
+ array size at least. It's necessary to write '\x00'==0 to get something
+ that's true only with -std. */
+int osf4_cc_array ['\x00' == 0 ? 1 : -1];
+
+/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters
+ inside strings and character constants. */
+#define FOO(x) 'x'
+int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1];
+
+int test (int i, double x);
+struct s1 {int (*f) (int a);};
+struct s2 {int (*f) (double a);};
+int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
+int argc;
+char **argv;
+int
+main ()
+{
+return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1];
+ ;
+ return 0;
+}
+_ACEOF
+for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \
+ -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
+do
+ CC="$ac_save_CC $ac_arg"
+ if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_c89=$ac_arg
+fi
+rm -f core conftest.err conftest.$ac_objext
+ test "x$ac_cv_prog_cc_c89" != "xno" && break
+done
+rm -f conftest.$ac_ext
+CC=$ac_save_CC
+
+fi
+# AC_CACHE_VAL
+case "x$ac_cv_prog_cc_c89" in
+ x)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
+$as_echo "none needed" >&6; } ;;
+ xno)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
+$as_echo "unsupported" >&6; } ;;
+ *)
+ CC="$CC $ac_cv_prog_cc_c89"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5
+$as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
+esac
+if test "x$ac_cv_prog_cc_c89" != xno; then :
+
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+depcc="$CC" am_compiler_list=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CC_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
+ case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CC_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CC_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CC_dependencies_compiler_type" >&6; }
+CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
+ am__fastdepCC_TRUE=
+ am__fastdepCC_FALSE='#'
+else
+ am__fastdepCC_TRUE='#'
+ am__fastdepCC_FALSE=
+fi
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a sed that does not truncate output" >&5
+$as_echo_n "checking for a sed that does not truncate output... " >&6; }
+if test "${ac_cv_path_SED+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_script=s/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb/
+ for ac_i in 1 2 3 4 5 6 7; do
+ ac_script="$ac_script$as_nl$ac_script"
+ done
+ echo "$ac_script" 2>/dev/null | sed 99q >conftest.sed
+ { ac_script=; unset ac_script;}
+ if test -z "$SED"; then
+ ac_path_SED_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in sed gsed; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_SED="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_SED" && $as_test_x "$ac_path_SED"; } || continue
+# Check for GNU ac_path_SED and select it if it is found.
+ # Check for GNU $ac_path_SED
+case `"$ac_path_SED" --version 2>&1` in
+*GNU*)
+ ac_cv_path_SED="$ac_path_SED" ac_path_SED_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo '' >> "conftest.nl"
+ "$ac_path_SED" -f conftest.sed < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
+ if test $ac_count -gt ${ac_path_SED_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_SED="$ac_path_SED"
+ ac_path_SED_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_SED_found && break 3
+ done
+ done
+ done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_SED"; then
+ as_fn_error $? "no acceptable sed could be found in \$PATH" "$LINENO" 5
+ fi
+else
+ ac_cv_path_SED=$SED
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_SED" >&5
+$as_echo "$ac_cv_path_SED" >&6; }
+ SED="$ac_cv_path_SED"
+ rm -f conftest.sed
+
+test -z "$SED" && SED=sed
+Xsed="$SED -e 1s/^X//"
+
+
+
+
+
+
+
+
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5
+$as_echo_n "checking for grep that handles long lines and -e... " >&6; }
+if test "${ac_cv_path_GREP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$GREP"; then
+ ac_path_GREP_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in grep ggrep; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue
+# Check for GNU ac_path_GREP and select it if it is found.
+ # Check for GNU $ac_path_GREP
+case `"$ac_path_GREP" --version 2>&1` in
+*GNU*)
+ ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo 'GREP' >> "conftest.nl"
+ "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
+ if test $ac_count -gt ${ac_path_GREP_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_GREP="$ac_path_GREP"
+ ac_path_GREP_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_GREP_found && break 3
+ done
+ done
+ done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_GREP"; then
+ as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+ fi
+else
+ ac_cv_path_GREP=$GREP
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5
+$as_echo "$ac_cv_path_GREP" >&6; }
+ GREP="$ac_cv_path_GREP"
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5
+$as_echo_n "checking for egrep... " >&6; }
+if test "${ac_cv_path_EGREP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if echo a | $GREP -E '(a|b)' >/dev/null 2>&1
+ then ac_cv_path_EGREP="$GREP -E"
+ else
+ if test -z "$EGREP"; then
+ ac_path_EGREP_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in egrep; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue
+# Check for GNU ac_path_EGREP and select it if it is found.
+ # Check for GNU $ac_path_EGREP
+case `"$ac_path_EGREP" --version 2>&1` in
+*GNU*)
+ ac_cv_path_EGREP="$ac_path_EGREP" ac_path_EGREP_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo 'EGREP' >> "conftest.nl"
+ "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
+ if test $ac_count -gt ${ac_path_EGREP_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_EGREP="$ac_path_EGREP"
+ ac_path_EGREP_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_EGREP_found && break 3
+ done
+ done
+ done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_EGREP"; then
+ as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+ fi
+else
+ ac_cv_path_EGREP=$EGREP
+fi
+
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5
+$as_echo "$ac_cv_path_EGREP" >&6; }
+ EGREP="$ac_cv_path_EGREP"
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for fgrep" >&5
+$as_echo_n "checking for fgrep... " >&6; }
+if test "${ac_cv_path_FGREP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if echo 'ab*c' | $GREP -F 'ab*c' >/dev/null 2>&1
+ then ac_cv_path_FGREP="$GREP -F"
+ else
+ if test -z "$FGREP"; then
+ ac_path_FGREP_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in fgrep; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_FGREP="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_FGREP" && $as_test_x "$ac_path_FGREP"; } || continue
+# Check for GNU ac_path_FGREP and select it if it is found.
+ # Check for GNU $ac_path_FGREP
+case `"$ac_path_FGREP" --version 2>&1` in
+*GNU*)
+ ac_cv_path_FGREP="$ac_path_FGREP" ac_path_FGREP_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo 'FGREP' >> "conftest.nl"
+ "$ac_path_FGREP" FGREP < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
+ if test $ac_count -gt ${ac_path_FGREP_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_FGREP="$ac_path_FGREP"
+ ac_path_FGREP_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_FGREP_found && break 3
+ done
+ done
+ done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_FGREP"; then
+ as_fn_error $? "no acceptable fgrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+ fi
+else
+ ac_cv_path_FGREP=$FGREP
+fi
+
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_FGREP" >&5
+$as_echo "$ac_cv_path_FGREP" >&6; }
+ FGREP="$ac_cv_path_FGREP"
+
+
+test -z "$GREP" && GREP=grep
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# Check whether --with-gnu-ld was given.
+if test "${with_gnu_ld+set}" = set; then :
+ withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes
+else
+ with_gnu_ld=no
+fi
+
+ac_prog=ld
+if test "$GCC" = yes; then
+ # Check if gcc -print-prog-name=ld gives a path.
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ld used by $CC" >&5
+$as_echo_n "checking for ld used by $CC... " >&6; }
+ case $host in
+ *-*-mingw*)
+ # gcc leaves a trailing carriage return which upsets mingw
+ ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+ *)
+ ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+ esac
+ case $ac_prog in
+ # Accept absolute paths.
+ [\\/]* | ?:[\\/]*)
+ re_direlt='/[^/][^/]*/\.\./'
+ # Canonicalize the pathname of ld
+ ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'`
+ while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do
+ ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"`
+ done
+ test -z "$LD" && LD="$ac_prog"
+ ;;
+ "")
+ # If it fails, then pretend we aren't using GCC.
+ ac_prog=ld
+ ;;
+ *)
+ # If it is relative, then search for the first ld in PATH.
+ with_gnu_ld=unknown
+ ;;
+ esac
+elif test "$with_gnu_ld" = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU ld" >&5
+$as_echo_n "checking for GNU ld... " >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for non-GNU ld" >&5
+$as_echo_n "checking for non-GNU ld... " >&6; }
+fi
+if test "${lt_cv_path_LD+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$LD"; then
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+ lt_cv_path_LD="$ac_dir/$ac_prog"
+ # Check to see if the program is GNU ld. I'd rather use --version,
+ # but apparently some variants of GNU ld only accept -v.
+ # Break only if it was the GNU/non-GNU ld that we prefer.
+ case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+ *GNU* | *'with BFD'*)
+ test "$with_gnu_ld" != no && break
+ ;;
+ *)
+ test "$with_gnu_ld" != yes && break
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+else
+ lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi
+fi
+
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LD" >&5
+$as_echo "$LD" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+test -z "$LD" && as_fn_error $? "no acceptable ld found in \$PATH" "$LINENO" 5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if the linker ($LD) is GNU ld" >&5
+$as_echo_n "checking if the linker ($LD) is GNU ld... " >&6; }
+if test "${lt_cv_prog_gnu_ld+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ # I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+ lt_cv_prog_gnu_ld=yes
+ ;;
+*)
+ lt_cv_prog_gnu_ld=no
+ ;;
+esac
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_gnu_ld" >&5
+$as_echo "$lt_cv_prog_gnu_ld" >&6; }
+with_gnu_ld=$lt_cv_prog_gnu_ld
+
+
+
+
+
+
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for BSD- or MS-compatible name lister (nm)" >&5
+$as_echo_n "checking for BSD- or MS-compatible name lister (nm)... " >&6; }
+if test "${lt_cv_path_NM+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$NM"; then
+ # Let the user override the test.
+ lt_cv_path_NM="$NM"
+else
+ lt_nm_to_check="${ac_tool_prefix}nm"
+ if test -n "$ac_tool_prefix" && test "$build" = "$host"; then
+ lt_nm_to_check="$lt_nm_to_check nm"
+ fi
+ for lt_tmp_nm in $lt_nm_to_check; do
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ tmp_nm="$ac_dir/$lt_tmp_nm"
+ if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then
+ # Check to see if the nm accepts a BSD-compat flag.
+ # Adding the `sed 1q' prevents false positives on HP-UX, which says:
+ # nm: unknown option "B" ignored
+ # Tru64's nm complains that /dev/null is an invalid object file
+ case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in
+ */dev/null* | *'Invalid file or object type'*)
+ lt_cv_path_NM="$tmp_nm -B"
+ break
+ ;;
+ *)
+ case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in
+ */dev/null*)
+ lt_cv_path_NM="$tmp_nm -p"
+ break
+ ;;
+ *)
+ lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but
+ continue # so that we can try to find one that supports BSD flags
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+ done
+ : ${lt_cv_path_NM=no}
+fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_path_NM" >&5
+$as_echo "$lt_cv_path_NM" >&6; }
+if test "$lt_cv_path_NM" != "no"; then
+ NM="$lt_cv_path_NM"
+else
+ # Didn't find any BSD compatible name lister, look for dumpbin.
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in "dumpbin -symbols" "link -dump -symbols"
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_DUMPBIN+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$DUMPBIN"; then
+ ac_cv_prog_DUMPBIN="$DUMPBIN" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_DUMPBIN="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+DUMPBIN=$ac_cv_prog_DUMPBIN
+if test -n "$DUMPBIN"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DUMPBIN" >&5
+$as_echo "$DUMPBIN" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$DUMPBIN" && break
+ done
+fi
+if test -z "$DUMPBIN"; then
+ ac_ct_DUMPBIN=$DUMPBIN
+ for ac_prog in "dumpbin -symbols" "link -dump -symbols"
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_DUMPBIN+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_DUMPBIN"; then
+ ac_cv_prog_ac_ct_DUMPBIN="$ac_ct_DUMPBIN" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_DUMPBIN="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_DUMPBIN=$ac_cv_prog_ac_ct_DUMPBIN
+if test -n "$ac_ct_DUMPBIN"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DUMPBIN" >&5
+$as_echo "$ac_ct_DUMPBIN" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_DUMPBIN" && break
+done
+
+ if test "x$ac_ct_DUMPBIN" = x; then
+ DUMPBIN=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ DUMPBIN=$ac_ct_DUMPBIN
+ fi
+fi
+
+
+ if test "$DUMPBIN" != ":"; then
+ NM="$DUMPBIN"
+ fi
+fi
+test -z "$NM" && NM=nm
+
+
+
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking the name lister ($NM) interface" >&5
+$as_echo_n "checking the name lister ($NM) interface... " >&6; }
+if test "${lt_cv_nm_interface+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_nm_interface="BSD nm"
+ echo "int some_variable = 0;" > conftest.$ac_ext
+ (eval echo "\"\$as_me:4689: $ac_compile\"" >&5)
+ (eval "$ac_compile" 2>conftest.err)
+ cat conftest.err >&5
+ (eval echo "\"\$as_me:4692: $NM \\\"conftest.$ac_objext\\\"\"" >&5)
+ (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out)
+ cat conftest.err >&5
+ (eval echo "\"\$as_me:4695: output\"" >&5)
+ cat conftest.out >&5
+ if $GREP 'External.*some_variable' conftest.out > /dev/null; then
+ lt_cv_nm_interface="MS dumpbin"
+ fi
+ rm -f conftest*
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_nm_interface" >&5
+$as_echo "$lt_cv_nm_interface" >&6; }
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ln -s works" >&5
+$as_echo_n "checking whether ln -s works... " >&6; }
+LN_S=$as_ln_s
+if test "$LN_S" = "ln -s"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no, using $LN_S" >&5
+$as_echo "no, using $LN_S" >&6; }
+fi
+
+# find the maximum length of command line arguments
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking the maximum length of command line arguments" >&5
+$as_echo_n "checking the maximum length of command line arguments... " >&6; }
+if test "${lt_cv_sys_max_cmd_len+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ i=0
+ teststring="ABCD"
+
+ case $build_os in
+ msdosdjgpp*)
+ # On DJGPP, this test can blow up pretty badly due to problems in libc
+ # (any single argument exceeding 2000 bytes causes a buffer overrun
+ # during glob expansion). Even if it were fixed, the result of this
+ # check would be larger than it should be.
+ lt_cv_sys_max_cmd_len=12288; # 12K is about right
+ ;;
+
+ gnu*)
+ # Under GNU Hurd, this test is not required because there is
+ # no limit to the length of command line arguments.
+ # Libtool will interpret -1 as no limit whatsoever
+ lt_cv_sys_max_cmd_len=-1;
+ ;;
+
+ cygwin* | mingw* | cegcc*)
+ # On Win9x/ME, this test blows up -- it succeeds, but takes
+ # about 5 minutes as the teststring grows exponentially.
+ # Worse, since 9x/ME are not pre-emptively multitasking,
+ # you end up with a "frozen" computer, even though with patience
+ # the test eventually succeeds (with a max line length of 256k).
+ # Instead, let's just punt: use the minimum linelength reported by
+ # all of the supported platforms: 8192 (on NT/2K/XP).
+ lt_cv_sys_max_cmd_len=8192;
+ ;;
+
+ amigaos*)
+ # On AmigaOS with pdksh, this test takes hours, literally.
+ # So we just punt and use a minimum line length of 8192.
+ lt_cv_sys_max_cmd_len=8192;
+ ;;
+
+ netbsd* | freebsd* | openbsd* | darwin* | dragonfly*)
+ # This has been around since 386BSD, at least. Likely further.
+ if test -x /sbin/sysctl; then
+ lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax`
+ elif test -x /usr/sbin/sysctl; then
+ lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax`
+ else
+ lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs
+ fi
+ # And add a safety zone
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+ ;;
+
+ interix*)
+ # We know the value 262144 and hardcode it with a safety zone (like BSD)
+ lt_cv_sys_max_cmd_len=196608
+ ;;
+
+ osf*)
+ # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure
+ # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not
+ # nice to cause kernel panics so lets avoid the loop below.
+ # First set a reasonable default.
+ lt_cv_sys_max_cmd_len=16384
+ #
+ if test -x /sbin/sysconfig; then
+ case `/sbin/sysconfig -q proc exec_disable_arg_limit` in
+ *1*) lt_cv_sys_max_cmd_len=-1 ;;
+ esac
+ fi
+ ;;
+ sco3.2v5*)
+ lt_cv_sys_max_cmd_len=102400
+ ;;
+ sysv5* | sco5v6* | sysv4.2uw2*)
+ kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null`
+ if test -n "$kargmax"; then
+ lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[ ]//'`
+ else
+ lt_cv_sys_max_cmd_len=32768
+ fi
+ ;;
+ *)
+ lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null`
+ if test -n "$lt_cv_sys_max_cmd_len"; then
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+ else
+ # Make teststring a little bigger before we do anything with it.
+ # a 1K string should be a reasonable start.
+ for i in 1 2 3 4 5 6 7 8 ; do
+ teststring=$teststring$teststring
+ done
+ SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}}
+ # If test is not a shell built-in, we'll probably end up computing a
+ # maximum length that is only half of the actual maximum length, but
+ # we can't tell.
+ while { test "X"`$SHELL $0 --fallback-echo "X$teststring$teststring" 2>/dev/null` \
+ = "XX$teststring$teststring"; } >/dev/null 2>&1 &&
+ test $i != 17 # 1/2 MB should be enough
+ do
+ i=`expr $i + 1`
+ teststring=$teststring$teststring
+ done
+ # Only check the string length outside the loop.
+ lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1`
+ teststring=
+ # Add a significant safety factor because C++ compilers can tack on
+ # massive amounts of additional arguments before passing them to the
+ # linker. It appears as though 1/2 is a usable value.
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2`
+ fi
+ ;;
+ esac
+
+fi
+
+if test -n $lt_cv_sys_max_cmd_len ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_sys_max_cmd_len" >&5
+$as_echo "$lt_cv_sys_max_cmd_len" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: none" >&5
+$as_echo "none" >&6; }
+fi
+max_cmd_len=$lt_cv_sys_max_cmd_len
+
+
+
+
+
+
+: ${CP="cp -f"}
+: ${MV="mv -f"}
+: ${RM="rm -f"}
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the shell understands some XSI constructs" >&5
+$as_echo_n "checking whether the shell understands some XSI constructs... " >&6; }
+# Try some XSI features
+xsi_shell=no
+( _lt_dummy="a/b/c"
+ test "${_lt_dummy##*/},${_lt_dummy%/*},"${_lt_dummy%"$_lt_dummy"}, \
+ = c,a/b,, \
+ && eval 'test $(( 1 + 1 )) -eq 2 \
+ && test "${#_lt_dummy}" -eq 5' ) >/dev/null 2>&1 \
+ && xsi_shell=yes
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $xsi_shell" >&5
+$as_echo "$xsi_shell" >&6; }
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the shell understands \"+=\"" >&5
+$as_echo_n "checking whether the shell understands \"+=\"... " >&6; }
+lt_shell_append=no
+( foo=bar; set foo baz; eval "$1+=\$2" && test "$foo" = barbaz ) \
+ >/dev/null 2>&1 \
+ && lt_shell_append=yes
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_shell_append" >&5
+$as_echo "$lt_shell_append" >&6; }
+
+
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+ lt_unset=unset
+else
+ lt_unset=false
+fi
+
+
+
+
+
+# test EBCDIC or ASCII
+case `echo X|tr X '\101'` in
+ A) # ASCII based system
+ # \n is not interpreted correctly by Solaris 8 /usr/ucb/tr
+ lt_SP2NL='tr \040 \012'
+ lt_NL2SP='tr \015\012 \040\040'
+ ;;
+ *) # EBCDIC based system
+ lt_SP2NL='tr \100 \n'
+ lt_NL2SP='tr \r\n \100\100'
+ ;;
+esac
+
+
+
+
+
+
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $LD option to reload object files" >&5
+$as_echo_n "checking for $LD option to reload object files... " >&6; }
+if test "${lt_cv_ld_reload_flag+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_ld_reload_flag='-r'
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_reload_flag" >&5
+$as_echo "$lt_cv_ld_reload_flag" >&6; }
+reload_flag=$lt_cv_ld_reload_flag
+case $reload_flag in
+"" | " "*) ;;
+*) reload_flag=" $reload_flag" ;;
+esac
+reload_cmds='$LD$reload_flag -o $output$reload_objs'
+case $host_os in
+ darwin*)
+ if test "$GCC" = yes; then
+ reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs'
+ else
+ reload_cmds='$LD$reload_flag -o $output$reload_objs'
+ fi
+ ;;
+esac
+
+
+
+
+
+
+
+
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}objdump", so it can be a program name with args.
+set dummy ${ac_tool_prefix}objdump; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_OBJDUMP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$OBJDUMP"; then
+ ac_cv_prog_OBJDUMP="$OBJDUMP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_OBJDUMP="${ac_tool_prefix}objdump"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+OBJDUMP=$ac_cv_prog_OBJDUMP
+if test -n "$OBJDUMP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OBJDUMP" >&5
+$as_echo "$OBJDUMP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_OBJDUMP"; then
+ ac_ct_OBJDUMP=$OBJDUMP
+ # Extract the first word of "objdump", so it can be a program name with args.
+set dummy objdump; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_OBJDUMP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_OBJDUMP"; then
+ ac_cv_prog_ac_ct_OBJDUMP="$ac_ct_OBJDUMP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_OBJDUMP="objdump"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_OBJDUMP=$ac_cv_prog_ac_ct_OBJDUMP
+if test -n "$ac_ct_OBJDUMP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OBJDUMP" >&5
+$as_echo "$ac_ct_OBJDUMP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_OBJDUMP" = x; then
+ OBJDUMP="false"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ OBJDUMP=$ac_ct_OBJDUMP
+ fi
+else
+ OBJDUMP="$ac_cv_prog_OBJDUMP"
+fi
+
+test -z "$OBJDUMP" && OBJDUMP=objdump
+
+
+
+
+
+
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to recognize dependent libraries" >&5
+$as_echo_n "checking how to recognize dependent libraries... " >&6; }
+if test "${lt_cv_deplibs_check_method+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_file_magic_cmd='$MAGIC_CMD'
+lt_cv_file_magic_test_file=
+lt_cv_deplibs_check_method='unknown'
+# Need to set the preceding variable on all platforms that support
+# interlibrary dependencies.
+# 'none' -- dependencies not supported.
+# `unknown' -- same as none, but documents that we really don't know.
+# 'pass_all' -- all dependencies passed with no checks.
+# 'test_compile' -- check by making test program.
+# 'file_magic [[regex]]' -- check by looking for files in library path
+# which responds to the $file_magic_cmd with a given extended regex.
+# If you have `file' or equivalent on your system and you're not sure
+# whether `pass_all' will *always* work, you probably want this one.
+
+case $host_os in
+aix[4-9]*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+beos*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+bsdi[45]*)
+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib)'
+ lt_cv_file_magic_cmd='/usr/bin/file -L'
+ lt_cv_file_magic_test_file=/shlib/libc.so
+ ;;
+
+cygwin*)
+ # func_win32_libid is a shell function defined in ltmain.sh
+ lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+ lt_cv_file_magic_cmd='func_win32_libid'
+ ;;
+
+mingw* | pw32*)
+ # Base MSYS/MinGW do not provide the 'file' command needed by
+ # func_win32_libid shell function, so use a weaker test based on 'objdump',
+ # unless we find 'file', for example because we are cross-compiling.
+ if ( file / ) >/dev/null 2>&1; then
+ lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+ lt_cv_file_magic_cmd='func_win32_libid'
+ else
+ lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?'
+ lt_cv_file_magic_cmd='$OBJDUMP -f'
+ fi
+ ;;
+
+cegcc)
+ # use the weaker test based on 'objdump'. See mingw*.
+ lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?'
+ lt_cv_file_magic_cmd='$OBJDUMP -f'
+ ;;
+
+darwin* | rhapsody*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+freebsd* | dragonfly*)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
+ case $host_cpu in
+ i*86 )
+ # Not sure whether the presence of OpenBSD here was a mistake.
+ # Let's accept both of them until this is cleared up.
+ lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[3-9]86 (compact )?demand paged shared library'
+ lt_cv_file_magic_cmd=/usr/bin/file
+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*`
+ ;;
+ esac
+ else
+ lt_cv_deplibs_check_method=pass_all
+ fi
+ ;;
+
+gnu*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+hpux10.20* | hpux11*)
+ lt_cv_file_magic_cmd=/usr/bin/file
+ case $host_cpu in
+ ia64*)
+ lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - IA64'
+ lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so
+ ;;
+ hppa*64*)
+ lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]'
+ lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl
+ ;;
+ *)
+ lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|PA-RISC[0-9].[0-9]) shared library'
+ lt_cv_file_magic_test_file=/usr/lib/libc.sl
+ ;;
+ esac
+ ;;
+
+interix[3-9]*)
+ # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|\.a)$'
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $LD in
+ *-32|*"-32 ") libmagic=32-bit;;
+ *-n32|*"-n32 ") libmagic=N32;;
+ *-64|*"-64 ") libmagic=64-bit;;
+ *) libmagic=never-match;;
+ esac
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$'
+ else
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|_pic\.a)$'
+ fi
+ ;;
+
+newos6*)
+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (executable|dynamic lib)'
+ lt_cv_file_magic_cmd=/usr/bin/file
+ lt_cv_file_magic_test_file=/usr/lib/libnls.so
+ ;;
+
+*nto* | *qnx*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+openbsd*)
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|\.so|_pic\.a)$'
+ else
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$'
+ fi
+ ;;
+
+osf3* | osf4* | osf5*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+rdos*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+solaris*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+sysv4 | sysv4.3*)
+ case $host_vendor in
+ motorola)
+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib) M[0-9][0-9]* Version [0-9]'
+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*`
+ ;;
+ ncr)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ sequent)
+ lt_cv_file_magic_cmd='/bin/file'
+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [LM]SB (shared object|dynamic lib )'
+ ;;
+ sni)
+ lt_cv_file_magic_cmd='/bin/file'
+ lt_cv_deplibs_check_method="file_magic ELF [0-9][0-9]*-bit [LM]SB dynamic lib"
+ lt_cv_file_magic_test_file=/lib/libc.so
+ ;;
+ siemens)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ pc)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ esac
+ ;;
+
+tpf*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+esac
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_deplibs_check_method" >&5
+$as_echo "$lt_cv_deplibs_check_method" >&6; }
+file_magic_cmd=$lt_cv_file_magic_cmd
+deplibs_check_method=$lt_cv_deplibs_check_method
+test -z "$deplibs_check_method" && deplibs_check_method=unknown
+
+
+
+
+
+
+
+
+
+
+
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}ar", so it can be a program name with args.
+set dummy ${ac_tool_prefix}ar; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_AR+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$AR"; then
+ ac_cv_prog_AR="$AR" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_AR="${ac_tool_prefix}ar"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+AR=$ac_cv_prog_AR
+if test -n "$AR"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AR" >&5
+$as_echo "$AR" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_AR"; then
+ ac_ct_AR=$AR
+ # Extract the first word of "ar", so it can be a program name with args.
+set dummy ar; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_AR+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_AR"; then
+ ac_cv_prog_ac_ct_AR="$ac_ct_AR" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_AR="ar"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_AR=$ac_cv_prog_ac_ct_AR
+if test -n "$ac_ct_AR"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_AR" >&5
+$as_echo "$ac_ct_AR" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_AR" = x; then
+ AR="false"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ AR=$ac_ct_AR
+ fi
+else
+ AR="$ac_cv_prog_AR"
+fi
+
+test -z "$AR" && AR=ar
+test -z "$AR_FLAGS" && AR_FLAGS=cru
+
+
+
+
+
+
+
+
+
+
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
+set dummy ${ac_tool_prefix}strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_STRIP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$STRIP"; then
+ ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_STRIP="${ac_tool_prefix}strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+STRIP=$ac_cv_prog_STRIP
+if test -n "$STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5
+$as_echo "$STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_STRIP"; then
+ ac_ct_STRIP=$STRIP
+ # Extract the first word of "strip", so it can be a program name with args.
+set dummy strip; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_STRIP"; then
+ ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_STRIP="strip"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
+if test -n "$ac_ct_STRIP"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5
+$as_echo "$ac_ct_STRIP" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_STRIP" = x; then
+ STRIP=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ STRIP=$ac_ct_STRIP
+ fi
+else
+ STRIP="$ac_cv_prog_STRIP"
+fi
+
+test -z "$STRIP" && STRIP=:
+
+
+
+
+
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args.
+set dummy ${ac_tool_prefix}ranlib; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_RANLIB+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$RANLIB"; then
+ ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+RANLIB=$ac_cv_prog_RANLIB
+if test -n "$RANLIB"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $RANLIB" >&5
+$as_echo "$RANLIB" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_RANLIB"; then
+ ac_ct_RANLIB=$RANLIB
+ # Extract the first word of "ranlib", so it can be a program name with args.
+set dummy ranlib; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_RANLIB"; then
+ ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_RANLIB="ranlib"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB
+if test -n "$ac_ct_RANLIB"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_RANLIB" >&5
+$as_echo "$ac_ct_RANLIB" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_RANLIB" = x; then
+ RANLIB=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ RANLIB=$ac_ct_RANLIB
+ fi
+else
+ RANLIB="$ac_cv_prog_RANLIB"
+fi
+
+test -z "$RANLIB" && RANLIB=:
+
+
+
+
+
+
+# Determine commands to create old-style static archives.
+old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs'
+old_postinstall_cmds='chmod 644 $oldlib'
+old_postuninstall_cmds=
+
+if test -n "$RANLIB"; then
+ case $host_os in
+ openbsd*)
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib"
+ ;;
+ *)
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib"
+ ;;
+ esac
+ old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib"
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+
+# Check for command to grab the raw symbol name followed by C symbol from nm.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking command to parse $NM output from $compiler object" >&5
+$as_echo_n "checking command to parse $NM output from $compiler object... " >&6; }
+if test "${lt_cv_sys_global_symbol_pipe+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+
+# These are sane defaults that work on at least a few old systems.
+# [They come from Ultrix. What could be older than Ultrix?!! ;)]
+
+# Character class describing NM global symbol codes.
+symcode='[BCDEGRST]'
+
+# Regexp to match symbols that can be accessed directly from C.
+sympat='\([_A-Za-z][_A-Za-z0-9]*\)'
+
+# Define system-specific variables.
+case $host_os in
+aix*)
+ symcode='[BCDT]'
+ ;;
+cygwin* | mingw* | pw32* | cegcc*)
+ symcode='[ABCDGISTW]'
+ ;;
+hpux*)
+ if test "$host_cpu" = ia64; then
+ symcode='[ABCDEGRST]'
+ fi
+ ;;
+irix* | nonstopux*)
+ symcode='[BCDEGRST]'
+ ;;
+osf*)
+ symcode='[BCDEGQRST]'
+ ;;
+solaris*)
+ symcode='[BDRT]'
+ ;;
+sco3.2v5*)
+ symcode='[DT]'
+ ;;
+sysv4.2uw2*)
+ symcode='[DT]'
+ ;;
+sysv5* | sco5v6* | unixware* | OpenUNIX*)
+ symcode='[ABDT]'
+ ;;
+sysv4)
+ symcode='[DFNSTU]'
+ ;;
+esac
+
+# If we're using GNU nm, then use its standard symbol codes.
+case `$NM -V 2>&1` in
+*GNU* | *'with BFD'*)
+ symcode='[ABCDGIRSTW]' ;;
+esac
+
+# Transform an extracted symbol line into a proper C declaration.
+# Some systems (esp. on ia64) link data and code symbols differently,
+# so use this general approach.
+lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'"
+
+# Transform an extracted symbol line into symbol name and symbol address
+lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"\2\", (void *) \&\2},/p'"
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \(lib[^ ]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"lib\2\", (void *) \&\2},/p'"
+
+# Handle CRLF in mingw tool chain
+opt_cr=
+case $build_os in
+mingw*)
+ opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp
+ ;;
+esac
+
+# Try without a prefix underscore, then with it.
+for ac_symprfx in "" "_"; do
+
+ # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol.
+ symxfrm="\\1 $ac_symprfx\\2 \\2"
+
+ # Write the raw and C identifiers.
+ if test "$lt_cv_nm_interface" = "MS dumpbin"; then
+ # Fake it for dumpbin and say T for any non-static function
+ # and D for any global variable.
+ # Also find C++ and __fastcall symbols from MSVC++,
+ # which start with @ or ?.
+ lt_cv_sys_global_symbol_pipe="$AWK '"\
+" {last_section=section; section=\$ 3};"\
+" /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\
+" \$ 0!~/External *\|/{next};"\
+" / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\
+" {if(hide[section]) next};"\
+" {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\
+" {split(\$ 0, a, /\||\r/); split(a[2], s)};"\
+" s[1]~/^[@?]/{print s[1], s[1]; next};"\
+" s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\
+" ' prfx=^$ac_symprfx"
+ else
+ lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[ ]\($symcode$symcode*\)[ ][ ]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'"
+ fi
+
+ # Check to see that the pipe works correctly.
+ pipe_works=no
+
+ rm -f conftest*
+ cat > conftest.$ac_ext <<_LT_EOF
+#ifdef __cplusplus
+extern "C" {
+#endif
+char nm_test_var;
+void nm_test_func(void);
+void nm_test_func(void){}
+#ifdef __cplusplus
+}
+#endif
+int main(){nm_test_var='a';nm_test_func();return(0);}
+_LT_EOF
+
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ # Now try to grab the symbols.
+ nlist=conftest.nm
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist\""; } >&5
+ (eval $NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && test -s "$nlist"; then
+ # Try sorting and uniquifying the output.
+ if sort "$nlist" | uniq > "$nlist"T; then
+ mv -f "$nlist"T "$nlist"
+ else
+ rm -f "$nlist"T
+ fi
+
+ # Make sure that we snagged all the symbols we need.
+ if $GREP ' nm_test_var$' "$nlist" >/dev/null; then
+ if $GREP ' nm_test_func$' "$nlist" >/dev/null; then
+ cat <<_LT_EOF > conftest.$ac_ext
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+_LT_EOF
+ # Now generate the symbol file.
+ eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext'
+
+ cat <<_LT_EOF >> conftest.$ac_ext
+
+/* The mapping between symbol names and symbols. */
+const struct {
+ const char *name;
+ void *address;
+}
+lt__PROGRAM__LTX_preloaded_symbols[] =
+{
+ { "@PROGRAM@", (void *) 0 },
+_LT_EOF
+ $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext
+ cat <<\_LT_EOF >> conftest.$ac_ext
+ {0, (void *) 0}
+};
+
+/* This works around a problem in FreeBSD linker */
+#ifdef FREEBSD_WORKAROUND
+static const void *lt_preloaded_setup() {
+ return lt__PROGRAM__LTX_preloaded_symbols;
+}
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+_LT_EOF
+ # Now try linking the two files.
+ mv conftest.$ac_objext conftstm.$ac_objext
+ lt_save_LIBS="$LIBS"
+ lt_save_CFLAGS="$CFLAGS"
+ LIBS="conftstm.$ac_objext"
+ CFLAGS="$CFLAGS$lt_prog_compiler_no_builtin_flag"
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5
+ (eval $ac_link) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && test -s conftest${ac_exeext}; then
+ pipe_works=yes
+ fi
+ LIBS="$lt_save_LIBS"
+ CFLAGS="$lt_save_CFLAGS"
+ else
+ echo "cannot find nm_test_func in $nlist" >&5
+ fi
+ else
+ echo "cannot find nm_test_var in $nlist" >&5
+ fi
+ else
+ echo "cannot run $lt_cv_sys_global_symbol_pipe" >&5
+ fi
+ else
+ echo "$progname: failed program was:" >&5
+ cat conftest.$ac_ext >&5
+ fi
+ rm -rf conftest* conftst*
+
+ # Do not use the global_symbol_pipe unless it works.
+ if test "$pipe_works" = yes; then
+ break
+ else
+ lt_cv_sys_global_symbol_pipe=
+ fi
+done
+
+fi
+
+if test -z "$lt_cv_sys_global_symbol_pipe"; then
+ lt_cv_sys_global_symbol_to_cdecl=
+fi
+if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: failed" >&5
+$as_echo "failed" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: ok" >&5
+$as_echo "ok" >&6; }
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# Check whether --enable-libtool-lock was given.
+if test "${enable_libtool_lock+set}" = set; then :
+ enableval=$enable_libtool_lock;
+fi
+
+test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes
+
+# Some flags need to be propagated to the compiler or linker for good
+# libtool support.
+case $host in
+ia64-*-hpux*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *ELF-32*)
+ HPUX_IA64_MODE="32"
+ ;;
+ *ELF-64*)
+ HPUX_IA64_MODE="64"
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+*-*-irix6*)
+ # Find out which ABI we are using.
+ echo '#line 5901 "configure"' > conftest.$ac_ext
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *32-bit*)
+ LD="${LD-ld} -melf32bsmip"
+ ;;
+ *N32*)
+ LD="${LD-ld} -melf32bmipn32"
+ ;;
+ *64-bit*)
+ LD="${LD-ld} -melf64bmip"
+ ;;
+ esac
+ else
+ case `/usr/bin/file conftest.$ac_objext` in
+ *32-bit*)
+ LD="${LD-ld} -32"
+ ;;
+ *N32*)
+ LD="${LD-ld} -n32"
+ ;;
+ *64-bit*)
+ LD="${LD-ld} -64"
+ ;;
+ esac
+ fi
+ fi
+ rm -rf conftest*
+ ;;
+
+x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \
+s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ case `/usr/bin/file conftest.o` in
+ *32-bit*)
+ case $host in
+ x86_64-*kfreebsd*-gnu)
+ LD="${LD-ld} -m elf_i386_fbsd"
+ ;;
+ x86_64-*linux*)
+ LD="${LD-ld} -m elf_i386"
+ ;;
+ ppc64-*linux*|powerpc64-*linux*)
+ LD="${LD-ld} -m elf32ppclinux"
+ ;;
+ s390x-*linux*)
+ LD="${LD-ld} -m elf_s390"
+ ;;
+ sparc64-*linux*)
+ LD="${LD-ld} -m elf32_sparc"
+ ;;
+ esac
+ ;;
+ *64-bit*)
+ case $host in
+ x86_64-*kfreebsd*-gnu)
+ LD="${LD-ld} -m elf_x86_64_fbsd"
+ ;;
+ x86_64-*linux*)
+ LD="${LD-ld} -m elf_x86_64"
+ ;;
+ ppc*-*linux*|powerpc*-*linux*)
+ LD="${LD-ld} -m elf64ppc"
+ ;;
+ s390*-*linux*|s390*-*tpf*)
+ LD="${LD-ld} -m elf64_s390"
+ ;;
+ sparc*-*linux*)
+ LD="${LD-ld} -m elf64_sparc"
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+
+*-*-sco3.2v5*)
+ # On SCO OpenServer 5, we need -belf to get full-featured binaries.
+ SAVE_CFLAGS="$CFLAGS"
+ CFLAGS="$CFLAGS -belf"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler needs -belf" >&5
+$as_echo_n "checking whether the C compiler needs -belf... " >&6; }
+if test "${lt_cv_cc_needs_belf+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ lt_cv_cc_needs_belf=yes
+else
+ lt_cv_cc_needs_belf=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+ ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_cc_needs_belf" >&5
+$as_echo "$lt_cv_cc_needs_belf" >&6; }
+ if test x"$lt_cv_cc_needs_belf" != x"yes"; then
+ # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf
+ CFLAGS="$SAVE_CFLAGS"
+ fi
+ ;;
+sparc*-*solaris*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ case `/usr/bin/file conftest.o` in
+ *64-bit*)
+ case $lt_cv_prog_gnu_ld in
+ yes*) LD="${LD-ld} -m elf64_sparc" ;;
+ *)
+ if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then
+ LD="${LD-ld} -64"
+ fi
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+esac
+
+need_locks="$enable_libtool_lock"
+
+
+ case $host_os in
+ rhapsody* | darwin*)
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}dsymutil", so it can be a program name with args.
+set dummy ${ac_tool_prefix}dsymutil; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_DSYMUTIL+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$DSYMUTIL"; then
+ ac_cv_prog_DSYMUTIL="$DSYMUTIL" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_DSYMUTIL="${ac_tool_prefix}dsymutil"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+DSYMUTIL=$ac_cv_prog_DSYMUTIL
+if test -n "$DSYMUTIL"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DSYMUTIL" >&5
+$as_echo "$DSYMUTIL" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_DSYMUTIL"; then
+ ac_ct_DSYMUTIL=$DSYMUTIL
+ # Extract the first word of "dsymutil", so it can be a program name with args.
+set dummy dsymutil; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_DSYMUTIL+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_DSYMUTIL"; then
+ ac_cv_prog_ac_ct_DSYMUTIL="$ac_ct_DSYMUTIL" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_DSYMUTIL="dsymutil"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_DSYMUTIL=$ac_cv_prog_ac_ct_DSYMUTIL
+if test -n "$ac_ct_DSYMUTIL"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DSYMUTIL" >&5
+$as_echo "$ac_ct_DSYMUTIL" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_DSYMUTIL" = x; then
+ DSYMUTIL=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ DSYMUTIL=$ac_ct_DSYMUTIL
+ fi
+else
+ DSYMUTIL="$ac_cv_prog_DSYMUTIL"
+fi
+
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}nmedit", so it can be a program name with args.
+set dummy ${ac_tool_prefix}nmedit; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_NMEDIT+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$NMEDIT"; then
+ ac_cv_prog_NMEDIT="$NMEDIT" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_NMEDIT="${ac_tool_prefix}nmedit"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+NMEDIT=$ac_cv_prog_NMEDIT
+if test -n "$NMEDIT"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $NMEDIT" >&5
+$as_echo "$NMEDIT" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_NMEDIT"; then
+ ac_ct_NMEDIT=$NMEDIT
+ # Extract the first word of "nmedit", so it can be a program name with args.
+set dummy nmedit; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_NMEDIT+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_NMEDIT"; then
+ ac_cv_prog_ac_ct_NMEDIT="$ac_ct_NMEDIT" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_NMEDIT="nmedit"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_NMEDIT=$ac_cv_prog_ac_ct_NMEDIT
+if test -n "$ac_ct_NMEDIT"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_NMEDIT" >&5
+$as_echo "$ac_ct_NMEDIT" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_NMEDIT" = x; then
+ NMEDIT=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ NMEDIT=$ac_ct_NMEDIT
+ fi
+else
+ NMEDIT="$ac_cv_prog_NMEDIT"
+fi
+
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}lipo", so it can be a program name with args.
+set dummy ${ac_tool_prefix}lipo; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_LIPO+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$LIPO"; then
+ ac_cv_prog_LIPO="$LIPO" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_LIPO="${ac_tool_prefix}lipo"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+LIPO=$ac_cv_prog_LIPO
+if test -n "$LIPO"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LIPO" >&5
+$as_echo "$LIPO" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_LIPO"; then
+ ac_ct_LIPO=$LIPO
+ # Extract the first word of "lipo", so it can be a program name with args.
+set dummy lipo; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_LIPO+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_LIPO"; then
+ ac_cv_prog_ac_ct_LIPO="$ac_ct_LIPO" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_LIPO="lipo"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_LIPO=$ac_cv_prog_ac_ct_LIPO
+if test -n "$ac_ct_LIPO"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_LIPO" >&5
+$as_echo "$ac_ct_LIPO" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_LIPO" = x; then
+ LIPO=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ LIPO=$ac_ct_LIPO
+ fi
+else
+ LIPO="$ac_cv_prog_LIPO"
+fi
+
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}otool", so it can be a program name with args.
+set dummy ${ac_tool_prefix}otool; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_OTOOL+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$OTOOL"; then
+ ac_cv_prog_OTOOL="$OTOOL" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_OTOOL="${ac_tool_prefix}otool"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+OTOOL=$ac_cv_prog_OTOOL
+if test -n "$OTOOL"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL" >&5
+$as_echo "$OTOOL" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_OTOOL"; then
+ ac_ct_OTOOL=$OTOOL
+ # Extract the first word of "otool", so it can be a program name with args.
+set dummy otool; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_OTOOL+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_OTOOL"; then
+ ac_cv_prog_ac_ct_OTOOL="$ac_ct_OTOOL" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_OTOOL="otool"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_OTOOL=$ac_cv_prog_ac_ct_OTOOL
+if test -n "$ac_ct_OTOOL"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL" >&5
+$as_echo "$ac_ct_OTOOL" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_OTOOL" = x; then
+ OTOOL=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ OTOOL=$ac_ct_OTOOL
+ fi
+else
+ OTOOL="$ac_cv_prog_OTOOL"
+fi
+
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}otool64", so it can be a program name with args.
+set dummy ${ac_tool_prefix}otool64; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_OTOOL64+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$OTOOL64"; then
+ ac_cv_prog_OTOOL64="$OTOOL64" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_OTOOL64="${ac_tool_prefix}otool64"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+OTOOL64=$ac_cv_prog_OTOOL64
+if test -n "$OTOOL64"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL64" >&5
+$as_echo "$OTOOL64" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_OTOOL64"; then
+ ac_ct_OTOOL64=$OTOOL64
+ # Extract the first word of "otool64", so it can be a program name with args.
+set dummy otool64; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_OTOOL64+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_OTOOL64"; then
+ ac_cv_prog_ac_ct_OTOOL64="$ac_ct_OTOOL64" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_OTOOL64="otool64"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_OTOOL64=$ac_cv_prog_ac_ct_OTOOL64
+if test -n "$ac_ct_OTOOL64"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL64" >&5
+$as_echo "$ac_ct_OTOOL64" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_OTOOL64" = x; then
+ OTOOL64=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ OTOOL64=$ac_ct_OTOOL64
+ fi
+else
+ OTOOL64="$ac_cv_prog_OTOOL64"
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -single_module linker flag" >&5
+$as_echo_n "checking for -single_module linker flag... " >&6; }
+if test "${lt_cv_apple_cc_single_mod+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_apple_cc_single_mod=no
+ if test -z "${LT_MULTI_MODULE}"; then
+ # By default we will add the -single_module flag. You can override
+ # by either setting the environment variable LT_MULTI_MODULE
+ # non-empty at configure time, or by adding -multi_module to the
+ # link flags.
+ rm -rf libconftest.dylib*
+ echo "int foo(void){return 1;}" > conftest.c
+ echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+-dynamiclib -Wl,-single_module conftest.c" >&5
+ $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+ -dynamiclib -Wl,-single_module conftest.c 2>conftest.err
+ _lt_result=$?
+ if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then
+ lt_cv_apple_cc_single_mod=yes
+ else
+ cat conftest.err >&5
+ fi
+ rm -rf libconftest.dylib*
+ rm -f conftest.*
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_apple_cc_single_mod" >&5
+$as_echo "$lt_cv_apple_cc_single_mod" >&6; }
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -exported_symbols_list linker flag" >&5
+$as_echo_n "checking for -exported_symbols_list linker flag... " >&6; }
+if test "${lt_cv_ld_exported_symbols_list+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_ld_exported_symbols_list=no
+ save_LDFLAGS=$LDFLAGS
+ echo "_main" > conftest.sym
+ LDFLAGS="$LDFLAGS -Wl,-exported_symbols_list,conftest.sym"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ lt_cv_ld_exported_symbols_list=yes
+else
+ lt_cv_ld_exported_symbols_list=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+ LDFLAGS="$save_LDFLAGS"
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_exported_symbols_list" >&5
+$as_echo "$lt_cv_ld_exported_symbols_list" >&6; }
+ case $host_os in
+ rhapsody* | darwin1.[012])
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}suppress' ;;
+ darwin1.*)
+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+ darwin*) # darwin 5.x on
+ # if running on 10.5 or later, the deployment target defaults
+ # to the OS version, if on x86, and 10.4, the deployment
+ # target defaults to 10.4. Don't you love it?
+ case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in
+ 10.0,*86*-darwin8*|10.0,*-darwin[91]*)
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+ 10.[012]*)
+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+ 10.*)
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+ esac
+ ;;
+ esac
+ if test "$lt_cv_apple_cc_single_mod" = "yes"; then
+ _lt_dar_single_mod='$single_module'
+ fi
+ if test "$lt_cv_ld_exported_symbols_list" = "yes"; then
+ _lt_dar_export_syms=' ${wl}-exported_symbols_list,$output_objdir/${libname}-symbols.expsym'
+ else
+ _lt_dar_export_syms='~$NMEDIT -s $output_objdir/${libname}-symbols.expsym ${lib}'
+ fi
+ if test "$DSYMUTIL" != ":"; then
+ _lt_dsymutil='~$DSYMUTIL $lib || :'
+ else
+ _lt_dsymutil=
+ fi
+ ;;
+ esac
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C preprocessor" >&5
+$as_echo_n "checking how to run the C preprocessor... " >&6; }
+# On Suns, sometimes $CPP names a directory.
+if test -n "$CPP" && test -d "$CPP"; then
+ CPP=
+fi
+if test -z "$CPP"; then
+ if test "${ac_cv_prog_CPP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ # Double quotes because CPP needs to be expanded
+ for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp"
+ do
+ ac_preproc_ok=false
+for ac_c_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+
+else
+ # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+ # Broken: success on invalid input.
+continue
+else
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.i conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then :
+ break
+fi
+
+ done
+ ac_cv_prog_CPP=$CPP
+
+fi
+ CPP=$ac_cv_prog_CPP
+else
+ ac_cv_prog_CPP=$CPP
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPP" >&5
+$as_echo "$CPP" >&6; }
+ac_preproc_ok=false
+for ac_c_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+
+else
+ # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+ # Broken: success on invalid input.
+continue
+else
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.i conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then :
+
+else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details" "$LINENO" 5 ; }
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5
+$as_echo_n "checking for ANSI C header files... " >&6; }
+if test "${ac_cv_header_stdc+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdlib.h>
+#include <stdarg.h>
+#include <string.h>
+#include <float.h>
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_header_stdc=yes
+else
+ ac_cv_header_stdc=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+
+if test $ac_cv_header_stdc = yes; then
+ # SunOS 4.x string.h does not declare mem*, contrary to ANSI.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <string.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "memchr" >/dev/null 2>&1; then :
+
+else
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdlib.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "free" >/dev/null 2>&1; then :
+
+else
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi.
+ if test "$cross_compiling" = yes; then :
+ :
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ctype.h>
+#include <stdlib.h>
+#if ((' ' & 0x0FF) == 0x020)
+# define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
+# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
+#else
+# define ISLOWER(c) \
+ (('a' <= (c) && (c) <= 'i') \
+ || ('j' <= (c) && (c) <= 'r') \
+ || ('s' <= (c) && (c) <= 'z'))
+# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c))
+#endif
+
+#define XOR(e, f) (((e) && !(f)) || (!(e) && (f)))
+int
+main ()
+{
+ int i;
+ for (i = 0; i < 256; i++)
+ if (XOR (islower (i), ISLOWER (i))
+ || toupper (i) != TOUPPER (i))
+ return 2;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_run "$LINENO"; then :
+
+else
+ ac_cv_header_stdc=no
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
+ conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+
+fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5
+$as_echo "$ac_cv_header_stdc" >&6; }
+if test $ac_cv_header_stdc = yes; then
+
+$as_echo "#define STDC_HEADERS 1" >>confdefs.h
+
+fi
+
+# On IRIX 5.3, sys/types and inttypes.h are conflicting.
+for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \
+ inttypes.h stdint.h unistd.h
+do :
+ as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default
+"
+if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+
+for ac_header in dlfcn.h
+do :
+ ac_fn_c_check_header_compile "$LINENO" "dlfcn.h" "ac_cv_header_dlfcn_h" "$ac_includes_default
+"
+if test "x$ac_cv_header_dlfcn_h" = x""yes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_DLFCN_H 1
+_ACEOF
+
+fi
+
+done
+
+
+
+# Set options
+
+
+
+ enable_dlopen=no
+
+
+ enable_win32_dll=no
+
+
+ # Check whether --enable-shared was given.
+if test "${enable_shared+set}" = set; then :
+ enableval=$enable_shared; p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_shared=yes ;;
+ no) enable_shared=no ;;
+ *)
+ enable_shared=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_shared=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac
+else
+ enable_shared=yes
+fi
+
+
+
+
+
+
+
+
+
+ # Check whether --enable-static was given.
+if test "${enable_static+set}" = set; then :
+ enableval=$enable_static; p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_static=yes ;;
+ no) enable_static=no ;;
+ *)
+ enable_static=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_static=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac
+else
+ enable_static=yes
+fi
+
+
+
+
+
+
+
+
+
+
+# Check whether --with-pic was given.
+if test "${with_pic+set}" = set; then :
+ withval=$with_pic; pic_mode="$withval"
+else
+ pic_mode=default
+fi
+
+
+test -z "$pic_mode" && pic_mode=default
+
+
+
+
+
+
+
+ # Check whether --enable-fast-install was given.
+if test "${enable_fast_install+set}" = set; then :
+ enableval=$enable_fast_install; p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_fast_install=yes ;;
+ no) enable_fast_install=no ;;
+ *)
+ enable_fast_install=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_fast_install=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac
+else
+ enable_fast_install=yes
+fi
+
+
+
+
+
+
+
+
+
+
+
+# This can be used to rebuild libtool when needed
+LIBTOOL_DEPS="$ltmain"
+
+# Always use our own libtool.
+LIBTOOL='$(SHELL) $(top_builddir)/libtool'
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+test -z "$LN_S" && LN_S="ln -s"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+if test -n "${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for objdir" >&5
+$as_echo_n "checking for objdir... " >&6; }
+if test "${lt_cv_objdir+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ rm -f .libs 2>/dev/null
+mkdir .libs 2>/dev/null
+if test -d .libs; then
+ lt_cv_objdir=.libs
+else
+ # MS-DOS does not allow filenames that begin with a dot.
+ lt_cv_objdir=_libs
+fi
+rmdir .libs 2>/dev/null
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_objdir" >&5
+$as_echo "$lt_cv_objdir" >&6; }
+objdir=$lt_cv_objdir
+
+
+
+
+
+cat >>confdefs.h <<_ACEOF
+#define LT_OBJDIR "$lt_cv_objdir/"
+_ACEOF
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+case $host_os in
+aix3*)
+ # AIX sometimes has problems with the GCC collect2 program. For some
+ # reason, if we set the COLLECT_NAMES environment variable, the problems
+ # vanish in a puff of smoke.
+ if test "X${COLLECT_NAMES+set}" != Xset; then
+ COLLECT_NAMES=
+ export COLLECT_NAMES
+ fi
+ ;;
+esac
+
+# Sed substitution that helps us do robust quoting. It backslashifies
+# metacharacters that are still active within double-quoted strings.
+sed_quote_subst='s/\(["`$\\]\)/\\\1/g'
+
+# Same as above, but do not quote variable references.
+double_quote_subst='s/\(["`\\]\)/\\\1/g'
+
+# Sed substitution to delay expansion of an escaped shell variable in a
+# double_quote_subst'ed string.
+delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g'
+
+# Sed substitution to delay expansion of an escaped single quote.
+delay_single_quote_subst='s/'\''/'\'\\\\\\\'\''/g'
+
+# Sed substitution to avoid accidental globbing in evaled expressions
+no_glob_subst='s/\*/\\\*/g'
+
+# Global variables:
+ofile=libtool
+can_build_shared=yes
+
+# All known linkers require a `.a' archive for static linking (except MSVC,
+# which needs '.lib').
+libext=a
+
+with_gnu_ld="$lt_cv_prog_gnu_ld"
+
+old_CC="$CC"
+old_CFLAGS="$CFLAGS"
+
+# Set sane defaults for various variables
+test -z "$CC" && CC=cc
+test -z "$LTCC" && LTCC=$CC
+test -z "$LTCFLAGS" && LTCFLAGS=$CFLAGS
+test -z "$LD" && LD=ld
+test -z "$ac_objext" && ac_objext=o
+
+for cc_temp in $compiler""; do
+ case $cc_temp in
+ compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+ distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+ \-*) ;;
+ *) break;;
+ esac
+done
+cc_basename=`$ECHO "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+
+
+# Only perform the check for file, if the check method requires it
+test -z "$MAGIC_CMD" && MAGIC_CMD=file
+case $deplibs_check_method in
+file_magic*)
+ if test "$file_magic_cmd" = '$MAGIC_CMD'; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ${ac_tool_prefix}file" >&5
+$as_echo_n "checking for ${ac_tool_prefix}file... " >&6; }
+if test "${lt_cv_path_MAGIC_CMD+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ case $MAGIC_CMD in
+[\\/*] | ?:[\\/]*)
+ lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path.
+ ;;
+*)
+ lt_save_MAGIC_CMD="$MAGIC_CMD"
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ ac_dummy="/usr/bin$PATH_SEPARATOR$PATH"
+ for ac_dir in $ac_dummy; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f $ac_dir/${ac_tool_prefix}file; then
+ lt_cv_path_MAGIC_CMD="$ac_dir/${ac_tool_prefix}file"
+ if test -n "$file_magic_test_file"; then
+ case $deplibs_check_method in
+ "file_magic "*)
+ file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"`
+ MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+ if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null |
+ $EGREP "$file_magic_regex" > /dev/null; then
+ :
+ else
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the command libtool uses to detect shared libraries,
+*** $file_magic_cmd, produces output that libtool cannot recognize.
+*** The result is that libtool may fail to recognize shared libraries
+*** as such. This will affect the creation of libtool libraries that
+*** depend on shared libraries, but programs linked with such libtool
+*** libraries will work regardless of this problem. Nevertheless, you
+*** may want to report the problem to your system manager and/or to
+*** bug-libtool at gnu.org
+
+_LT_EOF
+ fi ;;
+ esac
+ fi
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+ MAGIC_CMD="$lt_save_MAGIC_CMD"
+ ;;
+esac
+fi
+
+MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+if test -n "$MAGIC_CMD"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MAGIC_CMD" >&5
+$as_echo "$MAGIC_CMD" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+
+
+
+if test -z "$lt_cv_path_MAGIC_CMD"; then
+ if test -n "$ac_tool_prefix"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for file" >&5
+$as_echo_n "checking for file... " >&6; }
+if test "${lt_cv_path_MAGIC_CMD+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ case $MAGIC_CMD in
+[\\/*] | ?:[\\/]*)
+ lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path.
+ ;;
+*)
+ lt_save_MAGIC_CMD="$MAGIC_CMD"
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ ac_dummy="/usr/bin$PATH_SEPARATOR$PATH"
+ for ac_dir in $ac_dummy; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f $ac_dir/file; then
+ lt_cv_path_MAGIC_CMD="$ac_dir/file"
+ if test -n "$file_magic_test_file"; then
+ case $deplibs_check_method in
+ "file_magic "*)
+ file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"`
+ MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+ if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null |
+ $EGREP "$file_magic_regex" > /dev/null; then
+ :
+ else
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the command libtool uses to detect shared libraries,
+*** $file_magic_cmd, produces output that libtool cannot recognize.
+*** The result is that libtool may fail to recognize shared libraries
+*** as such. This will affect the creation of libtool libraries that
+*** depend on shared libraries, but programs linked with such libtool
+*** libraries will work regardless of this problem. Nevertheless, you
+*** may want to report the problem to your system manager and/or to
+*** bug-libtool at gnu.org
+
+_LT_EOF
+ fi ;;
+ esac
+ fi
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+ MAGIC_CMD="$lt_save_MAGIC_CMD"
+ ;;
+esac
+fi
+
+MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+if test -n "$MAGIC_CMD"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MAGIC_CMD" >&5
+$as_echo "$MAGIC_CMD" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ else
+ MAGIC_CMD=:
+ fi
+fi
+
+ fi
+ ;;
+esac
+
+# Use C for the default configuration in the libtool script
+
+lt_save_CC="$CC"
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+# Source file extension for C test sources.
+ac_ext=c
+
+# Object file extension for compiled C test sources.
+objext=o
+objext=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="int some_variable = 0;"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='int main(){return(0);}'
+
+
+
+
+
+
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+# Save the default compiler, since it gets overwritten when the other
+# tags are being tested, and _LT_TAGVAR(compiler, []) is a NOP.
+compiler_DEFAULT=$CC
+
+# save warnings/boilerplate of simple test code
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$RM conftest*
+
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$RM -r conftest*
+
+
+if test -n "$compiler"; then
+
+lt_prog_compiler_no_builtin_flag=
+
+if test "$GCC" = yes; then
+ lt_prog_compiler_no_builtin_flag=' -fno-builtin'
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler supports -fno-rtti -fno-exceptions" >&5
+$as_echo_n "checking if $compiler supports -fno-rtti -fno-exceptions... " >&6; }
+if test "${lt_cv_prog_compiler_rtti_exceptions+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_rtti_exceptions=no
+ ac_outfile=conftest.$ac_objext
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+ lt_compiler_flag="-fno-rtti -fno-exceptions"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ # The option is referenced via a variable to avoid confusing sed.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:7426: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>conftest.err)
+ ac_status=$?
+ cat conftest.err >&5
+ echo "$as_me:7430: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s "$ac_outfile"; then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings other than the usual output.
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_rtti_exceptions=yes
+ fi
+ fi
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_rtti_exceptions" >&5
+$as_echo "$lt_cv_prog_compiler_rtti_exceptions" >&6; }
+
+if test x"$lt_cv_prog_compiler_rtti_exceptions" = xyes; then
+ lt_prog_compiler_no_builtin_flag="$lt_prog_compiler_no_builtin_flag -fno-rtti -fno-exceptions"
+else
+ :
+fi
+
+fi
+
+
+
+
+
+
+ lt_prog_compiler_wl=
+lt_prog_compiler_pic=
+lt_prog_compiler_static=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $compiler option to produce PIC" >&5
+$as_echo_n "checking for $compiler option to produce PIC... " >&6; }
+
+ if test "$GCC" = yes; then
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_static='-static'
+
+ case $host_os in
+ aix*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ lt_prog_compiler_static='-Bstatic'
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ lt_prog_compiler_pic='-fPIC'
+ ;;
+ m68k)
+ # FIXME: we need at least 68020 code to build shared libraries, but
+ # adding the `-m68020' flag to GCC prevents building anything better,
+ # like `-m68040'.
+ lt_prog_compiler_pic='-m68020 -resident32 -malways-restore-a4'
+ ;;
+ esac
+ ;;
+
+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+ # PIC is the default for these OSes.
+ ;;
+
+ mingw* | cygwin* | pw32* | os2* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ # Although the cygwin gcc ignores -fPIC, still need this for old-style
+ # (--disable-auto-import) libraries
+ lt_prog_compiler_pic='-DDLL_EXPORT'
+ ;;
+
+ darwin* | rhapsody*)
+ # PIC is the default on this platform
+ # Common symbols not allowed in MH_DYLIB files
+ lt_prog_compiler_pic='-fno-common'
+ ;;
+
+ hpux*)
+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit
+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag
+ # sets the default TLS model and affects inlining.
+ case $host_cpu in
+ hppa*64*)
+ # +Z the default
+ ;;
+ *)
+ lt_prog_compiler_pic='-fPIC'
+ ;;
+ esac
+ ;;
+
+ interix[3-9]*)
+ # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+ # Instead, we relocate shared libraries at runtime.
+ ;;
+
+ msdosdjgpp*)
+ # Just because we use GCC doesn't mean we suddenly get shared libraries
+ # on systems that don't support them.
+ lt_prog_compiler_can_build_shared=no
+ enable_shared=no
+ ;;
+
+ *nto* | *qnx*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ lt_prog_compiler_pic='-fPIC -shared'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ lt_prog_compiler_pic=-Kconform_pic
+ fi
+ ;;
+
+ *)
+ lt_prog_compiler_pic='-fPIC'
+ ;;
+ esac
+ else
+ # PORTME Check for flag to pass linker flags through the system compiler.
+ case $host_os in
+ aix*)
+ lt_prog_compiler_wl='-Wl,'
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ lt_prog_compiler_static='-Bstatic'
+ else
+ lt_prog_compiler_static='-bnso -bI:/lib/syscalls.exp'
+ fi
+ ;;
+
+ mingw* | cygwin* | pw32* | os2* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ lt_prog_compiler_pic='-DDLL_EXPORT'
+ ;;
+
+ hpux9* | hpux10* | hpux11*)
+ lt_prog_compiler_wl='-Wl,'
+ # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+ # not for PA HP-UX.
+ case $host_cpu in
+ hppa*64*|ia64*)
+ # +Z the default
+ ;;
+ *)
+ lt_prog_compiler_pic='+Z'
+ ;;
+ esac
+ # Is there a better lt_prog_compiler_static that works with the bundled CC?
+ lt_prog_compiler_static='${wl}-a ${wl}archive'
+ ;;
+
+ irix5* | irix6* | nonstopux*)
+ lt_prog_compiler_wl='-Wl,'
+ # PIC (with -KPIC) is the default.
+ lt_prog_compiler_static='-non_shared'
+ ;;
+
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ # old Intel for x86_64 which still supported -KPIC.
+ ecc*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-static'
+ ;;
+ # icc used to be incompatible with GCC.
+ # ICC 10 doesn't accept -KPIC any more.
+ icc* | ifort*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-fPIC'
+ lt_prog_compiler_static='-static'
+ ;;
+ # Lahey Fortran 8.1.
+ lf95*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='--shared'
+ lt_prog_compiler_static='--static'
+ ;;
+ pgcc* | pgf77* | pgf90* | pgf95*)
+ # Portland Group compilers (*not* the Pentium gcc compiler,
+ # which looks to be a dead project)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-fpic'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+ ccc*)
+ lt_prog_compiler_wl='-Wl,'
+ # All Alpha code is PIC.
+ lt_prog_compiler_static='-non_shared'
+ ;;
+ xl*)
+ # IBM XL C 8.0/Fortran 10.1 on PPC
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-qpic'
+ lt_prog_compiler_static='-qstaticlink'
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C 5.9
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ lt_prog_compiler_wl='-Wl,'
+ ;;
+ *Sun\ F*)
+ # Sun Fortran 8.3 passes all unrecognized flags to the linker
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ lt_prog_compiler_wl=''
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+
+ newsos6)
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ *nto* | *qnx*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ lt_prog_compiler_pic='-fPIC -shared'
+ ;;
+
+ osf3* | osf4* | osf5*)
+ lt_prog_compiler_wl='-Wl,'
+ # All OSF/1 code is PIC.
+ lt_prog_compiler_static='-non_shared'
+ ;;
+
+ rdos*)
+ lt_prog_compiler_static='-non_shared'
+ ;;
+
+ solaris*)
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ case $cc_basename in
+ f77* | f90* | f95*)
+ lt_prog_compiler_wl='-Qoption ld ';;
+ *)
+ lt_prog_compiler_wl='-Wl,';;
+ esac
+ ;;
+
+ sunos4*)
+ lt_prog_compiler_wl='-Qoption ld '
+ lt_prog_compiler_pic='-PIC'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ sysv4 | sysv4.2uw2* | sysv4.3*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec ;then
+ lt_prog_compiler_pic='-Kconform_pic'
+ lt_prog_compiler_static='-Bstatic'
+ fi
+ ;;
+
+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ unicos*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_can_build_shared=no
+ ;;
+
+ uts4*)
+ lt_prog_compiler_pic='-pic'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ *)
+ lt_prog_compiler_can_build_shared=no
+ ;;
+ esac
+ fi
+
+case $host_os in
+ # For platforms which do not support PIC, -DPIC is meaningless:
+ *djgpp*)
+ lt_prog_compiler_pic=
+ ;;
+ *)
+ lt_prog_compiler_pic="$lt_prog_compiler_pic -DPIC"
+ ;;
+esac
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_prog_compiler_pic" >&5
+$as_echo "$lt_prog_compiler_pic" >&6; }
+
+
+
+
+
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$lt_prog_compiler_pic"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler PIC flag $lt_prog_compiler_pic works" >&5
+$as_echo_n "checking if $compiler PIC flag $lt_prog_compiler_pic works... " >&6; }
+if test "${lt_cv_prog_compiler_pic_works+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_pic_works=no
+ ac_outfile=conftest.$ac_objext
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+ lt_compiler_flag="$lt_prog_compiler_pic -DPIC"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ # The option is referenced via a variable to avoid confusing sed.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:7765: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>conftest.err)
+ ac_status=$?
+ cat conftest.err >&5
+ echo "$as_me:7769: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s "$ac_outfile"; then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings other than the usual output.
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_pic_works=yes
+ fi
+ fi
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_pic_works" >&5
+$as_echo "$lt_cv_prog_compiler_pic_works" >&6; }
+
+if test x"$lt_cv_prog_compiler_pic_works" = xyes; then
+ case $lt_prog_compiler_pic in
+ "" | " "*) ;;
+ *) lt_prog_compiler_pic=" $lt_prog_compiler_pic" ;;
+ esac
+else
+ lt_prog_compiler_pic=
+ lt_prog_compiler_can_build_shared=no
+fi
+
+fi
+
+
+
+
+
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$lt_prog_compiler_wl eval lt_tmp_static_flag=\"$lt_prog_compiler_static\"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler static flag $lt_tmp_static_flag works" >&5
+$as_echo_n "checking if $compiler static flag $lt_tmp_static_flag works... " >&6; }
+if test "${lt_cv_prog_compiler_static_works+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_static_works=no
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS $lt_tmp_static_flag"
+ echo "$lt_simple_link_test_code" > conftest.$ac_ext
+ if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+ # The linker can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ if test -s conftest.err; then
+ # Append any errors to the config.log.
+ cat conftest.err 1>&5
+ $ECHO "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_static_works=yes
+ fi
+ else
+ lt_cv_prog_compiler_static_works=yes
+ fi
+ fi
+ $RM -r conftest*
+ LDFLAGS="$save_LDFLAGS"
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_static_works" >&5
+$as_echo "$lt_cv_prog_compiler_static_works" >&6; }
+
+if test x"$lt_cv_prog_compiler_static_works" = xyes; then
+ :
+else
+ lt_prog_compiler_static=
+fi
+
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler supports -c -o file.$ac_objext" >&5
+$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; }
+if test "${lt_cv_prog_compiler_c_o+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_c_o=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:7870: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&5
+ echo "$as_me:7874: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_c_o=yes
+ fi
+ fi
+ chmod u+w . 2>&5
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_c_o" >&5
+$as_echo "$lt_cv_prog_compiler_c_o" >&6; }
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler supports -c -o file.$ac_objext" >&5
+$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; }
+if test "${lt_cv_prog_compiler_c_o+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_c_o=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:7925: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&5
+ echo "$as_me:7929: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_c_o=yes
+ fi
+ fi
+ chmod u+w . 2>&5
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_c_o" >&5
+$as_echo "$lt_cv_prog_compiler_c_o" >&6; }
+
+
+
+
+hard_links="nottested"
+if test "$lt_cv_prog_compiler_c_o" = no && test "$need_locks" != no; then
+ # do not overwrite the value of need_locks provided by the user
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if we can lock with hard links" >&5
+$as_echo_n "checking if we can lock with hard links... " >&6; }
+ hard_links=yes
+ $RM conftest*
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ touch conftest.a
+ ln conftest.a conftest.b 2>&5 || hard_links=no
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $hard_links" >&5
+$as_echo "$hard_links" >&6; }
+ if test "$hard_links" = no; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&5
+$as_echo "$as_me: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&2;}
+ need_locks=warn
+ fi
+else
+ need_locks=no
+fi
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+$as_echo_n "checking whether the $compiler linker ($LD) supports shared libraries... " >&6; }
+
+ runpath_var=
+ allow_undefined_flag=
+ always_export_symbols=no
+ archive_cmds=
+ archive_expsym_cmds=
+ compiler_needs_object=no
+ enable_shared_with_static_runtimes=no
+ export_dynamic_flag_spec=
+ export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ hardcode_automatic=no
+ hardcode_direct=no
+ hardcode_direct_absolute=no
+ hardcode_libdir_flag_spec=
+ hardcode_libdir_flag_spec_ld=
+ hardcode_libdir_separator=
+ hardcode_minus_L=no
+ hardcode_shlibpath_var=unsupported
+ inherit_rpath=no
+ link_all_deplibs=unknown
+ module_cmds=
+ module_expsym_cmds=
+ old_archive_from_new_cmds=
+ old_archive_from_expsyms_cmds=
+ thread_safe_flag_spec=
+ whole_archive_flag_spec=
+ # include_expsyms should be a list of space-separated symbols to be *always*
+ # included in the symbol list
+ include_expsyms=
+ # exclude_expsyms can be an extended regexp of symbols to exclude
+ # it will be wrapped by ` (' and `)$', so one must not match beginning or
+ # end of line. Example: `a|bc|.*d.*' will exclude the symbols `a' and `bc',
+ # as well as any symbol that contains `d'.
+ exclude_expsyms='_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*'
+ # Although _GLOBAL_OFFSET_TABLE_ is a valid symbol C name, most a.out
+ # platforms (ab)use it in PIC code, but their linkers get confused if
+ # the symbol is explicitly referenced. Since portable code cannot
+ # rely on this symbol name, it's probably fine to never include it in
+ # preloaded symbol tables.
+ # Exclude shared library initialization/finalization symbols.
+ extract_expsyms_cmds=
+
+ case $host_os in
+ cygwin* | mingw* | pw32* | cegcc*)
+ # FIXME: the MSVC++ port hasn't been tested in a loooong time
+ # When not using gcc, we currently assume that we are using
+ # Microsoft Visual C++.
+ if test "$GCC" != yes; then
+ with_gnu_ld=no
+ fi
+ ;;
+ interix*)
+ # we just hope/assume this is gcc and not c89 (= MSVC++)
+ with_gnu_ld=yes
+ ;;
+ openbsd*)
+ with_gnu_ld=no
+ ;;
+ linux* | k*bsd*-gnu)
+ link_all_deplibs=no
+ ;;
+ esac
+
+ ld_shlibs=yes
+ if test "$with_gnu_ld" = yes; then
+ # If archive_cmds runs LD, not CC, wlarc should be empty
+ wlarc='${wl}'
+
+ # Set some defaults for GNU ld with shared library support. These
+ # are reset later if shared libraries are not supported. Putting them
+ # here allows them to be overridden if necessary.
+ runpath_var=LD_RUN_PATH
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ export_dynamic_flag_spec='${wl}--export-dynamic'
+ # ancient GNU ld didn't support --whole-archive et. al.
+ if $LD --help 2>&1 | $GREP 'no-whole-archive' > /dev/null; then
+ whole_archive_flag_spec="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ else
+ whole_archive_flag_spec=
+ fi
+ supports_anon_versioning=no
+ case `$LD -v 2>&1` in
+ *GNU\ gold*) supports_anon_versioning=yes ;;
+ *\ [01].* | *\ 2.[0-9].* | *\ 2.10.*) ;; # catch versions < 2.11
+ *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ...
+ *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ...
+ *\ 2.11.*) ;; # other 2.11 versions
+ *) supports_anon_versioning=yes ;;
+ esac
+
+ # See if GNU ld supports shared libraries.
+ case $host_os in
+ aix[3-9]*)
+ # On AIX/PPC, the GNU linker is very broken
+ if test "$host_cpu" != ia64; then
+ ld_shlibs=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the GNU linker, at least up to release 2.9.1, is reported
+*** to be unable to reliably create shared libraries on AIX.
+*** Therefore, libtool is disabling shared libraries support. If you
+*** really care for shared libraries, you may want to modify your PATH
+*** so that a non-GNU linker is found, and then restart.
+
+_LT_EOF
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds=''
+ ;;
+ m68k)
+ archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_minus_L=yes
+ ;;
+ esac
+ ;;
+
+ beos*)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ allow_undefined_flag=unsupported
+ # Joseph Beckenbach <jrb3 at best.com> says some releases of gcc
+ # support --undefined. This deserves some investigation. FIXME
+ archive_cmds='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # _LT_TAGVAR(hardcode_libdir_flag_spec, ) is actually meaningless,
+ # as there is no search path for DLLs.
+ hardcode_libdir_flag_spec='-L$libdir'
+ allow_undefined_flag=unsupported
+ always_export_symbols=no
+ enable_shared_with_static_runtimes=yes
+ export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1 DATA/'\'' | $SED -e '\''/^[AITW][ ]/s/.*[ ]//'\'' | sort | uniq > $export_symbols'
+
+ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ # If the export-symbols file already is a .def file (1st line
+ # is EXPORTS), use it as is; otherwise, prepend...
+ archive_expsym_cmds='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+ cp $export_symbols $output_objdir/$soname.def;
+ else
+ echo EXPORTS > $output_objdir/$soname.def;
+ cat $export_symbols >> $output_objdir/$soname.def;
+ fi~
+ $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ interix[3-9]*)
+ hardcode_direct=no
+ hardcode_shlibpath_var=no
+ hardcode_libdir_flag_spec='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec='${wl}-E'
+ # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+ # Instead, shared libraries are loaded at an image base (0x10000000 by
+ # default) and relocated if they conflict, which is a slow very memory
+ # consuming and fragmenting process. To avoid this, we pick a random,
+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+ # time. Moving up from 0x10000000 also allows more sbrk(2) space.
+ archive_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ archive_expsym_cmds='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ ;;
+
+ gnu* | linux* | tpf* | k*bsd*-gnu | kopensolaris*-gnu)
+ tmp_diet=no
+ if test "$host_os" = linux-dietlibc; then
+ case $cc_basename in
+ diet\ *) tmp_diet=yes;; # linux-dietlibc with static linking (!diet-dyn)
+ esac
+ fi
+ if $LD --help 2>&1 | $EGREP ': supported targets:.* elf' > /dev/null \
+ && test "$tmp_diet" = no
+ then
+ tmp_addflag=
+ tmp_sharedflag='-shared'
+ case $cc_basename,$host_cpu in
+ pgcc*) # Portland Group C compiler
+ whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ tmp_addflag=' $pic_flag'
+ ;;
+ pgf77* | pgf90* | pgf95*) # Portland Group f77 and f90 compilers
+ whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ tmp_addflag=' $pic_flag -Mnomain' ;;
+ ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64
+ tmp_addflag=' -i_dynamic' ;;
+ efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64
+ tmp_addflag=' -i_dynamic -nofor_main' ;;
+ ifc* | ifort*) # Intel Fortran compiler
+ tmp_addflag=' -nofor_main' ;;
+ lf95*) # Lahey Fortran 8.1
+ whole_archive_flag_spec=
+ tmp_sharedflag='--shared' ;;
+ xl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ tmp_sharedflag='-qmkshrobj'
+ tmp_addflag= ;;
+ esac
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*) # Sun C 5.9
+ whole_archive_flag_spec='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ compiler_needs_object=yes
+ tmp_sharedflag='-G' ;;
+ *Sun\ F*) # Sun Fortran 8.3
+ tmp_sharedflag='-G' ;;
+ esac
+ archive_cmds='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+
+ if test "x$supports_anon_versioning" = xyes; then
+ archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+ fi
+
+ case $cc_basename in
+ xlf*)
+ # IBM XL Fortran 10.1 on PPC cannot create shared libs itself
+ whole_archive_flag_spec='--whole-archive$convenience --no-whole-archive'
+ hardcode_libdir_flag_spec=
+ hardcode_libdir_flag_spec_ld='-rpath $libdir'
+ archive_cmds='$LD -shared $libobjs $deplibs $compiler_flags -soname $soname -o $lib'
+ if test "x$supports_anon_versioning" = xyes; then
+ archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $LD -shared $libobjs $deplibs $compiler_flags -soname $soname -version-script $output_objdir/$libname.ver -o $lib'
+ fi
+ ;;
+ esac
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ archive_cmds='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
+ wlarc=
+ else
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ fi
+ ;;
+
+ solaris*)
+ if $LD -v 2>&1 | $GREP 'BFD 2\.8' > /dev/null; then
+ ld_shlibs=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: The releases 2.8.* of the GNU linker cannot reliably
+*** create shared libraries on Solaris systems. Therefore, libtool
+*** is disabling shared libraries support. We urge you to upgrade GNU
+*** binutils to release 2.9.1 or newer. Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+ elif $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*)
+ case `$LD -v 2>&1` in
+ *\ [01].* | *\ 2.[0-9].* | *\ 2.1[0-5].*)
+ ld_shlibs=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not
+*** reliably create shared libraries on SCO systems. Therefore, libtool
+*** is disabling shared libraries support. We urge you to upgrade GNU
+*** binutils to release 2.16.91.0.3 or newer. Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+ ;;
+ *)
+ # For security reasons, it is highly recommended that you always
+ # use absolute paths for naming shared libraries, and exclude the
+ # DT_RUNPATH tag from executables and libraries. But doing so
+ # requires that you compile everything twice, which is a pain.
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+ esac
+ ;;
+
+ sunos4*)
+ archive_cmds='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ wlarc=
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ *)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+ esac
+
+ if test "$ld_shlibs" = no; then
+ runpath_var=
+ hardcode_libdir_flag_spec=
+ export_dynamic_flag_spec=
+ whole_archive_flag_spec=
+ fi
+ else
+ # PORTME fill in a description of your system's linker (not GNU ld)
+ case $host_os in
+ aix3*)
+ allow_undefined_flag=unsupported
+ always_export_symbols=yes
+ archive_expsym_cmds='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname'
+ # Note: this linker hardcodes the directories in LIBPATH if there
+ # are no directories specified by -L.
+ hardcode_minus_L=yes
+ if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then
+ # Neither direct hardcoding nor static linking is supported with a
+ # broken collect2.
+ hardcode_direct=unsupported
+ fi
+ ;;
+
+ aix[4-9]*)
+ if test "$host_cpu" = ia64; then
+ # On IA64, the linker does run time linking by default, so we don't
+ # have to do anything special.
+ aix_use_runtimelinking=no
+ exp_sym_flag='-Bexport'
+ no_entry_flag=""
+ else
+ # If we're using GNU nm, then we don't want the "-C" option.
+ # -C means demangle to AIX nm, but means don't demangle with GNU nm
+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then
+ export_symbols_cmds='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ else
+ export_symbols_cmds='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ fi
+ aix_use_runtimelinking=no
+
+ # Test if we are trying to use run time linking or normal
+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+ # need to do runtime linking.
+ case $host_os in aix4.[23]|aix4.[23].*|aix[5-9]*)
+ for ld_flag in $LDFLAGS; do
+ if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then
+ aix_use_runtimelinking=yes
+ break
+ fi
+ done
+ ;;
+ esac
+
+ exp_sym_flag='-bexport'
+ no_entry_flag='-bnoentry'
+ fi
+
+ # When large executables or shared objects are built, AIX ld can
+ # have problems creating the table of contents. If linking a library
+ # or program results in "error TOC overflow" add -mminimal-toc to
+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not
+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+ archive_cmds=''
+ hardcode_direct=yes
+ hardcode_direct_absolute=yes
+ hardcode_libdir_separator=':'
+ link_all_deplibs=yes
+ file_list_spec='${wl}-f,'
+
+ if test "$GCC" = yes; then
+ case $host_os in aix4.[012]|aix4.[012].*)
+ # We only want to do this on AIX 4.2 and lower, the check
+ # below for broken collect2 doesn't work under 4.3+
+ collect2name=`${CC} -print-prog-name=collect2`
+ if test -f "$collect2name" &&
+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null
+ then
+ # We have reworked collect2
+ :
+ else
+ # We have old collect2
+ hardcode_direct=unsupported
+ # It fails to find uninstalled libraries when the uninstalled
+ # path is not listed in the libpath. Setting hardcode_minus_L
+ # to unsupported forces relinking
+ hardcode_minus_L=yes
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_libdir_separator=
+ fi
+ ;;
+ esac
+ shared_flag='-shared'
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag="$shared_flag "'${wl}-G'
+ fi
+ link_all_deplibs=no
+ else
+ # not using gcc
+ if test "$host_cpu" = ia64; then
+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+ # chokes on -Wl,-G. The following line is correct:
+ shared_flag='-G'
+ else
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag='${wl}-G'
+ else
+ shared_flag='${wl}-bM:SRE'
+ fi
+ fi
+ fi
+
+ export_dynamic_flag_spec='${wl}-bexpall'
+ # It seems that -bexpall does not export symbols beginning with
+ # underscore (_), so it is better to generate a list of symbols to export.
+ always_export_symbols=yes
+ if test "$aix_use_runtimelinking" = yes; then
+ # Warning - without using the other runtime loading flags (-brtl),
+ # -berok will link without error, but may produce a broken library.
+ allow_undefined_flag='-berok'
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+ hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath"
+ archive_expsym_cmds='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+ else
+ if test "$host_cpu" = ia64; then
+ hardcode_libdir_flag_spec='${wl}-R $libdir:/usr/lib:/lib'
+ allow_undefined_flag="-z nodefs"
+ archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+ else
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+ hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath"
+ # Warning - without using the other run time loading flags,
+ # -berok will link without error, but may produce a broken library.
+ no_undefined_flag=' ${wl}-bernotok'
+ allow_undefined_flag=' ${wl}-berok'
+ # Exported symbols can be pulled into shared objects from archives
+ whole_archive_flag_spec='$convenience'
+ archive_cmds_need_lc=yes
+ # This is similar to how AIX traditionally builds its shared libraries.
+ archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+ fi
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds=''
+ ;;
+ m68k)
+ archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_minus_L=yes
+ ;;
+ esac
+ ;;
+
+ bsdi[45]*)
+ export_dynamic_flag_spec=-rdynamic
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # When not using gcc, we currently assume that we are using
+ # Microsoft Visual C++.
+ # hardcode_libdir_flag_spec is actually meaningless, as there is
+ # no search path for DLLs.
+ hardcode_libdir_flag_spec=' '
+ allow_undefined_flag=unsupported
+ # Tell ltmain to make .lib files, not .a files.
+ libext=lib
+ # Tell ltmain to make .dll files, not .so files.
+ shrext_cmds=".dll"
+ # FIXME: Setting linknames here is a bad hack.
+ archive_cmds='$CC -o $lib $libobjs $compiler_flags `$ECHO "X$deplibs" | $Xsed -e '\''s/ -lc$//'\''` -link -dll~linknames='
+ # The linker will automatically build a .lib file if we build a DLL.
+ old_archive_from_new_cmds='true'
+ # FIXME: Should let the user specify the lib program.
+ old_archive_cmds='lib -OUT:$oldlib$oldobjs$old_deplibs'
+ fix_srcfile_path='`cygpath -w "$srcfile"`'
+ enable_shared_with_static_runtimes=yes
+ ;;
+
+ darwin* | rhapsody*)
+
+
+ archive_cmds_need_lc=no
+ hardcode_direct=no
+ hardcode_automatic=yes
+ hardcode_shlibpath_var=unsupported
+ whole_archive_flag_spec=''
+ link_all_deplibs=yes
+ allow_undefined_flag="$_lt_dar_allow_undefined"
+ case $cc_basename in
+ ifort*) _lt_dar_can_shared=yes ;;
+ *) _lt_dar_can_shared=$GCC ;;
+ esac
+ if test "$_lt_dar_can_shared" = "yes"; then
+ output_verbose_link_cmd=echo
+ archive_cmds="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}"
+ module_cmds="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}"
+ archive_expsym_cmds="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}"
+ module_expsym_cmds="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}"
+
+ else
+ ld_shlibs=no
+ fi
+
+ ;;
+
+ dgux*)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_shlibpath_var=no
+ ;;
+
+ freebsd1*)
+ ld_shlibs=no
+ ;;
+
+ # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor
+ # support. Future versions do this automatically, but an explicit c++rt0.o
+ # does not break anything, and helps significantly (at the cost of a little
+ # extra space).
+ freebsd2.2*)
+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o'
+ hardcode_libdir_flag_spec='-R$libdir'
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ # Unfortunately, older versions of FreeBSD 2 do not have this feature.
+ freebsd2*)
+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_direct=yes
+ hardcode_minus_L=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ # FreeBSD 3 and greater uses gcc -shared to do shared libraries.
+ freebsd* | dragonfly*)
+ archive_cmds='$CC -shared -o $lib $libobjs $deplibs $compiler_flags'
+ hardcode_libdir_flag_spec='-R$libdir'
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ hpux9*)
+ if test "$GCC" = yes; then
+ archive_cmds='$RM $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ else
+ archive_cmds='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ fi
+ hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
+ hardcode_libdir_separator=:
+ hardcode_direct=yes
+
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ hardcode_minus_L=yes
+ export_dynamic_flag_spec='${wl}-E'
+ ;;
+
+ hpux10*)
+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+ archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags'
+ fi
+ if test "$with_gnu_ld" = no; then
+ hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
+ hardcode_libdir_flag_spec_ld='+b $libdir'
+ hardcode_libdir_separator=:
+ hardcode_direct=yes
+ hardcode_direct_absolute=yes
+ export_dynamic_flag_spec='${wl}-E'
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ hardcode_minus_L=yes
+ fi
+ ;;
+
+ hpux11*)
+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+ case $host_cpu in
+ hppa*64*)
+ archive_cmds='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ ia64*)
+ archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ else
+ case $host_cpu in
+ hppa*64*)
+ archive_cmds='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ ia64*)
+ archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ fi
+ if test "$with_gnu_ld" = no; then
+ hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
+ hardcode_libdir_separator=:
+
+ case $host_cpu in
+ hppa*64*|ia64*)
+ hardcode_direct=no
+ hardcode_shlibpath_var=no
+ ;;
+ *)
+ hardcode_direct=yes
+ hardcode_direct_absolute=yes
+ export_dynamic_flag_spec='${wl}-E'
+
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ hardcode_minus_L=yes
+ ;;
+ esac
+ fi
+ ;;
+
+ irix5* | irix6* | nonstopux*)
+ if test "$GCC" = yes; then
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ # Try to use the -exported_symbol ld option, if it does not
+ # work, assume that -exports_file does not work either and
+ # implicitly export all symbols.
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+int foo(void) {}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib'
+
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+ LDFLAGS="$save_LDFLAGS"
+ else
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib'
+ fi
+ archive_cmds_need_lc='no'
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator=:
+ inherit_rpath=yes
+ link_all_deplibs=yes
+ ;;
+
+ netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out
+ else
+ archive_cmds='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF
+ fi
+ hardcode_libdir_flag_spec='-R$libdir'
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ newsos6)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_direct=yes
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator=:
+ hardcode_shlibpath_var=no
+ ;;
+
+ *nto* | *qnx*)
+ ;;
+
+ openbsd*)
+ if test -f /usr/libexec/ld.so; then
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ hardcode_direct_absolute=yes
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols'
+ hardcode_libdir_flag_spec='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec='${wl}-E'
+ else
+ case $host_os in
+ openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*)
+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_libdir_flag_spec='-R$libdir'
+ ;;
+ *)
+ archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+ hardcode_libdir_flag_spec='${wl}-rpath,$libdir'
+ ;;
+ esac
+ fi
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ os2*)
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_minus_L=yes
+ allow_undefined_flag=unsupported
+ archive_cmds='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def'
+ old_archive_from_new_cmds='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def'
+ ;;
+
+ osf3*)
+ if test "$GCC" = yes; then
+ allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*'
+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ else
+ allow_undefined_flag=' -expect_unresolved \*'
+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ fi
+ archive_cmds_need_lc='no'
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator=:
+ ;;
+
+ osf4* | osf5*) # as osf3* with the addition of -msym flag
+ if test "$GCC" = yes; then
+ allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*'
+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ else
+ allow_undefined_flag=' -expect_unresolved \*'
+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ archive_expsym_cmds='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~
+ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp'
+
+ # Both c and cxx compiler support -rpath directly
+ hardcode_libdir_flag_spec='-rpath $libdir'
+ fi
+ archive_cmds_need_lc='no'
+ hardcode_libdir_separator=:
+ ;;
+
+ solaris*)
+ no_undefined_flag=' -z defs'
+ if test "$GCC" = yes; then
+ wlarc='${wl}'
+ archive_cmds='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp'
+ else
+ case `$CC -V 2>&1` in
+ *"Compilers 5.0"*)
+ wlarc=''
+ archive_cmds='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp'
+ ;;
+ *)
+ wlarc='${wl}'
+ archive_cmds='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp'
+ ;;
+ esac
+ fi
+ hardcode_libdir_flag_spec='-R$libdir'
+ hardcode_shlibpath_var=no
+ case $host_os in
+ solaris2.[0-5] | solaris2.[0-5].*) ;;
+ *)
+ # The compiler driver will combine and reorder linker options,
+ # but understands `-z linker_flag'. GCC discards it without `$wl',
+ # but is careful enough not to reorder.
+ # Supported since Solaris 2.6 (maybe 2.5.1?)
+ if test "$GCC" = yes; then
+ whole_archive_flag_spec='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract'
+ else
+ whole_archive_flag_spec='-z allextract$convenience -z defaultextract'
+ fi
+ ;;
+ esac
+ link_all_deplibs=yes
+ ;;
+
+ sunos4*)
+ if test "x$host_vendor" = xsequent; then
+ # Use $CC to link under sequent, because it throws in some extra .o
+ # files that make .init and .fini sections work.
+ archive_cmds='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ archive_cmds='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags'
+ fi
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_direct=yes
+ hardcode_minus_L=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ sysv4)
+ case $host_vendor in
+ sni)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_direct=yes # is this really true???
+ ;;
+ siemens)
+ ## LD is ld it makes a PLAMLIB
+ ## CC just makes a GrossModule.
+ archive_cmds='$LD -G -o $lib $libobjs $deplibs $linker_flags'
+ reload_cmds='$CC -r -o $output$reload_objs'
+ hardcode_direct=no
+ ;;
+ motorola)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_direct=no #Motorola manual says yes, but my tests say they lie
+ ;;
+ esac
+ runpath_var='LD_RUN_PATH'
+ hardcode_shlibpath_var=no
+ ;;
+
+ sysv4.3*)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_shlibpath_var=no
+ export_dynamic_flag_spec='-Bexport'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_shlibpath_var=no
+ runpath_var=LD_RUN_PATH
+ hardcode_runpath_var=yes
+ ld_shlibs=yes
+ fi
+ ;;
+
+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*)
+ no_undefined_flag='${wl}-z,text'
+ archive_cmds_need_lc=no
+ hardcode_shlibpath_var=no
+ runpath_var='LD_RUN_PATH'
+
+ if test "$GCC" = yes; then
+ archive_cmds='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ archive_cmds='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ fi
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6*)
+ # Note: We can NOT use -z defs as we might desire, because we do not
+ # link with -lc, and that would cause any symbols used from libc to
+ # always be unresolved, which means just about no library would
+ # ever link correctly. If we're not using GNU ld we use -z text
+ # though, which does catch some bad symbols but isn't as heavy-handed
+ # as -z defs.
+ no_undefined_flag='${wl}-z,text'
+ allow_undefined_flag='${wl}-z,nodefs'
+ archive_cmds_need_lc=no
+ hardcode_shlibpath_var=no
+ hardcode_libdir_flag_spec='${wl}-R,$libdir'
+ hardcode_libdir_separator=':'
+ link_all_deplibs=yes
+ export_dynamic_flag_spec='${wl}-Bexport'
+ runpath_var='LD_RUN_PATH'
+
+ if test "$GCC" = yes; then
+ archive_cmds='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ archive_cmds='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ fi
+ ;;
+
+ uts4*)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_shlibpath_var=no
+ ;;
+
+ *)
+ ld_shlibs=no
+ ;;
+ esac
+
+ if test x$host_vendor = xsni; then
+ case $host in
+ sysv4 | sysv4.2uw2* | sysv4.3* | sysv5*)
+ export_dynamic_flag_spec='${wl}-Blargedynsym'
+ ;;
+ esac
+ fi
+ fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ld_shlibs" >&5
+$as_echo "$ld_shlibs" >&6; }
+test "$ld_shlibs" = no && can_build_shared=no
+
+with_gnu_ld=$with_gnu_ld
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$archive_cmds_need_lc" in
+x|xyes)
+ # Assume -lc should be added
+ archive_cmds_need_lc=yes
+
+ if test "$enable_shared" = yes && test "$GCC" = yes; then
+ case $archive_cmds in
+ *'~'*)
+ # FIXME: we may have to deal with multi-command sequences.
+ ;;
+ '$CC '*)
+ # Test whether the compiler implicitly links with -lc since on some
+ # systems, -lgcc has to come before -lc. If gcc already passes -lc
+ # to ld, don't add -lc before -lgcc.
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether -lc should be explicitly linked in" >&5
+$as_echo_n "checking whether -lc should be explicitly linked in... " >&6; }
+ $RM conftest*
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } 2>conftest.err; then
+ soname=conftest
+ lib=conftest
+ libobjs=conftest.$ac_objext
+ deplibs=
+ wl=$lt_prog_compiler_wl
+ pic_flag=$lt_prog_compiler_pic
+ compiler_flags=-v
+ linker_flags=-v
+ verstring=
+ output_objdir=.
+ libname=conftest
+ lt_save_allow_undefined_flag=$allow_undefined_flag
+ allow_undefined_flag=
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$archive_cmds 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1\""; } >&5
+ (eval $archive_cmds 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+ then
+ archive_cmds_need_lc=no
+ else
+ archive_cmds_need_lc=yes
+ fi
+ allow_undefined_flag=$lt_save_allow_undefined_flag
+ else
+ cat conftest.err 1>&5
+ fi
+ $RM conftest*
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $archive_cmds_need_lc" >&5
+$as_echo "$archive_cmds_need_lc" >&6; }
+ ;;
+ esac
+ fi
+ ;;
+esac
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking dynamic linker characteristics" >&5
+$as_echo_n "checking dynamic linker characteristics... " >&6; }
+
+if test "$GCC" = yes; then
+ case $host_os in
+ darwin*) lt_awk_arg="/^libraries:/,/LR/" ;;
+ *) lt_awk_arg="/^libraries:/" ;;
+ esac
+ lt_search_path_spec=`$CC -print-search-dirs | awk $lt_awk_arg | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$lt_search_path_spec" | $GREP ';' >/dev/null ; then
+ # if the path contains ";" then we assume it to be the separator
+ # otherwise default to the standard path separator (i.e. ":") - it is
+ # assumed that no part of a normal pathname contains ";" but that should
+ # okay in the real world where ";" in dirpaths is itself problematic.
+ lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ # Ok, now we have the path, separated by spaces, we can step through it
+ # and add multilib dir if necessary.
+ lt_tmp_lt_search_path_spec=
+ lt_multi_os_dir=`$CC $CPPFLAGS $CFLAGS $LDFLAGS -print-multi-os-directory 2>/dev/null`
+ for lt_sys_path in $lt_search_path_spec; do
+ if test -d "$lt_sys_path/$lt_multi_os_dir"; then
+ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path/$lt_multi_os_dir"
+ else
+ test -d "$lt_sys_path" && \
+ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path"
+ fi
+ done
+ lt_search_path_spec=`$ECHO $lt_tmp_lt_search_path_spec | awk '
+BEGIN {RS=" "; FS="/|\n";} {
+ lt_foo="";
+ lt_count=0;
+ for (lt_i = NF; lt_i > 0; lt_i--) {
+ if ($lt_i != "" && $lt_i != ".") {
+ if ($lt_i == "..") {
+ lt_count++;
+ } else {
+ if (lt_count == 0) {
+ lt_foo="/" $lt_i lt_foo;
+ } else {
+ lt_count--;
+ }
+ }
+ }
+ }
+ if (lt_foo != "") { lt_freq[lt_foo]++; }
+ if (lt_freq[lt_foo] == 1) { print lt_foo; }
+}'`
+ sys_lib_search_path_spec=`$ECHO $lt_search_path_spec`
+else
+ sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib"
+fi
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+ shlibpath_var=LIBPATH
+
+ # AIX 3 has no versioning support, so we append a major version to the name.
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+
+aix[4-9]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ hardcode_into_libs=yes
+ if test "$host_cpu" = ia64; then
+ # AIX 5 supports IA64
+ library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ else
+ # With GCC up to 2.95.x, collect2 would create an import file
+ # for dependence libraries. The import file would start with
+ # the line `#! .'. This would cause the generated library to
+ # depend on `.', always an invalid library. This was fixed in
+ # development snapshots of GCC prior to 3.0.
+ case $host_os in
+ aix4 | aix4.[01] | aix4.[01].*)
+ if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+ echo ' yes '
+ echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then
+ :
+ else
+ can_build_shared=no
+ fi
+ ;;
+ esac
+ # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+ # soname into executable. Probably we can add versioning support to
+ # collect2, so additional links can be useful in future.
+ if test "$aix_use_runtimelinking" = yes; then
+ # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+ # instead of lib<name>.a to let people know that these are not
+ # typical AIX shared libraries.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ else
+ # We preserve .a as extension for shared libraries through AIX4.2
+ # and later when we are not doing run time linking.
+ library_names_spec='${libname}${release}.a $libname.a'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ fi
+ shlibpath_var=LIBPATH
+ fi
+ ;;
+
+amigaos*)
+ case $host_cpu in
+ powerpc)
+ # Since July 2007 AmigaOS4 officially supports .so libraries.
+ # When compiling the executable, add -use-dynld -Lsobjs: to the compileline.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ ;;
+ m68k)
+ library_names_spec='$libname.ixlibrary $libname.a'
+ # Create ${libname}_ixlibrary.a entries in /sys/libs.
+ finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$ECHO "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+ ;;
+ esac
+ ;;
+
+beos*)
+ library_names_spec='${libname}${shared_ext}'
+ dynamic_linker="$host_os ld.so"
+ shlibpath_var=LIBRARY_PATH
+ ;;
+
+bsdi[45]*)
+ version_type=linux
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+ sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+ # the default ld.so.conf also contains /usr/contrib/lib and
+ # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+ # libtool to hard-code these into programs
+ ;;
+
+cygwin* | mingw* | pw32* | cegcc*)
+ version_type=windows
+ shrext_cmds=".dll"
+ need_version=no
+ need_lib_prefix=no
+
+ case $GCC,$host_os in
+ yes,cygwin* | yes,mingw* | yes,pw32* | yes,cegcc*)
+ library_names_spec='$libname.dll.a'
+ # DLL is installed to $(libdir)/../bin by postinstall_cmds
+ postinstall_cmds='base_file=`basename \${file}`~
+ dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i; echo \$dlname'\''`~
+ dldir=$destdir/`dirname \$dlpath`~
+ test -d \$dldir || mkdir -p \$dldir~
+ $install_prog $dir/$dlname \$dldir/$dlname~
+ chmod a+x \$dldir/$dlname~
+ if test -n '\''$stripme'\'' && test -n '\''$striplib'\''; then
+ eval '\''$striplib \$dldir/$dlname'\'' || exit \$?;
+ fi'
+ postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+ dlpath=$dir/\$dldll~
+ $RM \$dlpath'
+ shlibpath_overrides_runpath=yes
+
+ case $host_os in
+ cygwin*)
+ # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+ soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+ ;;
+ mingw* | cegcc*)
+ # MinGW DLLs use traditional 'lib' prefix
+ soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec=`$CC -print-search-dirs | $GREP "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$sys_lib_search_path_spec" | $GREP ';[c-zC-Z]:/' >/dev/null; then
+ # It is most probably a Windows format PATH printed by
+ # mingw gcc, but we are running on Cygwin. Gcc prints its search
+ # path with ; separators, and with drive letters. We can handle the
+ # drive letters (cygwin fileutils understands them), so leave them,
+ # especially as we might pass files found there to a mingw objdump,
+ # which wouldn't understand a cygwinified path. Ahh.
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ ;;
+ pw32*)
+ # pw32 DLLs use 'pw' prefix rather than 'lib'
+ library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ ;;
+ esac
+ ;;
+
+ *)
+ library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib'
+ ;;
+ esac
+ dynamic_linker='Win32 ld.exe'
+ # FIXME: first we should search . and the directory the executable is in
+ shlibpath_var=PATH
+ ;;
+
+darwin* | rhapsody*)
+ dynamic_linker="$host_os dyld"
+ version_type=darwin
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+ soname_spec='${libname}${release}${major}$shared_ext'
+ shlibpath_overrides_runpath=yes
+ shlibpath_var=DYLD_LIBRARY_PATH
+ shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /usr/local/lib"
+ sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+ ;;
+
+dgux*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+freebsd1*)
+ dynamic_linker=no
+ ;;
+
+freebsd* | dragonfly*)
+ # DragonFly does not have aout. When/if they implement a new
+ # versioning mechanism, adjust this.
+ if test -x /usr/bin/objformat; then
+ objformat=`/usr/bin/objformat`
+ else
+ case $host_os in
+ freebsd[123]*) objformat=aout ;;
+ *) objformat=elf ;;
+ esac
+ fi
+ version_type=freebsd-$objformat
+ case $version_type in
+ freebsd-elf*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ need_version=no
+ need_lib_prefix=no
+ ;;
+ freebsd-*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+ need_version=yes
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_os in
+ freebsd2*)
+ shlibpath_overrides_runpath=yes
+ ;;
+ freebsd3.[01]* | freebsdelf3.[01]*)
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ freebsd3.[2-9]* | freebsdelf3.[2-9]* | \
+ freebsd4.[0-5] | freebsdelf4.[0-5] | freebsd4.1.1 | freebsdelf4.1.1)
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+ *) # from 4.6 on, and DragonFly
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ esac
+ ;;
+
+gnu*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ hardcode_into_libs=yes
+ ;;
+
+hpux9* | hpux10* | hpux11*)
+ # Give a soname corresponding to the major version so that dld.sl refuses to
+ # link against other versions.
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ case $host_cpu in
+ ia64*)
+ shrext_cmds='.so'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.so"
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ if test "X$HPUX_IA64_MODE" = X32; then
+ sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+ else
+ sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+ fi
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ hppa*64*)
+ shrext_cmds='.sl'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ *)
+ shrext_cmds='.sl'
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=SHLIB_PATH
+ shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+ esac
+ # HP-UX runs *really* slowly unless shared libraries are mode 555.
+ postinstall_cmds='chmod 555 $lib'
+ ;;
+
+interix[3-9]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $host_os in
+ nonstopux*) version_type=nonstopux ;;
+ *)
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ version_type=linux
+ else
+ version_type=irix
+ fi ;;
+ esac
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+ case $host_os in
+ irix5* | nonstopux*)
+ libsuff= shlibsuff=
+ ;;
+ *)
+ case $LD in # libtool.m4 will add one of these switches to LD
+ *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+ libsuff= shlibsuff= libmagic=32-bit;;
+ *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+ libsuff=32 shlibsuff=N32 libmagic=N32;;
+ *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+ libsuff=64 shlibsuff=64 libmagic=64-bit;;
+ *) libsuff= shlibsuff= libmagic=never-match;;
+ esac
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+ sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+ hardcode_into_libs=yes
+ ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+ dynamic_linker=no
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ # Some binutils ld are patched to set DT_RUNPATH
+ save_LDFLAGS=$LDFLAGS
+ save_libdir=$libdir
+ eval "libdir=/foo; wl=\"$lt_prog_compiler_wl\"; \
+ LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec\""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then :
+ shlibpath_overrides_runpath=yes
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+ LDFLAGS=$save_LDFLAGS
+ libdir=$save_libdir
+
+ # This implies no fast_install, which is unacceptable.
+ # Some rework will be needed to allow for fast_install
+ # before this can be enabled.
+ hardcode_into_libs=yes
+
+ # Append ld.so.conf contents to the search path
+ if test -f /etc/ld.so.conf; then
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ fi
+
+ # We used to test for /lib/ld.so.1 and disable shared libraries on
+ # powerpc, because MkLinux only supported shared libraries with the
+ # GNU dynamic linker. Since this was broken with cross compilers,
+ # most powerpc-linux boxes support dynamic linking these days and
+ # people can always --disable-shared, the test was removed, and we
+ # assume the GNU/Linux dynamic linker is in use.
+ dynamic_linker='GNU/Linux ld.so'
+ ;;
+
+netbsdelf*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='NetBSD ld.elf_so'
+ ;;
+
+netbsd*)
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ dynamic_linker='NetBSD (a.out) ld.so'
+ else
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='NetBSD ld.elf_so'
+ fi
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+
+newsos6)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ ;;
+
+*nto* | *qnx*)
+ version_type=qnx
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='ldqnx.so'
+ ;;
+
+openbsd*)
+ version_type=sunos
+ sys_lib_dlsearch_path_spec="/usr/lib"
+ need_lib_prefix=no
+ # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+ case $host_os in
+ openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+ *) need_version=no ;;
+ esac
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ case $host_os in
+ openbsd2.[89] | openbsd2.[89].*)
+ shlibpath_overrides_runpath=no
+ ;;
+ *)
+ shlibpath_overrides_runpath=yes
+ ;;
+ esac
+ else
+ shlibpath_overrides_runpath=yes
+ fi
+ ;;
+
+os2*)
+ libname_spec='$name'
+ shrext_cmds=".dll"
+ need_lib_prefix=no
+ library_names_spec='$libname${shared_ext} $libname.a'
+ dynamic_linker='OS/2 ld.exe'
+ shlibpath_var=LIBPATH
+ ;;
+
+osf3* | osf4* | osf5*)
+ version_type=osf
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+ sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+ ;;
+
+rdos*)
+ dynamic_linker=no
+ ;;
+
+solaris*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ # ldd complains unless libraries are executable
+ postinstall_cmds='chmod +x $lib'
+ ;;
+
+sunos4*)
+ version_type=sunos
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ if test "$with_gnu_ld" = yes; then
+ need_lib_prefix=no
+ fi
+ need_version=yes
+ ;;
+
+sysv4 | sysv4.3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_vendor in
+ sni)
+ shlibpath_overrides_runpath=no
+ need_lib_prefix=no
+ runpath_var=LD_RUN_PATH
+ ;;
+ siemens)
+ need_lib_prefix=no
+ ;;
+ motorola)
+ need_lib_prefix=no
+ need_version=no
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+ ;;
+ esac
+ ;;
+
+sysv4*MP*)
+ if test -d /usr/nec ;then
+ version_type=linux
+ library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+ soname_spec='$libname${shared_ext}.$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ fi
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ version_type=freebsd-elf
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ if test "$with_gnu_ld" = yes; then
+ sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+ else
+ sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+ case $host_os in
+ sco3.2v5*)
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+ ;;
+ esac
+ fi
+ sys_lib_dlsearch_path_spec='/usr/lib'
+ ;;
+
+tpf*)
+ # TPF is a cross-target only. Preferred cross-host = GNU/Linux.
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+uts4*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+*)
+ dynamic_linker=no
+ ;;
+esac
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $dynamic_linker" >&5
+$as_echo "$dynamic_linker" >&6; }
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+ variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+
+if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then
+ sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec"
+fi
+if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then
+ sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec"
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to hardcode library paths into programs" >&5
+$as_echo_n "checking how to hardcode library paths into programs... " >&6; }
+hardcode_action=
+if test -n "$hardcode_libdir_flag_spec" ||
+ test -n "$runpath_var" ||
+ test "X$hardcode_automatic" = "Xyes" ; then
+
+ # We can hardcode non-existent directories.
+ if test "$hardcode_direct" != no &&
+ # If the only mechanism to avoid hardcoding is shlibpath_var, we
+ # have to relink, otherwise we might link with an installed library
+ # when we should be linking with a yet-to-be-installed one
+ ## test "$_LT_TAGVAR(hardcode_shlibpath_var, )" != no &&
+ test "$hardcode_minus_L" != no; then
+ # Linking always hardcodes the temporary library directory.
+ hardcode_action=relink
+ else
+ # We can link without hardcoding, and we can hardcode nonexisting dirs.
+ hardcode_action=immediate
+ fi
+else
+ # We cannot hardcode anything, or else we can only hardcode existing
+ # directories.
+ hardcode_action=unsupported
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $hardcode_action" >&5
+$as_echo "$hardcode_action" >&6; }
+
+if test "$hardcode_action" = relink ||
+ test "$inherit_rpath" = yes; then
+ # Fast installation is not supported
+ enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+ test "$enable_shared" = no; then
+ # Fast installation is not necessary
+ enable_fast_install=needless
+fi
+
+
+
+
+
+
+ if test "x$enable_dlopen" != xyes; then
+ enable_dlopen=unknown
+ enable_dlopen_self=unknown
+ enable_dlopen_self_static=unknown
+else
+ lt_cv_dlopen=no
+ lt_cv_dlopen_libs=
+
+ case $host_os in
+ beos*)
+ lt_cv_dlopen="load_add_on"
+ lt_cv_dlopen_libs=
+ lt_cv_dlopen_self=yes
+ ;;
+
+ mingw* | pw32* | cegcc*)
+ lt_cv_dlopen="LoadLibrary"
+ lt_cv_dlopen_libs=
+ ;;
+
+ cygwin*)
+ lt_cv_dlopen="dlopen"
+ lt_cv_dlopen_libs=
+ ;;
+
+ darwin*)
+ # if libdl is installed we need to link against it
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -ldl" >&5
+$as_echo_n "checking for dlopen in -ldl... " >&6; }
+if test "${ac_cv_lib_dl_dlopen+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldl $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+int
+main ()
+{
+return dlopen ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_dl_dlopen=yes
+else
+ ac_cv_lib_dl_dlopen=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dl_dlopen" >&5
+$as_echo "$ac_cv_lib_dl_dlopen" >&6; }
+if test "x$ac_cv_lib_dl_dlopen" = x""yes; then :
+ lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"
+else
+
+ lt_cv_dlopen="dyld"
+ lt_cv_dlopen_libs=
+ lt_cv_dlopen_self=yes
+
+fi
+
+ ;;
+
+ *)
+ ac_fn_c_check_func "$LINENO" "shl_load" "ac_cv_func_shl_load"
+if test "x$ac_cv_func_shl_load" = x""yes; then :
+ lt_cv_dlopen="shl_load"
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for shl_load in -ldld" >&5
+$as_echo_n "checking for shl_load in -ldld... " >&6; }
+if test "${ac_cv_lib_dld_shl_load+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldld $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char shl_load ();
+int
+main ()
+{
+return shl_load ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_dld_shl_load=yes
+else
+ ac_cv_lib_dld_shl_load=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dld_shl_load" >&5
+$as_echo "$ac_cv_lib_dld_shl_load" >&6; }
+if test "x$ac_cv_lib_dld_shl_load" = x""yes; then :
+ lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-ldld"
+else
+ ac_fn_c_check_func "$LINENO" "dlopen" "ac_cv_func_dlopen"
+if test "x$ac_cv_func_dlopen" = x""yes; then :
+ lt_cv_dlopen="dlopen"
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -ldl" >&5
+$as_echo_n "checking for dlopen in -ldl... " >&6; }
+if test "${ac_cv_lib_dl_dlopen+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldl $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+int
+main ()
+{
+return dlopen ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_dl_dlopen=yes
+else
+ ac_cv_lib_dl_dlopen=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dl_dlopen" >&5
+$as_echo "$ac_cv_lib_dl_dlopen" >&6; }
+if test "x$ac_cv_lib_dl_dlopen" = x""yes; then :
+ lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -lsvld" >&5
+$as_echo_n "checking for dlopen in -lsvld... " >&6; }
+if test "${ac_cv_lib_svld_dlopen+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lsvld $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+int
+main ()
+{
+return dlopen ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_svld_dlopen=yes
+else
+ ac_cv_lib_svld_dlopen=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_svld_dlopen" >&5
+$as_echo "$ac_cv_lib_svld_dlopen" >&6; }
+if test "x$ac_cv_lib_svld_dlopen" = x""yes; then :
+ lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld"
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dld_link in -ldld" >&5
+$as_echo_n "checking for dld_link in -ldld... " >&6; }
+if test "${ac_cv_lib_dld_dld_link+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldld $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dld_link ();
+int
+main ()
+{
+return dld_link ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_dld_dld_link=yes
+else
+ ac_cv_lib_dld_dld_link=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dld_dld_link" >&5
+$as_echo "$ac_cv_lib_dld_dld_link" >&6; }
+if test "x$ac_cv_lib_dld_dld_link" = x""yes; then :
+ lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-ldld"
+fi
+
+
+fi
+
+
+fi
+
+
+fi
+
+
+fi
+
+
+fi
+
+ ;;
+ esac
+
+ if test "x$lt_cv_dlopen" != xno; then
+ enable_dlopen=yes
+ else
+ enable_dlopen=no
+ fi
+
+ case $lt_cv_dlopen in
+ dlopen)
+ save_CPPFLAGS="$CPPFLAGS"
+ test "x$ac_cv_header_dlfcn_h" = xyes && CPPFLAGS="$CPPFLAGS -DHAVE_DLFCN_H"
+
+ save_LDFLAGS="$LDFLAGS"
+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\"
+
+ save_LIBS="$LIBS"
+ LIBS="$lt_cv_dlopen_libs $LIBS"
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether a program can dlopen itself" >&5
+$as_echo_n "checking whether a program can dlopen itself... " >&6; }
+if test "${lt_cv_dlopen_self+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then :
+ lt_cv_dlopen_self=cross
+else
+ lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
+ lt_status=$lt_dlunknown
+ cat > conftest.$ac_ext <<_LT_EOF
+#line 10309 "configure"
+#include "confdefs.h"
+
+#if HAVE_DLFCN_H
+#include <dlfcn.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef RTLD_GLOBAL
+# define LT_DLGLOBAL RTLD_GLOBAL
+#else
+# ifdef DL_GLOBAL
+# define LT_DLGLOBAL DL_GLOBAL
+# else
+# define LT_DLGLOBAL 0
+# endif
+#endif
+
+/* We may have to define LT_DLLAZY_OR_NOW in the command line if we
+ find out it does not work in some platform. */
+#ifndef LT_DLLAZY_OR_NOW
+# ifdef RTLD_LAZY
+# define LT_DLLAZY_OR_NOW RTLD_LAZY
+# else
+# ifdef DL_LAZY
+# define LT_DLLAZY_OR_NOW DL_LAZY
+# else
+# ifdef RTLD_NOW
+# define LT_DLLAZY_OR_NOW RTLD_NOW
+# else
+# ifdef DL_NOW
+# define LT_DLLAZY_OR_NOW DL_NOW
+# else
+# define LT_DLLAZY_OR_NOW 0
+# endif
+# endif
+# endif
+# endif
+#endif
+
+void fnord() { int i=42;}
+int main ()
+{
+ void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW);
+ int status = $lt_dlunknown;
+
+ if (self)
+ {
+ if (dlsym (self,"fnord")) status = $lt_dlno_uscore;
+ else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore;
+ /* dlclose (self); */
+ }
+ else
+ puts (dlerror ());
+
+ return status;
+}
+_LT_EOF
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5
+ (eval $ac_link) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && test -s conftest${ac_exeext} 2>/dev/null; then
+ (./conftest; exit; ) >&5 2>/dev/null
+ lt_status=$?
+ case x$lt_status in
+ x$lt_dlno_uscore) lt_cv_dlopen_self=yes ;;
+ x$lt_dlneed_uscore) lt_cv_dlopen_self=yes ;;
+ x$lt_dlunknown|x*) lt_cv_dlopen_self=no ;;
+ esac
+ else :
+ # compilation failed
+ lt_cv_dlopen_self=no
+ fi
+fi
+rm -fr conftest*
+
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_dlopen_self" >&5
+$as_echo "$lt_cv_dlopen_self" >&6; }
+
+ if test "x$lt_cv_dlopen_self" = xyes; then
+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether a statically linked program can dlopen itself" >&5
+$as_echo_n "checking whether a statically linked program can dlopen itself... " >&6; }
+if test "${lt_cv_dlopen_self_static+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then :
+ lt_cv_dlopen_self_static=cross
+else
+ lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
+ lt_status=$lt_dlunknown
+ cat > conftest.$ac_ext <<_LT_EOF
+#line 10405 "configure"
+#include "confdefs.h"
+
+#if HAVE_DLFCN_H
+#include <dlfcn.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef RTLD_GLOBAL
+# define LT_DLGLOBAL RTLD_GLOBAL
+#else
+# ifdef DL_GLOBAL
+# define LT_DLGLOBAL DL_GLOBAL
+# else
+# define LT_DLGLOBAL 0
+# endif
+#endif
+
+/* We may have to define LT_DLLAZY_OR_NOW in the command line if we
+ find out it does not work in some platform. */
+#ifndef LT_DLLAZY_OR_NOW
+# ifdef RTLD_LAZY
+# define LT_DLLAZY_OR_NOW RTLD_LAZY
+# else
+# ifdef DL_LAZY
+# define LT_DLLAZY_OR_NOW DL_LAZY
+# else
+# ifdef RTLD_NOW
+# define LT_DLLAZY_OR_NOW RTLD_NOW
+# else
+# ifdef DL_NOW
+# define LT_DLLAZY_OR_NOW DL_NOW
+# else
+# define LT_DLLAZY_OR_NOW 0
+# endif
+# endif
+# endif
+# endif
+#endif
+
+void fnord() { int i=42;}
+int main ()
+{
+ void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW);
+ int status = $lt_dlunknown;
+
+ if (self)
+ {
+ if (dlsym (self,"fnord")) status = $lt_dlno_uscore;
+ else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore;
+ /* dlclose (self); */
+ }
+ else
+ puts (dlerror ());
+
+ return status;
+}
+_LT_EOF
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5
+ (eval $ac_link) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && test -s conftest${ac_exeext} 2>/dev/null; then
+ (./conftest; exit; ) >&5 2>/dev/null
+ lt_status=$?
+ case x$lt_status in
+ x$lt_dlno_uscore) lt_cv_dlopen_self_static=yes ;;
+ x$lt_dlneed_uscore) lt_cv_dlopen_self_static=yes ;;
+ x$lt_dlunknown|x*) lt_cv_dlopen_self_static=no ;;
+ esac
+ else :
+ # compilation failed
+ lt_cv_dlopen_self_static=no
+ fi
+fi
+rm -fr conftest*
+
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_dlopen_self_static" >&5
+$as_echo "$lt_cv_dlopen_self_static" >&6; }
+ fi
+
+ CPPFLAGS="$save_CPPFLAGS"
+ LDFLAGS="$save_LDFLAGS"
+ LIBS="$save_LIBS"
+ ;;
+ esac
+
+ case $lt_cv_dlopen_self in
+ yes|no) enable_dlopen_self=$lt_cv_dlopen_self ;;
+ *) enable_dlopen_self=unknown ;;
+ esac
+
+ case $lt_cv_dlopen_self_static in
+ yes|no) enable_dlopen_self_static=$lt_cv_dlopen_self_static ;;
+ *) enable_dlopen_self_static=unknown ;;
+ esac
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+striplib=
+old_striplib=
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether stripping libraries is possible" >&5
+$as_echo_n "checking whether stripping libraries is possible... " >&6; }
+if test -n "$STRIP" && $STRIP -V 2>&1 | $GREP "GNU strip" >/dev/null; then
+ test -z "$old_striplib" && old_striplib="$STRIP --strip-debug"
+ test -z "$striplib" && striplib="$STRIP --strip-unneeded"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+else
+# FIXME - insert some real tests, host_os isn't really good enough
+ case $host_os in
+ darwin*)
+ if test -n "$STRIP" ; then
+ striplib="$STRIP -x"
+ old_striplib="$STRIP -S"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ fi
+ ;;
+ *)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ ;;
+ esac
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+ # Report which library types will actually be built
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if libtool supports shared libraries" >&5
+$as_echo_n "checking if libtool supports shared libraries... " >&6; }
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $can_build_shared" >&5
+$as_echo "$can_build_shared" >&6; }
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to build shared libraries" >&5
+$as_echo_n "checking whether to build shared libraries... " >&6; }
+ test "$can_build_shared" = "no" && enable_shared=no
+
+ # On AIX, shared libraries and static libraries use the same namespace, and
+ # are all built from PIC.
+ case $host_os in
+ aix3*)
+ test "$enable_shared" = yes && enable_static=no
+ if test -n "$RANLIB"; then
+ archive_cmds="$archive_cmds~\$RANLIB \$lib"
+ postinstall_cmds='$RANLIB $lib'
+ fi
+ ;;
+
+ aix[4-9]*)
+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+ test "$enable_shared" = yes && enable_static=no
+ fi
+ ;;
+ esac
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $enable_shared" >&5
+$as_echo "$enable_shared" >&6; }
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to build static libraries" >&5
+$as_echo_n "checking whether to build static libraries... " >&6; }
+ # Make sure either enable_shared or enable_static is yes.
+ test "$enable_shared" = yes || enable_static=yes
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $enable_static" >&5
+$as_echo "$enable_static" >&6; }
+
+
+
+
+fi
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+CC="$lt_save_CC"
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ac_config_commands="$ac_config_commands libtool"
+
+
+
+
+# Only expand once:
+
+
+
+ac_config_headers="$ac_config_headers libProgressBar/config.h"
+
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+if test -n "$ac_tool_prefix"; then
+ for ac_prog in gcc
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CC" && break
+ done
+fi
+if test -z "$CC"; then
+ ac_ct_CC=$CC
+ for ac_prog in gcc
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CC="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CC" && break
+done
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+fi
+
+
+test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "no acceptable C compiler found in \$PATH
+See \`config.log' for more details" "$LINENO" 5 ; }
+
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+ { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ sed '10a\
+... rest of stderr output deleted ...
+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5
+$as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
+if test "${ac_cv_c_compiler_gnu+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_compiler_gnu=yes
+else
+ ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_c_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5
+$as_echo "$ac_cv_c_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GCC=yes
+else
+ GCC=
+fi
+ac_test_CFLAGS=${CFLAGS+set}
+ac_save_CFLAGS=$CFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5
+$as_echo_n "checking whether $CC accepts -g... " >&6; }
+if test "${ac_cv_prog_cc_g+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_c_werror_flag=$ac_c_werror_flag
+ ac_c_werror_flag=yes
+ ac_cv_prog_cc_g=no
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
+else
+ CFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+
+else
+ ac_c_werror_flag=$ac_save_c_werror_flag
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_c_werror_flag=$ac_save_c_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5
+$as_echo "$ac_cv_prog_cc_g" >&6; }
+if test "$ac_test_CFLAGS" = set; then
+ CFLAGS=$ac_save_CFLAGS
+elif test $ac_cv_prog_cc_g = yes; then
+ if test "$GCC" = yes; then
+ CFLAGS="-g -O2"
+ else
+ CFLAGS="-g"
+ fi
+else
+ if test "$GCC" = yes; then
+ CFLAGS="-O2"
+ else
+ CFLAGS=
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5
+$as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
+if test "${ac_cv_prog_cc_c89+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_prog_cc_c89=no
+ac_save_CC=$CC
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdarg.h>
+#include <stdio.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */
+struct buf { int x; };
+FILE * (*rcsopen) (struct buf *, struct stat *, int);
+static char *e (p, i)
+ char **p;
+ int i;
+{
+ return p[i];
+}
+static char *f (char * (*g) (char **, int), char **p, ...)
+{
+ char *s;
+ va_list v;
+ va_start (v,p);
+ s = g (p, va_arg (v,int));
+ va_end (v);
+ return s;
+}
+
+/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has
+ function prototypes and stuff, but not '\xHH' hex character constants.
+ These don't provoke an error unfortunately, instead are silently treated
+ as 'x'. The following induces an error, until -std is added to get
+ proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an
+ array size at least. It's necessary to write '\x00'==0 to get something
+ that's true only with -std. */
+int osf4_cc_array ['\x00' == 0 ? 1 : -1];
+
+/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters
+ inside strings and character constants. */
+#define FOO(x) 'x'
+int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1];
+
+int test (int i, double x);
+struct s1 {int (*f) (int a);};
+struct s2 {int (*f) (double a);};
+int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
+int argc;
+char **argv;
+int
+main ()
+{
+return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1];
+ ;
+ return 0;
+}
+_ACEOF
+for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \
+ -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
+do
+ CC="$ac_save_CC $ac_arg"
+ if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_c89=$ac_arg
+fi
+rm -f core conftest.err conftest.$ac_objext
+ test "x$ac_cv_prog_cc_c89" != "xno" && break
+done
+rm -f conftest.$ac_ext
+CC=$ac_save_CC
+
+fi
+# AC_CACHE_VAL
+case "x$ac_cv_prog_cc_c89" in
+ x)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
+$as_echo "none needed" >&6; } ;;
+ xno)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
+$as_echo "unsupported" >&6; } ;;
+ *)
+ CC="$CC $ac_cv_prog_cc_c89"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5
+$as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
+esac
+if test "x$ac_cv_prog_cc_c89" != xno; then :
+
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+depcc="$CC" am_compiler_list=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CC_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
+ case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CC_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CC_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CC_dependencies_compiler_type" >&6; }
+CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
+ am__fastdepCC_TRUE=
+ am__fastdepCC_FALSE='#'
+else
+ am__fastdepCC_TRUE='#'
+ am__fastdepCC_FALSE=
+fi
+
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+if test -z "$CXX"; then
+ if test -n "$CCC"; then
+ CXX=$CCC
+ else
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in g++
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CXX"; then
+ ac_cv_prog_CXX="$CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CXX=$ac_cv_prog_CXX
+if test -n "$CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5
+$as_echo "$CXX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CXX" && break
+ done
+fi
+if test -z "$CXX"; then
+ ac_ct_CXX=$CXX
+ for ac_prog in g++
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CXX"; then
+ ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CXX="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
+if test -n "$ac_ct_CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5
+$as_echo "$ac_ct_CXX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CXX" && break
+done
+
+ if test "x$ac_ct_CXX" = x; then
+ CXX="g++"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CXX=$ac_ct_CXX
+ fi
+fi
+
+ fi
+fi
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+ { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ sed '10a\
+... rest of stderr output deleted ...
+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5
+$as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; }
+if test "${ac_cv_cxx_compiler_gnu+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_compiler_gnu=yes
+else
+ ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_cxx_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5
+$as_echo "$ac_cv_cxx_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GXX=yes
+else
+ GXX=
+fi
+ac_test_CXXFLAGS=${CXXFLAGS+set}
+ac_save_CXXFLAGS=$CXXFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5
+$as_echo_n "checking whether $CXX accepts -g... " >&6; }
+if test "${ac_cv_prog_cxx_g+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_cxx_werror_flag=$ac_cxx_werror_flag
+ ac_cxx_werror_flag=yes
+ ac_cv_prog_cxx_g=no
+ CXXFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_prog_cxx_g=yes
+else
+ CXXFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+
+else
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+ CXXFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_prog_cxx_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5
+$as_echo "$ac_cv_prog_cxx_g" >&6; }
+if test "$ac_test_CXXFLAGS" = set; then
+ CXXFLAGS=$ac_save_CXXFLAGS
+elif test $ac_cv_prog_cxx_g = yes; then
+ if test "$GXX" = yes; then
+ CXXFLAGS="-g -O2"
+ else
+ CXXFLAGS="-g"
+ fi
+else
+ if test "$GXX" = yes; then
+ CXXFLAGS="-O2"
+ else
+ CXXFLAGS=
+ fi
+fi
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+depcc="$CXX" am_compiler_list=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CXX_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
+ case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CXX_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CXX_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CXX_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CXX_dependencies_compiler_type" >&6; }
+CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CXX_dependencies_compiler_type" = gcc3; then
+ am__fastdepCXX_TRUE=
+ am__fastdepCXX_FALSE='#'
+else
+ am__fastdepCXX_TRUE='#'
+ am__fastdepCXX_FALSE=
+fi
+
+
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+if test -z "$CXX"; then
+ if test -n "$CCC"; then
+ CXX=$CCC
+ else
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CXX"; then
+ ac_cv_prog_CXX="$CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+CXX=$ac_cv_prog_CXX
+if test -n "$CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5
+$as_echo "$CXX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CXX" && break
+ done
+fi
+if test -z "$CXX"; then
+ ac_ct_CXX=$CXX
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
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+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CXX"; then
+ ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CXX="$ac_prog"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
+if test -n "$ac_ct_CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5
+$as_echo "$ac_ct_CXX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CXX" && break
+done
+
+ if test "x$ac_ct_CXX" = x; then
+ CXX="g++"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CXX=$ac_ct_CXX
+ fi
+fi
+
+ fi
+fi
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+ { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ sed '10a\
+... rest of stderr output deleted ...
+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5
+$as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; }
+if test "${ac_cv_cxx_compiler_gnu+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_compiler_gnu=yes
+else
+ ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_cxx_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5
+$as_echo "$ac_cv_cxx_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GXX=yes
+else
+ GXX=
+fi
+ac_test_CXXFLAGS=${CXXFLAGS+set}
+ac_save_CXXFLAGS=$CXXFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5
+$as_echo_n "checking whether $CXX accepts -g... " >&6; }
+if test "${ac_cv_prog_cxx_g+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_cxx_werror_flag=$ac_cxx_werror_flag
+ ac_cxx_werror_flag=yes
+ ac_cv_prog_cxx_g=no
+ CXXFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_prog_cxx_g=yes
+else
+ CXXFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+
+else
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+ CXXFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_prog_cxx_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5
+$as_echo "$ac_cv_prog_cxx_g" >&6; }
+if test "$ac_test_CXXFLAGS" = set; then
+ CXXFLAGS=$ac_save_CXXFLAGS
+elif test $ac_cv_prog_cxx_g = yes; then
+ if test "$GXX" = yes; then
+ CXXFLAGS="-g -O2"
+ else
+ CXXFLAGS="-g"
+ fi
+else
+ if test "$GXX" = yes; then
+ CXXFLAGS="-O2"
+ else
+ CXXFLAGS=
+ fi
+fi
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+depcc="$CXX" am_compiler_list=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CXX_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
+ case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
+ am__minus_obj=
+ ;;
+ none) break ;;
+ esac
+ if depmode=$depmode \
+ source=sub/conftest.c object=$am__obj \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CXX_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CXX_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CXX_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CXX_dependencies_compiler_type" >&6; }
+CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CXX_dependencies_compiler_type" = gcc3; then
+ am__fastdepCXX_TRUE=
+ am__fastdepCXX_FALSE='#'
+else
+ am__fastdepCXX_TRUE='#'
+ am__fastdepCXX_FALSE=
+fi
+
+
+if test -n "$CXX" && ( test "X$CXX" != "Xno" &&
+ ( (test "X$CXX" = "Xg++" && `g++ -v >/dev/null 2>&1` ) ||
+ (test "X$CXX" != "Xg++"))) ; then
+ ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C++ preprocessor" >&5
+$as_echo_n "checking how to run the C++ preprocessor... " >&6; }
+if test -z "$CXXCPP"; then
+ if test "${ac_cv_prog_CXXCPP+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ # Double quotes because CXXCPP needs to be expanded
+ for CXXCPP in "$CXX -E" "/lib/cpp"
+ do
+ ac_preproc_ok=false
+for ac_cxx_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if ac_fn_cxx_try_cpp "$LINENO"; then :
+
+else
+ # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if ac_fn_cxx_try_cpp "$LINENO"; then :
+ # Broken: success on invalid input.
+continue
+else
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.i conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then :
+ break
+fi
+
+ done
+ ac_cv_prog_CXXCPP=$CXXCPP
+
+fi
+ CXXCPP=$ac_cv_prog_CXXCPP
+else
+ ac_cv_prog_CXXCPP=$CXXCPP
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXXCPP" >&5
+$as_echo "$CXXCPP" >&6; }
+ac_preproc_ok=false
+for ac_cxx_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if ac_fn_cxx_try_cpp "$LINENO"; then :
+
+else
+ # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if ac_fn_cxx_try_cpp "$LINENO"; then :
+ # Broken: success on invalid input.
+continue
+else
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.i conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then :
+
+else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+_lt_caught_CXX_error=yes; }
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+else
+ _lt_caught_CXX_error=yes
+fi
+
+
+
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+archive_cmds_need_lc_CXX=no
+allow_undefined_flag_CXX=
+always_export_symbols_CXX=no
+archive_expsym_cmds_CXX=
+compiler_needs_object_CXX=no
+export_dynamic_flag_spec_CXX=
+hardcode_direct_CXX=no
+hardcode_direct_absolute_CXX=no
+hardcode_libdir_flag_spec_CXX=
+hardcode_libdir_flag_spec_ld_CXX=
+hardcode_libdir_separator_CXX=
+hardcode_minus_L_CXX=no
+hardcode_shlibpath_var_CXX=unsupported
+hardcode_automatic_CXX=no
+inherit_rpath_CXX=no
+module_cmds_CXX=
+module_expsym_cmds_CXX=
+link_all_deplibs_CXX=unknown
+old_archive_cmds_CXX=$old_archive_cmds
+no_undefined_flag_CXX=
+whole_archive_flag_spec_CXX=
+enable_shared_with_static_runtimes_CXX=no
+
+# Source file extension for C++ test sources.
+ac_ext=cpp
+
+# Object file extension for compiled C++ test sources.
+objext=o
+objext_CXX=$objext
+
+# No sense in running all these tests if we already determined that
+# the CXX compiler isn't working. Some variables (like enable_shared)
+# are currently assumed to apply to all compilers on this platform,
+# and will be corrupted by setting them based on a non-working compiler.
+if test "$_lt_caught_CXX_error" != yes; then
+ # Code to be used in simple compile tests
+ lt_simple_compile_test_code="int some_variable = 0;"
+
+ # Code to be used in simple link tests
+ lt_simple_link_test_code='int main(int, char *[]) { return(0); }'
+
+ # ltmain only uses $CC for tagged configurations so make sure $CC is set.
+
+
+
+
+
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+
+ # save warnings/boilerplate of simple test code
+ ac_outfile=conftest.$ac_objext
+echo "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$RM conftest*
+
+ ac_outfile=conftest.$ac_objext
+echo "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$RM -r conftest*
+
+
+ # Allow CC to be a program name with arguments.
+ lt_save_CC=$CC
+ lt_save_LD=$LD
+ lt_save_GCC=$GCC
+ GCC=$GXX
+ lt_save_with_gnu_ld=$with_gnu_ld
+ lt_save_path_LD=$lt_cv_path_LD
+ if test -n "${lt_cv_prog_gnu_ldcxx+set}"; then
+ lt_cv_prog_gnu_ld=$lt_cv_prog_gnu_ldcxx
+ else
+ $as_unset lt_cv_prog_gnu_ld
+ fi
+ if test -n "${lt_cv_path_LDCXX+set}"; then
+ lt_cv_path_LD=$lt_cv_path_LDCXX
+ else
+ $as_unset lt_cv_path_LD
+ fi
+ test -z "${LDCXX+set}" || LD=$LDCXX
+ CC=${CXX-"c++"}
+ compiler=$CC
+ compiler_CXX=$CC
+ for cc_temp in $compiler""; do
+ case $cc_temp in
+ compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+ distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+ \-*) ;;
+ *) break;;
+ esac
+done
+cc_basename=`$ECHO "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+
+
+ if test -n "$compiler"; then
+ # We don't want -fno-exception when compiling C++ code, so set the
+ # no_builtin_flag separately
+ if test "$GXX" = yes; then
+ lt_prog_compiler_no_builtin_flag_CXX=' -fno-builtin'
+ else
+ lt_prog_compiler_no_builtin_flag_CXX=
+ fi
+
+ if test "$GXX" = yes; then
+ # Set up default GNU C++ configuration
+
+
+
+# Check whether --with-gnu-ld was given.
+if test "${with_gnu_ld+set}" = set; then :
+ withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes
+else
+ with_gnu_ld=no
+fi
+
+ac_prog=ld
+if test "$GCC" = yes; then
+ # Check if gcc -print-prog-name=ld gives a path.
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ld used by $CC" >&5
+$as_echo_n "checking for ld used by $CC... " >&6; }
+ case $host in
+ *-*-mingw*)
+ # gcc leaves a trailing carriage return which upsets mingw
+ ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+ *)
+ ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+ esac
+ case $ac_prog in
+ # Accept absolute paths.
+ [\\/]* | ?:[\\/]*)
+ re_direlt='/[^/][^/]*/\.\./'
+ # Canonicalize the pathname of ld
+ ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'`
+ while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do
+ ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"`
+ done
+ test -z "$LD" && LD="$ac_prog"
+ ;;
+ "")
+ # If it fails, then pretend we aren't using GCC.
+ ac_prog=ld
+ ;;
+ *)
+ # If it is relative, then search for the first ld in PATH.
+ with_gnu_ld=unknown
+ ;;
+ esac
+elif test "$with_gnu_ld" = yes; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU ld" >&5
+$as_echo_n "checking for GNU ld... " >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for non-GNU ld" >&5
+$as_echo_n "checking for non-GNU ld... " >&6; }
+fi
+if test "${lt_cv_path_LD+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$LD"; then
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+ lt_cv_path_LD="$ac_dir/$ac_prog"
+ # Check to see if the program is GNU ld. I'd rather use --version,
+ # but apparently some variants of GNU ld only accept -v.
+ # Break only if it was the GNU/non-GNU ld that we prefer.
+ case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+ *GNU* | *'with BFD'*)
+ test "$with_gnu_ld" != no && break
+ ;;
+ *)
+ test "$with_gnu_ld" != yes && break
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+else
+ lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi
+fi
+
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LD" >&5
+$as_echo "$LD" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+test -z "$LD" && as_fn_error $? "no acceptable ld found in \$PATH" "$LINENO" 5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if the linker ($LD) is GNU ld" >&5
+$as_echo_n "checking if the linker ($LD) is GNU ld... " >&6; }
+if test "${lt_cv_prog_gnu_ld+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ # I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+ lt_cv_prog_gnu_ld=yes
+ ;;
+*)
+ lt_cv_prog_gnu_ld=no
+ ;;
+esac
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_gnu_ld" >&5
+$as_echo "$lt_cv_prog_gnu_ld" >&6; }
+with_gnu_ld=$lt_cv_prog_gnu_ld
+
+
+
+
+
+
+
+ # Check if GNU C++ uses GNU ld as the underlying linker, since the
+ # archiving commands below assume that GNU ld is being used.
+ if test "$with_gnu_ld" = yes; then
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+
+ # If archive_cmds runs LD, not CC, wlarc should be empty
+ # XXX I think wlarc can be eliminated in ltcf-cxx, but I need to
+ # investigate it a little bit more. (MM)
+ wlarc='${wl}'
+
+ # ancient GNU ld didn't support --whole-archive et. al.
+ if eval "`$CC -print-prog-name=ld` --help 2>&1" |
+ $GREP 'no-whole-archive' > /dev/null; then
+ whole_archive_flag_spec_CXX="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ else
+ whole_archive_flag_spec_CXX=
+ fi
+ else
+ with_gnu_ld=no
+ wlarc=
+
+ # A generic and very simple default shared library creation
+ # command for GNU C++ for the case where it uses the native
+ # linker, instead of GNU ld. If possible, this setting should
+ # overridden to take advantage of the native linker features on
+ # the platform it is being used on.
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+ fi
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+
+ else
+ GXX=no
+ with_gnu_ld=no
+ wlarc=
+ fi
+
+ # PORTME: fill in a description of your system's C++ link characteristics
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+$as_echo_n "checking whether the $compiler linker ($LD) supports shared libraries... " >&6; }
+ ld_shlibs_CXX=yes
+ case $host_os in
+ aix3*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ aix[4-9]*)
+ if test "$host_cpu" = ia64; then
+ # On IA64, the linker does run time linking by default, so we don't
+ # have to do anything special.
+ aix_use_runtimelinking=no
+ exp_sym_flag='-Bexport'
+ no_entry_flag=""
+ else
+ aix_use_runtimelinking=no
+
+ # Test if we are trying to use run time linking or normal
+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+ # need to do runtime linking.
+ case $host_os in aix4.[23]|aix4.[23].*|aix[5-9]*)
+ for ld_flag in $LDFLAGS; do
+ case $ld_flag in
+ *-brtl*)
+ aix_use_runtimelinking=yes
+ break
+ ;;
+ esac
+ done
+ ;;
+ esac
+
+ exp_sym_flag='-bexport'
+ no_entry_flag='-bnoentry'
+ fi
+
+ # When large executables or shared objects are built, AIX ld can
+ # have problems creating the table of contents. If linking a library
+ # or program results in "error TOC overflow" add -mminimal-toc to
+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not
+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+ archive_cmds_CXX=''
+ hardcode_direct_CXX=yes
+ hardcode_direct_absolute_CXX=yes
+ hardcode_libdir_separator_CXX=':'
+ link_all_deplibs_CXX=yes
+ file_list_spec_CXX='${wl}-f,'
+
+ if test "$GXX" = yes; then
+ case $host_os in aix4.[012]|aix4.[012].*)
+ # We only want to do this on AIX 4.2 and lower, the check
+ # below for broken collect2 doesn't work under 4.3+
+ collect2name=`${CC} -print-prog-name=collect2`
+ if test -f "$collect2name" &&
+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null
+ then
+ # We have reworked collect2
+ :
+ else
+ # We have old collect2
+ hardcode_direct_CXX=unsupported
+ # It fails to find uninstalled libraries when the uninstalled
+ # path is not listed in the libpath. Setting hardcode_minus_L
+ # to unsupported forces relinking
+ hardcode_minus_L_CXX=yes
+ hardcode_libdir_flag_spec_CXX='-L$libdir'
+ hardcode_libdir_separator_CXX=
+ fi
+ esac
+ shared_flag='-shared'
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag="$shared_flag "'${wl}-G'
+ fi
+ else
+ # not using gcc
+ if test "$host_cpu" = ia64; then
+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+ # chokes on -Wl,-G. The following line is correct:
+ shared_flag='-G'
+ else
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag='${wl}-G'
+ else
+ shared_flag='${wl}-bM:SRE'
+ fi
+ fi
+ fi
+
+ export_dynamic_flag_spec_CXX='${wl}-bexpall'
+ # It seems that -bexpall does not export symbols beginning with
+ # underscore (_), so it is better to generate a list of symbols to
+ # export.
+ always_export_symbols_CXX=yes
+ if test "$aix_use_runtimelinking" = yes; then
+ # Warning - without using the other runtime loading flags (-brtl),
+ # -berok will link without error, but may produce a broken library.
+ allow_undefined_flag_CXX='-berok'
+ # Determine the default libpath from the value encoded in an empty
+ # executable.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+ hardcode_libdir_flag_spec_CXX='${wl}-blibpath:$libdir:'"$aix_libpath"
+
+ archive_expsym_cmds_CXX='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+ else
+ if test "$host_cpu" = ia64; then
+ hardcode_libdir_flag_spec_CXX='${wl}-R $libdir:/usr/lib:/lib'
+ allow_undefined_flag_CXX="-z nodefs"
+ archive_expsym_cmds_CXX="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+ else
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+ hardcode_libdir_flag_spec_CXX='${wl}-blibpath:$libdir:'"$aix_libpath"
+ # Warning - without using the other run time loading flags,
+ # -berok will link without error, but may produce a broken library.
+ no_undefined_flag_CXX=' ${wl}-bernotok'
+ allow_undefined_flag_CXX=' ${wl}-berok'
+ # Exported symbols can be pulled into shared objects from archives
+ whole_archive_flag_spec_CXX='$convenience'
+ archive_cmds_need_lc_CXX=yes
+ # This is similar to how AIX traditionally builds its shared
+ # libraries.
+ archive_expsym_cmds_CXX="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+ fi
+ fi
+ ;;
+
+ beos*)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ allow_undefined_flag_CXX=unsupported
+ # Joseph Beckenbach <jrb3 at best.com> says some releases of gcc
+ # support --undefined. This deserves some investigation. FIXME
+ archive_cmds_CXX='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ else
+ ld_shlibs_CXX=no
+ fi
+ ;;
+
+ chorus*)
+ case $cc_basename in
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # _LT_TAGVAR(hardcode_libdir_flag_spec, CXX) is actually meaningless,
+ # as there is no search path for DLLs.
+ hardcode_libdir_flag_spec_CXX='-L$libdir'
+ allow_undefined_flag_CXX=unsupported
+ always_export_symbols_CXX=no
+ enable_shared_with_static_runtimes_CXX=yes
+
+ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ # If the export-symbols file already is a .def file (1st line
+ # is EXPORTS), use it as is; otherwise, prepend...
+ archive_expsym_cmds_CXX='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+ cp $export_symbols $output_objdir/$soname.def;
+ else
+ echo EXPORTS > $output_objdir/$soname.def;
+ cat $export_symbols >> $output_objdir/$soname.def;
+ fi~
+ $CC -shared -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ else
+ ld_shlibs_CXX=no
+ fi
+ ;;
+ darwin* | rhapsody*)
+
+
+ archive_cmds_need_lc_CXX=no
+ hardcode_direct_CXX=no
+ hardcode_automatic_CXX=yes
+ hardcode_shlibpath_var_CXX=unsupported
+ whole_archive_flag_spec_CXX=''
+ link_all_deplibs_CXX=yes
+ allow_undefined_flag_CXX="$_lt_dar_allow_undefined"
+ case $cc_basename in
+ ifort*) _lt_dar_can_shared=yes ;;
+ *) _lt_dar_can_shared=$GCC ;;
+ esac
+ if test "$_lt_dar_can_shared" = "yes"; then
+ output_verbose_link_cmd=echo
+ archive_cmds_CXX="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}"
+ module_cmds_CXX="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}"
+ archive_expsym_cmds_CXX="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}"
+ module_expsym_cmds_CXX="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}"
+ if test "$lt_cv_apple_cc_single_mod" != "yes"; then
+ archive_cmds_CXX="\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dsymutil}"
+ archive_expsym_cmds_CXX="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dar_export_syms}${_lt_dsymutil}"
+ fi
+
+ else
+ ld_shlibs_CXX=no
+ fi
+
+ ;;
+
+ dgux*)
+ case $cc_basename in
+ ec++*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ ghcx*)
+ # Green Hills C++ Compiler
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ freebsd[12]*)
+ # C++ shared libraries reported to be fairly broken before
+ # switch to ELF
+ ld_shlibs_CXX=no
+ ;;
+
+ freebsd-elf*)
+ archive_cmds_need_lc_CXX=no
+ ;;
+
+ freebsd* | dragonfly*)
+ # FreeBSD 3 and later use GNU C++ and GNU ld with standard ELF
+ # conventions
+ ld_shlibs_CXX=yes
+ ;;
+
+ gnu*)
+ ;;
+
+ hpux9*)
+ hardcode_libdir_flag_spec_CXX='${wl}+b ${wl}$libdir'
+ hardcode_libdir_separator_CXX=:
+ export_dynamic_flag_spec_CXX='${wl}-E'
+ hardcode_direct_CXX=yes
+ hardcode_minus_L_CXX=yes # Not in the search PATH,
+ # but as the default
+ # location of the library.
+
+ case $cc_basename in
+ CC*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ aCC*)
+ archive_cmds_CXX='$RM $output_objdir/$soname~$CC -b ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $EGREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ archive_cmds_CXX='$RM $output_objdir/$soname~$CC -shared -nostdlib -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ else
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ fi
+ ;;
+ esac
+ ;;
+
+ hpux10*|hpux11*)
+ if test $with_gnu_ld = no; then
+ hardcode_libdir_flag_spec_CXX='${wl}+b ${wl}$libdir'
+ hardcode_libdir_separator_CXX=:
+
+ case $host_cpu in
+ hppa*64*|ia64*)
+ ;;
+ *)
+ export_dynamic_flag_spec_CXX='${wl}-E'
+ ;;
+ esac
+ fi
+ case $host_cpu in
+ hppa*64*|ia64*)
+ hardcode_direct_CXX=no
+ hardcode_shlibpath_var_CXX=no
+ ;;
+ *)
+ hardcode_direct_CXX=yes
+ hardcode_direct_absolute_CXX=yes
+ hardcode_minus_L_CXX=yes # Not in the search PATH,
+ # but as the default
+ # location of the library.
+ ;;
+ esac
+
+ case $cc_basename in
+ CC*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ aCC*)
+ case $host_cpu in
+ hppa*64*)
+ archive_cmds_CXX='$CC -b ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ ia64*)
+ archive_cmds_CXX='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ esac
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $GREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ if test $with_gnu_ld = no; then
+ case $host_cpu in
+ hppa*64*)
+ archive_cmds_CXX='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ ia64*)
+ archive_cmds_CXX='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ esac
+ fi
+ else
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ fi
+ ;;
+ esac
+ ;;
+
+ interix[3-9]*)
+ hardcode_direct_CXX=no
+ hardcode_shlibpath_var_CXX=no
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec_CXX='${wl}-E'
+ # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+ # Instead, shared libraries are loaded at an image base (0x10000000 by
+ # default) and relocated if they conflict, which is a slow very memory
+ # consuming and fragmenting process. To avoid this, we pick a random,
+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+ # time. Moving up from 0x10000000 also allows more sbrk(2) space.
+ archive_cmds_CXX='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ archive_expsym_cmds_CXX='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ ;;
+ irix5* | irix6*)
+ case $cc_basename in
+ CC*)
+ # SGI C++
+ archive_cmds_CXX='$CC -shared -all -multigot $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+
+ # Archives containing C++ object files must be created using
+ # "CC -ar", where "CC" is the IRIX C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ old_archive_cmds_CXX='$CC -ar -WR,-u -o $oldlib $oldobjs'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ if test "$with_gnu_ld" = no; then
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ else
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` -o $lib'
+ fi
+ fi
+ link_all_deplibs_CXX=yes
+ ;;
+ esac
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator_CXX=:
+ inherit_rpath_CXX=yes
+ ;;
+
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ KCC*)
+ # Kuck and Associates, Inc. (KAI) C++ Compiler
+
+ # KCC will only create a shared library if the output file
+ # ends with ".so" (or ".sl" for HP-UX), so rename the library
+ # to its proper name (with version) after linking.
+ archive_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+ archive_expsym_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib ${wl}-retain-symbols-file,$export_symbols; mv \$templib $lib'
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 | $GREP "ld"`; rm -f libconftest$shared_ext; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+
+ # Archives containing C++ object files must be created using
+ # "CC -Bstatic", where "CC" is the KAI C++ compiler.
+ old_archive_cmds_CXX='$CC -Bstatic -o $oldlib $oldobjs'
+ ;;
+ icpc* | ecpc* )
+ # Intel C++
+ with_gnu_ld=yes
+ # version 8.0 and above of icpc choke on multiply defined symbols
+ # if we add $predep_objects and $postdep_objects, however 7.1 and
+ # earlier do not add the objects themselves.
+ case `$CC -V 2>&1` in
+ *"Version 7."*)
+ archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ ;;
+ *) # Version 8.0 or newer
+ tmp_idyn=
+ case $host_cpu in
+ ia64*) tmp_idyn=' -i_dynamic';;
+ esac
+ archive_cmds_CXX='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ ;;
+ esac
+ archive_cmds_need_lc_CXX=no
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+ whole_archive_flag_spec_CXX='${wl}--whole-archive$convenience ${wl}--no-whole-archive'
+ ;;
+ pgCC* | pgcpp*)
+ # Portland Group C++ compiler
+ case `$CC -V` in
+ *pgCC\ [1-5]* | *pgcpp\ [1-5]*)
+ prelink_cmds_CXX='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $objs $libobjs $compile_deplibs~
+ compile_command="$compile_command `find $tpldir -name \*.o | $NL2SP`"'
+ old_archive_cmds_CXX='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $oldobjs$old_deplibs~
+ $AR $AR_FLAGS $oldlib$oldobjs$old_deplibs `find $tpldir -name \*.o | $NL2SP`~
+ $RANLIB $oldlib'
+ archive_cmds_CXX='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~
+ $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+ archive_expsym_cmds_CXX='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~
+ $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+ ;;
+ *) # Version 6 will use weak symbols
+ archive_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+ ;;
+ esac
+
+ hardcode_libdir_flag_spec_CXX='${wl}--rpath ${wl}$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+ whole_archive_flag_spec_CXX='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ ;;
+ cxx*)
+ # Compaq C++
+ archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib ${wl}-retain-symbols-file $wl$export_symbols'
+
+ runpath_var=LD_RUN_PATH
+ hardcode_libdir_flag_spec_CXX='-rpath $libdir'
+ hardcode_libdir_separator_CXX=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld .*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ xl*)
+ # IBM XL 8.0 on PPC, with GNU ld
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+ archive_cmds_CXX='$CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ if test "x$supports_anon_versioning" = xyes; then
+ archive_expsym_cmds_CXX='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+ fi
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+ no_undefined_flag_CXX=' -zdefs'
+ archive_cmds_CXX='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file ${wl}$export_symbols'
+ hardcode_libdir_flag_spec_CXX='-R$libdir'
+ whole_archive_flag_spec_CXX='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ compiler_needs_object_CXX=yes
+
+ # Not sure whether something based on
+ # $CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1
+ # would be better.
+ output_verbose_link_cmd='echo'
+
+ # Archives containing C++ object files must be created using
+ # "CC -xar", where "CC" is the Sun C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ old_archive_cmds_CXX='$CC -xar -o $oldlib $oldobjs'
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+
+ lynxos*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+
+ m88k*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+
+ mvs*)
+ case $cc_basename in
+ cxx*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ netbsd*)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ archive_cmds_CXX='$LD -Bshareable -o $lib $predep_objects $libobjs $deplibs $postdep_objects $linker_flags'
+ wlarc=
+ hardcode_libdir_flag_spec_CXX='-R$libdir'
+ hardcode_direct_CXX=yes
+ hardcode_shlibpath_var_CXX=no
+ fi
+ # Workaround some broken pre-1.5 toolchains
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP conftest.$objext | $SED -e "s:-lgcc -lc -lgcc::"'
+ ;;
+
+ *nto* | *qnx*)
+ ld_shlibs_CXX=yes
+ ;;
+
+ openbsd2*)
+ # C++ shared libraries are fairly broken
+ ld_shlibs_CXX=no
+ ;;
+
+ openbsd*)
+ if test -f /usr/libexec/ld.so; then
+ hardcode_direct_CXX=yes
+ hardcode_shlibpath_var_CXX=no
+ hardcode_direct_absolute_CXX=yes
+ archive_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ archive_expsym_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file,$export_symbols -o $lib'
+ export_dynamic_flag_spec_CXX='${wl}-E'
+ whole_archive_flag_spec_CXX="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ fi
+ output_verbose_link_cmd=echo
+ else
+ ld_shlibs_CXX=no
+ fi
+ ;;
+
+ osf3* | osf4* | osf5*)
+ case $cc_basename in
+ KCC*)
+ # Kuck and Associates, Inc. (KAI) C++ Compiler
+
+ # KCC will only create a shared library if the output file
+ # ends with ".so" (or ".sl" for HP-UX), so rename the library
+ # to its proper name (with version) after linking.
+ archive_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo "$lib" | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ hardcode_libdir_separator_CXX=:
+
+ # Archives containing C++ object files must be created using
+ # the KAI C++ compiler.
+ case $host in
+ osf3*) old_archive_cmds_CXX='$CC -Bstatic -o $oldlib $oldobjs' ;;
+ *) old_archive_cmds_CXX='$CC -o $oldlib $oldobjs' ;;
+ esac
+ ;;
+ RCC*)
+ # Rational C++ 2.4.1
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ cxx*)
+ case $host in
+ osf3*)
+ allow_undefined_flag_CXX=' ${wl}-expect_unresolved ${wl}\*'
+ archive_cmds_CXX='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $soname `test -n "$verstring" && $ECHO "X${wl}-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ ;;
+ *)
+ allow_undefined_flag_CXX=' -expect_unresolved \*'
+ archive_cmds_CXX='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ archive_expsym_cmds_CXX='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done~
+ echo "-hidden">> $lib.exp~
+ $CC -shared$allow_undefined_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname ${wl}-input ${wl}$lib.exp `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~
+ $RM $lib.exp'
+ hardcode_libdir_flag_spec_CXX='-rpath $libdir'
+ ;;
+ esac
+
+ hardcode_libdir_separator_CXX=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld" | $GREP -v "ld:"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld.*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+ allow_undefined_flag_CXX=' ${wl}-expect_unresolved ${wl}\*'
+ case $host in
+ osf3*)
+ archive_cmds_CXX='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ ;;
+ esac
+
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator_CXX=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+
+ else
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ fi
+ ;;
+ esac
+ ;;
+
+ psos*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+
+ sunos4*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.x
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ lcc*)
+ # Lucid
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ solaris*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.2, 5.x and Centerline C++
+ archive_cmds_need_lc_CXX=yes
+ no_undefined_flag_CXX=' -zdefs'
+ archive_cmds_CXX='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ archive_expsym_cmds_CXX='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G${allow_undefined_flag} ${wl}-M ${wl}$lib.exp -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ hardcode_libdir_flag_spec_CXX='-R$libdir'
+ hardcode_shlibpath_var_CXX=no
+ case $host_os in
+ solaris2.[0-5] | solaris2.[0-5].*) ;;
+ *)
+ # The compiler driver will combine and reorder linker options,
+ # but understands `-z linker_flag'.
+ # Supported since Solaris 2.6 (maybe 2.5.1?)
+ whole_archive_flag_spec_CXX='-z allextract$convenience -z defaultextract'
+ ;;
+ esac
+ link_all_deplibs_CXX=yes
+
+ output_verbose_link_cmd='echo'
+
+ # Archives containing C++ object files must be created using
+ # "CC -xar", where "CC" is the Sun C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ old_archive_cmds_CXX='$CC -xar -o $oldlib $oldobjs'
+ ;;
+ gcx*)
+ # Green Hills C++ Compiler
+ archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+
+ # The C++ compiler must be used to create the archive.
+ old_archive_cmds_CXX='$CC $LDFLAGS -archive -o $oldlib $oldobjs'
+ ;;
+ *)
+ # GNU C++ compiler with Solaris linker
+ if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+ no_undefined_flag_CXX=' ${wl}-z ${wl}defs'
+ if $CC --version | $GREP -v '^2\.7' > /dev/null; then
+ archive_cmds_CXX='$CC -shared -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -shared -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+ else
+ # g++ 2.7 appears to require `-G' NOT `-shared' on this
+ # platform.
+ archive_cmds_CXX='$CC -G -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -G $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+ fi
+
+ hardcode_libdir_flag_spec_CXX='${wl}-R $wl$libdir'
+ case $host_os in
+ solaris2.[0-5] | solaris2.[0-5].*) ;;
+ *)
+ whole_archive_flag_spec_CXX='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract'
+ ;;
+ esac
+ fi
+ ;;
+ esac
+ ;;
+
+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*)
+ no_undefined_flag_CXX='${wl}-z,text'
+ archive_cmds_need_lc_CXX=no
+ hardcode_shlibpath_var_CXX=no
+ runpath_var='LD_RUN_PATH'
+
+ case $cc_basename in
+ CC*)
+ archive_cmds_CXX='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6*)
+ # Note: We can NOT use -z defs as we might desire, because we do not
+ # link with -lc, and that would cause any symbols used from libc to
+ # always be unresolved, which means just about no library would
+ # ever link correctly. If we're not using GNU ld we use -z text
+ # though, which does catch some bad symbols but isn't as heavy-handed
+ # as -z defs.
+ no_undefined_flag_CXX='${wl}-z,text'
+ allow_undefined_flag_CXX='${wl}-z,nodefs'
+ archive_cmds_need_lc_CXX=no
+ hardcode_shlibpath_var_CXX=no
+ hardcode_libdir_flag_spec_CXX='${wl}-R,$libdir'
+ hardcode_libdir_separator_CXX=':'
+ link_all_deplibs_CXX=yes
+ export_dynamic_flag_spec_CXX='${wl}-Bexport'
+ runpath_var='LD_RUN_PATH'
+
+ case $cc_basename in
+ CC*)
+ archive_cmds_CXX='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ ;;
+
+ tandem*)
+ case $cc_basename in
+ NCC*)
+ # NonStop-UX NCC 3.20
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ vxworks*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ld_shlibs_CXX" >&5
+$as_echo "$ld_shlibs_CXX" >&6; }
+ test "$ld_shlibs_CXX" = no && can_build_shared=no
+
+ GCC_CXX="$GXX"
+ LD_CXX="$LD"
+
+ ## CAVEAT EMPTOR:
+ ## There is no encapsulation within the following macros, do not change
+ ## the running order or otherwise move them around unless you know exactly
+ ## what you are doing...
+ # Dependencies to place before and after the object being linked:
+predep_objects_CXX=
+postdep_objects_CXX=
+predeps_CXX=
+postdeps_CXX=
+compiler_lib_search_path_CXX=
+
+cat > conftest.$ac_ext <<_LT_EOF
+class Foo
+{
+public:
+ Foo (void) { a = 0; }
+private:
+ int a;
+};
+_LT_EOF
+
+if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then
+ # Parse the compiler output and extract the necessary
+ # objects, libraries and library flags.
+
+ # Sentinel used to keep track of whether or not we are before
+ # the conftest object file.
+ pre_test_object_deps_done=no
+
+ for p in `eval "$output_verbose_link_cmd"`; do
+ case $p in
+
+ -L* | -R* | -l*)
+ # Some compilers place space between "-{L,R}" and the path.
+ # Remove the space.
+ if test $p = "-L" ||
+ test $p = "-R"; then
+ prev=$p
+ continue
+ else
+ prev=
+ fi
+
+ if test "$pre_test_object_deps_done" = no; then
+ case $p in
+ -L* | -R*)
+ # Internal compiler library paths should come after those
+ # provided the user. The postdeps already come after the
+ # user supplied libs so there is no need to process them.
+ if test -z "$compiler_lib_search_path_CXX"; then
+ compiler_lib_search_path_CXX="${prev}${p}"
+ else
+ compiler_lib_search_path_CXX="${compiler_lib_search_path_CXX} ${prev}${p}"
+ fi
+ ;;
+ # The "-l" case would never come before the object being
+ # linked, so don't bother handling this case.
+ esac
+ else
+ if test -z "$postdeps_CXX"; then
+ postdeps_CXX="${prev}${p}"
+ else
+ postdeps_CXX="${postdeps_CXX} ${prev}${p}"
+ fi
+ fi
+ ;;
+
+ *.$objext)
+ # This assumes that the test object file only shows up
+ # once in the compiler output.
+ if test "$p" = "conftest.$objext"; then
+ pre_test_object_deps_done=yes
+ continue
+ fi
+
+ if test "$pre_test_object_deps_done" = no; then
+ if test -z "$predep_objects_CXX"; then
+ predep_objects_CXX="$p"
+ else
+ predep_objects_CXX="$predep_objects_CXX $p"
+ fi
+ else
+ if test -z "$postdep_objects_CXX"; then
+ postdep_objects_CXX="$p"
+ else
+ postdep_objects_CXX="$postdep_objects_CXX $p"
+ fi
+ fi
+ ;;
+
+ *) ;; # Ignore the rest.
+
+ esac
+ done
+
+ # Clean up.
+ rm -f a.out a.exe
+else
+ echo "libtool.m4: error: problem compiling CXX test program"
+fi
+
+$RM -f confest.$objext
+
+# PORTME: override above test on systems where it is broken
+case $host_os in
+interix[3-9]*)
+ # Interix 3.5 installs completely hosed .la files for C++, so rather than
+ # hack all around it, let's just trust "g++" to DTRT.
+ predep_objects_CXX=
+ postdep_objects_CXX=
+ postdeps_CXX=
+ ;;
+
+linux*)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+
+ # The more standards-conforming stlport4 library is
+ # incompatible with the Cstd library. Avoid specifying
+ # it if it's in CXXFLAGS. Ignore libCrun as
+ # -library=stlport4 depends on it.
+ case " $CXX $CXXFLAGS " in
+ *" -library=stlport4 "*)
+ solaris_use_stlport4=yes
+ ;;
+ esac
+
+ if test "$solaris_use_stlport4" != yes; then
+ postdeps_CXX='-library=Cstd -library=Crun'
+ fi
+ ;;
+ esac
+ ;;
+
+solaris*)
+ case $cc_basename in
+ CC*)
+ # The more standards-conforming stlport4 library is
+ # incompatible with the Cstd library. Avoid specifying
+ # it if it's in CXXFLAGS. Ignore libCrun as
+ # -library=stlport4 depends on it.
+ case " $CXX $CXXFLAGS " in
+ *" -library=stlport4 "*)
+ solaris_use_stlport4=yes
+ ;;
+ esac
+
+ # Adding this requires a known-good setup of shared libraries for
+ # Sun compiler versions before 5.6, else PIC objects from an old
+ # archive will be linked into the output, leading to subtle bugs.
+ if test "$solaris_use_stlport4" != yes; then
+ postdeps_CXX='-library=Cstd -library=Crun'
+ fi
+ ;;
+ esac
+ ;;
+esac
+
+
+case " $postdeps_CXX " in
+*" -lc "*) archive_cmds_need_lc_CXX=no ;;
+esac
+ compiler_lib_search_dirs_CXX=
+if test -n "${compiler_lib_search_path_CXX}"; then
+ compiler_lib_search_dirs_CXX=`echo " ${compiler_lib_search_path_CXX}" | ${SED} -e 's! -L! !g' -e 's!^ !!'`
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ lt_prog_compiler_wl_CXX=
+lt_prog_compiler_pic_CXX=
+lt_prog_compiler_static_CXX=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $compiler option to produce PIC" >&5
+$as_echo_n "checking for $compiler option to produce PIC... " >&6; }
+
+ # C++ specific cases for pic, static, wl, etc.
+ if test "$GXX" = yes; then
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_static_CXX='-static'
+
+ case $host_os in
+ aix*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ lt_prog_compiler_static_CXX='-Bstatic'
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ lt_prog_compiler_pic_CXX='-fPIC'
+ ;;
+ m68k)
+ # FIXME: we need at least 68020 code to build shared libraries, but
+ # adding the `-m68020' flag to GCC prevents building anything better,
+ # like `-m68040'.
+ lt_prog_compiler_pic_CXX='-m68020 -resident32 -malways-restore-a4'
+ ;;
+ esac
+ ;;
+
+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+ # PIC is the default for these OSes.
+ ;;
+ mingw* | cygwin* | os2* | pw32* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ # Although the cygwin gcc ignores -fPIC, still need this for old-style
+ # (--disable-auto-import) libraries
+ lt_prog_compiler_pic_CXX='-DDLL_EXPORT'
+ ;;
+ darwin* | rhapsody*)
+ # PIC is the default on this platform
+ # Common symbols not allowed in MH_DYLIB files
+ lt_prog_compiler_pic_CXX='-fno-common'
+ ;;
+ *djgpp*)
+ # DJGPP does not support shared libraries at all
+ lt_prog_compiler_pic_CXX=
+ ;;
+ interix[3-9]*)
+ # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+ # Instead, we relocate shared libraries at runtime.
+ ;;
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ lt_prog_compiler_pic_CXX=-Kconform_pic
+ fi
+ ;;
+ hpux*)
+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit
+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag
+ # sets the default TLS model and affects inlining.
+ case $host_cpu in
+ hppa*64*)
+ ;;
+ *)
+ lt_prog_compiler_pic_CXX='-fPIC'
+ ;;
+ esac
+ ;;
+ *qnx* | *nto*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ lt_prog_compiler_pic_CXX='-fPIC -shared'
+ ;;
+ *)
+ lt_prog_compiler_pic_CXX='-fPIC'
+ ;;
+ esac
+ else
+ case $host_os in
+ aix[4-9]*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ lt_prog_compiler_static_CXX='-Bstatic'
+ else
+ lt_prog_compiler_static_CXX='-bnso -bI:/lib/syscalls.exp'
+ fi
+ ;;
+ chorus*)
+ case $cc_basename in
+ cxch68*)
+ # Green Hills C++ Compiler
+ # _LT_TAGVAR(lt_prog_compiler_static, CXX)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a"
+ ;;
+ esac
+ ;;
+ dgux*)
+ case $cc_basename in
+ ec++*)
+ lt_prog_compiler_pic_CXX='-KPIC'
+ ;;
+ ghcx*)
+ # Green Hills C++ Compiler
+ lt_prog_compiler_pic_CXX='-pic'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ freebsd* | dragonfly*)
+ # FreeBSD uses GNU C++
+ ;;
+ hpux9* | hpux10* | hpux11*)
+ case $cc_basename in
+ CC*)
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_static_CXX='${wl}-a ${wl}archive'
+ if test "$host_cpu" != ia64; then
+ lt_prog_compiler_pic_CXX='+Z'
+ fi
+ ;;
+ aCC*)
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_static_CXX='${wl}-a ${wl}archive'
+ case $host_cpu in
+ hppa*64*|ia64*)
+ # +Z the default
+ ;;
+ *)
+ lt_prog_compiler_pic_CXX='+Z'
+ ;;
+ esac
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ interix*)
+ # This is c89, which is MS Visual C++ (no shared libs)
+ # Anyone wants to do a port?
+ ;;
+ irix5* | irix6* | nonstopux*)
+ case $cc_basename in
+ CC*)
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_static_CXX='-non_shared'
+ # CC pic flag -KPIC is the default.
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ case $cc_basename in
+ KCC*)
+ # KAI C++ Compiler
+ lt_prog_compiler_wl_CXX='--backend -Wl,'
+ lt_prog_compiler_pic_CXX='-fPIC'
+ ;;
+ ecpc* )
+ # old Intel C++ for x86_64 which still supported -KPIC.
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-KPIC'
+ lt_prog_compiler_static_CXX='-static'
+ ;;
+ icpc* )
+ # Intel C++, used to be incompatible with GCC.
+ # ICC 10 doesn't accept -KPIC any more.
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-fPIC'
+ lt_prog_compiler_static_CXX='-static'
+ ;;
+ pgCC* | pgcpp*)
+ # Portland Group C++ compiler
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-fpic'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ ;;
+ cxx*)
+ # Compaq C++
+ # Make sure the PIC flag is empty. It appears that all Alpha
+ # Linux and Compaq Tru64 Unix objects are PIC.
+ lt_prog_compiler_pic_CXX=
+ lt_prog_compiler_static_CXX='-non_shared'
+ ;;
+ xlc* | xlC*)
+ # IBM XL 8.0 on PPC
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-qpic'
+ lt_prog_compiler_static_CXX='-qstaticlink'
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+ lt_prog_compiler_pic_CXX='-KPIC'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ lt_prog_compiler_wl_CXX='-Qoption ld '
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+ lynxos*)
+ ;;
+ m88k*)
+ ;;
+ mvs*)
+ case $cc_basename in
+ cxx*)
+ lt_prog_compiler_pic_CXX='-W c,exportall'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ netbsd* | netbsdelf*-gnu)
+ ;;
+ *qnx* | *nto*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ lt_prog_compiler_pic_CXX='-fPIC -shared'
+ ;;
+ osf3* | osf4* | osf5*)
+ case $cc_basename in
+ KCC*)
+ lt_prog_compiler_wl_CXX='--backend -Wl,'
+ ;;
+ RCC*)
+ # Rational C++ 2.4.1
+ lt_prog_compiler_pic_CXX='-pic'
+ ;;
+ cxx*)
+ # Digital/Compaq C++
+ lt_prog_compiler_wl_CXX='-Wl,'
+ # Make sure the PIC flag is empty. It appears that all Alpha
+ # Linux and Compaq Tru64 Unix objects are PIC.
+ lt_prog_compiler_pic_CXX=
+ lt_prog_compiler_static_CXX='-non_shared'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ psos*)
+ ;;
+ solaris*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.2, 5.x and Centerline C++
+ lt_prog_compiler_pic_CXX='-KPIC'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ lt_prog_compiler_wl_CXX='-Qoption ld '
+ ;;
+ gcx*)
+ # Green Hills C++ Compiler
+ lt_prog_compiler_pic_CXX='-PIC'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ sunos4*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.x
+ lt_prog_compiler_pic_CXX='-pic'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ ;;
+ lcc*)
+ # Lucid
+ lt_prog_compiler_pic_CXX='-pic'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+ case $cc_basename in
+ CC*)
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-KPIC'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ ;;
+ esac
+ ;;
+ tandem*)
+ case $cc_basename in
+ NCC*)
+ # NonStop-UX NCC 3.20
+ lt_prog_compiler_pic_CXX='-KPIC'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ vxworks*)
+ ;;
+ *)
+ lt_prog_compiler_can_build_shared_CXX=no
+ ;;
+ esac
+ fi
+
+case $host_os in
+ # For platforms which do not support PIC, -DPIC is meaningless:
+ *djgpp*)
+ lt_prog_compiler_pic_CXX=
+ ;;
+ *)
+ lt_prog_compiler_pic_CXX="$lt_prog_compiler_pic_CXX -DPIC"
+ ;;
+esac
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_prog_compiler_pic_CXX" >&5
+$as_echo "$lt_prog_compiler_pic_CXX" >&6; }
+
+
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$lt_prog_compiler_pic_CXX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler PIC flag $lt_prog_compiler_pic_CXX works" >&5
+$as_echo_n "checking if $compiler PIC flag $lt_prog_compiler_pic_CXX works... " >&6; }
+if test "${lt_cv_prog_compiler_pic_works_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_pic_works_CXX=no
+ ac_outfile=conftest.$ac_objext
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+ lt_compiler_flag="$lt_prog_compiler_pic_CXX -DPIC"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ # The option is referenced via a variable to avoid confusing sed.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:13771: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>conftest.err)
+ ac_status=$?
+ cat conftest.err >&5
+ echo "$as_me:13775: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s "$ac_outfile"; then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings other than the usual output.
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_pic_works_CXX=yes
+ fi
+ fi
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_pic_works_CXX" >&5
+$as_echo "$lt_cv_prog_compiler_pic_works_CXX" >&6; }
+
+if test x"$lt_cv_prog_compiler_pic_works_CXX" = xyes; then
+ case $lt_prog_compiler_pic_CXX in
+ "" | " "*) ;;
+ *) lt_prog_compiler_pic_CXX=" $lt_prog_compiler_pic_CXX" ;;
+ esac
+else
+ lt_prog_compiler_pic_CXX=
+ lt_prog_compiler_can_build_shared_CXX=no
+fi
+
+fi
+
+
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$lt_prog_compiler_wl_CXX eval lt_tmp_static_flag=\"$lt_prog_compiler_static_CXX\"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler static flag $lt_tmp_static_flag works" >&5
+$as_echo_n "checking if $compiler static flag $lt_tmp_static_flag works... " >&6; }
+if test "${lt_cv_prog_compiler_static_works_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_static_works_CXX=no
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS $lt_tmp_static_flag"
+ echo "$lt_simple_link_test_code" > conftest.$ac_ext
+ if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+ # The linker can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ if test -s conftest.err; then
+ # Append any errors to the config.log.
+ cat conftest.err 1>&5
+ $ECHO "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_static_works_CXX=yes
+ fi
+ else
+ lt_cv_prog_compiler_static_works_CXX=yes
+ fi
+ fi
+ $RM -r conftest*
+ LDFLAGS="$save_LDFLAGS"
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_static_works_CXX" >&5
+$as_echo "$lt_cv_prog_compiler_static_works_CXX" >&6; }
+
+if test x"$lt_cv_prog_compiler_static_works_CXX" = xyes; then
+ :
+else
+ lt_prog_compiler_static_CXX=
+fi
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler supports -c -o file.$ac_objext" >&5
+$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; }
+if test "${lt_cv_prog_compiler_c_o_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_c_o_CXX=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:13870: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&5
+ echo "$as_me:13874: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_c_o_CXX=yes
+ fi
+ fi
+ chmod u+w . 2>&5
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_c_o_CXX" >&5
+$as_echo "$lt_cv_prog_compiler_c_o_CXX" >&6; }
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler supports -c -o file.$ac_objext" >&5
+$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; }
+if test "${lt_cv_prog_compiler_c_o_CXX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_c_o_CXX=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:13922: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&5
+ echo "$as_me:13926: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_c_o_CXX=yes
+ fi
+ fi
+ chmod u+w . 2>&5
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_c_o_CXX" >&5
+$as_echo "$lt_cv_prog_compiler_c_o_CXX" >&6; }
+
+
+
+
+hard_links="nottested"
+if test "$lt_cv_prog_compiler_c_o_CXX" = no && test "$need_locks" != no; then
+ # do not overwrite the value of need_locks provided by the user
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if we can lock with hard links" >&5
+$as_echo_n "checking if we can lock with hard links... " >&6; }
+ hard_links=yes
+ $RM conftest*
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ touch conftest.a
+ ln conftest.a conftest.b 2>&5 || hard_links=no
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $hard_links" >&5
+$as_echo "$hard_links" >&6; }
+ if test "$hard_links" = no; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&5
+$as_echo "$as_me: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&2;}
+ need_locks=warn
+ fi
+else
+ need_locks=no
+fi
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+$as_echo_n "checking whether the $compiler linker ($LD) supports shared libraries... " >&6; }
+
+ export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ case $host_os in
+ aix[4-9]*)
+ # If we're using GNU nm, then we don't want the "-C" option.
+ # -C means demangle to AIX nm, but means don't demangle with GNU nm
+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then
+ export_symbols_cmds_CXX='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ else
+ export_symbols_cmds_CXX='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ fi
+ ;;
+ pw32*)
+ export_symbols_cmds_CXX="$ltdll_cmds"
+ ;;
+ cygwin* | mingw* | cegcc*)
+ export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1 DATA/;/^.*[ ]__nm__/s/^.*[ ]__nm__\([^ ]*\)[ ][^ ]*/\1 DATA/;/^I[ ]/d;/^[AITW][ ]/s/.* //'\'' | sort | uniq > $export_symbols'
+ ;;
+ linux* | k*bsd*-gnu)
+ link_all_deplibs_CXX=no
+ ;;
+ *)
+ export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ ;;
+ esac
+ exclude_expsyms_CXX='_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*'
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ld_shlibs_CXX" >&5
+$as_echo "$ld_shlibs_CXX" >&6; }
+test "$ld_shlibs_CXX" = no && can_build_shared=no
+
+with_gnu_ld_CXX=$with_gnu_ld
+
+
+
+
+
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$archive_cmds_need_lc_CXX" in
+x|xyes)
+ # Assume -lc should be added
+ archive_cmds_need_lc_CXX=yes
+
+ if test "$enable_shared" = yes && test "$GCC" = yes; then
+ case $archive_cmds_CXX in
+ *'~'*)
+ # FIXME: we may have to deal with multi-command sequences.
+ ;;
+ '$CC '*)
+ # Test whether the compiler implicitly links with -lc since on some
+ # systems, -lgcc has to come before -lc. If gcc already passes -lc
+ # to ld, don't add -lc before -lgcc.
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether -lc should be explicitly linked in" >&5
+$as_echo_n "checking whether -lc should be explicitly linked in... " >&6; }
+ $RM conftest*
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } 2>conftest.err; then
+ soname=conftest
+ lib=conftest
+ libobjs=conftest.$ac_objext
+ deplibs=
+ wl=$lt_prog_compiler_wl_CXX
+ pic_flag=$lt_prog_compiler_pic_CXX
+ compiler_flags=-v
+ linker_flags=-v
+ verstring=
+ output_objdir=.
+ libname=conftest
+ lt_save_allow_undefined_flag=$allow_undefined_flag_CXX
+ allow_undefined_flag_CXX=
+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$archive_cmds_CXX 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1\""; } >&5
+ (eval $archive_cmds_CXX 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+ then
+ archive_cmds_need_lc_CXX=no
+ else
+ archive_cmds_need_lc_CXX=yes
+ fi
+ allow_undefined_flag_CXX=$lt_save_allow_undefined_flag
+ else
+ cat conftest.err 1>&5
+ fi
+ $RM conftest*
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $archive_cmds_need_lc_CXX" >&5
+$as_echo "$archive_cmds_need_lc_CXX" >&6; }
+ ;;
+ esac
+ fi
+ ;;
+esac
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking dynamic linker characteristics" >&5
+$as_echo_n "checking dynamic linker characteristics... " >&6; }
+
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+ shlibpath_var=LIBPATH
+
+ # AIX 3 has no versioning support, so we append a major version to the name.
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+
+aix[4-9]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ hardcode_into_libs=yes
+ if test "$host_cpu" = ia64; then
+ # AIX 5 supports IA64
+ library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ else
+ # With GCC up to 2.95.x, collect2 would create an import file
+ # for dependence libraries. The import file would start with
+ # the line `#! .'. This would cause the generated library to
+ # depend on `.', always an invalid library. This was fixed in
+ # development snapshots of GCC prior to 3.0.
+ case $host_os in
+ aix4 | aix4.[01] | aix4.[01].*)
+ if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+ echo ' yes '
+ echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then
+ :
+ else
+ can_build_shared=no
+ fi
+ ;;
+ esac
+ # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+ # soname into executable. Probably we can add versioning support to
+ # collect2, so additional links can be useful in future.
+ if test "$aix_use_runtimelinking" = yes; then
+ # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+ # instead of lib<name>.a to let people know that these are not
+ # typical AIX shared libraries.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ else
+ # We preserve .a as extension for shared libraries through AIX4.2
+ # and later when we are not doing run time linking.
+ library_names_spec='${libname}${release}.a $libname.a'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ fi
+ shlibpath_var=LIBPATH
+ fi
+ ;;
+
+amigaos*)
+ case $host_cpu in
+ powerpc)
+ # Since July 2007 AmigaOS4 officially supports .so libraries.
+ # When compiling the executable, add -use-dynld -Lsobjs: to the compileline.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ ;;
+ m68k)
+ library_names_spec='$libname.ixlibrary $libname.a'
+ # Create ${libname}_ixlibrary.a entries in /sys/libs.
+ finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$ECHO "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+ ;;
+ esac
+ ;;
+
+beos*)
+ library_names_spec='${libname}${shared_ext}'
+ dynamic_linker="$host_os ld.so"
+ shlibpath_var=LIBRARY_PATH
+ ;;
+
+bsdi[45]*)
+ version_type=linux
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+ sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+ # the default ld.so.conf also contains /usr/contrib/lib and
+ # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+ # libtool to hard-code these into programs
+ ;;
+
+cygwin* | mingw* | pw32* | cegcc*)
+ version_type=windows
+ shrext_cmds=".dll"
+ need_version=no
+ need_lib_prefix=no
+
+ case $GCC,$host_os in
+ yes,cygwin* | yes,mingw* | yes,pw32* | yes,cegcc*)
+ library_names_spec='$libname.dll.a'
+ # DLL is installed to $(libdir)/../bin by postinstall_cmds
+ postinstall_cmds='base_file=`basename \${file}`~
+ dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i; echo \$dlname'\''`~
+ dldir=$destdir/`dirname \$dlpath`~
+ test -d \$dldir || mkdir -p \$dldir~
+ $install_prog $dir/$dlname \$dldir/$dlname~
+ chmod a+x \$dldir/$dlname~
+ if test -n '\''$stripme'\'' && test -n '\''$striplib'\''; then
+ eval '\''$striplib \$dldir/$dlname'\'' || exit \$?;
+ fi'
+ postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+ dlpath=$dir/\$dldll~
+ $RM \$dlpath'
+ shlibpath_overrides_runpath=yes
+
+ case $host_os in
+ cygwin*)
+ # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+ soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+ ;;
+ mingw* | cegcc*)
+ # MinGW DLLs use traditional 'lib' prefix
+ soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec=`$CC -print-search-dirs | $GREP "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$sys_lib_search_path_spec" | $GREP ';[c-zC-Z]:/' >/dev/null; then
+ # It is most probably a Windows format PATH printed by
+ # mingw gcc, but we are running on Cygwin. Gcc prints its search
+ # path with ; separators, and with drive letters. We can handle the
+ # drive letters (cygwin fileutils understands them), so leave them,
+ # especially as we might pass files found there to a mingw objdump,
+ # which wouldn't understand a cygwinified path. Ahh.
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ ;;
+ pw32*)
+ # pw32 DLLs use 'pw' prefix rather than 'lib'
+ library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ ;;
+ esac
+ ;;
+
+ *)
+ library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib'
+ ;;
+ esac
+ dynamic_linker='Win32 ld.exe'
+ # FIXME: first we should search . and the directory the executable is in
+ shlibpath_var=PATH
+ ;;
+
+darwin* | rhapsody*)
+ dynamic_linker="$host_os dyld"
+ version_type=darwin
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+ soname_spec='${libname}${release}${major}$shared_ext'
+ shlibpath_overrides_runpath=yes
+ shlibpath_var=DYLD_LIBRARY_PATH
+ shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+
+ sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+ ;;
+
+dgux*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+freebsd1*)
+ dynamic_linker=no
+ ;;
+
+freebsd* | dragonfly*)
+ # DragonFly does not have aout. When/if they implement a new
+ # versioning mechanism, adjust this.
+ if test -x /usr/bin/objformat; then
+ objformat=`/usr/bin/objformat`
+ else
+ case $host_os in
+ freebsd[123]*) objformat=aout ;;
+ *) objformat=elf ;;
+ esac
+ fi
+ version_type=freebsd-$objformat
+ case $version_type in
+ freebsd-elf*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ need_version=no
+ need_lib_prefix=no
+ ;;
+ freebsd-*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+ need_version=yes
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_os in
+ freebsd2*)
+ shlibpath_overrides_runpath=yes
+ ;;
+ freebsd3.[01]* | freebsdelf3.[01]*)
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ freebsd3.[2-9]* | freebsdelf3.[2-9]* | \
+ freebsd4.[0-5] | freebsdelf4.[0-5] | freebsd4.1.1 | freebsdelf4.1.1)
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+ *) # from 4.6 on, and DragonFly
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ esac
+ ;;
+
+gnu*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ hardcode_into_libs=yes
+ ;;
+
+hpux9* | hpux10* | hpux11*)
+ # Give a soname corresponding to the major version so that dld.sl refuses to
+ # link against other versions.
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ case $host_cpu in
+ ia64*)
+ shrext_cmds='.so'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.so"
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ if test "X$HPUX_IA64_MODE" = X32; then
+ sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+ else
+ sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+ fi
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ hppa*64*)
+ shrext_cmds='.sl'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ *)
+ shrext_cmds='.sl'
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=SHLIB_PATH
+ shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+ esac
+ # HP-UX runs *really* slowly unless shared libraries are mode 555.
+ postinstall_cmds='chmod 555 $lib'
+ ;;
+
+interix[3-9]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $host_os in
+ nonstopux*) version_type=nonstopux ;;
+ *)
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ version_type=linux
+ else
+ version_type=irix
+ fi ;;
+ esac
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+ case $host_os in
+ irix5* | nonstopux*)
+ libsuff= shlibsuff=
+ ;;
+ *)
+ case $LD in # libtool.m4 will add one of these switches to LD
+ *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+ libsuff= shlibsuff= libmagic=32-bit;;
+ *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+ libsuff=32 shlibsuff=N32 libmagic=N32;;
+ *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+ libsuff=64 shlibsuff=64 libmagic=64-bit;;
+ *) libsuff= shlibsuff= libmagic=never-match;;
+ esac
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+ sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+ hardcode_into_libs=yes
+ ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+ dynamic_linker=no
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ # Some binutils ld are patched to set DT_RUNPATH
+ save_LDFLAGS=$LDFLAGS
+ save_libdir=$libdir
+ eval "libdir=/foo; wl=\"$lt_prog_compiler_wl_CXX\"; \
+ LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec_CXX\""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+ if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then :
+ shlibpath_overrides_runpath=yes
+fi
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+ LDFLAGS=$save_LDFLAGS
+ libdir=$save_libdir
+
+ # This implies no fast_install, which is unacceptable.
+ # Some rework will be needed to allow for fast_install
+ # before this can be enabled.
+ hardcode_into_libs=yes
+
+ # Append ld.so.conf contents to the search path
+ if test -f /etc/ld.so.conf; then
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ fi
+
+ # We used to test for /lib/ld.so.1 and disable shared libraries on
+ # powerpc, because MkLinux only supported shared libraries with the
+ # GNU dynamic linker. Since this was broken with cross compilers,
+ # most powerpc-linux boxes support dynamic linking these days and
+ # people can always --disable-shared, the test was removed, and we
+ # assume the GNU/Linux dynamic linker is in use.
+ dynamic_linker='GNU/Linux ld.so'
+ ;;
+
+netbsdelf*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='NetBSD ld.elf_so'
+ ;;
+
+netbsd*)
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ dynamic_linker='NetBSD (a.out) ld.so'
+ else
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='NetBSD ld.elf_so'
+ fi
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+
+newsos6)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ ;;
+
+*nto* | *qnx*)
+ version_type=qnx
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='ldqnx.so'
+ ;;
+
+openbsd*)
+ version_type=sunos
+ sys_lib_dlsearch_path_spec="/usr/lib"
+ need_lib_prefix=no
+ # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+ case $host_os in
+ openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+ *) need_version=no ;;
+ esac
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ case $host_os in
+ openbsd2.[89] | openbsd2.[89].*)
+ shlibpath_overrides_runpath=no
+ ;;
+ *)
+ shlibpath_overrides_runpath=yes
+ ;;
+ esac
+ else
+ shlibpath_overrides_runpath=yes
+ fi
+ ;;
+
+os2*)
+ libname_spec='$name'
+ shrext_cmds=".dll"
+ need_lib_prefix=no
+ library_names_spec='$libname${shared_ext} $libname.a'
+ dynamic_linker='OS/2 ld.exe'
+ shlibpath_var=LIBPATH
+ ;;
+
+osf3* | osf4* | osf5*)
+ version_type=osf
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+ sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+ ;;
+
+rdos*)
+ dynamic_linker=no
+ ;;
+
+solaris*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ # ldd complains unless libraries are executable
+ postinstall_cmds='chmod +x $lib'
+ ;;
+
+sunos4*)
+ version_type=sunos
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ if test "$with_gnu_ld" = yes; then
+ need_lib_prefix=no
+ fi
+ need_version=yes
+ ;;
+
+sysv4 | sysv4.3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_vendor in
+ sni)
+ shlibpath_overrides_runpath=no
+ need_lib_prefix=no
+ runpath_var=LD_RUN_PATH
+ ;;
+ siemens)
+ need_lib_prefix=no
+ ;;
+ motorola)
+ need_lib_prefix=no
+ need_version=no
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+ ;;
+ esac
+ ;;
+
+sysv4*MP*)
+ if test -d /usr/nec ;then
+ version_type=linux
+ library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+ soname_spec='$libname${shared_ext}.$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ fi
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ version_type=freebsd-elf
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ if test "$with_gnu_ld" = yes; then
+ sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+ else
+ sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+ case $host_os in
+ sco3.2v5*)
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+ ;;
+ esac
+ fi
+ sys_lib_dlsearch_path_spec='/usr/lib'
+ ;;
+
+tpf*)
+ # TPF is a cross-target only. Preferred cross-host = GNU/Linux.
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+uts4*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+*)
+ dynamic_linker=no
+ ;;
+esac
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $dynamic_linker" >&5
+$as_echo "$dynamic_linker" >&6; }
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+ variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+
+if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then
+ sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec"
+fi
+if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then
+ sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec"
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to hardcode library paths into programs" >&5
+$as_echo_n "checking how to hardcode library paths into programs... " >&6; }
+hardcode_action_CXX=
+if test -n "$hardcode_libdir_flag_spec_CXX" ||
+ test -n "$runpath_var_CXX" ||
+ test "X$hardcode_automatic_CXX" = "Xyes" ; then
+
+ # We can hardcode non-existent directories.
+ if test "$hardcode_direct_CXX" != no &&
+ # If the only mechanism to avoid hardcoding is shlibpath_var, we
+ # have to relink, otherwise we might link with an installed library
+ # when we should be linking with a yet-to-be-installed one
+ ## test "$_LT_TAGVAR(hardcode_shlibpath_var, CXX)" != no &&
+ test "$hardcode_minus_L_CXX" != no; then
+ # Linking always hardcodes the temporary library directory.
+ hardcode_action_CXX=relink
+ else
+ # We can link without hardcoding, and we can hardcode nonexisting dirs.
+ hardcode_action_CXX=immediate
+ fi
+else
+ # We cannot hardcode anything, or else we can only hardcode existing
+ # directories.
+ hardcode_action_CXX=unsupported
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $hardcode_action_CXX" >&5
+$as_echo "$hardcode_action_CXX" >&6; }
+
+if test "$hardcode_action_CXX" = relink ||
+ test "$inherit_rpath_CXX" = yes; then
+ # Fast installation is not supported
+ enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+ test "$enable_shared" = no; then
+ # Fast installation is not necessary
+ enable_fast_install=needless
+fi
+
+
+
+
+
+
+
+ fi # test -n "$compiler"
+
+ CC=$lt_save_CC
+ LDCXX=$LD
+ LD=$lt_save_LD
+ GCC=$lt_save_GCC
+ with_gnu_ld=$lt_save_with_gnu_ld
+ lt_cv_path_LDCXX=$lt_cv_path_LD
+ lt_cv_path_LD=$lt_save_path_LD
+ lt_cv_prog_gnu_ldcxx=$lt_cv_prog_gnu_ld
+ lt_cv_prog_gnu_ld=$lt_save_with_gnu_ld
+fi # test "$_lt_caught_CXX_error" != yes
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+
+ISODATE=`date +%Y-%m-%d`
+
+
+ARCH=`uname -m | sed s/i.86/i386/ | sed s/x86_64/amd64/`
+
+
+# Extract the first word of "dpkg", so it can be a program name with args.
+set dummy dpkg; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_path_DEB_BUILDER+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ case $DEB_BUILDER in
+ [\\/]* | ?:[\\/]*)
+ ac_cv_path_DEB_BUILDER="$DEB_BUILDER" # Let the user override the test with a path.
+ ;;
+ *)
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_path_DEB_BUILDER="$as_dir/$ac_word$ac_exec_ext"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+fi
+DEB_BUILDER=$ac_cv_path_DEB_BUILDER
+if test -n "$DEB_BUILDER"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DEB_BUILDER" >&5
+$as_echo "$DEB_BUILDER" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+for ac_prog in rpmbuild rpm
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_path_RPM_BUILDER+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ case $RPM_BUILDER in
+ [\\/]* | ?:[\\/]*)
+ ac_cv_path_RPM_BUILDER="$RPM_BUILDER" # Let the user override the test with a path.
+ ;;
+ *)
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_path_RPM_BUILDER="$as_dir/$ac_word$ac_exec_ext"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+fi
+RPM_BUILDER=$ac_cv_path_RPM_BUILDER
+if test -n "$RPM_BUILDER"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $RPM_BUILDER" >&5
+$as_echo "$RPM_BUILDER" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$RPM_BUILDER" && break
+done
+
+
+# Extract the first word of "texi2dvi", so it can be a program name with args.
+set dummy texi2dvi; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_TEXI2DVI+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$TEXI2DVI"; then
+ ac_cv_prog_TEXI2DVI="$TEXI2DVI" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_TEXI2DVI="texi2dvi"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+TEXI2DVI=$ac_cv_prog_TEXI2DVI
+if test -n "$TEXI2DVI"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $TEXI2DVI" >&5
+$as_echo "$TEXI2DVI" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+# Extract the first word of "pdftex", so it can be a program name with args.
+set dummy pdftex; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_PDFTEX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$PDFTEX"; then
+ ac_cv_prog_PDFTEX="$PDFTEX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_PDFTEX="pdftex"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+PDFTEX=$ac_cv_prog_PDFTEX
+if test -n "$PDFTEX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PDFTEX" >&5
+$as_echo "$PDFTEX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+# Extract the first word of "kpsewhich", so it can be a program name with args.
+set dummy kpsewhich; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_KPSEWHICH+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$KPSEWHICH"; then
+ ac_cv_prog_KPSEWHICH="$KPSEWHICH" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_KPSEWHICH="kpsewhich"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+KPSEWHICH=$ac_cv_prog_KPSEWHICH
+if test -n "$KPSEWHICH"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $KPSEWHICH" >&5
+$as_echo "$KPSEWHICH" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+
+BUILD_DOC=true
+if test "x$TEXI2DVI" != "xtexi2dvi" || test "x$PDFTEX" != "xpdftex"; then :
+ BUILD_DOC=false
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: The 'texi2dvi' or 'pdftex' program could not be found. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases." >&5
+$as_echo "$as_me: WARNING: The 'texi2dvi' or 'pdftex' program could not be found. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases." >&2;}
+fi
+
+if test "x$KPSEWHICH" != "xkpsewhich" || test "$(kpsewhich -show-path=fmt)" == "/nonesuch"; then :
+ BUILD_DOC=false
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: The 'texi2dvi' or 'pdftex' is missing a correct latex installation. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases." >&5
+$as_echo "$as_me: WARNING: The 'texi2dvi' or 'pdftex' is missing a correct latex installation. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases." >&2;}
+fi
+ if $BUILD_DOC; then
+ BUILD_DOC_TRUE=
+ BUILD_DOC_FALSE='#'
+else
+ BUILD_DOC_TRUE='#'
+ BUILD_DOC_FALSE=
+fi
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for an ANSI C-conforming const" >&5
+$as_echo_n "checking for an ANSI C-conforming const... " >&6; }
+if test "${ac_cv_c_const+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+/* FIXME: Include the comments suggested by Paul. */
+#ifndef __cplusplus
+ /* Ultrix mips cc rejects this. */
+ typedef int charset[2];
+ const charset cs;
+ /* SunOS 4.1.1 cc rejects this. */
+ char const *const *pcpcc;
+ char **ppc;
+ /* NEC SVR4.0.2 mips cc rejects this. */
+ struct point {int x, y;};
+ static struct point const zero = {0,0};
+ /* AIX XL C 1.02.0.0 rejects this.
+ It does not let you subtract one const X* pointer from another in
+ an arm of an if-expression whose if-part is not a constant
+ expression */
+ const char *g = "string";
+ pcpcc = &g + (g ? g-g : 0);
+ /* HPUX 7.0 cc rejects these. */
+ ++pcpcc;
+ ppc = (char**) pcpcc;
+ pcpcc = (char const *const *) ppc;
+ { /* SCO 3.2v4 cc rejects this. */
+ char *t;
+ char const *s = 0 ? (char *) 0 : (char const *) 0;
+
+ *t++ = 0;
+ if (s) return 0;
+ }
+ { /* Someone thinks the Sun supposedly-ANSI compiler will reject this. */
+ int x[] = {25, 17};
+ const int *foo = &x[0];
+ ++foo;
+ }
+ { /* Sun SC1.0 ANSI compiler rejects this -- but not the above. */
+ typedef const int *iptr;
+ iptr p = 0;
+ ++p;
+ }
+ { /* AIX XL C 1.02.0.0 rejects this saying
+ "k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */
+ struct s { int j; const int *ap[3]; };
+ struct s *b; b->j = 5;
+ }
+ { /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */
+ const int foo = 10;
+ if (!foo) return 0;
+ }
+ return !cs[0] && !zero.x;
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_c_const=yes
+else
+ ac_cv_c_const=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_const" >&5
+$as_echo "$ac_cv_c_const" >&6; }
+if test $ac_cv_c_const = no; then
+
+$as_echo "#define const /**/" >>confdefs.h
+
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for inline" >&5
+$as_echo_n "checking for inline... " >&6; }
+if test "${ac_cv_c_inline+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_c_inline=no
+for ac_kw in inline __inline__ __inline; do
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifndef __cplusplus
+typedef int foo_t;
+static $ac_kw foo_t static_foo () {return 0; }
+$ac_kw foo_t foo () {return 0; }
+#endif
+
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_c_inline=$ac_kw
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ test "$ac_cv_c_inline" != no && break
+done
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_inline" >&5
+$as_echo "$ac_cv_c_inline" >&6; }
+
+case $ac_cv_c_inline in
+ inline | yes) ;;
+ *)
+ case $ac_cv_c_inline in
+ no) ac_val=;;
+ *) ac_val=$ac_cv_c_inline;;
+ esac
+ cat >>confdefs.h <<_ACEOF
+#ifndef __cplusplus
+#define inline $ac_val
+#endif
+_ACEOF
+ ;;
+esac
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether sys/types.h defines makedev" >&5
+$as_echo_n "checking whether sys/types.h defines makedev... " >&6; }
+if test "${ac_cv_header_sys_types_h_makedev+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <sys/types.h>
+int
+main ()
+{
+return makedev(0, 0);
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_header_sys_types_h_makedev=yes
+else
+ ac_cv_header_sys_types_h_makedev=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_sys_types_h_makedev" >&5
+$as_echo "$ac_cv_header_sys_types_h_makedev" >&6; }
+
+if test $ac_cv_header_sys_types_h_makedev = no; then
+ac_fn_c_check_header_mongrel "$LINENO" "sys/mkdev.h" "ac_cv_header_sys_mkdev_h" "$ac_includes_default"
+if test "x$ac_cv_header_sys_mkdev_h" = x""yes; then :
+
+$as_echo "#define MAJOR_IN_MKDEV 1" >>confdefs.h
+
+fi
+
+
+
+ if test $ac_cv_header_sys_mkdev_h = no; then
+ ac_fn_c_check_header_mongrel "$LINENO" "sys/sysmacros.h" "ac_cv_header_sys_sysmacros_h" "$ac_includes_default"
+if test "x$ac_cv_header_sys_sysmacros_h" = x""yes; then :
+
+$as_echo "#define MAJOR_IN_SYSMACROS 1" >>confdefs.h
+
+fi
+
+
+ fi
+fi
+
+# The Ultrix 4.2 mips builtin alloca declared by alloca.h only works
+# for constant arguments. Useless!
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for working alloca.h" >&5
+$as_echo_n "checking for working alloca.h... " >&6; }
+if test "${ac_cv_working_alloca_h+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <alloca.h>
+int
+main ()
+{
+char *p = (char *) alloca (2 * sizeof (int));
+ if (p) return 0;
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_working_alloca_h=yes
+else
+ ac_cv_working_alloca_h=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_working_alloca_h" >&5
+$as_echo "$ac_cv_working_alloca_h" >&6; }
+if test $ac_cv_working_alloca_h = yes; then
+
+$as_echo "#define HAVE_ALLOCA_H 1" >>confdefs.h
+
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for alloca" >&5
+$as_echo_n "checking for alloca... " >&6; }
+if test "${ac_cv_func_alloca_works+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#ifdef __GNUC__
+# define alloca __builtin_alloca
+#else
+# ifdef _MSC_VER
+# include <malloc.h>
+# define alloca _alloca
+# else
+# ifdef HAVE_ALLOCA_H
+# include <alloca.h>
+# else
+# ifdef _AIX
+ #pragma alloca
+# else
+# ifndef alloca /* predefined by HP cc +Olibcalls */
+char *alloca ();
+# endif
+# endif
+# endif
+# endif
+#endif
+
+int
+main ()
+{
+char *p = (char *) alloca (1);
+ if (p) return 0;
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_func_alloca_works=yes
+else
+ ac_cv_func_alloca_works=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_alloca_works" >&5
+$as_echo "$ac_cv_func_alloca_works" >&6; }
+
+if test $ac_cv_func_alloca_works = yes; then
+
+$as_echo "#define HAVE_ALLOCA 1" >>confdefs.h
+
+else
+ # The SVR3 libPW and SVR4 libucb both contain incompatible functions
+# that cause trouble. Some versions do not even contain alloca or
+# contain a buggy version. If you still want to use their alloca,
+# use ar to extract alloca.o from them instead of compiling alloca.c.
+
+ALLOCA=\${LIBOBJDIR}alloca.$ac_objext
+
+$as_echo "#define C_ALLOCA 1" >>confdefs.h
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether \`alloca.c' needs Cray hooks" >&5
+$as_echo_n "checking whether \`alloca.c' needs Cray hooks... " >&6; }
+if test "${ac_cv_os_cray+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#if defined CRAY && ! defined CRAY2
+webecray
+#else
+wenotbecray
+#endif
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "webecray" >/dev/null 2>&1; then :
+ ac_cv_os_cray=yes
+else
+ ac_cv_os_cray=no
+fi
+rm -f conftest*
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_os_cray" >&5
+$as_echo "$ac_cv_os_cray" >&6; }
+if test $ac_cv_os_cray = yes; then
+ for ac_func in _getb67 GETB67 getb67; do
+ as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
+if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
+
+cat >>confdefs.h <<_ACEOF
+#define CRAY_STACKSEG_END $ac_func
+_ACEOF
+
+ break
+fi
+
+ done
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking stack direction for C alloca" >&5
+$as_echo_n "checking stack direction for C alloca... " >&6; }
+if test "${ac_cv_c_stack_direction+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then :
+ ac_cv_c_stack_direction=0
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$ac_includes_default
+int
+find_stack_direction ()
+{
+ static char *addr = 0;
+ auto char dummy;
+ if (addr == 0)
+ {
+ addr = &dummy;
+ return find_stack_direction ();
+ }
+ else
+ return (&dummy > addr) ? 1 : -1;
+}
+
+int
+main ()
+{
+ return find_stack_direction () < 0;
+}
+_ACEOF
+if ac_fn_c_try_run "$LINENO"; then :
+ ac_cv_c_stack_direction=1
+else
+ ac_cv_c_stack_direction=-1
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
+ conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_stack_direction" >&5
+$as_echo "$ac_cv_c_stack_direction" >&6; }
+cat >>confdefs.h <<_ACEOF
+#define STACK_DIRECTION $ac_cv_c_stack_direction
+_ACEOF
+
+
+fi
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether struct tm is in sys/time.h or time.h" >&5
+$as_echo_n "checking whether struct tm is in sys/time.h or time.h... " >&6; }
+if test "${ac_cv_struct_tm+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <sys/types.h>
+#include <time.h>
+
+int
+main ()
+{
+struct tm tm;
+ int *p = &tm.tm_sec;
+ return !p;
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_struct_tm=time.h
+else
+ ac_cv_struct_tm=sys/time.h
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_struct_tm" >&5
+$as_echo "$ac_cv_struct_tm" >&6; }
+if test $ac_cv_struct_tm = sys/time.h; then
+
+$as_echo "#define TM_IN_SYS_TIME 1" >>confdefs.h
+
+fi
+
+ac_fn_c_check_member "$LINENO" "struct stat" "st_blocks" "ac_cv_member_struct_stat_st_blocks" "$ac_includes_default"
+if test "x$ac_cv_member_struct_stat_st_blocks" = x""yes; then :
+
+cat >>confdefs.h <<_ACEOF
+#define HAVE_STRUCT_STAT_ST_BLOCKS 1
+_ACEOF
+
+
+$as_echo "#define HAVE_ST_BLOCKS 1" >>confdefs.h
+
+else
+ case " $LIBOBJS " in
+ *" fileblocks.$ac_objext "* ) ;;
+ *) LIBOBJS="$LIBOBJS fileblocks.$ac_objext"
+ ;;
+esac
+
+fi
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ln -s works" >&5
+$as_echo_n "checking whether ln -s works... " >&6; }
+LN_S=$as_ln_s
+if test "$LN_S" = "ln -s"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no, using $LN_S" >&5
+$as_echo "no, using $LN_S" >&6; }
+fi
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5
+$as_echo_n "checking for ANSI C header files... " >&6; }
+if test "${ac_cv_header_stdc+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdlib.h>
+#include <stdarg.h>
+#include <string.h>
+#include <float.h>
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_header_stdc=yes
+else
+ ac_cv_header_stdc=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+
+if test $ac_cv_header_stdc = yes; then
+ # SunOS 4.x string.h does not declare mem*, contrary to ANSI.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <string.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "memchr" >/dev/null 2>&1; then :
+
+else
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdlib.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "free" >/dev/null 2>&1; then :
+
+else
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi.
+ if test "$cross_compiling" = yes; then :
+ :
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <ctype.h>
+#include <stdlib.h>
+#if ((' ' & 0x0FF) == 0x020)
+# define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
+# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
+#else
+# define ISLOWER(c) \
+ (('a' <= (c) && (c) <= 'i') \
+ || ('j' <= (c) && (c) <= 'r') \
+ || ('s' <= (c) && (c) <= 'z'))
+# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c))
+#endif
+
+#define XOR(e, f) (((e) && !(f)) || (!(e) && (f)))
+int
+main ()
+{
+ int i;
+ for (i = 0; i < 256; i++)
+ if (XOR (islower (i), ISLOWER (i))
+ || toupper (i) != TOUPPER (i))
+ return 2;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_run "$LINENO"; then :
+
+else
+ ac_cv_header_stdc=no
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
+ conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+
+fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5
+$as_echo "$ac_cv_header_stdc" >&6; }
+if test $ac_cv_header_stdc = yes; then
+
+$as_echo "#define STDC_HEADERS 1" >>confdefs.h
+
+fi
+
+for ac_header in \
+ unistd.h sys/param.h sys/time.h time.h sys/sysmacros.h \
+ string.h strings.h memory.h fcntl.h alloca.h \
+
+do :
+ as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+ac_fn_c_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default"
+if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+
+CXXFLAGS="-O6 -Wall --pedantic --ansi"
+
+hacked_prefix="${HACKED_PREFIX:-$prefix}"
+if test "x$hacked_prefix" == "xNONE"; then
+ hacked_prefix=$ac_default_prefix
+fi
+
+
+
+postrm_script=$srcdir/postrm
+
+postinst_script=$srcdir/postinst
+
+ac_config_files="$ac_config_files postinst prerm libProgressBar.lsm libProgressBar.spec control libProgressBar.pc Makefile libProgressBar/Makefile doc/Makefile doc/libProgressBar.3"
+
+cat >confcache <<\_ACEOF
+# This file is a shell script that caches the results of configure
+# tests run on this system so they can be shared between configure
+# scripts and configure runs, see configure's option --config-cache.
+# It is not useful on other systems. If it contains results you don't
+# want to keep, you may remove or edit it.
+#
+# config.status only pays attention to the cache file if you give it
+# the --recheck option to rerun configure.
+#
+# `ac_cv_env_foo' variables (set or unset) will be overridden when
+# loading this file, other *unset* `ac_cv_foo' will be assigned the
+# following values.
+
+_ACEOF
+
+# The following way of writing the cache mishandles newlines in values,
+# but we know of no workaround that is simple, portable, and efficient.
+# So, we kill variables containing newlines.
+# Ultrix sh set writes to stderr and can't be redirected directly,
+# and sets the high bit in the cache file unless we assign to the vars.
+(
+ for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) { eval $ac_var=; unset $ac_var;} ;;
+ esac ;;
+ esac
+ done
+
+ (set) 2>&1 |
+ case $as_nl`(ac_space=' '; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ # `set' does not quote correctly, so add quotes: double-quote
+ # substitution turns \\\\ into \\, and sed turns \\ into \.
+ sed -n \
+ "s/'/'\\\\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
+ ;; #(
+ *)
+ # `set' quotes correctly as required by POSIX, so do not add quotes.
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+) |
+ sed '
+ /^ac_cv_env_/b end
+ t clear
+ :clear
+ s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/
+ t end
+ s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/
+ :end' >>confcache
+if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
+ if test -w "$cache_file"; then
+ test "x$cache_file" != "x/dev/null" &&
+ { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
+$as_echo "$as_me: updating cache $cache_file" >&6;}
+ cat confcache >$cache_file
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
+$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
+ fi
+fi
+rm -f confcache
+
+test "x$prefix" = xNONE && prefix=$ac_default_prefix
+# Let make expand exec_prefix.
+test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
+
+DEFS=-DHAVE_CONFIG_H
+
+ac_libobjs=
+ac_ltlibobjs=
+U=
+for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
+ # 1. Remove the extension, and $U if already installed.
+ ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
+ ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
+ # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
+ # will be set to the directory where LIBOBJS objects are built.
+ as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext"
+ as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo'
+done
+LIBOBJS=$ac_libobjs
+
+LTLIBOBJS=$ac_ltlibobjs
+
+
+ if test -n "$EXEEXT"; then
+ am__EXEEXT_TRUE=
+ am__EXEEXT_FALSE='#'
+else
+ am__EXEEXT_TRUE='#'
+ am__EXEEXT_FALSE=
+fi
+
+if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
+ as_fn_error $? "conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
+ as_fn_error $? "conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
+ as_fn_error $? "conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
+ as_fn_error $? "conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
+ as_fn_error $? "conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${BUILD_DOC_TRUE}" && test -z "${BUILD_DOC_FALSE}"; then
+ as_fn_error $? "conditional \"BUILD_DOC\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+
+: ${CONFIG_STATUS=./config.status}
+ac_write_fail=0
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files $CONFIG_STATUS"
+{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5
+$as_echo "$as_me: creating $CONFIG_STATUS" >&6;}
+as_write_fail=0
+cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
+#! $SHELL
+# Generated by $as_me.
+# Run this file to recreate the current configuration.
+# Compiler output produced by configure, useful for debugging
+# configure, is in config.log if it exists.
+
+debug=false
+ac_cs_recheck=false
+ac_cs_silent=false
+
+SHELL=\${CONFIG_SHELL-$SHELL}
+export SHELL
+_ASEOF
+cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in #(
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+case $0 in #((
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
+# ----------------------------------------
+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+# script with STATUS, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ $as_echo "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} # as_fn_error
+
+
+# as_fn_set_status STATUS
+# -----------------------
+# Set $? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} # as_fn_set_status
+
+# as_fn_exit STATUS
+# -----------------
+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} # as_fn_exit
+
+# as_fn_unset VAR
+# ---------------
+# Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+# as_fn_append VAR VALUE
+# ----------------------
+# Append the text in VALUE to the end of the definition contained in VAR. Take
+# advantage of any shell optimizations that allow amortized linear growth over
+# repeated appends, instead of the typical quadratic growth present in naive
+# implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+# as_fn_arith ARG...
+# ------------------
+# Perform arithmetic evaluation on the ARGs, and store the result in the
+# global $as_val. Take advantage of shells that can avoid forks. The arguments
+# must be portable across $(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in #(((((
+-n*)
+ case `echo 'xy\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -p'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -p'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -p'
+ fi
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+
+# as_fn_mkdir_p
+# -------------
+# Create "$as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
+
+
+} # as_fn_mkdir_p
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p='mkdir -p "$as_dir"'
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+if test -x / >/dev/null 2>&1; then
+ as_test_x='test -x'
+else
+ if ls -dL / >/dev/null 2>&1; then
+ as_ls_L_option=L
+ else
+ as_ls_L_option=
+ fi
+ as_test_x='
+ eval sh -c '\''
+ if test -d "$1"; then
+ test -d "$1/.";
+ else
+ case $1 in #(
+ -*)set "./$1";;
+ esac;
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
+ ???[sx]*):;;*)false;;esac;fi
+ '\'' sh
+ '
+fi
+as_executable_p=$as_test_x
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+exec 6>&1
+## ----------------------------------- ##
+## Main body of $CONFIG_STATUS script. ##
+## ----------------------------------- ##
+_ASEOF
+test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# Save the log message, to keep $0 and so on meaningful, and to
+# report actual input values of CONFIG_FILES etc. instead of their
+# values after options handling.
+ac_log="
+This file was extended by Library for manage progress bars $as_me 1.2.0, which was
+generated by GNU Autoconf 2.67. Invocation command line was
+
+ CONFIG_FILES = $CONFIG_FILES
+ CONFIG_HEADERS = $CONFIG_HEADERS
+ CONFIG_LINKS = $CONFIG_LINKS
+ CONFIG_COMMANDS = $CONFIG_COMMANDS
+ $ $0 $@
+
+on `(hostname || uname -n) 2>/dev/null | sed 1q`
+"
+
+_ACEOF
+
+case $ac_config_files in *"
+"*) set x $ac_config_files; shift; ac_config_files=$*;;
+esac
+
+case $ac_config_headers in *"
+"*) set x $ac_config_headers; shift; ac_config_headers=$*;;
+esac
+
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+# Files that config.status was made for.
+config_files="$ac_config_files"
+config_headers="$ac_config_headers"
+config_commands="$ac_config_commands"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+ac_cs_usage="\
+\`$as_me' instantiates files and other configuration actions
+from templates according to the current configuration. Unless the files
+and actions are specified as TAGs, all are instantiated by default.
+
+Usage: $0 [OPTION]... [TAG]...
+
+ -h, --help print this help, then exit
+ -V, --version print version number and configuration settings, then exit
+ --config print configuration, then exit
+ -q, --quiet, --silent
+ do not print progress messages
+ -d, --debug don't remove temporary files
+ --recheck update $as_me by reconfiguring in the same conditions
+ --file=FILE[:TEMPLATE]
+ instantiate the configuration file FILE
+ --header=FILE[:TEMPLATE]
+ instantiate the configuration header FILE
+
+Configuration files:
+$config_files
+
+Configuration headers:
+$config_headers
+
+Configuration commands:
+$config_commands
+
+Report bugs to <alban.mancheron at inria.fr>."
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
+ac_cs_version="\\
+Library for manage progress bars config.status 1.2.0
+configured by $0, generated by GNU Autoconf 2.67,
+ with options \\"\$ac_cs_config\\"
+
+Copyright (C) 2010 Free Software Foundation, Inc.
+This config.status script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it."
+
+ac_pwd='$ac_pwd'
+srcdir='$srcdir'
+INSTALL='$INSTALL'
+MKDIR_P='$MKDIR_P'
+AWK='$AWK'
+test -n "\$AWK" || AWK=awk
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# The default lists apply if the user does not specify any file.
+ac_need_defaults=:
+while test $# != 0
+do
+ case $1 in
+ --*=?*)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
+ ac_shift=:
+ ;;
+ --*=)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=
+ ac_shift=:
+ ;;
+ *)
+ ac_option=$1
+ ac_optarg=$2
+ ac_shift=shift
+ ;;
+ esac
+
+ case $ac_option in
+ # Handling of the options.
+ -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
+ ac_cs_recheck=: ;;
+ --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
+ $as_echo "$ac_cs_version"; exit ;;
+ --config | --confi | --conf | --con | --co | --c )
+ $as_echo "$ac_cs_config"; exit ;;
+ --debug | --debu | --deb | --de | --d | -d )
+ debug=: ;;
+ --file | --fil | --fi | --f )
+ $ac_shift
+ case $ac_optarg in
+ *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ '') as_fn_error $? "missing file argument" ;;
+ esac
+ as_fn_append CONFIG_FILES " '$ac_optarg'"
+ ac_need_defaults=false;;
+ --header | --heade | --head | --hea )
+ $ac_shift
+ case $ac_optarg in
+ *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ as_fn_append CONFIG_HEADERS " '$ac_optarg'"
+ ac_need_defaults=false;;
+ --he | --h)
+ # Conflict between --help and --header
+ as_fn_error $? "ambiguous option: \`$1'
+Try \`$0 --help' for more information.";;
+ --help | --hel | -h )
+ $as_echo "$ac_cs_usage"; exit ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil | --si | --s)
+ ac_cs_silent=: ;;
+
+ # This is an error.
+ -*) as_fn_error $? "unrecognized option: \`$1'
+Try \`$0 --help' for more information." ;;
+
+ *) as_fn_append ac_config_targets " $1"
+ ac_need_defaults=false ;;
+
+ esac
+ shift
+done
+
+ac_configure_extra_args=
+
+if $ac_cs_silent; then
+ exec 6>/dev/null
+ ac_configure_extra_args="$ac_configure_extra_args --silent"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+if \$ac_cs_recheck; then
+ set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
+ shift
+ \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6
+ CONFIG_SHELL='$SHELL'
+ export CONFIG_SHELL
+ exec "\$@"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+exec 5>>config.log
+{
+ echo
+ sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX
+## Running $as_me. ##
+_ASBOX
+ $as_echo "$ac_log"
+} >&5
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+#
+# INIT-COMMANDS
+#
+AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"
+
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+sed_quote_subst='$sed_quote_subst'
+double_quote_subst='$double_quote_subst'
+delay_variable_subst='$delay_variable_subst'
+macro_version='`$ECHO "X$macro_version" | $Xsed -e "$delay_single_quote_subst"`'
+macro_revision='`$ECHO "X$macro_revision" | $Xsed -e "$delay_single_quote_subst"`'
+enable_shared='`$ECHO "X$enable_shared" | $Xsed -e "$delay_single_quote_subst"`'
+enable_static='`$ECHO "X$enable_static" | $Xsed -e "$delay_single_quote_subst"`'
+pic_mode='`$ECHO "X$pic_mode" | $Xsed -e "$delay_single_quote_subst"`'
+enable_fast_install='`$ECHO "X$enable_fast_install" | $Xsed -e "$delay_single_quote_subst"`'
+host_alias='`$ECHO "X$host_alias" | $Xsed -e "$delay_single_quote_subst"`'
+host='`$ECHO "X$host" | $Xsed -e "$delay_single_quote_subst"`'
+host_os='`$ECHO "X$host_os" | $Xsed -e "$delay_single_quote_subst"`'
+build_alias='`$ECHO "X$build_alias" | $Xsed -e "$delay_single_quote_subst"`'
+build='`$ECHO "X$build" | $Xsed -e "$delay_single_quote_subst"`'
+build_os='`$ECHO "X$build_os" | $Xsed -e "$delay_single_quote_subst"`'
+SED='`$ECHO "X$SED" | $Xsed -e "$delay_single_quote_subst"`'
+Xsed='`$ECHO "X$Xsed" | $Xsed -e "$delay_single_quote_subst"`'
+GREP='`$ECHO "X$GREP" | $Xsed -e "$delay_single_quote_subst"`'
+EGREP='`$ECHO "X$EGREP" | $Xsed -e "$delay_single_quote_subst"`'
+FGREP='`$ECHO "X$FGREP" | $Xsed -e "$delay_single_quote_subst"`'
+LD='`$ECHO "X$LD" | $Xsed -e "$delay_single_quote_subst"`'
+NM='`$ECHO "X$NM" | $Xsed -e "$delay_single_quote_subst"`'
+LN_S='`$ECHO "X$LN_S" | $Xsed -e "$delay_single_quote_subst"`'
+max_cmd_len='`$ECHO "X$max_cmd_len" | $Xsed -e "$delay_single_quote_subst"`'
+ac_objext='`$ECHO "X$ac_objext" | $Xsed -e "$delay_single_quote_subst"`'
+exeext='`$ECHO "X$exeext" | $Xsed -e "$delay_single_quote_subst"`'
+lt_unset='`$ECHO "X$lt_unset" | $Xsed -e "$delay_single_quote_subst"`'
+lt_SP2NL='`$ECHO "X$lt_SP2NL" | $Xsed -e "$delay_single_quote_subst"`'
+lt_NL2SP='`$ECHO "X$lt_NL2SP" | $Xsed -e "$delay_single_quote_subst"`'
+reload_flag='`$ECHO "X$reload_flag" | $Xsed -e "$delay_single_quote_subst"`'
+reload_cmds='`$ECHO "X$reload_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+OBJDUMP='`$ECHO "X$OBJDUMP" | $Xsed -e "$delay_single_quote_subst"`'
+deplibs_check_method='`$ECHO "X$deplibs_check_method" | $Xsed -e "$delay_single_quote_subst"`'
+file_magic_cmd='`$ECHO "X$file_magic_cmd" | $Xsed -e "$delay_single_quote_subst"`'
+AR='`$ECHO "X$AR" | $Xsed -e "$delay_single_quote_subst"`'
+AR_FLAGS='`$ECHO "X$AR_FLAGS" | $Xsed -e "$delay_single_quote_subst"`'
+STRIP='`$ECHO "X$STRIP" | $Xsed -e "$delay_single_quote_subst"`'
+RANLIB='`$ECHO "X$RANLIB" | $Xsed -e "$delay_single_quote_subst"`'
+old_postinstall_cmds='`$ECHO "X$old_postinstall_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+old_postuninstall_cmds='`$ECHO "X$old_postuninstall_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_cmds='`$ECHO "X$old_archive_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+CC='`$ECHO "X$CC" | $Xsed -e "$delay_single_quote_subst"`'
+CFLAGS='`$ECHO "X$CFLAGS" | $Xsed -e "$delay_single_quote_subst"`'
+compiler='`$ECHO "X$compiler" | $Xsed -e "$delay_single_quote_subst"`'
+GCC='`$ECHO "X$GCC" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_pipe='`$ECHO "X$lt_cv_sys_global_symbol_pipe" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_to_cdecl='`$ECHO "X$lt_cv_sys_global_symbol_to_cdecl" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_to_c_name_address='`$ECHO "X$lt_cv_sys_global_symbol_to_c_name_address" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='`$ECHO "X$lt_cv_sys_global_symbol_to_c_name_address_lib_prefix" | $Xsed -e "$delay_single_quote_subst"`'
+objdir='`$ECHO "X$objdir" | $Xsed -e "$delay_single_quote_subst"`'
+SHELL='`$ECHO "X$SHELL" | $Xsed -e "$delay_single_quote_subst"`'
+ECHO='`$ECHO "X$ECHO" | $Xsed -e "$delay_single_quote_subst"`'
+MAGIC_CMD='`$ECHO "X$MAGIC_CMD" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_no_builtin_flag='`$ECHO "X$lt_prog_compiler_no_builtin_flag" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_wl='`$ECHO "X$lt_prog_compiler_wl" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_pic='`$ECHO "X$lt_prog_compiler_pic" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_static='`$ECHO "X$lt_prog_compiler_static" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_prog_compiler_c_o='`$ECHO "X$lt_cv_prog_compiler_c_o" | $Xsed -e "$delay_single_quote_subst"`'
+need_locks='`$ECHO "X$need_locks" | $Xsed -e "$delay_single_quote_subst"`'
+DSYMUTIL='`$ECHO "X$DSYMUTIL" | $Xsed -e "$delay_single_quote_subst"`'
+NMEDIT='`$ECHO "X$NMEDIT" | $Xsed -e "$delay_single_quote_subst"`'
+LIPO='`$ECHO "X$LIPO" | $Xsed -e "$delay_single_quote_subst"`'
+OTOOL='`$ECHO "X$OTOOL" | $Xsed -e "$delay_single_quote_subst"`'
+OTOOL64='`$ECHO "X$OTOOL64" | $Xsed -e "$delay_single_quote_subst"`'
+libext='`$ECHO "X$libext" | $Xsed -e "$delay_single_quote_subst"`'
+shrext_cmds='`$ECHO "X$shrext_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+extract_expsyms_cmds='`$ECHO "X$extract_expsyms_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+archive_cmds_need_lc='`$ECHO "X$archive_cmds_need_lc" | $Xsed -e "$delay_single_quote_subst"`'
+enable_shared_with_static_runtimes='`$ECHO "X$enable_shared_with_static_runtimes" | $Xsed -e "$delay_single_quote_subst"`'
+export_dynamic_flag_spec='`$ECHO "X$export_dynamic_flag_spec" | $Xsed -e "$delay_single_quote_subst"`'
+whole_archive_flag_spec='`$ECHO "X$whole_archive_flag_spec" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_needs_object='`$ECHO "X$compiler_needs_object" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_from_new_cmds='`$ECHO "X$old_archive_from_new_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_from_expsyms_cmds='`$ECHO "X$old_archive_from_expsyms_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+archive_cmds='`$ECHO "X$archive_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+archive_expsym_cmds='`$ECHO "X$archive_expsym_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+module_cmds='`$ECHO "X$module_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+module_expsym_cmds='`$ECHO "X$module_expsym_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+with_gnu_ld='`$ECHO "X$with_gnu_ld" | $Xsed -e "$delay_single_quote_subst"`'
+allow_undefined_flag='`$ECHO "X$allow_undefined_flag" | $Xsed -e "$delay_single_quote_subst"`'
+no_undefined_flag='`$ECHO "X$no_undefined_flag" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_flag_spec='`$ECHO "X$hardcode_libdir_flag_spec" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_flag_spec_ld='`$ECHO "X$hardcode_libdir_flag_spec_ld" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_separator='`$ECHO "X$hardcode_libdir_separator" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_direct='`$ECHO "X$hardcode_direct" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_direct_absolute='`$ECHO "X$hardcode_direct_absolute" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_minus_L='`$ECHO "X$hardcode_minus_L" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_shlibpath_var='`$ECHO "X$hardcode_shlibpath_var" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_automatic='`$ECHO "X$hardcode_automatic" | $Xsed -e "$delay_single_quote_subst"`'
+inherit_rpath='`$ECHO "X$inherit_rpath" | $Xsed -e "$delay_single_quote_subst"`'
+link_all_deplibs='`$ECHO "X$link_all_deplibs" | $Xsed -e "$delay_single_quote_subst"`'
+fix_srcfile_path='`$ECHO "X$fix_srcfile_path" | $Xsed -e "$delay_single_quote_subst"`'
+always_export_symbols='`$ECHO "X$always_export_symbols" | $Xsed -e "$delay_single_quote_subst"`'
+export_symbols_cmds='`$ECHO "X$export_symbols_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+exclude_expsyms='`$ECHO "X$exclude_expsyms" | $Xsed -e "$delay_single_quote_subst"`'
+include_expsyms='`$ECHO "X$include_expsyms" | $Xsed -e "$delay_single_quote_subst"`'
+prelink_cmds='`$ECHO "X$prelink_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+file_list_spec='`$ECHO "X$file_list_spec" | $Xsed -e "$delay_single_quote_subst"`'
+variables_saved_for_relink='`$ECHO "X$variables_saved_for_relink" | $Xsed -e "$delay_single_quote_subst"`'
+need_lib_prefix='`$ECHO "X$need_lib_prefix" | $Xsed -e "$delay_single_quote_subst"`'
+need_version='`$ECHO "X$need_version" | $Xsed -e "$delay_single_quote_subst"`'
+version_type='`$ECHO "X$version_type" | $Xsed -e "$delay_single_quote_subst"`'
+runpath_var='`$ECHO "X$runpath_var" | $Xsed -e "$delay_single_quote_subst"`'
+shlibpath_var='`$ECHO "X$shlibpath_var" | $Xsed -e "$delay_single_quote_subst"`'
+shlibpath_overrides_runpath='`$ECHO "X$shlibpath_overrides_runpath" | $Xsed -e "$delay_single_quote_subst"`'
+libname_spec='`$ECHO "X$libname_spec" | $Xsed -e "$delay_single_quote_subst"`'
+library_names_spec='`$ECHO "X$library_names_spec" | $Xsed -e "$delay_single_quote_subst"`'
+soname_spec='`$ECHO "X$soname_spec" | $Xsed -e "$delay_single_quote_subst"`'
+postinstall_cmds='`$ECHO "X$postinstall_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+postuninstall_cmds='`$ECHO "X$postuninstall_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+finish_cmds='`$ECHO "X$finish_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+finish_eval='`$ECHO "X$finish_eval" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_into_libs='`$ECHO "X$hardcode_into_libs" | $Xsed -e "$delay_single_quote_subst"`'
+sys_lib_search_path_spec='`$ECHO "X$sys_lib_search_path_spec" | $Xsed -e "$delay_single_quote_subst"`'
+sys_lib_dlsearch_path_spec='`$ECHO "X$sys_lib_dlsearch_path_spec" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_action='`$ECHO "X$hardcode_action" | $Xsed -e "$delay_single_quote_subst"`'
+enable_dlopen='`$ECHO "X$enable_dlopen" | $Xsed -e "$delay_single_quote_subst"`'
+enable_dlopen_self='`$ECHO "X$enable_dlopen_self" | $Xsed -e "$delay_single_quote_subst"`'
+enable_dlopen_self_static='`$ECHO "X$enable_dlopen_self_static" | $Xsed -e "$delay_single_quote_subst"`'
+old_striplib='`$ECHO "X$old_striplib" | $Xsed -e "$delay_single_quote_subst"`'
+striplib='`$ECHO "X$striplib" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_lib_search_dirs='`$ECHO "X$compiler_lib_search_dirs" | $Xsed -e "$delay_single_quote_subst"`'
+predep_objects='`$ECHO "X$predep_objects" | $Xsed -e "$delay_single_quote_subst"`'
+postdep_objects='`$ECHO "X$postdep_objects" | $Xsed -e "$delay_single_quote_subst"`'
+predeps='`$ECHO "X$predeps" | $Xsed -e "$delay_single_quote_subst"`'
+postdeps='`$ECHO "X$postdeps" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_lib_search_path='`$ECHO "X$compiler_lib_search_path" | $Xsed -e "$delay_single_quote_subst"`'
+LD_CXX='`$ECHO "X$LD_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_cmds_CXX='`$ECHO "X$old_archive_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_CXX='`$ECHO "X$compiler_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+GCC_CXX='`$ECHO "X$GCC_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_no_builtin_flag_CXX='`$ECHO "X$lt_prog_compiler_no_builtin_flag_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_wl_CXX='`$ECHO "X$lt_prog_compiler_wl_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_pic_CXX='`$ECHO "X$lt_prog_compiler_pic_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_static_CXX='`$ECHO "X$lt_prog_compiler_static_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_prog_compiler_c_o_CXX='`$ECHO "X$lt_cv_prog_compiler_c_o_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+archive_cmds_need_lc_CXX='`$ECHO "X$archive_cmds_need_lc_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+enable_shared_with_static_runtimes_CXX='`$ECHO "X$enable_shared_with_static_runtimes_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+export_dynamic_flag_spec_CXX='`$ECHO "X$export_dynamic_flag_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+whole_archive_flag_spec_CXX='`$ECHO "X$whole_archive_flag_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_needs_object_CXX='`$ECHO "X$compiler_needs_object_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_from_new_cmds_CXX='`$ECHO "X$old_archive_from_new_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_from_expsyms_cmds_CXX='`$ECHO "X$old_archive_from_expsyms_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+archive_cmds_CXX='`$ECHO "X$archive_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+archive_expsym_cmds_CXX='`$ECHO "X$archive_expsym_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+module_cmds_CXX='`$ECHO "X$module_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+module_expsym_cmds_CXX='`$ECHO "X$module_expsym_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+with_gnu_ld_CXX='`$ECHO "X$with_gnu_ld_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+allow_undefined_flag_CXX='`$ECHO "X$allow_undefined_flag_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+no_undefined_flag_CXX='`$ECHO "X$no_undefined_flag_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_flag_spec_CXX='`$ECHO "X$hardcode_libdir_flag_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_flag_spec_ld_CXX='`$ECHO "X$hardcode_libdir_flag_spec_ld_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_separator_CXX='`$ECHO "X$hardcode_libdir_separator_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_direct_CXX='`$ECHO "X$hardcode_direct_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_direct_absolute_CXX='`$ECHO "X$hardcode_direct_absolute_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_minus_L_CXX='`$ECHO "X$hardcode_minus_L_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_shlibpath_var_CXX='`$ECHO "X$hardcode_shlibpath_var_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_automatic_CXX='`$ECHO "X$hardcode_automatic_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+inherit_rpath_CXX='`$ECHO "X$inherit_rpath_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+link_all_deplibs_CXX='`$ECHO "X$link_all_deplibs_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+fix_srcfile_path_CXX='`$ECHO "X$fix_srcfile_path_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+always_export_symbols_CXX='`$ECHO "X$always_export_symbols_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+export_symbols_cmds_CXX='`$ECHO "X$export_symbols_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+exclude_expsyms_CXX='`$ECHO "X$exclude_expsyms_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+include_expsyms_CXX='`$ECHO "X$include_expsyms_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+prelink_cmds_CXX='`$ECHO "X$prelink_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+file_list_spec_CXX='`$ECHO "X$file_list_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_action_CXX='`$ECHO "X$hardcode_action_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_lib_search_dirs_CXX='`$ECHO "X$compiler_lib_search_dirs_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+predep_objects_CXX='`$ECHO "X$predep_objects_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+postdep_objects_CXX='`$ECHO "X$postdep_objects_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+predeps_CXX='`$ECHO "X$predeps_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+postdeps_CXX='`$ECHO "X$postdeps_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_lib_search_path_CXX='`$ECHO "X$compiler_lib_search_path_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+
+LTCC='$LTCC'
+LTCFLAGS='$LTCFLAGS'
+compiler='$compiler_DEFAULT'
+
+# Quote evaled strings.
+for var in SED \
+GREP \
+EGREP \
+FGREP \
+LD \
+NM \
+LN_S \
+lt_SP2NL \
+lt_NL2SP \
+reload_flag \
+OBJDUMP \
+deplibs_check_method \
+file_magic_cmd \
+AR \
+AR_FLAGS \
+STRIP \
+RANLIB \
+CC \
+CFLAGS \
+compiler \
+lt_cv_sys_global_symbol_pipe \
+lt_cv_sys_global_symbol_to_cdecl \
+lt_cv_sys_global_symbol_to_c_name_address \
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix \
+SHELL \
+ECHO \
+lt_prog_compiler_no_builtin_flag \
+lt_prog_compiler_wl \
+lt_prog_compiler_pic \
+lt_prog_compiler_static \
+lt_cv_prog_compiler_c_o \
+need_locks \
+DSYMUTIL \
+NMEDIT \
+LIPO \
+OTOOL \
+OTOOL64 \
+shrext_cmds \
+export_dynamic_flag_spec \
+whole_archive_flag_spec \
+compiler_needs_object \
+with_gnu_ld \
+allow_undefined_flag \
+no_undefined_flag \
+hardcode_libdir_flag_spec \
+hardcode_libdir_flag_spec_ld \
+hardcode_libdir_separator \
+fix_srcfile_path \
+exclude_expsyms \
+include_expsyms \
+file_list_spec \
+variables_saved_for_relink \
+libname_spec \
+library_names_spec \
+soname_spec \
+finish_eval \
+old_striplib \
+striplib \
+compiler_lib_search_dirs \
+predep_objects \
+postdep_objects \
+predeps \
+postdeps \
+compiler_lib_search_path \
+LD_CXX \
+compiler_CXX \
+lt_prog_compiler_no_builtin_flag_CXX \
+lt_prog_compiler_wl_CXX \
+lt_prog_compiler_pic_CXX \
+lt_prog_compiler_static_CXX \
+lt_cv_prog_compiler_c_o_CXX \
+export_dynamic_flag_spec_CXX \
+whole_archive_flag_spec_CXX \
+compiler_needs_object_CXX \
+with_gnu_ld_CXX \
+allow_undefined_flag_CXX \
+no_undefined_flag_CXX \
+hardcode_libdir_flag_spec_CXX \
+hardcode_libdir_flag_spec_ld_CXX \
+hardcode_libdir_separator_CXX \
+fix_srcfile_path_CXX \
+exclude_expsyms_CXX \
+include_expsyms_CXX \
+file_list_spec_CXX \
+compiler_lib_search_dirs_CXX \
+predep_objects_CXX \
+postdep_objects_CXX \
+predeps_CXX \
+postdeps_CXX \
+compiler_lib_search_path_CXX; do
+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in
+ *[\\\\\\\`\\"\\\$]*)
+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$sed_quote_subst\\"\\\`\\\\\\""
+ ;;
+ *)
+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\""
+ ;;
+ esac
+done
+
+# Double-quote double-evaled strings.
+for var in reload_cmds \
+old_postinstall_cmds \
+old_postuninstall_cmds \
+old_archive_cmds \
+extract_expsyms_cmds \
+old_archive_from_new_cmds \
+old_archive_from_expsyms_cmds \
+archive_cmds \
+archive_expsym_cmds \
+module_cmds \
+module_expsym_cmds \
+export_symbols_cmds \
+prelink_cmds \
+postinstall_cmds \
+postuninstall_cmds \
+finish_cmds \
+sys_lib_search_path_spec \
+sys_lib_dlsearch_path_spec \
+old_archive_cmds_CXX \
+old_archive_from_new_cmds_CXX \
+old_archive_from_expsyms_cmds_CXX \
+archive_cmds_CXX \
+archive_expsym_cmds_CXX \
+module_cmds_CXX \
+module_expsym_cmds_CXX \
+export_symbols_cmds_CXX \
+prelink_cmds_CXX; do
+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in
+ *[\\\\\\\`\\"\\\$]*)
+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$double_quote_subst\\" -e \\"\\\$sed_quote_subst\\" -e \\"\\\$delay_variable_subst\\"\\\`\\\\\\""
+ ;;
+ *)
+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\""
+ ;;
+ esac
+done
+
+# Fix-up fallback echo if it was mangled by the above quoting rules.
+case \$lt_ECHO in
+*'\\\$0 --fallback-echo"') lt_ECHO=\`\$ECHO "X\$lt_ECHO" | \$Xsed -e 's/\\\\\\\\\\\\\\\$0 --fallback-echo"\$/\$0 --fallback-echo"/'\`
+ ;;
+esac
+
+ac_aux_dir='$ac_aux_dir'
+xsi_shell='$xsi_shell'
+lt_shell_append='$lt_shell_append'
+
+# See if we are running on zsh, and set the options which allow our
+# commands through without removal of \ escapes INIT.
+if test -n "\${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+fi
+
+
+ PACKAGE='$PACKAGE'
+ VERSION='$VERSION'
+ TIMESTAMP='$TIMESTAMP'
+ RM='$RM'
+ ofile='$ofile'
+
+
+
+
+
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+
+# Handling of arguments.
+for ac_config_target in $ac_config_targets
+do
+ case $ac_config_target in
+ "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+ "libtool") CONFIG_COMMANDS="$CONFIG_COMMANDS libtool" ;;
+ "libProgressBar/config.h") CONFIG_HEADERS="$CONFIG_HEADERS libProgressBar/config.h" ;;
+ "postinst") CONFIG_FILES="$CONFIG_FILES postinst" ;;
+ "prerm") CONFIG_FILES="$CONFIG_FILES prerm" ;;
+ "libProgressBar.lsm") CONFIG_FILES="$CONFIG_FILES libProgressBar.lsm" ;;
+ "libProgressBar.spec") CONFIG_FILES="$CONFIG_FILES libProgressBar.spec" ;;
+ "control") CONFIG_FILES="$CONFIG_FILES control" ;;
+ "libProgressBar.pc") CONFIG_FILES="$CONFIG_FILES libProgressBar.pc" ;;
+ "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
+ "libProgressBar/Makefile") CONFIG_FILES="$CONFIG_FILES libProgressBar/Makefile" ;;
+ "doc/Makefile") CONFIG_FILES="$CONFIG_FILES doc/Makefile" ;;
+ "doc/libProgressBar.3") CONFIG_FILES="$CONFIG_FILES doc/libProgressBar.3" ;;
+
+ *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5 ;;
+ esac
+done
+
+
+# If the user did not use the arguments to specify the items to instantiate,
+# then the envvar interface is used. Set only those that are not.
+# We use the long form for the default assignment because of an extremely
+# bizarre bug on SunOS 4.1.3.
+if $ac_need_defaults; then
+ test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
+ test "${CONFIG_HEADERS+set}" = set || CONFIG_HEADERS=$config_headers
+ test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands
+fi
+
+# Have a temporary directory for convenience. Make it in the build tree
+# simply because there is no reason against having it here, and in addition,
+# creating and moving files from /tmp can sometimes cause problems.
+# Hook for its removal unless debugging.
+# Note that there is a small window in which the directory will not be cleaned:
+# after its creation but before its name has been assigned to `$tmp'.
+$debug ||
+{
+ tmp=
+ trap 'exit_status=$?
+ { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status
+' 0
+ trap 'as_fn_exit 1' 1 2 13 15
+}
+# Create a (secure) tmp directory for tmp files.
+
+{
+ tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
+ test -n "$tmp" && test -d "$tmp"
+} ||
+{
+ tmp=./conf$$-$RANDOM
+ (umask 077 && mkdir "$tmp")
+} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
+
+# Set up the scripts for CONFIG_FILES section.
+# No need to generate them if there are no CONFIG_FILES.
+# This happens for instance with `./config.status config.h'.
+if test -n "$CONFIG_FILES"; then
+
+if $AWK 'BEGIN { getline <"/dev/null" }' </dev/null 2>/dev/null; then
+ ac_cs_awk_getline=:
+ ac_cs_awk_pipe_init=
+ ac_cs_awk_read_file='
+ while ((getline aline < (F[key])) > 0)
+ print(aline)
+ close(F[key])'
+ ac_cs_awk_pipe_fini=
+else
+ ac_cs_awk_getline=false
+ ac_cs_awk_pipe_init="print \"cat <<'|#_!!_#|' &&\""
+ ac_cs_awk_read_file='
+ print "|#_!!_#|"
+ print "cat " F[key] " &&"
+ '$ac_cs_awk_pipe_init
+ # The final `:' finishes the AND list.
+ ac_cs_awk_pipe_fini='END { print "|#_!!_#|"; print ":" }'
+fi
+ac_cr=`echo X | tr X '\015'`
+# On cygwin, bash can eat \r inside `` if the user requested igncr.
+# But we know of no other shell where ac_cr would be empty at this
+# point, so we can use a bashism as a fallback.
+if test "x$ac_cr" = x; then
+ eval ac_cr=\$\'\\r\'
+fi
+ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
+if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
+ ac_cs_awk_cr='\\r'
+else
+ ac_cs_awk_cr=$ac_cr
+fi
+
+echo 'BEGIN {' >"$tmp/subs1.awk" &&
+_ACEOF
+
+# Create commands to substitute file output variables.
+{
+ echo "cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1" &&
+ echo 'cat >>"\$tmp/subs1.awk" <<\\_ACAWK &&' &&
+ echo "$ac_subst_files" | sed 's/.*/F["&"]="$&"/' &&
+ echo "_ACAWK" &&
+ echo "_ACEOF"
+} >conf$$files.sh &&
+. ./conf$$files.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+rm -f conf$$files.sh
+
+{
+ echo "cat >conf$$subs.awk <<_ACEOF" &&
+ echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
+ echo "_ACEOF"
+} >conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'`
+ac_delim='%!_!# '
+for ac_last_try in false false false false false :; do
+ . ./conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+
+ ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
+ if test $ac_delim_n = $ac_delim_num; then
+ break
+ elif $ac_last_try; then
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ else
+ ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+ fi
+done
+rm -f conf$$subs.sh
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+cat >>"\$tmp/subs1.awk" <<\\_ACAWK &&
+_ACEOF
+sed -n '
+h
+s/^/S["/; s/!.*/"]=/
+p
+g
+s/^[^!]*!//
+:repl
+t repl
+s/'"$ac_delim"'$//
+t delim
+:nl
+h
+s/\(.\{148\}\)..*/\1/
+t more1
+s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/
+p
+n
+b repl
+:more1
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t nl
+:delim
+h
+s/\(.\{148\}\)..*/\1/
+t more2
+s/["\\]/\\&/g; s/^/"/; s/$/"/
+p
+b
+:more2
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t delim
+' <conf$$subs.awk | sed '
+/^[^""]/{
+ N
+ s/\n//
+}
+' >>$CONFIG_STATUS || ac_write_fail=1
+rm -f conf$$subs.awk
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+_ACAWK
+cat >>"\$tmp/subs1.awk" <<_ACAWK &&
+ for (key in S) S_is_set[key] = 1
+ FS = ""
+ \$ac_cs_awk_pipe_init
+}
+{
+ line = $ 0
+ nfields = split(line, field, "@")
+ substed = 0
+ len = length(field[1])
+ for (i = 2; i < nfields; i++) {
+ key = field[i]
+ keylen = length(key)
+ if (S_is_set[key]) {
+ value = S[key]
+ line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3)
+ len += length(value) + length(field[++i])
+ substed = 1
+ } else
+ len += 1 + keylen
+ }
+ if (nfields == 3 && !substed) {
+ key = field[2]
+ if (F[key] != "" && line ~ /^[ ]*@.*@[ ]*$/) {
+ \$ac_cs_awk_read_file
+ next
+ }
+ }
+ print line
+}
+\$ac_cs_awk_pipe_fini
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
+ sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g"
+else
+ cat
+fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \
+ || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
+_ACEOF
+
+# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
+# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
+# trailing colons and then remove the whole line if VPATH becomes empty
+# (actually we leave an empty line to preserve line numbers).
+if test "x$srcdir" = x.; then
+ ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{
+h
+s///
+s/^/:/
+s/[ ]*$/:/
+s/:\$(srcdir):/:/g
+s/:\${srcdir}:/:/g
+s/:@srcdir@:/:/g
+s/^:*//
+s/:*$//
+x
+s/\(=[ ]*\).*/\1/
+G
+s/\n//
+s/^[^=]*=[ ]*$//
+}'
+fi
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+fi # test -n "$CONFIG_FILES"
+
+# Set up the scripts for CONFIG_HEADERS section.
+# No need to generate them if there are no CONFIG_HEADERS.
+# This happens for instance with `./config.status Makefile'.
+if test -n "$CONFIG_HEADERS"; then
+cat >"$tmp/defines.awk" <<\_ACAWK ||
+BEGIN {
+_ACEOF
+
+# Transform confdefs.h into an awk script `defines.awk', embedded as
+# here-document in config.status, that substitutes the proper values into
+# config.h.in to produce config.h.
+
+# Create a delimiter string that does not exist in confdefs.h, to ease
+# handling of long lines.
+ac_delim='%!_!# '
+for ac_last_try in false false :; do
+ ac_t=`sed -n "/$ac_delim/p" confdefs.h`
+ if test -z "$ac_t"; then
+ break
+ elif $ac_last_try; then
+ as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5
+ else
+ ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+ fi
+done
+
+# For the awk script, D is an array of macro values keyed by name,
+# likewise P contains macro parameters if any. Preserve backslash
+# newline sequences.
+
+ac_word_re=[_$as_cr_Letters][_$as_cr_alnum]*
+sed -n '
+s/.\{148\}/&'"$ac_delim"'/g
+t rset
+:rset
+s/^[ ]*#[ ]*define[ ][ ]*/ /
+t def
+d
+:def
+s/\\$//
+t bsnl
+s/["\\]/\\&/g
+s/^ \('"$ac_word_re"'\)\(([^()]*)\)[ ]*\(.*\)/P["\1"]="\2"\
+D["\1"]=" \3"/p
+s/^ \('"$ac_word_re"'\)[ ]*\(.*\)/D["\1"]=" \2"/p
+d
+:bsnl
+s/["\\]/\\&/g
+s/^ \('"$ac_word_re"'\)\(([^()]*)\)[ ]*\(.*\)/P["\1"]="\2"\
+D["\1"]=" \3\\\\\\n"\\/p
+t cont
+s/^ \('"$ac_word_re"'\)[ ]*\(.*\)/D["\1"]=" \2\\\\\\n"\\/p
+t cont
+d
+:cont
+n
+s/.\{148\}/&'"$ac_delim"'/g
+t clear
+:clear
+s/\\$//
+t bsnlc
+s/["\\]/\\&/g; s/^/"/; s/$/"/p
+d
+:bsnlc
+s/["\\]/\\&/g; s/^/"/; s/$/\\\\\\n"\\/p
+b cont
+' <confdefs.h | sed '
+s/'"$ac_delim"'/"\\\
+"/g' >>$CONFIG_STATUS || ac_write_fail=1
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ for (key in D) D_is_set[key] = 1
+ FS = ""
+}
+/^[\t ]*#[\t ]*(define|undef)[\t ]+$ac_word_re([\t (]|\$)/ {
+ line = \$ 0
+ split(line, arg, " ")
+ if (arg[1] == "#") {
+ defundef = arg[2]
+ mac1 = arg[3]
+ } else {
+ defundef = substr(arg[1], 2)
+ mac1 = arg[2]
+ }
+ split(mac1, mac2, "(") #)
+ macro = mac2[1]
+ prefix = substr(line, 1, index(line, defundef) - 1)
+ if (D_is_set[macro]) {
+ # Preserve the white space surrounding the "#".
+ print prefix "define", macro P[macro] D[macro]
+ next
+ } else {
+ # Replace #undef with comments. This is necessary, for example,
+ # in the case of _POSIX_SOURCE, which is predefined and required
+ # on some systems where configure will not decide to define it.
+ if (defundef == "undef") {
+ print "/*", prefix defundef, macro, "*/"
+ next
+ }
+ }
+}
+{ print }
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+ as_fn_error $? "could not setup config headers machinery" "$LINENO" 5
+fi # test -n "$CONFIG_HEADERS"
+
+
+eval set X " :F $CONFIG_FILES :H $CONFIG_HEADERS :C $CONFIG_COMMANDS"
+shift
+for ac_tag
+do
+ case $ac_tag in
+ :[FHLC]) ac_mode=$ac_tag; continue;;
+ esac
+ case $ac_mode$ac_tag in
+ :[FHL]*:*);;
+ :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5 ;;
+ :[FH]-) ac_tag=-:-;;
+ :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
+ esac
+ ac_save_IFS=$IFS
+ IFS=:
+ set x $ac_tag
+ IFS=$ac_save_IFS
+ shift
+ ac_file=$1
+ shift
+
+ case $ac_mode in
+ :L) ac_source=$1;;
+ :[FH])
+ ac_file_inputs=
+ for ac_f
+ do
+ case $ac_f in
+ -) ac_f="$tmp/stdin";;
+ *) # Look for the file first in the build tree, then in the source tree
+ # (if the path is not absolute). The absolute path cannot be DOS-style,
+ # because $ac_f cannot contain `:'.
+ test -f "$ac_f" ||
+ case $ac_f in
+ [\\/$]*) false;;
+ *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
+ esac ||
+ as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5 ;;
+ esac
+ case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
+ as_fn_append ac_file_inputs " '$ac_f'"
+ done
+
+ # Let's still pretend it is `configure' which instantiates (i.e., don't
+ # use $as_me), people would be surprised to read:
+ # /* config.h. Generated by config.status. */
+ configure_input='Generated from '`
+ $as_echo "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g'
+ `' by configure.'
+ if test x"$ac_file" != x-; then
+ configure_input="$ac_file. $configure_input"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5
+$as_echo "$as_me: creating $ac_file" >&6;}
+ fi
+ # Neutralize special characters interpreted by sed in replacement strings.
+ case $configure_input in #(
+ *\&* | *\|* | *\\* )
+ ac_sed_conf_input=`$as_echo "$configure_input" |
+ sed 's/[\\\\&|]/\\\\&/g'`;; #(
+ *) ac_sed_conf_input=$configure_input;;
+ esac
+
+ case $ac_tag in
+ *:-:* | *:-) cat >"$tmp/stdin" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;;
+ esac
+ ;;
+ esac
+
+ ac_dir=`$as_dirname -- "$ac_file" ||
+$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$ac_file" : 'X\(//\)[^/]' \| \
+ X"$ac_file" : 'X\(//\)$' \| \
+ X"$ac_file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$ac_file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir="$ac_dir"; as_fn_mkdir_p
+ ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+ ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
+ # A ".." for each directory in $ac_dir_suffix.
+ ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
+ case $ac_top_builddir_sub in
+ "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+ *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+ esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+ .) # We are building in place.
+ ac_srcdir=.
+ ac_top_srcdir=$ac_top_builddir_sub
+ ac_abs_top_srcdir=$ac_pwd ;;
+ [\\/]* | ?:[\\/]* ) # Absolute name.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir
+ ac_abs_top_srcdir=$srcdir ;;
+ *) # Relative name.
+ ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_build_prefix$srcdir
+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+
+ case $ac_mode in
+ :F)
+ #
+ # CONFIG_FILE
+ #
+
+ case $INSTALL in
+ [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;;
+ *) ac_INSTALL=$ac_top_build_prefix$INSTALL ;;
+ esac
+ ac_MKDIR_P=$MKDIR_P
+ case $MKDIR_P in
+ [\\/$]* | ?:[\\/]* ) ;;
+ */*) ac_MKDIR_P=$ac_top_build_prefix$MKDIR_P ;;
+ esac
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# If the template does not know about datarootdir, expand it.
+# FIXME: This hack should be removed a few years after 2.60.
+ac_datarootdir_hack=; ac_datarootdir_seen=
+ac_sed_dataroot='
+/datarootdir/ {
+ p
+ q
+}
+/@datadir@/p
+/@docdir@/p
+/@infodir@/p
+/@localedir@/p
+/@mandir@/p'
+case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
+*datarootdir*) ac_datarootdir_seen=yes;;
+*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
+$as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ ac_datarootdir_hack='
+ s&@datadir@&$datadir&g
+ s&@docdir@&$docdir&g
+ s&@infodir@&$infodir&g
+ s&@localedir@&$localedir&g
+ s&@mandir@&$mandir&g
+ s&\\\${datarootdir}&$datarootdir&g' ;;
+esac
+_ACEOF
+
+# Neutralize VPATH when `$srcdir' = `.'.
+# Shell code in configure.ac might set extrasub.
+# FIXME: do we really want to maintain this feature?
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_sed_extra="$ac_vpsub
+$extrasub
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+:t
+/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
+s|@configure_input@|$ac_sed_conf_input|;t t
+s&@top_builddir@&$ac_top_builddir_sub&;t t
+s&@top_build_prefix@&$ac_top_build_prefix&;t t
+s&@srcdir@&$ac_srcdir&;t t
+s&@abs_srcdir@&$ac_abs_srcdir&;t t
+s&@top_srcdir@&$ac_top_srcdir&;t t
+s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t
+s&@builddir@&$ac_builddir&;t t
+s&@abs_builddir@&$ac_abs_builddir&;t t
+s&@abs_top_builddir@&$ac_abs_top_builddir&;t t
+s&@INSTALL@&$ac_INSTALL&;t t
+s&@MKDIR_P@&$ac_MKDIR_P&;t t
+$ac_datarootdir_hack
+"
+eval sed \"\$ac_sed_extra\" "$ac_file_inputs" |
+if $ac_cs_awk_getline; then
+ $AWK -f "$tmp/subs.awk"
+else
+ $AWK -f "$tmp/subs.awk" | $SHELL
+fi >$tmp/out \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+
+test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
+ { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } &&
+ { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } &&
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&5
+$as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&2;}
+
+ rm -f "$tmp/stdin"
+ case $ac_file in
+ -) cat "$tmp/out" && rm -f "$tmp/out";;
+ *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";;
+ esac \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ ;;
+ :H)
+ #
+ # CONFIG_HEADER
+ #
+ if test x"$ac_file" != x-; then
+ {
+ $as_echo "/* $configure_input */" \
+ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs"
+ } >"$tmp/config.h" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5
+$as_echo "$as_me: $ac_file is unchanged" >&6;}
+ else
+ rm -f "$ac_file"
+ mv "$tmp/config.h" "$ac_file" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ fi
+ else
+ $as_echo "/* $configure_input */" \
+ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \
+ || as_fn_error $? "could not create -" "$LINENO" 5
+ fi
+# Compute "$ac_file"'s index in $config_headers.
+_am_arg="$ac_file"
+_am_stamp_count=1
+for _am_header in $config_headers :; do
+ case $_am_header in
+ $_am_arg | $_am_arg:* )
+ break ;;
+ * )
+ _am_stamp_count=`expr $_am_stamp_count + 1` ;;
+ esac
+done
+echo "timestamp for $_am_arg" >`$as_dirname -- "$_am_arg" ||
+$as_expr X"$_am_arg" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$_am_arg" : 'X\(//\)[^/]' \| \
+ X"$_am_arg" : 'X\(//\)$' \| \
+ X"$_am_arg" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$_am_arg" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`/stamp-h$_am_stamp_count
+ ;;
+
+ :C) { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5
+$as_echo "$as_me: executing $ac_file commands" >&6;}
+ ;;
+ esac
+
+
+ case $ac_file$ac_mode in
+ "depfiles":C) test x"$AMDEP_TRUE" != x"" || {
+ # Autoconf 2.62 quotes --file arguments for eval, but not when files
+ # are listed without --file. Let's play safe and only enable the eval
+ # if we detect the quoting.
+ case $CONFIG_FILES in
+ *\'*) eval set x "$CONFIG_FILES" ;;
+ *) set x $CONFIG_FILES ;;
+ esac
+ shift
+ for mf
+ do
+ # Strip MF so we end up with the name of the file.
+ mf=`echo "$mf" | sed -e 's/:.*$//'`
+ # Check whether this is an Automake generated Makefile or not.
+ # We used to match only the files named `Makefile.in', but
+ # some people rename them; so instead we look at the file content.
+ # Grep'ing the first line is not enough: some people post-process
+ # each Makefile.in and add a new line on top of each file to say so.
+ # Grep'ing the whole file is not good either: AIX grep has a line
+ # limit of 2048, but all sed's we know have understand at least 4000.
+ if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
+ dirpart=`$as_dirname -- "$mf" ||
+$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$mf" : 'X\(//\)[^/]' \| \
+ X"$mf" : 'X\(//\)$' \| \
+ X"$mf" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$mf" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ else
+ continue
+ fi
+ # Extract the definition of DEPDIR, am__include, and am__quote
+ # from the Makefile without running `make'.
+ DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+ test -z "$DEPDIR" && continue
+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
+ test -z "am__include" && continue
+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # When using ansi2knr, U may be empty or an underscore; expand it
+ U=`sed -n 's/^U = //p' < "$mf"`
+ # Find all dependency output files, they are included files with
+ # $(DEPDIR) in their names. We invoke sed twice because it is the
+ # simplest approach to changing $(DEPDIR) to its actual value in the
+ # expansion.
+ for file in `sed -n "
+ s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+ # Make sure the directory exists.
+ test -f "$dirpart/$file" && continue
+ fdir=`$as_dirname -- "$file" ||
+$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$file" : 'X\(//\)[^/]' \| \
+ X"$file" : 'X\(//\)$' \| \
+ X"$file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir=$dirpart/$fdir; as_fn_mkdir_p
+ # echo "creating $dirpart/$file"
+ echo '# dummy' > "$dirpart/$file"
+ done
+ done
+}
+ ;;
+ "libtool":C)
+
+ # See if we are running on zsh, and set the options which allow our
+ # commands through without removal of \ escapes.
+ if test -n "${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+ fi
+
+ cfgfile="${ofile}T"
+ trap "$RM \"$cfgfile\"; exit 1" 1 2 15
+ $RM "$cfgfile"
+
+ cat <<_LT_EOF >> "$cfgfile"
+#! $SHELL
+
+# `$ECHO "$ofile" | sed 's%^.*/%%'` - Provide generalized library-building support services.
+# Generated automatically by $as_me ($PACKAGE$TIMESTAMP) $VERSION
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+# NOTE: Changes made to this file will be lost: look at ltmain.sh.
+#
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
+# 2006, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gordon Matzigkeit, 1996
+#
+# This file is part of GNU Libtool.
+#
+# GNU Libtool is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License as
+# published by the Free Software Foundation; either version 2 of
+# the License, or (at your option) any later version.
+#
+# As a special exception to the GNU General Public License,
+# if you distribute this file as part of a program or library that
+# is built using GNU Libtool, you may include this file under the
+# same distribution terms that you use for the rest of that program.
+#
+# GNU Libtool is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GNU Libtool; see the file COPYING. If not, a copy
+# can be downloaded from http://www.gnu.org/licenses/gpl.html, or
+# obtained by writing to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+
+# The names of the tagged configurations supported by this script.
+available_tags="CXX "
+
+# ### BEGIN LIBTOOL CONFIG
+
+# Which release of libtool.m4 was used?
+macro_version=$macro_version
+macro_revision=$macro_revision
+
+# Whether or not to build shared libraries.
+build_libtool_libs=$enable_shared
+
+# Whether or not to build static libraries.
+build_old_libs=$enable_static
+
+# What type of objects to build.
+pic_mode=$pic_mode
+
+# Whether or not to optimize for fast installation.
+fast_install=$enable_fast_install
+
+# The host system.
+host_alias=$host_alias
+host=$host
+host_os=$host_os
+
+# The build system.
+build_alias=$build_alias
+build=$build
+build_os=$build_os
+
+# A sed program that does not truncate output.
+SED=$lt_SED
+
+# Sed that helps us avoid accidentally triggering echo(1) options like -n.
+Xsed="\$SED -e 1s/^X//"
+
+# A grep program that handles long lines.
+GREP=$lt_GREP
+
+# An ERE matcher.
+EGREP=$lt_EGREP
+
+# A literal string matcher.
+FGREP=$lt_FGREP
+
+# A BSD- or MS-compatible name lister.
+NM=$lt_NM
+
+# Whether we need soft or hard links.
+LN_S=$lt_LN_S
+
+# What is the maximum length of a command?
+max_cmd_len=$max_cmd_len
+
+# Object file suffix (normally "o").
+objext=$ac_objext
+
+# Executable file suffix (normally "").
+exeext=$exeext
+
+# whether the shell understands "unset".
+lt_unset=$lt_unset
+
+# turn spaces into newlines.
+SP2NL=$lt_lt_SP2NL
+
+# turn newlines into spaces.
+NL2SP=$lt_lt_NL2SP
+
+# How to create reloadable object files.
+reload_flag=$lt_reload_flag
+reload_cmds=$lt_reload_cmds
+
+# An object symbol dumper.
+OBJDUMP=$lt_OBJDUMP
+
+# Method to check whether dependent libraries are shared objects.
+deplibs_check_method=$lt_deplibs_check_method
+
+# Command to use when deplibs_check_method == "file_magic".
+file_magic_cmd=$lt_file_magic_cmd
+
+# The archiver.
+AR=$lt_AR
+AR_FLAGS=$lt_AR_FLAGS
+
+# A symbol stripping program.
+STRIP=$lt_STRIP
+
+# Commands used to install an old-style archive.
+RANLIB=$lt_RANLIB
+old_postinstall_cmds=$lt_old_postinstall_cmds
+old_postuninstall_cmds=$lt_old_postuninstall_cmds
+
+# A C compiler.
+LTCC=$lt_CC
+
+# LTCC compiler flags.
+LTCFLAGS=$lt_CFLAGS
+
+# Take the output of nm and produce a listing of raw symbols and C names.
+global_symbol_pipe=$lt_lt_cv_sys_global_symbol_pipe
+
+# Transform the output of nm in a proper C declaration.
+global_symbol_to_cdecl=$lt_lt_cv_sys_global_symbol_to_cdecl
+
+# Transform the output of nm in a C name address pair.
+global_symbol_to_c_name_address=$lt_lt_cv_sys_global_symbol_to_c_name_address
+
+# Transform the output of nm in a C name address pair when lib prefix is needed.
+global_symbol_to_c_name_address_lib_prefix=$lt_lt_cv_sys_global_symbol_to_c_name_address_lib_prefix
+
+# The name of the directory that contains temporary libtool files.
+objdir=$objdir
+
+# Shell to use when invoking shell scripts.
+SHELL=$lt_SHELL
+
+# An echo program that does not interpret backslashes.
+ECHO=$lt_ECHO
+
+# Used to examine libraries when file_magic_cmd begins with "file".
+MAGIC_CMD=$MAGIC_CMD
+
+# Must we lock files when doing compilation?
+need_locks=$lt_need_locks
+
+# Tool to manipulate archived DWARF debug symbol files on Mac OS X.
+DSYMUTIL=$lt_DSYMUTIL
+
+# Tool to change global to local symbols on Mac OS X.
+NMEDIT=$lt_NMEDIT
+
+# Tool to manipulate fat objects and archives on Mac OS X.
+LIPO=$lt_LIPO
+
+# ldd/readelf like tool for Mach-O binaries on Mac OS X.
+OTOOL=$lt_OTOOL
+
+# ldd/readelf like tool for 64 bit Mach-O binaries on Mac OS X 10.4.
+OTOOL64=$lt_OTOOL64
+
+# Old archive suffix (normally "a").
+libext=$libext
+
+# Shared library suffix (normally ".so").
+shrext_cmds=$lt_shrext_cmds
+
+# The commands to extract the exported symbol list from a shared archive.
+extract_expsyms_cmds=$lt_extract_expsyms_cmds
+
+# Variables whose values should be saved in libtool wrapper scripts and
+# restored at link time.
+variables_saved_for_relink=$lt_variables_saved_for_relink
+
+# Do we need the "lib" prefix for modules?
+need_lib_prefix=$need_lib_prefix
+
+# Do we need a version for libraries?
+need_version=$need_version
+
+# Library versioning type.
+version_type=$version_type
+
+# Shared library runtime path variable.
+runpath_var=$runpath_var
+
+# Shared library path variable.
+shlibpath_var=$shlibpath_var
+
+# Is shlibpath searched before the hard-coded library search path?
+shlibpath_overrides_runpath=$shlibpath_overrides_runpath
+
+# Format of library name prefix.
+libname_spec=$lt_libname_spec
+
+# List of archive names. First name is the real one, the rest are links.
+# The last name is the one that the linker finds with -lNAME
+library_names_spec=$lt_library_names_spec
+
+# The coded name of the library, if different from the real name.
+soname_spec=$lt_soname_spec
+
+# Command to use after installation of a shared archive.
+postinstall_cmds=$lt_postinstall_cmds
+
+# Command to use after uninstallation of a shared archive.
+postuninstall_cmds=$lt_postuninstall_cmds
+
+# Commands used to finish a libtool library installation in a directory.
+finish_cmds=$lt_finish_cmds
+
+# As "finish_cmds", except a single script fragment to be evaled but
+# not shown.
+finish_eval=$lt_finish_eval
+
+# Whether we should hardcode library paths into libraries.
+hardcode_into_libs=$hardcode_into_libs
+
+# Compile-time system search path for libraries.
+sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+
+# Run-time system search path for libraries.
+sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec
+
+# Whether dlopen is supported.
+dlopen_support=$enable_dlopen
+
+# Whether dlopen of programs is supported.
+dlopen_self=$enable_dlopen_self
+
+# Whether dlopen of statically linked programs is supported.
+dlopen_self_static=$enable_dlopen_self_static
+
+# Commands to strip libraries.
+old_striplib=$lt_old_striplib
+striplib=$lt_striplib
+
+
+# The linker used to build libraries.
+LD=$lt_LD
+
+# Commands used to build an old-style archive.
+old_archive_cmds=$lt_old_archive_cmds
+
+# A language specific compiler.
+CC=$lt_compiler
+
+# Is the compiler the GNU compiler?
+with_gcc=$GCC
+
+# Compiler flag to turn off builtin functions.
+no_builtin_flag=$lt_lt_prog_compiler_no_builtin_flag
+
+# How to pass a linker flag through the compiler.
+wl=$lt_lt_prog_compiler_wl
+
+# Additional compiler flags for building library objects.
+pic_flag=$lt_lt_prog_compiler_pic
+
+# Compiler flag to prevent dynamic linking.
+link_static_flag=$lt_lt_prog_compiler_static
+
+# Does compiler simultaneously support -c and -o options?
+compiler_c_o=$lt_lt_cv_prog_compiler_c_o
+
+# Whether or not to add -lc for building shared libraries.
+build_libtool_need_lc=$archive_cmds_need_lc
+
+# Whether or not to disallow shared libs when runtime libs are static.
+allow_libtool_libs_with_static_runtimes=$enable_shared_with_static_runtimes
+
+# Compiler flag to allow reflexive dlopens.
+export_dynamic_flag_spec=$lt_export_dynamic_flag_spec
+
+# Compiler flag to generate shared objects directly from archives.
+whole_archive_flag_spec=$lt_whole_archive_flag_spec
+
+# Whether the compiler copes with passing no objects directly.
+compiler_needs_object=$lt_compiler_needs_object
+
+# Create an old-style archive from a shared archive.
+old_archive_from_new_cmds=$lt_old_archive_from_new_cmds
+
+# Create a temporary old-style archive to link instead of a shared archive.
+old_archive_from_expsyms_cmds=$lt_old_archive_from_expsyms_cmds
+
+# Commands used to build a shared archive.
+archive_cmds=$lt_archive_cmds
+archive_expsym_cmds=$lt_archive_expsym_cmds
+
+# Commands used to build a loadable module if different from building
+# a shared archive.
+module_cmds=$lt_module_cmds
+module_expsym_cmds=$lt_module_expsym_cmds
+
+# Whether we are building with GNU ld or not.
+with_gnu_ld=$lt_with_gnu_ld
+
+# Flag that allows shared libraries with undefined symbols to be built.
+allow_undefined_flag=$lt_allow_undefined_flag
+
+# Flag that enforces no undefined symbols.
+no_undefined_flag=$lt_no_undefined_flag
+
+# Flag to hardcode \$libdir into a binary during linking.
+# This must work even if \$libdir does not exist
+hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec
+
+# If ld is used when linking, flag to hardcode \$libdir into a binary
+# during linking. This must work even if \$libdir does not exist.
+hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld
+
+# Whether we need a single "-rpath" flag with a separated argument.
+hardcode_libdir_separator=$lt_hardcode_libdir_separator
+
+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes
+# DIR into the resulting binary.
+hardcode_direct=$hardcode_direct
+
+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes
+# DIR into the resulting binary and the resulting library dependency is
+# "absolute",i.e impossible to change by setting \${shlibpath_var} if the
+# library is relocated.
+hardcode_direct_absolute=$hardcode_direct_absolute
+
+# Set to "yes" if using the -LDIR flag during linking hardcodes DIR
+# into the resulting binary.
+hardcode_minus_L=$hardcode_minus_L
+
+# Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR
+# into the resulting binary.
+hardcode_shlibpath_var=$hardcode_shlibpath_var
+
+# Set to "yes" if building a shared library automatically hardcodes DIR
+# into the library and all subsequent libraries and executables linked
+# against it.
+hardcode_automatic=$hardcode_automatic
+
+# Set to yes if linker adds runtime paths of dependent libraries
+# to runtime path list.
+inherit_rpath=$inherit_rpath
+
+# Whether libtool must link a program against all its dependency libraries.
+link_all_deplibs=$link_all_deplibs
+
+# Fix the shell variable \$srcfile for the compiler.
+fix_srcfile_path=$lt_fix_srcfile_path
+
+# Set to "yes" if exported symbols are required.
+always_export_symbols=$always_export_symbols
+
+# The commands to list exported symbols.
+export_symbols_cmds=$lt_export_symbols_cmds
+
+# Symbols that should not be listed in the preloaded symbols.
+exclude_expsyms=$lt_exclude_expsyms
+
+# Symbols that must always be exported.
+include_expsyms=$lt_include_expsyms
+
+# Commands necessary for linking programs (against libraries) with templates.
+prelink_cmds=$lt_prelink_cmds
+
+# Specify filename containing input files.
+file_list_spec=$lt_file_list_spec
+
+# How to hardcode a shared library path into an executable.
+hardcode_action=$hardcode_action
+
+# The directories searched by this compiler when creating a shared library.
+compiler_lib_search_dirs=$lt_compiler_lib_search_dirs
+
+# Dependencies to place before and after the objects being linked to
+# create a shared library.
+predep_objects=$lt_predep_objects
+postdep_objects=$lt_postdep_objects
+predeps=$lt_predeps
+postdeps=$lt_postdeps
+
+# The library search path used internally by the compiler when linking
+# a shared library.
+compiler_lib_search_path=$lt_compiler_lib_search_path
+
+# ### END LIBTOOL CONFIG
+
+_LT_EOF
+
+ case $host_os in
+ aix3*)
+ cat <<\_LT_EOF >> "$cfgfile"
+# AIX sometimes has problems with the GCC collect2 program. For some
+# reason, if we set the COLLECT_NAMES environment variable, the problems
+# vanish in a puff of smoke.
+if test "X${COLLECT_NAMES+set}" != Xset; then
+ COLLECT_NAMES=
+ export COLLECT_NAMES
+fi
+_LT_EOF
+ ;;
+ esac
+
+
+ltmain="$ac_aux_dir/ltmain.sh"
+
+
+ # We use sed instead of cat because bash on DJGPP gets confused if
+ # if finds mixed CR/LF and LF-only lines. Since sed operates in
+ # text mode, it properly converts lines to CR/LF. This bash problem
+ # is reportedly fixed, but why not run on old versions too?
+ sed '/^# Generated shell functions inserted here/q' "$ltmain" >> "$cfgfile" \
+ || (rm -f "$cfgfile"; exit 1)
+
+ case $xsi_shell in
+ yes)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_dirname file append nondir_replacement
+# Compute the dirname of FILE. If nonempty, add APPEND to the result,
+# otherwise set result to NONDIR_REPLACEMENT.
+func_dirname ()
+{
+ case ${1} in
+ */*) func_dirname_result="${1%/*}${2}" ;;
+ * ) func_dirname_result="${3}" ;;
+ esac
+}
+
+# func_basename file
+func_basename ()
+{
+ func_basename_result="${1##*/}"
+}
+
+# func_dirname_and_basename file append nondir_replacement
+# perform func_basename and func_dirname in a single function
+# call:
+# dirname: Compute the dirname of FILE. If nonempty,
+# add APPEND to the result, otherwise set result
+# to NONDIR_REPLACEMENT.
+# value returned in "$func_dirname_result"
+# basename: Compute filename of FILE.
+# value retuned in "$func_basename_result"
+# Implementation must be kept synchronized with func_dirname
+# and func_basename. For efficiency, we do not delegate to
+# those functions but instead duplicate the functionality here.
+func_dirname_and_basename ()
+{
+ case ${1} in
+ */*) func_dirname_result="${1%/*}${2}" ;;
+ * ) func_dirname_result="${3}" ;;
+ esac
+ func_basename_result="${1##*/}"
+}
+
+# func_stripname prefix suffix name
+# strip PREFIX and SUFFIX off of NAME.
+# PREFIX and SUFFIX must not contain globbing or regex special
+# characters, hashes, percent signs, but SUFFIX may contain a leading
+# dot (in which case that matches only a dot).
+func_stripname ()
+{
+ # pdksh 5.2.14 does not do ${X%$Y} correctly if both X and Y are
+ # positional parameters, so assign one to ordinary parameter first.
+ func_stripname_result=${3}
+ func_stripname_result=${func_stripname_result#"${1}"}
+ func_stripname_result=${func_stripname_result%"${2}"}
+}
+
+# func_opt_split
+func_opt_split ()
+{
+ func_opt_split_opt=${1%%=*}
+ func_opt_split_arg=${1#*=}
+}
+
+# func_lo2o object
+func_lo2o ()
+{
+ case ${1} in
+ *.lo) func_lo2o_result=${1%.lo}.${objext} ;;
+ *) func_lo2o_result=${1} ;;
+ esac
+}
+
+# func_xform libobj-or-source
+func_xform ()
+{
+ func_xform_result=${1%.*}.lo
+}
+
+# func_arith arithmetic-term...
+func_arith ()
+{
+ func_arith_result=$(( $* ))
+}
+
+# func_len string
+# STRING may not start with a hyphen.
+func_len ()
+{
+ func_len_result=${#1}
+}
+
+_LT_EOF
+ ;;
+ *) # Bourne compatible functions.
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_dirname file append nondir_replacement
+# Compute the dirname of FILE. If nonempty, add APPEND to the result,
+# otherwise set result to NONDIR_REPLACEMENT.
+func_dirname ()
+{
+ # Extract subdirectory from the argument.
+ func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"`
+ if test "X$func_dirname_result" = "X${1}"; then
+ func_dirname_result="${3}"
+ else
+ func_dirname_result="$func_dirname_result${2}"
+ fi
+}
+
+# func_basename file
+func_basename ()
+{
+ func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"`
+}
+
+
+# func_stripname prefix suffix name
+# strip PREFIX and SUFFIX off of NAME.
+# PREFIX and SUFFIX must not contain globbing or regex special
+# characters, hashes, percent signs, but SUFFIX may contain a leading
+# dot (in which case that matches only a dot).
+# func_strip_suffix prefix name
+func_stripname ()
+{
+ case ${2} in
+ .*) func_stripname_result=`$ECHO "X${3}" \
+ | $Xsed -e "s%^${1}%%" -e "s%\\\\${2}\$%%"`;;
+ *) func_stripname_result=`$ECHO "X${3}" \
+ | $Xsed -e "s%^${1}%%" -e "s%${2}\$%%"`;;
+ esac
+}
+
+# sed scripts:
+my_sed_long_opt='1s/^\(-[^=]*\)=.*/\1/;q'
+my_sed_long_arg='1s/^-[^=]*=//'
+
+# func_opt_split
+func_opt_split ()
+{
+ func_opt_split_opt=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_opt"`
+ func_opt_split_arg=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_arg"`
+}
+
+# func_lo2o object
+func_lo2o ()
+{
+ func_lo2o_result=`$ECHO "X${1}" | $Xsed -e "$lo2o"`
+}
+
+# func_xform libobj-or-source
+func_xform ()
+{
+ func_xform_result=`$ECHO "X${1}" | $Xsed -e 's/\.[^.]*$/.lo/'`
+}
+
+# func_arith arithmetic-term...
+func_arith ()
+{
+ func_arith_result=`expr "$@"`
+}
+
+# func_len string
+# STRING may not start with a hyphen.
+func_len ()
+{
+ func_len_result=`expr "$1" : ".*" 2>/dev/null || echo $max_cmd_len`
+}
+
+_LT_EOF
+esac
+
+case $lt_shell_append in
+ yes)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$1+=\$2"
+}
+_LT_EOF
+ ;;
+ *)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$1=\$$1\$2"
+}
+
+_LT_EOF
+ ;;
+ esac
+
+
+ sed -n '/^# Generated shell functions inserted here/,$p' "$ltmain" >> "$cfgfile" \
+ || (rm -f "$cfgfile"; exit 1)
+
+ mv -f "$cfgfile" "$ofile" ||
+ (rm -f "$ofile" && cp "$cfgfile" "$ofile" && rm -f "$cfgfile")
+ chmod +x "$ofile"
+
+
+ cat <<_LT_EOF >> "$ofile"
+
+# ### BEGIN LIBTOOL TAG CONFIG: CXX
+
+# The linker used to build libraries.
+LD=$lt_LD_CXX
+
+# Commands used to build an old-style archive.
+old_archive_cmds=$lt_old_archive_cmds_CXX
+
+# A language specific compiler.
+CC=$lt_compiler_CXX
+
+# Is the compiler the GNU compiler?
+with_gcc=$GCC_CXX
+
+# Compiler flag to turn off builtin functions.
+no_builtin_flag=$lt_lt_prog_compiler_no_builtin_flag_CXX
+
+# How to pass a linker flag through the compiler.
+wl=$lt_lt_prog_compiler_wl_CXX
+
+# Additional compiler flags for building library objects.
+pic_flag=$lt_lt_prog_compiler_pic_CXX
+
+# Compiler flag to prevent dynamic linking.
+link_static_flag=$lt_lt_prog_compiler_static_CXX
+
+# Does compiler simultaneously support -c and -o options?
+compiler_c_o=$lt_lt_cv_prog_compiler_c_o_CXX
+
+# Whether or not to add -lc for building shared libraries.
+build_libtool_need_lc=$archive_cmds_need_lc_CXX
+
+# Whether or not to disallow shared libs when runtime libs are static.
+allow_libtool_libs_with_static_runtimes=$enable_shared_with_static_runtimes_CXX
+
+# Compiler flag to allow reflexive dlopens.
+export_dynamic_flag_spec=$lt_export_dynamic_flag_spec_CXX
+
+# Compiler flag to generate shared objects directly from archives.
+whole_archive_flag_spec=$lt_whole_archive_flag_spec_CXX
+
+# Whether the compiler copes with passing no objects directly.
+compiler_needs_object=$lt_compiler_needs_object_CXX
+
+# Create an old-style archive from a shared archive.
+old_archive_from_new_cmds=$lt_old_archive_from_new_cmds_CXX
+
+# Create a temporary old-style archive to link instead of a shared archive.
+old_archive_from_expsyms_cmds=$lt_old_archive_from_expsyms_cmds_CXX
+
+# Commands used to build a shared archive.
+archive_cmds=$lt_archive_cmds_CXX
+archive_expsym_cmds=$lt_archive_expsym_cmds_CXX
+
+# Commands used to build a loadable module if different from building
+# a shared archive.
+module_cmds=$lt_module_cmds_CXX
+module_expsym_cmds=$lt_module_expsym_cmds_CXX
+
+# Whether we are building with GNU ld or not.
+with_gnu_ld=$lt_with_gnu_ld_CXX
+
+# Flag that allows shared libraries with undefined symbols to be built.
+allow_undefined_flag=$lt_allow_undefined_flag_CXX
+
+# Flag that enforces no undefined symbols.
+no_undefined_flag=$lt_no_undefined_flag_CXX
+
+# Flag to hardcode \$libdir into a binary during linking.
+# This must work even if \$libdir does not exist
+hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec_CXX
+
+# If ld is used when linking, flag to hardcode \$libdir into a binary
+# during linking. This must work even if \$libdir does not exist.
+hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld_CXX
+
+# Whether we need a single "-rpath" flag with a separated argument.
+hardcode_libdir_separator=$lt_hardcode_libdir_separator_CXX
+
+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes
+# DIR into the resulting binary.
+hardcode_direct=$hardcode_direct_CXX
+
+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes
+# DIR into the resulting binary and the resulting library dependency is
+# "absolute",i.e impossible to change by setting \${shlibpath_var} if the
+# library is relocated.
+hardcode_direct_absolute=$hardcode_direct_absolute_CXX
+
+# Set to "yes" if using the -LDIR flag during linking hardcodes DIR
+# into the resulting binary.
+hardcode_minus_L=$hardcode_minus_L_CXX
+
+# Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR
+# into the resulting binary.
+hardcode_shlibpath_var=$hardcode_shlibpath_var_CXX
+
+# Set to "yes" if building a shared library automatically hardcodes DIR
+# into the library and all subsequent libraries and executables linked
+# against it.
+hardcode_automatic=$hardcode_automatic_CXX
+
+# Set to yes if linker adds runtime paths of dependent libraries
+# to runtime path list.
+inherit_rpath=$inherit_rpath_CXX
+
+# Whether libtool must link a program against all its dependency libraries.
+link_all_deplibs=$link_all_deplibs_CXX
+
+# Fix the shell variable \$srcfile for the compiler.
+fix_srcfile_path=$lt_fix_srcfile_path_CXX
+
+# Set to "yes" if exported symbols are required.
+always_export_symbols=$always_export_symbols_CXX
+
+# The commands to list exported symbols.
+export_symbols_cmds=$lt_export_symbols_cmds_CXX
+
+# Symbols that should not be listed in the preloaded symbols.
+exclude_expsyms=$lt_exclude_expsyms_CXX
+
+# Symbols that must always be exported.
+include_expsyms=$lt_include_expsyms_CXX
+
+# Commands necessary for linking programs (against libraries) with templates.
+prelink_cmds=$lt_prelink_cmds_CXX
+
+# Specify filename containing input files.
+file_list_spec=$lt_file_list_spec_CXX
+
+# How to hardcode a shared library path into an executable.
+hardcode_action=$hardcode_action_CXX
+
+# The directories searched by this compiler when creating a shared library.
+compiler_lib_search_dirs=$lt_compiler_lib_search_dirs_CXX
+
+# Dependencies to place before and after the objects being linked to
+# create a shared library.
+predep_objects=$lt_predep_objects_CXX
+postdep_objects=$lt_postdep_objects_CXX
+predeps=$lt_predeps_CXX
+postdeps=$lt_postdeps_CXX
+
+# The library search path used internally by the compiler when linking
+# a shared library.
+compiler_lib_search_path=$lt_compiler_lib_search_path_CXX
+
+# ### END LIBTOOL TAG CONFIG: CXX
+_LT_EOF
+
+ ;;
+ "postinst":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "prerm":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "libProgressBar.lsm":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "libProgressBar.spec":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "control":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "libProgressBar.pc":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "Makefile":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "libProgressBar/Makefile":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "doc/Makefile":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+ "doc/libProgressBar.3":F) \
+ chmod 755 postinst && chmod 755 prerm \
+ ;;
+
+ esac
+done # for ac_tag
+
+
+as_fn_exit 0
+_ACEOF
+ac_clean_files=$ac_clean_files_save
+
+test $ac_write_fail = 0 ||
+ as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5
+
+
+# configure is writing to config.log, and then calls config.status.
+# config.status does its own redirection, appending to config.log.
+# Unfortunately, on DOS this fails, as config.log is still kept open
+# by configure, so config.status won't be able to write to it; its
+# output is simply discarded. So we exec the FD to /dev/null,
+# effectively closing config.log, so it can be properly (re)opened and
+# appended to by config.status. When coming back to configure, we
+# need to make the FD available again.
+if test "$no_create" != yes; then
+ ac_cs_success=:
+ ac_config_status_args=
+ test "$silent" = yes &&
+ ac_config_status_args="$ac_config_status_args --quiet"
+ exec 5>/dev/null
+ $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
+ exec 5>>config.log
+ # Use ||, not &&, to avoid exiting from the if with $? = 1, which
+ # would make configure fail if this is the last instruction.
+ $ac_cs_success || as_fn_exit 1
+fi
+if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
+$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
+fi
+
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/configure.in b/src/libGkArrays/src/libProgressBar-1.2.0/configure.in
new file mode 100644
index 0000000..af8da41
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/configure.in
@@ -0,0 +1,101 @@
+dnl Process this file with autoconf to produce a configure script.
+
+m4_define([VERSION_MAJOR], [1])
+m4_define([VERSION_MINOR], [2])
+m4_define([VERSION_MICRO], [0])
+
+AC_INIT(
+ [Library for manage progress bars],
+ [VERSION_MAJOR.VERSION_MINOR.VERSION_MICRO],
+ [alban.mancheron at inria.fr],
+ [libProgressBar])
+AC_CONFIG_SRCDIR([libProgressBar/progressBar.cpp])
+AC_REVISION($Revision: 1.9 $)
+
+dnl The most recent interface number that this library implements.
+LIB_CURRENT=1
+dnl The implementation number of the current interface.
+LIB_REVISION=2
+dnl The difference between the newest and oldest interfaces that this library implements.
+LIB_AGE=1
+dnl LIB_VERSION is not the release number.
+dnl Please read libtool documentation about versionning
+LIB_VERSION=$LIB_CURRENT:$LIB_REVISION:$LIB_AGE
+dnl Ending numbers of library will be $((LIB_CURRENT-LIB_AGE)).$LIB_AGE.$LIB_REVISION
+
+AC_SUBST([VERSION])
+AC_SUBST([LIB_VERSION])
+AC_SUBST([LIB_VERSION_EXT], ["VERSION_MAJOR"_"VERSION_MINOR"_"VERSION_MICRO"])
+
+dnl Every other copy of the package version number gets its value from here
+AM_INIT_AUTOMAKE
+AM_PROG_LIBTOOL
+
+dnl create a config.h file (Automake will add -DHAVE_CONFIG_H)
+AC_CONFIG_HEADERS([libProgressBar/config.h])
+AC_CONFIG_MACRO_DIR([m4])
+
+AC_PROG_CC(gcc)
+AC_PROG_CXX(g++)
+
+ISODATE=`date +%Y-%m-%d`
+AC_SUBST(ISODATE)
+
+ARCH=`uname -m | sed s/i.86/i386/ | sed s/x86_64/amd64/`
+AC_SUBST(ARCH)
+
+AC_PATH_PROG(DEB_BUILDER, dpkg)
+AC_PATH_PROGS(RPM_BUILDER, [rpmbuild rpm])
+
+AC_CHECK_PROG([TEXI2DVI], [texi2dvi], [texi2dvi])
+AC_CHECK_PROG([PDFTEX], [pdftex], [pdftex])
+AC_CHECK_PROG([KPSEWHICH], [kpsewhich], [kpsewhich])
+
+BUILD_DOC=true
+AS_IF([test "x$TEXI2DVI" != "xtexi2dvi" || test "x$PDFTEX" != "xpdftex"],
+ [BUILD_DOC=false
+ AC_MSG_WARN([The 'texi2dvi' or 'pdftex' program could not be found. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases.])])
+
+AS_IF([test "x$KPSEWHICH" != "xkpsewhich" || test "$(kpsewhich -show-path=fmt)" == "/nonesuch"],
+ [BUILD_DOC=false
+ AC_MSG_WARN([The 'texi2dvi' or 'pdftex' is missing a correct latex installation. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases.])])
+AM_CONDITIONAL([BUILD_DOC], [$BUILD_DOC])
+
+AC_C_CONST
+AC_C_INLINE
+AC_HEADER_MAJOR
+AC_FUNC_ALLOCA
+AC_STRUCT_TM
+AC_STRUCT_ST_BLOCKS
+AC_PROG_INSTALL
+AC_PROG_LN_S
+
+dnl Checks for header files.
+AC_HEADER_STDC([])
+AC_CHECK_HEADERS([\
+ unistd.h sys/param.h sys/time.h time.h sys/sysmacros.h \
+ string.h strings.h memory.h fcntl.h alloca.h \
+])
+
+CXXFLAGS="-O6 -Wall --pedantic --ansi"
+
+hacked_prefix="${HACKED_PREFIX:-$prefix}"
+if test "x$hacked_prefix" == "xNONE"; then
+ hacked_prefix=$ac_default_prefix
+fi
+AC_SUBST(hacked_prefix)
+
+AC_SUBST_FILE(postrm_script)
+postrm_script=$srcdir/postrm
+AC_SUBST_FILE(postinst_script)
+postinst_script=$srcdir/postinst
+
+AC_CONFIG_FILES([\
+ postinst prerm \
+ libProgressBar.lsm libProgressBar.spec control \
+ libProgressBar.pc Makefile libProgressBar/Makefile \
+ doc/Makefile doc/libProgressBar.3 \
+], [ \
+ chmod 755 postinst && chmod 755 prerm \
+])
+AC_OUTPUT
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/control.in b/src/libGkArrays/src/libProgressBar-1.2.0/control.in
new file mode 100644
index 0000000..0e765a4
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/control.in
@@ -0,0 +1,18 @@
+Package: @PACKAGE@
+Version: @PACKAGE_VERSION@
+Section: libs
+Priority: optional
+Architecture: @ARCH@
+Essential: no
+Depends:
+Recommends:
+Suggests:
+Conflicts:
+Installed-Size: 284K
+Maintainer: DoccY <@PACKAGE_BUGREPORT@>
+Provides: @PACKAGE@
+Description: libProgressBar is a C++ library to manage... Progress bars!!!
+ .
+ If you want to easily display progress bar and if you are a
+ C++ programmer, this library is for you!
+ .
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/depcomp b/src/libGkArrays/src/libProgressBar-1.2.0/depcomp
new file mode 100755
index 0000000..df8eea7
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/depcomp
@@ -0,0 +1,630 @@
+#! /bin/sh
+# depcomp - compile a program generating dependencies as side-effects
+
+scriptversion=2009-04-28.21; # UTC
+
+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free
+# Software Foundation, Inc.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# Originally written by Alexandre Oliva <oliva at dcc.unicamp.br>.
+
+case $1 in
+ '')
+ echo "$0: No command. Try \`$0 --help' for more information." 1>&2
+ exit 1;
+ ;;
+ -h | --h*)
+ cat <<\EOF
+Usage: depcomp [--help] [--version] PROGRAM [ARGS]
+
+Run PROGRAMS ARGS to compile a file, generating dependencies
+as side-effects.
+
+Environment variables:
+ depmode Dependency tracking mode.
+ source Source file read by `PROGRAMS ARGS'.
+ object Object file output by `PROGRAMS ARGS'.
+ DEPDIR directory where to store dependencies.
+ depfile Dependency file to output.
+ tmpdepfile Temporary file to use when outputing dependencies.
+ libtool Whether libtool is used (yes/no).
+
+Report bugs to <bug-automake at gnu.org>.
+EOF
+ exit $?
+ ;;
+ -v | --v*)
+ echo "depcomp $scriptversion"
+ exit $?
+ ;;
+esac
+
+if test -z "$depmode" || test -z "$source" || test -z "$object"; then
+ echo "depcomp: Variables source, object and depmode must be set" 1>&2
+ exit 1
+fi
+
+# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
+depfile=${depfile-`echo "$object" |
+ sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
+tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
+
+rm -f "$tmpdepfile"
+
+# Some modes work just like other modes, but use different flags. We
+# parameterize here, but still list the modes in the big case below,
+# to make depend.m4 easier to write. Note that we *cannot* use a case
+# here, because this file can only contain one case statement.
+if test "$depmode" = hp; then
+ # HP compiler uses -M and no extra arg.
+ gccflag=-M
+ depmode=gcc
+fi
+
+if test "$depmode" = dashXmstdout; then
+ # This is just like dashmstdout with a different argument.
+ dashmflag=-xM
+ depmode=dashmstdout
+fi
+
+cygpath_u="cygpath -u -f -"
+if test "$depmode" = msvcmsys; then
+ # This is just like msvisualcpp but w/o cygpath translation.
+ # Just convert the backslash-escaped backslashes to single forward
+ # slashes to satisfy depend.m4
+ cygpath_u="sed s,\\\\\\\\,/,g"
+ depmode=msvisualcpp
+fi
+
+case "$depmode" in
+gcc3)
+## gcc 3 implements dependency tracking that does exactly what
+## we want. Yay! Note: for some reason libtool 1.4 doesn't like
+## it if -MD -MP comes after the -MF stuff. Hmm.
+## Unfortunately, FreeBSD c89 acceptance of flags depends upon
+## the command line argument order; so add the flags where they
+## appear in depend2.am. Note that the slowdown incurred here
+## affects only configure: in makefiles, %FASTDEP% shortcuts this.
+ for arg
+ do
+ case $arg in
+ -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;;
+ *) set fnord "$@" "$arg" ;;
+ esac
+ shift # fnord
+ shift # $arg
+ done
+ "$@"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ mv "$tmpdepfile" "$depfile"
+ ;;
+
+gcc)
+## There are various ways to get dependency output from gcc. Here's
+## why we pick this rather obscure method:
+## - Don't want to use -MD because we'd like the dependencies to end
+## up in a subdir. Having to rename by hand is ugly.
+## (We might end up doing this anyway to support other compilers.)
+## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
+## -MM, not -M (despite what the docs say).
+## - Using -M directly means running the compiler twice (even worse
+## than renaming).
+ if test -z "$gccflag"; then
+ gccflag=-MD,
+ fi
+ "$@" -Wp,"$gccflag$tmpdepfile"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
+## The second -e expression handles DOS-style file names with drive letters.
+ sed -e 's/^[^:]*: / /' \
+ -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
+## This next piece of magic avoids the `deleted header file' problem.
+## The problem is that when a header file which appears in a .P file
+## is deleted, the dependency causes make to die (because there is
+## typically no way to rebuild the header). We avoid this by adding
+## dummy dependencies for each header file. Too bad gcc doesn't do
+## this for us directly.
+ tr ' ' '
+' < "$tmpdepfile" |
+## Some versions of gcc put a space before the `:'. On the theory
+## that the space means something, we add a space to the output as
+## well.
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+hp)
+ # This case exists only to let depend.m4 do its work. It works by
+ # looking at the text of this script. This case will never be run,
+ # since it is checked for above.
+ exit 1
+ ;;
+
+sgi)
+ if test "$libtool" = yes; then
+ "$@" "-Wp,-MDupdate,$tmpdepfile"
+ else
+ "$@" -MDupdate "$tmpdepfile"
+ fi
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
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+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
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+ echo >> "$depfile"
+
+ # The second pass generates a dummy entry for each header file.
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+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
+ >> "$depfile"
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+ # The sourcefile does not contain any dependencies, so just
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+ # "include basename.Plo" scheme.
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+ rm -f "$tmpdepfile"
+ ;;
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+ # The C for AIX Compiler uses -M and outputs the dependencies
+ # in a .u file. In older versions, this file always lives in the
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+ # start of each line; $object doesn't have directory information.
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+
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+ fi
+
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+
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+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+ # Each line is of the form `foo.o: dependent.h',
+ # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
+ # Do two passes, one to just change these to
+ # `$object: dependent.h' and one to simply `dependent.h:'.
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+ # Some versions of the HPUX 10.20 sed can't process this invocation
+ # correctly. Breaking it into two sed invocations is a workaround.
+ sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
+ sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
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+ tmpdepfile1=$dir$base.d
+ tmpdepfile2=$dir.libs/$base.d
+ "$@" -Wc,+Maked
+ else
+ tmpdepfile1=$dir$base.d
+ tmpdepfile2=$dir$base.d
+ "$@" +Maked
+ fi
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2"
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+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2"
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+ done
+ if test -f "$tmpdepfile"; then
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+ # Add `dependent.h:' lines.
+ sed -ne '2,${
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+ s/ \\*$//
+ s/$/:/
+ p
+ }' "$tmpdepfile" >> "$depfile"
+ else
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile" "$tmpdepfile2"
+ ;;
+
+tru64)
+ # The Tru64 compiler uses -MD to generate dependencies as a side
+ # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
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+ # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
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+ rm -f "$tmpdepfile"
+ ;;
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+dashXmstdout)
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+
+makedepend)
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+ # Remove any Libtool call
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diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/doc/Makefile.am b/src/libGkArrays/src/libProgressBar-1.2.0/doc/Makefile.am
new file mode 100644
index 0000000..1122e04
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/doc/Makefile.am
@@ -0,0 +1,47 @@
+# build and install the .info pages
+info_TEXINFOS = libProgressBar.texinfo
+libProgressBar_TEXINFOS = lgpl.texinfo
+
+# install the man pages
+man_MANS = libProgressBar.3
+
+HTMLS = html
+DOCDIR = $(datadir)/$(PACKAGE)-$(VERSION)/
+DOCS = $(HTMLS) $(PSS) $(PDFS)
+
+AM_MAKEINFOFLAGS = --enable-encoding
+TEXI2DVI = texi2dvi -E -r
+
+all-local: info ps pdf html
+
+install-data-local: $(DOCS)
+ @$(NORMAL_INSTALL)
+ $(mkinstalldirs) $(DESTDIR)$(DOCDIR)
+ @for f in $^; do \
+ echo "test -f $$f && $(INSTALL_DATA) $$f $(DESTDIR)$(DOCDIR) || cp -R $$f $(DESTDIR)$(DOCDIR)"; \
+ test -f $$f && $(INSTALL_DATA) $$f $(DESTDIR)$(DOCDIR) || cp -R $$f $(DESTDIR)$(DOCDIR); \
+ done
+
+uninstall-local: $(DOCS)
+ @$(NORMAL_UNINSTALL)
+ @for f in $^; do \
+ echo "rm -f $(DESTDIR)$(DOCDIR)$$f"; \
+ rm -rf $(DESTDIR)$(DOCDIR)$$f; \
+ done
+ @rmdir $(DESTDIR)$(DOCDIR) 2> /dev/null && \
+ echo "$(DESTDIR)$(DOCDIR) is removed." || \
+ echo "$(DESTDIR)$(DOCDIR) is not empty or doesn't exist. So not removed."
+
+mostlyclean-local:
+ rm -rf $(DOCS)
+
+html: libProgressBar.texinfo
+ $(MAKEINFO) $(AM_MAKEINFOFLAGS) $(MAKEINFOFLAGS) -I $(srcdir) \
+ --html --number-sections `test -f '$<' || echo '$(srcdir)/'`$< -o $@
+
+EXTRA_DIST=$(man_MANS)
+
+MOSTLYCLEANFILES=$(man_MANS) *~
+CLEANFILES=*~
+DISTCLEANFILES=*~ $(PACKAGE).dvi
+MAINTAINERCLEANFILES=*~
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/doc/Makefile.in b/src/libGkArrays/src/libProgressBar-1.2.0/doc/Makefile.in
new file mode 100644
index 0000000..29a9c5b
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/doc/Makefile.in
@@ -0,0 +1,744 @@
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+
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+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
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+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
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+
+ at SET_MAKE@
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+subdir = doc
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+MAKEINFOHTML = $(MAKEINFO) --html
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+OTOOL64 = @OTOOL64@
+PACKAGE = @PACKAGE@
+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+PACKAGE_NAME = @PACKAGE_NAME@
+PACKAGE_STRING = @PACKAGE_STRING@
+PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_URL = @PACKAGE_URL@
+PACKAGE_VERSION = @PACKAGE_VERSION@
+PATH_SEPARATOR = @PATH_SEPARATOR@
+PDFTEX = @PDFTEX@
+RANLIB = @RANLIB@
+RPM_BUILDER = @RPM_BUILDER@
+SED = @SED@
+SET_MAKE = @SET_MAKE@
+SHELL = @SHELL@
+STRIP = @STRIP@
+TEXI2DVI = texi2dvi -E -r
+VERSION = @VERSION@
+abs_builddir = @abs_builddir@
+abs_srcdir = @abs_srcdir@
+abs_top_builddir = @abs_top_builddir@
+abs_top_srcdir = @abs_top_srcdir@
+ac_ct_CC = @ac_ct_CC@
+ac_ct_CXX = @ac_ct_CXX@
+ac_ct_DUMPBIN = @ac_ct_DUMPBIN@
+am__include = @am__include@
+am__leading_dot = @am__leading_dot@
+am__quote = @am__quote@
+am__tar = @am__tar@
+am__untar = @am__untar@
+bindir = @bindir@
+build = @build@
+build_alias = @build_alias@
+build_cpu = @build_cpu@
+build_os = @build_os@
+build_vendor = @build_vendor@
+builddir = @builddir@
+datadir = @datadir@
+datarootdir = @datarootdir@
+docdir = @docdir@
+dvidir = @dvidir@
+exec_prefix = @exec_prefix@
+hacked_prefix = @hacked_prefix@
+host = @host@
+host_alias = @host_alias@
+host_cpu = @host_cpu@
+host_os = @host_os@
+host_vendor = @host_vendor@
+htmldir = @htmldir@
+includedir = @includedir@
+infodir = @infodir@
+install_sh = @install_sh@
+libdir = @libdir@
+libexecdir = @libexecdir@
+localedir = @localedir@
+localstatedir = @localstatedir@
+lt_ECHO = @lt_ECHO@
+mandir = @mandir@
+mkdir_p = @mkdir_p@
+oldincludedir = @oldincludedir@
+pdfdir = @pdfdir@
+prefix = @prefix@
+program_transform_name = @program_transform_name@
+psdir = @psdir@
+sbindir = @sbindir@
+sharedstatedir = @sharedstatedir@
+srcdir = @srcdir@
+sysconfdir = @sysconfdir@
+target_alias = @target_alias@
+top_build_prefix = @top_build_prefix@
+top_builddir = @top_builddir@
+top_srcdir = @top_srcdir@
+
+# build and install the .info pages
+info_TEXINFOS = libProgressBar.texinfo
+libProgressBar_TEXINFOS = lgpl.texinfo
+
+# install the man pages
+man_MANS = libProgressBar.3
+HTMLS = html
+DOCDIR = $(datadir)/$(PACKAGE)-$(VERSION)/
+DOCS = $(HTMLS) $(PSS) $(PDFS)
+AM_MAKEINFOFLAGS = --enable-encoding
+EXTRA_DIST = $(man_MANS)
+MOSTLYCLEANFILES = $(man_MANS) *~
+CLEANFILES = *~
+DISTCLEANFILES = *~ $(PACKAGE).dvi
+MAINTAINERCLEANFILES = *~
+all: all-am
+
+.SUFFIXES:
+.SUFFIXES: .dvi .html .info .pdf .ps .texinfo
+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
+ @for dep in $?; do \
+ case '$(am__configure_deps)' in \
+ *$$dep*) \
+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+ && { if test -f $@; then exit 0; else break; fi; }; \
+ exit 1;; \
+ esac; \
+ done; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu doc/Makefile'; \
+ $(am__cd) $(top_srcdir) && \
+ $(AUTOMAKE) --gnu doc/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+ @case '$?' in \
+ *config.status*) \
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+ *) \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure: $(am__configure_deps)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+libProgressBar.3: $(top_builddir)/config.status $(srcdir)/libProgressBar.3.in
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
+
+mostlyclean-libtool:
+ -rm -f *.lo
+
+clean-libtool:
+ -rm -rf .libs _libs
+
+.texinfo.info:
+ restore=: && backupdir="$(am__leading_dot)am$$$$" && \
+ am__cwd=`pwd` && $(am__cd) $(srcdir) && \
+ rm -rf $$backupdir && mkdir $$backupdir && \
+ if ($(MAKEINFO) --version) >/dev/null 2>&1; then \
+ for f in $@ $@-[0-9] $@-[0-9][0-9] $(@:.info=).i[0-9] $(@:.info=).i[0-9][0-9]; do \
+ if test -f $$f; then mv $$f $$backupdir; restore=mv; else :; fi; \
+ done; \
+ else :; fi && \
+ cd "$$am__cwd"; \
+ if $(MAKEINFO) $(AM_MAKEINFOFLAGS) $(MAKEINFOFLAGS) -I $(srcdir) \
+ -o $@ $<; \
+ then \
+ rc=0; \
+ $(am__cd) $(srcdir); \
+ else \
+ rc=$$?; \
+ $(am__cd) $(srcdir) && \
+ $$restore $$backupdir/* `echo "./$@" | sed 's|[^/]*$$||'`; \
+ fi; \
+ rm -rf $$backupdir; exit $$rc
+
+.texinfo.dvi:
+ TEXINPUTS="$(am__TEXINFO_TEX_DIR)$(PATH_SEPARATOR)$$TEXINPUTS" \
+ MAKEINFO='$(MAKEINFO) $(AM_MAKEINFOFLAGS) $(MAKEINFOFLAGS) -I $(srcdir)' \
+ $(TEXI2DVI) $<
+
+.texinfo.pdf:
+ TEXINPUTS="$(am__TEXINFO_TEX_DIR)$(PATH_SEPARATOR)$$TEXINPUTS" \
+ MAKEINFO='$(MAKEINFO) $(AM_MAKEINFOFLAGS) $(MAKEINFOFLAGS) -I $(srcdir)' \
+ $(TEXI2PDF) $<
+
+.texinfo.html:
+ rm -rf $(@:.html=.htp)
+ if $(MAKEINFOHTML) $(AM_MAKEINFOHTMLFLAGS) $(MAKEINFOFLAGS) -I $(srcdir) \
+ -o $(@:.html=.htp) $<; \
+ then \
+ rm -rf $@; \
+ if test ! -d $(@:.html=.htp) && test -d $(@:.html=); then \
+ mv $(@:.html=) $@; else mv $(@:.html=.htp) $@; fi; \
+ else \
+ if test ! -d $(@:.html=.htp) && test -d $(@:.html=); then \
+ rm -rf $(@:.html=); else rm -Rf $(@:.html=.htp) $@; fi; \
+ exit 1; \
+ fi
+$(srcdir)/libProgressBar.info: libProgressBar.texinfo $(libProgressBar_TEXINFOS)
+libProgressBar.dvi: libProgressBar.texinfo $(libProgressBar_TEXINFOS)
+libProgressBar.pdf: libProgressBar.texinfo $(libProgressBar_TEXINFOS)
+libProgressBar.html: libProgressBar.texinfo $(libProgressBar_TEXINFOS)
+.dvi.ps:
+ TEXINPUTS="$(am__TEXINFO_TEX_DIR)$(PATH_SEPARATOR)$$TEXINPUTS" \
+ $(DVIPS) -o $@ $<
+
+uninstall-dvi-am:
+ @$(NORMAL_UNINSTALL)
+ @list='$(DVIS)'; test -n "$(dvidir)" || list=; \
+ for p in $$list; do \
+ $(am__strip_dir) \
+ echo " rm -f '$(DESTDIR)$(dvidir)/$$f'"; \
+ rm -f "$(DESTDIR)$(dvidir)/$$f"; \
+ done
+
+uninstall-html-am:
+ @$(NORMAL_UNINSTALL)
+ @list='$(HTMLS)'; test -n "$(htmldir)" || list=; \
+ for p in $$list; do \
+ $(am__strip_dir) \
+ echo " rm -rf '$(DESTDIR)$(htmldir)/$$f'"; \
+ rm -rf "$(DESTDIR)$(htmldir)/$$f"; \
+ done
+
+uninstall-info-am:
+ @$(PRE_UNINSTALL)
+ @if test -d '$(DESTDIR)$(infodir)' && \
+ (install-info --version && \
+ install-info --version 2>&1 | sed 1q | grep -i -v debian) >/dev/null 2>&1; then \
+ list='$(INFO_DEPS)'; \
+ for file in $$list; do \
+ relfile=`echo "$$file" | sed 's|^.*/||'`; \
+ echo " install-info --info-dir='$(DESTDIR)$(infodir)' --remove '$(DESTDIR)$(infodir)/$$relfile'"; \
+ if install-info --info-dir="$(DESTDIR)$(infodir)" --remove "$(DESTDIR)$(infodir)/$$relfile"; \
+ then :; else test ! -f "$(DESTDIR)$(infodir)/$$relfile" || exit 1; fi; \
+ done; \
+ else :; fi
+ @$(NORMAL_UNINSTALL)
+ @list='$(INFO_DEPS)'; \
+ for file in $$list; do \
+ relfile=`echo "$$file" | sed 's|^.*/||'`; \
+ relfile_i=`echo "$$relfile" | sed 's|\.info$$||;s|$$|.i|'`; \
+ (if test -d "$(DESTDIR)$(infodir)" && cd "$(DESTDIR)$(infodir)"; then \
+ echo " cd '$(DESTDIR)$(infodir)' && rm -f $$relfile $$relfile-[0-9] $$relfile-[0-9][0-9] $$relfile_i[0-9] $$relfile_i[0-9][0-9]"; \
+ rm -f $$relfile $$relfile-[0-9] $$relfile-[0-9][0-9] $$relfile_i[0-9] $$relfile_i[0-9][0-9]; \
+ else :; fi); \
+ done
+
+uninstall-pdf-am:
+ @$(NORMAL_UNINSTALL)
+ @list='$(PDFS)'; test -n "$(pdfdir)" || list=; \
+ for p in $$list; do \
+ $(am__strip_dir) \
+ echo " rm -f '$(DESTDIR)$(pdfdir)/$$f'"; \
+ rm -f "$(DESTDIR)$(pdfdir)/$$f"; \
+ done
+
+uninstall-ps-am:
+ @$(NORMAL_UNINSTALL)
+ @list='$(PSS)'; test -n "$(psdir)" || list=; \
+ for p in $$list; do \
+ $(am__strip_dir) \
+ echo " rm -f '$(DESTDIR)$(psdir)/$$f'"; \
+ rm -f "$(DESTDIR)$(psdir)/$$f"; \
+ done
+
+dist-info: $(INFO_DEPS)
+ @srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; \
+ list='$(INFO_DEPS)'; \
+ for base in $$list; do \
+ case $$base in \
+ $(srcdir)/*) base=`echo "$$base" | sed "s|^$$srcdirstrip/||"`;; \
+ esac; \
+ if test -f $$base; then d=.; else d=$(srcdir); fi; \
+ base_i=`echo "$$base" | sed 's|\.info$$||;s|$$|.i|'`; \
+ for file in $$d/$$base $$d/$$base-[0-9] $$d/$$base-[0-9][0-9] $$d/$$base_i[0-9] $$d/$$base_i[0-9][0-9]; do \
+ if test -f $$file; then \
+ relfile=`expr "$$file" : "$$d/\(.*\)"`; \
+ test -f "$(distdir)/$$relfile" || \
+ cp -p $$file "$(distdir)/$$relfile"; \
+ else :; fi; \
+ done; \
+ done
+
+mostlyclean-aminfo:
+ -rm -rf libProgressBar.aux libProgressBar.cp libProgressBar.cps \
+ libProgressBar.fn libProgressBar.fns libProgressBar.ky \
+ libProgressBar.kys libProgressBar.log libProgressBar.pg \
+ libProgressBar.pgs libProgressBar.tmp libProgressBar.toc \
+ libProgressBar.tp libProgressBar.tps libProgressBar.vr \
+ libProgressBar.vrs
+
+clean-aminfo:
+ -test -z "libProgressBar.dvi libProgressBar.pdf libProgressBar.ps \
+ libProgressBar.html" \
+ || rm -rf libProgressBar.dvi libProgressBar.pdf libProgressBar.ps \
+ libProgressBar.html
+
+maintainer-clean-aminfo:
+ @list='$(INFO_DEPS)'; for i in $$list; do \
+ i_i=`echo "$$i" | sed 's|\.info$$||;s|$$|.i|'`; \
+ echo " rm -f $$i $$i-[0-9] $$i-[0-9][0-9] $$i_i[0-9] $$i_i[0-9][0-9]"; \
+ rm -f $$i $$i-[0-9] $$i-[0-9][0-9] $$i_i[0-9] $$i_i[0-9][0-9]; \
+ done
+install-man3: $(man_MANS)
+ @$(NORMAL_INSTALL)
+ test -z "$(man3dir)" || $(MKDIR_P) "$(DESTDIR)$(man3dir)"
+ @list=''; test -n "$(man3dir)" || exit 0; \
+ { for i in $$list; do echo "$$i"; done; \
+ l2='$(man_MANS)'; for i in $$l2; do echo "$$i"; done | \
+ sed -n '/\.3[a-z]*$$/p'; \
+ } | while read p; do \
+ if test -f $$p; then d=; else d="$(srcdir)/"; fi; \
+ echo "$$d$$p"; echo "$$p"; \
+ done | \
+ sed -e 'n;s,.*/,,;p;h;s,.*\.,,;s,^[^3][0-9a-z]*$$,3,;x' \
+ -e 's,\.[0-9a-z]*$$,,;$(transform);G;s,\n,.,' | \
+ sed 'N;N;s,\n, ,g' | { \
+ list=; while read file base inst; do \
+ if test "$$base" = "$$inst"; then list="$$list $$file"; else \
+ echo " $(INSTALL_DATA) '$$file' '$(DESTDIR)$(man3dir)/$$inst'"; \
+ $(INSTALL_DATA) "$$file" "$(DESTDIR)$(man3dir)/$$inst" || exit $$?; \
+ fi; \
+ done; \
+ for i in $$list; do echo "$$i"; done | $(am__base_list) | \
+ while read files; do \
+ test -z "$$files" || { \
+ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(man3dir)'"; \
+ $(INSTALL_DATA) $$files "$(DESTDIR)$(man3dir)" || exit $$?; }; \
+ done; }
+
+uninstall-man3:
+ @$(NORMAL_UNINSTALL)
+ @list=''; test -n "$(man3dir)" || exit 0; \
+ files=`{ for i in $$list; do echo "$$i"; done; \
+ l2='$(man_MANS)'; for i in $$l2; do echo "$$i"; done | \
+ sed -n '/\.3[a-z]*$$/p'; \
+ } | sed -e 's,.*/,,;h;s,.*\.,,;s,^[^3][0-9a-z]*$$,3,;x' \
+ -e 's,\.[0-9a-z]*$$,,;$(transform);G;s,\n,.,'`; \
+ test -z "$$files" || { \
+ echo " ( cd '$(DESTDIR)$(man3dir)' && rm -f" $$files ")"; \
+ cd "$(DESTDIR)$(man3dir)" && rm -f $$files; }
+tags: TAGS
+TAGS:
+
+ctags: CTAGS
+CTAGS:
+
+
+distdir: $(DISTFILES)
+ @list='$(MANS)'; if test -n "$$list"; then \
+ list=`for p in $$list; do \
+ if test -f $$p; then d=; else d="$(srcdir)/"; fi; \
+ if test -f "$$d$$p"; then echo "$$d$$p"; else :; fi; done`; \
+ if test -n "$$list" && \
+ grep 'ab help2man is required to generate this page' $$list >/dev/null; then \
+ echo "error: found man pages containing the \`missing help2man' replacement text:" >&2; \
+ grep -l 'ab help2man is required to generate this page' $$list | sed 's/^/ /' >&2; \
+ echo " to fix them, install help2man, remove and regenerate the man pages;" >&2; \
+ echo " typically \`make maintainer-clean' will remove them" >&2; \
+ exit 1; \
+ else :; fi; \
+ else :; fi
+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+ list='$(DISTFILES)'; \
+ dist_files=`for file in $$list; do echo $$file; done | \
+ sed -e "s|^$$srcdirstrip/||;t" \
+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+ case $$dist_files in \
+ */*) $(MKDIR_P) `echo "$$dist_files" | \
+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+ sort -u` ;; \
+ esac; \
+ for file in $$dist_files; do \
+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+ if test -d $$d/$$file; then \
+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test -d "$(distdir)/$$file"; then \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ fi; \
+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ fi; \
+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+ else \
+ test -f "$(distdir)/$$file" \
+ || cp -p $$d/$$file "$(distdir)/$$file" \
+ || exit 1; \
+ fi; \
+ done
+ $(MAKE) $(AM_MAKEFLAGS) \
+ top_distdir="$(top_distdir)" distdir="$(distdir)" \
+ dist-info
+check-am: all-am
+check: check-am
+all-am: Makefile $(INFO_DEPS) $(MANS) all-local
+installdirs:
+ for dir in "$(DESTDIR)$(infodir)" "$(DESTDIR)$(man3dir)"; do \
+ test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+ done
+install: install-am
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+ @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
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+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+ `test -z '$(STRIP)' || \
+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+ -test -z "$(MOSTLYCLEANFILES)" || rm -f $(MOSTLYCLEANFILES)
+
+clean-generic:
+ -test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+ -test -z "$(DISTCLEANFILES)" || rm -f $(DISTCLEANFILES)
+
+maintainer-clean-generic:
+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+ -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
+clean: clean-am
+
+clean-am: clean-aminfo clean-generic clean-libtool mostlyclean-am
+
+distclean: distclean-am
+ -rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+dvi: dvi-am
+
+dvi-am: $(DVIS)
+
+html-am: $(HTMLS)
+
+info: info-am
+
+info-am: $(INFO_DEPS)
+
+install-data-am: install-data-local install-info-am install-man
+
+install-dvi: install-dvi-am
+
+install-dvi-am: $(DVIS)
+ @$(NORMAL_INSTALL)
+ test -z "$(dvidir)" || $(MKDIR_P) "$(DESTDIR)$(dvidir)"
+ @list='$(DVIS)'; test -n "$(dvidir)" || list=; \
+ for p in $$list; do \
+ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+ echo "$$d$$p"; \
+ done | $(am__base_list) | \
+ while read files; do \
+ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(dvidir)'"; \
+ $(INSTALL_DATA) $$files "$(DESTDIR)$(dvidir)" || exit $$?; \
+ done
+install-exec-am:
+
+install-html: install-html-am
+
+install-html-am: $(HTMLS)
+ @$(NORMAL_INSTALL)
+ test -z "$(htmldir)" || $(MKDIR_P) "$(DESTDIR)$(htmldir)"
+ @list='$(HTMLS)'; list2=; test -n "$(htmldir)" || list=; \
+ for p in $$list; do \
+ if test -f "$$p" || test -d "$$p"; then d=; else d="$(srcdir)/"; fi; \
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+ if test -d "$$d$$p"; then \
+ echo " $(MKDIR_P) '$(DESTDIR)$(htmldir)/$$f'"; \
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+ echo " $(INSTALL_DATA) '$$d$$p'/* '$(DESTDIR)$(htmldir)/$$f'"; \
+ $(INSTALL_DATA) "$$d$$p"/* "$(DESTDIR)$(htmldir)/$$f" || exit $$?; \
+ else \
+ list2="$$list2 $$d$$p"; \
+ fi; \
+ done; \
+ test -z "$$list2" || { echo "$$list2" | $(am__base_list) | \
+ while read files; do \
+ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(htmldir)'"; \
+ $(INSTALL_DATA) $$files "$(DESTDIR)$(htmldir)" || exit $$?; \
+ done; }
+install-info: install-info-am
+
+install-info-am: $(INFO_DEPS)
+ @$(NORMAL_INSTALL)
+ test -z "$(infodir)" || $(MKDIR_P) "$(DESTDIR)$(infodir)"
+ @srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; \
+ list='$(INFO_DEPS)'; test -n "$(infodir)" || list=; \
+ for file in $$list; do \
+ case $$file in \
+ $(srcdir)/*) file=`echo "$$file" | sed "s|^$$srcdirstrip/||"`;; \
+ esac; \
+ if test -f $$file; then d=.; else d=$(srcdir); fi; \
+ file_i=`echo "$$file" | sed 's|\.info$$||;s|$$|.i|'`; \
+ for ifile in $$d/$$file $$d/$$file-[0-9] $$d/$$file-[0-9][0-9] \
+ $$d/$$file_i[0-9] $$d/$$file_i[0-9][0-9] ; do \
+ if test -f $$ifile; then \
+ echo "$$ifile"; \
+ else : ; fi; \
+ done; \
+ done | $(am__base_list) | \
+ while read files; do \
+ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(infodir)'"; \
+ $(INSTALL_DATA) $$files "$(DESTDIR)$(infodir)" || exit $$?; done
+ @$(POST_INSTALL)
+ @if (install-info --version && \
+ install-info --version 2>&1 | sed 1q | grep -i -v debian) >/dev/null 2>&1; then \
+ list='$(INFO_DEPS)'; test -n "$(infodir)" || list=; \
+ for file in $$list; do \
+ relfile=`echo "$$file" | sed 's|^.*/||'`; \
+ echo " install-info --info-dir='$(DESTDIR)$(infodir)' '$(DESTDIR)$(infodir)/$$relfile'";\
+ install-info --info-dir="$(DESTDIR)$(infodir)" "$(DESTDIR)$(infodir)/$$relfile" || :;\
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+ for p in $$list; do \
+ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+ echo "$$d$$p"; \
+ done | $(am__base_list) | \
+ while read files; do \
+ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(pdfdir)'"; \
+ $(INSTALL_DATA) $$files "$(DESTDIR)$(pdfdir)" || exit $$?; done
+install-ps: install-ps-am
+
+install-ps-am: $(PSS)
+ @$(NORMAL_INSTALL)
+ test -z "$(psdir)" || $(MKDIR_P) "$(DESTDIR)$(psdir)"
+ @list='$(PSS)'; test -n "$(psdir)" || list=; \
+ for p in $$list; do \
+ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+ echo "$$d$$p"; \
+ done | $(am__base_list) | \
+ while read files; do \
+ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(psdir)'"; \
+ $(INSTALL_DATA) $$files "$(DESTDIR)$(psdir)" || exit $$?; done
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-aminfo \
+ maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-aminfo mostlyclean-generic \
+ mostlyclean-libtool mostlyclean-local
+
+pdf: pdf-am
+
+pdf-am: $(PDFS)
+
+ps: ps-am
+
+ps-am: $(PSS)
+
+uninstall-am: uninstall-dvi-am uninstall-html-am uninstall-info-am \
+ uninstall-local uninstall-man uninstall-pdf-am uninstall-ps-am
+
+uninstall-man: uninstall-man3
+
+.MAKE: install-am install-strip
+
+.PHONY: all all-am all-local check check-am clean clean-aminfo \
+ clean-generic clean-libtool dist-info distclean \
+ distclean-generic distclean-libtool distdir dvi dvi-am html \
+ html-am info info-am install install-am install-data \
+ install-data-am install-data-local install-dvi install-dvi-am \
+ install-exec install-exec-am install-html install-html-am \
+ install-info install-info-am install-man install-man3 \
+ install-pdf install-pdf-am install-ps install-ps-am \
+ install-strip installcheck installcheck-am installdirs \
+ maintainer-clean maintainer-clean-aminfo \
+ maintainer-clean-generic mostlyclean mostlyclean-aminfo \
+ mostlyclean-generic mostlyclean-libtool mostlyclean-local pdf \
+ pdf-am ps ps-am uninstall uninstall-am uninstall-dvi-am \
+ uninstall-html-am uninstall-info-am uninstall-local \
+ uninstall-man uninstall-man3 uninstall-pdf-am uninstall-ps-am
+
+
+all-local: info ps pdf html
+
+install-data-local: $(DOCS)
+ @$(NORMAL_INSTALL)
+ $(mkinstalldirs) $(DESTDIR)$(DOCDIR)
+ @for f in $^; do \
+ echo "test -f $$f && $(INSTALL_DATA) $$f $(DESTDIR)$(DOCDIR) || cp -R $$f $(DESTDIR)$(DOCDIR)"; \
+ test -f $$f && $(INSTALL_DATA) $$f $(DESTDIR)$(DOCDIR) || cp -R $$f $(DESTDIR)$(DOCDIR); \
+ done
+
+uninstall-local: $(DOCS)
+ @$(NORMAL_UNINSTALL)
+ @for f in $^; do \
+ echo "rm -f $(DESTDIR)$(DOCDIR)$$f"; \
+ rm -rf $(DESTDIR)$(DOCDIR)$$f; \
+ done
+ @rmdir $(DESTDIR)$(DOCDIR) 2> /dev/null && \
+ echo "$(DESTDIR)$(DOCDIR) is removed." || \
+ echo "$(DESTDIR)$(DOCDIR) is not empty or doesn't exist. So not removed."
+
+mostlyclean-local:
+ rm -rf $(DOCS)
+
+html: libProgressBar.texinfo
+ $(MAKEINFO) $(AM_MAKEINFOFLAGS) $(MAKEINFOFLAGS) -I $(srcdir) \
+ --html --number-sections `test -f '$<' || echo '$(srcdir)/'`$< -o $@
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/doc/lgpl.texinfo b/src/libGkArrays/src/libProgressBar-1.2.0/doc/lgpl.texinfo
new file mode 100644
index 0000000..2167662
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/doc/lgpl.texinfo
@@ -0,0 +1,190 @@
+ at c The GNU Lesser General Public License.
+ at center Version 3, 29 June 2007
+
+ at c This file is intended to be included within another document,
+ at c hence no sectioning command or @node.
+
+ at display
+Copyright @copyright{} 2007 Free Software Foundation, Inc. @url{http://fsf.org/}
+
+Everyone is permitted to copy and distribute verbatim copies of this
+license document, but changing it is not allowed.
+ at end display
+
+This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+ at enumerate 0
+ at item Additional Definitions.
+
+As used herein, ``this License'' refers to version 3 of the GNU Lesser
+General Public License, and the ``GNU GPL'' refers to version 3 of the GNU
+General Public License.
+
+``The Library'' refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+An ``Application'' is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+A ``Combined Work'' is a work produced by combining or linking an
+Application with the Library. The particular version of the Library
+with which the Combined Work was made is also called the ``Linked
+Version''.
+
+The ``Minimal Corresponding Source'' for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+The ``Corresponding Application Code'' for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+ at item Exception to Section 3 of the GNU GPL.
+
+You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+ at item Conveying Modified Versions.
+
+If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+ at enumerate a
+ at item
+under this License, provided that you make a good faith effort to
+ensure that, in the event an Application does not supply the
+function or data, the facility still operates, and performs
+whatever part of its purpose remains meaningful, or
+
+ at item
+under the GNU GPL, with none of the additional permissions of
+this License applicable to that copy.
+ at end enumerate
+
+ at item Object Code Incorporating Material from Library Header Files.
+
+The object code form of an Application may incorporate material from
+a header file that is part of the Library. You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+ at enumerate a
+ at item
+Give prominent notice with each copy of the object code that the
+Library is used in it and that the Library and its use are
+covered by this License.
+ at item
+Accompany the object code with a copy of the GNU GPL and this license
+document.
+ at end enumerate
+
+ at item Combined Works.
+
+You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+ at enumerate a
+ at item
+Give prominent notice with each copy of the Combined Work that
+the Library is used in it and that the Library and its use are
+covered by this License.
+ at item
+Accompany the Combined Work with a copy of the GNU GPL and this license
+document.
+ at item
+For a Combined Work that displays copyright notices during
+execution, include the copyright notice for the Library among
+these notices, as well as a reference directing the user to the
+copies of the GNU GPL and this license document.
+ at item
+Do one of the following:
+
+ at enumerate 0
+ at item
+Convey the Minimal Corresponding Source under the terms of this
+License, and the Corresponding Application Code in a form
+suitable for, and under terms that permit, the user to
+recombine or relink the Application with a modified version of
+the Linked Version to produce a modified Combined Work, in the
+manner specified by section 6 of the GNU GPL for conveying
+Corresponding Source.
+ at item
+Use a suitable shared library mechanism for linking with the
+Library. A suitable mechanism is one that (a) uses at run time
+a copy of the Library already present on the user's computer
+system, and (b) will operate properly with a modified version
+of the Library that is interface-compatible with the Linked
+Version.
+ at end enumerate
+
+ at item
+Provide Installation Information, but only if you would otherwise
+be required to provide such information under section 6 of the
+GNU GPL, and only to the extent that such information is
+necessary to install and execute a modified version of the
+Combined Work produced by recombining or relinking the
+Application with a modified version of the Linked Version. (If
+you use option 4d0, the Installation Information must accompany
+the Minimal Corresponding Source and Corresponding Application
+Code. If you use option 4d1, you must provide the Installation
+Information in the manner specified by section 6 of the GNU GPL
+for conveying Corresponding Source.)
+ at end enumerate
+
+ at item Combined Libraries.
+
+You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+ at enumerate a
+ at item
+Accompany the combined library with a copy of the same work based
+on the Library, uncombined with any other library facilities,
+conveyed under the terms of this License.
+ at item
+Give prominent notice with the combined library that part of it
+is a work based on the Library, and explaining where to find the
+accompanying uncombined form of the same work.
+ at end enumerate
+
+ at item Revised Versions of the GNU Lesser General Public License.
+
+The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License ``or any later version''
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.
+
+ at end enumerate
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/doc/libProgressBar.3 b/src/libGkArrays/src/libProgressBar-1.2.0/doc/libProgressBar.3
new file mode 100644
index 0000000..41639ba
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/doc/libProgressBar.3
@@ -0,0 +1,94 @@
+.\" hie, Emacs: -*- nroff -*-
+.\" libProgressBar is free software; you can redistribute it and/or modify
+.\" it under the terms of the GNU General Public License as published by
+.\" the Free Software Foundation; either version 2 of the License, or
+.\" (at your option) any later version.
+.\"
+.\" This program is distributed in the hope that it will be useful,
+.\" but WITHOUT ANY WARRANTY; without even the implied warranty of
+.\" MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+.\" GNU General Public License for more details.
+.\"
+.\" You should have received a copy of the GNU General Public License
+.\" along with this program; see the file COPYING. If not, write to
+.\" the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.
+.\"
+
+.TH libProgressBar 3 "2014-04-30" "libProgressBar version 1.2.0" "C++"
+
+.\" Please update the above date whenever this man page is modified.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins (default)
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+
+
+.\"
+.\" SECTION "NAME"
+.\"
+.SH "NAME"
+
+.ce 3
+.SB libProgressBar
+
+This library intends to create and manipulate... Progress bars!!!
+.ce 0
+
+.\"
+.\" SECTION "SEE ALSO"
+.\"
+.SH "SEE ALSO"
+
+The full documentation for
+.B libProgressBar
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B libProgressBar
+programs are properly installed at your site, the command
+.IP
+.B info libProgressBar
+.PP
+should give you access to the complete manual.
+.PP
+You can also find the ps and pdf versions of these manuals in /usr/local/share/libProgressBar/.
+
+.\"
+.\" SECTION "COPYRIGHT"
+.\"
+.SH "COPYRIGHT"
+
+Copyright @ 2007 -- Universit� des Antilles et de la Guyane
+
+Author: DoccY <alban.mancheron at inria.fr>
+.PP
+libProgressBar comes with ABSOLUTELY NO WARRANTY.
+.PP
+This is free library, and you are welcome to redistribute it under certain conditions.
+.PP
+See the GNU Lesser General Public License for more details.
+
+
+.\"
+.\" SECTION "BUGS"
+.\"
+.SH "BUGS"
+
+We thank you for reporting bugs to:
+.RS
+<alban.mancheron at inria.fr>
+
+
+.\"
+.\" SECTION "AUTHOR"
+.\"
+.SH "AUTHOR"
+
+DoccY <alban.mancheron at inria.fr>
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/doc/libProgressBar.3.in b/src/libGkArrays/src/libProgressBar-1.2.0/doc/libProgressBar.3.in
new file mode 100644
index 0000000..bb4a5b3
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/doc/libProgressBar.3.in
@@ -0,0 +1,94 @@
+.\" hie, Emacs: -*- nroff -*-
+.\" @PACKAGE@ is free software; you can redistribute it and/or modify
+.\" it under the terms of the GNU General Public License as published by
+.\" the Free Software Foundation; either version 2 of the License, or
+.\" (at your option) any later version.
+.\"
+.\" This program is distributed in the hope that it will be useful,
+.\" but WITHOUT ANY WARRANTY; without even the implied warranty of
+.\" MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+.\" GNU General Public License for more details.
+.\"
+.\" You should have received a copy of the GNU General Public License
+.\" along with this program; see the file COPYING. If not, write to
+.\" the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.
+.\"
+
+.TH @PACKAGE@ 3 "@ISODATE@" "@PACKAGE@ version @VERSION@" "C++"
+
+.\" Please update the above date whenever this man page is modified.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins (default)
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+
+
+.\"
+.\" SECTION "NAME"
+.\"
+.SH "NAME"
+
+.ce 3
+.SB @PACKAGE@
+
+This library intends to create and manipulate... Progress bars!!!
+.ce 0
+
+.\"
+.\" SECTION "SEE ALSO"
+.\"
+.SH "SEE ALSO"
+
+The full documentation for
+.B @PACKAGE@
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B @PACKAGE@
+programs are properly installed at your site, the command
+.IP
+.B info @PACKAGE@
+.PP
+should give you access to the complete manual.
+.PP
+You can also find the ps and pdf versions of these manuals in /usr/local/share/@PACKAGE@/.
+
+.\"
+.\" SECTION "COPYRIGHT"
+.\"
+.SH "COPYRIGHT"
+
+Copyright @ 2007 -- Universit� des Antilles et de la Guyane
+
+Author: DoccY <@PACKAGE_BUGREPORT@>
+.PP
+ at PACKAGE@ comes with ABSOLUTELY NO WARRANTY.
+.PP
+This is free library, and you are welcome to redistribute it under certain conditions.
+.PP
+See the GNU Lesser General Public License for more details.
+
+
+.\"
+.\" SECTION "BUGS"
+.\"
+.SH "BUGS"
+
+We thank you for reporting bugs to:
+.RS
+<@PACKAGE_BUGREPORT@>
+
+
+.\"
+.\" SECTION "AUTHOR"
+.\"
+.SH "AUTHOR"
+
+DoccY <alban.mancheron at inria.fr>
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/doc/libProgressBar.info b/src/libGkArrays/src/libProgressBar-1.2.0/doc/libProgressBar.info
new file mode 100644
index 0000000..4ff6fda
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/doc/libProgressBar.info
@@ -0,0 +1,294 @@
+This is libProgressBar.info, produced by makeinfo version 4.13 from
+libProgressBar.texinfo.
+
+This file documents the `libProgressBar' library.
+
+ Copyright � 2007 - Universit� des Antilles et de la Guyane/Institut
+National de Recherche en Informatique et en Automatique
+
+ Author: DoccY <alban.mancheron at inria.fr>
+
+ Permission is granted to make and distribute verbatim copies of this
+manual provided the copyright notice and this permission notice are
+preserved on all copies.
+
+ Permission is granted to copy and distribute modified versions of
+this manual under the conditions for verbatim copying, provided that
+the entire resulting derived work is distributed under the terms of a
+permission notice identical to this one.
+
+ Permission is granted to copy and distribute translations of this
+manual into another language, under the above conditions for modified
+versions, except that this permission notice may be stated in a
+translation approved by the Foundation.
+
+
+File: libProgressBar.info, Node: Top, Next: Instructions, Prev: (dir), Up: (dir)
+
+ This file documents the `libProgressBar' library.
+
+* Menu:
+
+* Instructions:: How to read this manual.
+* Copying:: How you can copy and share `libProgressBar'.
+* Overview:: Preliminary information.
+* Example:: An example of the use of `libProgressBar'.
+* Problems:: Reporting bugs.
+* Concept Index:: Index of concepts.
+
+
+File: libProgressBar.info, Node: Instructions, Next: Copying, Prev: Top, Up: Top
+
+1 How to Read This Manual
+*************************
+
+ You will find in the Copying section the GNU Lesser General Public
+License. In the Overview section, is given a quick description about
+what does `libProgressBar'. Then, you will have an example of use.
+
+ Indeed, we'll hope you having a good fun using `libProgressBar'.
+
+
+File: libProgressBar.info, Node: Copying, Next: Overview, Prev: Instructions, Up: Top
+
+2 Copying
+*********
+
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. `http://fsf.org/'
+
+ Everyone is permitted to copy and distribute verbatim copies of this
+ license document, but changing it is not allowed.
+
+ This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+ 0. Additional Definitions.
+
+ As used herein, "this License" refers to version 3 of the GNU
+ Lesser General Public License, and the "GNU GPL" refers to version
+ 3 of the GNU General Public License.
+
+ "The Library" refers to a covered work governed by this License,
+ other than an Application or a Combined Work as defined below.
+
+ An "Application" is any work that makes use of an interface
+ provided by the Library, but which is not otherwise based on the
+ Library. Defining a subclass of a class defined by the Library is
+ deemed a mode of using an interface provided by the Library.
+
+ A "Combined Work" is a work produced by combining or linking an
+ Application with the Library. The particular version of the
+ Library with which the Combined Work was made is also called the
+ "Linked Version".
+
+ The "Minimal Corresponding Source" for a Combined Work means the
+ Corresponding Source for the Combined Work, excluding any source
+ code for portions of the Combined Work that, considered in
+ isolation, are based on the Application, and not on the Linked
+ Version.
+
+ The "Corresponding Application Code" for a Combined Work means the
+ object code and/or source code for the Application, including any
+ data and utility programs needed for reproducing the Combined Work
+ from the Application, but excluding the System Libraries of the
+ Combined Work.
+
+ 1. Exception to Section 3 of the GNU GPL.
+
+ You may convey a covered work under sections 3 and 4 of this
+ License without being bound by section 3 of the GNU GPL.
+
+ 2. Conveying Modified Versions.
+
+ If you modify a copy of the Library, and, in your modifications, a
+ facility refers to a function or data to be supplied by an
+ Application that uses the facility (other than as an argument
+ passed when the facility is invoked), then you may convey a copy
+ of the modified version:
+
+ a. under this License, provided that you make a good faith
+ effort to ensure that, in the event an Application does not
+ supply the function or data, the facility still operates, and
+ performs whatever part of its purpose remains meaningful, or
+
+ b. under the GNU GPL, with none of the additional permissions of
+ this License applicable to that copy.
+
+ 3. Object Code Incorporating Material from Library Header Files.
+
+ The object code form of an Application may incorporate material
+ from a header file that is part of the Library. You may convey
+ such object code under terms of your choice, provided that, if the
+ incorporated material is not limited to numerical parameters, data
+ structure layouts and accessors, or small macros, inline functions
+ and templates (ten or fewer lines in length), you do both of the
+ following:
+
+ a. Give prominent notice with each copy of the object code that
+ the Library is used in it and that the Library and its use are
+ covered by this License.
+
+ b. Accompany the object code with a copy of the GNU GPL and this
+ license document.
+
+ 4. Combined Works.
+
+ You may convey a Combined Work under terms of your choice that,
+ taken together, effectively do not restrict modification of the
+ portions of the Library contained in the Combined Work and reverse
+ engineering for debugging such modifications, if you also do each
+ of the following:
+
+ a. Give prominent notice with each copy of the Combined Work that
+ the Library is used in it and that the Library and its use are
+ covered by this License.
+
+ b. Accompany the Combined Work with a copy of the GNU GPL and
+ this license document.
+
+ c. For a Combined Work that displays copyright notices during
+ execution, include the copyright notice for the Library among
+ these notices, as well as a reference directing the user to
+ the copies of the GNU GPL and this license document.
+
+ d. Do one of the following:
+
+ 0. Convey the Minimal Corresponding Source under the terms
+ of this License, and the Corresponding Application Code
+ in a form suitable for, and under terms that permit, the
+ user to recombine or relink the Application with a
+ modified version of the Linked Version to produce a
+ modified Combined Work, in the manner specified by
+ section 6 of the GNU GPL for conveying Corresponding
+ Source.
+
+ 1. Use a suitable shared library mechanism for linking with
+ the Library. A suitable mechanism is one that (a) uses
+ at run time a copy of the Library already present on the
+ user's computer system, and (b) will operate properly
+ with a modified version of the Library that is
+ interface-compatible with the Linked Version.
+
+ e. Provide Installation Information, but only if you would
+ otherwise be required to provide such information under
+ section 6 of the GNU GPL, and only to the extent that such
+ information is necessary to install and execute a modified
+ version of the Combined Work produced by recombining or
+ relinking the Application with a modified version of the
+ Linked Version. (If you use option 4d0, the Installation
+ Information must accompany the Minimal Corresponding Source
+ and Corresponding Application Code. If you use option 4d1,
+ you must provide the Installation Information in the manner
+ specified by section 6 of the GNU GPL for conveying
+ Corresponding Source.)
+
+ 5. Combined Libraries.
+
+ You may place library facilities that are a work based on the
+ Library side by side in a single library together with other
+ library facilities that are not Applications and are not covered
+ by this License, and convey such a combined library under terms of
+ your choice, if you do both of the following:
+
+ a. Accompany the combined library with a copy of the same work
+ based on the Library, uncombined with any other library
+ facilities, conveyed under the terms of this License.
+
+ b. Give prominent notice with the combined library that part of
+ it is a work based on the Library, and explaining where to
+ find the accompanying uncombined form of the same work.
+
+ 6. Revised Versions of the GNU Lesser General Public License.
+
+ The Free Software Foundation may publish revised and/or new
+ versions of the GNU Lesser General Public License from time to
+ time. Such new versions will be similar in spirit to the present
+ version, but may differ in detail to address new problems or
+ concerns.
+
+ Each version is given a distinguishing version number. If the
+ Library as you received it specifies that a certain numbered
+ version of the GNU Lesser General Public License "or any later
+ version" applies to it, you have the option of following the terms
+ and conditions either of that published version or of any later
+ version published by the Free Software Foundation. If the Library
+ as you received it does not specify a version number of the GNU
+ Lesser General Public License, you may choose any version of the
+ GNU Lesser General Public License ever published by the Free
+ Software Foundation.
+
+ If the Library as you received it specifies that a proxy can decide
+ whether future versions of the GNU Lesser General Public License
+ shall apply, that proxy's public statement of acceptance of any
+ version is permanent authorization for you to choose that version
+ for the Library.
+
+
+
+File: libProgressBar.info, Node: Overview, Next: Example, Prev: Copying, Up: Top
+
+3 Overview
+**********
+
+ TODO
+
+
+File: libProgressBar.info, Node: Example, Next: Problems, Prev: Overview, Up: Top
+
+4 Example of use
+****************
+
+ TODO
+
+
+File: libProgressBar.info, Node: Problems, Next: Concept Index, Prev: Example, Up: Top
+
+5 Reporting Bugs
+****************
+
+ If you find a bug in `libProgressBar', please send electronic mail to
+<alban.mancheron at inria.fr>. Include the version number. Also include
+in your message a decription of the encountered problem.
+
+
+ If you have other questions, comments or suggestions about
+`lbProgressBar', contact the author via electronic mail to
+<alban.mancheron at inria.fr>. The author will try to help you out,
+although he may not have time to fix your problems.
+
+
+File: libProgressBar.info, Node: Concept Index, Prev: Problems, Up: Top
+
+Concept Index
+*************
+
+ [index ]
+* Menu:
+
+* bugs: Problems. (line 6)
+* copying: Copying. (line 6)
+* example: Example. (line 6)
+* GNU LGPL: Copying. (line 6)
+* greetings: Overview. (line 6)
+* how to read: Instructions. (line 6)
+* manual, how to read: Instructions. (line 6)
+* overview: Overview. (line 6)
+* problems: Problems. (line 6)
+* reading: Instructions. (line 6)
+* usage: Example. (line 6)
+
+
+
+Tag Table:
+Node: Top977
+Node: Instructions1495
+Node: Copying1913
+Node: Overview10305
+Node: Example10425
+Node: Problems10558
+Node: Concept Index11130
+
+End Tag Table
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/doc/libProgressBar.texinfo b/src/libGkArrays/src/libProgressBar-1.2.0/doc/libProgressBar.texinfo
new file mode 100644
index 0000000..25c3a5d
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/doc/libProgressBar.texinfo
@@ -0,0 +1,165 @@
+\input texinfo @c -*-texinfo-*-
+ at documentlanguage en
+ at documentencoding ISO-8859-1
+ at c This file uses the @command command introduced in Texinfo 4.0.
+ at c %**start of header
+ at setfilename libProgressBar.info
+ at settitle A library to manage progress bars in C++: libProgressBar
+ at c finalout
+ at setchapternewpage odd
+ at iftex
+ at afourlatex
+ at internalpagesizes{247mm}{170mm}{-5.4mm}{-5.4mm}{5mm}{10mm}{297mm}{210mm}
+ at end iftex
+ at ifinfo
+ at firstparagraphindent insert
+ at end ifinfo
+ at setcontentsaftertitlepage
+ at c %**end of header
+
+ at set VERSION 1.0.0
+ at set author DoccY
+ at set mail @email{alban.mancheron@@inria.fr}
+ at set authormail @value{author} @value{mail}
+ at set Copyrights Copyright � 2007 -- Universit� des Antilles et de la Guyane/Institut National de Recherche en Informatique et en Automatique
+ at iftex
+ at clear mail
+ at clear Copyrights
+ at set mail <@email{alban.mancheron@@inria.fr}>
+ at set Copyrights Copyright @copyright{} 2007 -- Universit� des Antilles et de la Guyane/Institut National de Recherche en Informatique et en Automatique
+ at end iftex
+
+ at ifinfo
+This file documents the @command{libProgressBar} library.
+
+ at value{Copyrights}
+
+Author: @value{authormail}
+
+Permission is granted to make and distribute verbatim copies of
+this manual provided the copyright notice and this permission notice
+are preserved on all copies.
+
+ at ignore
+Permission is granted to process this file through TeX and print the
+results, provided the printed document carries copying permission
+notice identical to this one except for the removal of this paragraph
+(this paragraph not being relevant to the printed manual).
+
+ at end ignore
+Permission is granted to copy and distribute modified versions of this
+manual under the conditions for verbatim copying, provided that the entire
+resulting derived work is distributed under the terms of a permission
+notice identical to this one.
+
+Permission is granted to copy and distribute translations of this manual
+into another language, under the above conditions for modified versions,
+except that this permission notice may be stated in a translation approved
+by the Foundation.
+ at end ifinfo
+
+ at titlepage
+ at title @command{libProgressBar}
+ at subtitle library to manage progress bars.
+ at author by @value{authormail}
+
+
+ at page
+ at vskip 0pt plus 1filll
+
+ at value{Copyrights}
+
+Author: @value{authormail}
+
+Permission is granted to make and distribute verbatim copies of
+this manual provided the copyright notice and this permission notice
+are preserved on all copies.
+
+Permission is granted to copy and distribute modified versions of this
+manual under the conditions for verbatim copying, provided that the entire
+resulting derived work is distributed under the terms of a permission
+notice identical to this one.
+
+Permission is granted to copy and distribute translations of this manual
+into another language, under the above conditions for modified versions,
+except that this permission notice may be stated in a translation approved
+by the Foundation.
+
+ at end titlepage
+ at headings on
+
+ at c All the nodes can be updated using the EMACS command
+ at c texinfo-every-node-update, which is normally bound to C-c C-u C-e.
+ at node Top, Instructions, (dir), (dir)
+
+ at ifinfo
+This file documents the @command{libProgressBar} library.
+
+ at end ifinfo
+
+ at c All the menus can be updated with the EMACS command
+ at c texinfo-all-menus-update, which is normally bound to C-c C-u C-a.
+ at menu
+* Instructions:: How to read this manual.
+* Copying:: How you can copy and share @command{libProgressBar}.
+* Overview:: Preliminary information.
+* Example:: An example of the use of @command{libProgressBar}.
+* Problems:: Reporting bugs.
+* Concept Index:: Index of concepts.
+ at end menu
+
+ at node Instructions, Copying, Top, Top
+ at chapter How to Read This Manual
+
+ at cindex reading
+ at cindex manual, how to read
+ at cindex how to read
+You will find in the Copying section the GNU Lesser General Public License.
+In the Overview section, is given a quick description about what does
+ at command{libProgressBar}. Then, you will have an example of use.
+
+Indeed, we'll hope you having a good fun using @command{libProgressBar}.
+
+ at node Copying, Overview, Instructions, Top
+ at chapter Copying
+
+ at cindex copying
+ at cindex GNU LGPL
+ at include lgpl.texinfo
+
+ at node Overview, Example, Copying, Top
+ at chapter Overview
+ at cindex greetings
+ at cindex overview
+
+TODO
+
+ at node Example, Problems, Overview, Top
+ at chapter Example of use
+ at cindex example
+ at cindex usage
+
+TODO
+
+ at node Problems, Concept Index, Example, Top
+ at chapter Reporting Bugs
+ at cindex bugs
+ at cindex problems
+
+If you find a bug in @command{libProgressBar}, please send electronic mail to
+ at value{mail}. Include the version number.
+Also include in your message a decription of the encountered problem. at refill
+
+ at sp 1
+
+If you have other questions, comments or suggestions about
+ at command{lbProgressBar}, contact the author via electronic mail to
+ at value{mail}.
+The author will try to help you out, although he may not have time to
+fix your problems.
+
+ at node Concept Index, , Problems, Top
+ at unnumbered Concept Index
+ at printindex cp
+
+ at bye
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/doc/texinfo.tex b/src/libGkArrays/src/libProgressBar-1.2.0/doc/texinfo.tex
new file mode 100644
index 0000000..9140826
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/doc/texinfo.tex
@@ -0,0 +1,9291 @@
+% texinfo.tex -- TeX macros to handle Texinfo files.
+%
+% Load plain if necessary, i.e., if running under initex.
+\expandafter\ifx\csname fmtname\endcsname\relax\input plain\fi
+%
+\def\texinfoversion{2009-08-14.15}
+%
+% Copyright 1985, 1986, 1988, 1990, 1991, 1992, 1993, 1994, 1995,
+% 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006,
+% 2007, 2008, 2009 Free Software Foundation, Inc.
+%
+% This texinfo.tex file is free software: you can redistribute it and/or
+% modify it under the terms of the GNU General Public License as
+% published by the Free Software Foundation, either version 3 of the
+% License, or (at your option) any later version.
+%
+% This texinfo.tex file is distributed in the hope that it will be
+% useful, but WITHOUT ANY WARRANTY; without even the implied warranty
+% of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+% General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program. If not, see <http://www.gnu.org/licenses/>.
+%
+% As a special exception, when this file is read by TeX when processing
+% a Texinfo source document, you may use the result without
+% restriction. (This has been our intent since Texinfo was invented.)
+%
+% Please try the latest version of texinfo.tex before submitting bug
+% reports; you can get the latest version from:
+% http://www.gnu.org/software/texinfo/ (the Texinfo home page), or
+% ftp://tug.org/tex/texinfo.tex
+% (and all CTAN mirrors, see http://www.ctan.org).
+% The texinfo.tex in any given distribution could well be out
+% of date, so if that's what you're using, please check.
+%
+% Send bug reports to bug-texinfo at gnu.org. Please include including a
+% complete document in each bug report with which we can reproduce the
+% problem. Patches are, of course, greatly appreciated.
+%
+% To process a Texinfo manual with TeX, it's most reliable to use the
+% texi2dvi shell script that comes with the distribution. For a simple
+% manual foo.texi, however, you can get away with this:
+% tex foo.texi
+% texindex foo.??
+% tex foo.texi
+% tex foo.texi
+% dvips foo.dvi -o # or whatever; this makes foo.ps.
+% The extra TeX runs get the cross-reference information correct.
+% Sometimes one run after texindex suffices, and sometimes you need more
+% than two; texi2dvi does it as many times as necessary.
+%
+% It is possible to adapt texinfo.tex for other languages, to some
+% extent. You can get the existing language-specific files from the
+% full Texinfo distribution.
+%
+% The GNU Texinfo home page is http://www.gnu.org/software/texinfo.
+
+
+\message{Loading texinfo [version \texinfoversion]:}
+
+% If in a .fmt file, print the version number
+% and turn on active characters that we couldn't do earlier because
+% they might have appeared in the input file name.
+\everyjob{\message{[Texinfo version \texinfoversion]}%
+ \catcode`+=\active \catcode`\_=\active}
+
+
+\chardef\other=12
+
+% We never want plain's \outer definition of \+ in Texinfo.
+% For @tex, we can use \tabalign.
+\let\+ = \relax
+
+% Save some plain tex macros whose names we will redefine.
+\let\ptexb=\b
+\let\ptexbullet=\bullet
+\let\ptexc=\c
+\let\ptexcomma=\,
+\let\ptexdot=\.
+\let\ptexdots=\dots
+\let\ptexend=\end
+\let\ptexequiv=\equiv
+\let\ptexexclam=\!
+\let\ptexfootnote=\footnote
+\let\ptexgtr=>
+\let\ptexhat=^
+\let\ptexi=\i
+\let\ptexindent=\indent
+\let\ptexinsert=\insert
+\let\ptexlbrace=\{
+\let\ptexless=<
+\let\ptexnewwrite\newwrite
+\let\ptexnoindent=\noindent
+\let\ptexplus=+
+\let\ptexrbrace=\}
+\let\ptexslash=\/
+\let\ptexstar=\*
+\let\ptext=\t
+\let\ptextop=\top
+{\catcode`\'=\active
+\global\let\ptexquoteright'}% Math-mode def from plain.tex.
+\let\ptexraggedright=\raggedright
+
+% If this character appears in an error message or help string, it
+% starts a new line in the output.
+\newlinechar = `^^J
+
+% Use TeX 3.0's \inputlineno to get the line number, for better error
+% messages, but if we're using an old version of TeX, don't do anything.
+%
+\ifx\inputlineno\thisisundefined
+ \let\linenumber = \empty % Pre-3.0.
+\else
+ \def\linenumber{l.\the\inputlineno:\space}
+\fi
+
+% Set up fixed words for English if not already set.
+\ifx\putwordAppendix\undefined \gdef\putwordAppendix{Appendix}\fi
+\ifx\putwordChapter\undefined \gdef\putwordChapter{Chapter}\fi
+\ifx\putwordfile\undefined \gdef\putwordfile{file}\fi
+\ifx\putwordin\undefined \gdef\putwordin{in}\fi
+\ifx\putwordIndexIsEmpty\undefined \gdef\putwordIndexIsEmpty{(Index is empty)}\fi
+\ifx\putwordIndexNonexistent\undefined \gdef\putwordIndexNonexistent{(Index is nonexistent)}\fi
+\ifx\putwordInfo\undefined \gdef\putwordInfo{Info}\fi
+\ifx\putwordInstanceVariableof\undefined \gdef\putwordInstanceVariableof{Instance Variable of}\fi
+\ifx\putwordMethodon\undefined \gdef\putwordMethodon{Method on}\fi
+\ifx\putwordNoTitle\undefined \gdef\putwordNoTitle{No Title}\fi
+\ifx\putwordof\undefined \gdef\putwordof{of}\fi
+\ifx\putwordon\undefined \gdef\putwordon{on}\fi
+\ifx\putwordpage\undefined \gdef\putwordpage{page}\fi
+\ifx\putwordsection\undefined \gdef\putwordsection{section}\fi
+\ifx\putwordSection\undefined \gdef\putwordSection{Section}\fi
+\ifx\putwordsee\undefined \gdef\putwordsee{see}\fi
+\ifx\putwordSee\undefined \gdef\putwordSee{See}\fi
+\ifx\putwordShortTOC\undefined \gdef\putwordShortTOC{Short Contents}\fi
+\ifx\putwordTOC\undefined \gdef\putwordTOC{Table of Contents}\fi
+%
+\ifx\putwordMJan\undefined \gdef\putwordMJan{January}\fi
+\ifx\putwordMFeb\undefined \gdef\putwordMFeb{February}\fi
+\ifx\putwordMMar\undefined \gdef\putwordMMar{March}\fi
+\ifx\putwordMApr\undefined \gdef\putwordMApr{April}\fi
+\ifx\putwordMMay\undefined \gdef\putwordMMay{May}\fi
+\ifx\putwordMJun\undefined \gdef\putwordMJun{June}\fi
+\ifx\putwordMJul\undefined \gdef\putwordMJul{July}\fi
+\ifx\putwordMAug\undefined \gdef\putwordMAug{August}\fi
+\ifx\putwordMSep\undefined \gdef\putwordMSep{September}\fi
+\ifx\putwordMOct\undefined \gdef\putwordMOct{October}\fi
+\ifx\putwordMNov\undefined \gdef\putwordMNov{November}\fi
+\ifx\putwordMDec\undefined \gdef\putwordMDec{December}\fi
+%
+\ifx\putwordDefmac\undefined \gdef\putwordDefmac{Macro}\fi
+\ifx\putwordDefspec\undefined \gdef\putwordDefspec{Special Form}\fi
+\ifx\putwordDefvar\undefined \gdef\putwordDefvar{Variable}\fi
+\ifx\putwordDefopt\undefined \gdef\putwordDefopt{User Option}\fi
+\ifx\putwordDeffunc\undefined \gdef\putwordDeffunc{Function}\fi
+
+% Since the category of space is not known, we have to be careful.
+\chardef\spacecat = 10
+\def\spaceisspace{\catcode`\ =\spacecat}
+
+% sometimes characters are active, so we need control sequences.
+\chardef\colonChar = `\:
+\chardef\commaChar = `\,
+\chardef\dashChar = `\-
+\chardef\dotChar = `\.
+\chardef\exclamChar= `\!
+\chardef\lquoteChar= `\`
+\chardef\questChar = `\?
+\chardef\rquoteChar= `\'
+\chardef\semiChar = `\;
+\chardef\underChar = `\_
+
+% Ignore a token.
+%
+\def\gobble#1{}
+
+% The following is used inside several \edef's.
+\def\makecsname#1{\expandafter\noexpand\csname#1\endcsname}
+
+% Hyphenation fixes.
+\hyphenation{
+ Flor-i-da Ghost-script Ghost-view Mac-OS Post-Script
+ ap-pen-dix bit-map bit-maps
+ data-base data-bases eshell fall-ing half-way long-est man-u-script
+ man-u-scripts mini-buf-fer mini-buf-fers over-view par-a-digm
+ par-a-digms rath-er rec-tan-gu-lar ro-bot-ics se-vere-ly set-up spa-ces
+ spell-ing spell-ings
+ stand-alone strong-est time-stamp time-stamps which-ever white-space
+ wide-spread wrap-around
+}
+
+% Margin to add to right of even pages, to left of odd pages.
+\newdimen\bindingoffset
+\newdimen\normaloffset
+\newdimen\pagewidth \newdimen\pageheight
+
+% For a final copy, take out the rectangles
+% that mark overfull boxes (in case you have decided
+% that the text looks ok even though it passes the margin).
+%
+\def\finalout{\overfullrule=0pt}
+
+% @| inserts a changebar to the left of the current line. It should
+% surround any changed text. This approach does *not* work if the
+% change spans more than two lines of output. To handle that, we would
+% have adopt a much more difficult approach (putting marks into the main
+% vertical list for the beginning and end of each change).
+%
+\def\|{%
+ % \vadjust can only be used in horizontal mode.
+ \leavevmode
+ %
+ % Append this vertical mode material after the current line in the output.
+ \vadjust{%
+ % We want to insert a rule with the height and depth of the current
+ % leading; that is exactly what \strutbox is supposed to record.
+ \vskip-\baselineskip
+ %
+ % \vadjust-items are inserted at the left edge of the type. So
+ % the \llap here moves out into the left-hand margin.
+ \llap{%
+ %
+ % For a thicker or thinner bar, change the `1pt'.
+ \vrule height\baselineskip width1pt
+ %
+ % This is the space between the bar and the text.
+ \hskip 12pt
+ }%
+ }%
+}
+
+% Sometimes it is convenient to have everything in the transcript file
+% and nothing on the terminal. We don't just call \tracingall here,
+% since that produces some useless output on the terminal. We also make
+% some effort to order the tracing commands to reduce output in the log
+% file; cf. trace.sty in LaTeX.
+%
+\def\gloggingall{\begingroup \globaldefs = 1 \loggingall \endgroup}%
+\def\loggingall{%
+ \tracingstats2
+ \tracingpages1
+ \tracinglostchars2 % 2 gives us more in etex
+ \tracingparagraphs1
+ \tracingoutput1
+ \tracingmacros2
+ \tracingrestores1
+ \showboxbreadth\maxdimen \showboxdepth\maxdimen
+ \ifx\eTeXversion\undefined\else % etex gives us more logging
+ \tracingscantokens1
+ \tracingifs1
+ \tracinggroups1
+ \tracingnesting2
+ \tracingassigns1
+ \fi
+ \tracingcommands3 % 3 gives us more in etex
+ \errorcontextlines16
+}%
+
+% add check for \lastpenalty to plain's definitions. If the last thing
+% we did was a \nobreak, we don't want to insert more space.
+%
+\def\smallbreak{\ifnum\lastpenalty<10000\par\ifdim\lastskip<\smallskipamount
+ \removelastskip\penalty-50\smallskip\fi\fi}
+\def\medbreak{\ifnum\lastpenalty<10000\par\ifdim\lastskip<\medskipamount
+ \removelastskip\penalty-100\medskip\fi\fi}
+\def\bigbreak{\ifnum\lastpenalty<10000\par\ifdim\lastskip<\bigskipamount
+ \removelastskip\penalty-200\bigskip\fi\fi}
+
+% For @cropmarks command.
+% Do @cropmarks to get crop marks.
+%
+\newif\ifcropmarks
+\let\cropmarks = \cropmarkstrue
+%
+% Dimensions to add cropmarks at corners.
+% Added by P. A. MacKay, 12 Nov. 1986
+%
+\newdimen\outerhsize \newdimen\outervsize % set by the paper size routines
+\newdimen\cornerlong \cornerlong=1pc
+\newdimen\cornerthick \cornerthick=.3pt
+\newdimen\topandbottommargin \topandbottommargin=.75in
+
+% Output a mark which sets \thischapter, \thissection and \thiscolor.
+% We dump everything together because we only have one kind of mark.
+% This works because we only use \botmark / \topmark, not \firstmark.
+%
+% A mark contains a subexpression of the \ifcase ... \fi construct.
+% \get*marks macros below extract the needed part using \ifcase.
+%
+% Another complication is to let the user choose whether \thischapter
+% (\thissection) refers to the chapter (section) in effect at the top
+% of a page, or that at the bottom of a page. The solution is
+% described on page 260 of The TeXbook. It involves outputting two
+% marks for the sectioning macros, one before the section break, and
+% one after. I won't pretend I can describe this better than DEK...
+\def\domark{%
+ \toks0=\expandafter{\lastchapterdefs}%
+ \toks2=\expandafter{\lastsectiondefs}%
+ \toks4=\expandafter{\prevchapterdefs}%
+ \toks6=\expandafter{\prevsectiondefs}%
+ \toks8=\expandafter{\lastcolordefs}%
+ \mark{%
+ \the\toks0 \the\toks2
+ \noexpand\or \the\toks4 \the\toks6
+ \noexpand\else \the\toks8
+ }%
+}
+% \topmark doesn't work for the very first chapter (after the title
+% page or the contents), so we use \firstmark there -- this gets us
+% the mark with the chapter defs, unless the user sneaks in, e.g.,
+% @setcolor (or @url, or @link, etc.) between @contents and the very
+% first @chapter.
+\def\gettopheadingmarks{%
+ \ifcase0\topmark\fi
+ \ifx\thischapter\empty \ifcase0\firstmark\fi \fi
+}
+\def\getbottomheadingmarks{\ifcase1\botmark\fi}
+\def\getcolormarks{\ifcase2\topmark\fi}
+
+% Avoid "undefined control sequence" errors.
+\def\lastchapterdefs{}
+\def\lastsectiondefs{}
+\def\prevchapterdefs{}
+\def\prevsectiondefs{}
+\def\lastcolordefs{}
+
+% Main output routine.
+\chardef\PAGE = 255
+\output = {\onepageout{\pagecontents\PAGE}}
+
+\newbox\headlinebox
+\newbox\footlinebox
+
+% \onepageout takes a vbox as an argument. Note that \pagecontents
+% does insertions, but you have to call it yourself.
+\def\onepageout#1{%
+ \ifcropmarks \hoffset=0pt \else \hoffset=\normaloffset \fi
+ %
+ \ifodd\pageno \advance\hoffset by \bindingoffset
+ \else \advance\hoffset by -\bindingoffset\fi
+ %
+ % Do this outside of the \shipout so @code etc. will be expanded in
+ % the headline as they should be, not taken literally (outputting ''code).
+ \ifodd\pageno \getoddheadingmarks \else \getevenheadingmarks \fi
+ \setbox\headlinebox = \vbox{\let\hsize=\pagewidth \makeheadline}%
+ \ifodd\pageno \getoddfootingmarks \else \getevenfootingmarks \fi
+ \setbox\footlinebox = \vbox{\let\hsize=\pagewidth \makefootline}%
+ %
+ {%
+ % Have to do this stuff outside the \shipout because we want it to
+ % take effect in \write's, yet the group defined by the \vbox ends
+ % before the \shipout runs.
+ %
+ \indexdummies % don't expand commands in the output.
+ \normalturnoffactive % \ in index entries must not stay \, e.g., if
+ % the page break happens to be in the middle of an example.
+ % We don't want .vr (or whatever) entries like this:
+ % \entry{{\tt \indexbackslash }acronym}{32}{\code {\acronym}}
+ % "\acronym" won't work when it's read back in;
+ % it needs to be
+ % {\code {{\tt \backslashcurfont }acronym}
+ \shipout\vbox{%
+ % Do this early so pdf references go to the beginning of the page.
+ \ifpdfmakepagedest \pdfdest name{\the\pageno} xyz\fi
+ %
+ \ifcropmarks \vbox to \outervsize\bgroup
+ \hsize = \outerhsize
+ \vskip-\topandbottommargin
+ \vtop to0pt{%
+ \line{\ewtop\hfil\ewtop}%
+ \nointerlineskip
+ \line{%
+ \vbox{\moveleft\cornerthick\nstop}%
+ \hfill
+ \vbox{\moveright\cornerthick\nstop}%
+ }%
+ \vss}%
+ \vskip\topandbottommargin
+ \line\bgroup
+ \hfil % center the page within the outer (page) hsize.
+ \ifodd\pageno\hskip\bindingoffset\fi
+ \vbox\bgroup
+ \fi
+ %
+ \unvbox\headlinebox
+ \pagebody{#1}%
+ \ifdim\ht\footlinebox > 0pt
+ % Only leave this space if the footline is nonempty.
+ % (We lessened \vsize for it in \oddfootingyyy.)
+ % The \baselineskip=24pt in plain's \makefootline has no effect.
+ \vskip 24pt
+ \unvbox\footlinebox
+ \fi
+ %
+ \ifcropmarks
+ \egroup % end of \vbox\bgroup
+ \hfil\egroup % end of (centering) \line\bgroup
+ \vskip\topandbottommargin plus1fill minus1fill
+ \boxmaxdepth = \cornerthick
+ \vbox to0pt{\vss
+ \line{%
+ \vbox{\moveleft\cornerthick\nsbot}%
+ \hfill
+ \vbox{\moveright\cornerthick\nsbot}%
+ }%
+ \nointerlineskip
+ \line{\ewbot\hfil\ewbot}%
+ }%
+ \egroup % \vbox from first cropmarks clause
+ \fi
+ }% end of \shipout\vbox
+ }% end of group with \indexdummies
+ \advancepageno
+ \ifnum\outputpenalty>-20000 \else\dosupereject\fi
+}
+
+\newinsert\margin \dimen\margin=\maxdimen
+
+\def\pagebody#1{\vbox to\pageheight{\boxmaxdepth=\maxdepth #1}}
+{\catcode`\@ =11
+\gdef\pagecontents#1{\ifvoid\topins\else\unvbox\topins\fi
+% marginal hacks, juha at viisa.uucp (Juha Takala)
+\ifvoid\margin\else % marginal info is present
+ \rlap{\kern\hsize\vbox to\z@{\kern1pt\box\margin \vss}}\fi
+\dimen@=\dp#1\relax \unvbox#1\relax
+\ifvoid\footins\else\vskip\skip\footins\footnoterule \unvbox\footins\fi
+\ifr at ggedbottom \kern-\dimen@ \vfil \fi}
+}
+
+% Here are the rules for the cropmarks. Note that they are
+% offset so that the space between them is truly \outerhsize or \outervsize
+% (P. A. MacKay, 12 November, 1986)
+%
+\def\ewtop{\vrule height\cornerthick depth0pt width\cornerlong}
+\def\nstop{\vbox
+ {\hrule height\cornerthick depth\cornerlong width\cornerthick}}
+\def\ewbot{\vrule height0pt depth\cornerthick width\cornerlong}
+\def\nsbot{\vbox
+ {\hrule height\cornerlong depth\cornerthick width\cornerthick}}
+
+% Parse an argument, then pass it to #1. The argument is the rest of
+% the input line (except we remove a trailing comment). #1 should be a
+% macro which expects an ordinary undelimited TeX argument.
+%
+\def\parsearg{\parseargusing{}}
+\def\parseargusing#1#2{%
+ \def\argtorun{#2}%
+ \begingroup
+ \obeylines
+ \spaceisspace
+ #1%
+ \parseargline\empty% Insert the \empty token, see \finishparsearg below.
+}
+
+{\obeylines %
+ \gdef\parseargline#1^^M{%
+ \endgroup % End of the group started in \parsearg.
+ \argremovecomment #1\comment\ArgTerm%
+ }%
+}
+
+% First remove any @comment, then any @c comment.
+\def\argremovecomment#1\comment#2\ArgTerm{\argremovec #1\c\ArgTerm}
+\def\argremovec#1\c#2\ArgTerm{\argcheckspaces#1\^^M\ArgTerm}
+
+% Each occurrence of `\^^M' or `<space>\^^M' is replaced by a single space.
+%
+% \argremovec might leave us with trailing space, e.g.,
+% @end itemize @c foo
+% This space token undergoes the same procedure and is eventually removed
+% by \finishparsearg.
+%
+\def\argcheckspaces#1\^^M{\argcheckspacesX#1\^^M \^^M}
+\def\argcheckspacesX#1 \^^M{\argcheckspacesY#1\^^M}
+\def\argcheckspacesY#1\^^M#2\^^M#3\ArgTerm{%
+ \def\temp{#3}%
+ \ifx\temp\empty
+ % Do not use \next, perhaps the caller of \parsearg uses it; reuse \temp:
+ \let\temp\finishparsearg
+ \else
+ \let\temp\argcheckspaces
+ \fi
+ % Put the space token in:
+ \temp#1 #3\ArgTerm
+}
+
+% If a _delimited_ argument is enclosed in braces, they get stripped; so
+% to get _exactly_ the rest of the line, we had to prevent such situation.
+% We prepended an \empty token at the very beginning and we expand it now,
+% just before passing the control to \argtorun.
+% (Similarly, we have to think about #3 of \argcheckspacesY above: it is
+% either the null string, or it ends with \^^M---thus there is no danger
+% that a pair of braces would be stripped.
+%
+% But first, we have to remove the trailing space token.
+%
+\def\finishparsearg#1 \ArgTerm{\expandafter\argtorun\expandafter{#1}}
+
+% \parseargdef\foo{...}
+% is roughly equivalent to
+% \def\foo{\parsearg\Xfoo}
+% \def\Xfoo#1{...}
+%
+% Actually, I use \csname\string\foo\endcsname, ie. \\foo, as it is my
+% favourite TeX trick. --kasal, 16nov03
+
+\def\parseargdef#1{%
+ \expandafter \doparseargdef \csname\string#1\endcsname #1%
+}
+\def\doparseargdef#1#2{%
+ \def#2{\parsearg#1}%
+ \def#1##1%
+}
+
+% Several utility definitions with active space:
+{
+ \obeyspaces
+ \gdef\obeyedspace{ }
+
+ % Make each space character in the input produce a normal interword
+ % space in the output. Don't allow a line break at this space, as this
+ % is used only in environments like @example, where each line of input
+ % should produce a line of output anyway.
+ %
+ \gdef\sepspaces{\obeyspaces\let =\tie}
+
+ % If an index command is used in an @example environment, any spaces
+ % therein should become regular spaces in the raw index file, not the
+ % expansion of \tie (\leavevmode \penalty \@M \ ).
+ \gdef\unsepspaces{\let =\space}
+}
+
+
+\def\flushcr{\ifx\par\lisppar \def\next##1{}\else \let\next=\relax \fi \next}
+
+% Define the framework for environments in texinfo.tex. It's used like this:
+%
+% \envdef\foo{...}
+% \def\Efoo{...}
+%
+% It's the responsibility of \envdef to insert \begingroup before the
+% actual body; @end closes the group after calling \Efoo. \envdef also
+% defines \thisenv, so the current environment is known; @end checks
+% whether the environment name matches. The \checkenv macro can also be
+% used to check whether the current environment is the one expected.
+%
+% Non-false conditionals (@iftex, @ifset) don't fit into this, so they
+% are not treated as environments; they don't open a group. (The
+% implementation of @end takes care not to call \endgroup in this
+% special case.)
+
+
+% At run-time, environments start with this:
+\def\startenvironment#1{\begingroup\def\thisenv{#1}}
+% initialize
+\let\thisenv\empty
+
+% ... but they get defined via ``\envdef\foo{...}'':
+\long\def\envdef#1#2{\def#1{\startenvironment#1#2}}
+\def\envparseargdef#1#2{\parseargdef#1{\startenvironment#1#2}}
+
+% Check whether we're in the right environment:
+\def\checkenv#1{%
+ \def\temp{#1}%
+ \ifx\thisenv\temp
+ \else
+ \badenverr
+ \fi
+}
+
+% Environment mismatch, #1 expected:
+\def\badenverr{%
+ \errhelp = \EMsimple
+ \errmessage{This command can appear only \inenvironment\temp,
+ not \inenvironment\thisenv}%
+}
+\def\inenvironment#1{%
+ \ifx#1\empty
+ out of any environment%
+ \else
+ in environment \expandafter\string#1%
+ \fi
+}
+
+% @end foo executes the definition of \Efoo.
+% But first, it executes a specialized version of \checkenv
+%
+\parseargdef\end{%
+ \if 1\csname iscond.#1\endcsname
+ \else
+ % The general wording of \badenverr may not be ideal, but... --kasal, 06nov03
+ \expandafter\checkenv\csname#1\endcsname
+ \csname E#1\endcsname
+ \endgroup
+ \fi
+}
+
+\newhelp\EMsimple{Press RETURN to continue.}
+
+
+%% Simple single-character @ commands
+
+% @@ prints an @
+% Kludge this until the fonts are right (grr).
+\def\@{{\tt\char64}}
+
+% This is turned off because it was never documented
+% and you can use @w{...} around a quote to suppress ligatures.
+%% Define @` and @' to be the same as ` and '
+%% but suppressing ligatures.
+%\def\`{{`}}
+%\def\'{{'}}
+
+% Used to generate quoted braces.
+\def\mylbrace {{\tt\char123}}
+\def\myrbrace {{\tt\char125}}
+\let\{=\mylbrace
+\let\}=\myrbrace
+\begingroup
+ % Definitions to produce \{ and \} commands for indices,
+ % and @{ and @} for the aux/toc files.
+ \catcode`\{ = \other \catcode`\} = \other
+ \catcode`\[ = 1 \catcode`\] = 2
+ \catcode`\! = 0 \catcode`\\ = \other
+ !gdef!lbracecmd[\{]%
+ !gdef!rbracecmd[\}]%
+ !gdef!lbraceatcmd[@{]%
+ !gdef!rbraceatcmd[@}]%
+!endgroup
+
+% @comma{} to avoid , parsing problems.
+\let\comma = ,
+
+% Accents: @, @dotaccent @ringaccent @ubaraccent @udotaccent
+% Others are defined by plain TeX: @` @' @" @^ @~ @= @u @v @H.
+\let\, = \c
+\let\dotaccent = \.
+\def\ringaccent#1{{\accent23 #1}}
+\let\tieaccent = \t
+\let\ubaraccent = \b
+\let\udotaccent = \d
+
+% Other special characters: @questiondown @exclamdown @ordf @ordm
+% Plain TeX defines: @AA @AE @O @OE @L (plus lowercase versions) @ss.
+\def\questiondown{?`}
+\def\exclamdown{!`}
+\def\ordf{\leavevmode\raise1ex\hbox{\selectfonts\lllsize \underbar{a}}}
+\def\ordm{\leavevmode\raise1ex\hbox{\selectfonts\lllsize \underbar{o}}}
+
+% Dotless i and dotless j, used for accents.
+\def\imacro{i}
+\def\jmacro{j}
+\def\dotless#1{%
+ \def\temp{#1}%
+ \ifx\temp\imacro \ifmmode\imath \else\ptexi \fi
+ \else\ifx\temp\jmacro \ifmmode\jmath \else\j \fi
+ \else \errmessage{@dotless can be used only with i or j}%
+ \fi\fi
+}
+
+% The \TeX{} logo, as in plain, but resetting the spacing so that a
+% period following counts as ending a sentence. (Idea found in latex.)
+%
+\edef\TeX{\TeX \spacefactor=1000 }
+
+% @LaTeX{} logo. Not quite the same results as the definition in
+% latex.ltx, since we use a different font for the raised A; it's most
+% convenient for us to use an explicitly smaller font, rather than using
+% the \scriptstyle font (since we don't reset \scriptstyle and
+% \scriptscriptstyle).
+%
+\def\LaTeX{%
+ L\kern-.36em
+ {\setbox0=\hbox{T}%
+ \vbox to \ht0{\hbox{\selectfonts\lllsize A}\vss}}%
+ \kern-.15em
+ \TeX
+}
+
+% Be sure we're in horizontal mode when doing a tie, since we make space
+% equivalent to this in @example-like environments. Otherwise, a space
+% at the beginning of a line will start with \penalty -- and
+% since \penalty is valid in vertical mode, we'd end up putting the
+% penalty on the vertical list instead of in the new paragraph.
+{\catcode`@ = 11
+ % Avoid using \@M directly, because that causes trouble
+ % if the definition is written into an index file.
+ \global\let\tiepenalty = \@M
+ \gdef\tie{\leavevmode\penalty\tiepenalty\ }
+}
+
+% @: forces normal size whitespace following.
+\def\:{\spacefactor=1000 }
+
+% @* forces a line break.
+\def\*{\hfil\break\hbox{}\ignorespaces}
+
+% @/ allows a line break.
+\let\/=\allowbreak
+
+% @. is an end-of-sentence period.
+\def\.{.\spacefactor=\endofsentencespacefactor\space}
+
+% @! is an end-of-sentence bang.
+\def\!{!\spacefactor=\endofsentencespacefactor\space}
+
+% @? is an end-of-sentence query.
+\def\?{?\spacefactor=\endofsentencespacefactor\space}
+
+% @frenchspacing on|off says whether to put extra space after punctuation.
+%
+\def\onword{on}
+\def\offword{off}
+%
+\parseargdef\frenchspacing{%
+ \def\temp{#1}%
+ \ifx\temp\onword \plainfrenchspacing
+ \else\ifx\temp\offword \plainnonfrenchspacing
+ \else
+ \errhelp = \EMsimple
+ \errmessage{Unknown @frenchspacing option `\temp', must be on/off}%
+ \fi\fi
+}
+
+% @w prevents a word break. Without the \leavevmode, @w at the
+% beginning of a paragraph, when TeX is still in vertical mode, would
+% produce a whole line of output instead of starting the paragraph.
+\def\w#1{\leavevmode\hbox{#1}}
+
+% @group ... @end group forces ... to be all on one page, by enclosing
+% it in a TeX vbox. We use \vtop instead of \vbox to construct the box
+% to keep its height that of a normal line. According to the rules for
+% \topskip (p.114 of the TeXbook), the glue inserted is
+% max (\topskip - \ht (first item), 0). If that height is large,
+% therefore, no glue is inserted, and the space between the headline and
+% the text is small, which looks bad.
+%
+% Another complication is that the group might be very large. This can
+% cause the glue on the previous page to be unduly stretched, because it
+% does not have much material. In this case, it's better to add an
+% explicit \vfill so that the extra space is at the bottom. The
+% threshold for doing this is if the group is more than \vfilllimit
+% percent of a page (\vfilllimit can be changed inside of @tex).
+%
+\newbox\groupbox
+\def\vfilllimit{0.7}
+%
+\envdef\group{%
+ \ifnum\catcode`\^^M=\active \else
+ \errhelp = \groupinvalidhelp
+ \errmessage{@group invalid in context where filling is enabled}%
+ \fi
+ \startsavinginserts
+ %
+ \setbox\groupbox = \vtop\bgroup
+ % Do @comment since we are called inside an environment such as
+ % @example, where each end-of-line in the input causes an
+ % end-of-line in the output. We don't want the end-of-line after
+ % the `@group' to put extra space in the output. Since @group
+ % should appear on a line by itself (according to the Texinfo
+ % manual), we don't worry about eating any user text.
+ \comment
+}
+%
+% The \vtop produces a box with normal height and large depth; thus, TeX puts
+% \baselineskip glue before it, and (when the next line of text is done)
+% \lineskip glue after it. Thus, space below is not quite equal to space
+% above. But it's pretty close.
+\def\Egroup{%
+ % To get correct interline space between the last line of the group
+ % and the first line afterwards, we have to propagate \prevdepth.
+ \endgraf % Not \par, as it may have been set to \lisppar.
+ \global\dimen1 = \prevdepth
+ \egroup % End the \vtop.
+ % \dimen0 is the vertical size of the group's box.
+ \dimen0 = \ht\groupbox \advance\dimen0 by \dp\groupbox
+ % \dimen2 is how much space is left on the page (more or less).
+ \dimen2 = \pageheight \advance\dimen2 by -\pagetotal
+ % if the group doesn't fit on the current page, and it's a big big
+ % group, force a page break.
+ \ifdim \dimen0 > \dimen2
+ \ifdim \pagetotal < \vfilllimit\pageheight
+ \page
+ \fi
+ \fi
+ \box\groupbox
+ \prevdepth = \dimen1
+ \checkinserts
+}
+%
+% TeX puts in an \escapechar (i.e., `@') at the beginning of the help
+% message, so this ends up printing `@group can only ...'.
+%
+\newhelp\groupinvalidhelp{%
+group can only be used in environments such as @example,^^J%
+where each line of input produces a line of output.}
+
+% @need space-in-mils
+% forces a page break if there is not space-in-mils remaining.
+
+\newdimen\mil \mil=0.001in
+
+% Old definition--didn't work.
+%\parseargdef\need{\par %
+%% This method tries to make TeX break the page naturally
+%% if the depth of the box does not fit.
+%{\baselineskip=0pt%
+%\vtop to #1\mil{\vfil}\kern -#1\mil\nobreak
+%\prevdepth=-1000pt
+%}}
+
+\parseargdef\need{%
+ % Ensure vertical mode, so we don't make a big box in the middle of a
+ % paragraph.
+ \par
+ %
+ % If the @need value is less than one line space, it's useless.
+ \dimen0 = #1\mil
+ \dimen2 = \ht\strutbox
+ \advance\dimen2 by \dp\strutbox
+ \ifdim\dimen0 > \dimen2
+ %
+ % Do a \strut just to make the height of this box be normal, so the
+ % normal leading is inserted relative to the preceding line.
+ % And a page break here is fine.
+ \vtop to #1\mil{\strut\vfil}%
+ %
+ % TeX does not even consider page breaks if a penalty added to the
+ % main vertical list is 10000 or more. But in order to see if the
+ % empty box we just added fits on the page, we must make it consider
+ % page breaks. On the other hand, we don't want to actually break the
+ % page after the empty box. So we use a penalty of 9999.
+ %
+ % There is an extremely small chance that TeX will actually break the
+ % page at this \penalty, if there are no other feasible breakpoints in
+ % sight. (If the user is using lots of big @group commands, which
+ % almost-but-not-quite fill up a page, TeX will have a hard time doing
+ % good page breaking, for example.) However, I could not construct an
+ % example where a page broke at this \penalty; if it happens in a real
+ % document, then we can reconsider our strategy.
+ \penalty9999
+ %
+ % Back up by the size of the box, whether we did a page break or not.
+ \kern -#1\mil
+ %
+ % Do not allow a page break right after this kern.
+ \nobreak
+ \fi
+}
+
+% @br forces paragraph break (and is undocumented).
+
+\let\br = \par
+
+% @page forces the start of a new page.
+%
+\def\page{\par\vfill\supereject}
+
+% @exdent text....
+% outputs text on separate line in roman font, starting at standard page margin
+
+% This records the amount of indent in the innermost environment.
+% That's how much \exdent should take out.
+\newskip\exdentamount
+
+% This defn is used inside fill environments such as @defun.
+\parseargdef\exdent{\hfil\break\hbox{\kern -\exdentamount{\rm#1}}\hfil\break}
+
+% This defn is used inside nofill environments such as @example.
+\parseargdef\nofillexdent{{\advance \leftskip by -\exdentamount
+ \leftline{\hskip\leftskip{\rm#1}}}}
+
+% @inmargin{WHICH}{TEXT} puts TEXT in the WHICH margin next to the current
+% paragraph. For more general purposes, use the \margin insertion
+% class. WHICH is `l' or `r'.
+%
+\newskip\inmarginspacing \inmarginspacing=1cm
+\def\strutdepth{\dp\strutbox}
+%
+\def\doinmargin#1#2{\strut\vadjust{%
+ \nobreak
+ \kern-\strutdepth
+ \vtop to \strutdepth{%
+ \baselineskip=\strutdepth
+ \vss
+ % if you have multiple lines of stuff to put here, you'll need to
+ % make the vbox yourself of the appropriate size.
+ \ifx#1l%
+ \llap{\ignorespaces #2\hskip\inmarginspacing}%
+ \else
+ \rlap{\hskip\hsize \hskip\inmarginspacing \ignorespaces #2}%
+ \fi
+ \null
+ }%
+}}
+\def\inleftmargin{\doinmargin l}
+\def\inrightmargin{\doinmargin r}
+%
+% @inmargin{TEXT [, RIGHT-TEXT]}
+% (if RIGHT-TEXT is given, use TEXT for left page, RIGHT-TEXT for right;
+% else use TEXT for both).
+%
+\def\inmargin#1{\parseinmargin #1,,\finish}
+\def\parseinmargin#1,#2,#3\finish{% not perfect, but better than nothing.
+ \setbox0 = \hbox{\ignorespaces #2}%
+ \ifdim\wd0 > 0pt
+ \def\lefttext{#1}% have both texts
+ \def\righttext{#2}%
+ \else
+ \def\lefttext{#1}% have only one text
+ \def\righttext{#1}%
+ \fi
+ %
+ \ifodd\pageno
+ \def\temp{\inrightmargin\righttext}% odd page -> outside is right margin
+ \else
+ \def\temp{\inleftmargin\lefttext}%
+ \fi
+ \temp
+}
+
+% @include FILE -- \input text of FILE.
+%
+\def\include{\parseargusing\filenamecatcodes\includezzz}
+\def\includezzz#1{%
+ \pushthisfilestack
+ \def\thisfile{#1}%
+ {%
+ \makevalueexpandable % we want to expand any @value in FILE.
+ \turnoffactive % and allow special characters in the expansion
+ \indexnofonts % Allow `@@' and other weird things in file names.
+ \edef\temp{\noexpand\input #1 }%
+ %
+ % This trickery is to read FILE outside of a group, in case it makes
+ % definitions, etc.
+ \expandafter
+ }\temp
+ \popthisfilestack
+}
+\def\filenamecatcodes{%
+ \catcode`\\=\other
+ \catcode`~=\other
+ \catcode`^=\other
+ \catcode`_=\other
+ \catcode`|=\other
+ \catcode`<=\other
+ \catcode`>=\other
+ \catcode`+=\other
+ \catcode`-=\other
+ \catcode`\`=\other
+ \catcode`\'=\other
+}
+
+\def\pushthisfilestack{%
+ \expandafter\pushthisfilestackX\popthisfilestack\StackTerm
+}
+\def\pushthisfilestackX{%
+ \expandafter\pushthisfilestackY\thisfile\StackTerm
+}
+\def\pushthisfilestackY #1\StackTerm #2\StackTerm {%
+ \gdef\popthisfilestack{\gdef\thisfile{#1}\gdef\popthisfilestack{#2}}%
+}
+
+\def\popthisfilestack{\errthisfilestackempty}
+\def\errthisfilestackempty{\errmessage{Internal error:
+ the stack of filenames is empty.}}
+
+\def\thisfile{}
+
+% @center line
+% outputs that line, centered.
+%
+\parseargdef\center{%
+ \ifhmode
+ \let\next\centerH
+ \else
+ \let\next\centerV
+ \fi
+ \next{\hfil \ignorespaces#1\unskip \hfil}%
+}
+\def\centerH#1{%
+ {%
+ \hfil\break
+ \advance\hsize by -\leftskip
+ \advance\hsize by -\rightskip
+ \line{#1}%
+ \break
+ }%
+}
+\def\centerV#1{\line{\kern\leftskip #1\kern\rightskip}}
+
+% @sp n outputs n lines of vertical space
+
+\parseargdef\sp{\vskip #1\baselineskip}
+
+% @comment ...line which is ignored...
+% @c is the same as @comment
+% @ignore ... @end ignore is another way to write a comment
+
+\def\comment{\begingroup \catcode`\^^M=\other%
+\catcode`\@=\other \catcode`\{=\other \catcode`\}=\other%
+\commentxxx}
+{\catcode`\^^M=\other \gdef\commentxxx#1^^M{\endgroup}}
+
+\let\c=\comment
+
+% @paragraphindent NCHARS
+% We'll use ems for NCHARS, close enough.
+% NCHARS can also be the word `asis' or `none'.
+% We cannot feasibly implement @paragraphindent asis, though.
+%
+\def\asisword{asis} % no translation, these are keywords
+\def\noneword{none}
+%
+\parseargdef\paragraphindent{%
+ \def\temp{#1}%
+ \ifx\temp\asisword
+ \else
+ \ifx\temp\noneword
+ \defaultparindent = 0pt
+ \else
+ \defaultparindent = #1em
+ \fi
+ \fi
+ \parindent = \defaultparindent
+}
+
+% @exampleindent NCHARS
+% We'll use ems for NCHARS like @paragraphindent.
+% It seems @exampleindent asis isn't necessary, but
+% I preserve it to make it similar to @paragraphindent.
+\parseargdef\exampleindent{%
+ \def\temp{#1}%
+ \ifx\temp\asisword
+ \else
+ \ifx\temp\noneword
+ \lispnarrowing = 0pt
+ \else
+ \lispnarrowing = #1em
+ \fi
+ \fi
+}
+
+% @firstparagraphindent WORD
+% If WORD is `none', then suppress indentation of the first paragraph
+% after a section heading. If WORD is `insert', then do indent at such
+% paragraphs.
+%
+% The paragraph indentation is suppressed or not by calling
+% \suppressfirstparagraphindent, which the sectioning commands do.
+% We switch the definition of this back and forth according to WORD.
+% By default, we suppress indentation.
+%
+\def\suppressfirstparagraphindent{\dosuppressfirstparagraphindent}
+\def\insertword{insert}
+%
+\parseargdef\firstparagraphindent{%
+ \def\temp{#1}%
+ \ifx\temp\noneword
+ \let\suppressfirstparagraphindent = \dosuppressfirstparagraphindent
+ \else\ifx\temp\insertword
+ \let\suppressfirstparagraphindent = \relax
+ \else
+ \errhelp = \EMsimple
+ \errmessage{Unknown @firstparagraphindent option `\temp'}%
+ \fi\fi
+}
+
+% Here is how we actually suppress indentation. Redefine \everypar to
+% \kern backwards by \parindent, and then reset itself to empty.
+%
+% We also make \indent itself not actually do anything until the next
+% paragraph.
+%
+\gdef\dosuppressfirstparagraphindent{%
+ \gdef\indent{%
+ \restorefirstparagraphindent
+ \indent
+ }%
+ \gdef\noindent{%
+ \restorefirstparagraphindent
+ \noindent
+ }%
+ \global\everypar = {%
+ \kern -\parindent
+ \restorefirstparagraphindent
+ }%
+}
+
+\gdef\restorefirstparagraphindent{%
+ \global \let \indent = \ptexindent
+ \global \let \noindent = \ptexnoindent
+ \global \everypar = {}%
+}
+
+
+% @asis just yields its argument. Used with @table, for example.
+%
+\def\asis#1{#1}
+
+% @math outputs its argument in math mode.
+%
+% One complication: _ usually means subscripts, but it could also mean
+% an actual _ character, as in @math{@var{some_variable} + 1}. So make
+% _ active, and distinguish by seeing if the current family is \slfam,
+% which is what @var uses.
+{
+ \catcode`\_ = \active
+ \gdef\mathunderscore{%
+ \catcode`\_=\active
+ \def_{\ifnum\fam=\slfam \_\else\sb\fi}%
+ }
+}
+% Another complication: we want \\ (and @\) to output a \ character.
+% FYI, plain.tex uses \\ as a temporary control sequence (why?), but
+% this is not advertised and we don't care. Texinfo does not
+% otherwise define @\.
+%
+% The \mathchar is class=0=ordinary, family=7=ttfam, position=5C=\.
+\def\mathbackslash{\ifnum\fam=\ttfam \mathchar"075C \else\backslash \fi}
+%
+\def\math{%
+ \tex
+ \mathunderscore
+ \let\\ = \mathbackslash
+ \mathactive
+ % make the texinfo accent commands work in math mode
+ \let\"=\ddot
+ \let\'=\acute
+ \let\==\bar
+ \let\^=\hat
+ \let\`=\grave
+ \let\u=\breve
+ \let\v=\check
+ \let\~=\tilde
+ \let\dotaccent=\dot
+ $\finishmath
+}
+\def\finishmath#1{#1$\endgroup} % Close the group opened by \tex.
+
+% Some active characters (such as <) are spaced differently in math.
+% We have to reset their definitions in case the @math was an argument
+% to a command which sets the catcodes (such as @item or @section).
+%
+{
+ \catcode`^ = \active
+ \catcode`< = \active
+ \catcode`> = \active
+ \catcode`+ = \active
+ \catcode`' = \active
+ \gdef\mathactive{%
+ \let^ = \ptexhat
+ \let< = \ptexless
+ \let> = \ptexgtr
+ \let+ = \ptexplus
+ \let' = \ptexquoteright
+ }
+}
+
+% Some math mode symbols.
+\def\bullet{$\ptexbullet$}
+\def\geq{\ifmmode \ge\else $\ge$\fi}
+\def\leq{\ifmmode \le\else $\le$\fi}
+\def\minus{\ifmmode -\else $-$\fi}
+
+% @dots{} outputs an ellipsis using the current font.
+% We do .5em per period so that it has the same spacing in the cm
+% typewriter fonts as three actual period characters; on the other hand,
+% in other typewriter fonts three periods are wider than 1.5em. So do
+% whichever is larger.
+%
+\def\dots{%
+ \leavevmode
+ \setbox0=\hbox{...}% get width of three periods
+ \ifdim\wd0 > 1.5em
+ \dimen0 = \wd0
+ \else
+ \dimen0 = 1.5em
+ \fi
+ \hbox to \dimen0{%
+ \hskip 0pt plus.25fil
+ .\hskip 0pt plus1fil
+ .\hskip 0pt plus1fil
+ .\hskip 0pt plus.5fil
+ }%
+}
+
+% @enddots{} is an end-of-sentence ellipsis.
+%
+\def\enddots{%
+ \dots
+ \spacefactor=\endofsentencespacefactor
+}
+
+% @comma{} is so commas can be inserted into text without messing up
+% Texinfo's parsing.
+%
+\let\comma = ,
+
+% @refill is a no-op.
+\let\refill=\relax
+
+% If working on a large document in chapters, it is convenient to
+% be able to disable indexing, cross-referencing, and contents, for test runs.
+% This is done with @novalidate (before @setfilename).
+%
+\newif\iflinks \linkstrue % by default we want the aux files.
+\let\novalidate = \linksfalse
+
+% @setfilename is done at the beginning of every texinfo file.
+% So open here the files we need to have open while reading the input.
+% This makes it possible to make a .fmt file for texinfo.
+\def\setfilename{%
+ \fixbackslash % Turn off hack to swallow `\input texinfo'.
+ \iflinks
+ \tryauxfile
+ % Open the new aux file. TeX will close it automatically at exit.
+ \immediate\openout\auxfile=\jobname.aux
+ \fi % \openindices needs to do some work in any case.
+ \openindices
+ \let\setfilename=\comment % Ignore extra @setfilename cmds.
+ %
+ % If texinfo.cnf is present on the system, read it.
+ % Useful for site-wide @afourpaper, etc.
+ \openin 1 texinfo.cnf
+ \ifeof 1 \else \input texinfo.cnf \fi
+ \closein 1
+ %
+ \comment % Ignore the actual filename.
+}
+
+% Called from \setfilename.
+%
+\def\openindices{%
+ \newindex{cp}%
+ \newcodeindex{fn}%
+ \newcodeindex{vr}%
+ \newcodeindex{tp}%
+ \newcodeindex{ky}%
+ \newcodeindex{pg}%
+}
+
+% @bye.
+\outer\def\bye{\pagealignmacro\tracingstats=1\ptexend}
+
+
+\message{pdf,}
+% adobe `portable' document format
+\newcount\tempnum
+\newcount\lnkcount
+\newtoks\filename
+\newcount\filenamelength
+\newcount\pgn
+\newtoks\toksA
+\newtoks\toksB
+\newtoks\toksC
+\newtoks\toksD
+\newbox\boxA
+\newcount\countA
+\newif\ifpdf
+\newif\ifpdfmakepagedest
+
+% when pdftex is run in dvi mode, \pdfoutput is defined (so \pdfoutput=1
+% can be set). So we test for \relax and 0 as well as \undefined,
+% borrowed from ifpdf.sty.
+\ifx\pdfoutput\undefined
+\else
+ \ifx\pdfoutput\relax
+ \else
+ \ifcase\pdfoutput
+ \else
+ \pdftrue
+ \fi
+ \fi
+\fi
+
+% PDF uses PostScript string constants for the names of xref targets,
+% for display in the outlines, and in other places. Thus, we have to
+% double any backslashes. Otherwise, a name like "\node" will be
+% interpreted as a newline (\n), followed by o, d, e. Not good.
+% http://www.ntg.nl/pipermail/ntg-pdftex/2004-July/000654.html
+% (and related messages, the final outcome is that it is up to the TeX
+% user to double the backslashes and otherwise make the string valid, so
+% that's what we do).
+
+% double active backslashes.
+%
+{\catcode`\@=0 \catcode`\\=\active
+ @gdef at activebackslashdouble{%
+ @catcode`@\=@active
+ @let\=@doublebackslash}
+}
+
+% To handle parens, we must adopt a different approach, since parens are
+% not active characters. hyperref.dtx (which has the same problem as
+% us) handles it with this amazing macro to replace tokens, with minor
+% changes for Texinfo. It is included here under the GPL by permission
+% from the author, Heiko Oberdiek.
+%
+% #1 is the tokens to replace.
+% #2 is the replacement.
+% #3 is the control sequence with the string.
+%
+\def\HyPsdSubst#1#2#3{%
+ \def\HyPsdReplace##1#1##2\END{%
+ ##1%
+ \ifx\\##2\\%
+ \else
+ #2%
+ \HyReturnAfterFi{%
+ \HyPsdReplace##2\END
+ }%
+ \fi
+ }%
+ \xdef#3{\expandafter\HyPsdReplace#3#1\END}%
+}
+\long\def\HyReturnAfterFi#1\fi{\fi#1}
+
+% #1 is a control sequence in which to do the replacements.
+\def\backslashparens#1{%
+ \xdef#1{#1}% redefine it as its expansion; the definition is simply
+ % \lastnode when called from \setref -> \pdfmkdest.
+ \HyPsdSubst{(}{\realbackslash(}{#1}%
+ \HyPsdSubst{)}{\realbackslash)}{#1}%
+}
+
+\newhelp\nopdfimagehelp{Texinfo supports .png, .jpg, .jpeg, and .pdf images
+with PDF output, and none of those formats could be found. (.eps cannot
+be supported due to the design of the PDF format; use regular TeX (DVI
+output) for that.)}
+
+\ifpdf
+ %
+ % Color manipulation macros based on pdfcolor.tex,
+ % except using rgb instead of cmyk; the latter is said to render as a
+ % very dark gray on-screen and a very dark halftone in print, instead
+ % of actual black.
+ \def\rgbDarkRed{0.50 0.09 0.12}
+ \def\rgbBlack{0 0 0}
+ %
+ % k sets the color for filling (usual text, etc.);
+ % K sets the color for stroking (thin rules, e.g., normal _'s).
+ \def\pdfsetcolor#1{\pdfliteral{#1 rg #1 RG}}
+ %
+ % Set color, and create a mark which defines \thiscolor accordingly,
+ % so that \makeheadline knows which color to restore.
+ \def\setcolor#1{%
+ \xdef\lastcolordefs{\gdef\noexpand\thiscolor{#1}}%
+ \domark
+ \pdfsetcolor{#1}%
+ }
+ %
+ \def\maincolor{\rgbBlack}
+ \pdfsetcolor{\maincolor}
+ \edef\thiscolor{\maincolor}
+ \def\lastcolordefs{}
+ %
+ \def\makefootline{%
+ \baselineskip24pt
+ \line{\pdfsetcolor{\maincolor}\the\footline}%
+ }
+ %
+ \def\makeheadline{%
+ \vbox to 0pt{%
+ \vskip-22.5pt
+ \line{%
+ \vbox to8.5pt{}%
+ % Extract \thiscolor definition from the marks.
+ \getcolormarks
+ % Typeset the headline with \maincolor, then restore the color.
+ \pdfsetcolor{\maincolor}\the\headline\pdfsetcolor{\thiscolor}%
+ }%
+ \vss
+ }%
+ \nointerlineskip
+ }
+ %
+ %
+ \pdfcatalog{/PageMode /UseOutlines}
+ %
+ % #1 is image name, #2 width (might be empty/whitespace), #3 height (ditto).
+ \def\dopdfimage#1#2#3{%
+ \def\imagewidth{#2}\setbox0 = \hbox{\ignorespaces #2}%
+ \def\imageheight{#3}\setbox2 = \hbox{\ignorespaces #3}%
+ %
+ % pdftex (and the PDF format) support .png, .jpg, .pdf (among
+ % others). Let's try in that order.
+ \let\pdfimgext=\empty
+ \begingroup
+ \openin 1 #1.png \ifeof 1
+ \openin 1 #1.jpg \ifeof 1
+ \openin 1 #1.jpeg \ifeof 1
+ \openin 1 #1.JPG \ifeof 1
+ \openin 1 #1.pdf \ifeof 1
+ \openin 1 #1.PDF \ifeof 1
+ \errhelp = \nopdfimagehelp
+ \errmessage{Could not find image file #1 for pdf}%
+ \else \gdef\pdfimgext{PDF}%
+ \fi
+ \else \gdef\pdfimgext{pdf}%
+ \fi
+ \else \gdef\pdfimgext{JPG}%
+ \fi
+ \else \gdef\pdfimgext{jpeg}%
+ \fi
+ \else \gdef\pdfimgext{jpg}%
+ \fi
+ \else \gdef\pdfimgext{png}%
+ \fi
+ \closein 1
+ \endgroup
+ %
+ % without \immediate, ancient pdftex seg faults when the same image is
+ % included twice. (Version 3.14159-pre-1.0-unofficial-20010704.)
+ \ifnum\pdftexversion < 14
+ \immediate\pdfimage
+ \else
+ \immediate\pdfximage
+ \fi
+ \ifdim \wd0 >0pt width \imagewidth \fi
+ \ifdim \wd2 >0pt height \imageheight \fi
+ \ifnum\pdftexversion<13
+ #1.\pdfimgext
+ \else
+ {#1.\pdfimgext}%
+ \fi
+ \ifnum\pdftexversion < 14 \else
+ \pdfrefximage \pdflastximage
+ \fi}
+ %
+ \def\pdfmkdest#1{{%
+ % We have to set dummies so commands such as @code, and characters
+ % such as \, aren't expanded when present in a section title.
+ \indexnofonts
+ \turnoffactive
+ \activebackslashdouble
+ \makevalueexpandable
+ \def\pdfdestname{#1}%
+ \backslashparens\pdfdestname
+ \safewhatsit{\pdfdest name{\pdfdestname} xyz}%
+ }}
+ %
+ % used to mark target names; must be expandable.
+ \def\pdfmkpgn#1{#1}
+ %
+ % by default, use a color that is dark enough to print on paper as
+ % nearly black, but still distinguishable for online viewing.
+ \def\urlcolor{\rgbDarkRed}
+ \def\linkcolor{\rgbDarkRed}
+ \def\endlink{\setcolor{\maincolor}\pdfendlink}
+ %
+ % Adding outlines to PDF; macros for calculating structure of outlines
+ % come from Petr Olsak
+ \def\expnumber#1{\expandafter\ifx\csname#1\endcsname\relax 0%
+ \else \csname#1\endcsname \fi}
+ \def\advancenumber#1{\tempnum=\expnumber{#1}\relax
+ \advance\tempnum by 1
+ \expandafter\xdef\csname#1\endcsname{\the\tempnum}}
+ %
+ % #1 is the section text, which is what will be displayed in the
+ % outline by the pdf viewer. #2 is the pdf expression for the number
+ % of subentries (or empty, for subsubsections). #3 is the node text,
+ % which might be empty if this toc entry had no corresponding node.
+ % #4 is the page number
+ %
+ \def\dopdfoutline#1#2#3#4{%
+ % Generate a link to the node text if that exists; else, use the
+ % page number. We could generate a destination for the section
+ % text in the case where a section has no node, but it doesn't
+ % seem worth the trouble, since most documents are normally structured.
+ \def\pdfoutlinedest{#3}%
+ \ifx\pdfoutlinedest\empty
+ \def\pdfoutlinedest{#4}%
+ \else
+ % Doubled backslashes in the name.
+ {\activebackslashdouble \xdef\pdfoutlinedest{#3}%
+ \backslashparens\pdfoutlinedest}%
+ \fi
+ %
+ % Also double the backslashes in the display string.
+ {\activebackslashdouble \xdef\pdfoutlinetext{#1}%
+ \backslashparens\pdfoutlinetext}%
+ %
+ \pdfoutline goto name{\pdfmkpgn{\pdfoutlinedest}}#2{\pdfoutlinetext}%
+ }
+ %
+ \def\pdfmakeoutlines{%
+ \begingroup
+ % Thanh's hack / proper braces in bookmarks
+ \edef\mylbrace{\iftrue \string{\else}\fi}\let\{=\mylbrace
+ \edef\myrbrace{\iffalse{\else\string}\fi}\let\}=\myrbrace
+ %
+ % Read toc silently, to get counts of subentries for \pdfoutline.
+ \def\numchapentry##1##2##3##4{%
+ \def\thischapnum{##2}%
+ \def\thissecnum{0}%
+ \def\thissubsecnum{0}%
+ }%
+ \def\numsecentry##1##2##3##4{%
+ \advancenumber{chap\thischapnum}%
+ \def\thissecnum{##2}%
+ \def\thissubsecnum{0}%
+ }%
+ \def\numsubsecentry##1##2##3##4{%
+ \advancenumber{sec\thissecnum}%
+ \def\thissubsecnum{##2}%
+ }%
+ \def\numsubsubsecentry##1##2##3##4{%
+ \advancenumber{subsec\thissubsecnum}%
+ }%
+ \def\thischapnum{0}%
+ \def\thissecnum{0}%
+ \def\thissubsecnum{0}%
+ %
+ % use \def rather than \let here because we redefine \chapentry et
+ % al. a second time, below.
+ \def\appentry{\numchapentry}%
+ \def\appsecentry{\numsecentry}%
+ \def\appsubsecentry{\numsubsecentry}%
+ \def\appsubsubsecentry{\numsubsubsecentry}%
+ \def\unnchapentry{\numchapentry}%
+ \def\unnsecentry{\numsecentry}%
+ \def\unnsubsecentry{\numsubsecentry}%
+ \def\unnsubsubsecentry{\numsubsubsecentry}%
+ \readdatafile{toc}%
+ %
+ % Read toc second time, this time actually producing the outlines.
+ % The `-' means take the \expnumber as the absolute number of
+ % subentries, which we calculated on our first read of the .toc above.
+ %
+ % We use the node names as the destinations.
+ \def\numchapentry##1##2##3##4{%
+ \dopdfoutline{##1}{count-\expnumber{chap##2}}{##3}{##4}}%
+ \def\numsecentry##1##2##3##4{%
+ \dopdfoutline{##1}{count-\expnumber{sec##2}}{##3}{##4}}%
+ \def\numsubsecentry##1##2##3##4{%
+ \dopdfoutline{##1}{count-\expnumber{subsec##2}}{##3}{##4}}%
+ \def\numsubsubsecentry##1##2##3##4{% count is always zero
+ \dopdfoutline{##1}{}{##3}{##4}}%
+ %
+ % PDF outlines are displayed using system fonts, instead of
+ % document fonts. Therefore we cannot use special characters,
+ % since the encoding is unknown. For example, the eogonek from
+ % Latin 2 (0xea) gets translated to a | character. Info from
+ % Staszek Wawrykiewicz, 19 Jan 2004 04:09:24 +0100.
+ %
+ % xx to do this right, we have to translate 8-bit characters to
+ % their "best" equivalent, based on the @documentencoding. Right
+ % now, I guess we'll just let the pdf reader have its way.
+ \indexnofonts
+ \setupdatafile
+ \catcode`\\=\active \otherbackslash
+ \input \tocreadfilename
+ \endgroup
+ }
+ %
+ \def\skipspaces#1{\def\PP{#1}\def\D{|}%
+ \ifx\PP\D\let\nextsp\relax
+ \else\let\nextsp\skipspaces
+ \ifx\p\space\else\addtokens{\filename}{\PP}%
+ \advance\filenamelength by 1
+ \fi
+ \fi
+ \nextsp}
+ \def\getfilename#1{\filenamelength=0\expandafter\skipspaces#1|\relax}
+ \ifnum\pdftexversion < 14
+ \let \startlink \pdfannotlink
+ \else
+ \let \startlink \pdfstartlink
+ \fi
+ % make a live url in pdf output.
+ \def\pdfurl#1{%
+ \begingroup
+ % it seems we really need yet another set of dummies; have not
+ % tried to figure out what each command should do in the context
+ % of @url. for now, just make @/ a no-op, that's the only one
+ % people have actually reported a problem with.
+ %
+ \normalturnoffactive
+ \def\@{@}%
+ \let\/=\empty
+ \makevalueexpandable
+ % do we want to go so far as to use \indexnofonts instead of just
+ % special-casing \var here?
+ \def\var##1{##1}%
+ %
+ \leavevmode\setcolor{\urlcolor}%
+ \startlink attr{/Border [0 0 0]}%
+ user{/Subtype /Link /A << /S /URI /URI (#1) >>}%
+ \endgroup}
+ \def\pdfgettoks#1.{\setbox\boxA=\hbox{\toksA={#1.}\toksB={}\maketoks}}
+ \def\addtokens#1#2{\edef\addtoks{\noexpand#1={\the#1#2}}\addtoks}
+ \def\adn#1{\addtokens{\toksC}{#1}\global\countA=1\let\next=\maketoks}
+ \def\poptoks#1#2|ENDTOKS|{\let\first=#1\toksD={#1}\toksA={#2}}
+ \def\maketoks{%
+ \expandafter\poptoks\the\toksA|ENDTOKS|\relax
+ \ifx\first0\adn0
+ \else\ifx\first1\adn1 \else\ifx\first2\adn2 \else\ifx\first3\adn3
+ \else\ifx\first4\adn4 \else\ifx\first5\adn5 \else\ifx\first6\adn6
+ \else\ifx\first7\adn7 \else\ifx\first8\adn8 \else\ifx\first9\adn9
+ \else
+ \ifnum0=\countA\else\makelink\fi
+ \ifx\first.\let\next=\done\else
+ \let\next=\maketoks
+ \addtokens{\toksB}{\the\toksD}
+ \ifx\first,\addtokens{\toksB}{\space}\fi
+ \fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \next}
+ \def\makelink{\addtokens{\toksB}%
+ {\noexpand\pdflink{\the\toksC}}\toksC={}\global\countA=0}
+ \def\pdflink#1{%
+ \startlink attr{/Border [0 0 0]} goto name{\pdfmkpgn{#1}}
+ \setcolor{\linkcolor}#1\endlink}
+ \def\done{\edef\st{\global\noexpand\toksA={\the\toksB}}\st}
+\else
+ % non-pdf mode
+ \let\pdfmkdest = \gobble
+ \let\pdfurl = \gobble
+ \let\endlink = \relax
+ \let\setcolor = \gobble
+ \let\pdfsetcolor = \gobble
+ \let\pdfmakeoutlines = \relax
+\fi % \ifx\pdfoutput
+
+
+\message{fonts,}
+
+% Change the current font style to #1, remembering it in \curfontstyle.
+% For now, we do not accumulate font styles: @b{@i{foo}} prints foo in
+% italics, not bold italics.
+%
+\def\setfontstyle#1{%
+ \def\curfontstyle{#1}% not as a control sequence, because we are \edef'd.
+ \csname ten#1\endcsname % change the current font
+}
+
+% Select #1 fonts with the current style.
+%
+\def\selectfonts#1{\csname #1fonts\endcsname \csname\curfontstyle\endcsname}
+
+\def\rm{\fam=0 \setfontstyle{rm}}
+\def\it{\fam=\itfam \setfontstyle{it}}
+\def\sl{\fam=\slfam \setfontstyle{sl}}
+\def\bf{\fam=\bffam \setfontstyle{bf}}\def\bfstylename{bf}
+\def\tt{\fam=\ttfam \setfontstyle{tt}}
+
+% Unfortunately, we have to override this for titles and the like, since
+% in those cases "rm" is bold. Sigh.
+\def\rmisbold{\rm\def\curfontstyle{bf}}
+
+% Texinfo sort of supports the sans serif font style, which plain TeX does not.
+% So we set up a \sf.
+\newfam\sffam
+\def\sf{\fam=\sffam \setfontstyle{sf}}
+\let\li = \sf % Sometimes we call it \li, not \sf.
+
+% We don't need math for this font style.
+\def\ttsl{\setfontstyle{ttsl}}
+
+
+% Default leading.
+\newdimen\textleading \textleading = 13.2pt
+
+% Set the baselineskip to #1, and the lineskip and strut size
+% correspondingly. There is no deep meaning behind these magic numbers
+% used as factors; they just match (closely enough) what Knuth defined.
+%
+\def\lineskipfactor{.08333}
+\def\strutheightpercent{.70833}
+\def\strutdepthpercent {.29167}
+%
+% can get a sort of poor man's double spacing by redefining this.
+\def\baselinefactor{1}
+%
+\def\setleading#1{%
+ \dimen0 = #1\relax
+ \normalbaselineskip = \baselinefactor\dimen0
+ \normallineskip = \lineskipfactor\normalbaselineskip
+ \normalbaselines
+ \setbox\strutbox =\hbox{%
+ \vrule width0pt height\strutheightpercent\baselineskip
+ depth \strutdepthpercent \baselineskip
+ }%
+}
+
+% PDF CMaps. See also LaTeX's t1.cmap.
+%
+% do nothing with this by default.
+\expandafter\let\csname cmapOT1\endcsname\gobble
+\expandafter\let\csname cmapOT1IT\endcsname\gobble
+\expandafter\let\csname cmapOT1TT\endcsname\gobble
+
+% if we are producing pdf, and we have \pdffontattr, then define cmaps.
+% (\pdffontattr was introduced many years ago, but people still run
+% older pdftex's; it's easy to conditionalize, so we do.)
+\ifpdf \ifx\pdffontattr\undefined \else
+ \begingroup
+ \catcode`\^^M=\active \def^^M{^^J}% Output line endings as the ^^J char.
+ \catcode`\%=12 \immediate\pdfobj stream {%!PS-Adobe-3.0 Resource-CMap
+%%DocumentNeededResources: ProcSet (CIDInit)
+%%IncludeResource: ProcSet (CIDInit)
+%%BeginResource: CMap (TeX-OT1-0)
+%%Title: (TeX-OT1-0 TeX OT1 0)
+%%Version: 1.000
+%%EndComments
+/CIDInit /ProcSet findresource begin
+12 dict begin
+begincmap
+/CIDSystemInfo
+<< /Registry (TeX)
+/Ordering (OT1)
+/Supplement 0
+>> def
+/CMapName /TeX-OT1-0 def
+/CMapType 2 def
+1 begincodespacerange
+<00> <7F>
+endcodespacerange
+8 beginbfrange
+<00> <01> <0393>
+<09> <0A> <03A8>
+<23> <26> <0023>
+<28> <3B> <0028>
+<3F> <5B> <003F>
+<5D> <5E> <005D>
+<61> <7A> <0061>
+<7B> <7C> <2013>
+endbfrange
+40 beginbfchar
+<02> <0398>
+<03> <039B>
+<04> <039E>
+<05> <03A0>
+<06> <03A3>
+<07> <03D2>
+<08> <03A6>
+<0B> <00660066>
+<0C> <00660069>
+<0D> <0066006C>
+<0E> <006600660069>
+<0F> <00660066006C>
+<10> <0131>
+<11> <0237>
+<12> <0060>
+<13> <00B4>
+<14> <02C7>
+<15> <02D8>
+<16> <00AF>
+<17> <02DA>
+<18> <00B8>
+<19> <00DF>
+<1A> <00E6>
+<1B> <0153>
+<1C> <00F8>
+<1D> <00C6>
+<1E> <0152>
+<1F> <00D8>
+<21> <0021>
+<22> <201D>
+<27> <2019>
+<3C> <00A1>
+<3D> <003D>
+<3E> <00BF>
+<5C> <201C>
+<5F> <02D9>
+<60> <2018>
+<7D> <02DD>
+<7E> <007E>
+<7F> <00A8>
+endbfchar
+endcmap
+CMapName currentdict /CMap defineresource pop
+end
+end
+%%EndResource
+%%EOF
+ }\endgroup
+ \expandafter\edef\csname cmapOT1\endcsname#1{%
+ \pdffontattr#1{/ToUnicode \the\pdflastobj\space 0 R}%
+ }%
+%
+% \cmapOT1IT
+ \begingroup
+ \catcode`\^^M=\active \def^^M{^^J}% Output line endings as the ^^J char.
+ \catcode`\%=12 \immediate\pdfobj stream {%!PS-Adobe-3.0 Resource-CMap
+%%DocumentNeededResources: ProcSet (CIDInit)
+%%IncludeResource: ProcSet (CIDInit)
+%%BeginResource: CMap (TeX-OT1IT-0)
+%%Title: (TeX-OT1IT-0 TeX OT1IT 0)
+%%Version: 1.000
+%%EndComments
+/CIDInit /ProcSet findresource begin
+12 dict begin
+begincmap
+/CIDSystemInfo
+<< /Registry (TeX)
+/Ordering (OT1IT)
+/Supplement 0
+>> def
+/CMapName /TeX-OT1IT-0 def
+/CMapType 2 def
+1 begincodespacerange
+<00> <7F>
+endcodespacerange
+8 beginbfrange
+<00> <01> <0393>
+<09> <0A> <03A8>
+<25> <26> <0025>
+<28> <3B> <0028>
+<3F> <5B> <003F>
+<5D> <5E> <005D>
+<61> <7A> <0061>
+<7B> <7C> <2013>
+endbfrange
+42 beginbfchar
+<02> <0398>
+<03> <039B>
+<04> <039E>
+<05> <03A0>
+<06> <03A3>
+<07> <03D2>
+<08> <03A6>
+<0B> <00660066>
+<0C> <00660069>
+<0D> <0066006C>
+<0E> <006600660069>
+<0F> <00660066006C>
+<10> <0131>
+<11> <0237>
+<12> <0060>
+<13> <00B4>
+<14> <02C7>
+<15> <02D8>
+<16> <00AF>
+<17> <02DA>
+<18> <00B8>
+<19> <00DF>
+<1A> <00E6>
+<1B> <0153>
+<1C> <00F8>
+<1D> <00C6>
+<1E> <0152>
+<1F> <00D8>
+<21> <0021>
+<22> <201D>
+<23> <0023>
+<24> <00A3>
+<27> <2019>
+<3C> <00A1>
+<3D> <003D>
+<3E> <00BF>
+<5C> <201C>
+<5F> <02D9>
+<60> <2018>
+<7D> <02DD>
+<7E> <007E>
+<7F> <00A8>
+endbfchar
+endcmap
+CMapName currentdict /CMap defineresource pop
+end
+end
+%%EndResource
+%%EOF
+ }\endgroup
+ \expandafter\edef\csname cmapOT1IT\endcsname#1{%
+ \pdffontattr#1{/ToUnicode \the\pdflastobj\space 0 R}%
+ }%
+%
+% \cmapOT1TT
+ \begingroup
+ \catcode`\^^M=\active \def^^M{^^J}% Output line endings as the ^^J char.
+ \catcode`\%=12 \immediate\pdfobj stream {%!PS-Adobe-3.0 Resource-CMap
+%%DocumentNeededResources: ProcSet (CIDInit)
+%%IncludeResource: ProcSet (CIDInit)
+%%BeginResource: CMap (TeX-OT1TT-0)
+%%Title: (TeX-OT1TT-0 TeX OT1TT 0)
+%%Version: 1.000
+%%EndComments
+/CIDInit /ProcSet findresource begin
+12 dict begin
+begincmap
+/CIDSystemInfo
+<< /Registry (TeX)
+/Ordering (OT1TT)
+/Supplement 0
+>> def
+/CMapName /TeX-OT1TT-0 def
+/CMapType 2 def
+1 begincodespacerange
+<00> <7F>
+endcodespacerange
+5 beginbfrange
+<00> <01> <0393>
+<09> <0A> <03A8>
+<21> <26> <0021>
+<28> <5F> <0028>
+<61> <7E> <0061>
+endbfrange
+32 beginbfchar
+<02> <0398>
+<03> <039B>
+<04> <039E>
+<05> <03A0>
+<06> <03A3>
+<07> <03D2>
+<08> <03A6>
+<0B> <2191>
+<0C> <2193>
+<0D> <0027>
+<0E> <00A1>
+<0F> <00BF>
+<10> <0131>
+<11> <0237>
+<12> <0060>
+<13> <00B4>
+<14> <02C7>
+<15> <02D8>
+<16> <00AF>
+<17> <02DA>
+<18> <00B8>
+<19> <00DF>
+<1A> <00E6>
+<1B> <0153>
+<1C> <00F8>
+<1D> <00C6>
+<1E> <0152>
+<1F> <00D8>
+<20> <2423>
+<27> <2019>
+<60> <2018>
+<7F> <00A8>
+endbfchar
+endcmap
+CMapName currentdict /CMap defineresource pop
+end
+end
+%%EndResource
+%%EOF
+ }\endgroup
+ \expandafter\edef\csname cmapOT1TT\endcsname#1{%
+ \pdffontattr#1{/ToUnicode \the\pdflastobj\space 0 R}%
+ }%
+\fi\fi
+
+
+% Set the font macro #1 to the font named #2, adding on the
+% specified font prefix (normally `cm').
+% #3 is the font's design size, #4 is a scale factor, #5 is the CMap
+% encoding (currently only OT1, OT1IT and OT1TT are allowed, pass
+% empty to omit).
+\def\setfont#1#2#3#4#5{%
+ \font#1=\fontprefix#2#3 scaled #4
+ \csname cmap#5\endcsname#1%
+}
+% This is what gets called when #5 of \setfont is empty.
+\let\cmap\gobble
+% emacs-page end of cmaps
+
+% Use cm as the default font prefix.
+% To specify the font prefix, you must define \fontprefix
+% before you read in texinfo.tex.
+\ifx\fontprefix\undefined
+\def\fontprefix{cm}
+\fi
+% Support font families that don't use the same naming scheme as CM.
+\def\rmshape{r}
+\def\rmbshape{bx} %where the normal face is bold
+\def\bfshape{b}
+\def\bxshape{bx}
+\def\ttshape{tt}
+\def\ttbshape{tt}
+\def\ttslshape{sltt}
+\def\itshape{ti}
+\def\itbshape{bxti}
+\def\slshape{sl}
+\def\slbshape{bxsl}
+\def\sfshape{ss}
+\def\sfbshape{ss}
+\def\scshape{csc}
+\def\scbshape{csc}
+
+% Definitions for a main text size of 11pt. This is the default in
+% Texinfo.
+%
+\def\definetextfontsizexi{%
+% Text fonts (11.2pt, magstep1).
+\def\textnominalsize{11pt}
+\edef\mainmagstep{\magstephalf}
+\setfont\textrm\rmshape{10}{\mainmagstep}{OT1}
+\setfont\texttt\ttshape{10}{\mainmagstep}{OT1TT}
+\setfont\textbf\bfshape{10}{\mainmagstep}{OT1}
+\setfont\textit\itshape{10}{\mainmagstep}{OT1IT}
+\setfont\textsl\slshape{10}{\mainmagstep}{OT1}
+\setfont\textsf\sfshape{10}{\mainmagstep}{OT1}
+\setfont\textsc\scshape{10}{\mainmagstep}{OT1}
+\setfont\textttsl\ttslshape{10}{\mainmagstep}{OT1TT}
+\font\texti=cmmi10 scaled \mainmagstep
+\font\textsy=cmsy10 scaled \mainmagstep
+\def\textecsize{1095}
+
+% A few fonts for @defun names and args.
+\setfont\defbf\bfshape{10}{\magstep1}{OT1}
+\setfont\deftt\ttshape{10}{\magstep1}{OT1TT}
+\setfont\defttsl\ttslshape{10}{\magstep1}{OT1TT}
+\def\df{\let\tentt=\deftt \let\tenbf = \defbf \let\tenttsl=\defttsl \bf}
+
+% Fonts for indices, footnotes, small examples (9pt).
+\def\smallnominalsize{9pt}
+\setfont\smallrm\rmshape{9}{1000}{OT1}
+\setfont\smalltt\ttshape{9}{1000}{OT1TT}
+\setfont\smallbf\bfshape{10}{900}{OT1}
+\setfont\smallit\itshape{9}{1000}{OT1IT}
+\setfont\smallsl\slshape{9}{1000}{OT1}
+\setfont\smallsf\sfshape{9}{1000}{OT1}
+\setfont\smallsc\scshape{10}{900}{OT1}
+\setfont\smallttsl\ttslshape{10}{900}{OT1TT}
+\font\smalli=cmmi9
+\font\smallsy=cmsy9
+\def\smallecsize{0900}
+
+% Fonts for small examples (8pt).
+\def\smallernominalsize{8pt}
+\setfont\smallerrm\rmshape{8}{1000}{OT1}
+\setfont\smallertt\ttshape{8}{1000}{OT1TT}
+\setfont\smallerbf\bfshape{10}{800}{OT1}
+\setfont\smallerit\itshape{8}{1000}{OT1IT}
+\setfont\smallersl\slshape{8}{1000}{OT1}
+\setfont\smallersf\sfshape{8}{1000}{OT1}
+\setfont\smallersc\scshape{10}{800}{OT1}
+\setfont\smallerttsl\ttslshape{10}{800}{OT1TT}
+\font\smalleri=cmmi8
+\font\smallersy=cmsy8
+\def\smallerecsize{0800}
+
+% Fonts for title page (20.4pt):
+\def\titlenominalsize{20pt}
+\setfont\titlerm\rmbshape{12}{\magstep3}{OT1}
+\setfont\titleit\itbshape{10}{\magstep4}{OT1IT}
+\setfont\titlesl\slbshape{10}{\magstep4}{OT1}
+\setfont\titlett\ttbshape{12}{\magstep3}{OT1TT}
+\setfont\titlettsl\ttslshape{10}{\magstep4}{OT1TT}
+\setfont\titlesf\sfbshape{17}{\magstep1}{OT1}
+\let\titlebf=\titlerm
+\setfont\titlesc\scbshape{10}{\magstep4}{OT1}
+\font\titlei=cmmi12 scaled \magstep3
+\font\titlesy=cmsy10 scaled \magstep4
+\def\titleecsize{2074}
+
+% Chapter (and unnumbered) fonts (17.28pt).
+\def\chapnominalsize{17pt}
+\setfont\chaprm\rmbshape{12}{\magstep2}{OT1}
+\setfont\chapit\itbshape{10}{\magstep3}{OT1IT}
+\setfont\chapsl\slbshape{10}{\magstep3}{OT1}
+\setfont\chaptt\ttbshape{12}{\magstep2}{OT1TT}
+\setfont\chapttsl\ttslshape{10}{\magstep3}{OT1TT}
+\setfont\chapsf\sfbshape{17}{1000}{OT1}
+\let\chapbf=\chaprm
+\setfont\chapsc\scbshape{10}{\magstep3}{OT1}
+\font\chapi=cmmi12 scaled \magstep2
+\font\chapsy=cmsy10 scaled \magstep3
+\def\chapecsize{1728}
+
+% Section fonts (14.4pt).
+\def\secnominalsize{14pt}
+\setfont\secrm\rmbshape{12}{\magstep1}{OT1}
+\setfont\secit\itbshape{10}{\magstep2}{OT1IT}
+\setfont\secsl\slbshape{10}{\magstep2}{OT1}
+\setfont\sectt\ttbshape{12}{\magstep1}{OT1TT}
+\setfont\secttsl\ttslshape{10}{\magstep2}{OT1TT}
+\setfont\secsf\sfbshape{12}{\magstep1}{OT1}
+\let\secbf\secrm
+\setfont\secsc\scbshape{10}{\magstep2}{OT1}
+\font\seci=cmmi12 scaled \magstep1
+\font\secsy=cmsy10 scaled \magstep2
+\def\sececsize{1440}
+
+% Subsection fonts (13.15pt).
+\def\ssecnominalsize{13pt}
+\setfont\ssecrm\rmbshape{12}{\magstephalf}{OT1}
+\setfont\ssecit\itbshape{10}{1315}{OT1IT}
+\setfont\ssecsl\slbshape{10}{1315}{OT1}
+\setfont\ssectt\ttbshape{12}{\magstephalf}{OT1TT}
+\setfont\ssecttsl\ttslshape{10}{1315}{OT1TT}
+\setfont\ssecsf\sfbshape{12}{\magstephalf}{OT1}
+\let\ssecbf\ssecrm
+\setfont\ssecsc\scbshape{10}{1315}{OT1}
+\font\sseci=cmmi12 scaled \magstephalf
+\font\ssecsy=cmsy10 scaled 1315
+\def\ssececsize{1200}
+
+% Reduced fonts for @acro in text (10pt).
+\def\reducednominalsize{10pt}
+\setfont\reducedrm\rmshape{10}{1000}{OT1}
+\setfont\reducedtt\ttshape{10}{1000}{OT1TT}
+\setfont\reducedbf\bfshape{10}{1000}{OT1}
+\setfont\reducedit\itshape{10}{1000}{OT1IT}
+\setfont\reducedsl\slshape{10}{1000}{OT1}
+\setfont\reducedsf\sfshape{10}{1000}{OT1}
+\setfont\reducedsc\scshape{10}{1000}{OT1}
+\setfont\reducedttsl\ttslshape{10}{1000}{OT1TT}
+\font\reducedi=cmmi10
+\font\reducedsy=cmsy10
+\def\reducedecsize{1000}
+
+% reset the current fonts
+\textfonts
+\rm
+} % end of 11pt text font size definitions
+
+
+% Definitions to make the main text be 10pt Computer Modern, with
+% section, chapter, etc., sizes following suit. This is for the GNU
+% Press printing of the Emacs 22 manual. Maybe other manuals in the
+% future. Used with @smallbook, which sets the leading to 12pt.
+%
+\def\definetextfontsizex{%
+% Text fonts (10pt).
+\def\textnominalsize{10pt}
+\edef\mainmagstep{1000}
+\setfont\textrm\rmshape{10}{\mainmagstep}{OT1}
+\setfont\texttt\ttshape{10}{\mainmagstep}{OT1TT}
+\setfont\textbf\bfshape{10}{\mainmagstep}{OT1}
+\setfont\textit\itshape{10}{\mainmagstep}{OT1IT}
+\setfont\textsl\slshape{10}{\mainmagstep}{OT1}
+\setfont\textsf\sfshape{10}{\mainmagstep}{OT1}
+\setfont\textsc\scshape{10}{\mainmagstep}{OT1}
+\setfont\textttsl\ttslshape{10}{\mainmagstep}{OT1TT}
+\font\texti=cmmi10 scaled \mainmagstep
+\font\textsy=cmsy10 scaled \mainmagstep
+\def\textecsize{1000}
+
+% A few fonts for @defun names and args.
+\setfont\defbf\bfshape{10}{\magstephalf}{OT1}
+\setfont\deftt\ttshape{10}{\magstephalf}{OT1TT}
+\setfont\defttsl\ttslshape{10}{\magstephalf}{OT1TT}
+\def\df{\let\tentt=\deftt \let\tenbf = \defbf \let\tenttsl=\defttsl \bf}
+
+% Fonts for indices, footnotes, small examples (9pt).
+\def\smallnominalsize{9pt}
+\setfont\smallrm\rmshape{9}{1000}{OT1}
+\setfont\smalltt\ttshape{9}{1000}{OT1TT}
+\setfont\smallbf\bfshape{10}{900}{OT1}
+\setfont\smallit\itshape{9}{1000}{OT1IT}
+\setfont\smallsl\slshape{9}{1000}{OT1}
+\setfont\smallsf\sfshape{9}{1000}{OT1}
+\setfont\smallsc\scshape{10}{900}{OT1}
+\setfont\smallttsl\ttslshape{10}{900}{OT1TT}
+\font\smalli=cmmi9
+\font\smallsy=cmsy9
+\def\smallecsize{0900}
+
+% Fonts for small examples (8pt).
+\def\smallernominalsize{8pt}
+\setfont\smallerrm\rmshape{8}{1000}{OT1}
+\setfont\smallertt\ttshape{8}{1000}{OT1TT}
+\setfont\smallerbf\bfshape{10}{800}{OT1}
+\setfont\smallerit\itshape{8}{1000}{OT1IT}
+\setfont\smallersl\slshape{8}{1000}{OT1}
+\setfont\smallersf\sfshape{8}{1000}{OT1}
+\setfont\smallersc\scshape{10}{800}{OT1}
+\setfont\smallerttsl\ttslshape{10}{800}{OT1TT}
+\font\smalleri=cmmi8
+\font\smallersy=cmsy8
+\def\smallerecsize{0800}
+
+% Fonts for title page (20.4pt):
+\def\titlenominalsize{20pt}
+\setfont\titlerm\rmbshape{12}{\magstep3}{OT1}
+\setfont\titleit\itbshape{10}{\magstep4}{OT1IT}
+\setfont\titlesl\slbshape{10}{\magstep4}{OT1}
+\setfont\titlett\ttbshape{12}{\magstep3}{OT1TT}
+\setfont\titlettsl\ttslshape{10}{\magstep4}{OT1TT}
+\setfont\titlesf\sfbshape{17}{\magstep1}{OT1}
+\let\titlebf=\titlerm
+\setfont\titlesc\scbshape{10}{\magstep4}{OT1}
+\font\titlei=cmmi12 scaled \magstep3
+\font\titlesy=cmsy10 scaled \magstep4
+\def\titleecsize{2074}
+
+% Chapter fonts (14.4pt).
+\def\chapnominalsize{14pt}
+\setfont\chaprm\rmbshape{12}{\magstep1}{OT1}
+\setfont\chapit\itbshape{10}{\magstep2}{OT1IT}
+\setfont\chapsl\slbshape{10}{\magstep2}{OT1}
+\setfont\chaptt\ttbshape{12}{\magstep1}{OT1TT}
+\setfont\chapttsl\ttslshape{10}{\magstep2}{OT1TT}
+\setfont\chapsf\sfbshape{12}{\magstep1}{OT1}
+\let\chapbf\chaprm
+\setfont\chapsc\scbshape{10}{\magstep2}{OT1}
+\font\chapi=cmmi12 scaled \magstep1
+\font\chapsy=cmsy10 scaled \magstep2
+\def\chapecsize{1440}
+
+% Section fonts (12pt).
+\def\secnominalsize{12pt}
+\setfont\secrm\rmbshape{12}{1000}{OT1}
+\setfont\secit\itbshape{10}{\magstep1}{OT1IT}
+\setfont\secsl\slbshape{10}{\magstep1}{OT1}
+\setfont\sectt\ttbshape{12}{1000}{OT1TT}
+\setfont\secttsl\ttslshape{10}{\magstep1}{OT1TT}
+\setfont\secsf\sfbshape{12}{1000}{OT1}
+\let\secbf\secrm
+\setfont\secsc\scbshape{10}{\magstep1}{OT1}
+\font\seci=cmmi12
+\font\secsy=cmsy10 scaled \magstep1
+\def\sececsize{1200}
+
+% Subsection fonts (10pt).
+\def\ssecnominalsize{10pt}
+\setfont\ssecrm\rmbshape{10}{1000}{OT1}
+\setfont\ssecit\itbshape{10}{1000}{OT1IT}
+\setfont\ssecsl\slbshape{10}{1000}{OT1}
+\setfont\ssectt\ttbshape{10}{1000}{OT1TT}
+\setfont\ssecttsl\ttslshape{10}{1000}{OT1TT}
+\setfont\ssecsf\sfbshape{10}{1000}{OT1}
+\let\ssecbf\ssecrm
+\setfont\ssecsc\scbshape{10}{1000}{OT1}
+\font\sseci=cmmi10
+\font\ssecsy=cmsy10
+\def\ssececsize{1000}
+
+% Reduced fonts for @acro in text (9pt).
+\def\reducednominalsize{9pt}
+\setfont\reducedrm\rmshape{9}{1000}{OT1}
+\setfont\reducedtt\ttshape{9}{1000}{OT1TT}
+\setfont\reducedbf\bfshape{10}{900}{OT1}
+\setfont\reducedit\itshape{9}{1000}{OT1IT}
+\setfont\reducedsl\slshape{9}{1000}{OT1}
+\setfont\reducedsf\sfshape{9}{1000}{OT1}
+\setfont\reducedsc\scshape{10}{900}{OT1}
+\setfont\reducedttsl\ttslshape{10}{900}{OT1TT}
+\font\reducedi=cmmi9
+\font\reducedsy=cmsy9
+\def\reducedecsize{0900}
+
+% reduce space between paragraphs
+\divide\parskip by 2
+
+% reset the current fonts
+\textfonts
+\rm
+} % end of 10pt text font size definitions
+
+
+% We provide the user-level command
+% @fonttextsize 10
+% (or 11) to redefine the text font size. pt is assumed.
+%
+\def\xword{10}
+\def\xiword{11}
+%
+\parseargdef\fonttextsize{%
+ \def\textsizearg{#1}%
+ \wlog{doing @fonttextsize \textsizearg}%
+ %
+ % Set \globaldefs so that documents can use this inside @tex, since
+ % makeinfo 4.8 does not support it, but we need it nonetheless.
+ %
+ \begingroup \globaldefs=1
+ \ifx\textsizearg\xword \definetextfontsizex
+ \else \ifx\textsizearg\xiword \definetextfontsizexi
+ \else
+ \errhelp=\EMsimple
+ \errmessage{@fonttextsize only supports `10' or `11', not `\textsizearg'}
+ \fi\fi
+ \endgroup
+}
+
+
+% In order for the font changes to affect most math symbols and letters,
+% we have to define the \textfont of the standard families. Since
+% texinfo doesn't allow for producing subscripts and superscripts except
+% in the main text, we don't bother to reset \scriptfont and
+% \scriptscriptfont (which would also require loading a lot more fonts).
+%
+\def\resetmathfonts{%
+ \textfont0=\tenrm \textfont1=\teni \textfont2=\tensy
+ \textfont\itfam=\tenit \textfont\slfam=\tensl \textfont\bffam=\tenbf
+ \textfont\ttfam=\tentt \textfont\sffam=\tensf
+}
+
+% The font-changing commands redefine the meanings of \tenSTYLE, instead
+% of just \STYLE. We do this because \STYLE needs to also set the
+% current \fam for math mode. Our \STYLE (e.g., \rm) commands hardwire
+% \tenSTYLE to set the current font.
+%
+% Each font-changing command also sets the names \lsize (one size lower)
+% and \lllsize (three sizes lower). These relative commands are used in
+% the LaTeX logo and acronyms.
+%
+% This all needs generalizing, badly.
+%
+\def\textfonts{%
+ \let\tenrm=\textrm \let\tenit=\textit \let\tensl=\textsl
+ \let\tenbf=\textbf \let\tentt=\texttt \let\smallcaps=\textsc
+ \let\tensf=\textsf \let\teni=\texti \let\tensy=\textsy
+ \let\tenttsl=\textttsl
+ \def\curfontsize{text}%
+ \def\lsize{reduced}\def\lllsize{smaller}%
+ \resetmathfonts \setleading{\textleading}}
+\def\titlefonts{%
+ \let\tenrm=\titlerm \let\tenit=\titleit \let\tensl=\titlesl
+ \let\tenbf=\titlebf \let\tentt=\titlett \let\smallcaps=\titlesc
+ \let\tensf=\titlesf \let\teni=\titlei \let\tensy=\titlesy
+ \let\tenttsl=\titlettsl
+ \def\curfontsize{title}%
+ \def\lsize{chap}\def\lllsize{subsec}%
+ \resetmathfonts \setleading{25pt}}
+\def\titlefont#1{{\titlefonts\rmisbold #1}}
+\def\chapfonts{%
+ \let\tenrm=\chaprm \let\tenit=\chapit \let\tensl=\chapsl
+ \let\tenbf=\chapbf \let\tentt=\chaptt \let\smallcaps=\chapsc
+ \let\tensf=\chapsf \let\teni=\chapi \let\tensy=\chapsy
+ \let\tenttsl=\chapttsl
+ \def\curfontsize{chap}%
+ \def\lsize{sec}\def\lllsize{text}%
+ \resetmathfonts \setleading{19pt}}
+\def\secfonts{%
+ \let\tenrm=\secrm \let\tenit=\secit \let\tensl=\secsl
+ \let\tenbf=\secbf \let\tentt=\sectt \let\smallcaps=\secsc
+ \let\tensf=\secsf \let\teni=\seci \let\tensy=\secsy
+ \let\tenttsl=\secttsl
+ \def\curfontsize{sec}%
+ \def\lsize{subsec}\def\lllsize{reduced}%
+ \resetmathfonts \setleading{16pt}}
+\def\subsecfonts{%
+ \let\tenrm=\ssecrm \let\tenit=\ssecit \let\tensl=\ssecsl
+ \let\tenbf=\ssecbf \let\tentt=\ssectt \let\smallcaps=\ssecsc
+ \let\tensf=\ssecsf \let\teni=\sseci \let\tensy=\ssecsy
+ \let\tenttsl=\ssecttsl
+ \def\curfontsize{ssec}%
+ \def\lsize{text}\def\lllsize{small}%
+ \resetmathfonts \setleading{15pt}}
+\let\subsubsecfonts = \subsecfonts
+\def\reducedfonts{%
+ \let\tenrm=\reducedrm \let\tenit=\reducedit \let\tensl=\reducedsl
+ \let\tenbf=\reducedbf \let\tentt=\reducedtt \let\reducedcaps=\reducedsc
+ \let\tensf=\reducedsf \let\teni=\reducedi \let\tensy=\reducedsy
+ \let\tenttsl=\reducedttsl
+ \def\curfontsize{reduced}%
+ \def\lsize{small}\def\lllsize{smaller}%
+ \resetmathfonts \setleading{10.5pt}}
+\def\smallfonts{%
+ \let\tenrm=\smallrm \let\tenit=\smallit \let\tensl=\smallsl
+ \let\tenbf=\smallbf \let\tentt=\smalltt \let\smallcaps=\smallsc
+ \let\tensf=\smallsf \let\teni=\smalli \let\tensy=\smallsy
+ \let\tenttsl=\smallttsl
+ \def\curfontsize{small}%
+ \def\lsize{smaller}\def\lllsize{smaller}%
+ \resetmathfonts \setleading{10.5pt}}
+\def\smallerfonts{%
+ \let\tenrm=\smallerrm \let\tenit=\smallerit \let\tensl=\smallersl
+ \let\tenbf=\smallerbf \let\tentt=\smallertt \let\smallcaps=\smallersc
+ \let\tensf=\smallersf \let\teni=\smalleri \let\tensy=\smallersy
+ \let\tenttsl=\smallerttsl
+ \def\curfontsize{smaller}%
+ \def\lsize{smaller}\def\lllsize{smaller}%
+ \resetmathfonts \setleading{9.5pt}}
+
+% Fonts for short table of contents.
+\setfont\shortcontrm\rmshape{12}{1000}{OT1}
+\setfont\shortcontbf\bfshape{10}{\magstep1}{OT1} % no cmb12
+\setfont\shortcontsl\slshape{12}{1000}{OT1}
+\setfont\shortconttt\ttshape{12}{1000}{OT1TT}
+
+% Define these just so they can be easily changed for other fonts.
+\def\angleleft{$\langle$}
+\def\angleright{$\rangle$}
+
+% Set the fonts to use with the @small... environments.
+\let\smallexamplefonts = \smallfonts
+
+% About \smallexamplefonts. If we use \smallfonts (9pt), @smallexample
+% can fit this many characters:
+% 8.5x11=86 smallbook=72 a4=90 a5=69
+% If we use \scriptfonts (8pt), then we can fit this many characters:
+% 8.5x11=90+ smallbook=80 a4=90+ a5=77
+% For me, subjectively, the few extra characters that fit aren't worth
+% the additional smallness of 8pt. So I'm making the default 9pt.
+%
+% By the way, for comparison, here's what fits with @example (10pt):
+% 8.5x11=71 smallbook=60 a4=75 a5=58
+% --karl, 24jan03.
+
+% Set up the default fonts, so we can use them for creating boxes.
+%
+\definetextfontsizexi
+
+
+\message{markup,}
+
+% Check if we are currently using a typewriter font. Since all the
+% Computer Modern typewriter fonts have zero interword stretch (and
+% shrink), and it is reasonable to expect all typewriter fonts to have
+% this property, we can check that font parameter.
+%
+\def\ifmonospace{\ifdim\fontdimen3\font=0pt }
+
+% Markup style infrastructure. \defmarkupstylesetup\INITMACRO will
+% define and register \INITMACRO to be called on markup style changes.
+% \INITMACRO can check \currentmarkupstyle for the innermost
+% style and the set of \ifmarkupSTYLE switches for all styles
+% currently in effect.
+\newif\ifmarkupvar
+\newif\ifmarkupsamp
+\newif\ifmarkupkey
+%\newif\ifmarkupfile % @file == @samp.
+%\newif\ifmarkupoption % @option == @samp.
+\newif\ifmarkupcode
+\newif\ifmarkupkbd
+%\newif\ifmarkupenv % @env == @code.
+%\newif\ifmarkupcommand % @command == @code.
+\newif\ifmarkuptex % @tex (and part of @math, for now).
+\newif\ifmarkupexample
+\newif\ifmarkupverb
+\newif\ifmarkupverbatim
+
+\let\currentmarkupstyle\empty
+
+\def\setupmarkupstyle#1{%
+ \csname markup#1true\endcsname
+ \def\currentmarkupstyle{#1}%
+ \markupstylesetup
+}
+
+\let\markupstylesetup\empty
+
+\def\defmarkupstylesetup#1{%
+ \expandafter\def\expandafter\markupstylesetup
+ \expandafter{\markupstylesetup #1}%
+ \def#1%
+}
+
+% Markup style setup for left and right quotes.
+\defmarkupstylesetup\markupsetuplq{%
+ \expandafter\let\expandafter \temp \csname markupsetuplq\currentmarkupstyle\endcsname
+ \ifx\temp\relax \markupsetuplqdefault \else \temp \fi
+}
+
+\defmarkupstylesetup\markupsetuprq{%
+ \expandafter\let\expandafter \temp \csname markupsetuprq\currentmarkupstyle\endcsname
+ \ifx\temp\relax \markupsetuprqdefault \else \temp \fi
+}
+
+{
+\catcode`\'=\active
+\catcode`\`=\active
+
+\gdef\markupsetuplqdefault{\let`\lq}
+\gdef\markupsetuprqdefault{\let'\rq}
+
+\gdef\markupsetcodequoteleft{\let`\codequoteleft}
+\gdef\markupsetcodequoteright{\let'\codequoteright}
+
+\gdef\markupsetnoligaturesquoteleft{\let`\noligaturesquoteleft}
+}
+
+\let\markupsetuplqcode \markupsetcodequoteleft
+\let\markupsetuprqcode \markupsetcodequoteright
+\let\markupsetuplqexample \markupsetcodequoteleft
+\let\markupsetuprqexample \markupsetcodequoteright
+\let\markupsetuplqverb \markupsetcodequoteleft
+\let\markupsetuprqverb \markupsetcodequoteright
+\let\markupsetuplqverbatim \markupsetcodequoteleft
+\let\markupsetuprqverbatim \markupsetcodequoteright
+
+\let\markupsetuplqsamp \markupsetnoligaturesquoteleft
+\let\markupsetuplqkbd \markupsetnoligaturesquoteleft
+
+% Allow an option to not replace quotes with a regular directed right
+% quote/apostrophe (char 0x27), but instead use the undirected quote
+% from cmtt (char 0x0d). The undirected quote is ugly, so don't make it
+% the default, but it works for pasting with more pdf viewers (at least
+% evince), the lilypond developers report. xpdf does work with the
+% regular 0x27.
+%
+\def\codequoteright{%
+ \expandafter\ifx\csname SETtxicodequoteundirected\endcsname\relax
+ \expandafter\ifx\csname SETcodequoteundirected\endcsname\relax
+ '%
+ \else \char'15 \fi
+ \else \char'15 \fi
+}
+%
+% and a similar option for the left quote char vs. a grave accent.
+% Modern fonts display ASCII 0x60 as a grave accent, so some people like
+% the code environments to do likewise.
+%
+\def\codequoteleft{%
+ \expandafter\ifx\csname SETtxicodequotebacktick\endcsname\relax
+ \expandafter\ifx\csname SETcodequotebacktick\endcsname\relax
+ % [Knuth] pp. 380,381,391
+ % \relax disables Spanish ligatures ?` and !` of \tt font.
+ \relax`%
+ \else \char'22 \fi
+ \else \char'22 \fi
+}
+
+% [Knuth] pp. 380,381,391, disable Spanish ligatures ?` and !` of \tt font.
+\def\noligaturesquoteleft{\relax\lq}
+
+% Count depth in font-changes, for error checks
+\newcount\fontdepth \fontdepth=0
+
+%% Add scribe-like font environments, plus @l for inline lisp (usually sans
+%% serif) and @ii for TeX italic
+
+% \smartitalic{ARG} outputs arg in italics, followed by an italic correction
+% unless the following character is such as not to need one.
+\def\smartitalicx{\ifx\next,\else\ifx\next-\else\ifx\next.\else
+ \ptexslash\fi\fi\fi}
+\def\smartslanted#1{{\ifusingtt\ttsl\sl #1}\futurelet\next\smartitalicx}
+\def\smartitalic#1{{\ifusingtt\ttsl\it #1}\futurelet\next\smartitalicx}
+
+% like \smartslanted except unconditionally uses \ttsl.
+% @var is set to this for defun arguments.
+\def\ttslanted#1{{\ttsl #1}\futurelet\next\smartitalicx}
+
+% @cite is like \smartslanted except unconditionally use \sl. We never want
+% ttsl for book titles, do we?
+\def\cite#1{{\sl #1}\futurelet\next\smartitalicx}
+
+\let\i=\smartitalic
+\let\slanted=\smartslanted
+\def\var#1{{\setupmarkupstyle{var}\smartslanted{#1}}}
+\let\dfn=\smartslanted
+\let\emph=\smartitalic
+
+% Explicit font changes: @r, @sc, undocumented @ii.
+\def\r#1{{\rm #1}} % roman font
+\def\sc#1{{\smallcaps#1}} % smallcaps font
+\def\ii#1{{\it #1}} % italic font
+
+% @b, explicit bold. Also @strong.
+\def\b#1{{\bf #1}}
+\let\strong=\b
+
+% @sansserif, explicit sans.
+\def\sansserif#1{{\sf #1}}
+
+% We can't just use \exhyphenpenalty, because that only has effect at
+% the end of a paragraph. Restore normal hyphenation at the end of the
+% group within which \nohyphenation is presumably called.
+%
+\def\nohyphenation{\hyphenchar\font = -1 \aftergroup\restorehyphenation}
+\def\restorehyphenation{\hyphenchar\font = `- }
+
+% Set sfcode to normal for the chars that usually have another value.
+% Can't use plain's \frenchspacing because it uses the `\x notation, and
+% sometimes \x has an active definition that messes things up.
+%
+\catcode`@=11
+ \def\plainfrenchspacing{%
+ \sfcode\dotChar =\@m \sfcode\questChar=\@m \sfcode\exclamChar=\@m
+ \sfcode\colonChar=\@m \sfcode\semiChar =\@m \sfcode\commaChar =\@m
+ \def\endofsentencespacefactor{1000}% for @. and friends
+ }
+ \def\plainnonfrenchspacing{%
+ \sfcode`\.3000\sfcode`\?3000\sfcode`\!3000
+ \sfcode`\:2000\sfcode`\;1500\sfcode`\,1250
+ \def\endofsentencespacefactor{3000}% for @. and friends
+ }
+\catcode`@=\other
+\def\endofsentencespacefactor{3000}% default
+
+% @t, explicit typewriter.
+\def\t#1{%
+ {\tt \rawbackslash \plainfrenchspacing #1}%
+ \null
+}
+
+% @samp.
+\def\samp#1{{\setupmarkupstyle{samp}\lq\tclose{#1}\rq\null}}
+
+% definition of @key that produces a lozenge. Doesn't adjust to text size.
+%\setfont\keyrm\rmshape{8}{1000}{OT1}
+%\font\keysy=cmsy9
+%\def\key#1{{\keyrm\textfont2=\keysy \leavevmode\hbox{%
+% \raise0.4pt\hbox{\angleleft}\kern-.08em\vtop{%
+% \vbox{\hrule\kern-0.4pt
+% \hbox{\raise0.4pt\hbox{\vphantom{\angleleft}}#1}}%
+% \kern-0.4pt\hrule}%
+% \kern-.06em\raise0.4pt\hbox{\angleright}}}}
+
+% definition of @key with no lozenge. If the current font is already
+% monospace, don't change it; that way, we respect @kbdinputstyle. But
+% if it isn't monospace, then use \tt.
+%
+\def\key#1{{\setupmarkupstyle{key}%
+ \nohyphenation
+ \ifmonospace\else\tt\fi
+ #1}\null}
+
+% ctrl is no longer a Texinfo command.
+\def\ctrl #1{{\tt \rawbackslash \hat}#1}
+
+% @file, @option are the same as @samp.
+\let\file=\samp
+\let\option=\samp
+
+% @code is a modification of @t,
+% which makes spaces the same size as normal in the surrounding text.
+\def\tclose#1{%
+ {%
+ % Change normal interword space to be same as for the current font.
+ \spaceskip = \fontdimen2\font
+ %
+ % Switch to typewriter.
+ \tt
+ %
+ % But `\ ' produces the large typewriter interword space.
+ \def\ {{\spaceskip = 0pt{} }}%
+ %
+ % Turn off hyphenation.
+ \nohyphenation
+ %
+ \rawbackslash
+ \plainfrenchspacing
+ #1%
+ }%
+ \null
+}
+
+% We *must* turn on hyphenation at `-' and `_' in @code.
+% Otherwise, it is too hard to avoid overfull hboxes
+% in the Emacs manual, the Library manual, etc.
+
+% Unfortunately, TeX uses one parameter (\hyphenchar) to control
+% both hyphenation at - and hyphenation within words.
+% We must therefore turn them both off (\tclose does that)
+% and arrange explicitly to hyphenate at a dash.
+% -- rms.
+{
+ \catcode`\-=\active \catcode`\_=\active
+ \catcode`\'=\active \catcode`\`=\active
+ \global\let'=\rq \global\let`=\lq % default definitions
+ %
+ \global\def\code{\begingroup
+ \setupmarkupstyle{code}%
+ % The following should really be moved into \setupmarkupstyle handlers.
+ \catcode\dashChar=\active \catcode\underChar=\active
+ \ifallowcodebreaks
+ \let-\codedash
+ \let_\codeunder
+ \else
+ \let-\realdash
+ \let_\realunder
+ \fi
+ \codex
+ }
+}
+
+\def\realdash{-}
+\def\codedash{-\discretionary{}{}{}}
+\def\codeunder{%
+ % this is all so @math{@code{var_name}+1} can work. In math mode, _
+ % is "active" (mathcode"8000) and \normalunderscore (or \char95, etc.)
+ % will therefore expand the active definition of _, which is us
+ % (inside @code that is), therefore an endless loop.
+ \ifusingtt{\ifmmode
+ \mathchar"075F % class 0=ordinary, family 7=ttfam, pos 0x5F=_.
+ \else\normalunderscore \fi
+ \discretionary{}{}{}}%
+ {\_}%
+}
+\def\codex #1{\tclose{#1}\endgroup}
+
+% An additional complication: the above will allow breaks after, e.g.,
+% each of the four underscores in __typeof__. This is undesirable in
+% some manuals, especially if they don't have long identifiers in
+% general. @allowcodebreaks provides a way to control this.
+%
+\newif\ifallowcodebreaks \allowcodebreakstrue
+
+\def\keywordtrue{true}
+\def\keywordfalse{false}
+
+\parseargdef\allowcodebreaks{%
+ \def\txiarg{#1}%
+ \ifx\txiarg\keywordtrue
+ \allowcodebreakstrue
+ \else\ifx\txiarg\keywordfalse
+ \allowcodebreaksfalse
+ \else
+ \errhelp = \EMsimple
+ \errmessage{Unknown @allowcodebreaks option `\txiarg'}%
+ \fi\fi
+}
+
+% @kbd is like @code, except that if the argument is just one @key command,
+% then @kbd has no effect.
+\def\kbd#1{{\setupmarkupstyle{kbd}\def\look{#1}\expandafter\kbdfoo\look??\par}}
+
+% @kbdinputstyle -- arg is `distinct' (@kbd uses slanted tty font always),
+% `example' (@kbd uses ttsl only inside of @example and friends),
+% or `code' (@kbd uses normal tty font always).
+\parseargdef\kbdinputstyle{%
+ \def\txiarg{#1}%
+ \ifx\txiarg\worddistinct
+ \gdef\kbdexamplefont{\ttsl}\gdef\kbdfont{\ttsl}%
+ \else\ifx\txiarg\wordexample
+ \gdef\kbdexamplefont{\ttsl}\gdef\kbdfont{\tt}%
+ \else\ifx\txiarg\wordcode
+ \gdef\kbdexamplefont{\tt}\gdef\kbdfont{\tt}%
+ \else
+ \errhelp = \EMsimple
+ \errmessage{Unknown @kbdinputstyle option `\txiarg'}%
+ \fi\fi\fi
+}
+\def\worddistinct{distinct}
+\def\wordexample{example}
+\def\wordcode{code}
+
+% Default is `distinct'.
+\kbdinputstyle distinct
+
+\def\xkey{\key}
+\def\kbdfoo#1#2#3\par{\def\one{#1}\def\three{#3}\def\threex{??}%
+\ifx\one\xkey\ifx\threex\three \key{#2}%
+\else{\tclose{\kbdfont\setupmarkupstyle{kbd}\look}}\fi
+\else{\tclose{\kbdfont\setupmarkupstyle{kbd}\look}}\fi}
+
+% For @indicateurl, @env, @command quotes seem unnecessary, so use \code.
+\let\indicateurl=\code
+\let\env=\code
+\let\command=\code
+
+% @clicksequence{File @click{} Open ...}
+\def\clicksequence#1{\begingroup #1\endgroup}
+
+% @clickstyle @arrow (by default)
+\parseargdef\clickstyle{\def\click{#1}}
+\def\click{\arrow}
+
+% @uref (abbreviation for `urlref') takes an optional (comma-separated)
+% second argument specifying the text to display and an optional third
+% arg as text to display instead of (rather than in addition to) the url
+% itself. First (mandatory) arg is the url. Perhaps eventually put in
+% a hypertex \special here.
+%
+\def\uref#1{\douref #1,,,\finish}
+\def\douref#1,#2,#3,#4\finish{\begingroup
+ \unsepspaces
+ \pdfurl{#1}%
+ \setbox0 = \hbox{\ignorespaces #3}%
+ \ifdim\wd0 > 0pt
+ \unhbox0 % third arg given, show only that
+ \else
+ \setbox0 = \hbox{\ignorespaces #2}%
+ \ifdim\wd0 > 0pt
+ \ifpdf
+ \unhbox0 % PDF: 2nd arg given, show only it
+ \else
+ \unhbox0\ (\code{#1})% DVI: 2nd arg given, show both it and url
+ \fi
+ \else
+ \code{#1}% only url given, so show it
+ \fi
+ \fi
+ \endlink
+\endgroup}
+
+% @url synonym for @uref, since that's how everyone uses it.
+%
+\let\url=\uref
+
+% rms does not like angle brackets --karl, 17may97.
+% So now @email is just like @uref, unless we are pdf.
+%
+%\def\email#1{\angleleft{\tt #1}\angleright}
+\ifpdf
+ \def\email#1{\doemail#1,,\finish}
+ \def\doemail#1,#2,#3\finish{\begingroup
+ \unsepspaces
+ \pdfurl{mailto:#1}%
+ \setbox0 = \hbox{\ignorespaces #2}%
+ \ifdim\wd0>0pt\unhbox0\else\code{#1}\fi
+ \endlink
+ \endgroup}
+\else
+ \let\email=\uref
+\fi
+
+% Typeset a dimension, e.g., `in' or `pt'. The only reason for the
+% argument is to make the input look right: @dmn{pt} instead of @dmn{}pt.
+%
+\def\dmn#1{\thinspace #1}
+
+% @l was never documented to mean ``switch to the Lisp font'',
+% and it is not used as such in any manual I can find. We need it for
+% Polish suppressed-l. --karl, 22sep96.
+%\def\l#1{{\li #1}\null}
+
+% @acronym for "FBI", "NATO", and the like.
+% We print this one point size smaller, since it's intended for
+% all-uppercase.
+%
+\def\acronym#1{\doacronym #1,,\finish}
+\def\doacronym#1,#2,#3\finish{%
+ {\selectfonts\lsize #1}%
+ \def\temp{#2}%
+ \ifx\temp\empty \else
+ \space ({\unsepspaces \ignorespaces \temp \unskip})%
+ \fi
+}
+
+% @abbr for "Comput. J." and the like.
+% No font change, but don't do end-of-sentence spacing.
+%
+\def\abbr#1{\doabbr #1,,\finish}
+\def\doabbr#1,#2,#3\finish{%
+ {\plainfrenchspacing #1}%
+ \def\temp{#2}%
+ \ifx\temp\empty \else
+ \space ({\unsepspaces \ignorespaces \temp \unskip})%
+ \fi
+}
+
+
+\message{glyphs,}
+
+% @point{}, @result{}, @expansion{}, @print{}, @equiv{}.
+%
+% Since these characters are used in examples, they should be an even number of
+% \tt widths. Each \tt character is 1en, so two makes it 1em.
+%
+\def\point{$\star$}
+\def\arrow{\leavevmode\raise.05ex\hbox to 1em{\hfil$\rightarrow$\hfil}}
+\def\result{\leavevmode\raise.05ex\hbox to 1em{\hfil$\Rightarrow$\hfil}}
+\def\expansion{\leavevmode\hbox to 1em{\hfil$\mapsto$\hfil}}
+\def\print{\leavevmode\lower.1ex\hbox to 1em{\hfil$\dashv$\hfil}}
+\def\equiv{\leavevmode\hbox to 1em{\hfil$\ptexequiv$\hfil}}
+
+% The @error{} command.
+% Adapted from the TeXbook's \boxit.
+%
+\newbox\errorbox
+%
+{\tentt \global\dimen0 = 3em}% Width of the box.
+\dimen2 = .55pt % Thickness of rules
+% The text. (`r' is open on the right, `e' somewhat less so on the left.)
+\setbox0 = \hbox{\kern-.75pt \reducedsf error\kern-1.5pt}
+%
+\setbox\errorbox=\hbox to \dimen0{\hfil
+ \hsize = \dimen0 \advance\hsize by -5.8pt % Space to left+right.
+ \advance\hsize by -2\dimen2 % Rules.
+ \vbox{%
+ \hrule height\dimen2
+ \hbox{\vrule width\dimen2 \kern3pt % Space to left of text.
+ \vtop{\kern2.4pt \box0 \kern2.4pt}% Space above/below.
+ \kern3pt\vrule width\dimen2}% Space to right.
+ \hrule height\dimen2}
+ \hfil}
+%
+\def\error{\leavevmode\lower.7ex\copy\errorbox}
+
+% @pounds{} is a sterling sign, which Knuth put in the CM italic font.
+%
+\def\pounds{{\it\$}}
+
+% @euro{} comes from a separate font, depending on the current style.
+% We use the free feym* fonts from the eurosym package by Henrik
+% Theiling, which support regular, slanted, bold and bold slanted (and
+% "outlined" (blackboard board, sort of) versions, which we don't need).
+% It is available from http://www.ctan.org/tex-archive/fonts/eurosym.
+%
+% Although only regular is the truly official Euro symbol, we ignore
+% that. The Euro is designed to be slightly taller than the regular
+% font height.
+%
+% feymr - regular
+% feymo - slanted
+% feybr - bold
+% feybo - bold slanted
+%
+% There is no good (free) typewriter version, to my knowledge.
+% A feymr10 euro is ~7.3pt wide, while a normal cmtt10 char is ~5.25pt wide.
+% Hmm.
+%
+% Also doesn't work in math. Do we need to do math with euro symbols?
+% Hope not.
+%
+%
+\def\euro{{\eurofont e}}
+\def\eurofont{%
+ % We set the font at each command, rather than predefining it in
+ % \textfonts and the other font-switching commands, so that
+ % installations which never need the symbol don't have to have the
+ % font installed.
+ %
+ % There is only one designed size (nominal 10pt), so we always scale
+ % that to the current nominal size.
+ %
+ % By the way, simply using "at 1em" works for cmr10 and the like, but
+ % does not work for cmbx10 and other extended/shrunken fonts.
+ %
+ \def\eurosize{\csname\curfontsize nominalsize\endcsname}%
+ %
+ \ifx\curfontstyle\bfstylename
+ % bold:
+ \font\thiseurofont = \ifusingit{feybo10}{feybr10} at \eurosize
+ \else
+ % regular:
+ \font\thiseurofont = \ifusingit{feymo10}{feymr10} at \eurosize
+ \fi
+ \thiseurofont
+}
+
+% Glyphs from the EC fonts. We don't use \let for the aliases, because
+% sometimes we redefine the original macro, and the alias should reflect
+% the redefinition.
+%
+% Use LaTeX names for the Icelandic letters.
+\def\DH{{\ecfont \char"D0}} % Eth
+\def\dh{{\ecfont \char"F0}} % eth
+\def\TH{{\ecfont \char"DE}} % Thorn
+\def\th{{\ecfont \char"FE}} % thorn
+%
+\def\guillemetleft{{\ecfont \char"13}}
+\def\guillemotleft{\guillemetleft}
+\def\guillemetright{{\ecfont \char"14}}
+\def\guillemotright{\guillemetright}
+\def\guilsinglleft{{\ecfont \char"0E}}
+\def\guilsinglright{{\ecfont \char"0F}}
+\def\quotedblbase{{\ecfont \char"12}}
+\def\quotesinglbase{{\ecfont \char"0D}}
+%
+% This positioning is not perfect (see the ogonek LaTeX package), but
+% we have the precomposed glyphs for the most common cases. We put the
+% tests to use those glyphs in the single \ogonek macro so we have fewer
+% dummy definitions to worry about for index entries, etc.
+%
+% ogonek is also used with other letters in Lithuanian (IOU), but using
+% the precomposed glyphs for those is not so easy since they aren't in
+% the same EC font.
+\def\ogonek#1{{%
+ \def\temp{#1}%
+ \ifx\temp\macrocharA\Aogonek
+ \else\ifx\temp\macrochara\aogonek
+ \else\ifx\temp\macrocharE\Eogonek
+ \else\ifx\temp\macrochare\eogonek
+ \else
+ \ecfont \setbox0=\hbox{#1}%
+ \ifdim\ht0=1ex\accent"0C #1%
+ \else\ooalign{\unhbox0\crcr\hidewidth\char"0C \hidewidth}%
+ \fi
+ \fi\fi\fi\fi
+ }%
+}
+\def\Aogonek{{\ecfont \char"81}}\def\macrocharA{A}
+\def\aogonek{{\ecfont \char"A1}}\def\macrochara{a}
+\def\Eogonek{{\ecfont \char"86}}\def\macrocharE{E}
+\def\eogonek{{\ecfont \char"A6}}\def\macrochare{e}
+%
+% Use the ec* fonts (cm-super in outline format) for non-CM glyphs.
+\def\ecfont{%
+ % We can't distinguish serif/sans and italic/slanted, but this
+ % is used for crude hacks anyway (like adding French and German
+ % quotes to documents typeset with CM, where we lose kerning), so
+ % hopefully nobody will notice/care.
+ \edef\ecsize{\csname\curfontsize ecsize\endcsname}%
+ \edef\nominalsize{\csname\curfontsize nominalsize\endcsname}%
+ \ifx\curfontstyle\bfstylename
+ % bold:
+ \font\thisecfont = ecb\ifusingit{i}{x}\ecsize \space at \nominalsize
+ \else
+ % regular:
+ \font\thisecfont = ec\ifusingit{ti}{rm}\ecsize \space at \nominalsize
+ \fi
+ \thisecfont
+}
+
+% @registeredsymbol - R in a circle. The font for the R should really
+% be smaller yet, but lllsize is the best we can do for now.
+% Adapted from the plain.tex definition of \copyright.
+%
+\def\registeredsymbol{%
+ $^{{\ooalign{\hfil\raise.07ex\hbox{\selectfonts\lllsize R}%
+ \hfil\crcr\Orb}}%
+ }$%
+}
+
+% @textdegree - the normal degrees sign.
+%
+\def\textdegree{$^\circ$}
+
+% Laurent Siebenmann reports \Orb undefined with:
+% Textures 1.7.7 (preloaded format=plain 93.10.14) (68K) 16 APR 2004 02:38
+% so we'll define it if necessary.
+%
+\ifx\Orb\undefined
+\def\Orb{\mathhexbox20D}
+\fi
+
+% Quotes.
+\chardef\quotedblleft="5C
+\chardef\quotedblright=`\"
+\chardef\quoteleft=`\`
+\chardef\quoteright=`\'
+
+
+\message{page headings,}
+
+\newskip\titlepagetopglue \titlepagetopglue = 1.5in
+\newskip\titlepagebottomglue \titlepagebottomglue = 2pc
+
+% First the title page. Must do @settitle before @titlepage.
+\newif\ifseenauthor
+\newif\iffinishedtitlepage
+
+% Do an implicit @contents or @shortcontents after @end titlepage if the
+% user says @setcontentsaftertitlepage or @setshortcontentsaftertitlepage.
+%
+\newif\ifsetcontentsaftertitlepage
+ \let\setcontentsaftertitlepage = \setcontentsaftertitlepagetrue
+\newif\ifsetshortcontentsaftertitlepage
+ \let\setshortcontentsaftertitlepage = \setshortcontentsaftertitlepagetrue
+
+\parseargdef\shorttitlepage{\begingroup\hbox{}\vskip 1.5in \chaprm \centerline{#1}%
+ \endgroup\page\hbox{}\page}
+
+\envdef\titlepage{%
+ % Open one extra group, as we want to close it in the middle of \Etitlepage.
+ \begingroup
+ \parindent=0pt \textfonts
+ % Leave some space at the very top of the page.
+ \vglue\titlepagetopglue
+ % No rule at page bottom unless we print one at the top with @title.
+ \finishedtitlepagetrue
+ %
+ % Most title ``pages'' are actually two pages long, with space
+ % at the top of the second. We don't want the ragged left on the second.
+ \let\oldpage = \page
+ \def\page{%
+ \iffinishedtitlepage\else
+ \finishtitlepage
+ \fi
+ \let\page = \oldpage
+ \page
+ \null
+ }%
+}
+
+\def\Etitlepage{%
+ \iffinishedtitlepage\else
+ \finishtitlepage
+ \fi
+ % It is important to do the page break before ending the group,
+ % because the headline and footline are only empty inside the group.
+ % If we use the new definition of \page, we always get a blank page
+ % after the title page, which we certainly don't want.
+ \oldpage
+ \endgroup
+ %
+ % Need this before the \...aftertitlepage checks so that if they are
+ % in effect the toc pages will come out with page numbers.
+ \HEADINGSon
+ %
+ % If they want short, they certainly want long too.
+ \ifsetshortcontentsaftertitlepage
+ \shortcontents
+ \contents
+ \global\let\shortcontents = \relax
+ \global\let\contents = \relax
+ \fi
+ %
+ \ifsetcontentsaftertitlepage
+ \contents
+ \global\let\contents = \relax
+ \global\let\shortcontents = \relax
+ \fi
+}
+
+\def\finishtitlepage{%
+ \vskip4pt \hrule height 2pt width \hsize
+ \vskip\titlepagebottomglue
+ \finishedtitlepagetrue
+}
+
+%%% Macros to be used within @titlepage:
+
+\let\subtitlerm=\tenrm
+\def\subtitlefont{\subtitlerm \normalbaselineskip = 13pt \normalbaselines}
+
+\parseargdef\title{%
+ \checkenv\titlepage
+ \leftline{\titlefonts\rmisbold #1}
+ % print a rule at the page bottom also.
+ \finishedtitlepagefalse
+ \vskip4pt \hrule height 4pt width \hsize \vskip4pt
+}
+
+\parseargdef\subtitle{%
+ \checkenv\titlepage
+ {\subtitlefont \rightline{#1}}%
+}
+
+% @author should come last, but may come many times.
+% It can also be used inside @quotation.
+%
+\parseargdef\author{%
+ \def\temp{\quotation}%
+ \ifx\thisenv\temp
+ \def\quotationauthor{#1}% printed in \Equotation.
+ \else
+ \checkenv\titlepage
+ \ifseenauthor\else \vskip 0pt plus 1filll \seenauthortrue \fi
+ {\secfonts\rmisbold \leftline{#1}}%
+ \fi
+}
+
+
+%%% Set up page headings and footings.
+
+\let\thispage=\folio
+
+\newtoks\evenheadline % headline on even pages
+\newtoks\oddheadline % headline on odd pages
+\newtoks\evenfootline % footline on even pages
+\newtoks\oddfootline % footline on odd pages
+
+% Now make TeX use those variables
+\headline={{\textfonts\rm \ifodd\pageno \the\oddheadline
+ \else \the\evenheadline \fi}}
+\footline={{\textfonts\rm \ifodd\pageno \the\oddfootline
+ \else \the\evenfootline \fi}\HEADINGShook}
+\let\HEADINGShook=\relax
+
+% Commands to set those variables.
+% For example, this is what @headings on does
+% @evenheading @thistitle|@thispage|@thischapter
+% @oddheading @thischapter|@thispage|@thistitle
+% @evenfooting @thisfile||
+% @oddfooting ||@thisfile
+
+
+\def\evenheading{\parsearg\evenheadingxxx}
+\def\evenheadingxxx #1{\evenheadingyyy #1\|\|\|\|\finish}
+\def\evenheadingyyy #1\|#2\|#3\|#4\finish{%
+\global\evenheadline={\rlap{\centerline{#2}}\line{#1\hfil#3}}}
+
+\def\oddheading{\parsearg\oddheadingxxx}
+\def\oddheadingxxx #1{\oddheadingyyy #1\|\|\|\|\finish}
+\def\oddheadingyyy #1\|#2\|#3\|#4\finish{%
+\global\oddheadline={\rlap{\centerline{#2}}\line{#1\hfil#3}}}
+
+\parseargdef\everyheading{\oddheadingxxx{#1}\evenheadingxxx{#1}}%
+
+\def\evenfooting{\parsearg\evenfootingxxx}
+\def\evenfootingxxx #1{\evenfootingyyy #1\|\|\|\|\finish}
+\def\evenfootingyyy #1\|#2\|#3\|#4\finish{%
+\global\evenfootline={\rlap{\centerline{#2}}\line{#1\hfil#3}}}
+
+\def\oddfooting{\parsearg\oddfootingxxx}
+\def\oddfootingxxx #1{\oddfootingyyy #1\|\|\|\|\finish}
+\def\oddfootingyyy #1\|#2\|#3\|#4\finish{%
+ \global\oddfootline = {\rlap{\centerline{#2}}\line{#1\hfil#3}}%
+ %
+ % Leave some space for the footline. Hopefully ok to assume
+ % @evenfooting will not be used by itself.
+ \global\advance\pageheight by -12pt
+ \global\advance\vsize by -12pt
+}
+
+\parseargdef\everyfooting{\oddfootingxxx{#1}\evenfootingxxx{#1}}
+
+% @evenheadingmarks top \thischapter <- chapter at the top of a page
+% @evenheadingmarks bottom \thischapter <- chapter at the bottom of a page
+%
+% The same set of arguments for:
+%
+% @oddheadingmarks
+% @evenfootingmarks
+% @oddfootingmarks
+% @everyheadingmarks
+% @everyfootingmarks
+
+\def\evenheadingmarks{\headingmarks{even}{heading}}
+\def\oddheadingmarks{\headingmarks{odd}{heading}}
+\def\evenfootingmarks{\headingmarks{even}{footing}}
+\def\oddfootingmarks{\headingmarks{odd}{footing}}
+\def\everyheadingmarks#1 {\headingmarks{even}{heading}{#1}
+ \headingmarks{odd}{heading}{#1} }
+\def\everyfootingmarks#1 {\headingmarks{even}{footing}{#1}
+ \headingmarks{odd}{footing}{#1} }
+% #1 = even/odd, #2 = heading/footing, #3 = top/bottom.
+\def\headingmarks#1#2#3 {%
+ \expandafter\let\expandafter\temp \csname get#3headingmarks\endcsname
+ \global\expandafter\let\csname get#1#2marks\endcsname \temp
+}
+
+\everyheadingmarks bottom
+\everyfootingmarks bottom
+
+% @headings double turns headings on for double-sided printing.
+% @headings single turns headings on for single-sided printing.
+% @headings off turns them off.
+% @headings on same as @headings double, retained for compatibility.
+% @headings after turns on double-sided headings after this page.
+% @headings doubleafter turns on double-sided headings after this page.
+% @headings singleafter turns on single-sided headings after this page.
+% By default, they are off at the start of a document,
+% and turned `on' after @end titlepage.
+
+\def\headings #1 {\csname HEADINGS#1\endcsname}
+
+\def\HEADINGSoff{%
+\global\evenheadline={\hfil} \global\evenfootline={\hfil}
+\global\oddheadline={\hfil} \global\oddfootline={\hfil}}
+\HEADINGSoff
+% When we turn headings on, set the page number to 1.
+% For double-sided printing, put current file name in lower left corner,
+% chapter name on inside top of right hand pages, document
+% title on inside top of left hand pages, and page numbers on outside top
+% edge of all pages.
+\def\HEADINGSdouble{%
+\global\pageno=1
+\global\evenfootline={\hfil}
+\global\oddfootline={\hfil}
+\global\evenheadline={\line{\folio\hfil\thistitle}}
+\global\oddheadline={\line{\thischapter\hfil\folio}}
+\global\let\contentsalignmacro = \chapoddpage
+}
+\let\contentsalignmacro = \chappager
+
+% For single-sided printing, chapter title goes across top left of page,
+% page number on top right.
+\def\HEADINGSsingle{%
+\global\pageno=1
+\global\evenfootline={\hfil}
+\global\oddfootline={\hfil}
+\global\evenheadline={\line{\thischapter\hfil\folio}}
+\global\oddheadline={\line{\thischapter\hfil\folio}}
+\global\let\contentsalignmacro = \chappager
+}
+\def\HEADINGSon{\HEADINGSdouble}
+
+\def\HEADINGSafter{\let\HEADINGShook=\HEADINGSdoublex}
+\let\HEADINGSdoubleafter=\HEADINGSafter
+\def\HEADINGSdoublex{%
+\global\evenfootline={\hfil}
+\global\oddfootline={\hfil}
+\global\evenheadline={\line{\folio\hfil\thistitle}}
+\global\oddheadline={\line{\thischapter\hfil\folio}}
+\global\let\contentsalignmacro = \chapoddpage
+}
+
+\def\HEADINGSsingleafter{\let\HEADINGShook=\HEADINGSsinglex}
+\def\HEADINGSsinglex{%
+\global\evenfootline={\hfil}
+\global\oddfootline={\hfil}
+\global\evenheadline={\line{\thischapter\hfil\folio}}
+\global\oddheadline={\line{\thischapter\hfil\folio}}
+\global\let\contentsalignmacro = \chappager
+}
+
+% Subroutines used in generating headings
+% This produces Day Month Year style of output.
+% Only define if not already defined, in case a txi-??.tex file has set
+% up a different format (e.g., txi-cs.tex does this).
+\ifx\today\undefined
+\def\today{%
+ \number\day\space
+ \ifcase\month
+ \or\putwordMJan\or\putwordMFeb\or\putwordMMar\or\putwordMApr
+ \or\putwordMMay\or\putwordMJun\or\putwordMJul\or\putwordMAug
+ \or\putwordMSep\or\putwordMOct\or\putwordMNov\or\putwordMDec
+ \fi
+ \space\number\year}
+\fi
+
+% @settitle line... specifies the title of the document, for headings.
+% It generates no output of its own.
+\def\thistitle{\putwordNoTitle}
+\def\settitle{\parsearg{\gdef\thistitle}}
+
+
+\message{tables,}
+% Tables -- @table, @ftable, @vtable, @item(x).
+
+% default indentation of table text
+\newdimen\tableindent \tableindent=.8in
+% default indentation of @itemize and @enumerate text
+\newdimen\itemindent \itemindent=.3in
+% margin between end of table item and start of table text.
+\newdimen\itemmargin \itemmargin=.1in
+
+% used internally for \itemindent minus \itemmargin
+\newdimen\itemmax
+
+% Note @table, @ftable, and @vtable define @item, @itemx, etc., with
+% these defs.
+% They also define \itemindex
+% to index the item name in whatever manner is desired (perhaps none).
+
+\newif\ifitemxneedsnegativevskip
+
+\def\itemxpar{\par\ifitemxneedsnegativevskip\nobreak\vskip-\parskip\nobreak\fi}
+
+\def\internalBitem{\smallbreak \parsearg\itemzzz}
+\def\internalBitemx{\itemxpar \parsearg\itemzzz}
+
+\def\itemzzz #1{\begingroup %
+ \advance\hsize by -\rightskip
+ \advance\hsize by -\tableindent
+ \setbox0=\hbox{\itemindicate{#1}}%
+ \itemindex{#1}%
+ \nobreak % This prevents a break before @itemx.
+ %
+ % If the item text does not fit in the space we have, put it on a line
+ % by itself, and do not allow a page break either before or after that
+ % line. We do not start a paragraph here because then if the next
+ % command is, e.g., @kindex, the whatsit would get put into the
+ % horizontal list on a line by itself, resulting in extra blank space.
+ \ifdim \wd0>\itemmax
+ %
+ % Make this a paragraph so we get the \parskip glue and wrapping,
+ % but leave it ragged-right.
+ \begingroup
+ \advance\leftskip by-\tableindent
+ \advance\hsize by\tableindent
+ \advance\rightskip by0pt plus1fil
+ \leavevmode\unhbox0\par
+ \endgroup
+ %
+ % We're going to be starting a paragraph, but we don't want the
+ % \parskip glue -- logically it's part of the @item we just started.
+ \nobreak \vskip-\parskip
+ %
+ % Stop a page break at the \parskip glue coming up. However, if
+ % what follows is an environment such as @example, there will be no
+ % \parskip glue; then the negative vskip we just inserted would
+ % cause the example and the item to crash together. So we use this
+ % bizarre value of 10001 as a signal to \aboveenvbreak to insert
+ % \parskip glue after all. Section titles are handled this way also.
+ %
+ \penalty 10001
+ \endgroup
+ \itemxneedsnegativevskipfalse
+ \else
+ % The item text fits into the space. Start a paragraph, so that the
+ % following text (if any) will end up on the same line.
+ \noindent
+ % Do this with kerns and \unhbox so that if there is a footnote in
+ % the item text, it can migrate to the main vertical list and
+ % eventually be printed.
+ \nobreak\kern-\tableindent
+ \dimen0 = \itemmax \advance\dimen0 by \itemmargin \advance\dimen0 by -\wd0
+ \unhbox0
+ \nobreak\kern\dimen0
+ \endgroup
+ \itemxneedsnegativevskiptrue
+ \fi
+}
+
+\def\item{\errmessage{@item while not in a list environment}}
+\def\itemx{\errmessage{@itemx while not in a list environment}}
+
+% @table, @ftable, @vtable.
+\envdef\table{%
+ \let\itemindex\gobble
+ \tablecheck{table}%
+}
+\envdef\ftable{%
+ \def\itemindex ##1{\doind {fn}{\code{##1}}}%
+ \tablecheck{ftable}%
+}
+\envdef\vtable{%
+ \def\itemindex ##1{\doind {vr}{\code{##1}}}%
+ \tablecheck{vtable}%
+}
+\def\tablecheck#1{%
+ \ifnum \the\catcode`\^^M=\active
+ \endgroup
+ \errmessage{This command won't work in this context; perhaps the problem is
+ that we are \inenvironment\thisenv}%
+ \def\next{\doignore{#1}}%
+ \else
+ \let\next\tablex
+ \fi
+ \next
+}
+\def\tablex#1{%
+ \def\itemindicate{#1}%
+ \parsearg\tabley
+}
+\def\tabley#1{%
+ {%
+ \makevalueexpandable
+ \edef\temp{\noexpand\tablez #1\space\space\space}%
+ \expandafter
+ }\temp \endtablez
+}
+\def\tablez #1 #2 #3 #4\endtablez{%
+ \aboveenvbreak
+ \ifnum 0#1>0 \advance \leftskip by #1\mil \fi
+ \ifnum 0#2>0 \tableindent=#2\mil \fi
+ \ifnum 0#3>0 \advance \rightskip by #3\mil \fi
+ \itemmax=\tableindent
+ \advance \itemmax by -\itemmargin
+ \advance \leftskip by \tableindent
+ \exdentamount=\tableindent
+ \parindent = 0pt
+ \parskip = \smallskipamount
+ \ifdim \parskip=0pt \parskip=2pt \fi
+ \let\item = \internalBitem
+ \let\itemx = \internalBitemx
+}
+\def\Etable{\endgraf\afterenvbreak}
+\let\Eftable\Etable
+\let\Evtable\Etable
+\let\Eitemize\Etable
+\let\Eenumerate\Etable
+
+% This is the counter used by @enumerate, which is really @itemize
+
+\newcount \itemno
+
+\envdef\itemize{\parsearg\doitemize}
+
+\def\doitemize#1{%
+ \aboveenvbreak
+ \itemmax=\itemindent
+ \advance\itemmax by -\itemmargin
+ \advance\leftskip by \itemindent
+ \exdentamount=\itemindent
+ \parindent=0pt
+ \parskip=\smallskipamount
+ \ifdim\parskip=0pt \parskip=2pt \fi
+ %
+ % Try typesetting the item mark that if the document erroneously says
+ % something like @itemize @samp (intending @table), there's an error
+ % right away at the @itemize. It's not the best error message in the
+ % world, but it's better than leaving it to the @item. This means if
+ % the user wants an empty mark, they have to say @w{} not just @w.
+ \def\itemcontents{#1}%
+ \setbox0 = \hbox{\itemcontents}%
+ %
+ % @itemize with no arg is equivalent to @itemize @bullet.
+ \ifx\itemcontents\empty\def\itemcontents{\bullet}\fi
+ %
+ \let\item=\itemizeitem
+}
+
+% Definition of @item while inside @itemize and @enumerate.
+%
+\def\itemizeitem{%
+ \advance\itemno by 1 % for enumerations
+ {\let\par=\endgraf \smallbreak}% reasonable place to break
+ {%
+ % If the document has an @itemize directly after a section title, a
+ % \nobreak will be last on the list, and \sectionheading will have
+ % done a \vskip-\parskip. In that case, we don't want to zero
+ % parskip, or the item text will crash with the heading. On the
+ % other hand, when there is normal text preceding the item (as there
+ % usually is), we do want to zero parskip, or there would be too much
+ % space. In that case, we won't have a \nobreak before. At least
+ % that's the theory.
+ \ifnum\lastpenalty<10000 \parskip=0in \fi
+ \noindent
+ \hbox to 0pt{\hss \itemcontents \kern\itemmargin}%
+ %
+ \vadjust{\penalty 1200}}% not good to break after first line of item.
+ \flushcr
+}
+
+% \splitoff TOKENS\endmark defines \first to be the first token in
+% TOKENS, and \rest to be the remainder.
+%
+\def\splitoff#1#2\endmark{\def\first{#1}\def\rest{#2}}%
+
+% Allow an optional argument of an uppercase letter, lowercase letter,
+% or number, to specify the first label in the enumerated list. No
+% argument is the same as `1'.
+%
+\envparseargdef\enumerate{\enumeratey #1 \endenumeratey}
+\def\enumeratey #1 #2\endenumeratey{%
+ % If we were given no argument, pretend we were given `1'.
+ \def\thearg{#1}%
+ \ifx\thearg\empty \def\thearg{1}\fi
+ %
+ % Detect if the argument is a single token. If so, it might be a
+ % letter. Otherwise, the only valid thing it can be is a number.
+ % (We will always have one token, because of the test we just made.
+ % This is a good thing, since \splitoff doesn't work given nothing at
+ % all -- the first parameter is undelimited.)
+ \expandafter\splitoff\thearg\endmark
+ \ifx\rest\empty
+ % Only one token in the argument. It could still be anything.
+ % A ``lowercase letter'' is one whose \lccode is nonzero.
+ % An ``uppercase letter'' is one whose \lccode is both nonzero, and
+ % not equal to itself.
+ % Otherwise, we assume it's a number.
+ %
+ % We need the \relax at the end of the \ifnum lines to stop TeX from
+ % continuing to look for a <number>.
+ %
+ \ifnum\lccode\expandafter`\thearg=0\relax
+ \numericenumerate % a number (we hope)
+ \else
+ % It's a letter.
+ \ifnum\lccode\expandafter`\thearg=\expandafter`\thearg\relax
+ \lowercaseenumerate % lowercase letter
+ \else
+ \uppercaseenumerate % uppercase letter
+ \fi
+ \fi
+ \else
+ % Multiple tokens in the argument. We hope it's a number.
+ \numericenumerate
+ \fi
+}
+
+% An @enumerate whose labels are integers. The starting integer is
+% given in \thearg.
+%
+\def\numericenumerate{%
+ \itemno = \thearg
+ \startenumeration{\the\itemno}%
+}
+
+% The starting (lowercase) letter is in \thearg.
+\def\lowercaseenumerate{%
+ \itemno = \expandafter`\thearg
+ \startenumeration{%
+ % Be sure we're not beyond the end of the alphabet.
+ \ifnum\itemno=0
+ \errmessage{No more lowercase letters in @enumerate; get a bigger
+ alphabet}%
+ \fi
+ \char\lccode\itemno
+ }%
+}
+
+% The starting (uppercase) letter is in \thearg.
+\def\uppercaseenumerate{%
+ \itemno = \expandafter`\thearg
+ \startenumeration{%
+ % Be sure we're not beyond the end of the alphabet.
+ \ifnum\itemno=0
+ \errmessage{No more uppercase letters in @enumerate; get a bigger
+ alphabet}
+ \fi
+ \char\uccode\itemno
+ }%
+}
+
+% Call \doitemize, adding a period to the first argument and supplying the
+% common last two arguments. Also subtract one from the initial value in
+% \itemno, since @item increments \itemno.
+%
+\def\startenumeration#1{%
+ \advance\itemno by -1
+ \doitemize{#1.}\flushcr
+}
+
+% @alphaenumerate and @capsenumerate are abbreviations for giving an arg
+% to @enumerate.
+%
+\def\alphaenumerate{\enumerate{a}}
+\def\capsenumerate{\enumerate{A}}
+\def\Ealphaenumerate{\Eenumerate}
+\def\Ecapsenumerate{\Eenumerate}
+
+
+% @multitable macros
+% Amy Hendrickson, 8/18/94, 3/6/96
+%
+% @multitable ... @end multitable will make as many columns as desired.
+% Contents of each column will wrap at width given in preamble. Width
+% can be specified either with sample text given in a template line,
+% or in percent of \hsize, the current width of text on page.
+
+% Table can continue over pages but will only break between lines.
+
+% To make preamble:
+%
+% Either define widths of columns in terms of percent of \hsize:
+% @multitable @columnfractions .25 .3 .45
+% @item ...
+%
+% Numbers following @columnfractions are the percent of the total
+% current hsize to be used for each column. You may use as many
+% columns as desired.
+
+
+% Or use a template:
+% @multitable {Column 1 template} {Column 2 template} {Column 3 template}
+% @item ...
+% using the widest term desired in each column.
+
+% Each new table line starts with @item, each subsequent new column
+% starts with @tab. Empty columns may be produced by supplying @tab's
+% with nothing between them for as many times as empty columns are needed,
+% ie, @tab at tab@tab will produce two empty columns.
+
+% @item, @tab do not need to be on their own lines, but it will not hurt
+% if they are.
+
+% Sample multitable:
+
+% @multitable {Column 1 template} {Column 2 template} {Column 3 template}
+% @item first col stuff @tab second col stuff @tab third col
+% @item
+% first col stuff
+% @tab
+% second col stuff
+% @tab
+% third col
+% @item first col stuff @tab second col stuff
+% @tab Many paragraphs of text may be used in any column.
+%
+% They will wrap at the width determined by the template.
+% @item at tab@tab This will be in third column.
+% @end multitable
+
+% Default dimensions may be reset by user.
+% @multitableparskip is vertical space between paragraphs in table.
+% @multitableparindent is paragraph indent in table.
+% @multitablecolmargin is horizontal space to be left between columns.
+% @multitablelinespace is space to leave between table items, baseline
+% to baseline.
+% 0pt means it depends on current normal line spacing.
+%
+\newskip\multitableparskip
+\newskip\multitableparindent
+\newdimen\multitablecolspace
+\newskip\multitablelinespace
+\multitableparskip=0pt
+\multitableparindent=6pt
+\multitablecolspace=12pt
+\multitablelinespace=0pt
+
+% Macros used to set up halign preamble:
+%
+\let\endsetuptable\relax
+\def\xendsetuptable{\endsetuptable}
+\let\columnfractions\relax
+\def\xcolumnfractions{\columnfractions}
+\newif\ifsetpercent
+
+% #1 is the @columnfraction, usually a decimal number like .5, but might
+% be just 1. We just use it, whatever it is.
+%
+\def\pickupwholefraction#1 {%
+ \global\advance\colcount by 1
+ \expandafter\xdef\csname col\the\colcount\endcsname{#1\hsize}%
+ \setuptable
+}
+
+\newcount\colcount
+\def\setuptable#1{%
+ \def\firstarg{#1}%
+ \ifx\firstarg\xendsetuptable
+ \let\go = \relax
+ \else
+ \ifx\firstarg\xcolumnfractions
+ \global\setpercenttrue
+ \else
+ \ifsetpercent
+ \let\go\pickupwholefraction
+ \else
+ \global\advance\colcount by 1
+ \setbox0=\hbox{#1\unskip\space}% Add a normal word space as a
+ % separator; typically that is always in the input, anyway.
+ \expandafter\xdef\csname col\the\colcount\endcsname{\the\wd0}%
+ \fi
+ \fi
+ \ifx\go\pickupwholefraction
+ % Put the argument back for the \pickupwholefraction call, so
+ % we'll always have a period there to be parsed.
+ \def\go{\pickupwholefraction#1}%
+ \else
+ \let\go = \setuptable
+ \fi%
+ \fi
+ \go
+}
+
+% multitable-only commands.
+%
+% @headitem starts a heading row, which we typeset in bold.
+% Assignments have to be global since we are inside the implicit group
+% of an alignment entry. \everycr resets \everytab so we don't have to
+% undo it ourselves.
+\def\headitemfont{\b}% for people to use in the template row; not changeable
+\def\headitem{%
+ \checkenv\multitable
+ \crcr
+ \global\everytab={\bf}% can't use \headitemfont since the parsing differs
+ \the\everytab % for the first item
+}%
+%
+% A \tab used to include \hskip1sp. But then the space in a template
+% line is not enough. That is bad. So let's go back to just `&' until
+% we again encounter the problem the 1sp was intended to solve.
+% --karl, nathan at acm.org, 20apr99.
+\def\tab{\checkenv\multitable &\the\everytab}%
+
+% @multitable ... @end multitable definitions:
+%
+\newtoks\everytab % insert after every tab.
+%
+\envdef\multitable{%
+ \vskip\parskip
+ \startsavinginserts
+ %
+ % @item within a multitable starts a normal row.
+ % We use \def instead of \let so that if one of the multitable entries
+ % contains an @itemize, we don't choke on the \item (seen as \crcr aka
+ % \endtemplate) expanding \doitemize.
+ \def\item{\crcr}%
+ %
+ \tolerance=9500
+ \hbadness=9500
+ \setmultitablespacing
+ \parskip=\multitableparskip
+ \parindent=\multitableparindent
+ \overfullrule=0pt
+ \global\colcount=0
+ %
+ \everycr = {%
+ \noalign{%
+ \global\everytab={}%
+ \global\colcount=0 % Reset the column counter.
+ % Check for saved footnotes, etc.
+ \checkinserts
+ % Keeps underfull box messages off when table breaks over pages.
+ %\filbreak
+ % Maybe so, but it also creates really weird page breaks when the
+ % table breaks over pages. Wouldn't \vfil be better? Wait until the
+ % problem manifests itself, so it can be fixed for real --karl.
+ }%
+ }%
+ %
+ \parsearg\domultitable
+}
+\def\domultitable#1{%
+ % To parse everything between @multitable and @item:
+ \setuptable#1 \endsetuptable
+ %
+ % This preamble sets up a generic column definition, which will
+ % be used as many times as user calls for columns.
+ % \vtop will set a single line and will also let text wrap and
+ % continue for many paragraphs if desired.
+ \halign\bgroup &%
+ \global\advance\colcount by 1
+ \multistrut
+ \vtop{%
+ % Use the current \colcount to find the correct column width:
+ \hsize=\expandafter\csname col\the\colcount\endcsname
+ %
+ % In order to keep entries from bumping into each other
+ % we will add a \leftskip of \multitablecolspace to all columns after
+ % the first one.
+ %
+ % If a template has been used, we will add \multitablecolspace
+ % to the width of each template entry.
+ %
+ % If the user has set preamble in terms of percent of \hsize we will
+ % use that dimension as the width of the column, and the \leftskip
+ % will keep entries from bumping into each other. Table will start at
+ % left margin and final column will justify at right margin.
+ %
+ % Make sure we don't inherit \rightskip from the outer environment.
+ \rightskip=0pt
+ \ifnum\colcount=1
+ % The first column will be indented with the surrounding text.
+ \advance\hsize by\leftskip
+ \else
+ \ifsetpercent \else
+ % If user has not set preamble in terms of percent of \hsize
+ % we will advance \hsize by \multitablecolspace.
+ \advance\hsize by \multitablecolspace
+ \fi
+ % In either case we will make \leftskip=\multitablecolspace:
+ \leftskip=\multitablecolspace
+ \fi
+ % Ignoring space at the beginning and end avoids an occasional spurious
+ % blank line, when TeX decides to break the line at the space before the
+ % box from the multistrut, so the strut ends up on a line by itself.
+ % For example:
+ % @multitable @columnfractions .11 .89
+ % @item @code{#}
+ % @tab Legal holiday which is valid in major parts of the whole country.
+ % Is automatically provided with highlighting sequences respectively
+ % marking characters.
+ \noindent\ignorespaces##\unskip\multistrut
+ }\cr
+}
+\def\Emultitable{%
+ \crcr
+ \egroup % end the \halign
+ \global\setpercentfalse
+}
+
+\def\setmultitablespacing{%
+ \def\multistrut{\strut}% just use the standard line spacing
+ %
+ % Compute \multitablelinespace (if not defined by user) for use in
+ % \multitableparskip calculation. We used define \multistrut based on
+ % this, but (ironically) that caused the spacing to be off.
+ % See bug-texinfo report from Werner Lemberg, 31 Oct 2004 12:52:20 +0100.
+\ifdim\multitablelinespace=0pt
+\setbox0=\vbox{X}\global\multitablelinespace=\the\baselineskip
+\global\advance\multitablelinespace by-\ht0
+\fi
+%% Test to see if parskip is larger than space between lines of
+%% table. If not, do nothing.
+%% If so, set to same dimension as multitablelinespace.
+\ifdim\multitableparskip>\multitablelinespace
+\global\multitableparskip=\multitablelinespace
+\global\advance\multitableparskip-7pt %% to keep parskip somewhat smaller
+ %% than skip between lines in the table.
+\fi%
+\ifdim\multitableparskip=0pt
+\global\multitableparskip=\multitablelinespace
+\global\advance\multitableparskip-7pt %% to keep parskip somewhat smaller
+ %% than skip between lines in the table.
+\fi}
+
+
+\message{conditionals,}
+
+% @iftex, @ifnotdocbook, @ifnothtml, @ifnotinfo, @ifnotplaintext,
+% @ifnotxml always succeed. They currently do nothing; we don't
+% attempt to check whether the conditionals are properly nested. But we
+% have to remember that they are conditionals, so that @end doesn't
+% attempt to close an environment group.
+%
+\def\makecond#1{%
+ \expandafter\let\csname #1\endcsname = \relax
+ \expandafter\let\csname iscond.#1\endcsname = 1
+}
+\makecond{iftex}
+\makecond{ifnotdocbook}
+\makecond{ifnothtml}
+\makecond{ifnotinfo}
+\makecond{ifnotplaintext}
+\makecond{ifnotxml}
+
+% Ignore @ignore, @ifhtml, @ifinfo, and the like.
+%
+\def\direntry{\doignore{direntry}}
+\def\documentdescription{\doignore{documentdescription}}
+\def\docbook{\doignore{docbook}}
+\def\html{\doignore{html}}
+\def\ifdocbook{\doignore{ifdocbook}}
+\def\ifhtml{\doignore{ifhtml}}
+\def\ifinfo{\doignore{ifinfo}}
+\def\ifnottex{\doignore{ifnottex}}
+\def\ifplaintext{\doignore{ifplaintext}}
+\def\ifxml{\doignore{ifxml}}
+\def\ignore{\doignore{ignore}}
+\def\menu{\doignore{menu}}
+\def\xml{\doignore{xml}}
+
+% Ignore text until a line `@end #1', keeping track of nested conditionals.
+%
+% A count to remember the depth of nesting.
+\newcount\doignorecount
+
+\def\doignore#1{\begingroup
+ % Scan in ``verbatim'' mode:
+ \obeylines
+ \catcode`\@ = \other
+ \catcode`\{ = \other
+ \catcode`\} = \other
+ %
+ % Make sure that spaces turn into tokens that match what \doignoretext wants.
+ \spaceisspace
+ %
+ % Count number of #1's that we've seen.
+ \doignorecount = 0
+ %
+ % Swallow text until we reach the matching `@end #1'.
+ \dodoignore{#1}%
+}
+
+{ \catcode`_=11 % We want to use \_STOP_ which cannot appear in texinfo source.
+ \obeylines %
+ %
+ \gdef\dodoignore#1{%
+ % #1 contains the command name as a string, e.g., `ifinfo'.
+ %
+ % Define a command to find the next `@end #1'.
+ \long\def\doignoretext##1^^M at end #1{%
+ \doignoretextyyy##1^^M@#1\_STOP_}%
+ %
+ % And this command to find another #1 command, at the beginning of a
+ % line. (Otherwise, we would consider a line `@c @ifset', for
+ % example, to count as an @ifset for nesting.)
+ \long\def\doignoretextyyy##1^^M@#1##2\_STOP_{\doignoreyyy{##2}\_STOP_}%
+ %
+ % And now expand that command.
+ \doignoretext ^^M%
+ }%
+}
+
+\def\doignoreyyy#1{%
+ \def\temp{#1}%
+ \ifx\temp\empty % Nothing found.
+ \let\next\doignoretextzzz
+ \else % Found a nested condition, ...
+ \advance\doignorecount by 1
+ \let\next\doignoretextyyy % ..., look for another.
+ % If we're here, #1 ends with ^^M\ifinfo (for example).
+ \fi
+ \next #1% the token \_STOP_ is present just after this macro.
+}
+
+% We have to swallow the remaining "\_STOP_".
+%
+\def\doignoretextzzz#1{%
+ \ifnum\doignorecount = 0 % We have just found the outermost @end.
+ \let\next\enddoignore
+ \else % Still inside a nested condition.
+ \advance\doignorecount by -1
+ \let\next\doignoretext % Look for the next @end.
+ \fi
+ \next
+}
+
+% Finish off ignored text.
+{ \obeylines%
+ % Ignore anything after the last `@end #1'; this matters in verbatim
+ % environments, where otherwise the newline after an ignored conditional
+ % would result in a blank line in the output.
+ \gdef\enddoignore#1^^M{\endgroup\ignorespaces}%
+}
+
+
+% @set VAR sets the variable VAR to an empty value.
+% @set VAR REST-OF-LINE sets VAR to the value REST-OF-LINE.
+%
+% Since we want to separate VAR from REST-OF-LINE (which might be
+% empty), we can't just use \parsearg; we have to insert a space of our
+% own to delimit the rest of the line, and then take it out again if we
+% didn't need it.
+% We rely on the fact that \parsearg sets \catcode`\ =10.
+%
+\parseargdef\set{\setyyy#1 \endsetyyy}
+\def\setyyy#1 #2\endsetyyy{%
+ {%
+ \makevalueexpandable
+ \def\temp{#2}%
+ \edef\next{\gdef\makecsname{SET#1}}%
+ \ifx\temp\empty
+ \next{}%
+ \else
+ \setzzz#2\endsetzzz
+ \fi
+ }%
+}
+% Remove the trailing space \setxxx inserted.
+\def\setzzz#1 \endsetzzz{\next{#1}}
+
+% @clear VAR clears (i.e., unsets) the variable VAR.
+%
+\parseargdef\clear{%
+ {%
+ \makevalueexpandable
+ \global\expandafter\let\csname SET#1\endcsname=\relax
+ }%
+}
+
+% @value{foo} gets the text saved in variable foo.
+\def\value{\begingroup\makevalueexpandable\valuexxx}
+\def\valuexxx#1{\expandablevalue{#1}\endgroup}
+{
+ \catcode`\- = \active \catcode`\_ = \active
+ %
+ \gdef\makevalueexpandable{%
+ \let\value = \expandablevalue
+ % We don't want these characters active, ...
+ \catcode`\-=\other \catcode`\_=\other
+ % ..., but we might end up with active ones in the argument if
+ % we're called from @code, as @code{@value{foo-bar_}}, though.
+ % So \let them to their normal equivalents.
+ \let-\realdash \let_\normalunderscore
+ }
+}
+
+% We have this subroutine so that we can handle at least some @value's
+% properly in indexes (we call \makevalueexpandable in \indexdummies).
+% The command has to be fully expandable (if the variable is set), since
+% the result winds up in the index file. This means that if the
+% variable's value contains other Texinfo commands, it's almost certain
+% it will fail (although perhaps we could fix that with sufficient work
+% to do a one-level expansion on the result, instead of complete).
+%
+\def\expandablevalue#1{%
+ \expandafter\ifx\csname SET#1\endcsname\relax
+ {[No value for ``#1'']}%
+ \message{Variable `#1', used in @value, is not set.}%
+ \else
+ \csname SET#1\endcsname
+ \fi
+}
+
+% @ifset VAR ... @end ifset reads the `...' iff VAR has been defined
+% with @set.
+%
+% To get special treatment of `@end ifset,' call \makeond and the redefine.
+%
+\makecond{ifset}
+\def\ifset{\parsearg{\doifset{\let\next=\ifsetfail}}}
+\def\doifset#1#2{%
+ {%
+ \makevalueexpandable
+ \let\next=\empty
+ \expandafter\ifx\csname SET#2\endcsname\relax
+ #1% If not set, redefine \next.
+ \fi
+ \expandafter
+ }\next
+}
+\def\ifsetfail{\doignore{ifset}}
+
+% @ifclear VAR ... @end ifclear reads the `...' iff VAR has never been
+% defined with @set, or has been undefined with @clear.
+%
+% The `\else' inside the `\doifset' parameter is a trick to reuse the
+% above code: if the variable is not set, do nothing, if it is set,
+% then redefine \next to \ifclearfail.
+%
+\makecond{ifclear}
+\def\ifclear{\parsearg{\doifset{\else \let\next=\ifclearfail}}}
+\def\ifclearfail{\doignore{ifclear}}
+
+% @dircategory CATEGORY -- specify a category of the dir file
+% which this file should belong to. Ignore this in TeX.
+\let\dircategory=\comment
+
+% @defininfoenclose.
+\let\definfoenclose=\comment
+
+
+\message{indexing,}
+% Index generation facilities
+
+% Define \newwrite to be identical to plain tex's \newwrite
+% except not \outer, so it can be used within macros and \if's.
+\edef\newwrite{\makecsname{ptexnewwrite}}
+
+% \newindex {foo} defines an index named foo.
+% It automatically defines \fooindex such that
+% \fooindex ...rest of line... puts an entry in the index foo.
+% It also defines \fooindfile to be the number of the output channel for
+% the file that accumulates this index. The file's extension is foo.
+% The name of an index should be no more than 2 characters long
+% for the sake of vms.
+%
+\def\newindex#1{%
+ \iflinks
+ \expandafter\newwrite \csname#1indfile\endcsname
+ \openout \csname#1indfile\endcsname \jobname.#1 % Open the file
+ \fi
+ \expandafter\xdef\csname#1index\endcsname{% % Define @#1index
+ \noexpand\doindex{#1}}
+}
+
+% @defindex foo == \newindex{foo}
+%
+\def\defindex{\parsearg\newindex}
+
+% Define @defcodeindex, like @defindex except put all entries in @code.
+%
+\def\defcodeindex{\parsearg\newcodeindex}
+%
+\def\newcodeindex#1{%
+ \iflinks
+ \expandafter\newwrite \csname#1indfile\endcsname
+ \openout \csname#1indfile\endcsname \jobname.#1
+ \fi
+ \expandafter\xdef\csname#1index\endcsname{%
+ \noexpand\docodeindex{#1}}%
+}
+
+
+% @synindex foo bar makes index foo feed into index bar.
+% Do this instead of @defindex foo if you don't want it as a separate index.
+%
+% @syncodeindex foo bar similar, but put all entries made for index foo
+% inside @code.
+%
+\def\synindex#1 #2 {\dosynindex\doindex{#1}{#2}}
+\def\syncodeindex#1 #2 {\dosynindex\docodeindex{#1}{#2}}
+
+% #1 is \doindex or \docodeindex, #2 the index getting redefined (foo),
+% #3 the target index (bar).
+\def\dosynindex#1#2#3{%
+ % Only do \closeout if we haven't already done it, else we'll end up
+ % closing the target index.
+ \expandafter \ifx\csname donesynindex#2\endcsname \relax
+ % The \closeout helps reduce unnecessary open files; the limit on the
+ % Acorn RISC OS is a mere 16 files.
+ \expandafter\closeout\csname#2indfile\endcsname
+ \expandafter\let\csname donesynindex#2\endcsname = 1
+ \fi
+ % redefine \fooindfile:
+ \expandafter\let\expandafter\temp\expandafter=\csname#3indfile\endcsname
+ \expandafter\let\csname#2indfile\endcsname=\temp
+ % redefine \fooindex:
+ \expandafter\xdef\csname#2index\endcsname{\noexpand#1{#3}}%
+}
+
+% Define \doindex, the driver for all \fooindex macros.
+% Argument #1 is generated by the calling \fooindex macro,
+% and it is "foo", the name of the index.
+
+% \doindex just uses \parsearg; it calls \doind for the actual work.
+% This is because \doind is more useful to call from other macros.
+
+% There is also \dosubind {index}{topic}{subtopic}
+% which makes an entry in a two-level index such as the operation index.
+
+\def\doindex#1{\edef\indexname{#1}\parsearg\singleindexer}
+\def\singleindexer #1{\doind{\indexname}{#1}}
+
+% like the previous two, but they put @code around the argument.
+\def\docodeindex#1{\edef\indexname{#1}\parsearg\singlecodeindexer}
+\def\singlecodeindexer #1{\doind{\indexname}{\code{#1}}}
+
+% Take care of Texinfo commands that can appear in an index entry.
+% Since there are some commands we want to expand, and others we don't,
+% we have to laboriously prevent expansion for those that we don't.
+%
+\def\indexdummies{%
+ \escapechar = `\\ % use backslash in output files.
+ \def\@{@}% change to @@ when we switch to @ as escape char in index files.
+ \def\ {\realbackslash\space }%
+ %
+ % Need these in case \tex is in effect and \{ is a \delimiter again.
+ % But can't use \lbracecmd and \rbracecmd because texindex assumes
+ % braces and backslashes are used only as delimiters.
+ \let\{ = \mylbrace
+ \let\} = \myrbrace
+ %
+ % I don't entirely understand this, but when an index entry is
+ % generated from a macro call, the \endinput which \scanmacro inserts
+ % causes processing to be prematurely terminated. This is,
+ % apparently, because \indexsorttmp is fully expanded, and \endinput
+ % is an expandable command. The redefinition below makes \endinput
+ % disappear altogether for that purpose -- although logging shows that
+ % processing continues to some further point. On the other hand, it
+ % seems \endinput does not hurt in the printed index arg, since that
+ % is still getting written without apparent harm.
+ %
+ % Sample source (mac-idx3.tex, reported by Graham Percival to
+ % help-texinfo, 22may06):
+ % @macro funindex {WORD}
+ % @findex xyz
+ % @end macro
+ % ...
+ % @funindex commtest
+ %
+ % The above is not enough to reproduce the bug, but it gives the flavor.
+ %
+ % Sample whatsit resulting:
+ % . at write3{\entry{xyz}{@folio }{@code {xyz at endinput }}}
+ %
+ % So:
+ \let\endinput = \empty
+ %
+ % Do the redefinitions.
+ \commondummies
+}
+
+% For the aux and toc files, @ is the escape character. So we want to
+% redefine everything using @ as the escape character (instead of
+% \realbackslash, still used for index files). When everything uses @,
+% this will be simpler.
+%
+\def\atdummies{%
+ \def\@{@@}%
+ \def\ {@ }%
+ \let\{ = \lbraceatcmd
+ \let\} = \rbraceatcmd
+ %
+ % Do the redefinitions.
+ \commondummies
+ \otherbackslash
+}
+
+% Called from \indexdummies and \atdummies.
+%
+\def\commondummies{%
+ %
+ % \definedummyword defines \#1 as \string\#1\space, thus effectively
+ % preventing its expansion. This is used only for control% words,
+ % not control letters, because the \space would be incorrect for
+ % control characters, but is needed to separate the control word
+ % from whatever follows.
+ %
+ % For control letters, we have \definedummyletter, which omits the
+ % space.
+ %
+ % These can be used both for control words that take an argument and
+ % those that do not. If it is followed by {arg} in the input, then
+ % that will dutifully get written to the index (or wherever).
+ %
+ \def\definedummyword ##1{\def##1{\string##1\space}}%
+ \def\definedummyletter##1{\def##1{\string##1}}%
+ \let\definedummyaccent\definedummyletter
+ %
+ \commondummiesnofonts
+ %
+ \definedummyletter\_%
+ %
+ % Non-English letters.
+ \definedummyword\AA
+ \definedummyword\AE
+ \definedummyword\DH
+ \definedummyword\L
+ \definedummyword\O
+ \definedummyword\OE
+ \definedummyword\TH
+ \definedummyword\aa
+ \definedummyword\ae
+ \definedummyword\dh
+ \definedummyword\exclamdown
+ \definedummyword\l
+ \definedummyword\o
+ \definedummyword\oe
+ \definedummyword\ordf
+ \definedummyword\ordm
+ \definedummyword\questiondown
+ \definedummyword\ss
+ \definedummyword\th
+ %
+ % Although these internal commands shouldn't show up, sometimes they do.
+ \definedummyword\bf
+ \definedummyword\gtr
+ \definedummyword\hat
+ \definedummyword\less
+ \definedummyword\sf
+ \definedummyword\sl
+ \definedummyword\tclose
+ \definedummyword\tt
+ %
+ \definedummyword\LaTeX
+ \definedummyword\TeX
+ %
+ % Assorted special characters.
+ \definedummyword\bullet
+ \definedummyword\comma
+ \definedummyword\copyright
+ \definedummyword\registeredsymbol
+ \definedummyword\dots
+ \definedummyword\enddots
+ \definedummyword\equiv
+ \definedummyword\error
+ \definedummyword\euro
+ \definedummyword\guillemetleft
+ \definedummyword\guillemetright
+ \definedummyword\guilsinglleft
+ \definedummyword\guilsinglright
+ \definedummyword\expansion
+ \definedummyword\minus
+ \definedummyword\ogonek
+ \definedummyword\pounds
+ \definedummyword\point
+ \definedummyword\print
+ \definedummyword\quotedblbase
+ \definedummyword\quotedblleft
+ \definedummyword\quotedblright
+ \definedummyword\quoteleft
+ \definedummyword\quoteright
+ \definedummyword\quotesinglbase
+ \definedummyword\result
+ \definedummyword\textdegree
+ %
+ % We want to disable all macros so that they are not expanded by \write.
+ \macrolist
+ %
+ \normalturnoffactive
+ %
+ % Handle some cases of @value -- where it does not contain any
+ % (non-fully-expandable) commands.
+ \makevalueexpandable
+}
+
+% \commondummiesnofonts: common to \commondummies and \indexnofonts.
+%
+\def\commondummiesnofonts{%
+ % Control letters and accents.
+ \definedummyletter\!%
+ \definedummyaccent\"%
+ \definedummyaccent\'%
+ \definedummyletter\*%
+ \definedummyaccent\,%
+ \definedummyletter\.%
+ \definedummyletter\/%
+ \definedummyletter\:%
+ \definedummyaccent\=%
+ \definedummyletter\?%
+ \definedummyaccent\^%
+ \definedummyaccent\`%
+ \definedummyaccent\~%
+ \definedummyword\u
+ \definedummyword\v
+ \definedummyword\H
+ \definedummyword\dotaccent
+ \definedummyword\ogonek
+ \definedummyword\ringaccent
+ \definedummyword\tieaccent
+ \definedummyword\ubaraccent
+ \definedummyword\udotaccent
+ \definedummyword\dotless
+ %
+ % Texinfo font commands.
+ \definedummyword\b
+ \definedummyword\i
+ \definedummyword\r
+ \definedummyword\sc
+ \definedummyword\t
+ %
+ % Commands that take arguments.
+ \definedummyword\acronym
+ \definedummyword\cite
+ \definedummyword\code
+ \definedummyword\command
+ \definedummyword\dfn
+ \definedummyword\email
+ \definedummyword\emph
+ \definedummyword\env
+ \definedummyword\file
+ \definedummyword\kbd
+ \definedummyword\key
+ \definedummyword\math
+ \definedummyword\option
+ \definedummyword\pxref
+ \definedummyword\ref
+ \definedummyword\samp
+ \definedummyword\strong
+ \definedummyword\tie
+ \definedummyword\uref
+ \definedummyword\url
+ \definedummyword\var
+ \definedummyword\verb
+ \definedummyword\w
+ \definedummyword\xref
+}
+
+% \indexnofonts is used when outputting the strings to sort the index
+% by, and when constructing control sequence names. It eliminates all
+% control sequences and just writes whatever the best ASCII sort string
+% would be for a given command (usually its argument).
+%
+\def\indexnofonts{%
+ % Accent commands should become @asis.
+ \def\definedummyaccent##1{\let##1\asis}%
+ % We can just ignore other control letters.
+ \def\definedummyletter##1{\let##1\empty}%
+ % Hopefully, all control words can become @asis.
+ \let\definedummyword\definedummyaccent
+ %
+ \commondummiesnofonts
+ %
+ % Don't no-op \tt, since it isn't a user-level command
+ % and is used in the definitions of the active chars like <, >, |, etc.
+ % Likewise with the other plain tex font commands.
+ %\let\tt=\asis
+ %
+ \def\ { }%
+ \def\@{@}%
+ % how to handle braces?
+ \def\_{\normalunderscore}%
+ %
+ % Non-English letters.
+ \def\AA{AA}%
+ \def\AE{AE}%
+ \def\DH{DZZ}%
+ \def\L{L}%
+ \def\OE{OE}%
+ \def\O{O}%
+ \def\TH{ZZZ}%
+ \def\aa{aa}%
+ \def\ae{ae}%
+ \def\dh{dzz}%
+ \def\exclamdown{!}%
+ \def\l{l}%
+ \def\oe{oe}%
+ \def\ordf{a}%
+ \def\ordm{o}%
+ \def\o{o}%
+ \def\questiondown{?}%
+ \def\ss{ss}%
+ \def\th{zzz}%
+ %
+ \def\LaTeX{LaTeX}%
+ \def\TeX{TeX}%
+ %
+ % Assorted special characters.
+ % (The following {} will end up in the sort string, but that's ok.)
+ \def\bullet{bullet}%
+ \def\comma{,}%
+ \def\copyright{copyright}%
+ \def\dots{...}%
+ \def\enddots{...}%
+ \def\equiv{==}%
+ \def\error{error}%
+ \def\euro{euro}%
+ \def\expansion{==>}%
+ \def\guillemetleft{<<}%
+ \def\guillemetright{>>}%
+ \def\guilsinglleft{<}%
+ \def\guilsinglright{>}%
+ \def\minus{-}%
+ \def\point{.}%
+ \def\pounds{pounds}%
+ \def\print{-|}%
+ \def\quotedblbase{"}%
+ \def\quotedblleft{"}%
+ \def\quotedblright{"}%
+ \def\quoteleft{`}%
+ \def\quoteright{'}%
+ \def\quotesinglbase{,}%
+ \def\registeredsymbol{R}%
+ \def\result{=>}%
+ \def\textdegree{o}%
+ %
+ % We need to get rid of all macros, leaving only the arguments (if present).
+ % Of course this is not nearly correct, but it is the best we can do for now.
+ % makeinfo does not expand macros in the argument to @deffn, which ends up
+ % writing an index entry, and texindex isn't prepared for an index sort entry
+ % that starts with \.
+ %
+ % Since macro invocations are followed by braces, we can just redefine them
+ % to take a single TeX argument. The case of a macro invocation that
+ % goes to end-of-line is not handled.
+ %
+ \macrolist
+}
+
+\let\indexbackslash=0 %overridden during \printindex.
+\let\SETmarginindex=\relax % put index entries in margin (undocumented)?
+
+% Most index entries go through here, but \dosubind is the general case.
+% #1 is the index name, #2 is the entry text.
+\def\doind#1#2{\dosubind{#1}{#2}{}}
+
+% Workhorse for all \fooindexes.
+% #1 is name of index, #2 is stuff to put there, #3 is subentry --
+% empty if called from \doind, as we usually are (the main exception
+% is with most defuns, which call us directly).
+%
+\def\dosubind#1#2#3{%
+ \iflinks
+ {%
+ % Store the main index entry text (including the third arg).
+ \toks0 = {#2}%
+ % If third arg is present, precede it with a space.
+ \def\thirdarg{#3}%
+ \ifx\thirdarg\empty \else
+ \toks0 = \expandafter{\the\toks0 \space #3}%
+ \fi
+ %
+ \edef\writeto{\csname#1indfile\endcsname}%
+ %
+ \safewhatsit\dosubindwrite
+ }%
+ \fi
+}
+
+% Write the entry in \toks0 to the index file:
+%
+\def\dosubindwrite{%
+ % Put the index entry in the margin if desired.
+ \ifx\SETmarginindex\relax\else
+ \insert\margin{\hbox{\vrule height8pt depth3pt width0pt \the\toks0}}%
+ \fi
+ %
+ % Remember, we are within a group.
+ \indexdummies % Must do this here, since \bf, etc expand at this stage
+ \def\backslashcurfont{\indexbackslash}% \indexbackslash isn't defined now
+ % so it will be output as is; and it will print as backslash.
+ %
+ % Process the index entry with all font commands turned off, to
+ % get the string to sort by.
+ {\indexnofonts
+ \edef\temp{\the\toks0}% need full expansion
+ \xdef\indexsorttmp{\temp}%
+ }%
+ %
+ % Set up the complete index entry, with both the sort key and
+ % the original text, including any font commands. We write
+ % three arguments to \entry to the .?? file (four in the
+ % subentry case), texindex reduces to two when writing the .??s
+ % sorted result.
+ \edef\temp{%
+ \write\writeto{%
+ \string\entry{\indexsorttmp}{\noexpand\folio}{\the\toks0}}%
+ }%
+ \temp
+}
+
+% Take care of unwanted page breaks/skips around a whatsit:
+%
+% If a skip is the last thing on the list now, preserve it
+% by backing up by \lastskip, doing the \write, then inserting
+% the skip again. Otherwise, the whatsit generated by the
+% \write or \pdfdest will make \lastskip zero. The result is that
+% sequences like this:
+% @end defun
+% @tindex whatever
+% @defun ...
+% will have extra space inserted, because the \medbreak in the
+% start of the @defun won't see the skip inserted by the @end of
+% the previous defun.
+%
+% But don't do any of this if we're not in vertical mode. We
+% don't want to do a \vskip and prematurely end a paragraph.
+%
+% Avoid page breaks due to these extra skips, too.
+%
+% But wait, there is a catch there:
+% We'll have to check whether \lastskip is zero skip. \ifdim is not
+% sufficient for this purpose, as it ignores stretch and shrink parts
+% of the skip. The only way seems to be to check the textual
+% representation of the skip.
+%
+% The following is almost like \def\zeroskipmacro{0.0pt} except that
+% the ``p'' and ``t'' characters have catcode \other, not 11 (letter).
+%
+\edef\zeroskipmacro{\expandafter\the\csname z at skip\endcsname}
+%
+\newskip\whatsitskip
+\newcount\whatsitpenalty
+%
+% ..., ready, GO:
+%
+\def\safewhatsit#1{%
+\ifhmode
+ #1%
+\else
+ % \lastskip and \lastpenalty cannot both be nonzero simultaneously.
+ \whatsitskip = \lastskip
+ \edef\lastskipmacro{\the\lastskip}%
+ \whatsitpenalty = \lastpenalty
+ %
+ % If \lastskip is nonzero, that means the last item was a
+ % skip. And since a skip is discardable, that means this
+ % -\whatsitskip glue we're inserting is preceded by a
+ % non-discardable item, therefore it is not a potential
+ % breakpoint, therefore no \nobreak needed.
+ \ifx\lastskipmacro\zeroskipmacro
+ \else
+ \vskip-\whatsitskip
+ \fi
+ %
+ #1%
+ %
+ \ifx\lastskipmacro\zeroskipmacro
+ % If \lastskip was zero, perhaps the last item was a penalty, and
+ % perhaps it was >=10000, e.g., a \nobreak. In that case, we want
+ % to re-insert the same penalty (values >10000 are used for various
+ % signals); since we just inserted a non-discardable item, any
+ % following glue (such as a \parskip) would be a breakpoint. For example:
+ %
+ % @deffn deffn-whatever
+ % @vindex index-whatever
+ % Description.
+ % would allow a break between the index-whatever whatsit
+ % and the "Description." paragraph.
+ \ifnum\whatsitpenalty>9999 \penalty\whatsitpenalty \fi
+ \else
+ % On the other hand, if we had a nonzero \lastskip,
+ % this make-up glue would be preceded by a non-discardable item
+ % (the whatsit from the \write), so we must insert a \nobreak.
+ \nobreak\vskip\whatsitskip
+ \fi
+\fi
+}
+
+% The index entry written in the file actually looks like
+% \entry {sortstring}{page}{topic}
+% or
+% \entry {sortstring}{page}{topic}{subtopic}
+% The texindex program reads in these files and writes files
+% containing these kinds of lines:
+% \initial {c}
+% before the first topic whose initial is c
+% \entry {topic}{pagelist}
+% for a topic that is used without subtopics
+% \primary {topic}
+% for the beginning of a topic that is used with subtopics
+% \secondary {subtopic}{pagelist}
+% for each subtopic.
+
+% Define the user-accessible indexing commands
+% @findex, @vindex, @kindex, @cindex.
+
+\def\findex {\fnindex}
+\def\kindex {\kyindex}
+\def\cindex {\cpindex}
+\def\vindex {\vrindex}
+\def\tindex {\tpindex}
+\def\pindex {\pgindex}
+
+\def\cindexsub {\begingroup\obeylines\cindexsub}
+{\obeylines %
+\gdef\cindexsub "#1" #2^^M{\endgroup %
+\dosubind{cp}{#2}{#1}}}
+
+% Define the macros used in formatting output of the sorted index material.
+
+% @printindex causes a particular index (the ??s file) to get printed.
+% It does not print any chapter heading (usually an @unnumbered).
+%
+\parseargdef\printindex{\begingroup
+ \dobreak \chapheadingskip{10000}%
+ %
+ \smallfonts \rm
+ \tolerance = 9500
+ \plainfrenchspacing
+ \everypar = {}% don't want the \kern\-parindent from indentation suppression.
+ %
+ % See if the index file exists and is nonempty.
+ % Change catcode of @ here so that if the index file contains
+ % \initial {@}
+ % as its first line, TeX doesn't complain about mismatched braces
+ % (because it thinks @} is a control sequence).
+ \catcode`\@ = 11
+ \openin 1 \jobname.#1s
+ \ifeof 1
+ % \enddoublecolumns gets confused if there is no text in the index,
+ % and it loses the chapter title and the aux file entries for the
+ % index. The easiest way to prevent this problem is to make sure
+ % there is some text.
+ \putwordIndexNonexistent
+ \else
+ %
+ % If the index file exists but is empty, then \openin leaves \ifeof
+ % false. We have to make TeX try to read something from the file, so
+ % it can discover if there is anything in it.
+ \read 1 to \temp
+ \ifeof 1
+ \putwordIndexIsEmpty
+ \else
+ % Index files are almost Texinfo source, but we use \ as the escape
+ % character. It would be better to use @, but that's too big a change
+ % to make right now.
+ \def\indexbackslash{\backslashcurfont}%
+ \catcode`\\ = 0
+ \escapechar = `\\
+ \begindoublecolumns
+ \input \jobname.#1s
+ \enddoublecolumns
+ \fi
+ \fi
+ \closein 1
+\endgroup}
+
+% These macros are used by the sorted index file itself.
+% Change them to control the appearance of the index.
+
+\def\initial#1{{%
+ % Some minor font changes for the special characters.
+ \let\tentt=\sectt \let\tt=\sectt \let\sf=\sectt
+ %
+ % Remove any glue we may have, we'll be inserting our own.
+ \removelastskip
+ %
+ % We like breaks before the index initials, so insert a bonus.
+ \nobreak
+ \vskip 0pt plus 3\baselineskip
+ \penalty 0
+ \vskip 0pt plus -3\baselineskip
+ %
+ % Typeset the initial. Making this add up to a whole number of
+ % baselineskips increases the chance of the dots lining up from column
+ % to column. It still won't often be perfect, because of the stretch
+ % we need before each entry, but it's better.
+ %
+ % No shrink because it confuses \balancecolumns.
+ \vskip 1.67\baselineskip plus .5\baselineskip
+ \leftline{\secbf #1}%
+ % Do our best not to break after the initial.
+ \nobreak
+ \vskip .33\baselineskip plus .1\baselineskip
+}}
+
+% \entry typesets a paragraph consisting of the text (#1), dot leaders, and
+% then page number (#2) flushed to the right margin. It is used for index
+% and table of contents entries. The paragraph is indented by \leftskip.
+%
+% A straightforward implementation would start like this:
+% \def\entry#1#2{...
+% But this freezes the catcodes in the argument, and can cause problems to
+% @code, which sets - active. This problem was fixed by a kludge---
+% ``-'' was active throughout whole index, but this isn't really right.
+%
+% The right solution is to prevent \entry from swallowing the whole text.
+% --kasal, 21nov03
+\def\entry{%
+ \begingroup
+ %
+ % Start a new paragraph if necessary, so our assignments below can't
+ % affect previous text.
+ \par
+ %
+ % Do not fill out the last line with white space.
+ \parfillskip = 0in
+ %
+ % No extra space above this paragraph.
+ \parskip = 0in
+ %
+ % Do not prefer a separate line ending with a hyphen to fewer lines.
+ \finalhyphendemerits = 0
+ %
+ % \hangindent is only relevant when the entry text and page number
+ % don't both fit on one line. In that case, bob suggests starting the
+ % dots pretty far over on the line. Unfortunately, a large
+ % indentation looks wrong when the entry text itself is broken across
+ % lines. So we use a small indentation and put up with long leaders.
+ %
+ % \hangafter is reset to 1 (which is the value we want) at the start
+ % of each paragraph, so we need not do anything with that.
+ \hangindent = 2em
+ %
+ % When the entry text needs to be broken, just fill out the first line
+ % with blank space.
+ \rightskip = 0pt plus1fil
+ %
+ % A bit of stretch before each entry for the benefit of balancing
+ % columns.
+ \vskip 0pt plus1pt
+ %
+ % Swallow the left brace of the text (first parameter):
+ \afterassignment\doentry
+ \let\temp =
+}
+\def\doentry{%
+ \bgroup % Instead of the swallowed brace.
+ \noindent
+ \aftergroup\finishentry
+ % And now comes the text of the entry.
+}
+\def\finishentry#1{%
+ % #1 is the page number.
+ %
+ % The following is kludged to not output a line of dots in the index if
+ % there are no page numbers. The next person who breaks this will be
+ % cursed by a Unix daemon.
+ \setbox\boxA = \hbox{#1}%
+ \ifdim\wd\boxA = 0pt
+ \ %
+ \else
+ %
+ % If we must, put the page number on a line of its own, and fill out
+ % this line with blank space. (The \hfil is overwhelmed with the
+ % fill leaders glue in \indexdotfill if the page number does fit.)
+ \hfil\penalty50
+ \null\nobreak\indexdotfill % Have leaders before the page number.
+ %
+ % The `\ ' here is removed by the implicit \unskip that TeX does as
+ % part of (the primitive) \par. Without it, a spurious underfull
+ % \hbox ensues.
+ \ifpdf
+ \pdfgettoks#1.%
+ \ \the\toksA
+ \else
+ \ #1%
+ \fi
+ \fi
+ \par
+ \endgroup
+}
+
+% Like plain.tex's \dotfill, except uses up at least 1 em.
+\def\indexdotfill{\cleaders
+ \hbox{$\mathsurround=0pt \mkern1.5mu.\mkern1.5mu$}\hskip 1em plus 1fill}
+
+\def\primary #1{\line{#1\hfil}}
+
+\newskip\secondaryindent \secondaryindent=0.5cm
+\def\secondary#1#2{{%
+ \parfillskip=0in
+ \parskip=0in
+ \hangindent=1in
+ \hangafter=1
+ \noindent\hskip\secondaryindent\hbox{#1}\indexdotfill
+ \ifpdf
+ \pdfgettoks#2.\ \the\toksA % The page number ends the paragraph.
+ \else
+ #2
+ \fi
+ \par
+}}
+
+% Define two-column mode, which we use to typeset indexes.
+% Adapted from the TeXbook, page 416, which is to say,
+% the manmac.tex format used to print the TeXbook itself.
+\catcode`\@=11
+
+\newbox\partialpage
+\newdimen\doublecolumnhsize
+
+\def\begindoublecolumns{\begingroup % ended by \enddoublecolumns
+ % Grab any single-column material above us.
+ \output = {%
+ %
+ % Here is a possibility not foreseen in manmac: if we accumulate a
+ % whole lot of material, we might end up calling this \output
+ % routine twice in a row (see the doublecol-lose test, which is
+ % essentially a couple of indexes with @setchapternewpage off). In
+ % that case we just ship out what is in \partialpage with the normal
+ % output routine. Generally, \partialpage will be empty when this
+ % runs and this will be a no-op. See the indexspread.tex test case.
+ \ifvoid\partialpage \else
+ \onepageout{\pagecontents\partialpage}%
+ \fi
+ %
+ \global\setbox\partialpage = \vbox{%
+ % Unvbox the main output page.
+ \unvbox\PAGE
+ \kern-\topskip \kern\baselineskip
+ }%
+ }%
+ \eject % run that output routine to set \partialpage
+ %
+ % Use the double-column output routine for subsequent pages.
+ \output = {\doublecolumnout}%
+ %
+ % Change the page size parameters. We could do this once outside this
+ % routine, in each of @smallbook, @afourpaper, and the default 8.5x11
+ % format, but then we repeat the same computation. Repeating a couple
+ % of assignments once per index is clearly meaningless for the
+ % execution time, so we may as well do it in one place.
+ %
+ % First we halve the line length, less a little for the gutter between
+ % the columns. We compute the gutter based on the line length, so it
+ % changes automatically with the paper format. The magic constant
+ % below is chosen so that the gutter has the same value (well, +-<1pt)
+ % as it did when we hard-coded it.
+ %
+ % We put the result in a separate register, \doublecolumhsize, so we
+ % can restore it in \pagesofar, after \hsize itself has (potentially)
+ % been clobbered.
+ %
+ \doublecolumnhsize = \hsize
+ \advance\doublecolumnhsize by -.04154\hsize
+ \divide\doublecolumnhsize by 2
+ \hsize = \doublecolumnhsize
+ %
+ % Double the \vsize as well. (We don't need a separate register here,
+ % since nobody clobbers \vsize.)
+ \vsize = 2\vsize
+}
+
+% The double-column output routine for all double-column pages except
+% the last.
+%
+\def\doublecolumnout{%
+ \splittopskip=\topskip \splitmaxdepth=\maxdepth
+ % Get the available space for the double columns -- the normal
+ % (undoubled) page height minus any material left over from the
+ % previous page.
+ \dimen@ = \vsize
+ \divide\dimen@ by 2
+ \advance\dimen@ by -\ht\partialpage
+ %
+ % box0 will be the left-hand column, box2 the right.
+ \setbox0=\vsplit255 to\dimen@ \setbox2=\vsplit255 to\dimen@
+ \onepageout\pagesofar
+ \unvbox255
+ \penalty\outputpenalty
+}
+%
+% Re-output the contents of the output page -- any previous material,
+% followed by the two boxes we just split, in box0 and box2.
+\def\pagesofar{%
+ \unvbox\partialpage
+ %
+ \hsize = \doublecolumnhsize
+ \wd0=\hsize \wd2=\hsize
+ \hbox to\pagewidth{\box0\hfil\box2}%
+}
+%
+% All done with double columns.
+\def\enddoublecolumns{%
+ % The following penalty ensures that the page builder is exercised
+ % _before_ we change the output routine. This is necessary in the
+ % following situation:
+ %
+ % The last section of the index consists only of a single entry.
+ % Before this section, \pagetotal is less than \pagegoal, so no
+ % break occurs before the last section starts. However, the last
+ % section, consisting of \initial and the single \entry, does not
+ % fit on the page and has to be broken off. Without the following
+ % penalty the page builder will not be exercised until \eject
+ % below, and by that time we'll already have changed the output
+ % routine to the \balancecolumns version, so the next-to-last
+ % double-column page will be processed with \balancecolumns, which
+ % is wrong: The two columns will go to the main vertical list, with
+ % the broken-off section in the recent contributions. As soon as
+ % the output routine finishes, TeX starts reconsidering the page
+ % break. The two columns and the broken-off section both fit on the
+ % page, because the two columns now take up only half of the page
+ % goal. When TeX sees \eject from below which follows the final
+ % section, it invokes the new output routine that we've set after
+ % \balancecolumns below; \onepageout will try to fit the two columns
+ % and the final section into the vbox of \pageheight (see
+ % \pagebody), causing an overfull box.
+ %
+ % Note that glue won't work here, because glue does not exercise the
+ % page builder, unlike penalties (see The TeXbook, pp. 280-281).
+ \penalty0
+ %
+ \output = {%
+ % Split the last of the double-column material. Leave it on the
+ % current page, no automatic page break.
+ \balancecolumns
+ %
+ % If we end up splitting too much material for the current page,
+ % though, there will be another page break right after this \output
+ % invocation ends. Having called \balancecolumns once, we do not
+ % want to call it again. Therefore, reset \output to its normal
+ % definition right away. (We hope \balancecolumns will never be
+ % called on to balance too much material, but if it is, this makes
+ % the output somewhat more palatable.)
+ \global\output = {\onepageout{\pagecontents\PAGE}}%
+ }%
+ \eject
+ \endgroup % started in \begindoublecolumns
+ %
+ % \pagegoal was set to the doubled \vsize above, since we restarted
+ % the current page. We're now back to normal single-column
+ % typesetting, so reset \pagegoal to the normal \vsize (after the
+ % \endgroup where \vsize got restored).
+ \pagegoal = \vsize
+}
+%
+% Called at the end of the double column material.
+\def\balancecolumns{%
+ \setbox0 = \vbox{\unvbox255}% like \box255 but more efficient, see p.120.
+ \dimen@ = \ht0
+ \advance\dimen@ by \topskip
+ \advance\dimen@ by-\baselineskip
+ \divide\dimen@ by 2 % target to split to
+ %debug\message{final 2-column material height=\the\ht0, target=\the\dimen at .}%
+ \splittopskip = \topskip
+ % Loop until we get a decent breakpoint.
+ {%
+ \vbadness = 10000
+ \loop
+ \global\setbox3 = \copy0
+ \global\setbox1 = \vsplit3 to \dimen@
+ \ifdim\ht3>\dimen@
+ \global\advance\dimen@ by 1pt
+ \repeat
+ }%
+ %debug\message{split to \the\dimen@, column heights: \the\ht1, \the\ht3.}%
+ \setbox0=\vbox to\dimen@{\unvbox1}%
+ \setbox2=\vbox to\dimen@{\unvbox3}%
+ %
+ \pagesofar
+}
+\catcode`\@ = \other
+
+
+\message{sectioning,}
+% Chapters, sections, etc.
+
+% \unnumberedno is an oxymoron, of course. But we count the unnumbered
+% sections so that we can refer to them unambiguously in the pdf
+% outlines by their "section number". We avoid collisions with chapter
+% numbers by starting them at 10000. (If a document ever has 10000
+% chapters, we're in trouble anyway, I'm sure.)
+\newcount\unnumberedno \unnumberedno = 10000
+\newcount\chapno
+\newcount\secno \secno=0
+\newcount\subsecno \subsecno=0
+\newcount\subsubsecno \subsubsecno=0
+
+% This counter is funny since it counts through charcodes of letters A, B, ...
+\newcount\appendixno \appendixno = `\@
+%
+% \def\appendixletter{\char\the\appendixno}
+% We do the following ugly conditional instead of the above simple
+% construct for the sake of pdftex, which needs the actual
+% letter in the expansion, not just typeset.
+%
+\def\appendixletter{%
+ \ifnum\appendixno=`A A%
+ \else\ifnum\appendixno=`B B%
+ \else\ifnum\appendixno=`C C%
+ \else\ifnum\appendixno=`D D%
+ \else\ifnum\appendixno=`E E%
+ \else\ifnum\appendixno=`F F%
+ \else\ifnum\appendixno=`G G%
+ \else\ifnum\appendixno=`H H%
+ \else\ifnum\appendixno=`I I%
+ \else\ifnum\appendixno=`J J%
+ \else\ifnum\appendixno=`K K%
+ \else\ifnum\appendixno=`L L%
+ \else\ifnum\appendixno=`M M%
+ \else\ifnum\appendixno=`N N%
+ \else\ifnum\appendixno=`O O%
+ \else\ifnum\appendixno=`P P%
+ \else\ifnum\appendixno=`Q Q%
+ \else\ifnum\appendixno=`R R%
+ \else\ifnum\appendixno=`S S%
+ \else\ifnum\appendixno=`T T%
+ \else\ifnum\appendixno=`U U%
+ \else\ifnum\appendixno=`V V%
+ \else\ifnum\appendixno=`W W%
+ \else\ifnum\appendixno=`X X%
+ \else\ifnum\appendixno=`Y Y%
+ \else\ifnum\appendixno=`Z Z%
+ % The \the is necessary, despite appearances, because \appendixletter is
+ % expanded while writing the .toc file. \char\appendixno is not
+ % expandable, thus it is written literally, thus all appendixes come out
+ % with the same letter (or @) in the toc without it.
+ \else\char\the\appendixno
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi}
+
+% Each @chapter defines these (using marks) as the number+name, number
+% and name of the chapter. Page headings and footings can use
+% these. @section does likewise.
+\def\thischapter{}
+\def\thischapternum{}
+\def\thischaptername{}
+\def\thissection{}
+\def\thissectionnum{}
+\def\thissectionname{}
+
+\newcount\absseclevel % used to calculate proper heading level
+\newcount\secbase\secbase=0 % @raisesections/@lowersections modify this count
+
+% @raisesections: treat @section as chapter, @subsection as section, etc.
+\def\raisesections{\global\advance\secbase by -1}
+\let\up=\raisesections % original BFox name
+
+% @lowersections: treat @chapter as section, @section as subsection, etc.
+\def\lowersections{\global\advance\secbase by 1}
+\let\down=\lowersections % original BFox name
+
+% we only have subsub.
+\chardef\maxseclevel = 3
+%
+% A numbered section within an unnumbered changes to unnumbered too.
+% To achive this, remember the "biggest" unnum. sec. we are currently in:
+\chardef\unmlevel = \maxseclevel
+%
+% Trace whether the current chapter is an appendix or not:
+% \chapheadtype is "N" or "A", unnumbered chapters are ignored.
+\def\chapheadtype{N}
+
+% Choose a heading macro
+% #1 is heading type
+% #2 is heading level
+% #3 is text for heading
+\def\genhead#1#2#3{%
+ % Compute the abs. sec. level:
+ \absseclevel=#2
+ \advance\absseclevel by \secbase
+ % Make sure \absseclevel doesn't fall outside the range:
+ \ifnum \absseclevel < 0
+ \absseclevel = 0
+ \else
+ \ifnum \absseclevel > 3
+ \absseclevel = 3
+ \fi
+ \fi
+ % The heading type:
+ \def\headtype{#1}%
+ \if \headtype U%
+ \ifnum \absseclevel < \unmlevel
+ \chardef\unmlevel = \absseclevel
+ \fi
+ \else
+ % Check for appendix sections:
+ \ifnum \absseclevel = 0
+ \edef\chapheadtype{\headtype}%
+ \else
+ \if \headtype A\if \chapheadtype N%
+ \errmessage{@appendix... within a non-appendix chapter}%
+ \fi\fi
+ \fi
+ % Check for numbered within unnumbered:
+ \ifnum \absseclevel > \unmlevel
+ \def\headtype{U}%
+ \else
+ \chardef\unmlevel = 3
+ \fi
+ \fi
+ % Now print the heading:
+ \if \headtype U%
+ \ifcase\absseclevel
+ \unnumberedzzz{#3}%
+ \or \unnumberedseczzz{#3}%
+ \or \unnumberedsubseczzz{#3}%
+ \or \unnumberedsubsubseczzz{#3}%
+ \fi
+ \else
+ \if \headtype A%
+ \ifcase\absseclevel
+ \appendixzzz{#3}%
+ \or \appendixsectionzzz{#3}%
+ \or \appendixsubseczzz{#3}%
+ \or \appendixsubsubseczzz{#3}%
+ \fi
+ \else
+ \ifcase\absseclevel
+ \chapterzzz{#3}%
+ \or \seczzz{#3}%
+ \or \numberedsubseczzz{#3}%
+ \or \numberedsubsubseczzz{#3}%
+ \fi
+ \fi
+ \fi
+ \suppressfirstparagraphindent
+}
+
+% an interface:
+\def\numhead{\genhead N}
+\def\apphead{\genhead A}
+\def\unnmhead{\genhead U}
+
+% @chapter, @appendix, @unnumbered. Increment top-level counter, reset
+% all lower-level sectioning counters to zero.
+%
+% Also set \chaplevelprefix, which we prepend to @float sequence numbers
+% (e.g., figures), q.v. By default (before any chapter), that is empty.
+\let\chaplevelprefix = \empty
+%
+\outer\parseargdef\chapter{\numhead0{#1}} % normally numhead0 calls chapterzzz
+\def\chapterzzz#1{%
+ % section resetting is \global in case the chapter is in a group, such
+ % as an @include file.
+ \global\secno=0 \global\subsecno=0 \global\subsubsecno=0
+ \global\advance\chapno by 1
+ %
+ % Used for \float.
+ \gdef\chaplevelprefix{\the\chapno.}%
+ \resetallfloatnos
+ %
+ % \putwordChapter can contain complex things in translations.
+ \toks0=\expandafter{\putwordChapter}%
+ \message{\the\toks0 \space \the\chapno}%
+ %
+ % Write the actual heading.
+ \chapmacro{#1}{Ynumbered}{\the\chapno}%
+ %
+ % So @section and the like are numbered underneath this chapter.
+ \global\let\section = \numberedsec
+ \global\let\subsection = \numberedsubsec
+ \global\let\subsubsection = \numberedsubsubsec
+}
+
+\outer\parseargdef\appendix{\apphead0{#1}} % normally calls appendixzzz
+%
+\def\appendixzzz#1{%
+ \global\secno=0 \global\subsecno=0 \global\subsubsecno=0
+ \global\advance\appendixno by 1
+ \gdef\chaplevelprefix{\appendixletter.}%
+ \resetallfloatnos
+ %
+ % \putwordAppendix can contain complex things in translations.
+ \toks0=\expandafter{\putwordAppendix}%
+ \message{\the\toks0 \space \appendixletter}%
+ %
+ \chapmacro{#1}{Yappendix}{\appendixletter}%
+ %
+ \global\let\section = \appendixsec
+ \global\let\subsection = \appendixsubsec
+ \global\let\subsubsection = \appendixsubsubsec
+}
+
+\outer\parseargdef\unnumbered{\unnmhead0{#1}} % normally unnmhead0 calls unnumberedzzz
+\def\unnumberedzzz#1{%
+ \global\secno=0 \global\subsecno=0 \global\subsubsecno=0
+ \global\advance\unnumberedno by 1
+ %
+ % Since an unnumbered has no number, no prefix for figures.
+ \global\let\chaplevelprefix = \empty
+ \resetallfloatnos
+ %
+ % This used to be simply \message{#1}, but TeX fully expands the
+ % argument to \message. Therefore, if #1 contained @-commands, TeX
+ % expanded them. For example, in `@unnumbered The @cite{Book}', TeX
+ % expanded @cite (which turns out to cause errors because \cite is meant
+ % to be executed, not expanded).
+ %
+ % Anyway, we don't want the fully-expanded definition of @cite to appear
+ % as a result of the \message, we just want `@cite' itself. We use
+ % \the<toks register> to achieve this: TeX expands \the<toks> only once,
+ % simply yielding the contents of <toks register>. (We also do this for
+ % the toc entries.)
+ \toks0 = {#1}%
+ \message{(\the\toks0)}%
+ %
+ \chapmacro{#1}{Ynothing}{\the\unnumberedno}%
+ %
+ \global\let\section = \unnumberedsec
+ \global\let\subsection = \unnumberedsubsec
+ \global\let\subsubsection = \unnumberedsubsubsec
+}
+
+% @centerchap is like @unnumbered, but the heading is centered.
+\outer\parseargdef\centerchap{%
+ % Well, we could do the following in a group, but that would break
+ % an assumption that \chapmacro is called at the outermost level.
+ % Thus we are safer this way: --kasal, 24feb04
+ \let\centerparametersmaybe = \centerparameters
+ \unnmhead0{#1}%
+ \let\centerparametersmaybe = \relax
+}
+
+% @top is like @unnumbered.
+\let\top\unnumbered
+
+% Sections.
+\outer\parseargdef\numberedsec{\numhead1{#1}} % normally calls seczzz
+\def\seczzz#1{%
+ \global\subsecno=0 \global\subsubsecno=0 \global\advance\secno by 1
+ \sectionheading{#1}{sec}{Ynumbered}{\the\chapno.\the\secno}%
+}
+
+\outer\parseargdef\appendixsection{\apphead1{#1}} % normally calls appendixsectionzzz
+\def\appendixsectionzzz#1{%
+ \global\subsecno=0 \global\subsubsecno=0 \global\advance\secno by 1
+ \sectionheading{#1}{sec}{Yappendix}{\appendixletter.\the\secno}%
+}
+\let\appendixsec\appendixsection
+
+\outer\parseargdef\unnumberedsec{\unnmhead1{#1}} % normally calls unnumberedseczzz
+\def\unnumberedseczzz#1{%
+ \global\subsecno=0 \global\subsubsecno=0 \global\advance\secno by 1
+ \sectionheading{#1}{sec}{Ynothing}{\the\unnumberedno.\the\secno}%
+}
+
+% Subsections.
+\outer\parseargdef\numberedsubsec{\numhead2{#1}} % normally calls numberedsubseczzz
+\def\numberedsubseczzz#1{%
+ \global\subsubsecno=0 \global\advance\subsecno by 1
+ \sectionheading{#1}{subsec}{Ynumbered}{\the\chapno.\the\secno.\the\subsecno}%
+}
+
+\outer\parseargdef\appendixsubsec{\apphead2{#1}} % normally calls appendixsubseczzz
+\def\appendixsubseczzz#1{%
+ \global\subsubsecno=0 \global\advance\subsecno by 1
+ \sectionheading{#1}{subsec}{Yappendix}%
+ {\appendixletter.\the\secno.\the\subsecno}%
+}
+
+\outer\parseargdef\unnumberedsubsec{\unnmhead2{#1}} %normally calls unnumberedsubseczzz
+\def\unnumberedsubseczzz#1{%
+ \global\subsubsecno=0 \global\advance\subsecno by 1
+ \sectionheading{#1}{subsec}{Ynothing}%
+ {\the\unnumberedno.\the\secno.\the\subsecno}%
+}
+
+% Subsubsections.
+\outer\parseargdef\numberedsubsubsec{\numhead3{#1}} % normally numberedsubsubseczzz
+\def\numberedsubsubseczzz#1{%
+ \global\advance\subsubsecno by 1
+ \sectionheading{#1}{subsubsec}{Ynumbered}%
+ {\the\chapno.\the\secno.\the\subsecno.\the\subsubsecno}%
+}
+
+\outer\parseargdef\appendixsubsubsec{\apphead3{#1}} % normally appendixsubsubseczzz
+\def\appendixsubsubseczzz#1{%
+ \global\advance\subsubsecno by 1
+ \sectionheading{#1}{subsubsec}{Yappendix}%
+ {\appendixletter.\the\secno.\the\subsecno.\the\subsubsecno}%
+}
+
+\outer\parseargdef\unnumberedsubsubsec{\unnmhead3{#1}} %normally unnumberedsubsubseczzz
+\def\unnumberedsubsubseczzz#1{%
+ \global\advance\subsubsecno by 1
+ \sectionheading{#1}{subsubsec}{Ynothing}%
+ {\the\unnumberedno.\the\secno.\the\subsecno.\the\subsubsecno}%
+}
+
+% These macros control what the section commands do, according
+% to what kind of chapter we are in (ordinary, appendix, or unnumbered).
+% Define them by default for a numbered chapter.
+\let\section = \numberedsec
+\let\subsection = \numberedsubsec
+\let\subsubsection = \numberedsubsubsec
+
+% Define @majorheading, @heading and @subheading
+
+% NOTE on use of \vbox for chapter headings, section headings, and such:
+% 1) We use \vbox rather than the earlier \line to permit
+% overlong headings to fold.
+% 2) \hyphenpenalty is set to 10000 because hyphenation in a
+% heading is obnoxious; this forbids it.
+% 3) Likewise, headings look best if no \parindent is used, and
+% if justification is not attempted. Hence \raggedright.
+
+\def\majorheading{%
+ {\advance\chapheadingskip by 10pt \chapbreak }%
+ \parsearg\chapheadingzzz
+}
+
+\def\chapheading{\chapbreak \parsearg\chapheadingzzz}
+\def\chapheadingzzz#1{%
+ {\chapfonts \vbox{\hyphenpenalty=10000\tolerance=5000
+ \parindent=0pt\ptexraggedright
+ \rmisbold #1\hfill}}%
+ \bigskip \par\penalty 200\relax
+ \suppressfirstparagraphindent
+}
+
+% @heading, @subheading, @subsubheading.
+\parseargdef\heading{\sectionheading{#1}{sec}{Yomitfromtoc}{}
+ \suppressfirstparagraphindent}
+\parseargdef\subheading{\sectionheading{#1}{subsec}{Yomitfromtoc}{}
+ \suppressfirstparagraphindent}
+\parseargdef\subsubheading{\sectionheading{#1}{subsubsec}{Yomitfromtoc}{}
+ \suppressfirstparagraphindent}
+
+% These macros generate a chapter, section, etc. heading only
+% (including whitespace, linebreaking, etc. around it),
+% given all the information in convenient, parsed form.
+
+%%% Args are the skip and penalty (usually negative)
+\def\dobreak#1#2{\par\ifdim\lastskip<#1\removelastskip\penalty#2\vskip#1\fi}
+
+%%% Define plain chapter starts, and page on/off switching for it
+% Parameter controlling skip before chapter headings (if needed)
+
+\newskip\chapheadingskip
+
+\def\chapbreak{\dobreak \chapheadingskip {-4000}}
+\def\chappager{\par\vfill\supereject}
+% Because \domark is called before \chapoddpage, the filler page will
+% get the headings for the next chapter, which is wrong. But we don't
+% care -- we just disable all headings on the filler page.
+\def\chapoddpage{%
+ \chappager
+ \ifodd\pageno \else
+ \begingroup
+ \evenheadline={\hfil}\evenfootline={\hfil}%
+ \oddheadline={\hfil}\oddfootline={\hfil}%
+ \hbox to 0pt{}%
+ \chappager
+ \endgroup
+ \fi
+}
+
+\def\setchapternewpage #1 {\csname CHAPPAG#1\endcsname}
+
+\def\CHAPPAGoff{%
+\global\let\contentsalignmacro = \chappager
+\global\let\pchapsepmacro=\chapbreak
+\global\let\pagealignmacro=\chappager}
+
+\def\CHAPPAGon{%
+\global\let\contentsalignmacro = \chappager
+\global\let\pchapsepmacro=\chappager
+\global\let\pagealignmacro=\chappager
+\global\def\HEADINGSon{\HEADINGSsingle}}
+
+\def\CHAPPAGodd{%
+\global\let\contentsalignmacro = \chapoddpage
+\global\let\pchapsepmacro=\chapoddpage
+\global\let\pagealignmacro=\chapoddpage
+\global\def\HEADINGSon{\HEADINGSdouble}}
+
+\CHAPPAGon
+
+% Chapter opening.
+%
+% #1 is the text, #2 is the section type (Ynumbered, Ynothing,
+% Yappendix, Yomitfromtoc), #3 the chapter number.
+%
+% To test against our argument.
+\def\Ynothingkeyword{Ynothing}
+\def\Yomitfromtockeyword{Yomitfromtoc}
+\def\Yappendixkeyword{Yappendix}
+%
+\def\chapmacro#1#2#3{%
+ % Insert the first mark before the heading break (see notes for \domark).
+ \let\prevchapterdefs=\lastchapterdefs
+ \let\prevsectiondefs=\lastsectiondefs
+ \gdef\lastsectiondefs{\gdef\thissectionname{}\gdef\thissectionnum{}%
+ \gdef\thissection{}}%
+ %
+ \def\temptype{#2}%
+ \ifx\temptype\Ynothingkeyword
+ \gdef\lastchapterdefs{\gdef\thischaptername{#1}\gdef\thischapternum{}%
+ \gdef\thischapter{\thischaptername}}%
+ \else\ifx\temptype\Yomitfromtockeyword
+ \gdef\lastchapterdefs{\gdef\thischaptername{#1}\gdef\thischapternum{}%
+ \gdef\thischapter{}}%
+ \else\ifx\temptype\Yappendixkeyword
+ \toks0={#1}%
+ \xdef\lastchapterdefs{%
+ \gdef\noexpand\thischaptername{\the\toks0}%
+ \gdef\noexpand\thischapternum{\appendixletter}%
+ % \noexpand\putwordAppendix avoids expanding indigestible
+ % commands in some of the translations.
+ \gdef\noexpand\thischapter{\noexpand\putwordAppendix{}
+ \noexpand\thischapternum:
+ \noexpand\thischaptername}%
+ }%
+ \else
+ \toks0={#1}%
+ \xdef\lastchapterdefs{%
+ \gdef\noexpand\thischaptername{\the\toks0}%
+ \gdef\noexpand\thischapternum{\the\chapno}%
+ % \noexpand\putwordChapter avoids expanding indigestible
+ % commands in some of the translations.
+ \gdef\noexpand\thischapter{\noexpand\putwordChapter{}
+ \noexpand\thischapternum:
+ \noexpand\thischaptername}%
+ }%
+ \fi\fi\fi
+ %
+ % Output the mark. Pass it through \safewhatsit, to take care of
+ % the preceding space.
+ \safewhatsit\domark
+ %
+ % Insert the chapter heading break.
+ \pchapsepmacro
+ %
+ % Now the second mark, after the heading break. No break points
+ % between here and the heading.
+ \let\prevchapterdefs=\lastchapterdefs
+ \let\prevsectiondefs=\lastsectiondefs
+ \domark
+ %
+ {%
+ \chapfonts \rmisbold
+ %
+ % Have to define \lastsection before calling \donoderef, because the
+ % xref code eventually uses it. On the other hand, it has to be called
+ % after \pchapsepmacro, or the headline will change too soon.
+ \gdef\lastsection{#1}%
+ %
+ % Only insert the separating space if we have a chapter/appendix
+ % number, and don't print the unnumbered ``number''.
+ \ifx\temptype\Ynothingkeyword
+ \setbox0 = \hbox{}%
+ \def\toctype{unnchap}%
+ \else\ifx\temptype\Yomitfromtockeyword
+ \setbox0 = \hbox{}% contents like unnumbered, but no toc entry
+ \def\toctype{omit}%
+ \else\ifx\temptype\Yappendixkeyword
+ \setbox0 = \hbox{\putwordAppendix{} #3\enspace}%
+ \def\toctype{app}%
+ \else
+ \setbox0 = \hbox{#3\enspace}%
+ \def\toctype{numchap}%
+ \fi\fi\fi
+ %
+ % Write the toc entry for this chapter. Must come before the
+ % \donoderef, because we include the current node name in the toc
+ % entry, and \donoderef resets it to empty.
+ \writetocentry{\toctype}{#1}{#3}%
+ %
+ % For pdftex, we have to write out the node definition (aka, make
+ % the pdfdest) after any page break, but before the actual text has
+ % been typeset. If the destination for the pdf outline is after the
+ % text, then jumping from the outline may wind up with the text not
+ % being visible, for instance under high magnification.
+ \donoderef{#2}%
+ %
+ % Typeset the actual heading.
+ \nobreak % Avoid page breaks at the interline glue.
+ \vbox{\hyphenpenalty=10000 \tolerance=5000 \parindent=0pt \ptexraggedright
+ \hangindent=\wd0 \centerparametersmaybe
+ \unhbox0 #1\par}%
+ }%
+ \nobreak\bigskip % no page break after a chapter title
+ \nobreak
+}
+
+% @centerchap -- centered and unnumbered.
+\let\centerparametersmaybe = \relax
+\def\centerparameters{%
+ \advance\rightskip by 3\rightskip
+ \leftskip = \rightskip
+ \parfillskip = 0pt
+}
+
+
+% I don't think this chapter style is supported any more, so I'm not
+% updating it with the new noderef stuff. We'll see. --karl, 11aug03.
+%
+\def\setchapterstyle #1 {\csname CHAPF#1\endcsname}
+%
+\def\unnchfopen #1{%
+\chapoddpage {\chapfonts \vbox{\hyphenpenalty=10000\tolerance=5000
+ \parindent=0pt\ptexraggedright
+ \rmisbold #1\hfill}}\bigskip \par\nobreak
+}
+\def\chfopen #1#2{\chapoddpage {\chapfonts
+\vbox to 3in{\vfil \hbox to\hsize{\hfil #2} \hbox to\hsize{\hfil #1} \vfil}}%
+\par\penalty 5000 %
+}
+\def\centerchfopen #1{%
+\chapoddpage {\chapfonts \vbox{\hyphenpenalty=10000\tolerance=5000
+ \parindent=0pt
+ \hfill {\rmisbold #1}\hfill}}\bigskip \par\nobreak
+}
+\def\CHAPFopen{%
+ \global\let\chapmacro=\chfopen
+ \global\let\centerchapmacro=\centerchfopen}
+
+
+% Section titles. These macros combine the section number parts and
+% call the generic \sectionheading to do the printing.
+%
+\newskip\secheadingskip
+\def\secheadingbreak{\dobreak \secheadingskip{-1000}}
+
+% Subsection titles.
+\newskip\subsecheadingskip
+\def\subsecheadingbreak{\dobreak \subsecheadingskip{-500}}
+
+% Subsubsection titles.
+\def\subsubsecheadingskip{\subsecheadingskip}
+\def\subsubsecheadingbreak{\subsecheadingbreak}
+
+
+% Print any size, any type, section title.
+%
+% #1 is the text, #2 is the section level (sec/subsec/subsubsec), #3 is
+% the section type for xrefs (Ynumbered, Ynothing, Yappendix), #4 is the
+% section number.
+%
+\def\seckeyword{sec}
+%
+\def\sectionheading#1#2#3#4{%
+ {%
+ % Switch to the right set of fonts.
+ \csname #2fonts\endcsname \rmisbold
+ %
+ \def\sectionlevel{#2}%
+ \def\temptype{#3}%
+ %
+ % Insert first mark before the heading break (see notes for \domark).
+ \let\prevsectiondefs=\lastsectiondefs
+ \ifx\temptype\Ynothingkeyword
+ \ifx\sectionlevel\seckeyword
+ \gdef\lastsectiondefs{\gdef\thissectionname{#1}\gdef\thissectionnum{}%
+ \gdef\thissection{\thissectionname}}%
+ \fi
+ \else\ifx\temptype\Yomitfromtockeyword
+ % Don't redefine \thissection.
+ \else\ifx\temptype\Yappendixkeyword
+ \ifx\sectionlevel\seckeyword
+ \toks0={#1}%
+ \xdef\lastsectiondefs{%
+ \gdef\noexpand\thissectionname{\the\toks0}%
+ \gdef\noexpand\thissectionnum{#4}%
+ % \noexpand\putwordSection avoids expanding indigestible
+ % commands in some of the translations.
+ \gdef\noexpand\thissection{\noexpand\putwordSection{}
+ \noexpand\thissectionnum:
+ \noexpand\thissectionname}%
+ }%
+ \fi
+ \else
+ \ifx\sectionlevel\seckeyword
+ \toks0={#1}%
+ \xdef\lastsectiondefs{%
+ \gdef\noexpand\thissectionname{\the\toks0}%
+ \gdef\noexpand\thissectionnum{#4}%
+ % \noexpand\putwordSection avoids expanding indigestible
+ % commands in some of the translations.
+ \gdef\noexpand\thissection{\noexpand\putwordSection{}
+ \noexpand\thissectionnum:
+ \noexpand\thissectionname}%
+ }%
+ \fi
+ \fi\fi\fi
+ %
+ % Go into vertical mode. Usually we'll already be there, but we
+ % don't want the following whatsit to end up in a preceding paragraph
+ % if the document didn't happen to have a blank line.
+ \par
+ %
+ % Output the mark. Pass it through \safewhatsit, to take care of
+ % the preceding space.
+ \safewhatsit\domark
+ %
+ % Insert space above the heading.
+ \csname #2headingbreak\endcsname
+ %
+ % Now the second mark, after the heading break. No break points
+ % between here and the heading.
+ \let\prevsectiondefs=\lastsectiondefs
+ \domark
+ %
+ % Only insert the space after the number if we have a section number.
+ \ifx\temptype\Ynothingkeyword
+ \setbox0 = \hbox{}%
+ \def\toctype{unn}%
+ \gdef\lastsection{#1}%
+ \else\ifx\temptype\Yomitfromtockeyword
+ % for @headings -- no section number, don't include in toc,
+ % and don't redefine \lastsection.
+ \setbox0 = \hbox{}%
+ \def\toctype{omit}%
+ \let\sectionlevel=\empty
+ \else\ifx\temptype\Yappendixkeyword
+ \setbox0 = \hbox{#4\enspace}%
+ \def\toctype{app}%
+ \gdef\lastsection{#1}%
+ \else
+ \setbox0 = \hbox{#4\enspace}%
+ \def\toctype{num}%
+ \gdef\lastsection{#1}%
+ \fi\fi\fi
+ %
+ % Write the toc entry (before \donoderef). See comments in \chapmacro.
+ \writetocentry{\toctype\sectionlevel}{#1}{#4}%
+ %
+ % Write the node reference (= pdf destination for pdftex).
+ % Again, see comments in \chapmacro.
+ \donoderef{#3}%
+ %
+ % Interline glue will be inserted when the vbox is completed.
+ % That glue will be a valid breakpoint for the page, since it'll be
+ % preceded by a whatsit (usually from the \donoderef, or from the
+ % \writetocentry if there was no node). We don't want to allow that
+ % break, since then the whatsits could end up on page n while the
+ % section is on page n+1, thus toc/etc. are wrong. Debian bug 276000.
+ \nobreak
+ %
+ % Output the actual section heading.
+ \vbox{\hyphenpenalty=10000 \tolerance=5000 \parindent=0pt \ptexraggedright
+ \hangindent=\wd0 % zero if no section number
+ \unhbox0 #1}%
+ }%
+ % Add extra space after the heading -- half of whatever came above it.
+ % Don't allow stretch, though.
+ \kern .5 \csname #2headingskip\endcsname
+ %
+ % Do not let the kern be a potential breakpoint, as it would be if it
+ % was followed by glue.
+ \nobreak
+ %
+ % We'll almost certainly start a paragraph next, so don't let that
+ % glue accumulate. (Not a breakpoint because it's preceded by a
+ % discardable item.)
+ \vskip-\parskip
+ %
+ % This is purely so the last item on the list is a known \penalty >
+ % 10000. This is so \startdefun can avoid allowing breakpoints after
+ % section headings. Otherwise, it would insert a valid breakpoint between:
+ %
+ % @section sec-whatever
+ % @deffn def-whatever
+ \penalty 10001
+}
+
+
+\message{toc,}
+% Table of contents.
+\newwrite\tocfile
+
+% Write an entry to the toc file, opening it if necessary.
+% Called from @chapter, etc.
+%
+% Example usage: \writetocentry{sec}{Section Name}{\the\chapno.\the\secno}
+% We append the current node name (if any) and page number as additional
+% arguments for the \{chap,sec,...}entry macros which will eventually
+% read this. The node name is used in the pdf outlines as the
+% destination to jump to.
+%
+% We open the .toc file for writing here instead of at @setfilename (or
+% any other fixed time) so that @contents can be anywhere in the document.
+% But if #1 is `omit', then we don't do anything. This is used for the
+% table of contents chapter openings themselves.
+%
+\newif\iftocfileopened
+\def\omitkeyword{omit}%
+%
+\def\writetocentry#1#2#3{%
+ \edef\writetoctype{#1}%
+ \ifx\writetoctype\omitkeyword \else
+ \iftocfileopened\else
+ \immediate\openout\tocfile = \jobname.toc
+ \global\tocfileopenedtrue
+ \fi
+ %
+ \iflinks
+ {\atdummies
+ \edef\temp{%
+ \write\tocfile{@#1entry{#2}{#3}{\lastnode}{\noexpand\folio}}}%
+ \temp
+ }%
+ \fi
+ \fi
+ %
+ % Tell \shipout to create a pdf destination on each page, if we're
+ % writing pdf. These are used in the table of contents. We can't
+ % just write one on every page because the title pages are numbered
+ % 1 and 2 (the page numbers aren't printed), and so are the first
+ % two pages of the document. Thus, we'd have two destinations named
+ % `1', and two named `2'.
+ \ifpdf \global\pdfmakepagedesttrue \fi
+}
+
+
+% These characters do not print properly in the Computer Modern roman
+% fonts, so we must take special care. This is more or less redundant
+% with the Texinfo input format setup at the end of this file.
+%
+\def\activecatcodes{%
+ \catcode`\"=\active
+ \catcode`\$=\active
+ \catcode`\<=\active
+ \catcode`\>=\active
+ \catcode`\\=\active
+ \catcode`\^=\active
+ \catcode`\_=\active
+ \catcode`\|=\active
+ \catcode`\~=\active
+}
+
+
+% Read the toc file, which is essentially Texinfo input.
+\def\readtocfile{%
+ \setupdatafile
+ \activecatcodes
+ \input \tocreadfilename
+}
+
+\newskip\contentsrightmargin \contentsrightmargin=1in
+\newcount\savepageno
+\newcount\lastnegativepageno \lastnegativepageno = -1
+
+% Prepare to read what we've written to \tocfile.
+%
+\def\startcontents#1{%
+ % If @setchapternewpage on, and @headings double, the contents should
+ % start on an odd page, unlike chapters. Thus, we maintain
+ % \contentsalignmacro in parallel with \pagealignmacro.
+ % From: Torbjorn Granlund <tege at matematik.su.se>
+ \contentsalignmacro
+ \immediate\closeout\tocfile
+ %
+ % Don't need to put `Contents' or `Short Contents' in the headline.
+ % It is abundantly clear what they are.
+ \chapmacro{#1}{Yomitfromtoc}{}%
+ %
+ \savepageno = \pageno
+ \begingroup % Set up to handle contents files properly.
+ \raggedbottom % Worry more about breakpoints than the bottom.
+ \advance\hsize by -\contentsrightmargin % Don't use the full line length.
+ %
+ % Roman numerals for page numbers.
+ \ifnum \pageno>0 \global\pageno = \lastnegativepageno \fi
+}
+
+% redefined for the two-volume lispref. We always output on
+% \jobname.toc even if this is redefined.
+%
+\def\tocreadfilename{\jobname.toc}
+
+% Normal (long) toc.
+%
+\def\contents{%
+ \startcontents{\putwordTOC}%
+ \openin 1 \tocreadfilename\space
+ \ifeof 1 \else
+ \readtocfile
+ \fi
+ \vfill \eject
+ \contentsalignmacro % in case @setchapternewpage odd is in effect
+ \ifeof 1 \else
+ \pdfmakeoutlines
+ \fi
+ \closein 1
+ \endgroup
+ \lastnegativepageno = \pageno
+ \global\pageno = \savepageno
+}
+
+% And just the chapters.
+\def\summarycontents{%
+ \startcontents{\putwordShortTOC}%
+ %
+ \let\numchapentry = \shortchapentry
+ \let\appentry = \shortchapentry
+ \let\unnchapentry = \shortunnchapentry
+ % We want a true roman here for the page numbers.
+ \secfonts
+ \let\rm=\shortcontrm \let\bf=\shortcontbf
+ \let\sl=\shortcontsl \let\tt=\shortconttt
+ \rm
+ \hyphenpenalty = 10000
+ \advance\baselineskip by 1pt % Open it up a little.
+ \def\numsecentry##1##2##3##4{}
+ \let\appsecentry = \numsecentry
+ \let\unnsecentry = \numsecentry
+ \let\numsubsecentry = \numsecentry
+ \let\appsubsecentry = \numsecentry
+ \let\unnsubsecentry = \numsecentry
+ \let\numsubsubsecentry = \numsecentry
+ \let\appsubsubsecentry = \numsecentry
+ \let\unnsubsubsecentry = \numsecentry
+ \openin 1 \tocreadfilename\space
+ \ifeof 1 \else
+ \readtocfile
+ \fi
+ \closein 1
+ \vfill \eject
+ \contentsalignmacro % in case @setchapternewpage odd is in effect
+ \endgroup
+ \lastnegativepageno = \pageno
+ \global\pageno = \savepageno
+}
+\let\shortcontents = \summarycontents
+
+% Typeset the label for a chapter or appendix for the short contents.
+% The arg is, e.g., `A' for an appendix, or `3' for a chapter.
+%
+\def\shortchaplabel#1{%
+ % This space should be enough, since a single number is .5em, and the
+ % widest letter (M) is 1em, at least in the Computer Modern fonts.
+ % But use \hss just in case.
+ % (This space doesn't include the extra space that gets added after
+ % the label; that gets put in by \shortchapentry above.)
+ %
+ % We'd like to right-justify chapter numbers, but that looks strange
+ % with appendix letters. And right-justifying numbers and
+ % left-justifying letters looks strange when there is less than 10
+ % chapters. Have to read the whole toc once to know how many chapters
+ % there are before deciding ...
+ \hbox to 1em{#1\hss}%
+}
+
+% These macros generate individual entries in the table of contents.
+% The first argument is the chapter or section name.
+% The last argument is the page number.
+% The arguments in between are the chapter number, section number, ...
+
+% Chapters, in the main contents.
+\def\numchapentry#1#2#3#4{\dochapentry{#2\labelspace#1}{#4}}
+%
+% Chapters, in the short toc.
+% See comments in \dochapentry re vbox and related settings.
+\def\shortchapentry#1#2#3#4{%
+ \tocentry{\shortchaplabel{#2}\labelspace #1}{\doshortpageno\bgroup#4\egroup}%
+}
+
+% Appendices, in the main contents.
+% Need the word Appendix, and a fixed-size box.
+%
+\def\appendixbox#1{%
+ % We use M since it's probably the widest letter.
+ \setbox0 = \hbox{\putwordAppendix{} M}%
+ \hbox to \wd0{\putwordAppendix{} #1\hss}}
+%
+\def\appentry#1#2#3#4{\dochapentry{\appendixbox{#2}\labelspace#1}{#4}}
+
+% Unnumbered chapters.
+\def\unnchapentry#1#2#3#4{\dochapentry{#1}{#4}}
+\def\shortunnchapentry#1#2#3#4{\tocentry{#1}{\doshortpageno\bgroup#4\egroup}}
+
+% Sections.
+\def\numsecentry#1#2#3#4{\dosecentry{#2\labelspace#1}{#4}}
+\let\appsecentry=\numsecentry
+\def\unnsecentry#1#2#3#4{\dosecentry{#1}{#4}}
+
+% Subsections.
+\def\numsubsecentry#1#2#3#4{\dosubsecentry{#2\labelspace#1}{#4}}
+\let\appsubsecentry=\numsubsecentry
+\def\unnsubsecentry#1#2#3#4{\dosubsecentry{#1}{#4}}
+
+% And subsubsections.
+\def\numsubsubsecentry#1#2#3#4{\dosubsubsecentry{#2\labelspace#1}{#4}}
+\let\appsubsubsecentry=\numsubsubsecentry
+\def\unnsubsubsecentry#1#2#3#4{\dosubsubsecentry{#1}{#4}}
+
+% This parameter controls the indentation of the various levels.
+% Same as \defaultparindent.
+\newdimen\tocindent \tocindent = 15pt
+
+% Now for the actual typesetting. In all these, #1 is the text and #2 is the
+% page number.
+%
+% If the toc has to be broken over pages, we want it to be at chapters
+% if at all possible; hence the \penalty.
+\def\dochapentry#1#2{%
+ \penalty-300 \vskip1\baselineskip plus.33\baselineskip minus.25\baselineskip
+ \begingroup
+ \chapentryfonts
+ \tocentry{#1}{\dopageno\bgroup#2\egroup}%
+ \endgroup
+ \nobreak\vskip .25\baselineskip plus.1\baselineskip
+}
+
+\def\dosecentry#1#2{\begingroup
+ \secentryfonts \leftskip=\tocindent
+ \tocentry{#1}{\dopageno\bgroup#2\egroup}%
+\endgroup}
+
+\def\dosubsecentry#1#2{\begingroup
+ \subsecentryfonts \leftskip=2\tocindent
+ \tocentry{#1}{\dopageno\bgroup#2\egroup}%
+\endgroup}
+
+\def\dosubsubsecentry#1#2{\begingroup
+ \subsubsecentryfonts \leftskip=3\tocindent
+ \tocentry{#1}{\dopageno\bgroup#2\egroup}%
+\endgroup}
+
+% We use the same \entry macro as for the index entries.
+\let\tocentry = \entry
+
+% Space between chapter (or whatever) number and the title.
+\def\labelspace{\hskip1em \relax}
+
+\def\dopageno#1{{\rm #1}}
+\def\doshortpageno#1{{\rm #1}}
+
+\def\chapentryfonts{\secfonts \rm}
+\def\secentryfonts{\textfonts}
+\def\subsecentryfonts{\textfonts}
+\def\subsubsecentryfonts{\textfonts}
+
+
+\message{environments,}
+% @foo ... @end foo.
+
+% @tex ... @end tex escapes into raw Tex temporarily.
+% One exception: @ is still an escape character, so that @end tex works.
+% But \@ or @@ will get a plain tex @ character.
+
+\envdef\tex{%
+ \setupmarkupstyle{tex}%
+ \catcode `\\=0 \catcode `\{=1 \catcode `\}=2
+ \catcode `\$=3 \catcode `\&=4 \catcode `\#=6
+ \catcode `\^=7 \catcode `\_=8 \catcode `\~=\active \let~=\tie
+ \catcode `\%=14
+ \catcode `\+=\other
+ \catcode `\"=\other
+ \catcode `\|=\other
+ \catcode `\<=\other
+ \catcode `\>=\other
+ \catcode`\`=\other
+ \catcode`\'=\other
+ \escapechar=`\\
+ %
+ \let\b=\ptexb
+ \let\bullet=\ptexbullet
+ \let\c=\ptexc
+ \let\,=\ptexcomma
+ \let\.=\ptexdot
+ \let\dots=\ptexdots
+ \let\equiv=\ptexequiv
+ \let\!=\ptexexclam
+ \let\i=\ptexi
+ \let\indent=\ptexindent
+ \let\noindent=\ptexnoindent
+ \let\{=\ptexlbrace
+ \let\+=\tabalign
+ \let\}=\ptexrbrace
+ \let\/=\ptexslash
+ \let\*=\ptexstar
+ \let\t=\ptext
+ \expandafter \let\csname top\endcsname=\ptextop % outer
+ \let\frenchspacing=\plainfrenchspacing
+ %
+ \def\endldots{\mathinner{\ldots\ldots\ldots\ldots}}%
+ \def\enddots{\relax\ifmmode\endldots\else$\mathsurround=0pt \endldots\,$\fi}%
+ \def\@{@}%
+}
+% There is no need to define \Etex.
+
+% Define @lisp ... @end lisp.
+% @lisp environment forms a group so it can rebind things,
+% including the definition of @end lisp (which normally is erroneous).
+
+% Amount to narrow the margins by for @lisp.
+\newskip\lispnarrowing \lispnarrowing=0.4in
+
+% This is the definition that ^^M gets inside @lisp, @example, and other
+% such environments. \null is better than a space, since it doesn't
+% have any width.
+\def\lisppar{\null\endgraf}
+
+% This space is always present above and below environments.
+\newskip\envskipamount \envskipamount = 0pt
+
+% Make spacing and below environment symmetrical. We use \parskip here
+% to help in doing that, since in @example-like environments \parskip
+% is reset to zero; thus the \afterenvbreak inserts no space -- but the
+% start of the next paragraph will insert \parskip.
+%
+\def\aboveenvbreak{{%
+ % =10000 instead of <10000 because of a special case in \itemzzz and
+ % \sectionheading, q.v.
+ \ifnum \lastpenalty=10000 \else
+ \advance\envskipamount by \parskip
+ \endgraf
+ \ifdim\lastskip<\envskipamount
+ \removelastskip
+ % it's not a good place to break if the last penalty was \nobreak
+ % or better ...
+ \ifnum\lastpenalty<10000 \penalty-50 \fi
+ \vskip\envskipamount
+ \fi
+ \fi
+}}
+
+\let\afterenvbreak = \aboveenvbreak
+
+% \nonarrowing is a flag. If "set", @lisp etc don't narrow margins; it will
+% also clear it, so that its embedded environments do the narrowing again.
+\let\nonarrowing=\relax
+
+% @cartouche ... @end cartouche: draw rectangle w/rounded corners around
+% environment contents.
+\font\circle=lcircle10
+\newdimen\circthick
+\newdimen\cartouter\newdimen\cartinner
+\newskip\normbskip\newskip\normpskip\newskip\normlskip
+\circthick=\fontdimen8\circle
+%
+\def\ctl{{\circle\char'013\hskip -6pt}}% 6pt from pl file: 1/2charwidth
+\def\ctr{{\hskip 6pt\circle\char'010}}
+\def\cbl{{\circle\char'012\hskip -6pt}}
+\def\cbr{{\hskip 6pt\circle\char'011}}
+\def\carttop{\hbox to \cartouter{\hskip\lskip
+ \ctl\leaders\hrule height\circthick\hfil\ctr
+ \hskip\rskip}}
+\def\cartbot{\hbox to \cartouter{\hskip\lskip
+ \cbl\leaders\hrule height\circthick\hfil\cbr
+ \hskip\rskip}}
+%
+\newskip\lskip\newskip\rskip
+
+\envdef\cartouche{%
+ \ifhmode\par\fi % can't be in the midst of a paragraph.
+ \startsavinginserts
+ \lskip=\leftskip \rskip=\rightskip
+ \leftskip=0pt\rightskip=0pt % we want these *outside*.
+ \cartinner=\hsize \advance\cartinner by-\lskip
+ \advance\cartinner by-\rskip
+ \cartouter=\hsize
+ \advance\cartouter by 18.4pt % allow for 3pt kerns on either
+ % side, and for 6pt waste from
+ % each corner char, and rule thickness
+ \normbskip=\baselineskip \normpskip=\parskip \normlskip=\lineskip
+ % Flag to tell @lisp, etc., not to narrow margin.
+ \let\nonarrowing = t%
+ \vbox\bgroup
+ \baselineskip=0pt\parskip=0pt\lineskip=0pt
+ \carttop
+ \hbox\bgroup
+ \hskip\lskip
+ \vrule\kern3pt
+ \vbox\bgroup
+ \kern3pt
+ \hsize=\cartinner
+ \baselineskip=\normbskip
+ \lineskip=\normlskip
+ \parskip=\normpskip
+ \vskip -\parskip
+ \comment % For explanation, see the end of \def\group.
+}
+\def\Ecartouche{%
+ \ifhmode\par\fi
+ \kern3pt
+ \egroup
+ \kern3pt\vrule
+ \hskip\rskip
+ \egroup
+ \cartbot
+ \egroup
+ \checkinserts
+}
+
+
+% This macro is called at the beginning of all the @example variants,
+% inside a group.
+\newdimen\nonfillparindent
+\def\nonfillstart{%
+ \aboveenvbreak
+ \hfuzz = 12pt % Don't be fussy
+ \sepspaces % Make spaces be word-separators rather than space tokens.
+ \let\par = \lisppar % don't ignore blank lines
+ \obeylines % each line of input is a line of output
+ \parskip = 0pt
+ % Turn off paragraph indentation but redefine \indent to emulate
+ % the normal \indent.
+ \nonfillparindent=\parindent
+ \parindent = 0pt
+ \let\indent\nonfillindent
+ %
+ \emergencystretch = 0pt % don't try to avoid overfull boxes
+ \ifx\nonarrowing\relax
+ \advance \leftskip by \lispnarrowing
+ \exdentamount=\lispnarrowing
+ \else
+ \let\nonarrowing = \relax
+ \fi
+ \let\exdent=\nofillexdent
+}
+
+\begingroup
+\obeyspaces
+% We want to swallow spaces (but not other tokens) after the fake
+% @indent in our nonfill-environments, where spaces are normally
+% active and set to @tie, resulting in them not being ignored after
+% @indent.
+\gdef\nonfillindent{\futurelet\temp\nonfillindentcheck}%
+\gdef\nonfillindentcheck{%
+\ifx\temp %
+\expandafter\nonfillindentgobble%
+\else%
+\leavevmode\nonfillindentbox%
+\fi%
+}%
+\endgroup
+\def\nonfillindentgobble#1{\nonfillindent}
+\def\nonfillindentbox{\hbox to \nonfillparindent{\hss}}
+
+% If you want all examples etc. small: @set dispenvsize small.
+% If you want even small examples the full size: @set dispenvsize nosmall.
+% This affects the following displayed environments:
+% @example, @display, @format, @lisp
+%
+\def\smallword{small}
+\def\nosmallword{nosmall}
+\let\SETdispenvsize\relax
+\def\setnormaldispenv{%
+ \ifx\SETdispenvsize\smallword
+ % end paragraph for sake of leading, in case document has no blank
+ % line. This is redundant with what happens in \aboveenvbreak, but
+ % we need to do it before changing the fonts, and it's inconvenient
+ % to change the fonts afterward.
+ \ifnum \lastpenalty=10000 \else \endgraf \fi
+ \smallexamplefonts \rm
+ \fi
+}
+\def\setsmalldispenv{%
+ \ifx\SETdispenvsize\nosmallword
+ \else
+ \ifnum \lastpenalty=10000 \else \endgraf \fi
+ \smallexamplefonts \rm
+ \fi
+}
+
+% We often define two environments, @foo and @smallfoo.
+% Let's do it by one command:
+\def\makedispenv #1#2{
+ \expandafter\envdef\csname#1\endcsname {\setnormaldispenv #2}
+ \expandafter\envdef\csname small#1\endcsname {\setsmalldispenv #2}
+ \expandafter\let\csname E#1\endcsname \afterenvbreak
+ \expandafter\let\csname Esmall#1\endcsname \afterenvbreak
+}
+
+% Define two synonyms:
+\def\maketwodispenvs #1#2#3{
+ \makedispenv{#1}{#3}
+ \makedispenv{#2}{#3}
+}
+
+% @lisp: indented, narrowed, typewriter font; @example: same as @lisp.
+%
+% @smallexample and @smalllisp: use smaller fonts.
+% Originally contributed by Pavel at xerox.
+%
+\maketwodispenvs {lisp}{example}{%
+ \nonfillstart
+ \tt\setupmarkupstyle{example}%
+ \let\kbdfont = \kbdexamplefont % Allow @kbd to do something special.
+ \gobble % eat return
+}
+% @display/@smalldisplay: same as @lisp except keep current font.
+%
+\makedispenv {display}{%
+ \nonfillstart
+ \gobble
+}
+
+% @format/@smallformat: same as @display except don't narrow margins.
+%
+\makedispenv{format}{%
+ \let\nonarrowing = t%
+ \nonfillstart
+ \gobble
+}
+
+% @flushleft: same as @format, but doesn't obey \SETdispenvsize.
+\envdef\flushleft{%
+ \let\nonarrowing = t%
+ \nonfillstart
+ \gobble
+}
+\let\Eflushleft = \afterenvbreak
+
+% @flushright.
+%
+\envdef\flushright{%
+ \let\nonarrowing = t%
+ \nonfillstart
+ \advance\leftskip by 0pt plus 1fill
+ \gobble
+}
+\let\Eflushright = \afterenvbreak
+
+
+% @raggedright does more-or-less normal line breaking but no right
+% justification. From plain.tex.
+\envdef\raggedright{%
+ \rightskip0pt plus2em \spaceskip.3333em \xspaceskip.5em\relax
+}
+\let\Eraggedright\par
+
+\envdef\raggedleft{%
+ \parindent=0pt \leftskip0pt plus2em
+ \spaceskip.3333em \xspaceskip.5em \parfillskip=0pt
+ \hbadness=10000 % Last line will usually be underfull, so turn off
+ % badness reporting.
+}
+\let\Eraggedleft\par
+
+\envdef\raggedcenter{%
+ \parindent=0pt \rightskip0pt plus1em \leftskip0pt plus1em
+ \spaceskip.3333em \xspaceskip.5em \parfillskip=0pt
+ \hbadness=10000 % Last line will usually be underfull, so turn off
+ % badness reporting.
+}
+\let\Eraggedcenter\par
+
+
+% @quotation does normal linebreaking (hence we can't use \nonfillstart)
+% and narrows the margins. We keep \parskip nonzero in general, since
+% we're doing normal filling. So, when using \aboveenvbreak and
+% \afterenvbreak, temporarily make \parskip 0.
+%
+\def\quotationstart{%
+ {\parskip=0pt \aboveenvbreak}% because \aboveenvbreak inserts \parskip
+ \parindent=0pt
+ %
+ % @cartouche defines \nonarrowing to inhibit narrowing at next level down.
+ \ifx\nonarrowing\relax
+ \advance\leftskip by \lispnarrowing
+ \advance\rightskip by \lispnarrowing
+ \exdentamount = \lispnarrowing
+ \else
+ \let\nonarrowing = \relax
+ \fi
+ \parsearg\quotationlabel
+}
+
+\envdef\quotation{%
+ \setnormaldispenv
+ \quotationstart
+}
+
+\envdef\smallquotation{%
+ \setsmalldispenv
+ \quotationstart
+}
+\let\Esmallquotation = \Equotation
+
+% We have retained a nonzero parskip for the environment, since we're
+% doing normal filling.
+%
+\def\Equotation{%
+ \par
+ \ifx\quotationauthor\undefined\else
+ % indent a bit.
+ \leftline{\kern 2\leftskip \sl ---\quotationauthor}%
+ \fi
+ {\parskip=0pt \afterenvbreak}%
+}
+
+% If we're given an argument, typeset it in bold with a colon after.
+\def\quotationlabel#1{%
+ \def\temp{#1}%
+ \ifx\temp\empty \else
+ {\bf #1: }%
+ \fi
+}
+
+
+% LaTeX-like @verbatim... at end verbatim and @verb{<char>...<char>}
+% If we want to allow any <char> as delimiter,
+% we need the curly braces so that makeinfo sees the @verb command, eg:
+% `@verbx...x' would look like the '@verbx' command. --janneke at gnu.org
+%
+% [Knuth]: Donald Ervin Knuth, 1996. The TeXbook.
+%
+% [Knuth] p.344; only we need to do the other characters Texinfo sets
+% active too. Otherwise, they get lost as the first character on a
+% verbatim line.
+\def\dospecials{%
+ \do\ \do\\\do\{\do\}\do\$\do\&%
+ \do\#\do\^\do\^^K\do\_\do\^^A\do\%\do\~%
+ \do\<\do\>\do\|\do\@\do+\do\"%
+ % Don't do the quotes -- if we do, @set txicodequoteundirected and
+ % @set txicodequotebacktick will not have effect on @verb and
+ % @verbatim, and ?` and !` ligatures won't get disabled.
+ %\do\`\do\'%
+}
+%
+% [Knuth] p. 380
+\def\uncatcodespecials{%
+ \def\do##1{\catcode`##1=\other}\dospecials}
+%
+% Setup for the @verb command.
+%
+% Eight spaces for a tab
+\begingroup
+ \catcode`\^^I=\active
+ \gdef\tabeightspaces{\catcode`\^^I=\active\def^^I{\ \ \ \ \ \ \ \ }}
+\endgroup
+%
+\def\setupverb{%
+ \tt % easiest (and conventionally used) font for verbatim
+ \def\par{\leavevmode\endgraf}%
+ \setupmarkupstyle{verb}%
+ \tabeightspaces
+ % Respect line breaks,
+ % print special symbols as themselves, and
+ % make each space count
+ % must do in this order:
+ \obeylines \uncatcodespecials \sepspaces
+}
+
+% Setup for the @verbatim environment
+%
+% Real tab expansion
+\newdimen\tabw \setbox0=\hbox{\tt\space} \tabw=8\wd0 % tab amount
+%
+\def\starttabbox{\setbox0=\hbox\bgroup}
+%
+\begingroup
+ \catcode`\^^I=\active
+ \gdef\tabexpand{%
+ \catcode`\^^I=\active
+ \def^^I{\leavevmode\egroup
+ \dimen0=\wd0 % the width so far, or since the previous tab
+ \divide\dimen0 by\tabw
+ \multiply\dimen0 by\tabw % compute previous multiple of \tabw
+ \advance\dimen0 by\tabw % advance to next multiple of \tabw
+ \wd0=\dimen0 \box0 \starttabbox
+ }%
+ }
+\endgroup
+
+% start the verbatim environment.
+\def\setupverbatim{%
+ \let\nonarrowing = t%
+ \nonfillstart
+ % Easiest (and conventionally used) font for verbatim
+ \tt
+ \def\par{\leavevmode\egroup\box0\endgraf}%
+ \tabexpand
+ \setupmarkupstyle{verbatim}%
+ % Respect line breaks,
+ % print special symbols as themselves, and
+ % make each space count
+ % must do in this order:
+ \obeylines \uncatcodespecials \sepspaces
+ \everypar{\starttabbox}%
+}
+
+% Do the @verb magic: verbatim text is quoted by unique
+% delimiter characters. Before first delimiter expect a
+% right brace, after last delimiter expect closing brace:
+%
+% \def\doverb'{'<char>#1<char>'}'{#1}
+%
+% [Knuth] p. 382; only eat outer {}
+\begingroup
+ \catcode`[=1\catcode`]=2\catcode`\{=\other\catcode`\}=\other
+ \gdef\doverb{#1[\def\next##1#1}[##1\endgroup]\next]
+\endgroup
+%
+\def\verb{\begingroup\setupverb\doverb}
+%
+%
+% Do the @verbatim magic: define the macro \doverbatim so that
+% the (first) argument ends when '@end verbatim' is reached, ie:
+%
+% \def\doverbatim#1 at end verbatim{#1}
+%
+% For Texinfo it's a lot easier than for LaTeX,
+% because texinfo's \verbatim doesn't stop at '\end{verbatim}':
+% we need not redefine '\', '{' and '}'.
+%
+% Inspired by LaTeX's verbatim command set [latex.ltx]
+%
+\begingroup
+ \catcode`\ =\active
+ \obeylines %
+ % ignore everything up to the first ^^M, that's the newline at the end
+ % of the @verbatim input line itself. Otherwise we get an extra blank
+ % line in the output.
+ \xdef\doverbatim#1^^M#2 at end verbatim{#2\noexpand\end\gobble verbatim}%
+ % We really want {...\end verbatim} in the body of the macro, but
+ % without the active space; thus we have to use \xdef and \gobble.
+\endgroup
+%
+\envdef\verbatim{%
+ \setupverbatim\doverbatim
+}
+\let\Everbatim = \afterenvbreak
+
+
+% @verbatiminclude FILE - insert text of file in verbatim environment.
+%
+\def\verbatiminclude{\parseargusing\filenamecatcodes\doverbatiminclude}
+%
+\def\doverbatiminclude#1{%
+ {%
+ \makevalueexpandable
+ \setupverbatim
+ \indexnofonts % Allow `@@' and other weird things in file names.
+ \input #1
+ \afterenvbreak
+ }%
+}
+
+% @copying ... @end copying.
+% Save the text away for @insertcopying later.
+%
+% We save the uninterpreted tokens, rather than creating a box.
+% Saving the text in a box would be much easier, but then all the
+% typesetting commands (@smallbook, font changes, etc.) have to be done
+% beforehand -- and a) we want @copying to be done first in the source
+% file; b) letting users define the frontmatter in as flexible order as
+% possible is very desirable.
+%
+\def\copying{\checkenv{}\begingroup\scanargctxt\docopying}
+\def\docopying#1 at end copying{\endgroup\def\copyingtext{#1}}
+%
+\def\insertcopying{%
+ \begingroup
+ \parindent = 0pt % paragraph indentation looks wrong on title page
+ \scanexp\copyingtext
+ \endgroup
+}
+
+
+\message{defuns,}
+% @defun etc.
+
+\newskip\defbodyindent \defbodyindent=.4in
+\newskip\defargsindent \defargsindent=50pt
+\newskip\deflastargmargin \deflastargmargin=18pt
+\newcount\defunpenalty
+
+% Start the processing of @deffn:
+\def\startdefun{%
+ \ifnum\lastpenalty<10000
+ \medbreak
+ \defunpenalty=10003 % Will keep this @deffn together with the
+ % following @def command, see below.
+ \else
+ % If there are two @def commands in a row, we'll have a \nobreak,
+ % which is there to keep the function description together with its
+ % header. But if there's nothing but headers, we need to allow a
+ % break somewhere. Check specifically for penalty 10002, inserted
+ % by \printdefunline, instead of 10000, since the sectioning
+ % commands also insert a nobreak penalty, and we don't want to allow
+ % a break between a section heading and a defun.
+ %
+ % As a minor refinement, we avoid "club" headers by signalling
+ % with penalty of 10003 after the very first @deffn in the
+ % sequence (see above), and penalty of 10002 after any following
+ % @def command.
+ \ifnum\lastpenalty=10002 \penalty2000 \else \defunpenalty=10002 \fi
+ %
+ % Similarly, after a section heading, do not allow a break.
+ % But do insert the glue.
+ \medskip % preceded by discardable penalty, so not a breakpoint
+ \fi
+ %
+ \parindent=0in
+ \advance\leftskip by \defbodyindent
+ \exdentamount=\defbodyindent
+}
+
+\def\dodefunx#1{%
+ % First, check whether we are in the right environment:
+ \checkenv#1%
+ %
+ % As above, allow line break if we have multiple x headers in a row.
+ % It's not a great place, though.
+ \ifnum\lastpenalty=10002 \penalty3000 \else \defunpenalty=10002 \fi
+ %
+ % And now, it's time to reuse the body of the original defun:
+ \expandafter\gobbledefun#1%
+}
+\def\gobbledefun#1\startdefun{}
+
+% \printdefunline \deffnheader{text}
+%
+\def\printdefunline#1#2{%
+ \begingroup
+ % call \deffnheader:
+ #1#2 \endheader
+ % common ending:
+ \interlinepenalty = 10000
+ \advance\rightskip by 0pt plus 1fil
+ \endgraf
+ \nobreak\vskip -\parskip
+ \penalty\defunpenalty % signal to \startdefun and \dodefunx
+ % Some of the @defun-type tags do not enable magic parentheses,
+ % rendering the following check redundant. But we don't optimize.
+ \checkparencounts
+ \endgroup
+}
+
+\def\Edefun{\endgraf\medbreak}
+
+% \makedefun{deffn} creates \deffn, \deffnx and \Edeffn;
+% the only thing remaining is to define \deffnheader.
+%
+\def\makedefun#1{%
+ \expandafter\let\csname E#1\endcsname = \Edefun
+ \edef\temp{\noexpand\domakedefun
+ \makecsname{#1}\makecsname{#1x}\makecsname{#1header}}%
+ \temp
+}
+
+% \domakedefun \deffn \deffnx \deffnheader
+%
+% Define \deffn and \deffnx, without parameters.
+% \deffnheader has to be defined explicitly.
+%
+\def\domakedefun#1#2#3{%
+ \envdef#1{%
+ \startdefun
+ \parseargusing\activeparens{\printdefunline#3}%
+ }%
+ \def#2{\dodefunx#1}%
+ \def#3%
+}
+
+%%% Untyped functions:
+
+% @deffn category name args
+\makedefun{deffn}{\deffngeneral{}}
+
+% @deffn category class name args
+\makedefun{defop}#1 {\defopon{#1\ \putwordon}}
+
+% \defopon {category on}class name args
+\def\defopon#1#2 {\deffngeneral{\putwordon\ \code{#2}}{#1\ \code{#2}} }
+
+% \deffngeneral {subind}category name args
+%
+\def\deffngeneral#1#2 #3 #4\endheader{%
+ % Remember that \dosubind{fn}{foo}{} is equivalent to \doind{fn}{foo}.
+ \dosubind{fn}{\code{#3}}{#1}%
+ \defname{#2}{}{#3}\magicamp\defunargs{#4\unskip}%
+}
+
+%%% Typed functions:
+
+% @deftypefn category type name args
+\makedefun{deftypefn}{\deftypefngeneral{}}
+
+% @deftypeop category class type name args
+\makedefun{deftypeop}#1 {\deftypeopon{#1\ \putwordon}}
+
+% \deftypeopon {category on}class type name args
+\def\deftypeopon#1#2 {\deftypefngeneral{\putwordon\ \code{#2}}{#1\ \code{#2}} }
+
+% \deftypefngeneral {subind}category type name args
+%
+\def\deftypefngeneral#1#2 #3 #4 #5\endheader{%
+ \dosubind{fn}{\code{#4}}{#1}%
+ \defname{#2}{#3}{#4}\defunargs{#5\unskip}%
+}
+
+%%% Typed variables:
+
+% @deftypevr category type var args
+\makedefun{deftypevr}{\deftypecvgeneral{}}
+
+% @deftypecv category class type var args
+\makedefun{deftypecv}#1 {\deftypecvof{#1\ \putwordof}}
+
+% \deftypecvof {category of}class type var args
+\def\deftypecvof#1#2 {\deftypecvgeneral{\putwordof\ \code{#2}}{#1\ \code{#2}} }
+
+% \deftypecvgeneral {subind}category type var args
+%
+\def\deftypecvgeneral#1#2 #3 #4 #5\endheader{%
+ \dosubind{vr}{\code{#4}}{#1}%
+ \defname{#2}{#3}{#4}\defunargs{#5\unskip}%
+}
+
+%%% Untyped variables:
+
+% @defvr category var args
+\makedefun{defvr}#1 {\deftypevrheader{#1} {} }
+
+% @defcv category class var args
+\makedefun{defcv}#1 {\defcvof{#1\ \putwordof}}
+
+% \defcvof {category of}class var args
+\def\defcvof#1#2 {\deftypecvof{#1}#2 {} }
+
+%%% Type:
+% @deftp category name args
+\makedefun{deftp}#1 #2 #3\endheader{%
+ \doind{tp}{\code{#2}}%
+ \defname{#1}{}{#2}\defunargs{#3\unskip}%
+}
+
+% Remaining @defun-like shortcuts:
+\makedefun{defun}{\deffnheader{\putwordDeffunc} }
+\makedefun{defmac}{\deffnheader{\putwordDefmac} }
+\makedefun{defspec}{\deffnheader{\putwordDefspec} }
+\makedefun{deftypefun}{\deftypefnheader{\putwordDeffunc} }
+\makedefun{defvar}{\defvrheader{\putwordDefvar} }
+\makedefun{defopt}{\defvrheader{\putwordDefopt} }
+\makedefun{deftypevar}{\deftypevrheader{\putwordDefvar} }
+\makedefun{defmethod}{\defopon\putwordMethodon}
+\makedefun{deftypemethod}{\deftypeopon\putwordMethodon}
+\makedefun{defivar}{\defcvof\putwordInstanceVariableof}
+\makedefun{deftypeivar}{\deftypecvof\putwordInstanceVariableof}
+
+% \defname, which formats the name of the @def (not the args).
+% #1 is the category, such as "Function".
+% #2 is the return type, if any.
+% #3 is the function name.
+%
+% We are followed by (but not passed) the arguments, if any.
+%
+\def\defname#1#2#3{%
+ % Get the values of \leftskip and \rightskip as they were outside the @def...
+ \advance\leftskip by -\defbodyindent
+ %
+ % How we'll format the type name. Putting it in brackets helps
+ % distinguish it from the body text that may end up on the next line
+ % just below it.
+ \def\temp{#1}%
+ \setbox0=\hbox{\kern\deflastargmargin \ifx\temp\empty\else [\rm\temp]\fi}
+ %
+ % Figure out line sizes for the paragraph shape.
+ % The first line needs space for \box0; but if \rightskip is nonzero,
+ % we need only space for the part of \box0 which exceeds it:
+ \dimen0=\hsize \advance\dimen0 by -\wd0 \advance\dimen0 by \rightskip
+ % The continuations:
+ \dimen2=\hsize \advance\dimen2 by -\defargsindent
+ % (plain.tex says that \dimen1 should be used only as global.)
+ \parshape 2 0in \dimen0 \defargsindent \dimen2
+ %
+ % Put the type name to the right margin.
+ \noindent
+ \hbox to 0pt{%
+ \hfil\box0 \kern-\hsize
+ % \hsize has to be shortened this way:
+ \kern\leftskip
+ % Intentionally do not respect \rightskip, since we need the space.
+ }%
+ %
+ % Allow all lines to be underfull without complaint:
+ \tolerance=10000 \hbadness=10000
+ \exdentamount=\defbodyindent
+ {%
+ % defun fonts. We use typewriter by default (used to be bold) because:
+ % . we're printing identifiers, they should be in tt in principle.
+ % . in languages with many accents, such as Czech or French, it's
+ % common to leave accents off identifiers. The result looks ok in
+ % tt, but exceedingly strange in rm.
+ % . we don't want -- and --- to be treated as ligatures.
+ % . this still does not fix the ?` and !` ligatures, but so far no
+ % one has made identifiers using them :).
+ \df \tt
+ \def\temp{#2}% return value type
+ \ifx\temp\empty\else \tclose{\temp} \fi
+ #3% output function name
+ }%
+ {\rm\enskip}% hskip 0.5 em of \tenrm
+ %
+ \boldbrax
+ % arguments will be output next, if any.
+}
+
+% Print arguments in slanted roman (not ttsl), inconsistently with using
+% tt for the name. This is because literal text is sometimes needed in
+% the argument list (groff manual), and ttsl and tt are not very
+% distinguishable. Prevent hyphenation at `-' chars.
+%
+\def\defunargs#1{%
+ % use sl by default (not ttsl),
+ % tt for the names.
+ \df \sl \hyphenchar\font=0
+ %
+ % On the other hand, if an argument has two dashes (for instance), we
+ % want a way to get ttsl. Let's try @var for that.
+ \def\var##1{{\setupmarkupstyle{var}\ttslanted{##1}}}%
+ #1%
+ \sl\hyphenchar\font=45
+}
+
+% We want ()&[] to print specially on the defun line.
+%
+\def\activeparens{%
+ \catcode`\(=\active \catcode`\)=\active
+ \catcode`\[=\active \catcode`\]=\active
+ \catcode`\&=\active
+}
+
+% Make control sequences which act like normal parenthesis chars.
+\let\lparen = ( \let\rparen = )
+
+% Be sure that we always have a definition for `(', etc. For example,
+% if the fn name has parens in it, \boldbrax will not be in effect yet,
+% so TeX would otherwise complain about undefined control sequence.
+{
+ \activeparens
+ \global\let(=\lparen \global\let)=\rparen
+ \global\let[=\lbrack \global\let]=\rbrack
+ \global\let& = \&
+
+ \gdef\boldbrax{\let(=\opnr\let)=\clnr\let[=\lbrb\let]=\rbrb}
+ \gdef\magicamp{\let&=\amprm}
+}
+
+\newcount\parencount
+
+% If we encounter &foo, then turn on ()-hacking afterwards
+\newif\ifampseen
+\def\amprm#1 {\ampseentrue{\bf\ }}
+
+\def\parenfont{%
+ \ifampseen
+ % At the first level, print parens in roman,
+ % otherwise use the default font.
+ \ifnum \parencount=1 \rm \fi
+ \else
+ % The \sf parens (in \boldbrax) actually are a little bolder than
+ % the contained text. This is especially needed for [ and ] .
+ \sf
+ \fi
+}
+\def\infirstlevel#1{%
+ \ifampseen
+ \ifnum\parencount=1
+ #1%
+ \fi
+ \fi
+}
+\def\bfafterword#1 {#1 \bf}
+
+\def\opnr{%
+ \global\advance\parencount by 1
+ {\parenfont(}%
+ \infirstlevel \bfafterword
+}
+\def\clnr{%
+ {\parenfont)}%
+ \infirstlevel \sl
+ \global\advance\parencount by -1
+}
+
+\newcount\brackcount
+\def\lbrb{%
+ \global\advance\brackcount by 1
+ {\bf[}%
+}
+\def\rbrb{%
+ {\bf]}%
+ \global\advance\brackcount by -1
+}
+
+\def\checkparencounts{%
+ \ifnum\parencount=0 \else \badparencount \fi
+ \ifnum\brackcount=0 \else \badbrackcount \fi
+}
+% these should not use \errmessage; the glibc manual, at least, actually
+% has such constructs (when documenting function pointers).
+\def\badparencount{%
+ \message{Warning: unbalanced parentheses in @def...}%
+ \global\parencount=0
+}
+\def\badbrackcount{%
+ \message{Warning: unbalanced square brackets in @def...}%
+ \global\brackcount=0
+}
+
+
+\message{macros,}
+% @macro.
+
+% To do this right we need a feature of e-TeX, \scantokens,
+% which we arrange to emulate with a temporary file in ordinary TeX.
+\ifx\eTeXversion\undefined
+ \newwrite\macscribble
+ \def\scantokens#1{%
+ \toks0={#1}%
+ \immediate\openout\macscribble=\jobname.tmp
+ \immediate\write\macscribble{\the\toks0}%
+ \immediate\closeout\macscribble
+ \input \jobname.tmp
+ }
+\fi
+
+\def\scanmacro#1{%
+ \begingroup
+ \newlinechar`\^^M
+ \let\xeatspaces\eatspaces
+ % Undo catcode changes of \startcontents and \doprintindex
+ % When called from @insertcopying or (short)caption, we need active
+ % backslash to get it printed correctly. Previously, we had
+ % \catcode`\\=\other instead. We'll see whether a problem appears
+ % with macro expansion. --kasal, 19aug04
+ \catcode`\@=0 \catcode`\\=\active \escapechar=`\@
+ % ... and \example
+ \spaceisspace
+ %
+ % Append \endinput to make sure that TeX does not see the ending newline.
+ % I've verified that it is necessary both for e-TeX and for ordinary TeX
+ % --kasal, 29nov03
+ \scantokens{#1\endinput}%
+ \endgroup
+}
+
+\def\scanexp#1{%
+ \edef\temp{\noexpand\scanmacro{#1}}%
+ \temp
+}
+
+\newcount\paramno % Count of parameters
+\newtoks\macname % Macro name
+\newif\ifrecursive % Is it recursive?
+
+% List of all defined macros in the form
+% \definedummyword\macro1\definedummyword\macro2...
+% Currently is also contains all @aliases; the list can be split
+% if there is a need.
+\def\macrolist{}
+
+% Add the macro to \macrolist
+\def\addtomacrolist#1{\expandafter \addtomacrolistxxx \csname#1\endcsname}
+\def\addtomacrolistxxx#1{%
+ \toks0 = \expandafter{\macrolist\definedummyword#1}%
+ \xdef\macrolist{\the\toks0}%
+}
+
+% Utility routines.
+% This does \let #1 = #2, with \csnames; that is,
+% \let \csname#1\endcsname = \csname#2\endcsname
+% (except of course we have to play expansion games).
+%
+\def\cslet#1#2{%
+ \expandafter\let
+ \csname#1\expandafter\endcsname
+ \csname#2\endcsname
+}
+
+% Trim leading and trailing spaces off a string.
+% Concepts from aro-bend problem 15 (see CTAN).
+{\catcode`\@=11
+\gdef\eatspaces #1{\expandafter\trim@\expandafter{#1 }}
+\gdef\trim@ #1{\trim@@ @#1 @ #1 @ @@}
+\gdef\trim@@ #1@ #2@ #3@@{\trim@@@\empty #2 @}
+\def\unbrace#1{#1}
+\unbrace{\gdef\trim@@@ #1 } #2@{#1}
+}
+
+% Trim a single trailing ^^M off a string.
+{\catcode`\^^M=\other \catcode`\Q=3%
+\gdef\eatcr #1{\eatcra #1Q^^MQ}%
+\gdef\eatcra#1^^MQ{\eatcrb#1Q}%
+\gdef\eatcrb#1Q#2Q{#1}%
+}
+
+% Macro bodies are absorbed as an argument in a context where
+% all characters are catcode 10, 11 or 12, except \ which is active
+% (as in normal texinfo). It is necessary to change the definition of \.
+
+% Non-ASCII encodings make 8-bit characters active, so un-activate
+% them to avoid their expansion. Must do this non-globally, to
+% confine the change to the current group.
+
+% It's necessary to have hard CRs when the macro is executed. This is
+% done by making ^^M (\endlinechar) catcode 12 when reading the macro
+% body, and then making it the \newlinechar in \scanmacro.
+
+\def\scanctxt{%
+ \catcode`\"=\other
+ \catcode`\+=\other
+ \catcode`\<=\other
+ \catcode`\>=\other
+ \catcode`\@=\other
+ \catcode`\^=\other
+ \catcode`\_=\other
+ \catcode`\|=\other
+ \catcode`\~=\other
+ \ifx\declaredencoding\ascii \else \setnonasciicharscatcodenonglobal\other \fi
+}
+
+\def\scanargctxt{%
+ \scanctxt
+ \catcode`\\=\other
+ \catcode`\^^M=\other
+}
+
+\def\macrobodyctxt{%
+ \scanctxt
+ \catcode`\{=\other
+ \catcode`\}=\other
+ \catcode`\^^M=\other
+ \usembodybackslash
+}
+
+\def\macroargctxt{%
+ \scanctxt
+ \catcode`\\=\other
+}
+
+% \mbodybackslash is the definition of \ in @macro bodies.
+% It maps \foo\ => \csname macarg.foo\endcsname => #N
+% where N is the macro parameter number.
+% We define \csname macarg.\endcsname to be \realbackslash, so
+% \\ in macro replacement text gets you a backslash.
+
+{\catcode`@=0 @catcode`@\=@active
+ @gdef at usembodybackslash{@let\=@mbodybackslash}
+ @gdef at mbodybackslash#1\{@csname macarg.#1 at endcsname}
+}
+\expandafter\def\csname macarg.\endcsname{\realbackslash}
+
+\def\macro{\recursivefalse\parsearg\macroxxx}
+\def\rmacro{\recursivetrue\parsearg\macroxxx}
+
+\def\macroxxx#1{%
+ \getargs{#1}% now \macname is the macname and \argl the arglist
+ \ifx\argl\empty % no arguments
+ \paramno=0%
+ \else
+ \expandafter\parsemargdef \argl;%
+ \fi
+ \if1\csname ismacro.\the\macname\endcsname
+ \message{Warning: redefining \the\macname}%
+ \else
+ \expandafter\ifx\csname \the\macname\endcsname \relax
+ \else \errmessage{Macro name \the\macname\space already defined}\fi
+ \global\cslet{macsave.\the\macname}{\the\macname}%
+ \global\expandafter\let\csname ismacro.\the\macname\endcsname=1%
+ \addtomacrolist{\the\macname}%
+ \fi
+ \begingroup \macrobodyctxt
+ \ifrecursive \expandafter\parsermacbody
+ \else \expandafter\parsemacbody
+ \fi}
+
+\parseargdef\unmacro{%
+ \if1\csname ismacro.#1\endcsname
+ \global\cslet{#1}{macsave.#1}%
+ \global\expandafter\let \csname ismacro.#1\endcsname=0%
+ % Remove the macro name from \macrolist:
+ \begingroup
+ \expandafter\let\csname#1\endcsname \relax
+ \let\definedummyword\unmacrodo
+ \xdef\macrolist{\macrolist}%
+ \endgroup
+ \else
+ \errmessage{Macro #1 not defined}%
+ \fi
+}
+
+% Called by \do from \dounmacro on each macro. The idea is to omit any
+% macro definitions that have been changed to \relax.
+%
+\def\unmacrodo#1{%
+ \ifx #1\relax
+ % remove this
+ \else
+ \noexpand\definedummyword \noexpand#1%
+ \fi
+}
+
+% This makes use of the obscure feature that if the last token of a
+% <parameter list> is #, then the preceding argument is delimited by
+% an opening brace, and that opening brace is not consumed.
+\def\getargs#1{\getargsxxx#1{}}
+\def\getargsxxx#1#{\getmacname #1 \relax\getmacargs}
+\def\getmacname #1 #2\relax{\macname={#1}}
+\def\getmacargs#1{\def\argl{#1}}
+
+% Parse the optional {params} list. Set up \paramno and \paramlist
+% so \defmacro knows what to do. Define \macarg.blah for each blah
+% in the params list, to be ##N where N is the position in that list.
+% That gets used by \mbodybackslash (above).
+
+% We need to get `macro parameter char #' into several definitions.
+% The technique used is stolen from LaTeX: let \hash be something
+% unexpandable, insert that wherever you need a #, and then redefine
+% it to # just before using the token list produced.
+%
+% The same technique is used to protect \eatspaces till just before
+% the macro is used.
+
+\def\parsemargdef#1;{\paramno=0\def\paramlist{}%
+ \let\hash\relax\let\xeatspaces\relax\parsemargdefxxx#1,;,}
+\def\parsemargdefxxx#1,{%
+ \if#1;\let\next=\relax
+ \else \let\next=\parsemargdefxxx
+ \advance\paramno by 1%
+ \expandafter\edef\csname macarg.\eatspaces{#1}\endcsname
+ {\xeatspaces{\hash\the\paramno}}%
+ \edef\paramlist{\paramlist\hash\the\paramno,}%
+ \fi\next}
+
+% These two commands read recursive and nonrecursive macro bodies.
+% (They're different since rec and nonrec macros end differently.)
+
+\long\def\parsemacbody#1 at end macro%
+{\xdef\temp{\eatcr{#1}}\endgroup\defmacro}%
+\long\def\parsermacbody#1 at end rmacro%
+{\xdef\temp{\eatcr{#1}}\endgroup\defmacro}%
+
+% This defines the macro itself. There are six cases: recursive and
+% nonrecursive macros of zero, one, and many arguments.
+% Much magic with \expandafter here.
+% \xdef is used so that macro definitions will survive the file
+% they're defined in; @include reads the file inside a group.
+\def\defmacro{%
+ \let\hash=##% convert placeholders to macro parameter chars
+ \ifrecursive
+ \ifcase\paramno
+ % 0
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \noexpand\scanmacro{\temp}}%
+ \or % 1
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \bgroup\noexpand\macroargctxt
+ \noexpand\braceorline
+ \expandafter\noexpand\csname\the\macname xxx\endcsname}%
+ \expandafter\xdef\csname\the\macname xxx\endcsname##1{%
+ \egroup\noexpand\scanmacro{\temp}}%
+ \else % many
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \bgroup\noexpand\macroargctxt
+ \noexpand\csname\the\macname xx\endcsname}%
+ \expandafter\xdef\csname\the\macname xx\endcsname##1{%
+ \expandafter\noexpand\csname\the\macname xxx\endcsname ##1,}%
+ \expandafter\expandafter
+ \expandafter\xdef
+ \expandafter\expandafter
+ \csname\the\macname xxx\endcsname
+ \paramlist{\egroup\noexpand\scanmacro{\temp}}%
+ \fi
+ \else
+ \ifcase\paramno
+ % 0
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \noexpand\norecurse{\the\macname}%
+ \noexpand\scanmacro{\temp}\egroup}%
+ \or % 1
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \bgroup\noexpand\macroargctxt
+ \noexpand\braceorline
+ \expandafter\noexpand\csname\the\macname xxx\endcsname}%
+ \expandafter\xdef\csname\the\macname xxx\endcsname##1{%
+ \egroup
+ \noexpand\norecurse{\the\macname}%
+ \noexpand\scanmacro{\temp}\egroup}%
+ \else % many
+ \expandafter\xdef\csname\the\macname\endcsname{%
+ \bgroup\noexpand\macroargctxt
+ \expandafter\noexpand\csname\the\macname xx\endcsname}%
+ \expandafter\xdef\csname\the\macname xx\endcsname##1{%
+ \expandafter\noexpand\csname\the\macname xxx\endcsname ##1,}%
+ \expandafter\expandafter
+ \expandafter\xdef
+ \expandafter\expandafter
+ \csname\the\macname xxx\endcsname
+ \paramlist{%
+ \egroup
+ \noexpand\norecurse{\the\macname}%
+ \noexpand\scanmacro{\temp}\egroup}%
+ \fi
+ \fi}
+
+\def\norecurse#1{\bgroup\cslet{#1}{macsave.#1}}
+
+% \braceorline decides whether the next nonwhitespace character is a
+% {. If so it reads up to the closing }, if not, it reads the whole
+% line. Whatever was read is then fed to the next control sequence
+% as an argument (by \parsebrace or \parsearg)
+\def\braceorline#1{\let\macnamexxx=#1\futurelet\nchar\braceorlinexxx}
+\def\braceorlinexxx{%
+ \ifx\nchar\bgroup\else
+ \expandafter\parsearg
+ \fi \macnamexxx}
+
+
+% @alias.
+% We need some trickery to remove the optional spaces around the equal
+% sign. Just make them active and then expand them all to nothing.
+\def\alias{\parseargusing\obeyspaces\aliasxxx}
+\def\aliasxxx #1{\aliasyyy#1\relax}
+\def\aliasyyy #1=#2\relax{%
+ {%
+ \expandafter\let\obeyedspace=\empty
+ \addtomacrolist{#1}%
+ \xdef\next{\global\let\makecsname{#1}=\makecsname{#2}}%
+ }%
+ \next
+}
+
+
+\message{cross references,}
+
+\newwrite\auxfile
+\newif\ifhavexrefs % True if xref values are known.
+\newif\ifwarnedxrefs % True if we warned once that they aren't known.
+
+% @inforef is relatively simple.
+\def\inforef #1{\inforefzzz #1,,,,**}
+\def\inforefzzz #1,#2,#3,#4**{\putwordSee{} \putwordInfo{} \putwordfile{} \file{\ignorespaces #3{}},
+ node \samp{\ignorespaces#1{}}}
+
+% @node's only job in TeX is to define \lastnode, which is used in
+% cross-references. The @node line might or might not have commas, and
+% might or might not have spaces before the first comma, like:
+% @node foo , bar , ...
+% We don't want such trailing spaces in the node name.
+%
+\parseargdef\node{\checkenv{}\donode #1 ,\finishnodeparse}
+%
+% also remove a trailing comma, in case of something like this:
+% @node Help-Cross, , , Cross-refs
+\def\donode#1 ,#2\finishnodeparse{\dodonode #1,\finishnodeparse}
+\def\dodonode#1,#2\finishnodeparse{\gdef\lastnode{#1}}
+
+\let\nwnode=\node
+\let\lastnode=\empty
+
+% Write a cross-reference definition for the current node. #1 is the
+% type (Ynumbered, Yappendix, Ynothing).
+%
+\def\donoderef#1{%
+ \ifx\lastnode\empty\else
+ \setref{\lastnode}{#1}%
+ \global\let\lastnode=\empty
+ \fi
+}
+
+% @anchor{NAME} -- define xref target at arbitrary point.
+%
+\newcount\savesfregister
+%
+\def\savesf{\relax \ifhmode \savesfregister=\spacefactor \fi}
+\def\restoresf{\relax \ifhmode \spacefactor=\savesfregister \fi}
+\def\anchor#1{\savesf \setref{#1}{Ynothing}\restoresf \ignorespaces}
+
+% \setref{NAME}{SNT} defines a cross-reference point NAME (a node or an
+% anchor), which consists of three parts:
+% 1) NAME-title - the current sectioning name taken from \lastsection,
+% or the anchor name.
+% 2) NAME-snt - section number and type, passed as the SNT arg, or
+% empty for anchors.
+% 3) NAME-pg - the page number.
+%
+% This is called from \donoderef, \anchor, and \dofloat. In the case of
+% floats, there is an additional part, which is not written here:
+% 4) NAME-lof - the text as it should appear in a @listoffloats.
+%
+\def\setref#1#2{%
+ \pdfmkdest{#1}%
+ \iflinks
+ {%
+ \atdummies % preserve commands, but don't expand them
+ \edef\writexrdef##1##2{%
+ \write\auxfile{@xrdef{#1-% #1 of \setref, expanded by the \edef
+ ##1}{##2}}% these are parameters of \writexrdef
+ }%
+ \toks0 = \expandafter{\lastsection}%
+ \immediate \writexrdef{title}{\the\toks0 }%
+ \immediate \writexrdef{snt}{\csname #2\endcsname}% \Ynumbered etc.
+ \safewhatsit{\writexrdef{pg}{\folio}}% will be written later, during \shipout
+ }%
+ \fi
+}
+
+% @xref, @pxref, and @ref generate cross-references. For \xrefX, #1 is
+% the node name, #2 the name of the Info cross-reference, #3 the printed
+% node name, #4 the name of the Info file, #5 the name of the printed
+% manual. All but the node name can be omitted.
+%
+\def\pxref#1{\putwordsee{} \xrefX[#1,,,,,,,]}
+\def\xref#1{\putwordSee{} \xrefX[#1,,,,,,,]}
+\def\ref#1{\xrefX[#1,,,,,,,]}
+\def\xrefX[#1,#2,#3,#4,#5,#6]{\begingroup
+ \unsepspaces
+ \def\printedmanual{\ignorespaces #5}%
+ \def\printedrefname{\ignorespaces #3}%
+ \setbox1=\hbox{\printedmanual\unskip}%
+ \setbox0=\hbox{\printedrefname\unskip}%
+ \ifdim \wd0 = 0pt
+ % No printed node name was explicitly given.
+ \expandafter\ifx\csname SETxref-automatic-section-title\endcsname\relax
+ % Use the node name inside the square brackets.
+ \def\printedrefname{\ignorespaces #1}%
+ \else
+ % Use the actual chapter/section title appear inside
+ % the square brackets. Use the real section title if we have it.
+ \ifdim \wd1 > 0pt
+ % It is in another manual, so we don't have it.
+ \def\printedrefname{\ignorespaces #1}%
+ \else
+ \ifhavexrefs
+ % We know the real title if we have the xref values.
+ \def\printedrefname{\refx{#1-title}{}}%
+ \else
+ % Otherwise just copy the Info node name.
+ \def\printedrefname{\ignorespaces #1}%
+ \fi%
+ \fi
+ \fi
+ \fi
+ %
+ % Make link in pdf output.
+ \ifpdf
+ {\indexnofonts
+ \turnoffactive
+ % This expands tokens, so do it after making catcode changes, so _
+ % etc. don't get their TeX definitions.
+ \getfilename{#4}%
+ %
+ % See comments at \activebackslashdouble.
+ {\activebackslashdouble \xdef\pdfxrefdest{#1}%
+ \backslashparens\pdfxrefdest}%
+ %
+ \leavevmode
+ \startlink attr{/Border [0 0 0]}%
+ \ifnum\filenamelength>0
+ goto file{\the\filename.pdf} name{\pdfxrefdest}%
+ \else
+ goto name{\pdfmkpgn{\pdfxrefdest}}%
+ \fi
+ }%
+ \setcolor{\linkcolor}%
+ \fi
+ %
+ % Float references are printed completely differently: "Figure 1.2"
+ % instead of "[somenode], p.3". We distinguish them by the
+ % LABEL-title being set to a magic string.
+ {%
+ % Have to otherify everything special to allow the \csname to
+ % include an _ in the xref name, etc.
+ \indexnofonts
+ \turnoffactive
+ \expandafter\global\expandafter\let\expandafter\Xthisreftitle
+ \csname XR#1-title\endcsname
+ }%
+ \iffloat\Xthisreftitle
+ % If the user specified the print name (third arg) to the ref,
+ % print it instead of our usual "Figure 1.2".
+ \ifdim\wd0 = 0pt
+ \refx{#1-snt}{}%
+ \else
+ \printedrefname
+ \fi
+ %
+ % if the user also gave the printed manual name (fifth arg), append
+ % "in MANUALNAME".
+ \ifdim \wd1 > 0pt
+ \space \putwordin{} \cite{\printedmanual}%
+ \fi
+ \else
+ % node/anchor (non-float) references.
+ %
+ % If we use \unhbox0 and \unhbox1 to print the node names, TeX does not
+ % insert empty discretionaries after hyphens, which means that it will
+ % not find a line break at a hyphen in a node names. Since some manuals
+ % are best written with fairly long node names, containing hyphens, this
+ % is a loss. Therefore, we give the text of the node name again, so it
+ % is as if TeX is seeing it for the first time.
+ \ifdim \wd1 > 0pt
+ \putwordSection{} ``\printedrefname'' \putwordin{} \cite{\printedmanual}%
+ \else
+ % _ (for example) has to be the character _ for the purposes of the
+ % control sequence corresponding to the node, but it has to expand
+ % into the usual \leavevmode...\vrule stuff for purposes of
+ % printing. So we \turnoffactive for the \refx-snt, back on for the
+ % printing, back off for the \refx-pg.
+ {\turnoffactive
+ % Only output a following space if the -snt ref is nonempty; for
+ % @unnumbered and @anchor, it won't be.
+ \setbox2 = \hbox{\ignorespaces \refx{#1-snt}{}}%
+ \ifdim \wd2 > 0pt \refx{#1-snt}\space\fi
+ }%
+ % output the `[mynode]' via a macro so it can be overridden.
+ \xrefprintnodename\printedrefname
+ %
+ % But we always want a comma and a space:
+ ,\space
+ %
+ % output the `page 3'.
+ \turnoffactive \putwordpage\tie\refx{#1-pg}{}%
+ \fi
+ \fi
+ \endlink
+\endgroup}
+
+% This macro is called from \xrefX for the `[nodename]' part of xref
+% output. It's a separate macro only so it can be changed more easily,
+% since square brackets don't work well in some documents. Particularly
+% one that Bob is working on :).
+%
+\def\xrefprintnodename#1{[#1]}
+
+% Things referred to by \setref.
+%
+\def\Ynothing{}
+\def\Yomitfromtoc{}
+\def\Ynumbered{%
+ \ifnum\secno=0
+ \putwordChapter at tie \the\chapno
+ \else \ifnum\subsecno=0
+ \putwordSection at tie \the\chapno.\the\secno
+ \else \ifnum\subsubsecno=0
+ \putwordSection at tie \the\chapno.\the\secno.\the\subsecno
+ \else
+ \putwordSection at tie \the\chapno.\the\secno.\the\subsecno.\the\subsubsecno
+ \fi\fi\fi
+}
+\def\Yappendix{%
+ \ifnum\secno=0
+ \putwordAppendix at tie @char\the\appendixno{}%
+ \else \ifnum\subsecno=0
+ \putwordSection at tie @char\the\appendixno.\the\secno
+ \else \ifnum\subsubsecno=0
+ \putwordSection at tie @char\the\appendixno.\the\secno.\the\subsecno
+ \else
+ \putwordSection at tie
+ @char\the\appendixno.\the\secno.\the\subsecno.\the\subsubsecno
+ \fi\fi\fi
+}
+
+% Define \refx{NAME}{SUFFIX} to reference a cross-reference string named NAME.
+% If its value is nonempty, SUFFIX is output afterward.
+%
+\def\refx#1#2{%
+ {%
+ \indexnofonts
+ \otherbackslash
+ \expandafter\global\expandafter\let\expandafter\thisrefX
+ \csname XR#1\endcsname
+ }%
+ \ifx\thisrefX\relax
+ % If not defined, say something at least.
+ \angleleft un\-de\-fined\angleright
+ \iflinks
+ \ifhavexrefs
+ \message{\linenumber Undefined cross reference `#1'.}%
+ \else
+ \ifwarnedxrefs\else
+ \global\warnedxrefstrue
+ \message{Cross reference values unknown; you must run TeX again.}%
+ \fi
+ \fi
+ \fi
+ \else
+ % It's defined, so just use it.
+ \thisrefX
+ \fi
+ #2% Output the suffix in any case.
+}
+
+% This is the macro invoked by entries in the aux file. Usually it's
+% just a \def (we prepend XR to the control sequence name to avoid
+% collisions). But if this is a float type, we have more work to do.
+%
+\def\xrdef#1#2{%
+ {% The node name might contain 8-bit characters, which in our current
+ % implementation are changed to commands like @'e. Don't let these
+ % mess up the control sequence name.
+ \indexnofonts
+ \turnoffactive
+ \xdef\safexrefname{#1}%
+ }%
+ %
+ \expandafter\gdef\csname XR\safexrefname\endcsname{#2}% remember this xref
+ %
+ % Was that xref control sequence that we just defined for a float?
+ \expandafter\iffloat\csname XR\safexrefname\endcsname
+ % it was a float, and we have the (safe) float type in \iffloattype.
+ \expandafter\let\expandafter\floatlist
+ \csname floatlist\iffloattype\endcsname
+ %
+ % Is this the first time we've seen this float type?
+ \expandafter\ifx\floatlist\relax
+ \toks0 = {\do}% yes, so just \do
+ \else
+ % had it before, so preserve previous elements in list.
+ \toks0 = \expandafter{\floatlist\do}%
+ \fi
+ %
+ % Remember this xref in the control sequence \floatlistFLOATTYPE,
+ % for later use in \listoffloats.
+ \expandafter\xdef\csname floatlist\iffloattype\endcsname{\the\toks0
+ {\safexrefname}}%
+ \fi
+}
+
+% Read the last existing aux file, if any. No error if none exists.
+%
+\def\tryauxfile{%
+ \openin 1 \jobname.aux
+ \ifeof 1 \else
+ \readdatafile{aux}%
+ \global\havexrefstrue
+ \fi
+ \closein 1
+}
+
+\def\setupdatafile{%
+ \catcode`\^^@=\other
+ \catcode`\^^A=\other
+ \catcode`\^^B=\other
+ \catcode`\^^C=\other
+ \catcode`\^^D=\other
+ \catcode`\^^E=\other
+ \catcode`\^^F=\other
+ \catcode`\^^G=\other
+ \catcode`\^^H=\other
+ \catcode`\^^K=\other
+ \catcode`\^^L=\other
+ \catcode`\^^N=\other
+ \catcode`\^^P=\other
+ \catcode`\^^Q=\other
+ \catcode`\^^R=\other
+ \catcode`\^^S=\other
+ \catcode`\^^T=\other
+ \catcode`\^^U=\other
+ \catcode`\^^V=\other
+ \catcode`\^^W=\other
+ \catcode`\^^X=\other
+ \catcode`\^^Z=\other
+ \catcode`\^^[=\other
+ \catcode`\^^\=\other
+ \catcode`\^^]=\other
+ \catcode`\^^^=\other
+ \catcode`\^^_=\other
+ % It was suggested to set the catcode of ^ to 7, which would allow ^^e4 etc.
+ % in xref tags, i.e., node names. But since ^^e4 notation isn't
+ % supported in the main text, it doesn't seem desirable. Furthermore,
+ % that is not enough: for node names that actually contain a ^
+ % character, we would end up writing a line like this: 'xrdef {'hat
+ % b-title}{'hat b} and \xrdef does a \csname...\endcsname on the first
+ % argument, and \hat is not an expandable control sequence. It could
+ % all be worked out, but why? Either we support ^^ or we don't.
+ %
+ % The other change necessary for this was to define \auxhat:
+ % \def\auxhat{\def^{'hat }}% extra space so ok if followed by letter
+ % and then to call \auxhat in \setq.
+ %
+ \catcode`\^=\other
+ %
+ % Special characters. Should be turned off anyway, but...
+ \catcode`\~=\other
+ \catcode`\[=\other
+ \catcode`\]=\other
+ \catcode`\"=\other
+ \catcode`\_=\other
+ \catcode`\|=\other
+ \catcode`\<=\other
+ \catcode`\>=\other
+ \catcode`\$=\other
+ \catcode`\#=\other
+ \catcode`\&=\other
+ \catcode`\%=\other
+ \catcode`+=\other % avoid \+ for paranoia even though we've turned it off
+ %
+ % This is to support \ in node names and titles, since the \
+ % characters end up in a \csname. It's easier than
+ % leaving it active and making its active definition an actual \
+ % character. What I don't understand is why it works in the *value*
+ % of the xrdef. Seems like it should be a catcode12 \, and that
+ % should not typeset properly. But it works, so I'm moving on for
+ % now. --karl, 15jan04.
+ \catcode`\\=\other
+ %
+ % Make the characters 128-255 be printing characters.
+ {%
+ \count1=128
+ \def\loop{%
+ \catcode\count1=\other
+ \advance\count1 by 1
+ \ifnum \count1<256 \loop \fi
+ }%
+ }%
+ %
+ % @ is our escape character in .aux files, and we need braces.
+ \catcode`\{=1
+ \catcode`\}=2
+ \catcode`\@=0
+}
+
+\def\readdatafile#1{%
+\begingroup
+ \setupdatafile
+ \input\jobname.#1
+\endgroup}
+
+
+\message{insertions,}
+% including footnotes.
+
+\newcount \footnoteno
+
+% The trailing space in the following definition for supereject is
+% vital for proper filling; pages come out unaligned when you do a
+% pagealignmacro call if that space before the closing brace is
+% removed. (Generally, numeric constants should always be followed by a
+% space to prevent strange expansion errors.)
+\def\supereject{\par\penalty -20000\footnoteno =0 }
+
+% @footnotestyle is meaningful for info output only.
+\let\footnotestyle=\comment
+
+{\catcode `\@=11
+%
+% Auto-number footnotes. Otherwise like plain.
+\gdef\footnote{%
+ \let\indent=\ptexindent
+ \let\noindent=\ptexnoindent
+ \global\advance\footnoteno by \@ne
+ \edef\thisfootno{$^{\the\footnoteno}$}%
+ %
+ % In case the footnote comes at the end of a sentence, preserve the
+ % extra spacing after we do the footnote number.
+ \let\@sf\empty
+ \ifhmode\edef\@sf{\spacefactor\the\spacefactor}\ptexslash\fi
+ %
+ % Remove inadvertent blank space before typesetting the footnote number.
+ \unskip
+ \thisfootno\@sf
+ \dofootnote
+}%
+
+% Don't bother with the trickery in plain.tex to not require the
+% footnote text as a parameter. Our footnotes don't need to be so general.
+%
+% Oh yes, they do; otherwise, @ifset (and anything else that uses
+% \parseargline) fails inside footnotes because the tokens are fixed when
+% the footnote is read. --karl, 16nov96.
+%
+\gdef\dofootnote{%
+ \insert\footins\bgroup
+ % We want to typeset this text as a normal paragraph, even if the
+ % footnote reference occurs in (for example) a display environment.
+ % So reset some parameters.
+ \hsize=\pagewidth
+ \interlinepenalty\interfootnotelinepenalty
+ \splittopskip\ht\strutbox % top baseline for broken footnotes
+ \splitmaxdepth\dp\strutbox
+ \floatingpenalty\@MM
+ \leftskip\z at skip
+ \rightskip\z at skip
+ \spaceskip\z at skip
+ \xspaceskip\z at skip
+ \parindent\defaultparindent
+ %
+ \smallfonts \rm
+ %
+ % Because we use hanging indentation in footnotes, a @noindent appears
+ % to exdent this text, so make it be a no-op. makeinfo does not use
+ % hanging indentation so @noindent can still be needed within footnote
+ % text after an @example or the like (not that this is good style).
+ \let\noindent = \relax
+ %
+ % Hang the footnote text off the number. Use \everypar in case the
+ % footnote extends for more than one paragraph.
+ \everypar = {\hang}%
+ \textindent{\thisfootno}%
+ %
+ % Don't crash into the line above the footnote text. Since this
+ % expands into a box, it must come within the paragraph, lest it
+ % provide a place where TeX can split the footnote.
+ \footstrut
+ \futurelet\next\fo at t
+}
+}%end \catcode `\@=11
+
+% In case a @footnote appears in a vbox, save the footnote text and create
+% the real \insert just after the vbox finished. Otherwise, the insertion
+% would be lost.
+% Similarly, if a @footnote appears inside an alignment, save the footnote
+% text to a box and make the \insert when a row of the table is finished.
+% And the same can be done for other insert classes. --kasal, 16nov03.
+
+% Replace the \insert primitive by a cheating macro.
+% Deeper inside, just make sure that the saved insertions are not spilled
+% out prematurely.
+%
+\def\startsavinginserts{%
+ \ifx \insert\ptexinsert
+ \let\insert\saveinsert
+ \else
+ \let\checkinserts\relax
+ \fi
+}
+
+% This \insert replacement works for both \insert\footins{foo} and
+% \insert\footins\bgroup foo\egroup, but it doesn't work for \insert27{foo}.
+%
+\def\saveinsert#1{%
+ \edef\next{\noexpand\savetobox \makeSAVEname#1}%
+ \afterassignment\next
+ % swallow the left brace
+ \let\temp =
+}
+\def\makeSAVEname#1{\makecsname{SAVE\expandafter\gobble\string#1}}
+\def\savetobox#1{\global\setbox#1 = \vbox\bgroup \unvbox#1}
+
+\def\checksaveins#1{\ifvoid#1\else \placesaveins#1\fi}
+
+\def\placesaveins#1{%
+ \ptexinsert \csname\expandafter\gobblesave\string#1\endcsname
+ {\box#1}%
+}
+
+% eat @SAVE -- beware, all of them have catcode \other:
+{
+ \def\dospecials{\do S\do A\do V\do E} \uncatcodespecials % ;-)
+ \gdef\gobblesave @SAVE{}
+}
+
+% initialization:
+\def\newsaveins #1{%
+ \edef\next{\noexpand\newsaveinsX \makeSAVEname#1}%
+ \next
+}
+\def\newsaveinsX #1{%
+ \csname newbox\endcsname #1%
+ \expandafter\def\expandafter\checkinserts\expandafter{\checkinserts
+ \checksaveins #1}%
+}
+
+% initialize:
+\let\checkinserts\empty
+\newsaveins\footins
+\newsaveins\margin
+
+
+% @image. We use the macros from epsf.tex to support this.
+% If epsf.tex is not installed and @image is used, we complain.
+%
+% Check for and read epsf.tex up front. If we read it only at @image
+% time, we might be inside a group, and then its definitions would get
+% undone and the next image would fail.
+\openin 1 = epsf.tex
+\ifeof 1 \else
+ % Do not bother showing banner with epsf.tex v2.7k (available in
+ % doc/epsf.tex and on ctan).
+ \def\epsfannounce{\toks0 = }%
+ \input epsf.tex
+\fi
+\closein 1
+%
+% We will only complain once about lack of epsf.tex.
+\newif\ifwarnednoepsf
+\newhelp\noepsfhelp{epsf.tex must be installed for images to
+ work. It is also included in the Texinfo distribution, or you can get
+ it from ftp://tug.org/tex/epsf.tex.}
+%
+\def\image#1{%
+ \ifx\epsfbox\undefined
+ \ifwarnednoepsf \else
+ \errhelp = \noepsfhelp
+ \errmessage{epsf.tex not found, images will be ignored}%
+ \global\warnednoepsftrue
+ \fi
+ \else
+ \imagexxx #1,,,,,\finish
+ \fi
+}
+%
+% Arguments to @image:
+% #1 is (mandatory) image filename; we tack on .eps extension.
+% #2 is (optional) width, #3 is (optional) height.
+% #4 is (ignored optional) html alt text.
+% #5 is (ignored optional) extension.
+% #6 is just the usual extra ignored arg for parsing this stuff.
+\newif\ifimagevmode
+\def\imagexxx#1,#2,#3,#4,#5,#6\finish{\begingroup
+ \catcode`\^^M = 5 % in case we're inside an example
+ \normalturnoffactive % allow _ et al. in names
+ % If the image is by itself, center it.
+ \ifvmode
+ \imagevmodetrue
+ \nobreak\medskip
+ % Usually we'll have text after the image which will insert
+ % \parskip glue, so insert it here too to equalize the space
+ % above and below.
+ \nobreak\vskip\parskip
+ \nobreak
+ \fi
+ %
+ % Leave vertical mode so that indentation from an enclosing
+ % environment such as @quotation is respected. On the other hand, if
+ % it's at the top level, we don't want the normal paragraph indentation.
+ \noindent
+ %
+ % Output the image.
+ \ifpdf
+ \dopdfimage{#1}{#2}{#3}%
+ \else
+ % \epsfbox itself resets \epsf?size at each figure.
+ \setbox0 = \hbox{\ignorespaces #2}\ifdim\wd0 > 0pt \epsfxsize=#2\relax \fi
+ \setbox0 = \hbox{\ignorespaces #3}\ifdim\wd0 > 0pt \epsfysize=#3\relax \fi
+ \epsfbox{#1.eps}%
+ \fi
+ %
+ \ifimagevmode \medskip \fi % space after the standalone image
+\endgroup}
+
+
+% @float FLOATTYPE,LABEL,LOC ... @end float for displayed figures, tables,
+% etc. We don't actually implement floating yet, we always include the
+% float "here". But it seemed the best name for the future.
+%
+\envparseargdef\float{\eatcommaspace\eatcommaspace\dofloat#1, , ,\finish}
+
+% There may be a space before second and/or third parameter; delete it.
+\def\eatcommaspace#1, {#1,}
+
+% #1 is the optional FLOATTYPE, the text label for this float, typically
+% "Figure", "Table", "Example", etc. Can't contain commas. If omitted,
+% this float will not be numbered and cannot be referred to.
+%
+% #2 is the optional xref label. Also must be present for the float to
+% be referable.
+%
+% #3 is the optional positioning argument; for now, it is ignored. It
+% will somehow specify the positions allowed to float to (here, top, bottom).
+%
+% We keep a separate counter for each FLOATTYPE, which we reset at each
+% chapter-level command.
+\let\resetallfloatnos=\empty
+%
+\def\dofloat#1,#2,#3,#4\finish{%
+ \let\thiscaption=\empty
+ \let\thisshortcaption=\empty
+ %
+ % don't lose footnotes inside @float.
+ %
+ % BEWARE: when the floats start float, we have to issue warning whenever an
+ % insert appears inside a float which could possibly float. --kasal, 26may04
+ %
+ \startsavinginserts
+ %
+ % We can't be used inside a paragraph.
+ \par
+ %
+ \vtop\bgroup
+ \def\floattype{#1}%
+ \def\floatlabel{#2}%
+ \def\floatloc{#3}% we do nothing with this yet.
+ %
+ \ifx\floattype\empty
+ \let\safefloattype=\empty
+ \else
+ {%
+ % the floattype might have accents or other special characters,
+ % but we need to use it in a control sequence name.
+ \indexnofonts
+ \turnoffactive
+ \xdef\safefloattype{\floattype}%
+ }%
+ \fi
+ %
+ % If label is given but no type, we handle that as the empty type.
+ \ifx\floatlabel\empty \else
+ % We want each FLOATTYPE to be numbered separately (Figure 1,
+ % Table 1, Figure 2, ...). (And if no label, no number.)
+ %
+ \expandafter\getfloatno\csname\safefloattype floatno\endcsname
+ \global\advance\floatno by 1
+ %
+ {%
+ % This magic value for \lastsection is output by \setref as the
+ % XREFLABEL-title value. \xrefX uses it to distinguish float
+ % labels (which have a completely different output format) from
+ % node and anchor labels. And \xrdef uses it to construct the
+ % lists of floats.
+ %
+ \edef\lastsection{\floatmagic=\safefloattype}%
+ \setref{\floatlabel}{Yfloat}%
+ }%
+ \fi
+ %
+ % start with \parskip glue, I guess.
+ \vskip\parskip
+ %
+ % Don't suppress indentation if a float happens to start a section.
+ \restorefirstparagraphindent
+}
+
+% we have these possibilities:
+% @float Foo,lbl & @caption{Cap}: Foo 1.1: Cap
+% @float Foo,lbl & no caption: Foo 1.1
+% @float Foo & @caption{Cap}: Foo: Cap
+% @float Foo & no caption: Foo
+% @float ,lbl & Caption{Cap}: 1.1: Cap
+% @float ,lbl & no caption: 1.1
+% @float & @caption{Cap}: Cap
+% @float & no caption:
+%
+\def\Efloat{%
+ \let\floatident = \empty
+ %
+ % In all cases, if we have a float type, it comes first.
+ \ifx\floattype\empty \else \def\floatident{\floattype}\fi
+ %
+ % If we have an xref label, the number comes next.
+ \ifx\floatlabel\empty \else
+ \ifx\floattype\empty \else % if also had float type, need tie first.
+ \appendtomacro\floatident{\tie}%
+ \fi
+ % the number.
+ \appendtomacro\floatident{\chaplevelprefix\the\floatno}%
+ \fi
+ %
+ % Start the printed caption with what we've constructed in
+ % \floatident, but keep it separate; we need \floatident again.
+ \let\captionline = \floatident
+ %
+ \ifx\thiscaption\empty \else
+ \ifx\floatident\empty \else
+ \appendtomacro\captionline{: }% had ident, so need a colon between
+ \fi
+ %
+ % caption text.
+ \appendtomacro\captionline{\scanexp\thiscaption}%
+ \fi
+ %
+ % If we have anything to print, print it, with space before.
+ % Eventually this needs to become an \insert.
+ \ifx\captionline\empty \else
+ \vskip.5\parskip
+ \captionline
+ %
+ % Space below caption.
+ \vskip\parskip
+ \fi
+ %
+ % If have an xref label, write the list of floats info. Do this
+ % after the caption, to avoid chance of it being a breakpoint.
+ \ifx\floatlabel\empty \else
+ % Write the text that goes in the lof to the aux file as
+ % \floatlabel-lof. Besides \floatident, we include the short
+ % caption if specified, else the full caption if specified, else nothing.
+ {%
+ \atdummies
+ %
+ % since we read the caption text in the macro world, where ^^M
+ % is turned into a normal character, we have to scan it back, so
+ % we don't write the literal three characters "^^M" into the aux file.
+ \scanexp{%
+ \xdef\noexpand\gtemp{%
+ \ifx\thisshortcaption\empty
+ \thiscaption
+ \else
+ \thisshortcaption
+ \fi
+ }%
+ }%
+ \immediate\write\auxfile{@xrdef{\floatlabel-lof}{\floatident
+ \ifx\gtemp\empty \else : \gtemp \fi}}%
+ }%
+ \fi
+ \egroup % end of \vtop
+ %
+ % place the captured inserts
+ %
+ % BEWARE: when the floats start floating, we have to issue warning
+ % whenever an insert appears inside a float which could possibly
+ % float. --kasal, 26may04
+ %
+ \checkinserts
+}
+
+% Append the tokens #2 to the definition of macro #1, not expanding either.
+%
+\def\appendtomacro#1#2{%
+ \expandafter\def\expandafter#1\expandafter{#1#2}%
+}
+
+% @caption, @shortcaption
+%
+\def\caption{\docaption\thiscaption}
+\def\shortcaption{\docaption\thisshortcaption}
+\def\docaption{\checkenv\float \bgroup\scanargctxt\defcaption}
+\def\defcaption#1#2{\egroup \def#1{#2}}
+
+% The parameter is the control sequence identifying the counter we are
+% going to use. Create it if it doesn't exist and assign it to \floatno.
+\def\getfloatno#1{%
+ \ifx#1\relax
+ % Haven't seen this figure type before.
+ \csname newcount\endcsname #1%
+ %
+ % Remember to reset this floatno at the next chap.
+ \expandafter\gdef\expandafter\resetallfloatnos
+ \expandafter{\resetallfloatnos #1=0 }%
+ \fi
+ \let\floatno#1%
+}
+
+% \setref calls this to get the XREFLABEL-snt value. We want an @xref
+% to the FLOATLABEL to expand to "Figure 3.1". We call \setref when we
+% first read the @float command.
+%
+\def\Yfloat{\floattype at tie \chaplevelprefix\the\floatno}%
+
+% Magic string used for the XREFLABEL-title value, so \xrefX can
+% distinguish floats from other xref types.
+\def\floatmagic{!!float!!}
+
+% #1 is the control sequence we are passed; we expand into a conditional
+% which is true if #1 represents a float ref. That is, the magic
+% \lastsection value which we \setref above.
+%
+\def\iffloat#1{\expandafter\doiffloat#1==\finish}
+%
+% #1 is (maybe) the \floatmagic string. If so, #2 will be the
+% (safe) float type for this float. We set \iffloattype to #2.
+%
+\def\doiffloat#1=#2=#3\finish{%
+ \def\temp{#1}%
+ \def\iffloattype{#2}%
+ \ifx\temp\floatmagic
+}
+
+% @listoffloats FLOATTYPE - print a list of floats like a table of contents.
+%
+\parseargdef\listoffloats{%
+ \def\floattype{#1}% floattype
+ {%
+ % the floattype might have accents or other special characters,
+ % but we need to use it in a control sequence name.
+ \indexnofonts
+ \turnoffactive
+ \xdef\safefloattype{\floattype}%
+ }%
+ %
+ % \xrdef saves the floats as a \do-list in \floatlistSAFEFLOATTYPE.
+ \expandafter\ifx\csname floatlist\safefloattype\endcsname \relax
+ \ifhavexrefs
+ % if the user said @listoffloats foo but never @float foo.
+ \message{\linenumber No `\safefloattype' floats to list.}%
+ \fi
+ \else
+ \begingroup
+ \leftskip=\tocindent % indent these entries like a toc
+ \let\do=\listoffloatsdo
+ \csname floatlist\safefloattype\endcsname
+ \endgroup
+ \fi
+}
+
+% This is called on each entry in a list of floats. We're passed the
+% xref label, in the form LABEL-title, which is how we save it in the
+% aux file. We strip off the -title and look up \XRLABEL-lof, which
+% has the text we're supposed to typeset here.
+%
+% Figures without xref labels will not be included in the list (since
+% they won't appear in the aux file).
+%
+\def\listoffloatsdo#1{\listoffloatsdoentry#1\finish}
+\def\listoffloatsdoentry#1-title\finish{{%
+ % Can't fully expand XR#1-lof because it can contain anything. Just
+ % pass the control sequence. On the other hand, XR#1-pg is just the
+ % page number, and we want to fully expand that so we can get a link
+ % in pdf output.
+ \toksA = \expandafter{\csname XR#1-lof\endcsname}%
+ %
+ % use the same \entry macro we use to generate the TOC and index.
+ \edef\writeentry{\noexpand\entry{\the\toksA}{\csname XR#1-pg\endcsname}}%
+ \writeentry
+}}
+
+
+\message{localization,}
+
+% For single-language documents, @documentlanguage is usually given very
+% early, just after @documentencoding. Single argument is the language
+% (de) or locale (de_DE) abbreviation.
+%
+{
+ \catcode`\_ = \active
+ \globaldefs=1
+\parseargdef\documentlanguage{\begingroup
+ \let_=\normalunderscore % normal _ character for filenames
+ \tex % read txi-??.tex file in plain TeX.
+ % Read the file by the name they passed if it exists.
+ \openin 1 txi-#1.tex
+ \ifeof 1
+ \documentlanguagetrywithoutunderscore{#1_\finish}%
+ \else
+ \globaldefs = 1 % everything in the txi-LL files needs to persist
+ \input txi-#1.tex
+ \fi
+ \closein 1
+ \endgroup % end raw TeX
+\endgroup}
+%
+% If they passed de_DE, and txi-de_DE.tex doesn't exist,
+% try txi-de.tex.
+%
+\gdef\documentlanguagetrywithoutunderscore#1_#2\finish{%
+ \openin 1 txi-#1.tex
+ \ifeof 1
+ \errhelp = \nolanghelp
+ \errmessage{Cannot read language file txi-#1.tex}%
+ \else
+ \globaldefs = 1 % everything in the txi-LL files needs to persist
+ \input txi-#1.tex
+ \fi
+ \closein 1
+}
+}% end of special _ catcode
+%
+\newhelp\nolanghelp{The given language definition file cannot be found or
+is empty. Maybe you need to install it? Putting it in the current
+directory should work if nowhere else does.}
+
+% This macro is called from txi-??.tex files; the first argument is the
+% \language name to set (without the "\lang@" prefix), the second and
+% third args are \{left,right}hyphenmin.
+%
+% The language names to pass are determined when the format is built.
+% See the etex.log file created at that time, e.g.,
+% /usr/local/texlive/2008/texmf-var/web2c/pdftex/etex.log.
+%
+% With TeX Live 2008, etex now includes hyphenation patterns for all
+% available languages. This means we can support hyphenation in
+% Texinfo, at least to some extent. (This still doesn't solve the
+% accented characters problem.)
+%
+\catcode`@=11
+\def\txisetlanguage#1#2#3{%
+ % do not set the language if the name is undefined in the current TeX.
+ \expandafter\ifx\csname lang@#1\endcsname \relax
+ \message{no patterns for #1}%
+ \else
+ \global\language = \csname lang@#1\endcsname
+ \fi
+ % but there is no harm in adjusting the hyphenmin values regardless.
+ \global\lefthyphenmin = #2\relax
+ \global\righthyphenmin = #3\relax
+}
+
+% Helpers for encodings.
+% Set the catcode of characters 128 through 255 to the specified number.
+%
+\def\setnonasciicharscatcode#1{%
+ \count255=128
+ \loop\ifnum\count255<256
+ \global\catcode\count255=#1\relax
+ \advance\count255 by 1
+ \repeat
+}
+
+\def\setnonasciicharscatcodenonglobal#1{%
+ \count255=128
+ \loop\ifnum\count255<256
+ \catcode\count255=#1\relax
+ \advance\count255 by 1
+ \repeat
+}
+
+% @documentencoding sets the definition of non-ASCII characters
+% according to the specified encoding.
+%
+\parseargdef\documentencoding{%
+ % Encoding being declared for the document.
+ \def\declaredencoding{\csname #1.enc\endcsname}%
+ %
+ % Supported encodings: names converted to tokens in order to be able
+ % to compare them with \ifx.
+ \def\ascii{\csname US-ASCII.enc\endcsname}%
+ \def\latnine{\csname ISO-8859-15.enc\endcsname}%
+ \def\latone{\csname ISO-8859-1.enc\endcsname}%
+ \def\lattwo{\csname ISO-8859-2.enc\endcsname}%
+ \def\utfeight{\csname UTF-8.enc\endcsname}%
+ %
+ \ifx \declaredencoding \ascii
+ \asciichardefs
+ %
+ \else \ifx \declaredencoding \lattwo
+ \setnonasciicharscatcode\active
+ \lattwochardefs
+ %
+ \else \ifx \declaredencoding \latone
+ \setnonasciicharscatcode\active
+ \latonechardefs
+ %
+ \else \ifx \declaredencoding \latnine
+ \setnonasciicharscatcode\active
+ \latninechardefs
+ %
+ \else \ifx \declaredencoding \utfeight
+ \setnonasciicharscatcode\active
+ \utfeightchardefs
+ %
+ \else
+ \message{Unknown document encoding #1, ignoring.}%
+ %
+ \fi % utfeight
+ \fi % latnine
+ \fi % latone
+ \fi % lattwo
+ \fi % ascii
+}
+
+% A message to be logged when using a character that isn't available
+% the default font encoding (OT1).
+%
+\def\missingcharmsg#1{\message{Character missing in OT1 encoding: #1.}}
+
+% Take account of \c (plain) vs. \, (Texinfo) difference.
+\def\cedilla#1{\ifx\c\ptexc\c{#1}\else\,{#1}\fi}
+
+% First, make active non-ASCII characters in order for them to be
+% correctly categorized when TeX reads the replacement text of
+% macros containing the character definitions.
+\setnonasciicharscatcode\active
+%
+% Latin1 (ISO-8859-1) character definitions.
+\def\latonechardefs{%
+ \gdef^^a0{~}
+ \gdef^^a1{\exclamdown}
+ \gdef^^a2{\missingcharmsg{CENT SIGN}}
+ \gdef^^a3{{\pounds}}
+ \gdef^^a4{\missingcharmsg{CURRENCY SIGN}}
+ \gdef^^a5{\missingcharmsg{YEN SIGN}}
+ \gdef^^a6{\missingcharmsg{BROKEN BAR}}
+ \gdef^^a7{\S}
+ \gdef^^a8{\"{}}
+ \gdef^^a9{\copyright}
+ \gdef^^aa{\ordf}
+ \gdef^^ab{\guillemetleft}
+ \gdef^^ac{$\lnot$}
+ \gdef^^ad{\-}
+ \gdef^^ae{\registeredsymbol}
+ \gdef^^af{\={}}
+ %
+ \gdef^^b0{\textdegree}
+ \gdef^^b1{$\pm$}
+ \gdef^^b2{$^2$}
+ \gdef^^b3{$^3$}
+ \gdef^^b4{\'{}}
+ \gdef^^b5{$\mu$}
+ \gdef^^b6{\P}
+ %
+ \gdef^^b7{$^.$}
+ \gdef^^b8{\cedilla\ }
+ \gdef^^b9{$^1$}
+ \gdef^^ba{\ordm}
+ %
+ \gdef^^bb{\guilletright}
+ \gdef^^bc{$1\over4$}
+ \gdef^^bd{$1\over2$}
+ \gdef^^be{$3\over4$}
+ \gdef^^bf{\questiondown}
+ %
+ \gdef^^c0{\`A}
+ \gdef^^c1{\'A}
+ \gdef^^c2{\^A}
+ \gdef^^c3{\~A}
+ \gdef^^c4{\"A}
+ \gdef^^c5{\ringaccent A}
+ \gdef^^c6{\AE}
+ \gdef^^c7{\cedilla C}
+ \gdef^^c8{\`E}
+ \gdef^^c9{\'E}
+ \gdef^^ca{\^E}
+ \gdef^^cb{\"E}
+ \gdef^^cc{\`I}
+ \gdef^^cd{\'I}
+ \gdef^^ce{\^I}
+ \gdef^^cf{\"I}
+ %
+ \gdef^^d0{\DH}
+ \gdef^^d1{\~N}
+ \gdef^^d2{\`O}
+ \gdef^^d3{\'O}
+ \gdef^^d4{\^O}
+ \gdef^^d5{\~O}
+ \gdef^^d6{\"O}
+ \gdef^^d7{$\times$}
+ \gdef^^d8{\O}
+ \gdef^^d9{\`U}
+ \gdef^^da{\'U}
+ \gdef^^db{\^U}
+ \gdef^^dc{\"U}
+ \gdef^^dd{\'Y}
+ \gdef^^de{\TH}
+ \gdef^^df{\ss}
+ %
+ \gdef^^e0{\`a}
+ \gdef^^e1{\'a}
+ \gdef^^e2{\^a}
+ \gdef^^e3{\~a}
+ \gdef^^e4{\"a}
+ \gdef^^e5{\ringaccent a}
+ \gdef^^e6{\ae}
+ \gdef^^e7{\cedilla c}
+ \gdef^^e8{\`e}
+ \gdef^^e9{\'e}
+ \gdef^^ea{\^e}
+ \gdef^^eb{\"e}
+ \gdef^^ec{\`{\dotless i}}
+ \gdef^^ed{\'{\dotless i}}
+ \gdef^^ee{\^{\dotless i}}
+ \gdef^^ef{\"{\dotless i}}
+ %
+ \gdef^^f0{\dh}
+ \gdef^^f1{\~n}
+ \gdef^^f2{\`o}
+ \gdef^^f3{\'o}
+ \gdef^^f4{\^o}
+ \gdef^^f5{\~o}
+ \gdef^^f6{\"o}
+ \gdef^^f7{$\div$}
+ \gdef^^f8{\o}
+ \gdef^^f9{\`u}
+ \gdef^^fa{\'u}
+ \gdef^^fb{\^u}
+ \gdef^^fc{\"u}
+ \gdef^^fd{\'y}
+ \gdef^^fe{\th}
+ \gdef^^ff{\"y}
+}
+
+% Latin9 (ISO-8859-15) encoding character definitions.
+\def\latninechardefs{%
+ % Encoding is almost identical to Latin1.
+ \latonechardefs
+ %
+ \gdef^^a4{\euro}
+ \gdef^^a6{\v S}
+ \gdef^^a8{\v s}
+ \gdef^^b4{\v Z}
+ \gdef^^b8{\v z}
+ \gdef^^bc{\OE}
+ \gdef^^bd{\oe}
+ \gdef^^be{\"Y}
+}
+
+% Latin2 (ISO-8859-2) character definitions.
+\def\lattwochardefs{%
+ \gdef^^a0{~}
+ \gdef^^a1{\ogonek{A}}
+ \gdef^^a2{\u{}}
+ \gdef^^a3{\L}
+ \gdef^^a4{\missingcharmsg{CURRENCY SIGN}}
+ \gdef^^a5{\v L}
+ \gdef^^a6{\'S}
+ \gdef^^a7{\S}
+ \gdef^^a8{\"{}}
+ \gdef^^a9{\v S}
+ \gdef^^aa{\cedilla S}
+ \gdef^^ab{\v T}
+ \gdef^^ac{\'Z}
+ \gdef^^ad{\-}
+ \gdef^^ae{\v Z}
+ \gdef^^af{\dotaccent Z}
+ %
+ \gdef^^b0{\textdegree}
+ \gdef^^b1{\ogonek{a}}
+ \gdef^^b2{\ogonek{ }}
+ \gdef^^b3{\l}
+ \gdef^^b4{\'{}}
+ \gdef^^b5{\v l}
+ \gdef^^b6{\'s}
+ \gdef^^b7{\v{}}
+ \gdef^^b8{\cedilla\ }
+ \gdef^^b9{\v s}
+ \gdef^^ba{\cedilla s}
+ \gdef^^bb{\v t}
+ \gdef^^bc{\'z}
+ \gdef^^bd{\H{}}
+ \gdef^^be{\v z}
+ \gdef^^bf{\dotaccent z}
+ %
+ \gdef^^c0{\'R}
+ \gdef^^c1{\'A}
+ \gdef^^c2{\^A}
+ \gdef^^c3{\u A}
+ \gdef^^c4{\"A}
+ \gdef^^c5{\'L}
+ \gdef^^c6{\'C}
+ \gdef^^c7{\cedilla C}
+ \gdef^^c8{\v C}
+ \gdef^^c9{\'E}
+ \gdef^^ca{\ogonek{E}}
+ \gdef^^cb{\"E}
+ \gdef^^cc{\v E}
+ \gdef^^cd{\'I}
+ \gdef^^ce{\^I}
+ \gdef^^cf{\v D}
+ %
+ \gdef^^d0{\DH}
+ \gdef^^d1{\'N}
+ \gdef^^d2{\v N}
+ \gdef^^d3{\'O}
+ \gdef^^d4{\^O}
+ \gdef^^d5{\H O}
+ \gdef^^d6{\"O}
+ \gdef^^d7{$\times$}
+ \gdef^^d8{\v R}
+ \gdef^^d9{\ringaccent U}
+ \gdef^^da{\'U}
+ \gdef^^db{\H U}
+ \gdef^^dc{\"U}
+ \gdef^^dd{\'Y}
+ \gdef^^de{\cedilla T}
+ \gdef^^df{\ss}
+ %
+ \gdef^^e0{\'r}
+ \gdef^^e1{\'a}
+ \gdef^^e2{\^a}
+ \gdef^^e3{\u a}
+ \gdef^^e4{\"a}
+ \gdef^^e5{\'l}
+ \gdef^^e6{\'c}
+ \gdef^^e7{\cedilla c}
+ \gdef^^e8{\v c}
+ \gdef^^e9{\'e}
+ \gdef^^ea{\ogonek{e}}
+ \gdef^^eb{\"e}
+ \gdef^^ec{\v e}
+ \gdef^^ed{\'\i}
+ \gdef^^ee{\^\i}
+ \gdef^^ef{\v d}
+ %
+ \gdef^^f0{\dh}
+ \gdef^^f1{\'n}
+ \gdef^^f2{\v n}
+ \gdef^^f3{\'o}
+ \gdef^^f4{\^o}
+ \gdef^^f5{\H o}
+ \gdef^^f6{\"o}
+ \gdef^^f7{$\div$}
+ \gdef^^f8{\v r}
+ \gdef^^f9{\ringaccent u}
+ \gdef^^fa{\'u}
+ \gdef^^fb{\H u}
+ \gdef^^fc{\"u}
+ \gdef^^fd{\'y}
+ \gdef^^fe{\cedilla t}
+ \gdef^^ff{\dotaccent{}}
+}
+
+% UTF-8 character definitions.
+%
+% This code to support UTF-8 is based on LaTeX's utf8.def, with some
+% changes for Texinfo conventions. It is included here under the GPL by
+% permission from Frank Mittelbach and the LaTeX team.
+%
+\newcount\countUTFx
+\newcount\countUTFy
+\newcount\countUTFz
+
+\gdef\UTFviiiTwoOctets#1#2{\expandafter
+ \UTFviiiDefined\csname u8:#1\string #2\endcsname}
+%
+\gdef\UTFviiiThreeOctets#1#2#3{\expandafter
+ \UTFviiiDefined\csname u8:#1\string #2\string #3\endcsname}
+%
+\gdef\UTFviiiFourOctets#1#2#3#4{\expandafter
+ \UTFviiiDefined\csname u8:#1\string #2\string #3\string #4\endcsname}
+
+\gdef\UTFviiiDefined#1{%
+ \ifx #1\relax
+ \message{\linenumber Unicode char \string #1 not defined for Texinfo}%
+ \else
+ \expandafter #1%
+ \fi
+}
+
+\begingroup
+ \catcode`\~13
+ \catcode`\"12
+
+ \def\UTFviiiLoop{%
+ \global\catcode\countUTFx\active
+ \uccode`\~\countUTFx
+ \uppercase\expandafter{\UTFviiiTmp}%
+ \advance\countUTFx by 1
+ \ifnum\countUTFx < \countUTFy
+ \expandafter\UTFviiiLoop
+ \fi}
+
+ \countUTFx = "C2
+ \countUTFy = "E0
+ \def\UTFviiiTmp{%
+ \xdef~{\noexpand\UTFviiiTwoOctets\string~}}
+ \UTFviiiLoop
+
+ \countUTFx = "E0
+ \countUTFy = "F0
+ \def\UTFviiiTmp{%
+ \xdef~{\noexpand\UTFviiiThreeOctets\string~}}
+ \UTFviiiLoop
+
+ \countUTFx = "F0
+ \countUTFy = "F4
+ \def\UTFviiiTmp{%
+ \xdef~{\noexpand\UTFviiiFourOctets\string~}}
+ \UTFviiiLoop
+\endgroup
+
+\begingroup
+ \catcode`\"=12
+ \catcode`\<=12
+ \catcode`\.=12
+ \catcode`\,=12
+ \catcode`\;=12
+ \catcode`\!=12
+ \catcode`\~=13
+
+ \gdef\DeclareUnicodeCharacter#1#2{%
+ \countUTFz = "#1\relax
+ \wlog{\space\space defining Unicode char U+#1 (decimal \the\countUTFz)}%
+ \begingroup
+ \parseXMLCharref
+ \def\UTFviiiTwoOctets##1##2{%
+ \csname u8:##1\string ##2\endcsname}%
+ \def\UTFviiiThreeOctets##1##2##3{%
+ \csname u8:##1\string ##2\string ##3\endcsname}%
+ \def\UTFviiiFourOctets##1##2##3##4{%
+ \csname u8:##1\string ##2\string ##3\string ##4\endcsname}%
+ \expandafter\expandafter\expandafter\expandafter
+ \expandafter\expandafter\expandafter
+ \gdef\UTFviiiTmp{#2}%
+ \endgroup}
+
+ \gdef\parseXMLCharref{%
+ \ifnum\countUTFz < "A0\relax
+ \errhelp = \EMsimple
+ \errmessage{Cannot define Unicode char value < 00A0}%
+ \else\ifnum\countUTFz < "800\relax
+ \parseUTFviiiA,%
+ \parseUTFviiiB C\UTFviiiTwoOctets.,%
+ \else\ifnum\countUTFz < "10000\relax
+ \parseUTFviiiA;%
+ \parseUTFviiiA,%
+ \parseUTFviiiB E\UTFviiiThreeOctets.{,;}%
+ \else
+ \parseUTFviiiA;%
+ \parseUTFviiiA,%
+ \parseUTFviiiA!%
+ \parseUTFviiiB F\UTFviiiFourOctets.{!,;}%
+ \fi\fi\fi
+ }
+
+ \gdef\parseUTFviiiA#1{%
+ \countUTFx = \countUTFz
+ \divide\countUTFz by 64
+ \countUTFy = \countUTFz
+ \multiply\countUTFz by 64
+ \advance\countUTFx by -\countUTFz
+ \advance\countUTFx by 128
+ \uccode `#1\countUTFx
+ \countUTFz = \countUTFy}
+
+ \gdef\parseUTFviiiB#1#2#3#4{%
+ \advance\countUTFz by "#10\relax
+ \uccode `#3\countUTFz
+ \uppercase{\gdef\UTFviiiTmp{#2#3#4}}}
+\endgroup
+
+\def\utfeightchardefs{%
+ \DeclareUnicodeCharacter{00A0}{\tie}
+ \DeclareUnicodeCharacter{00A1}{\exclamdown}
+ \DeclareUnicodeCharacter{00A3}{\pounds}
+ \DeclareUnicodeCharacter{00A8}{\"{ }}
+ \DeclareUnicodeCharacter{00A9}{\copyright}
+ \DeclareUnicodeCharacter{00AA}{\ordf}
+ \DeclareUnicodeCharacter{00AB}{\guillemetleft}
+ \DeclareUnicodeCharacter{00AD}{\-}
+ \DeclareUnicodeCharacter{00AE}{\registeredsymbol}
+ \DeclareUnicodeCharacter{00AF}{\={ }}
+
+ \DeclareUnicodeCharacter{00B0}{\ringaccent{ }}
+ \DeclareUnicodeCharacter{00B4}{\'{ }}
+ \DeclareUnicodeCharacter{00B8}{\cedilla{ }}
+ \DeclareUnicodeCharacter{00BA}{\ordm}
+ \DeclareUnicodeCharacter{00BB}{\guillemetright}
+ \DeclareUnicodeCharacter{00BF}{\questiondown}
+
+ \DeclareUnicodeCharacter{00C0}{\`A}
+ \DeclareUnicodeCharacter{00C1}{\'A}
+ \DeclareUnicodeCharacter{00C2}{\^A}
+ \DeclareUnicodeCharacter{00C3}{\~A}
+ \DeclareUnicodeCharacter{00C4}{\"A}
+ \DeclareUnicodeCharacter{00C5}{\AA}
+ \DeclareUnicodeCharacter{00C6}{\AE}
+ \DeclareUnicodeCharacter{00C7}{\cedilla{C}}
+ \DeclareUnicodeCharacter{00C8}{\`E}
+ \DeclareUnicodeCharacter{00C9}{\'E}
+ \DeclareUnicodeCharacter{00CA}{\^E}
+ \DeclareUnicodeCharacter{00CB}{\"E}
+ \DeclareUnicodeCharacter{00CC}{\`I}
+ \DeclareUnicodeCharacter{00CD}{\'I}
+ \DeclareUnicodeCharacter{00CE}{\^I}
+ \DeclareUnicodeCharacter{00CF}{\"I}
+
+ \DeclareUnicodeCharacter{00D0}{\DH}
+ \DeclareUnicodeCharacter{00D1}{\~N}
+ \DeclareUnicodeCharacter{00D2}{\`O}
+ \DeclareUnicodeCharacter{00D3}{\'O}
+ \DeclareUnicodeCharacter{00D4}{\^O}
+ \DeclareUnicodeCharacter{00D5}{\~O}
+ \DeclareUnicodeCharacter{00D6}{\"O}
+ \DeclareUnicodeCharacter{00D8}{\O}
+ \DeclareUnicodeCharacter{00D9}{\`U}
+ \DeclareUnicodeCharacter{00DA}{\'U}
+ \DeclareUnicodeCharacter{00DB}{\^U}
+ \DeclareUnicodeCharacter{00DC}{\"U}
+ \DeclareUnicodeCharacter{00DD}{\'Y}
+ \DeclareUnicodeCharacter{00DE}{\TH}
+ \DeclareUnicodeCharacter{00DF}{\ss}
+
+ \DeclareUnicodeCharacter{00E0}{\`a}
+ \DeclareUnicodeCharacter{00E1}{\'a}
+ \DeclareUnicodeCharacter{00E2}{\^a}
+ \DeclareUnicodeCharacter{00E3}{\~a}
+ \DeclareUnicodeCharacter{00E4}{\"a}
+ \DeclareUnicodeCharacter{00E5}{\aa}
+ \DeclareUnicodeCharacter{00E6}{\ae}
+ \DeclareUnicodeCharacter{00E7}{\cedilla{c}}
+ \DeclareUnicodeCharacter{00E8}{\`e}
+ \DeclareUnicodeCharacter{00E9}{\'e}
+ \DeclareUnicodeCharacter{00EA}{\^e}
+ \DeclareUnicodeCharacter{00EB}{\"e}
+ \DeclareUnicodeCharacter{00EC}{\`{\dotless{i}}}
+ \DeclareUnicodeCharacter{00ED}{\'{\dotless{i}}}
+ \DeclareUnicodeCharacter{00EE}{\^{\dotless{i}}}
+ \DeclareUnicodeCharacter{00EF}{\"{\dotless{i}}}
+
+ \DeclareUnicodeCharacter{00F0}{\dh}
+ \DeclareUnicodeCharacter{00F1}{\~n}
+ \DeclareUnicodeCharacter{00F2}{\`o}
+ \DeclareUnicodeCharacter{00F3}{\'o}
+ \DeclareUnicodeCharacter{00F4}{\^o}
+ \DeclareUnicodeCharacter{00F5}{\~o}
+ \DeclareUnicodeCharacter{00F6}{\"o}
+ \DeclareUnicodeCharacter{00F8}{\o}
+ \DeclareUnicodeCharacter{00F9}{\`u}
+ \DeclareUnicodeCharacter{00FA}{\'u}
+ \DeclareUnicodeCharacter{00FB}{\^u}
+ \DeclareUnicodeCharacter{00FC}{\"u}
+ \DeclareUnicodeCharacter{00FD}{\'y}
+ \DeclareUnicodeCharacter{00FE}{\th}
+ \DeclareUnicodeCharacter{00FF}{\"y}
+
+ \DeclareUnicodeCharacter{0100}{\=A}
+ \DeclareUnicodeCharacter{0101}{\=a}
+ \DeclareUnicodeCharacter{0102}{\u{A}}
+ \DeclareUnicodeCharacter{0103}{\u{a}}
+ \DeclareUnicodeCharacter{0104}{\ogonek{A}}
+ \DeclareUnicodeCharacter{0105}{\ogonek{a}}
+ \DeclareUnicodeCharacter{0106}{\'C}
+ \DeclareUnicodeCharacter{0107}{\'c}
+ \DeclareUnicodeCharacter{0108}{\^C}
+ \DeclareUnicodeCharacter{0109}{\^c}
+ \DeclareUnicodeCharacter{0118}{\ogonek{E}}
+ \DeclareUnicodeCharacter{0119}{\ogonek{e}}
+ \DeclareUnicodeCharacter{010A}{\dotaccent{C}}
+ \DeclareUnicodeCharacter{010B}{\dotaccent{c}}
+ \DeclareUnicodeCharacter{010C}{\v{C}}
+ \DeclareUnicodeCharacter{010D}{\v{c}}
+ \DeclareUnicodeCharacter{010E}{\v{D}}
+
+ \DeclareUnicodeCharacter{0112}{\=E}
+ \DeclareUnicodeCharacter{0113}{\=e}
+ \DeclareUnicodeCharacter{0114}{\u{E}}
+ \DeclareUnicodeCharacter{0115}{\u{e}}
+ \DeclareUnicodeCharacter{0116}{\dotaccent{E}}
+ \DeclareUnicodeCharacter{0117}{\dotaccent{e}}
+ \DeclareUnicodeCharacter{011A}{\v{E}}
+ \DeclareUnicodeCharacter{011B}{\v{e}}
+ \DeclareUnicodeCharacter{011C}{\^G}
+ \DeclareUnicodeCharacter{011D}{\^g}
+ \DeclareUnicodeCharacter{011E}{\u{G}}
+ \DeclareUnicodeCharacter{011F}{\u{g}}
+
+ \DeclareUnicodeCharacter{0120}{\dotaccent{G}}
+ \DeclareUnicodeCharacter{0121}{\dotaccent{g}}
+ \DeclareUnicodeCharacter{0124}{\^H}
+ \DeclareUnicodeCharacter{0125}{\^h}
+ \DeclareUnicodeCharacter{0128}{\~I}
+ \DeclareUnicodeCharacter{0129}{\~{\dotless{i}}}
+ \DeclareUnicodeCharacter{012A}{\=I}
+ \DeclareUnicodeCharacter{012B}{\={\dotless{i}}}
+ \DeclareUnicodeCharacter{012C}{\u{I}}
+ \DeclareUnicodeCharacter{012D}{\u{\dotless{i}}}
+
+ \DeclareUnicodeCharacter{0130}{\dotaccent{I}}
+ \DeclareUnicodeCharacter{0131}{\dotless{i}}
+ \DeclareUnicodeCharacter{0132}{IJ}
+ \DeclareUnicodeCharacter{0133}{ij}
+ \DeclareUnicodeCharacter{0134}{\^J}
+ \DeclareUnicodeCharacter{0135}{\^{\dotless{j}}}
+ \DeclareUnicodeCharacter{0139}{\'L}
+ \DeclareUnicodeCharacter{013A}{\'l}
+
+ \DeclareUnicodeCharacter{0141}{\L}
+ \DeclareUnicodeCharacter{0142}{\l}
+ \DeclareUnicodeCharacter{0143}{\'N}
+ \DeclareUnicodeCharacter{0144}{\'n}
+ \DeclareUnicodeCharacter{0147}{\v{N}}
+ \DeclareUnicodeCharacter{0148}{\v{n}}
+ \DeclareUnicodeCharacter{014C}{\=O}
+ \DeclareUnicodeCharacter{014D}{\=o}
+ \DeclareUnicodeCharacter{014E}{\u{O}}
+ \DeclareUnicodeCharacter{014F}{\u{o}}
+
+ \DeclareUnicodeCharacter{0150}{\H{O}}
+ \DeclareUnicodeCharacter{0151}{\H{o}}
+ \DeclareUnicodeCharacter{0152}{\OE}
+ \DeclareUnicodeCharacter{0153}{\oe}
+ \DeclareUnicodeCharacter{0154}{\'R}
+ \DeclareUnicodeCharacter{0155}{\'r}
+ \DeclareUnicodeCharacter{0158}{\v{R}}
+ \DeclareUnicodeCharacter{0159}{\v{r}}
+ \DeclareUnicodeCharacter{015A}{\'S}
+ \DeclareUnicodeCharacter{015B}{\'s}
+ \DeclareUnicodeCharacter{015C}{\^S}
+ \DeclareUnicodeCharacter{015D}{\^s}
+ \DeclareUnicodeCharacter{015E}{\cedilla{S}}
+ \DeclareUnicodeCharacter{015F}{\cedilla{s}}
+
+ \DeclareUnicodeCharacter{0160}{\v{S}}
+ \DeclareUnicodeCharacter{0161}{\v{s}}
+ \DeclareUnicodeCharacter{0162}{\cedilla{t}}
+ \DeclareUnicodeCharacter{0163}{\cedilla{T}}
+ \DeclareUnicodeCharacter{0164}{\v{T}}
+
+ \DeclareUnicodeCharacter{0168}{\~U}
+ \DeclareUnicodeCharacter{0169}{\~u}
+ \DeclareUnicodeCharacter{016A}{\=U}
+ \DeclareUnicodeCharacter{016B}{\=u}
+ \DeclareUnicodeCharacter{016C}{\u{U}}
+ \DeclareUnicodeCharacter{016D}{\u{u}}
+ \DeclareUnicodeCharacter{016E}{\ringaccent{U}}
+ \DeclareUnicodeCharacter{016F}{\ringaccent{u}}
+
+ \DeclareUnicodeCharacter{0170}{\H{U}}
+ \DeclareUnicodeCharacter{0171}{\H{u}}
+ \DeclareUnicodeCharacter{0174}{\^W}
+ \DeclareUnicodeCharacter{0175}{\^w}
+ \DeclareUnicodeCharacter{0176}{\^Y}
+ \DeclareUnicodeCharacter{0177}{\^y}
+ \DeclareUnicodeCharacter{0178}{\"Y}
+ \DeclareUnicodeCharacter{0179}{\'Z}
+ \DeclareUnicodeCharacter{017A}{\'z}
+ \DeclareUnicodeCharacter{017B}{\dotaccent{Z}}
+ \DeclareUnicodeCharacter{017C}{\dotaccent{z}}
+ \DeclareUnicodeCharacter{017D}{\v{Z}}
+ \DeclareUnicodeCharacter{017E}{\v{z}}
+
+ \DeclareUnicodeCharacter{01C4}{D\v{Z}}
+ \DeclareUnicodeCharacter{01C5}{D\v{z}}
+ \DeclareUnicodeCharacter{01C6}{d\v{z}}
+ \DeclareUnicodeCharacter{01C7}{LJ}
+ \DeclareUnicodeCharacter{01C8}{Lj}
+ \DeclareUnicodeCharacter{01C9}{lj}
+ \DeclareUnicodeCharacter{01CA}{NJ}
+ \DeclareUnicodeCharacter{01CB}{Nj}
+ \DeclareUnicodeCharacter{01CC}{nj}
+ \DeclareUnicodeCharacter{01CD}{\v{A}}
+ \DeclareUnicodeCharacter{01CE}{\v{a}}
+ \DeclareUnicodeCharacter{01CF}{\v{I}}
+
+ \DeclareUnicodeCharacter{01D0}{\v{\dotless{i}}}
+ \DeclareUnicodeCharacter{01D1}{\v{O}}
+ \DeclareUnicodeCharacter{01D2}{\v{o}}
+ \DeclareUnicodeCharacter{01D3}{\v{U}}
+ \DeclareUnicodeCharacter{01D4}{\v{u}}
+
+ \DeclareUnicodeCharacter{01E2}{\={\AE}}
+ \DeclareUnicodeCharacter{01E3}{\={\ae}}
+ \DeclareUnicodeCharacter{01E6}{\v{G}}
+ \DeclareUnicodeCharacter{01E7}{\v{g}}
+ \DeclareUnicodeCharacter{01E8}{\v{K}}
+ \DeclareUnicodeCharacter{01E9}{\v{k}}
+
+ \DeclareUnicodeCharacter{01F0}{\v{\dotless{j}}}
+ \DeclareUnicodeCharacter{01F1}{DZ}
+ \DeclareUnicodeCharacter{01F2}{Dz}
+ \DeclareUnicodeCharacter{01F3}{dz}
+ \DeclareUnicodeCharacter{01F4}{\'G}
+ \DeclareUnicodeCharacter{01F5}{\'g}
+ \DeclareUnicodeCharacter{01F8}{\`N}
+ \DeclareUnicodeCharacter{01F9}{\`n}
+ \DeclareUnicodeCharacter{01FC}{\'{\AE}}
+ \DeclareUnicodeCharacter{01FD}{\'{\ae}}
+ \DeclareUnicodeCharacter{01FE}{\'{\O}}
+ \DeclareUnicodeCharacter{01FF}{\'{\o}}
+
+ \DeclareUnicodeCharacter{021E}{\v{H}}
+ \DeclareUnicodeCharacter{021F}{\v{h}}
+
+ \DeclareUnicodeCharacter{0226}{\dotaccent{A}}
+ \DeclareUnicodeCharacter{0227}{\dotaccent{a}}
+ \DeclareUnicodeCharacter{0228}{\cedilla{E}}
+ \DeclareUnicodeCharacter{0229}{\cedilla{e}}
+ \DeclareUnicodeCharacter{022E}{\dotaccent{O}}
+ \DeclareUnicodeCharacter{022F}{\dotaccent{o}}
+
+ \DeclareUnicodeCharacter{0232}{\=Y}
+ \DeclareUnicodeCharacter{0233}{\=y}
+ \DeclareUnicodeCharacter{0237}{\dotless{j}}
+
+ \DeclareUnicodeCharacter{02DB}{\ogonek{ }}
+
+ \DeclareUnicodeCharacter{1E02}{\dotaccent{B}}
+ \DeclareUnicodeCharacter{1E03}{\dotaccent{b}}
+ \DeclareUnicodeCharacter{1E04}{\udotaccent{B}}
+ \DeclareUnicodeCharacter{1E05}{\udotaccent{b}}
+ \DeclareUnicodeCharacter{1E06}{\ubaraccent{B}}
+ \DeclareUnicodeCharacter{1E07}{\ubaraccent{b}}
+ \DeclareUnicodeCharacter{1E0A}{\dotaccent{D}}
+ \DeclareUnicodeCharacter{1E0B}{\dotaccent{d}}
+ \DeclareUnicodeCharacter{1E0C}{\udotaccent{D}}
+ \DeclareUnicodeCharacter{1E0D}{\udotaccent{d}}
+ \DeclareUnicodeCharacter{1E0E}{\ubaraccent{D}}
+ \DeclareUnicodeCharacter{1E0F}{\ubaraccent{d}}
+
+ \DeclareUnicodeCharacter{1E1E}{\dotaccent{F}}
+ \DeclareUnicodeCharacter{1E1F}{\dotaccent{f}}
+
+ \DeclareUnicodeCharacter{1E20}{\=G}
+ \DeclareUnicodeCharacter{1E21}{\=g}
+ \DeclareUnicodeCharacter{1E22}{\dotaccent{H}}
+ \DeclareUnicodeCharacter{1E23}{\dotaccent{h}}
+ \DeclareUnicodeCharacter{1E24}{\udotaccent{H}}
+ \DeclareUnicodeCharacter{1E25}{\udotaccent{h}}
+ \DeclareUnicodeCharacter{1E26}{\"H}
+ \DeclareUnicodeCharacter{1E27}{\"h}
+
+ \DeclareUnicodeCharacter{1E30}{\'K}
+ \DeclareUnicodeCharacter{1E31}{\'k}
+ \DeclareUnicodeCharacter{1E32}{\udotaccent{K}}
+ \DeclareUnicodeCharacter{1E33}{\udotaccent{k}}
+ \DeclareUnicodeCharacter{1E34}{\ubaraccent{K}}
+ \DeclareUnicodeCharacter{1E35}{\ubaraccent{k}}
+ \DeclareUnicodeCharacter{1E36}{\udotaccent{L}}
+ \DeclareUnicodeCharacter{1E37}{\udotaccent{l}}
+ \DeclareUnicodeCharacter{1E3A}{\ubaraccent{L}}
+ \DeclareUnicodeCharacter{1E3B}{\ubaraccent{l}}
+ \DeclareUnicodeCharacter{1E3E}{\'M}
+ \DeclareUnicodeCharacter{1E3F}{\'m}
+
+ \DeclareUnicodeCharacter{1E40}{\dotaccent{M}}
+ \DeclareUnicodeCharacter{1E41}{\dotaccent{m}}
+ \DeclareUnicodeCharacter{1E42}{\udotaccent{M}}
+ \DeclareUnicodeCharacter{1E43}{\udotaccent{m}}
+ \DeclareUnicodeCharacter{1E44}{\dotaccent{N}}
+ \DeclareUnicodeCharacter{1E45}{\dotaccent{n}}
+ \DeclareUnicodeCharacter{1E46}{\udotaccent{N}}
+ \DeclareUnicodeCharacter{1E47}{\udotaccent{n}}
+ \DeclareUnicodeCharacter{1E48}{\ubaraccent{N}}
+ \DeclareUnicodeCharacter{1E49}{\ubaraccent{n}}
+
+ \DeclareUnicodeCharacter{1E54}{\'P}
+ \DeclareUnicodeCharacter{1E55}{\'p}
+ \DeclareUnicodeCharacter{1E56}{\dotaccent{P}}
+ \DeclareUnicodeCharacter{1E57}{\dotaccent{p}}
+ \DeclareUnicodeCharacter{1E58}{\dotaccent{R}}
+ \DeclareUnicodeCharacter{1E59}{\dotaccent{r}}
+ \DeclareUnicodeCharacter{1E5A}{\udotaccent{R}}
+ \DeclareUnicodeCharacter{1E5B}{\udotaccent{r}}
+ \DeclareUnicodeCharacter{1E5E}{\ubaraccent{R}}
+ \DeclareUnicodeCharacter{1E5F}{\ubaraccent{r}}
+
+ \DeclareUnicodeCharacter{1E60}{\dotaccent{S}}
+ \DeclareUnicodeCharacter{1E61}{\dotaccent{s}}
+ \DeclareUnicodeCharacter{1E62}{\udotaccent{S}}
+ \DeclareUnicodeCharacter{1E63}{\udotaccent{s}}
+ \DeclareUnicodeCharacter{1E6A}{\dotaccent{T}}
+ \DeclareUnicodeCharacter{1E6B}{\dotaccent{t}}
+ \DeclareUnicodeCharacter{1E6C}{\udotaccent{T}}
+ \DeclareUnicodeCharacter{1E6D}{\udotaccent{t}}
+ \DeclareUnicodeCharacter{1E6E}{\ubaraccent{T}}
+ \DeclareUnicodeCharacter{1E6F}{\ubaraccent{t}}
+
+ \DeclareUnicodeCharacter{1E7C}{\~V}
+ \DeclareUnicodeCharacter{1E7D}{\~v}
+ \DeclareUnicodeCharacter{1E7E}{\udotaccent{V}}
+ \DeclareUnicodeCharacter{1E7F}{\udotaccent{v}}
+
+ \DeclareUnicodeCharacter{1E80}{\`W}
+ \DeclareUnicodeCharacter{1E81}{\`w}
+ \DeclareUnicodeCharacter{1E82}{\'W}
+ \DeclareUnicodeCharacter{1E83}{\'w}
+ \DeclareUnicodeCharacter{1E84}{\"W}
+ \DeclareUnicodeCharacter{1E85}{\"w}
+ \DeclareUnicodeCharacter{1E86}{\dotaccent{W}}
+ \DeclareUnicodeCharacter{1E87}{\dotaccent{w}}
+ \DeclareUnicodeCharacter{1E88}{\udotaccent{W}}
+ \DeclareUnicodeCharacter{1E89}{\udotaccent{w}}
+ \DeclareUnicodeCharacter{1E8A}{\dotaccent{X}}
+ \DeclareUnicodeCharacter{1E8B}{\dotaccent{x}}
+ \DeclareUnicodeCharacter{1E8C}{\"X}
+ \DeclareUnicodeCharacter{1E8D}{\"x}
+ \DeclareUnicodeCharacter{1E8E}{\dotaccent{Y}}
+ \DeclareUnicodeCharacter{1E8F}{\dotaccent{y}}
+
+ \DeclareUnicodeCharacter{1E90}{\^Z}
+ \DeclareUnicodeCharacter{1E91}{\^z}
+ \DeclareUnicodeCharacter{1E92}{\udotaccent{Z}}
+ \DeclareUnicodeCharacter{1E93}{\udotaccent{z}}
+ \DeclareUnicodeCharacter{1E94}{\ubaraccent{Z}}
+ \DeclareUnicodeCharacter{1E95}{\ubaraccent{z}}
+ \DeclareUnicodeCharacter{1E96}{\ubaraccent{h}}
+ \DeclareUnicodeCharacter{1E97}{\"t}
+ \DeclareUnicodeCharacter{1E98}{\ringaccent{w}}
+ \DeclareUnicodeCharacter{1E99}{\ringaccent{y}}
+
+ \DeclareUnicodeCharacter{1EA0}{\udotaccent{A}}
+ \DeclareUnicodeCharacter{1EA1}{\udotaccent{a}}
+
+ \DeclareUnicodeCharacter{1EB8}{\udotaccent{E}}
+ \DeclareUnicodeCharacter{1EB9}{\udotaccent{e}}
+ \DeclareUnicodeCharacter{1EBC}{\~E}
+ \DeclareUnicodeCharacter{1EBD}{\~e}
+
+ \DeclareUnicodeCharacter{1ECA}{\udotaccent{I}}
+ \DeclareUnicodeCharacter{1ECB}{\udotaccent{i}}
+ \DeclareUnicodeCharacter{1ECC}{\udotaccent{O}}
+ \DeclareUnicodeCharacter{1ECD}{\udotaccent{o}}
+
+ \DeclareUnicodeCharacter{1EE4}{\udotaccent{U}}
+ \DeclareUnicodeCharacter{1EE5}{\udotaccent{u}}
+
+ \DeclareUnicodeCharacter{1EF2}{\`Y}
+ \DeclareUnicodeCharacter{1EF3}{\`y}
+ \DeclareUnicodeCharacter{1EF4}{\udotaccent{Y}}
+
+ \DeclareUnicodeCharacter{1EF8}{\~Y}
+ \DeclareUnicodeCharacter{1EF9}{\~y}
+
+ \DeclareUnicodeCharacter{2013}{--}
+ \DeclareUnicodeCharacter{2014}{---}
+ \DeclareUnicodeCharacter{2018}{\quoteleft}
+ \DeclareUnicodeCharacter{2019}{\quoteright}
+ \DeclareUnicodeCharacter{201A}{\quotesinglbase}
+ \DeclareUnicodeCharacter{201C}{\quotedblleft}
+ \DeclareUnicodeCharacter{201D}{\quotedblright}
+ \DeclareUnicodeCharacter{201E}{\quotedblbase}
+ \DeclareUnicodeCharacter{2022}{\bullet}
+ \DeclareUnicodeCharacter{2026}{\dots}
+ \DeclareUnicodeCharacter{2039}{\guilsinglleft}
+ \DeclareUnicodeCharacter{203A}{\guilsinglright}
+ \DeclareUnicodeCharacter{20AC}{\euro}
+
+ \DeclareUnicodeCharacter{2192}{\expansion}
+ \DeclareUnicodeCharacter{21D2}{\result}
+
+ \DeclareUnicodeCharacter{2212}{\minus}
+ \DeclareUnicodeCharacter{2217}{\point}
+ \DeclareUnicodeCharacter{2261}{\equiv}
+}% end of \utfeightchardefs
+
+
+% US-ASCII character definitions.
+\def\asciichardefs{% nothing need be done
+ \relax
+}
+
+% Make non-ASCII characters printable again for compatibility with
+% existing Texinfo documents that may use them, even without declaring a
+% document encoding.
+%
+\setnonasciicharscatcode \other
+
+
+\message{formatting,}
+
+\newdimen\defaultparindent \defaultparindent = 15pt
+
+\chapheadingskip = 15pt plus 4pt minus 2pt
+\secheadingskip = 12pt plus 3pt minus 2pt
+\subsecheadingskip = 9pt plus 2pt minus 2pt
+
+% Prevent underfull vbox error messages.
+\vbadness = 10000
+
+% Don't be so finicky about underfull hboxes, either.
+\hbadness = 2000
+
+% Following George Bush, get rid of widows and orphans.
+\widowpenalty=10000
+\clubpenalty=10000
+
+% Use TeX 3.0's \emergencystretch to help line breaking, but if we're
+% using an old version of TeX, don't do anything. We want the amount of
+% stretch added to depend on the line length, hence the dependence on
+% \hsize. We call this whenever the paper size is set.
+%
+\def\setemergencystretch{%
+ \ifx\emergencystretch\thisisundefined
+ % Allow us to assign to \emergencystretch anyway.
+ \def\emergencystretch{\dimen0}%
+ \else
+ \emergencystretch = .15\hsize
+ \fi
+}
+
+% Parameters in order: 1) textheight; 2) textwidth;
+% 3) voffset; 4) hoffset; 5) binding offset; 6) topskip;
+% 7) physical page height; 8) physical page width.
+%
+% We also call \setleading{\textleading}, so the caller should define
+% \textleading. The caller should also set \parskip.
+%
+\def\internalpagesizes#1#2#3#4#5#6#7#8{%
+ \voffset = #3\relax
+ \topskip = #6\relax
+ \splittopskip = \topskip
+ %
+ \vsize = #1\relax
+ \advance\vsize by \topskip
+ \outervsize = \vsize
+ \advance\outervsize by 2\topandbottommargin
+ \pageheight = \vsize
+ %
+ \hsize = #2\relax
+ \outerhsize = \hsize
+ \advance\outerhsize by 0.5in
+ \pagewidth = \hsize
+ %
+ \normaloffset = #4\relax
+ \bindingoffset = #5\relax
+ %
+ \ifpdf
+ \pdfpageheight #7\relax
+ \pdfpagewidth #8\relax
+ % if we don't reset these, they will remain at "1 true in" of
+ % whatever layout pdftex was dumped with.
+ \pdfhorigin = 1 true in
+ \pdfvorigin = 1 true in
+ \fi
+ %
+ \setleading{\textleading}
+ %
+ \parindent = \defaultparindent
+ \setemergencystretch
+}
+
+% @letterpaper (the default).
+\def\letterpaper{{\globaldefs = 1
+ \parskip = 3pt plus 2pt minus 1pt
+ \textleading = 13.2pt
+ %
+ % If page is nothing but text, make it come out even.
+ \internalpagesizes{607.2pt}{6in}% that's 46 lines
+ {\voffset}{.25in}%
+ {\bindingoffset}{36pt}%
+ {11in}{8.5in}%
+}}
+
+% Use @smallbook to reset parameters for 7x9.25 trim size.
+\def\smallbook{{\globaldefs = 1
+ \parskip = 2pt plus 1pt
+ \textleading = 12pt
+ %
+ \internalpagesizes{7.5in}{5in}%
+ {-.2in}{0in}%
+ {\bindingoffset}{16pt}%
+ {9.25in}{7in}%
+ %
+ \lispnarrowing = 0.3in
+ \tolerance = 700
+ \hfuzz = 1pt
+ \contentsrightmargin = 0pt
+ \defbodyindent = .5cm
+}}
+
+% Use @smallerbook to reset parameters for 6x9 trim size.
+% (Just testing, parameters still in flux.)
+\def\smallerbook{{\globaldefs = 1
+ \parskip = 1.5pt plus 1pt
+ \textleading = 12pt
+ %
+ \internalpagesizes{7.4in}{4.8in}%
+ {-.2in}{-.4in}%
+ {0pt}{14pt}%
+ {9in}{6in}%
+ %
+ \lispnarrowing = 0.25in
+ \tolerance = 700
+ \hfuzz = 1pt
+ \contentsrightmargin = 0pt
+ \defbodyindent = .4cm
+}}
+
+% Use @afourpaper to print on European A4 paper.
+\def\afourpaper{{\globaldefs = 1
+ \parskip = 3pt plus 2pt minus 1pt
+ \textleading = 13.2pt
+ %
+ % Double-side printing via postscript on Laserjet 4050
+ % prints double-sided nicely when \bindingoffset=10mm and \hoffset=-6mm.
+ % To change the settings for a different printer or situation, adjust
+ % \normaloffset until the front-side and back-side texts align. Then
+ % do the same for \bindingoffset. You can set these for testing in
+ % your texinfo source file like this:
+ % @tex
+ % \global\normaloffset = -6mm
+ % \global\bindingoffset = 10mm
+ % @end tex
+ \internalpagesizes{673.2pt}{160mm}% that's 51 lines
+ {\voffset}{\hoffset}%
+ {\bindingoffset}{44pt}%
+ {297mm}{210mm}%
+ %
+ \tolerance = 700
+ \hfuzz = 1pt
+ \contentsrightmargin = 0pt
+ \defbodyindent = 5mm
+}}
+
+% Use @afivepaper to print on European A5 paper.
+% From romildo at urano.iceb.ufop.br, 2 July 2000.
+% He also recommends making @example and @lisp be small.
+\def\afivepaper{{\globaldefs = 1
+ \parskip = 2pt plus 1pt minus 0.1pt
+ \textleading = 12.5pt
+ %
+ \internalpagesizes{160mm}{120mm}%
+ {\voffset}{\hoffset}%
+ {\bindingoffset}{8pt}%
+ {210mm}{148mm}%
+ %
+ \lispnarrowing = 0.2in
+ \tolerance = 800
+ \hfuzz = 1.2pt
+ \contentsrightmargin = 0pt
+ \defbodyindent = 2mm
+ \tableindent = 12mm
+}}
+
+% A specific text layout, 24x15cm overall, intended for A4 paper.
+\def\afourlatex{{\globaldefs = 1
+ \afourpaper
+ \internalpagesizes{237mm}{150mm}%
+ {\voffset}{4.6mm}%
+ {\bindingoffset}{7mm}%
+ {297mm}{210mm}%
+ %
+ % Must explicitly reset to 0 because we call \afourpaper.
+ \globaldefs = 0
+}}
+
+% Use @afourwide to print on A4 paper in landscape format.
+\def\afourwide{{\globaldefs = 1
+ \afourpaper
+ \internalpagesizes{241mm}{165mm}%
+ {\voffset}{-2.95mm}%
+ {\bindingoffset}{7mm}%
+ {297mm}{210mm}%
+ \globaldefs = 0
+}}
+
+% @pagesizes TEXTHEIGHT[,TEXTWIDTH]
+% Perhaps we should allow setting the margins, \topskip, \parskip,
+% and/or leading, also. Or perhaps we should compute them somehow.
+%
+\parseargdef\pagesizes{\pagesizesyyy #1,,\finish}
+\def\pagesizesyyy#1,#2,#3\finish{{%
+ \setbox0 = \hbox{\ignorespaces #2}\ifdim\wd0 > 0pt \hsize=#2\relax \fi
+ \globaldefs = 1
+ %
+ \parskip = 3pt plus 2pt minus 1pt
+ \setleading{\textleading}%
+ %
+ \dimen0 = #1\relax
+ \advance\dimen0 by \voffset
+ %
+ \dimen2 = \hsize
+ \advance\dimen2 by \normaloffset
+ %
+ \internalpagesizes{#1}{\hsize}%
+ {\voffset}{\normaloffset}%
+ {\bindingoffset}{44pt}%
+ {\dimen0}{\dimen2}%
+}}
+
+% Set default to letter.
+%
+\letterpaper
+
+
+\message{and turning on texinfo input format.}
+
+% DEL is a comment character, in case @c does not suffice.
+\catcode`\^^? = 14
+
+% Define macros to output various characters with catcode for normal text.
+\catcode`\"=\other
+\catcode`\~=\other
+\catcode`\^=\other
+\catcode`\_=\other
+\catcode`\|=\other
+\catcode`\<=\other
+\catcode`\>=\other
+\catcode`\+=\other
+\catcode`\$=\other
+\def\normaldoublequote{"}
+\def\normaltilde{~}
+\def\normalcaret{^}
+\def\normalunderscore{_}
+\def\normalverticalbar{|}
+\def\normalless{<}
+\def\normalgreater{>}
+\def\normalplus{+}
+\def\normaldollar{$}%$ font-lock fix
+
+% This macro is used to make a character print one way in \tt
+% (where it can probably be output as-is), and another way in other fonts,
+% where something hairier probably needs to be done.
+%
+% #1 is what to print if we are indeed using \tt; #2 is what to print
+% otherwise. Since all the Computer Modern typewriter fonts have zero
+% interword stretch (and shrink), and it is reasonable to expect all
+% typewriter fonts to have this, we can check that font parameter.
+%
+\def\ifusingtt#1#2{\ifdim \fontdimen3\font=0pt #1\else #2\fi}
+
+% Same as above, but check for italic font. Actually this also catches
+% non-italic slanted fonts since it is impossible to distinguish them from
+% italic fonts. But since this is only used by $ and it uses \sl anyway
+% this is not a problem.
+\def\ifusingit#1#2{\ifdim \fontdimen1\font>0pt #1\else #2\fi}
+
+% Turn off all special characters except @
+% (and those which the user can use as if they were ordinary).
+% Most of these we simply print from the \tt font, but for some, we can
+% use math or other variants that look better in normal text.
+
+\catcode`\"=\active
+\def\activedoublequote{{\tt\char34}}
+\let"=\activedoublequote
+\catcode`\~=\active
+\def~{{\tt\char126}}
+\chardef\hat=`\^
+\catcode`\^=\active
+\def^{{\tt \hat}}
+
+\catcode`\_=\active
+\def_{\ifusingtt\normalunderscore\_}
+\let\realunder=_
+% Subroutine for the previous macro.
+\def\_{\leavevmode \kern.07em \vbox{\hrule width.3em height.1ex}\kern .07em }
+
+\catcode`\|=\active
+\def|{{\tt\char124}}
+\chardef \less=`\<
+\catcode`\<=\active
+\def<{{\tt \less}}
+\chardef \gtr=`\>
+\catcode`\>=\active
+\def>{{\tt \gtr}}
+\catcode`\+=\active
+\def+{{\tt \char 43}}
+\catcode`\$=\active
+\def${\ifusingit{{\sl\$}}\normaldollar}%$ font-lock fix
+
+% If a .fmt file is being used, characters that might appear in a file
+% name cannot be active until we have parsed the command line.
+% So turn them off again, and have \everyjob (or @setfilename) turn them on.
+% \otherifyactive is called near the end of this file.
+\def\otherifyactive{\catcode`+=\other \catcode`\_=\other}
+
+% Used sometimes to turn off (effectively) the active characters even after
+% parsing them.
+\def\turnoffactive{%
+ \normalturnoffactive
+ \otherbackslash
+}
+
+\catcode`\@=0
+
+% \backslashcurfont outputs one backslash character in current font,
+% as in \char`\\.
+\global\chardef\backslashcurfont=`\\
+\global\let\rawbackslashxx=\backslashcurfont % let existing .??s files work
+
+% \realbackslash is an actual character `\' with catcode other, and
+% \doublebackslash is two of them (for the pdf outlines).
+{\catcode`\\=\other @gdef at realbackslash{\} @gdef at doublebackslash{\\}}
+
+% In texinfo, backslash is an active character; it prints the backslash
+% in fixed width font.
+\catcode`\\=\active
+ at def@normalbackslash{{@tt at backslashcurfont}}
+% On startup, @fixbackslash assigns:
+% @let \ = @normalbackslash
+
+% \rawbackslash defines an active \ to do \backslashcurfont.
+% \otherbackslash defines an active \ to be a literal `\' character with
+% catcode other.
+ at gdef@rawbackslash{@let\=@backslashcurfont}
+ at gdef@otherbackslash{@let\=@realbackslash}
+
+% Same as @turnoffactive except outputs \ as {\tt\char`\\} instead of
+% the literal character `\'.
+%
+ at def@normalturnoffactive{%
+ @let\=@normalbackslash
+ @let"=@normaldoublequote
+ @let~=@normaltilde
+ @let^=@normalcaret
+ @let_=@normalunderscore
+ @let|=@normalverticalbar
+ @let<=@normalless
+ @let>=@normalgreater
+ @let+=@normalplus
+ @let$=@normaldollar %$ font-lock fix
+ @markupsetuplqdefault
+ @markupsetuprqdefault
+ @unsepspaces
+}
+
+% Make _ and + \other characters, temporarily.
+% This is canceled by @fixbackslash.
+ at otherifyactive
+
+% If a .fmt file is being used, we don't want the `\input texinfo' to show up.
+% That is what \eatinput is for; after that, the `\' should revert to printing
+% a backslash.
+%
+ at gdef@eatinput input texinfo{@fixbackslash}
+ at global@let\ = @eatinput
+
+% On the other hand, perhaps the file did not have a `\input texinfo'. Then
+% the first `\' in the file would cause an error. This macro tries to fix
+% that, assuming it is called before the first `\' could plausibly occur.
+% Also turn back on active characters that might appear in the input
+% file name, in case not using a pre-dumped format.
+%
+ at gdef@fixbackslash{%
+ @ifx\@eatinput @let\ = @normalbackslash @fi
+ @catcode`+=@active
+ @catcode`@_=@active
+}
+
+% Say @foo, not \foo, in error messages.
+ at escapechar = `@@
+
+% These look ok in all fonts, so just make them not special.
+ at catcode`@& = @other
+ at catcode`@# = @other
+ at catcode`@% = @other
+
+ at c Finally, make ` and ' active, so that txicodequoteundirected and
+ at c txicodequotebacktick work right in, e.g., @w{@code{`foo'}}. If we
+ at c don't make ` and ' active, @code will not get them as active chars.
+ at c Do this last of all since we use ` in the previous @catcode assignments.
+ at catcode`@'=@active
+ at catcode`@`=@active
+ at markupsetuplqdefault
+ at markupsetuprqdefault
+
+ at c Local variables:
+ at c eval: (add-hook 'write-file-hooks 'time-stamp)
+ at c page-delimiter: "^\\\\message"
+ at c time-stamp-start: "def\\\\texinfoversion{"
+ at c time-stamp-format: "%:y-%02m-%02d.%02H"
+ at c time-stamp-end: "}"
+ at c End:
+
+ at c vim:sw=2:
+
+ at ignore
+ arch-tag: e1b36e32-c96e-4135-a41a-0b2efa2ea115
+ at end ignore
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/install-sh b/src/libGkArrays/src/libProgressBar-1.2.0/install-sh
new file mode 100755
index 0000000..6781b98
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/install-sh
@@ -0,0 +1,520 @@
+#!/bin/sh
+# install - install a program, script, or datafile
+
+scriptversion=2009-04-28.21; # UTC
+
+# This originates from X11R5 (mit/util/scripts/install.sh), which was
+# later released in X11R6 (xc/config/util/install.sh) with the
+# following copyright and license.
+#
+# Copyright (C) 1994 X Consortium
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to
+# deal in the Software without restriction, including without limitation the
+# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+# sell copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
+# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
+# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Except as contained in this notice, the name of the X Consortium shall not
+# be used in advertising or otherwise to promote the sale, use or other deal-
+# ings in this Software without prior written authorization from the X Consor-
+# tium.
+#
+#
+# FSF changes to this file are in the public domain.
+#
+# Calling this script install-sh is preferred over install.sh, to prevent
+# `make' implicit rules from creating a file called install from it
+# when there is no Makefile.
+#
+# This script is compatible with the BSD install script, but was written
+# from scratch.
+
+nl='
+'
+IFS=" "" $nl"
+
+# set DOITPROG to echo to test this script
+
+# Don't use :- since 4.3BSD and earlier shells don't like it.
+doit=${DOITPROG-}
+if test -z "$doit"; then
+ doit_exec=exec
+else
+ doit_exec=$doit
+fi
+
+# Put in absolute file names if you don't have them in your path;
+# or use environment vars.
+
+chgrpprog=${CHGRPPROG-chgrp}
+chmodprog=${CHMODPROG-chmod}
+chownprog=${CHOWNPROG-chown}
+cmpprog=${CMPPROG-cmp}
+cpprog=${CPPROG-cp}
+mkdirprog=${MKDIRPROG-mkdir}
+mvprog=${MVPROG-mv}
+rmprog=${RMPROG-rm}
+stripprog=${STRIPPROG-strip}
+
+posix_glob='?'
+initialize_posix_glob='
+ test "$posix_glob" != "?" || {
+ if (set -f) 2>/dev/null; then
+ posix_glob=
+ else
+ posix_glob=:
+ fi
+ }
+'
+
+posix_mkdir=
+
+# Desired mode of installed file.
+mode=0755
+
+chgrpcmd=
+chmodcmd=$chmodprog
+chowncmd=
+mvcmd=$mvprog
+rmcmd="$rmprog -f"
+stripcmd=
+
+src=
+dst=
+dir_arg=
+dst_arg=
+
+copy_on_change=false
+no_target_directory=
+
+usage="\
+Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
+ or: $0 [OPTION]... SRCFILES... DIRECTORY
+ or: $0 [OPTION]... -t DIRECTORY SRCFILES...
+ or: $0 [OPTION]... -d DIRECTORIES...
+
+In the 1st form, copy SRCFILE to DSTFILE.
+In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
+In the 4th, create DIRECTORIES.
+
+Options:
+ --help display this help and exit.
+ --version display version info and exit.
+
+ -c (ignored)
+ -C install only if different (preserve the last data modification time)
+ -d create directories instead of installing files.
+ -g GROUP $chgrpprog installed files to GROUP.
+ -m MODE $chmodprog installed files to MODE.
+ -o USER $chownprog installed files to USER.
+ -s $stripprog installed files.
+ -t DIRECTORY install into DIRECTORY.
+ -T report an error if DSTFILE is a directory.
+
+Environment variables override the default commands:
+ CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG
+ RMPROG STRIPPROG
+"
+
+while test $# -ne 0; do
+ case $1 in
+ -c) ;;
+
+ -C) copy_on_change=true;;
+
+ -d) dir_arg=true;;
+
+ -g) chgrpcmd="$chgrpprog $2"
+ shift;;
+
+ --help) echo "$usage"; exit $?;;
+
+ -m) mode=$2
+ case $mode in
+ *' '* | *' '* | *'
+'* | *'*'* | *'?'* | *'['*)
+ echo "$0: invalid mode: $mode" >&2
+ exit 1;;
+ esac
+ shift;;
+
+ -o) chowncmd="$chownprog $2"
+ shift;;
+
+ -s) stripcmd=$stripprog;;
+
+ -t) dst_arg=$2
+ shift;;
+
+ -T) no_target_directory=true;;
+
+ --version) echo "$0 $scriptversion"; exit $?;;
+
+ --) shift
+ break;;
+
+ -*) echo "$0: invalid option: $1" >&2
+ exit 1;;
+
+ *) break;;
+ esac
+ shift
+done
+
+if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
+ # When -d is used, all remaining arguments are directories to create.
+ # When -t is used, the destination is already specified.
+ # Otherwise, the last argument is the destination. Remove it from $@.
+ for arg
+ do
+ if test -n "$dst_arg"; then
+ # $@ is not empty: it contains at least $arg.
+ set fnord "$@" "$dst_arg"
+ shift # fnord
+ fi
+ shift # arg
+ dst_arg=$arg
+ done
+fi
+
+if test $# -eq 0; then
+ if test -z "$dir_arg"; then
+ echo "$0: no input file specified." >&2
+ exit 1
+ fi
+ # It's OK to call `install-sh -d' without argument.
+ # This can happen when creating conditional directories.
+ exit 0
+fi
+
+if test -z "$dir_arg"; then
+ trap '(exit $?); exit' 1 2 13 15
+
+ # Set umask so as not to create temps with too-generous modes.
+ # However, 'strip' requires both read and write access to temps.
+ case $mode in
+ # Optimize common cases.
+ *644) cp_umask=133;;
+ *755) cp_umask=22;;
+
+ *[0-7])
+ if test -z "$stripcmd"; then
+ u_plus_rw=
+ else
+ u_plus_rw='% 200'
+ fi
+ cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
+ *)
+ if test -z "$stripcmd"; then
+ u_plus_rw=
+ else
+ u_plus_rw=,u+rw
+ fi
+ cp_umask=$mode$u_plus_rw;;
+ esac
+fi
+
+for src
+do
+ # Protect names starting with `-'.
+ case $src in
+ -*) src=./$src;;
+ esac
+
+ if test -n "$dir_arg"; then
+ dst=$src
+ dstdir=$dst
+ test -d "$dstdir"
+ dstdir_status=$?
+ else
+
+ # Waiting for this to be detected by the "$cpprog $src $dsttmp" command
+ # might cause directories to be created, which would be especially bad
+ # if $src (and thus $dsttmp) contains '*'.
+ if test ! -f "$src" && test ! -d "$src"; then
+ echo "$0: $src does not exist." >&2
+ exit 1
+ fi
+
+ if test -z "$dst_arg"; then
+ echo "$0: no destination specified." >&2
+ exit 1
+ fi
+
+ dst=$dst_arg
+ # Protect names starting with `-'.
+ case $dst in
+ -*) dst=./$dst;;
+ esac
+
+ # If destination is a directory, append the input filename; won't work
+ # if double slashes aren't ignored.
+ if test -d "$dst"; then
+ if test -n "$no_target_directory"; then
+ echo "$0: $dst_arg: Is a directory" >&2
+ exit 1
+ fi
+ dstdir=$dst
+ dst=$dstdir/`basename "$src"`
+ dstdir_status=0
+ else
+ # Prefer dirname, but fall back on a substitute if dirname fails.
+ dstdir=`
+ (dirname "$dst") 2>/dev/null ||
+ expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$dst" : 'X\(//\)[^/]' \| \
+ X"$dst" : 'X\(//\)$' \| \
+ X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
+ echo X"$dst" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'
+ `
+
+ test -d "$dstdir"
+ dstdir_status=$?
+ fi
+ fi
+
+ obsolete_mkdir_used=false
+
+ if test $dstdir_status != 0; then
+ case $posix_mkdir in
+ '')
+ # Create intermediate dirs using mode 755 as modified by the umask.
+ # This is like FreeBSD 'install' as of 1997-10-28.
+ umask=`umask`
+ case $stripcmd.$umask in
+ # Optimize common cases.
+ *[2367][2367]) mkdir_umask=$umask;;
+ .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
+
+ *[0-7])
+ mkdir_umask=`expr $umask + 22 \
+ - $umask % 100 % 40 + $umask % 20 \
+ - $umask % 10 % 4 + $umask % 2
+ `;;
+ *) mkdir_umask=$umask,go-w;;
+ esac
+
+ # With -d, create the new directory with the user-specified mode.
+ # Otherwise, rely on $mkdir_umask.
+ if test -n "$dir_arg"; then
+ mkdir_mode=-m$mode
+ else
+ mkdir_mode=
+ fi
+
+ posix_mkdir=false
+ case $umask in
+ *[123567][0-7][0-7])
+ # POSIX mkdir -p sets u+wx bits regardless of umask, which
+ # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
+ ;;
+ *)
+ tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
+ trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
+
+ if (umask $mkdir_umask &&
+ exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
+ then
+ if test -z "$dir_arg" || {
+ # Check for POSIX incompatibilities with -m.
+ # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
+ # other-writeable bit of parent directory when it shouldn't.
+ # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
+ ls_ld_tmpdir=`ls -ld "$tmpdir"`
+ case $ls_ld_tmpdir in
+ d????-?r-*) different_mode=700;;
+ d????-?--*) different_mode=755;;
+ *) false;;
+ esac &&
+ $mkdirprog -m$different_mode -p -- "$tmpdir" && {
+ ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
+ test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
+ }
+ }
+ then posix_mkdir=:
+ fi
+ rmdir "$tmpdir/d" "$tmpdir"
+ else
+ # Remove any dirs left behind by ancient mkdir implementations.
+ rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
+ fi
+ trap '' 0;;
+ esac;;
+ esac
+
+ if
+ $posix_mkdir && (
+ umask $mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
+ )
+ then :
+ else
+
+ # The umask is ridiculous, or mkdir does not conform to POSIX,
+ # or it failed possibly due to a race condition. Create the
+ # directory the slow way, step by step, checking for races as we go.
+
+ case $dstdir in
+ /*) prefix='/';;
+ -*) prefix='./';;
+ *) prefix='';;
+ esac
+
+ eval "$initialize_posix_glob"
+
+ oIFS=$IFS
+ IFS=/
+ $posix_glob set -f
+ set fnord $dstdir
+ shift
+ $posix_glob set +f
+ IFS=$oIFS
+
+ prefixes=
+
+ for d
+ do
+ test -z "$d" && continue
+
+ prefix=$prefix$d
+ if test -d "$prefix"; then
+ prefixes=
+ else
+ if $posix_mkdir; then
+ (umask=$mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
+ # Don't fail if two instances are running concurrently.
+ test -d "$prefix" || exit 1
+ else
+ case $prefix in
+ *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
+ *) qprefix=$prefix;;
+ esac
+ prefixes="$prefixes '$qprefix'"
+ fi
+ fi
+ prefix=$prefix/
+ done
+
+ if test -n "$prefixes"; then
+ # Don't fail if two instances are running concurrently.
+ (umask $mkdir_umask &&
+ eval "\$doit_exec \$mkdirprog $prefixes") ||
+ test -d "$dstdir" || exit 1
+ obsolete_mkdir_used=true
+ fi
+ fi
+ fi
+
+ if test -n "$dir_arg"; then
+ { test -z "$chowncmd" || $doit $chowncmd "$dst"; } &&
+ { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } &&
+ { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false ||
+ test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1
+ else
+
+ # Make a couple of temp file names in the proper directory.
+ dsttmp=$dstdir/_inst.$$_
+ rmtmp=$dstdir/_rm.$$_
+
+ # Trap to clean up those temp files at exit.
+ trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
+
+ # Copy the file name to the temp name.
+ (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") &&
+
+ # and set any options; do chmod last to preserve setuid bits.
+ #
+ # If any of these fail, we abort the whole thing. If we want to
+ # ignore errors from any of these, just make sure not to ignore
+ # errors from the above "$doit $cpprog $src $dsttmp" command.
+ #
+ { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&
+ { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&
+ { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&
+ { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
+
+ # If -C, don't bother to copy if it wouldn't change the file.
+ if $copy_on_change &&
+ old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
+ new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
+
+ eval "$initialize_posix_glob" &&
+ $posix_glob set -f &&
+ set X $old && old=:$2:$4:$5:$6 &&
+ set X $new && new=:$2:$4:$5:$6 &&
+ $posix_glob set +f &&
+
+ test "$old" = "$new" &&
+ $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
+ then
+ rm -f "$dsttmp"
+ else
+ # Rename the file to the real destination.
+ $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||
+
+ # The rename failed, perhaps because mv can't rename something else
+ # to itself, or perhaps because mv is so ancient that it does not
+ # support -f.
+ {
+ # Now remove or move aside any old file at destination location.
+ # We try this two ways since rm can't unlink itself on some
+ # systems and the destination file might be busy for other
+ # reasons. In this case, the final cleanup might fail but the new
+ # file should still install successfully.
+ {
+ test ! -f "$dst" ||
+ $doit $rmcmd -f "$dst" 2>/dev/null ||
+ { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
+ { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
+ } ||
+ { echo "$0: cannot unlink or rename $dst" >&2
+ (exit 1); exit 1
+ }
+ } &&
+
+ # Now rename the file to the real destination.
+ $doit $mvcmd "$dsttmp" "$dst"
+ }
+ fi || exit 1
+
+ trap '' 0
+ fi
+done
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar.lsm.in b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar.lsm.in
new file mode 100644
index 0000000..d2dba3b
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar.lsm.in
@@ -0,0 +1,24 @@
+Begin3
+Title: @PACKAGE_NAME@
+Version: @PACKAGE_VERSION@
+Entered-date: @ISODATE@
+Description: libProgressBar is a C++ library to manage... Progress bars!!!
+
+ If you want to easily display progress bar and if you are a
+ C++ programmer, this library is for you!
+
+Keywords: progress bar c++
+Author: DoccY <@PACKAGE_BUGREPORT@>
+Maintained-by: DoccY <@PACKAGE_BUGREPORT@>
+Primary-site: ???
+ 410k @PACKAGE at -@PACKAGE_VERSION at .tar.gz
+ 1k @PACKAGE at .lsm
+Alternate-site:
+Original-site:
+Platforms: Built with GNU C++ compiler. g++ version 4.1 works,
+ Since the source code support the -Wall, -pedantic and -ansi
+ options, non-GNU C++ compiler might work too, but I haven't
+ tried it. Valgrind says that no memory leaks are possible on
+ each test I have done.
+Copying-policy: GNU Lesser General Public Licence
+End
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar.pc.in b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar.pc.in
new file mode 100644
index 0000000..f83e93b
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar.pc.in
@@ -0,0 +1,10 @@
+prefix=@hacked_prefix@
+exec_prefix=@exec_prefix@
+libdir=@libdir@
+includedir=@includedir@
+
+Name: libProgressBar
+Description: C++ library to manage progress bar.
+Version: @VERSION@
+Libs: -L${libdir} -lProgressBar
+Cflags: -I${includedir}/@PACKAGE at -@VERSION@
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar.spec.in b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar.spec.in
new file mode 100644
index 0000000..d82a7b6
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar.spec.in
@@ -0,0 +1,107 @@
+# libProgressBar.spec
+#
+# Copyright (c) 2007 -- Universite des Antilles et de la Guyane
+# Copyright (c) 2007 -- Institut National de Recherche en Informatique et en Automatique
+# Author: DoccY <alban.mancheron at inria.fr>
+#
+# $Id: libProgressBar.spec.in,v 1.3 2007/09/27 14:53:27 mancheron Exp $
+#
+
+%define name @PACKAGE@
+%define version @VERSION@
+%define packager @PACKAGE_BUGREPORT@
+%define release 1
+%define manifest %{_builddir}/%{name}-%{version}-%{release}.manifest
+%define _prefix /usr/local
+%define _topdir %(echo "$PWD")/%{name}-%{version}
+%define _builddir %{_topdir}/BUILD
+%define _rpmdir %{_topdir}/RPMS
+%define _sourcedir %{_topdir}/SOURCES
+%define _specdir %{_topdir}/SPECS
+%define _srcrpmdir %{_topdir}/SRPMS
+
+# required items
+Name: %{name}
+Version: %{version}
+Release: %{release}
+License: LGPL
+Group: Development/Libraries
+
+# optional items
+#Vendor: DoccY
+#Distribution:
+#Icon:
+#URL:
+Packager: DoccY <${packager}>
+
+# source + patches
+Source: %{name}-%{version}.tar.gz
+#Source1:
+#Patch:
+#Patch1:
+
+# RPM info
+Provides: %{name}-%{version}
+AutoReqProv: yes
+#Requires:
+#Conflicts:
+#Prereq:
+
+Prefix: ${_prefix}
+BuildRoot: /var/tmp/%{name}-%{version}
+
+Summary: libProgressBar is a C++ library to manage... Progress bars!!!
+
+%description
+If you want to easily display progress bar and if you are a C++ programmer,
+this library is for you!
+
+%prep
+%setup -q
+#%patch0 -p1
+
+%build
+%configure
+make
+
+%install
+rm -rf $RPM_BUILD_ROOT
+mkdir -p $RPM_BUILD_ROOT
+%makeinstall
+
+# __os_install_post is implicitly expanded after the
+# %install section... do it now, and then disable it,
+# so all work is done before building manifest.
+
+%{?__os_install_post}
+%define __os_install_post %{nil}
+
+# build the file list automagically into %{manifest}
+
+cd $RPM_BUILD_ROOT
+rm -f %{manifest}
+find . -type d \
+ | sed '1,2d;s,^\.,\%attr(-\,root\,root) \%dir ,' >> %{manifest}
+find . -type f \
+ | sed 's,^\.,\%attr(-\,root\,root) ,' >> %{manifest}
+find . -type l \
+ | sed 's,^\.,\%attr(-\,root\,root) ,' >> %{manifest}
+
+#%pre
+#%post
+ at postinst_script@
+#%preun
+#%postun
+ at postrm_script@
+
+%clean
+rm -f %{manifest}
+rm -rf $RPM_BUILD_ROOT
+
+%files -f %{manifest}
+%defattr(-,root,root)
+%doc %{_datadir}/%{name}-%{version}
+#%docdir
+#%config
+
+%changelog
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/Makefile.am b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/Makefile.am
new file mode 100644
index 0000000..d4b6852
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/Makefile.am
@@ -0,0 +1,24 @@
+library_includedir=@includedir@/@PACKAGE at -@VERSION@
+library_include_HEADERS = progressBar.h
+lib_LTLIBRARIES = libProgressBar.la
+libProgressBar_la_SOURCES = progressBar.h progressBar.cpp
+libProgressBar_la_configdir = @libdir@/@PACKAGE at -@VERSION@/include
+libProgressBar_la_config_DATA = config.h
+libProgressBar_la_LDFLAGS = -version-info @LIB_VERSION@ -release @VERSION@ $(AM_LDFLAGS)
+
+noinst_PROGRAMS=testProgressBar
+testProgressBar_SOURCES=testPB.cpp
+testProgressBar_LDADD=libProgressBar.la
+testProgressBar_LDFLAGS=-lProgressBar $(AM_LDFLAGS)
+
+install-data-hook:
+ $(LN_S) -f @PACKAGE at -@VERSION@ $(DESTDIR)@includedir@/@PACKAGE@
+
+uninstall-hook:
+ test "`readlink $(DESTDIR)@includedir@/@PACKAGE@`" != @PACKAGE at -@VERSION@ \
+ || $(RM) -f $(DESTDIR)@includedir@/@PACKAGE@
+
+MOSTLYCLEANFILES=*~
+CLEANFILES=*~
+DISTCLEANFILES=*~
+MAINTAINERCLEANFILES=*~
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/Makefile.in b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/Makefile.in
new file mode 100644
index 0000000..16f7fa7
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/Makefile.in
@@ -0,0 +1,661 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+
+
+
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+noinst_PROGRAMS = testProgressBar$(EXEEXT)
+subdir = libProgressBar
+DIST_COMMON = $(library_include_HEADERS) $(srcdir)/Makefile.am \
+ $(srcdir)/Makefile.in $(srcdir)/config.h.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \
+ $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+ $(ACLOCAL_M4)
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_HEADER = config.h
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+ $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+ *) f=$$p;; \
+ esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+ srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+ for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+ for p in $$list; do echo "$$p $$p"; done | \
+ sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+ $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+ if (++n[$$2] == $(am__install_max)) \
+ { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+ END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+ sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+ sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
+am__installdirs = "$(DESTDIR)$(libdir)" \
+ "$(DESTDIR)$(libProgressBar_la_configdir)" \
+ "$(DESTDIR)$(library_includedir)"
+LTLIBRARIES = $(lib_LTLIBRARIES)
+libProgressBar_la_LIBADD =
+am_libProgressBar_la_OBJECTS = progressBar.lo
+libProgressBar_la_OBJECTS = $(am_libProgressBar_la_OBJECTS)
+libProgressBar_la_LINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \
+ $(CXXFLAGS) $(libProgressBar_la_LDFLAGS) $(LDFLAGS) -o $@
+PROGRAMS = $(noinst_PROGRAMS)
+am_testProgressBar_OBJECTS = testPB.$(OBJEXT)
+testProgressBar_OBJECTS = $(am_testProgressBar_OBJECTS)
+testProgressBar_DEPENDENCIES = libProgressBar.la
+testProgressBar_LINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \
+ $(CXXFLAGS) $(testProgressBar_LDFLAGS) $(LDFLAGS) -o $@
+DEFAULT_INCLUDES = -I. at am__isrc@
+depcomp = $(SHELL) $(top_srcdir)/depcomp
+am__depfiles_maybe = depfiles
+am__mv = mv -f
+CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
+ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+LTCXXCOMPILE = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+ --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
+ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+CXXLD = $(CXX)
+CXXLINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+ --mode=link $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) \
+ $(LDFLAGS) -o $@
+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+LTCOMPILE = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+ --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
+ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+CCLD = $(CC)
+LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+ --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \
+ $(LDFLAGS) -o $@
+SOURCES = $(libProgressBar_la_SOURCES) $(testProgressBar_SOURCES)
+DIST_SOURCES = $(libProgressBar_la_SOURCES) $(testProgressBar_SOURCES)
+DATA = $(libProgressBar_la_config_DATA)
+HEADERS = $(library_include_HEADERS)
+ETAGS = etags
+CTAGS = ctags
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = @ACLOCAL@
+ALLOCA = @ALLOCA@
+AMTAR = @AMTAR@
+AR = @AR@
+ARCH = @ARCH@
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
+AWK = @AWK@
+CC = @CC@
+CCDEPMODE = @CCDEPMODE@
+CFLAGS = @CFLAGS@
+CPP = @CPP@
+CPPFLAGS = @CPPFLAGS@
+CXX = @CXX@
+CXXCPP = @CXXCPP@
+CXXDEPMODE = @CXXDEPMODE@
+CXXFLAGS = @CXXFLAGS@
+CYGPATH_W = @CYGPATH_W@
+DEB_BUILDER = @DEB_BUILDER@
+DEFS = @DEFS@
+DEPDIR = @DEPDIR@
+DSYMUTIL = @DSYMUTIL@
+DUMPBIN = @DUMPBIN@
+ECHO_C = @ECHO_C@
+ECHO_N = @ECHO_N@
+ECHO_T = @ECHO_T@
+EGREP = @EGREP@
+EXEEXT = @EXEEXT@
+FGREP = @FGREP@
+GREP = @GREP@
+INSTALL = @INSTALL@
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+ISODATE = @ISODATE@
+KPSEWHICH = @KPSEWHICH@
+LD = @LD@
+LDFLAGS = @LDFLAGS@
+LIBOBJS = @LIBOBJS@
+LIBS = @LIBS@
+LIBTOOL = @LIBTOOL@
+LIB_VERSION = @LIB_VERSION@
+LIB_VERSION_EXT = @LIB_VERSION_EXT@
+LIPO = @LIPO@
+LN_S = @LN_S@
+LTLIBOBJS = @LTLIBOBJS@
+MAKEINFO = @MAKEINFO@
+MKDIR_P = @MKDIR_P@
+NM = @NM@
+NMEDIT = @NMEDIT@
+OBJDUMP = @OBJDUMP@
+OBJEXT = @OBJEXT@
+OTOOL = @OTOOL@
+OTOOL64 = @OTOOL64@
+PACKAGE = @PACKAGE@
+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+PACKAGE_NAME = @PACKAGE_NAME@
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diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/config.h.in b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/config.h.in
new file mode 100644
index 0000000..8942d1b
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/config.h.in
@@ -0,0 +1,126 @@
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+
+/* Define to 1 if you have the <sys/stat.h> header file. */
+#undef HAVE_SYS_STAT_H
+
+/* Define to 1 if you have the <sys/sysmacros.h> header file. */
+#undef HAVE_SYS_SYSMACROS_H
+
+/* Define to 1 if you have the <sys/time.h> header file. */
+#undef HAVE_SYS_TIME_H
+
+/* Define to 1 if you have the <sys/types.h> header file. */
+#undef HAVE_SYS_TYPES_H
+
+/* Define to 1 if you have the <time.h> header file. */
+#undef HAVE_TIME_H
+
+/* Define to 1 if you have the <unistd.h> header file. */
+#undef HAVE_UNISTD_H
+
+/* Define to the sub-directory in which libtool stores uninstalled libraries.
+ */
+#undef LT_OBJDIR
+
+/* Define to 1 if `major', `minor', and `makedev' are declared in <mkdev.h>.
+ */
+#undef MAJOR_IN_MKDEV
+
+/* Define to 1 if `major', `minor', and `makedev' are declared in
+ <sysmacros.h>. */
+#undef MAJOR_IN_SYSMACROS
+
+/* Name of package */
+#undef PACKAGE
+
+/* Define to the address where bug reports for this package should be sent. */
+#undef PACKAGE_BUGREPORT
+
+/* Define to the full name of this package. */
+#undef PACKAGE_NAME
+
+/* Define to the full name and version of this package. */
+#undef PACKAGE_STRING
+
+/* Define to the one symbol short name of this package. */
+#undef PACKAGE_TARNAME
+
+/* Define to the home page for this package. */
+#undef PACKAGE_URL
+
+/* Define to the version of this package. */
+#undef PACKAGE_VERSION
+
+/* If using the C implementation of alloca, define if you know the
+ direction of stack growth for your system; otherwise it will be
+ automatically deduced at runtime.
+ STACK_DIRECTION > 0 => grows toward higher addresses
+ STACK_DIRECTION < 0 => grows toward lower addresses
+ STACK_DIRECTION = 0 => direction of growth unknown */
+#undef STACK_DIRECTION
+
+/* Define to 1 if you have the ANSI C header files. */
+#undef STDC_HEADERS
+
+/* Define to 1 if your <sys/time.h> declares `struct tm'. */
+#undef TM_IN_SYS_TIME
+
+/* Version number of package */
+#undef VERSION
+
+/* Define to empty if `const' does not conform to ANSI C. */
+#undef const
+
+/* Define to `__inline__' or `__inline' if that's what the C compiler
+ calls it, or to nothing if 'inline' is not supported under any name. */
+#ifndef __cplusplus
+#undef inline
+#endif
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/progressBar.cpp b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/progressBar.cpp
new file mode 100644
index 0000000..eca752e
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/progressBar.cpp
@@ -0,0 +1,191 @@
+/******************************************************************************
+* *
+* Copyright � 2007 -- Universit� de Antilles et de la Guyane *
+* Copyright � 2007 -- Institut National de Recherche en Informatique *
+* et en Automatique *
+* *
+* Author: DoccY <alban.mancheron at inria.fr> *
+* *
+* This File initially comes from StatiSTARS. *
+* *
+* This library is free software; you can redistribute it and/or modify it *
+* under the terms of the GNU Library General Public License as published by *
+* the Free Software Foundation; either version 2 of the License, or (at your *
+* option) any later version. *
+* *
+* This library is distributed in the hope that it will be useful, but WITHOUT *
+* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or *
+* FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public *
+* License for more details. *
+* *
+* You should have received a copy of the GNU Library General Public License *
+* along with this library; if not, write: *
+* *
+* the Free Software Foundation, Inc., *
+* 59 Temple Place - Suite 330, *
+* Boston, MA 02111-1307, USA. *
+* *
+******************************************************************************/
+
+/*
+ * =============================================
+ *
+ * $Id: progressBar.cpp,v 1.4 2013/11/29 16:46:35 doccy Exp $
+ *
+ * ---------------------------------------------
+ *
+ * $Log: progressBar.cpp,v $
+ * Revision 1.4 2013/11/29 16:46:35 doccy
+ * Update:
+ * - Time display enhancement.
+ * - Allows systems without tex distribution to install the library (doc is just not built).
+ * - Add a method/constructor option to add/set an initial a value to the timer.
+ * - Add a 'C' function to get version number.
+ *
+ * Revision 1.3 2007/09/27 14:40:50 mancheron
+ * Ajout de la m�thode GetTime() qui permet de r�cup�rer le temps
+ * �coul� (en s.) depuis le d�but du processus en progr�s.
+ *
+ * Revision 1.2 2007-09-09 21:16:29 mancheron
+ * Modulation de l'affichage (avec ou sans temps/pourcentage).
+ *
+ * Revision 1.1 2007-08-15 16:36:23 mancheron
+ * *** empty log message ***
+ *
+ * =============================================
+ *
+ */
+
+#include "progressBar.h"
+
+using namespace DoccY;
+
+extern "C" {
+ char *libProgressBarVersion() {
+ return (char*)PACKAGE_VERSION;
+ }
+}
+
+void ProgressBar::ShowPercent() {
+ display |= 1;
+} /* Fin ShowPercent */
+
+void ProgressBar::HidePercent() {
+ display &= (unsigned char) -2;
+} /* Fin HidePercent */
+
+void ProgressBar::ShowTime() {
+ display |= 2;
+} /* Fin ShowTime */
+
+void ProgressBar::HideTime() {
+ display &= (unsigned char) -3;
+} /* Fin HideTime */
+
+double ProgressBar::GetTime() const {
+ return (clock() - start)/double(CLOCKS_PER_SEC);
+} /* Fin GetTime */
+
+void ProgressBar::AddTime(clock_t sec) {
+ start -= sec * CLOCKS_PER_SEC;
+}
+
+void ProgressBar::Reset() {
+ val = 0;
+ start = clock();
+} /* Fin Reset */
+
+void ProgressBar::SetVal(unsigned int v, bool update) {
+ val = min(v, max_val);
+ if (update) {
+ this->update();
+ } /* Fin Si */
+} /* Fin SetVal */
+
+void ProgressBar::Step(bool update) {
+ val = min(val+1, max_val);
+ if (update) {
+ this->update();
+ } /* Fin Si */
+} /* Fin Step */
+
+ProgressBar::ProgressBar(const string &t, const unsigned int m, const unsigned int w, ostream &os, bool startnewline, clock_t start):
+ symbol('='), delim1('['), delim2(']'), title(t), val(0), max_val(m),
+ width(w), output(os), start(clock() - start*CLOCKS_PER_SEC), display(1) {
+ if (startnewline) {
+ output << endl;
+ } /* Fin Si */
+} /* Fin ProgressBar */
+
+ProgressBar::ProgressBar(const char s, const char d1, const char d2, const string &t,
+ unsigned int v, const unsigned int m, const unsigned int w,
+ ostream &os, bool startnewline, clock_t start):
+ symbol(s), delim1(d1), delim2(d2), title(t), val(min(v, m)), max_val(m),
+ width(w), output(os), start(clock() - start*CLOCKS_PER_SEC), display(1) {
+ if (startnewline) {
+ output << endl;
+ } /* Fin Si */
+} /* Fin ProgressBar */
+
+ProgressBar::~ProgressBar() {
+ clear();
+} /* Fin ~ProgressBar */
+
+void ProgressBar::update(bool goback) const {
+ unsigned int lg;
+ unsigned int v;
+ stringstream tps;
+ if (display & 1) {
+ tps << setw(4) << setfill(' ') << val * 100 / max_val << " %";
+ } /* Fin Si */
+ if (display & 2) {
+ double temps = (clock() - start)/double(CLOCKS_PER_SEC);
+ if (display & 1) {
+ tps << " (";
+ } else {
+ tps << " ";
+ }
+ if (temps < 60.0) {
+ tps.precision((temps < 10.0)?2:1);
+ tps.setf(stringstream::fixed,stringstream::floatfield);
+ tps << temps << "s";
+ } else {
+ tps.precision(0);
+ if (temps < 3600.0) {
+ tps << int(temps)/60 << "m"
+ << setfill('0') << setw(2) << int(temps)%60;
+ } else {
+ if (temps < 86400.0) {
+ tps << int(temps)/3600 << "h"
+ << setfill('0') << setw(2) << int(temps)%3600/60;
+ } else {
+ tps << int(temps)/86400 << "d"
+ << setfill('0') << setw(2) << int(temps)%86400/3600;
+ } /* Fin Si */
+ } /* Fin Si */
+ } /* Fin Si */
+ if (display & 1) {
+ tps << ")";
+ }
+ } /* Fin Si */
+ lg = width - title.size() - 4 - tps.str().length();
+ v = val * lg / max_val;
+ output << title << " " << delim1;
+ if (v) {
+ output << setw(v) << setfill(symbol) << symbol;
+ } /* Fin Si */
+ output << setw(lg - v + 1) << setfill(' ') << delim2;
+ output << tps.str() << flush;
+ if (goback) {
+ fill('\b');
+ } /* Fin Si */
+} /* Fin update */
+
+void ProgressBar::clear() const {
+ fill(' ');
+ fill('\b');
+} /* Fin clear */
+
+void ProgressBar::fill(const char c) const {
+ output << setw(width - 1) << setfill(c) << c << flush;
+} /* Fin fill */
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/progressBar.h b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/progressBar.h
new file mode 100644
index 0000000..321b4bf
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/progressBar.h
@@ -0,0 +1,269 @@
+/******************************************************************************
+* *
+* Copyright � 2007 -- Universit� de Antilles et de la Guyane *
+* Copyright � 2007 -- Institut National de Recherche en Informatique *
+* et en Automatique *
+* *
+* Author: DoccY <alban.mancheron at inria.fr> *
+* *
+* This File initially comes from StatiSTARS. *
+* *
+* This library is free software; you can redistribute it and/or modify it *
+* under the terms of the GNU Library General Public License as published by *
+* the Free Software Foundation; either version 2 of the License, or (at your *
+* option) any later version. *
+* *
+* This library is distributed in the hope that it will be useful, but WITHOUT *
+* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or *
+* FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public *
+* License for more details. *
+* *
+* You should have received a copy of the GNU Library General Public License *
+* along with this library; if not, write: *
+* *
+* the Free Software Foundation, Inc., *
+* 59 Temple Place - Suite 330, *
+* Boston, MA 02111-1307, USA. *
+* *
+******************************************************************************/
+
+/*
+ * =============================================
+ *
+ * $Id: progressBar.h,v 1.4 2013/11/29 16:46:35 doccy Exp $
+ *
+ * ---------------------------------------------
+ *
+ * $Log: progressBar.h,v $
+ * Revision 1.4 2013/11/29 16:46:35 doccy
+ * Update:
+ * - Time display enhancement.
+ * - Allows systems without tex distribution to install the library (doc is just not built).
+ * - Add a method/constructor option to add/set an initial a value to the timer.
+ * - Add a 'C' function to get version number.
+ *
+ * Revision 1.3 2007/09/27 14:40:50 mancheron
+ * Ajout de la m�thode GetTime() qui permet de r�cup�rer le temps
+ * �coul� (en s.) depuis le d�but du processus en progr�s.
+ *
+ * Revision 1.2 2007-09-09 21:16:29 mancheron
+ * Modulation de l'affichage (avec ou sans temps/pourcentage).
+ *
+ * Revision 1.1 2007-08-15 16:36:23 mancheron
+ * *** empty log message ***
+ *
+ * =============================================
+ *
+ */
+
+#ifndef __PROGRESSBAR_H
+#define __PROGRESSBAR_H
+
+#include <iostream>
+#include <iomanip>
+#include <string>
+#include <sstream>
+#include <ctime>
+#include <config.h>
+
+using namespace std;
+
+/**
+ * @Namespace DoccY
+ * For my personal convenience, I have decided to put all my C++ contributions
+ * (at this time, it is the only one...) in this namespace.
+ */
+namespace DoccY {
+
+ extern "C" {
+ /* One can use this function to test the library availability */
+ char *libProgressBarVersion();
+ }
+
+ /**
+ * Class ProgressBar.
+ * @Author DoccY <alban.mancheron at inria.fr>
+ * @Copyright � 2007 --
+ * Universit� de Antilles et de la Guyane
+ * Institut National de Recherche en Informatique et en Automatique
+ * @brief A C++ class to manage... progress bars.
+ */
+ class ProgressBar {
+
+ private:
+
+ /**
+ * Symbol used for show the progression (default: '=').
+ */
+ const char symbol;
+
+ /**
+ * Starting delimiter (default: '[').
+ */
+ const char delim1;
+
+ /**
+ * Ending delimiter (default: ']').
+ */
+ const char delim2;
+
+ /**
+ * ProgressBar Title.
+ */
+ const string title;
+
+ /**
+ * Current value of the process.
+ */
+ unsigned int val;
+
+ /**
+ * Max value (at the end of the process).
+ */
+ const unsigned int max_val;
+
+ /**
+ * Width of the progress bar.
+ * This parameter must be large enough to write the title
+ * and the optional time and percents (@see display).
+ */
+ const unsigned int width;
+
+ /**
+ * Output stream to display the progress bar.
+ */
+ ostream &output;
+
+ /**
+ * Starting time of the process.
+ */
+ clock_t start;
+
+ /**
+ * Optional informations to display:
+ * if (display & 1), then show percents;
+ * if (display & 2), then show consumed time.
+ */
+ unsigned char display;
+
+ public:
+ /**
+ * Constructor (standard)
+ * @param t ProgressBar title (@see title).
+ * @param m Max value at the end of the process (@see max_val).
+ * @param w Width of the Progress Bar (@see width).
+ * @param os Output stream to display the progress bar (@see output)
+ * [default: ios::cerr].
+ * @param startnewline Tell if the progress bar starts by an new line
+ * [default: true]. This parameter is usefull when
+ * managing many progress bars.
+ * @param start Set starting time to this value (in seconds) [default: 0].
+ */
+ ProgressBar(const string &t, const unsigned int m, const unsigned int w, ostream &os = cerr, bool startnewline = true, clock_t start = 0);
+
+ /**
+ * Constructor (custom)
+ * @param s Symbol used for show the progression (@see symbol)
+ * [default: '='].
+ * @param d1 Starting delimiter (@see delim1) [default: '['].
+ * @param d2 Ending delimiter (@see delim2) [default: '['].
+ * @param t ProgressBar title (@see title) [default: "ProgressBar"].
+ * @param v Initial value at the begining of the process (@see val)
+ * [default: 0].
+ * @param m Max value at the end of the process (@see max_val)
+ * [default: 100].
+ * @param w Width of the Progress Bar (@see width) [default: 80].
+ * @param os Output stream to display the progress bar (@see output)
+ * [default: ios::cerr].
+ * @param startnewline Tell if the progress bar starts by an new line
+ * [default: true]. This parameter is usefull when
+ * managing many progress bars.
+ * @param start Set starting time to this value (in seconds) [default: 0].
+ */
+ ProgressBar(const char s = '=', const char d1 = '[', const char d2 = ']',
+ const string &t = "ProgressBar",
+ unsigned int v = 0, const unsigned int m = 100, const unsigned int w = 80,
+ ostream &os = cerr, bool startnewline = true, clock_t start = 0);
+
+ /**
+ * Destructor
+ */
+ ~ProgressBar();
+
+ /**
+ * Enable percentage display (@see display).
+ */
+ void ShowPercent();
+
+ /**
+ * Disable percentage display (@see display).
+ */
+ void HidePercent();
+
+ /**
+ * Enable consumed time display (@see display).
+ */
+ void ShowTime();
+
+ /**
+ * Disable consumed time display (@see display).
+ */
+ void HideTime();
+
+ /**
+ * Get consumed time in seconds (@see start).
+ */
+ double GetTime() const;
+
+ /**
+ * Add sec seconds to expanded time (@see start).
+ */
+ void AddTime(clock_t sec);
+
+ /**
+ * Reset the progress bar (@see val, @see start).
+ */
+ void Reset();
+
+ /**
+ * Set the current value of the process.
+ * @param v The current value (@see val).
+ * @param update Refresh the progress bar display.
+ */
+ void SetVal(unsigned int v, bool update = false);
+
+ /**
+ * Increment by one the current value of the process
+ * (@see val).
+ * @param update Refresh the progress bar display.
+ */
+ void Step(bool update = true);
+
+ /**
+ * Refresh the progress bar display.
+ * @param goback If true, rewind the cursor at the
+ * beginning of the progress bar.
+ */
+ void update(bool goback = true) const;
+
+ /**
+ * Clear the progress bar from the display. This
+ * doesn't reset either the timer, or the current
+ * value!!!
+ */
+ void clear() const;
+
+ /**
+ * Fill the progress bar with some symbol.
+ * @param c Symbol used to fill the progress bar
+ * [default: ' '].
+ */
+ void fill(const char c = ' ') const;
+ }; /* Fin ProgressBar */
+
+} /* Fin espace de nom DoccY */
+
+#endif /* __PROGRESSBAR_H */
+// Local Variables:
+// mode:c++
+// End:
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/testPB.cpp b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/testPB.cpp
new file mode 100644
index 0000000..477b3d3
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/libProgressBar/testPB.cpp
@@ -0,0 +1,125 @@
+/******************************************************************************
+* *
+* Copyright � 2007 -- Universit� de Antilles et de la Guyane *
+* Copyright � 2007 -- Institut National de Recherche en Informatique *
+* et en Automatique *
+* *
+* Author: DoccY <alban.mancheron at inria.fr> *
+* *
+* This File initially comes from StatiSTARS. *
+* *
+* This library is free software; you can redistribute it and/or modify it *
+* under the terms of the GNU Library General Public License as published by *
+* the Free Software Foundation; either version 2 of the License, or (at your *
+* option) any later version. *
+* *
+* This library is distributed in the hope that it will be useful, but WITHOUT *
+* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or *
+* FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public *
+* License for more details. *
+* *
+* You should have received a copy of the GNU Library General Public License *
+* along with this library; if not, write: *
+* *
+* the Free Software Foundation, Inc., *
+* 59 Temple Place - Suite 330, *
+* Boston, MA 02111-1307, USA. *
+* *
+******************************************************************************/
+
+/*
+ * =============================================
+ *
+ * $Id: testPB.cpp,v 1.3 2013/11/29 16:46:35 doccy Exp $
+ *
+ * ---------------------------------------------
+ *
+ * $Log: testPB.cpp,v $
+ * Revision 1.3 2013/11/29 16:46:35 doccy
+ * Update:
+ * - Time display enhancement.
+ * - Allows systems without tex distribution to install the library (doc is just not built).
+ * - Add a method/constructor option to add/set an initial a value to the timer.
+ * - Add a 'C' function to get version number.
+ *
+ * Revision 1.2 2007/09/27 14:40:50 mancheron
+ * Ajout de la m�thode GetTime() qui permet de r�cup�rer le temps
+ * �coul� (en s.) depuis le d�but du processus en progr�s.
+ *
+ * =============================================
+ *
+ */
+
+#include "progressBar.h"
+
+#define MAX_VAL 1000
+
+using namespace DoccY;
+
+void testPB(ProgressBar &pb, double tps, bool fake = false) {
+
+ pb.Reset();
+ double ftps = tps / MAX_VAL;
+ if (fake) {
+ tps = 30;
+ }
+ tps /= MAX_VAL;
+ for(unsigned int i = 0; i < MAX_VAL; i++) {
+ clock_t timer = clock();
+ pb.Step();
+ if (fake) {
+ pb.AddTime(ftps);
+ }
+ while ((clock() - timer)/double(CLOCKS_PER_SEC) < tps);
+ } /* Fin Pour */
+ if (fake) {
+ pb.Reset();
+ pb.AddTime(ftps * MAX_VAL);
+ pb.SetVal(MAX_VAL);
+ }
+ pb.update(false);
+ cout << endl;
+
+} /* Fin testPB */
+
+int main(int argc, char** argv) {
+
+ ProgressBar PB("ProgressBar Test Program", MAX_VAL, 80, cout, true);
+ for (int i = 1; i <= 8; i++) {
+ cout << setfill(' ') << setw(10) << i*10;
+ }
+ cout << endl;
+ for (int i = 0; i < 8; i++) {
+ cout << setfill('-') << setw(10) << "+";
+ }
+ cout << endl;
+
+ cout << "Test with percent and without time [default] (10s):" << endl;
+ testPB(PB, 2.5);
+
+ cout << "Test with percent and time (10s):" << endl;
+ PB.ShowTime();
+ testPB(PB, 2.5);
+
+ cout << "Test without percent and with time (10s):" << endl;
+ PB.HidePercent();
+ testPB(PB, 2.5);
+
+ cout << "Test without percent and without time (10s)" << endl;
+ PB.HideTime();
+ testPB(PB, 2.5);
+
+ cout << "Test without percent and with time (2 min)" << endl;
+ PB.ShowPercent();
+ PB.ShowTime();
+ testPB(PB, 120.0);
+
+ cout << "Test without percent and with time (1h30 [displayed in 30s])" << endl;
+ testPB(PB, (1*60.0+30.0)*60.0, true);
+ cout << "Test without percent and with time (15h15 [displayed in 30s])" << endl;
+ testPB(PB, (15*60.0+15.0)*60.0, true);
+ cout << "Test without percent and with time (22d22 [displayed 30s])" << endl;
+ testPB(PB, (22.0*24.0+22.0)*3600.0, true);
+
+ return 0;
+}
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/ltmain.sh b/src/libGkArrays/src/libProgressBar-1.2.0/ltmain.sh
new file mode 100755
index 0000000..d88da2c
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/ltmain.sh
@@ -0,0 +1,8413 @@
+# Generated from ltmain.m4sh.
+
+# ltmain.sh (GNU libtool) 2.2.6b
+# Written by Gordon Matzigkeit <gord at gnu.ai.mit.edu>, 1996
+
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, 2006, 2007 2008 Free Software Foundation, Inc.
+# This is free software; see the source for copying conditions. There is NO
+# warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+# GNU Libtool is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# As a special exception to the GNU General Public License,
+# if you distribute this file as part of a program or library that
+# is built using GNU Libtool, you may include this file under the
+# same distribution terms that you use for the rest of that program.
+#
+# GNU Libtool is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GNU Libtool; see the file COPYING. If not, a copy
+# can be downloaded from http://www.gnu.org/licenses/gpl.html,
+# or obtained by writing to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# Usage: $progname [OPTION]... [MODE-ARG]...
+#
+# Provide generalized library-building support services.
+#
+# --config show all configuration variables
+# --debug enable verbose shell tracing
+# -n, --dry-run display commands without modifying any files
+# --features display basic configuration information and exit
+# --mode=MODE use operation mode MODE
+# --preserve-dup-deps don't remove duplicate dependency libraries
+# --quiet, --silent don't print informational messages
+# --tag=TAG use configuration variables from tag TAG
+# -v, --verbose print informational messages (default)
+# --version print version information
+# -h, --help print short or long help message
+#
+# MODE must be one of the following:
+#
+# clean remove files from the build directory
+# compile compile a source file into a libtool object
+# execute automatically set library path, then run a program
+# finish complete the installation of libtool libraries
+# install install libraries or executables
+# link create a library or an executable
+# uninstall remove libraries from an installed directory
+#
+# MODE-ARGS vary depending on the MODE.
+# Try `$progname --help --mode=MODE' for a more detailed description of MODE.
+#
+# When reporting a bug, please describe a test case to reproduce it and
+# include the following information:
+#
+# host-triplet: $host
+# shell: $SHELL
+# compiler: $LTCC
+# compiler flags: $LTCFLAGS
+# linker: $LD (gnu? $with_gnu_ld)
+# $progname: (GNU libtool) 2.2.6b Debian-2.2.6b-2
+# automake: $automake_version
+# autoconf: $autoconf_version
+#
+# Report bugs to <bug-libtool at gnu.org>.
+
+PROGRAM=ltmain.sh
+PACKAGE=libtool
+VERSION="2.2.6b Debian-2.2.6b-2"
+TIMESTAMP=""
+package_revision=1.3017
+
+# Be Bourne compatible
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in *posix*) set -o posix;; esac
+fi
+BIN_SH=xpg4; export BIN_SH # for Tru64
+DUALCASE=1; export DUALCASE # for MKS sh
+
+# NLS nuisances: We save the old values to restore during execute mode.
+# Only set LANG and LC_ALL to C if already set.
+# These must not be set unconditionally because not all systems understand
+# e.g. LANG=C (notably SCO).
+lt_user_locale=
+lt_safe_locale=
+for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES
+do
+ eval "if test \"\${$lt_var+set}\" = set; then
+ save_$lt_var=\$$lt_var
+ $lt_var=C
+ export $lt_var
+ lt_user_locale=\"$lt_var=\\\$save_\$lt_var; \$lt_user_locale\"
+ lt_safe_locale=\"$lt_var=C; \$lt_safe_locale\"
+ fi"
+done
+
+$lt_unset CDPATH
+
+
+
+
+
+: ${CP="cp -f"}
+: ${ECHO="echo"}
+: ${EGREP="/bin/grep -E"}
+: ${FGREP="/bin/grep -F"}
+: ${GREP="/bin/grep"}
+: ${LN_S="ln -s"}
+: ${MAKE="make"}
+: ${MKDIR="mkdir"}
+: ${MV="mv -f"}
+: ${RM="rm -f"}
+: ${SED="/bin/sed"}
+: ${SHELL="${CONFIG_SHELL-/bin/sh}"}
+: ${Xsed="$SED -e 1s/^X//"}
+
+# Global variables:
+EXIT_SUCCESS=0
+EXIT_FAILURE=1
+EXIT_MISMATCH=63 # $? = 63 is used to indicate version mismatch to missing.
+EXIT_SKIP=77 # $? = 77 is used to indicate a skipped test to automake.
+
+exit_status=$EXIT_SUCCESS
+
+# Make sure IFS has a sensible default
+lt_nl='
+'
+IFS=" $lt_nl"
+
+dirname="s,/[^/]*$,,"
+basename="s,^.*/,,"
+
+# func_dirname_and_basename file append nondir_replacement
+# perform func_basename and func_dirname in a single function
+# call:
+# dirname: Compute the dirname of FILE. If nonempty,
+# add APPEND to the result, otherwise set result
+# to NONDIR_REPLACEMENT.
+# value returned in "$func_dirname_result"
+# basename: Compute filename of FILE.
+# value retuned in "$func_basename_result"
+# Implementation must be kept synchronized with func_dirname
+# and func_basename. For efficiency, we do not delegate to
+# those functions but instead duplicate the functionality here.
+func_dirname_and_basename ()
+{
+ # Extract subdirectory from the argument.
+ func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"`
+ if test "X$func_dirname_result" = "X${1}"; then
+ func_dirname_result="${3}"
+ else
+ func_dirname_result="$func_dirname_result${2}"
+ fi
+ func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"`
+}
+
+# Generated shell functions inserted here.
+
+# Work around backward compatibility issue on IRIX 6.5. On IRIX 6.4+, sh
+# is ksh but when the shell is invoked as "sh" and the current value of
+# the _XPG environment variable is not equal to 1 (one), the special
+# positional parameter $0, within a function call, is the name of the
+# function.
+progpath="$0"
+
+# The name of this program:
+# In the unlikely event $progname began with a '-', it would play havoc with
+# func_echo (imagine progname=-n), so we prepend ./ in that case:
+func_dirname_and_basename "$progpath"
+progname=$func_basename_result
+case $progname in
+ -*) progname=./$progname ;;
+esac
+
+# Make sure we have an absolute path for reexecution:
+case $progpath in
+ [\\/]*|[A-Za-z]:\\*) ;;
+ *[\\/]*)
+ progdir=$func_dirname_result
+ progdir=`cd "$progdir" && pwd`
+ progpath="$progdir/$progname"
+ ;;
+ *)
+ save_IFS="$IFS"
+ IFS=:
+ for progdir in $PATH; do
+ IFS="$save_IFS"
+ test -x "$progdir/$progname" && break
+ done
+ IFS="$save_IFS"
+ test -n "$progdir" || progdir=`pwd`
+ progpath="$progdir/$progname"
+ ;;
+esac
+
+# Sed substitution that helps us do robust quoting. It backslashifies
+# metacharacters that are still active within double-quoted strings.
+Xsed="${SED}"' -e 1s/^X//'
+sed_quote_subst='s/\([`"$\\]\)/\\\1/g'
+
+# Same as above, but do not quote variable references.
+double_quote_subst='s/\(["`\\]\)/\\\1/g'
+
+# Re-`\' parameter expansions in output of double_quote_subst that were
+# `\'-ed in input to the same. If an odd number of `\' preceded a '$'
+# in input to double_quote_subst, that '$' was protected from expansion.
+# Since each input `\' is now two `\'s, look for any number of runs of
+# four `\'s followed by two `\'s and then a '$'. `\' that '$'.
+bs='\\'
+bs2='\\\\'
+bs4='\\\\\\\\'
+dollar='\$'
+sed_double_backslash="\
+ s/$bs4/&\\
+/g
+ s/^$bs2$dollar/$bs&/
+ s/\\([^$bs]\\)$bs2$dollar/\\1$bs2$bs$dollar/g
+ s/\n//g"
+
+# Standard options:
+opt_dry_run=false
+opt_help=false
+opt_quiet=false
+opt_verbose=false
+opt_warning=:
+
+# func_echo arg...
+# Echo program name prefixed message, along with the current mode
+# name if it has been set yet.
+func_echo ()
+{
+ $ECHO "$progname${mode+: }$mode: $*"
+}
+
+# func_verbose arg...
+# Echo program name prefixed message in verbose mode only.
+func_verbose ()
+{
+ $opt_verbose && func_echo ${1+"$@"}
+
+ # A bug in bash halts the script if the last line of a function
+ # fails when set -e is in force, so we need another command to
+ # work around that:
+ :
+}
+
+# func_error arg...
+# Echo program name prefixed message to standard error.
+func_error ()
+{
+ $ECHO "$progname${mode+: }$mode: "${1+"$@"} 1>&2
+}
+
+# func_warning arg...
+# Echo program name prefixed warning message to standard error.
+func_warning ()
+{
+ $opt_warning && $ECHO "$progname${mode+: }$mode: warning: "${1+"$@"} 1>&2
+
+ # bash bug again:
+ :
+}
+
+# func_fatal_error arg...
+# Echo program name prefixed message to standard error, and exit.
+func_fatal_error ()
+{
+ func_error ${1+"$@"}
+ exit $EXIT_FAILURE
+}
+
+# func_fatal_help arg...
+# Echo program name prefixed message to standard error, followed by
+# a help hint, and exit.
+func_fatal_help ()
+{
+ func_error ${1+"$@"}
+ func_fatal_error "$help"
+}
+help="Try \`$progname --help' for more information." ## default
+
+
+# func_grep expression filename
+# Check whether EXPRESSION matches any line of FILENAME, without output.
+func_grep ()
+{
+ $GREP "$1" "$2" >/dev/null 2>&1
+}
+
+
+# func_mkdir_p directory-path
+# Make sure the entire path to DIRECTORY-PATH is available.
+func_mkdir_p ()
+{
+ my_directory_path="$1"
+ my_dir_list=
+
+ if test -n "$my_directory_path" && test "$opt_dry_run" != ":"; then
+
+ # Protect directory names starting with `-'
+ case $my_directory_path in
+ -*) my_directory_path="./$my_directory_path" ;;
+ esac
+
+ # While some portion of DIR does not yet exist...
+ while test ! -d "$my_directory_path"; do
+ # ...make a list in topmost first order. Use a colon delimited
+ # list incase some portion of path contains whitespace.
+ my_dir_list="$my_directory_path:$my_dir_list"
+
+ # If the last portion added has no slash in it, the list is done
+ case $my_directory_path in */*) ;; *) break ;; esac
+
+ # ...otherwise throw away the child directory and loop
+ my_directory_path=`$ECHO "X$my_directory_path" | $Xsed -e "$dirname"`
+ done
+ my_dir_list=`$ECHO "X$my_dir_list" | $Xsed -e 's,:*$,,'`
+
+ save_mkdir_p_IFS="$IFS"; IFS=':'
+ for my_dir in $my_dir_list; do
+ IFS="$save_mkdir_p_IFS"
+ # mkdir can fail with a `File exist' error if two processes
+ # try to create one of the directories concurrently. Don't
+ # stop in that case!
+ $MKDIR "$my_dir" 2>/dev/null || :
+ done
+ IFS="$save_mkdir_p_IFS"
+
+ # Bail out if we (or some other process) failed to create a directory.
+ test -d "$my_directory_path" || \
+ func_fatal_error "Failed to create \`$1'"
+ fi
+}
+
+
+# func_mktempdir [string]
+# Make a temporary directory that won't clash with other running
+# libtool processes, and avoids race conditions if possible. If
+# given, STRING is the basename for that directory.
+func_mktempdir ()
+{
+ my_template="${TMPDIR-/tmp}/${1-$progname}"
+
+ if test "$opt_dry_run" = ":"; then
+ # Return a directory name, but don't create it in dry-run mode
+ my_tmpdir="${my_template}-$$"
+ else
+
+ # If mktemp works, use that first and foremost
+ my_tmpdir=`mktemp -d "${my_template}-XXXXXXXX" 2>/dev/null`
+
+ if test ! -d "$my_tmpdir"; then
+ # Failing that, at least try and use $RANDOM to avoid a race
+ my_tmpdir="${my_template}-${RANDOM-0}$$"
+
+ save_mktempdir_umask=`umask`
+ umask 0077
+ $MKDIR "$my_tmpdir"
+ umask $save_mktempdir_umask
+ fi
+
+ # If we're not in dry-run mode, bomb out on failure
+ test -d "$my_tmpdir" || \
+ func_fatal_error "cannot create temporary directory \`$my_tmpdir'"
+ fi
+
+ $ECHO "X$my_tmpdir" | $Xsed
+}
+
+
+# func_quote_for_eval arg
+# Aesthetically quote ARG to be evaled later.
+# This function returns two values: FUNC_QUOTE_FOR_EVAL_RESULT
+# is double-quoted, suitable for a subsequent eval, whereas
+# FUNC_QUOTE_FOR_EVAL_UNQUOTED_RESULT has merely all characters
+# which are still active within double quotes backslashified.
+func_quote_for_eval ()
+{
+ case $1 in
+ *[\\\`\"\$]*)
+ func_quote_for_eval_unquoted_result=`$ECHO "X$1" | $Xsed -e "$sed_quote_subst"` ;;
+ *)
+ func_quote_for_eval_unquoted_result="$1" ;;
+ esac
+
+ case $func_quote_for_eval_unquoted_result in
+ # Double-quote args containing shell metacharacters to delay
+ # word splitting, command substitution and and variable
+ # expansion for a subsequent eval.
+ # Many Bourne shells cannot handle close brackets correctly
+ # in scan sets, so we specify it separately.
+ *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"")
+ func_quote_for_eval_result="\"$func_quote_for_eval_unquoted_result\""
+ ;;
+ *)
+ func_quote_for_eval_result="$func_quote_for_eval_unquoted_result"
+ esac
+}
+
+
+# func_quote_for_expand arg
+# Aesthetically quote ARG to be evaled later; same as above,
+# but do not quote variable references.
+func_quote_for_expand ()
+{
+ case $1 in
+ *[\\\`\"]*)
+ my_arg=`$ECHO "X$1" | $Xsed \
+ -e "$double_quote_subst" -e "$sed_double_backslash"` ;;
+ *)
+ my_arg="$1" ;;
+ esac
+
+ case $my_arg in
+ # Double-quote args containing shell metacharacters to delay
+ # word splitting and command substitution for a subsequent eval.
+ # Many Bourne shells cannot handle close brackets correctly
+ # in scan sets, so we specify it separately.
+ *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"")
+ my_arg="\"$my_arg\""
+ ;;
+ esac
+
+ func_quote_for_expand_result="$my_arg"
+}
+
+
+# func_show_eval cmd [fail_exp]
+# Unless opt_silent is true, then output CMD. Then, if opt_dryrun is
+# not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP
+# is given, then evaluate it.
+func_show_eval ()
+{
+ my_cmd="$1"
+ my_fail_exp="${2-:}"
+
+ ${opt_silent-false} || {
+ func_quote_for_expand "$my_cmd"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+
+ if ${opt_dry_run-false}; then :; else
+ eval "$my_cmd"
+ my_status=$?
+ if test "$my_status" -eq 0; then :; else
+ eval "(exit $my_status); $my_fail_exp"
+ fi
+ fi
+}
+
+
+# func_show_eval_locale cmd [fail_exp]
+# Unless opt_silent is true, then output CMD. Then, if opt_dryrun is
+# not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP
+# is given, then evaluate it. Use the saved locale for evaluation.
+func_show_eval_locale ()
+{
+ my_cmd="$1"
+ my_fail_exp="${2-:}"
+
+ ${opt_silent-false} || {
+ func_quote_for_expand "$my_cmd"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+
+ if ${opt_dry_run-false}; then :; else
+ eval "$lt_user_locale
+ $my_cmd"
+ my_status=$?
+ eval "$lt_safe_locale"
+ if test "$my_status" -eq 0; then :; else
+ eval "(exit $my_status); $my_fail_exp"
+ fi
+ fi
+}
+
+
+
+
+
+# func_version
+# Echo version message to standard output and exit.
+func_version ()
+{
+ $SED -n '/^# '$PROGRAM' (GNU /,/# warranty; / {
+ s/^# //
+ s/^# *$//
+ s/\((C)\)[ 0-9,-]*\( [1-9][0-9]*\)/\1\2/
+ p
+ }' < "$progpath"
+ exit $?
+}
+
+# func_usage
+# Echo short help message to standard output and exit.
+func_usage ()
+{
+ $SED -n '/^# Usage:/,/# -h/ {
+ s/^# //
+ s/^# *$//
+ s/\$progname/'$progname'/
+ p
+ }' < "$progpath"
+ $ECHO
+ $ECHO "run \`$progname --help | more' for full usage"
+ exit $?
+}
+
+# func_help
+# Echo long help message to standard output and exit.
+func_help ()
+{
+ $SED -n '/^# Usage:/,/# Report bugs to/ {
+ s/^# //
+ s/^# *$//
+ s*\$progname*'$progname'*
+ s*\$host*'"$host"'*
+ s*\$SHELL*'"$SHELL"'*
+ s*\$LTCC*'"$LTCC"'*
+ s*\$LTCFLAGS*'"$LTCFLAGS"'*
+ s*\$LD*'"$LD"'*
+ s/\$with_gnu_ld/'"$with_gnu_ld"'/
+ s/\$automake_version/'"`(automake --version) 2>/dev/null |$SED 1q`"'/
+ s/\$autoconf_version/'"`(autoconf --version) 2>/dev/null |$SED 1q`"'/
+ p
+ }' < "$progpath"
+ exit $?
+}
+
+# func_missing_arg argname
+# Echo program name prefixed message to standard error and set global
+# exit_cmd.
+func_missing_arg ()
+{
+ func_error "missing argument for $1"
+ exit_cmd=exit
+}
+
+exit_cmd=:
+
+
+
+
+
+# Check that we have a working $ECHO.
+if test "X$1" = X--no-reexec; then
+ # Discard the --no-reexec flag, and continue.
+ shift
+elif test "X$1" = X--fallback-echo; then
+ # Avoid inline document here, it may be left over
+ :
+elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t'; then
+ # Yippee, $ECHO works!
+ :
+else
+ # Restart under the correct shell, and then maybe $ECHO will work.
+ exec $SHELL "$progpath" --no-reexec ${1+"$@"}
+fi
+
+if test "X$1" = X--fallback-echo; then
+ # used as fallback echo
+ shift
+ cat <<EOF
+$*
+EOF
+ exit $EXIT_SUCCESS
+fi
+
+magic="%%%MAGIC variable%%%"
+magic_exe="%%%MAGIC EXE variable%%%"
+
+# Global variables.
+# $mode is unset
+nonopt=
+execute_dlfiles=
+preserve_args=
+lo2o="s/\\.lo\$/.${objext}/"
+o2lo="s/\\.${objext}\$/.lo/"
+extracted_archives=
+extracted_serial=0
+
+opt_dry_run=false
+opt_duplicate_deps=false
+opt_silent=false
+opt_debug=:
+
+# If this variable is set in any of the actions, the command in it
+# will be execed at the end. This prevents here-documents from being
+# left over by shells.
+exec_cmd=
+
+# func_fatal_configuration arg...
+# Echo program name prefixed message to standard error, followed by
+# a configuration failure hint, and exit.
+func_fatal_configuration ()
+{
+ func_error ${1+"$@"}
+ func_error "See the $PACKAGE documentation for more information."
+ func_fatal_error "Fatal configuration error."
+}
+
+
+# func_config
+# Display the configuration for all the tags in this script.
+func_config ()
+{
+ re_begincf='^# ### BEGIN LIBTOOL'
+ re_endcf='^# ### END LIBTOOL'
+
+ # Default configuration.
+ $SED "1,/$re_begincf CONFIG/d;/$re_endcf CONFIG/,\$d" < "$progpath"
+
+ # Now print the configurations for the tags.
+ for tagname in $taglist; do
+ $SED -n "/$re_begincf TAG CONFIG: $tagname\$/,/$re_endcf TAG CONFIG: $tagname\$/p" < "$progpath"
+ done
+
+ exit $?
+}
+
+# func_features
+# Display the features supported by this script.
+func_features ()
+{
+ $ECHO "host: $host"
+ if test "$build_libtool_libs" = yes; then
+ $ECHO "enable shared libraries"
+ else
+ $ECHO "disable shared libraries"
+ fi
+ if test "$build_old_libs" = yes; then
+ $ECHO "enable static libraries"
+ else
+ $ECHO "disable static libraries"
+ fi
+
+ exit $?
+}
+
+# func_enable_tag tagname
+# Verify that TAGNAME is valid, and either flag an error and exit, or
+# enable the TAGNAME tag. We also add TAGNAME to the global $taglist
+# variable here.
+func_enable_tag ()
+{
+ # Global variable:
+ tagname="$1"
+
+ re_begincf="^# ### BEGIN LIBTOOL TAG CONFIG: $tagname\$"
+ re_endcf="^# ### END LIBTOOL TAG CONFIG: $tagname\$"
+ sed_extractcf="/$re_begincf/,/$re_endcf/p"
+
+ # Validate tagname.
+ case $tagname in
+ *[!-_A-Za-z0-9,/]*)
+ func_fatal_error "invalid tag name: $tagname"
+ ;;
+ esac
+
+ # Don't test for the "default" C tag, as we know it's
+ # there but not specially marked.
+ case $tagname in
+ CC) ;;
+ *)
+ if $GREP "$re_begincf" "$progpath" >/dev/null 2>&1; then
+ taglist="$taglist $tagname"
+
+ # Evaluate the configuration. Be careful to quote the path
+ # and the sed script, to avoid splitting on whitespace, but
+ # also don't use non-portable quotes within backquotes within
+ # quotes we have to do it in 2 steps:
+ extractedcf=`$SED -n -e "$sed_extractcf" < "$progpath"`
+ eval "$extractedcf"
+ else
+ func_error "ignoring unknown tag $tagname"
+ fi
+ ;;
+ esac
+}
+
+# Parse options once, thoroughly. This comes as soon as possible in
+# the script to make things like `libtool --version' happen quickly.
+{
+
+ # Shorthand for --mode=foo, only valid as the first argument
+ case $1 in
+ clean|clea|cle|cl)
+ shift; set dummy --mode clean ${1+"$@"}; shift
+ ;;
+ compile|compil|compi|comp|com|co|c)
+ shift; set dummy --mode compile ${1+"$@"}; shift
+ ;;
+ execute|execut|execu|exec|exe|ex|e)
+ shift; set dummy --mode execute ${1+"$@"}; shift
+ ;;
+ finish|finis|fini|fin|fi|f)
+ shift; set dummy --mode finish ${1+"$@"}; shift
+ ;;
+ install|instal|insta|inst|ins|in|i)
+ shift; set dummy --mode install ${1+"$@"}; shift
+ ;;
+ link|lin|li|l)
+ shift; set dummy --mode link ${1+"$@"}; shift
+ ;;
+ uninstall|uninstal|uninsta|uninst|unins|unin|uni|un|u)
+ shift; set dummy --mode uninstall ${1+"$@"}; shift
+ ;;
+ esac
+
+ # Parse non-mode specific arguments:
+ while test "$#" -gt 0; do
+ opt="$1"
+ shift
+
+ case $opt in
+ --config) func_config ;;
+
+ --debug) preserve_args="$preserve_args $opt"
+ func_echo "enabling shell trace mode"
+ opt_debug='set -x'
+ $opt_debug
+ ;;
+
+ -dlopen) test "$#" -eq 0 && func_missing_arg "$opt" && break
+ execute_dlfiles="$execute_dlfiles $1"
+ shift
+ ;;
+
+ --dry-run | -n) opt_dry_run=: ;;
+ --features) func_features ;;
+ --finish) mode="finish" ;;
+
+ --mode) test "$#" -eq 0 && func_missing_arg "$opt" && break
+ case $1 in
+ # Valid mode arguments:
+ clean) ;;
+ compile) ;;
+ execute) ;;
+ finish) ;;
+ install) ;;
+ link) ;;
+ relink) ;;
+ uninstall) ;;
+
+ # Catch anything else as an error
+ *) func_error "invalid argument for $opt"
+ exit_cmd=exit
+ break
+ ;;
+ esac
+
+ mode="$1"
+ shift
+ ;;
+
+ --preserve-dup-deps)
+ opt_duplicate_deps=: ;;
+
+ --quiet|--silent) preserve_args="$preserve_args $opt"
+ opt_silent=:
+ ;;
+
+ --verbose| -v) preserve_args="$preserve_args $opt"
+ opt_silent=false
+ ;;
+
+ --tag) test "$#" -eq 0 && func_missing_arg "$opt" && break
+ preserve_args="$preserve_args $opt $1"
+ func_enable_tag "$1" # tagname is set here
+ shift
+ ;;
+
+ # Separate optargs to long options:
+ -dlopen=*|--mode=*|--tag=*)
+ func_opt_split "$opt"
+ set dummy "$func_opt_split_opt" "$func_opt_split_arg" ${1+"$@"}
+ shift
+ ;;
+
+ -\?|-h) func_usage ;;
+ --help) opt_help=: ;;
+ --version) func_version ;;
+
+ -*) func_fatal_help "unrecognized option \`$opt'" ;;
+
+ *) nonopt="$opt"
+ break
+ ;;
+ esac
+ done
+
+
+ case $host in
+ *cygwin* | *mingw* | *pw32* | *cegcc*)
+ # don't eliminate duplications in $postdeps and $predeps
+ opt_duplicate_compiler_generated_deps=:
+ ;;
+ *)
+ opt_duplicate_compiler_generated_deps=$opt_duplicate_deps
+ ;;
+ esac
+
+ # Having warned about all mis-specified options, bail out if
+ # anything was wrong.
+ $exit_cmd $EXIT_FAILURE
+}
+
+# func_check_version_match
+# Ensure that we are using m4 macros, and libtool script from the same
+# release of libtool.
+func_check_version_match ()
+{
+ if test "$package_revision" != "$macro_revision"; then
+ if test "$VERSION" != "$macro_version"; then
+ if test -z "$macro_version"; then
+ cat >&2 <<_LT_EOF
+$progname: Version mismatch error. This is $PACKAGE $VERSION, but the
+$progname: definition of this LT_INIT comes from an older release.
+$progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION
+$progname: and run autoconf again.
+_LT_EOF
+ else
+ cat >&2 <<_LT_EOF
+$progname: Version mismatch error. This is $PACKAGE $VERSION, but the
+$progname: definition of this LT_INIT comes from $PACKAGE $macro_version.
+$progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION
+$progname: and run autoconf again.
+_LT_EOF
+ fi
+ else
+ cat >&2 <<_LT_EOF
+$progname: Version mismatch error. This is $PACKAGE $VERSION, revision $package_revision,
+$progname: but the definition of this LT_INIT comes from revision $macro_revision.
+$progname: You should recreate aclocal.m4 with macros from revision $package_revision
+$progname: of $PACKAGE $VERSION and run autoconf again.
+_LT_EOF
+ fi
+
+ exit $EXIT_MISMATCH
+ fi
+}
+
+
+## ----------- ##
+## Main. ##
+## ----------- ##
+
+$opt_help || {
+ # Sanity checks first:
+ func_check_version_match
+
+ if test "$build_libtool_libs" != yes && test "$build_old_libs" != yes; then
+ func_fatal_configuration "not configured to build any kind of library"
+ fi
+
+ test -z "$mode" && func_fatal_error "error: you must specify a MODE."
+
+
+ # Darwin sucks
+ eval std_shrext=\"$shrext_cmds\"
+
+
+ # Only execute mode is allowed to have -dlopen flags.
+ if test -n "$execute_dlfiles" && test "$mode" != execute; then
+ func_error "unrecognized option \`-dlopen'"
+ $ECHO "$help" 1>&2
+ exit $EXIT_FAILURE
+ fi
+
+ # Change the help message to a mode-specific one.
+ generic_help="$help"
+ help="Try \`$progname --help --mode=$mode' for more information."
+}
+
+
+# func_lalib_p file
+# True iff FILE is a libtool `.la' library or `.lo' object file.
+# This function is only a basic sanity check; it will hardly flush out
+# determined imposters.
+func_lalib_p ()
+{
+ test -f "$1" &&
+ $SED -e 4q "$1" 2>/dev/null \
+ | $GREP "^# Generated by .*$PACKAGE" > /dev/null 2>&1
+}
+
+# func_lalib_unsafe_p file
+# True iff FILE is a libtool `.la' library or `.lo' object file.
+# This function implements the same check as func_lalib_p without
+# resorting to external programs. To this end, it redirects stdin and
+# closes it afterwards, without saving the original file descriptor.
+# As a safety measure, use it only where a negative result would be
+# fatal anyway. Works if `file' does not exist.
+func_lalib_unsafe_p ()
+{
+ lalib_p=no
+ if test -f "$1" && test -r "$1" && exec 5<&0 <"$1"; then
+ for lalib_p_l in 1 2 3 4
+ do
+ read lalib_p_line
+ case "$lalib_p_line" in
+ \#\ Generated\ by\ *$PACKAGE* ) lalib_p=yes; break;;
+ esac
+ done
+ exec 0<&5 5<&-
+ fi
+ test "$lalib_p" = yes
+}
+
+# func_ltwrapper_script_p file
+# True iff FILE is a libtool wrapper script
+# This function is only a basic sanity check; it will hardly flush out
+# determined imposters.
+func_ltwrapper_script_p ()
+{
+ func_lalib_p "$1"
+}
+
+# func_ltwrapper_executable_p file
+# True iff FILE is a libtool wrapper executable
+# This function is only a basic sanity check; it will hardly flush out
+# determined imposters.
+func_ltwrapper_executable_p ()
+{
+ func_ltwrapper_exec_suffix=
+ case $1 in
+ *.exe) ;;
+ *) func_ltwrapper_exec_suffix=.exe ;;
+ esac
+ $GREP "$magic_exe" "$1$func_ltwrapper_exec_suffix" >/dev/null 2>&1
+}
+
+# func_ltwrapper_scriptname file
+# Assumes file is an ltwrapper_executable
+# uses $file to determine the appropriate filename for a
+# temporary ltwrapper_script.
+func_ltwrapper_scriptname ()
+{
+ func_ltwrapper_scriptname_result=""
+ if func_ltwrapper_executable_p "$1"; then
+ func_dirname_and_basename "$1" "" "."
+ func_stripname '' '.exe' "$func_basename_result"
+ func_ltwrapper_scriptname_result="$func_dirname_result/$objdir/${func_stripname_result}_ltshwrapper"
+ fi
+}
+
+# func_ltwrapper_p file
+# True iff FILE is a libtool wrapper script or wrapper executable
+# This function is only a basic sanity check; it will hardly flush out
+# determined imposters.
+func_ltwrapper_p ()
+{
+ func_ltwrapper_script_p "$1" || func_ltwrapper_executable_p "$1"
+}
+
+
+# func_execute_cmds commands fail_cmd
+# Execute tilde-delimited COMMANDS.
+# If FAIL_CMD is given, eval that upon failure.
+# FAIL_CMD may read-access the current command in variable CMD!
+func_execute_cmds ()
+{
+ $opt_debug
+ save_ifs=$IFS; IFS='~'
+ for cmd in $1; do
+ IFS=$save_ifs
+ eval cmd=\"$cmd\"
+ func_show_eval "$cmd" "${2-:}"
+ done
+ IFS=$save_ifs
+}
+
+
+# func_source file
+# Source FILE, adding directory component if necessary.
+# Note that it is not necessary on cygwin/mingw to append a dot to
+# FILE even if both FILE and FILE.exe exist: automatic-append-.exe
+# behavior happens only for exec(3), not for open(2)! Also, sourcing
+# `FILE.' does not work on cygwin managed mounts.
+func_source ()
+{
+ $opt_debug
+ case $1 in
+ */* | *\\*) . "$1" ;;
+ *) . "./$1" ;;
+ esac
+}
+
+
+# func_infer_tag arg
+# Infer tagged configuration to use if any are available and
+# if one wasn't chosen via the "--tag" command line option.
+# Only attempt this if the compiler in the base compile
+# command doesn't match the default compiler.
+# arg is usually of the form 'gcc ...'
+func_infer_tag ()
+{
+ $opt_debug
+ if test -n "$available_tags" && test -z "$tagname"; then
+ CC_quoted=
+ for arg in $CC; do
+ func_quote_for_eval "$arg"
+ CC_quoted="$CC_quoted $func_quote_for_eval_result"
+ done
+ case $@ in
+ # Blanks in the command may have been stripped by the calling shell,
+ # but not from the CC environment variable when configure was run.
+ " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*) ;;
+ # Blanks at the start of $base_compile will cause this to fail
+ # if we don't check for them as well.
+ *)
+ for z in $available_tags; do
+ if $GREP "^# ### BEGIN LIBTOOL TAG CONFIG: $z$" < "$progpath" > /dev/null; then
+ # Evaluate the configuration.
+ eval "`${SED} -n -e '/^# ### BEGIN LIBTOOL TAG CONFIG: '$z'$/,/^# ### END LIBTOOL TAG CONFIG: '$z'$/p' < $progpath`"
+ CC_quoted=
+ for arg in $CC; do
+ # Double-quote args containing other shell metacharacters.
+ func_quote_for_eval "$arg"
+ CC_quoted="$CC_quoted $func_quote_for_eval_result"
+ done
+ case "$@ " in
+ " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*)
+ # The compiler in the base compile command matches
+ # the one in the tagged configuration.
+ # Assume this is the tagged configuration we want.
+ tagname=$z
+ break
+ ;;
+ esac
+ fi
+ done
+ # If $tagname still isn't set, then no tagged configuration
+ # was found and let the user know that the "--tag" command
+ # line option must be used.
+ if test -z "$tagname"; then
+ func_echo "unable to infer tagged configuration"
+ func_fatal_error "specify a tag with \`--tag'"
+# else
+# func_verbose "using $tagname tagged configuration"
+ fi
+ ;;
+ esac
+ fi
+}
+
+
+
+# func_write_libtool_object output_name pic_name nonpic_name
+# Create a libtool object file (analogous to a ".la" file),
+# but don't create it if we're doing a dry run.
+func_write_libtool_object ()
+{
+ write_libobj=${1}
+ if test "$build_libtool_libs" = yes; then
+ write_lobj=\'${2}\'
+ else
+ write_lobj=none
+ fi
+
+ if test "$build_old_libs" = yes; then
+ write_oldobj=\'${3}\'
+ else
+ write_oldobj=none
+ fi
+
+ $opt_dry_run || {
+ cat >${write_libobj}T <<EOF
+# $write_libobj - a libtool object file
+# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object=$write_lobj
+
+# Name of the non-PIC object
+non_pic_object=$write_oldobj
+
+EOF
+ $MV "${write_libobj}T" "${write_libobj}"
+ }
+}
+
+# func_mode_compile arg...
+func_mode_compile ()
+{
+ $opt_debug
+ # Get the compilation command and the source file.
+ base_compile=
+ srcfile="$nonopt" # always keep a non-empty value in "srcfile"
+ suppress_opt=yes
+ suppress_output=
+ arg_mode=normal
+ libobj=
+ later=
+ pie_flag=
+
+ for arg
+ do
+ case $arg_mode in
+ arg )
+ # do not "continue". Instead, add this to base_compile
+ lastarg="$arg"
+ arg_mode=normal
+ ;;
+
+ target )
+ libobj="$arg"
+ arg_mode=normal
+ continue
+ ;;
+
+ normal )
+ # Accept any command-line options.
+ case $arg in
+ -o)
+ test -n "$libobj" && \
+ func_fatal_error "you cannot specify \`-o' more than once"
+ arg_mode=target
+ continue
+ ;;
+
+ -pie | -fpie | -fPIE)
+ pie_flag="$pie_flag $arg"
+ continue
+ ;;
+
+ -shared | -static | -prefer-pic | -prefer-non-pic)
+ later="$later $arg"
+ continue
+ ;;
+
+ -no-suppress)
+ suppress_opt=no
+ continue
+ ;;
+
+ -Xcompiler)
+ arg_mode=arg # the next one goes into the "base_compile" arg list
+ continue # The current "srcfile" will either be retained or
+ ;; # replaced later. I would guess that would be a bug.
+
+ -Wc,*)
+ func_stripname '-Wc,' '' "$arg"
+ args=$func_stripname_result
+ lastarg=
+ save_ifs="$IFS"; IFS=','
+ for arg in $args; do
+ IFS="$save_ifs"
+ func_quote_for_eval "$arg"
+ lastarg="$lastarg $func_quote_for_eval_result"
+ done
+ IFS="$save_ifs"
+ func_stripname ' ' '' "$lastarg"
+ lastarg=$func_stripname_result
+
+ # Add the arguments to base_compile.
+ base_compile="$base_compile $lastarg"
+ continue
+ ;;
+
+ *)
+ # Accept the current argument as the source file.
+ # The previous "srcfile" becomes the current argument.
+ #
+ lastarg="$srcfile"
+ srcfile="$arg"
+ ;;
+ esac # case $arg
+ ;;
+ esac # case $arg_mode
+
+ # Aesthetically quote the previous argument.
+ func_quote_for_eval "$lastarg"
+ base_compile="$base_compile $func_quote_for_eval_result"
+ done # for arg
+
+ case $arg_mode in
+ arg)
+ func_fatal_error "you must specify an argument for -Xcompile"
+ ;;
+ target)
+ func_fatal_error "you must specify a target with \`-o'"
+ ;;
+ *)
+ # Get the name of the library object.
+ test -z "$libobj" && {
+ func_basename "$srcfile"
+ libobj="$func_basename_result"
+ }
+ ;;
+ esac
+
+ # Recognize several different file suffixes.
+ # If the user specifies -o file.o, it is replaced with file.lo
+ case $libobj in
+ *.[cCFSifmso] | \
+ *.ada | *.adb | *.ads | *.asm | \
+ *.c++ | *.cc | *.ii | *.class | *.cpp | *.cxx | \
+ *.[fF][09]? | *.for | *.java | *.obj | *.sx)
+ func_xform "$libobj"
+ libobj=$func_xform_result
+ ;;
+ esac
+
+ case $libobj in
+ *.lo) func_lo2o "$libobj"; obj=$func_lo2o_result ;;
+ *)
+ func_fatal_error "cannot determine name of library object from \`$libobj'"
+ ;;
+ esac
+
+ func_infer_tag $base_compile
+
+ for arg in $later; do
+ case $arg in
+ -shared)
+ test "$build_libtool_libs" != yes && \
+ func_fatal_configuration "can not build a shared library"
+ build_old_libs=no
+ continue
+ ;;
+
+ -static)
+ build_libtool_libs=no
+ build_old_libs=yes
+ continue
+ ;;
+
+ -prefer-pic)
+ pic_mode=yes
+ continue
+ ;;
+
+ -prefer-non-pic)
+ pic_mode=no
+ continue
+ ;;
+ esac
+ done
+
+ func_quote_for_eval "$libobj"
+ test "X$libobj" != "X$func_quote_for_eval_result" \
+ && $ECHO "X$libobj" | $GREP '[]~#^*{};<>?"'"'"' &()|`$[]' \
+ && func_warning "libobj name \`$libobj' may not contain shell special characters."
+ func_dirname_and_basename "$obj" "/" ""
+ objname="$func_basename_result"
+ xdir="$func_dirname_result"
+ lobj=${xdir}$objdir/$objname
+
+ test -z "$base_compile" && \
+ func_fatal_help "you must specify a compilation command"
+
+ # Delete any leftover library objects.
+ if test "$build_old_libs" = yes; then
+ removelist="$obj $lobj $libobj ${libobj}T"
+ else
+ removelist="$lobj $libobj ${libobj}T"
+ fi
+
+ # On Cygwin there's no "real" PIC flag so we must build both object types
+ case $host_os in
+ cygwin* | mingw* | pw32* | os2* | cegcc*)
+ pic_mode=default
+ ;;
+ esac
+ if test "$pic_mode" = no && test "$deplibs_check_method" != pass_all; then
+ # non-PIC code in shared libraries is not supported
+ pic_mode=default
+ fi
+
+ # Calculate the filename of the output object if compiler does
+ # not support -o with -c
+ if test "$compiler_c_o" = no; then
+ output_obj=`$ECHO "X$srcfile" | $Xsed -e 's%^.*/%%' -e 's%\.[^.]*$%%'`.${objext}
+ lockfile="$output_obj.lock"
+ else
+ output_obj=
+ need_locks=no
+ lockfile=
+ fi
+
+ # Lock this critical section if it is needed
+ # We use this script file to make the link, it avoids creating a new file
+ if test "$need_locks" = yes; then
+ until $opt_dry_run || ln "$progpath" "$lockfile" 2>/dev/null; do
+ func_echo "Waiting for $lockfile to be removed"
+ sleep 2
+ done
+ elif test "$need_locks" = warn; then
+ if test -f "$lockfile"; then
+ $ECHO "\
+*** ERROR, $lockfile exists and contains:
+`cat $lockfile 2>/dev/null`
+
+This indicates that another process is trying to use the same
+temporary object file, and libtool could not work around it because
+your compiler does not support \`-c' and \`-o' together. If you
+repeat this compilation, it may succeed, by chance, but you had better
+avoid parallel builds (make -j) in this platform, or get a better
+compiler."
+
+ $opt_dry_run || $RM $removelist
+ exit $EXIT_FAILURE
+ fi
+ removelist="$removelist $output_obj"
+ $ECHO "$srcfile" > "$lockfile"
+ fi
+
+ $opt_dry_run || $RM $removelist
+ removelist="$removelist $lockfile"
+ trap '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' 1 2 15
+
+ if test -n "$fix_srcfile_path"; then
+ eval srcfile=\"$fix_srcfile_path\"
+ fi
+ func_quote_for_eval "$srcfile"
+ qsrcfile=$func_quote_for_eval_result
+
+ # Only build a PIC object if we are building libtool libraries.
+ if test "$build_libtool_libs" = yes; then
+ # Without this assignment, base_compile gets emptied.
+ fbsd_hideous_sh_bug=$base_compile
+
+ if test "$pic_mode" != no; then
+ command="$base_compile $qsrcfile $pic_flag"
+ else
+ # Don't build PIC code
+ command="$base_compile $qsrcfile"
+ fi
+
+ func_mkdir_p "$xdir$objdir"
+
+ if test -z "$output_obj"; then
+ # Place PIC objects in $objdir
+ command="$command -o $lobj"
+ fi
+
+ func_show_eval_locale "$command" \
+ 'test -n "$output_obj" && $RM $removelist; exit $EXIT_FAILURE'
+
+ if test "$need_locks" = warn &&
+ test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then
+ $ECHO "\
+*** ERROR, $lockfile contains:
+`cat $lockfile 2>/dev/null`
+
+but it should contain:
+$srcfile
+
+This indicates that another process is trying to use the same
+temporary object file, and libtool could not work around it because
+your compiler does not support \`-c' and \`-o' together. If you
+repeat this compilation, it may succeed, by chance, but you had better
+avoid parallel builds (make -j) in this platform, or get a better
+compiler."
+
+ $opt_dry_run || $RM $removelist
+ exit $EXIT_FAILURE
+ fi
+
+ # Just move the object if needed, then go on to compile the next one
+ if test -n "$output_obj" && test "X$output_obj" != "X$lobj"; then
+ func_show_eval '$MV "$output_obj" "$lobj"' \
+ 'error=$?; $opt_dry_run || $RM $removelist; exit $error'
+ fi
+
+ # Allow error messages only from the first compilation.
+ if test "$suppress_opt" = yes; then
+ suppress_output=' >/dev/null 2>&1'
+ fi
+ fi
+
+ # Only build a position-dependent object if we build old libraries.
+ if test "$build_old_libs" = yes; then
+ if test "$pic_mode" != yes; then
+ # Don't build PIC code
+ command="$base_compile $qsrcfile$pie_flag"
+ else
+ command="$base_compile $qsrcfile $pic_flag"
+ fi
+ if test "$compiler_c_o" = yes; then
+ command="$command -o $obj"
+ fi
+
+ # Suppress compiler output if we already did a PIC compilation.
+ command="$command$suppress_output"
+ func_show_eval_locale "$command" \
+ '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE'
+
+ if test "$need_locks" = warn &&
+ test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then
+ $ECHO "\
+*** ERROR, $lockfile contains:
+`cat $lockfile 2>/dev/null`
+
+but it should contain:
+$srcfile
+
+This indicates that another process is trying to use the same
+temporary object file, and libtool could not work around it because
+your compiler does not support \`-c' and \`-o' together. If you
+repeat this compilation, it may succeed, by chance, but you had better
+avoid parallel builds (make -j) in this platform, or get a better
+compiler."
+
+ $opt_dry_run || $RM $removelist
+ exit $EXIT_FAILURE
+ fi
+
+ # Just move the object if needed
+ if test -n "$output_obj" && test "X$output_obj" != "X$obj"; then
+ func_show_eval '$MV "$output_obj" "$obj"' \
+ 'error=$?; $opt_dry_run || $RM $removelist; exit $error'
+ fi
+ fi
+
+ $opt_dry_run || {
+ func_write_libtool_object "$libobj" "$objdir/$objname" "$objname"
+
+ # Unlock the critical section if it was locked
+ if test "$need_locks" != no; then
+ removelist=$lockfile
+ $RM "$lockfile"
+ fi
+ }
+
+ exit $EXIT_SUCCESS
+}
+
+$opt_help || {
+test "$mode" = compile && func_mode_compile ${1+"$@"}
+}
+
+func_mode_help ()
+{
+ # We need to display help for each of the modes.
+ case $mode in
+ "")
+ # Generic help is extracted from the usage comments
+ # at the start of this file.
+ func_help
+ ;;
+
+ clean)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=clean RM [RM-OPTION]... FILE...
+
+Remove files from the build directory.
+
+RM is the name of the program to use to delete files associated with each FILE
+(typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed
+to RM.
+
+If FILE is a libtool library, object or program, all the files associated
+with it are deleted. Otherwise, only FILE itself is deleted using RM."
+ ;;
+
+ compile)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=compile COMPILE-COMMAND... SOURCEFILE
+
+Compile a source file into a libtool library object.
+
+This mode accepts the following additional options:
+
+ -o OUTPUT-FILE set the output file name to OUTPUT-FILE
+ -no-suppress do not suppress compiler output for multiple passes
+ -prefer-pic try to building PIC objects only
+ -prefer-non-pic try to building non-PIC objects only
+ -shared do not build a \`.o' file suitable for static linking
+ -static only build a \`.o' file suitable for static linking
+
+COMPILE-COMMAND is a command to be used in creating a \`standard' object file
+from the given SOURCEFILE.
+
+The output file name is determined by removing the directory component from
+SOURCEFILE, then substituting the C source code suffix \`.c' with the
+library object suffix, \`.lo'."
+ ;;
+
+ execute)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=execute COMMAND [ARGS]...
+
+Automatically set library path, then run a program.
+
+This mode accepts the following additional options:
+
+ -dlopen FILE add the directory containing FILE to the library path
+
+This mode sets the library path environment variable according to \`-dlopen'
+flags.
+
+If any of the ARGS are libtool executable wrappers, then they are translated
+into their corresponding uninstalled binary, and any of their required library
+directories are added to the library path.
+
+Then, COMMAND is executed, with ARGS as arguments."
+ ;;
+
+ finish)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=finish [LIBDIR]...
+
+Complete the installation of libtool libraries.
+
+Each LIBDIR is a directory that contains libtool libraries.
+
+The commands that this mode executes may require superuser privileges. Use
+the \`--dry-run' option if you just want to see what would be executed."
+ ;;
+
+ install)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=install INSTALL-COMMAND...
+
+Install executables or libraries.
+
+INSTALL-COMMAND is the installation command. The first component should be
+either the \`install' or \`cp' program.
+
+The following components of INSTALL-COMMAND are treated specially:
+
+ -inst-prefix PREFIX-DIR Use PREFIX-DIR as a staging area for installation
+
+The rest of the components are interpreted as arguments to that command (only
+BSD-compatible install options are recognized)."
+ ;;
+
+ link)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=link LINK-COMMAND...
+
+Link object files or libraries together to form another library, or to
+create an executable program.
+
+LINK-COMMAND is a command using the C compiler that you would use to create
+a program from several object files.
+
+The following components of LINK-COMMAND are treated specially:
+
+ -all-static do not do any dynamic linking at all
+ -avoid-version do not add a version suffix if possible
+ -dlopen FILE \`-dlpreopen' FILE if it cannot be dlopened at runtime
+ -dlpreopen FILE link in FILE and add its symbols to lt_preloaded_symbols
+ -export-dynamic allow symbols from OUTPUT-FILE to be resolved with dlsym(3)
+ -export-symbols SYMFILE
+ try to export only the symbols listed in SYMFILE
+ -export-symbols-regex REGEX
+ try to export only the symbols matching REGEX
+ -LLIBDIR search LIBDIR for required installed libraries
+ -lNAME OUTPUT-FILE requires the installed library libNAME
+ -module build a library that can dlopened
+ -no-fast-install disable the fast-install mode
+ -no-install link a not-installable executable
+ -no-undefined declare that a library does not refer to external symbols
+ -o OUTPUT-FILE create OUTPUT-FILE from the specified objects
+ -objectlist FILE Use a list of object files found in FILE to specify objects
+ -precious-files-regex REGEX
+ don't remove output files matching REGEX
+ -release RELEASE specify package release information
+ -rpath LIBDIR the created library will eventually be installed in LIBDIR
+ -R[ ]LIBDIR add LIBDIR to the runtime path of programs and libraries
+ -shared only do dynamic linking of libtool libraries
+ -shrext SUFFIX override the standard shared library file extension
+ -static do not do any dynamic linking of uninstalled libtool libraries
+ -static-libtool-libs
+ do not do any dynamic linking of libtool libraries
+ -version-info CURRENT[:REVISION[:AGE]]
+ specify library version info [each variable defaults to 0]
+ -weak LIBNAME declare that the target provides the LIBNAME interface
+
+All other options (arguments beginning with \`-') are ignored.
+
+Every other argument is treated as a filename. Files ending in \`.la' are
+treated as uninstalled libtool libraries, other files are standard or library
+object files.
+
+If the OUTPUT-FILE ends in \`.la', then a libtool library is created,
+only library objects (\`.lo' files) may be specified, and \`-rpath' is
+required, except when creating a convenience library.
+
+If OUTPUT-FILE ends in \`.a' or \`.lib', then a standard library is created
+using \`ar' and \`ranlib', or on Windows using \`lib'.
+
+If OUTPUT-FILE ends in \`.lo' or \`.${objext}', then a reloadable object file
+is created, otherwise an executable program is created."
+ ;;
+
+ uninstall)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=uninstall RM [RM-OPTION]... FILE...
+
+Remove libraries from an installation directory.
+
+RM is the name of the program to use to delete files associated with each FILE
+(typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed
+to RM.
+
+If FILE is a libtool library, all the files associated with it are deleted.
+Otherwise, only FILE itself is deleted using RM."
+ ;;
+
+ *)
+ func_fatal_help "invalid operation mode \`$mode'"
+ ;;
+ esac
+
+ $ECHO
+ $ECHO "Try \`$progname --help' for more information about other modes."
+
+ exit $?
+}
+
+ # Now that we've collected a possible --mode arg, show help if necessary
+ $opt_help && func_mode_help
+
+
+# func_mode_execute arg...
+func_mode_execute ()
+{
+ $opt_debug
+ # The first argument is the command name.
+ cmd="$nonopt"
+ test -z "$cmd" && \
+ func_fatal_help "you must specify a COMMAND"
+
+ # Handle -dlopen flags immediately.
+ for file in $execute_dlfiles; do
+ test -f "$file" \
+ || func_fatal_help "\`$file' is not a file"
+
+ dir=
+ case $file in
+ *.la)
+ # Check to see that this really is a libtool archive.
+ func_lalib_unsafe_p "$file" \
+ || func_fatal_help "\`$lib' is not a valid libtool archive"
+
+ # Read the libtool library.
+ dlname=
+ library_names=
+ func_source "$file"
+
+ # Skip this library if it cannot be dlopened.
+ if test -z "$dlname"; then
+ # Warn if it was a shared library.
+ test -n "$library_names" && \
+ func_warning "\`$file' was not linked with \`-export-dynamic'"
+ continue
+ fi
+
+ func_dirname "$file" "" "."
+ dir="$func_dirname_result"
+
+ if test -f "$dir/$objdir/$dlname"; then
+ dir="$dir/$objdir"
+ else
+ if test ! -f "$dir/$dlname"; then
+ func_fatal_error "cannot find \`$dlname' in \`$dir' or \`$dir/$objdir'"
+ fi
+ fi
+ ;;
+
+ *.lo)
+ # Just add the directory containing the .lo file.
+ func_dirname "$file" "" "."
+ dir="$func_dirname_result"
+ ;;
+
+ *)
+ func_warning "\`-dlopen' is ignored for non-libtool libraries and objects"
+ continue
+ ;;
+ esac
+
+ # Get the absolute pathname.
+ absdir=`cd "$dir" && pwd`
+ test -n "$absdir" && dir="$absdir"
+
+ # Now add the directory to shlibpath_var.
+ if eval "test -z \"\$$shlibpath_var\""; then
+ eval "$shlibpath_var=\"\$dir\""
+ else
+ eval "$shlibpath_var=\"\$dir:\$$shlibpath_var\""
+ fi
+ done
+
+ # This variable tells wrapper scripts just to set shlibpath_var
+ # rather than running their programs.
+ libtool_execute_magic="$magic"
+
+ # Check if any of the arguments is a wrapper script.
+ args=
+ for file
+ do
+ case $file in
+ -*) ;;
+ *)
+ # Do a test to see if this is really a libtool program.
+ if func_ltwrapper_script_p "$file"; then
+ func_source "$file"
+ # Transform arg to wrapped name.
+ file="$progdir/$program"
+ elif func_ltwrapper_executable_p "$file"; then
+ func_ltwrapper_scriptname "$file"
+ func_source "$func_ltwrapper_scriptname_result"
+ # Transform arg to wrapped name.
+ file="$progdir/$program"
+ fi
+ ;;
+ esac
+ # Quote arguments (to preserve shell metacharacters).
+ func_quote_for_eval "$file"
+ args="$args $func_quote_for_eval_result"
+ done
+
+ if test "X$opt_dry_run" = Xfalse; then
+ if test -n "$shlibpath_var"; then
+ # Export the shlibpath_var.
+ eval "export $shlibpath_var"
+ fi
+
+ # Restore saved environment variables
+ for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES
+ do
+ eval "if test \"\${save_$lt_var+set}\" = set; then
+ $lt_var=\$save_$lt_var; export $lt_var
+ else
+ $lt_unset $lt_var
+ fi"
+ done
+
+ # Now prepare to actually exec the command.
+ exec_cmd="\$cmd$args"
+ else
+ # Display what would be done.
+ if test -n "$shlibpath_var"; then
+ eval "\$ECHO \"\$shlibpath_var=\$$shlibpath_var\""
+ $ECHO "export $shlibpath_var"
+ fi
+ $ECHO "$cmd$args"
+ exit $EXIT_SUCCESS
+ fi
+}
+
+test "$mode" = execute && func_mode_execute ${1+"$@"}
+
+
+# func_mode_finish arg...
+func_mode_finish ()
+{
+ $opt_debug
+ libdirs="$nonopt"
+ admincmds=
+
+ if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then
+ for dir
+ do
+ libdirs="$libdirs $dir"
+ done
+
+ for libdir in $libdirs; do
+ if test -n "$finish_cmds"; then
+ # Do each command in the finish commands.
+ func_execute_cmds "$finish_cmds" 'admincmds="$admincmds
+'"$cmd"'"'
+ fi
+ if test -n "$finish_eval"; then
+ # Do the single finish_eval.
+ eval cmds=\"$finish_eval\"
+ $opt_dry_run || eval "$cmds" || admincmds="$admincmds
+ $cmds"
+ fi
+ done
+ fi
+
+ # Exit here if they wanted silent mode.
+ $opt_silent && exit $EXIT_SUCCESS
+
+ $ECHO "X----------------------------------------------------------------------" | $Xsed
+ $ECHO "Libraries have been installed in:"
+ for libdir in $libdirs; do
+ $ECHO " $libdir"
+ done
+ $ECHO
+ $ECHO "If you ever happen to want to link against installed libraries"
+ $ECHO "in a given directory, LIBDIR, you must either use libtool, and"
+ $ECHO "specify the full pathname of the library, or use the \`-LLIBDIR'"
+ $ECHO "flag during linking and do at least one of the following:"
+ if test -n "$shlibpath_var"; then
+ $ECHO " - add LIBDIR to the \`$shlibpath_var' environment variable"
+ $ECHO " during execution"
+ fi
+ if test -n "$runpath_var"; then
+ $ECHO " - add LIBDIR to the \`$runpath_var' environment variable"
+ $ECHO " during linking"
+ fi
+ if test -n "$hardcode_libdir_flag_spec"; then
+ libdir=LIBDIR
+ eval flag=\"$hardcode_libdir_flag_spec\"
+
+ $ECHO " - use the \`$flag' linker flag"
+ fi
+ if test -n "$admincmds"; then
+ $ECHO " - have your system administrator run these commands:$admincmds"
+ fi
+ if test -f /etc/ld.so.conf; then
+ $ECHO " - have your system administrator add LIBDIR to \`/etc/ld.so.conf'"
+ fi
+ $ECHO
+
+ $ECHO "See any operating system documentation about shared libraries for"
+ case $host in
+ solaris2.[6789]|solaris2.1[0-9])
+ $ECHO "more information, such as the ld(1), crle(1) and ld.so(8) manual"
+ $ECHO "pages."
+ ;;
+ *)
+ $ECHO "more information, such as the ld(1) and ld.so(8) manual pages."
+ ;;
+ esac
+ $ECHO "X----------------------------------------------------------------------" | $Xsed
+ exit $EXIT_SUCCESS
+}
+
+test "$mode" = finish && func_mode_finish ${1+"$@"}
+
+
+# func_mode_install arg...
+func_mode_install ()
+{
+ $opt_debug
+ # There may be an optional sh(1) argument at the beginning of
+ # install_prog (especially on Windows NT).
+ if test "$nonopt" = "$SHELL" || test "$nonopt" = /bin/sh ||
+ # Allow the use of GNU shtool's install command.
+ $ECHO "X$nonopt" | $GREP shtool >/dev/null; then
+ # Aesthetically quote it.
+ func_quote_for_eval "$nonopt"
+ install_prog="$func_quote_for_eval_result "
+ arg=$1
+ shift
+ else
+ install_prog=
+ arg=$nonopt
+ fi
+
+ # The real first argument should be the name of the installation program.
+ # Aesthetically quote it.
+ func_quote_for_eval "$arg"
+ install_prog="$install_prog$func_quote_for_eval_result"
+
+ # We need to accept at least all the BSD install flags.
+ dest=
+ files=
+ opts=
+ prev=
+ install_type=
+ isdir=no
+ stripme=
+ for arg
+ do
+ if test -n "$dest"; then
+ files="$files $dest"
+ dest=$arg
+ continue
+ fi
+
+ case $arg in
+ -d) isdir=yes ;;
+ -f)
+ case " $install_prog " in
+ *[\\\ /]cp\ *) ;;
+ *) prev=$arg ;;
+ esac
+ ;;
+ -g | -m | -o)
+ prev=$arg
+ ;;
+ -s)
+ stripme=" -s"
+ continue
+ ;;
+ -*)
+ ;;
+ *)
+ # If the previous option needed an argument, then skip it.
+ if test -n "$prev"; then
+ prev=
+ else
+ dest=$arg
+ continue
+ fi
+ ;;
+ esac
+
+ # Aesthetically quote the argument.
+ func_quote_for_eval "$arg"
+ install_prog="$install_prog $func_quote_for_eval_result"
+ done
+
+ test -z "$install_prog" && \
+ func_fatal_help "you must specify an install program"
+
+ test -n "$prev" && \
+ func_fatal_help "the \`$prev' option requires an argument"
+
+ if test -z "$files"; then
+ if test -z "$dest"; then
+ func_fatal_help "no file or destination specified"
+ else
+ func_fatal_help "you must specify a destination"
+ fi
+ fi
+
+ # Strip any trailing slash from the destination.
+ func_stripname '' '/' "$dest"
+ dest=$func_stripname_result
+
+ # Check to see that the destination is a directory.
+ test -d "$dest" && isdir=yes
+ if test "$isdir" = yes; then
+ destdir="$dest"
+ destname=
+ else
+ func_dirname_and_basename "$dest" "" "."
+ destdir="$func_dirname_result"
+ destname="$func_basename_result"
+
+ # Not a directory, so check to see that there is only one file specified.
+ set dummy $files; shift
+ test "$#" -gt 1 && \
+ func_fatal_help "\`$dest' is not a directory"
+ fi
+ case $destdir in
+ [\\/]* | [A-Za-z]:[\\/]*) ;;
+ *)
+ for file in $files; do
+ case $file in
+ *.lo) ;;
+ *)
+ func_fatal_help "\`$destdir' must be an absolute directory name"
+ ;;
+ esac
+ done
+ ;;
+ esac
+
+ # This variable tells wrapper scripts just to set variables rather
+ # than running their programs.
+ libtool_install_magic="$magic"
+
+ staticlibs=
+ future_libdirs=
+ current_libdirs=
+ for file in $files; do
+
+ # Do each installation.
+ case $file in
+ *.$libext)
+ # Do the static libraries later.
+ staticlibs="$staticlibs $file"
+ ;;
+
+ *.la)
+ # Check to see that this really is a libtool archive.
+ func_lalib_unsafe_p "$file" \
+ || func_fatal_help "\`$file' is not a valid libtool archive"
+
+ library_names=
+ old_library=
+ relink_command=
+ func_source "$file"
+
+ # Add the libdir to current_libdirs if it is the destination.
+ if test "X$destdir" = "X$libdir"; then
+ case "$current_libdirs " in
+ *" $libdir "*) ;;
+ *) current_libdirs="$current_libdirs $libdir" ;;
+ esac
+ else
+ # Note the libdir as a future libdir.
+ case "$future_libdirs " in
+ *" $libdir "*) ;;
+ *) future_libdirs="$future_libdirs $libdir" ;;
+ esac
+ fi
+
+ func_dirname "$file" "/" ""
+ dir="$func_dirname_result"
+ dir="$dir$objdir"
+
+ if test -n "$relink_command"; then
+ # Determine the prefix the user has applied to our future dir.
+ inst_prefix_dir=`$ECHO "X$destdir" | $Xsed -e "s%$libdir\$%%"`
+
+ # Don't allow the user to place us outside of our expected
+ # location b/c this prevents finding dependent libraries that
+ # are installed to the same prefix.
+ # At present, this check doesn't affect windows .dll's that
+ # are installed into $libdir/../bin (currently, that works fine)
+ # but it's something to keep an eye on.
+ test "$inst_prefix_dir" = "$destdir" && \
+ func_fatal_error "error: cannot install \`$file' to a directory not ending in $libdir"
+
+ if test -n "$inst_prefix_dir"; then
+ # Stick the inst_prefix_dir data into the link command.
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%"`
+ else
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%%"`
+ fi
+
+ func_warning "relinking \`$file'"
+ func_show_eval "$relink_command" \
+ 'func_fatal_error "error: relink \`$file'\'' with the above command before installing it"'
+ fi
+
+ # See the names of the shared library.
+ set dummy $library_names; shift
+ if test -n "$1"; then
+ realname="$1"
+ shift
+
+ srcname="$realname"
+ test -n "$relink_command" && srcname="$realname"T
+
+ # Install the shared library and build the symlinks.
+ func_show_eval "$install_prog $dir/$srcname $destdir/$realname" \
+ 'exit $?'
+ tstripme="$stripme"
+ case $host_os in
+ cygwin* | mingw* | pw32* | cegcc*)
+ case $realname in
+ *.dll.a)
+ tstripme=""
+ ;;
+ esac
+ ;;
+ esac
+ if test -n "$tstripme" && test -n "$striplib"; then
+ func_show_eval "$striplib $destdir/$realname" 'exit $?'
+ fi
+
+ if test "$#" -gt 0; then
+ # Delete the old symlinks, and create new ones.
+ # Try `ln -sf' first, because the `ln' binary might depend on
+ # the symlink we replace! Solaris /bin/ln does not understand -f,
+ # so we also need to try rm && ln -s.
+ for linkname
+ do
+ test "$linkname" != "$realname" \
+ && func_show_eval "(cd $destdir && { $LN_S -f $realname $linkname || { $RM $linkname && $LN_S $realname $linkname; }; })"
+ done
+ fi
+
+ # Do each command in the postinstall commands.
+ lib="$destdir/$realname"
+ func_execute_cmds "$postinstall_cmds" 'exit $?'
+ fi
+
+ # Install the pseudo-library for information purposes.
+ func_basename "$file"
+ name="$func_basename_result"
+ instname="$dir/$name"i
+ func_show_eval "$install_prog $instname $destdir/$name" 'exit $?'
+
+ # Maybe install the static library, too.
+ test -n "$old_library" && staticlibs="$staticlibs $dir/$old_library"
+ ;;
+
+ *.lo)
+ # Install (i.e. copy) a libtool object.
+
+ # Figure out destination file name, if it wasn't already specified.
+ if test -n "$destname"; then
+ destfile="$destdir/$destname"
+ else
+ func_basename "$file"
+ destfile="$func_basename_result"
+ destfile="$destdir/$destfile"
+ fi
+
+ # Deduce the name of the destination old-style object file.
+ case $destfile in
+ *.lo)
+ func_lo2o "$destfile"
+ staticdest=$func_lo2o_result
+ ;;
+ *.$objext)
+ staticdest="$destfile"
+ destfile=
+ ;;
+ *)
+ func_fatal_help "cannot copy a libtool object to \`$destfile'"
+ ;;
+ esac
+
+ # Install the libtool object if requested.
+ test -n "$destfile" && \
+ func_show_eval "$install_prog $file $destfile" 'exit $?'
+
+ # Install the old object if enabled.
+ if test "$build_old_libs" = yes; then
+ # Deduce the name of the old-style object file.
+ func_lo2o "$file"
+ staticobj=$func_lo2o_result
+ func_show_eval "$install_prog \$staticobj \$staticdest" 'exit $?'
+ fi
+ exit $EXIT_SUCCESS
+ ;;
+
+ *)
+ # Figure out destination file name, if it wasn't already specified.
+ if test -n "$destname"; then
+ destfile="$destdir/$destname"
+ else
+ func_basename "$file"
+ destfile="$func_basename_result"
+ destfile="$destdir/$destfile"
+ fi
+
+ # If the file is missing, and there is a .exe on the end, strip it
+ # because it is most likely a libtool script we actually want to
+ # install
+ stripped_ext=""
+ case $file in
+ *.exe)
+ if test ! -f "$file"; then
+ func_stripname '' '.exe' "$file"
+ file=$func_stripname_result
+ stripped_ext=".exe"
+ fi
+ ;;
+ esac
+
+ # Do a test to see if this is really a libtool program.
+ case $host in
+ *cygwin* | *mingw*)
+ if func_ltwrapper_executable_p "$file"; then
+ func_ltwrapper_scriptname "$file"
+ wrapper=$func_ltwrapper_scriptname_result
+ else
+ func_stripname '' '.exe' "$file"
+ wrapper=$func_stripname_result
+ fi
+ ;;
+ *)
+ wrapper=$file
+ ;;
+ esac
+ if func_ltwrapper_script_p "$wrapper"; then
+ notinst_deplibs=
+ relink_command=
+
+ func_source "$wrapper"
+
+ # Check the variables that should have been set.
+ test -z "$generated_by_libtool_version" && \
+ func_fatal_error "invalid libtool wrapper script \`$wrapper'"
+
+ finalize=yes
+ for lib in $notinst_deplibs; do
+ # Check to see that each library is installed.
+ libdir=
+ if test -f "$lib"; then
+ func_source "$lib"
+ fi
+ libfile="$libdir/"`$ECHO "X$lib" | $Xsed -e 's%^.*/%%g'` ### testsuite: skip nested quoting test
+ if test -n "$libdir" && test ! -f "$libfile"; then
+ func_warning "\`$lib' has not been installed in \`$libdir'"
+ finalize=no
+ fi
+ done
+
+ relink_command=
+ func_source "$wrapper"
+
+ outputname=
+ if test "$fast_install" = no && test -n "$relink_command"; then
+ $opt_dry_run || {
+ if test "$finalize" = yes; then
+ tmpdir=`func_mktempdir`
+ func_basename "$file$stripped_ext"
+ file="$func_basename_result"
+ outputname="$tmpdir/$file"
+ # Replace the output file specification.
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e 's%@OUTPUT@%'"$outputname"'%g'`
+
+ $opt_silent || {
+ func_quote_for_expand "$relink_command"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+ if eval "$relink_command"; then :
+ else
+ func_error "error: relink \`$file' with the above command before installing it"
+ $opt_dry_run || ${RM}r "$tmpdir"
+ continue
+ fi
+ file="$outputname"
+ else
+ func_warning "cannot relink \`$file'"
+ fi
+ }
+ else
+ # Install the binary that we compiled earlier.
+ file=`$ECHO "X$file$stripped_ext" | $Xsed -e "s%\([^/]*\)$%$objdir/\1%"`
+ fi
+ fi
+
+ # remove .exe since cygwin /usr/bin/install will append another
+ # one anyway
+ case $install_prog,$host in
+ */usr/bin/install*,*cygwin*)
+ case $file:$destfile in
+ *.exe:*.exe)
+ # this is ok
+ ;;
+ *.exe:*)
+ destfile=$destfile.exe
+ ;;
+ *:*.exe)
+ func_stripname '' '.exe' "$destfile"
+ destfile=$func_stripname_result
+ ;;
+ esac
+ ;;
+ esac
+ func_show_eval "$install_prog\$stripme \$file \$destfile" 'exit $?'
+ $opt_dry_run || if test -n "$outputname"; then
+ ${RM}r "$tmpdir"
+ fi
+ ;;
+ esac
+ done
+
+ for file in $staticlibs; do
+ func_basename "$file"
+ name="$func_basename_result"
+
+ # Set up the ranlib parameters.
+ oldlib="$destdir/$name"
+
+ func_show_eval "$install_prog \$file \$oldlib" 'exit $?'
+
+ if test -n "$stripme" && test -n "$old_striplib"; then
+ func_show_eval "$old_striplib $oldlib" 'exit $?'
+ fi
+
+ # Do each command in the postinstall commands.
+ func_execute_cmds "$old_postinstall_cmds" 'exit $?'
+ done
+
+ test -n "$future_libdirs" && \
+ func_warning "remember to run \`$progname --finish$future_libdirs'"
+
+ if test -n "$current_libdirs"; then
+ # Maybe just do a dry run.
+ $opt_dry_run && current_libdirs=" -n$current_libdirs"
+ exec_cmd='$SHELL $progpath $preserve_args --finish$current_libdirs'
+ else
+ exit $EXIT_SUCCESS
+ fi
+}
+
+test "$mode" = install && func_mode_install ${1+"$@"}
+
+
+# func_generate_dlsyms outputname originator pic_p
+# Extract symbols from dlprefiles and create ${outputname}S.o with
+# a dlpreopen symbol table.
+func_generate_dlsyms ()
+{
+ $opt_debug
+ my_outputname="$1"
+ my_originator="$2"
+ my_pic_p="${3-no}"
+ my_prefix=`$ECHO "$my_originator" | sed 's%[^a-zA-Z0-9]%_%g'`
+ my_dlsyms=
+
+ if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
+ if test -n "$NM" && test -n "$global_symbol_pipe"; then
+ my_dlsyms="${my_outputname}S.c"
+ else
+ func_error "not configured to extract global symbols from dlpreopened files"
+ fi
+ fi
+
+ if test -n "$my_dlsyms"; then
+ case $my_dlsyms in
+ "") ;;
+ *.c)
+ # Discover the nlist of each of the dlfiles.
+ nlist="$output_objdir/${my_outputname}.nm"
+
+ func_show_eval "$RM $nlist ${nlist}S ${nlist}T"
+
+ # Parse the name list into a source file.
+ func_verbose "creating $output_objdir/$my_dlsyms"
+
+ $opt_dry_run || $ECHO > "$output_objdir/$my_dlsyms" "\
+/* $my_dlsyms - symbol resolution table for \`$my_outputname' dlsym emulation. */
+/* Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION */
+
+#ifdef __cplusplus
+extern \"C\" {
+#endif
+
+/* External symbol declarations for the compiler. */\
+"
+
+ if test "$dlself" = yes; then
+ func_verbose "generating symbol list for \`$output'"
+
+ $opt_dry_run || echo ': @PROGRAM@ ' > "$nlist"
+
+ # Add our own program objects to the symbol list.
+ progfiles=`$ECHO "X$objs$old_deplibs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+ for progfile in $progfiles; do
+ func_verbose "extracting global C symbols from \`$progfile'"
+ $opt_dry_run || eval "$NM $progfile | $global_symbol_pipe >> '$nlist'"
+ done
+
+ if test -n "$exclude_expsyms"; then
+ $opt_dry_run || {
+ eval '$EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T'
+ eval '$MV "$nlist"T "$nlist"'
+ }
+ fi
+
+ if test -n "$export_symbols_regex"; then
+ $opt_dry_run || {
+ eval '$EGREP -e "$export_symbols_regex" "$nlist" > "$nlist"T'
+ eval '$MV "$nlist"T "$nlist"'
+ }
+ fi
+
+ # Prepare the list of exported symbols
+ if test -z "$export_symbols"; then
+ export_symbols="$output_objdir/$outputname.exp"
+ $opt_dry_run || {
+ $RM $export_symbols
+ eval "${SED} -n -e '/^: @PROGRAM@ $/d' -e 's/^.* \(.*\)$/\1/p' "'< "$nlist" > "$export_symbols"'
+ case $host in
+ *cygwin* | *mingw* | *cegcc* )
+ eval "echo EXPORTS "'> "$output_objdir/$outputname.def"'
+ eval 'cat "$export_symbols" >> "$output_objdir/$outputname.def"'
+ ;;
+ esac
+ }
+ else
+ $opt_dry_run || {
+ eval "${SED} -e 's/\([].[*^$]\)/\\\\\1/g' -e 's/^/ /' -e 's/$/$/'"' < "$export_symbols" > "$output_objdir/$outputname.exp"'
+ eval '$GREP -f "$output_objdir/$outputname.exp" < "$nlist" > "$nlist"T'
+ eval '$MV "$nlist"T "$nlist"'
+ case $host in
+ *cygwin | *mingw* | *cegcc* )
+ eval "echo EXPORTS "'> "$output_objdir/$outputname.def"'
+ eval 'cat "$nlist" >> "$output_objdir/$outputname.def"'
+ ;;
+ esac
+ }
+ fi
+ fi
+
+ for dlprefile in $dlprefiles; do
+ func_verbose "extracting global C symbols from \`$dlprefile'"
+ func_basename "$dlprefile"
+ name="$func_basename_result"
+ $opt_dry_run || {
+ eval '$ECHO ": $name " >> "$nlist"'
+ eval "$NM $dlprefile 2>/dev/null | $global_symbol_pipe >> '$nlist'"
+ }
+ done
+
+ $opt_dry_run || {
+ # Make sure we have at least an empty file.
+ test -f "$nlist" || : > "$nlist"
+
+ if test -n "$exclude_expsyms"; then
+ $EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T
+ $MV "$nlist"T "$nlist"
+ fi
+
+ # Try sorting and uniquifying the output.
+ if $GREP -v "^: " < "$nlist" |
+ if sort -k 3 </dev/null >/dev/null 2>&1; then
+ sort -k 3
+ else
+ sort +2
+ fi |
+ uniq > "$nlist"S; then
+ :
+ else
+ $GREP -v "^: " < "$nlist" > "$nlist"S
+ fi
+
+ if test -f "$nlist"S; then
+ eval "$global_symbol_to_cdecl"' < "$nlist"S >> "$output_objdir/$my_dlsyms"'
+ else
+ $ECHO '/* NONE */' >> "$output_objdir/$my_dlsyms"
+ fi
+
+ $ECHO >> "$output_objdir/$my_dlsyms" "\
+
+/* The mapping between symbol names and symbols. */
+typedef struct {
+ const char *name;
+ void *address;
+} lt_dlsymlist;
+"
+ case $host in
+ *cygwin* | *mingw* | *cegcc* )
+ $ECHO >> "$output_objdir/$my_dlsyms" "\
+/* DATA imports from DLLs on WIN32 con't be const, because
+ runtime relocations are performed -- see ld's documentation
+ on pseudo-relocs. */"
+ lt_dlsym_const= ;;
+ *osf5*)
+ echo >> "$output_objdir/$my_dlsyms" "\
+/* This system does not cope well with relocations in const data */"
+ lt_dlsym_const= ;;
+ *)
+ lt_dlsym_const=const ;;
+ esac
+
+ $ECHO >> "$output_objdir/$my_dlsyms" "\
+extern $lt_dlsym_const lt_dlsymlist
+lt_${my_prefix}_LTX_preloaded_symbols[];
+$lt_dlsym_const lt_dlsymlist
+lt_${my_prefix}_LTX_preloaded_symbols[] =
+{\
+ { \"$my_originator\", (void *) 0 },"
+
+ case $need_lib_prefix in
+ no)
+ eval "$global_symbol_to_c_name_address" < "$nlist" >> "$output_objdir/$my_dlsyms"
+ ;;
+ *)
+ eval "$global_symbol_to_c_name_address_lib_prefix" < "$nlist" >> "$output_objdir/$my_dlsyms"
+ ;;
+ esac
+ $ECHO >> "$output_objdir/$my_dlsyms" "\
+ {0, (void *) 0}
+};
+
+/* This works around a problem in FreeBSD linker */
+#ifdef FREEBSD_WORKAROUND
+static const void *lt_preloaded_setup() {
+ return lt_${my_prefix}_LTX_preloaded_symbols;
+}
+#endif
+
+#ifdef __cplusplus
+}
+#endif\
+"
+ } # !$opt_dry_run
+
+ pic_flag_for_symtable=
+ case "$compile_command " in
+ *" -static "*) ;;
+ *)
+ case $host in
+ # compiling the symbol table file with pic_flag works around
+ # a FreeBSD bug that causes programs to crash when -lm is
+ # linked before any other PIC object. But we must not use
+ # pic_flag when linking with -static. The problem exists in
+ # FreeBSD 2.2.6 and is fixed in FreeBSD 3.1.
+ *-*-freebsd2*|*-*-freebsd3.0*|*-*-freebsdelf3.0*)
+ pic_flag_for_symtable=" $pic_flag -DFREEBSD_WORKAROUND" ;;
+ *-*-hpux*)
+ pic_flag_for_symtable=" $pic_flag" ;;
+ *)
+ if test "X$my_pic_p" != Xno; then
+ pic_flag_for_symtable=" $pic_flag"
+ fi
+ ;;
+ esac
+ ;;
+ esac
+ symtab_cflags=
+ for arg in $LTCFLAGS; do
+ case $arg in
+ -pie | -fpie | -fPIE) ;;
+ *) symtab_cflags="$symtab_cflags $arg" ;;
+ esac
+ done
+
+ # Now compile the dynamic symbol file.
+ func_show_eval '(cd $output_objdir && $LTCC$symtab_cflags -c$no_builtin_flag$pic_flag_for_symtable "$my_dlsyms")' 'exit $?'
+
+ # Clean up the generated files.
+ func_show_eval '$RM "$output_objdir/$my_dlsyms" "$nlist" "${nlist}S" "${nlist}T"'
+
+ # Transform the symbol file into the correct name.
+ symfileobj="$output_objdir/${my_outputname}S.$objext"
+ case $host in
+ *cygwin* | *mingw* | *cegcc* )
+ if test -f "$output_objdir/$my_outputname.def"; then
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"`
+ finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"`
+ else
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"`
+ finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"`
+ fi
+ ;;
+ *)
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"`
+ finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"`
+ ;;
+ esac
+ ;;
+ *)
+ func_fatal_error "unknown suffix for \`$my_dlsyms'"
+ ;;
+ esac
+ else
+ # We keep going just in case the user didn't refer to
+ # lt_preloaded_symbols. The linker will fail if global_symbol_pipe
+ # really was required.
+
+ # Nullify the symbol file.
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e "s% @SYMFILE@%%"`
+ finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s% @SYMFILE@%%"`
+ fi
+}
+
+# func_win32_libid arg
+# return the library type of file 'arg'
+#
+# Need a lot of goo to handle *both* DLLs and import libs
+# Has to be a shell function in order to 'eat' the argument
+# that is supplied when $file_magic_command is called.
+func_win32_libid ()
+{
+ $opt_debug
+ win32_libid_type="unknown"
+ win32_fileres=`file -L $1 2>/dev/null`
+ case $win32_fileres in
+ *ar\ archive\ import\ library*) # definitely import
+ win32_libid_type="x86 archive import"
+ ;;
+ *ar\ archive*) # could be an import, or static
+ if eval $OBJDUMP -f $1 | $SED -e '10q' 2>/dev/null |
+ $EGREP 'file format pe-i386(.*architecture: i386)?' >/dev/null ; then
+ win32_nmres=`eval $NM -f posix -A $1 |
+ $SED -n -e '
+ 1,100{
+ / I /{
+ s,.*,import,
+ p
+ q
+ }
+ }'`
+ case $win32_nmres in
+ import*) win32_libid_type="x86 archive import";;
+ *) win32_libid_type="x86 archive static";;
+ esac
+ fi
+ ;;
+ *DLL*)
+ win32_libid_type="x86 DLL"
+ ;;
+ *executable*) # but shell scripts are "executable" too...
+ case $win32_fileres in
+ *MS\ Windows\ PE\ Intel*)
+ win32_libid_type="x86 DLL"
+ ;;
+ esac
+ ;;
+ esac
+ $ECHO "$win32_libid_type"
+}
+
+
+
+# func_extract_an_archive dir oldlib
+func_extract_an_archive ()
+{
+ $opt_debug
+ f_ex_an_ar_dir="$1"; shift
+ f_ex_an_ar_oldlib="$1"
+ func_show_eval "(cd \$f_ex_an_ar_dir && $AR x \"\$f_ex_an_ar_oldlib\")" 'exit $?'
+ if ($AR t "$f_ex_an_ar_oldlib" | sort | sort -uc >/dev/null 2>&1); then
+ :
+ else
+ func_fatal_error "object name conflicts in archive: $f_ex_an_ar_dir/$f_ex_an_ar_oldlib"
+ fi
+}
+
+
+# func_extract_archives gentop oldlib ...
+func_extract_archives ()
+{
+ $opt_debug
+ my_gentop="$1"; shift
+ my_oldlibs=${1+"$@"}
+ my_oldobjs=""
+ my_xlib=""
+ my_xabs=""
+ my_xdir=""
+
+ for my_xlib in $my_oldlibs; do
+ # Extract the objects.
+ case $my_xlib in
+ [\\/]* | [A-Za-z]:[\\/]*) my_xabs="$my_xlib" ;;
+ *) my_xabs=`pwd`"/$my_xlib" ;;
+ esac
+ func_basename "$my_xlib"
+ my_xlib="$func_basename_result"
+ my_xlib_u=$my_xlib
+ while :; do
+ case " $extracted_archives " in
+ *" $my_xlib_u "*)
+ func_arith $extracted_serial + 1
+ extracted_serial=$func_arith_result
+ my_xlib_u=lt$extracted_serial-$my_xlib ;;
+ *) break ;;
+ esac
+ done
+ extracted_archives="$extracted_archives $my_xlib_u"
+ my_xdir="$my_gentop/$my_xlib_u"
+
+ func_mkdir_p "$my_xdir"
+
+ case $host in
+ *-darwin*)
+ func_verbose "Extracting $my_xabs"
+ # Do not bother doing anything if just a dry run
+ $opt_dry_run || {
+ darwin_orig_dir=`pwd`
+ cd $my_xdir || exit $?
+ darwin_archive=$my_xabs
+ darwin_curdir=`pwd`
+ darwin_base_archive=`basename "$darwin_archive"`
+ darwin_arches=`$LIPO -info "$darwin_archive" 2>/dev/null | $GREP Architectures 2>/dev/null || true`
+ if test -n "$darwin_arches"; then
+ darwin_arches=`$ECHO "$darwin_arches" | $SED -e 's/.*are://'`
+ darwin_arch=
+ func_verbose "$darwin_base_archive has multiple architectures $darwin_arches"
+ for darwin_arch in $darwin_arches ; do
+ func_mkdir_p "unfat-$$/${darwin_base_archive}-${darwin_arch}"
+ $LIPO -thin $darwin_arch -output "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" "${darwin_archive}"
+ cd "unfat-$$/${darwin_base_archive}-${darwin_arch}"
+ func_extract_an_archive "`pwd`" "${darwin_base_archive}"
+ cd "$darwin_curdir"
+ $RM "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}"
+ done # $darwin_arches
+ ## Okay now we've a bunch of thin objects, gotta fatten them up :)
+ darwin_filelist=`find unfat-$$ -type f -name \*.o -print -o -name \*.lo -print | $SED -e "$basename" | sort -u`
+ darwin_file=
+ darwin_files=
+ for darwin_file in $darwin_filelist; do
+ darwin_files=`find unfat-$$ -name $darwin_file -print | $NL2SP`
+ $LIPO -create -output "$darwin_file" $darwin_files
+ done # $darwin_filelist
+ $RM -rf unfat-$$
+ cd "$darwin_orig_dir"
+ else
+ cd $darwin_orig_dir
+ func_extract_an_archive "$my_xdir" "$my_xabs"
+ fi # $darwin_arches
+ } # !$opt_dry_run
+ ;;
+ *)
+ func_extract_an_archive "$my_xdir" "$my_xabs"
+ ;;
+ esac
+ my_oldobjs="$my_oldobjs "`find $my_xdir -name \*.$objext -print -o -name \*.lo -print | $NL2SP`
+ done
+
+ func_extract_archives_result="$my_oldobjs"
+}
+
+
+
+# func_emit_wrapper_part1 [arg=no]
+#
+# Emit the first part of a libtool wrapper script on stdout.
+# For more information, see the description associated with
+# func_emit_wrapper(), below.
+func_emit_wrapper_part1 ()
+{
+ func_emit_wrapper_part1_arg1=no
+ if test -n "$1" ; then
+ func_emit_wrapper_part1_arg1=$1
+ fi
+
+ $ECHO "\
+#! $SHELL
+
+# $output - temporary wrapper script for $objdir/$outputname
+# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
+#
+# The $output program cannot be directly executed until all the libtool
+# libraries that it depends on are installed.
+#
+# This wrapper script should never be moved out of the build directory.
+# If it is, it will not operate correctly.
+
+# Sed substitution that helps us do robust quoting. It backslashifies
+# metacharacters that are still active within double-quoted strings.
+Xsed='${SED} -e 1s/^X//'
+sed_quote_subst='$sed_quote_subst'
+
+# Be Bourne compatible
+if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Zsh 3.x and 4.x performs word splitting on \${1+\"\$@\"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '\${1+\"\$@\"}'='\"\$@\"'
+ setopt NO_GLOB_SUBST
+else
+ case \`(set -o) 2>/dev/null\` in *posix*) set -o posix;; esac
+fi
+BIN_SH=xpg4; export BIN_SH # for Tru64
+DUALCASE=1; export DUALCASE # for MKS sh
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+relink_command=\"$relink_command\"
+
+# This environment variable determines our operation mode.
+if test \"\$libtool_install_magic\" = \"$magic\"; then
+ # install mode needs the following variables:
+ generated_by_libtool_version='$macro_version'
+ notinst_deplibs='$notinst_deplibs'
+else
+ # When we are sourced in execute mode, \$file and \$ECHO are already set.
+ if test \"\$libtool_execute_magic\" != \"$magic\"; then
+ ECHO=\"$qecho\"
+ file=\"\$0\"
+ # Make sure echo works.
+ if test \"X\$1\" = X--no-reexec; then
+ # Discard the --no-reexec flag, and continue.
+ shift
+ elif test \"X\`{ \$ECHO '\t'; } 2>/dev/null\`\" = 'X\t'; then
+ # Yippee, \$ECHO works!
+ :
+ else
+ # Restart under the correct shell, and then maybe \$ECHO will work.
+ exec $SHELL \"\$0\" --no-reexec \${1+\"\$@\"}
+ fi
+ fi\
+"
+ $ECHO "\
+
+ # Find the directory that this script lives in.
+ thisdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*$%%'\`
+ test \"x\$thisdir\" = \"x\$file\" && thisdir=.
+
+ # Follow symbolic links until we get to the real thisdir.
+ file=\`ls -ld \"\$file\" | ${SED} -n 's/.*-> //p'\`
+ while test -n \"\$file\"; do
+ destdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*\$%%'\`
+
+ # If there was a directory component, then change thisdir.
+ if test \"x\$destdir\" != \"x\$file\"; then
+ case \"\$destdir\" in
+ [\\\\/]* | [A-Za-z]:[\\\\/]*) thisdir=\"\$destdir\" ;;
+ *) thisdir=\"\$thisdir/\$destdir\" ;;
+ esac
+ fi
+
+ file=\`\$ECHO \"X\$file\" | \$Xsed -e 's%^.*/%%'\`
+ file=\`ls -ld \"\$thisdir/\$file\" | ${SED} -n 's/.*-> //p'\`
+ done
+"
+}
+# end: func_emit_wrapper_part1
+
+# func_emit_wrapper_part2 [arg=no]
+#
+# Emit the second part of a libtool wrapper script on stdout.
+# For more information, see the description associated with
+# func_emit_wrapper(), below.
+func_emit_wrapper_part2 ()
+{
+ func_emit_wrapper_part2_arg1=no
+ if test -n "$1" ; then
+ func_emit_wrapper_part2_arg1=$1
+ fi
+
+ $ECHO "\
+
+ # Usually 'no', except on cygwin/mingw when embedded into
+ # the cwrapper.
+ WRAPPER_SCRIPT_BELONGS_IN_OBJDIR=$func_emit_wrapper_part2_arg1
+ if test \"\$WRAPPER_SCRIPT_BELONGS_IN_OBJDIR\" = \"yes\"; then
+ # special case for '.'
+ if test \"\$thisdir\" = \".\"; then
+ thisdir=\`pwd\`
+ fi
+ # remove .libs from thisdir
+ case \"\$thisdir\" in
+ *[\\\\/]$objdir ) thisdir=\`\$ECHO \"X\$thisdir\" | \$Xsed -e 's%[\\\\/][^\\\\/]*$%%'\` ;;
+ $objdir ) thisdir=. ;;
+ esac
+ fi
+
+ # Try to get the absolute directory name.
+ absdir=\`cd \"\$thisdir\" && pwd\`
+ test -n \"\$absdir\" && thisdir=\"\$absdir\"
+"
+
+ if test "$fast_install" = yes; then
+ $ECHO "\
+ program=lt-'$outputname'$exeext
+ progdir=\"\$thisdir/$objdir\"
+
+ if test ! -f \"\$progdir/\$program\" ||
+ { file=\`ls -1dt \"\$progdir/\$program\" \"\$progdir/../\$program\" 2>/dev/null | ${SED} 1q\`; \\
+ test \"X\$file\" != \"X\$progdir/\$program\"; }; then
+
+ file=\"\$\$-\$program\"
+
+ if test ! -d \"\$progdir\"; then
+ $MKDIR \"\$progdir\"
+ else
+ $RM \"\$progdir/\$file\"
+ fi"
+
+ $ECHO "\
+
+ # relink executable if necessary
+ if test -n \"\$relink_command\"; then
+ if relink_command_output=\`eval \$relink_command 2>&1\`; then :
+ else
+ $ECHO \"\$relink_command_output\" >&2
+ $RM \"\$progdir/\$file\"
+ exit 1
+ fi
+ fi
+
+ $MV \"\$progdir/\$file\" \"\$progdir/\$program\" 2>/dev/null ||
+ { $RM \"\$progdir/\$program\";
+ $MV \"\$progdir/\$file\" \"\$progdir/\$program\"; }
+ $RM \"\$progdir/\$file\"
+ fi"
+ else
+ $ECHO "\
+ program='$outputname'
+ progdir=\"\$thisdir/$objdir\"
+"
+ fi
+
+ $ECHO "\
+
+ if test -f \"\$progdir/\$program\"; then"
+
+ # Export our shlibpath_var if we have one.
+ if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then
+ $ECHO "\
+ # Add our own library path to $shlibpath_var
+ $shlibpath_var=\"$temp_rpath\$$shlibpath_var\"
+
+ # Some systems cannot cope with colon-terminated $shlibpath_var
+ # The second colon is a workaround for a bug in BeOS R4 sed
+ $shlibpath_var=\`\$ECHO \"X\$$shlibpath_var\" | \$Xsed -e 's/::*\$//'\`
+
+ export $shlibpath_var
+"
+ fi
+
+ # fixup the dll searchpath if we need to.
+ if test -n "$dllsearchpath"; then
+ $ECHO "\
+ # Add the dll search path components to the executable PATH
+ PATH=$dllsearchpath:\$PATH
+"
+ fi
+
+ $ECHO "\
+ if test \"\$libtool_execute_magic\" != \"$magic\"; then
+ # Run the actual program with our arguments.
+"
+ case $host in
+ # Backslashes separate directories on plain windows
+ *-*-mingw | *-*-os2* | *-cegcc*)
+ $ECHO "\
+ exec \"\$progdir\\\\\$program\" \${1+\"\$@\"}
+"
+ ;;
+
+ *)
+ $ECHO "\
+ exec \"\$progdir/\$program\" \${1+\"\$@\"}
+"
+ ;;
+ esac
+ $ECHO "\
+ \$ECHO \"\$0: cannot exec \$program \$*\" 1>&2
+ exit 1
+ fi
+ else
+ # The program doesn't exist.
+ \$ECHO \"\$0: error: \\\`\$progdir/\$program' does not exist\" 1>&2
+ \$ECHO \"This script is just a wrapper for \$program.\" 1>&2
+ $ECHO \"See the $PACKAGE documentation for more information.\" 1>&2
+ exit 1
+ fi
+fi\
+"
+}
+# end: func_emit_wrapper_part2
+
+
+# func_emit_wrapper [arg=no]
+#
+# Emit a libtool wrapper script on stdout.
+# Don't directly open a file because we may want to
+# incorporate the script contents within a cygwin/mingw
+# wrapper executable. Must ONLY be called from within
+# func_mode_link because it depends on a number of variables
+# set therein.
+#
+# ARG is the value that the WRAPPER_SCRIPT_BELONGS_IN_OBJDIR
+# variable will take. If 'yes', then the emitted script
+# will assume that the directory in which it is stored is
+# the $objdir directory. This is a cygwin/mingw-specific
+# behavior.
+func_emit_wrapper ()
+{
+ func_emit_wrapper_arg1=no
+ if test -n "$1" ; then
+ func_emit_wrapper_arg1=$1
+ fi
+
+ # split this up so that func_emit_cwrapperexe_src
+ # can call each part independently.
+ func_emit_wrapper_part1 "${func_emit_wrapper_arg1}"
+ func_emit_wrapper_part2 "${func_emit_wrapper_arg1}"
+}
+
+
+# func_to_host_path arg
+#
+# Convert paths to host format when used with build tools.
+# Intended for use with "native" mingw (where libtool itself
+# is running under the msys shell), or in the following cross-
+# build environments:
+# $build $host
+# mingw (msys) mingw [e.g. native]
+# cygwin mingw
+# *nix + wine mingw
+# where wine is equipped with the `winepath' executable.
+# In the native mingw case, the (msys) shell automatically
+# converts paths for any non-msys applications it launches,
+# but that facility isn't available from inside the cwrapper.
+# Similar accommodations are necessary for $host mingw and
+# $build cygwin. Calling this function does no harm for other
+# $host/$build combinations not listed above.
+#
+# ARG is the path (on $build) that should be converted to
+# the proper representation for $host. The result is stored
+# in $func_to_host_path_result.
+func_to_host_path ()
+{
+ func_to_host_path_result="$1"
+ if test -n "$1" ; then
+ case $host in
+ *mingw* )
+ lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g'
+ case $build in
+ *mingw* ) # actually, msys
+ # awkward: cmd appends spaces to result
+ lt_sed_strip_trailing_spaces="s/[ ]*\$//"
+ func_to_host_path_tmp1=`( cmd //c echo "$1" |\
+ $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""`
+ func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ ;;
+ *cygwin* )
+ func_to_host_path_tmp1=`cygpath -w "$1"`
+ func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ ;;
+ * )
+ # Unfortunately, winepath does not exit with a non-zero
+ # error code, so we are forced to check the contents of
+ # stdout. On the other hand, if the command is not
+ # found, the shell will set an exit code of 127 and print
+ # *an error message* to stdout. So we must check for both
+ # error code of zero AND non-empty stdout, which explains
+ # the odd construction:
+ func_to_host_path_tmp1=`winepath -w "$1" 2>/dev/null`
+ if test "$?" -eq 0 && test -n "${func_to_host_path_tmp1}"; then
+ func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ else
+ # Allow warning below.
+ func_to_host_path_result=""
+ fi
+ ;;
+ esac
+ if test -z "$func_to_host_path_result" ; then
+ func_error "Could not determine host path corresponding to"
+ func_error " '$1'"
+ func_error "Continuing, but uninstalled executables may not work."
+ # Fallback:
+ func_to_host_path_result="$1"
+ fi
+ ;;
+ esac
+ fi
+}
+# end: func_to_host_path
+
+# func_to_host_pathlist arg
+#
+# Convert pathlists to host format when used with build tools.
+# See func_to_host_path(), above. This function supports the
+# following $build/$host combinations (but does no harm for
+# combinations not listed here):
+# $build $host
+# mingw (msys) mingw [e.g. native]
+# cygwin mingw
+# *nix + wine mingw
+#
+# Path separators are also converted from $build format to
+# $host format. If ARG begins or ends with a path separator
+# character, it is preserved (but converted to $host format)
+# on output.
+#
+# ARG is a pathlist (on $build) that should be converted to
+# the proper representation on $host. The result is stored
+# in $func_to_host_pathlist_result.
+func_to_host_pathlist ()
+{
+ func_to_host_pathlist_result="$1"
+ if test -n "$1" ; then
+ case $host in
+ *mingw* )
+ lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g'
+ # Remove leading and trailing path separator characters from
+ # ARG. msys behavior is inconsistent here, cygpath turns them
+ # into '.;' and ';.', and winepath ignores them completely.
+ func_to_host_pathlist_tmp2="$1"
+ # Once set for this call, this variable should not be
+ # reassigned. It is used in tha fallback case.
+ func_to_host_pathlist_tmp1=`echo "$func_to_host_pathlist_tmp2" |\
+ $SED -e 's|^:*||' -e 's|:*$||'`
+ case $build in
+ *mingw* ) # Actually, msys.
+ # Awkward: cmd appends spaces to result.
+ lt_sed_strip_trailing_spaces="s/[ ]*\$//"
+ func_to_host_pathlist_tmp2=`( cmd //c echo "$func_to_host_pathlist_tmp1" |\
+ $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""`
+ func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ ;;
+ *cygwin* )
+ func_to_host_pathlist_tmp2=`cygpath -w -p "$func_to_host_pathlist_tmp1"`
+ func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ ;;
+ * )
+ # unfortunately, winepath doesn't convert pathlists
+ func_to_host_pathlist_result=""
+ func_to_host_pathlist_oldIFS=$IFS
+ IFS=:
+ for func_to_host_pathlist_f in $func_to_host_pathlist_tmp1 ; do
+ IFS=$func_to_host_pathlist_oldIFS
+ if test -n "$func_to_host_pathlist_f" ; then
+ func_to_host_path "$func_to_host_pathlist_f"
+ if test -n "$func_to_host_path_result" ; then
+ if test -z "$func_to_host_pathlist_result" ; then
+ func_to_host_pathlist_result="$func_to_host_path_result"
+ else
+ func_to_host_pathlist_result="$func_to_host_pathlist_result;$func_to_host_path_result"
+ fi
+ fi
+ fi
+ IFS=:
+ done
+ IFS=$func_to_host_pathlist_oldIFS
+ ;;
+ esac
+ if test -z "$func_to_host_pathlist_result" ; then
+ func_error "Could not determine the host path(s) corresponding to"
+ func_error " '$1'"
+ func_error "Continuing, but uninstalled executables may not work."
+ # Fallback. This may break if $1 contains DOS-style drive
+ # specifications. The fix is not to complicate the expression
+ # below, but for the user to provide a working wine installation
+ # with winepath so that path translation in the cross-to-mingw
+ # case works properly.
+ lt_replace_pathsep_nix_to_dos="s|:|;|g"
+ func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp1" |\
+ $SED -e "$lt_replace_pathsep_nix_to_dos"`
+ fi
+ # Now, add the leading and trailing path separators back
+ case "$1" in
+ :* ) func_to_host_pathlist_result=";$func_to_host_pathlist_result"
+ ;;
+ esac
+ case "$1" in
+ *: ) func_to_host_pathlist_result="$func_to_host_pathlist_result;"
+ ;;
+ esac
+ ;;
+ esac
+ fi
+}
+# end: func_to_host_pathlist
+
+# func_emit_cwrapperexe_src
+# emit the source code for a wrapper executable on stdout
+# Must ONLY be called from within func_mode_link because
+# it depends on a number of variable set therein.
+func_emit_cwrapperexe_src ()
+{
+ cat <<EOF
+
+/* $cwrappersource - temporary wrapper executable for $objdir/$outputname
+ Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
+
+ The $output program cannot be directly executed until all the libtool
+ libraries that it depends on are installed.
+
+ This wrapper executable should never be moved out of the build directory.
+ If it is, it will not operate correctly.
+
+ Currently, it simply execs the wrapper *script* "$SHELL $output",
+ but could eventually absorb all of the scripts functionality and
+ exec $objdir/$outputname directly.
+*/
+EOF
+ cat <<"EOF"
+#include <stdio.h>
+#include <stdlib.h>
+#ifdef _MSC_VER
+# include <direct.h>
+# include <process.h>
+# include <io.h>
+# define setmode _setmode
+#else
+# include <unistd.h>
+# include <stdint.h>
+# ifdef __CYGWIN__
+# include <io.h>
+# define HAVE_SETENV
+# ifdef __STRICT_ANSI__
+char *realpath (const char *, char *);
+int putenv (char *);
+int setenv (const char *, const char *, int);
+# endif
+# endif
+#endif
+#include <malloc.h>
+#include <stdarg.h>
+#include <assert.h>
+#include <string.h>
+#include <ctype.h>
+#include <errno.h>
+#include <fcntl.h>
+#include <sys/stat.h>
+
+#if defined(PATH_MAX)
+# define LT_PATHMAX PATH_MAX
+#elif defined(MAXPATHLEN)
+# define LT_PATHMAX MAXPATHLEN
+#else
+# define LT_PATHMAX 1024
+#endif
+
+#ifndef S_IXOTH
+# define S_IXOTH 0
+#endif
+#ifndef S_IXGRP
+# define S_IXGRP 0
+#endif
+
+#ifdef _MSC_VER
+# define S_IXUSR _S_IEXEC
+# define stat _stat
+# ifndef _INTPTR_T_DEFINED
+# define intptr_t int
+# endif
+#endif
+
+#ifndef DIR_SEPARATOR
+# define DIR_SEPARATOR '/'
+# define PATH_SEPARATOR ':'
+#endif
+
+#if defined (_WIN32) || defined (__MSDOS__) || defined (__DJGPP__) || \
+ defined (__OS2__)
+# define HAVE_DOS_BASED_FILE_SYSTEM
+# define FOPEN_WB "wb"
+# ifndef DIR_SEPARATOR_2
+# define DIR_SEPARATOR_2 '\\'
+# endif
+# ifndef PATH_SEPARATOR_2
+# define PATH_SEPARATOR_2 ';'
+# endif
+#endif
+
+#ifndef DIR_SEPARATOR_2
+# define IS_DIR_SEPARATOR(ch) ((ch) == DIR_SEPARATOR)
+#else /* DIR_SEPARATOR_2 */
+# define IS_DIR_SEPARATOR(ch) \
+ (((ch) == DIR_SEPARATOR) || ((ch) == DIR_SEPARATOR_2))
+#endif /* DIR_SEPARATOR_2 */
+
+#ifndef PATH_SEPARATOR_2
+# define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR)
+#else /* PATH_SEPARATOR_2 */
+# define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR_2)
+#endif /* PATH_SEPARATOR_2 */
+
+#ifdef __CYGWIN__
+# define FOPEN_WB "wb"
+#endif
+
+#ifndef FOPEN_WB
+# define FOPEN_WB "w"
+#endif
+#ifndef _O_BINARY
+# define _O_BINARY 0
+#endif
+
+#define XMALLOC(type, num) ((type *) xmalloc ((num) * sizeof(type)))
+#define XFREE(stale) do { \
+ if (stale) { free ((void *) stale); stale = 0; } \
+} while (0)
+
+#undef LTWRAPPER_DEBUGPRINTF
+#if defined DEBUGWRAPPER
+# define LTWRAPPER_DEBUGPRINTF(args) ltwrapper_debugprintf args
+static void
+ltwrapper_debugprintf (const char *fmt, ...)
+{
+ va_list args;
+ va_start (args, fmt);
+ (void) vfprintf (stderr, fmt, args);
+ va_end (args);
+}
+#else
+# define LTWRAPPER_DEBUGPRINTF(args)
+#endif
+
+const char *program_name = NULL;
+
+void *xmalloc (size_t num);
+char *xstrdup (const char *string);
+const char *base_name (const char *name);
+char *find_executable (const char *wrapper);
+char *chase_symlinks (const char *pathspec);
+int make_executable (const char *path);
+int check_executable (const char *path);
+char *strendzap (char *str, const char *pat);
+void lt_fatal (const char *message, ...);
+void lt_setenv (const char *name, const char *value);
+char *lt_extend_str (const char *orig_value, const char *add, int to_end);
+void lt_opt_process_env_set (const char *arg);
+void lt_opt_process_env_prepend (const char *arg);
+void lt_opt_process_env_append (const char *arg);
+int lt_split_name_value (const char *arg, char** name, char** value);
+void lt_update_exe_path (const char *name, const char *value);
+void lt_update_lib_path (const char *name, const char *value);
+
+static const char *script_text_part1 =
+EOF
+
+ func_emit_wrapper_part1 yes |
+ $SED -e 's/\([\\"]\)/\\\1/g' \
+ -e 's/^/ "/' -e 's/$/\\n"/'
+ echo ";"
+ cat <<EOF
+
+static const char *script_text_part2 =
+EOF
+ func_emit_wrapper_part2 yes |
+ $SED -e 's/\([\\"]\)/\\\1/g' \
+ -e 's/^/ "/' -e 's/$/\\n"/'
+ echo ";"
+
+ cat <<EOF
+const char * MAGIC_EXE = "$magic_exe";
+const char * LIB_PATH_VARNAME = "$shlibpath_var";
+EOF
+
+ if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then
+ func_to_host_pathlist "$temp_rpath"
+ cat <<EOF
+const char * LIB_PATH_VALUE = "$func_to_host_pathlist_result";
+EOF
+ else
+ cat <<"EOF"
+const char * LIB_PATH_VALUE = "";
+EOF
+ fi
+
+ if test -n "$dllsearchpath"; then
+ func_to_host_pathlist "$dllsearchpath:"
+ cat <<EOF
+const char * EXE_PATH_VARNAME = "PATH";
+const char * EXE_PATH_VALUE = "$func_to_host_pathlist_result";
+EOF
+ else
+ cat <<"EOF"
+const char * EXE_PATH_VARNAME = "";
+const char * EXE_PATH_VALUE = "";
+EOF
+ fi
+
+ if test "$fast_install" = yes; then
+ cat <<EOF
+const char * TARGET_PROGRAM_NAME = "lt-$outputname"; /* hopefully, no .exe */
+EOF
+ else
+ cat <<EOF
+const char * TARGET_PROGRAM_NAME = "$outputname"; /* hopefully, no .exe */
+EOF
+ fi
+
+
+ cat <<"EOF"
+
+#define LTWRAPPER_OPTION_PREFIX "--lt-"
+#define LTWRAPPER_OPTION_PREFIX_LENGTH 5
+
+static const size_t opt_prefix_len = LTWRAPPER_OPTION_PREFIX_LENGTH;
+static const char *ltwrapper_option_prefix = LTWRAPPER_OPTION_PREFIX;
+
+static const char *dumpscript_opt = LTWRAPPER_OPTION_PREFIX "dump-script";
+
+static const size_t env_set_opt_len = LTWRAPPER_OPTION_PREFIX_LENGTH + 7;
+static const char *env_set_opt = LTWRAPPER_OPTION_PREFIX "env-set";
+ /* argument is putenv-style "foo=bar", value of foo is set to bar */
+
+static const size_t env_prepend_opt_len = LTWRAPPER_OPTION_PREFIX_LENGTH + 11;
+static const char *env_prepend_opt = LTWRAPPER_OPTION_PREFIX "env-prepend";
+ /* argument is putenv-style "foo=bar", new value of foo is bar${foo} */
+
+static const size_t env_append_opt_len = LTWRAPPER_OPTION_PREFIX_LENGTH + 10;
+static const char *env_append_opt = LTWRAPPER_OPTION_PREFIX "env-append";
+ /* argument is putenv-style "foo=bar", new value of foo is ${foo}bar */
+
+int
+main (int argc, char *argv[])
+{
+ char **newargz;
+ int newargc;
+ char *tmp_pathspec;
+ char *actual_cwrapper_path;
+ char *actual_cwrapper_name;
+ char *target_name;
+ char *lt_argv_zero;
+ intptr_t rval = 127;
+
+ int i;
+
+ program_name = (char *) xstrdup (base_name (argv[0]));
+ LTWRAPPER_DEBUGPRINTF (("(main) argv[0] : %s\n", argv[0]));
+ LTWRAPPER_DEBUGPRINTF (("(main) program_name : %s\n", program_name));
+
+ /* very simple arg parsing; don't want to rely on getopt */
+ for (i = 1; i < argc; i++)
+ {
+ if (strcmp (argv[i], dumpscript_opt) == 0)
+ {
+EOF
+ case "$host" in
+ *mingw* | *cygwin* )
+ # make stdout use "unix" line endings
+ echo " setmode(1,_O_BINARY);"
+ ;;
+ esac
+
+ cat <<"EOF"
+ printf ("%s", script_text_part1);
+ printf ("%s", script_text_part2);
+ return 0;
+ }
+ }
+
+ newargz = XMALLOC (char *, argc + 1);
+ tmp_pathspec = find_executable (argv[0]);
+ if (tmp_pathspec == NULL)
+ lt_fatal ("Couldn't find %s", argv[0]);
+ LTWRAPPER_DEBUGPRINTF (("(main) found exe (before symlink chase) at : %s\n",
+ tmp_pathspec));
+
+ actual_cwrapper_path = chase_symlinks (tmp_pathspec);
+ LTWRAPPER_DEBUGPRINTF (("(main) found exe (after symlink chase) at : %s\n",
+ actual_cwrapper_path));
+ XFREE (tmp_pathspec);
+
+ actual_cwrapper_name = xstrdup( base_name (actual_cwrapper_path));
+ strendzap (actual_cwrapper_path, actual_cwrapper_name);
+
+ /* wrapper name transforms */
+ strendzap (actual_cwrapper_name, ".exe");
+ tmp_pathspec = lt_extend_str (actual_cwrapper_name, ".exe", 1);
+ XFREE (actual_cwrapper_name);
+ actual_cwrapper_name = tmp_pathspec;
+ tmp_pathspec = 0;
+
+ /* target_name transforms -- use actual target program name; might have lt- prefix */
+ target_name = xstrdup (base_name (TARGET_PROGRAM_NAME));
+ strendzap (target_name, ".exe");
+ tmp_pathspec = lt_extend_str (target_name, ".exe", 1);
+ XFREE (target_name);
+ target_name = tmp_pathspec;
+ tmp_pathspec = 0;
+
+ LTWRAPPER_DEBUGPRINTF (("(main) libtool target name: %s\n",
+ target_name));
+EOF
+
+ cat <<EOF
+ newargz[0] =
+ XMALLOC (char, (strlen (actual_cwrapper_path) +
+ strlen ("$objdir") + 1 + strlen (actual_cwrapper_name) + 1));
+ strcpy (newargz[0], actual_cwrapper_path);
+ strcat (newargz[0], "$objdir");
+ strcat (newargz[0], "/");
+EOF
+
+ cat <<"EOF"
+ /* stop here, and copy so we don't have to do this twice */
+ tmp_pathspec = xstrdup (newargz[0]);
+
+ /* do NOT want the lt- prefix here, so use actual_cwrapper_name */
+ strcat (newargz[0], actual_cwrapper_name);
+
+ /* DO want the lt- prefix here if it exists, so use target_name */
+ lt_argv_zero = lt_extend_str (tmp_pathspec, target_name, 1);
+ XFREE (tmp_pathspec);
+ tmp_pathspec = NULL;
+EOF
+
+ case $host_os in
+ mingw*)
+ cat <<"EOF"
+ {
+ char* p;
+ while ((p = strchr (newargz[0], '\\')) != NULL)
+ {
+ *p = '/';
+ }
+ while ((p = strchr (lt_argv_zero, '\\')) != NULL)
+ {
+ *p = '/';
+ }
+ }
+EOF
+ ;;
+ esac
+
+ cat <<"EOF"
+ XFREE (target_name);
+ XFREE (actual_cwrapper_path);
+ XFREE (actual_cwrapper_name);
+
+ lt_setenv ("BIN_SH", "xpg4"); /* for Tru64 */
+ lt_setenv ("DUALCASE", "1"); /* for MSK sh */
+ lt_update_lib_path (LIB_PATH_VARNAME, LIB_PATH_VALUE);
+ lt_update_exe_path (EXE_PATH_VARNAME, EXE_PATH_VALUE);
+
+ newargc=0;
+ for (i = 1; i < argc; i++)
+ {
+ if (strncmp (argv[i], env_set_opt, env_set_opt_len) == 0)
+ {
+ if (argv[i][env_set_opt_len] == '=')
+ {
+ const char *p = argv[i] + env_set_opt_len + 1;
+ lt_opt_process_env_set (p);
+ }
+ else if (argv[i][env_set_opt_len] == '\0' && i + 1 < argc)
+ {
+ lt_opt_process_env_set (argv[++i]); /* don't copy */
+ }
+ else
+ lt_fatal ("%s missing required argument", env_set_opt);
+ continue;
+ }
+ if (strncmp (argv[i], env_prepend_opt, env_prepend_opt_len) == 0)
+ {
+ if (argv[i][env_prepend_opt_len] == '=')
+ {
+ const char *p = argv[i] + env_prepend_opt_len + 1;
+ lt_opt_process_env_prepend (p);
+ }
+ else if (argv[i][env_prepend_opt_len] == '\0' && i + 1 < argc)
+ {
+ lt_opt_process_env_prepend (argv[++i]); /* don't copy */
+ }
+ else
+ lt_fatal ("%s missing required argument", env_prepend_opt);
+ continue;
+ }
+ if (strncmp (argv[i], env_append_opt, env_append_opt_len) == 0)
+ {
+ if (argv[i][env_append_opt_len] == '=')
+ {
+ const char *p = argv[i] + env_append_opt_len + 1;
+ lt_opt_process_env_append (p);
+ }
+ else if (argv[i][env_append_opt_len] == '\0' && i + 1 < argc)
+ {
+ lt_opt_process_env_append (argv[++i]); /* don't copy */
+ }
+ else
+ lt_fatal ("%s missing required argument", env_append_opt);
+ continue;
+ }
+ if (strncmp (argv[i], ltwrapper_option_prefix, opt_prefix_len) == 0)
+ {
+ /* however, if there is an option in the LTWRAPPER_OPTION_PREFIX
+ namespace, but it is not one of the ones we know about and
+ have already dealt with, above (inluding dump-script), then
+ report an error. Otherwise, targets might begin to believe
+ they are allowed to use options in the LTWRAPPER_OPTION_PREFIX
+ namespace. The first time any user complains about this, we'll
+ need to make LTWRAPPER_OPTION_PREFIX a configure-time option
+ or a configure.ac-settable value.
+ */
+ lt_fatal ("Unrecognized option in %s namespace: '%s'",
+ ltwrapper_option_prefix, argv[i]);
+ }
+ /* otherwise ... */
+ newargz[++newargc] = xstrdup (argv[i]);
+ }
+ newargz[++newargc] = NULL;
+
+ LTWRAPPER_DEBUGPRINTF (("(main) lt_argv_zero : %s\n", (lt_argv_zero ? lt_argv_zero : "<NULL>")));
+ for (i = 0; i < newargc; i++)
+ {
+ LTWRAPPER_DEBUGPRINTF (("(main) newargz[%d] : %s\n", i, (newargz[i] ? newargz[i] : "<NULL>")));
+ }
+
+EOF
+
+ case $host_os in
+ mingw*)
+ cat <<"EOF"
+ /* execv doesn't actually work on mingw as expected on unix */
+ rval = _spawnv (_P_WAIT, lt_argv_zero, (const char * const *) newargz);
+ if (rval == -1)
+ {
+ /* failed to start process */
+ LTWRAPPER_DEBUGPRINTF (("(main) failed to launch target \"%s\": errno = %d\n", lt_argv_zero, errno));
+ return 127;
+ }
+ return rval;
+EOF
+ ;;
+ *)
+ cat <<"EOF"
+ execv (lt_argv_zero, newargz);
+ return rval; /* =127, but avoids unused variable warning */
+EOF
+ ;;
+ esac
+
+ cat <<"EOF"
+}
+
+void *
+xmalloc (size_t num)
+{
+ void *p = (void *) malloc (num);
+ if (!p)
+ lt_fatal ("Memory exhausted");
+
+ return p;
+}
+
+char *
+xstrdup (const char *string)
+{
+ return string ? strcpy ((char *) xmalloc (strlen (string) + 1),
+ string) : NULL;
+}
+
+const char *
+base_name (const char *name)
+{
+ const char *base;
+
+#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
+ /* Skip over the disk name in MSDOS pathnames. */
+ if (isalpha ((unsigned char) name[0]) && name[1] == ':')
+ name += 2;
+#endif
+
+ for (base = name; *name; name++)
+ if (IS_DIR_SEPARATOR (*name))
+ base = name + 1;
+ return base;
+}
+
+int
+check_executable (const char *path)
+{
+ struct stat st;
+
+ LTWRAPPER_DEBUGPRINTF (("(check_executable) : %s\n",
+ path ? (*path ? path : "EMPTY!") : "NULL!"));
+ if ((!path) || (!*path))
+ return 0;
+
+ if ((stat (path, &st) >= 0)
+ && (st.st_mode & (S_IXUSR | S_IXGRP | S_IXOTH)))
+ return 1;
+ else
+ return 0;
+}
+
+int
+make_executable (const char *path)
+{
+ int rval = 0;
+ struct stat st;
+
+ LTWRAPPER_DEBUGPRINTF (("(make_executable) : %s\n",
+ path ? (*path ? path : "EMPTY!") : "NULL!"));
+ if ((!path) || (!*path))
+ return 0;
+
+ if (stat (path, &st) >= 0)
+ {
+ rval = chmod (path, st.st_mode | S_IXOTH | S_IXGRP | S_IXUSR);
+ }
+ return rval;
+}
+
+/* Searches for the full path of the wrapper. Returns
+ newly allocated full path name if found, NULL otherwise
+ Does not chase symlinks, even on platforms that support them.
+*/
+char *
+find_executable (const char *wrapper)
+{
+ int has_slash = 0;
+ const char *p;
+ const char *p_next;
+ /* static buffer for getcwd */
+ char tmp[LT_PATHMAX + 1];
+ int tmp_len;
+ char *concat_name;
+
+ LTWRAPPER_DEBUGPRINTF (("(find_executable) : %s\n",
+ wrapper ? (*wrapper ? wrapper : "EMPTY!") : "NULL!"));
+
+ if ((wrapper == NULL) || (*wrapper == '\0'))
+ return NULL;
+
+ /* Absolute path? */
+#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
+ if (isalpha ((unsigned char) wrapper[0]) && wrapper[1] == ':')
+ {
+ concat_name = xstrdup (wrapper);
+ if (check_executable (concat_name))
+ return concat_name;
+ XFREE (concat_name);
+ }
+ else
+ {
+#endif
+ if (IS_DIR_SEPARATOR (wrapper[0]))
+ {
+ concat_name = xstrdup (wrapper);
+ if (check_executable (concat_name))
+ return concat_name;
+ XFREE (concat_name);
+ }
+#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
+ }
+#endif
+
+ for (p = wrapper; *p; p++)
+ if (*p == '/')
+ {
+ has_slash = 1;
+ break;
+ }
+ if (!has_slash)
+ {
+ /* no slashes; search PATH */
+ const char *path = getenv ("PATH");
+ if (path != NULL)
+ {
+ for (p = path; *p; p = p_next)
+ {
+ const char *q;
+ size_t p_len;
+ for (q = p; *q; q++)
+ if (IS_PATH_SEPARATOR (*q))
+ break;
+ p_len = q - p;
+ p_next = (*q == '\0' ? q : q + 1);
+ if (p_len == 0)
+ {
+ /* empty path: current directory */
+ if (getcwd (tmp, LT_PATHMAX) == NULL)
+ lt_fatal ("getcwd failed");
+ tmp_len = strlen (tmp);
+ concat_name =
+ XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1);
+ memcpy (concat_name, tmp, tmp_len);
+ concat_name[tmp_len] = '/';
+ strcpy (concat_name + tmp_len + 1, wrapper);
+ }
+ else
+ {
+ concat_name =
+ XMALLOC (char, p_len + 1 + strlen (wrapper) + 1);
+ memcpy (concat_name, p, p_len);
+ concat_name[p_len] = '/';
+ strcpy (concat_name + p_len + 1, wrapper);
+ }
+ if (check_executable (concat_name))
+ return concat_name;
+ XFREE (concat_name);
+ }
+ }
+ /* not found in PATH; assume curdir */
+ }
+ /* Relative path | not found in path: prepend cwd */
+ if (getcwd (tmp, LT_PATHMAX) == NULL)
+ lt_fatal ("getcwd failed");
+ tmp_len = strlen (tmp);
+ concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1);
+ memcpy (concat_name, tmp, tmp_len);
+ concat_name[tmp_len] = '/';
+ strcpy (concat_name + tmp_len + 1, wrapper);
+
+ if (check_executable (concat_name))
+ return concat_name;
+ XFREE (concat_name);
+ return NULL;
+}
+
+char *
+chase_symlinks (const char *pathspec)
+{
+#ifndef S_ISLNK
+ return xstrdup (pathspec);
+#else
+ char buf[LT_PATHMAX];
+ struct stat s;
+ char *tmp_pathspec = xstrdup (pathspec);
+ char *p;
+ int has_symlinks = 0;
+ while (strlen (tmp_pathspec) && !has_symlinks)
+ {
+ LTWRAPPER_DEBUGPRINTF (("checking path component for symlinks: %s\n",
+ tmp_pathspec));
+ if (lstat (tmp_pathspec, &s) == 0)
+ {
+ if (S_ISLNK (s.st_mode) != 0)
+ {
+ has_symlinks = 1;
+ break;
+ }
+
+ /* search backwards for last DIR_SEPARATOR */
+ p = tmp_pathspec + strlen (tmp_pathspec) - 1;
+ while ((p > tmp_pathspec) && (!IS_DIR_SEPARATOR (*p)))
+ p--;
+ if ((p == tmp_pathspec) && (!IS_DIR_SEPARATOR (*p)))
+ {
+ /* no more DIR_SEPARATORS left */
+ break;
+ }
+ *p = '\0';
+ }
+ else
+ {
+ char *errstr = strerror (errno);
+ lt_fatal ("Error accessing file %s (%s)", tmp_pathspec, errstr);
+ }
+ }
+ XFREE (tmp_pathspec);
+
+ if (!has_symlinks)
+ {
+ return xstrdup (pathspec);
+ }
+
+ tmp_pathspec = realpath (pathspec, buf);
+ if (tmp_pathspec == 0)
+ {
+ lt_fatal ("Could not follow symlinks for %s", pathspec);
+ }
+ return xstrdup (tmp_pathspec);
+#endif
+}
+
+char *
+strendzap (char *str, const char *pat)
+{
+ size_t len, patlen;
+
+ assert (str != NULL);
+ assert (pat != NULL);
+
+ len = strlen (str);
+ patlen = strlen (pat);
+
+ if (patlen <= len)
+ {
+ str += len - patlen;
+ if (strcmp (str, pat) == 0)
+ *str = '\0';
+ }
+ return str;
+}
+
+static void
+lt_error_core (int exit_status, const char *mode,
+ const char *message, va_list ap)
+{
+ fprintf (stderr, "%s: %s: ", program_name, mode);
+ vfprintf (stderr, message, ap);
+ fprintf (stderr, ".\n");
+
+ if (exit_status >= 0)
+ exit (exit_status);
+}
+
+void
+lt_fatal (const char *message, ...)
+{
+ va_list ap;
+ va_start (ap, message);
+ lt_error_core (EXIT_FAILURE, "FATAL", message, ap);
+ va_end (ap);
+}
+
+void
+lt_setenv (const char *name, const char *value)
+{
+ LTWRAPPER_DEBUGPRINTF (("(lt_setenv) setting '%s' to '%s'\n",
+ (name ? name : "<NULL>"),
+ (value ? value : "<NULL>")));
+ {
+#ifdef HAVE_SETENV
+ /* always make a copy, for consistency with !HAVE_SETENV */
+ char *str = xstrdup (value);
+ setenv (name, str, 1);
+#else
+ int len = strlen (name) + 1 + strlen (value) + 1;
+ char *str = XMALLOC (char, len);
+ sprintf (str, "%s=%s", name, value);
+ if (putenv (str) != EXIT_SUCCESS)
+ {
+ XFREE (str);
+ }
+#endif
+ }
+}
+
+char *
+lt_extend_str (const char *orig_value, const char *add, int to_end)
+{
+ char *new_value;
+ if (orig_value && *orig_value)
+ {
+ int orig_value_len = strlen (orig_value);
+ int add_len = strlen (add);
+ new_value = XMALLOC (char, add_len + orig_value_len + 1);
+ if (to_end)
+ {
+ strcpy (new_value, orig_value);
+ strcpy (new_value + orig_value_len, add);
+ }
+ else
+ {
+ strcpy (new_value, add);
+ strcpy (new_value + add_len, orig_value);
+ }
+ }
+ else
+ {
+ new_value = xstrdup (add);
+ }
+ return new_value;
+}
+
+int
+lt_split_name_value (const char *arg, char** name, char** value)
+{
+ const char *p;
+ int len;
+ if (!arg || !*arg)
+ return 1;
+
+ p = strchr (arg, (int)'=');
+
+ if (!p)
+ return 1;
+
+ *value = xstrdup (++p);
+
+ len = strlen (arg) - strlen (*value);
+ *name = XMALLOC (char, len);
+ strncpy (*name, arg, len-1);
+ (*name)[len - 1] = '\0';
+
+ return 0;
+}
+
+void
+lt_opt_process_env_set (const char *arg)
+{
+ char *name = NULL;
+ char *value = NULL;
+
+ if (lt_split_name_value (arg, &name, &value) != 0)
+ {
+ XFREE (name);
+ XFREE (value);
+ lt_fatal ("bad argument for %s: '%s'", env_set_opt, arg);
+ }
+
+ lt_setenv (name, value);
+ XFREE (name);
+ XFREE (value);
+}
+
+void
+lt_opt_process_env_prepend (const char *arg)
+{
+ char *name = NULL;
+ char *value = NULL;
+ char *new_value = NULL;
+
+ if (lt_split_name_value (arg, &name, &value) != 0)
+ {
+ XFREE (name);
+ XFREE (value);
+ lt_fatal ("bad argument for %s: '%s'", env_prepend_opt, arg);
+ }
+
+ new_value = lt_extend_str (getenv (name), value, 0);
+ lt_setenv (name, new_value);
+ XFREE (new_value);
+ XFREE (name);
+ XFREE (value);
+}
+
+void
+lt_opt_process_env_append (const char *arg)
+{
+ char *name = NULL;
+ char *value = NULL;
+ char *new_value = NULL;
+
+ if (lt_split_name_value (arg, &name, &value) != 0)
+ {
+ XFREE (name);
+ XFREE (value);
+ lt_fatal ("bad argument for %s: '%s'", env_append_opt, arg);
+ }
+
+ new_value = lt_extend_str (getenv (name), value, 1);
+ lt_setenv (name, new_value);
+ XFREE (new_value);
+ XFREE (name);
+ XFREE (value);
+}
+
+void
+lt_update_exe_path (const char *name, const char *value)
+{
+ LTWRAPPER_DEBUGPRINTF (("(lt_update_exe_path) modifying '%s' by prepending '%s'\n",
+ (name ? name : "<NULL>"),
+ (value ? value : "<NULL>")));
+
+ if (name && *name && value && *value)
+ {
+ char *new_value = lt_extend_str (getenv (name), value, 0);
+ /* some systems can't cope with a ':'-terminated path #' */
+ int len = strlen (new_value);
+ while (((len = strlen (new_value)) > 0) && IS_PATH_SEPARATOR (new_value[len-1]))
+ {
+ new_value[len-1] = '\0';
+ }
+ lt_setenv (name, new_value);
+ XFREE (new_value);
+ }
+}
+
+void
+lt_update_lib_path (const char *name, const char *value)
+{
+ LTWRAPPER_DEBUGPRINTF (("(lt_update_lib_path) modifying '%s' by prepending '%s'\n",
+ (name ? name : "<NULL>"),
+ (value ? value : "<NULL>")));
+
+ if (name && *name && value && *value)
+ {
+ char *new_value = lt_extend_str (getenv (name), value, 0);
+ lt_setenv (name, new_value);
+ XFREE (new_value);
+ }
+}
+
+
+EOF
+}
+# end: func_emit_cwrapperexe_src
+
+# func_mode_link arg...
+func_mode_link ()
+{
+ $opt_debug
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*)
+ # It is impossible to link a dll without this setting, and
+ # we shouldn't force the makefile maintainer to figure out
+ # which system we are compiling for in order to pass an extra
+ # flag for every libtool invocation.
+ # allow_undefined=no
+
+ # FIXME: Unfortunately, there are problems with the above when trying
+ # to make a dll which has undefined symbols, in which case not
+ # even a static library is built. For now, we need to specify
+ # -no-undefined on the libtool link line when we can be certain
+ # that all symbols are satisfied, otherwise we get a static library.
+ allow_undefined=yes
+ ;;
+ *)
+ allow_undefined=yes
+ ;;
+ esac
+ libtool_args=$nonopt
+ base_compile="$nonopt $@"
+ compile_command=$nonopt
+ finalize_command=$nonopt
+
+ compile_rpath=
+ finalize_rpath=
+ compile_shlibpath=
+ finalize_shlibpath=
+ convenience=
+ old_convenience=
+ deplibs=
+ old_deplibs=
+ compiler_flags=
+ linker_flags=
+ dllsearchpath=
+ lib_search_path=`pwd`
+ inst_prefix_dir=
+ new_inherited_linker_flags=
+
+ avoid_version=no
+ dlfiles=
+ dlprefiles=
+ dlself=no
+ export_dynamic=no
+ export_symbols=
+ export_symbols_regex=
+ generated=
+ libobjs=
+ ltlibs=
+ module=no
+ no_install=no
+ objs=
+ non_pic_objects=
+ precious_files_regex=
+ prefer_static_libs=no
+ preload=no
+ prev=
+ prevarg=
+ release=
+ rpath=
+ xrpath=
+ perm_rpath=
+ temp_rpath=
+ thread_safe=no
+ vinfo=
+ vinfo_number=no
+ weak_libs=
+ single_module="${wl}-single_module"
+ func_infer_tag $base_compile
+
+ # We need to know -static, to get the right output filenames.
+ for arg
+ do
+ case $arg in
+ -shared)
+ test "$build_libtool_libs" != yes && \
+ func_fatal_configuration "can not build a shared library"
+ build_old_libs=no
+ break
+ ;;
+ -all-static | -static | -static-libtool-libs)
+ case $arg in
+ -all-static)
+ if test "$build_libtool_libs" = yes && test -z "$link_static_flag"; then
+ func_warning "complete static linking is impossible in this configuration"
+ fi
+ if test -n "$link_static_flag"; then
+ dlopen_self=$dlopen_self_static
+ fi
+ prefer_static_libs=yes
+ ;;
+ -static)
+ if test -z "$pic_flag" && test -n "$link_static_flag"; then
+ dlopen_self=$dlopen_self_static
+ fi
+ prefer_static_libs=built
+ ;;
+ -static-libtool-libs)
+ if test -z "$pic_flag" && test -n "$link_static_flag"; then
+ dlopen_self=$dlopen_self_static
+ fi
+ prefer_static_libs=yes
+ ;;
+ esac
+ build_libtool_libs=no
+ build_old_libs=yes
+ break
+ ;;
+ esac
+ done
+
+ # See if our shared archives depend on static archives.
+ test -n "$old_archive_from_new_cmds" && build_old_libs=yes
+
+ # Go through the arguments, transforming them on the way.
+ while test "$#" -gt 0; do
+ arg="$1"
+ shift
+ func_quote_for_eval "$arg"
+ qarg=$func_quote_for_eval_unquoted_result
+ func_append libtool_args " $func_quote_for_eval_result"
+
+ # If the previous option needs an argument, assign it.
+ if test -n "$prev"; then
+ case $prev in
+ output)
+ func_append compile_command " @OUTPUT@"
+ func_append finalize_command " @OUTPUT@"
+ ;;
+ esac
+
+ case $prev in
+ dlfiles|dlprefiles)
+ if test "$preload" = no; then
+ # Add the symbol object into the linking commands.
+ func_append compile_command " @SYMFILE@"
+ func_append finalize_command " @SYMFILE@"
+ preload=yes
+ fi
+ case $arg in
+ *.la | *.lo) ;; # We handle these cases below.
+ force)
+ if test "$dlself" = no; then
+ dlself=needless
+ export_dynamic=yes
+ fi
+ prev=
+ continue
+ ;;
+ self)
+ if test "$prev" = dlprefiles; then
+ dlself=yes
+ elif test "$prev" = dlfiles && test "$dlopen_self" != yes; then
+ dlself=yes
+ else
+ dlself=needless
+ export_dynamic=yes
+ fi
+ prev=
+ continue
+ ;;
+ *)
+ if test "$prev" = dlfiles; then
+ dlfiles="$dlfiles $arg"
+ else
+ dlprefiles="$dlprefiles $arg"
+ fi
+ prev=
+ continue
+ ;;
+ esac
+ ;;
+ expsyms)
+ export_symbols="$arg"
+ test -f "$arg" \
+ || func_fatal_error "symbol file \`$arg' does not exist"
+ prev=
+ continue
+ ;;
+ expsyms_regex)
+ export_symbols_regex="$arg"
+ prev=
+ continue
+ ;;
+ framework)
+ case $host in
+ *-*-darwin*)
+ case "$deplibs " in
+ *" $qarg.ltframework "*) ;;
+ *) deplibs="$deplibs $qarg.ltframework" # this is fixed later
+ ;;
+ esac
+ ;;
+ esac
+ prev=
+ continue
+ ;;
+ inst_prefix)
+ inst_prefix_dir="$arg"
+ prev=
+ continue
+ ;;
+ objectlist)
+ if test -f "$arg"; then
+ save_arg=$arg
+ moreargs=
+ for fil in `cat "$save_arg"`
+ do
+# moreargs="$moreargs $fil"
+ arg=$fil
+ # A libtool-controlled object.
+
+ # Check to see that this really is a libtool object.
+ if func_lalib_unsafe_p "$arg"; then
+ pic_object=
+ non_pic_object=
+
+ # Read the .lo file
+ func_source "$arg"
+
+ if test -z "$pic_object" ||
+ test -z "$non_pic_object" ||
+ test "$pic_object" = none &&
+ test "$non_pic_object" = none; then
+ func_fatal_error "cannot find name of object for \`$arg'"
+ fi
+
+ # Extract subdirectory from the argument.
+ func_dirname "$arg" "/" ""
+ xdir="$func_dirname_result"
+
+ if test "$pic_object" != none; then
+ # Prepend the subdirectory the object is found in.
+ pic_object="$xdir$pic_object"
+
+ if test "$prev" = dlfiles; then
+ if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then
+ dlfiles="$dlfiles $pic_object"
+ prev=
+ continue
+ else
+ # If libtool objects are unsupported, then we need to preload.
+ prev=dlprefiles
+ fi
+ fi
+
+ # CHECK ME: I think I busted this. -Ossama
+ if test "$prev" = dlprefiles; then
+ # Preload the old-style object.
+ dlprefiles="$dlprefiles $pic_object"
+ prev=
+ fi
+
+ # A PIC object.
+ func_append libobjs " $pic_object"
+ arg="$pic_object"
+ fi
+
+ # Non-PIC object.
+ if test "$non_pic_object" != none; then
+ # Prepend the subdirectory the object is found in.
+ non_pic_object="$xdir$non_pic_object"
+
+ # A standard non-PIC object
+ func_append non_pic_objects " $non_pic_object"
+ if test -z "$pic_object" || test "$pic_object" = none ; then
+ arg="$non_pic_object"
+ fi
+ else
+ # If the PIC object exists, use it instead.
+ # $xdir was prepended to $pic_object above.
+ non_pic_object="$pic_object"
+ func_append non_pic_objects " $non_pic_object"
+ fi
+ else
+ # Only an error if not doing a dry-run.
+ if $opt_dry_run; then
+ # Extract subdirectory from the argument.
+ func_dirname "$arg" "/" ""
+ xdir="$func_dirname_result"
+
+ func_lo2o "$arg"
+ pic_object=$xdir$objdir/$func_lo2o_result
+ non_pic_object=$xdir$func_lo2o_result
+ func_append libobjs " $pic_object"
+ func_append non_pic_objects " $non_pic_object"
+ else
+ func_fatal_error "\`$arg' is not a valid libtool object"
+ fi
+ fi
+ done
+ else
+ func_fatal_error "link input file \`$arg' does not exist"
+ fi
+ arg=$save_arg
+ prev=
+ continue
+ ;;
+ precious_regex)
+ precious_files_regex="$arg"
+ prev=
+ continue
+ ;;
+ release)
+ release="-$arg"
+ prev=
+ continue
+ ;;
+ rpath | xrpath)
+ # We need an absolute path.
+ case $arg in
+ [\\/]* | [A-Za-z]:[\\/]*) ;;
+ *)
+ func_fatal_error "only absolute run-paths are allowed"
+ ;;
+ esac
+ if test "$prev" = rpath; then
+ case "$rpath " in
+ *" $arg "*) ;;
+ *) rpath="$rpath $arg" ;;
+ esac
+ else
+ case "$xrpath " in
+ *" $arg "*) ;;
+ *) xrpath="$xrpath $arg" ;;
+ esac
+ fi
+ prev=
+ continue
+ ;;
+ shrext)
+ shrext_cmds="$arg"
+ prev=
+ continue
+ ;;
+ weak)
+ weak_libs="$weak_libs $arg"
+ prev=
+ continue
+ ;;
+ xcclinker)
+ linker_flags="$linker_flags $qarg"
+ compiler_flags="$compiler_flags $qarg"
+ prev=
+ func_append compile_command " $qarg"
+ func_append finalize_command " $qarg"
+ continue
+ ;;
+ xcompiler)
+ compiler_flags="$compiler_flags $qarg"
+ prev=
+ func_append compile_command " $qarg"
+ func_append finalize_command " $qarg"
+ continue
+ ;;
+ xlinker)
+ linker_flags="$linker_flags $qarg"
+ compiler_flags="$compiler_flags $wl$qarg"
+ prev=
+ func_append compile_command " $wl$qarg"
+ func_append finalize_command " $wl$qarg"
+ continue
+ ;;
+ *)
+ eval "$prev=\"\$arg\""
+ prev=
+ continue
+ ;;
+ esac
+ fi # test -n "$prev"
+
+ prevarg="$arg"
+
+ case $arg in
+ -all-static)
+ if test -n "$link_static_flag"; then
+ # See comment for -static flag below, for more details.
+ func_append compile_command " $link_static_flag"
+ func_append finalize_command " $link_static_flag"
+ fi
+ continue
+ ;;
+
+ -allow-undefined)
+ # FIXME: remove this flag sometime in the future.
+ func_fatal_error "\`-allow-undefined' must not be used because it is the default"
+ ;;
+
+ -avoid-version)
+ avoid_version=yes
+ continue
+ ;;
+
+ -dlopen)
+ prev=dlfiles
+ continue
+ ;;
+
+ -dlpreopen)
+ prev=dlprefiles
+ continue
+ ;;
+
+ -export-dynamic)
+ export_dynamic=yes
+ continue
+ ;;
+
+ -export-symbols | -export-symbols-regex)
+ if test -n "$export_symbols" || test -n "$export_symbols_regex"; then
+ func_fatal_error "more than one -exported-symbols argument is not allowed"
+ fi
+ if test "X$arg" = "X-export-symbols"; then
+ prev=expsyms
+ else
+ prev=expsyms_regex
+ fi
+ continue
+ ;;
+
+ -framework)
+ prev=framework
+ continue
+ ;;
+
+ -inst-prefix-dir)
+ prev=inst_prefix
+ continue
+ ;;
+
+ # The native IRIX linker understands -LANG:*, -LIST:* and -LNO:*
+ # so, if we see these flags be careful not to treat them like -L
+ -L[A-Z][A-Z]*:*)
+ case $with_gcc/$host in
+ no/*-*-irix* | /*-*-irix*)
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ ;;
+ esac
+ continue
+ ;;
+
+ -L*)
+ func_stripname '-L' '' "$arg"
+ dir=$func_stripname_result
+ if test -z "$dir"; then
+ if test "$#" -gt 0; then
+ func_fatal_error "require no space between \`-L' and \`$1'"
+ else
+ func_fatal_error "need path for \`-L' option"
+ fi
+ fi
+ # We need an absolute path.
+ case $dir in
+ [\\/]* | [A-Za-z]:[\\/]*) ;;
+ *)
+ absdir=`cd "$dir" && pwd`
+ test -z "$absdir" && \
+ func_fatal_error "cannot determine absolute directory name of \`$dir'"
+ dir="$absdir"
+ ;;
+ esac
+ case "$deplibs " in
+ *" -L$dir "*) ;;
+ *)
+ deplibs="$deplibs -L$dir"
+ lib_search_path="$lib_search_path $dir"
+ ;;
+ esac
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*)
+ testbindir=`$ECHO "X$dir" | $Xsed -e 's*/lib$*/bin*'`
+ case :$dllsearchpath: in
+ *":$dir:"*) ;;
+ ::) dllsearchpath=$dir;;
+ *) dllsearchpath="$dllsearchpath:$dir";;
+ esac
+ case :$dllsearchpath: in
+ *":$testbindir:"*) ;;
+ ::) dllsearchpath=$testbindir;;
+ *) dllsearchpath="$dllsearchpath:$testbindir";;
+ esac
+ ;;
+ esac
+ continue
+ ;;
+
+ -l*)
+ if test "X$arg" = "X-lc" || test "X$arg" = "X-lm"; then
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-beos* | *-cegcc*)
+ # These systems don't actually have a C or math library (as such)
+ continue
+ ;;
+ *-*-os2*)
+ # These systems don't actually have a C library (as such)
+ test "X$arg" = "X-lc" && continue
+ ;;
+ *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
+ # Do not include libc due to us having libc/libc_r.
+ test "X$arg" = "X-lc" && continue
+ ;;
+ *-*-rhapsody* | *-*-darwin1.[012])
+ # Rhapsody C and math libraries are in the System framework
+ deplibs="$deplibs System.ltframework"
+ continue
+ ;;
+ *-*-sco3.2v5* | *-*-sco5v6*)
+ # Causes problems with __ctype
+ test "X$arg" = "X-lc" && continue
+ ;;
+ *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*)
+ # Compiler inserts libc in the correct place for threads to work
+ test "X$arg" = "X-lc" && continue
+ ;;
+ esac
+ elif test "X$arg" = "X-lc_r"; then
+ case $host in
+ *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
+ # Do not include libc_r directly, use -pthread flag.
+ continue
+ ;;
+ esac
+ fi
+ deplibs="$deplibs $arg"
+ continue
+ ;;
+
+ -module)
+ module=yes
+ continue
+ ;;
+
+ # Tru64 UNIX uses -model [arg] to determine the layout of C++
+ # classes, name mangling, and exception handling.
+ # Darwin uses the -arch flag to determine output architecture.
+ -model|-arch|-isysroot)
+ compiler_flags="$compiler_flags $arg"
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ prev=xcompiler
+ continue
+ ;;
+
+ -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads)
+ compiler_flags="$compiler_flags $arg"
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ case "$new_inherited_linker_flags " in
+ *" $arg "*) ;;
+ * ) new_inherited_linker_flags="$new_inherited_linker_flags $arg" ;;
+ esac
+ continue
+ ;;
+
+ -multi_module)
+ single_module="${wl}-multi_module"
+ continue
+ ;;
+
+ -no-fast-install)
+ fast_install=no
+ continue
+ ;;
+
+ -no-install)
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-darwin* | *-cegcc*)
+ # The PATH hackery in wrapper scripts is required on Windows
+ # and Darwin in order for the loader to find any dlls it needs.
+ func_warning "\`-no-install' is ignored for $host"
+ func_warning "assuming \`-no-fast-install' instead"
+ fast_install=no
+ ;;
+ *) no_install=yes ;;
+ esac
+ continue
+ ;;
+
+ -no-undefined)
+ allow_undefined=no
+ continue
+ ;;
+
+ -objectlist)
+ prev=objectlist
+ continue
+ ;;
+
+ -o) prev=output ;;
+
+ -precious-files-regex)
+ prev=precious_regex
+ continue
+ ;;
+
+ -release)
+ prev=release
+ continue
+ ;;
+
+ -rpath)
+ prev=rpath
+ continue
+ ;;
+
+ -R)
+ prev=xrpath
+ continue
+ ;;
+
+ -R*)
+ func_stripname '-R' '' "$arg"
+ dir=$func_stripname_result
+ # We need an absolute path.
+ case $dir in
+ [\\/]* | [A-Za-z]:[\\/]*) ;;
+ *)
+ func_fatal_error "only absolute run-paths are allowed"
+ ;;
+ esac
+ case "$xrpath " in
+ *" $dir "*) ;;
+ *) xrpath="$xrpath $dir" ;;
+ esac
+ continue
+ ;;
+
+ -shared)
+ # The effects of -shared are defined in a previous loop.
+ continue
+ ;;
+
+ -shrext)
+ prev=shrext
+ continue
+ ;;
+
+ -static | -static-libtool-libs)
+ # The effects of -static are defined in a previous loop.
+ # We used to do the same as -all-static on platforms that
+ # didn't have a PIC flag, but the assumption that the effects
+ # would be equivalent was wrong. It would break on at least
+ # Digital Unix and AIX.
+ continue
+ ;;
+
+ -thread-safe)
+ thread_safe=yes
+ continue
+ ;;
+
+ -version-info)
+ prev=vinfo
+ continue
+ ;;
+
+ -version-number)
+ prev=vinfo
+ vinfo_number=yes
+ continue
+ ;;
+
+ -weak)
+ prev=weak
+ continue
+ ;;
+
+ -Wc,*)
+ func_stripname '-Wc,' '' "$arg"
+ args=$func_stripname_result
+ arg=
+ save_ifs="$IFS"; IFS=','
+ for flag in $args; do
+ IFS="$save_ifs"
+ func_quote_for_eval "$flag"
+ arg="$arg $wl$func_quote_for_eval_result"
+ compiler_flags="$compiler_flags $func_quote_for_eval_result"
+ done
+ IFS="$save_ifs"
+ func_stripname ' ' '' "$arg"
+ arg=$func_stripname_result
+ ;;
+
+ -Wl,*)
+ func_stripname '-Wl,' '' "$arg"
+ args=$func_stripname_result
+ arg=
+ save_ifs="$IFS"; IFS=','
+ for flag in $args; do
+ IFS="$save_ifs"
+ func_quote_for_eval "$flag"
+ arg="$arg $wl$func_quote_for_eval_result"
+ compiler_flags="$compiler_flags $wl$func_quote_for_eval_result"
+ linker_flags="$linker_flags $func_quote_for_eval_result"
+ done
+ IFS="$save_ifs"
+ func_stripname ' ' '' "$arg"
+ arg=$func_stripname_result
+ ;;
+
+ -Xcompiler)
+ prev=xcompiler
+ continue
+ ;;
+
+ -Xlinker)
+ prev=xlinker
+ continue
+ ;;
+
+ -XCClinker)
+ prev=xcclinker
+ continue
+ ;;
+
+ # -msg_* for osf cc
+ -msg_*)
+ func_quote_for_eval "$arg"
+ arg="$func_quote_for_eval_result"
+ ;;
+
+ # -64, -mips[0-9] enable 64-bit mode on the SGI compiler
+ # -r[0-9][0-9]* specifies the processor on the SGI compiler
+ # -xarch=*, -xtarget=* enable 64-bit mode on the Sun compiler
+ # +DA*, +DD* enable 64-bit mode on the HP compiler
+ # -q* pass through compiler args for the IBM compiler
+ # -m*, -t[45]*, -txscale* pass through architecture-specific
+ # compiler args for GCC
+ # -F/path gives path to uninstalled frameworks, gcc on darwin
+ # -p, -pg, --coverage, -fprofile-* pass through profiling flag for GCC
+ # @file GCC response files
+ -64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*| \
+ -t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*)
+ func_quote_for_eval "$arg"
+ arg="$func_quote_for_eval_result"
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ compiler_flags="$compiler_flags $arg"
+ continue
+ ;;
+
+ # Some other compiler flag.
+ -* | +*)
+ func_quote_for_eval "$arg"
+ arg="$func_quote_for_eval_result"
+ ;;
+
+ *.$objext)
+ # A standard object.
+ objs="$objs $arg"
+ ;;
+
+ *.lo)
+ # A libtool-controlled object.
+
+ # Check to see that this really is a libtool object.
+ if func_lalib_unsafe_p "$arg"; then
+ pic_object=
+ non_pic_object=
+
+ # Read the .lo file
+ func_source "$arg"
+
+ if test -z "$pic_object" ||
+ test -z "$non_pic_object" ||
+ test "$pic_object" = none &&
+ test "$non_pic_object" = none; then
+ func_fatal_error "cannot find name of object for \`$arg'"
+ fi
+
+ # Extract subdirectory from the argument.
+ func_dirname "$arg" "/" ""
+ xdir="$func_dirname_result"
+
+ if test "$pic_object" != none; then
+ # Prepend the subdirectory the object is found in.
+ pic_object="$xdir$pic_object"
+
+ if test "$prev" = dlfiles; then
+ if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then
+ dlfiles="$dlfiles $pic_object"
+ prev=
+ continue
+ else
+ # If libtool objects are unsupported, then we need to preload.
+ prev=dlprefiles
+ fi
+ fi
+
+ # CHECK ME: I think I busted this. -Ossama
+ if test "$prev" = dlprefiles; then
+ # Preload the old-style object.
+ dlprefiles="$dlprefiles $pic_object"
+ prev=
+ fi
+
+ # A PIC object.
+ func_append libobjs " $pic_object"
+ arg="$pic_object"
+ fi
+
+ # Non-PIC object.
+ if test "$non_pic_object" != none; then
+ # Prepend the subdirectory the object is found in.
+ non_pic_object="$xdir$non_pic_object"
+
+ # A standard non-PIC object
+ func_append non_pic_objects " $non_pic_object"
+ if test -z "$pic_object" || test "$pic_object" = none ; then
+ arg="$non_pic_object"
+ fi
+ else
+ # If the PIC object exists, use it instead.
+ # $xdir was prepended to $pic_object above.
+ non_pic_object="$pic_object"
+ func_append non_pic_objects " $non_pic_object"
+ fi
+ else
+ # Only an error if not doing a dry-run.
+ if $opt_dry_run; then
+ # Extract subdirectory from the argument.
+ func_dirname "$arg" "/" ""
+ xdir="$func_dirname_result"
+
+ func_lo2o "$arg"
+ pic_object=$xdir$objdir/$func_lo2o_result
+ non_pic_object=$xdir$func_lo2o_result
+ func_append libobjs " $pic_object"
+ func_append non_pic_objects " $non_pic_object"
+ else
+ func_fatal_error "\`$arg' is not a valid libtool object"
+ fi
+ fi
+ ;;
+
+ *.$libext)
+ # An archive.
+ deplibs="$deplibs $arg"
+ old_deplibs="$old_deplibs $arg"
+ continue
+ ;;
+
+ *.la)
+ # A libtool-controlled library.
+
+ if test "$prev" = dlfiles; then
+ # This library was specified with -dlopen.
+ dlfiles="$dlfiles $arg"
+ prev=
+ elif test "$prev" = dlprefiles; then
+ # The library was specified with -dlpreopen.
+ dlprefiles="$dlprefiles $arg"
+ prev=
+ else
+ deplibs="$deplibs $arg"
+ fi
+ continue
+ ;;
+
+ # Some other compiler argument.
+ *)
+ # Unknown arguments in both finalize_command and compile_command need
+ # to be aesthetically quoted because they are evaled later.
+ func_quote_for_eval "$arg"
+ arg="$func_quote_for_eval_result"
+ ;;
+ esac # arg
+
+ # Now actually substitute the argument into the commands.
+ if test -n "$arg"; then
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ fi
+ done # argument parsing loop
+
+ test -n "$prev" && \
+ func_fatal_help "the \`$prevarg' option requires an argument"
+
+ if test "$export_dynamic" = yes && test -n "$export_dynamic_flag_spec"; then
+ eval arg=\"$export_dynamic_flag_spec\"
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ fi
+
+ oldlibs=
+ # calculate the name of the file, without its directory
+ func_basename "$output"
+ outputname="$func_basename_result"
+ libobjs_save="$libobjs"
+
+ if test -n "$shlibpath_var"; then
+ # get the directories listed in $shlibpath_var
+ eval shlib_search_path=\`\$ECHO \"X\${$shlibpath_var}\" \| \$Xsed -e \'s/:/ /g\'\`
+ else
+ shlib_search_path=
+ fi
+ eval sys_lib_search_path=\"$sys_lib_search_path_spec\"
+ eval sys_lib_dlsearch_path=\"$sys_lib_dlsearch_path_spec\"
+
+ func_dirname "$output" "/" ""
+ output_objdir="$func_dirname_result$objdir"
+ # Create the object directory.
+ func_mkdir_p "$output_objdir"
+
+ # Determine the type of output
+ case $output in
+ "")
+ func_fatal_help "you must specify an output file"
+ ;;
+ *.$libext) linkmode=oldlib ;;
+ *.lo | *.$objext) linkmode=obj ;;
+ *.la) linkmode=lib ;;
+ *) linkmode=prog ;; # Anything else should be a program.
+ esac
+
+ specialdeplibs=
+
+ libs=
+ # Find all interdependent deplibs by searching for libraries
+ # that are linked more than once (e.g. -la -lb -la)
+ for deplib in $deplibs; do
+ if $opt_duplicate_deps ; then
+ case "$libs " in
+ *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+ esac
+ fi
+ libs="$libs $deplib"
+ done
+
+ if test "$linkmode" = lib; then
+ libs="$predeps $libs $compiler_lib_search_path $postdeps"
+
+ # Compute libraries that are listed more than once in $predeps
+ # $postdeps and mark them as special (i.e., whose duplicates are
+ # not to be eliminated).
+ pre_post_deps=
+ if $opt_duplicate_compiler_generated_deps; then
+ for pre_post_dep in $predeps $postdeps; do
+ case "$pre_post_deps " in
+ *" $pre_post_dep "*) specialdeplibs="$specialdeplibs $pre_post_deps" ;;
+ esac
+ pre_post_deps="$pre_post_deps $pre_post_dep"
+ done
+ fi
+ pre_post_deps=
+ fi
+
+ deplibs=
+ newdependency_libs=
+ newlib_search_path=
+ need_relink=no # whether we're linking any uninstalled libtool libraries
+ notinst_deplibs= # not-installed libtool libraries
+ notinst_path= # paths that contain not-installed libtool libraries
+
+ case $linkmode in
+ lib)
+ passes="conv dlpreopen link"
+ for file in $dlfiles $dlprefiles; do
+ case $file in
+ *.la) ;;
+ *)
+ func_fatal_help "libraries can \`-dlopen' only libtool libraries: $file"
+ ;;
+ esac
+ done
+ ;;
+ prog)
+ compile_deplibs=
+ finalize_deplibs=
+ alldeplibs=no
+ newdlfiles=
+ newdlprefiles=
+ passes="conv scan dlopen dlpreopen link"
+ ;;
+ *) passes="conv"
+ ;;
+ esac
+
+ for pass in $passes; do
+ # The preopen pass in lib mode reverses $deplibs; put it back here
+ # so that -L comes before libs that need it for instance...
+ if test "$linkmode,$pass" = "lib,link"; then
+ ## FIXME: Find the place where the list is rebuilt in the wrong
+ ## order, and fix it there properly
+ tmp_deplibs=
+ for deplib in $deplibs; do
+ tmp_deplibs="$deplib $tmp_deplibs"
+ done
+ deplibs="$tmp_deplibs"
+ fi
+
+ if test "$linkmode,$pass" = "lib,link" ||
+ test "$linkmode,$pass" = "prog,scan"; then
+ libs="$deplibs"
+ deplibs=
+ fi
+ if test "$linkmode" = prog; then
+ case $pass in
+ dlopen) libs="$dlfiles" ;;
+ dlpreopen) libs="$dlprefiles" ;;
+ link)
+ libs="$deplibs %DEPLIBS%"
+ test "X$link_all_deplibs" != Xno && libs="$libs $dependency_libs"
+ ;;
+ esac
+ fi
+ if test "$linkmode,$pass" = "lib,dlpreopen"; then
+ # Collect and forward deplibs of preopened libtool libs
+ for lib in $dlprefiles; do
+ # Ignore non-libtool-libs
+ dependency_libs=
+ case $lib in
+ *.la) func_source "$lib" ;;
+ esac
+
+ # Collect preopened libtool deplibs, except any this library
+ # has declared as weak libs
+ for deplib in $dependency_libs; do
+ deplib_base=`$ECHO "X$deplib" | $Xsed -e "$basename"`
+ case " $weak_libs " in
+ *" $deplib_base "*) ;;
+ *) deplibs="$deplibs $deplib" ;;
+ esac
+ done
+ done
+ libs="$dlprefiles"
+ fi
+ if test "$pass" = dlopen; then
+ # Collect dlpreopened libraries
+ save_deplibs="$deplibs"
+ deplibs=
+ fi
+
+ for deplib in $libs; do
+ lib=
+ found=no
+ case $deplib in
+ -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads)
+ if test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ compiler_flags="$compiler_flags $deplib"
+ if test "$linkmode" = lib ; then
+ case "$new_inherited_linker_flags " in
+ *" $deplib "*) ;;
+ * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;;
+ esac
+ fi
+ fi
+ continue
+ ;;
+ -l*)
+ if test "$linkmode" != lib && test "$linkmode" != prog; then
+ func_warning "\`-l' is ignored for archives/objects"
+ continue
+ fi
+ func_stripname '-l' '' "$deplib"
+ name=$func_stripname_result
+ if test "$linkmode" = lib; then
+ searchdirs="$newlib_search_path $lib_search_path $compiler_lib_search_dirs $sys_lib_search_path $shlib_search_path"
+ else
+ searchdirs="$newlib_search_path $lib_search_path $sys_lib_search_path $shlib_search_path"
+ fi
+ for searchdir in $searchdirs; do
+ for search_ext in .la $std_shrext .so .a; do
+ # Search the libtool library
+ lib="$searchdir/lib${name}${search_ext}"
+ if test -f "$lib"; then
+ if test "$search_ext" = ".la"; then
+ found=yes
+ else
+ found=no
+ fi
+ break 2
+ fi
+ done
+ done
+ if test "$found" != yes; then
+ # deplib doesn't seem to be a libtool library
+ if test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ deplibs="$deplib $deplibs"
+ test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs"
+ fi
+ continue
+ else # deplib is a libtool library
+ # If $allow_libtool_libs_with_static_runtimes && $deplib is a stdlib,
+ # We need to do some special things here, and not later.
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $deplib "*)
+ if func_lalib_p "$lib"; then
+ library_names=
+ old_library=
+ func_source "$lib"
+ for l in $old_library $library_names; do
+ ll="$l"
+ done
+ if test "X$ll" = "X$old_library" ; then # only static version available
+ found=no
+ func_dirname "$lib" "" "."
+ ladir="$func_dirname_result"
+ lib=$ladir/$old_library
+ if test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ deplibs="$deplib $deplibs"
+ test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs"
+ fi
+ continue
+ fi
+ fi
+ ;;
+ *) ;;
+ esac
+ fi
+ fi
+ ;; # -l
+ *.ltframework)
+ if test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ deplibs="$deplib $deplibs"
+ if test "$linkmode" = lib ; then
+ case "$new_inherited_linker_flags " in
+ *" $deplib "*) ;;
+ * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;;
+ esac
+ fi
+ fi
+ continue
+ ;;
+ -L*)
+ case $linkmode in
+ lib)
+ deplibs="$deplib $deplibs"
+ test "$pass" = conv && continue
+ newdependency_libs="$deplib $newdependency_libs"
+ func_stripname '-L' '' "$deplib"
+ newlib_search_path="$newlib_search_path $func_stripname_result"
+ ;;
+ prog)
+ if test "$pass" = conv; then
+ deplibs="$deplib $deplibs"
+ continue
+ fi
+ if test "$pass" = scan; then
+ deplibs="$deplib $deplibs"
+ else
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ fi
+ func_stripname '-L' '' "$deplib"
+ newlib_search_path="$newlib_search_path $func_stripname_result"
+ ;;
+ *)
+ func_warning "\`-L' is ignored for archives/objects"
+ ;;
+ esac # linkmode
+ continue
+ ;; # -L
+ -R*)
+ if test "$pass" = link; then
+ func_stripname '-R' '' "$deplib"
+ dir=$func_stripname_result
+ # Make sure the xrpath contains only unique directories.
+ case "$xrpath " in
+ *" $dir "*) ;;
+ *) xrpath="$xrpath $dir" ;;
+ esac
+ fi
+ deplibs="$deplib $deplibs"
+ continue
+ ;;
+ *.la) lib="$deplib" ;;
+ *.$libext)
+ if test "$pass" = conv; then
+ deplibs="$deplib $deplibs"
+ continue
+ fi
+ case $linkmode in
+ lib)
+ # Linking convenience modules into shared libraries is allowed,
+ # but linking other static libraries is non-portable.
+ case " $dlpreconveniencelibs " in
+ *" $deplib "*) ;;
+ *)
+ valid_a_lib=no
+ case $deplibs_check_method in
+ match_pattern*)
+ set dummy $deplibs_check_method; shift
+ match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"`
+ if eval "\$ECHO \"X$deplib\"" 2>/dev/null | $Xsed -e 10q \
+ | $EGREP "$match_pattern_regex" > /dev/null; then
+ valid_a_lib=yes
+ fi
+ ;;
+ pass_all)
+ valid_a_lib=yes
+ ;;
+ esac
+ if test "$valid_a_lib" != yes; then
+ $ECHO
+ $ECHO "*** Warning: Trying to link with static lib archive $deplib."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have"
+ $ECHO "*** because the file extensions .$libext of this argument makes me believe"
+ $ECHO "*** that it is just a static archive that I should not use here."
+ else
+ $ECHO
+ $ECHO "*** Warning: Linking the shared library $output against the"
+ $ECHO "*** static library $deplib is not portable!"
+ deplibs="$deplib $deplibs"
+ fi
+ ;;
+ esac
+ continue
+ ;;
+ prog)
+ if test "$pass" != link; then
+ deplibs="$deplib $deplibs"
+ else
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ fi
+ continue
+ ;;
+ esac # linkmode
+ ;; # *.$libext
+ *.lo | *.$objext)
+ if test "$pass" = conv; then
+ deplibs="$deplib $deplibs"
+ elif test "$linkmode" = prog; then
+ if test "$pass" = dlpreopen || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then
+ # If there is no dlopen support or we're linking statically,
+ # we need to preload.
+ newdlprefiles="$newdlprefiles $deplib"
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ newdlfiles="$newdlfiles $deplib"
+ fi
+ fi
+ continue
+ ;;
+ %DEPLIBS%)
+ alldeplibs=yes
+ continue
+ ;;
+ esac # case $deplib
+
+ if test "$found" = yes || test -f "$lib"; then :
+ else
+ func_fatal_error "cannot find the library \`$lib' or unhandled argument \`$deplib'"
+ fi
+
+ # Check to see that this really is a libtool archive.
+ func_lalib_unsafe_p "$lib" \
+ || func_fatal_error "\`$lib' is not a valid libtool archive"
+
+ func_dirname "$lib" "" "."
+ ladir="$func_dirname_result"
+
+ dlname=
+ dlopen=
+ dlpreopen=
+ libdir=
+ library_names=
+ old_library=
+ inherited_linker_flags=
+ # If the library was installed with an old release of libtool,
+ # it will not redefine variables installed, or shouldnotlink
+ installed=yes
+ shouldnotlink=no
+ avoidtemprpath=
+
+
+ # Read the .la file
+ func_source "$lib"
+
+ # Convert "-framework foo" to "foo.ltframework"
+ if test -n "$inherited_linker_flags"; then
+ tmp_inherited_linker_flags=`$ECHO "X$inherited_linker_flags" | $Xsed -e 's/-framework \([^ $]*\)/\1.ltframework/g'`
+ for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
+ case " $new_inherited_linker_flags " in
+ *" $tmp_inherited_linker_flag "*) ;;
+ *) new_inherited_linker_flags="$new_inherited_linker_flags $tmp_inherited_linker_flag";;
+ esac
+ done
+ fi
+ dependency_libs=`$ECHO "X $dependency_libs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ if test "$linkmode,$pass" = "lib,link" ||
+ test "$linkmode,$pass" = "prog,scan" ||
+ { test "$linkmode" != prog && test "$linkmode" != lib; }; then
+ test -n "$dlopen" && dlfiles="$dlfiles $dlopen"
+ test -n "$dlpreopen" && dlprefiles="$dlprefiles $dlpreopen"
+ fi
+
+ if test "$pass" = conv; then
+ # Only check for convenience libraries
+ deplibs="$lib $deplibs"
+ if test -z "$libdir"; then
+ if test -z "$old_library"; then
+ func_fatal_error "cannot find name of link library for \`$lib'"
+ fi
+ # It is a libtool convenience library, so add in its objects.
+ convenience="$convenience $ladir/$objdir/$old_library"
+ old_convenience="$old_convenience $ladir/$objdir/$old_library"
+ tmp_libs=
+ for deplib in $dependency_libs; do
+ deplibs="$deplib $deplibs"
+ if $opt_duplicate_deps ; then
+ case "$tmp_libs " in
+ *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+ esac
+ fi
+ tmp_libs="$tmp_libs $deplib"
+ done
+ elif test "$linkmode" != prog && test "$linkmode" != lib; then
+ func_fatal_error "\`$lib' is not a convenience library"
+ fi
+ continue
+ fi # $pass = conv
+
+
+ # Get the name of the library we link against.
+ linklib=
+ for l in $old_library $library_names; do
+ linklib="$l"
+ done
+ if test -z "$linklib"; then
+ func_fatal_error "cannot find name of link library for \`$lib'"
+ fi
+
+ # This library was specified with -dlopen.
+ if test "$pass" = dlopen; then
+ if test -z "$libdir"; then
+ func_fatal_error "cannot -dlopen a convenience library: \`$lib'"
+ fi
+ if test -z "$dlname" ||
+ test "$dlopen_support" != yes ||
+ test "$build_libtool_libs" = no; then
+ # If there is no dlname, no dlopen support or we're linking
+ # statically, we need to preload. We also need to preload any
+ # dependent libraries so libltdl's deplib preloader doesn't
+ # bomb out in the load deplibs phase.
+ dlprefiles="$dlprefiles $lib $dependency_libs"
+ else
+ newdlfiles="$newdlfiles $lib"
+ fi
+ continue
+ fi # $pass = dlopen
+
+ # We need an absolute path.
+ case $ladir in
+ [\\/]* | [A-Za-z]:[\\/]*) abs_ladir="$ladir" ;;
+ *)
+ abs_ladir=`cd "$ladir" && pwd`
+ if test -z "$abs_ladir"; then
+ func_warning "cannot determine absolute directory name of \`$ladir'"
+ func_warning "passing it literally to the linker, although it might fail"
+ abs_ladir="$ladir"
+ fi
+ ;;
+ esac
+ func_basename "$lib"
+ laname="$func_basename_result"
+
+ # Find the relevant object directory and library name.
+ if test "X$installed" = Xyes; then
+ if test ! -f "$libdir/$linklib" && test -f "$abs_ladir/$linklib"; then
+ func_warning "library \`$lib' was moved."
+ dir="$ladir"
+ absdir="$abs_ladir"
+ libdir="$abs_ladir"
+ else
+ dir="$libdir"
+ absdir="$libdir"
+ fi
+ test "X$hardcode_automatic" = Xyes && avoidtemprpath=yes
+ else
+ if test ! -f "$ladir/$objdir/$linklib" && test -f "$abs_ladir/$linklib"; then
+ dir="$ladir"
+ absdir="$abs_ladir"
+ # Remove this search path later
+ notinst_path="$notinst_path $abs_ladir"
+ else
+ dir="$ladir/$objdir"
+ absdir="$abs_ladir/$objdir"
+ # Remove this search path later
+ notinst_path="$notinst_path $abs_ladir"
+ fi
+ fi # $installed = yes
+ func_stripname 'lib' '.la' "$laname"
+ name=$func_stripname_result
+
+ # This library was specified with -dlpreopen.
+ if test "$pass" = dlpreopen; then
+ if test -z "$libdir" && test "$linkmode" = prog; then
+ func_fatal_error "only libraries may -dlpreopen a convenience library: \`$lib'"
+ fi
+ # Prefer using a static library (so that no silly _DYNAMIC symbols
+ # are required to link).
+ if test -n "$old_library"; then
+ newdlprefiles="$newdlprefiles $dir/$old_library"
+ # Keep a list of preopened convenience libraries to check
+ # that they are being used correctly in the link pass.
+ test -z "$libdir" && \
+ dlpreconveniencelibs="$dlpreconveniencelibs $dir/$old_library"
+ # Otherwise, use the dlname, so that lt_dlopen finds it.
+ elif test -n "$dlname"; then
+ newdlprefiles="$newdlprefiles $dir/$dlname"
+ else
+ newdlprefiles="$newdlprefiles $dir/$linklib"
+ fi
+ fi # $pass = dlpreopen
+
+ if test -z "$libdir"; then
+ # Link the convenience library
+ if test "$linkmode" = lib; then
+ deplibs="$dir/$old_library $deplibs"
+ elif test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$dir/$old_library $compile_deplibs"
+ finalize_deplibs="$dir/$old_library $finalize_deplibs"
+ else
+ deplibs="$lib $deplibs" # used for prog,scan pass
+ fi
+ continue
+ fi
+
+
+ if test "$linkmode" = prog && test "$pass" != link; then
+ newlib_search_path="$newlib_search_path $ladir"
+ deplibs="$lib $deplibs"
+
+ linkalldeplibs=no
+ if test "$link_all_deplibs" != no || test -z "$library_names" ||
+ test "$build_libtool_libs" = no; then
+ linkalldeplibs=yes
+ fi
+
+ tmp_libs=
+ for deplib in $dependency_libs; do
+ case $deplib in
+ -L*) func_stripname '-L' '' "$deplib"
+ newlib_search_path="$newlib_search_path $func_stripname_result"
+ ;;
+ esac
+ # Need to link against all dependency_libs?
+ if test "$linkalldeplibs" = yes; then
+ deplibs="$deplib $deplibs"
+ else
+ # Need to hardcode shared library paths
+ # or/and link against static libraries
+ newdependency_libs="$deplib $newdependency_libs"
+ fi
+ if $opt_duplicate_deps ; then
+ case "$tmp_libs " in
+ *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+ esac
+ fi
+ tmp_libs="$tmp_libs $deplib"
+ done # for deplib
+ continue
+ fi # $linkmode = prog...
+
+ if test "$linkmode,$pass" = "prog,link"; then
+ if test -n "$library_names" &&
+ { { test "$prefer_static_libs" = no ||
+ test "$prefer_static_libs,$installed" = "built,yes"; } ||
+ test -z "$old_library"; }; then
+ # We need to hardcode the library path
+ if test -n "$shlibpath_var" && test -z "$avoidtemprpath" ; then
+ # Make sure the rpath contains only unique directories.
+ case "$temp_rpath:" in
+ *"$absdir:"*) ;;
+ *) temp_rpath="$temp_rpath$absdir:" ;;
+ esac
+ fi
+
+ # Hardcode the library path.
+ # Skip directories that are in the system default run-time
+ # search path.
+ case " $sys_lib_dlsearch_path " in
+ *" $absdir "*) ;;
+ *)
+ case "$compile_rpath " in
+ *" $absdir "*) ;;
+ *) compile_rpath="$compile_rpath $absdir"
+ esac
+ ;;
+ esac
+ case " $sys_lib_dlsearch_path " in
+ *" $libdir "*) ;;
+ *)
+ case "$finalize_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_rpath="$finalize_rpath $libdir"
+ esac
+ ;;
+ esac
+ fi # $linkmode,$pass = prog,link...
+
+ if test "$alldeplibs" = yes &&
+ { test "$deplibs_check_method" = pass_all ||
+ { test "$build_libtool_libs" = yes &&
+ test -n "$library_names"; }; }; then
+ # We only need to search for static libraries
+ continue
+ fi
+ fi
+
+ link_static=no # Whether the deplib will be linked statically
+ use_static_libs=$prefer_static_libs
+ if test "$use_static_libs" = built && test "$installed" = yes; then
+ use_static_libs=no
+ fi
+ if test -n "$library_names" &&
+ { test "$use_static_libs" = no || test -z "$old_library"; }; then
+ case $host in
+ *cygwin* | *mingw* | *cegcc*)
+ # No point in relinking DLLs because paths are not encoded
+ notinst_deplibs="$notinst_deplibs $lib"
+ need_relink=no
+ ;;
+ *)
+ if test "$installed" = no; then
+ notinst_deplibs="$notinst_deplibs $lib"
+ need_relink=yes
+ fi
+ ;;
+ esac
+ # This is a shared library
+
+ # Warn about portability, can't link against -module's on some
+ # systems (darwin). Don't bleat about dlopened modules though!
+ dlopenmodule=""
+ for dlpremoduletest in $dlprefiles; do
+ if test "X$dlpremoduletest" = "X$lib"; then
+ dlopenmodule="$dlpremoduletest"
+ break
+ fi
+ done
+ if test -z "$dlopenmodule" && test "$shouldnotlink" = yes && test "$pass" = link; then
+ $ECHO
+ if test "$linkmode" = prog; then
+ $ECHO "*** Warning: Linking the executable $output against the loadable module"
+ else
+ $ECHO "*** Warning: Linking the shared library $output against the loadable module"
+ fi
+ $ECHO "*** $linklib is not portable!"
+ fi
+ if test "$linkmode" = lib &&
+ test "$hardcode_into_libs" = yes; then
+ # Hardcode the library path.
+ # Skip directories that are in the system default run-time
+ # search path.
+ case " $sys_lib_dlsearch_path " in
+ *" $absdir "*) ;;
+ *)
+ case "$compile_rpath " in
+ *" $absdir "*) ;;
+ *) compile_rpath="$compile_rpath $absdir"
+ esac
+ ;;
+ esac
+ case " $sys_lib_dlsearch_path " in
+ *" $libdir "*) ;;
+ *)
+ case "$finalize_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_rpath="$finalize_rpath $libdir"
+ esac
+ ;;
+ esac
+ fi
+
+ if test -n "$old_archive_from_expsyms_cmds"; then
+ # figure out the soname
+ set dummy $library_names
+ shift
+ realname="$1"
+ shift
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ # use dlname if we got it. it's perfectly good, no?
+ if test -n "$dlname"; then
+ soname="$dlname"
+ elif test -n "$soname_spec"; then
+ # bleh windows
+ case $host in
+ *cygwin* | mingw* | *cegcc*)
+ func_arith $current - $age
+ major=$func_arith_result
+ versuffix="-$major"
+ ;;
+ esac
+ eval soname=\"$soname_spec\"
+ else
+ soname="$realname"
+ fi
+
+ # Make a new name for the extract_expsyms_cmds to use
+ soroot="$soname"
+ func_basename "$soroot"
+ soname="$func_basename_result"
+ func_stripname 'lib' '.dll' "$soname"
+ newlib=libimp-$func_stripname_result.a
+
+ # If the library has no export list, then create one now
+ if test -f "$output_objdir/$soname-def"; then :
+ else
+ func_verbose "extracting exported symbol list from \`$soname'"
+ func_execute_cmds "$extract_expsyms_cmds" 'exit $?'
+ fi
+
+ # Create $newlib
+ if test -f "$output_objdir/$newlib"; then :; else
+ func_verbose "generating import library for \`$soname'"
+ func_execute_cmds "$old_archive_from_expsyms_cmds" 'exit $?'
+ fi
+ # make sure the library variables are pointing to the new library
+ dir=$output_objdir
+ linklib=$newlib
+ fi # test -n "$old_archive_from_expsyms_cmds"
+
+ if test "$linkmode" = prog || test "$mode" != relink; then
+ add_shlibpath=
+ add_dir=
+ add=
+ lib_linked=yes
+ case $hardcode_action in
+ immediate | unsupported)
+ if test "$hardcode_direct" = no; then
+ add="$dir/$linklib"
+ case $host in
+ *-*-sco3.2v5.0.[024]*) add_dir="-L$dir" ;;
+ *-*-sysv4*uw2*) add_dir="-L$dir" ;;
+ *-*-sysv5OpenUNIX* | *-*-sysv5UnixWare7.[01].[10]* | \
+ *-*-unixware7*) add_dir="-L$dir" ;;
+ *-*-darwin* )
+ # if the lib is a (non-dlopened) module then we can not
+ # link against it, someone is ignoring the earlier warnings
+ if /usr/bin/file -L $add 2> /dev/null |
+ $GREP ": [^:]* bundle" >/dev/null ; then
+ if test "X$dlopenmodule" != "X$lib"; then
+ $ECHO "*** Warning: lib $linklib is a module, not a shared library"
+ if test -z "$old_library" ; then
+ $ECHO
+ $ECHO "*** And there doesn't seem to be a static archive available"
+ $ECHO "*** The link will probably fail, sorry"
+ else
+ add="$dir/$old_library"
+ fi
+ elif test -n "$old_library"; then
+ add="$dir/$old_library"
+ fi
+ fi
+ esac
+ elif test "$hardcode_minus_L" = no; then
+ case $host in
+ *-*-sunos*) add_shlibpath="$dir" ;;
+ esac
+ add_dir="-L$dir"
+ add="-l$name"
+ elif test "$hardcode_shlibpath_var" = no; then
+ add_shlibpath="$dir"
+ add="-l$name"
+ else
+ lib_linked=no
+ fi
+ ;;
+ relink)
+ if test "$hardcode_direct" = yes &&
+ test "$hardcode_direct_absolute" = no; then
+ add="$dir/$linklib"
+ elif test "$hardcode_minus_L" = yes; then
+ add_dir="-L$dir"
+ # Try looking first in the location we're being installed to.
+ if test -n "$inst_prefix_dir"; then
+ case $libdir in
+ [\\/]*)
+ add_dir="$add_dir -L$inst_prefix_dir$libdir"
+ ;;
+ esac
+ fi
+ add="-l$name"
+ elif test "$hardcode_shlibpath_var" = yes; then
+ add_shlibpath="$dir"
+ add="-l$name"
+ else
+ lib_linked=no
+ fi
+ ;;
+ *) lib_linked=no ;;
+ esac
+
+ if test "$lib_linked" != yes; then
+ func_fatal_configuration "unsupported hardcode properties"
+ fi
+
+ if test -n "$add_shlibpath"; then
+ case :$compile_shlibpath: in
+ *":$add_shlibpath:"*) ;;
+ *) compile_shlibpath="$compile_shlibpath$add_shlibpath:" ;;
+ esac
+ fi
+ if test "$linkmode" = prog; then
+ test -n "$add_dir" && compile_deplibs="$add_dir $compile_deplibs"
+ test -n "$add" && compile_deplibs="$add $compile_deplibs"
+ else
+ test -n "$add_dir" && deplibs="$add_dir $deplibs"
+ test -n "$add" && deplibs="$add $deplibs"
+ if test "$hardcode_direct" != yes &&
+ test "$hardcode_minus_L" != yes &&
+ test "$hardcode_shlibpath_var" = yes; then
+ case :$finalize_shlibpath: in
+ *":$libdir:"*) ;;
+ *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;;
+ esac
+ fi
+ fi
+ fi
+
+ if test "$linkmode" = prog || test "$mode" = relink; then
+ add_shlibpath=
+ add_dir=
+ add=
+ # Finalize command for both is simple: just hardcode it.
+ if test "$hardcode_direct" = yes &&
+ test "$hardcode_direct_absolute" = no; then
+ add="$libdir/$linklib"
+ elif test "$hardcode_minus_L" = yes; then
+ add_dir="-L$libdir"
+ add="-l$name"
+ elif test "$hardcode_shlibpath_var" = yes; then
+ case :$finalize_shlibpath: in
+ *":$libdir:"*) ;;
+ *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;;
+ esac
+ add="-l$name"
+ elif test "$hardcode_automatic" = yes; then
+ if test -n "$inst_prefix_dir" &&
+ test -f "$inst_prefix_dir$libdir/$linklib" ; then
+ add="$inst_prefix_dir$libdir/$linklib"
+ else
+ add="$libdir/$linklib"
+ fi
+ else
+ # We cannot seem to hardcode it, guess we'll fake it.
+ add_dir="-L$libdir"
+ # Try looking first in the location we're being installed to.
+ if test -n "$inst_prefix_dir"; then
+ case $libdir in
+ [\\/]*)
+ add_dir="$add_dir -L$inst_prefix_dir$libdir"
+ ;;
+ esac
+ fi
+ add="-l$name"
+ fi
+
+ if test "$linkmode" = prog; then
+ test -n "$add_dir" && finalize_deplibs="$add_dir $finalize_deplibs"
+ test -n "$add" && finalize_deplibs="$add $finalize_deplibs"
+ else
+ test -n "$add_dir" && deplibs="$add_dir $deplibs"
+ test -n "$add" && deplibs="$add $deplibs"
+ fi
+ fi
+ elif test "$linkmode" = prog; then
+ # Here we assume that one of hardcode_direct or hardcode_minus_L
+ # is not unsupported. This is valid on all known static and
+ # shared platforms.
+ if test "$hardcode_direct" != unsupported; then
+ test -n "$old_library" && linklib="$old_library"
+ compile_deplibs="$dir/$linklib $compile_deplibs"
+ finalize_deplibs="$dir/$linklib $finalize_deplibs"
+ else
+ compile_deplibs="-l$name -L$dir $compile_deplibs"
+ finalize_deplibs="-l$name -L$dir $finalize_deplibs"
+ fi
+ elif test "$build_libtool_libs" = yes; then
+ # Not a shared library
+ if test "$deplibs_check_method" != pass_all; then
+ # We're trying link a shared library against a static one
+ # but the system doesn't support it.
+
+ # Just print a warning and add the library to dependency_libs so
+ # that the program can be linked against the static library.
+ $ECHO
+ $ECHO "*** Warning: This system can not link to static lib archive $lib."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have."
+ if test "$module" = yes; then
+ $ECHO "*** But as you try to build a module library, libtool will still create "
+ $ECHO "*** a static module, that should work as long as the dlopening application"
+ $ECHO "*** is linked with the -dlopen flag to resolve symbols at runtime."
+ if test -z "$global_symbol_pipe"; then
+ $ECHO
+ $ECHO "*** However, this would only work if libtool was able to extract symbol"
+ $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could"
+ $ECHO "*** not find such a program. So, this module is probably useless."
+ $ECHO "*** \`nm' from GNU binutils and a full rebuild may help."
+ fi
+ if test "$build_old_libs" = no; then
+ build_libtool_libs=module
+ build_old_libs=yes
+ else
+ build_libtool_libs=no
+ fi
+ fi
+ else
+ deplibs="$dir/$old_library $deplibs"
+ link_static=yes
+ fi
+ fi # link shared/static library?
+
+ if test "$linkmode" = lib; then
+ if test -n "$dependency_libs" &&
+ { test "$hardcode_into_libs" != yes ||
+ test "$build_old_libs" = yes ||
+ test "$link_static" = yes; }; then
+ # Extract -R from dependency_libs
+ temp_deplibs=
+ for libdir in $dependency_libs; do
+ case $libdir in
+ -R*) func_stripname '-R' '' "$libdir"
+ temp_xrpath=$func_stripname_result
+ case " $xrpath " in
+ *" $temp_xrpath "*) ;;
+ *) xrpath="$xrpath $temp_xrpath";;
+ esac;;
+ *) temp_deplibs="$temp_deplibs $libdir";;
+ esac
+ done
+ dependency_libs="$temp_deplibs"
+ fi
+
+ newlib_search_path="$newlib_search_path $absdir"
+ # Link against this library
+ test "$link_static" = no && newdependency_libs="$abs_ladir/$laname $newdependency_libs"
+ # ... and its dependency_libs
+ tmp_libs=
+ for deplib in $dependency_libs; do
+ newdependency_libs="$deplib $newdependency_libs"
+ if $opt_duplicate_deps ; then
+ case "$tmp_libs " in
+ *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+ esac
+ fi
+ tmp_libs="$tmp_libs $deplib"
+ done
+
+ if test "$link_all_deplibs" != no; then
+ # Add the search paths of all dependency libraries
+ for deplib in $dependency_libs; do
+ path=
+ case $deplib in
+ -L*) path="$deplib" ;;
+ *.la)
+ func_dirname "$deplib" "" "."
+ dir="$func_dirname_result"
+ # We need an absolute path.
+ case $dir in
+ [\\/]* | [A-Za-z]:[\\/]*) absdir="$dir" ;;
+ *)
+ absdir=`cd "$dir" && pwd`
+ if test -z "$absdir"; then
+ func_warning "cannot determine absolute directory name of \`$dir'"
+ absdir="$dir"
+ fi
+ ;;
+ esac
+ if $GREP "^installed=no" $deplib > /dev/null; then
+ case $host in
+ *-*-darwin*)
+ depdepl=
+ eval deplibrary_names=`${SED} -n -e 's/^library_names=\(.*\)$/\1/p' $deplib`
+ if test -n "$deplibrary_names" ; then
+ for tmp in $deplibrary_names ; do
+ depdepl=$tmp
+ done
+ if test -f "$absdir/$objdir/$depdepl" ; then
+ depdepl="$absdir/$objdir/$depdepl"
+ darwin_install_name=`${OTOOL} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'`
+ if test -z "$darwin_install_name"; then
+ darwin_install_name=`${OTOOL64} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'`
+ fi
+ compiler_flags="$compiler_flags ${wl}-dylib_file ${wl}${darwin_install_name}:${depdepl}"
+ linker_flags="$linker_flags -dylib_file ${darwin_install_name}:${depdepl}"
+ path=
+ fi
+ fi
+ ;;
+ *)
+ path="-L$absdir/$objdir"
+ ;;
+ esac
+ else
+ eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib`
+ test -z "$libdir" && \
+ func_fatal_error "\`$deplib' is not a valid libtool archive"
+ test "$absdir" != "$libdir" && \
+ func_warning "\`$deplib' seems to be moved"
+
+ path="-L$absdir"
+ fi
+ ;;
+ esac
+ case " $deplibs " in
+ *" $path "*) ;;
+ *) deplibs="$path $deplibs" ;;
+ esac
+ done
+ fi # link_all_deplibs != no
+ fi # linkmode = lib
+ done # for deplib in $libs
+ if test "$pass" = link; then
+ if test "$linkmode" = "prog"; then
+ compile_deplibs="$new_inherited_linker_flags $compile_deplibs"
+ finalize_deplibs="$new_inherited_linker_flags $finalize_deplibs"
+ else
+ compiler_flags="$compiler_flags "`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ fi
+ fi
+ dependency_libs="$newdependency_libs"
+ if test "$pass" = dlpreopen; then
+ # Link the dlpreopened libraries before other libraries
+ for deplib in $save_deplibs; do
+ deplibs="$deplib $deplibs"
+ done
+ fi
+ if test "$pass" != dlopen; then
+ if test "$pass" != conv; then
+ # Make sure lib_search_path contains only unique directories.
+ lib_search_path=
+ for dir in $newlib_search_path; do
+ case "$lib_search_path " in
+ *" $dir "*) ;;
+ *) lib_search_path="$lib_search_path $dir" ;;
+ esac
+ done
+ newlib_search_path=
+ fi
+
+ if test "$linkmode,$pass" != "prog,link"; then
+ vars="deplibs"
+ else
+ vars="compile_deplibs finalize_deplibs"
+ fi
+ for var in $vars dependency_libs; do
+ # Add libraries to $var in reverse order
+ eval tmp_libs=\"\$$var\"
+ new_libs=
+ for deplib in $tmp_libs; do
+ # FIXME: Pedantically, this is the right thing to do, so
+ # that some nasty dependency loop isn't accidentally
+ # broken:
+ #new_libs="$deplib $new_libs"
+ # Pragmatically, this seems to cause very few problems in
+ # practice:
+ case $deplib in
+ -L*) new_libs="$deplib $new_libs" ;;
+ -R*) ;;
+ *)
+ # And here is the reason: when a library appears more
+ # than once as an explicit dependence of a library, or
+ # is implicitly linked in more than once by the
+ # compiler, it is considered special, and multiple
+ # occurrences thereof are not removed. Compare this
+ # with having the same library being listed as a
+ # dependency of multiple other libraries: in this case,
+ # we know (pedantically, we assume) the library does not
+ # need to be listed more than once, so we keep only the
+ # last copy. This is not always right, but it is rare
+ # enough that we require users that really mean to play
+ # such unportable linking tricks to link the library
+ # using -Wl,-lname, so that libtool does not consider it
+ # for duplicate removal.
+ case " $specialdeplibs " in
+ *" $deplib "*) new_libs="$deplib $new_libs" ;;
+ *)
+ case " $new_libs " in
+ *" $deplib "*) ;;
+ *) new_libs="$deplib $new_libs" ;;
+ esac
+ ;;
+ esac
+ ;;
+ esac
+ done
+ tmp_libs=
+ for deplib in $new_libs; do
+ case $deplib in
+ -L*)
+ case " $tmp_libs " in
+ *" $deplib "*) ;;
+ *) tmp_libs="$tmp_libs $deplib" ;;
+ esac
+ ;;
+ *) tmp_libs="$tmp_libs $deplib" ;;
+ esac
+ done
+ eval $var=\"$tmp_libs\"
+ done # for var
+ fi
+ # Last step: remove runtime libs from dependency_libs
+ # (they stay in deplibs)
+ tmp_libs=
+ for i in $dependency_libs ; do
+ case " $predeps $postdeps $compiler_lib_search_path " in
+ *" $i "*)
+ i=""
+ ;;
+ esac
+ if test -n "$i" ; then
+ tmp_libs="$tmp_libs $i"
+ fi
+ done
+ dependency_libs=$tmp_libs
+ done # for pass
+ if test "$linkmode" = prog; then
+ dlfiles="$newdlfiles"
+ fi
+ if test "$linkmode" = prog || test "$linkmode" = lib; then
+ dlprefiles="$newdlprefiles"
+ fi
+
+ case $linkmode in
+ oldlib)
+ if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
+ func_warning "\`-dlopen' is ignored for archives"
+ fi
+
+ case " $deplibs" in
+ *\ -l* | *\ -L*)
+ func_warning "\`-l' and \`-L' are ignored for archives" ;;
+ esac
+
+ test -n "$rpath" && \
+ func_warning "\`-rpath' is ignored for archives"
+
+ test -n "$xrpath" && \
+ func_warning "\`-R' is ignored for archives"
+
+ test -n "$vinfo" && \
+ func_warning "\`-version-info/-version-number' is ignored for archives"
+
+ test -n "$release" && \
+ func_warning "\`-release' is ignored for archives"
+
+ test -n "$export_symbols$export_symbols_regex" && \
+ func_warning "\`-export-symbols' is ignored for archives"
+
+ # Now set the variables for building old libraries.
+ build_libtool_libs=no
+ oldlibs="$output"
+ objs="$objs$old_deplibs"
+ ;;
+
+ lib)
+ # Make sure we only generate libraries of the form `libNAME.la'.
+ case $outputname in
+ lib*)
+ func_stripname 'lib' '.la' "$outputname"
+ name=$func_stripname_result
+ eval shared_ext=\"$shrext_cmds\"
+ eval libname=\"$libname_spec\"
+ ;;
+ *)
+ test "$module" = no && \
+ func_fatal_help "libtool library \`$output' must begin with \`lib'"
+
+ if test "$need_lib_prefix" != no; then
+ # Add the "lib" prefix for modules if required
+ func_stripname '' '.la' "$outputname"
+ name=$func_stripname_result
+ eval shared_ext=\"$shrext_cmds\"
+ eval libname=\"$libname_spec\"
+ else
+ func_stripname '' '.la' "$outputname"
+ libname=$func_stripname_result
+ fi
+ ;;
+ esac
+
+ if test -n "$objs"; then
+ if test "$deplibs_check_method" != pass_all; then
+ func_fatal_error "cannot build libtool library \`$output' from non-libtool objects on this host:$objs"
+ else
+ $ECHO
+ $ECHO "*** Warning: Linking the shared library $output against the non-libtool"
+ $ECHO "*** objects $objs is not portable!"
+ libobjs="$libobjs $objs"
+ fi
+ fi
+
+ test "$dlself" != no && \
+ func_warning "\`-dlopen self' is ignored for libtool libraries"
+
+ set dummy $rpath
+ shift
+ test "$#" -gt 1 && \
+ func_warning "ignoring multiple \`-rpath's for a libtool library"
+
+ install_libdir="$1"
+
+ oldlibs=
+ if test -z "$rpath"; then
+ if test "$build_libtool_libs" = yes; then
+ # Building a libtool convenience library.
+ # Some compilers have problems with a `.al' extension so
+ # convenience libraries should have the same extension an
+ # archive normally would.
+ oldlibs="$output_objdir/$libname.$libext $oldlibs"
+ build_libtool_libs=convenience
+ build_old_libs=yes
+ fi
+
+ test -n "$vinfo" && \
+ func_warning "\`-version-info/-version-number' is ignored for convenience libraries"
+
+ test -n "$release" && \
+ func_warning "\`-release' is ignored for convenience libraries"
+ else
+
+ # Parse the version information argument.
+ save_ifs="$IFS"; IFS=':'
+ set dummy $vinfo 0 0 0
+ shift
+ IFS="$save_ifs"
+
+ test -n "$7" && \
+ func_fatal_help "too many parameters to \`-version-info'"
+
+ # convert absolute version numbers to libtool ages
+ # this retains compatibility with .la files and attempts
+ # to make the code below a bit more comprehensible
+
+ case $vinfo_number in
+ yes)
+ number_major="$1"
+ number_minor="$2"
+ number_revision="$3"
+ #
+ # There are really only two kinds -- those that
+ # use the current revision as the major version
+ # and those that subtract age and use age as
+ # a minor version. But, then there is irix
+ # which has an extra 1 added just for fun
+ #
+ case $version_type in
+ darwin|linux|osf|windows|none)
+ func_arith $number_major + $number_minor
+ current=$func_arith_result
+ age="$number_minor"
+ revision="$number_revision"
+ ;;
+ freebsd-aout|freebsd-elf|sunos)
+ current="$number_major"
+ revision="$number_minor"
+ age="0"
+ ;;
+ irix|nonstopux)
+ func_arith $number_major + $number_minor
+ current=$func_arith_result
+ age="$number_minor"
+ revision="$number_minor"
+ lt_irix_increment=no
+ ;;
+ *)
+ func_fatal_configuration "$modename: unknown library version type \`$version_type'"
+ ;;
+ esac
+ ;;
+ no)
+ current="$1"
+ revision="$2"
+ age="$3"
+ ;;
+ esac
+
+ # Check that each of the things are valid numbers.
+ case $current in
+ 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
+ *)
+ func_error "CURRENT \`$current' must be a nonnegative integer"
+ func_fatal_error "\`$vinfo' is not valid version information"
+ ;;
+ esac
+
+ case $revision in
+ 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
+ *)
+ func_error "REVISION \`$revision' must be a nonnegative integer"
+ func_fatal_error "\`$vinfo' is not valid version information"
+ ;;
+ esac
+
+ case $age in
+ 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
+ *)
+ func_error "AGE \`$age' must be a nonnegative integer"
+ func_fatal_error "\`$vinfo' is not valid version information"
+ ;;
+ esac
+
+ if test "$age" -gt "$current"; then
+ func_error "AGE \`$age' is greater than the current interface number \`$current'"
+ func_fatal_error "\`$vinfo' is not valid version information"
+ fi
+
+ # Calculate the version variables.
+ major=
+ versuffix=
+ verstring=
+ case $version_type in
+ none) ;;
+
+ darwin)
+ # Like Linux, but with the current version available in
+ # verstring for coding it into the library header
+ func_arith $current - $age
+ major=.$func_arith_result
+ versuffix="$major.$age.$revision"
+ # Darwin ld doesn't like 0 for these options...
+ func_arith $current + 1
+ minor_current=$func_arith_result
+ xlcverstring="${wl}-compatibility_version ${wl}$minor_current ${wl}-current_version ${wl}$minor_current.$revision"
+ verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
+ ;;
+
+ freebsd-aout)
+ major=".$current"
+ versuffix=".$current.$revision";
+ ;;
+
+ freebsd-elf)
+ major=".$current"
+ versuffix=".$current"
+ ;;
+
+ irix | nonstopux)
+ if test "X$lt_irix_increment" = "Xno"; then
+ func_arith $current - $age
+ else
+ func_arith $current - $age + 1
+ fi
+ major=$func_arith_result
+
+ case $version_type in
+ nonstopux) verstring_prefix=nonstopux ;;
+ *) verstring_prefix=sgi ;;
+ esac
+ verstring="$verstring_prefix$major.$revision"
+
+ # Add in all the interfaces that we are compatible with.
+ loop=$revision
+ while test "$loop" -ne 0; do
+ func_arith $revision - $loop
+ iface=$func_arith_result
+ func_arith $loop - 1
+ loop=$func_arith_result
+ verstring="$verstring_prefix$major.$iface:$verstring"
+ done
+
+ # Before this point, $major must not contain `.'.
+ major=.$major
+ versuffix="$major.$revision"
+ ;;
+
+ linux)
+ func_arith $current - $age
+ major=.$func_arith_result
+ versuffix="$major.$age.$revision"
+ ;;
+
+ osf)
+ func_arith $current - $age
+ major=.$func_arith_result
+ versuffix=".$current.$age.$revision"
+ verstring="$current.$age.$revision"
+
+ # Add in all the interfaces that we are compatible with.
+ loop=$age
+ while test "$loop" -ne 0; do
+ func_arith $current - $loop
+ iface=$func_arith_result
+ func_arith $loop - 1
+ loop=$func_arith_result
+ verstring="$verstring:${iface}.0"
+ done
+
+ # Make executables depend on our current version.
+ verstring="$verstring:${current}.0"
+ ;;
+
+ qnx)
+ major=".$current"
+ versuffix=".$current"
+ ;;
+
+ sunos)
+ major=".$current"
+ versuffix=".$current.$revision"
+ ;;
+
+ windows)
+ # Use '-' rather than '.', since we only want one
+ # extension on DOS 8.3 filesystems.
+ func_arith $current - $age
+ major=$func_arith_result
+ versuffix="-$major"
+ ;;
+
+ *)
+ func_fatal_configuration "unknown library version type \`$version_type'"
+ ;;
+ esac
+
+ # Clear the version info if we defaulted, and they specified a release.
+ if test -z "$vinfo" && test -n "$release"; then
+ major=
+ case $version_type in
+ darwin)
+ # we can't check for "0.0" in archive_cmds due to quoting
+ # problems, so we reset it completely
+ verstring=
+ ;;
+ *)
+ verstring="0.0"
+ ;;
+ esac
+ if test "$need_version" = no; then
+ versuffix=
+ else
+ versuffix=".0.0"
+ fi
+ fi
+
+ # Remove version info from name if versioning should be avoided
+ if test "$avoid_version" = yes && test "$need_version" = no; then
+ major=
+ versuffix=
+ verstring=""
+ fi
+
+ # Check to see if the archive will have undefined symbols.
+ if test "$allow_undefined" = yes; then
+ if test "$allow_undefined_flag" = unsupported; then
+ func_warning "undefined symbols not allowed in $host shared libraries"
+ build_libtool_libs=no
+ build_old_libs=yes
+ fi
+ else
+ # Don't allow undefined symbols.
+ allow_undefined_flag="$no_undefined_flag"
+ fi
+
+ fi
+
+ func_generate_dlsyms "$libname" "$libname" "yes"
+ libobjs="$libobjs $symfileobj"
+ test "X$libobjs" = "X " && libobjs=
+
+ if test "$mode" != relink; then
+ # Remove our outputs, but don't remove object files since they
+ # may have been created when compiling PIC objects.
+ removelist=
+ tempremovelist=`$ECHO "$output_objdir/*"`
+ for p in $tempremovelist; do
+ case $p in
+ *.$objext | *.gcno)
+ ;;
+ $output_objdir/$outputname | $output_objdir/$libname.* | $output_objdir/${libname}${release}.*)
+ if test "X$precious_files_regex" != "X"; then
+ if $ECHO "$p" | $EGREP -e "$precious_files_regex" >/dev/null 2>&1
+ then
+ continue
+ fi
+ fi
+ removelist="$removelist $p"
+ ;;
+ *) ;;
+ esac
+ done
+ test -n "$removelist" && \
+ func_show_eval "${RM}r \$removelist"
+ fi
+
+ # Now set the variables for building old libraries.
+ if test "$build_old_libs" = yes && test "$build_libtool_libs" != convenience ; then
+ oldlibs="$oldlibs $output_objdir/$libname.$libext"
+
+ # Transform .lo files to .o files.
+ oldobjs="$objs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}'$/d' -e "$lo2o" | $NL2SP`
+ fi
+
+ # Eliminate all temporary directories.
+ #for path in $notinst_path; do
+ # lib_search_path=`$ECHO "X$lib_search_path " | $Xsed -e "s% $path % %g"`
+ # deplibs=`$ECHO "X$deplibs " | $Xsed -e "s% -L$path % %g"`
+ # dependency_libs=`$ECHO "X$dependency_libs " | $Xsed -e "s% -L$path % %g"`
+ #done
+
+ if test -n "$xrpath"; then
+ # If the user specified any rpath flags, then add them.
+ temp_xrpath=
+ for libdir in $xrpath; do
+ temp_xrpath="$temp_xrpath -R$libdir"
+ case "$finalize_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_rpath="$finalize_rpath $libdir" ;;
+ esac
+ done
+ if test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes; then
+ dependency_libs="$temp_xrpath $dependency_libs"
+ fi
+ fi
+
+ # Make sure dlfiles contains only unique files that won't be dlpreopened
+ old_dlfiles="$dlfiles"
+ dlfiles=
+ for lib in $old_dlfiles; do
+ case " $dlprefiles $dlfiles " in
+ *" $lib "*) ;;
+ *) dlfiles="$dlfiles $lib" ;;
+ esac
+ done
+
+ # Make sure dlprefiles contains only unique files
+ old_dlprefiles="$dlprefiles"
+ dlprefiles=
+ for lib in $old_dlprefiles; do
+ case "$dlprefiles " in
+ *" $lib "*) ;;
+ *) dlprefiles="$dlprefiles $lib" ;;
+ esac
+ done
+
+ if test "$build_libtool_libs" = yes; then
+ if test -n "$rpath"; then
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-beos* | *-cegcc*)
+ # these systems don't actually have a c library (as such)!
+ ;;
+ *-*-rhapsody* | *-*-darwin1.[012])
+ # Rhapsody C library is in the System framework
+ deplibs="$deplibs System.ltframework"
+ ;;
+ *-*-netbsd*)
+ # Don't link with libc until the a.out ld.so is fixed.
+ ;;
+ *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
+ # Do not include libc due to us having libc/libc_r.
+ ;;
+ *-*-sco3.2v5* | *-*-sco5v6*)
+ # Causes problems with __ctype
+ ;;
+ *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*)
+ # Compiler inserts libc in the correct place for threads to work
+ ;;
+ *)
+ # Add libc to deplibs on all other systems if necessary.
+ if test "$build_libtool_need_lc" = "yes"; then
+ deplibs="$deplibs -lc"
+ fi
+ ;;
+ esac
+ fi
+
+ # Transform deplibs into only deplibs that can be linked in shared.
+ name_save=$name
+ libname_save=$libname
+ release_save=$release
+ versuffix_save=$versuffix
+ major_save=$major
+ # I'm not sure if I'm treating the release correctly. I think
+ # release should show up in the -l (ie -lgmp5) so we don't want to
+ # add it in twice. Is that correct?
+ release=""
+ versuffix=""
+ major=""
+ newdeplibs=
+ droppeddeps=no
+ case $deplibs_check_method in
+ pass_all)
+ # Don't check for shared/static. Everything works.
+ # This might be a little naive. We might want to check
+ # whether the library exists or not. But this is on
+ # osf3 & osf4 and I'm not really sure... Just
+ # implementing what was already the behavior.
+ newdeplibs=$deplibs
+ ;;
+ test_compile)
+ # This code stresses the "libraries are programs" paradigm to its
+ # limits. Maybe even breaks it. We compile a program, linking it
+ # against the deplibs as a proxy for the library. Then we can check
+ # whether they linked in statically or dynamically with ldd.
+ $opt_dry_run || $RM conftest.c
+ cat > conftest.c <<EOF
+ int main() { return 0; }
+EOF
+ $opt_dry_run || $RM conftest
+ if $LTCC $LTCFLAGS -o conftest conftest.c $deplibs; then
+ ldd_output=`ldd conftest`
+ for i in $deplibs; do
+ case $i in
+ -l*)
+ func_stripname -l '' "$i"
+ name=$func_stripname_result
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $i "*)
+ newdeplibs="$newdeplibs $i"
+ i=""
+ ;;
+ esac
+ fi
+ if test -n "$i" ; then
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ deplib_matches=`eval "\\$ECHO \"$library_names_spec\""`
+ set dummy $deplib_matches; shift
+ deplib_match=$1
+ if test `expr "$ldd_output" : ".*$deplib_match"` -ne 0 ; then
+ newdeplibs="$newdeplibs $i"
+ else
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning: dynamic linker does not accept needed library $i."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which I believe you do not have"
+ $ECHO "*** because a test_compile did reveal that the linker did not use it for"
+ $ECHO "*** its dynamic dependency list that programs get resolved with at runtime."
+ fi
+ fi
+ ;;
+ *)
+ newdeplibs="$newdeplibs $i"
+ ;;
+ esac
+ done
+ else
+ # Error occurred in the first compile. Let's try to salvage
+ # the situation: Compile a separate program for each library.
+ for i in $deplibs; do
+ case $i in
+ -l*)
+ func_stripname -l '' "$i"
+ name=$func_stripname_result
+ $opt_dry_run || $RM conftest
+ if $LTCC $LTCFLAGS -o conftest conftest.c $i; then
+ ldd_output=`ldd conftest`
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $i "*)
+ newdeplibs="$newdeplibs $i"
+ i=""
+ ;;
+ esac
+ fi
+ if test -n "$i" ; then
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ deplib_matches=`eval "\\$ECHO \"$library_names_spec\""`
+ set dummy $deplib_matches; shift
+ deplib_match=$1
+ if test `expr "$ldd_output" : ".*$deplib_match"` -ne 0 ; then
+ newdeplibs="$newdeplibs $i"
+ else
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning: dynamic linker does not accept needed library $i."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have"
+ $ECHO "*** because a test_compile did reveal that the linker did not use this one"
+ $ECHO "*** as a dynamic dependency that programs can get resolved with at runtime."
+ fi
+ fi
+ else
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning! Library $i is needed by this library but I was not able to"
+ $ECHO "*** make it link in! You will probably need to install it or some"
+ $ECHO "*** library that it depends on before this library will be fully"
+ $ECHO "*** functional. Installing it before continuing would be even better."
+ fi
+ ;;
+ *)
+ newdeplibs="$newdeplibs $i"
+ ;;
+ esac
+ done
+ fi
+ ;;
+ file_magic*)
+ set dummy $deplibs_check_method; shift
+ file_magic_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"`
+ for a_deplib in $deplibs; do
+ case $a_deplib in
+ -l*)
+ func_stripname -l '' "$a_deplib"
+ name=$func_stripname_result
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $a_deplib "*)
+ newdeplibs="$newdeplibs $a_deplib"
+ a_deplib=""
+ ;;
+ esac
+ fi
+ if test -n "$a_deplib" ; then
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do
+ potential_libs=`ls $i/$libname[.-]* 2>/dev/null`
+ for potent_lib in $potential_libs; do
+ # Follow soft links.
+ if ls -lLd "$potent_lib" 2>/dev/null |
+ $GREP " -> " >/dev/null; then
+ continue
+ fi
+ # The statement above tries to avoid entering an
+ # endless loop below, in case of cyclic links.
+ # We might still enter an endless loop, since a link
+ # loop can be closed while we follow links,
+ # but so what?
+ potlib="$potent_lib"
+ while test -h "$potlib" 2>/dev/null; do
+ potliblink=`ls -ld $potlib | ${SED} 's/.* -> //'`
+ case $potliblink in
+ [\\/]* | [A-Za-z]:[\\/]*) potlib="$potliblink";;
+ *) potlib=`$ECHO "X$potlib" | $Xsed -e 's,[^/]*$,,'`"$potliblink";;
+ esac
+ done
+ if eval $file_magic_cmd \"\$potlib\" 2>/dev/null |
+ $SED -e 10q |
+ $EGREP "$file_magic_regex" > /dev/null; then
+ newdeplibs="$newdeplibs $a_deplib"
+ a_deplib=""
+ break 2
+ fi
+ done
+ done
+ fi
+ if test -n "$a_deplib" ; then
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning: linker path does not have real file for library $a_deplib."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have"
+ $ECHO "*** because I did check the linker path looking for a file starting"
+ if test -z "$potlib" ; then
+ $ECHO "*** with $libname but no candidates were found. (...for file magic test)"
+ else
+ $ECHO "*** with $libname and none of the candidates passed a file format test"
+ $ECHO "*** using a file magic. Last file checked: $potlib"
+ fi
+ fi
+ ;;
+ *)
+ # Add a -L argument.
+ newdeplibs="$newdeplibs $a_deplib"
+ ;;
+ esac
+ done # Gone through all deplibs.
+ ;;
+ match_pattern*)
+ set dummy $deplibs_check_method; shift
+ match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"`
+ for a_deplib in $deplibs; do
+ case $a_deplib in
+ -l*)
+ func_stripname -l '' "$a_deplib"
+ name=$func_stripname_result
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $a_deplib "*)
+ newdeplibs="$newdeplibs $a_deplib"
+ a_deplib=""
+ ;;
+ esac
+ fi
+ if test -n "$a_deplib" ; then
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do
+ potential_libs=`ls $i/$libname[.-]* 2>/dev/null`
+ for potent_lib in $potential_libs; do
+ potlib="$potent_lib" # see symlink-check above in file_magic test
+ if eval "\$ECHO \"X$potent_lib\"" 2>/dev/null | $Xsed -e 10q | \
+ $EGREP "$match_pattern_regex" > /dev/null; then
+ newdeplibs="$newdeplibs $a_deplib"
+ a_deplib=""
+ break 2
+ fi
+ done
+ done
+ fi
+ if test -n "$a_deplib" ; then
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning: linker path does not have real file for library $a_deplib."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have"
+ $ECHO "*** because I did check the linker path looking for a file starting"
+ if test -z "$potlib" ; then
+ $ECHO "*** with $libname but no candidates were found. (...for regex pattern test)"
+ else
+ $ECHO "*** with $libname and none of the candidates passed a file format test"
+ $ECHO "*** using a regex pattern. Last file checked: $potlib"
+ fi
+ fi
+ ;;
+ *)
+ # Add a -L argument.
+ newdeplibs="$newdeplibs $a_deplib"
+ ;;
+ esac
+ done # Gone through all deplibs.
+ ;;
+ none | unknown | *)
+ newdeplibs=""
+ tmp_deplibs=`$ECHO "X $deplibs" | $Xsed \
+ -e 's/ -lc$//' -e 's/ -[LR][^ ]*//g'`
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ for i in $predeps $postdeps ; do
+ # can't use Xsed below, because $i might contain '/'
+ tmp_deplibs=`$ECHO "X $tmp_deplibs" | $Xsed -e "s,$i,,"`
+ done
+ fi
+ if $ECHO "X $tmp_deplibs" | $Xsed -e 's/[ ]//g' |
+ $GREP . >/dev/null; then
+ $ECHO
+ if test "X$deplibs_check_method" = "Xnone"; then
+ $ECHO "*** Warning: inter-library dependencies are not supported in this platform."
+ else
+ $ECHO "*** Warning: inter-library dependencies are not known to be supported."
+ fi
+ $ECHO "*** All declared inter-library dependencies are being dropped."
+ droppeddeps=yes
+ fi
+ ;;
+ esac
+ versuffix=$versuffix_save
+ major=$major_save
+ release=$release_save
+ libname=$libname_save
+ name=$name_save
+
+ case $host in
+ *-*-rhapsody* | *-*-darwin1.[012])
+ # On Rhapsody replace the C library with the System framework
+ newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's/ -lc / System.ltframework /'`
+ ;;
+ esac
+
+ if test "$droppeddeps" = yes; then
+ if test "$module" = yes; then
+ $ECHO
+ $ECHO "*** Warning: libtool could not satisfy all declared inter-library"
+ $ECHO "*** dependencies of module $libname. Therefore, libtool will create"
+ $ECHO "*** a static module, that should work as long as the dlopening"
+ $ECHO "*** application is linked with the -dlopen flag."
+ if test -z "$global_symbol_pipe"; then
+ $ECHO
+ $ECHO "*** However, this would only work if libtool was able to extract symbol"
+ $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could"
+ $ECHO "*** not find such a program. So, this module is probably useless."
+ $ECHO "*** \`nm' from GNU binutils and a full rebuild may help."
+ fi
+ if test "$build_old_libs" = no; then
+ oldlibs="$output_objdir/$libname.$libext"
+ build_libtool_libs=module
+ build_old_libs=yes
+ else
+ build_libtool_libs=no
+ fi
+ else
+ $ECHO "*** The inter-library dependencies that have been dropped here will be"
+ $ECHO "*** automatically added whenever a program is linked with this library"
+ $ECHO "*** or is declared to -dlopen it."
+
+ if test "$allow_undefined" = no; then
+ $ECHO
+ $ECHO "*** Since this library must not contain undefined symbols,"
+ $ECHO "*** because either the platform does not support them or"
+ $ECHO "*** it was explicitly requested with -no-undefined,"
+ $ECHO "*** libtool will only create a static version of it."
+ if test "$build_old_libs" = no; then
+ oldlibs="$output_objdir/$libname.$libext"
+ build_libtool_libs=module
+ build_old_libs=yes
+ else
+ build_libtool_libs=no
+ fi
+ fi
+ fi
+ fi
+ # Done checking deplibs!
+ deplibs=$newdeplibs
+ fi
+ # Time to change all our "foo.ltframework" stuff back to "-framework foo"
+ case $host in
+ *-*-darwin*)
+ newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ new_inherited_linker_flags=`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ deplibs=`$ECHO "X $deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ ;;
+ esac
+
+ # move library search paths that coincide with paths to not yet
+ # installed libraries to the beginning of the library search list
+ new_libs=
+ for path in $notinst_path; do
+ case " $new_libs " in
+ *" -L$path/$objdir "*) ;;
+ *)
+ case " $deplibs " in
+ *" -L$path/$objdir "*)
+ new_libs="$new_libs -L$path/$objdir" ;;
+ esac
+ ;;
+ esac
+ done
+ for deplib in $deplibs; do
+ case $deplib in
+ -L*)
+ case " $new_libs " in
+ *" $deplib "*) ;;
+ *) new_libs="$new_libs $deplib" ;;
+ esac
+ ;;
+ *) new_libs="$new_libs $deplib" ;;
+ esac
+ done
+ deplibs="$new_libs"
+
+ # All the library-specific variables (install_libdir is set above).
+ library_names=
+ old_library=
+ dlname=
+
+ # Test again, we may have decided not to build it any more
+ if test "$build_libtool_libs" = yes; then
+ if test "$hardcode_into_libs" = yes; then
+ # Hardcode the library paths
+ hardcode_libdirs=
+ dep_rpath=
+ rpath="$finalize_rpath"
+ test "$mode" != relink && rpath="$compile_rpath$rpath"
+ for libdir in $rpath; do
+ if test -n "$hardcode_libdir_flag_spec"; then
+ if test -n "$hardcode_libdir_separator"; then
+ if test -z "$hardcode_libdirs"; then
+ hardcode_libdirs="$libdir"
+ else
+ # Just accumulate the unique libdirs.
+ case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
+ *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
+ ;;
+ *)
+ hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir"
+ ;;
+ esac
+ fi
+ else
+ eval flag=\"$hardcode_libdir_flag_spec\"
+ dep_rpath="$dep_rpath $flag"
+ fi
+ elif test -n "$runpath_var"; then
+ case "$perm_rpath " in
+ *" $libdir "*) ;;
+ *) perm_rpath="$perm_rpath $libdir" ;;
+ esac
+ fi
+ done
+ # Substitute the hardcoded libdirs into the rpath.
+ if test -n "$hardcode_libdir_separator" &&
+ test -n "$hardcode_libdirs"; then
+ libdir="$hardcode_libdirs"
+ if test -n "$hardcode_libdir_flag_spec_ld"; then
+ eval dep_rpath=\"$hardcode_libdir_flag_spec_ld\"
+ else
+ eval dep_rpath=\"$hardcode_libdir_flag_spec\"
+ fi
+ fi
+ if test -n "$runpath_var" && test -n "$perm_rpath"; then
+ # We should set the runpath_var.
+ rpath=
+ for dir in $perm_rpath; do
+ rpath="$rpath$dir:"
+ done
+ eval "$runpath_var='$rpath\$$runpath_var'; export $runpath_var"
+ fi
+ test -n "$dep_rpath" && deplibs="$dep_rpath $deplibs"
+ fi
+
+ shlibpath="$finalize_shlibpath"
+ test "$mode" != relink && shlibpath="$compile_shlibpath$shlibpath"
+ if test -n "$shlibpath"; then
+ eval "$shlibpath_var='$shlibpath\$$shlibpath_var'; export $shlibpath_var"
+ fi
+
+ # Get the real and link names of the library.
+ eval shared_ext=\"$shrext_cmds\"
+ eval library_names=\"$library_names_spec\"
+ set dummy $library_names
+ shift
+ realname="$1"
+ shift
+
+ if test -n "$soname_spec"; then
+ eval soname=\"$soname_spec\"
+ else
+ soname="$realname"
+ fi
+ if test -z "$dlname"; then
+ dlname=$soname
+ fi
+
+ lib="$output_objdir/$realname"
+ linknames=
+ for link
+ do
+ linknames="$linknames $link"
+ done
+
+ # Use standard objects if they are pic
+ test -z "$pic_flag" && libobjs=`$ECHO "X$libobjs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+ test "X$libobjs" = "X " && libobjs=
+
+ delfiles=
+ if test -n "$export_symbols" && test -n "$include_expsyms"; then
+ $opt_dry_run || cp "$export_symbols" "$output_objdir/$libname.uexp"
+ export_symbols="$output_objdir/$libname.uexp"
+ delfiles="$delfiles $export_symbols"
+ fi
+
+ orig_export_symbols=
+ case $host_os in
+ cygwin* | mingw* | cegcc*)
+ if test -n "$export_symbols" && test -z "$export_symbols_regex"; then
+ # exporting using user supplied symfile
+ if test "x`$SED 1q $export_symbols`" != xEXPORTS; then
+ # and it's NOT already a .def file. Must figure out
+ # which of the given symbols are data symbols and tag
+ # them as such. So, trigger use of export_symbols_cmds.
+ # export_symbols gets reassigned inside the "prepare
+ # the list of exported symbols" if statement, so the
+ # include_expsyms logic still works.
+ orig_export_symbols="$export_symbols"
+ export_symbols=
+ always_export_symbols=yes
+ fi
+ fi
+ ;;
+ esac
+
+ # Prepare the list of exported symbols
+ if test -z "$export_symbols"; then
+ if test "$always_export_symbols" = yes || test -n "$export_symbols_regex"; then
+ func_verbose "generating symbol list for \`$libname.la'"
+ export_symbols="$output_objdir/$libname.exp"
+ $opt_dry_run || $RM $export_symbols
+ cmds=$export_symbols_cmds
+ save_ifs="$IFS"; IFS='~'
+ for cmd in $cmds; do
+ IFS="$save_ifs"
+ eval cmd=\"$cmd\"
+ func_len " $cmd"
+ len=$func_len_result
+ if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then
+ func_show_eval "$cmd" 'exit $?'
+ skipped_export=false
+ else
+ # The command line is too long to execute in one step.
+ func_verbose "using reloadable object file for export list..."
+ skipped_export=:
+ # Break out early, otherwise skipped_export may be
+ # set to false by a later but shorter cmd.
+ break
+ fi
+ done
+ IFS="$save_ifs"
+ if test -n "$export_symbols_regex" && test "X$skipped_export" != "X:"; then
+ func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"'
+ func_show_eval '$MV "${export_symbols}T" "$export_symbols"'
+ fi
+ fi
+ fi
+
+ if test -n "$export_symbols" && test -n "$include_expsyms"; then
+ tmp_export_symbols="$export_symbols"
+ test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols"
+ $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"'
+ fi
+
+ if test "X$skipped_export" != "X:" && test -n "$orig_export_symbols"; then
+ # The given exports_symbols file has to be filtered, so filter it.
+ func_verbose "filter symbol list for \`$libname.la' to tag DATA exports"
+ # FIXME: $output_objdir/$libname.filter potentially contains lots of
+ # 's' commands which not all seds can handle. GNU sed should be fine
+ # though. Also, the filter scales superlinearly with the number of
+ # global variables. join(1) would be nice here, but unfortunately
+ # isn't a blessed tool.
+ $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter
+ delfiles="$delfiles $export_symbols $output_objdir/$libname.filter"
+ export_symbols=$output_objdir/$libname.def
+ $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols
+ fi
+
+ tmp_deplibs=
+ for test_deplib in $deplibs; do
+ case " $convenience " in
+ *" $test_deplib "*) ;;
+ *)
+ tmp_deplibs="$tmp_deplibs $test_deplib"
+ ;;
+ esac
+ done
+ deplibs="$tmp_deplibs"
+
+ if test -n "$convenience"; then
+ if test -n "$whole_archive_flag_spec" &&
+ test "$compiler_needs_object" = yes &&
+ test -z "$libobjs"; then
+ # extract the archives, so we have objects to list.
+ # TODO: could optimize this to just extract one archive.
+ whole_archive_flag_spec=
+ fi
+ if test -n "$whole_archive_flag_spec"; then
+ save_libobjs=$libobjs
+ eval libobjs=\"\$libobjs $whole_archive_flag_spec\"
+ test "X$libobjs" = "X " && libobjs=
+ else
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $convenience
+ libobjs="$libobjs $func_extract_archives_result"
+ test "X$libobjs" = "X " && libobjs=
+ fi
+ fi
+
+ if test "$thread_safe" = yes && test -n "$thread_safe_flag_spec"; then
+ eval flag=\"$thread_safe_flag_spec\"
+ linker_flags="$linker_flags $flag"
+ fi
+
+ # Make a backup of the uninstalled library when relinking
+ if test "$mode" = relink; then
+ $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}U && $MV $realname ${realname}U)' || exit $?
+ fi
+
+ # Do each of the archive commands.
+ if test "$module" = yes && test -n "$module_cmds" ; then
+ if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then
+ eval test_cmds=\"$module_expsym_cmds\"
+ cmds=$module_expsym_cmds
+ else
+ eval test_cmds=\"$module_cmds\"
+ cmds=$module_cmds
+ fi
+ else
+ if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then
+ eval test_cmds=\"$archive_expsym_cmds\"
+ cmds=$archive_expsym_cmds
+ else
+ eval test_cmds=\"$archive_cmds\"
+ cmds=$archive_cmds
+ fi
+ fi
+
+ if test "X$skipped_export" != "X:" &&
+ func_len " $test_cmds" &&
+ len=$func_len_result &&
+ test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then
+ :
+ else
+ # The command line is too long to link in one step, link piecewise
+ # or, if using GNU ld and skipped_export is not :, use a linker
+ # script.
+
+ # Save the value of $output and $libobjs because we want to
+ # use them later. If we have whole_archive_flag_spec, we
+ # want to use save_libobjs as it was before
+ # whole_archive_flag_spec was expanded, because we can't
+ # assume the linker understands whole_archive_flag_spec.
+ # This may have to be revisited, in case too many
+ # convenience libraries get linked in and end up exceeding
+ # the spec.
+ if test -z "$convenience" || test -z "$whole_archive_flag_spec"; then
+ save_libobjs=$libobjs
+ fi
+ save_output=$output
+ output_la=`$ECHO "X$output" | $Xsed -e "$basename"`
+
+ # Clear the reloadable object creation command queue and
+ # initialize k to one.
+ test_cmds=
+ concat_cmds=
+ objlist=
+ last_robj=
+ k=1
+
+ if test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "$with_gnu_ld" = yes; then
+ output=${output_objdir}/${output_la}.lnkscript
+ func_verbose "creating GNU ld script: $output"
+ $ECHO 'INPUT (' > $output
+ for obj in $save_libobjs
+ do
+ $ECHO "$obj" >> $output
+ done
+ $ECHO ')' >> $output
+ delfiles="$delfiles $output"
+ elif test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "X$file_list_spec" != X; then
+ output=${output_objdir}/${output_la}.lnk
+ func_verbose "creating linker input file list: $output"
+ : > $output
+ set x $save_libobjs
+ shift
+ firstobj=
+ if test "$compiler_needs_object" = yes; then
+ firstobj="$1 "
+ shift
+ fi
+ for obj
+ do
+ $ECHO "$obj" >> $output
+ done
+ delfiles="$delfiles $output"
+ output=$firstobj\"$file_list_spec$output\"
+ else
+ if test -n "$save_libobjs"; then
+ func_verbose "creating reloadable object files..."
+ output=$output_objdir/$output_la-${k}.$objext
+ eval test_cmds=\"$reload_cmds\"
+ func_len " $test_cmds"
+ len0=$func_len_result
+ len=$len0
+
+ # Loop over the list of objects to be linked.
+ for obj in $save_libobjs
+ do
+ func_len " $obj"
+ func_arith $len + $func_len_result
+ len=$func_arith_result
+ if test "X$objlist" = X ||
+ test "$len" -lt "$max_cmd_len"; then
+ func_append objlist " $obj"
+ else
+ # The command $test_cmds is almost too long, add a
+ # command to the queue.
+ if test "$k" -eq 1 ; then
+ # The first file doesn't have a previous command to add.
+ eval concat_cmds=\"$reload_cmds $objlist $last_robj\"
+ else
+ # All subsequent reloadable object files will link in
+ # the last one created.
+ eval concat_cmds=\"\$concat_cmds~$reload_cmds $objlist $last_robj~\$RM $last_robj\"
+ fi
+ last_robj=$output_objdir/$output_la-${k}.$objext
+ func_arith $k + 1
+ k=$func_arith_result
+ output=$output_objdir/$output_la-${k}.$objext
+ objlist=$obj
+ func_len " $last_robj"
+ func_arith $len0 + $func_len_result
+ len=$func_arith_result
+ fi
+ done
+ # Handle the remaining objects by creating one last
+ # reloadable object file. All subsequent reloadable object
+ # files will link in the last one created.
+ test -z "$concat_cmds" || concat_cmds=$concat_cmds~
+ eval concat_cmds=\"\${concat_cmds}$reload_cmds $objlist $last_robj\"
+ if test -n "$last_robj"; then
+ eval concat_cmds=\"\${concat_cmds}~\$RM $last_robj\"
+ fi
+ delfiles="$delfiles $output"
+
+ else
+ output=
+ fi
+
+ if ${skipped_export-false}; then
+ func_verbose "generating symbol list for \`$libname.la'"
+ export_symbols="$output_objdir/$libname.exp"
+ $opt_dry_run || $RM $export_symbols
+ libobjs=$output
+ # Append the command to create the export file.
+ test -z "$concat_cmds" || concat_cmds=$concat_cmds~
+ eval concat_cmds=\"\$concat_cmds$export_symbols_cmds\"
+ if test -n "$last_robj"; then
+ eval concat_cmds=\"\$concat_cmds~\$RM $last_robj\"
+ fi
+ fi
+
+ test -n "$save_libobjs" &&
+ func_verbose "creating a temporary reloadable object file: $output"
+
+ # Loop through the commands generated above and execute them.
+ save_ifs="$IFS"; IFS='~'
+ for cmd in $concat_cmds; do
+ IFS="$save_ifs"
+ $opt_silent || {
+ func_quote_for_expand "$cmd"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+ $opt_dry_run || eval "$cmd" || {
+ lt_exit=$?
+
+ # Restore the uninstalled library and exit
+ if test "$mode" = relink; then
+ ( cd "$output_objdir" && \
+ $RM "${realname}T" && \
+ $MV "${realname}U" "$realname" )
+ fi
+
+ exit $lt_exit
+ }
+ done
+ IFS="$save_ifs"
+
+ if test -n "$export_symbols_regex" && ${skipped_export-false}; then
+ func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"'
+ func_show_eval '$MV "${export_symbols}T" "$export_symbols"'
+ fi
+ fi
+
+ if ${skipped_export-false}; then
+ if test -n "$export_symbols" && test -n "$include_expsyms"; then
+ tmp_export_symbols="$export_symbols"
+ test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols"
+ $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"'
+ fi
+
+ if test -n "$orig_export_symbols"; then
+ # The given exports_symbols file has to be filtered, so filter it.
+ func_verbose "filter symbol list for \`$libname.la' to tag DATA exports"
+ # FIXME: $output_objdir/$libname.filter potentially contains lots of
+ # 's' commands which not all seds can handle. GNU sed should be fine
+ # though. Also, the filter scales superlinearly with the number of
+ # global variables. join(1) would be nice here, but unfortunately
+ # isn't a blessed tool.
+ $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter
+ delfiles="$delfiles $export_symbols $output_objdir/$libname.filter"
+ export_symbols=$output_objdir/$libname.def
+ $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols
+ fi
+ fi
+
+ libobjs=$output
+ # Restore the value of output.
+ output=$save_output
+
+ if test -n "$convenience" && test -n "$whole_archive_flag_spec"; then
+ eval libobjs=\"\$libobjs $whole_archive_flag_spec\"
+ test "X$libobjs" = "X " && libobjs=
+ fi
+ # Expand the library linking commands again to reset the
+ # value of $libobjs for piecewise linking.
+
+ # Do each of the archive commands.
+ if test "$module" = yes && test -n "$module_cmds" ; then
+ if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then
+ cmds=$module_expsym_cmds
+ else
+ cmds=$module_cmds
+ fi
+ else
+ if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then
+ cmds=$archive_expsym_cmds
+ else
+ cmds=$archive_cmds
+ fi
+ fi
+ fi
+
+ if test -n "$delfiles"; then
+ # Append the command to remove temporary files to $cmds.
+ eval cmds=\"\$cmds~\$RM $delfiles\"
+ fi
+
+ # Add any objects from preloaded convenience libraries
+ if test -n "$dlprefiles"; then
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $dlprefiles
+ libobjs="$libobjs $func_extract_archives_result"
+ test "X$libobjs" = "X " && libobjs=
+ fi
+
+ save_ifs="$IFS"; IFS='~'
+ for cmd in $cmds; do
+ IFS="$save_ifs"
+ eval cmd=\"$cmd\"
+ $opt_silent || {
+ func_quote_for_expand "$cmd"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+ $opt_dry_run || eval "$cmd" || {
+ lt_exit=$?
+
+ # Restore the uninstalled library and exit
+ if test "$mode" = relink; then
+ ( cd "$output_objdir" && \
+ $RM "${realname}T" && \
+ $MV "${realname}U" "$realname" )
+ fi
+
+ exit $lt_exit
+ }
+ done
+ IFS="$save_ifs"
+
+ # Restore the uninstalled library and exit
+ if test "$mode" = relink; then
+ $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}T && $MV $realname ${realname}T && $MV ${realname}U $realname)' || exit $?
+
+ if test -n "$convenience"; then
+ if test -z "$whole_archive_flag_spec"; then
+ func_show_eval '${RM}r "$gentop"'
+ fi
+ fi
+
+ exit $EXIT_SUCCESS
+ fi
+
+ # Create links to the real library.
+ for linkname in $linknames; do
+ if test "$realname" != "$linkname"; then
+ func_show_eval '(cd "$output_objdir" && $RM "$linkname" && $LN_S "$realname" "$linkname")' 'exit $?'
+ fi
+ done
+
+ # If -module or -export-dynamic was specified, set the dlname.
+ if test "$module" = yes || test "$export_dynamic" = yes; then
+ # On all known operating systems, these are identical.
+ dlname="$soname"
+ fi
+ fi
+ ;;
+
+ obj)
+ if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
+ func_warning "\`-dlopen' is ignored for objects"
+ fi
+
+ case " $deplibs" in
+ *\ -l* | *\ -L*)
+ func_warning "\`-l' and \`-L' are ignored for objects" ;;
+ esac
+
+ test -n "$rpath" && \
+ func_warning "\`-rpath' is ignored for objects"
+
+ test -n "$xrpath" && \
+ func_warning "\`-R' is ignored for objects"
+
+ test -n "$vinfo" && \
+ func_warning "\`-version-info' is ignored for objects"
+
+ test -n "$release" && \
+ func_warning "\`-release' is ignored for objects"
+
+ case $output in
+ *.lo)
+ test -n "$objs$old_deplibs" && \
+ func_fatal_error "cannot build library object \`$output' from non-libtool objects"
+
+ libobj=$output
+ func_lo2o "$libobj"
+ obj=$func_lo2o_result
+ ;;
+ *)
+ libobj=
+ obj="$output"
+ ;;
+ esac
+
+ # Delete the old objects.
+ $opt_dry_run || $RM $obj $libobj
+
+ # Objects from convenience libraries. This assumes
+ # single-version convenience libraries. Whenever we create
+ # different ones for PIC/non-PIC, this we'll have to duplicate
+ # the extraction.
+ reload_conv_objs=
+ gentop=
+ # reload_cmds runs $LD directly, so let us get rid of
+ # -Wl from whole_archive_flag_spec and hope we can get by with
+ # turning comma into space..
+ wl=
+
+ if test -n "$convenience"; then
+ if test -n "$whole_archive_flag_spec"; then
+ eval tmp_whole_archive_flags=\"$whole_archive_flag_spec\"
+ reload_conv_objs=$reload_objs\ `$ECHO "X$tmp_whole_archive_flags" | $Xsed -e 's|,| |g'`
+ else
+ gentop="$output_objdir/${obj}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $convenience
+ reload_conv_objs="$reload_objs $func_extract_archives_result"
+ fi
+ fi
+
+ # Create the old-style object.
+ reload_objs="$objs$old_deplibs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}$'/d' -e '/\.lib$/d' -e "$lo2o" | $NL2SP`" $reload_conv_objs" ### testsuite: skip nested quoting test
+
+ output="$obj"
+ func_execute_cmds "$reload_cmds" 'exit $?'
+
+ # Exit if we aren't doing a library object file.
+ if test -z "$libobj"; then
+ if test -n "$gentop"; then
+ func_show_eval '${RM}r "$gentop"'
+ fi
+
+ exit $EXIT_SUCCESS
+ fi
+
+ if test "$build_libtool_libs" != yes; then
+ if test -n "$gentop"; then
+ func_show_eval '${RM}r "$gentop"'
+ fi
+
+ # Create an invalid libtool object if no PIC, so that we don't
+ # accidentally link it into a program.
+ # $show "echo timestamp > $libobj"
+ # $opt_dry_run || eval "echo timestamp > $libobj" || exit $?
+ exit $EXIT_SUCCESS
+ fi
+
+ if test -n "$pic_flag" || test "$pic_mode" != default; then
+ # Only do commands if we really have different PIC objects.
+ reload_objs="$libobjs $reload_conv_objs"
+ output="$libobj"
+ func_execute_cmds "$reload_cmds" 'exit $?'
+ fi
+
+ if test -n "$gentop"; then
+ func_show_eval '${RM}r "$gentop"'
+ fi
+
+ exit $EXIT_SUCCESS
+ ;;
+
+ prog)
+ case $host in
+ *cygwin*) func_stripname '' '.exe' "$output"
+ output=$func_stripname_result.exe;;
+ esac
+ test -n "$vinfo" && \
+ func_warning "\`-version-info' is ignored for programs"
+
+ test -n "$release" && \
+ func_warning "\`-release' is ignored for programs"
+
+ test "$preload" = yes \
+ && test "$dlopen_support" = unknown \
+ && test "$dlopen_self" = unknown \
+ && test "$dlopen_self_static" = unknown && \
+ func_warning "\`LT_INIT([dlopen])' not used. Assuming no dlopen support."
+
+ case $host in
+ *-*-rhapsody* | *-*-darwin1.[012])
+ # On Rhapsody replace the C library is the System framework
+ compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'`
+ finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'`
+ ;;
+ esac
+
+ case $host in
+ *-*-darwin*)
+ # Don't allow lazy linking, it breaks C++ global constructors
+ # But is supposedly fixed on 10.4 or later (yay!).
+ if test "$tagname" = CXX ; then
+ case ${MACOSX_DEPLOYMENT_TARGET-10.0} in
+ 10.[0123])
+ compile_command="$compile_command ${wl}-bind_at_load"
+ finalize_command="$finalize_command ${wl}-bind_at_load"
+ ;;
+ esac
+ fi
+ # Time to change all our "foo.ltframework" stuff back to "-framework foo"
+ compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ ;;
+ esac
+
+
+ # move library search paths that coincide with paths to not yet
+ # installed libraries to the beginning of the library search list
+ new_libs=
+ for path in $notinst_path; do
+ case " $new_libs " in
+ *" -L$path/$objdir "*) ;;
+ *)
+ case " $compile_deplibs " in
+ *" -L$path/$objdir "*)
+ new_libs="$new_libs -L$path/$objdir" ;;
+ esac
+ ;;
+ esac
+ done
+ for deplib in $compile_deplibs; do
+ case $deplib in
+ -L*)
+ case " $new_libs " in
+ *" $deplib "*) ;;
+ *) new_libs="$new_libs $deplib" ;;
+ esac
+ ;;
+ *) new_libs="$new_libs $deplib" ;;
+ esac
+ done
+ compile_deplibs="$new_libs"
+
+
+ compile_command="$compile_command $compile_deplibs"
+ finalize_command="$finalize_command $finalize_deplibs"
+
+ if test -n "$rpath$xrpath"; then
+ # If the user specified any rpath flags, then add them.
+ for libdir in $rpath $xrpath; do
+ # This is the magic to use -rpath.
+ case "$finalize_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_rpath="$finalize_rpath $libdir" ;;
+ esac
+ done
+ fi
+
+ # Now hardcode the library paths
+ rpath=
+ hardcode_libdirs=
+ for libdir in $compile_rpath $finalize_rpath; do
+ if test -n "$hardcode_libdir_flag_spec"; then
+ if test -n "$hardcode_libdir_separator"; then
+ if test -z "$hardcode_libdirs"; then
+ hardcode_libdirs="$libdir"
+ else
+ # Just accumulate the unique libdirs.
+ case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
+ *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
+ ;;
+ *)
+ hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir"
+ ;;
+ esac
+ fi
+ else
+ eval flag=\"$hardcode_libdir_flag_spec\"
+ rpath="$rpath $flag"
+ fi
+ elif test -n "$runpath_var"; then
+ case "$perm_rpath " in
+ *" $libdir "*) ;;
+ *) perm_rpath="$perm_rpath $libdir" ;;
+ esac
+ fi
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*)
+ testbindir=`${ECHO} "$libdir" | ${SED} -e 's*/lib$*/bin*'`
+ case :$dllsearchpath: in
+ *":$libdir:"*) ;;
+ ::) dllsearchpath=$libdir;;
+ *) dllsearchpath="$dllsearchpath:$libdir";;
+ esac
+ case :$dllsearchpath: in
+ *":$testbindir:"*) ;;
+ ::) dllsearchpath=$testbindir;;
+ *) dllsearchpath="$dllsearchpath:$testbindir";;
+ esac
+ ;;
+ esac
+ done
+ # Substitute the hardcoded libdirs into the rpath.
+ if test -n "$hardcode_libdir_separator" &&
+ test -n "$hardcode_libdirs"; then
+ libdir="$hardcode_libdirs"
+ eval rpath=\" $hardcode_libdir_flag_spec\"
+ fi
+ compile_rpath="$rpath"
+
+ rpath=
+ hardcode_libdirs=
+ for libdir in $finalize_rpath; do
+ if test -n "$hardcode_libdir_flag_spec"; then
+ if test -n "$hardcode_libdir_separator"; then
+ if test -z "$hardcode_libdirs"; then
+ hardcode_libdirs="$libdir"
+ else
+ # Just accumulate the unique libdirs.
+ case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
+ *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
+ ;;
+ *)
+ hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir"
+ ;;
+ esac
+ fi
+ else
+ eval flag=\"$hardcode_libdir_flag_spec\"
+ rpath="$rpath $flag"
+ fi
+ elif test -n "$runpath_var"; then
+ case "$finalize_perm_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_perm_rpath="$finalize_perm_rpath $libdir" ;;
+ esac
+ fi
+ done
+ # Substitute the hardcoded libdirs into the rpath.
+ if test -n "$hardcode_libdir_separator" &&
+ test -n "$hardcode_libdirs"; then
+ libdir="$hardcode_libdirs"
+ eval rpath=\" $hardcode_libdir_flag_spec\"
+ fi
+ finalize_rpath="$rpath"
+
+ if test -n "$libobjs" && test "$build_old_libs" = yes; then
+ # Transform all the library objects into standard objects.
+ compile_command=`$ECHO "X$compile_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+ finalize_command=`$ECHO "X$finalize_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+ fi
+
+ func_generate_dlsyms "$outputname" "@PROGRAM@" "no"
+
+ # template prelinking step
+ if test -n "$prelink_cmds"; then
+ func_execute_cmds "$prelink_cmds" 'exit $?'
+ fi
+
+ wrappers_required=yes
+ case $host in
+ *cygwin* | *mingw* )
+ if test "$build_libtool_libs" != yes; then
+ wrappers_required=no
+ fi
+ ;;
+ *cegcc)
+ # Disable wrappers for cegcc, we are cross compiling anyway.
+ wrappers_required=no
+ ;;
+ *)
+ if test "$need_relink" = no || test "$build_libtool_libs" != yes; then
+ wrappers_required=no
+ fi
+ ;;
+ esac
+ if test "$wrappers_required" = no; then
+ # Replace the output file specification.
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'`
+ link_command="$compile_command$compile_rpath"
+
+ # We have no uninstalled library dependencies, so finalize right now.
+ exit_status=0
+ func_show_eval "$link_command" 'exit_status=$?'
+
+ # Delete the generated files.
+ if test -f "$output_objdir/${outputname}S.${objext}"; then
+ func_show_eval '$RM "$output_objdir/${outputname}S.${objext}"'
+ fi
+
+ exit $exit_status
+ fi
+
+ if test -n "$compile_shlibpath$finalize_shlibpath"; then
+ compile_command="$shlibpath_var=\"$compile_shlibpath$finalize_shlibpath\$$shlibpath_var\" $compile_command"
+ fi
+ if test -n "$finalize_shlibpath"; then
+ finalize_command="$shlibpath_var=\"$finalize_shlibpath\$$shlibpath_var\" $finalize_command"
+ fi
+
+ compile_var=
+ finalize_var=
+ if test -n "$runpath_var"; then
+ if test -n "$perm_rpath"; then
+ # We should set the runpath_var.
+ rpath=
+ for dir in $perm_rpath; do
+ rpath="$rpath$dir:"
+ done
+ compile_var="$runpath_var=\"$rpath\$$runpath_var\" "
+ fi
+ if test -n "$finalize_perm_rpath"; then
+ # We should set the runpath_var.
+ rpath=
+ for dir in $finalize_perm_rpath; do
+ rpath="$rpath$dir:"
+ done
+ finalize_var="$runpath_var=\"$rpath\$$runpath_var\" "
+ fi
+ fi
+
+ if test "$no_install" = yes; then
+ # We don't need to create a wrapper script.
+ link_command="$compile_var$compile_command$compile_rpath"
+ # Replace the output file specification.
+ link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'`
+ # Delete the old output file.
+ $opt_dry_run || $RM $output
+ # Link the executable and exit
+ func_show_eval "$link_command" 'exit $?'
+ exit $EXIT_SUCCESS
+ fi
+
+ if test "$hardcode_action" = relink; then
+ # Fast installation is not supported
+ link_command="$compile_var$compile_command$compile_rpath"
+ relink_command="$finalize_var$finalize_command$finalize_rpath"
+
+ func_warning "this platform does not like uninstalled shared libraries"
+ func_warning "\`$output' will be relinked during installation"
+ else
+ if test "$fast_install" != no; then
+ link_command="$finalize_var$compile_command$finalize_rpath"
+ if test "$fast_install" = yes; then
+ relink_command=`$ECHO "X$compile_var$compile_command$compile_rpath" | $Xsed -e 's%@OUTPUT@%\$progdir/\$file%g'`
+ else
+ # fast_install is set to needless
+ relink_command=
+ fi
+ else
+ link_command="$compile_var$compile_command$compile_rpath"
+ relink_command="$finalize_var$finalize_command$finalize_rpath"
+ fi
+ fi
+
+ # Replace the output file specification.
+ link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output_objdir/$outputname"'%g'`
+
+ # Delete the old output files.
+ $opt_dry_run || $RM $output $output_objdir/$outputname $output_objdir/lt-$outputname
+
+ func_show_eval "$link_command" 'exit $?'
+
+ # Now create the wrapper script.
+ func_verbose "creating $output"
+
+ # Quote the relink command for shipping.
+ if test -n "$relink_command"; then
+ # Preserve any variables that may affect compiler behavior
+ for var in $variables_saved_for_relink; do
+ if eval test -z \"\${$var+set}\"; then
+ relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command"
+ elif eval var_value=\$$var; test -z "$var_value"; then
+ relink_command="$var=; export $var; $relink_command"
+ else
+ func_quote_for_eval "$var_value"
+ relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command"
+ fi
+ done
+ relink_command="(cd `pwd`; $relink_command)"
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e "$sed_quote_subst"`
+ fi
+
+ # Quote $ECHO for shipping.
+ if test "X$ECHO" = "X$SHELL $progpath --fallback-echo"; then
+ case $progpath in
+ [\\/]* | [A-Za-z]:[\\/]*) qecho="$SHELL $progpath --fallback-echo";;
+ *) qecho="$SHELL `pwd`/$progpath --fallback-echo";;
+ esac
+ qecho=`$ECHO "X$qecho" | $Xsed -e "$sed_quote_subst"`
+ else
+ qecho=`$ECHO "X$ECHO" | $Xsed -e "$sed_quote_subst"`
+ fi
+
+ # Only actually do things if not in dry run mode.
+ $opt_dry_run || {
+ # win32 will think the script is a binary if it has
+ # a .exe suffix, so we strip it off here.
+ case $output in
+ *.exe) func_stripname '' '.exe' "$output"
+ output=$func_stripname_result ;;
+ esac
+ # test for cygwin because mv fails w/o .exe extensions
+ case $host in
+ *cygwin*)
+ exeext=.exe
+ func_stripname '' '.exe' "$outputname"
+ outputname=$func_stripname_result ;;
+ *) exeext= ;;
+ esac
+ case $host in
+ *cygwin* | *mingw* )
+ func_dirname_and_basename "$output" "" "."
+ output_name=$func_basename_result
+ output_path=$func_dirname_result
+ cwrappersource="$output_path/$objdir/lt-$output_name.c"
+ cwrapper="$output_path/$output_name.exe"
+ $RM $cwrappersource $cwrapper
+ trap "$RM $cwrappersource $cwrapper; exit $EXIT_FAILURE" 1 2 15
+
+ func_emit_cwrapperexe_src > $cwrappersource
+
+ # The wrapper executable is built using the $host compiler,
+ # because it contains $host paths and files. If cross-
+ # compiling, it, like the target executable, must be
+ # executed on the $host or under an emulation environment.
+ $opt_dry_run || {
+ $LTCC $LTCFLAGS -o $cwrapper $cwrappersource
+ $STRIP $cwrapper
+ }
+
+ # Now, create the wrapper script for func_source use:
+ func_ltwrapper_scriptname $cwrapper
+ $RM $func_ltwrapper_scriptname_result
+ trap "$RM $func_ltwrapper_scriptname_result; exit $EXIT_FAILURE" 1 2 15
+ $opt_dry_run || {
+ # note: this script will not be executed, so do not chmod.
+ if test "x$build" = "x$host" ; then
+ $cwrapper --lt-dump-script > $func_ltwrapper_scriptname_result
+ else
+ func_emit_wrapper no > $func_ltwrapper_scriptname_result
+ fi
+ }
+ ;;
+ * )
+ $RM $output
+ trap "$RM $output; exit $EXIT_FAILURE" 1 2 15
+
+ func_emit_wrapper no > $output
+ chmod +x $output
+ ;;
+ esac
+ }
+ exit $EXIT_SUCCESS
+ ;;
+ esac
+
+ # See if we need to build an old-fashioned archive.
+ for oldlib in $oldlibs; do
+
+ if test "$build_libtool_libs" = convenience; then
+ oldobjs="$libobjs_save $symfileobj"
+ addlibs="$convenience"
+ build_libtool_libs=no
+ else
+ if test "$build_libtool_libs" = module; then
+ oldobjs="$libobjs_save"
+ build_libtool_libs=no
+ else
+ oldobjs="$old_deplibs $non_pic_objects"
+ if test "$preload" = yes && test -f "$symfileobj"; then
+ oldobjs="$oldobjs $symfileobj"
+ fi
+ fi
+ addlibs="$old_convenience"
+ fi
+
+ if test -n "$addlibs"; then
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $addlibs
+ oldobjs="$oldobjs $func_extract_archives_result"
+ fi
+
+ # Do each command in the archive commands.
+ if test -n "$old_archive_from_new_cmds" && test "$build_libtool_libs" = yes; then
+ cmds=$old_archive_from_new_cmds
+ else
+
+ # Add any objects from preloaded convenience libraries
+ if test -n "$dlprefiles"; then
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $dlprefiles
+ oldobjs="$oldobjs $func_extract_archives_result"
+ fi
+
+ # POSIX demands no paths to be encoded in archives. We have
+ # to avoid creating archives with duplicate basenames if we
+ # might have to extract them afterwards, e.g., when creating a
+ # static archive out of a convenience library, or when linking
+ # the entirety of a libtool archive into another (currently
+ # not supported by libtool).
+ if (for obj in $oldobjs
+ do
+ func_basename "$obj"
+ $ECHO "$func_basename_result"
+ done | sort | sort -uc >/dev/null 2>&1); then
+ :
+ else
+ $ECHO "copying selected object files to avoid basename conflicts..."
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+ func_mkdir_p "$gentop"
+ save_oldobjs=$oldobjs
+ oldobjs=
+ counter=1
+ for obj in $save_oldobjs
+ do
+ func_basename "$obj"
+ objbase="$func_basename_result"
+ case " $oldobjs " in
+ " ") oldobjs=$obj ;;
+ *[\ /]"$objbase "*)
+ while :; do
+ # Make sure we don't pick an alternate name that also
+ # overlaps.
+ newobj=lt$counter-$objbase
+ func_arith $counter + 1
+ counter=$func_arith_result
+ case " $oldobjs " in
+ *[\ /]"$newobj "*) ;;
+ *) if test ! -f "$gentop/$newobj"; then break; fi ;;
+ esac
+ done
+ func_show_eval "ln $obj $gentop/$newobj || cp $obj $gentop/$newobj"
+ oldobjs="$oldobjs $gentop/$newobj"
+ ;;
+ *) oldobjs="$oldobjs $obj" ;;
+ esac
+ done
+ fi
+ eval cmds=\"$old_archive_cmds\"
+
+ func_len " $cmds"
+ len=$func_len_result
+ if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then
+ cmds=$old_archive_cmds
+ else
+ # the command line is too long to link in one step, link in parts
+ func_verbose "using piecewise archive linking..."
+ save_RANLIB=$RANLIB
+ RANLIB=:
+ objlist=
+ concat_cmds=
+ save_oldobjs=$oldobjs
+ oldobjs=
+ # Is there a better way of finding the last object in the list?
+ for obj in $save_oldobjs
+ do
+ last_oldobj=$obj
+ done
+ eval test_cmds=\"$old_archive_cmds\"
+ func_len " $test_cmds"
+ len0=$func_len_result
+ len=$len0
+ for obj in $save_oldobjs
+ do
+ func_len " $obj"
+ func_arith $len + $func_len_result
+ len=$func_arith_result
+ func_append objlist " $obj"
+ if test "$len" -lt "$max_cmd_len"; then
+ :
+ else
+ # the above command should be used before it gets too long
+ oldobjs=$objlist
+ if test "$obj" = "$last_oldobj" ; then
+ RANLIB=$save_RANLIB
+ fi
+ test -z "$concat_cmds" || concat_cmds=$concat_cmds~
+ eval concat_cmds=\"\${concat_cmds}$old_archive_cmds\"
+ objlist=
+ len=$len0
+ fi
+ done
+ RANLIB=$save_RANLIB
+ oldobjs=$objlist
+ if test "X$oldobjs" = "X" ; then
+ eval cmds=\"\$concat_cmds\"
+ else
+ eval cmds=\"\$concat_cmds~\$old_archive_cmds\"
+ fi
+ fi
+ fi
+ func_execute_cmds "$cmds" 'exit $?'
+ done
+
+ test -n "$generated" && \
+ func_show_eval "${RM}r$generated"
+
+ # Now create the libtool archive.
+ case $output in
+ *.la)
+ old_library=
+ test "$build_old_libs" = yes && old_library="$libname.$libext"
+ func_verbose "creating $output"
+
+ # Preserve any variables that may affect compiler behavior
+ for var in $variables_saved_for_relink; do
+ if eval test -z \"\${$var+set}\"; then
+ relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command"
+ elif eval var_value=\$$var; test -z "$var_value"; then
+ relink_command="$var=; export $var; $relink_command"
+ else
+ func_quote_for_eval "$var_value"
+ relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command"
+ fi
+ done
+ # Quote the link command for shipping.
+ relink_command="(cd `pwd`; $SHELL $progpath $preserve_args --mode=relink $libtool_args @inst_prefix_dir@)"
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e "$sed_quote_subst"`
+ if test "$hardcode_automatic" = yes ; then
+ relink_command=
+ fi
+
+ # Only create the output if not a dry run.
+ $opt_dry_run || {
+ for installed in no yes; do
+ if test "$installed" = yes; then
+ if test -z "$install_libdir"; then
+ break
+ fi
+ output="$output_objdir/$outputname"i
+ # Replace all uninstalled libtool libraries with the installed ones
+ newdependency_libs=
+ for deplib in $dependency_libs; do
+ case $deplib in
+ *.la)
+ func_basename "$deplib"
+ name="$func_basename_result"
+ eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib`
+ test -z "$libdir" && \
+ func_fatal_error "\`$deplib' is not a valid libtool archive"
+ newdependency_libs="$newdependency_libs $libdir/$name"
+ ;;
+ *) newdependency_libs="$newdependency_libs $deplib" ;;
+ esac
+ done
+ dependency_libs="$newdependency_libs"
+ newdlfiles=
+
+ for lib in $dlfiles; do
+ case $lib in
+ *.la)
+ func_basename "$lib"
+ name="$func_basename_result"
+ eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib`
+ test -z "$libdir" && \
+ func_fatal_error "\`$lib' is not a valid libtool archive"
+ newdlfiles="$newdlfiles $libdir/$name"
+ ;;
+ *) newdlfiles="$newdlfiles $lib" ;;
+ esac
+ done
+ dlfiles="$newdlfiles"
+ newdlprefiles=
+ for lib in $dlprefiles; do
+ case $lib in
+ *.la)
+ # Only pass preopened files to the pseudo-archive (for
+ # eventual linking with the app. that links it) if we
+ # didn't already link the preopened objects directly into
+ # the library:
+ func_basename "$lib"
+ name="$func_basename_result"
+ eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib`
+ test -z "$libdir" && \
+ func_fatal_error "\`$lib' is not a valid libtool archive"
+ newdlprefiles="$newdlprefiles $libdir/$name"
+ ;;
+ esac
+ done
+ dlprefiles="$newdlprefiles"
+ else
+ newdlfiles=
+ for lib in $dlfiles; do
+ case $lib in
+ [\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;;
+ *) abs=`pwd`"/$lib" ;;
+ esac
+ newdlfiles="$newdlfiles $abs"
+ done
+ dlfiles="$newdlfiles"
+ newdlprefiles=
+ for lib in $dlprefiles; do
+ case $lib in
+ [\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;;
+ *) abs=`pwd`"/$lib" ;;
+ esac
+ newdlprefiles="$newdlprefiles $abs"
+ done
+ dlprefiles="$newdlprefiles"
+ fi
+ $RM $output
+ # place dlname in correct position for cygwin
+ tdlname=$dlname
+ case $host,$output,$installed,$module,$dlname in
+ *cygwin*,*lai,yes,no,*.dll | *mingw*,*lai,yes,no,*.dll | *cegcc*,*lai,yes,no,*.dll) tdlname=../bin/$dlname ;;
+ esac
+ $ECHO > $output "\
+# $outputname - a libtool library file
+# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# The name that we can dlopen(3).
+dlname='$tdlname'
+
+# Names of this library.
+library_names='$library_names'
+
+# The name of the static archive.
+old_library='$old_library'
+
+# Linker flags that can not go in dependency_libs.
+inherited_linker_flags='$new_inherited_linker_flags'
+
+# Libraries that this one depends upon.
+dependency_libs='$dependency_libs'
+
+# Names of additional weak libraries provided by this library
+weak_library_names='$weak_libs'
+
+# Version information for $libname.
+current=$current
+age=$age
+revision=$revision
+
+# Is this an already installed library?
+installed=$installed
+
+# Should we warn about portability when linking against -modules?
+shouldnotlink=$module
+
+# Files to dlopen/dlpreopen
+dlopen='$dlfiles'
+dlpreopen='$dlprefiles'
+
+# Directory that this library needs to be installed in:
+libdir='$install_libdir'"
+ if test "$installed" = no && test "$need_relink" = yes; then
+ $ECHO >> $output "\
+relink_command=\"$relink_command\""
+ fi
+ done
+ }
+
+ # Do a symbolic link so that the libtool archive can be found in
+ # LD_LIBRARY_PATH before the program is installed.
+ func_show_eval '( cd "$output_objdir" && $RM "$outputname" && $LN_S "../$outputname" "$outputname" )' 'exit $?'
+ ;;
+ esac
+ exit $EXIT_SUCCESS
+}
+
+{ test "$mode" = link || test "$mode" = relink; } &&
+ func_mode_link ${1+"$@"}
+
+
+# func_mode_uninstall arg...
+func_mode_uninstall ()
+{
+ $opt_debug
+ RM="$nonopt"
+ files=
+ rmforce=
+ exit_status=0
+
+ # This variable tells wrapper scripts just to set variables rather
+ # than running their programs.
+ libtool_install_magic="$magic"
+
+ for arg
+ do
+ case $arg in
+ -f) RM="$RM $arg"; rmforce=yes ;;
+ -*) RM="$RM $arg" ;;
+ *) files="$files $arg" ;;
+ esac
+ done
+
+ test -z "$RM" && \
+ func_fatal_help "you must specify an RM program"
+
+ rmdirs=
+
+ origobjdir="$objdir"
+ for file in $files; do
+ func_dirname "$file" "" "."
+ dir="$func_dirname_result"
+ if test "X$dir" = X.; then
+ objdir="$origobjdir"
+ else
+ objdir="$dir/$origobjdir"
+ fi
+ func_basename "$file"
+ name="$func_basename_result"
+ test "$mode" = uninstall && objdir="$dir"
+
+ # Remember objdir for removal later, being careful to avoid duplicates
+ if test "$mode" = clean; then
+ case " $rmdirs " in
+ *" $objdir "*) ;;
+ *) rmdirs="$rmdirs $objdir" ;;
+ esac
+ fi
+
+ # Don't error if the file doesn't exist and rm -f was used.
+ if { test -L "$file"; } >/dev/null 2>&1 ||
+ { test -h "$file"; } >/dev/null 2>&1 ||
+ test -f "$file"; then
+ :
+ elif test -d "$file"; then
+ exit_status=1
+ continue
+ elif test "$rmforce" = yes; then
+ continue
+ fi
+
+ rmfiles="$file"
+
+ case $name in
+ *.la)
+ # Possibly a libtool archive, so verify it.
+ if func_lalib_p "$file"; then
+ func_source $dir/$name
+
+ # Delete the libtool libraries and symlinks.
+ for n in $library_names; do
+ rmfiles="$rmfiles $objdir/$n"
+ done
+ test -n "$old_library" && rmfiles="$rmfiles $objdir/$old_library"
+
+ case "$mode" in
+ clean)
+ case " $library_names " in
+ # " " in the beginning catches empty $dlname
+ *" $dlname "*) ;;
+ *) rmfiles="$rmfiles $objdir/$dlname" ;;
+ esac
+ test -n "$libdir" && rmfiles="$rmfiles $objdir/$name $objdir/${name}i"
+ ;;
+ uninstall)
+ if test -n "$library_names"; then
+ # Do each command in the postuninstall commands.
+ func_execute_cmds "$postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1'
+ fi
+
+ if test -n "$old_library"; then
+ # Do each command in the old_postuninstall commands.
+ func_execute_cmds "$old_postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1'
+ fi
+ # FIXME: should reinstall the best remaining shared library.
+ ;;
+ esac
+ fi
+ ;;
+
+ *.lo)
+ # Possibly a libtool object, so verify it.
+ if func_lalib_p "$file"; then
+
+ # Read the .lo file
+ func_source $dir/$name
+
+ # Add PIC object to the list of files to remove.
+ if test -n "$pic_object" &&
+ test "$pic_object" != none; then
+ rmfiles="$rmfiles $dir/$pic_object"
+ fi
+
+ # Add non-PIC object to the list of files to remove.
+ if test -n "$non_pic_object" &&
+ test "$non_pic_object" != none; then
+ rmfiles="$rmfiles $dir/$non_pic_object"
+ fi
+ fi
+ ;;
+
+ *)
+ if test "$mode" = clean ; then
+ noexename=$name
+ case $file in
+ *.exe)
+ func_stripname '' '.exe' "$file"
+ file=$func_stripname_result
+ func_stripname '' '.exe' "$name"
+ noexename=$func_stripname_result
+ # $file with .exe has already been added to rmfiles,
+ # add $file without .exe
+ rmfiles="$rmfiles $file"
+ ;;
+ esac
+ # Do a test to see if this is a libtool program.
+ if func_ltwrapper_p "$file"; then
+ if func_ltwrapper_executable_p "$file"; then
+ func_ltwrapper_scriptname "$file"
+ relink_command=
+ func_source $func_ltwrapper_scriptname_result
+ rmfiles="$rmfiles $func_ltwrapper_scriptname_result"
+ else
+ relink_command=
+ func_source $dir/$noexename
+ fi
+
+ # note $name still contains .exe if it was in $file originally
+ # as does the version of $file that was added into $rmfiles
+ rmfiles="$rmfiles $objdir/$name $objdir/${name}S.${objext}"
+ if test "$fast_install" = yes && test -n "$relink_command"; then
+ rmfiles="$rmfiles $objdir/lt-$name"
+ fi
+ if test "X$noexename" != "X$name" ; then
+ rmfiles="$rmfiles $objdir/lt-${noexename}.c"
+ fi
+ fi
+ fi
+ ;;
+ esac
+ func_show_eval "$RM $rmfiles" 'exit_status=1'
+ done
+ objdir="$origobjdir"
+
+ # Try to remove the ${objdir}s in the directories where we deleted files
+ for dir in $rmdirs; do
+ if test -d "$dir"; then
+ func_show_eval "rmdir $dir >/dev/null 2>&1"
+ fi
+ done
+
+ exit $exit_status
+}
+
+{ test "$mode" = uninstall || test "$mode" = clean; } &&
+ func_mode_uninstall ${1+"$@"}
+
+test -z "$mode" && {
+ help="$generic_help"
+ func_fatal_help "you must specify a MODE"
+}
+
+test -z "$exec_cmd" && \
+ func_fatal_help "invalid operation mode \`$mode'"
+
+if test -n "$exec_cmd"; then
+ eval exec "$exec_cmd"
+ exit $EXIT_FAILURE
+fi
+
+exit $exit_status
+
+
+# The TAGs below are defined such that we never get into a situation
+# in which we disable both kinds of libraries. Given conflicting
+# choices, we go for a static library, that is the most portable,
+# since we can't tell whether shared libraries were disabled because
+# the user asked for that or because the platform doesn't support
+# them. This is particularly important on AIX, because we don't
+# support having both static and shared libraries enabled at the same
+# time on that platform, so we default to a shared-only configuration.
+# If a disable-shared tag is given, we'll fallback to a static-only
+# configuration. But we'll never go from static-only to shared-only.
+
+# ### BEGIN LIBTOOL TAG CONFIG: disable-shared
+build_libtool_libs=no
+build_old_libs=yes
+# ### END LIBTOOL TAG CONFIG: disable-shared
+
+# ### BEGIN LIBTOOL TAG CONFIG: disable-static
+build_old_libs=`case $build_libtool_libs in yes) echo no;; *) echo yes;; esac`
+# ### END LIBTOOL TAG CONFIG: disable-static
+
+# Local Variables:
+# mode:shell-script
+# sh-indentation:2
+# End:
+# vi:sw=2
+
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/missing b/src/libGkArrays/src/libProgressBar-1.2.0/missing
new file mode 100755
index 0000000..28055d2
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/missing
@@ -0,0 +1,376 @@
+#! /bin/sh
+# Common stub for a few missing GNU programs while installing.
+
+scriptversion=2009-04-28.21; # UTC
+
+# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
+# 2008, 2009 Free Software Foundation, Inc.
+# Originally by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+if test $# -eq 0; then
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+fi
+
+run=:
+sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
+sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
+
+# In the cases where this matters, `missing' is being run in the
+# srcdir already.
+if test -f configure.ac; then
+ configure_ac=configure.ac
+else
+ configure_ac=configure.in
+fi
+
+msg="missing on your system"
+
+case $1 in
+--run)
+ # Try to run requested program, and just exit if it succeeds.
+ run=
+ shift
+ "$@" && exit 0
+ # Exit code 63 means version mismatch. This often happens
+ # when the user try to use an ancient version of a tool on
+ # a file that requires a minimum version. In this case we
+ # we should proceed has if the program had been absent, or
+ # if --run hadn't been passed.
+ if test $? = 63; then
+ run=:
+ msg="probably too old"
+ fi
+ ;;
+
+ -h|--h|--he|--hel|--help)
+ echo "\
+$0 [OPTION]... PROGRAM [ARGUMENT]...
+
+Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
+error status if there is no known handling for PROGRAM.
+
+Options:
+ -h, --help display this help and exit
+ -v, --version output version information and exit
+ --run try to run the given command, and emulate it if it fails
+
+Supported PROGRAM values:
+ aclocal touch file \`aclocal.m4'
+ autoconf touch file \`configure'
+ autoheader touch file \`config.h.in'
+ autom4te touch the output file, or create a stub one
+ automake touch all \`Makefile.in' files
+ bison create \`y.tab.[ch]', if possible, from existing .[ch]
+ flex create \`lex.yy.c', if possible, from existing .c
+ help2man touch the output file
+ lex create \`lex.yy.c', if possible, from existing .c
+ makeinfo touch the output file
+ tar try tar, gnutar, gtar, then tar without non-portable flags
+ yacc create \`y.tab.[ch]', if possible, from existing .[ch]
+
+Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
+\`g' are ignored when checking the name.
+
+Send bug reports to <bug-automake at gnu.org>."
+ exit $?
+ ;;
+
+ -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
+ echo "missing $scriptversion (GNU Automake)"
+ exit $?
+ ;;
+
+ -*)
+ echo 1>&2 "$0: Unknown \`$1' option"
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+ ;;
+
+esac
+
+# normalize program name to check for.
+program=`echo "$1" | sed '
+ s/^gnu-//; t
+ s/^gnu//; t
+ s/^g//; t'`
+
+# Now exit if we have it, but it failed. Also exit now if we
+# don't have it and --version was passed (most likely to detect
+# the program). This is about non-GNU programs, so use $1 not
+# $program.
+case $1 in
+ lex*|yacc*)
+ # Not GNU programs, they don't have --version.
+ ;;
+
+ tar*)
+ if test -n "$run"; then
+ echo 1>&2 "ERROR: \`tar' requires --run"
+ exit 1
+ elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+ exit 1
+ fi
+ ;;
+
+ *)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+ # Could not run --version or --help. This is probably someone
+ # running `$TOOL --version' or `$TOOL --help' to check whether
+ # $TOOL exists and not knowing $TOOL uses missing.
+ exit 1
+ fi
+ ;;
+esac
+
+# If it does not exist, or fails to run (possibly an outdated version),
+# try to emulate it.
+case $program in
+ aclocal*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acinclude.m4' or \`${configure_ac}'. You might want
+ to install the \`Automake' and \`Perl' packages. Grab them from
+ any GNU archive site."
+ touch aclocal.m4
+ ;;
+
+ autoconf*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`${configure_ac}'. You might want to install the
+ \`Autoconf' and \`GNU m4' packages. Grab them from any GNU
+ archive site."
+ touch configure
+ ;;
+
+ autoheader*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acconfig.h' or \`${configure_ac}'. You might want
+ to install the \`Autoconf' and \`GNU m4' packages. Grab them
+ from any GNU archive site."
+ files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
+ test -z "$files" && files="config.h"
+ touch_files=
+ for f in $files; do
+ case $f in
+ *:*) touch_files="$touch_files "`echo "$f" |
+ sed -e 's/^[^:]*://' -e 's/:.*//'`;;
+ *) touch_files="$touch_files $f.in";;
+ esac
+ done
+ touch $touch_files
+ ;;
+
+ automake*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
+ You might want to install the \`Automake' and \`Perl' packages.
+ Grab them from any GNU archive site."
+ find . -type f -name Makefile.am -print |
+ sed 's/\.am$/.in/' |
+ while read f; do touch "$f"; done
+ ;;
+
+ autom4te*)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, but is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them.
+ You can get \`$1' as part of \`Autoconf' from any GNU
+ archive site."
+
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo "#! /bin/sh"
+ echo "# Created by GNU Automake missing as a replacement of"
+ echo "# $ $@"
+ echo "exit 0"
+ chmod +x $file
+ exit 1
+ fi
+ ;;
+
+ bison*|yacc*)
+ echo 1>&2 "\
+WARNING: \`$1' $msg. You should only need it if
+ you modified a \`.y' file. You may need the \`Bison' package
+ in order for those modifications to take effect. You can get
+ \`Bison' from any GNU archive site."
+ rm -f y.tab.c y.tab.h
+ if test $# -ne 1; then
+ eval LASTARG="\${$#}"
+ case $LASTARG in
+ *.y)
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" y.tab.c
+ fi
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" y.tab.h
+ fi
+ ;;
+ esac
+ fi
+ if test ! -f y.tab.h; then
+ echo >y.tab.h
+ fi
+ if test ! -f y.tab.c; then
+ echo 'main() { return 0; }' >y.tab.c
+ fi
+ ;;
+
+ lex*|flex*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.l' file. You may need the \`Flex' package
+ in order for those modifications to take effect. You can get
+ \`Flex' from any GNU archive site."
+ rm -f lex.yy.c
+ if test $# -ne 1; then
+ eval LASTARG="\${$#}"
+ case $LASTARG in
+ *.l)
+ SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" lex.yy.c
+ fi
+ ;;
+ esac
+ fi
+ if test ! -f lex.yy.c; then
+ echo 'main() { return 0; }' >lex.yy.c
+ fi
+ ;;
+
+ help2man*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a dependency of a manual page. You may need the
+ \`Help2man' package in order for those modifications to take
+ effect. You can get \`Help2man' from any GNU archive site."
+
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo ".ab help2man is required to generate this page"
+ exit $?
+ fi
+ ;;
+
+ makeinfo*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.texi' or \`.texinfo' file, or any other file
+ indirectly affecting the aspect of the manual. The spurious
+ call might also be the consequence of using a buggy \`make' (AIX,
+ DU, IRIX). You might want to install the \`Texinfo' package or
+ the \`GNU make' package. Grab either from any GNU archive site."
+ # The file to touch is that specified with -o ...
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -z "$file"; then
+ # ... or it is the one specified with @setfilename ...
+ infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
+ file=`sed -n '
+ /^@setfilename/{
+ s/.* \([^ ]*\) *$/\1/
+ p
+ q
+ }' $infile`
+ # ... or it is derived from the source name (dir/f.texi becomes f.info)
+ test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
+ fi
+ # If the file does not exist, the user really needs makeinfo;
+ # let's fail without touching anything.
+ test -f $file || exit 1
+ touch $file
+ ;;
+
+ tar*)
+ shift
+
+ # We have already tried tar in the generic part.
+ # Look for gnutar/gtar before invocation to avoid ugly error
+ # messages.
+ if (gnutar --version > /dev/null 2>&1); then
+ gnutar "$@" && exit 0
+ fi
+ if (gtar --version > /dev/null 2>&1); then
+ gtar "$@" && exit 0
+ fi
+ firstarg="$1"
+ if shift; then
+ case $firstarg in
+ *o*)
+ firstarg=`echo "$firstarg" | sed s/o//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ case $firstarg in
+ *h*)
+ firstarg=`echo "$firstarg" | sed s/h//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ fi
+
+ echo 1>&2 "\
+WARNING: I can't seem to be able to run \`tar' with the given arguments.
+ You may want to install GNU tar or Free paxutils, or check the
+ command line arguments."
+ exit 1
+ ;;
+
+ *)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, and is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them. Check the \`README' file,
+ it often tells you about the needed prerequisites for installing
+ this package. You may also peek at any GNU archive site, in case
+ some other package would contain this missing \`$1' program."
+ exit 1
+ ;;
+esac
+
+exit 0
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/mkinstalldirs b/src/libGkArrays/src/libProgressBar-1.2.0/mkinstalldirs
new file mode 100755
index 0000000..4191a45
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/mkinstalldirs
@@ -0,0 +1,162 @@
+#! /bin/sh
+# mkinstalldirs --- make directory hierarchy
+
+scriptversion=2009-04-28.21; # UTC
+
+# Original author: Noah Friedman <friedman at prep.ai.mit.edu>
+# Created: 1993-05-16
+# Public domain.
+#
+# This file is maintained in Automake, please report
+# bugs to <bug-automake at gnu.org> or send patches to
+# <automake-patches at gnu.org>.
+
+nl='
+'
+IFS=" "" $nl"
+errstatus=0
+dirmode=
+
+usage="\
+Usage: mkinstalldirs [-h] [--help] [--version] [-m MODE] DIR ...
+
+Create each directory DIR (with mode MODE, if specified), including all
+leading file name components.
+
+Report bugs to <bug-automake at gnu.org>."
+
+# process command line arguments
+while test $# -gt 0 ; do
+ case $1 in
+ -h | --help | --h*) # -h for help
+ echo "$usage"
+ exit $?
+ ;;
+ -m) # -m PERM arg
+ shift
+ test $# -eq 0 && { echo "$usage" 1>&2; exit 1; }
+ dirmode=$1
+ shift
+ ;;
+ --version)
+ echo "$0 $scriptversion"
+ exit $?
+ ;;
+ --) # stop option processing
+ shift
+ break
+ ;;
+ -*) # unknown option
+ echo "$usage" 1>&2
+ exit 1
+ ;;
+ *) # first non-opt arg
+ break
+ ;;
+ esac
+done
+
+for file
+do
+ if test -d "$file"; then
+ shift
+ else
+ break
+ fi
+done
+
+case $# in
+ 0) exit 0 ;;
+esac
+
+# Solaris 8's mkdir -p isn't thread-safe. If you mkdir -p a/b and
+# mkdir -p a/c at the same time, both will detect that a is missing,
+# one will create a, then the other will try to create a and die with
+# a "File exists" error. This is a problem when calling mkinstalldirs
+# from a parallel make. We use --version in the probe to restrict
+# ourselves to GNU mkdir, which is thread-safe.
+case $dirmode in
+ '')
+ if mkdir -p --version . >/dev/null 2>&1 && test ! -d ./--version; then
+ echo "mkdir -p -- $*"
+ exec mkdir -p -- "$@"
+ else
+ # On NextStep and OpenStep, the `mkdir' command does not
+ # recognize any option. It will interpret all options as
+ # directories to create, and then abort because `.' already
+ # exists.
+ test -d ./-p && rmdir ./-p
+ test -d ./--version && rmdir ./--version
+ fi
+ ;;
+ *)
+ if mkdir -m "$dirmode" -p --version . >/dev/null 2>&1 &&
+ test ! -d ./--version; then
+ echo "mkdir -m $dirmode -p -- $*"
+ exec mkdir -m "$dirmode" -p -- "$@"
+ else
+ # Clean up after NextStep and OpenStep mkdir.
+ for d in ./-m ./-p ./--version "./$dirmode";
+ do
+ test -d $d && rmdir $d
+ done
+ fi
+ ;;
+esac
+
+for file
+do
+ case $file in
+ /*) pathcomp=/ ;;
+ *) pathcomp= ;;
+ esac
+ oIFS=$IFS
+ IFS=/
+ set fnord $file
+ shift
+ IFS=$oIFS
+
+ for d
+ do
+ test "x$d" = x && continue
+
+ pathcomp=$pathcomp$d
+ case $pathcomp in
+ -*) pathcomp=./$pathcomp ;;
+ esac
+
+ if test ! -d "$pathcomp"; then
+ echo "mkdir $pathcomp"
+
+ mkdir "$pathcomp" || lasterr=$?
+
+ if test ! -d "$pathcomp"; then
+ errstatus=$lasterr
+ else
+ if test ! -z "$dirmode"; then
+ echo "chmod $dirmode $pathcomp"
+ lasterr=
+ chmod "$dirmode" "$pathcomp" || lasterr=$?
+
+ if test ! -z "$lasterr"; then
+ errstatus=$lasterr
+ fi
+ fi
+ fi
+ fi
+
+ pathcomp=$pathcomp/
+ done
+done
+
+exit $errstatus
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/postinst.in b/src/libGkArrays/src/libProgressBar-1.2.0/postinst.in
new file mode 100644
index 0000000..4ff7947
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/postinst.in
@@ -0,0 +1,4 @@
+#!/bin/sh
+set -e
+echo "@hacked_prefix@/lib" > /etc/ld.so.conf.d/@PACKAGE at -@VERSION at .conf
+ldconfig
diff --git a/src/libGkArrays/src/libProgressBar-1.2.0/prerm.in b/src/libGkArrays/src/libProgressBar-1.2.0/prerm.in
new file mode 100644
index 0000000..4a3afe1
--- /dev/null
+++ b/src/libGkArrays/src/libProgressBar-1.2.0/prerm.in
@@ -0,0 +1,4 @@
+#!/bin/sh
+set -e
+rm /etc/ld.so.conf.d/@PACKAGE at -@VERSION at .conf
+ldconfig
diff --git a/src/libGkArrays/src/readsReader.cpp b/src/libGkArrays/src/readsReader.cpp
new file mode 100644
index 0000000..6811652
--- /dev/null
+++ b/src/libGkArrays/src/readsReader.cpp
@@ -0,0 +1,405 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at etud.univ-montp2.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+#include <iostream>
+#include "readsReader.h"
+
+using namespace std;
+
+namespace gkarrays {
+
+ void readIterator::setPrintWarnings(bool isVisible)
+ {
+ this->warningsVisible = isVisible;
+ }
+
+ bool readIterator::printWarnings() {
+ return warningsVisible;
+ }
+
+ singleReadIterator::singleReadIterator(const char* filename, uint k,
+ uint length, bool printWarnings,
+ bool autoDiscard,
+ bool autoFirstIteration):
+ k(k),length(length),autoDiscard(autoDiscard) {
+ readsFile = gzopen(filename, "r");
+ seq = kseq_init(readsFile);
+ finished = false;
+ filenameConstructor = true;
+ tagNumber = 0;
+ setPrintWarnings(printWarnings);
+ if (autoFirstIteration) ++(*this);
+ }
+
+ singleReadIterator::singleReadIterator(kseq_t *seq, uint k, uint length):k(k),
+ length(length),
+ seq(seq),
+ filenameConstructor(false) {
+ autoDiscard = true;
+ tagNumber = 0;
+ setPrintWarnings(false);
+ }
+
+ singleReadIterator::singleReadIterator(const singleReadIterator& mit):k(mit.k),
+ length(mit.length),
+ seq(mit.seq),
+ finished(mit.finished),
+ filenameConstructor(false),
+ autoDiscard(mit.autoDiscard),
+ tagNumber(mit.tagNumber)
+ {}
+
+ singleReadIterator::~singleReadIterator() {
+ if (seq && filenameConstructor) {
+ kseq_destroy(seq);
+ gzclose(readsFile);
+ }
+ }
+
+ readIterator& singleReadIterator::operator++() {
+
+ if (finished || kseq_read(seq) <= 0) {
+ finished = true;
+ } else {
+ tagNumber++;
+ if (isDiscarded() && autoDiscard) {
+ if(printWarnings()) {
+ cerr << "Warning: read number " << tagNumber
+ << " is ignored";
+ if (k > getLength()) {
+ cerr << " because its length is lower than the k-mer length"
+ << endl;
+ } else if (getLength() < length) {
+ cerr << " because its length is shorter than expected"
+ << endl;
+ }
+ }
+ // Read should be ignored (its length isn't good), go to the next one
+ ++(*this);
+ }
+ }
+ return *this;
+ }
+
+ singleReadIterator singleReadIterator::operator++(int) {
+ singleReadIterator orig = *this;
+ ++(*this);
+ return orig;
+ }
+
+ bool singleReadIterator::operator==(const singleReadIterator& rhs) {
+ return ((seq == NULL || finished) && (rhs.seq == NULL || rhs.finished))
+ || (seq == rhs.seq);
+ }
+ bool singleReadIterator::operator!=(const singleReadIterator& rhs) {
+ return ! (*this == rhs);
+ }
+
+ kseq_t &singleReadIterator::operator*() {
+ return *seq;
+ }
+
+ size_t singleReadIterator::getLength() {
+ return seq->seq.l;
+ }
+
+ char *singleReadIterator::getName() {
+ return seq->name.s;
+ }
+
+ char *singleReadIterator::getQuality() {
+ return seq->qual.s;
+ }
+
+ uint singleReadIterator::getReadNumber() {
+ // minus 1 because we want the numbering to start from 0
+ return tagNumber-1;
+ }
+
+ char *singleReadIterator::getSequence() {
+ return seq->seq.s;
+ }
+
+ bool singleReadIterator::isFinished() {
+ return finished;
+ }
+
+ bool singleReadIterator::isDiscarded() {
+ return (getLength() < length || getLength() < k);
+ }
+
+ void singleReadIterator::setAutoDiscard(bool value){
+ autoDiscard = value;
+ }
+
+ ////////////////////////////////////////////////////////////
+
+ pairedEndReadIterator::pairedEndReadIterator(const char* filename1,
+ const char* filename2,
+ uint k, uint length,
+ bool printWarnings):
+ k(k),length(length)
+ {
+ this->readIterator1 = new singleReadIterator(filename1,k,length,printWarnings,false,false);
+ this->readIterator2 = new singleReadIterator(filename2,k,length,printWarnings,false,false);
+ this->is_it1CurrentIterator = false;
+ this->setPrintWarnings(printWarnings);
+ ++(*this);
+ }
+
+ pairedEndReadIterator::pairedEndReadIterator(const pairedEndReadIterator& mit){
+ this->readIterator1 = mit.readIterator1;
+ this->readIterator2 = mit.readIterator2;
+ this->is_it1CurrentIterator = mit.is_it1CurrentIterator;
+ }
+
+ pairedEndReadIterator::~pairedEndReadIterator()
+ {
+ delete readIterator1;
+ delete readIterator2;
+ }
+
+ readIterator& pairedEndReadIterator::operator++()
+ {
+ bool isReadPairValid = false;
+
+ if(!isFinished()) {
+ if(!is_it1CurrentIterator) {
+ while(!isReadPairValid && !isFinished()) {
+ ++(*readIterator1);
+ ++(*readIterator2);
+ if(isFinished()) break;
+ if(!readIterator1->isDiscarded() && !readIterator2->isDiscarded()){
+ isReadPairValid = true;
+ } else if(printWarnings()) {
+ cerr << "Warning: both reads of the pair number " << readIterator1->getReadNumber()
+ << " are ignored";
+ if (k > readIterator1->getLength()) {
+ cerr << " because the first read length is lower than the k-mer length"
+ << endl;
+ } else if (k > readIterator2->getLength()){
+ cerr << " because the second read length is lower than the k-mer length"
+ << endl;
+ } else if (readIterator1->getLength() < length) {
+ cerr << " because the first read length is shorter than expected"
+ << endl;
+ } else if (readIterator2->getLength() < length) {
+ cerr << " because the second read length is shorter than expected"
+ << endl;
+ }
+ }
+ }
+ is_it1CurrentIterator = true;
+ } else {
+ is_it1CurrentIterator = false;
+ }
+ }
+ return *this;
+ }
+
+ pairedEndReadIterator pairedEndReadIterator::operator++(int)
+ {
+ pairedEndReadIterator orig = *this;
+ ++(*this);
+ return orig;
+ }
+
+ bool pairedEndReadIterator::operator==(const pairedEndReadIterator& rhs) {
+ if(is_it1CurrentIterator){
+ return readIterator1 == rhs.readIterator1;
+ } else {
+ return readIterator2 == rhs.readIterator2;
+ }
+ }
+
+ bool pairedEndReadIterator::operator!=(const pairedEndReadIterator& rhs) {
+ return !(*this == rhs);
+ }
+
+ kseq_t &pairedEndReadIterator::operator*() {
+ if(is_it1CurrentIterator){
+ return *(*readIterator1);
+ } else {
+ return *(*readIterator2);
+ }
+ }
+
+ size_t pairedEndReadIterator::getLength() {
+ return getCurrentReadIterator()->getLength();
+ }
+
+ char *pairedEndReadIterator::getName() {
+ return getCurrentReadIterator()->getName();
+ }
+
+ readIterator& pairedEndReadIterator::getPair() {
+ if(is_it1CurrentIterator) {
+ is_it1CurrentIterator = false;
+ } else {
+ is_it1CurrentIterator = true;
+ }
+ return *this;
+ }
+
+ char *pairedEndReadIterator::getQuality() {
+ return getCurrentReadIterator()->getQuality();
+ }
+
+ uint pairedEndReadIterator::getReadNumber() {
+ if(is_it1CurrentIterator) {
+ return readIterator1->getReadNumber() + readIterator2->getReadNumber();
+ } else {
+ return readIterator1->getReadNumber() + readIterator2->getReadNumber() + 1;
+ }
+ }
+
+ char *pairedEndReadIterator::getSequence() {
+ return getCurrentReadIterator()->getSequence();
+ }
+
+ bool pairedEndReadIterator::isFinished() {
+ return readIterator1->isFinished() || readIterator2->isFinished();
+ }
+
+ bool pairedEndReadIterator::isTheFirstMemberOfPair() {
+ return is_it1CurrentIterator;
+ }
+
+ singleReadIterator *pairedEndReadIterator::getCurrentReadIterator() {
+ if(is_it1CurrentIterator) {
+ return readIterator1;
+ } else {
+ return readIterator2;
+ }
+ }
+
+
+ readsReader::readsReader(char *filename, uint k, uint length)
+ {
+ this->filename1 = filename;
+ this->k = k;
+ this->length = length;
+ this->is_pairedEnd = false;
+ }
+
+ readsReader::readsReader(char *filename1, char *filename2, uint k, uint length)
+ {
+ this->filename1 = filename1;
+ this->filename2 = filename2;
+ this->k = k;
+ this->length = length;
+ this->is_pairedEnd = true;
+ }
+
+ readIterator *readsReader::begin(bool printWarnings) {
+ if(is_pairedEnd){
+ return new pairedEndReadIterator(filename1,filename2,k,length,printWarnings);
+ } else {
+ return new singleReadIterator(filename1,k,length,printWarnings);
+ }
+ }
+
+ bool readsReader::isPairedEnd() {
+ return is_pairedEnd;
+ }
+
+}
diff --git a/src/libGkArrays/src/readsReader.h b/src/libGkArrays/src/readsReader.h
new file mode 100644
index 0000000..97a941d
--- /dev/null
+++ b/src/libGkArrays/src/readsReader.h
@@ -0,0 +1,432 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at etud.univ-montp2.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef READSREADER_H
+#define READSREADER_H
+
+#include <iterator>
+#include <zlib.h>
+#include "kseq/kseq.h"
+
+KSEQ_INIT(gzFile, gzread)
+
+namespace gkarrays {
+ /**
+ * readIterator allows to retrieve information on each read by traversing
+ * them in order, one after one.
+ * If the k-mer length or the read length are given, only reads that are
+ * long enough to fulfill those values are considered.
+ */
+ class readIterator: public std::iterator<std::forward_iterator_tag, kseq_t> {
+ bool warningsVisible;
+ public:
+ /**
+ * Virtual destructor, necessary in c++
+ */
+ virtual ~readIterator(){}
+
+ /**
+ * Go to next sequence
+ */
+ virtual readIterator& operator++() = 0;
+
+ /**
+ * @return the kseq_t related to the current read
+ */
+ virtual kseq_t& operator*() = 0;
+
+ /**
+ * @return the length of the read
+ */
+ virtual size_t getLength() = 0;
+
+ /**
+ * @return the name of the read
+ */
+ virtual char *getName() = 0;
+
+ /**
+ * @return the quality of the read
+ */
+ virtual char *getQuality() = 0;
+
+ /**
+ * @return the number of the read in the file
+ */
+ virtual uint getReadNumber() = 0;
+
+ /**
+ * @return the sequence of the read
+ */
+ virtual char *getSequence() = 0;
+
+ /**
+ * @return true iff we have read the whole file
+ */
+ virtual bool isFinished() = 0;
+
+ /**
+ * @return true if warnings are visible
+ * false either.
+ */
+ bool printWarnings();
+
+ /**
+ * @param isVisible Printwarnins visible value.
+ */
+ void setPrintWarnings(bool isVisible);
+ };
+
+ /**
+ * singleReadIterator allows to retrieve information on each read by traversing
+ * them in order, one after one.
+ * If the k-mer length or the read length are given, only reads that are
+ * long enough to fulfill those values are considered.
+ */
+ class singleReadIterator: public readIterator {
+ uint k;
+ uint length;
+ kseq_t *seq;
+ bool finished;
+ bool filenameConstructor;
+ gzFile readsFile;
+ bool autoDiscard; // if autoDiscard is true, the iterator will skip bad reads
+ uint tagNumber;
+ public:
+ /**
+ * Constructor. Reads are retrieved from the given file.
+ * @param filename: file we must iterate on
+ * @param k: k-mer length used (0 if unknown or not applicable)
+ * @param length: Read length (0 for variable)
+ * @param printWarnings: if true print warnings when skipping a read
+ * @param autoDiscard: if true skip automatically bad reads
+ * @param autoFirstIteration: automatically perform the first iteration
+ * (meaning that it initializes the data structure)
+ */
+ singleReadIterator(const char* filename, uint k=0, uint length=0,
+ bool printWarnings=false, bool autoDiscard=true,
+ bool autoFirstIteration=true);
+
+ /**
+ * Constructor. singleReadIterator starts at the given sequence.
+ * @param seq: the sequence to start at.
+ * @param k: k-mer length used (0 if unknown or not applicable)
+ * @param length: Read length (0 for variable)
+ */
+ singleReadIterator(kseq_t* seq, uint k=0, uint length=0);
+
+ /**
+ * Copy constructor
+ */
+ singleReadIterator(const singleReadIterator& mit);
+
+ /**
+ * Destructor
+ */
+ ~singleReadIterator();
+
+ /**
+ * Go to next sequence prefix
+ */
+ virtual readIterator& operator++();
+ /**
+ * Go to next sequence postfix
+ */
+ virtual singleReadIterator operator++(int);
+
+ virtual bool operator==(const singleReadIterator& rhs);
+ virtual bool operator!=(const singleReadIterator& rhs);
+ virtual kseq_t& operator*();
+
+ /**
+ * @return the name of the read
+ */
+ virtual char *getName();
+
+ /**
+ * @return the quality of the read
+ */
+ virtual char *getQuality();
+
+ /**
+ * @return the sequence of the read
+ */
+ virtual char *getSequence();
+
+ /**
+ * @return the number of the read in the file
+ */
+ virtual uint getReadNumber();
+
+ /**
+ * @return the length of the read
+ */
+ virtual size_t getLength();
+
+ /**
+ * @return true iff we have read the whole file
+ */
+ virtual bool isFinished();
+
+ /**
+ * @return true if real tag length is inferior to k or to wanted length
+ */
+ bool isDiscarded();
+
+ /**
+ * @param value Value to set AutoDiscard mode
+ */
+ void setAutoDiscard(bool value);
+
+ };
+
+ /**
+ * pairedEndReadIterator allows to retrieve information on each read by traversing
+ * them in order, one after one in the case of paired-end reads.
+ * If the k-mer length or the read length are given, only reads that are
+ * long enough to fulfill those values are considered.
+ */
+ class pairedEndReadIterator: public readIterator {
+ singleReadIterator *readIterator1;
+ singleReadIterator *readIterator2;
+ bool is_it1CurrentIterator;
+ uint k;
+ uint length;
+
+ public:
+ /**
+ * Constructor. Reads are retrieved from the given file.
+ * @param filename1: file we must iterate on
+ * @param filename2: second file (for paired-end) we must iterate on
+ * @param k: k-mer length used (0 if unknown or not applicable)
+ * @param length: Read length (0 for variable)
+ * @param printWarnings: if true print warnings when skipping a read
+ */
+ pairedEndReadIterator(const char* filename1, const char* filename2, uint k=0,
+ uint length=0, bool printWarnings=false);
+
+ /**
+ * Copy constructor
+ */
+ pairedEndReadIterator(const pairedEndReadIterator& mit);
+
+ /**
+ * Destructor
+ */
+ virtual ~pairedEndReadIterator();
+
+ /**
+ * Go to next sequence prefix
+ */
+ virtual readIterator& operator++();
+ /**
+ * Go to next sequence postfix
+ */
+ virtual pairedEndReadIterator operator++(int);
+ virtual bool operator==(const pairedEndReadIterator& rhs);
+ virtual bool operator!=(const pairedEndReadIterator& rhs);
+ virtual kseq_t& operator*();
+
+ /**
+ * @return the length of the read
+ */
+ virtual size_t getLength();
+
+ /**
+ * @return the name of the read
+ */
+ virtual char *getName();
+
+ /**
+ * @return the paired iterator with the current one
+ */
+ readIterator& getPair();
+
+ /**
+ * @return the quality of the read
+ */
+ virtual char *getQuality();
+
+ /**
+ * @return the number of the read in the file
+ */
+ virtual uint getReadNumber();
+
+ /**
+ * @return the sequence of the read
+ */
+ virtual char *getSequence();
+
+ /**
+ * @return true iff we have read the whole file
+ */
+ virtual bool isFinished();
+
+ /**
+ * @return true if the current read is the first
+ * member of the pair
+ */
+ bool isTheFirstMemberOfPair();
+
+ private:
+
+ /**
+ * @return the current singleReadIterator according to the isIt1CurrentIterator boolean
+ */
+ singleReadIterator *getCurrentReadIterator();
+ };
+
+ /**
+ * readsReader is a class that allows you to store informations about
+ * an RNA_Seq experiment. It works both for single reads and paired-end reads.
+ * You can get an iterator using method begin() in order to go trough all reads.
+ */
+ class readsReader {
+
+ char *filename1;
+ char *filename2; // in case of paired end;
+ uint k;
+ uint length;
+ bool is_pairedEnd;
+
+ public :
+ /**
+ * Single reads constructor
+ * @param filename The name of the file containg reads
+ * @param k length of k-mers we have to use (0 for variable-length reads)
+ * @param length length of the reads. If a shorter read is found,
+ * it raises an error. If a longer read is found, only the prefix
+ * of tag_length characters is kept.
+ * If tag_length == 0 (default), just gess what the read length
+ * is.
+ */
+ readsReader(char *filename, uint k=0, uint length=0);
+
+ /**
+ * Single reads constructor
+ * @param filename1 The name of the first file containing reads
+ * @param filename2 The name of the second file containing reads
+ * @param k length of k-mers we have to use (0 for variable-length reads)
+ * @param length length of the reads. If a shorter read is found,
+ * it raises an error. If a longer read is found, only the prefix
+ * of tag_length characters is kept.
+ * If tag_length == 0 (default), just gess what the read length
+ * is.
+ */
+ readsReader(char *filename1, char *filename2, uint k=0, uint length=0);
+
+ /**
+ * @param printWarnings Value of printWarnings option
+ * @return an read iterator that goes through the read file(s)
+ */
+ readIterator *begin(bool printWarnings=false);
+
+ /**
+ * @return true is the reads are paired-end (i.e there is two reads files)
+ */
+ bool isPairedEnd();
+
+ };
+}
+
+#endif
diff --git a/src/libGkArrays/src/solArray.cpp b/src/libGkArrays/src/solArray.cpp
new file mode 100644
index 0000000..6e437f9
--- /dev/null
+++ b/src/libGkArrays/src/solArray.cpp
@@ -0,0 +1,186 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <cstddef>
+#include <cstdlib>
+#include "solArray.h"
+#include "utils.h"
+
+namespace gkarrays {
+
+ SolArray::SolArray():type(SMALL_ARRAY),large(NULL),small(NULL),bv(NULL),len(0) {}
+
+ SolArray::SolArray(uintSA nbElements, array_type t) {
+ init(nbElements, nbElements, t);
+ }
+
+ SolArray::SolArray(uintSA nbElements, uintSA max, array_type t) {
+ init(nbElements, max, t);
+ }
+
+ SolArray::SolArray(SolArray &sa):type(sa.type), large(sa.large), small(sa.small),
+ bv(sa.bv), len(sa.len){}
+
+ SolArray::SolArray(void *ptr, array_type t, uintSA nbElements) throw (invalid_argument)
+ :type(t),
+ len(nbElements)
+ {
+ small = NULL;
+ large = NULL;
+ bv = NULL;
+ switch(type) {
+ case SMALL_ARRAY:
+ small = (uint *)ptr;
+ break;
+ case LARGE_ARRAY:
+ large = (uintSA *)ptr;
+ break;
+ default:
+ throw invalid_argument("Cannot create a bit vector array with an already allocated memory zone");
+ }
+ }
+
+ SolArray::~SolArray() {
+ if (large)
+ free(large);
+ if (small)
+ free(small);
+ if (bv)
+ delete bv;
+ }
+
+ void SolArray::init(uintSA nbElements, uintSA max, array_type t) {
+ len = nbElements;
+ type = t;
+ small = NULL;
+ bv = NULL;
+ large = NULL;
+ switch(type) {
+ case LARGE_ARRAY:
+ large = Calloc<uintSA>(nbElements);
+ break;
+ case SMALL_ARRAY:
+ small = Calloc<uint>(nbElements);
+ break;
+ default:
+ // Compute the number of bits needed
+ uint nb_bits = BitVector<uintSA, uintSA>::GetMinimalBit(max);
+ nb_bits = (nb_bits / 8 + (nb_bits % 8 == 0 ? 0 : 1)) * 8;
+ bv = new BitVector<uintSA, uintSA>(nbElements, nb_bits);
+ }
+ }
+
+ void SolArray::realloc(uintSA nbElements) throw (logic_error) {
+ len = nbElements;
+ switch(type) {
+ case SMALL_ARRAY:
+ small = (uint*) ::realloc(small, nbElements * sizeof(uint));
+ break;
+ case LARGE_ARRAY:
+ large = (uintSA*) ::realloc(large, nbElements * sizeof(uintSA));
+ break;
+ default:
+ bv->Resize(nbElements);
+ }
+ }
+}
+
diff --git a/src/libGkArrays/src/solArray.h b/src/libGkArrays/src/solArray.h
new file mode 100644
index 0000000..7f05193
--- /dev/null
+++ b/src/libGkArrays/src/solArray.h
@@ -0,0 +1,260 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef SOL_ARRAY_H
+#define SOL_ARRAY_H
+
+#include <stdexcept>
+#include "gkArraysTypes.h"
+#include "bitvector.hxx"
+
+using namespace std;
+
+namespace gkarrays {
+
+ typedef enum {SMALL_ARRAY, LARGE_ARRAY, OPTIMAL_ARRAY} array_type;
+
+ /**
+ * Small Or Large (SOL) Array storing integers. A SOL array can either
+ * store 32-bit, 64-bit integers, or fixed length integers on a different number
+ * of bits, depending on the user choice.
+ * This class allows to deal with the same variable whatever the type of
+ * integers we are storing.
+ */
+ class SolArray {
+ public:
+ array_type type;
+ uintSA *large;
+ uint *small;
+ BitVector<uintSA, uintSA> *bv;
+ uintSA len;
+
+ /**
+ * Default constructor
+ * @post getType() == SMALL_ARRAY && length() == 0
+ */
+ SolArray();
+
+ /**
+ * @param nbElements: number of elements to be stored in the array.
+ * @param t: type of the array to be constructed.
+ * This specifies if we need to build a small array (32-bit integers)
+ * a large array (64-bit integers) or an optimal array which uses the
+ * optimal number of bits in memory (but which is longer)
+ */
+ SolArray(uintSA nbElements, array_type t);
+
+ /**
+ * @param nbElements: number of elements to be stored in the array.
+ * @param max: maximal value stored in the array
+ * @param t: type of the array to be constructed.
+ * This specifies if we need to build a small array (32-bit integers)
+ * a large array (64-bit integers) or an optimal array which uses the
+ * optimal number of bits in memory (but which is longer)
+ */
+ SolArray(uintSA nbElements, uintSA max, array_type t);
+
+ /**
+ * @param ptr: pointer to an already allocated memory
+ * @param t: type of the array to be built
+ * @param nbElements: Number of elements that can be stored in the array
+ * @pre t == SMALL_ARRAY || t == LARGE_ARRAY (doestn't work for bit vectors -- yet?)
+ */
+ SolArray(void *ptr, array_type t, uintSA nbElements) throw (invalid_argument);
+
+ /**
+ * Copy constructor.
+ * Warning, the arrays are not copied, only the pointers are (to avoid
+ * huge memory consumption).
+ */
+ SolArray(SolArray &sa);
+
+ ~SolArray();
+
+ /**
+ * @param nbElements: number of elements to be stored in the array.
+ * @param max: maximal value stored in the array.
+ * @param t: type of the array to be constructed
+ * @pre The previous arrays must have been deleted if needed.
+ * @post length() == nbElements && getType() == t
+ */
+ void init(uintSA nbElements, uintSA max, array_type t) ;
+
+ /**
+ * @param pos: position in the array
+ * @pre pos >= 0 && pos < length()
+ * @return the value in the array at position pos
+ */
+ uintSA get(uintSA pos);
+
+ /**
+ * @return the type of the SolArray that was constructed .
+ */
+ array_type getType();
+
+ /**
+ * @return The number of elements we can store in the array.
+ */
+ uintSA length();
+
+ /**
+ * @param nbElements: number of elements the array must be reallocated to
+ * @pre getType() != OPTIMAL_ARRAY
+ * @post length() == nbElements AND the memory has been reallocated.
+ */
+ void realloc(uintSA nbElements) throw (logic_error);
+
+ /**
+ * @param pos: position in the array
+ * @param value: value to be stored.
+ * @pre pos >= 0 && pos < length()
+ * @post get(pos) == value
+ */
+ void set(uintSA pos, uintSA value);
+
+ /**
+ * A shortcut to the get method.
+ */
+ uintSA operator[](uintSA pos);
+ };
+
+
+ inline uintSA SolArray::get(uintSA pos) {
+ switch(type) {
+ case SMALL_ARRAY:
+ return small[pos];
+ case LARGE_ARRAY:
+ return large[pos];
+ default:
+ return bv->GetValue(pos);
+ }
+ }
+
+ inline array_type SolArray::getType() {
+ return type;
+ }
+
+ inline uintSA SolArray::length() {
+ return len;
+ }
+
+ inline void SolArray::set(uintSA pos, uintSA value) {
+ switch(type) {
+ case SMALL_ARRAY:
+ small[pos] = value;
+ break;
+ case LARGE_ARRAY:
+ large[pos] = value;
+ break;
+ case OPTIMAL_ARRAY:
+ bv->SetValue(pos, value);
+ break;
+ }
+ }
+
+ inline uintSA SolArray::operator[](uintSA pos) {
+ return get(pos);
+ }
+}
+#endif
+
+// Local Variables:
+// mode:c++
+// End:
diff --git a/src/libGkArrays/src/sux/COPYING.LIB b/src/libGkArrays/src/sux/COPYING.LIB
new file mode 100644
index 0000000..b1e3f5a
--- /dev/null
+++ b/src/libGkArrays/src/sux/COPYING.LIB
@@ -0,0 +1,504 @@
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
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+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the
+ library `Frob' (a library for tweaking knobs) written by James Random Hacker.
+
+ <signature of Ty Coon>, 1 April 1990
+ Ty Coon, President of Vice
+
+That's all there is to it!
+
+
diff --git a/src/libGkArrays/src/sux/Makefile.am b/src/libGkArrays/src/sux/Makefile.am
new file mode 100644
index 0000000..41c79d4
--- /dev/null
+++ b/src/libGkArrays/src/sux/Makefile.am
@@ -0,0 +1,113 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thierry LECROQ <thierry.lecroq at univ-rouen.fr> #
+# Martine LÉONARD <Martine.Leonard at univ-rouen.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie de la librairie Gk-arrays. #
+# #
+# La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de #
+# lectures de séquences issues du séquençage haut-débit. #
+# #
+# Ce logiciel est régi par la licence CeCILL-C soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL-C, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the Gk-arrays library. #
+# #
+# The Gk-arrays library aims at indexing k-factors from a huge set of #
+# sequencing reads. #
+# #
+# This software is governed by the CeCILL-C license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL-C #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL-C license and that you accept its terms. #
+# #
+###############################################################################
+#
+# $Id: Makefile.am 215 2011-02-14 14:39:11Z salson $
+#
+###############################################################################
+
+suxdir = $(includedir)/@PACKAGE at -@VERSION@/sux
+sux_HEADERS = macros.h popcount.h rank9b.h
+EXTRA_DIST = rank9b.cpp
+
+MOSTLYCLEANFILES=*~
+CLEANFILES=*~
+DISTCLEANFILES=*~
+MAINTAINERCLEANFILES=*~
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new file mode 100644
index 0000000..552b1ba
--- /dev/null
+++ b/src/libGkArrays/src/sux/Makefile.in
@@ -0,0 +1,577 @@
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+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
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+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thierry LECROQ <thierry.lecroq at univ-rouen.fr> #
+# Martine LÉONARD <Martine.Leonard at univ-rouen.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie de la librairie Gk-arrays. #
+# #
+# La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de #
+# lectures de séquences issues du séquençage haut-débit. #
+# #
+# Ce logiciel est régi par la licence CeCILL-C soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
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+# titulaire des droits patrimoniaux et les concédants successifs. #
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+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
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+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
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+# avertis possédant des connaissances informatiques approfondies. Les #
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+# ------------------------------------------------------------------------- #
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+# This File is part of the Gk-arrays library. #
+# #
+# The Gk-arrays library aims at indexing k-factors from a huge set of #
+# sequencing reads. #
+# #
+# This software is governed by the CeCILL-C license under French law and #
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+# modify and/ or redistribute the software under the terms of the CeCILL-C #
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+ fi; \
+ fi
+ctags: CTAGS
+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
+ $(TAGS_FILES) $(LISP)
+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in files) print i; }; }'`; \
+ test -z "$(CTAGS_ARGS)$$unique" \
+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+ $$unique
+
+GTAGS:
+ here=`$(am__cd) $(top_builddir) && pwd` \
+ && $(am__cd) $(top_srcdir) \
+ && gtags -i $(GTAGS_ARGS) "$$here"
+
+distclean-tags:
+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(DISTFILES)
+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+ list='$(DISTFILES)'; \
+ dist_files=`for file in $$list; do echo $$file; done | \
+ sed -e "s|^$$srcdirstrip/||;t" \
+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+ case $$dist_files in \
+ */*) $(MKDIR_P) `echo "$$dist_files" | \
+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+ sort -u` ;; \
+ esac; \
+ for file in $$dist_files; do \
+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+ if test -d $$d/$$file; then \
+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test -d "$(distdir)/$$file"; then \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ fi; \
+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ fi; \
+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+ else \
+ test -f "$(distdir)/$$file" \
+ || cp -p $$d/$$file "$(distdir)/$$file" \
+ || exit 1; \
+ fi; \
+ done
+check-am: all-am
+check: check-am
+all-am: Makefile $(HEADERS)
+installdirs:
+ for dir in "$(DESTDIR)$(suxdir)"; do \
+ test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+ done
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+ @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+ `test -z '$(STRIP)' || \
+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+ -test -z "$(MOSTLYCLEANFILES)" || rm -f $(MOSTLYCLEANFILES)
+
+clean-generic:
+ -test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+ -test -z "$(DISTCLEANFILES)" || rm -f $(DISTCLEANFILES)
+
+maintainer-clean-generic:
+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+ -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
+clean: clean-am
+
+clean-am: clean-generic clean-libtool mostlyclean-am
+
+distclean: distclean-am
+ -rm -f Makefile
+distclean-am: clean-am distclean-generic distclean-tags
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am: install-suxHEADERS
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic mostlyclean-libtool
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-suxHEADERS
+
+.MAKE: install-am install-strip
+
+.PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \
+ clean-libtool ctags distclean distclean-generic \
+ distclean-libtool distclean-tags distdir dvi dvi-am html \
+ html-am info info-am install install-am install-data \
+ install-data-am install-dvi install-dvi-am install-exec \
+ install-exec-am install-html install-html-am install-info \
+ install-info-am install-man install-pdf install-pdf-am \
+ install-ps install-ps-am install-strip install-suxHEADERS \
+ installcheck installcheck-am installdirs maintainer-clean \
+ maintainer-clean-generic mostlyclean mostlyclean-generic \
+ mostlyclean-libtool pdf pdf-am ps ps-am tags uninstall \
+ uninstall-am uninstall-suxHEADERS
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/src/libGkArrays/src/sux/README b/src/libGkArrays/src/sux/README
new file mode 100644
index 0000000..ad02a89
--- /dev/null
+++ b/src/libGkArrays/src/sux/README
@@ -0,0 +1,74 @@
+Welcome to the C++ part of the sux project.
+
+We provide two implementations of rank/select queries for bit arrays of up
+to 2^64 bits. The constructor requires a pointer to a uint_64 array and
+a number of bits. The classes provide obvious rank/select methods.
+Please see my paper "Broadword Implementation of Rank/Select Queries"
+for details about the implementations.
+
+We also provide an implementation of Jacobson's balanced parentheses data
+structure. Please see my paper "Broadword Implementation of Parenthesis
+Queries" for details about the implementations.
+
+The documentation is definitely lacking. It is coming: it is also likely
+that a scheme similar to Sux4J will be implemented--e.g., select9 will
+be implemented by a separate class that will require a rank9 instance
+in its constructor.
+
+- rank9sel.cpp/rank9sel.h uses broadword algorithms, rank9 as basic structure,
+ and adds select9 (+25%-+37.5% depending on data) which provides constant
+ time selection using further broadword techniques. There is also a version
+ limited to 32-bit addressing.
+
+- simple_select.cpp/simple_select.h uses broadword bit search to implement a
+ very efficient selection structure that on uniformly distributed arrays
+ uses ~13.8% additional space and is very fast. simple_select_zero.cpp
+ does the same for selecting zeroes.
+
+- rank9b.cpp/rank9b.h uses broadword algorithms, rank9 as basic ranking
+ structure (+25% in size), and performs selection using hinted binary
+ search (at most +12.5% in size). Mainly useful for testing. There is also
+ a version limited to 32-bit addressing.
+
+- sparse.cpp/sparse.h implements an opportunistic data structure: the
+ original bit array is not required. It uses simple_select_half--a
+ data structure identical to simple_select but with constants hardwired
+ for density 1/2.
+
+- jacobson.cpp/jacobson.h implements Jacobson's o(n) constant-time rank
+ structure.
+
+By defining some symbols you can conditionally compile different behaviours:
+
+- RANKPOPCOUNT in rank9.cpp will use popcounts for ranking instead of broadword algorithms;
+- RANKPOPCOUNT2 in rank9.cpp will use *unrolled* popcounts;
+- NOINVENTORY for rank9.cpp will eliminate the inventory and use a pure binary search.
+
+- SELPOPCOUNT will use popcounts for selection instead of broadword algorithms;
+
+- bal_paren.cpp/bal_paren.h implements Jacobson's o(n) constant-time rank
+ structure. In that case, SLOW_NO_TABS compiles in for-loop instead of
+ broadword implementations.
+
+All classes are heavily asserted. For testing speed, remember to use
+-DNDEBUG.
+
+The files testcount64.cpp and testselect64.cpp provide testing in isolation
+for rank/select techniques inside a word. testranksel.cpp can be compiled
+with more or less any structure by defining CLASS to the structure name,
+and provides testing of rank/select primitives (please see the makefile).
+Beside the number of bits, you can provide one or two probabilities. Bits
+will be set to one with the given probability in the first half of the test
+array, and with the second probability in the second half (if no second
+probability is specified, it is assumed to be equal to the first one). This
+setup is necessary to show the slow behaviour of naive implementations on
+half-almost-empty-half-almost-full arrays.
+
+testbalparen.cpp tests the speed of finding a matching close parenthesis,
+and requires the number of parentheses in the test stirng. By providing an
+additional twist between 0 and 1 you can skew the string distribution
+towards strings with deeper nestings (1 means no twist).
+
+Enjoy,
+
+ seba (vigna at acm.org)
\ No newline at end of file
diff --git a/src/libGkArrays/src/sux/macros.h b/src/libGkArrays/src/sux/macros.h
new file mode 100644
index 0000000..7dcce30
--- /dev/null
+++ b/src/libGkArrays/src/sux/macros.h
@@ -0,0 +1,26 @@
+#ifndef ranksel_macros_h
+#define ranksel_macros_h
+
+#define ONES_STEP_4 ( 0x1111111111111111ULL )
+#define ONES_STEP_8 ( 0x0101010101010101ULL )
+#define ONES_STEP_9 ( 1ULL << 0 | 1ULL << 9 | 1ULL << 18 | 1ULL << 27 | 1ULL << 36 | 1ULL << 45 | 1ULL << 54 )
+#define ONES_STEP_16 ( 1ULL << 0 | 1ULL << 16 | 1ULL << 32 | 1ULL << 48 )
+#define MSBS_STEP_4 ( 0x8ULL * ONES_STEP_4 )
+#define MSBS_STEP_8 ( 0x80ULL * ONES_STEP_8 )
+#define MSBS_STEP_9 ( 0x100ULL * ONES_STEP_9 )
+#define MSBS_STEP_16 ( 0x8000ULL * ONES_STEP_16 )
+#define INCR_STEP_8 ( 0x80ULL << 56 | 0x40ULL << 48 | 0x20ULL << 40 | 0x10ULL << 32 | 0x8ULL << 24 | 0x4ULL << 16 | 0x2ULL << 8 | 0x1 )
+
+#define ONES_STEP_32 ( 0x0000000100000001ULL )
+#define MSBS_STEP_32 ( 0x8000000080000000ULL )
+
+#define COMPARE_STEP_8(x,y) ( ( ( ( ( (x) | MSBS_STEP_8 ) - ( (y) & ~MSBS_STEP_8 ) ) ^ (x) ^ ~(y) ) & MSBS_STEP_8 ) >> 7 )
+#define LEQ_STEP_8(x,y) ( ( ( ( ( (y) | MSBS_STEP_8 ) - ( (x) & ~MSBS_STEP_8 ) ) ^ (x) ^ (y) ) & MSBS_STEP_8 ) >> 7 )
+
+#define UCOMPARE_STEP_9(x,y) ( ( ( ( ( ( (x) | MSBS_STEP_9 ) - ( (y) & ~MSBS_STEP_9 ) ) | ( x ^ y ) ) ^ ( x | ~y ) ) & MSBS_STEP_9 ) >> 8 )
+#define UCOMPARE_STEP_16(x,y) ( ( ( ( ( ( (x) | MSBS_STEP_16 ) - ( (y) & ~MSBS_STEP_16 ) ) | ( x ^ y ) ) ^ ( x | ~y ) ) & MSBS_STEP_16 ) >> 15 )
+#define ULEQ_STEP_9(x,y) ( ( ( ( ( ( (y) | MSBS_STEP_9 ) - ( (x) & ~MSBS_STEP_9 ) ) | ( x ^ y ) ) ^ ( x & ~y ) ) & MSBS_STEP_9 ) >> 8 )
+#define ULEQ_STEP_16(x,y) ( ( ( ( ( ( (y) | MSBS_STEP_16 ) - ( (x) & ~MSBS_STEP_16 ) ) | ( x ^ y ) ) ^ ( x & ~y ) ) & MSBS_STEP_16 ) >> 15 )
+#define ZCOMPARE_STEP_8(x) ( ( ( x | ( ( x | MSBS_STEP_8 ) - ONES_STEP_8 ) ) & MSBS_STEP_8 ) >> 7 )
+
+#endif
diff --git a/src/libGkArrays/src/sux/popcount.h b/src/libGkArrays/src/sux/popcount.h
new file mode 100644
index 0000000..197ce54
--- /dev/null
+++ b/src/libGkArrays/src/sux/popcount.h
@@ -0,0 +1,15 @@
+#ifndef popcount_h
+#define popcount_h
+
+const unsigned char popcount[] = {
+0,1,1,2,1,2,2,3,1,2,2,3,2,3,3,4,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,
+1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,
+1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,
+2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,
+1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,
+2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,
+2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,
+3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,4,5,5,6,5,6,6,7,5,6,6,7,6,7,7,8,
+};
+
+#endif
diff --git a/src/libGkArrays/src/sux/rank9b.cpp b/src/libGkArrays/src/sux/rank9b.cpp
new file mode 100644
index 0000000..42cdf24
--- /dev/null
+++ b/src/libGkArrays/src/sux/rank9b.cpp
@@ -0,0 +1,236 @@
+/*
+ * Sux: Succinct data structures
+ *
+ * Copyright (C) 2007-2010 Sebastiano Vigna
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * This library is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+ * or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#include <cstdio>
+#include <ctime>
+#include <cassert>
+#include <cstdlib>
+#include <cstring>
+#include <climits>
+#include <sys/time.h>
+#include <sys/resource.h>
+#include "rank9b.h"
+
+uint64_t shifts, dichotomous;
+
+rank9b::rank9b( const uint64_t * const bits, const uint64_t num_bits ) {
+ this->bits = bits;
+ num_words = ( num_bits + 63 ) / 64;
+ num_counts = ( ( num_bits + 64 * 8 - 1 ) / ( 64 * 8 ) ) * 2;
+
+ // Init rank/select structure
+ counts = new uint64_t[ num_counts + 1 ];
+ memset( counts, 0, ( num_counts + 1 ) * sizeof *counts );
+
+ uint64_t c = 0;
+ uint64_t pos = 0;
+ for( uint64_t i = 0; i < num_words; i += 8, pos += 2 ) {
+ counts[ pos ] = c;
+ c += count( bits[ i ] );
+ for( int j = 1; j < 8; j++ ) {
+ counts[ pos + 1 ] |= ( c - counts[ pos ] ) << 9 * ( j - 1 );
+ if ( i + j < num_words ) c += count( bits[ i + j ] );
+ }
+ }
+
+ counts[ num_counts ] = c;
+
+ assert( c <= num_bits );
+
+#ifndef NOINVENTORY
+
+ ones_per_inventory = ( c * 16 * 64 + num_bits - 1 ) / num_bits;
+ // Make ones_per_inventory into a power of 2
+ for( log2_ones_per_inventory = 64; log2_ones_per_inventory-- != 1; ) if ( ones_per_inventory & 1ULL << log2_ones_per_inventory ) break;
+ ones_per_inventory = 1ULL << log2_ones_per_inventory;
+ inventory_size = ( c + ones_per_inventory - 1 ) / ones_per_inventory;
+
+ assert( ones_per_inventory <= 16 * 64 );
+
+ inventory = new uint64_t[ inventory_size + 1 ];
+ uint64_t d = 0;
+ const uint64_t mask = ones_per_inventory - 1;
+ for( uint64_t i = 0; i < num_words; i++ )
+ for( int j = 0; j < 64; j++ )
+ if ( bits[ i ] & 1ULL << j ) {
+ if ( ( d & mask ) == 0 ) {
+ inventory[ d >> log2_ones_per_inventory ] = ( i / 8 ) * 2;
+ assert( counts[ ( i / 8 ) * 2 ] <= d );
+ assert( counts[ ( i / 8 ) * 2 + 2 ] > d );
+ }
+
+ d++;
+ }
+
+ assert( c == d );
+ inventory[ inventory_size ] = ( num_words / 8 ) * 2;
+
+
+#ifdef DEBUG
+ printf("First inventories: %lld %lld %lld %lld\n", inventory[ 0 ], inventory[ 1 ], inventory[ 2 ], inventory[ 3 ] );
+#endif
+
+#endif
+
+#ifndef NDEBUG
+ uint64_t r, t;
+ for( uint64_t i = 0; i < c; i++ ) {
+ t = select( i );
+ r = rank( t );
+ if ( r != i ) {
+ printf( "i: %lld s: %lld r: %lld\n", i, t, r );
+ assert( r == i );
+ }
+ }
+
+ for( uint64_t i = 0; i < num_bits; i++ ) {
+ r = rank( i );
+ if ( r < c ) {
+ t = select( r );
+ if ( t < i ) {
+ printf( "i: %lld r: %lld s: %lld\n", i, r, t );
+ assert( t >= i );
+ }
+ }
+ }
+#endif
+}
+
+rank9b::~rank9b() {
+ delete [] counts;
+#ifndef NOINVENTORY
+ delete [] inventory;
+#endif
+}
+
+
+uint64_t rank9b::rank( const uint64_t k ) {
+ const uint64_t word = k / 64;
+ const uint64_t block = word / 4 & ~1;
+ const int offset = word % 8 - 1;
+
+#ifdef RANKPOPCOUNT
+ uint64_t b = bits[ word ] & ( ( 1ULL << k % 64 ) - 1 );
+ int c = 0;
+ for( int i = ( k % 64 + 7 ) / 8; i-- != 0; ) {
+ c += popcount[ b & 0xFF ];
+ b >>= 8;
+ }
+ return counts[ block ] + ( counts[ block + 1 ] >> ( offset + ( offset >> sizeof offset * 8 - 4 & 0x8 ) ) * 9 & 0x1FF ) + c;
+#else
+#ifdef RANKPOPCOUNT2
+ const uint64_t b = bits[ word ] & ( ( 1ULL << k % 64 ) - 1 );
+ return counts[ block ] + ( counts[ block + 1 ] >> ( offset + ( offset >> sizeof offset * 8 - 4 & 0x8 ) ) * 9 & 0x1FF ) +
+ popcount[ b & 0xFF ] + popcount[ b >> 8 & 0xFF ] + popcount[ b >> 16 & 0xFF ] + popcount[ b >> 24 & 0xFF ] +
+ popcount[ b >> 32 & 0xFF ] + popcount[ b >> 40 & 0xFF ] + popcount[ b >> 48 & 0xFF ] + popcount[ b >> 56 & 0xFF ];
+#else
+ return counts[ block ] + ( counts[ block + 1 ] >> ( offset + ( offset >> sizeof offset * 8 - 4 & 0x8 ) ) * 9 & 0x1FF ) + count( bits[ word ] & ( ( 1ULL << k % 64 ) - 1 ) );
+#endif
+#endif
+}
+
+
+
+uint64_t rank9b::select( const uint64_t rank ) {
+#ifndef NOINVENTORY
+ const uint64_t inventory_index_left = rank >> log2_ones_per_inventory;
+ assert( inventory_index_left < inventory_size );
+
+ uint64_t block_left = inventory[ inventory_index_left ];
+ uint64_t block_right = inventory[ inventory_index_left + 1 ];
+#else
+ uint64_t block_left = 0, block_right = num_words / 8 * 2;
+#endif
+#ifdef DEBUG
+ printf( "Initially, rank: %lld block_left: %lld block_right: %lld counts_left: %lld counts_right: %lld\n", rank, block_left, block_right, counts[ block_left ], counts[ block_right ] );
+#endif
+
+ if ( rank >= counts[ block_right ] ) {
+#ifdef COUNTS
+ shifts++;
+#endif
+ block_right = ( block_left = block_right ) + 2;
+#ifdef DEBUG
+printf( "After shift, rank: %lld block_left: %lld block_right: %lld counts_left: %lld counts_right: %lld\n", rank, block_left, block_right, counts[ block_left ], counts[ block_right ] );
+#endif
+ }
+ else {
+ uint64_t block_middle;
+
+ while( block_right - block_left > 2 ) {
+ block_middle = ( block_right + block_left ) / 2 & ~1;
+ if ( rank >= counts[ block_middle ] ) block_left = block_middle;
+ else block_right = block_middle;
+#ifdef COUNTS
+ dichotomous++;
+#endif
+ }
+ }
+
+ assert( counts[ block_left ] <= rank );
+ assert( counts[ block_right ] > rank );
+
+ const uint64_t rank_in_block = rank - counts[ block_left ];
+
+#ifdef DEBUG
+ printf( "After search, rank: %lld block_left: %lld block_right: %lld counts_left: %lld counts_right: %lld rank_in_block: %lld\n", rank, block_left, block_right, counts[ block_left ], counts[ block_right ], rank_in_block );
+#endif
+
+ assert( counts[ block_left ] <= rank );
+ assert( counts[ block_right ] > rank );
+ assert( block_right - block_left == 2 );
+ assert( rank_in_block < counts[ block_right ] - counts[ block_left ] );
+ assert( rank_in_block < 512 );
+
+ const uint64_t rank_in_block_step_9 = rank_in_block * ONES_STEP_9;
+ const uint64_t subcounts = counts[ block_left + 1 ];
+ const uint64_t offset_in_block = ( ULEQ_STEP_9( subcounts, rank_in_block_step_9 ) * ONES_STEP_9 >> 54 & 0x7 );
+
+ const uint64_t word = block_left * 4 + offset_in_block;
+ const uint64_t rank_in_word = rank_in_block - ( subcounts >> ( offset_in_block - 1 & 7 ) * 9 & 0x1FF );
+#ifdef DEBUG
+ printf( "rank_in_block: %lld offset_in_block: %lld rank_in_word: %lld compare: %016llx shift: %lld\n", rank_in_block, offset_in_block, rank_in_word, UCOMPARE_STEP_9( rank_in_block_step_9, subcounts ), subcounts >> ( offset_in_block - 1 ) * 9 & 0x1FF );
+#endif
+ assert( offset_in_block >= 0 );
+ assert( offset_in_block <= 7 );
+
+#ifdef DEBUG
+ printf( "rank_in_block: %lld offset_in_block: %lld rank_in_word: %lld\n", rank_in_block, offset_in_block, rank_in_word );
+ printf( "subcounts: " );
+ for( int i = 0; i < 7; i++ ) printf( "%lld ", subcounts >> i * 9 & 0x1FF );
+ printf( "\n" );
+ fflush( stdout );
+#endif
+
+ assert( rank_in_word < 64 );
+ assert( rank_in_word >= 0 );
+
+ return word * 64 + select_in_word( bits[ word ], rank_in_word );
+}
+
+uint64_t rank9b::bit_count() {
+#ifdef NOINVENTORY
+ return num_counts * 64;
+#else
+ return ( num_counts + inventory_size ) * 64;
+#endif
+}
+
+void rank9b::print_counts() {}
diff --git a/src/libGkArrays/src/sux/rank9b.h b/src/libGkArrays/src/sux/rank9b.h
new file mode 100644
index 0000000..8099c94
--- /dev/null
+++ b/src/libGkArrays/src/sux/rank9b.h
@@ -0,0 +1,89 @@
+/*
+ * Sux: Succinct data structures
+ *
+ * Copyright (C) 2007-2010 Sebastiano Vigna
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 3 of the License, or (at your option)
+ * any later version.
+ *
+ * This library is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+ * or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifndef rank9b_h
+#define rank9b_h
+#include <stdint.h>
+#include <assert.h>
+#include "popcount.h"
+#include "macros.h"
+
+class rank9b {
+private:
+ const uint64_t *bits;
+ uint64_t *counts, *inventory;
+ uint64_t num_words, num_counts, inventory_size, ones_per_inventory, log2_ones_per_inventory, num_ones;
+
+ /** Counts the number of bits in x. */
+ __inline static int count( const uint64_t x ) {
+ register uint64_t byte_sums = x - ( ( x & 0xa * ONES_STEP_4 ) >> 1 );
+ byte_sums = ( byte_sums & 3 * ONES_STEP_4 ) + ( ( byte_sums >> 2 ) & 3 * ONES_STEP_4 );
+ byte_sums = ( byte_sums + ( byte_sums >> 4 ) ) & 0x0f * ONES_STEP_8;
+ return byte_sums * ONES_STEP_8 >> 56;
+ }
+
+ /* Selects the k-th (k>=0) bit in l. Returns 72 if no such bit exists. */
+
+ __inline static int select_in_word( const uint64_t x, const int k ) {
+ assert( k < count( x ) );
+
+#ifdef SELPOPCOUNT
+ for( int i = 0, c = k; i < 64; i+=8 )
+ if ( ( c -= popcount[ x >> i & 0xFF ] ) < 0 ) {
+ c += popcount[ x >> i & 0xFF ];
+ for( int j = 0; j < 8; j++ ) if ( ( x & 1ULL << ( i + j ) ) && c-- == 0 ) return i + j;
+ }
+ return -1;
+#endif
+
+ // Phase 1: sums by byte
+ register uint64_t byte_sums = x - ( ( x & 0xa * ONES_STEP_4 ) >> 1 );
+ byte_sums = ( byte_sums & 3 * ONES_STEP_4 ) + ( ( byte_sums >> 2 ) & 3 * ONES_STEP_4 );
+ byte_sums = ( byte_sums + ( byte_sums >> 4 ) ) & 0x0f * ONES_STEP_8;
+ byte_sums *= ONES_STEP_8;
+
+ // Phase 2: compare each byte sum with k
+ const uint64_t k_step_8 = k * ONES_STEP_8;
+ const uint64_t place = ( LEQ_STEP_8( byte_sums, k_step_8 ) * ONES_STEP_8 >> 53 ) & ~0x7;
+
+ // Phase 3: Locate the relevant byte and make 8 copies with incrental masks
+ const int byte_rank = k - ( ( ( byte_sums << 8 ) >> place ) & 0xFF );
+
+ const uint64_t spread_bits = ( x >> place & 0xFF ) * ONES_STEP_8 & INCR_STEP_8;
+ const uint64_t bit_sums = ZCOMPARE_STEP_8( spread_bits ) * ONES_STEP_8;
+
+ // Compute the inside-byte location and return the sum
+ const uint64_t byte_rank_step_8 = byte_rank * ONES_STEP_8;
+
+ return place + ( LEQ_STEP_8( bit_sums, byte_rank_step_8 ) * ONES_STEP_8 >> 56 );
+ }
+
+
+public:
+ rank9b( const uint64_t * const bits, const uint64_t num_bits );
+ ~rank9b();
+ uint64_t rank( const uint64_t pos );
+ uint64_t select( const uint64_t rank );
+ // Just for analysis purposes
+ void print_counts();
+ uint64_t bit_count();
+};
+
+#endif
diff --git a/src/libGkArrays/src/utils.cpp b/src/libGkArrays/src/utils.cpp
new file mode 100644
index 0000000..9be8c63
--- /dev/null
+++ b/src/libGkArrays/src/utils.cpp
@@ -0,0 +1,214 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at etud.univ-montp2.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "utils.h"
+
+#include <iostream>
+#include <string>
+#include <cstdlib>
+
+using namespace std;
+
+namespace gkarrays {
+
+ void dnaFiltration(char *dna, uintSA length) {
+ for (uintSA i = 0; i < length; i++) {
+ dna[i] = intToNuc(convNuc(dna[i]));
+ }
+ }
+
+ uintSA DNAtoInt(char *dna, uintSA dna_length){
+ uintSA dna_int = 0;
+ for (uintSA i=0 ; i< dna_length ; i++){
+ dna_int <<= 2;
+ dna_int |= convNuc(dna[i]);
+ }
+ return dna_int;
+ }
+
+ int comparUint(const void *a1, const void* a2){
+ return (int) (* (uint *)a1 - * (uint *) a2);
+ }
+
+ int comparUintSA(const void *a1, const void* a2){
+ return (int) (* (uintSA *)a1 - * (uintSA *) a2);
+ }
+
+ uint convNuc(char nuc){
+ switch (nuc){
+ case 'a' : case 'A' : return 0 ;
+ case 'c' : case 'C' : return 1 ;
+ case 'g' : case 'G' : return 2 ;
+ case 't' : case 'T' : return 3 ;
+ default : return 0;
+ }
+ return 0;
+ }
+
+ char intToNuc(uint c) {
+ switch(c) {
+ case 0: return 'A';
+ case 1: return 'C';
+ case 2: return 'G';
+ case 3: return 'T';
+ default: cerr << "Invalid number (0-3): " << c <<endl; exit(5);
+ }
+ }
+
+ void intToDNA(uint64 code, uint dna_length, char *dna) {
+ uint64 mask = 3;
+ for (uint i=0; i < dna_length; i++) {
+ dna[dna_length-i-1] = intToNuc(code & mask);
+ code >>=2;
+ }
+ }
+
+ uint64 factorsToInt(uintSA pos, uchar *dna, uint length) {
+ assert(length >= 4 && length <= 32);
+
+ uintSA posFirstFactor = 4 - (pos % 4);
+ uintSA numFirstFactor = pos / 4;
+ uintSA posLastFactor = (length - posFirstFactor) % 4;
+ uint64 factor = dna[numFirstFactor] & ((1 << (posFirstFactor*2)) - 1);
+ for(uintSA i = 1 ; i <= (length-posFirstFactor)/4 ; i++){
+ factor <<= 8;
+ factor |= dna[numFirstFactor+i];
+ }
+ factor <<= posLastFactor*2;
+
+ factor |= dna[numFirstFactor+(length-posFirstFactor)/4+1] >> (8-2*posLastFactor) & ((1 << (posLastFactor*2)) - 1);
+
+ return factor;
+ }
+
+ //identique a factorsToInt pour le cas stranded
+ uint64 factorsToIntNoStranded(uintSA pos, uchar *dna, uint length) {
+ uint64 f1=factorsToInt(pos,dna,length);
+ return min(f1, intRevcomp(f1, length));
+ }
+
+ uint64 intRevcomp(uint64 factor, uint length) {
+ uint64 mask;
+ if (length == 32)
+ mask = ~0;
+ else
+ mask = ((uint64) 1 << (2*length)) - 1;
+
+ factor ^= mask;
+
+ uint64 mask_lsb;
+ // Corresponds to the rightmost nucleotide
+ mask_lsb = 3;
+ uint64 shift = 0;
+ uint64 result=0;
+ for(uint j(0);j<length;j++){
+ result <<= 2;
+ // get the leftmost nucleotide and put it at the end
+ result |= (factor & mask_lsb) >> shift;
+ mask_lsb <<= 2;
+ shift += 2;
+ }
+
+ return result;
+ }
+}
diff --git a/src/libGkArrays/src/utils.h b/src/libGkArrays/src/utils.h
new file mode 100644
index 0000000..5334a0d
--- /dev/null
+++ b/src/libGkArrays/src/utils.h
@@ -0,0 +1,229 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at etud.univ-montp2.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+/*
+ * =============================================
+ *
+ * $Id: utils.h 397 2011-04-14 08:47:49Z nphilippe $
+ *
+ * =============================================
+ */
+
+#ifndef UTILS_H
+#define UTILS_H
+
+#ifdef HAVE_CONFIG_H
+# include <config.h>
+#endif
+#include <gkArraysTypes.h>
+#include <cstdlib>
+#include <stdexcept>
+#include <cassert>
+
+#ifndef NDEBUG
+#define PRINT_VAR(v) std::cerr << #v << " = " << v << std::endl;
+#define ASSERT_MSG(condition, message) \
+ if (!(condition)) { std::cerr << message << std::endl; assert(condition); }
+#else
+#define ASSERT_MSG(condition, message) ((void)0)
+#define PRINT_VAR(v) ((void)0)
+
+#endif
+
+namespace gkarrays {
+
+ template <typename T>
+ inline T *Malloc() {
+ T *ptr;
+ if (!(ptr = (T *) malloc(sizeof(T)))) {
+ throw std::bad_alloc();
+ }
+ return ptr;
+ }
+
+ template <typename T>
+ inline T *Calloc(size_t nb) {
+ T *ptr;
+ if (!(ptr = (T *) calloc(nb, sizeof(T)))) {
+ throw std::bad_alloc();
+ }
+ return ptr;
+ }
+
+ template <typename T>
+ inline T *Realloc(T *ptr, size_t nb) {
+ if (!(ptr = (T *) realloc((void *) ptr, nb * sizeof(T)))) {
+ throw std::bad_alloc();
+ }
+ return ptr;
+ }
+
+ int comparUint(const void *a1, const void* a2);
+
+ int comparUintSA(const void *a1, const void* a2);
+
+ uint convNuc(char nuc);
+
+ char intToNuc(uint c);
+
+ /**
+ * Modify the parameter so that every lowercase nucleotide
+ * is changed to an uppercase nucleotide
+ * and every unknown letter (other than A, C, G or T) is changed to A.
+ * The second parameter corresponds to the length of the DNA string
+ * to be treated.
+ */
+ void dnaFiltration(char *, uintSA);
+
+ uintSA DNAtoInt(char *dna, uintSA dna_length);
+
+ void intToDNA(uint64 code, uint dna_length, char *dna);
+
+ /**
+ * @param pos: position in the string
+ * @param dna: DNA string, where each nucleotide is encoded on 2 bits
+ * @param length: length of the factor to extract
+ * @return a numeric representation of the DNA factor
+ * @pre length >= 4 && length <= 32
+ */
+ /**
+ * @param pos: position in the string
+ * @param dna: DNA string, where each nucleotide is encoded on 2 bits
+ * @param length: length of the factor to extract
+ * @return a numeric representation of the DNA factor
+ * @pre length >= 4 && length <= 32
+ */
+ uint64 factorsToInt(uintSA pos, uchar *dna, uint length);
+
+ /**
+ * @param pos: position in the string
+ * @param dna: DNA string, where each nucleotide is encoded on 2 bits
+ * @param length: length of the factor to extract
+ * @return a numeric representation of the DNA factor such that
+ * a factor and its reverse complement share the same value.
+ * @pre length >= 4 && length <= 32
+ */
+ uint64 factorsToIntNoStranded(uintSA pos, uchar *dna, uint length);
+
+ /**
+ * @param factor: a numeric representation of a DNA factor
+ * @param length: length of the DNA factor
+ * @return the numeric representation of the DNA factor's revcomp.
+ */
+ uint64 intRevcomp(uint64 factor, uint length);
+
+ /**
+ * @return the integer corresponding to the complementary nucleotide
+ * @post intToNuc(complementaryNuc(convNuc(c))) == c'
+ * where c is a nucleotide and c' its complementary
+ */
+ inline uintSA complementaryNuc(int i){
+ return i ^ 3;
+ }
+
+}
+#endif
+
+// Local Variables:
+// mode:c++
+// End:
diff --git a/src/libGkArrays/tests/Makefile.am b/src/libGkArrays/tests/Makefile.am
new file mode 100644
index 0000000..41b6b61
--- /dev/null
+++ b/src/libGkArrays/tests/Makefile.am
@@ -0,0 +1,131 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thierry LECROQ <thierry.lecroq at univ-rouen.fr> #
+# Martine LÉONARD <Martine.Leonard at univ-rouen.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie de la librairie Gk-arrays. #
+# #
+# La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de #
+# lectures de séquences issues du séquençage haut-débit. #
+# #
+# Ce logiciel est régi par la licence CeCILL-C soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL-C, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the Gk-arrays library. #
+# #
+# The Gk-arrays library aims at indexing k-factors from a huge set of #
+# sequencing reads. #
+# #
+# This software is governed by the CeCILL-C license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL-C #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL-C license and that you accept its terms. #
+# #
+###############################################################################
+
+TESTS = testPairedEnd testVariableFixed testConsistency
+check_PROGRAMS = variableAndFixedLength $(TESTS)
+
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+AM_CPPFLAGS = -I at abs_srcdir@/../src -DDATADIR=\"$(srcdir)/\"
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+
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+
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+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
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+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thierry LECROQ <thierry.lecroq at univ-rouen.fr> #
+# Martine LÉONARD <Martine.Leonard at univ-rouen.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie de la librairie Gk-arrays. #
+# #
+# La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de #
+# lectures de séquences issues du séquençage haut-débit. #
+# #
+# Ce logiciel est régi par la licence CeCILL-C soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
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+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL-C, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the Gk-arrays library. #
+# #
+# The Gk-arrays library aims at indexing k-factors from a huge set of #
+# sequencing reads. #
+# #
+# This software is governed by the CeCILL-C license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL-C #
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diff --git a/src/libGkArrays/tests/checkConsistency.cpp b/src/libGkArrays/tests/checkConsistency.cpp
new file mode 100644
index 0000000..5f39fe3
--- /dev/null
+++ b/src/libGkArrays/tests/checkConsistency.cpp
@@ -0,0 +1,332 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#undef NDEBUG
+#include "checkConsistency.h"
+#include <gkArrays.h>
+#include <utils.h>
+#include <cstring>
+#include <iostream>
+#include "testing.h"
+
+using namespace std;
+using namespace gkarrays;
+
+void checkConsistency(const char *file, uint k, uint read_length, bool use_bitvector,
+ bool stranded, uint nb_threads) {
+
+#undef TAP_ADDITIONAL_INFOS
+#define TAP_ADDITIONAL_INFOS "file = " << file << ", read_length = " << read_length <<", k = " << k <<", stranded = " << stranded << ", bit_vector = " << use_bitvector <<", nb_threads = " << nb_threads
+
+ RECORD_TAP_TEST(TEST_SORTED_STRING, "Check that strings are sorted in gkSA");
+ RECORD_TAP_TEST(TEST_GKCFA, "Check GkCFA values");
+ RECORD_TAP_TEST(TEST_GKISA, "Check GkIFA values");
+ RECORD_TAP_TEST(TEST_GKCFALENGTH, "Check GkCFA length");
+ RECORD_TAP_TEST(TEST_READING_READS, "Compare reading sequences from file and retrieving them from the structure");
+ RECORD_TAP_TEST(TEST_READ_LENGTH, "Check read length");
+ RECORD_TAP_TEST(TEST_EPOTN, "Check endPosOfTagNum");
+ RECORD_TAP_TEST(TEST_SPOTN, "Check startPosOfTagNum");
+ RECORD_TAP_TEST(TEST_SQPOTN, "Check startQPosOfTagNum");
+ RECORD_TAP_TEST(TEST_SUPPORT_LENGTH, "Check support length");
+ RECORD_TAP_TEST(TEST_TAGNUM, "Check read number");
+ RECORD_TAP_TEST(TEST_TAGPOS, "Check tag position computation");
+ RECORD_TAP_TEST(TEST_NBOCCS_TAGS, "Check number of occurrences among reads");
+ RECORD_TAP_TEST(TEST_SUPPORT, "Check support");
+ RECORD_TAP_TEST(TEST_KMER, "Check k-mer extraction from the structure");
+ RECORD_TAP_TEST(TEST_FIND_MYSELF, "Check I find myself among the occurrences");
+ RECORD_TAP_TEST(TEST_NBTAGS_FOUND, "Check number of occurrences among reads (with multiplicity");
+ RECORD_TAP_TEST(TEST_PPOSITION, "Check isPposition is true when needed");
+ RECORD_TAP_TEST(TEST_PPOS_TO_QPOS, "Check conversion of Pposition in Qposition");
+ RECORD_TAP_TEST(TEST_NOT_PPOSITION, "Check isPposition is false when needed");
+ RECORD_TAP_TEST(TEST_NB_READS, "Check number of reads");
+
+ gkArrays *gk = new gkArrays((char *)file, k, use_bitvector, read_length, stranded,
+ nb_threads);
+ readIterator *it = gk->getReads()->begin();
+ uint nb_reads = 0;
+ uint current_length;
+ uintSA cumulative_length = 0;
+ uintSA cumulativePpos = 0;
+
+ // Testing GkISA, GkSA and GkCFPS
+ char *previous_factor = gk->getTextFactor(gk->getGkSA(0), k);
+ uintSA nb_distinct_factors = 0;
+ uintSA nb_factors_current_bucket = 1;
+ for (uintSA i = 1; i < gk->getGkSALength(); i++) {
+ char *current_factor = gk->getTextFactor(gk->getGkSA(i), k);
+ int compar = strcmp(previous_factor, current_factor);
+ TAP_TEST(compar <= 0, TEST_SORTED_STRING,
+ "i = " << i << ", gkSA[i] = " << gk->getGkSA(i) << ", we should have "
+ << previous_factor << "<=" << current_factor);
+
+ if (compar < 0) {
+ TAP_TEST(gk->getGkCFA(nb_distinct_factors) == nb_factors_current_bucket,
+ TEST_GKCFA,
+ "i = " << i << ", gkSA[i] = " << gk->getGkSA(i) << ", we should have "
+ << gk->getGkCFA(nb_distinct_factors) << "=="
+ << nb_factors_current_bucket);
+ nb_distinct_factors++;
+ nb_factors_current_bucket = 1;
+ } else
+ nb_factors_current_bucket++;
+
+ TAP_TEST(gk->getGkISA(gk->convertPposToQpos(gk->getGkSA(i))) == nb_distinct_factors,
+ TEST_GKISA,
+ "gk->getGkISA(gk->convertPposToQpos(gk->getGkSA(i))) = " << gk->getGkISA(gk->convertPposToQpos(gk->getGkSA(i))) << ", nb_distinct_factors = " << nb_distinct_factors);
+ delete [] previous_factor;
+ previous_factor = current_factor;
+ }
+ TAP_TEST(gk->getGkCFALength() == nb_distinct_factors+1,
+ TEST_GKCFALENGTH,
+ "|GkCFA| = " << gk->getGkCFALength() << ", nb_distinct_factors = " << nb_distinct_factors);
+
+ while (!it->isFinished()) {
+ char *current_read = gk->getTag(nb_reads);
+ char *it_read = it->getSequence();
+ current_length = gk->getTagLength(nb_reads);
+ if (read_length) {
+ dnaFiltration(it_read, read_length);
+ TAP_TEST(strncmp(current_read, it_read, read_length) == 0,
+ TEST_READING_READS,
+ "Read n°" << nb_reads << " read " << it_read
+ << ", in GkArrays: " << current_read);
+ TAP_TEST(current_length == read_length,
+ TEST_READ_LENGTH,
+ "read_length (parameter) = " << read_length
+ << " current_length (given by gkA) = "
+ << current_length);
+ } else {
+ dnaFiltration(it_read, strlen(it_read));
+ TAP_TEST(strcmp(current_read, it_read) == 0,
+ TEST_READING_READS,
+ "current_read = " << current_read <<", it->getSequence() = " << it_read);
+ TAP_TEST(strlen(current_read) == current_length,
+ TEST_READ_LENGTH,
+ "length of read is " << strlen(current_read) <<", should have been "
+ << current_length << " (according to gkA)");
+ }
+ TAP_TEST(gk->getEndPosOfTagNum(nb_reads) == cumulative_length + current_length - 1,
+ TEST_EPOTN,
+ "nb_reads = " << nb_reads
+ << ", gk->getEndPosOfTagNum(nb_reads) = "
+ << gk->getEndPosOfTagNum(nb_reads)
+ << "cumulative_length + current_length - 1 = "
+ << cumulative_length + current_length - 1);
+ TAP_TEST(gk->getStartPosOfTagNum(nb_reads) == cumulative_length,
+ TEST_SPOTN,
+ "nb_reads = " << nb_reads
+ << ", gk->getStartPosOfTagNum(nb_reads) = "
+ << gk->getStartPosOfTagNum(nb_reads)
+ << "cumulative_length = " << cumulative_length);
+ TAP_TEST(gk->getStartQPosOfTagNum(nb_reads) == cumulativePpos,
+ TEST_SQPOTN,
+ "nb_reads = " << nb_reads
+ << ", gk->getStartQPosOfTagNum(nb_reads) = "
+ << gk->getStartQPosOfTagNum(nb_reads)
+ << "cumulativePpos = " << cumulativePpos);
+
+ TAP_TEST(gk->getSupportLength(nb_reads) == current_length - k + 1,
+ TEST_SUPPORT_LENGTH,
+ "nb_reads = " << nb_reads << " support length: "
+ << gk->getSupportLength(nb_reads) << ", current_length - k + 1 = "
+ << current_length - k + 1);
+
+ for (uint i = 0; i < current_length; i++) {
+ for (uint j = 1; j < current_length - i; j++) {
+ char *factor = gk->getTagFactor(nb_reads, i, j);
+ assert(strncmp(factor, ¤t_read[i], j) == 0);
+ delete [] factor;
+ }
+ }
+
+ for (uint i = 0; i < current_length; i++) {
+ std::pair<uint, uint> tagNumPos = gk->getTagNumAndPosFromAbsolutePos(cumulative_length + i);
+ TAP_TEST(gk->getTagNum(cumulative_length + i) == nb_reads,
+ TEST_TAGNUM,
+ "cumulative_length = " << cumulative_length << ", i = " << i <<", nb_reads = " << nb_reads <<", gk->getTagNum(cumulative_length + i) = " << gk->getTagNum(cumulative_length + i));
+ TAP_TEST(i == tagNumPos.second,
+ TEST_TAGPOS,
+ "i = " << i <<", tagNumPos.second = " << tagNumPos.second);
+ TAP_TEST(nb_reads == tagNumPos.first, TEST_TAGNUM,
+ "nb_reads = " << nb_reads <<", tagNumPos.first = " << tagNumPos.first);
+ }
+
+ uint *support = gk->getSupport(nb_reads);
+
+ for (uint i = 0; i < current_length - k + 1; i++) {
+ uint nb_tags = gk->getNbTagsWithFactor(nb_reads, i, false);
+ char *kmer = gk->getTagFactor(nb_reads, i, k);
+ uint *tags_num = gk->getTagNumWithFactor(nb_reads, i);
+ uint nb_occs = gk->getNbTagsWithFactor(nb_reads, i, true);
+ pair<uint, uint> *tags = gk->getTagsWithFactor(nb_reads, i);
+ bool found_me = false;
+ uint nb_found = 0;
+
+ TAP_TEST(nb_occs >= nb_tags, TEST_NBOCCS_TAGS,
+ "i = " << i << "nb_occs = " << nb_occs <<", nb_tags = " << nb_tags);
+ TAP_TEST(support[i] == nb_occs, TEST_SUPPORT,
+ "i = " << i << ", support[i] = " << support[i]
+ << ", nb_occs = " << nb_occs);
+
+ for (uint j = 0; j < nb_occs; j++) {
+ if (tags[j].first == nb_reads)
+ found_me = true;
+
+ // Search this tag in tags_num
+ uint p;
+ for (p = 0; p < nb_tags && tags_num[p] != tags[j].first ; p++) {}
+ if (p < nb_tags) {
+ // Count the read found
+ nb_found++;
+ // And change it in the array so that we don't count it twice.
+ tags_num[p] = ~0;
+ }
+
+ char *current_kmer = gk->getTagFactor(tags[j].first, tags[j].second, k);
+ TAP_TEST(strcmp(current_kmer, kmer) == 0,
+ TEST_KMER,
+ "current_kmer = " << current_kmer << ", kmer = " << kmer << ", j = " << j << ", nb_occs = " << nb_occs);
+ delete [] current_kmer;
+ }
+
+ TAP_TEST(found_me, TEST_FIND_MYSELF,
+ "i = " << i);
+ TAP_TEST(nb_found == nb_tags,
+ TEST_NBTAGS_FOUND,
+ "nb_found = " << nb_found <<", nb_tags = " << nb_tags );
+ TAP_TEST(gk->isPposition(cumulative_length + i),
+ TEST_PPOSITION,
+ "i = " << i <<", cumulative_length = " << cumulative_length);
+ TAP_TEST(gk->convertPposToQpos(cumulative_length + i) == cumulativePpos + i,
+ TEST_PPOS_TO_QPOS,
+ "i = " << i <<", cumulative_length = " << cumulative_length
+ <<", cumulativePpos = " << cumulativePpos <<
+ "gk->convertPposToQpos(cumulative_length + i) = "
+ << gk->convertPposToQpos(cumulative_length + i));
+ delete [] kmer;
+ free(tags_num);
+ delete [] tags;
+ }
+
+ delete [] support;
+
+ for (uint i = current_length - k + 1; i < current_length; i++) {
+ TAP_TEST(! gk->isPposition(cumulative_length+i), TEST_NOT_PPOSITION,
+ "cumulative_length = " << cumulative_length << ", i = " << i);
+ }
+
+ cumulative_length += current_length;
+ cumulativePpos += current_length - k + 1;
+ nb_reads++;
+ ++(*it);
+
+ delete [] current_read;
+ }
+
+ delete it;
+
+ TAP_TEST(nb_reads == gk->getNbTags(),
+ TEST_NB_READS,
+ "nb_reads = " << nb_reads <<", gk->getNbTags() = "
+ << gk->getNbTags());
+
+ delete gk;
+}
diff --git a/src/libGkArrays/tests/checkConsistency.h b/src/libGkArrays/tests/checkConsistency.h
new file mode 100644
index 0000000..517fc7b
--- /dev/null
+++ b/src/libGkArrays/tests/checkConsistency.h
@@ -0,0 +1,139 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <gkArraysTypes.h>
+
+enum {TEST_SORTED_STRING,
+ TEST_GKCFA,
+ TEST_GKISA,
+ TEST_GKCFALENGTH,
+ TEST_READING_READS,
+ TEST_READ_LENGTH,
+ TEST_EPOTN,
+ TEST_SPOTN,
+ TEST_SQPOTN,
+ TEST_SUPPORT_LENGTH,
+ TEST_TAGNUM,
+ TEST_TAGPOS,
+ TEST_NBOCCS_TAGS,
+ TEST_SUPPORT,
+ TEST_KMER,
+ TEST_FIND_MYSELF,
+ TEST_NBTAGS_FOUND,
+ TEST_PPOSITION,
+ TEST_PPOS_TO_QPOS,
+ TEST_NOT_PPOSITION,
+ TEST_NB_READS,
+ NB_TESTS
+};
+
+/**
+ * Check that the values returned by the Gk-arrays are consistent.
+ * - getTag(i) == it.getSequence(), where it is a readIterator incremented at
+ * the same time as i
+ * - getTagLength(i) == strlen(getTag(i))
+ * - getStartPosOfTagNum(i) == pos, where pos is incremented by getTagLength(i) after
+ * each comparison
+ * - o
+ */
+void checkConsistency(const char *file, uint k, uint read_length=0,
+ bool use_bitvector=false, bool stranded = true,
+ uint nb_threads=1);
diff --git a/src/libGkArrays/tests/checkPairedEnd.cpp b/src/libGkArrays/tests/checkPairedEnd.cpp
new file mode 100644
index 0000000..d43942a
--- /dev/null
+++ b/src/libGkArrays/tests/checkPairedEnd.cpp
@@ -0,0 +1,146 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#undef NDEBUG
+#include "checkPairedEnd.h"
+#include <readsReader.h>
+#include <utils.h>
+#include <cstring>
+#include <iostream>
+#include "testing.h"
+
+using namespace std;
+using namespace gkarrays;
+
+void checkPairedEnd(const char *tags_file1, const char *tags_file2, uint threshold, uint tag_length) {
+
+#undef TAP_ADDITIONAL_INFOS
+#define TAP_ADDITIONAL_INFOS "file1 = " << tags_file1 << ", tags_file2 = " << tags_file2 <<", k = " << threshold <<", read length = " << tag_length
+
+ RECORD_TAP_TEST(TEST_SEQUENCE_CONSISTENCY,
+ "Test that sequences are the same by reading a single file or by reading files as paired-end reads");
+
+ singleReadIterator *it1 = new singleReadIterator(tags_file1,threshold,tag_length,false,false,true);
+ singleReadIterator *it2 = new singleReadIterator(tags_file2,threshold,tag_length,false,false,true);
+ readIterator *it12 = new pairedEndReadIterator(tags_file1,tags_file2,threshold,tag_length,false);
+
+ bool firstMemberOfPair = true;
+ while(!it1->isFinished() && !it2->isFinished() && !it12->isFinished()) {
+ while(it1->isDiscarded() || it2->isDiscarded()){
+ ++(*it1);
+ ++(*it2);
+ }
+ if(firstMemberOfPair) {
+ TAP_TEST(strcmp(it1->getSequence(),it12->getSequence()) == 0, TEST_SEQUENCE_CONSISTENCY, "seq1 = " << it1->getSequence() << ", seq2 = " << it2->getSequence());
+ firstMemberOfPair = false;
+ ++(*it1);
+ } else {
+ TAP_TEST(strcmp(it2->getSequence(),it12->getSequence()) == 0, TEST_SEQUENCE_CONSISTENCY, "seq1 = " << it2->getSequence() << ", seq2 = " << it2->getSequence());
+ firstMemberOfPair = true;
+ ++(*it2);
+ }
+ ++(*it12);
+ }
+ //assert(it1->isFinished() && it2->isFinished() && it12->isFinished());
+ delete it1;
+ delete it2;
+ delete it12;
+}
diff --git a/src/libGkArrays/tests/checkPairedEnd.h b/src/libGkArrays/tests/checkPairedEnd.h
new file mode 100644
index 0000000..ea9f59a
--- /dev/null
+++ b/src/libGkArrays/tests/checkPairedEnd.h
@@ -0,0 +1,107 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <gkArraysTypes.h>
+
+#define TEST_SEQUENCE_CONSISTENCY 0
+#define NB_TESTS 1
+
+void checkPairedEnd(const char *tags_file1, const char *tags_file2, uint threshold, uint tag_length);
diff --git a/src/libGkArrays/tests/compareVariableFixed.cpp b/src/libGkArrays/tests/compareVariableFixed.cpp
new file mode 100644
index 0000000..04d085c
--- /dev/null
+++ b/src/libGkArrays/tests/compareVariableFixed.cpp
@@ -0,0 +1,190 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+#undef NDEBUG
+#include <iostream>
+#include <cstdlib>
+#include <ctime>
+#ifdef HAVE_CONFIG_H
+# include <config.h>
+#endif
+#include "compareVariableFixed.h"
+#include <gkArrays.h>
+#include <gkArraysTypes.h>
+#include <utils.h>
+#include <sys/time.h>
+#include "testing.h"
+
+#ifndef ullong
+#define ullong unsigned long long
+#endif
+
+using namespace std;
+using namespace gkarrays;
+
+void compareVariableFixed(const char *file, uint read_length, uint k, bool stranded,
+ bool bit_vector, uint nb_threads) {
+
+ RECORD_TAP_TEST(TEST_NBTAGS, "Check number of tags");
+ RECORD_TAP_TEST(TEST_TAG_NUM, "Check that tag numbers are consistent");
+ RECORD_TAP_TEST(TEST_TAG_LENGTH, "Check tag lengths");
+ RECORD_TAP_TEST(TEST_GKSALENGTH, "Check GkSA length");
+ RECORD_TAP_TEST(TEST_GKSA, "Check GkSA values");
+ RECORD_TAP_TEST(TEST_GKISA, "Check GkISA values");
+ RECORD_TAP_TEST(TEST_GKCFALENGTH, "Check GkCFA length");
+ RECORD_TAP_TEST(TEST_GKCFA, "Check GkCFA values");
+
+#undef TAP_ADDITIONAL_INFOS
+#define TAP_ADDITIONAL_INFOS "file = " << file << ", read_length = " << read_length <<", k = " << k <<", stranded = " << stranded << ", bit_vector = " << bit_vector <<", nb_threads = " << nb_threads
+
+ gkArrays *gkFixed = new gkArrays((char *)file, k, bit_vector, read_length, stranded,
+ nb_threads);
+ gkArrays *gkVariable = new gkArrays((char *)file, k, bit_vector, 0, stranded, nb_threads);
+
+ TAP_TEST(gkFixed->getNbTags() == gkVariable->getNbTags(),
+ TEST_NBTAGS,
+ "Nb fixed tags (" << gkFixed->getNbTags() << ") != Nb variable tags ("
+ << gkVariable->getNbTags() << ")");
+
+ uint nbtags = gkFixed->getNbTags();
+
+ for (uintSA i = 0; i < nbtags; i++) {
+ for (uintSA j = 0; j < (uintSA) read_length; j++)
+ TAP_TEST(i == gkFixed->getTagNum(i * read_length + j) && i == gkVariable->getTagNum(i * read_length + j ),
+ TEST_TAG_NUM,
+ "i = " << i << ", j = " << j << ", num_fixed = " << gkFixed->getTagNum(i * read_length + j) << ", num_var = " << gkVariable->getTagNum(i * read_length + j));
+
+ TAP_TEST(gkFixed->getTagLength(i) == (uintSA)read_length && gkVariable->getTagLength(i) == (uintSA)read_length,
+ TEST_TAG_LENGTH,
+ "i = " << i << " fixed tag length: " << gkFixed->getTagLength(i) <<", variable tag length: " << gkVariable->getTagLength(i));
+ }
+
+
+ TAP_TEST(gkFixed->getGkSALength() == gkVariable->getGkSALength(),
+ TEST_GKSALENGTH,
+ "fixed gkSA length = " << gkFixed->getGkSALength() << ", variable gkSA length = " << gkVariable->getGkSALength());
+
+ uintSA max = gkFixed->getGkSALength();
+
+ for (uintSA i = 0; i < max; i++) {
+ TAP_TEST(gkFixed->getGkSA(i) == gkVariable->getGkSA(i),
+ TEST_GKSA,
+ "i = " << i);
+ TAP_TEST(gkFixed->getGkISA(i) == gkVariable->getGkISA(i),
+ TEST_GKISA,
+ "i = " << i << ", GkISA[i] (fixed) = " << gkFixed->getGkISA(i)
+ << ", GkISA[i] (variable) = " << gkVariable->getGkISA(i));
+ }
+
+ TAP_TEST(gkFixed->getGkCFALength() == gkVariable->getGkCFALength(),
+ TEST_GKCFALENGTH,
+ "fixed GkCFA length = " << gkFixed->getGkCFALength() << ", variable GkCFA length = " << gkVariable->getGkCFALength());
+
+ max = gkFixed->getGkCFALength();
+
+ for (uintSA i = 0; i < max; i++) {
+ TAP_TEST(gkFixed->getGkCFA(i) == gkVariable->getGkCFA(i),
+ TEST_GKCFA,
+ "i = " << i);
+ }
+
+ delete gkFixed;
+ delete gkVariable;
+}
diff --git a/src/libGkArrays/tests/compareVariableFixed.h b/src/libGkArrays/tests/compareVariableFixed.h
new file mode 100644
index 0000000..8b72e59
--- /dev/null
+++ b/src/libGkArrays/tests/compareVariableFixed.h
@@ -0,0 +1,121 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <gkArraysTypes.h>
+
+
+enum { TEST_NBTAGS,
+ TEST_TAG_NUM,
+ TEST_TAG_LENGTH,
+ TEST_GKSALENGTH,
+ TEST_GKSA,
+ TEST_GKISA,
+ TEST_GKCFALENGTH,
+ TEST_GKCFA, NB_TESTS };
+
+/**
+ * Creates two Gk-Arrays, one variable-length and another one fixed-length.
+ * Compare that basic queries (number of reads, read number, read length,
+ * gkSA, gkISA and gkCFA) are identical
+ */
+void compareVariableFixed(const char *file, uint read_length, uint k,
+ bool stranded=true, bool bit_vector = false,
+ uint nb_threads = 1);
diff --git a/src/libGkArrays/tests/dataset/data1.fa b/src/libGkArrays/tests/dataset/data1.fa
new file mode 100644
index 0000000..a591e29
--- /dev/null
+++ b/src/libGkArrays/tests/dataset/data1.fa
@@ -0,0 +1,7 @@
+>seq1
+GGAGTCCTTTAGGGCATCCATCAGCTTGTTTGCCGTCTTCCCAGCAAAAGCTCTCGGTAACCCAAAATGTACTGCCTTCTTCACAGAATGCTCCAGCAGAA
+>seq1-2
+GGAGTCCTTTAGGGCATCCATCAGCTTGTTTGCCGTCTTCCCAGCAAAAGCTCTCGGTAACCCAAAATGTACTGCCTTCTTCACAGAATGCTCCAGCAGAA
+>seq2
+NCGGGGTATCATCTGCAGAGACTGGCAGGGGTGGGGGTTCTGCCCGGCTCTCCCTGTTCGAAGCAGGCTCTCCATCTACCTTTTGTTTTGACTTTGACTCC
+
diff --git a/src/libGkArrays/tests/dataset/data2.fa b/src/libGkArrays/tests/dataset/data2.fa
new file mode 100644
index 0000000..6822fbe
--- /dev/null
+++ b/src/libGkArrays/tests/dataset/data2.fa
@@ -0,0 +1,7 @@
+>seq3
+CGGTAATCGTAGGTACATGTTAGCGTGTAGCACATAGTCGCGCTATGCTAGTCATGGTAACCCAAAATGTACTGCCTTCTTCACAGAATGCTCCAGCAGAA
+>seq3-5
+GGAGTCCTTTAGGGCATCCATCAGCTTGTTTGCCGTCTTACCAGCCGTAAATGCTGGCTATATCGGATCGGGGTTATAGCTGCTATAATGCTCCAGCAGAA
+>seq4
+AGGCCTGTAAGCTTGAAGGTGTGTCGGCTAGCTAATTGCTGATCGGGCTCTCCCTGTTCGAAGCAGGCTCTCCATCTACCTTTTGTTTTGACTTTGACTCC
+
diff --git a/src/libGkArrays/tests/dataset/variable.fa b/src/libGkArrays/tests/dataset/variable.fa
new file mode 100644
index 0000000..59a403e
--- /dev/null
+++ b/src/libGkArrays/tests/dataset/variable.fa
@@ -0,0 +1,10 @@
+>seq1
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>seq2
+tttttttttt
+>seq3
+ACTAGACATCTGACTATCGATCACTACGATCTAGCGACTTCAGCACTACGAGCATCTAGCATCATCAGCGACT
+>seq4
+AAAAAAAAAAGGGGGGGGGGCCCCCCCCCCTTTTTTTTTT
+>seq5
+ACTGCAGTACTGCAGTACTGCAGTACTGCAGTACTGCAGTACTGCAGTACTGCAGTACTGCAGTACTGCAGTACTGCAGTACTGCAGT
\ No newline at end of file
diff --git a/src/libGkArrays/tests/testConsistency.cpp b/src/libGkArrays/tests/testConsistency.cpp
new file mode 100644
index 0000000..ed3c19c
--- /dev/null
+++ b/src/libGkArrays/tests/testConsistency.cpp
@@ -0,0 +1,141 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "checkConsistency.h"
+#include <iostream>
+#include <cstring>
+#include <cstdlib>
+#include "testing.h"
+using namespace std;
+
+TAP_DECLARATIONS
+
+/**
+ * No parameter: Launch by default
+ *
+ */
+int main(int argc, char **argv) {
+ TAP_START(NB_TESTS);
+ if (argc == 1) {
+ for (int t = 1; t <= 3; t++) {
+ for (int k = 4; k < 30; k++) {
+ for (int i=0; i < 2; i++) {
+ bool bit_vector = (i == 0);
+ checkConsistency(DATADIR"dataset/data1.fa", k, 30, bit_vector, true, t);
+ checkConsistency(DATADIR"dataset/data1.fa", k, 50, bit_vector, true, t);
+ checkConsistency(DATADIR"dataset/data1.fa", k, 101, bit_vector, true, t);
+ checkConsistency(DATADIR"dataset/data1.fa", k, 0, bit_vector, true, t);
+ checkConsistency(DATADIR"dataset/variable.fa", k, 0, bit_vector, true, t);
+ }
+ }
+ }
+ } else {
+ if (strcmp(argv[1], "-h") == 0) {
+ cerr << "Usage: " << argv[0] << " file read_length k nb_threads" << endl;
+ } else if (argc >= 5) {
+ checkConsistency(argv[1], atoi(argv[3]), atoi(argv[2]), false, true,
+ atoi(argv[4]));
+ checkConsistency(argv[1], atoi(argv[3]), atoi(argv[2]), true, true,
+ atoi(argv[4]));
+ }
+ }
+ TAP_END_TEST_EXIT
+}
diff --git a/src/libGkArrays/tests/testPairedEnd.cpp b/src/libGkArrays/tests/testPairedEnd.cpp
new file mode 100644
index 0000000..9e6a7ff
--- /dev/null
+++ b/src/libGkArrays/tests/testPairedEnd.cpp
@@ -0,0 +1,123 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "checkPairedEnd.h"
+#include <iostream>
+#include <cstring>
+#include <cstdlib>
+#include "testing.h"
+using namespace std;
+
+TAP_DECLARATIONS
+
+/**
+ * No parameter: Launch by default
+ *
+ */
+int main(int argc, char **argv) {
+ TAP_START(NB_TESTS);
+ for (int l = 3; l < 31; l++) {
+ for (int k = 4; k < 30; k++) {
+ checkPairedEnd(DATADIR"dataset/data1.fa", DATADIR"dataset/data2.fa", k, l);
+ }
+ }
+ TAP_END_TEST_EXIT
+}
diff --git a/src/libGkArrays/tests/testVariable.h b/src/libGkArrays/tests/testVariable.h
new file mode 100644
index 0000000..fee1b18
--- /dev/null
+++ b/src/libGkArrays/tests/testVariable.h
@@ -0,0 +1,106 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+
+/**
+ * Performs some tests on dataset/variable.fa which is a small test
+ * with two variable length reads.
+ */
+void testVariable_fa();
diff --git a/src/libGkArrays/tests/testVariableFixed.cpp b/src/libGkArrays/tests/testVariableFixed.cpp
new file mode 100644
index 0000000..32617be
--- /dev/null
+++ b/src/libGkArrays/tests/testVariableFixed.cpp
@@ -0,0 +1,118 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+#include "compareVariableFixed.h"
+#include "testing.h"
+
+TAP_DECLARATIONS
+
+int main(int argc, char **argv) {
+ TAP_START(NB_TESTS);
+ for (uint k = 4; k <= 30; k++) {
+ for (uint t = 1; t <= 3; t++) {
+ for (int i = 0; i < 2; i++) {
+ bool bit_vector = (i == 0);
+ compareVariableFixed(DATADIR"dataset/data1.fa", 101, k, false, bit_vector, t);
+ compareVariableFixed(DATADIR"dataset/data1.fa", 101, k, true, bit_vector, t);
+ }
+ }
+ }
+ TAP_END_TEST_EXIT
+}
diff --git a/src/libGkArrays/tests/testing.h b/src/libGkArrays/tests/testing.h
new file mode 100644
index 0000000..0e88c9c
--- /dev/null
+++ b/src/libGkArrays/tests/testing.h
@@ -0,0 +1,65 @@
+#ifndef TESTING_H
+#define TESTING_H
+
+#include <iostream>
+#include <fstream>
+#include <cstdlib>
+using namespace std;
+
+
+extern int *test_results;
+extern string *test_messages;
+
+#define TAP_DECLARATIONS int *test_results; \
+ string *test_messages;
+
+#define TAP_MAX_FAILED 20
+
+#define TAP_ADDITIONAL_INFOS ""
+#define TAP_START(nb_test) test_results = (int *)calloc(nb_test, sizeof(int)); \
+ test_messages = new string[nb_test];
+
+#define RECORD_TAP_TEST(id, msg) test_messages[id] = msg;
+
+#define TAP_TEST(test, id, msg) if (test_results[id] <= TAP_MAX_FAILED) { \
+ if (! (test)) { \
+ test_results[id]++; \
+ cerr << "Test " << #test << " failed (" << __FILE__ << ":" \
+ << __LINE__ << "): " << msg << endl; \
+ cerr << "\tadditional infos: " << TAP_ADDITIONAL_INFOS << endl; \
+ }}
+
+#define TAP_END_TEST tap_end_test(__FILE__)
+
+inline bool tap_end_test(const char *filename) {
+ bool ok = true;
+ ofstream tap_file;
+ string tap_filename(filename);
+ tap_filename.append(".tap");
+ tap_file.open(tap_filename.c_str(), ios_base::out);
+ tap_file << "1.." << NB_TESTS << endl;
+ for (int i = 0; i < NB_TESTS; i++) {
+ if (test_results[i] == 0)
+ tap_file << "ok " << i+1;
+ else {
+ ok = false;
+ tap_file << "not ok " << i+1;
+ }
+ if (! test_messages[i].empty()) {
+ tap_file << " - " << test_messages[i];
+ }
+ tap_file << endl;
+ }
+ tap_file.close();
+ free(test_results);
+ delete [] test_messages;
+ return ok;
+}
+
+#define TAP_END_TEST_EXIT if(tap_end_test(__FILE__)) { \
+ exit(0); \
+ } else { \
+ exit(1); \
+ }
+
+#endif
diff --git a/src/libGkArrays/tests/variableAndFixedLength.cpp b/src/libGkArrays/tests/variableAndFixedLength.cpp
new file mode 100644
index 0000000..d2469f3
--- /dev/null
+++ b/src/libGkArrays/tests/variableAndFixedLength.cpp
@@ -0,0 +1,131 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thierry LECROQ <thierry.lecroq at univ-rouen.fr> *
+* Martine LÉONARD <Martine.Leonard at univ-rouen.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: Gk-Arrays list <crac-gkarrays at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie de la librairie Gk-arrays. *
+* *
+* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
+* lectures de séquences issues du séquençage haut-débit. *
+* *
+* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the Gk-arrays library. *
+* *
+* The Gk-arrays library aims at indexing k-factors from a huge set of *
+* sequencing reads. *
+* *
+* This software is governed by the CeCILL-C license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL-C *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL-C license and that you accept its terms. *
+* *
+******************************************************************************/
+#include <iostream>
+#include <cstdlib>
+#include <compareVariableFixed.h>
+#include "testing.h"
+
+TAP_DECLARATIONS
+
+using namespace std;
+
+int main(int argc, char **argv) {
+ TAP_START(NB_TESTS);
+ if (argc < 4) {
+ cerr << "Usage: " << argv[0] << " <file> <read_length> <k>" << endl
+ << endl
+ << "Test the variable and fixed implementation using a dataset." << endl
+ << "The dataset must contain fixed-length reads since the goal" << endl
+ << "is to compare the results and check if they are consistent." << endl
+ << endl
+ << " <file>: text file containing the reads in FASTA/FASTQ format. " << endl
+ << " <read_length>: integer giving the length of the reads" << endl
+ << " <k>: integer setting the length of indexed k-mers." << endl;
+ exit(1);
+ }
+ uint k = atol(argv[3]);
+
+ int read_length = atoi(argv[2]);
+
+ compareVariableFixed(argv[1], read_length, k);
+
+ TAP_END_TEST_EXIT
+}
diff --git a/src/libReadsInfo/BioTagIndelInfo.cpp b/src/libReadsInfo/BioTagIndelInfo.cpp
new file mode 100644
index 0000000..ffd5642
--- /dev/null
+++ b/src/libReadsInfo/BioTagIndelInfo.cpp
@@ -0,0 +1,105 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "BioTagIndelInfo.h"
+
+BioIndelInfo::BioIndelInfo(ChrPosition chrPos, uint position, uint nb_ins,
+ uint nb_del, float score, bool is_duplicated):
+ IndelInfo(chrPos, position, nb_ins, nb_del, score, is_duplicated) {}
+
diff --git a/src/libReadsInfo/BioTagIndelInfo.h b/src/libReadsInfo/BioTagIndelInfo.h
new file mode 100644
index 0000000..28abc1b
--- /dev/null
+++ b/src/libReadsInfo/BioTagIndelInfo.h
@@ -0,0 +1,112 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef BIOINDEL_INFO_H
+#define BIOINDEL_INFO_H
+#include "IndelInfo.h"
+#include "../libSSA/chrPosition.h"
+
+class BioIndelInfo : public IndelInfo {
+ public:
+ BioIndelInfo(ChrPosition chrPos, uint position, uint nb_ins, uint nb_del,
+ float score, bool is_duplicated);
+};
+
+
+#endif
diff --git a/src/libReadsInfo/BioUndeterminedInfo.cpp b/src/libReadsInfo/BioUndeterminedInfo.cpp
new file mode 100644
index 0000000..21a04c3
--- /dev/null
+++ b/src/libReadsInfo/BioUndeterminedInfo.cpp
@@ -0,0 +1,138 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "BioUndeterminedInfo.h"
+
+BioUndeterminedInfo::BioUndeterminedInfo(ChrPosition *pos, uint position, char *message)
+ :pos(pos), message(message)
+{
+ setPosition(position);
+}
+
+BioUndeterminedInfo::~BioUndeterminedInfo() {
+ if (pos != NULL)
+ delete pos;
+ delete [] message;
+}
+
+ChrPosition *BioUndeterminedInfo::getChrPosition() {
+ return pos;
+}
+
+char *BioUndeterminedInfo::getMessage() {
+ return message;
+}
+
+void BioUndeterminedInfo::output(ostream &os) {
+ os << *this;
+}
+
+void BioUndeterminedInfo::samOutput(ostream &os, int strand) {
+ os << "BioUndetermined:" << getPosition(strand)
+ << ":[" << getMessage() << "]";
+}
+
+ostream &operator<<(ostream &os, BioUndeterminedInfo& i) {
+ if (i.getChrPosition() != NULL)
+ os << *i.getChrPosition() << " ";
+ os << "pos_break=" << i.getPosition() ;
+ os << " [" << i.getMessage()<< "]";
+ return os;
+}
+
diff --git a/src/libReadsInfo/BioUndeterminedInfo.h b/src/libReadsInfo/BioUndeterminedInfo.h
new file mode 100644
index 0000000..70e4bc9
--- /dev/null
+++ b/src/libReadsInfo/BioUndeterminedInfo.h
@@ -0,0 +1,123 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef BIO_UNDETERMINED_H
+#define BIO_UNDETERMINED_H
+#include "genericInfo.h"
+#include "../libSSA/chrPosition.h"
+
+class BioUndeterminedInfo : public GenericInfo {
+ private:
+ ChrPosition *pos;
+ uint position;
+ char *message;
+ public:
+ BioUndeterminedInfo(ChrPosition *pos, uint position, char *message);
+ ~BioUndeterminedInfo();
+
+ ChrPosition *getChrPosition();
+ char *getMessage();
+
+ void output(ostream &);
+ void samOutput(ostream &, int=1);
+};
+
+ostream &operator<<(ostream &os, BioUndeterminedInfo &);
+
+#endif
diff --git a/src/libReadsInfo/Cigar.cpp b/src/libReadsInfo/Cigar.cpp
new file mode 100644
index 0000000..86a677a
--- /dev/null
+++ b/src/libReadsInfo/Cigar.cpp
@@ -0,0 +1,226 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "Cigar.h"
+#include <cassert>
+
+Cigar::Cigar():nb_M(0), nb_I(0), nb_D(0), nb_S(0), nb_P(0), nb_H(0), nb_EQ(0), nb_X(0), nb_N(0), nb_chimeras(0){}
+
+
+void Cigar::append(uint nb, char op) {
+ assert(op == 'M' || op == 'I' || op == 'D' || op == 'S' || op == '='
+ || op == 'P' || op == 'H' || op == 'X' || op == 'N');
+ cigar_type ct = {nb, op};
+ append(ct);
+}
+
+void Cigar::append(cigar_type cigar) {
+ update_counters(cigar);
+ this->cigar.push_back(cigar);
+}
+
+void Cigar::filter() {
+ char old_type = 0;
+ uint old_nb = 0;
+ vector<cigar_type>::iterator it = cigar.begin();
+ while (it < cigar.end()) {
+ // Two identical consecutive types
+ if (it->type == old_type
+ && (it->type != 'N' || (it->nb > 0 && old_nb > 0))) {
+ it->nb += old_nb;
+ it = cigar.erase(it-1);
+ } else if (it->type != 'N' && it->nb == 0) {
+ it = cigar.erase(it)-1;
+ }
+
+ old_type = it->type;
+ old_nb = it->nb;
+ it++;
+ }
+}
+
+void Cigar::prepend(uint nb, char op) {
+ assert(op == 'M' || op == 'I' || op == 'D' || op == 'S' || op == '='
+ || op == 'P' || op == 'H' || op == 'X' || op == 'N');
+ cigar_type ct = {nb, op};
+ prepend(ct);
+}
+
+void Cigar::prepend(cigar_type cigar) {
+ update_counters(cigar);
+ this->cigar.insert(this->cigar.begin(), cigar);
+}
+
+ /* Queries */
+
+uint Cigar::count() const {
+ return cigar.size();
+}
+
+const cigar_type& Cigar::get(uint i) const{
+ return cigar[i];
+}
+
+uint Cigar::getReferenceAlignementLength() const {
+ return nb_M + nb_D + nb_N + nb_EQ + nb_X;
+}
+
+uint Cigar::getNbDeletions() const {
+ return nb_D + nb_N;
+}
+
+uint Cigar::getNbPositionsRead() const {
+ return nb_M + nb_EQ + nb_X + nb_I + nb_S;
+}
+
+uint Cigar::getEditDistance() const {
+ return nb_X + nb_I + nb_D + nb_N;
+}
+
+uint Cigar::getNbChimeras() const {
+ return nb_chimeras;
+}
+
+void Cigar::reverse() {
+ vector<cigar_type> reverse_cigar;
+ for(int i = cigar.size(); i > 0; i--) {
+ reverse_cigar.push_back(cigar[i-1]);
+ }
+ cigar = reverse_cigar;
+}
+
+cigar_type &Cigar::operator[](uint i) {
+ return cigar[i];
+}
+
+
+ostream &operator<<(ostream &os, const Cigar &c) {
+ if (c.count() > 0) {
+ for (uint i=0; i < c.count(); i++) {
+ os << c.get(i);
+ }
+ } else {
+ os << "*";
+ }
+ return os;
+}
+
+void Cigar::update_counters(const cigar_type &cigar) {
+ if(cigar.type == 'M') {
+ nb_M += cigar.nb;
+ } else if(cigar.type == '=') {
+ nb_EQ += cigar.nb;
+ } else if(cigar.type == 'X') {
+ nb_X += cigar.nb;
+ } else if(cigar.type == 'I') {
+ nb_I += cigar.nb;
+ } else if(cigar.type == 'D') {
+ nb_D += cigar.nb;
+ } else if(cigar.type == 'N') {
+ if(cigar.nb == 0) {
+ nb_chimeras += 1;
+ } else {
+ nb_N += cigar.nb;
+ }
+ } else if(cigar.type == 'S') {
+ nb_S += cigar.nb;
+ } else if(cigar.type == 'H') {
+ nb_H += cigar.nb;
+ }
+}
diff --git a/src/libReadsInfo/Cigar.h b/src/libReadsInfo/Cigar.h
new file mode 100644
index 0000000..544181a
--- /dev/null
+++ b/src/libReadsInfo/Cigar.h
@@ -0,0 +1,222 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef CIGAR_H
+#define CIGAR_H
+#include <iostream>
+#include <vector>
+#include "cigarTypes.h"
+
+class Cigar {
+ private:
+ /* Storing the whole CIGAR string */
+ vector<cigar_type> cigar;
+
+ /* Counters for each operator */
+ uint nb_M, nb_I, nb_D, nb_S, nb_P, nb_H, nb_EQ, nb_X, nb_N, nb_chimeras;
+
+ void update_counters(const cigar_type &cigar);
+
+ public:
+
+ Cigar();
+
+ /* Command */
+ /**
+ * Append a new element in the CIGAR string
+ * @param nb: the number related to the CIGAR operator (eg. 10 in 10M)
+ * @param operator: the operator to be used
+ * @pre op in (M, I, D, S, P, H, =, X, N)
+ * @post count() == old count() + 1
+ * AND get(count()-1) == {nb, op}
+ */
+ void append(uint nb, char op);
+
+ /**
+ * Append a new element in the CIGAR string
+ * @param cigar: the CIGAR operator (with the number)
+ * @post count() == old count() + 1
+ * AND get(count()-1) == cigar
+ */
+ void append(cigar_type cigar);
+
+ /**
+ * Filter consecutive operators with the same type, remove
+ * operators whose length is 0 (apart from N).
+ * @post count() <= old count()
+ * AND get(i).type != get(i+1).type (when get(i).type != 'N') for i = 0 ... count()-2
+ * AND get(i).nb != 0 (when get(i).type != 'N') for i = 0 ... count()-1
+ */
+ void filter();
+
+ /**
+ * Prepend a new element in the CIGAR string
+ * @param nb: the number related to the CIGAR operator (eg. 10 in 10M)
+ * @param operator: the operator to be used
+ * @pre op in (M, I, D, S, P, H, =, X, N)
+ * @post count() == old count() + 1
+ * AND get(0) == {nb, op}
+ */
+ void prepend(uint nb, char op);
+
+ /**
+ * Prepend a new element in the CIGAR string
+ * @param cigar: the CIGAR operator (with the number)
+ * @post count() == old count() - 1
+ * AND get(0) == cigar
+ */
+ void prepend(cigar_type cigar);
+
+ /* Queries */
+
+ /**
+ * @return Number of operators in the string
+ */
+ uint count() const;
+
+ /**
+ * @param i: Element from the CIGAR string to retrieve
+ * @pre 0 <= i < count()
+ * @return the i-th element in CIGAR.
+ */
+ const cigar_type& get(uint i) const;
+
+ /**
+ * @return the length of the alignement on the reference
+ * (ie sume of the numbers associated with a M, D, N, = or X operator).
+ */
+ uint getReferenceAlignementLength() const;
+
+ /*
+ * @retrun the number of deleted nucleotids from the reference.
+ * (ie sum of the numbers associated with a D or N operator).
+ */
+ uint getNbDeletions() const;
+
+ /**
+ * @return the number of positions that are in the read
+ * (ie sum of the numbers associated with a M, I, S, = or X operator).
+ */
+ uint getNbPositionsRead() const;
+
+ /**
+ * @return the number of positions that are in the read
+ * (ie sum of the numbers associated with a X, I, D, or N operator).
+ */
+ uint getEditDistance() const;
+
+ /**
+ * @return the number of chimeras in the Cigar chain
+ * (ie sum of '0N' elements)
+ */
+ uint getNbChimeras() const;
+
+ /**
+ * Reverse the cigar elements.
+ * Example : 8S5M1D3M => 3M1D5M8S
+ */
+ void reverse();
+
+ cigar_type &operator[](uint i);
+};
+
+ostream &operator<<(ostream &, const Cigar &);
+
+
+#endif
diff --git a/src/libReadsInfo/DuplicationInfo.cpp b/src/libReadsInfo/DuplicationInfo.cpp
new file mode 100644
index 0000000..a7b379a
--- /dev/null
+++ b/src/libReadsInfo/DuplicationInfo.cpp
@@ -0,0 +1,116 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "DuplicationInfo.h"
+
+DuplicationInfo::DuplicationInfo(){}
+DuplicationInfo::~DuplicationInfo(){}
+
+// uint DuplicationInfo::getNbDuplication() {
+// return nb_copies;
+// }
+
+void DuplicationInfo::output(ostream &os) {
+ os << *this;
+}
+
+ostream &operator<<(ostream &os, DuplicationInfo &info) {
+// os << "nb_copies = " << info.getNbDuplication() ;
+ return os;
+}
diff --git a/src/libReadsInfo/DuplicationInfo.h b/src/libReadsInfo/DuplicationInfo.h
new file mode 100644
index 0000000..4128b79
--- /dev/null
+++ b/src/libReadsInfo/DuplicationInfo.h
@@ -0,0 +1,117 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef DUPLICATION_INFO_H
+#define DUPLICATION_INFO_H
+#include "genericInfo.h"
+
+class DuplicationInfo : public GenericInfo {
+ private:
+ public:
+ DuplicationInfo();
+ ~DuplicationInfo();
+
+/* uint getNbDuplication(); */
+
+ void output(ostream &);
+};
+
+ostream &operator<<(ostream &, DuplicationInfo &);
+
+#endif
diff --git a/src/libReadsInfo/IndelInfo.cpp b/src/libReadsInfo/IndelInfo.cpp
new file mode 100644
index 0000000..dcc4a1a
--- /dev/null
+++ b/src/libReadsInfo/IndelInfo.cpp
@@ -0,0 +1,185 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <cassert>
+#include "IndelInfo.h"
+
+IndelInfo::IndelInfo(ChrPosition chrPos, uint position, uint nb_ins, uint nb_del,
+ float score, bool is_duplicated):
+ chrPos(chrPos),nb_ins(nb_ins),nb_del(nb_del),score(score),is_duplicated(is_duplicated) {
+ setPosition(position);
+}
+
+IndelInfo::~IndelInfo() {
+// delete chrPos;
+}
+
+uint IndelInfo::getNbIns() {
+ return nb_ins;
+}
+
+uint IndelInfo::getNbDel() {
+ return nb_del;
+}
+
+ChrPosition &IndelInfo::getChrPosition() {
+ return chrPos;
+}
+
+float IndelInfo::getScore() {
+ return score;
+}
+
+bool IndelInfo::isDuplicated() {
+ return is_duplicated;
+}
+
+void IndelInfo::output(ostream &os) {
+ os << *this;
+}
+
+void IndelInfo::samOutput(ostream &os, int strand) {
+ if (getNbIns() > 0 && getNbIns() < (uint)~0) {
+ os << "Ins:" << getScore() << ":" << getPosition(strand) << ":" << getChrPosition()
+ << ":" << getNbIns();
+ } else if (getNbDel() > 0 && getNbDel() < (uint) ~0) {
+ os << "Del:" << getScore() << ":" << getPosition(strand) << ":" << getChrPosition()
+ << ":" << getNbDel();
+ } else {
+ cerr << "Nothing was expected here : " << __FILE__ << ":" << __LINE__ << endl;
+ }
+}
+
+cigar_type IndelInfo::getCigarInfo() {
+ cigar_type cigar;
+ if (getNbIns() == 0 && getNbDel() == 0) {
+ cigar.nb = 1;
+ cigar.type = 'X';
+ } else if (getNbIns() != (uint)~0 && getNbIns() > 0) {
+ cigar.nb = getNbIns();
+ cigar.type = 'I';
+ } else {
+ assert(getNbDel() != (uint)~0);
+ cigar.nb = getNbDel();
+ cigar.type = 'D';
+ }
+ return cigar;
+};
+
+
+ostream &operator<<(ostream &os, IndelInfo& i) {
+ if (i.isDuplicated()){
+ os <<"duplicate ";
+ }else{
+ os <<"single ";
+ }
+ os << i.getChrPosition() << " pos_indel="<<i.getPosition()<<" nb_ins=";
+ uint nb = i.getNbIns();
+ if (nb == (uint)~0)
+ os << "unknown";
+ else
+ os << nb;
+ os <<" nb_del=";
+ nb = i.getNbDel();
+ if (nb == (uint)~0)
+ os << "unknown";
+ else
+ os << nb;
+ return os;
+}
diff --git a/src/libReadsInfo/IndelInfo.h b/src/libReadsInfo/IndelInfo.h
new file mode 100644
index 0000000..40b40f5
--- /dev/null
+++ b/src/libReadsInfo/IndelInfo.h
@@ -0,0 +1,136 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef INDEL_INFO_H
+#define INDEL_INFO_H
+#include "genericInfo.h"
+#include "../libSSA/chrPosition.h"
+
+class IndelInfo : public GenericInfo {
+private:
+ ChrPosition chrPos;
+ uint nb_ins;
+ uint nb_del;
+ float score;
+ bool is_duplicated;
+
+public:
+ IndelInfo(ChrPosition chrPos, uint position, uint nb_ins, uint nb_del,
+ float score, bool is_duplicated);
+ ~IndelInfo();
+
+ uint getNbIns();
+ uint getNbDel();
+ ChrPosition &getChrPosition();
+
+ /**
+ * Return the score of the indel
+ */
+ float getScore();
+
+ virtual bool isDuplicated();
+
+ virtual void output(ostream &);
+ virtual void samOutput(ostream &, int=1);
+ virtual cigar_type getCigarInfo();
+};
+
+ostream &operator<<(ostream &os, IndelInfo& i);
+
+#endif
diff --git a/src/libReadsInfo/Makefile.am b/src/libReadsInfo/Makefile.am
new file mode 100644
index 0000000..d3f6035
--- /dev/null
+++ b/src/libReadsInfo/Makefile.am
@@ -0,0 +1,132 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+
+noinst_LIBRARIES = libReadsInfo.a
+
+libReadsInfo_a_SOURCES = \
+ BioTagIndelInfo.cpp BioTagIndelInfo.h \
+ BioUndeterminedInfo.cpp BioUndeterminedInfo.h \
+ cigarTypes.cpp cigarTypes.h \
+ Cigar.cpp Cigar.h \
+ DuplicationInfo.cpp DuplicationInfo.h \
+ genericInfo.cpp genericInfo.h \
+ IndelInfo.cpp IndelInfo.h \
+ repetitionInfo.cpp repetitionInfo.h \
+ SeqErrInfo.cpp SeqErrInfo.h \
+ SNPInfo.cpp SNPInfo.h \
+ SpliceInfo.cpp SpliceInfo.h \
+ SpliceInterInfo.cpp SpliceInterInfo.h \
+ SpliceIntraInfo.cpp SpliceIntraInfo.h \
+ SpliceNoCoverInfo.cpp SpliceNoCoverInfo.h \
+ SplicingInfo.cpp SplicingInfo.h \
+ samLine.cpp samLine.h \
+ tagInfo.cpp tagInfo.h \
+ undeterminedErrorInfo.cpp undeterminedErrorInfo.h
+
+libReadsInfo_a_CPPFLAGS = -I at abs_top_srcdir@ -I at abs_top_srcdir@/src -I at abs_top_srcdir@/src/libSSA
+if INCLUDED_GKARRAYS
+ libReadsInfo_a_CPPFLAGS += -I at abs_srcdir@/../libGkArrays/src/
+endif
+
+
+MOSTLYCLEANFILES=*~
+CLEANFILES=*~ $(EXTRA_PROGRAMS)
+DISTCLEANFILES=*~
+MAINTAINERCLEANFILES=*~
diff --git a/src/libReadsInfo/Makefile.in b/src/libReadsInfo/Makefile.in
new file mode 100644
index 0000000..b49f051
--- /dev/null
+++ b/src/libReadsInfo/Makefile.in
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+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
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+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
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+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
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+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
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+ libReadsInfo_a-Cigar.$(OBJEXT) \
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+ DuplicationInfo.cpp DuplicationInfo.h \
+ genericInfo.cpp genericInfo.h \
+ IndelInfo.cpp IndelInfo.h \
+ repetitionInfo.cpp repetitionInfo.h \
+ SeqErrInfo.cpp SeqErrInfo.h \
+ SNPInfo.cpp SNPInfo.h \
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+ SpliceInterInfo.cpp SpliceInterInfo.h \
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+ SpliceNoCoverInfo.cpp SpliceNoCoverInfo.h \
+ SplicingInfo.cpp SplicingInfo.h \
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+ tagInfo.cpp tagInfo.h \
+ undeterminedErrorInfo.cpp undeterminedErrorInfo.h
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+
+libReadsInfo_a-SNPInfo.o: SNPInfo.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-SNPInfo.o -MD -MP -MF $(DEPDIR)/libReadsInfo_a-SNPInfo.Tpo -c -o libReadsInfo_a-SNPInfo.o `test -f 'SNPInfo.cpp' || echo '$(srcdir)/'`SNPInfo.cpp
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-SNPInfo.Tpo $(DEPDIR)/libReadsInfo_a-SNPInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='SNPInfo.cpp' object='libReadsInfo_a-SNPInfo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-SNPInfo.o `test -f 'SNPInfo.cpp' || echo '$(srcdir)/'`SNPInfo.cpp
+
+libReadsInfo_a-SNPInfo.obj: SNPInfo.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-SNPInfo.obj -MD -MP -MF $(DEPDIR)/libReadsInfo_a-SNPInfo.Tpo -c -o libReadsInfo_a-SNPInfo.obj `if test -f 'SNPInfo.cpp'; then $(CYGPATH_W) 'SNPInfo.cpp'; else $(CYGPATH_W) '$(srcdir)/SNPInfo.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-SNPInfo.Tpo $(DEPDIR)/libReadsInfo_a-SNPInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='SNPInfo.cpp' object='libReadsInfo_a-SNPInfo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-SNPInfo.obj `if test -f 'SNPInfo.cpp'; then $(CYGPATH_W) 'SNPInfo.cpp'; else $(CYGPATH_W) '$(srcdir)/SNPInfo.cpp'; fi`
+
+libReadsInfo_a-SpliceInfo.o: SpliceInfo.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-SpliceInfo.o -MD -MP -MF $(DEPDIR)/libReadsInfo_a-SpliceInfo.Tpo -c -o libReadsInfo_a-SpliceInfo.o `test -f 'SpliceInfo.cpp' || echo '$(srcdir)/'`SpliceInfo.cpp
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-SpliceInfo.Tpo $(DEPDIR)/libReadsInfo_a-SpliceInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='SpliceInfo.cpp' object='libReadsInfo_a-SpliceInfo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-SpliceInfo.o `test -f 'SpliceInfo.cpp' || echo '$(srcdir)/'`SpliceInfo.cpp
+
+libReadsInfo_a-SpliceInfo.obj: SpliceInfo.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-SpliceInfo.obj -MD -MP -MF $(DEPDIR)/libReadsInfo_a-SpliceInfo.Tpo -c -o libReadsInfo_a-SpliceInfo.obj `if test -f 'SpliceInfo.cpp'; then $(CYGPATH_W) 'SpliceInfo.cpp'; else $(CYGPATH_W) '$(srcdir)/SpliceInfo.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-SpliceInfo.Tpo $(DEPDIR)/libReadsInfo_a-SpliceInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='SpliceInfo.cpp' object='libReadsInfo_a-SpliceInfo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-SpliceInfo.obj `if test -f 'SpliceInfo.cpp'; then $(CYGPATH_W) 'SpliceInfo.cpp'; else $(CYGPATH_W) '$(srcdir)/SpliceInfo.cpp'; fi`
+
+libReadsInfo_a-SpliceInterInfo.o: SpliceInterInfo.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-SpliceInterInfo.o -MD -MP -MF $(DEPDIR)/libReadsInfo_a-SpliceInterInfo.Tpo -c -o libReadsInfo_a-SpliceInterInfo.o `test -f 'SpliceInterInfo.cpp' || echo '$(srcdir)/'`SpliceInterInfo.cpp
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-SpliceInterInfo.Tpo $(DEPDIR)/libReadsInfo_a-SpliceInterInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='SpliceInterInfo.cpp' object='libReadsInfo_a-SpliceInterInfo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-SpliceInterInfo.o `test -f 'SpliceInterInfo.cpp' || echo '$(srcdir)/'`SpliceInterInfo.cpp
+
+libReadsInfo_a-SpliceInterInfo.obj: SpliceInterInfo.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-SpliceInterInfo.obj -MD -MP -MF $(DEPDIR)/libReadsInfo_a-SpliceInterInfo.Tpo -c -o libReadsInfo_a-SpliceInterInfo.obj `if test -f 'SpliceInterInfo.cpp'; then $(CYGPATH_W) 'SpliceInterInfo.cpp'; else $(CYGPATH_W) '$(srcdir)/SpliceInterInfo.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-SpliceInterInfo.Tpo $(DEPDIR)/libReadsInfo_a-SpliceInterInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='SpliceInterInfo.cpp' object='libReadsInfo_a-SpliceInterInfo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-SpliceInterInfo.obj `if test -f 'SpliceInterInfo.cpp'; then $(CYGPATH_W) 'SpliceInterInfo.cpp'; else $(CYGPATH_W) '$(srcdir)/SpliceInterInfo.cpp'; fi`
+
+libReadsInfo_a-SpliceIntraInfo.o: SpliceIntraInfo.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-SpliceIntraInfo.o -MD -MP -MF $(DEPDIR)/libReadsInfo_a-SpliceIntraInfo.Tpo -c -o libReadsInfo_a-SpliceIntraInfo.o `test -f 'SpliceIntraInfo.cpp' || echo '$(srcdir)/'`SpliceIntraInfo.cpp
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-SpliceIntraInfo.Tpo $(DEPDIR)/libReadsInfo_a-SpliceIntraInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='SpliceIntraInfo.cpp' object='libReadsInfo_a-SpliceIntraInfo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-SpliceIntraInfo.o `test -f 'SpliceIntraInfo.cpp' || echo '$(srcdir)/'`SpliceIntraInfo.cpp
+
+libReadsInfo_a-SpliceIntraInfo.obj: SpliceIntraInfo.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-SpliceIntraInfo.obj -MD -MP -MF $(DEPDIR)/libReadsInfo_a-SpliceIntraInfo.Tpo -c -o libReadsInfo_a-SpliceIntraInfo.obj `if test -f 'SpliceIntraInfo.cpp'; then $(CYGPATH_W) 'SpliceIntraInfo.cpp'; else $(CYGPATH_W) '$(srcdir)/SpliceIntraInfo.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-SpliceIntraInfo.Tpo $(DEPDIR)/libReadsInfo_a-SpliceIntraInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='SpliceIntraInfo.cpp' object='libReadsInfo_a-SpliceIntraInfo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-SpliceIntraInfo.obj `if test -f 'SpliceIntraInfo.cpp'; then $(CYGPATH_W) 'SpliceIntraInfo.cpp'; else $(CYGPATH_W) '$(srcdir)/SpliceIntraInfo.cpp'; fi`
+
+libReadsInfo_a-SpliceNoCoverInfo.o: SpliceNoCoverInfo.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-SpliceNoCoverInfo.o -MD -MP -MF $(DEPDIR)/libReadsInfo_a-SpliceNoCoverInfo.Tpo -c -o libReadsInfo_a-SpliceNoCoverInfo.o `test -f 'SpliceNoCoverInfo.cpp' || echo '$(srcdir)/'`SpliceNoCoverInfo.cpp
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-SpliceNoCoverInfo.Tpo $(DEPDIR)/libReadsInfo_a-SpliceNoCoverInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='SpliceNoCoverInfo.cpp' object='libReadsInfo_a-SpliceNoCoverInfo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-SpliceNoCoverInfo.o `test -f 'SpliceNoCoverInfo.cpp' || echo '$(srcdir)/'`SpliceNoCoverInfo.cpp
+
+libReadsInfo_a-SpliceNoCoverInfo.obj: SpliceNoCoverInfo.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-SpliceNoCoverInfo.obj -MD -MP -MF $(DEPDIR)/libReadsInfo_a-SpliceNoCoverInfo.Tpo -c -o libReadsInfo_a-SpliceNoCoverInfo.obj `if test -f 'SpliceNoCoverInfo.cpp'; then $(CYGPATH_W) 'SpliceNoCoverInfo.cpp'; else $(CYGPATH_W) '$(srcdir)/SpliceNoCoverInfo.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-SpliceNoCoverInfo.Tpo $(DEPDIR)/libReadsInfo_a-SpliceNoCoverInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='SpliceNoCoverInfo.cpp' object='libReadsInfo_a-SpliceNoCoverInfo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-SpliceNoCoverInfo.obj `if test -f 'SpliceNoCoverInfo.cpp'; then $(CYGPATH_W) 'SpliceNoCoverInfo.cpp'; else $(CYGPATH_W) '$(srcdir)/SpliceNoCoverInfo.cpp'; fi`
+
+libReadsInfo_a-SplicingInfo.o: SplicingInfo.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-SplicingInfo.o -MD -MP -MF $(DEPDIR)/libReadsInfo_a-SplicingInfo.Tpo -c -o libReadsInfo_a-SplicingInfo.o `test -f 'SplicingInfo.cpp' || echo '$(srcdir)/'`SplicingInfo.cpp
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-SplicingInfo.Tpo $(DEPDIR)/libReadsInfo_a-SplicingInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='SplicingInfo.cpp' object='libReadsInfo_a-SplicingInfo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-SplicingInfo.o `test -f 'SplicingInfo.cpp' || echo '$(srcdir)/'`SplicingInfo.cpp
+
+libReadsInfo_a-SplicingInfo.obj: SplicingInfo.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-SplicingInfo.obj -MD -MP -MF $(DEPDIR)/libReadsInfo_a-SplicingInfo.Tpo -c -o libReadsInfo_a-SplicingInfo.obj `if test -f 'SplicingInfo.cpp'; then $(CYGPATH_W) 'SplicingInfo.cpp'; else $(CYGPATH_W) '$(srcdir)/SplicingInfo.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-SplicingInfo.Tpo $(DEPDIR)/libReadsInfo_a-SplicingInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='SplicingInfo.cpp' object='libReadsInfo_a-SplicingInfo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-SplicingInfo.obj `if test -f 'SplicingInfo.cpp'; then $(CYGPATH_W) 'SplicingInfo.cpp'; else $(CYGPATH_W) '$(srcdir)/SplicingInfo.cpp'; fi`
+
+libReadsInfo_a-samLine.o: samLine.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-samLine.o -MD -MP -MF $(DEPDIR)/libReadsInfo_a-samLine.Tpo -c -o libReadsInfo_a-samLine.o `test -f 'samLine.cpp' || echo '$(srcdir)/'`samLine.cpp
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-samLine.Tpo $(DEPDIR)/libReadsInfo_a-samLine.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='samLine.cpp' object='libReadsInfo_a-samLine.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-samLine.o `test -f 'samLine.cpp' || echo '$(srcdir)/'`samLine.cpp
+
+libReadsInfo_a-samLine.obj: samLine.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-samLine.obj -MD -MP -MF $(DEPDIR)/libReadsInfo_a-samLine.Tpo -c -o libReadsInfo_a-samLine.obj `if test -f 'samLine.cpp'; then $(CYGPATH_W) 'samLine.cpp'; else $(CYGPATH_W) '$(srcdir)/samLine.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-samLine.Tpo $(DEPDIR)/libReadsInfo_a-samLine.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='samLine.cpp' object='libReadsInfo_a-samLine.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-samLine.obj `if test -f 'samLine.cpp'; then $(CYGPATH_W) 'samLine.cpp'; else $(CYGPATH_W) '$(srcdir)/samLine.cpp'; fi`
+
+libReadsInfo_a-tagInfo.o: tagInfo.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-tagInfo.o -MD -MP -MF $(DEPDIR)/libReadsInfo_a-tagInfo.Tpo -c -o libReadsInfo_a-tagInfo.o `test -f 'tagInfo.cpp' || echo '$(srcdir)/'`tagInfo.cpp
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-tagInfo.Tpo $(DEPDIR)/libReadsInfo_a-tagInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='tagInfo.cpp' object='libReadsInfo_a-tagInfo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-tagInfo.o `test -f 'tagInfo.cpp' || echo '$(srcdir)/'`tagInfo.cpp
+
+libReadsInfo_a-tagInfo.obj: tagInfo.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-tagInfo.obj -MD -MP -MF $(DEPDIR)/libReadsInfo_a-tagInfo.Tpo -c -o libReadsInfo_a-tagInfo.obj `if test -f 'tagInfo.cpp'; then $(CYGPATH_W) 'tagInfo.cpp'; else $(CYGPATH_W) '$(srcdir)/tagInfo.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-tagInfo.Tpo $(DEPDIR)/libReadsInfo_a-tagInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='tagInfo.cpp' object='libReadsInfo_a-tagInfo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-tagInfo.obj `if test -f 'tagInfo.cpp'; then $(CYGPATH_W) 'tagInfo.cpp'; else $(CYGPATH_W) '$(srcdir)/tagInfo.cpp'; fi`
+
+libReadsInfo_a-undeterminedErrorInfo.o: undeterminedErrorInfo.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-undeterminedErrorInfo.o -MD -MP -MF $(DEPDIR)/libReadsInfo_a-undeterminedErrorInfo.Tpo -c -o libReadsInfo_a-undeterminedErrorInfo.o `test -f 'undeterminedErrorInfo.cpp' || echo '$(srcdir)/'`undeterminedErrorInfo.cpp
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-undeterminedErrorInfo.Tpo $(DEPDIR)/libReadsInfo_a-undeterminedErrorInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='undeterminedErrorInfo.cpp' object='libReadsInfo_a-undeterminedErrorInfo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-undeterminedErrorInfo.o `test -f 'undeterminedErrorInfo.cpp' || echo '$(srcdir)/'`undeterminedErrorInfo.cpp
+
+libReadsInfo_a-undeterminedErrorInfo.obj: undeterminedErrorInfo.cpp
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT libReadsInfo_a-undeterminedErrorInfo.obj -MD -MP -MF $(DEPDIR)/libReadsInfo_a-undeterminedErrorInfo.Tpo -c -o libReadsInfo_a-undeterminedErrorInfo.obj `if test -f 'undeterminedErrorInfo.cpp'; then $(CYGPATH_W) 'undeterminedErrorInfo.cpp'; else $(CYGPATH_W) '$(srcdir)/undeterminedErrorInfo.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/libReadsInfo_a-undeterminedErrorInfo.Tpo $(DEPDIR)/libReadsInfo_a-undeterminedErrorInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='undeterminedErrorInfo.cpp' object='libReadsInfo_a-undeterminedErrorInfo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libReadsInfo_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o libReadsInfo_a-undeterminedErrorInfo.obj `if test -f 'undeterminedErrorInfo.cpp'; then $(CYGPATH_W) 'undeterminedErrorInfo.cpp'; else $(CYGPATH_W) '$(srcdir)/undeterminedErrorInfo.cpp'; fi`
+
+mostlyclean-libtool:
+ -rm -f *.lo
+
+clean-libtool:
+ -rm -rf .libs _libs
+
+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in files) print i; }; }'`; \
+ mkid -fID $$unique
+tags: TAGS
+
+TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
+ $(TAGS_FILES) $(LISP)
+ set x; \
+ here=`pwd`; \
+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in files) print i; }; }'`; \
+ shift; \
+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
+ test -n "$$unique" || unique=$$empty_fix; \
+ if test $$# -gt 0; then \
+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+ "$$@" $$unique; \
+ else \
+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+ $$unique; \
+ fi; \
+ fi
+ctags: CTAGS
+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
+ $(TAGS_FILES) $(LISP)
+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in files) print i; }; }'`; \
+ test -z "$(CTAGS_ARGS)$$unique" \
+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+ $$unique
+
+GTAGS:
+ here=`$(am__cd) $(top_builddir) && pwd` \
+ && $(am__cd) $(top_srcdir) \
+ && gtags -i $(GTAGS_ARGS) "$$here"
+
+distclean-tags:
+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(DISTFILES)
+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+ list='$(DISTFILES)'; \
+ dist_files=`for file in $$list; do echo $$file; done | \
+ sed -e "s|^$$srcdirstrip/||;t" \
+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+ case $$dist_files in \
+ */*) $(MKDIR_P) `echo "$$dist_files" | \
+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
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+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
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+ else \
+ test -f "$(distdir)/$$file" \
+ || cp -p $$d/$$file "$(distdir)/$$file" \
+ || exit 1; \
+ fi; \
+ done
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+ `test -z '$(STRIP)' || \
+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+ -test -z "$(MOSTLYCLEANFILES)" || rm -f $(MOSTLYCLEANFILES)
+
+clean-generic:
+ -test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
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+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+ -test -z "$(DISTCLEANFILES)" || rm -f $(DISTCLEANFILES)
+
+maintainer-clean-generic:
+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+ -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
+clean: clean-am
+
+clean-am: clean-generic clean-libtool clean-noinstLIBRARIES \
+ mostlyclean-am
+
+distclean: distclean-am
+ -rm -rf ./$(DEPDIR)
+ -rm -f Makefile
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+ distclean-tags
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+dvi: dvi-am
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+dvi-am:
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+
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+install-ps-am:
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+maintainer-clean: maintainer-clean-am
+ -rm -rf ./$(DEPDIR)
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-compile mostlyclean-generic \
+ mostlyclean-libtool
+
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+ps-am:
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+
+.MAKE: install-am install-strip
+
+.PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \
+ clean-libtool clean-noinstLIBRARIES ctags distclean \
+ distclean-compile distclean-generic distclean-libtool \
+ distclean-tags distdir dvi dvi-am html html-am info info-am \
+ install install-am install-data install-data-am install-dvi \
+ install-dvi-am install-exec install-exec-am install-html \
+ install-html-am install-info install-info-am install-man \
+ install-pdf install-pdf-am install-ps install-ps-am \
+ install-strip installcheck installcheck-am installdirs \
+ maintainer-clean maintainer-clean-generic mostlyclean \
+ mostlyclean-compile mostlyclean-generic mostlyclean-libtool \
+ pdf pdf-am ps ps-am tags uninstall uninstall-am
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/src/libReadsInfo/SNPInfo.cpp b/src/libReadsInfo/SNPInfo.cpp
new file mode 100644
index 0000000..1907eb1
--- /dev/null
+++ b/src/libReadsInfo/SNPInfo.cpp
@@ -0,0 +1,208 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "SNPInfo.h"
+#include "libSSA/utils.h"
+
+SNPInfo::SNPInfo(ChrPosition chrPos, uint position,
+ float score, bool is_duplicated,
+ char actual_nuc, char expected_nuc):
+ chrPos(chrPos), score(score),
+ is_duplicated(is_duplicated),
+ actual_nuc(actual_nuc),
+ expected_nuc(expected_nuc)
+{
+ setPosition(position);
+ if (actual_nuc == 0) {
+ if (expected_nuc == 0) {
+ type = SNP_UNKNOWN;
+ } else {
+ type = SNP_DELETION;
+ }
+ } else {
+ if (expected_nuc == 0) {
+ type = SNP_INSERTION;
+ } else {
+ type = SNP_SUBSTITUTION;
+ }
+ }
+}
+
+SNPInfo::~SNPInfo() {
+}
+
+char SNPInfo::getActualNucleotide(int strand) {
+ if (getSNPType() == SNP_UNKNOWN || getSNPType() == SNP_DELETION)
+ return '?';
+ return (strand == 1) ? actual_nuc : complementDNA(actual_nuc);;
+}
+
+char SNPInfo::getExpectedNucleotide(int strand) {
+ if (getSNPType() == SNP_UNKNOWN || getSNPType() == SNP_INSERTION)
+ return '?';
+ return (strand == 1) ? expected_nuc : complementDNA(expected_nuc);
+}
+
+ChrPosition &SNPInfo::getChrPosition() {
+ return chrPos;
+}
+
+float SNPInfo::getScore() {
+ return score;
+}
+
+snp_type SNPInfo::getSNPType() {
+ return type;
+}
+
+bool SNPInfo::isDuplicated() {
+ return is_duplicated;
+}
+
+void SNPInfo::output(ostream &os) {
+ os << *this;
+}
+
+void SNPInfo::samOutput(ostream &os, int strand) {
+ os << "SNP:" << getScore() << ":" << getPosition(strand) << ":" << getChrPosition()
+ << ":" << getExpectedNucleotide(strand) << ":" << getActualNucleotide(strand);
+}
+
+cigar_type SNPInfo::getCigarInfo() {
+ cigar_type cigar;
+ cigar.nb = 1;
+ cigar.type = 0; // Just initializing so that gcc is happy
+ if (getSNPType() == SNP_SUBSTITUTION) {
+ cigar.type = 'X';
+ } else if (getSNPType() == SNP_DELETION) {
+ cigar.type = 'D';
+ } else if (getSNPType() == SNP_INSERTION) {
+ cigar.type = 'I';
+ }
+ return cigar;
+}
+
+ostream &operator<<(ostream &os, SNPInfo& i) {
+ if (i.isDuplicated()){
+ os << "duplicate ";
+ }else{
+ os << "single ";
+ }
+ os << i.getChrPosition()
+ << " pos_SNV="<<i.getPosition()
+ << " ";
+ if (i.getSNPType() == SNP_UNKNOWN)
+ os << "?->?";
+ else {
+ if (i.getSNPType() == SNP_INSERTION)
+ os << "?";
+ else
+ os << i.getExpectedNucleotide() ;
+
+ os << "->";
+
+ if (i.getSNPType() == SNP_DELETION)
+ os << "?";
+ else
+ os << i.getActualNucleotide();
+ os << " score=" << i.getScore() ;
+
+ }
+ return os;
+}
diff --git a/src/libReadsInfo/SNPInfo.h b/src/libReadsInfo/SNPInfo.h
new file mode 100644
index 0000000..9b4c4ee
--- /dev/null
+++ b/src/libReadsInfo/SNPInfo.h
@@ -0,0 +1,150 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef SNP_INFO_H
+#define SNP_INFO_H
+#include "../types.h"
+#include "genericInfo.h"
+#include "../libSSA/chrPosition.h"
+#include "cigarTypes.h"
+
+class SNPInfo : public GenericInfo {
+private:
+ ChrPosition chrPos;
+ float score;
+ snp_type type;
+ bool is_duplicated;
+ char actual_nuc;
+ char expected_nuc;
+
+public:
+ SNPInfo(ChrPosition chrPos, uint position, float score,
+ bool is_duplicated,
+ char actual_nuc=0, char expected_nuc=0);
+ ~SNPInfo();
+
+ /**
+ * Return the nucleotide actually found in the sequence,
+ * or 0 if getSNPType() == SNP_DELETION || getSNPType() == SNP_UNKNOWN
+ * @param strand: if strand == -1 return the complementary of the nucleotide
+ * instead of the nucleotide itself
+ */
+ char getActualNucleotide(int strand=1);
+
+ /**
+ * Return the nucleotide as expected in the reference genome
+ * or 0 if getSNPType() == SNP_INSERTION || getSNPType() == SNP_UNKNOWN
+ * @param strand: if strand == -1 return the complementary of the nucleotide
+ * instead of the nucleotide itself
+ */
+ char getExpectedNucleotide(int strand=1);
+
+ ChrPosition &getChrPosition();
+ float getScore();
+ snp_type getSNPType();
+ bool isDuplicated();
+
+ void output(ostream &);
+ void samOutput(ostream &, int=1);
+ cigar_type getCigarInfo();
+};
+
+ostream &operator<<(ostream &os, SNPInfo &);
+
+#endif
diff --git a/src/libReadsInfo/SeqErrInfo.cpp b/src/libReadsInfo/SeqErrInfo.cpp
new file mode 100644
index 0000000..2c71e7d
--- /dev/null
+++ b/src/libReadsInfo/SeqErrInfo.cpp
@@ -0,0 +1,222 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "SeqErrInfo.h"
+#include "../libSSA/utils.h"
+
+SeqErrInfo::SeqErrInfo(ChrPosition chrPos, uint position, uint nb_ins,
+ uint nb_del, float score, bool is_duplicated,
+ char *genome, char *tag,
+ uint g_length, uint t_length):
+ IndelInfo(chrPos, position, nb_ins, nb_del, score, is_duplicated),
+ genome_sequence(genome),
+ err_sequence(tag), g_seq_length(g_length), t_seq_length(t_length)
+{
+ genome_sequence_revcomp = NULL;
+ err_sequence_revcomp = NULL;
+ if (genome_sequence) {
+ genome_sequence_revcomp = new char[g_seq_length+1];
+ genome_sequence_revcomp[g_seq_length] = 0;
+ for (uint i=0; i < g_seq_length; i++)
+ genome_sequence_revcomp[g_seq_length - i - 1] = complementDNA(genome_sequence[i]);
+ }
+
+ if (err_sequence) {
+ err_sequence_revcomp = new char[t_seq_length+1];
+ err_sequence_revcomp[t_seq_length] = 0;
+ for (uint i = 0; i < t_seq_length; i++)
+ err_sequence_revcomp[t_seq_length - i - 1] = complementDNA(err_sequence[i]);
+ }
+}
+
+SeqErrInfo::~SeqErrInfo() {
+ if (genome_sequence != NULL && genome_sequence[0]!=0) {
+ free(genome_sequence);
+ delete [] genome_sequence_revcomp;
+ }
+ if (err_sequence != NULL && err_sequence[0]!=0) {
+ delete [] err_sequence;
+ delete [] err_sequence_revcomp;
+ }
+}
+
+char *SeqErrInfo::getErrorSequence(int strand) {
+ return (strand == 1) ? err_sequence : err_sequence_revcomp;
+}
+
+uint SeqErrInfo::getErrorSequenceLength() {
+ return t_seq_length;
+}
+
+char *SeqErrInfo::getGenomeSequence(int strand) {
+ return (strand == 1) ? genome_sequence : genome_sequence_revcomp;
+}
+
+uint SeqErrInfo::getGenomeSequenceLength() {
+ return g_seq_length;
+}
+
+// bool SeqErrInfo::isDuplicated() {
+// return is_duplicated;
+// }
+
+void SeqErrInfo::samOutput(ostream &os, int strand) {
+ if (getErrorSequenceLength() == getGenomeSequenceLength()
+ && getErrorSequenceLength() < (uint)~0)
+ // Substitution
+ os << "Error:Sub:" << getPosition(strand) << ":" << getScore() << ":"
+ << getGenomeSequence(strand) << ":"
+ << getErrorSequence(strand);
+ else if ((getNbIns() == (uint)~0) && (getNbDel() == (uint)~0))
+ // Unknown
+ os << "Error:Unknown:" << getPosition(strand) << ":" << getScore();
+ else if (getNbDel() > 0)
+ // Deletion
+ os << "Error:Del:" << getPosition(strand) << ":" << getScore() << ":"
+ << getNbDel() << ":"
+ << (getGenomeSequence() == NULL ? "<snip>" : getGenomeSequence(strand));
+ else if (getNbIns() > 0)
+ os << "Error:Ins:" << getPosition(strand) << ":" << getScore() << ":"
+ << getNbIns() << ":"
+ << (getErrorSequence() == NULL ? "<snip>" : getErrorSequence(strand));
+}
+
+ostream &operator<<(ostream &os, SeqErrInfo& i) {
+ if (i.isDuplicated()){
+ os <<"duplicate ";
+ }else{
+ os <<"single ";
+ }
+ os << i.getChrPosition()
+ << " pos_error="<<i.getPosition()
+ << " nb_ins=";
+ uint nb = i.getNbIns();
+ if (nb == (uint)~0)
+ os << "unknown";
+ else
+ os << nb;
+ os <<" nb_del=";
+ nb = i.getNbDel();
+ if (nb == (uint)~0)
+ os << "unknown";
+ else
+ os << nb;
+
+ if ((i.getGenomeSequence() == NULL
+ || i.getGenomeSequence()[0]==0)
+ && (i.getErrorSequence() == NULL
+ || i.getErrorSequence()[0]==0))
+ return os;
+
+ os << " ";
+
+ if (i.getGenomeSequence() == NULL)
+ os << "?";
+ else
+ os << i.getGenomeSequence();
+
+ os << "->";
+
+ if (i.getErrorSequence() == NULL)
+ os << "?";
+ else
+ os << i.getErrorSequence();
+ os << " score=" << i.getScore();
+ return os;
+}
diff --git a/src/libReadsInfo/SeqErrInfo.h b/src/libReadsInfo/SeqErrInfo.h
new file mode 100644
index 0000000..59d9656
--- /dev/null
+++ b/src/libReadsInfo/SeqErrInfo.h
@@ -0,0 +1,154 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef SEQERR_INFO_H
+#define SEQERR_INFO_H
+#include "IndelInfo.h"
+#include "../libSSA/chrPosition.h"
+
+class SeqErrInfo : public IndelInfo {
+ private:
+ float score;
+ char *genome_sequence;
+ char *err_sequence;
+ char *genome_sequence_revcomp;
+ char *err_sequence_revcomp;
+ uint g_seq_length;
+ uint t_seq_length;
+
+ public:
+ SeqErrInfo(ChrPosition chrPos, uint position, uint nb_ins, uint nb_del,
+ float score, bool is_duplicated,
+ char *genome=NULL, char *tag=NULL, uint g_length=~0, uint t_length=~0);
+
+ ~SeqErrInfo();
+
+ /**
+ * @return err_sequence, the sequence, corresponding to the error,
+ * on the tag.
+ */
+ char *getErrorSequence(int strand = 1);
+
+ /**
+ * @return t_seq_length, the length of the string returned by
+ * getErrorSequence().
+ */
+ uint getErrorSequenceLength();
+
+ /**
+ * @return err_sequence, the sequence, corresponding to the error,
+ * on the genome.
+ */
+ char *getGenomeSequence(int strand = 1);
+
+ /**
+ * @return g_seq_length, the length of the array returned by
+ * getGenomeSequence (\0 excluded).
+ */
+ uint getGenomeSequenceLength();
+
+
+ /* bool isDuplicated(); */
+
+ void samOutput(ostream &os, int=1);
+};
+
+ostream &operator<<(ostream &os, SeqErrInfo& i);
+
+#endif
diff --git a/src/libReadsInfo/SpliceInfo.cpp b/src/libReadsInfo/SpliceInfo.cpp
new file mode 100644
index 0000000..0a91c61
--- /dev/null
+++ b/src/libReadsInfo/SpliceInfo.cpp
@@ -0,0 +1,108 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "SpliceInfo.h"
+
+SpliceInfo::SpliceInfo(ChrPosition chrPos, uint position, uint gap_length, bool is_duplicated)
+ : SplicingInfo(chrPos, position, gap_length, is_duplicated){}
+
+void SpliceInfo::samOutput(ostream &os, int strand) {
+ os << "Junction:normal:";
+ SplicingInfo::samOutput(os, strand);
+}
diff --git a/src/libReadsInfo/SpliceInfo.h b/src/libReadsInfo/SpliceInfo.h
new file mode 100644
index 0000000..fb0f375
--- /dev/null
+++ b/src/libReadsInfo/SpliceInfo.h
@@ -0,0 +1,111 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef SPLICE_INFO_H
+#define SPLICE_INFO_H
+#include "SplicingInfo.h"
+#include "../libSSA/chrPosition.h"
+
+class SpliceInfo : public SplicingInfo {
+ public:
+ SpliceInfo(ChrPosition chrPos, uint position, uint gap_length, bool is_duplicated);
+ void samOutput(ostream &os, int=1);
+};
+
+#endif
diff --git a/src/libReadsInfo/SpliceInterInfo.cpp b/src/libReadsInfo/SpliceInterInfo.cpp
new file mode 100644
index 0000000..a5eb413
--- /dev/null
+++ b/src/libReadsInfo/SpliceInterInfo.cpp
@@ -0,0 +1,149 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "SpliceInterInfo.h"
+
+SpliceInterInfo::SpliceInterInfo(ChrPosition chrPos, uint position, ChrPosition chrPos2, bool is_duplicated):
+ chrPos(chrPos),chrPos2(chrPos2), is_duplicated(is_duplicated){
+ setPosition(position);
+ is_valid = true;
+}
+
+SpliceInterInfo::~SpliceInterInfo() {
+}
+
+ChrPosition &SpliceInterInfo::getChromosomeDest() {
+ return chrPos2;
+}
+
+ChrPosition &SpliceInterInfo::getChrPosition() {
+ return chrPos;
+}
+
+cigar_type SpliceInterInfo::getCigarInfo() {
+ cigar_type cigar;
+ // Special case for pointing a chimera and so that
+ // usual softwares processing SAM do not complain.
+ cigar.nb = 0;
+ cigar.type = 'N';
+ return cigar;
+}
+
+bool SpliceInterInfo::isDuplicated() {
+ return is_duplicated;
+}
+
+void SpliceInterInfo::output(ostream &os) {
+ os << *this;
+}
+
+void SpliceInterInfo::samOutput(ostream &os, int strand) {
+ os << "chimera:" << getPosition(strand) << ":" << getChrPosition() << ":"
+ << getChromosomeDest();
+}
+
+ostream &operator<<(ostream &os, SpliceInterInfo &i) {
+ if (i.isDuplicated()){
+ os << "duplicate ";
+ }else{
+ os << "single ";
+ }
+ os << i.getChrPosition() <<" "<<i.getChromosomeDest() << " pos_junction="<<i.getPosition();
+ return os;
+}
diff --git a/src/libReadsInfo/SpliceInterInfo.h b/src/libReadsInfo/SpliceInterInfo.h
new file mode 100644
index 0000000..1a2a693
--- /dev/null
+++ b/src/libReadsInfo/SpliceInterInfo.h
@@ -0,0 +1,127 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef SPLICEINTER_INFO_H
+#define SPLICEINTER_INFO_H
+#include "genericInfo.h"
+#include "../libSSA/chrPosition.h"
+
+class SpliceInterInfo : public GenericInfo {
+private:
+ ChrPosition chrPos;
+ ChrPosition chrPos2;
+ bool is_duplicated;
+ bool is_valid;
+public:
+ SpliceInterInfo(ChrPosition chrPos, uint position, ChrPosition chrPos2, bool is_duplicated);
+ ~SpliceInterInfo();
+
+ ChrPosition &getChromosomeDest();
+ ChrPosition &getChrPosition();
+
+ virtual cigar_type getCigarInfo();
+ bool isDuplicated();
+
+ void output(ostream &os);
+ void samOutput(ostream &os, int=1);
+};
+
+ostream &operator<<(ostream &os, SpliceInterInfo &);
+
+#endif
diff --git a/src/libReadsInfo/SpliceIntraInfo.cpp b/src/libReadsInfo/SpliceIntraInfo.cpp
new file mode 100644
index 0000000..2bc9585
--- /dev/null
+++ b/src/libReadsInfo/SpliceIntraInfo.cpp
@@ -0,0 +1,108 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "SpliceIntraInfo.h"
+
+SpliceIntraInfo::SpliceIntraInfo(ChrPosition chrPos, uint position, uint gap_length, bool is_duplicated)
+ : SplicingInfo(chrPos, position, gap_length, is_duplicated){}
+
+void SpliceIntraInfo::samOutput(ostream &os, int strand) {
+ os << "Junction:intra:";
+ SplicingInfo::samOutput(os, strand);
+}
diff --git a/src/libReadsInfo/SpliceIntraInfo.h b/src/libReadsInfo/SpliceIntraInfo.h
new file mode 100644
index 0000000..345718e
--- /dev/null
+++ b/src/libReadsInfo/SpliceIntraInfo.h
@@ -0,0 +1,111 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef SPLICEINTRA_INFO_H
+#define SPLICEINTRA_INFO_H
+#include "SplicingInfo.h"
+#include "../libSSA/chrPosition.h"
+
+class SpliceIntraInfo : public SplicingInfo {
+ public:
+ SpliceIntraInfo(ChrPosition chrPos, uint position, uint gap_length, bool is_duplicated);
+ void samOutput(ostream &os, int=1);
+};
+
+#endif
diff --git a/src/libReadsInfo/SpliceNoCoverInfo.cpp b/src/libReadsInfo/SpliceNoCoverInfo.cpp
new file mode 100644
index 0000000..04269ff
--- /dev/null
+++ b/src/libReadsInfo/SpliceNoCoverInfo.cpp
@@ -0,0 +1,108 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "SpliceNoCoverInfo.h"
+
+SpliceNoCoverInfo::SpliceNoCoverInfo(ChrPosition chrPos, uint position, uint gap_length, bool is_duplicated)
+ : SplicingInfo(chrPos, position, gap_length, is_duplicated){}
+
+void SpliceNoCoverInfo::samOutput(ostream &os, int strand) {
+ os << "Junction:coverless:";
+ SplicingInfo::samOutput(os, strand);
+}
diff --git a/src/libReadsInfo/SpliceNoCoverInfo.h b/src/libReadsInfo/SpliceNoCoverInfo.h
new file mode 100644
index 0000000..1ca02dd
--- /dev/null
+++ b/src/libReadsInfo/SpliceNoCoverInfo.h
@@ -0,0 +1,111 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef SPLICE_NO_COVER_INFO_H
+#define SPLICE_NO_COVER_INFO_H
+#include "SplicingInfo.h"
+#include "../libSSA/chrPosition.h"
+
+class SpliceNoCoverInfo : public SplicingInfo {
+ public:
+ SpliceNoCoverInfo(ChrPosition chrPos, uint position, uint gap_length, bool is_duplicated);
+ void samOutput(ostream &os, int=1);
+};
+
+#endif
diff --git a/src/libReadsInfo/SplicingInfo.cpp b/src/libReadsInfo/SplicingInfo.cpp
new file mode 100644
index 0000000..12d0571
--- /dev/null
+++ b/src/libReadsInfo/SplicingInfo.cpp
@@ -0,0 +1,146 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "SplicingInfo.h"
+
+SplicingInfo::SplicingInfo(ChrPosition chrPos, uint position, uint gap_length, bool is_duplicated)
+ :chrPos(chrPos),gap_length(gap_length),is_duplicated(is_duplicated){
+ setPosition(position);
+}
+
+SplicingInfo::~SplicingInfo() {
+}
+
+uint SplicingInfo::getGapLength() {
+ return gap_length;
+}
+
+ChrPosition &SplicingInfo::getChrPosition() {
+ return chrPos;
+}
+
+bool SplicingInfo::isDuplicated(){
+ return is_duplicated;
+}
+
+void SplicingInfo::output(ostream &os) {
+ os << *this;
+}
+
+void SplicingInfo::samOutput(ostream &os, int strand) {
+ os << getPosition(strand) << ":" << getChrPosition() << ":" << getGapLength();
+}
+
+cigar_type SplicingInfo::getCigarInfo() {
+ cigar_type cigar;
+ cigar.nb = getGapLength();
+ cigar.type = 'N';
+ return cigar;
+}
+
+ostream &operator<<(ostream &os, SplicingInfo &i) {
+ if (i.isDuplicated()){
+ os <<"duplicate ";
+ }else{
+ os <<"single ";
+ }
+ os << i.getChrPosition() << " pos_junction="<<i.getPosition() << " gap_length="<<i.getGapLength();
+ return os;
+}
+
diff --git a/src/libReadsInfo/SplicingInfo.h b/src/libReadsInfo/SplicingInfo.h
new file mode 100644
index 0000000..b06b505
--- /dev/null
+++ b/src/libReadsInfo/SplicingInfo.h
@@ -0,0 +1,127 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef SPLICING_INFO_H
+#define SPLICING_INFO_H
+#include "genericInfo.h"
+#include "../libSSA/chrPosition.h"
+#include "cigarTypes.h"
+
+class SplicingInfo : public GenericInfo {
+private:
+ ChrPosition chrPos;
+ uint gap_length;
+ bool is_duplicated;
+
+ public:
+ SplicingInfo(ChrPosition chrPos, uint position, uint gap_length, bool is_duplicated);
+ ~SplicingInfo();
+
+ uint getGapLength();
+ ChrPosition &getChrPosition();
+ bool isDuplicated();
+
+ virtual void output(ostream &os);
+ virtual void samOutput(ostream &os, int=1);
+ virtual cigar_type getCigarInfo();
+};
+
+ostream &operator<<(ostream &os, SplicingInfo &);
+
+#endif
diff --git a/src/libReadsInfo/cigarTypes.cpp b/src/libReadsInfo/cigarTypes.cpp
new file mode 100644
index 0000000..7813c19
--- /dev/null
+++ b/src/libReadsInfo/cigarTypes.cpp
@@ -0,0 +1,144 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "cigarTypes.h"
+#include "../const.h"
+#include <cstdlib>
+
+
+cigar_type *add_cigar(cigar_type *ct, uint &index, uint nb, char type) {
+ cigar_type cigar;
+ cigar.nb = nb;
+ cigar.type = type;
+ return add_cigar(ct, index, cigar);
+}
+
+cigar_type *add_cigar(cigar_type *ct, uint &index, cigar_type cigar) {
+ if (index > 0 && index % NB_CIGAR_ELEM == 0)
+ ct = (cigar_type *)realloc(ct, (index+NB_CIGAR_ELEM) * sizeof(cigar_type));
+ ct[index++] = cigar;
+ return ct;
+}
+
+cigar_type cigar_string_to_cigar_type(char *str) {
+ uint pos=0;
+ char type;
+ uint nb;
+ while (str[pos]>= '0' && str[pos] <= '9')
+ pos++;
+ type=str[pos];
+ str[pos]=0;
+ nb = atoi(str);
+ cigar_type ct= {nb,type};
+ return ct;
+}
+
+
+ostream &operator<<(ostream &os, const cigar_type &cigar) {
+ os << cigar.nb << cigar.type;
+ return os;
+}
+
+bool operator==(const cigar_type& lhs, const cigar_type& rhs) {
+ return lhs.nb == rhs.nb && lhs.type == rhs.type;
+}
+
+bool operator!=(const cigar_type& lhs, const cigar_type& rhs) {
+ return lhs.nb != rhs.nb || lhs.type != rhs.type;
+}
diff --git a/src/libReadsInfo/cigarTypes.h b/src/libReadsInfo/cigarTypes.h
new file mode 100644
index 0000000..f18376a
--- /dev/null
+++ b/src/libReadsInfo/cigarTypes.h
@@ -0,0 +1,135 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef CIGAR_TYPES_H
+#define CIGAR_TYPES_H
+#include <iostream>
+#include "../types.h"
+using namespace std;
+
+typedef struct s_cigar_type {
+ uint nb;
+ char type;
+} cigar_type;
+
+
+bool operator==(const cigar_type& lhs, const cigar_type& rhs);
+bool operator!=(const cigar_type& lhs, const cigar_type& rhs);
+
+/**
+ * Add a new cigar_type in an array of cigar_type.
+ * The second parameter is the current index in the array to be modified.
+ * The number of elements in the array is a multiple of NB_CIGAR_ELEM.
+ * If the array is not big enough to contain the new element it is enlarged.
+ * The index is updated.
+ */
+cigar_type *add_cigar(cigar_type *, uint &, uint, char);
+
+cigar_type *add_cigar(cigar_type *, uint &, cigar_type);
+
+/**
+ * Convert a cigar string (whose format is <nb><type>, eg. 12M) to a cigar_type
+ */
+cigar_type cigar_string_to_cigar_type(char *);
+
+/**
+ * Redefinition of operator << for elements of type cigar_type
+ */
+ostream &operator<<(ostream &, const cigar_type &);
+#endif
diff --git a/src/libReadsInfo/genericInfo.cpp b/src/libReadsInfo/genericInfo.cpp
new file mode 100644
index 0000000..b2857d3
--- /dev/null
+++ b/src/libReadsInfo/genericInfo.cpp
@@ -0,0 +1,156 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "genericInfo.h"
+
+GenericInfo::GenericInfo() {
+ stranded_pos = ~0;
+}
+
+GenericInfo::~GenericInfo() {}
+
+void GenericInfo::cigarString(ostream &os) {
+ os << getCigarInfo();
+}
+
+cigar_type GenericInfo::getCigarInfo() {
+ cigar_type cigar;
+ cigar.nb = 0;
+ cigar.type = 0;
+ return cigar;
+}
+
+uint GenericInfo::getPosition(int strand) {
+ return (strand == 1) ? position
+ : (((uint)stranded_pos != (uint)~0)
+ ? stranded_pos
+ : getReadLength() - 1 - position);
+}
+
+uint GenericInfo::getReadLength() {
+ return read_length;
+}
+
+void GenericInfo::setPosition(uint p) {
+ position = p;
+}
+
+void GenericInfo::setReadLength(uint l) {
+ read_length = l;
+}
+
+void GenericInfo::setStrandedPosition(uint pos) {
+ stranded_pos = pos;
+}
+
+uint GenericInfo::getBreakId() {
+ return breakId;
+}
+
+void GenericInfo::setBreakId(uint id) {
+ breakId = id;
+}
+
+uint GenericInfo::getCauseId() {
+ return causeId;
+}
+
+void GenericInfo::setCauseId(uint id) {
+ causeId = id;
+}
diff --git a/src/libReadsInfo/genericInfo.h b/src/libReadsInfo/genericInfo.h
new file mode 100644
index 0000000..c9fe520
--- /dev/null
+++ b/src/libReadsInfo/genericInfo.h
@@ -0,0 +1,139 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef GENERIC_INFO_H
+#define GENERIC_INFO_H
+#include <iostream>
+#include <ostream>
+#include "cigarTypes.h"
+using namespace std;
+
+
+class GenericInfo {
+ private:
+ uint read_length;
+ uint position;
+ int stranded_pos; /* Stores the position for reverse strand
+ * it may be difficult to compute it directly
+ * from position because of overlapping kmers.*/
+ uint breakId;
+ uint causeId;
+
+ public:
+ GenericInfo();
+ virtual ~GenericInfo();
+ virtual void output(ostream &) {};
+ virtual void samOutput(ostream &, int=1) {};
+ void cigarString(ostream &);
+ int getKMerOverlap();
+ uint getBreakId();
+ uint getCauseId();
+ uint getPosition(int strand=1);
+ uint getReadLength();
+ virtual cigar_type getCigarInfo();
+
+ void setPosition(uint);
+ void setReadLength(uint);
+ void setStrandedPosition(uint);
+ void setBreakId(uint);
+ void setCauseId(uint);
+};
+
+
+#endif
diff --git a/src/libReadsInfo/repetitionInfo.cpp b/src/libReadsInfo/repetitionInfo.cpp
new file mode 100644
index 0000000..edc1e84
--- /dev/null
+++ b/src/libReadsInfo/repetitionInfo.cpp
@@ -0,0 +1,145 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "repetitionInfo.h"
+
+RepetitionInfo::RepetitionInfo(int pos_in, int pos_out):pos_in(pos_in),pos_out(pos_out){}
+
+RepetitionInfo::~RepetitionInfo() {}
+
+int RepetitionInfo::getStartPosition() {
+ return pos_in;
+}
+
+int RepetitionInfo::getEndPosition() {
+ return pos_out;
+}
+
+void RepetitionInfo::output(ostream &os) {
+ os << *this;
+}
+
+void RepetitionInfo::samOutput(ostream &os, int strand) {
+ //os << "Repetition:";
+ if (getStartPosition() == -1)
+ os << "unknown";
+ else
+ os << getStartPosition();
+ os << ":";
+ if (getEndPosition() == -1)
+ os << "unknown";
+ else
+ os << getEndPosition();
+}
+
+ostream &operator<<(ostream &os, RepetitionInfo &i) {
+ os << "start_pos_repeat=";
+ int pos=i.getStartPosition();
+ if (pos == -1)
+ os << "unknown";
+ else
+ os << pos;
+ os<<" end_pos_repeat=";
+ pos=i.getEndPosition();
+ if (pos == -1)
+ os << "unknown";
+ else
+ os << pos;
+ return os;
+}
diff --git a/src/libReadsInfo/repetitionInfo.h b/src/libReadsInfo/repetitionInfo.h
new file mode 100644
index 0000000..5bdd602
--- /dev/null
+++ b/src/libReadsInfo/repetitionInfo.h
@@ -0,0 +1,121 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef REPETITION_INFO_H
+#define REPETITION_INFO_H
+#include "genericInfo.h"
+
+class RepetitionInfo : public GenericInfo {
+ private:
+ int pos_in;
+ int pos_out;
+ public:
+ RepetitionInfo(int pos_in, int pos_out);
+ ~RepetitionInfo();
+
+ int getStartPosition();
+ int getEndPosition();
+
+ virtual void output(ostream &);
+ virtual void samOutput(ostream &, int=1);
+};
+
+ostream &operator<<(ostream &, RepetitionInfo &);
+
+#endif
diff --git a/src/libReadsInfo/samLine.cpp b/src/libReadsInfo/samLine.cpp
new file mode 100644
index 0000000..d40eba6
--- /dev/null
+++ b/src/libReadsInfo/samLine.cpp
@@ -0,0 +1,421 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at univ-montp2.fr *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "samLine.h"
+#include "../libSSA/utils.h"
+#include <sstream>
+#include <cstring>
+
+
+SamLine::SamLine() {
+ // init SAM fields with default values
+ rname = "*";
+ qname = "*";
+ rnext = "*";
+ seq = "*";
+ qual = "*";
+ flag = 0;
+ pos = 0;
+ mapQ = 255;
+ //mapQ = 0;
+ pnext = 0;
+ tlen = 0;
+ //is_mapped = true;
+}
+
+// Query template NAME
+void SamLine::setQname(const string& qname) {
+ this->qname = qname;
+}
+const string& SamLine::getQname() const {
+ return qname;
+}
+
+// bitwize FLAG
+void SamLine::setFlag(uint flag){
+ this->flag = flag;
+}
+uint SamLine::getFlag() const {
+ return flag;
+}
+
+// generic flag bit methods
+bool SamLine::isFlagBitSet(uint bit) const {
+ return flag & bit;
+}
+void SamLine::setFlagBit(uint bit) {
+ flag = flag | bit;
+}
+void SamLine::unsetFlagBit(uint bit) {
+ flag = flag^bit;
+}
+
+// Flag operations
+// bit 1
+bool SamLine::isTemplateHavingMultipleSegments() const {
+ return isFlagBitSet(1);
+}
+void SamLine::setTemplateHavingMultipleSegments() {
+ setFlagBit(1);
+}
+void SamLine::unsetTemplateHavingMultipleSegments() {
+ unsetFlagBit(1);
+}
+
+// bit 2
+bool SamLine::isEachSegmentsMapped() const {
+ return isFlagBitSet(2);
+}
+void SamLine::setEachSegmentsMapped() {
+ setFlagBit(2);
+}
+void SamLine::unsetEachSegmentsMapped() {
+ unsetFlagBit(2);
+}
+
+// bit 4
+bool SamLine::isSegmentUnmapped() const {
+ return isFlagBitSet(4);
+}
+void SamLine::setSegmentUnmapped() {
+ setFlagBit(4);
+}
+void SamLine::unsetSegmentUnmapped() {
+ unsetFlagBit(4);
+}
+
+// bit 8
+bool SamLine::isNextSegmentUnmapped() const {
+ return isFlagBitSet(8);
+}
+void SamLine::setNextSegmentUnmapped() {
+ setFlagBit(8);
+}
+void SamLine::unsetNextSegmentUnmapped() {
+ unsetFlagBit(8);
+}
+
+// bit 16
+bool SamLine::isSeqReverseComplemented() const {
+ return isFlagBitSet(16);
+}
+void SamLine::setSeqReverseComplemented() {
+ setFlagBit(16);
+}
+void SamLine::unsetSeqReverseComplemented() {
+ unsetFlagBit(16);
+}
+
+// bit 32
+bool SamLine::isNextSeqReverseComplemented() const {
+ return isFlagBitSet(32);
+}
+void SamLine::setNextSeqReverseComplemented() {
+ setFlagBit(32);
+}
+void SamLine::unsetNextSeqReverseComplemented() {
+ unsetFlagBit(32);
+}
+
+// bit 64
+bool SamLine::isFirstSegmentInTheTemplate() const {
+ return isFlagBitSet(64);
+}
+void SamLine::setFirstSegmentInTheTemplate() {
+ setFlagBit(64);
+}
+void SamLine::unsetFirstSegmentInTheTemplate() {
+ unsetFlagBit(64);
+}
+
+// bit 128
+bool SamLine::isLastSegmentInTheTemplate() const {
+ return isFlagBitSet(128);
+}
+void SamLine::setLastSegmentInTheTemplate() {
+ setFlagBit(128);
+}
+void SamLine::unsetLastSegmentInTheTemplate() {
+ unsetFlagBit(128);
+}
+
+// bit 256
+bool SamLine::isSecondaryAlignement() const {
+ return isFlagBitSet(256);
+}
+void SamLine::setSecondaryAlignement() {
+ setFlagBit(256);
+}
+void SamLine::unsetSecondaryAlignement() {
+ unsetFlagBit(256);
+}
+
+// bit 512
+bool SamLine::isFailingQualityControl() const {
+ return isFlagBitSet(512);
+}
+void SamLine::setFailingQualityControl() {
+ setFlagBit(512);
+}
+void SamLine::unsetFailingQualityControl() {
+ unsetFlagBit(512);
+}
+
+// bit 1024
+bool SamLine::isPCRDuplicated() const {
+ return isFlagBitSet(1024);
+}
+void SamLine::setPCRDuplicated() {
+ setFlagBit(1024);
+}
+void SamLine::unsetPCRDuplicated() {
+ unsetFlagBit(1024);
+}
+
+// bit 2048
+bool SamLine::isChimericAlignement() const {
+ return isFlagBitSet(2048);
+}
+void SamLine::setChimericAlignement() {
+ setFlagBit(2048);
+}
+void SamLine::unsetChimericAlignement() {
+ unsetFlagBit(2048);
+}
+
+// Reference sequence NAME
+void SamLine::setRname(const string& rname) {
+ this->rname = rname;
+}
+const string& SamLine::getRname() const {
+ return rname;
+}
+
+// 1-based leftmost mapping POSition
+void SamLine::setPos(uint pos) {
+ this->pos = pos;
+}
+uint SamLine::getPos() const {
+ return pos;
+}
+
+// MAPping Quality
+void SamLine::setMapQ(uint mapQ) {
+ this->mapQ = mapQ;
+}
+uint SamLine::getMapQ() const {
+ return mapQ;
+}
+
+// CIGAR string
+void SamLine::setCigar(const Cigar &cigar) {
+ this->cigar = cigar;
+}
+const Cigar& SamLine::getCigar() const {
+ return cigar;
+}
+
+// Ref. name of the mate/next segment
+void SamLine::setRnext(const string& rnext) {
+ this->rnext = rnext;
+}
+const string& SamLine::getRnext() const{
+ return rnext;
+}
+
+// Position of the mate/next segment
+void SamLine::setPnext(uint pnext) {
+ this->pnext = pnext;
+}
+uint SamLine::getPnext() const{
+ return pnext;
+}
+
+// observed Template LENgth
+void SamLine::setTlen(int tlen) {
+ this->tlen = tlen;
+}
+int SamLine::getTlen() const{
+ return tlen;
+}
+
+// segment SEQuence
+void SamLine::setSeq(const string& seq) {
+ this->seq = seq;
+}
+const string& SamLine::getSeq() const {
+ return seq;
+}
+void SamLine::reverseComplementeSeq() {
+ string new_seq;
+ for (int i = seq.length() - 1; i >= 0; i--) {
+ new_seq.push_back(complementDNA(seq[i]));
+ }
+ setSeq(new_seq);
+}
+
+// ASCII of Phred-scaled base QUALity+33
+void SamLine::setQual(const string& qual) {
+ this->qual = qual;
+}
+const string& SamLine::getQual() const {
+ return qual;
+}
+void SamLine::reverseQual() {
+ string new_qual;
+ for (int i = qual.length() - 1; i >= 0; i--) {
+ new_qual.push_back(qual[i]);
+ }
+ setQual(new_qual);
+}
+
+// Optional fields
+bool SamLine::addOptionalField(const char *tag, int val) {
+ ostringstream convert;
+ convert << "i:" << val;
+ optionalFields[tag] = convert.str();
+ return true;
+}
+bool SamLine::addOptionalField(const char *tag, const string& val) {
+ string new_val = val;
+ optionalFields[tag] = new_val.insert(0,"Z:");
+ return true;
+}
+bool SamLine::addOptionalField(const char *tag, const char* val) {
+ string new_val = val;
+ optionalFields[tag] = new_val.insert(0,"Z:");
+ return true;
+}
+const string& SamLine::getOptionalField(const char *tag) {
+ return optionalFields[tag];
+}
+bool SamLine::isOptionalFieldDefined(const char *tag) {
+ return optionalFields.count(tag) > 0;
+}
+
+void SamLine::removeAllUserOptionalFields() {
+ map<string,string>::iterator it=optionalFields.begin();
+ while(it != optionalFields.end()) {
+ if(it->first[0] == 'X' || it->first[0] == 'Y' || it->first[0] == 'Z')
+ optionalFields.erase(it++);
+ else
+ ++it;
+ }
+}
+
+// write the SAM line in the file
+ostream &SamLine::writeLine(ostream &os){
+ os << getQname() << "\t"
+ << getFlag() << "\t"
+ << getRname() << "\t"
+ << getPos() << "\t"
+ << getMapQ() << "\t"
+ << getCigar() << "\t"
+ << getRnext() << "\t"
+ << getPnext() << "\t"
+ << getTlen() << "\t"
+ << getSeq() << "\t"
+ << getQual();
+ for (map<string,string>::iterator it=optionalFields.begin(); it!=optionalFields.end(); ++it)
+ os << "\t" << it->first << ":" << it->second;
+ os << endl;
+ return os;
+}
+
diff --git a/src/libReadsInfo/samLine.h b/src/libReadsInfo/samLine.h
new file mode 100644
index 0000000..ec4618f
--- /dev/null
+++ b/src/libReadsInfo/samLine.h
@@ -0,0 +1,270 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at univ-montp2.fr *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef SAMLINE_H
+#define SAMLINE_H
+#include <string>
+#include <map>
+#include <ostream>
+#include <vector>
+
+#include "Cigar.h"
+
+using namespace std;
+
+
+class SamLine {
+private:
+ string rname;
+ string qname;
+ string rnext;
+ string seq;
+ string qual;
+ uint flag;
+ uint pos;
+ uint mapQ;
+ uint pnext;
+ int tlen;
+ Cigar cigar;
+ map<string, string> optionalFields;
+
+ bool isFlagBitSet(uint bit) const;
+ void setFlagBit(uint bit);
+ void unsetFlagBit(uint bit);
+
+public:
+ SamLine();
+
+ // Query template NAME
+ void setQname(const string& qname);
+ const string& getQname() const;
+
+ // bitwize FLAG
+ void setFlag(uint flag);
+ uint getFlag() const;
+
+ // Flag operations
+ // Bit Description
+ // 0x1 template having multiple segments in sequencing
+ // 0x2 each segment properly aligned according to the aligner
+ // 0x4 segment unmapped
+ // 0x8 next segment in the template unmapped
+ // 0x10 SEQ being reverse complemented
+ // 0x20 SEQ of the next segment in the template being reversed
+ // 0x40 the
rst segment in the template
+ // 0x80 the last segment in the template
+ // 0x100 secondary alignment
+ // 0x200 not passing quality controls
+ // 0x400 PCR or optical duplicate
+ // 0x800 supplementary alignment
+ // bit 1
+ bool isTemplateHavingMultipleSegments() const;
+ void setTemplateHavingMultipleSegments();
+ void unsetTemplateHavingMultipleSegments();
+
+ // bit 2
+ bool isEachSegmentsMapped() const;
+ void setEachSegmentsMapped();
+ void unsetEachSegmentsMapped();
+
+ // bit 4
+ bool isSegmentUnmapped() const;
+ void setSegmentUnmapped();
+ void unsetSegmentUnmapped();
+
+ // bit 8
+ bool isNextSegmentUnmapped() const;
+ void setNextSegmentUnmapped();
+ void unsetNextSegmentUnmapped();
+
+ // bit 16
+ bool isSeqReverseComplemented() const;
+ void setSeqReverseComplemented();
+ void unsetSeqReverseComplemented();
+
+ // bit 32
+ bool isNextSeqReverseComplemented() const;
+ void setNextSeqReverseComplemented();
+ void unsetNextSeqReverseComplemented();
+
+ // bit 64
+ bool isFirstSegmentInTheTemplate() const;
+ void setFirstSegmentInTheTemplate();
+ void unsetFirstSegmentInTheTemplate();
+
+ // bit 128
+ bool isLastSegmentInTheTemplate() const;
+ void setLastSegmentInTheTemplate();
+ void unsetLastSegmentInTheTemplate();
+
+ // bit 256
+ bool isSecondaryAlignement() const;
+ void setSecondaryAlignement();
+ void unsetSecondaryAlignement();
+
+ // bit 512
+ bool isFailingQualityControl() const;
+ void setFailingQualityControl();
+ void unsetFailingQualityControl();
+
+ // bit 1024
+ bool isPCRDuplicated() const;
+ void setPCRDuplicated();
+ void unsetPCRDuplicated();
+
+ // bit 2048
+ bool isChimericAlignement() const;
+ void setChimericAlignement();
+ void unsetChimericAlignement();
+
+ // Reference sequence NAME
+ void setRname(const string& rname);
+ const string& getRname() const;
+
+ // 1-based leftmost mapping POSition
+ void setPos(uint pos);
+ uint getPos() const;
+
+ // MAPping Quality
+ void setMapQ(uint mapQ);
+ uint getMapQ() const;
+
+ // CIGAR string
+ void setCigar(const Cigar& cigar);
+ const Cigar& getCigar() const;
+
+ // Ref. name of the mate/next segment
+ void setRnext(const string& rnext);
+ const string& getRnext() const;
+
+ // Position of the mate/next segment
+ void setPnext(uint pnext);
+ uint getPnext() const;
+
+ // observed Template LENgth
+ void setTlen(int tlen);
+ int getTlen() const;
+
+ // segment SEQuence
+ void setSeq(const string& seq);
+ const string& getSeq() const;
+ void reverseComplementeSeq();
+
+ // ASCII of Phred-scaled base QUALity+33
+ void setQual(const string& qual);
+ const string& getQual() const;
+ void reverseQual();
+
+ // Optional fields
+ bool addOptionalField(const char *tag, int val);
+ bool addOptionalField(const char *tag, const string& val);
+ bool addOptionalField(const char *tag, const char* val);
+ const string& getOptionalField(const char *tag);
+ bool isOptionalFieldDefined(const char *tag);
+
+ // Remove all fields that are user reserved.
+ // That means the tag used matches : X?, Y? or Z?
+ void removeAllUserOptionalFields();
+
+ // write the SAM line in the file
+ ostream &writeLine(ostream &os);
+};
+
+#endif
diff --git a/src/libReadsInfo/tagInfo.cpp b/src/libReadsInfo/tagInfo.cpp
new file mode 100644
index 0000000..486191f
--- /dev/null
+++ b/src/libReadsInfo/tagInfo.cpp
@@ -0,0 +1,1735 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at univ-montp2.fr *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <stdlib.h>
+#include "tagInfo.h"
+#include "../const.h"
+#include "../libSSA/utils.h"
+#include "../utils.h"
+#include "Cigar.h"
+#include <limits.h>
+#include <string>
+#include <sstream>
+
+TagInfo::TagInfo(LocateOnGenome *genome, Support *s)
+ :code(0),genome(genome), nb_each_type(NULL),info_each_type(NULL), nb_causes(0),
+ support(s), current_break(0), read_name(NULL), read_quality(NULL){
+
+ if (support->isNone())
+ addNone();
+ if (support->isDuplicate())
+ addDuplication();
+ if (support->isMultiple())
+ addMultiple();
+ if (support->isSingle()){
+ addSingle();
+ if (support->hasRepeat())
+ addRepetition(support->getStartPosRepeat(),
+ support->getEndPosRepeat());
+ else if (support->isContinuous()) {
+ if (! support->isAlmostNormal()){
+ addNormal();
+ }else{
+ addAlmostNormal();
+ }
+ }
+ }
+
+ chrpos[START_BREAK] = (ChrPosition **)calloc(support->getNbBreaks(),
+ sizeof(ChrPosition*));
+ chrpos[END_BREAK] = (ChrPosition **)calloc(support->getNbBreaks(),
+ sizeof(ChrPosition*));
+}
+
+
+TagInfo::~TagInfo() {
+ if (nb_each_type != NULL) {
+ for (uint i=0; i < INFO_NB_TYPES; i++) {
+ for (uint j=0; j < nb_each_type[i]; j++) {
+ delete info_each_type[i][j];
+ }
+ if (nb_each_type[i])
+ free(info_each_type[i]);
+ }
+ free(info_each_type);
+ free(types_in_order);
+ free(nb_causes_per_break);
+ }
+ for (uint j = 0; j < NB_POS_BREAK; j++) {
+ for (uint i=0; i < support->getNbBreaks(); i++)
+ if (chrpos[j][i])
+ delete (chrpos[j][i]);
+ free(chrpos[j]);
+ }
+
+ if (read_quality)
+ delete [] read_quality;
+ if (read_name)
+ delete [] read_name;
+
+ if (nb_each_type != NULL)
+ free(nb_each_type);
+}
+
+void TagInfo::addGenericElement(byte type, GenericInfo *gi) {
+ if (nb_each_type == NULL) {
+ nb_each_type = (byte *)calloc(INFO_NB_TYPES,sizeof(byte));
+ info_each_type = (GenericInfo ***)malloc(sizeof(GenericInfo**)*INFO_NB_TYPES);
+ types_in_order = (byte *)malloc(sizeof(byte) * NB_INFO_STORED);
+ nb_causes_per_break = (byte *)calloc(NB_INFO_BREAKS+1, sizeof(byte));
+ nb_causes = 0;
+ }
+
+ if (nb_each_type[type] == 0)
+ info_each_type[type] = (GenericInfo **)malloc(NB_ELEMENTS_PER_TYPE * sizeof(gi));
+ else if (nb_each_type[type] % NB_ELEMENTS_PER_TYPE == 0)
+ info_each_type[type] = (GenericInfo **)realloc(info_each_type[type]
+ , (nb_each_type[type]
+ +NB_ELEMENTS_PER_TYPE)*sizeof(gi));
+
+ if (type != INFO_REPETITION && type != INFO_DUPLICATION) {
+ if (current_break > 0 && current_break % NB_INFO_BREAKS == 0
+ && nb_causes_per_break[current_break] == 0) {
+ nb_causes_per_break = (byte *)realloc(nb_causes_per_break,
+ (current_break + NB_INFO_BREAKS+1) * sizeof(byte));
+ for (uint i=current_break ; i <= current_break + NB_INFO_BREAKS; i++)
+ nb_causes_per_break[i] = 0;
+ }
+ nb_causes_per_break[current_break]++;
+
+ if (nb_causes > 0 && nb_causes % NB_INFO_STORED == 0) {
+ types_in_order = (byte *) realloc(types_in_order,
+ (nb_causes + NB_INFO_STORED) * sizeof(byte));
+ }
+
+ gi->setBreakId(current_break);
+ gi->setCauseId(nb_causes);
+
+ types_in_order[nb_causes++] = type;
+ }
+
+#ifdef DBG
+ cerr << "Adding element " <<(int)type<<" for tag " << num << endl;
+#endif
+
+ gi->setReadLength(support->getTagLength());
+ info_each_type[type][nb_each_type[type]] = gi;
+ nb_each_type[type]++;
+}
+
+byte TagInfo::getNbGenericElement(uint type) {
+ if (nb_each_type == NULL)
+ return 0;
+ return nb_each_type[type];
+}
+
+GenericInfo **TagInfo::getGenericInfos(uint type) {
+ if (nb_each_type == NULL || nb_each_type[type] == -2)
+ return NULL;
+ return info_each_type[type];
+}
+
+void TagInfo::changeGenericElement(byte type, byte newType, int oldMask,
+ int newMask,uint i, GenericInfo *newGi) {
+ GenericInfo *oldGi = info_each_type[type][i];
+ uint causeId = oldGi->getCauseId();
+
+ // We change the type of the element in types in order
+ types_in_order[causeId] = newType;
+
+ // Set read length breakId and causeId from the old element
+ newGi->setReadLength(oldGi->getReadLength());
+ newGi->setBreakId(oldGi->getBreakId());
+ newGi->setCauseId(oldGi->getCauseId());
+
+ // Delete the old Generic Element
+ delete oldGi;
+ memmove(&(info_each_type[type][i]), &(info_each_type[type][i+1]), (nb_each_type[type] - i - 1)*sizeof(oldGi));
+ if (nb_each_type[type] == 1)
+ free(info_each_type[type]);
+ nb_each_type[type]--;
+
+ // update code: we have a new type
+ code |= newMask;
+ // And we may remove the previous one (if there is no more)
+ if (nb_each_type[type] == 0)
+ code ^= oldMask;
+
+ // Insert the new Generic Element in the right place of InfoEachType
+ // Update info_each_type size if needed
+ if (nb_each_type[newType] == 0) {
+ info_each_type[newType] = (GenericInfo **)malloc(NB_ELEMENTS_PER_TYPE * sizeof(newGi));
+ info_each_type[newType][nb_each_type[newType]] = newGi;
+ } else {
+ if (nb_each_type[newType] % NB_ELEMENTS_PER_TYPE == 0)
+ info_each_type[newType] = (GenericInfo **)realloc(info_each_type[newType]
+ , (nb_each_type[newType]
+ +NB_ELEMENTS_PER_TYPE)*sizeof(newGi));
+
+ // Count elements of newType in array types in order to get the place to insert the new element
+ uint nbNewType = 0;
+ for(uint j=0; j<causeId; j++) {
+ if(types_in_order[j] == newType) {
+ nbNewType++;
+ }
+ }
+ // Move the element of new type in order to insert the new generic info in the right place
+ memmove(&(info_each_type[newType][nbNewType+1]), &(info_each_type[newType][nbNewType]), (nb_each_type[newType] - nbNewType)*sizeof(newGi));
+ // Delete the element duplicated by the memmove
+ //if (nb_each_type[newType] > 1)
+ // delete info_each_type[newType][nbNewType];
+ info_each_type[newType][nbNewType] = newGi;
+ }
+ nb_each_type[newType]++;
+}
+
+void TagInfo::changeGenericElement(byte type, byte newType, int oldMask,
+ int newMask, uint break_id, uint cause_num,
+ GenericInfo *newGi) {
+ for (uint i = 0; i < nb_each_type[type]; i++) {
+ if (info_each_type[type][i]->getBreakId() == break_id) {
+ // We found a cause in the same break
+ if (cause_num == 0) {
+ // Additionnally it is the same cause in this break.
+ // We found what we were looking for!
+ changeGenericElement(type, newType, oldMask, newMask, i, newGi);
+ return;
+ } else {
+ cause_num--;
+ }
+ }
+ }
+}
+
+int TagInfo::getCode() {
+ return code;
+}
+
+float TagInfo::getAverageLowInside(uint i) {
+ return support->getBreak(i)->getAverageLowInside();
+}
+
+float TagInfo::getAverageHighInside(uint i) {
+ return support->getBreak(i)->getAverageHighInside();
+}
+
+SupportBreak *TagInfo::getBreak(uint i, int strand) {
+ if (strand == 1)
+ return support->getBreak(i);
+ return support->getBreak(getNbBreaks() - i - 1);
+}
+
+byte TagInfo::getCauseType(uint i, int strand) {
+ if (strand == 1)
+ return types_in_order[i];
+ else
+ return types_in_order[getNbCauses() - i - 1];
+}
+
+ChrPosition *TagInfo::getChrPosEndBreak(uint i) {
+ bool new_value = ! chrpos[END_BREAK][i]
+ || getBreak(i)->getPositionLocation(END_BREAK) != chrpos[END_BREAK][i]->getRelativePosition();
+ if (new_value) {
+ if (chrpos[END_BREAK][i])
+ delete chrpos[END_BREAK][i];
+ chrpos[END_BREAK][i] = support->getBreak(i)->getChrPosition(END_BREAK);
+ }
+ return chrpos[END_BREAK][i];
+}
+
+ChrPosition *TagInfo::getChrPosStartBreak(uint i) {
+ bool new_value = ! chrpos[START_BREAK][i]
+ || getBreak(i)->getPositionLocation(START_BREAK) != chrpos[START_BREAK][i]->getRelativePosition();
+ if (new_value) {
+ if (chrpos[START_BREAK][i])
+ delete chrpos[START_BREAK][i];
+ chrpos[START_BREAK][i] = support->getBreak(i)->getChrPosition(START_BREAK);
+ }
+ return chrpos[START_BREAK][i];
+}
+
+uint TagInfo::getCurrentBreak() {
+ return current_break;
+}
+
+int TagInfo::getEndPosRepeat() {
+ return support->getEndPosRepeat();
+}
+
+gap_size_t TagInfo::getGenomeGapLength(uint i) {
+ return support->getBreak(i)->getGenomeGapLength();
+}
+
+// bool TagInfo::getIsExtended(uint i) {
+// return is_extended[i];
+// }
+
+uint *TagInfo::getLocalisations() {
+ return support->getNbLocs();
+}
+
+ChrPosition *TagInfo::getLocation() {
+ return support->getLocation();
+}
+
+uint TagInfo::getLocationEndBreak(uint i) {
+ return support->getBreak(i)->getPositionLocation(END_BREAK);
+}
+
+uint TagInfo::getLocationStartBreak(uint i) {
+ return support->getBreak(i)->getPositionLocation(START_BREAK);
+}
+
+uint TagInfo::getNbBreaks() {
+ return support->getNbBreaks();;
+}
+
+uint TagInfo::getNbDuplicate() {
+ return support->getNbDuplicate();
+}
+
+uint TagInfo::getNbMultiple() {
+ return support->getNbMultiple();
+}
+
+uint TagInfo::getNbSingle() {
+ return support->getNbSingle();
+}
+
+uint TagInfo::getPositionEndBreak(uint i, int strand) {
+ if (strand == 1)
+ return support->getBreak(i)->getPositionEndBreak();
+ return support->getBreak(getNbBreaks() - i - 1)->getPositionEndBreak(strand);
+}
+
+uint TagInfo::getPositionOfLocation(){
+ return support->getPositionOfLocation();
+}
+
+uint TagInfo::getPositionStartBreak(uint i, int strand) {
+ if (strand == 1)
+ return support->getBreak(i)->getPositionStartBreak();
+ return support->getBreak(getNbBreaks() - i - 1)->getPositionStartBreak(strand);
+}
+
+char *TagInfo::getReadName() {
+ return read_name;
+}
+
+char *TagInfo::getReadQuality() {
+ return read_quality;
+}
+
+float TagInfo::getScoreComputedInterExon(uint i) {
+ return support->getBreak(i)->getScoreComputedInterExon();
+}
+
+float TagInfo::getScoreComputedIntraExon(uint i) {
+ return support->getBreak(i)->getScoreComputedIntraExon();
+}
+
+float TagInfo::getScoreInsideAverages(uint i) {
+ return support->getBreak(i)->getScoreInsideAverages();
+}
+
+float TagInfo::getScoreInsideBreak(uint i) {
+ return support->getBreak(i)->getScoreInsideBreak();
+}
+
+float TagInfo::getScoreOutsideBreak(uint i) {
+ return support->getBreak(i)->getScoreOutsideBreak();
+}
+
+int TagInfo::getStartPosRepeat() {
+ return support->getStartPosRepeat();;
+}
+
+uint *TagInfo::getSupport() {
+ return support->getSupport();
+}
+
+Support *TagInfo::getSupportObject() {
+ return support;
+}
+
+uint TagInfo::getSupportLength() {
+ return support->getLength();
+}
+
+char *TagInfo::getTag() {
+ return support->getTag();
+}
+
+ulong TagInfo::getTagPosition() {
+ return getLocation()->getRelativePosition();
+}
+
+char *TagInfo::getTagChromosome() {
+ return getLocation()->getChrPosition();
+}
+
+uint TagInfo::getTagBreakLength(uint i) {
+ return support->getBreak(i)->getTagBreakLength();
+}
+
+bool TagInfo::getTagStrand() {
+ return getLocation()->getStrand();
+}
+
+uint TagInfo::getThreshold() {
+ return support->getThreshold();
+}
+
+/* bool functions */
+bool TagInfo::isAlmostNormal() {
+ return (code & MASK_ALMOST_NORMAL);
+}
+
+bool TagInfo::isDuplicated(uint i) {
+ return support->getBreak(i)->isDuplicated();
+}
+
+bool TagInfo::isExplainable() {
+ return (code & (MASK_ALMOST_NORMAL | MASK_NORMAL | MASK_DUPLICATION | MASK_REPETITION
+ | MASK_SNP | MASK_SEQ_ERR | MASK_SPLICE
+ | MASK_INTRA_TRANSPLICING | MASK_INTER_TRANSPLICING
+ | MASK_BIOLOGICAL_TAG_INDEL | MASK_BIOLOGICAL_UNDETERMINED));
+}
+
+bool TagInfo::isNormal() {
+ return (code & MASK_NORMAL);
+}
+
+bool TagInfo::isMultiple() {
+ return (code & MASK_MULTIPLE);
+}
+
+bool TagInfo::isNone() {
+ return (code & MASK_NONE);
+}
+
+bool TagInfo::isRepeated(uint i) {
+ return support->getBreak(i)->isRepeated();
+}
+
+bool TagInfo::isSingle() {
+ return (code & MASK_SINGLE);
+}
+
+bool TagInfo::isSupportFallingLeft(uint i, int strand) {
+ return support->getBreak(i)->isSupportFallingLeft(strand);
+}
+
+bool TagInfo::isSupportFallingRight(uint i, int strand) {
+ return support->getBreak(i)->isSupportFallingRight(strand);
+}
+
+bool TagInfo::hasRepetition() {
+ return (code & MASK_REPETITION);
+}
+
+bool TagInfo::isDuplication() {
+ return (code & MASK_DUPLICATION);
+}
+
+bool TagInfo::hasSNP() {
+ return (code & MASK_SNP);
+}
+
+bool TagInfo::hasBioTagIndel() {
+ return (code & MASK_BIOLOGICAL_TAG_INDEL);
+}
+
+bool TagInfo::hasBioUndetermined() {
+ return (code & MASK_BIOLOGICAL_UNDETERMINED);
+}
+
+
+bool TagInfo::hasSeqErr() {
+ return (code & MASK_SEQ_ERR);
+}
+
+
+bool TagInfo::hasSplice() {
+ return (code & MASK_SPLICE);
+}
+
+bool TagInfo::hasSpliceIntraChr() {
+ return (code & MASK_INTRA_TRANSPLICING);
+}
+
+bool TagInfo::hasSpliceInterChr() {
+ return (code & MASK_INTER_TRANSPLICING);
+}
+
+bool TagInfo::hasSpliceNoCover() {
+ return (code & MASK_SPLICE_NO_COVER);
+}
+
+bool TagInfo::hasNothing() {
+ return code == 0;
+}
+
+bool TagInfo::hasUndeterminedError() {
+ return (code & MASK_UNDETERMINED_ERROR);
+}
+
+/* getNb* commands */
+
+byte TagInfo::getNbBioUndetermined() {
+ return getNbGenericElement(INFO_BIOLOGICAL_UNDETERMINED);
+}
+
+byte TagInfo::getNbRepetition() {
+ return getNbGenericElement(INFO_REPETITION);
+}
+
+byte TagInfo::getNbSNP() {
+ return getNbGenericElement(INFO_SNP);
+}
+
+byte TagInfo::getNbBioTagIndel() {
+ return getNbGenericElement(INFO_BIOLOGICAL_TAG_INDEL);
+}
+
+uint TagInfo::getNbCauses() {
+ return nb_causes;
+}
+
+byte TagInfo::getNbCausesInBreak(uint i, int strand) {
+ if (strand == 1)
+ return nb_causes_per_break[i];
+ else
+ return nb_causes_per_break[getNbBreaks() - i -1];
+}
+
+byte TagInfo::getNbSeqErr() {
+ return getNbGenericElement(INFO_SEQ_ERR);
+}
+
+byte TagInfo::getNbSplice() {
+ return getNbGenericElement(INFO_SPLICE);
+}
+
+byte TagInfo::getNbSpliceIntra() {
+ return getNbGenericElement(INFO_INTRASPLICE);
+}
+
+byte TagInfo::getNbSpliceInter() {
+ return getNbGenericElement(INFO_INTERSPLICE);
+}
+
+byte TagInfo::getNbSpliceNoCover() {
+ return getNbGenericElement(INFO_SPLICE_NO_COVER);
+}
+
+byte TagInfo::getNbUndeterminedError() {
+ return getNbGenericElement(INFO_UNDETERMINED_ERROR);
+}
+
+/* getInfos* commands */
+
+DuplicationInfo **TagInfo::getInfosDuplication() {
+ return (DuplicationInfo **) getGenericInfos(INFO_DUPLICATION);
+}
+
+RepetitionInfo **TagInfo::getInfosRepetition() {
+ return (RepetitionInfo **)getGenericInfos(INFO_REPETITION);
+}
+
+SNPInfo **TagInfo::getInfosSNP() {
+ return (SNPInfo **)getGenericInfos(INFO_SNP);
+}
+
+BioIndelInfo **TagInfo::getInfosBioTagIndel() {
+ return (BioIndelInfo **)getGenericInfos(INFO_BIOLOGICAL_TAG_INDEL);
+}
+
+BioUndeterminedInfo **TagInfo::getInfosBioUndetermined() {
+ return (BioUndeterminedInfo **)getGenericInfos(INFO_BIOLOGICAL_UNDETERMINED);
+}
+
+SeqErrInfo **TagInfo::getInfosSeqErr() {
+ return (SeqErrInfo **)getGenericInfos(INFO_SEQ_ERR);
+}
+
+SpliceInfo **TagInfo::getInfosSplice() {
+ return (SpliceInfo **)getGenericInfos(INFO_SPLICE);
+}
+
+SpliceIntraInfo **TagInfo::getInfosSpliceIntra() {
+ return (SpliceIntraInfo **)getGenericInfos(INFO_INTRASPLICE);
+}
+
+SpliceInterInfo **TagInfo::getInfosSpliceInter() {
+ return (SpliceInterInfo **)getGenericInfos(INFO_INTERSPLICE);
+}
+
+SpliceNoCoverInfo **TagInfo::getInfosSpliceNoCover() {
+ return (SpliceNoCoverInfo **)getGenericInfos(INFO_SPLICE_NO_COVER);
+}
+
+UndeterminedErrorInfo **TagInfo::getInfosUndeterminedError() {
+ return (UndeterminedErrorInfo **)getGenericInfos(INFO_UNDETERMINED_ERROR);
+}
+
+/* add commands */
+
+void TagInfo::addDuplication() {
+ code |= MASK_DUPLICATION;
+ // addGenericElement(INFO_DUPLICATION, new DuplicationInfo());
+#ifdef DBG
+ cerr << "Adding Duplication for tag " << num << endl;
+#endif
+}
+
+void TagInfo::addAlmostNormal() {
+ code |= MASK_ALMOST_NORMAL;
+#ifdef DBG
+ cerr << "Adding almostNormal for tag " << num << endl;
+#endif
+}
+
+void TagInfo::addMultiple() {
+ code |= MASK_MULTIPLE;
+#ifdef DBG
+ cerr << "Adding Multiple for tag " << num << endl;
+#endif
+}
+
+
+void TagInfo::addNormal() {
+ code |= MASK_NORMAL;
+#ifdef DBG
+ cerr << "Adding Normal for tag " << num << endl;
+#endif
+}
+
+void TagInfo::addNone() {
+ code |= MASK_NONE;
+#ifdef DBG
+ cerr << "Adding None for tag " << num << endl;
+#endif
+}
+
+void TagInfo::addRepetition(int position_in, int position_out) {
+ code |= MASK_REPETITION;
+ addGenericElement(INFO_REPETITION, new RepetitionInfo( position_in, position_out));
+}
+
+void TagInfo::addSingle() {
+ code |= MASK_SINGLE;
+}
+
+void TagInfo::addSNP(char tag_nuc, error_context snpID ) {
+ ChrPosition chrPos;
+ int shift = 0;
+ char genome_nuc = 0;
+
+ pair<ChrPosition, uchar *> result = retrieveChrPosAndNuc(snpID, 1, shift);
+
+ if (result.second) {
+ genome_nuc = result.second[0];
+ free(result.second);
+ }
+ chrPos = result.first;
+
+ // if (genome_nuc == tag_nuc) {
+ // cerr << "Warning: Discarding SNP at position "
+ // << getPositionEndBreak(current_break) - shift << " in read "
+ // << support->getTagNum() << endl;
+ // const char mymsg[] = "Should be a SNP. But doesn't make sense!";
+ // uint len = strlen(mymsg);
+ // char *msg = new char [len+1];
+ // strcpy(msg, mymsg);
+ // msg[len] = 0;
+ // addGenericElement(INFO_UNDETERMINED_ERROR, new UndeterminedErrorInfo(msg));
+ // return ;
+ // }
+
+ code |= MASK_SNP;
+ addGenericElement(INFO_SNP, new SNPInfo(chrPos,
+ getPositionEndBreak(current_break) - shift,
+ getScoreComputedIntraExon(current_break),
+ isDuplicated(current_break),
+ tag_nuc, genome_nuc));
+}
+
+void TagInfo::addSNP(uint pos, char base_read, char base_genome,
+ ChrPosition &chrPos, float score) {
+ code |= MASK_SNP;
+ addGenericElement(INFO_SNP,
+ new SNPInfo(chrPos, pos, score, isDuplicated(current_break),
+ base_read, base_genome));
+}
+
+void TagInfo::addBioTagIndel(uint nb_ins, uint nb_del) {
+ code |= MASK_BIOLOGICAL_TAG_INDEL;
+
+ ChrPosition chrPos = *getChrPosStartBreak(current_break);
+
+ if (chrPos.getStrand() == -1) {
+ chrPos += - nb_del;
+ } else {
+ chrPos = *getChrPosEndBreak(current_break) - nb_del;
+ }
+ addGenericElement(INFO_BIOLOGICAL_TAG_INDEL,
+ new BioIndelInfo(chrPos,
+ getPositionEndBreak(current_break),
+ nb_ins, nb_del, getScoreComputedIntraExon(current_break),isDuplicated(current_break)));
+}
+
+void TagInfo::addBioUndetermined(ChrPosition *chrPos, uint position,
+ const char *message, ...) {
+ code |= MASK_BIOLOGICAL_UNDETERMINED;
+ char *error = new char[MAX_SIZE_MESSAGE_UNDETERMINED_ERROR];
+ va_list args;
+ va_start(args, message);
+ vsprintf(error, message, args);
+ addGenericElement(INFO_BIOLOGICAL_UNDETERMINED, new BioUndeterminedInfo(chrPos, position, error));
+ va_end(args);
+}
+
+void TagInfo::addSeqErr(error_context errorID, uint position, uint nb_ins,
+ uint nb_del, float score,
+ uint genome_seq_length,
+ char *tag_seq, uint tag_seq_length) {
+ if (tag_seq == NULL)
+ tag_seq_length =~0;
+ ChrPosition chrPos;
+ uchar *genome_seq = NULL;
+ int shift=0;
+
+ if (errorID == UNKNOWN_START_MISSING)
+ chrPos = *getChrPosEndBreak(current_break);
+ else if (errorID == UNKNOWN_END_MISSING)
+ chrPos = *getChrPosStartBreak(current_break);
+ else {
+ pair<ChrPosition, uchar *> result = retrieveChrPosAndNuc(errorID,
+ genome_seq_length,
+ shift);
+ genome_seq = result.second;
+
+ // if (genome_seq) {
+ // if (tag_seq && ! strcmp((char *)result.second, tag_seq)) {
+ // cerr << "Warning: Discarding error at position " << position << " in read "
+ // << support->getTagNum() << endl;
+ // delete [] tag_seq;
+ // free(result.second);
+ // const char mymsg[] = "Should be an error. But doesn't make sense!";
+ // uint len = strlen(mymsg);
+ // char *msg = new char [len+1];
+ // strcpy(msg, mymsg);
+ // msg[len] = 0;
+ // addGenericElement(INFO_UNDETERMINED_ERROR, new UndeterminedErrorInfo(msg));
+
+ // return ;
+ // }
+ // }
+ chrPos = ChrPosition(result.first);
+ }
+ if (genome_seq_length == 0)
+ genome_seq_length = ~0;
+
+ code |= MASK_SEQ_ERR;
+ addGenericElement(INFO_SEQ_ERR, new SeqErrInfo(chrPos,
+ position, nb_ins, nb_del,
+ score, isDuplicated(current_break),
+ (char *)genome_seq, tag_seq,
+ genome_seq_length, tag_seq_length));
+}
+
+
+void TagInfo::addSplice(uint gap_length) {
+ code |= MASK_SPLICE;
+
+ ChrPosition pos = *getChrPosStartBreak(current_break);
+ if (pos.getStrand() == 1) {
+ pos += getThreshold() - 1;
+ } else {
+ pos = *getChrPosEndBreak(current_break) + getThreshold() - 1;
+ }
+
+ addGenericElement(INFO_SPLICE,
+ new SpliceInfo(pos, getPositionEndBreak(current_break), gap_length,isDuplicated(current_break)));
+}
+
+void TagInfo::addSpliceNoCover(uint gap_length) {
+ code |= MASK_SPLICE_NO_COVER;
+
+ ChrPosition pos = *getChrPosStartBreak(current_break);
+ if (pos.getStrand() == 1) {
+ pos += getThreshold() - 1;
+ } else {
+ pos = *getChrPosEndBreak(current_break) + getThreshold() - 1;
+ }
+
+ addGenericElement(INFO_SPLICE_NO_COVER,
+ new SpliceNoCoverInfo(pos, getPositionEndBreak(current_break),
+ gap_length,isDuplicated(current_break)));
+}
+
+void TagInfo::addSpliceIntra(uint gap_length) {
+ code |= MASK_INTRA_TRANSPLICING;
+
+ ChrPosition pos = *getChrPosStartBreak(current_break);
+ if (pos.getStrand() == 1) {
+ pos += getThreshold() - 1;
+ } else {
+ pos = *getChrPosEndBreak(current_break) + getThreshold() - 1;
+ }
+
+ addGenericElement(INFO_INTRASPLICE,
+ new SpliceIntraInfo(pos, getPositionEndBreak(current_break),
+ gap_length,isDuplicated(current_break)));
+}
+
+void TagInfo::addSpliceInter() {
+ code |= MASK_INTER_TRANSPLICING;
+
+ ChrPosition chrPos1 = *getChrPosStartBreak(current_break), chrPos2;
+ if (chrPos1.getStrand() == 1) {
+ chrPos1 += getThreshold() - 1;
+ }
+ chrPos2 = *getChrPosEndBreak(current_break);
+
+ if (chrPos2.getStrand() == -1){
+ chrPos2 += getThreshold() - 1;
+ }
+
+ // only for the data simulated otherwise there are many FP
+ // the reason is because all chimera are built on the strand +
+ // so the reading is inversed if strand(chrPos1) == -1
+ // if (chrPos1.getStrand() == -1) {
+ // ChrPosition tmp = chrPos1;
+ // chrPos1 = chrPos2;
+ // chrPos2 = tmp;
+ // }
+
+ addGenericElement(INFO_INTERSPLICE,
+ new SpliceInterInfo(chrPos1, getPositionEndBreak(current_break),
+ chrPos2, isDuplicated(current_break)));
+}
+
+
+void TagInfo::addUndeterminedError(const char *format, ...) {
+ code |= MASK_UNDETERMINED_ERROR;
+ char *error = new char[MAX_SIZE_MESSAGE_UNDETERMINED_ERROR];
+ va_list args;
+ va_start(args, format);
+ vsprintf(error, format, args);
+ addGenericElement(INFO_UNDETERMINED_ERROR, new UndeterminedErrorInfo(error));
+ va_end(args);
+}
+
+void TagInfo::removeSpliceInter(uint i,const char* info) {
+ if (i >= 0 && i < getNbSpliceInter()) {
+ SpliceInterInfo *spliceInter = getInfosSpliceInter()[i];
+ ChrPosition *chrPos = new ChrPosition(spliceInter->getChrPosition());
+ uint position = spliceInter->getPosition();
+
+ char *error = new char[MAX_SIZE_MESSAGE_UNDETERMINED_ERROR];
+ strcpy(error,info);
+
+ changeGenericElement(INFO_INTERSPLICE,INFO_BIOLOGICAL_UNDETERMINED,
+ MASK_INTER_TRANSPLICING, MASK_BIOLOGICAL_UNDETERMINED,
+ i,new BioUndeterminedInfo(chrPos, position, error));
+ }
+ // TODO if not raise an exception
+}
+
+SamLine *TagInfo::getSamLine(ChrPosition *loc, ulong pos_of_original_loc_in_read) {
+ SamLine *sam = new SamLine();
+
+ if(!loc) {
+ loc = getLocation();
+ pos_of_original_loc_in_read = getSupportObject()->getPositionOfLocation();
+ }
+
+ //uint flag = 0;
+ ChrPosition *loc_to_display = loc ; // Location to be displayed
+ bool unmapped = ! loc || isNone(); // || (isMultiple() && !support->getParameters()->treat_multiple);
+ int strand = 1;
+ int bases5_not_in_chromosome = 0; // Bases that are mapped 5' but not
+ // actually in the chromsome (must ignore
+ // the 5' bases)
+ ostringstream string_stream;
+ string qname;
+ string rname;
+ string sequence = getTag();
+
+ if (!getReadName()) {
+ qname = intToString(support->getTagNum());
+ } else {
+ qname = getReadName();
+ }
+ sam->setQname(qname);
+ sam->setSeq(sequence);
+
+ if(getReadQuality()) {
+ string quality = getReadQuality();
+ sam->setQual(quality);
+ }
+
+ if (unmapped) {
+ sam->setSegmentUnmapped();
+ } else {
+ int first_nice_break = -1; // First nice break on strand +1 (5' end)
+ int last_nice_break = -1; // Last nice break on strand -1 (5' end)
+ int cause_type;
+ int num_cause = 0;
+
+ // Look for the first nice break
+ for (int i = 0; i < (int)getNbBreaks(); i++) {
+ cause_type = getCauseType(num_cause);
+ num_cause += getNbCausesInBreak(i);
+
+ // Is it a nice break? In that case, update the variables
+ if ((getBreak(i)->isNiceBreak() || cause_type == INFO_INTERSPLICE)
+ && cause_type != INFO_UNDETERMINED_ERROR
+ && cause_type != INFO_BIOLOGICAL_UNDETERMINED) {
+ if (first_nice_break == -1 && getBreak(i)->getStrandLocation(START_BREAK) == 1)
+ first_nice_break = i;
+ if (getBreak(i)->getStrandLocation(END_BREAK) == -1)
+ last_nice_break = i;
+ }
+ }
+
+ // Define the location of the first nice break
+ if (first_nice_break > -1 || last_nice_break > -1) {
+ uint pos5_nice; // 5' position of the 5'-most nice break
+ uint end5; // last valid position starting from pos5_nice
+ // and going to the 5' end.
+ if (first_nice_break > -1)
+ strand = 1;
+ else if (last_nice_break > -1)
+ strand = -1;
+
+ // Define some variables so that we don't need to take care of strand
+ // afterwards
+ pos_location_break type_loc = (strand == 1) ? START_BREAK : END_BREAK;
+ int id_nice_break = (strand == 1) ? first_nice_break : last_nice_break;
+
+ // We take the location of the first nice
+ // break and we shift it to the left (5') as much as we can
+ loc_to_display = getBreak(id_nice_break)->getChrPosition(type_loc);
+ pos5_nice = getBreak(id_nice_break)->getPositionStartBreak(strand) - 1;
+ end5 = (((strand == 1 && id_nice_break > 0)
+ || (strand == -1 && id_nice_break < (int)getNbBreaks() - 1))
+ ? getBreak(id_nice_break - strand)->getPositionEndBreak(strand) + 1
+ : 0);
+ if (end5 > pos5_nice)
+ end5 = pos5_nice;
+
+ if (loc_to_display->getRelativePosition() < (pos5_nice - end5)) {
+ // Oops we are before the chromosome!
+ bases5_not_in_chromosome = (pos5_nice - end5) - loc_to_display->getRelativePosition();
+ // Go back a little!
+ end5 += bases5_not_in_chromosome;
+ }
+ *loc_to_display -= (pos5_nice - end5);
+ }
+
+ if (loc_to_display->getStrand() == -1) {
+ sam->setSeqReverseComplemented();
+ //flag = 16;
+ strand = -1;
+ }
+ }
+
+ if (!unmapped) {
+ // String for what is matched, what is inserted, what is deleted
+ // M : alignment match (sequence match or mismatch
+ // I : insertion
+ // D : deletion
+ // N : intron -> 0N special case for telling there is a chimera
+ // = : seq. match
+ // X : seq. mismatch
+ // S : soft clipping (unaligned)
+ byte current_cause_type[INFO_NB_TYPES];
+ uint current_cause = 0;
+ SeqErrInfo **infos = getInfosSeqErr();
+ int nb_suspicious_breaks = 0; /* number of breaks where the mapping
+ may not be very accurate
+ */
+ for (uint i=0; i < INFO_NB_TYPES; i++)
+ current_cause_type[i]= (strand == 1) ? 0 : getNbGenericElement(i)-1;
+
+ bool ended = false;
+ Cigar cigar;
+
+ bool started_for_real = false; /* put at true when we have something else
+ than no start break or undetermined
+ */
+ uint last_match_pos = 0; // Last time a match was seen.
+
+ // Do we have at least one nice break?
+ if (loc != loc_to_display) {
+ for (uint i=0; i < getNbBreaks(); i++) {
+ SupportBreak *sb = getBreak(i, strand);
+
+ for (uint j = 0; j < getNbCausesInBreak(i, strand); j++) {
+ byte cause = getCauseType(current_cause, strand);
+ bool is_undetermined =
+ cause == INFO_BIOLOGICAL_UNDETERMINED
+ || cause == INFO_UNDETERMINED_ERROR
+ || (cause == INFO_SEQ_ERR
+ && infos[current_cause_type[cause]]->getNbIns() == (uint) ~0
+ && infos[current_cause_type[cause]]->getNbDel() == (uint) ~0);
+
+ if (getPositionStartBreak(i, strand) == 0
+ || (is_undetermined && !started_for_real)) {
+ last_match_pos = getPositionEndBreak(i, strand)+1;
+ } else {
+ // First time we arrive here.
+ // Write down the S we may have
+ if (! started_for_real && last_match_pos > 0) {
+ cigar.append(last_match_pos, 'S');
+ }
+
+ started_for_real = true;
+
+ if (j > 0
+ && ((cause == INFO_SNP
+ && getCauseType(current_cause-1, strand) == INFO_SNP)
+ || (cause == INFO_SEQ_ERR
+ && getCauseType(current_cause-1, strand) == INFO_SEQ_ERR))) {
+ // Double SNP or double error
+ // We need to take into account the bases that are matched
+ // between the two mutations
+ cigar.append(getPositionEndBreak(i, strand)
+ - (getPositionStartBreak(i, strand)
+ + sb->getThreshold()),
+ 'M');
+ } else {
+ // Write down the numbers of match we have.
+
+ if (is_undetermined
+ // either a too large insertion in the read
+ // that is not compatible with the gap length
+ // -> doesn't make sense.
+ && ((sb->getNbGenomeIndels() < 0
+ && - sb->getNbGenomeIndels()
+ > (int) (getPositionEndBreak(i, strand)
+ - getPositionStartBreak(i, strand)))
+ // or too large genome gap that cannot be considered
+ // as a splice
+ || (sb->getNbGenomeIndels() > 0
+ && sb->getNbGenomeIndels() > (int)getSupportObject()->getParameters()->max_splice_length)
+ // or we are dealing with a kind of chimera
+ || sb->isChimera())){
+ // Since these cases are not coherent,
+ // we tell to ignore the read until the end.
+ cigar.append(getPositionStartBreak(i, strand)
+ + sb->getThreshold() -2
+ - last_match_pos + 1, 'M');
+ cigar.append(getSupportObject()->getTagLength()
+ - (getPositionStartBreak(i, strand)
+ + sb->getThreshold() -1),
+ 'S');
+ ended = true;
+ // Leave the two outer loops
+ i = getNbBreaks();
+ break;
+ }
+ // Large insertion in read are not like usual insertions
+ // they should be considered like chimera and therefore
+ // like large... deletions!
+ // same for insertions that lead to a negative gap length on the
+ // genome
+ bool large_insertion = sb->getNbGenomeIndels() <= 0
+ && (((- sb->getNbGenomeIndels()
+ >= (int)(getPositionEndBreak(i, strand)
+ - getPositionStartBreak(i, strand)+1))
+ || (sb->getGenomeGapLength() <= 0))
+ || (sb->isChimera() && sb->isBiologicalInterEvent()));
+
+ uint min_last_pos =
+ min(getPositionStartBreak(i, strand) + sb->getThreshold() -2,
+ sb->hasNoEndBreak(strand)
+ ? getSupportObject()->getTagLength() - 1
+ : getPositionEndBreak(i, strand)
+ - (sb->getNbGenomeIndels() < 0 && ! large_insertion
+ ? - sb->getNbGenomeIndels() : 1));
+
+ uint nb_match = min_last_pos
+ // Beware short gaps!
+ - last_match_pos + 1;
+ // In case of deletion, we may have one more match, in fact
+ if ((sb->getNbGenomeIndels() > 0 || large_insertion)
+ && min_last_pos < (getPositionStartBreak(i, strand)
+ + sb->getThreshold()
+ -2))
+ nb_match++;
+ cigar.append(nb_match, 'M');
+ }
+
+
+ // Take care of gaps that can be larger than expected
+ // Of course we don't consider large gaps that contain several causes
+ // nor end breaks
+ if (getNbCausesInBreak(i, strand) == 1
+ && ! sb->hasNoEndBreak(strand)) {
+ uint expected_max_gap_length = sb->getThreshold();
+ if (sb->getNbGenomeIndels() > 0)
+ expected_max_gap_length--;
+ else if (sb->getNbGenomeIndels() < 0)
+ expected_max_gap_length += -sb->getNbGenomeIndels() - 1;
+ if (expected_max_gap_length < sb->getTagBreakLength()) {
+ if (is_undetermined)
+ nb_suspicious_breaks++;
+ cigar.append(sb->getTagBreakLength() - expected_max_gap_length,
+ 'X');
+ }
+ }
+
+ if (! is_undetermined) {
+ // SNP, splice, indel, seq err (sub + indel), chimera
+ cigar.append(getGenericInfos(cause)[current_cause_type[cause]]->getCigarInfo());
+ } else {
+ // Bio undetermined, undetermined, seq err
+
+ if (sb->hasNoEndBreak(strand)) {
+ // end of read
+ ended = true;
+ cigar.append(getSupportObject()->getTagLength() - 1
+ - (getPositionStartBreak(i, strand)
+ + sb->getThreshold()-1) + 1, 'S');
+ } else {
+ if (sb->getNbGenomeIndels() > 0) {
+ // We have a kind of splice
+ cigar.append(sb->getNbGenomeIndels(), 'N');
+ } else if (sb->getNbGenomeIndels() < 0
+ && sb->getGenomeGapLength() > 0)
+ cigar.append(-sb->getNbGenomeIndels(), 'I');
+ else {
+ // Well, well, well, ... don't know what to say about
+ // that gap. Unfortunately there is no "unknown" operator
+ // in CIGAR. We use X instead...
+ cigar.append(1, 'X');
+ }
+ }
+ }
+ if (strand == -1)
+ getGenericInfos(cause)[current_cause_type[cause]]
+ ->setStrandedPosition(sb->getPositionEndBreak(strand));
+ }
+
+ current_cause_type[cause] += strand;
+ current_cause++;
+ }
+ if (! ended)
+ last_match_pos = getPositionEndBreak(i, strand) + 1;
+ }
+
+ // And treat all the remaining bases that may have mapped
+ // at the end of the read after the breaks (but be careful to ignored
+ // breaks)
+ if (! ended) {
+ cigar.append(getSupportObject()->getTagLength() - last_match_pos,
+ 'M');
+ }
+ } else {
+ // If we only had undetermined breaks, we have no reliable way
+ // of identifying the read's location.
+ // Therefore, we are falling back to the location found
+ // in Support (chosen in the longest run of single locations).
+ // We will set the cigar so that it corresponds to this fact.
+
+ // In that case loc == loc_to_display. Separate them, so that by
+ // modifying one, we don't modify the other
+ loc_to_display = new ChrPosition(*loc);
+
+ // Check how far we can extend that to the left and to the right
+ // (BTW choose the leftmost position)
+ uint pos_shift[2];
+ // Index of the left (5') end and the right (3') end
+ int left_idx = (strand == 1) ? 0 : 1;
+ int right_idx = (strand == 1) ? 1: 0;
+
+ pos_shift[0]= pos_of_original_loc_in_read;
+ pos_shift[1] = pos_of_original_loc_in_read;
+
+ // If we have no break the leftmost and rightmost positions
+ // are quite easy to find.
+ if (getNbBreaks() == 0) {
+ pos_shift[0] = 0;
+ pos_shift[1] = getSupportLength() - 1;
+ } else {
+ while (pos_shift[left_idx] > 0
+ && pos_shift[left_idx] < getSupportLength() - 1
+ && getLocalisations()[pos_shift[left_idx]] > 0)
+ pos_shift[left_idx] -= strand;
+ if (getLocalisations()[pos_shift[left_idx]] == 0)
+ pos_shift[left_idx] += strand;
+
+ while (pos_shift[right_idx] > 0
+ && pos_shift[right_idx] < getSupportLength() - 1
+ && getLocalisations()[pos_shift[right_idx]] > 0)
+ pos_shift[right_idx] += strand;
+ if (getLocalisations()[pos_shift[right_idx]] == 0)
+ pos_shift[right_idx] -= strand;
+ }
+
+ // Take the leftmost (5') position
+ if (loc_to_display->getRelativePosition() < strand * (pos_of_original_loc_in_read
+ - pos_shift[left_idx])) {
+ // Oops we are before the start of the chromosome !
+ pos_shift[left_idx] = pos_of_original_loc_in_read - loc_to_display->getRelativePosition() * strand;
+ }
+ *loc_to_display -= strand * (pos_of_original_loc_in_read
+ - pos_shift[left_idx]);
+ pos_of_original_loc_in_read = pos_shift[left_idx];
+
+ int bases[2] = {0,0};
+ bases[0] = pos_shift[0];
+ if (getSupportObject()->getTagLength() -1
+ > (pos_shift[1] + getThreshold() - 1))
+ bases[1] = getSupportObject()->getTagLength() -1
+ - (pos_shift[1] + getThreshold() - 1);
+
+ // set CIGAR
+ if (bases[left_idx])
+ cigar.append(bases[left_idx], 'S');
+ // The match is only considered between the leftmost and rightmost
+ // positions
+ cigar.append((support->getTagLength()
+ - bases[left_idx]
+ - bases[right_idx]), 'M');
+ if (bases[right_idx])
+ cigar.append(bases[right_idx], 'S');
+
+ }
+
+ // If we had bases to ignore in 5'
+ if (bases5_not_in_chromosome) {
+ if (cigar[0].type == 'S') {
+ assert(cigar.count() >= 2);
+ cigar[0].nb += bases5_not_in_chromosome;
+ cigar[1].nb -= bases5_not_in_chromosome;
+ } else {
+ // We have a match from the beginning. We need to add a S at the start!
+ cigar[0].nb -= bases5_not_in_chromosome;
+ // Add the S
+ cigar.prepend(bases5_not_in_chromosome, 'S');
+ }
+ }
+
+ // Join duplicates, remove empty operators, ...
+ cigar.filter();
+
+ //sam->setFlag(flag);
+ rname = loc_to_display->getChrPosition();
+ sam->setRname(rname);
+ sam->setPos(loc_to_display->getRelativePosition() + 1);
+ sam->setMapQ(254 - (getNbBreaks() > 0
+ ? 204.*nb_suspicious_breaks/getNbBreaks()
+ : 0));
+ sam->setCigar(cigar);
+ }
+
+ // reverse complemente sequence and quality
+ if (sam->isSeqReverseComplemented()) {
+ sam->reverseComplementeSeq();
+ sam->reverseQual();
+ }
+
+ // Unique, duplicate, multiple
+ sam->addOptionalField("XU",isSingle());
+ sam->addOptionalField("XD",isDuplication());
+ sam->addOptionalField("XM",isMultiple());
+ uint xn_value = 0;
+ if (isNormal()) {
+ xn_value = 1;
+ } else if (isAlmostNormal()) {
+ xn_value = 2;
+ }
+ sam->addOptionalField("XN",xn_value);
+
+ // k-mer chosen
+ // if (pos_of_loc_cause_in_read != (uint)~0) {
+ // os << "XL:Z:" << loc_cause << "\t";
+ // os << "XP:i:" << pos_of_loc_cause_in_read << "\t";
+ // }
+ if (loc) {
+ string_stream.str("");
+ string_stream << *loc;
+ sam->addOptionalField("XO",string_stream.str());
+ sam->addOptionalField("XQ",getSupportObject()->getPositionOfLocation());
+ }
+
+ // Number of causes
+ sam->addOptionalField("XC",getNbCauses());
+
+ // Reptition, XX field
+ if(hasRepetition()) {
+ string_stream.str("");
+ for (uint i = 0; i < nb_each_type[INFO_REPETITION]; i++) {
+ if(string_stream.str() != "")
+ string_stream << ";";
+ info_each_type[INFO_REPETITION][i]->samOutput(string_stream, strand);
+ }
+ sam->addOptionalField("XX",string_stream.str());
+ }
+
+ // Display causes in optional field XE if there is any
+ if(getNbCauses() > 0) {
+ byte *current_each_type = (byte *)calloc(INFO_NB_TYPES, sizeof(byte));
+ uint this_break_id = 0;
+ uint current_nb_causes_this_break = 0;
+ string_stream.str("");
+ for (uint i = 0; i < getNbCauses(); i++) {
+ current_nb_causes_this_break++;
+ // add separator in case of multiple events
+ if(string_stream.str() != "")
+ string_stream << ";";
+ string_stream << i << ":" << this_break_id << ":";
+ info_each_type[types_in_order[i]][current_each_type[types_in_order[i]]]->samOutput(string_stream, strand);
+ current_each_type[types_in_order[i]]++;
+ if (nb_causes_per_break[this_break_id] == current_nb_causes_this_break) {
+ this_break_id++;
+ current_nb_causes_this_break = 0;
+ }
+ }
+ sam->addOptionalField("XE",string_stream.str());
+ free(current_each_type);
+ }
+
+ if (getSupportObject()->getParameters()->detailed_sam) {
+ if(getNbBreaks() > 0) {
+ string_stream.str("");
+ for (uint i = 0; i < getNbBreaks(); i++) {
+ if(string_stream.rdbuf()->in_avail() > 0)
+ string_stream << ";";
+ string_stream << i
+ << ":is_duplicated=" << getBreak(i, strand)->isDuplicated()
+ << ";genome_indels=" << getBreak(i, strand)->getNbGenomeIndels()
+ << ";score_intra=" << getBreak(i, strand)->getScoreComputedIntraExon()
+ << ";score_inter=" << getBreak(i, strand)->getScoreComputedInterExon()
+ << ";deviation=" << getBreak(i, strand)->getScoreInsideAverages()
+ << ";falling_left=" << getBreak(i, strand)->isSupportFallingLeft(strand)
+ << ";falling_right=" << getBreak(i, strand)->isSupportFallingRight(strand)
+ << ";inside_first_quartile="
+ << getBreak(i, strand)->getInsideQuartile1()
+ << ";inside_last_quartile="
+ << getBreak(i, strand)->getInsideQuartile4()
+ << ";inside_score=" << getBreak(i, strand)->getInsideScore()
+ << ";outside_score=" << getBreak(i, strand)->getOutsideScore()
+ << ";average_low_inside=" << getBreak(i, strand)->getAverageLowInside()
+ << ";average_high_inside=" << getBreak(i, strand)->getAverageHighInside()
+ << ";has_no_start_break=" << getBreak(i, strand)->hasNoStartBreak(strand)
+ << ";has_no_end_break=" << getBreak(i, strand)->hasNoEndBreak(strand)
+ << ";is_deviated=" << getBreak(i, strand)->isDeviated()
+ << ";is_nice_break=" << getBreak(i, strand)->isNiceBreak()
+ << ";is_very_nice_break=" << getBreak(i, strand)->isVeryNiceBreak()
+ << ";pos_start_break=" << getPositionStartBreak(i, strand)
+ << ";pos_end_break=" << getPositionEndBreak(i, strand);
+ }
+ sam->addOptionalField("XB",string_stream.str());
+ }
+
+ // if read is reversed we also reverse the support and the localisation
+ string_stream.str("");
+ string_stream << "p_support=";
+
+ //if (sam->isSeqReverseComplemented()) {
+ // for (uint j=getSupportLength() -1; j > 0; j--) {
+ // string_stream << getSupport()[j] << "," ;
+ // }
+ // string_stream << getSupport()[0] << ";p_loc=";
+ // for (uint j=getSupportLength() -1; j > 0; j--) {
+ // string_stream << getLocalisations()[j] << "," ;
+ // }
+ // string_stream << getLocalisations()[0];
+ //} else {
+ // We used to reverse the support and the ploc, but not anymore.
+ // See bug #16102 for more informations
+ for (uint j=0; j < getSupportLength()-1; j++) {
+ string_stream << getSupport()[j] << "," ;
+ }
+ string_stream << getSupport()[getSupportLength()-1] << ";p_loc=";
+ for (uint j=0; j < getSupportLength()-1; j++) {
+ string_stream << getLocalisations()[j] << "," ;
+ }
+ string_stream << getLocalisations()[getSupportLength()-1];
+ //}
+ sam->addOptionalField("XR",string_stream.str());
+ }
+
+ if (loc_to_display != loc)
+ delete loc_to_display;
+
+ return sam;
+}
+
+vector<SamLine*> *TagInfo::getChimericAlignements(SamLine *base_line, uint cigar_index, uint splice_id, uint left_softclip, uint *right_softclip) {
+ if(cigar_index >= base_line->getCigar().count()) {
+ // If there is no more 0N (chimeras)
+ return new vector<SamLine*>();
+ } else {
+ // Clone base line
+ SamLine *chimeric_alignement = new SamLine(*base_line);
+ // Create a new cigar for this slice
+ Cigar new_cigar;
+
+ // Create the cigar for this slice util we found an other chimera
+ while(cigar_index < base_line->getCigar().count() && getInfosSpliceInter()[0]->getCigarInfo() != base_line->getCigar().get(cigar_index)) {
+ new_cigar.append(base_line->getCigar().get(cigar_index));
+ cigar_index++;
+ }
+
+ uint nb_positions_read_before_softclipping = new_cigar.getNbPositionsRead();
+
+ // RECURSION
+ vector<SamLine*> *sam_lines = getChimericAlignements(base_line,cigar_index+1,splice_id+1,left_softclip+nb_positions_read_before_softclipping,right_softclip);
+
+ // Add right softclip calculated from previous child
+ if(*right_softclip > 0) {
+ new_cigar.append(*right_softclip,'S');
+ }
+ // Update right softclip with length of this slice
+ *right_softclip+=nb_positions_read_before_softclipping;
+
+
+ // If the strand has change we need to reverse seq and qual to always
+ // be on strand forward only when this is not the primary alignement
+ if(splice_id > 0) {
+ chimeric_alignement->setChimericAlignement();
+ // If this is not the primary line
+ // Update chromosome and start position
+ // with chimera info
+ string new_rname = getInfosSpliceInter()[splice_id-1]->getChromosomeDest().getChrPosition();
+ base_line->setRname(new_rname);
+ chimeric_alignement->setPos(getInfosSpliceInter()[splice_id-1]->getChromosomeDest().getRelativePosition());
+ new_cigar.prepend(left_softclip,'S');
+ if(getInfosSpliceInter()[splice_id-1]->getChromosomeDest().getStrand() == -1 && !chimeric_alignement->isSeqReverseComplemented()) {
+ chimeric_alignement->setSeqReverseComplemented();
+ chimeric_alignement->reverseComplementeSeq();
+ chimeric_alignement->reverseQual();
+ new_cigar.reverse();
+ } else if(getInfosSpliceInter()[splice_id-1]->getChromosomeDest().getStrand() == 1 && chimeric_alignement->isSeqReverseComplemented()) {
+ chimeric_alignement->unsetSeqReverseComplemented();
+ chimeric_alignement->reverseComplementeSeq();
+ chimeric_alignement->reverseQual();
+ new_cigar.reverse();
+ }
+ // We remove CRAC extend fields
+ chimeric_alignement->removeAllUserOptionalFields();
+ }
+ //
+ // set cigar
+ chimeric_alignement->setCigar(new_cigar);
+
+ // Add the line to the vector
+ sam_lines->insert(sam_lines->begin(),chimeric_alignement);
+ return sam_lines;
+ }
+}
+
+
+vector<SamLine*> *TagInfo::getSamLines() {
+ //sam_alignements sam_alignements;
+ vector<SamLine*> *sam_lines;
+ // Multiple alignements
+ // we consider several alignments only if there is no break (otherwise it is a little bit tricky)
+ if ((
+ (support->getParameters()->treat_multiple && (support->isMultiple() || support->isDuplicate()))
+ //|| (support->isDuplicate() && !support->isMultiple())
+ )
+ && support->isContinuous()
+ && !support->isSingle()) {
+ sam_lines = new vector<SamLine*>;
+ uint pos_loc;
+ pair<ChrPosition **,uint> locs = support->getLocations(pos_loc);
+ for(ulong i = 0; i < locs.second; i++) {
+ SamLine *multiple_alignement = getSamLine(locs.first[i], pos_loc);
+ // If this is not the primary line
+ if(i>0) {
+ multiple_alignement->setSecondaryAlignement();
+ }
+ sam_lines->push_back(multiple_alignement);
+ delete locs.first[i];
+ }
+ if (locs.first!=NULL)
+ free(locs.first);
+
+ // Set flags for "Next hit" : CC, CP
+ vector<SamLine*>::iterator it = sam_lines->begin() ;
+ vector<SamLine*>::iterator next_it = sam_lines->begin() ;
+ next_it++;
+ for (; next_it != sam_lines->end(); ++next_it) {
+ if((*next_it)->getRname() == (*it)->getRname()) {
+ (*it)->addOptionalField("CC","=");
+ } else {
+ (*it)->addOptionalField("CC",(*next_it)->getRname());
+ }
+ (*it)->addOptionalField("CP",(*next_it)->getPos());
+ it++;
+ }
+ }
+ // Hack for chimeric alignement
+ // Since SAM format now supports chimeric alignement
+ // we need to provide one SAM line for each alignement
+ else {
+ SamLine *base_line = getSamLine();
+
+ if(base_line->getCigar().getNbChimeras() > 0) {
+ uint right_softclip = 0;
+ sam_lines = getChimericAlignements(base_line, 0, 0, 0, &right_softclip);
+ delete base_line;
+
+ // Generating SA optional field
+ ostringstream string_stream;
+ for (vector<SamLine*>::iterator it = sam_lines->begin() ; it != sam_lines->end(); ++it) {
+ string_stream.str(""); // reset buffer
+ for (vector<SamLine*>::iterator it2 = sam_lines->begin() ; it2 != sam_lines->end(); ++it2) {
+ // We do not print the current line info to SA field
+ // that would be redoundant
+ if(it != it2) {
+ // Add a semicolon separator if this is not the first alignement
+ if (string_stream.str().size() > 0) {
+ string_stream << ";";
+ }
+ // print canonical alignemnt with coma separated fields
+ string_stream << (*it2)->getRname() << ',' << (*it2)->getPos() << ',';
+ if((*it2)->isSeqReverseComplemented()) {
+ string_stream << "-";
+ } else {
+ string_stream << "+";
+ }
+ string_stream << ',' << (*it2)->getCigar() << ',' <<(*it2)->getMapQ() << ',' << (*it2)->getCigar().getEditDistance();
+ }
+ }
+ (*it)->addOptionalField("SA",string_stream.str());
+ }
+ } else {
+ sam_lines = new vector<SamLine*>;
+ sam_lines->push_back(base_line);
+ }
+ }
+
+
+ // Set optional fields
+ for (vector<SamLine*>::iterator it = sam_lines->begin() ; it != sam_lines->end(); ++it) {
+ (*it)->addOptionalField("NM",(*it)->getCigar().getEditDistance());
+ (*it)->addOptionalField("IH",sam_lines->size());
+ (*it)->addOptionalField("NH",support->getNbLocsMax());
+ }
+
+ return sam_lines;
+}
+
+ostream &TagInfo::samOutput(ostream &os) {
+ vector<SamLine*> *sam_lines = getSamLines();
+ for (vector<SamLine*>::iterator it = sam_lines->begin() ; it != sam_lines->end(); ++it) {
+ (*it)->writeLine(os);
+ delete (*it);
+ }
+ delete sam_lines;
+ return os;
+}
+
+void TagInfo::setCurrentBreak(uint i) {
+ current_break = i;
+}
+
+void TagInfo::setReadName(char *name) {
+ if (read_name)
+ delete [] read_name;
+ if (name) {
+ read_name = new char[strlen(name)+1];
+ strcpy(read_name, name);
+ } else
+ read_name = NULL;
+}
+
+void TagInfo::setReadQuality(char *quality) {
+ if (read_quality)
+ delete [] read_quality;
+ if (quality) {
+ uint tag_length = strlen(getTag());
+ read_quality = new char[tag_length+1]();
+ strncpy(read_quality, quality, tag_length);
+ } else
+ read_quality = NULL;
+}
+
+void TagInfo::setReadNumber(uint tagId) {
+ this->tagId = tagId;
+}
+
+uint TagInfo::getReadNumber() {
+ return tagId;
+}
+
+ostream &operator<<(ostream &os, TagInfo &info) {
+ // uint current_break = info.getCurrentBreak();
+ // if (info.getNbBreaks() > 0 && current_break < info.getNbBreaks()) {
+ // os << "gap_indel=" << (int) (info.getTagBreakLength(current_break)
+ // - info.getThreshold())
+ // << " score_intra=" << info.getScoreComputedIntraExon(current_break)
+ // << " score_inter=" << info.getScoreComputedInterExon(current_break)
+ // << " deviation=" << info.getScoreInsideAverages(current_break)
+ // << " falling_left=" << info.isSupportFallingLeft(current_break)
+ // << " falling_right=" << info.isSupportFallingRight(current_break)
+ // << " inside_first_quartile="
+ // << info.getBreak(current_break)->getInsideQuartile1()
+ // << " inside_last_quartile="
+ // << info.getBreak(current_break)->getInsideQuartile4()
+ // << " " << endl;
+ // }
+
+ if (info.getLocation() != NULL){
+ os << *info.getLocation() << " ";
+ os << "pos_location=" << info.getPositionOfLocation() << " ";
+ }
+
+ os << info.getTag() << " " ;
+
+ for (uint j=0; j < info.getSupportLength()-1; j++) {
+ os << info.getSupport()[j] << "," ;
+ }
+ os << info.getSupport()[info.getSupportLength()-1] << " ";
+ for (uint j=0; j < info.getSupportLength()-1; j++) {
+ os << info.getLocalisations()[j] << "," ;
+ }
+ os << info.getLocalisations()[info.getSupportLength()-1];
+ return os;
+}
+
+
+// PRIVATE
+
+pair<ChrPosition, uchar *> TagInfo::retrieveChrPosAndNuc(error_context type,
+ uint nb_nuc,
+ int &shift) {
+ uint absolute_genome_loc;
+ ChrPosition chrPos = *getChrPosStartBreak(current_break);
+ uchar *dna = NULL;
+ if (type == SECOND_SUBSTITUTION) {
+ shift = (int) getTagBreakLength(current_break) - getThreshold();
+ }
+ if (chrPos.getStrand() == -1) {
+ if (type != FIRST_SUBSTITUTION || type == INSERTION
+ || type == DELETION) {
+ chrPos += -1;
+ absolute_genome_loc = getLocationStartBreak(current_break) - 1;
+ } else {
+ chrPos = *getChrPosEndBreak(current_break) + getThreshold();
+ absolute_genome_loc = getLocationEndBreak(current_break) + getThreshold();
+ }
+ } else {
+ chrPos = *getChrPosEndBreak(current_break) - shift - 1;
+ absolute_genome_loc = getLocationEndBreak(current_break) - shift - 1;
+ }
+ if (type == DELETION)
+ shift = -1;
+ if (type != INSERTION && nb_nuc > 0) {
+ if (nb_nuc <= support->getParameters()->max_bases_retrieved)
+ dna = genome->getGenomeSubstring(absolute_genome_loc,
+ nb_nuc, chrPos.getStrand());
+ else
+ cerr << "Warning substring of length "
+ << nb_nuc << " not retrieved from genome (read "
+ << support->getTagNum() << ")" << endl;
+ }
+ return pair<ChrPosition, uchar *>(chrPos, dna);
+}
+
diff --git a/src/libReadsInfo/tagInfo.h b/src/libReadsInfo/tagInfo.h
new file mode 100644
index 0000000..b2921f6
--- /dev/null
+++ b/src/libReadsInfo/tagInfo.h
@@ -0,0 +1,472 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at univ-montp2.fr *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef TAG_INFO_H
+#define TAG_INFO_H
+#include <iostream>
+#include <stdarg.h>
+#include "SNPInfo.h"
+#include "BioTagIndelInfo.h"
+#include "BioUndeterminedInfo.h"
+#include "DuplicationInfo.h"
+#include "SpliceInfo.h"
+#include "SpliceInterInfo.h"
+#include "SpliceNoCoverInfo.h"
+#include "SpliceIntraInfo.h"
+#include "SeqErrInfo.h"
+#include "repetitionInfo.h"
+#include "undeterminedErrorInfo.h"
+#include "genericInfo.h"
+#include "../libSSA/chrPosition.h"
+#include "../libSSA/locateOnGenome.h"
+#include "../types.h"
+#include "../Support.h"
+#include "../SupportBreak.h"
+#include "../Parameters.h"
+#include "samLine.h"
+
+using namespace std;
+
+class TagInfo {
+ private:
+ int code;
+ LocateOnGenome *genome;
+ byte *nb_each_type;
+ GenericInfo ***info_each_type; /* Stores the info on breaks depending on
+ * the type it corresponds to */
+ uint nb_causes; /* Number of causes found in the read
+ * INFO_DUPLICATION and INFO_REPETITION are not stored
+ * are not taken into account
+ */
+ byte *types_in_order; /* Stores in which order the add* function have been
+ called.
+ Each cell stores a type (INFO_SNP, INFO_SEQ_ERR, ...).
+ INFO_DUPLICATION and INFO_REPETITION are not stored
+ This array has nb_causes cells.
+ */
+ byte *nb_causes_per_break; /* Number of causes in each break
+ * INFO_DUPLICATION and INFO_REPETITION are not stored
+ * are not taken into account
+ * This array has at least
+ * getNbBreaks() cells */
+
+ Support *support;
+ uint current_break; /* The current break id processed */
+
+ ChrPosition **chrpos[NB_POS_BREAK];
+
+ void addGenericElement(byte type, GenericInfo *gi);
+
+ byte getNbGenericElement(uint type);
+ GenericInfo **getGenericInfos(uint type);
+
+ char *read_name, *read_quality;
+ uint tagId;
+
+
+
+ public:
+ /**
+ * The support is not copied but is deleted when this is deleted
+ */
+ TagInfo(LocateOnGenome *genome, Support *s);
+
+ ~TagInfo();
+
+ float getAverageHighInside(uint);
+ float getAverageLowInside(uint);
+ SupportBreak *getBreak(uint, int = 1);
+ /**
+ * @return the type of the i-th cause
+ */
+ byte getCauseType(uint i, int=1);
+ ChrPosition *getChrPosEndBreak(uint);
+ ChrPosition *getChrPosStartBreak(uint);
+ uint getCurrentBreak();
+ float getDeviationInsideBreak(uint);
+ int getEndPosRepeat();
+ gap_size_t getGenomeGapLength(uint);
+/* bool getIsExtended(uint); */
+ uint *getLocalisations();
+ ChrPosition *getLocation();
+ uint getLocationEndBreak(uint);
+ uint getLocationStartBreak(uint);
+ uint getNbBreaks();
+ uint getNbCauses();
+ byte getNbCausesInBreak(uint, int = 1);
+ uint getNbDuplicate();
+ uint getNbMultiple();
+ uint getNbSingle();
+ uint getPositionOfLocation();
+ char *getReadName();
+ char *getReadQuality();
+ int getStartPosRepeat();
+ uint *getSupport();
+ Support *getSupportObject();
+ uint getSupportLength();
+ /* uint getPositionEndBreak(uint); */
+ uint getPositionEndBreak(uint, int=1);
+ /* uint getPositionStartBreak(uint); */
+ uint getPositionStartBreak(uint, int=1);
+ float getScoreComputedIntraExon(uint);
+ float getScoreComputedInterExon(uint);
+ float getScoreInsideBreak(uint);
+ float getScoreInsideAverages(uint);
+ float getScoreOutsideBreak(uint);
+ char *getTag();
+ char *getTagChromosome();
+ uint getTagBreakLength(uint);
+ ulong getTagPosition();
+ bool getTagStrand();
+ uint getThreshold();
+
+ bool isAlmostNormal();
+ bool isDuplicated(uint);
+ bool isExplainable();
+ bool isNormal();
+ bool isMultiple();
+ bool isNone();
+ bool isRepeated(uint);
+ bool isSingle();
+ bool isSupportFallingLeft(uint, int=1);
+ bool isSupportFallingRight(uint, int=1);
+ bool isDuplication();
+ bool hasSNP();
+ bool hasBioTagIndel();
+ bool hasBioUndetermined();
+ bool hasSeqErr();
+ bool hasRepetition();
+ bool hasSplice();
+ bool hasSpliceIntraChr();
+ bool hasSpliceInterChr();
+ bool hasSpliceNoCover();
+ bool hasNothing();
+ bool hasUndeterminedError();
+ int getCode();
+
+ DuplicationInfo **getInfosDuplication();
+
+ RepetitionInfo **getInfosRepetition();
+ byte getNbRepetition();
+
+ SNPInfo **getInfosSNP();
+ byte getNbSNP();
+
+ BioIndelInfo **getInfosBioTagIndel();
+ byte getNbBioTagIndel();
+
+ BioUndeterminedInfo **getInfosBioUndetermined();
+ byte getNbBioUndetermined();
+
+ SeqErrInfo **getInfosSeqErr();
+ byte getNbSeqErr();
+
+ UndeterminedErrorInfo **getInfosUndeterminedError();
+ byte getNbUndeterminedError();
+
+ SpliceInfo **getInfosSplice();
+ byte getNbSplice();
+
+ SpliceIntraInfo **getInfosSpliceIntra();
+ byte getNbSpliceIntra();
+
+ SpliceInterInfo **getInfosSpliceInter();
+ byte getNbSpliceInter();
+
+ SpliceNoCoverInfo **getInfosSpliceNoCover();
+ byte getNbSpliceNoCover();
+
+ /// COMMANDS ///
+
+ void addDuplication();
+
+ void addAlmostNormal();
+ void addNormal();
+ void addMultiple();
+ void addNone();
+
+ /**
+ * position_in: position in the tag where the repetition starts (default: -1
+ * unkown)
+ * position_out: position in the tag where the repetition ends.
+ */
+ void addRepetition(int position_in=-1, int position_out=-1);
+
+ void addSingle();
+
+ /**
+ * tag_nuc: nucleotide found in the tag, or 0 if unknown (or deletion)
+ * genome_nuc: nucleotide found in the genome, or 0 if unknown (or insertion)
+ * snpID: identify which kind of SNP (depending on in which context it occurs)
+ */
+ void addSNP(char tag_nuc=0,
+ error_context snpID=FIRST_SUBSTITUTION);
+
+ /**
+ * Another version of addSNP, less easy to use but that allows to give all
+ * the necessary informations without letting the other addSNP version
+ * computing them.
+ * @param pos : position of the SNP in the read
+ * @param base_read : nucleotide from the read (or 0 if it doesn't exist)
+ * @param base_genome: corresponding nucleotide on the genome
+ * (or 0 if it doesn't exist)
+ * @param chrPos : location of the SNP on the genome
+ * @param score: score of the SNP.
+ */
+ void addSNP(uint pos, char base_read, char base_genome, ChrPosition &chrPos,
+ float score);
+
+ /**
+ * nb_ins: number of insertions
+ * nb_del: number of deletions
+ */
+ void addBioTagIndel(uint nb_ins, uint nb_del);
+
+ /**
+ * We know that there is a biological cause, but since
+ * it is at the beginning or at the end of the support, it is impossible
+ * to determined accurately the biological cause.
+ */
+ void addBioUndetermined(ChrPosition *, uint, const char *, ...);
+
+ /**
+ * position: position in the tag where the sequence error is
+ * nb_ins: number of insertions
+ * nb_del: number of deletions
+ */
+ void addSeqErr(error_context , uint position, uint nb_ins, uint nb_del,
+ float score,
+ uint genome_seq_length=~0,
+ char *tag_seq=NULL, uint tag_seq_length=~0);
+
+
+ /**
+ * position: position where the splice is
+ * gap_length: length of the intron
+ */
+ void addSplice(uint gap_length);
+ void addSpliceIntra(uint gap_length);
+ void addSpliceInter();
+ void addSpliceNoCover(uint gap_length);
+
+ void addUndeterminedError(const char *format, ...);
+
+ /**
+ * Change a GenericInfo with an other one.
+ * The new GenericInfo will be inserted at the same place as the old one,
+ * Indeed, it will apply to the same break.
+ * This function is useful when we are reclassifying breaks afterwards.
+ *
+ * @param type the type of the old genericInfo to replace
+ * @param newType the new type that will replace the current type
+ * @param oldMask: old mask corresponding to the old cause to be replaced
+ * (see constant whose name starts with MASK_ in const.h)
+ * @param newMask: new mask corresponding to the new cause replacing the new one
+ * @param i the index of the GenericInfo in info_each_type[type] array.
+ * @param newGi the new GenericElement to insert in array info_each_type[newType]
+ *
+ * @post getNbGenericElement(type) == old getNbGenericElement(type) - 1
+ * && getNbGenericElement(newType) == old getNbGenericElement(newType) + 1
+ * && (old getNbGenericElement(type) == 1 ==> getCode() & type == 0)
+ * && getCode() & newType == newType
+ */
+ void changeGenericElement(byte type, byte newType, int oldMask, int newMask,
+ uint i, GenericInfo *newGi);
+
+ /**
+ * Same function as above.
+ * The difference resides in the parameter given.
+ * On that version, you must provide the break ID, the cause lies in, and additionally
+ * the number of a cause of that type in this break (starts at 0).
+ *
+ * @param type the type of the old genericInfo to replace
+ * @param newType the new type that will replace the current type
+ * @param oldMask: old mask corresponding to the old cause to be replaced
+ * (see constant whose name starts with MASK_ in const.h)
+ * @param newMask: new mask corresponding to the new cause replacing the new one
+ * @param break_id The ID of the break where we must change something
+ * @param cause_num The number of the cause (starts at 0) we want to change, having
+ * the same type, in break break_id.
+ * @param newGi the new GenericElement to insert in array info_each_type[newType]
+ */
+ void changeGenericElement(byte type, byte newType, int oldMask, int newMask,
+ uint break_id, uint cause_num, GenericInfo *newGi);
+
+
+ /**
+ * Remove a splice Inter and add a bioUndetermined info instead.
+ *
+ * @param i the indice of the spliceInter if Info_each_type array
+ * @param info a string containing the reason of the reclassification
+ */
+ void removeSpliceInter(uint i,const char* info);
+
+ /**
+ * SAM output for the given read
+ * XU: Is it single located?
+ * XD: It it duplicated?
+ * XM: Is it multiple?
+ * XN: Is it normal? (1: normal, 2: almost, 0: no)
+ * XL: location taken to minimise the probability of FP.
+ * XP: position in the read of XL
+ * XO: Location taken in Support as a single location
+ * XQ: position in the read of XO
+ * XC: Number of causes in the read
+ * XE: Detail of a cause
+ * XB: Large details for a cause
+ */
+ ostream &samOutput(ostream &os);
+
+ /*
+ * Return a set of sam line that corresponds to the alignement of the read.
+ * Multiple line for one read can occur in two situations:
+ * 1. the read has multiple locations on the genome
+ * 2. the read has a chimeric alignement
+ * The primary line of the read is always returned if first postion
+ * of the vector.
+ */
+ vector<SamLine*> *getSamLines();
+
+ /**
+ * Tells which break we are working on.
+ * The given integer is the break number.
+ * @post Calling one of addSNP, addGenomeIndel, ... will affect one of those causes
+ * to the current break
+ */
+ void setCurrentBreak(uint);
+
+ void setReadName(char *name);
+ void setReadQuality(char *);
+ void setReadNumber(uint tagId);
+ uint getReadNumber();
+
+ friend ostream &operator<<(ostream &os, TagInfo &);
+
+ private:
+ pair<ChrPosition, uchar *> retrieveChrPosAndNuc(error_context type,
+ uint nb_nuc,
+ int &shift);
+
+
+ /**
+ * This method constructs from a single SamLine object a set of SamLines
+ * that corresponds to the chimericAlignement of the read if there is one.
+ * This method is recursive and called by the "getSamLine()" method of this
+ * very Class.
+ */
+ vector<SamLine*> *getChimericAlignements(SamLine *base_line, uint cigar_index, uint splice_id, uint left_softclip, uint *right_softclip);
+
+ /**
+ * Return a prototype of SAMLine that can be used to create
+ * multiple alignement for one tagInfo.
+ * @loc is the location of a chosen kmer in the read which represents
+ * the read location
+ * @pos_loc the kmer position in the read
+ */
+ SamLine *getSamLine(ChrPosition *loc = NULL, ulong pos_loc = 0);
+
+
+
+};
+
+ostream &operator<<(ostream &os, TagInfo &);
+
+
+#endif
diff --git a/src/libReadsInfo/undeterminedErrorInfo.cpp b/src/libReadsInfo/undeterminedErrorInfo.cpp
new file mode 100644
index 0000000..8269f09
--- /dev/null
+++ b/src/libReadsInfo/undeterminedErrorInfo.cpp
@@ -0,0 +1,125 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <iostream>
+#include "undeterminedErrorInfo.h"
+using namespace std;
+
+UndeterminedErrorInfo::UndeterminedErrorInfo(char*message):message(message){}
+
+UndeterminedErrorInfo::~UndeterminedErrorInfo() {
+ delete [] message;
+}
+
+char *UndeterminedErrorInfo::getMessage() {
+ return message;
+}
+
+void UndeterminedErrorInfo::output(ostream &os) {
+ os << *this;
+}
+
+void UndeterminedErrorInfo::samOutput(ostream &os, int strand) {
+ os << "Undetermined:[" << getMessage() << "]";
+}
+
+ostream &operator<<(ostream &os, UndeterminedErrorInfo &i) {
+ os << i.getMessage() ;
+ return os;
+}
diff --git a/src/libReadsInfo/undeterminedErrorInfo.h b/src/libReadsInfo/undeterminedErrorInfo.h
new file mode 100644
index 0000000..08a14ee
--- /dev/null
+++ b/src/libReadsInfo/undeterminedErrorInfo.h
@@ -0,0 +1,119 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef UNDETERMINED_ERROR_INFO_H
+#define UNDETERMINED_ERROR_INFO_H
+#include "genericInfo.h"
+
+class UndeterminedErrorInfo : public GenericInfo {
+ private:
+ char *message;
+ public:
+ UndeterminedErrorInfo(char *message);
+ ~UndeterminedErrorInfo();
+
+ char *getMessage();
+
+ void output(ostream &);
+ void samOutput(ostream &, int=1);
+};
+
+ostream &operator<<(ostream &, UndeterminedErrorInfo &);
+
+#endif
diff --git a/src/libSSA/GenomeInfo.cpp b/src/libSSA/GenomeInfo.cpp
new file mode 100644
index 0000000..ac48bcb
--- /dev/null
+++ b/src/libSSA/GenomeInfo.cpp
@@ -0,0 +1,273 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "GenomeInfo.h"
+#include <cassert>
+#include <fstream>
+
+ /**
+ * Array containing the sequence names
+ */
+ uchar **chr_names;
+ /**
+ * Number of sequences
+ */
+ ulong nb_chr;
+ /**
+ * Array containing the length (in nt) of each sequence
+ */
+ ulong *length_chr;
+ /**
+ * Array containing the cumulative length of each sequence.
+ * First cell's value is 0
+ */
+ ulong *total_length;
+
+
+ /**
+ * Read the file whose name is stored in <basename>.conf.
+ * Retrieves the information from the file and store them
+ * in the class.
+ * @param basename: name of the file without the .conf extension
+ */
+GenomeInfo::GenomeInfo(char *basename) {
+ char *genomeConf = new char[strlen(basename)+6];
+ fstream file;
+ sprintf(genomeConf, "%s.conf", basename);
+
+ file.open(genomeConf, ios::in);
+ if (! file.is_open()) {
+ cerr << "Cannot open chromosomes file: " << genomeConf << endl;
+ exit(2);
+ }
+
+ delete [] genomeConf;
+
+ // Store the number of sequences
+ file >> skipws >> nb_chr;
+
+ // Allocate memory for the arrays
+ chr_names = new uchar*[nb_chr];
+ total_length = new ulong[nb_chr+1];
+ length_chr = new ulong[nb_chr];
+ total_length[0] = 0;
+
+ int i = 0;
+ file.width(MAX_LENGTH_CHR_NAME);
+ while (! file.eof()) {
+ chr_names[i] = new uchar[MAX_LENGTH_CHR_NAME];
+ file >> skipws >> chr_names[i];
+ file >> skipws >> length_chr[i];
+ total_length[i+1] = total_length[i]+ length_chr[i];
+ i++;
+ }
+ file.close();
+}
+
+GenomeInfo::GenomeInfo(uchar **chr_names, ulong nb_chr, ulong *length_chr):
+ chr_names(chr_names), nb_chr(nb_chr), length_chr(length_chr) {
+ total_length = new ulong[nb_chr+1];
+ total_length[0] = 0;
+ for (ulong i = 0; i < nb_chr; i++) {
+ total_length[i+1] = total_length[i] + length_chr[i];
+ }
+}
+
+GenomeInfo::~GenomeInfo() {
+ for (uint i = 0; i < nb_chr; i++)
+ delete [] chr_names[i];
+ delete [] chr_names;
+ delete [] total_length;
+ delete [] length_chr;
+}
+
+uchar *GenomeInfo::getChrName(ulong i) {
+ assert(i >= 0 && i < getNbChr());
+
+ return chr_names[i];
+}
+
+pair<const uchar *,const ulong> GenomeInfo::getChrNameFromPosition(ulong pos) {
+ pair<ulong, ulong> tmp_pair = getNumFromPosition(pos);
+ uchar *chr_name;
+
+ if (tmp_pair.first >= getNbChr()) {
+ chr_name = NULL;
+ } else {
+ chr_name = getChrName(tmp_pair.first);
+ }
+ return (pair<const uchar *, const ulong>(chr_name, tmp_pair.second));
+}
+
+ulong GenomeInfo::getChrLength(ulong i) {
+ assert(i >= 0 && i < getNbChr());
+
+ return length_chr[i];
+}
+
+ulong GenomeInfo::getGenomeLength() {
+ return total_length[getNbChr()];
+}
+
+ulong GenomeInfo::getGenomePosition(uchar *chr, ulong position) {
+ return getGenomePosition(getNumFromName(chr), position);
+}
+
+ulong GenomeInfo::getGenomePosition(ulong id, ulong position) {
+ if (id < getNbChr() && position < length_chr[id]) {
+ return total_length[id] + position;
+ }
+ return ~0;
+}
+
+ulong GenomeInfo::getNbChr() {
+ return nb_chr;
+}
+
+ulong GenomeInfo::getNumFromName(uchar *name) {
+ ulong num_chr = 0;
+ while (num_chr < getNbChr()
+ && strcmp((char *)chr_names[num_chr], (char *)name) != 0){
+ num_chr++;
+ }
+ if (num_chr >= getNbChr()) {
+ return getNbChr();
+ }
+ return num_chr;
+}
+
+pair<const ulong, const ulong> GenomeInfo::getNumFromPosition(ulong pos) {
+ ulong num_chr = 0;
+
+ while (num_chr < getNbChr() && pos >= total_length[num_chr+1]) {
+ num_chr++;
+ }
+ return pair<const ulong, const ulong>(num_chr, pos - total_length[num_chr]);
+}
+
+bool GenomeInfo::isValidPosition(ulong pos) {
+ return pos < getGenomeLength();
+}
+
+
+void GenomeInfo::save(char *name, const char *ext) {
+ char *confName = new char[strlen(name) + strlen(ext)];
+ ofstream conf;
+ sprintf(confName, "%s%s", name, ext);
+ conf.open(confName, ios_base::out | ios_base::binary);
+ if (! conf.is_open()) {
+ cerr << "Can't write file " << confName << endl;
+ exit(3);
+ }
+ delete [] confName;
+
+ // Writing configuration file
+ conf << *this;
+ conf.close();
+
+}
+
+ostream &operator<<(ostream &os, GenomeInfo &g) {
+ os << g.getNbChr();
+ for (uint i=0; i < g.getNbChr(); i++) {
+ os << endl << g.getChrName(i)
+ << endl << g.getChrLength(i);
+ }
+ return os;
+}
diff --git a/src/libSSA/GenomeInfo.h b/src/libSSA/GenomeInfo.h
new file mode 100644
index 0000000..7f17f4e
--- /dev/null
+++ b/src/libSSA/GenomeInfo.h
@@ -0,0 +1,246 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef GENOME_INFO_H
+#define GENOME_INFO_H
+
+#include <utility>
+#include <iostream>
+#include "basic.h"
+
+using namespace std;
+
+/**
+ * Maximal length of a chromosome (or sequence) name.
+ */
+#define MAX_LENGTH_CHR_NAME 60
+
+/**
+ * A class that gives access to the information stored in .conf file
+ */
+class GenomeInfo {
+private:
+ /**
+ * Array containing the sequence names
+ */
+ uchar **chr_names;
+ /**
+ * Number of sequences
+ */
+ ulong nb_chr;
+ /**
+ * Array containing the length (in nt) of each sequence
+ */
+ ulong *length_chr;
+ /**
+ * Array containing the cumulative length of each sequence.
+ * First cell's value is 0
+ */
+ ulong *total_length;
+
+
+public:
+
+ /**
+ * Read the file whose name is stored in <basename>.conf.
+ * Retrieves the information from the file and store them
+ * in the class.
+ * @param basename: name of the file without the .conf extension
+ */
+ GenomeInfo(char *basename);
+
+ /**
+ * Construct the class given the sequences names, their number
+ * and their lengths.
+ * Beware: the arrays are not copied.
+ * @param chr_names: Names of the sequences
+ * @param nb_chr: Number of sequences
+ * @param length_chr: Length of the sequences
+ */
+ GenomeInfo(uchar **chr_names, ulong nb_chr, ulong *length_chr);
+
+ ~GenomeInfo();
+
+ /**
+ * @pre i >= 0 && i < getNbChr()
+ * @return The name of the sequence number i
+ */
+ uchar *getChrName(ulong i);
+
+ /**
+ * @param pos: a position in the genome
+ * @return the name of the chromosome associated to that position and
+ * the relative position in the chromosome.
+ * If the position isn't in the genome, the chromosome name is set
+ * to NULL
+ */
+ pair<const uchar *,const ulong> getChrNameFromPosition(ulong pos);
+
+ /**
+ * @pre i >= 0 && i < getNbChr()
+ * @return The length of the sequence number i (whose name is getChrName(i))
+ */
+ ulong getChrLength(ulong i);
+
+ /**
+ * @return the total length of the chromosome ie. the cumulated length of
+ * the chromosomes.
+ */
+ ulong getGenomeLength();
+
+ /**
+ * @param chr: Name of the chromosome
+ * @param position: Position in the chromosome
+ * @return The position in the genome of <position> in chromosome <chr>
+ * or ~0 if no such chromosome or position in the chromosome exist.
+ * @post p = getChrNameFromPosition(pos)
+ * <==> pos == getGenomePosition(p.first, p.second)
+ */
+ ulong getGenomePosition(uchar *chr, ulong position);
+
+ /**
+ * @param id: Id of the chromosome
+ * @param position: Position in the chromosome
+ * @return The position in the genome of <position> in chromosome number <id>
+ * or ~0 if no such chromosome or position in the chromosome exist.
+ * @post p = getChrNameFromPosition(pos)
+ * <==> pos == getGenomePosition(p.first, p.second)
+ */
+ ulong getGenomePosition(ulong id, ulong position);
+
+ /**
+ * @return The number of sequences stored
+ */
+ ulong getNbChr();
+
+ /**
+ * @param name: Name of a sequence
+ * @return the number associated to the sequence or getNbChr() if no such
+ * name corresponds to a known sequence.
+ * @post getChrName(getNumFromName(name)) and name are equals
+ */
+ ulong getNumFromName(uchar *name);
+
+ /**
+ * @param pos: a position in the genome
+ * @return the number of the chromosome associated to that position, and
+ * the relative position in the chromosome.
+ * If the position isn't in the genome, the chromosome number is
+ * set to getNbChr().
+ * @post getNumFromName(getChrNameFromPosition(pos).first)
+ * == getNumFromPosition(pos).first
+ */
+ pair<const ulong, const ulong> getNumFromPosition(ulong pos);
+
+ /**
+ * @return true iff pos < getGenomeLength()
+ */
+ bool isValidPosition(ulong pos);
+
+ /**
+ * Save to the file whose name given in parameter
+ * @param filename: the filename you must save to
+ * @param ext: extension put after the filename (default .conf)
+ */
+ void save(char *name, const char *ext=".conf");
+};
+
+ostream &operator<<(ostream &os, GenomeInfo &g);
+
+#endif
diff --git a/src/libSSA/HuffAlphabetRank.cpp b/src/libSSA/HuffAlphabetRank.cpp
new file mode 100644
index 0000000..82fc435
--- /dev/null
+++ b/src/libSSA/HuffAlphabetRank.cpp
@@ -0,0 +1,344 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "HuffAlphabetRank.h"
+#include <cstdlib>
+
+ THuffAlphabetRank::THuffAlphabetRank(uchar *s, ulong n, TCodeEntry *codetable, ulong level, ulong factor) {
+ left = NULL;
+ right = NULL;
+ bitrank = NULL;
+// parent = NULL;
+ ch = s[0];
+ this->codetable = codetable;
+ ulong *Binbits = (ulong *)calloc(n/W+1, sizeof(ulong));;
+ ulong sum=0,i;
+
+ for (i=0;i<n;i++)
+ if ((codetable[s[i]].code & (1u << level)) ) {
+ SetField(Binbits,1,i,true);
+ sum++;
+ } else
+ SetField(Binbits,1,i,false);
+ leaf=true;
+ for (i=1;i<n;i++)
+ if (s[i] != ch)
+ leaf = false;
+ if (leaf) {
+ free(Binbits);
+ delete [] s;
+ return;
+ }
+
+ uchar *sfirst=NULL, *ssecond=NULL;
+ if (n-sum > 0) {
+ sfirst = new uchar[n-sum];
+ }
+ if (sum > 0) {
+ ssecond = new uchar[sum];
+ }
+ ulong j=0,k=0;
+ for (i=0;i<n;i++)
+ if (GetField(Binbits,1,i)) ssecond[k++] = s[i];
+ else sfirst[j++] = s[i];
+
+ delete [] s;
+ bitrank = new BitRankW32Int(Binbits,n,true,factor);
+ if (j > 0) {
+ left = new THuffAlphabetRank(sfirst,j,codetable,level+1,factor);
+ } else if (sfirst) {
+ delete [] sfirst;
+ }
+ if (k>0) {
+ right = new THuffAlphabetRank(ssecond,k,codetable,level+1,factor);
+ } else if (ssecond) {
+ delete [] ssecond;
+ }
+// if (level == 0)
+// init_leaves();
+ }
+
+// void THuffAlphabetRank::init_leaves() {
+// leaves = new THuffAlphabetRank[size_uchar];
+// for (uchar c = 0; c < size_uchar; c++) {
+// leaves[c] = getLeaf(c);
+// }
+// }
+
+THuffAlphabetRank *THuffAlphabetRank::getLeaf(uchar c) {
+ if (codetable[c].count == 0) return NULL;
+ ulong level = 0;
+ ulong code = codetable[c].code;
+ THuffAlphabetRank *currentNode = this;
+ while (! currentNode->leaf) {
+ if ((code & (1u<<level)) == 0) {
+ currentNode = currentNode->left;
+ } else {
+ currentNode = currentNode->right;
+ }
+ ++level;
+ }
+ return currentNode;
+}
+
+ ulong THuffAlphabetRank::rank(uchar c, ulong i) { // returns the number of characters c before and including position i
+ THuffAlphabetRank *temp=this;
+ if (codetable[c].count == 0) return 0;
+ ulong level = 0;
+ ulong code = codetable[c].code;
+ while (!temp->leaf) {
+ if ((code & (1u<<level)) == 0) {
+ i = i-temp->bitrank->rank(i);
+ temp = temp->left;
+ }
+ else {
+ i = temp->bitrank->rank(i)-1;
+ temp = temp->right;
+ }
+ ++level;
+ }
+ return i+1;
+ }
+
+// ulong THuffAlphabetRank::select(uchar c, ulong i) {
+// THuffAlphabetRank *node = leaves[c];
+
+// if (node->parent == NULL)
+// return i;
+
+// bool bit = node->parent->right == node;
+
+// while(node->parent != NULL) {
+// node = node->parent;
+// node->bitrank->select
+// }
+// }
+
+
+ bool THuffAlphabetRank::IsCharAtPos(uchar c, ulong i) {
+ THuffAlphabetRank *temp=this;
+ if (codetable[c].count == 0) return false;
+ ulong level = 0;
+ ulong code = codetable[c].code;
+ while (!temp->leaf) {
+ if ((code & (1u<<level))==0) {
+ if (temp->bitrank->IsBitSet(i)) return false;
+ i = i-temp->bitrank->rank(i);
+ temp = temp->left;
+ }
+ else {
+ if (!temp->bitrank->IsBitSet(i)) return false;
+ i = temp->bitrank->rank(i)-1;
+ temp = temp->right;
+ }
+ ++level;
+ }
+ return true;
+ }
+ uchar THuffAlphabetRank::charAtPos(ulong i) {
+ THuffAlphabetRank *temp=this;
+ while (!temp->leaf) {
+ if (temp->bitrank->IsBitSet(i)) {
+ i = temp->bitrank->rank(i)-1;
+ temp = temp->right;
+ } else {
+ i = i-temp->bitrank->rank(i);
+ temp = temp->left;
+ }
+ }
+ return temp->ch;
+ }
+ uchar THuffAlphabetRank::charAtPos2(ulong i, ulong *rank) {
+ THuffAlphabetRank *temp=this;
+ while (!temp->leaf) {
+ if (temp->bitrank->IsBitSet(i)) {
+ i = temp->bitrank->rank(i)-1;
+ temp = temp->right;
+ } else {
+ i = i-temp->bitrank->rank(i);
+ temp = temp->left;
+ }
+ }
+ (*rank)=i;
+ return temp->ch;
+ }
+
+ ulong THuffAlphabetRank::SpaceRequirementInBits() {
+ ulong bits=sizeof(THuffAlphabetRank)*8;
+ if (left!=NULL) bits+=left->SpaceRequirementInBits();
+ if (right!=NULL) bits+=right->SpaceRequirementInBits();
+ if (bitrank != NULL)
+ bits += bitrank->SpaceRequirementInBits();
+ return bits;
+ }
+ bool THuffAlphabetRank::Test(uchar *s, ulong n) {
+ // testing that the code works correctly
+ uchar C[size_uchar];
+ ulong i,j;
+ bool correct=true;
+ for (j=0;j<size_uchar;j++)
+ C[j] = 0;
+ for (i=0;i<n;i++) {
+ C[s[i]]++;
+ if (C[s[i]]!=rank(s[i],i)) {
+ correct = false;
+ printf("%u (%c): %d<>%u\n",i,s[i],C[s[i]],rank(s[i],i));
+ }
+ }
+ return correct;
+ }
+ THuffAlphabetRank::~THuffAlphabetRank() {
+ if (left!=NULL) delete left;
+ if (right!=NULL) delete right;
+ if (bitrank!=NULL)
+ delete bitrank;
+ }
+
+ int THuffAlphabetRank::save(FILE *f) {
+ uchar sons;
+ if (f == NULL) return 20;
+ if (fwrite (&leaf,sizeof(uchar),1,f) != 1) return 21;
+ if (fwrite (&ch,sizeof(uchar),1,f) != 1) return 21;
+ if (!leaf) {
+ if (bitrank->save(f) != 0) return 21;
+ sons=0;
+ if (left != NULL) sons=sons | 1;
+ if (right != NULL) sons=sons | 2;
+ if (fwrite (&sons,sizeof(uchar),1,f) != 1) return 21;
+ if (left != NULL)
+ if (left->save(f)!=0) return 21;
+ if (right != NULL)
+ if (right->save(f)!=0) return 21;
+ }
+ return 0;
+ }
+
+ int THuffAlphabetRank::load(FILE *f, TCodeEntry *_codetable) {
+ int error;
+ uchar sons;
+ left = NULL;
+ right = NULL;
+// parent = NULL;
+ bitrank = NULL;
+
+ if (f == NULL) return 23;
+ if (fread (&leaf,sizeof(uchar),1,f) != 1) return 25;
+ if (fread (&ch,sizeof(uchar),1,f) != 1) return 25;
+ codetable=_codetable;
+ if (!leaf){
+ bitrank= new BitRankW32Int(f,&error);
+ if (error != 0) return error;
+ if (fread (&sons,sizeof(uchar),1,f) != 1) return 25;
+ if ((sons&1) > 0 ) {
+ left = new THuffAlphabetRank(f, _codetable, &error);
+// left->parent = this;
+ if (error != 0) return error;
+ }
+ if ((sons&2) > 0 ) {
+ right = new THuffAlphabetRank(f, _codetable, &error);
+// right->parent = this;
+ if (error != 0) return error;
+ }
+ }
+ return 0;
+ }
+ THuffAlphabetRank::THuffAlphabetRank(FILE *f, TCodeEntry *_codetable, int *error) {
+ *error = load(f, _codetable);
+// init_leaves();
+ }
diff --git a/src/libSSA/HuffAlphabetRank.h b/src/libSSA/HuffAlphabetRank.h
new file mode 100644
index 0000000..3084ed9
--- /dev/null
+++ b/src/libSSA/HuffAlphabetRank.h
@@ -0,0 +1,134 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef HuffAlphabetRank_h
+#define HuffAlphabetRank_h
+
+#include "Huffman_Codes.h"
+#include "basic.h"
+#include "bitrankw32int.h"
+
+class THuffAlphabetRank {
+// using fixed 0...255 alphabet
+private:
+ TCodeEntry *codetable;
+ BitRankW32Int *bitrank;
+ uchar ch;
+ bool leaf;
+ THuffAlphabetRank *left;
+ THuffAlphabetRank *right;
+/* THuffAlphabetRank *parent; */
+
+/* THuffAlphabetRank *leaves; */
+/* void init_leaves(); */
+public:
+ THuffAlphabetRank(uchar *s, ulong n, TCodeEntry *codetable, ulong level, ulong factor);
+ THuffAlphabetRank *getLeaf(uchar c);
+ ulong rank(uchar c, ulong i); // returns the number of characters c before and including position i
+ bool IsCharAtPos(uchar c, ulong i);
+ uchar charAtPos(ulong i);
+ uchar charAtPos2(ulong i, ulong *rank);
+ ulong SpaceRequirementInBits();
+ bool Test(uchar *s, ulong n);
+ ~THuffAlphabetRank();
+ int save(FILE *f);
+ int load(FILE *f, TCodeEntry *_codetable);
+ THuffAlphabetRank(FILE *f, TCodeEntry *_codetable, int *error);
+};
+#endif
diff --git a/src/libSSA/Huffman_Codes.cpp b/src/libSSA/Huffman_Codes.cpp
new file mode 100644
index 0000000..23e3143
--- /dev/null
+++ b/src/libSSA/Huffman_Codes.cpp
@@ -0,0 +1,180 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "Huffman_Codes.h"
+//
+// This routine does a quick count of all the
+// characters in the input text.
+//
+
+
+void count_chars(uchar *text, ulong n, TCodeEntry *counts )
+{
+ ulong i;
+ for (i = 0 ; i < size_uchar ; i++ )
+ counts[ i ].count = 0;
+ for (i=0; i<n; i++)
+ counts[text[i]].count++;
+}
+
+TCodeEntry *makecodetable(uchar *text, ulong n)
+{
+ TCodeEntry *result = new TCodeEntry[ size_uchar ];
+
+ count_chars( text, n, result );
+/* ulong count=0;
+ for (int i=0;i<256; i++) {
+ count += result[i].count;
+ if (result[i].count>0)
+ printf("%c,%d: %d\n",i , i,result[i].count);
+ }
+ printf("count=%d\n",count);*/
+ priority_queue< node, vector< node >, greater<node> > q;
+//
+// First I push all the leaf nodes into the queue
+//
+ for ( ulong i = 0 ; i < size_uchar ; i++ )
+ if ( result[ i ].count )
+ q.push(node( i, result[ i ].count ) );
+//
+// This loop removes the two smallest nodes from the
+// queue. It creates a new internal node that has
+// those two nodes as children. The new internal node
+// is then inserted into the priority queue. When there
+// is only one node in the priority queue, the tree
+// is complete.
+//
+
+ while ( q.size() > 1 ) {
+ node *child0 = new node( q.top() );
+ q.pop();
+ node *child1 = new node( q.top() );
+ q.pop();
+ q.push( node( child0, child1 ) );
+ }
+//
+// Now I compute and return the codetable
+//
+// cout << "Char Symbol Code" << endl;
+// q.top().traverse();
+ q.top().maketable(0u,0u, result);
+ q.top().deleteme();
+ q.pop();
+ return result;
+}
+
+int save_codetable(FILE *f,TCodeEntry *codetable) {
+ if (f == NULL) return 20;
+ for (int i=0; i<size_uchar;i++) {
+ if (codetable[i].save(f) != 0) return 21;
+ }
+ return 0;
+}
+
+
+int load_codetable(FILE *f,TCodeEntry **codetable) {
+ if (f == NULL) return 23;
+ TCodeEntry *result = new TCodeEntry[ size_uchar ];
+ for (int i=0; i<size_uchar;i++) {
+ if (result[i].load(f) != 0) return 25;
+ }
+ (*codetable)=result;
+ return 0;
+}
+
diff --git a/src/libSSA/Huffman_Codes.h b/src/libSSA/Huffman_Codes.h
new file mode 100644
index 0000000..88a4158
--- /dev/null
+++ b/src/libSSA/Huffman_Codes.h
@@ -0,0 +1,233 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef maketable_h
+#define maketable_h
+
+#include <iostream>
+#include <iomanip>
+#include <fstream>
+#include <vector>
+#include <stack>
+#include <string>
+#include <queue>
+#include "basic.h"
+
+using namespace std;
+
+
+// To append codes
+
+//ulong SetBit(ulong x, ulong pos, ulong bit) {
+// return x | (bit << pos);
+//}
+
+// codetable := new TCodeEntry[256]
+
+class TCodeEntry {
+ public:
+ ulong count;
+ ulong bits;
+ ulong code;
+ TCodeEntry() {count=0;bits=0;code=0u;};
+ int save(FILE *f) {
+ if (f == NULL) return 20;
+ if (fwrite (&count,sizeof(ulong),1,f) != 1) return 21;
+ if (fwrite (&bits,sizeof(ulong),1,f) != 1) return 21;
+ if (fwrite (&code,sizeof(ulong),1,f) != 1) return 21;
+ return 0;
+ };
+ int load(FILE *f) {
+ if (f == NULL) return 23;
+ if (fread (&count,sizeof(ulong),1,f) != 1) return 25;
+ if (fread (&bits,sizeof(ulong),1,f) != 1) return 25;
+ if (fread (&code,sizeof(ulong),1,f) != 1) return 25;
+ return 0;
+ };
+};
+
+//
+// The node class is used to represent both leaf
+// and internal nodes. leaf nodes have 0s in the
+// child pointers, and their value member corresponds
+// to the character they encode. internal nodes
+// don't have anything meaningful in their value
+// member, but their child pointers point to
+// other nodes.
+//
+
+class node {
+private:
+ int weight;
+ uchar value;
+ const node *child0;
+ const node *child1;
+//
+// Construct a new leaf node for character c
+//
+public:
+ node( uchar c = 0, int i = -1 ) {
+ value = c;
+ weight = i;
+ child0 = 0;
+ child1 = 0;
+ }
+//
+// Construct a new internal node that has
+// children c1 and c2.
+//
+ node( const node* c0, const node *c1 ) {
+ value = 0;
+ weight = c0->weight + c1->weight;
+ child0 = c0;
+ child1 = c1;
+ }
+
+//
+// The comparison operators used to order the
+// priority queue.
+//
+ bool operator>( const node &a ) const {
+ return weight > a.weight;
+ }
+//
+// The traverse member function is used to
+// print out the code for a given node. It
+// is designed to print the entire tree if
+// called for the root node.
+//
+
+ void traverse( string code = "" ) const
+ {
+ if ( child0 ) {
+ child0->traverse( code + "0" );
+ child1->traverse( code + "1" );
+ } else {
+ cout << " " << value << " " << (int) value << " ";
+ cout << setw( 2 ) << weight;
+ cout << " " << code << endl;
+ }
+ }
+ void maketable( ulong code, ulong bits, TCodeEntry *codetable ) const
+ {
+ if ( child0 ) {
+ child0->maketable( code | (0 << bits) , bits+1, codetable );
+ child1->maketable( code | (1 << bits) , bits+1, codetable );
+ }
+ else {
+ codetable[value].code = code;
+ codetable[value].bits = bits;
+ }
+ }
+ void deleteme() const {
+ if ( child0 ) {
+ if (child0->child0)
+ child0->deleteme();
+ if (child1->child0)
+ child1->deleteme();
+ delete child0;
+ delete child1;
+ }
+ }
+};
+
+TCodeEntry *makecodetable(uchar *text, ulong n);
+int save_codetable(FILE *f,TCodeEntry *codetable);
+int load_codetable(FILE *f,TCodeEntry **codetable);
+#endif
diff --git a/src/libSSA/Makefile.am b/src/libSSA/Makefile.am
new file mode 100644
index 0000000..33ff26d
--- /dev/null
+++ b/src/libSSA/Makefile.am
@@ -0,0 +1,246 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+
+bin_PROGRAMS = crac-index
+crac_index_SOURCES = cracIndex.cpp cracIndex.h
+
+AM_CPPFLAGS = -I at abs_top_srcdir@ -I at abs_srcdir@/karkkainen_bwt -I at abs_top_srcdir@/src/libGkArrays/src
+AM_LDFLAGS = -lm -lpthread -lSSA -L at abs_builddir@/
+LDADD = libSSA.a
+
+KARKKAINEN_BWT = \
+ karkkainen_bwt/blockwise_sa.h \
+ karkkainen_bwt/zbox.h \
+ karkkainen_bwt/assert_helpers.h \
+ karkkainen_bwt/random_source.h \
+ karkkainen_bwt/binary_sa_search.h \
+ karkkainen_bwt/multikey_qsort.h \
+ karkkainen_bwt/auto_array.h \
+ karkkainen_bwt/diff_sample.h \
+ karkkainen_bwt/alphabet.h \
+ karkkainen_bwt/timer.h
+
+SEQAN_INDEX = \
+ seqan/index.h \
+ seqan/index/index_qgram_find.h \
+ seqan/index/index_sa_lss.h \
+ seqan/index/index_generated_forwards.h \
+ seqan/index/shape_base.h \
+ seqan/index/shape_predefined.h \
+ seqan/index/index_manual_forwards.h \
+ seqan/index/shape_gapped.h \
+ seqan/index/index_find.h \
+ seqan/index/index_base.h
+
+SEQAN_SEQUENCE = \
+ seqan/sequence.h \
+ seqan/sequence/string_pointer.h \
+ seqan/sequence/sequence_forwards.h \
+ seqan/sequence/string_alloc.h \
+ seqan/sequence/string_base.h \
+ seqan/sequence/sequence_shortcuts.h \
+ seqan/sequence/sequence_generated_forwards.h \
+ seqan/sequence/sequence_multiple.h \
+ seqan/sequence/string_packed.h \
+ seqan/sequence/lexical.h \
+ seqan/sequence/string_value_expand.h \
+ seqan/sequence/std_string.h \
+ seqan/sequence/string_array.h \
+ seqan/sequence/segment_prefix.h \
+ seqan/sequence/segment_base.h \
+ seqan/sequence/segment_infix.h \
+ seqan/sequence/segment_suffix.h \
+ seqan/sequence/sequence_interface.h \
+ seqan/sequence/string_cstyle.h \
+ seqan/sequence/string_stack.h
+
+SEQAN_FILE = \
+ seqan/file.h \
+ seqan/file/file_format_fasta_align.h \
+ seqan/file/file_format_raw.h \
+ seqan/file/file_format.h \
+ seqan/file/file_format_guess.h \
+ seqan/file/cstream.h \
+ seqan/file/file_base.h \
+ seqan/file/file_format_fasta.h \
+ seqan/file/file_generated_forwards.h \
+ seqan/file/file_forwards.h \
+ seqan/file/file_array.h \
+ seqan/file/chunk_collector.h \
+ seqan/file/stream.h \
+ seqan/file/file_format_cgviz.h \
+ seqan/file/stream_algorithms.h \
+ seqan/file/meta.h
+
+SEQAN_FIND = \
+ seqan/find.h \
+ seqan/find/find_score.h \
+ seqan/find/find_set_horspool.h \
+ seqan/find/find_generated_forwards.h \
+ seqan/find/find_base.h \
+ seqan/find/find_multi.h \
+ seqan/find/find_horspool.h \
+ seqan/find/find_multiple_shiftand.h
+
+SEQAN_BASIC = \
+ seqan/basic.h \
+ seqan/basic/basic_operator.h \
+ seqan/basic/basic_allocator_multipool.h \
+ seqan/basic/basic_compare.h \
+ seqan/basic/basic_allocator_singlepool.h \
+ seqan/basic/basic_allocator_to_std.h \
+ seqan/basic/basic_alphabet_interface2.h \
+ seqan/basic/basic_pointer.h \
+ seqan/basic/basic_alphabet_simple_tabs.h \
+ seqan/basic/basic_iterator.h \
+ seqan/basic/basic_converter.h \
+ seqan/basic/basic_alphabet_interface.h \
+ seqan/basic/basic_metaprogramming.h \
+ seqan/basic/basic_profile.h \
+ seqan/basic/basic_proxy.h \
+ seqan/basic/basic_alphabet_trait_basic.h \
+ seqan/basic/basic_allocator_simple.h \
+ seqan/basic/basic_alphabet_simple.h \
+ seqan/basic/basic_host.h \
+ seqan/basic/basic_counted_ptr.h \
+ seqan/basic/basic_allocator_interface.h \
+ seqan/basic/basic_iterator_position.h \
+ seqan/basic/basic_iterator_adaptor.h \
+ seqan/basic/basic_iterator_adapt_std.h \
+ seqan/basic/basic_iterator_simple.h \
+ seqan/basic/basic_forwards.h \
+ seqan/basic/basic_debug.h \
+ seqan/basic/basic_generated_forwards.h \
+ seqan/basic/basic_transport.h \
+ seqan/basic/basic_type.h \
+ seqan/basic/basic_holder.h \
+ seqan/basic/basic_aggregates.h \
+ seqan/basic/basic_definition.h \
+ seqan/basic/basic_volatile_ptr.h \
+ seqan/basic/basic_iterator_base.h \
+ seqan/basic/basic_tag.h
+
+SEQAN = \
+ seqan/platform.h \
+ $(SEQAN_INDEX) \
+ $(SEQAN_SEQUENCE) \
+ $(SEQAN_FILE) \
+ $(SEQAN_FIND) \
+ $(SEQAN_BASIC)
+
+noinst_LIBRARIES = libSSA.a
+libSSA_a_SOURCES = \
+ basic.h \
+ bitarray.cpp bitarray.h \
+ bitrankw32int.cpp bitrankw32int.h \
+ chrPosition.cpp chrPosition.h \
+ HuffAlphabetRank.cpp HuffAlphabetRank.h \
+ Huffman_Codes.cpp Huffman_Codes.h \
+ locateOnGenome.cpp locateOnGenome.h \
+ locateTags.cpp locateTags.h \
+ SSA.cpp SSA.h \
+ utils.cpp utils.h \
+ GenomeInfo.cpp GenomeInfo.h \
+ $(SEQAN) $(KARKKAINEN_BWT) $(KSEQ)
+
+MOSTLYCLEANFILES=*~
+CLEANFILES=*~ $(EXTRA_PROGRAMS)
+DISTCLEANFILES=*~
+MAINTAINERCLEANFILES=*~
diff --git a/src/libSSA/Makefile.in b/src/libSSA/Makefile.in
new file mode 100644
index 0000000..06dcc02
--- /dev/null
+++ b/src/libSSA/Makefile.in
@@ -0,0 +1,804 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+
+VPATH = @srcdir@
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+LDADD = libSSA.a
+KARKKAINEN_BWT = \
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+ karkkainen_bwt/zbox.h \
+ karkkainen_bwt/assert_helpers.h \
+ karkkainen_bwt/random_source.h \
+ karkkainen_bwt/binary_sa_search.h \
+ karkkainen_bwt/multikey_qsort.h \
+ karkkainen_bwt/auto_array.h \
+ karkkainen_bwt/diff_sample.h \
+ karkkainen_bwt/alphabet.h \
+ karkkainen_bwt/timer.h
+
+SEQAN_INDEX = \
+ seqan/index.h \
+ seqan/index/index_qgram_find.h \
+ seqan/index/index_sa_lss.h \
+ seqan/index/index_generated_forwards.h \
+ seqan/index/shape_base.h \
+ seqan/index/shape_predefined.h \
+ seqan/index/index_manual_forwards.h \
+ seqan/index/shape_gapped.h \
+ seqan/index/index_find.h \
+ seqan/index/index_base.h
+
+SEQAN_SEQUENCE = \
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+ seqan/sequence/string_pointer.h \
+ seqan/sequence/sequence_forwards.h \
+ seqan/sequence/string_alloc.h \
+ seqan/sequence/string_base.h \
+ seqan/sequence/sequence_shortcuts.h \
+ seqan/sequence/sequence_generated_forwards.h \
+ seqan/sequence/sequence_multiple.h \
+ seqan/sequence/string_packed.h \
+ seqan/sequence/lexical.h \
+ seqan/sequence/string_value_expand.h \
+ seqan/sequence/std_string.h \
+ seqan/sequence/string_array.h \
+ seqan/sequence/segment_prefix.h \
+ seqan/sequence/segment_base.h \
+ seqan/sequence/segment_infix.h \
+ seqan/sequence/segment_suffix.h \
+ seqan/sequence/sequence_interface.h \
+ seqan/sequence/string_cstyle.h \
+ seqan/sequence/string_stack.h
+
+SEQAN_FILE = \
+ seqan/file.h \
+ seqan/file/file_format_fasta_align.h \
+ seqan/file/file_format_raw.h \
+ seqan/file/file_format.h \
+ seqan/file/file_format_guess.h \
+ seqan/file/cstream.h \
+ seqan/file/file_base.h \
+ seqan/file/file_format_fasta.h \
+ seqan/file/file_generated_forwards.h \
+ seqan/file/file_forwards.h \
+ seqan/file/file_array.h \
+ seqan/file/chunk_collector.h \
+ seqan/file/stream.h \
+ seqan/file/file_format_cgviz.h \
+ seqan/file/stream_algorithms.h \
+ seqan/file/meta.h
+
+SEQAN_FIND = \
+ seqan/find.h \
+ seqan/find/find_score.h \
+ seqan/find/find_set_horspool.h \
+ seqan/find/find_generated_forwards.h \
+ seqan/find/find_base.h \
+ seqan/find/find_multi.h \
+ seqan/find/find_horspool.h \
+ seqan/find/find_multiple_shiftand.h
+
+SEQAN_BASIC = \
+ seqan/basic.h \
+ seqan/basic/basic_operator.h \
+ seqan/basic/basic_allocator_multipool.h \
+ seqan/basic/basic_compare.h \
+ seqan/basic/basic_allocator_singlepool.h \
+ seqan/basic/basic_allocator_to_std.h \
+ seqan/basic/basic_alphabet_interface2.h \
+ seqan/basic/basic_pointer.h \
+ seqan/basic/basic_alphabet_simple_tabs.h \
+ seqan/basic/basic_iterator.h \
+ seqan/basic/basic_converter.h \
+ seqan/basic/basic_alphabet_interface.h \
+ seqan/basic/basic_metaprogramming.h \
+ seqan/basic/basic_profile.h \
+ seqan/basic/basic_proxy.h \
+ seqan/basic/basic_alphabet_trait_basic.h \
+ seqan/basic/basic_allocator_simple.h \
+ seqan/basic/basic_alphabet_simple.h \
+ seqan/basic/basic_host.h \
+ seqan/basic/basic_counted_ptr.h \
+ seqan/basic/basic_allocator_interface.h \
+ seqan/basic/basic_iterator_position.h \
+ seqan/basic/basic_iterator_adaptor.h \
+ seqan/basic/basic_iterator_adapt_std.h \
+ seqan/basic/basic_iterator_simple.h \
+ seqan/basic/basic_forwards.h \
+ seqan/basic/basic_debug.h \
+ seqan/basic/basic_generated_forwards.h \
+ seqan/basic/basic_transport.h \
+ seqan/basic/basic_type.h \
+ seqan/basic/basic_holder.h \
+ seqan/basic/basic_aggregates.h \
+ seqan/basic/basic_definition.h \
+ seqan/basic/basic_volatile_ptr.h \
+ seqan/basic/basic_iterator_base.h \
+ seqan/basic/basic_tag.h
+
+SEQAN = \
+ seqan/platform.h \
+ $(SEQAN_INDEX) \
+ $(SEQAN_SEQUENCE) \
+ $(SEQAN_FILE) \
+ $(SEQAN_FIND) \
+ $(SEQAN_BASIC)
+
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+ bitrankw32int.cpp bitrankw32int.h \
+ chrPosition.cpp chrPosition.h \
+ HuffAlphabetRank.cpp HuffAlphabetRank.h \
+ Huffman_Codes.cpp Huffman_Codes.h \
+ locateOnGenome.cpp locateOnGenome.h \
+ locateTags.cpp locateTags.h \
+ SSA.cpp SSA.h \
+ utils.cpp utils.h \
+ GenomeInfo.cpp GenomeInfo.h \
+ $(SEQAN) $(KARKKAINEN_BWT) $(KSEQ)
+
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+DISTCLEANFILES = *~
+MAINTAINERCLEANFILES = *~
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+
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+ $(libSSA_a_AR) libSSA.a $(libSSA_a_OBJECTS) $(libSSA_a_LIBADD)
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+ test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
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+ sed 's/$(EXEEXT)$$//' | \
+ while read p p1; do if test -f $$p || test -f $$p1; \
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+ sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
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+ sed 'N;N;N;s,\n, ,g' | \
+ $(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
+ { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
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+ END { for (d in files) print "f", d, files[d] }' | \
+ while read type dir files; do \
+ if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
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+clean-binPROGRAMS:
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+ echo " rm -f" $$list; \
+ rm -f $$list || exit $$?; \
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+ list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
+ echo " rm -f" $$list; \
+ rm -f $$list
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+ @rm -f crac-index$(EXEEXT)
+ $(CXXLINK) $(crac_index_OBJECTS) $(crac_index_LDADD) $(LIBS)
+
+mostlyclean-compile:
+ -rm -f *.$(OBJEXT)
+
+distclean-compile:
+ -rm -f *.tab.c
+
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/GenomeInfo.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/HuffAlphabetRank.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/Huffman_Codes.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/SSA.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/bitarray.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/bitrankw32int.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/chrPosition.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cracIndex.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/locateOnGenome.Po at am__quote@
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+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/utils.Po at am__quote@
+
+.cpp.o:
+ at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+
+.cpp.obj:
+ at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+
+.cpp.lo:
+ at am__fastdepCXX_TRUE@ $(LTCXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Plo
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=yes @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(LTCXXCOMPILE) -c -o $@ $<
+
+mostlyclean-libtool:
+ -rm -f *.lo
+
+clean-libtool:
+ -rm -rf .libs _libs
+
+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in files) print i; }; }'`; \
+ mkid -fID $$unique
+tags: TAGS
+
+TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
+ $(TAGS_FILES) $(LISP)
+ set x; \
+ here=`pwd`; \
+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in files) print i; }; }'`; \
+ shift; \
+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
+ test -n "$$unique" || unique=$$empty_fix; \
+ if test $$# -gt 0; then \
+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+ "$$@" $$unique; \
+ else \
+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+ $$unique; \
+ fi; \
+ fi
+ctags: CTAGS
+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
+ $(TAGS_FILES) $(LISP)
+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in files) print i; }; }'`; \
+ test -z "$(CTAGS_ARGS)$$unique" \
+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+ $$unique
+
+GTAGS:
+ here=`$(am__cd) $(top_builddir) && pwd` \
+ && $(am__cd) $(top_srcdir) \
+ && gtags -i $(GTAGS_ARGS) "$$here"
+
+distclean-tags:
+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(DISTFILES)
+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+ list='$(DISTFILES)'; \
+ dist_files=`for file in $$list; do echo $$file; done | \
+ sed -e "s|^$$srcdirstrip/||;t" \
+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+ case $$dist_files in \
+ */*) $(MKDIR_P) `echo "$$dist_files" | \
+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+ sort -u` ;; \
+ esac; \
+ for file in $$dist_files; do \
+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+ if test -d $$d/$$file; then \
+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test -d "$(distdir)/$$file"; then \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ fi; \
+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ fi; \
+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+ else \
+ test -f "$(distdir)/$$file" \
+ || cp -p $$d/$$file "$(distdir)/$$file" \
+ || exit 1; \
+ fi; \
+ done
+check-am: all-am
+check: check-am
+all-am: Makefile $(LIBRARIES) $(PROGRAMS)
+installdirs:
+ for dir in "$(DESTDIR)$(bindir)"; do \
+ test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+ done
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+ `test -z '$(STRIP)' || \
+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+ -test -z "$(MOSTLYCLEANFILES)" || rm -f $(MOSTLYCLEANFILES)
+
+clean-generic:
+ -test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+ -test -z "$(DISTCLEANFILES)" || rm -f $(DISTCLEANFILES)
+
+maintainer-clean-generic:
+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+ -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
+clean: clean-am
+
+clean-am: clean-binPROGRAMS clean-generic clean-libtool \
+ clean-noinstLIBRARIES mostlyclean-am
+
+distclean: distclean-am
+ -rm -rf ./$(DEPDIR)
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+distclean-am: clean-am distclean-compile distclean-generic \
+ distclean-tags
+
+dvi: dvi-am
+
+dvi-am:
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+html: html-am
+
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+ mostlyclean-libtool
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+.MAKE: install-am install-strip
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+.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
+ clean-generic clean-libtool clean-noinstLIBRARIES ctags \
+ distclean distclean-compile distclean-generic \
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+ html-am info info-am install install-am install-binPROGRAMS \
+ install-data install-data-am install-dvi install-dvi-am \
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+ install-pdf-am install-ps install-ps-am install-strip \
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+ maintainer-clean-generic mostlyclean mostlyclean-compile \
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+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/src/libSSA/SSA.cpp b/src/libSSA/SSA.cpp
new file mode 100644
index 0000000..057bae2
--- /dev/null
+++ b/src/libSSA/SSA.cpp
@@ -0,0 +1,685 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <cmath>
+#include <cstdlib>
+#include <cstdio>
+#include <sys/types.h>
+#include <sys/times.h>
+#include <cassert>
+#include <cstring>
+#include <stdint.h>
+#include "SSA.h"
+#include "utils.h"
+//---------------------------------------------------------------------------
+
+/* Three function to variables to manage parameters */
+static bool is_delimeter(char *delimiters, char c) {
+ int i=0,len_delimiters=strlen(delimiters);
+ bool is=false;
+ for (i=0;i<len_delimiters;i++)
+ if (c == delimiters[i]) is=true;
+ return is;
+}
+
+static void parse_parameters(char *options, int *num_parameters, char ***parameters, char *delimiters) {
+ int i=0,j=0,temp=0,num=0, len_options=strlen(options);
+ char *options_temp;
+ while (i<len_options) {
+ while ((i<len_options) && is_delimeter(delimiters,options[i])) i++;
+ temp=i;
+ while ((i<len_options) && !is_delimeter(delimiters,options[i])) i++;
+ if (i!=temp) num++;
+ }
+ (*parameters) = (char **) malloc(num*sizeof(char * ));
+ i=0;
+ while (i<len_options) {
+ while ((i<len_options) && is_delimeter(delimiters,options[i])) i++;
+ temp=i;
+ while ((i<len_options) && !is_delimeter(delimiters,options[i])) i++;
+ if (i!=temp) {
+ (*parameters)[j]=(char *) malloc((i-temp+1)*sizeof(char));
+ options_temp = options+temp;
+ strncpy((*parameters)[j], options_temp, i-temp);
+ ((*parameters)[j])[i-temp] = '\0';
+ j++;
+ }
+ }
+ *num_parameters = num;
+}
+
+static void free_parameters(int num_parameters,char ***parameters) {
+ int i=0;
+ for (i=0; i<num_parameters;i++)
+ free((*parameters)[i]);
+ free((*parameters));
+}
+
+void swap(ulong *pos, ulong i, ulong j) {
+ ulong tmp = pos[i];
+ pos[i] = pos[j];
+ pos[j] = tmp;
+}
+
+int compare (const void * a, const void * b)
+{
+ if (*(ulong *)a < *(ulong *)b)
+ return -1;
+ else if (*(ulong *)a == *(ulong *)b)
+ return 0;
+ else
+ return 1;
+}
+
+
+void sortPositions(ulong *pos, ulong *suffixes, ulong length, ulong mult) {
+ memcpy(suffixes, pos, length*sizeof(ulong));
+ qsort(suffixes, length, sizeof(ulong), compare);
+
+ ulong min, max;
+ ulong index;
+ bool found;
+ uint *ranks = new uint[length];
+ for (ulong i =0; i < length ; i++) {
+ min = 0;
+ max = length-1;
+ found = false;
+ // cerr << i << " (searching "<<pos[i]<<")"<< endl;
+ while (! found) {
+ index = (min+max)/2;
+ if (pos[i] < suffixes[index]) {
+ max = index-1;
+ } else if (pos[i] > suffixes[index]) {
+ min = index+1;
+ } else {
+ found = true;
+ }
+ }
+ ranks[index] = i;
+ }
+
+ for (ulong i = 0; i < length; i++) {
+ suffixes[i] = ranks[i]*mult;
+ }
+ delete [] ranks;
+
+
+}
+
+/**********************************************************************************************************
+ * succinct full-text index *
+ **********************************************************************************************************/
+
+
+TFMindex::TFMindex(uchar *bwt, ulong length, ulong samplerate, bool free_text,ulong factor, int *error, uchar terminator) {
+ this->n = length;
+ this->samplerate = samplerate;
+ // uchar *bwt = BWT(text,free_text,factor);
+
+ if (bwt == NULL) *error = 1;
+ uint terminator_pos = 0;
+ map0 = terminator;
+ // caller can delete text now
+ ulong i;
+ for (i=0;i<size_uchar+1;i++)
+ C[i]=0;
+ for (i=0;i<n;++i) {
+ if (bwt[i] == terminator) {
+ terminator_pos = i;
+ }
+ C[bwt[i]]++;
+ }
+ ulong prev=C[0], temp;
+ C[0]=0;
+ for (i=1;i<size_uchar+1;i++) {
+ temp = C[i];
+ C[i]=C[i-1]+prev;
+ prev = temp;
+ }
+ codetable = makecodetable(bwt,n);
+
+
+ // for (uint i = 0; i < size_uchar; i++) {
+ // cout << (uchar)i << " " << codetable[i].code << " " << codetable[i].bits << endl;
+ // }
+ alphabetrank = new THuffAlphabetRank(bwt,n,codetable,0,factor);
+
+ // Computing the position in F where the terminator is.
+ terminator_pos = C[alphabetrank->charAtPos(terminator_pos)] + alphabetrank->rank(alphabetrank->charAtPos(terminator_pos), terminator_pos)-1;
+
+ ulong *sampledpositions = (ulong *)calloc(this->n/W+1, sizeof(ulong));
+ this->suffixes = new ulong[(this->n-1)/samplerate+1];
+ this->positions = new ulong[(this->n-1)/samplerate+2];
+ for (i=0;i<this->n/W+1;i++)
+ sampledpositions[i]=0u;
+ ulong sa_value = this->n-1;
+ ulong pos = terminator_pos;
+
+ for (i=0;i<this->n;i++) {
+ if (sa_value % samplerate == 0) {
+ SetField(sampledpositions,1,pos,1);
+ // this->suffixes[pos] = sa_value;
+ this->positions[sa_value/samplerate] = pos;
+ }
+ pos = C[alphabetrank->charAtPos(pos)] + alphabetrank->rank(alphabetrank->charAtPos(pos), pos)-1;
+ sa_value--;
+ }
+
+ sortPositions(positions,suffixes,(this->n-1)/samplerate+1, samplerate);
+ positions[(this->n-1)/samplerate+1] = positions[0];
+
+ this->sampled = new BitRankW32Int(sampledpositions,this->n,true,factor);
+ // delete [] bwt;
+ *error=0;
+}
+
+ulong TFMindex::count(uchar *pattern, ulong m) {
+ // use the FM-search replacing function Occ(c,1,i) with alphabetrank->rank(c,i)
+ ulong sp, ep;
+ getRange(pattern, m, sp, ep);
+ if (sp<=ep) {
+ return ep-sp+1;
+ } else {
+ return 0;
+ }
+}
+
+ulong TFMindex::countReverseComp(uchar *pattern, ulong m) {
+ ulong sp = 1;
+ ulong ep = get_length();
+ for (ulong i = 0; i < m && sp <= ep ; i++) {
+ iterCountReverseComp(pattern[i], sp, ep);
+ }
+ if (sp <= ep)
+ return ep - sp + 1;
+ return 0;
+}
+
+void TFMindex::getRange(uchar *pattern, ulong m, ulong &sp, ulong &ep) {
+ uchar *pat=pattern;
+ if (map0 != 0 )
+ pat = pattern0(pattern,m);
+ uchar c = pat[m-1]; ulong i=m-1;
+ sp = C[c];
+ ep = C[c+1]-1;
+ while (sp<=ep && i>=1) {
+ c = pat[--i];
+ // cout << "sp = " << sp <<", ep = " << ep << endl;
+ iterCount(c, sp, ep);
+ }
+ if (map0 != 0) free(pat);
+}
+
+void TFMindex::getReverseCompRange(uchar *pattern, ulong m, ulong &sp, ulong &ep) {
+ uchar c = complementDNA(pattern[0]);
+ sp = C[c];
+ ep = C[c+1]-1;
+ for (ulong i = 1; i < m && sp <= ep ; i++) {
+ iterCountReverseComp(pattern[i], sp, ep);
+ }
+}
+
+void TFMindex::iterCount(uchar c, ulong &sp, ulong &ep) {
+ sp = C[c]+ (sp == 0 ? 0 : alphabetrank->rank(c,sp-1));
+ ep = C[c]+alphabetrank->rank(c,ep);
+ // Before decrementing ep, make sure it is non-zero
+ if (ep > 0)
+ ep--;
+ else {
+ // ep should be negative (but we can't), meaning that we have an empty
+ // range. We modify sp so that we have an empty range (buurk!)
+ sp = 1;
+ }
+}
+
+void TFMindex::iterCountReverseComp(uchar c, ulong &sp, ulong &ep) {
+ uchar c2 = complementDNA(c);
+ iterCount(c2, sp, ep);
+}
+
+ulong TFMindex::locateReverseComp(uchar *pattern, ulong m, ulong **occ,ulong nb_displayed) {
+ ulong sp, ep;
+ getReverseCompRange(pattern, m, sp, ep);
+ if (sp <= ep)
+ return returnLocate(sp, ep, nb_displayed, occ);
+ else
+ return 0;
+}
+
+ulong TFMindex::returnLocate(ulong sp, ulong ep, ulong nb_displayed, ulong **occ, long m) {
+ ulong locate=0;
+ uchar c;
+ ulong i=sp, j;
+ ulong dist,rank_tmp;
+ *occ = (ulong *)malloc(sizeof(ulong)*(ep-sp+1));
+ while (i<=ep && locate < nb_displayed) {
+ j=i,dist=0;
+ while (!sampled->IsBitSet(j)) {
+ c = alphabetrank->charAtPos2(j,&rank_tmp);
+ j = C[c]+rank_tmp; // LF-mapping The rank_tmp is already decremented by 1
+ ++dist;
+ }
+ (*occ)[locate]=suffixes[sampled->rank(j)-1]+dist+m;
+ locate ++ ;
+ ++i;
+ }
+ return locate;
+}
+
+ulong TFMindex::locate(uchar *pattern, ulong m, ulong **occ,ulong nb_displayed) {
+ // use the FM-search replacing function Occ(c,1,i) with alphabetrank->rank(c,i)
+ ulong sp, ep, i;
+ uchar c;
+ getRange(pattern, m, sp, ep);
+ if (nb_displayed == 0)
+ nb_displayed = ep-sp+1;
+
+ if (sp<=ep) {
+ ulong matches = ep-sp+1;
+ ulong locate=0;
+ *occ = (ulong *) malloc(matches*sizeof(ulong));
+ i=sp;
+ ulong j,dist,rank_tmp;
+ while (i<=ep && locate < nb_displayed) {
+ j=i,dist=0;
+ while (!sampled->IsBitSet(j)) {
+ c = alphabetrank->charAtPos2(j,&rank_tmp);
+ j = C[c]+rank_tmp; // LF-mapping The rank_tmp is already decremented by 1
+ ++dist;
+ }
+ (*occ)[locate]=suffixes[sampled->rank(j)-1]+dist;
+ locate ++ ;
+ ++i;
+ }
+ return locate;
+ } else {
+ *occ = NULL;
+ return 0;
+ }
+}
+
+int TFMindex::display(uchar *pattern, ulong m, ulong numc, ulong *numocc, uchar **snippet_text, ulong **snippet_lengths, ulong **occ) {
+ // use the FM-search replacing function Occ(c,1,i) with alphabetrank->rank(c,i)
+ ulong sp, ep;
+ getRange(pattern, m, sp, ep);
+ uchar c; ulong i;
+ if (sp<=ep) {
+ (*numocc) = ep-sp+1;
+ ulong locate=0;
+ *occ = (ulong *) malloc((*numocc)*sizeof(ulong));
+ *snippet_lengths = (ulong *) malloc((*numocc)*sizeof(ulong));
+ *snippet_text = (uchar *) malloc((*numocc)*(m+2*numc)*sizeof(uchar));
+ uchar *text_aux=*snippet_text;
+
+ i=sp;
+ ulong j,dist,x,rank_tmp;
+ while (i<=ep) {
+ j=i,dist=0;
+ while (!sampled->IsBitSet(j)) {
+ c = alphabetrank->charAtPos2(j,&rank_tmp);
+ j = C[c]+rank_tmp; // LF-mapping The rank_tmp is already decremented by 1
+ ++dist;
+ }
+ x = suffixes[sampled->rank(j)-1]+dist;
+ (*occ)[locate]= x;
+ ulong from;
+ if (x>numc) from = x-numc;
+ else from=0;
+ ulong to=min(x+m+numc-1,n-2); // n-1 is '\0'
+ ulong len =to-from+1;
+ ulong skip;
+ ulong j = positions[to/samplerate+1];
+ if ((to/samplerate+1) == ((n-1)/samplerate+1))
+ skip = n-1 - to;
+ else
+ skip = samplerate-to%samplerate-1;
+ for (ulong dist=0;dist<skip+len;dist++) {
+ c = alphabetrank->charAtPos2(j,&rank_tmp);
+ j = C[c]+rank_tmp; // LF-mapping The rank_tmp is already decremented by 1
+ if (dist>= skip) {
+ if (c == map0)
+ text_aux[len-dist-1+skip]='\0';
+ else
+ text_aux[len-dist-1+skip]=c;
+ }
+ }
+ (*snippet_lengths)[locate]=len;
+ text_aux+=m+2*numc;
+
+ locate ++ ;
+ i++;
+ }
+ } else {
+ *snippet_lengths = NULL;
+ *snippet_text = NULL;
+ *occ = NULL;
+ (*numocc) = 0;
+ }
+ return 0;
+}
+
+ulong TFMindex::get_length () {
+ return n-1;
+}
+
+TFMindex::~TFMindex() {
+ delete alphabetrank;
+ delete sampled;
+ delete [] codetable;
+ delete [] suffixes;
+ delete [] positions;
+}
+
+ulong TFMindex::SpaceRequirement(){
+ return sizeof(TFMindex)+alphabetrank->SpaceRequirementInBits()/8+
+ sampled->SpaceRequirementInBits()/8+sizeof(codetable)*size_uchar+
+ ((this->n-1)/samplerate+1)*2*sizeof(ulong);
+}
+
+ulong TFMindex::SpaceRequirement_locate(){
+ return sizeof(TFMindex)+alphabetrank->SpaceRequirementInBits()/8+
+ sampled->SpaceRequirementInBits()/8+sizeof(codetable)*size_uchar+
+ ((this->n-1)/samplerate+1)*sizeof(ulong);
+}
+
+ulong TFMindex::SpaceRequirement_count(){
+ return sizeof(TFMindex)+alphabetrank->SpaceRequirementInBits()/8+
+ sizeof(codetable)*size_uchar;
+}
+
+int TFMindex::extract(ulong from, ulong to, uchar **snippet) {
+ if (to> n) to=n-2; // n-1 is '\0'
+ if (from > to) {
+ *snippet = NULL;
+ return 0;
+ }
+ ulong len =to-from+1;
+ *snippet = (uchar *) malloc((len+1)*sizeof(uchar));
+ (*snippet)[len] = 0;
+ uchar c;
+ ulong skip,rank_tmp;
+ ulong j = positions[to/samplerate+1];
+ if ((to/samplerate+1) == ((n-1)/samplerate+1))
+ skip = n-1 - to;
+ else
+ skip = samplerate-to%samplerate-1;
+ for (ulong dist=0;dist<skip+len;dist++) {
+ c = alphabetrank->charAtPos2(j,&rank_tmp);
+ j = C[c]+rank_tmp; // LF-mapping The rank_tmp is already decremented by 1
+ if (dist>= skip) {
+ if (c == map0)
+ (*snippet)[len-dist-1+skip]='\0';
+ else
+ (*snippet)[len-dist-1+skip]=c;
+ }
+ }
+ return len;
+}
+
+int TFMindex::save(char *filename) {
+ char fnamext[1024];
+ FILE *f;
+ sprintf (fnamext,"%s.ssa",filename);
+ f = fopen (fnamext,"w");
+ if (f == NULL) return 20;
+ if (fwrite (&n,sizeof(ulong),1,f) != 1) return 21;
+ if (fwrite (&samplerate,sizeof(ulong),1,f) != 1) return 21;
+ if (fwrite (&map0,sizeof(uchar),1,f) != 1) return 21;
+ if (fwrite (C,sizeof(ulong),size_uchar+1,f) != size_uchar+1) return 21;
+ if (save_codetable(f,codetable) !=0) return 21;
+ if (alphabetrank->save(f) !=0) return 21;
+ if (sampled->save(f) !=0) return 21;
+ if (fwrite (suffixes,sizeof(ulong),(this->n-1)/samplerate+1,f) != (this->n-1)/samplerate+1) return 21;
+ if (fwrite (positions,sizeof(ulong),(this->n-1)/samplerate+2,f) != (this->n-1)/samplerate+2) return 21;
+ fclose(f);
+ return 0;
+}
+
+int TFMindex::load(char *filename) {
+ char fnamext[1024];
+ FILE *f;
+ int error;
+ sprintf (fnamext,"%s.ssa",filename);
+ f = fopen (fnamext,"r");
+ if (f == NULL) return 23;
+ if (fread (&n,sizeof(ulong),1,f) != 1) return 25;
+ if (fread (&samplerate,sizeof(ulong),1,f) != 1) return 25;
+ if (fread (&map0,sizeof(uchar),1,f) != 1) return 25;
+ if (fread (C,sizeof(ulong),size_uchar+1,f) != size_uchar+1) return 25;
+ if (load_codetable(f,&codetable) !=0) return 25;
+ alphabetrank = new THuffAlphabetRank(f,codetable,&error);
+ if (error !=0) return error;
+ sampled = new BitRankW32Int(f,&error);
+ if (error !=0) return error;
+ this->suffixes = new ulong[(this->n-1)/samplerate+1];
+ if (!this->suffixes) return 1;
+ if (fread (suffixes,sizeof(ulong),(this->n-1)/samplerate+1,f) != (this->n-1)/samplerate+1) return 25;
+ this->positions = new ulong[(this->n-1)/samplerate+2];
+ if (!this->positions) return 1;
+ if (fread (positions,sizeof(ulong),(this->n-1)/samplerate+2,f) != (this->n-1)/samplerate+2) return 25;
+ fclose(f);
+ return 0;
+}
+
+TFMindex::TFMindex(char *filename, int *error) {
+ *error = load(filename);
+}
+
+////////////////////////
+////Building the Index//
+////////////////////////
+int build_index(uchar *text, ulong length, char *build_options, void **index){
+ ulong samplerate=64;
+ ulong factor=4;
+ int error;
+ char delimiters[] = " =;";
+ int j,num_parameters;
+ char ** parameters;
+ int free_text=false; /* don't free text by default */
+ uchar terminator = 0;
+
+ if (build_options != NULL) {
+ parse_parameters(build_options,&num_parameters, ¶meters, delimiters);
+ for (j=0; j<num_parameters;j++) {
+ if ((strcmp(parameters[j], "samplerate") == 0 ) && (j < num_parameters-1) ) {
+ samplerate=atoi(parameters[j+1]);
+ j++;
+ } else if ((strcmp(parameters[j], "factor") == 0 ) && (j < num_parameters-1) ) {
+ factor=atoi(parameters[j+1]);
+ j++;
+ } else if (strcmp(parameters[j], "free_text") == 0 )
+ free_text=true;
+ else if (strcmp(parameters[j], "terminator") == 0 && (j < num_parameters - 1))
+ terminator = parameters[j+1][0];
+ }
+ free_parameters(num_parameters, ¶meters);
+ }
+ TFMindex *FMindex = new TFMindex(text,length,samplerate,free_text,factor,&error, terminator);
+ (*index) = FMindex;
+ if (error != 0) return error;
+ return 0;
+}
+int save_index(void *index, char *filename) {
+ TFMindex *_index=(TFMindex *) index;
+ return _index->save(filename);
+}
+int load_index(char *filename, void **index){
+ int error;
+ TFMindex *FMindex = new TFMindex(filename, &error);
+ (*index) = FMindex;
+ return error;
+}
+
+int free_index(void *index){
+ TFMindex *_index=(TFMindex *) index;
+ delete _index;
+ return 0;
+}
+
+int index_size(void *index, ulong *size) {
+ TFMindex *_index=(TFMindex *) index;
+ (*size) = _index->SpaceRequirement();
+ return 0;
+}
+int index_size_count(void *index, ulong *size) {
+ TFMindex *_index=(TFMindex *) index;
+ (*size) = _index->SpaceRequirement_count();
+ return 0;
+}
+int index_size_locate(void *index, ulong *size) {
+ TFMindex *_index=(TFMindex *) index;
+ (*size) = _index->SpaceRequirement_locate();
+ return 0;
+}
+////////////////////////
+////Querying the Index//
+////////////////////////
+int count(void *index, uchar *pattern, ulong length, ulong *numocc){
+ TFMindex *_index=(TFMindex *) index;
+ (*numocc)= _index->count(pattern,length);
+ return 0;
+}
+int locate(void *index, uchar *pattern, ulong length, ulong **occ, ulong *numocc, ulong nb_displayed){
+ TFMindex *_index=(TFMindex *) index;
+ (*numocc)= _index->locate(pattern,length,occ, nb_displayed);
+ return 0;
+}
+/////////////////////////
+//Accessing the indexed//
+/////////////////////////
+int extract(void *index, ulong from, ulong to, uchar **snippet, ulong *snippet_length){
+ TFMindex *_index=(TFMindex *) index;
+ (*snippet_length)= _index->extract(from,to, snippet);
+ return 0 ;
+}
+int display(void *index, uchar *pattern, ulong length, ulong numc, ulong *numocc, uchar **snippet_text, ulong **snippet_lengths) {
+ TFMindex *_index=(TFMindex *) index;
+ ulong *occ;
+ int aux = _index->display(pattern, length, numc, numocc, snippet_text, snippet_lengths, &occ);
+ free(occ);
+ return aux;
+}
+int get_length(void *index, ulong *length){
+ TFMindex *_index=(TFMindex *) index;
+ (*length)=(_index)->get_length();
+ return 0;
+}
+////////////////////
+////Error handling//
+////////////////////
+const char *error_index(int e){
+ switch(e) {
+ case 0: return "No error";
+ case 1: return "Out of memory";
+ case 2: return "The text must end with a \\0";
+ case 5: return "You can't free the text if you don't copy it";
+ case 20: return "Cannot create files";
+ case 21: return "Error writing the index";
+ case 22: return "Error writing the index";
+ case 23: return "Cannot open index";
+ case 24: return "Cannot open text";
+ case 25: return "Error reading the index";
+ case 26: return "Error reading the index";
+ case 27: return "Error reading the text";
+ case 28: return "Error reading the text";
+ case 99: return "Not implemented";
+ default: return "Unknown error";
+ }
+}
+
diff --git a/src/libSSA/SSA.h b/src/libSSA/SSA.h
new file mode 100644
index 0000000..8851a60
--- /dev/null
+++ b/src/libSSA/SSA.h
@@ -0,0 +1,214 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef SSA_H
+#define SSA_H
+#include "HuffAlphabetRank.h"
+#include "basic.h"
+#include "bitarray.h"
+#include "Huffman_Codes.h"
+
+class TFMindex {
+ private:
+ ulong n;
+ ulong samplerate;
+ ulong C[size_uchar+1];
+ TCodeEntry *codetable;
+ THuffAlphabetRank *alphabetrank;
+ BitRankW32Int *sampled;
+ ulong *suffixes;
+ ulong *positions;
+ uchar map0;
+ int remap0(uchar *text, ulong n) {
+ int i;
+ ulong j;
+ ulong Freq_old[size_uchar];
+ for(i=0;i<size_uchar;i++)
+ Freq_old[i]=0;
+ for(j=0;j<n;j++) {
+ Freq_old[text[j]]++;
+ }
+ i=-1;
+ // remap alphabet
+ if (Freq_old[0]==0) return 0; //test if some character of T is zero
+ for(j=1;j<size_uchar;j++)
+ if(Freq_old[j]==0) {
+ i=j;
+ break;
+ }
+ if (i == -1 ) return i;
+ // remap text
+ for(j=0;j<n;j++)
+ if (text[j] == 0) text[j] = i;
+ return i;
+ }
+ uchar *pattern0(uchar *pattern, ulong m) {
+ uchar *pat0;
+ pat0 = (uchar *) malloc (sizeof(uchar)*m);
+ for (ulong j=0;j<m;j++) {
+ if (pattern[j] == 0) pat0[j]=map0;
+ else pat0[j]=pattern[j];
+ }
+ return pat0;
+ }
+public:
+
+ TFMindex(uchar *bwt, ulong length, ulong samplerate, bool free_text,ulong factor, int *error, uchar terminator=0);
+
+ ulong count(uchar *pattern, ulong m);
+ ulong countReverseComp(uchar *pattern, ulong m);
+
+ void getRange(uchar *pattern, ulong m, ulong &sp, ulong &ep);
+ void getReverseCompRange(uchar *pattern, ulong m, ulong &sp, ulong &ep);
+
+ void iterCount(uchar c, ulong &sp, ulong &ep);
+ void iterCountReverseComp(uchar c, ulong &sp, ulong &ep);
+
+ ulong returnLocate(ulong sp, ulong ep, ulong nb_displayed, ulong **occ, long m=0);
+
+ ulong locate(uchar *pattern, ulong m, ulong **occ, ulong nb_displayed=0);
+ ulong locateReverseComp(uchar *pattern, ulong m, ulong **occ,ulong nb_displayed=0);
+
+ int display(uchar *pattern, ulong m, ulong numc, ulong *numocc, uchar **snippet_text, ulong **snippet_lengths, ulong **occ);
+
+ ulong get_length ();
+
+ ~TFMindex() ;
+
+ ulong SpaceRequirement();
+
+ ulong SpaceRequirement_locate();
+
+ ulong SpaceRequirement_count();
+
+ int extract(ulong from, ulong to, uchar **snippet);
+
+ int save(char *filename);
+
+ int load(char *filename);
+
+ TFMindex(char *filename, int *error);
+};
+
+
+int build_index(uchar *text, ulong length, char *build_options, void **index);
+int save_index(void *index, char *filename);
+int load_index(char *filename, void **index);
+int free_index(void *index);
+int index_size(void *index, ulong *size);
+int index_size_count(void *index, ulong *size);
+int index_size_locate(void *index, ulong *size);
+////////////////////////
+////Querying the Index//
+////////////////////////
+int count(void *index, uchar *pattern, ulong length, ulong *numocc);
+int locate(void *index, uchar *pattern, ulong length, ulong **occ, ulong *numocc, ulong nb_displayed=0);
+/////////////////////////
+//Accessing the indexed//
+/////////////////////////
+int extract(void *index, ulong from, ulong to, uchar **snippet, ulong *snippet_length);
+int display(void *index, uchar *pattern, ulong length, ulong numc, ulong *numocc, uchar **snippet_text, ulong **snippet_lengths);
+
+int get_length(void *index, ulong *length);
+////////////////////
+////Error handling//
+////////////////////
+const char *error_index(int e);
+
+#endif
diff --git a/src/libSSA/basic.h b/src/libSSA/basic.h
new file mode 100644
index 0000000..2489d89
--- /dev/null
+++ b/src/libSSA/basic.h
@@ -0,0 +1,243 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef BASICSINCLUDED
+#define BASICSINCLUDED
+
+#include <sys/types.h>
+#include <sys/resource.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#define mask31 0x0000001F
+
+
+/*numero de bits del entero de la maquina*/
+#define W 32
+/* W-1 */
+#define Wminusone 31
+/*numero de bits del entero de la maquina*/
+#define WW 64
+/*bits para hacer la mascara para contar mas rapido*/
+#define bitsM 8
+/*bytes que hacen una palabra */
+#define BW 4
+#define ulong uint
+typedef unsigned char uchar;
+typedef u_int8_t byte;
+#define size_uchar 256
+
+
+typedef struct t_stack_element {
+ void *node;
+ byte counter;
+ ulong sp, ep;
+ unsigned char *str;
+ ulong n;
+} stack_element;
+
+
+const unsigned char __popcount_tab[] =
+{
+0,1,1,2,1,2,2,3,1,2,2,3,2,3,3,4,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,
+1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,
+1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,
+2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,
+1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,
+2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,
+2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,
+3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,4,5,5,6,5,6,6,7,5,6,6,7,6,7,7,8,
+};
+
+const unsigned char select_tab[] =
+{
+0,1,2,1,3,1,2,1,4,1,2,1,3,1,2,1,5,1,2,1,3,1,2,1,4,1,2,1,3,1,2,1,
+6,1,2,1,3,1,2,1,4,1,2,1,3,1,2,1,5,1,2,1,3,1,2,1,4,1,2,1,3,1,2,1,
+7,1,2,1,3,1,2,1,4,1,2,1,3,1,2,1,5,1,2,1,3,1,2,1,4,1,2,1,3,1,2,1,
+6,1,2,1,3,1,2,1,4,1,2,1,3,1,2,1,5,1,2,1,3,1,2,1,4,1,2,1,3,1,2,1,
+8,1,2,1,3,1,2,1,4,1,2,1,3,1,2,1,5,1,2,1,3,1,2,1,4,1,2,1,3,1,2,1,
+6,1,2,1,3,1,2,1,4,1,2,1,3,1,2,1,5,1,2,1,3,1,2,1,4,1,2,1,3,1,2,1,
+7,1,2,1,3,1,2,1,4,1,2,1,3,1,2,1,5,1,2,1,3,1,2,1,4,1,2,1,3,1,2,1,
+6,1,2,1,3,1,2,1,4,1,2,1,3,1,2,1,5,1,2,1,3,1,2,1,4,1,2,1,3,1,2,1,
+};
+
+
+/* bits needed to represent a number between 0 and n */
+inline uint bits (uint n){
+ uint b = 0;
+ while (n) { b++; n >>= 1; }
+ return b;
+}
+
+/* reads bit p from e */
+#define bitget(e,p) ((((e)[(p)/W] >> ((p)%W))) & 1)
+/* sets bit p in e */
+#define bitset(e,p) ((e)[(p)/W] |= (1<<((p)%W)))
+/* cleans bit p in e */
+#define bitclean(e,p) ((e)[(p)/W] &= ~(1<<((p)%W)))
+
+/* numero de enteros necesarios para representar e elementos de largo n */
+#define enteros(e,n) ((e)*(n))/W+(((e)*(n))%W > 0)
+
+inline ulong GetField(ulong *A, register ulong len, register ulong index) {
+ register ulong i=index*len/W, j=index*len-W*i, result;
+ if (j+len <= W)
+ result = (A[i] << (W-j-len)) >> (W-len);
+ else {
+ result = A[i] >> j;
+ result = result | (A[i+1] << (WW-j-len)) >> (W-len);
+ }
+ return result;
+}
+
+inline void SetField(ulong *A,register ulong len, register ulong index,register ulong x) {
+ ulong i=index*len/W, j=index*len-i*W;
+ ulong mask = ((j+len) < W ? ~0u << (j+len) : 0) | ((W-j) < W ? ~0u >> (W-j) : 0);
+ A[i] = (A[i] & mask) | x << j;
+ if (j+len>W) {
+ mask = ((~0u) << (len+j-W));
+ A[i+1] = (A[i+1] & mask)| x >> (W-j);
+ }
+}
+
+inline unsigned GetFieldW32(unsigned *A,register unsigned index) {
+ return A[index];
+}
+
+inline void SetField32(unsigned *A, register unsigned index,register unsigned x) {
+ A[index]=x;
+}
+
+inline unsigned GetFieldW16(unsigned *A,register unsigned index) {
+ register unsigned i=index/2, j=(index&1)<<4, result;
+ result = (A[i] << (16-j)) >> (16);
+ return result;
+}
+
+inline unsigned GetFieldW4(unsigned *A,register unsigned index) {
+ register unsigned i=index/8, j=(index&0x7)<<2;
+ /*register unsigned i=index/8, j=index*4-32*i; */
+ return (A[i] << (28-j)) >> (28);
+}
+
+
+inline uint popcount32 (register int x){
+ return __popcount_tab[(x >> 0) & 0xff] + __popcount_tab[(x >> 8) & 0xff] + __popcount_tab[(x >> 16) & 0xff] + __popcount_tab[(x >> 24) & 0xff];
+}
+
+inline uint popcount16 (register int x){
+ return __popcount_tab[x & 0xff] + __popcount_tab[(x >> 8) & 0xff];
+}
+
+inline uint popcount8 (register int x){
+ return __popcount_tab[x & 0xff];
+}
+
+inline int len_uchar(unsigned char *s) {
+ int i;
+ for (i=0;;i++)
+ if (s[i] == '\0') return i;
+}
+
+#define mmax(x,y) ((x)>(y)?(x):(y))
+#define mmin(x,y) ((x)<(y)?(x):(y))
+
+#endif
+
diff --git a/src/libSSA/bitarray.cpp b/src/libSSA/bitarray.cpp
new file mode 100644
index 0000000..2406790
--- /dev/null
+++ b/src/libSSA/bitarray.cpp
@@ -0,0 +1,461 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <cassert>
+#include <cmath>
+#include <sys/types.h>
+#include "bitarray.h"
+#include "basic.h"
+
+/////////////
+//Rank(B,i)//
+/////////////
+//This Class use a superblock size of 256 bits
+//and a block size of 32 bits also
+//we use a 32 bit to represent Rs and
+//we use a 8 bit to represent Rb
+
+// The bitarray goes form 0..n-1
+BitRankF::BitRankF(ulong *bitarray, ulong n, bool owner) {
+ data=bitarray;
+ this->owner = owner;
+ this->n=n;
+ b=32; // b is a word
+ factor=8; // 8 word in 256 bits
+ s=b*factor;
+ ulong aux=(n+1)%W;
+ if (aux != 0)
+ integers = (n+1)/W+1;
+ else
+ integers = (n+1)/W;
+ BuildRank();
+}
+
+BitRankF::~BitRankF() {
+ delete [] Rs;
+ delete [] Rb;
+ if (owner) delete [] data;
+}
+
+ulong BitRankF::SpaceRequirementInBits() {
+ return (owner?n:0)+(n/s)*sizeof(ulong)*8 +(n/b)*sizeof(uchar)*8+sizeof(BitRankF)*8;
+}
+//Build the rank (blocks and superblocks)
+void BitRankF::BuildRank(){
+ ulong num_sblock = n/s;
+ ulong num_block = n/b;
+ Rs = new ulong[num_sblock+1];//+1 we add the 0 pos
+ Rb = new uchar[num_block+1];//+1 we add the 0 pos
+ ulong j;
+ Rs[0]=0;
+ for (j=1;j<=num_sblock;j++)
+ Rs[j]=BuildRankSub((j-1)*factor,factor)+Rs[j-1];
+
+ Rb[0]=0;
+ for (ulong k=1;k<=num_block;k++) {
+ j = k / factor;
+ Rb[k]=BuildRankSub(j*factor,k%factor);
+ }
+}
+
+int BitRankF::save(FILE *f) {
+ if (f == NULL) return 20;
+ if (fwrite (&n,sizeof(ulong),1,f) != 1) return 21;
+ if (fwrite (data,sizeof(ulong),n/W+1,f) != n/W+1) return 21;
+ if (fwrite (Rs,sizeof(ulong),n/s+1,f) != n/s+1) return 21;
+ if (fwrite (Rb,sizeof(uchar),n/b+1,f) != n/b+1) return 21;
+ return 0;
+}
+
+int BitRankF::load(FILE *f) {
+ if (f == NULL) return 23;
+ if (fread (&n,sizeof(ulong),1,f) != 1) return 25;
+ b=32; // b is a word
+ factor=8; // 8 word in 256 bits
+ s=b*factor;
+ ulong aux=(n+1)%W;
+ if (aux != 0)
+ integers = (n+1)/W+1;
+ else
+ integers = (n+1)/W;
+ data= new ulong[n/W+1];
+ if (!data) return 1;
+ if (fread (data,sizeof(ulong),n/W+1,f) != n/W+1) return 25;
+ this->owner = true;
+ Rs= new ulong[n/s+1];
+ if (!Rs) return 1;
+ if (fread (Rs,sizeof(ulong),n/s+1,f) != n/s+1) return 25;
+ Rb= new uchar[n/b+1];
+ if (!Rb) return 1;
+ if (fread (Rb,sizeof(uchar),n/b+1,f) != n/b+1) return 25;
+ return 0;
+}
+
+BitRankF::BitRankF(FILE *f, int *error) {
+ *error = BitRankF::load(f);
+}
+
+ulong BitRankF::BuildRankSub(ulong ini,ulong bloques){
+ ulong rank=0,aux;
+ for(ulong i=ini;i<ini+bloques;i++) {
+ if (i < integers) {
+ aux=data[i];
+ rank+=popcount32(aux);
+ }
+ }
+ return rank; //return the numbers of 1's in the interval
+}
+
+
+//this rank ask from 0 to n-1
+ulong BitRankF::rank(ulong i) {
+ ++i; // the following gives sum of 1s before i
+ return Rs[i>>8]+Rb[i>>5]
+ +popcount32(data[i>>5] & ((1<<(i & mask31))-1));
+}
+
+//this rank ask from 0 to n-1
+ulong BitRankF::rank2(ulong i) {
+ ++i;
+ ulong resp=Rs[i>>factor];
+ ulong aux=(i/s)*factor;
+ for (ulong a=aux;a<i/W;a++)
+ resp+=popcount32(data[a]);
+ resp+=popcount32(data[i/W] & ((1<<(i & mask31))-1));
+ return resp;
+}
+
+
+ulong BitRankF::prev(ulong start) {
+ // returns the position of the previous 1 bit before and including start.
+ // tuned to 32 bit machine
+
+ ulong i = start >> 5;
+ int offset = (start % W);
+ ulong answer = start;
+ ulong val = data[i] << (Wminusone-offset);
+
+ if (!val) { val = data[--i]; answer -= 1+offset; }
+
+ while (!val) { val = data[--i]; answer -= W; }
+
+ if (!(val & 0xFFFF0000)) { val <<= 16; answer -= 16; }
+ if (!(val & 0xFF000000)) { val <<= 8; answer -= 8; }
+
+ while (!(val & 0x80000000)) { val <<= 1; answer--; }
+ return answer;
+}
+
+ulong BitRankF::select(ulong x) {
+ // returns i such that x=rank(i) && rank(i-1)<x or n if that i not exist
+ // first binary search over first level rank structure
+ // then sequential search using popcount over a int
+ // then sequential search using popcount over a char
+ // then sequential search bit a bit
+
+ //binary search over first level rank structure
+ ulong l=0, r=n/s;
+ ulong mid=(l+r)/2;
+ ulong rankmid = Rs[mid];
+ while (l<=r) {
+ if (rankmid<x)
+ l = mid+1;
+ else
+ r = mid-1;
+ mid = (l+r)/2;
+ rankmid = Rs[mid];
+ }
+ //sequential search using popcount over a int
+ ulong left;
+ left=mid*factor;
+ x-=rankmid;
+ ulong j=data[left];
+ ulong ones = popcount32(j);
+ while (ones < x) {
+ x-=ones;left++;
+ if (left > integers) return n;
+ j = data[left];
+ ones = popcount32(j);
+ }
+ //sequential search using popcount over a char
+ left=left*b;
+ rankmid = popcount8(j);
+ if (rankmid < x) {
+ j=j>>8;
+ x-=rankmid;
+ left+=8;
+ rankmid = popcount8(j);
+ if (rankmid < x) {
+ j=j>>8;
+ x-=rankmid;
+ left+=8;
+ rankmid = popcount8(j);
+ if (rankmid < x) {
+ j=j>>8;
+ x-=rankmid;
+ left+=8;
+ }
+ }
+ }
+
+ // then sequential search bit a bit
+ while (x>0) {
+ if (j&1) x--;
+ j=j>>1;
+ left++;
+ }
+ return left-1;
+}
+
+bool BitRankF::IsBitSet(ulong i) {
+ return (1u << (i % W)) & data[i/W];
+}
+
+
+
+
+/* Implementation of Bitselect Next */
+BitSelectNext::BitSelectNext(ulong *bit, ulong n, bool owner) {
+ this->owner = owner;
+ this->datos=bit;
+ this->n=n;
+ ulong aux=(n+1)%W;
+ if (aux != 0)
+ integers = (n+1)/W+1;
+ else
+ integers = (n+1)/W;
+}
+
+//Select Next
+//this selectnext ask from 1 to n
+ulong BitSelectNext::select_next(ulong k) {
+ ulong count = k-1;
+ ulong des,aux2;
+ des=count%W;
+ aux2= datos[count/W] >> des;
+ if (aux2 > 0) {
+ if ((aux2&0xff) > 0) return count+select_tab[aux2&0xff];
+ else if ((aux2&0xff00) > 0) return count+8+select_tab[(aux2>>8)&0xff];
+ else if ((aux2&0xff0000) > 0) return count+16+select_tab[(aux2>>16)&0xff];
+ else {return count+24+select_tab[(aux2>>24)&0xff];}
+ }
+
+ for (ulong i=count/W+1;i<integers;i++) {
+ aux2=datos[i];
+ if (aux2 > 0) {
+ if ((aux2&0xff) > 0) return i*W+select_tab[aux2&0xff];
+ else if ((aux2&0xff00) > 0) return i*W+8+select_tab[(aux2>>8)&0xff];
+ else if ((aux2&0xff0000) > 0) return i*W+16+select_tab[(aux2>>16)&0xff];
+ else {return i*W+24+select_tab[(aux2>>24)&0xff];}
+ }
+ }
+ return n+1;
+}
+
+
+BitSelectNext::~BitSelectNext() {
+ if (owner) delete datos;
+}
+// The bitarray have positions from 0..n-1
+BitRankFSparse::BitRankFSparse(ulong *bitarray, ulong n){
+ ulong ones=0;
+ ulong i,j,*sblockbit,*blockbit;
+ assert(bitget(bitarray,n-1));
+ for (i=0;i<n;i++)
+ if (bitget(bitarray,i)) ones++;
+ L=(ulong)ceil(sqrt(n/ones));
+ sblockbit=new ulong[(n/L)/W+1];
+ ulong aux=0;
+ for (i=0;i<(n/L)/W+1;i++) sblockbit[i] = 0;
+ for (i=0;i*L<n;i++){
+ assert(i*L<n);
+ for (j=i*L;j<mmin(n,(i+1)*L);j++) {
+ if (bitget(bitarray,j)) { bitset(sblockbit,i); aux++; break; }
+ }
+ //printf("maximo j revisado=%d\n", j);
+
+ }
+ sblock = new BitRankF(sblockbit,n/L,true);
+ blockbit=new ulong[(L*sblock->rank(n/L))/W+1];
+ for (i=0;i<(L*sblock->rank(n/L))/W+1;i++) blockbit[i] = 0;
+ ulong loc=0;
+ for (i=0;i*L<n;i++){
+ assert(i*L<n);
+ if (bitget(sblockbit,i)) {
+ for (j=i*L;j<mmin(n,(i+1)*L);j++) {
+ if (bitget(bitarray,j)) bitset(blockbit,j-i*L+loc);
+ }
+ loc+=L;
+ // printf("maximo j revisado=%d\n", j);
+ }
+ }
+ block = new BitRankF(blockbit,L*sblock->rank(n/L),true);
+
+ //printf("largo de bloque %lu\n", L);
+ //printf("numero de bloques activos%lu %lu\n", aux, sblock-> rank(n/L));
+
+}
+
+BitRankFSparse::~BitRankFSparse() {
+ delete sblock;
+ delete block;
+}
+
+bool BitRankFSparse::IsBitSet(ulong i){
+ ulong numblock=i/L;
+ if (sblock->IsBitSet(numblock) == false) return false;
+ else {
+ ulong one_blocks=sblock->rank(numblock);
+ ulong zero_blocks=numblock-one_blocks+1;
+ //printf("mmm i=%d, zero_blocks=%d, L=%d, res=%d \n",i,zero_blocks,L, i-zero_blocks*L);
+ return block->IsBitSet(i-zero_blocks*L);
+ }
+}
+
+ulong BitRankFSparse::rank(ulong i){
+ ulong numblock=i/L;
+ ulong one_blocks=sblock->rank(numblock);
+ if (sblock->IsBitSet(numblock) == false) {
+ return block->rank(one_blocks*L-1);
+ } else {
+ ulong zero_blocks=numblock-one_blocks+1;
+ return block->rank(i-zero_blocks*L);
+ }
+}
+
+ulong BitRankFSparse::select(ulong i){
+ ulong pos1=block->select(i);
+ ulong one_blocks=pos1/L+1;
+ ulong pos2=sblock->select(one_blocks);
+ ulong zero_blocks=pos2-one_blocks+1;
+ return pos1+zero_blocks*L;
+}
+
+ulong BitRankFSparse::SpaceRequirementInBits(){
+ return block->SpaceRequirementInBits()+sblock->SpaceRequirementInBits()+sizeof(BitRankFSparse)*8;
+}
+
+ulong BitRankFSparse::prev(ulong start) {
+ // returns the position of the previous 1 bit before and including start.
+ // tuned to 32 bit machine
+ ulong temp,zero_blocks;
+ ulong numblock=start/L+1;
+ ulong one_blocks=sblock->rank(numblock-1);
+ zero_blocks=numblock-one_blocks;
+ if (sblock->IsBitSet(numblock-1) == false) {
+ temp = block->prev(one_blocks*L-1);
+ numblock = sblock->prev(numblock-1)+1;
+ zero_blocks=numblock-(one_blocks-1)-1;
+ //printf("Caso1 ");
+ return temp+zero_blocks*L;
+ } else {
+ temp = block->prev(start-zero_blocks*L);
+ if (temp < (one_blocks-1)*L) {
+ numblock = sblock->prev(numblock-2)+1;
+ zero_blocks=numblock-(one_blocks-1);
+ //printf("Caso2 ");
+ return temp+zero_blocks*L;
+ } else {
+ zero_blocks=numblock-(one_blocks-1)-1;
+ //printf("Caso3 ");
+ return temp+zero_blocks*L;
+ }
+ }
+}
+
diff --git a/src/libSSA/bitarray.h b/src/libSSA/bitarray.h
new file mode 100644
index 0000000..5046832
--- /dev/null
+++ b/src/libSSA/bitarray.h
@@ -0,0 +1,159 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef bitarray_h
+#define bitarray_h
+
+#include "basic.h"
+
+class BitRankF {
+private:
+ ulong *data; //here is the bit-array
+ bool owner;
+ ulong n,integers;
+ ulong factor,b,s;
+ ulong *Rs; //superblock array
+ uchar *Rb; //block array
+ ulong BuildRankSub(ulong ini,ulong fin); //internal use of BuildRank
+ void BuildRank(); //crea indice para rank
+public:
+ BitRankF(ulong *bitarray, ulong n, bool owner);
+ ~BitRankF(); //destructor
+ bool IsBitSet(ulong i);
+ ulong rank(ulong i); //Rank from 0 to n-1
+ ulong rank2(ulong i); //Rank from 0 to n-1
+ ulong prev(ulong start); // gives the largest index i<=start such that IsBitSet(i)=true
+ ulong select(ulong x); // gives the position of the x:th 1.
+ ulong SpaceRequirementInBits();
+ /*load-save functions*/
+ int save(FILE *f);
+ int load(FILE *f);
+ BitRankF(FILE *f, int *error);
+};
+
+
+class BitSelectNext {
+private:
+ ulong *datos; //arreglo de bits
+ bool owner;
+ ulong n;
+ ulong integers;
+public:
+ // Crea arreglo segun numero de bits, semilla aleatoria y probabilidad
+ BitSelectNext(ulong *bit, ulong n, bool owner);
+ ~BitSelectNext(); //destructor
+ ulong select_next(ulong i); // select_next
+};
+
+class BitRankFSparse {
+private:
+ BitRankF *block;
+ BitRankF *sblock;
+ ulong L;
+public:
+ BitRankFSparse(ulong *bitarray, ulong n);
+ ~BitRankFSparse(); //destructor
+ bool IsBitSet(ulong i);
+ ulong rank(ulong i); //Rank from 0 to n-1
+ ulong prev(ulong start); // gives the largest index i<=start such that IsBitSet(i)=true
+ ulong select(ulong x); // gives the position of the x:th 1.
+ ulong SpaceRequirementInBits();
+};
+
+#endif
diff --git a/src/libSSA/bitrankw32int.cpp b/src/libSSA/bitrankw32int.cpp
new file mode 100644
index 0000000..dbffd36
--- /dev/null
+++ b/src/libSSA/bitrankw32int.cpp
@@ -0,0 +1,293 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "bitrankw32int.h"
+#include "assert.h"
+#include "math.h"
+#include <sys/types.h>
+#include <cstdlib>
+
+/////////////
+//Rank(B,i)//
+/////////////
+//_factor = 0 => s=W*lgn
+//_factor = P => s=W*P
+//Is interesting to notice
+//factor=2 => overhead 50%
+//factor=3 => overhead 33%
+//factor=4 => overhead 25%
+//factor=20=> overhead 5%
+
+BitRankW32Int::BitRankW32Int( ulong *bitarray, ulong _n, bool owner, ulong _factor){
+ data=bitarray;
+ this->owner = owner;
+ this->n=_n;
+ ulong lgn=bits(n-1);
+ this->factor=_factor;
+ if (_factor==0) this->factor=lgn;
+ else this->factor=_factor;
+ b=32;
+ s=b*this->factor;
+ integers = n/W+1;
+ BuildRank();
+}
+
+BitRankW32Int::~BitRankW32Int() {
+ delete [] Rs;
+ if (owner) free(data);
+}
+
+//Metodo que realiza la busqueda d
+void BitRankW32Int::BuildRank(){
+ ulong num_sblock = n/s;
+ Rs = new ulong[num_sblock+1];// +1 pues sumo la pos cero
+ for(ulong i=0;i<num_sblock+1;i++)
+ Rs[i]=0;
+ ulong j;
+ Rs[0]=0;
+ for (j=1;j<=num_sblock;j++) {
+ Rs[j]=Rs[j-1];
+ Rs[j]+=BuildRankSub((j-1)*factor,factor);
+ }
+}
+
+ulong BitRankW32Int::BuildRankSub(ulong ini,ulong bloques){
+ ulong rank=0,aux;
+ for(ulong i=ini;i<ini+bloques;i++) {
+ if (i < integers) {
+ aux=data[i];
+ rank+=popcount32(aux);
+ }
+ }
+ return rank; //retorna el numero de 1's del intervalo
+
+}
+
+ulong BitRankW32Int::rank(ulong i) {
+ ++i;
+ ulong resp=Rs[i/s];
+ ulong aux=(i/s)*factor;
+ for (ulong a=aux;a<i/W;a++)
+ resp+=popcount32(data[a]);
+ resp+=popcount32(data[i/W] & ((1<<(i & mask31))-1));
+ return resp;
+}
+
+bool BitRankW32Int::IsBitSet(ulong i) {
+ return (1u << (i % W)) & data[i/W];
+}
+
+int BitRankW32Int::save(FILE *f) {
+ if (f == NULL) return 20;
+ if (fwrite (&n,sizeof(ulong),1,f) != 1) return 21;
+ if (fwrite (&factor,sizeof(ulong),1,f) != 1) return 21;
+ if (fwrite (data,sizeof(ulong),n/W+1,f) != n/W+1) return 21;
+ if (fwrite (Rs,sizeof(ulong),n/s+1,f) != n/s+1) return 21;
+ return 0;
+}
+
+int BitRankW32Int::load(FILE *f) {
+ if (f == NULL) return 23;
+ if (fread (&n,sizeof(ulong),1,f) != 1) return 25;
+ b=32; // b is a word
+ if (fread (&factor,sizeof(ulong),1,f) != 1) return 25;
+ s=b*factor;
+ ulong aux=(n+1)%W;
+ if (aux != 0)
+ integers = (n+1)/W+1;
+ else
+ integers = (n+1)/W;
+ data= (ulong *)calloc(n/W+1, sizeof(ulong));
+ if (!data) return 1;
+ if (fread (data,sizeof(ulong),n/W+1,f) != n/W+1) return 25;
+ this->owner = true;
+ Rs= new ulong[n/s+1];
+ if (!Rs) return 1;
+ if (fread (Rs,sizeof(ulong),n/s+1,f) != n/s+1) return 25;
+ return 0;
+}
+
+BitRankW32Int::BitRankW32Int(FILE *f, int *error) {
+ *error = BitRankW32Int::load(f);
+}
+
+ulong BitRankW32Int::SpaceRequirementInBits() {
+ return (owner?n:0)+(n/s)*sizeof(ulong)*8 +sizeof(BitRankW32Int)*8;
+}
+
+ulong BitRankW32Int::prev(ulong start) {
+ // returns the position of the previous 1 bit before and including start.
+ // tuned to 32 bit machine
+
+ ulong i = start >> 5;
+ int offset = (start % W);
+ ulong answer = start;
+ ulong val = data[i] << (Wminusone-offset);
+
+ if (!val) { val = data[--i]; answer -= 1+offset; }
+
+ while (!val) { val = data[--i]; answer -= W; }
+
+ if (!(val & 0xFFFF0000)) { val <<= 16; answer -= 16; }
+ if (!(val & 0xFF000000)) { val <<= 8; answer -= 8; }
+
+ while (!(val & 0x80000000)) { val <<= 1; answer--; }
+ return answer;
+}
+
+ulong BitRankW32Int::select(ulong x) {
+ // returns i such that x=rank(i) && rank(i-1)<x or n if that i not exist
+ // first binary search over first level rank structure
+ // then sequential search using popcount over a int
+ // then sequential search using popcount over a char
+ // then sequential search bit a bit
+
+ //binary search over first level rank structure
+ ulong l=0, r=n/s;
+ ulong mid=(l+r)/2;
+ ulong rankmid = Rs[mid];
+ while (l<=r) {
+ if (rankmid<x)
+ l = mid+1;
+ else
+ r = mid-1;
+ mid = (l+r)/2;
+ rankmid = Rs[mid];
+ }
+ //sequential search using popcount over a int
+ ulong left;
+ left=mid*factor;
+ x-=rankmid;
+ ulong j=data[left];
+ ulong ones = popcount32(j);
+ while (ones < x) {
+ x-=ones;left++;
+ if (left > integers) return n;
+ j = data[left];
+ ones = popcount32(j);
+ }
+ //sequential search using popcount over a char
+ left=left*b;
+ rankmid = popcount8(j);
+ if (rankmid < x) {
+ j=j>>8;
+ x-=rankmid;
+ left+=8;
+ rankmid = popcount8(j);
+ if (rankmid < x) {
+ j=j>>8;
+ x-=rankmid;
+ left+=8;
+ rankmid = popcount8(j);
+ if (rankmid < x) {
+ j=j>>8;
+ x-=rankmid;
+ left+=8;
+ }
+ }
+ }
+
+ // then sequential search bit a bit
+ while (x>0) {
+ if (j&1) x--;
+ j=j>>1;
+ left++;
+ }
+ return left-1;
+}
diff --git a/src/libSSA/bitrankw32int.h b/src/libSSA/bitrankw32int.h
new file mode 100644
index 0000000..20a2304
--- /dev/null
+++ b/src/libSSA/bitrankw32int.h
@@ -0,0 +1,141 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef BitRankW32Int_h
+#define BitRankW32Int_h
+
+#include "basic.h"
+/////////////
+//Rank(B,i)//
+/////////////
+//_factor = 0 => s=W*lgn
+//_factor = P => s=W*P
+//Is interesting to notice
+//factor=2 => overhead 50%
+//factor=3 => overhead 33%
+//factor=4 => overhead 25%
+//factor=20=> overhead 5%
+
+class BitRankW32Int {
+private:
+ ulong *data;
+ bool owner;
+ ulong n,integers;
+ ulong factor,b,s;
+ ulong *Rs; //superblock array
+
+ ulong BuildRankSub(ulong ini,ulong fin); //uso interno para contruir el indice rank
+ void BuildRank(); //crea indice para rank
+public:
+ BitRankW32Int(ulong *bitarray, ulong n, bool owner, ulong factor);
+ ~BitRankW32Int(); //destructor
+ bool IsBitSet(ulong i);
+ ulong rank(ulong i); //Nivel 1 bin, nivel 2 sec-pop y nivel 3 sec-bit
+
+ ulong prev(ulong start); // gives the largest index i<=start such that IsBitSet(i)=true
+ ulong select(ulong x); // gives the position of the x:th 1.
+ ulong SpaceRequirementInBits();
+ /*load-save functions*/
+ int save(FILE *f);
+ int load(FILE *f);
+ BitRankW32Int(FILE *f, int *error);
+};
+
+#endif
+
diff --git a/src/libSSA/chrPosition.cpp b/src/libSSA/chrPosition.cpp
new file mode 100644
index 0000000..c98ff29
--- /dev/null
+++ b/src/libSSA/chrPosition.cpp
@@ -0,0 +1,165 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "chrPosition.h"
+
+ChrPosition::ChrPosition():rel_position(0), chr(NULL), strand(0) {}
+
+ChrPosition::ChrPosition(ulong rel_position, char *chr, int strand):
+rel_position(rel_position), chr(chr), strand(strand) {}
+
+ChrPosition::ChrPosition(const ChrPosition &pos) {
+ rel_position = pos.getRelativePosition();
+ chr = pos.getChrPosition();
+ strand = pos.getStrand();
+}
+
+ulong ChrPosition::getRelativePosition() const {
+ return rel_position;
+}
+
+char *ChrPosition::getChrPosition() const {
+ return chr;
+}
+
+int ChrPosition::getStrand() const {
+ return strand;
+}
+
+ostream &operator<<(ostream &os, ChrPosition &p) {
+ os << p.getChrPosition() << "|"<< p.getStrand() << "," << p.getRelativePosition();
+ return os;
+}
+
+ChrPosition ChrPosition::operator+(int i) {
+ return ChrPosition(*this) += i;
+// return pos;
+}
+
+ChrPosition &ChrPosition::operator+=(int i) {
+ rel_position += i;
+ return *this;
+}
+
+ChrPosition ChrPosition::operator-(int i) {
+ return ChrPosition(*this) -= i;
+}
+
+ChrPosition &ChrPosition::operator-=(int i) {
+ *this += -i;
+ return *this;
+}
+
+ChrPosition ChrPosition::operator+(ulong i) {
+ return ChrPosition(*this) += i;
+}
+
+ChrPosition &ChrPosition::operator+=(ulong i) {
+ rel_position += i;
+ return *this;
+}
+
+ChrPosition ChrPosition::operator-(ulong i) {
+ return ChrPosition(*this) -= i;
+}
+
+ChrPosition &ChrPosition::operator-=(ulong i) {
+ *this += -i;
+ return *this;
+}
diff --git a/src/libSSA/chrPosition.h b/src/libSSA/chrPosition.h
new file mode 100644
index 0000000..e8ef666
--- /dev/null
+++ b/src/libSSA/chrPosition.h
@@ -0,0 +1,136 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef CHR_POSITION_H
+#define CHR_POSITION_H
+#include <iostream>
+#include "basic.h"
+using namespace std;
+
+class ChrPosition {
+ private:
+ ulong rel_position;
+ char *chr;
+ int strand;
+
+ public:
+ ChrPosition();
+ ChrPosition(ulong rel_position, char *chr, int strand);
+ ChrPosition(const ChrPosition &);
+
+ ulong getRelativePosition() const;
+ char *getChrPosition() const;
+ int getStrand() const;
+
+ /**
+ * Shifts the position by the specified int
+ */
+ ChrPosition operator+(int);
+ ChrPosition &operator+=(int);
+ ChrPosition operator-(int);
+ ChrPosition &operator-=(int);
+
+ ChrPosition operator+(ulong);
+ ChrPosition &operator+=(ulong);
+ ChrPosition operator-(ulong);
+ ChrPosition &operator-=(ulong);
+};
+
+ostream &operator<<(ostream &, ChrPosition &);
+#endif
diff --git a/src/libSSA/cracIndex.cpp b/src/libSSA/cracIndex.cpp
new file mode 100644
index 0000000..d00f4dc
--- /dev/null
+++ b/src/libSSA/cracIndex.cpp
@@ -0,0 +1,418 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <iostream>
+#include <fstream>
+#include <getopt.h>
+#include <list>
+#include <cstring>
+#include <cstdlib>
+#include <ctime>
+using namespace std;
+
+
+extern "C" {
+#include <sys/types.h>
+#include <unistd.h>
+}
+
+#include <blockwise_sa.h>
+#include <SSA.h>
+#include <config.h>
+#include <seqan/sequence.h>
+#include <seqan/file.h>
+
+#include <cracIndex.h>
+#include <GenomeInfo.h>
+#include <utils.h>
+
+typedef String<Dna, Packed<> > TStr;
+
+using namespace seqan;
+
+int verbose = 0;
+
+void usage(char *prog) {
+ cerr << endl << prog << " version " << PACKAGE_VERSION;
+ cerr << "\tCompiled on " <<__DATE__ << endl << endl;
+ cerr << "Usage : "<<prog << " [options] <command> <output file> <input file>+"
+ << endl << endl
+ << " command must be one of:" << endl
+ << " index: create an index on the specified input file(s)."
+ << endl << endl
+ << " get: get a (multi)FASTA file containing the original sequences."
+ << endl << endl
+ << " options can be (for the index command only):" << endl << endl
+ << " -b <bucket_size>\t the size of the bucket for the index construction"
+ << endl
+ << " \t (default " << THIS_BUCKET_SIZE << ")" << endl
+ << " -d <diff-cover> \t parameter for the index construction (default "
+ << COVER << ")"
+ << endl
+ << " -v \t verbose mode"
+ << endl << endl
+ << " Examples: " << endl
+ << "\tIndexing:" << endl
+ << "\t\t" << prog << " index myIndex sequence1.fa sequence2.fa sequence3.fa"
+ << endl
+ << "\t\t\tYou can specify FASTA or MultiFASTA file(s)." << endl
+ << "\t\t\tIn this example, two files will be created:" << endl
+ << "\t\t\t- myIndex.ssa (index storing the compressed sequences)" << endl
+ << "\t\t\t- myIndex.conf (information on sequence names and length)" << endl
+ << "\tExtracting:" << endl
+ << "\t\t" << prog << " get sequences.fa myIndex" << endl
+ << "\t\t\tSequences indexed in myIndex will be extracted" << endl
+ << "\t\t\tto the sequences.fa file" << endl;
+ exit(1);
+}
+
+
+void index(char **input_files, int nb_input_files, char *output_file,
+ uint cover, uint bucket_size) {
+ unsigned long long n = 0;
+ void *index;
+ ifstream file;
+ ofstream conf;
+ TStr *text = new TStr();
+ uchar *bwt;
+ int i = 0;
+ list<pair<uint, String<char> > > sequences;
+
+ for (i = 0; i < nb_input_files; i++) {
+ if (verbose)
+ cerr << "Reading file " << input_files[i] << endl;
+
+ file.open(input_files[i], ios_base::in | ios_base::binary);
+ if (file.is_open()) {
+ String<Dna5> current_seq;
+ String<char> fasta_tag;
+ uint current_length;
+ do {
+ readMeta(file, fasta_tag, Fasta());
+ read(file, current_seq, Fasta());
+ current_length = length(current_seq);
+ if (verbose && current_length)
+ cerr << "\tSequence of length " << current_length << endl;
+ if (current_length) {
+ // Search sequence name in fasta_tag
+ Iterator<String<char> >::Type it = begin(fasta_tag);
+ while (it != end(fasta_tag) && value(it) != ' ')
+ it++;
+ fasta_tag = prefix(fasta_tag, it);
+
+ if (length(fasta_tag) > MAX_LENGTH_CHR_NAME) {
+ cerr << "Warning the name of the sequence is too long and will be cut:" << endl
+ << "\t" << fasta_tag << endl;
+ fasta_tag = prefix(fasta_tag, MAX_LENGTH_CHR_NAME-1);
+ }
+
+ sequences.push_back(pair<uint, String<char> >(current_length,
+ fasta_tag));
+
+ uint this_seq_length = length(current_seq);
+ for (uint i = 0; i < this_seq_length; i++) {
+ // Replace N with a random nucleotide... that's not great. I know.
+ // But the text is encoded on two bits.
+ if (current_seq[i] == 'N') {
+ current_seq[i] = randomDNA();
+ }
+ }
+
+ n += current_length;
+ *text += current_seq;
+ }
+ } while (current_length > 0);
+ file.close();
+ } else {
+ cerr<<"Unable to open the input file " << input_files[i] << endl;
+ exit(2);
+ }
+ }
+
+
+ // Creating configuration file
+ char *confName = new char[strlen(output_file)+6];
+ sprintf(confName, "%s.conf", output_file);
+ conf.open(confName, ios_base::out | ios_base::binary);
+ if (! conf.is_open()) {
+ cerr << "Can't write configuration file " << confName << endl;
+ exit(3);
+ }
+ delete [] confName;
+
+ // Writing configuration file
+ list<pair<uint, String<char> > >::iterator it = sequences.begin();
+ conf << sequences.size();
+ while (it != sequences.end()) {
+ conf << endl << (*it).second
+ << endl << (*it).first;
+ it++;
+ }
+ conf.close();
+
+ if (n > ((unsigned long long) 1 << 32) - 1) {
+ cerr << "Your genome sequence is too large. I cannot index it. Sorry" << endl;
+ exit(4);
+ }
+
+ if (verbose)
+ cerr << "Initialising KBSA" << endl;
+
+ BlockwiseSA<TStr> *kSA = new KarkkainenBlockwiseSA<TStr>(*text, bucket_size, cover);
+
+ if (verbose)
+ cerr << "Building BWT. Do you know what the BWT is?" << endl
+ << "You can have a look at http://enwp.org/Burrows-Wheeler%20transform" << endl;
+
+ // Build the BWT of chars.
+ bwt = new unsigned char[n+1];
+ for (uint i = 0; i <= n; i++) {
+ uint current = kSA->nextSuffix();
+ if (current == 0)
+ bwt[i] = 255;
+ else {
+ bwt[i] = convert<char>((*text)[current - 1]);
+ }
+ }
+ delete kSA;
+ delete text;
+
+ if (verbose)
+ cerr << "Building the BWT-based index." << endl
+ << "Do you know what an FM-index is?" << endl
+ << "You can have a look at http://enwp.org/FM-index" << endl;
+
+ // build_index has been modified so that it takes a BWT as parameter
+ char *params = new char[13];
+ sprintf(params, "terminator %c",255);
+ build_index((unsigned char *)bwt, n+1, params, &index);
+ if (verbose)
+ cerr << "Saving the index in the output file" << endl;
+ save_index(index, output_file);
+ delete [] params;
+ free_index(index);
+}
+
+
+void get(char *input, char *output) {
+ void *index;
+ unsigned int n;
+ uchar *chars;
+ uint total_pos;
+ uint current_pos;
+ ofstream fasta;
+ GenomeInfo *gInfo;
+
+ if (verbose)
+ cerr << "Reading informations on sequences" << endl;
+ gInfo = new GenomeInfo(input);
+
+ fasta.open(output, ios_base::out | ios_base::binary);
+ if (! fasta.is_open()) {
+ cerr << "Can't write FASTA file " << output << endl;
+ exit(3);
+ }
+
+ if (verbose)
+ cerr << "Loading index" << endl;
+ load_index(input,&index);
+ get_length(index, &n);
+ if (verbose)
+ cerr << "Extracting the sequences from the index" << endl;
+ extract(index, 0, n-1, &chars, &n);
+
+ uint i = 0;
+ uchar substr[NB_CHAR_FASTA_LINE+1];
+ substr[NB_CHAR_FASTA_LINE]=0;
+ total_pos = 0;
+ while (i < gInfo->getNbChr()) {
+ current_pos = 0;
+ // Output FASTA header for the sequence
+ if (verbose)
+ cerr << "Retrieving " << gInfo->getChrName(i) << endl;
+ fasta << ">" << gInfo->getChrName(i) << endl;
+ // Reading each sequence
+ while (current_pos + NB_CHAR_FASTA_LINE < gInfo->getChrLength(i)) {
+ // Writing each line separately
+ strncpy((char *)substr, (char *)&chars[total_pos], NB_CHAR_FASTA_LINE);
+ fasta << substr << endl;
+ total_pos += NB_CHAR_FASTA_LINE;
+ current_pos += NB_CHAR_FASTA_LINE;
+ }
+ // Read the remaining (if any)
+ if (current_pos < gInfo->getChrLength(i)) {
+ strncpy((char *) substr, (char *) & chars[total_pos], gInfo->getChrLength(i) - current_pos);
+ substr[gInfo->getChrLength(i) - current_pos] = 0;
+ fasta << substr << endl;
+ total_pos += gInfo->getChrLength(i) - current_pos;
+ }
+ i++;
+ }
+ fasta.close();
+ free(chars);
+
+ free_index(index);
+
+ delete gInfo;
+}
+
+
+int main(int argc, char **argv) {
+ uint bucket_size = THIS_BUCKET_SIZE;
+ uint cover = COVER;
+ char *output_file = NULL;
+ int command=-1; // O: index, 1: get
+ int option_index;
+ int opt;
+
+ static const char *short_options = "d:b:hv";
+ static struct option long_options[] =
+ {{"help", no_argument, NULL, 'h'},
+ {"diff-cover", required_argument, NULL, 'd'},
+ {"bucket-size", required_argument, NULL, 'b'},
+ { 0, 0, 0, 0 } //terminator
+ };
+
+ while ((opt = getopt_long(argc, argv, short_options, long_options, &option_index)) != -1){
+ switch(opt) {
+ case 'd' :
+ cover = atoi(optarg);
+ break;
+ case 'b' :
+ bucket_size = atoi(optarg);
+ break;
+ case 'v':
+ verbose = 1;
+ break;
+ case 'h' :
+ default:
+ usage(argv[0]);
+ }
+ }
+
+ if (argc - optind < 3) {
+ usage(argv[0]);
+ }
+
+ // Get the command argument
+ if (! strcmp(argv[optind], "index")) {
+ command = 0;
+ } else if (! strcmp(argv[optind], "get")) {
+ command = 1;
+ } else {
+ cerr << "Unknown command " << argv[optind] << endl;
+ usage(argv[0]);
+ }
+ optind++;
+
+ // Get the output file
+ output_file = argv[optind++];
+
+ // Input files are what is remaining...
+
+ if (command == 0) {
+ // index
+ index(&argv[optind], argc - optind, output_file, cover, bucket_size);
+ } else {
+ // get
+ get(argv[optind], output_file);
+ }
+
+ exit(0);
+}
diff --git a/src/libSSA/cracIndex.h b/src/libSSA/cracIndex.h
new file mode 100644
index 0000000..0f7f772
--- /dev/null
+++ b/src/libSSA/cracIndex.h
@@ -0,0 +1,141 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef CRAC_INDEX
+#define CRAC_INDEX
+
+/**
+ * Default bucket size for the index construction
+ */
+#define THIS_BUCKET_SIZE 100000000
+
+/**
+ * Default cover for the index construction
+ */
+#define COVER 1024
+
+
+
+/**
+ * Maximal number of letters to write for a sequence in a FASTA file
+ */
+#define NB_CHAR_FASTA_LINE 80
+
+
+/**
+ * Create an index for the FASTA files
+ *
+ * @param input_files: FASTA files containing the sequences to be indexed
+ * @param nb_input_files: Number of input files in the array
+ * @param output_file: Output file basename
+ * @param cover: parameter for the construction
+ * @param bucket_size: parameter for the construction
+ */
+void index(char **input_files, int nb_input_files, char *output_file,
+ uint cover, uint bucket_size);
+
+/**
+ * From the index, create a FASTA file containing all the indexed sequences
+ *
+ * @param input: the index basename
+ * @param output: the FASTA filename
+ */
+void get(char *input, char *output);
+
+#endif
diff --git a/src/libSSA/karkkainen_bwt/alphabet.h b/src/libSSA/karkkainen_bwt/alphabet.h
new file mode 100644
index 0000000..b464ddf
--- /dev/null
+++ b/src/libSSA/karkkainen_bwt/alphabet.h
@@ -0,0 +1,252 @@
+#ifndef ALPHABETS_H_
+#define ALPHABETS_H_
+
+#include <stdexcept>
+#include <string>
+#include <seqan/sequence.h>
+#include <seqan/file.h>
+#include <sstream>
+#include "assert_helpers.h"
+
+using namespace std;
+using namespace seqan;
+
+/**
+ * Return a new TStr containing the reverse-complement of s. Ns go to
+ * Ns.
+ */
+template<typename TStr>
+static inline TStr reverseComplement(const TStr& s, bool color) {
+ typedef typename Value<TStr>::Type TVal;
+ TStr s_rc;
+ size_t slen = length(s);
+ resize(s_rc, slen);
+ if(color) {
+ for(size_t i = 0; i < slen; i++) {
+ s_rc[i] = s[slen-i-1];
+ }
+ } else {
+ for(size_t i = 0; i < slen; i++) {
+ int sv = (int)s[slen-i-1];
+ if(sv == 4) {
+ s_rc[i] = (TVal)4;
+ } else {
+ s_rc[i] = (TVal)(sv ^ 3);
+ }
+ }
+ }
+ return s_rc;
+}
+
+/**
+ * Reverse-complement s in-place. Ns go to Ns.
+ */
+template<typename TStr>
+static inline void reverseComplementInPlace(TStr& s, bool color) {
+ typedef typename Value<TStr>::Type TVal;
+ if(color) {
+ reverseInPlace(s);
+ return;
+ }
+ size_t len = length(s);
+ size_t i;
+ for(i = 0; i < (len>>1); i++) {
+ int sv = (int)s[len-i-1];
+ int sf = (int)s[i];
+ if(sv == 4) {
+ s[i] = (TVal)4;
+ } else {
+ s[i] = (TVal)(sv ^ 3);
+ }
+ if(sf == 4) {
+ s[len-i-1] = (TVal)4;
+ } else {
+ s[len-i-1] = (TVal)(sf ^ 3);
+ }
+ }
+ if((len & 1) != 0 && (int)s[len >> 1] != 4) {
+ s[len >> 1] = (TVal)((int)s[len >> 1] ^ 3);
+ }
+}
+
+/// Reverse a string in-place
+template <typename TStr>
+static inline void reverseInPlace(TStr& s) {
+ typedef typename Value<TStr>::Type TVal;
+ size_t len = length(s);
+ for(size_t i = 0; i < (len>>1); i++) {
+ TVal tmp = s[i];
+ s[i] = s[len-i-1];
+ s[len-i-1] = tmp;
+ }
+}
+
+/**
+ * Return the reverse-complement of s.
+ */
+template<typename TStr>
+static inline TStr reverseCopy(const TStr& s) {
+ typedef typename Value<TStr>::Type TVal;
+ TStr s_rc;
+ size_t slen = length(s);
+ resize(s_rc, slen);
+ for(size_t i = 0; i < slen; i++) {
+ s_rc[i] = (TVal)((int)s[slen-i-1]);
+ }
+ return s_rc;
+}
+
+/**
+ * Return true iff the first string is dollar-less-than the second.
+ * This means that we pretend that a 'dollar sign' character,
+ * lexicographically larger than all other characters, exists at the
+ * end of both strings.
+ */
+template <typename TStr>
+static inline bool
+dollarLt(const TStr& l, const TStr& r) {
+ return isPrefix(r, l) || (l < r && !isPrefix(l, r));
+}
+
+/**
+ * Return true iff the first string is dollar-greater-than the second.
+ * This means that we pretend that a 'dollar sign' character,
+ * lexicographically larger than all other characters, exists at the
+ * end of both strings.
+ */
+template <typename TStr>
+static inline bool
+dollarGt(const TStr& l, const TStr& r) {
+ return !dollarLt(l, r);
+}
+
+/**
+ * Return a copy of the suffix of l starting at 'off'.
+ */
+template <typename TStr>
+static inline std::string
+suffixStr(const TStr& l, size_t off) {
+ typedef typename Value<TStr>::Type TVal;
+ std::string ret;
+ size_t len = seqan::length(l);
+ for(size_t i = off; i < len; i++) {
+ ret.push_back((char)(TVal)l[i]);
+ }
+ return ret;
+}
+
+/**
+ * Calculate the entropy of the given read. Handle Ns by charging them
+ * to the most frequent non-N character.
+ */
+static inline float entropyDna5(const String<Dna5>& read) {
+ size_t cs[5] = {0, 0, 0, 0, 0};
+ size_t readLen = seqan::length(read);
+ for(size_t i = 0; i < readLen; i++) {
+ int c = (int)read[i];
+ assert_lt(c, 5);
+ assert_geq(c, 0);
+ cs[c]++;
+ }
+ if(cs[4] > 0) {
+ // Charge the Ns to the non-N character with maximal count and
+ // then exclude them from the entropy calculation (i.e.,
+ // penalize Ns as much as possible)
+ if(cs[0] >= cs[1] && cs[0] >= cs[2] && cs[0] >= cs[3]) {
+ // Charge Ns to As
+ cs[0] += cs[4];
+ } else if(cs[1] >= cs[2] && cs[1] >= cs[3]) {
+ // Charge Ns to Cs
+ cs[1] += cs[4];
+ } else if(cs[2] >= cs[3]) {
+ // Charge Ns to Gs
+ cs[2] += cs[4];
+ } else {
+ // Charge Ns to Ts
+ cs[3] += cs[4];
+ }
+ }
+ float ent = 0.0;
+ for(int i = 0; i < 4; i++) {
+ if(cs[i] > 0) {
+ float frac = (float)cs[i] / (float)readLen;
+ ent += (frac * log(frac));
+ }
+ }
+ ent = -ent;
+ assert_geq(ent, 0.0);
+ return ent;
+}
+
+/**
+ * Return the DNA complement of the given ASCII char.
+ */
+static inline char comp(char c) {
+ switch(c) {
+ case 'a': return 't';
+ case 'A': return 'T';
+ case 'c': return 'g';
+ case 'C': return 'G';
+ case 'g': return 'c';
+ case 'G': return 'C';
+ case 't': return 'a';
+ case 'T': return 'A';
+ default: return c;
+ }
+}
+
+extern uint8_t dna4Cat[];
+extern uint8_t charToDna5[];
+extern uint8_t asc2col[];
+extern uint8_t rcCharToDna5[];
+
+/// Convert an ascii char to a DNA category. Categories are:
+/// 0 -> invalid
+/// 1 -> unambiguous a, c, g or t
+/// 2 -> ambiguous
+/// 3 -> unmatchable
+extern uint8_t asc2dnacat[];
+
+/// Convert an ascii char to a color category. Categories are:
+/// 0 -> invalid
+/// 1 -> unambiguous 0, 1, 2 or 3
+/// 2 -> ambiguous (not applicable for colors)
+/// 3 -> unmatchable
+extern uint8_t asc2colcat[];
+
+/// Convert a 2-bit nucleotide (and 4=N) and a color to the
+/// corresponding 2-bit nucleotide
+extern uint8_t nuccol2nuc[5][5];
+
+/**
+ * Return true iff c is an unambiguous Dna character.
+ */
+static inline bool isUnambigDna(char c) {
+ return asc2dnacat[(int)c] == 1;
+}
+
+/**
+ * Return true iff c is a Dna character.
+ */
+static inline bool isDna(char c) {
+ return asc2dnacat[(int)c] > 0;
+}
+
+/**
+ * Return true iff c is an unambiguous color character (0,1,2,3).
+ */
+static inline bool isUnambigColor(char c) {
+ return asc2colcat[(int)c] == 1;
+}
+
+/**
+ * Return true iff c is a color character.
+ */
+static inline bool isColor(char c) {
+ return asc2colcat[(int)c] > 0;
+}
+
+/// Convert a pair of 2-bit (and 4=N) encoded DNA bases to a color
+extern uint8_t dinuc2color[5][5];
+
+#endif /*ALPHABETS_H_*/
diff --git a/src/libSSA/karkkainen_bwt/assert_helpers.h b/src/libSSA/karkkainen_bwt/assert_helpers.h
new file mode 100644
index 0000000..cb46fa0
--- /dev/null
+++ b/src/libSSA/karkkainen_bwt/assert_helpers.h
@@ -0,0 +1,259 @@
+#ifndef ASSERT_HELPERS_H_
+#define ASSERT_HELPERS_H_
+
+#include <stdexcept>
+#include <string>
+#include <cassert>
+
+/**
+ * Assertion for release-enabled assertions
+ */
+class ReleaseAssertException : public std::runtime_error {
+public:
+ ReleaseAssertException(const std::string& msg = "") : std::runtime_error(msg) {}
+};
+
+/**
+ * Macros for release-enabled assertions, and helper macros to make
+ * all assertion error messages more helpful.
+ */
+#ifndef NDEBUG
+#define ASSERT_ONLY(x...) x
+#else
+#define ASSERT_ONLY(x...)
+#endif
+
+#define rt_assert(b) \
+ if(!(b)) { \
+ std::cout << "rt_assert at " << __FILE__ << ":" << __LINE__ << std::endl; \
+ throw ReleaseAssertException(); \
+ }
+#define rt_assert_msg(b,msg) \
+ if(!(b)) { \
+ std::cout << msg << " at " << __FILE__ << ":" << __LINE__ << std::endl; \
+ throw ReleaseAssertException(msg); \
+ }
+
+#define rt_assert_eq(ex,ac) \
+ if(!((ex) == (ac))) { \
+ std::cout << "rt_assert_eq: expected (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ throw ReleaseAssertException(); \
+ }
+#define rt_assert_eq_msg(ex,ac,msg) \
+ if(!((ex) == (ac))) { \
+ std::cout << "rt_assert_eq: " << msg << ": (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ throw ReleaseAssertException(msg); \
+ }
+
+#ifndef NDEBUG
+#define assert_eq(ex,ac) \
+ if(!((ex) == (ac))) { \
+ std::cout << "assert_eq: expected (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ assert(0); \
+ }
+#define assert_eq_msg(ex,ac,msg) \
+ if(!((ex) == (ac))) { \
+ std::cout << "assert_eq: " << msg << ": (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ assert(0); \
+ }
+#else
+#define assert_eq(ex,ac)
+#define assert_eq_msg(ex,ac,msg)
+#endif
+
+#define rt_assert_neq(ex,ac) \
+ if(!((ex) != (ac))) { \
+ std::cout << "rt_assert_neq: expected not (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ throw ReleaseAssertException(); \
+ }
+#define rt_assert_neq_msg(ex,ac,msg) \
+ if(!((ex) != (ac))) { \
+ std::cout << "rt_assert_neq: " << msg << ": (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ throw ReleaseAssertException(msg); \
+ }
+
+#ifndef NDEBUG
+#define assert_neq(ex,ac) \
+ if(!((ex) != (ac))) { \
+ std::cout << "assert_neq: expected not (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ assert(0); \
+ }
+#define assert_neq_msg(ex,ac,msg) \
+ if(!((ex) != (ac))) { \
+ std::cout << "assert_neq: " << msg << ": (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ assert(0); \
+ }
+#else
+#define assert_neq(ex,ac)
+#define assert_neq_msg(ex,ac,msg)
+#endif
+
+#define rt_assert_gt(a,b) \
+ if(!((a) > (b))) { \
+ std::cout << "rt_assert_gt: expected (" << (a) << ") > (" << (b) << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ throw ReleaseAssertException(); \
+ }
+#define rt_assert_gt_msg(a,b,msg) \
+ if(!((a) > (b))) { \
+ std::cout << "rt_assert_gt: " << msg << ": (" << (a) << ") > (" << (b) << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ throw ReleaseAssertException(msg); \
+ }
+
+#ifndef NDEBUG
+#define assert_gt(a,b) \
+ if(!((a) > (b))) { \
+ std::cout << "assert_gt: expected (" << (a) << ") > (" << (b) << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ assert(0); \
+ }
+#define assert_gt_msg(a,b,msg) \
+ if(!((a) > (b))) { \
+ std::cout << "assert_gt: " << msg << ": (" << (a) << ") > (" << (b) << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ assert(0); \
+ }
+#else
+#define assert_gt(a,b)
+#define assert_gt_msg(a,b,msg)
+#endif
+
+#define rt_assert_geq(a,b) \
+ if(!((a) >= (b))) { \
+ std::cout << "rt_assert_geq: expected (" << (a) << ") >= (" << (b) << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ throw ReleaseAssertException(); \
+ }
+#define rt_assert_geq_msg(a,b,msg) \
+ if(!((a) >= (b))) { \
+ std::cout << "rt_assert_geq: " << msg << ": (" << (a) << ") >= (" << (b) << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ throw ReleaseAssertException(msg); \
+ }
+
+#ifndef NDEBUG
+#define assert_geq(a,b) \
+ if(!((a) >= (b))) { \
+ std::cout << "assert_geq: expected (" << (a) << ") >= (" << (b) << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ assert(0); \
+ }
+#define assert_geq_msg(a,b,msg) \
+ if(!((a) >= (b))) { \
+ std::cout << "assert_geq: " << msg << ": (" << (a) << ") >= (" << (b) << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ assert(0); \
+ }
+#else
+#define assert_geq(a,b)
+#define assert_geq_msg(a,b,msg)
+#endif
+
+#define rt_assert_lt(a,b) \
+ if(!(a < b)) { \
+ std::cout << "rt_assert_lt: expected (" << a << ") < (" << b << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ throw ReleaseAssertException(); \
+ }
+#define rt_assert_lt_msg(a,b,msg) \
+ if(!(a < b)) { \
+ std::cout << "rt_assert_lt: " << msg << ": (" << a << ") < (" << b << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ throw ReleaseAssertException(msg); \
+ }
+
+#ifndef NDEBUG
+#define assert_lt(a,b) \
+ if(!(a < b)) { \
+ std::cout << "assert_lt: expected (" << a << ") < (" << b << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ assert(0); \
+ }
+#define assert_lt_msg(a,b,msg) \
+ if(!(a < b)) { \
+ std::cout << "assert_lt: " << msg << ": (" << a << ") < (" << b << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ assert(0); \
+ }
+#else
+#define assert_lt(a,b)
+#define assert_lt_msg(a,b,msg)
+#endif
+
+#define rt_assert_leq(a,b) \
+ if(!((a) <= (b))) { \
+ std::cout << "rt_assert_leq: expected (" << (a) << ") <= (" << (b) << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ throw ReleaseAssertException(); \
+ }
+#define rt_assert_leq_msg(a,b,msg) \
+ if(!((a) <= (b))) { \
+ std::cout << "rt_assert_leq: " << msg << ": (" << (a) << ") <= (" << (b) << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ throw ReleaseAssertException(msg); \
+ }
+
+#ifndef NDEBUG
+#define assert_leq(a,b) \
+ if(!((a) <= (b))) { \
+ std::cout << "assert_leq: expected (" << (a) << ") <= (" << (b) << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ assert(0); \
+ }
+#define assert_leq_msg(a,b,msg) \
+ if(!((a) <= (b))) { \
+ std::cout << "assert_leq: " << msg << ": (" << (a) << ") <= (" << (b) << ")" << std::endl; \
+ std::cout << __FILE__ << ":" << __LINE__ << std::endl; \
+ assert(0); \
+ }
+#else
+#define assert_leq(a,b)
+#define assert_leq_msg(a,b,msg)
+#endif
+
+#ifndef NDEBUG
+#define assert_in(c, s) assert_in2(c, s, __FILE__, __LINE__)
+static inline void assert_in2(char c, const char *str, const char *file, int line) {
+ const char *s = str;
+ while(*s != '\0') {
+ if(c == *s) return;
+ s++;
+ }
+ std::cout << "assert_in: (" << c << ") not in (" << str << ")" << std::endl;
+ std::cout << file << ":" << line << std::endl;
+ assert(0);
+}
+#else
+#define assert_in(c, s)
+#endif
+
+#ifndef NDEBUG
+#define assert_range(b, e, v) assert_range_helper(b, e, v, __FILE__, __LINE__)
+template<typename T>
+inline static void assert_range_helper(const T& begin,
+ const T& end,
+ const T& val,
+ const char *file,
+ int line)
+{
+ if(val < begin || val > end) {
+ std::cout << "assert_range: (" << val << ") not in ["
+ << begin << ", " << end << "]" << std::endl;
+ std::cout << file << ":" << line << std::endl;
+ assert(0);
+ }
+}
+#else
+#define assert_range(b, e, v)
+#endif
+
+#endif /*ASSERT_HELPERS_H_*/
diff --git a/src/libSSA/karkkainen_bwt/auto_array.h b/src/libSSA/karkkainen_bwt/auto_array.h
new file mode 100644
index 0000000..afbc08a
--- /dev/null
+++ b/src/libSSA/karkkainen_bwt/auto_array.h
@@ -0,0 +1,38 @@
+/*
+ * auto_array.h
+ *
+ * Created on: Oct 12, 2009
+ * Author: Ben Langmead
+ */
+
+#include <cstring>
+
+#ifndef AUTO_ARRAY_H_
+#define AUTO_ARRAY_H_
+
+/**
+ * A simple fixed-length array of type T, automatically freed in the
+ * destructor.
+ */
+template<typename T>
+class AutoArray {
+public:
+ AutoArray(size_t sz) {
+ t_ = NULL;
+ t_ = new T[sz];
+ memset(t_, 0, sz*sizeof(T));
+ sz_ = sz;
+ }
+ ~AutoArray() { if(t_ != NULL) delete[] t_; }
+ T& operator[](size_t sz) {
+ return t_[sz];
+ }
+ const T& operator[](size_t sz) const {
+ return t_[sz];
+ }
+private:
+ T *t_;
+ size_t sz_;
+};
+
+#endif /* AUTO_ARRAY_H_ */
diff --git a/src/libSSA/karkkainen_bwt/binary_sa_search.h b/src/libSSA/karkkainen_bwt/binary_sa_search.h
new file mode 100644
index 0000000..49b7c6d
--- /dev/null
+++ b/src/libSSA/karkkainen_bwt/binary_sa_search.h
@@ -0,0 +1,76 @@
+#ifndef BINARY_SA_SEARCH_H_
+#define BINARY_SA_SEARCH_H_
+
+#include <stdint.h>
+#include <iostream>
+#include <seqan/sequence.h>
+#include "alphabet.h"
+#include "assert_helpers.h"
+
+/**
+ * Do a binary search using the suffix of 'host' beginning at offset
+ * 'qry' as the query and 'sa' as an already-lexicographically-sorted
+ * list of suffixes of host. 'sa' may be all suffixes of host or just
+ * a subset. Returns the index in sa of the smallest suffix of host
+ * that is larger than qry, or length(sa) if all suffixes of host are
+ * less than qry.
+ *
+ * We use the Manber and Myers optimization of maintaining a pair of
+ * counters for the longest lcp observed so far on the left- and right-
+ * hand sides and using the min of the two as a way of skipping over
+ * characters at the beginning of a new round.
+ *
+ * Returns 0xffffffff if the query suffix matches an element of sa.
+ */
+template<typename TStr, typename TSufElt> inline
+uint32_t binarySASearch(const TStr& host,
+ uint32_t qry,
+ const String<TSufElt>& sa)
+{
+ uint32_t lLcp = 0, rLcp = 0; // greatest observed LCPs on left and right
+ uint32_t l = 0, r = length(sa)+1; // binary-search window
+ uint32_t hostLen = length(host);
+ while(true) {
+ assert_gt(r, l);
+ uint32_t m = (l+r) >> 1;
+ if(m == l) {
+ // Binary-search window has closed: we have an answer
+ if(m > 0 && sa[m-1] == qry) return 0xffffffff; // qry matches
+ assert_leq(m, length(sa));
+ return m; // Return index of right-hand suffix
+ }
+ assert_gt(m, 0);
+ uint32_t suf = sa[m-1];
+ if(suf == qry) return 0xffffffff; // query matches an elt of sa
+ uint32_t lcp = min(lLcp, rLcp);
+#ifndef NDEBUG
+ if(prefix(suffix(host, qry), lcp) != prefix(suffix(host, suf), lcp)) {
+ assert(0);
+ }
+#endif
+ // Keep advancing lcp, but stop when query mismatches host or
+ // when the counter falls off either the query or the suffix
+ while(suf+lcp < hostLen && qry+lcp < hostLen && host[suf+lcp] == host[qry+lcp]) {
+ lcp++;
+ }
+ // Fell off the end of either the query or the sa elt?
+ bool fell = (suf+lcp == hostLen || qry+lcp == hostLen);
+ if((fell && qry+lcp == hostLen) || (!fell && host[suf+lcp] < host[qry+lcp])) {
+ // Query is greater than sa elt
+ l = m; // update left bound
+ lLcp = max(lLcp, lcp); // update left lcp
+ }
+ else if((fell && suf+lcp == hostLen) || (!fell && host[suf+lcp] > host[qry+lcp])) {
+ // Query is less than sa elt
+ r = m; // update right bound
+ rLcp = max(rLcp, lcp); // update right lcp
+ } else {
+ assert(false); // Must be one or the other!
+ }
+ }
+ // Shouldn't get here
+ assert(false);
+ return 0xffffffff;
+}
+
+#endif /*BINARY_SA_SEARCH_H_*/
diff --git a/src/libSSA/karkkainen_bwt/blockwise_sa.h b/src/libSSA/karkkainen_bwt/blockwise_sa.h
new file mode 100644
index 0000000..3341fea
--- /dev/null
+++ b/src/libSSA/karkkainen_bwt/blockwise_sa.h
@@ -0,0 +1,902 @@
+#ifndef BLOCKWISE_SA_H_
+#define BLOCKWISE_SA_H_
+
+#include <stdint.h>
+#include <stdlib.h>
+#include <iostream>
+#include <sstream>
+#include <stdexcept>
+#include <vector>
+#include <seqan/sequence.h>
+#include <seqan/index.h>
+#include "assert_helpers.h"
+#include "diff_sample.h"
+#include "multikey_qsort.h"
+#include "random_source.h"
+#include "binary_sa_search.h"
+#include "zbox.h"
+#include "alphabet.h"
+#include "timer.h"
+#include "auto_array.h"
+
+using namespace std;
+using namespace seqan;
+
+// Helpers for printing verbose messages
+
+#ifndef VMSG_NL
+#define VMSG_NL(args...) \
+if(this->verbose()) { \
+ stringstream tmp; \
+ tmp << args << endl; \
+ this->verbose(tmp.str()); \
+}
+#endif
+
+#ifndef VMSG
+#define VMSG(args...) \
+if(this->verbose()) { \
+ stringstream tmp; \
+ tmp << args; \
+ this->verbose(tmp.str()); \
+}
+#endif
+
+/**
+ * Abstract parent class for blockwise suffix-array building schemes.
+ */
+template<typename TStr>
+class BlockwiseSA {
+public:
+ BlockwiseSA(const TStr& __text,
+ uint32_t __bucketSz,
+ bool __sanityCheck = false,
+ bool __passMemExc = false,
+ bool __verbose = false,
+ ostream& __logger = cout) :
+ _text(__text),
+ _bucketSz(max<uint32_t>(__bucketSz, 2u)),
+ _sanityCheck(__sanityCheck),
+ _passMemExc(__passMemExc),
+ _verbose(__verbose),
+ _itrBucket(),
+ _itrBucketPos(0xffffffff),
+ _itrPushedBackSuffix(0xffffffff),
+ _logger(__logger)
+ { }
+
+ virtual ~BlockwiseSA() { }
+
+ /**
+ * Get the next suffix; compute the next bucket if necessary.
+ */
+ uint32_t nextSuffix() {
+ if(_itrPushedBackSuffix != 0xffffffff) {
+ uint32_t tmp = _itrPushedBackSuffix;
+ _itrPushedBackSuffix = 0xffffffff;
+ return tmp;
+ }
+ while(_itrBucketPos >= length(_itrBucket) ||
+ length(_itrBucket) == 0)
+ {
+ if(!hasMoreBlocks()) {
+ throw out_of_range("No more suffixes");
+ }
+ nextBlock();
+ _itrBucketPos = 0;
+ }
+ return _itrBucket[_itrBucketPos++];
+ }
+
+ /**
+ * Return true iff the next call to nextSuffix will succeed.
+ */
+ bool hasMoreSuffixes() {
+ if(_itrPushedBackSuffix != 0xffffffff) return true;
+ try {
+ _itrPushedBackSuffix = nextSuffix();
+ } catch(out_of_range& e) {
+ assert_eq(0xffffffff, _itrPushedBackSuffix);
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Reset the suffix iterator so that the next call to nextSuffix()
+ * returns the lexicographically-first suffix.
+ */
+ void resetSuffixItr() {
+ clear(_itrBucket);
+ _itrBucketPos = 0xffffffff;
+ _itrPushedBackSuffix = 0xffffffff;
+ reset();
+ assert(suffixItrIsReset());
+ }
+
+ /**
+ * Returns true iff the next call to nextSuffix() returns the
+ * lexicographically-first suffix.
+ */
+ bool suffixItrIsReset() {
+ return length(_itrBucket) == 0 &&
+ _itrBucketPos == 0xffffffff &&
+ _itrPushedBackSuffix == 0xffffffff &&
+ isReset();
+ }
+
+ const TStr& text() const { return _text; }
+ uint32_t bucketSz() const { return _bucketSz; }
+ bool sanityCheck() const { return _sanityCheck; }
+ bool verbose() const { return _verbose; }
+ ostream& log() const { return _logger; }
+ uint32_t size() const { return length(_text)+1; }
+
+protected:
+ /// Reset back to the first block
+ virtual void reset() = 0;
+ /// Return true iff reset to the first block
+ virtual bool isReset() = 0;
+
+ /**
+ * Grab the next block of sorted suffixes. The block is guaranteed
+ * to have at most _bucketSz elements.
+ */
+ virtual void nextBlock() = 0;
+ /// Return true iff more blocks are available
+ virtual bool hasMoreBlocks() const = 0;
+ /// Optionally output a verbose message
+ void verbose(const string& s) const {
+ if(this->verbose()) {
+ this->log() << s;
+ this->log().flush();
+ }
+ }
+
+ const TStr& _text; /// original string
+ const uint32_t _bucketSz; /// target maximum bucket size
+ const bool _sanityCheck; /// whether to perform sanity checks
+ const bool _passMemExc; /// true -> pass on memory exceptions
+ const bool _verbose; /// be talkative
+ String<uint32_t> _itrBucket; /// current bucket
+ uint32_t _itrBucketPos;/// offset into current bucket
+ uint32_t _itrPushedBackSuffix; /// temporary slot for lookahead
+ ostream& _logger; /// write log messages here
+};
+
+/**
+ * Abstract parent class for a blockwise suffix array builder that
+ * always doles out blocks in lexicographical order.
+ */
+template<typename TStr>
+class InorderBlockwiseSA : public BlockwiseSA<TStr> {
+public:
+ InorderBlockwiseSA(const TStr& __text,
+ uint32_t __bucketSz,
+ bool __sanityCheck = false,
+ bool __passMemExc = false,
+ bool __verbose = false,
+ ostream& __logger = cout) :
+ BlockwiseSA<TStr>(__text, __bucketSz, __sanityCheck, __passMemExc, __verbose, __logger)
+ { }
+};
+
+/**
+ * Build the SA a block at a time according to the scheme outlined in
+ * Karkkainen's "Fast BWT" paper.
+ */
+template<typename TStr>
+class KarkkainenBlockwiseSA : public InorderBlockwiseSA<TStr> {
+public:
+ typedef DifferenceCoverSample<TStr> TDC;
+
+ KarkkainenBlockwiseSA(const TStr& __text,
+ uint32_t __bucketSz,
+ uint32_t __dcV,
+ uint32_t __seed = 0,
+ bool __sanityCheck = false,
+ bool __passMemExc = false,
+ bool __verbose = false,
+ ostream& __logger = cout) :
+ InorderBlockwiseSA<TStr>(__text, __bucketSz, __sanityCheck, __passMemExc, __verbose, __logger),
+ _sampleSuffs(), _cur(0), _dcV(__dcV), _dc(NULL), _built(false)
+ { _randomSrc.init(__seed); reset(); }
+
+ ~KarkkainenBlockwiseSA() {
+ if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
+ }
+
+ /**
+ * Allocate an amount of memory that simulates the peak memory
+ * usage of the DifferenceCoverSample with the given text and v.
+ * Throws bad_alloc if it's not going to fit in memory. Returns
+ * the approximate number of bytes the Cover takes at all times.
+ */
+ static size_t simulateAllocs(const TStr& text, uint32_t bucketSz) {
+ size_t len = length(text);
+ // _sampleSuffs and _itrBucket are in memory at the peak
+ size_t bsz = bucketSz;
+ size_t sssz = len / max<uint32_t>(bucketSz-1, 1);
+ AutoArray<uint32_t> tmp(bsz + sssz + (1024 * 1024 /*out of caution*/));
+ return bsz;
+ }
+
+ /// Defined in blockwise_sa.cpp
+ virtual void nextBlock();
+
+ /// Defined in blockwise_sa.cpp
+ virtual void qsort(String<uint32_t>& bucket);
+
+ /// Return true iff more blocks are available
+ virtual bool hasMoreBlocks() const {
+ return _cur <= length(_sampleSuffs);
+ }
+
+ /// Return the difference-cover period
+ uint32_t dcV() const { return _dcV; }
+
+protected:
+
+ /**
+ * Initialize the state of the blockwise suffix sort. If the
+ * difference cover sample and the sample set have not yet been
+ * built, build them. Then reset the block cursor to point to
+ * the first block.
+ */
+ virtual void reset() {
+ if(!_built) {
+ build();
+ }
+ assert(_built);
+ _cur = 0;
+ }
+
+ /// Return true iff we're about to dole out the first bucket
+ virtual bool isReset() {
+ return _cur == 0;
+ }
+
+private:
+
+ /**
+ * Calculate the difference-cover sample and sample suffixes.
+ */
+ void build() {
+ // Calculate difference-cover sample
+ assert(_dc == NULL);
+ if(_dcV != 0) {
+ _dc = new TDC(this->text(), _dcV, this->verbose(), this->sanityCheck());
+ _dc->build();
+ }
+ // Calculate sample suffixes
+ if(this->bucketSz() <= length(this->text())) {
+ VMSG_NL("Building samples");
+ buildSamples();
+ } else {
+ VMSG_NL("Skipping building samples since text length " <<
+ length(this->text()) << " is less than bucket size: " <<
+ this->bucketSz());
+ }
+ _built = true;
+ }
+
+ /**
+ * Calculate the lcp between two suffixes using the difference
+ * cover as a tie-breaker. If the tie-breaker is employed, then
+ * the calculated lcp may be an underestimate.
+ *
+ * Defined in blockwise_sa.cpp
+ */
+ inline bool tieBreakingLcp(uint32_t aOff,
+ uint32_t bOff,
+ uint32_t& lcp,
+ bool& lcpIsSoft);
+
+ /**
+ * Compare two suffixes using the difference-cover sample.
+ */
+ inline bool suffixCmp(uint32_t cmp,
+ uint32_t i,
+ int64_t& j,
+ int64_t& k,
+ bool& kSoft,
+ const String<uint32_t>& z);
+
+ void buildSamples();
+
+ String<uint32_t> _sampleSuffs; /// sample suffixes
+ uint32_t _cur; /// offset to 1st elt of next block
+ const uint32_t _dcV; /// difference-cover periodicity
+ TDC* _dc; /// queryable difference-cover data
+ bool _built; /// whether samples/DC have been built
+ RandomSource _randomSrc; /// source of pseudo-randoms
+};
+
+/**
+ * Qsort the set of suffixes whose offsets are in 'bucket'.
+ */
+template<typename TStr>
+void KarkkainenBlockwiseSA<TStr>::qsort(String<uint32_t>& bucket) {
+ typedef typename Value<TStr>::Type TAlphabet;
+ const TStr& t = this->text();
+ uint32_t *s = begin(bucket);
+ uint32_t slen = seqan::length(bucket);
+ uint32_t len = seqan::length(t);
+ if(_dc != NULL) {
+ // Use the difference cover as a tie-breaker if we have it
+ VMSG_NL(" (Using difference cover)");
+ // Extract the 'host' array because it's faster to work
+ // with than the String<> container
+ uint8_t *host = (uint8_t*)t.data_begin;
+ mkeyQSortSufDcU8(t, host, len, s, slen, *_dc,
+ ValueSize<TAlphabet>::VALUE,
+ this->verbose(), this->sanityCheck());
+ } else {
+ VMSG_NL(" (Not using difference cover)");
+ // We don't have a difference cover - just do a normal
+ // suffix sort
+ mkeyQSortSuf(t, s, slen, ValueSize<TAlphabet>::VALUE,
+ this->verbose(), this->sanityCheck());
+ }
+}
+
+/**
+ * Qsort the set of suffixes whose offsets are in 'bucket'. This
+ * specialization for packed strings does not attempt to extract and
+ * operate directly on the host string; the fact that the string is
+ * packed means that the array cannot be sorted directly.
+ */
+template<>
+void KarkkainenBlockwiseSA<String<Dna, Packed<> > >::qsort(String<uint32_t>& bucket) {
+ const String<Dna, Packed<> >& t = this->text();
+ uint32_t *s = begin(bucket);
+ uint32_t slen = seqan::length(bucket);
+ uint32_t len = seqan::length(t);
+ if(_dc != NULL) {
+ // Use the difference cover as a tie-breaker if we have it
+ VMSG_NL(" (Using difference cover)");
+ // Can't use the text's 'host' array because the backing
+ // store for the packed string is not one-char-per-elt.
+ mkeyQSortSufDcU8(t, t, len, s, slen, *_dc,
+ ValueSize<Dna>::VALUE,
+ this->verbose(), this->sanityCheck());
+ } else {
+ VMSG_NL(" (Not using difference cover)");
+ // We don't have a difference cover - just do a normal
+ // suffix sort
+ mkeyQSortSuf(t, s, slen, ValueSize<Dna>::VALUE,
+ this->verbose(), this->sanityCheck());
+ }
+}
+
+/**
+ * Select a set of bucket-delineating sample suffixes such that no
+ * bucket is greater than the requested upper limit. Some care is
+ * taken to make each bucket's size close to the limit without
+ * going over.
+ */
+template<typename TStr>
+void KarkkainenBlockwiseSA<TStr>::buildSamples() {
+ typedef typename Value<TStr>::Type TAlphabet;
+ const TStr& t = this->text();
+ uint32_t bsz = this->bucketSz()-1; // subtract 1 to leave room for sample
+ uint32_t len = length(this->text());
+ // Prepare _sampleSuffs array
+ clear(_sampleSuffs);
+ uint32_t numSamples = ((len/bsz)+1)<<1; // ~len/bsz x 2
+ assert_gt(numSamples, 0);
+ VMSG_NL("Reserving space for " << numSamples << " sample suffixes");
+ if(this->_passMemExc) {
+ reserve(_sampleSuffs, numSamples, Exact());
+ // Randomly generate samples. Allow duplicates for now.
+ VMSG_NL("Generating random suffixes");
+ for(size_t i = 0; i < numSamples; i++) {
+ appendValue(_sampleSuffs, _randomSrc.nextU32() % len);
+ }
+ } else {
+ try {
+ reserve(_sampleSuffs, numSamples, Exact());
+ // Randomly generate samples. Allow duplicates for now.
+ VMSG_NL("Generating random suffixes");
+ for(size_t i = 0; i < numSamples; i++) {
+ appendValue(_sampleSuffs, _randomSrc.nextU32() % len);
+ }
+ } catch(bad_alloc &e) {
+ if(this->_passMemExc) {
+ throw e; // rethrow immediately
+ } else {
+ cerr << "Could not allocate sample suffix container of " << (numSamples * 4) << " bytes." << endl
+ << "Please try using a smaller number of blocks by specifying a larger --bmax or" << endl
+ << "a smaller --bmaxdivn" << endl;
+ throw 1;
+ }
+ }
+ }
+ // Remove duplicates; very important to do this before the call to
+ // mkeyQSortSuf so that it doesn't try to calculate lexicographical
+ // relationships between very long, identical strings, which takes
+ // an extremely long time in general, and causes the stack to grow
+ // linearly with the size of the input
+ {
+ Timer timer(cout, "QSorting sample offsets, eliminating duplicates time: ", this->verbose());
+ VMSG_NL("QSorting " << length(_sampleSuffs) << " sample offsets, eliminating duplicates");
+ sort(begin(_sampleSuffs), end(_sampleSuffs));
+ size_t sslen = length(_sampleSuffs);
+ for(size_t i = 0; i < sslen-1; i++) {
+ if(_sampleSuffs[i] == _sampleSuffs[i+1]) {
+ erase(_sampleSuffs, i--);
+ sslen--;
+ }
+ }
+ }
+ // Multikey quicksort the samples
+ {
+ Timer timer(cout, " Multikey QSorting samples time: ", this->verbose());
+ VMSG_NL("Multikey QSorting " << length(_sampleSuffs) << " samples");
+ this->qsort(_sampleSuffs);
+ }
+ // Calculate bucket sizes
+ VMSG_NL("Calculating bucket sizes");
+ int limit = 5;
+ // Iterate until all buckets are less than
+ while(--limit >= 0) {
+ // Calculate bucket sizes by doing a binary search for each
+ // suffix and noting where it lands
+ uint32_t numBuckets = length(_sampleSuffs)+1;
+ String<uint32_t> bucketSzs; // holds computed bucket sizes
+ String<uint32_t> bucketReps; // holds 1 member of each bucket (for splitting)
+ try {
+ // Allocate and initialize containers for holding bucket
+ // sizes and representatives.
+ fill(bucketSzs, numBuckets, 0, Exact());
+ fill(bucketReps, numBuckets, 0xffffffff, Exact());
+ } catch(bad_alloc &e) {
+ if(this->_passMemExc) {
+ throw e; // rethrow immediately
+ } else {
+ cerr << "Could not allocate sizes, representatives (" << ((numBuckets*8)>>10) << " KB) for blocks." << endl
+ << "Please try using a smaller number of blocks by specifying a larger --bmax or a" << endl
+ << "smaller --bmaxdivn." << endl;
+ throw 1;
+ }
+ }
+ // Iterate through every suffix in the text, determine which
+ // bucket it falls into by doing a binary search across the
+ // sorted list of samples, and increment a counter associated
+ // with that bucket. Also, keep one representative for each
+ // bucket so that we can split it later. We loop in ten
+ // stretches so that we can print out a helpful progress
+ // message. (This step can take a long time.)
+ {
+ VMSG_NL(" Binary sorting into buckets");
+ Timer timer(cout, " Binary sorting into buckets time: ", this->verbose());
+ uint32_t lenDiv10 = (len + 9) / 10;
+ for(uint32_t iten = 0, ten = 0; iten < len; iten += lenDiv10, ten++) {
+ uint32_t itenNext = iten + lenDiv10;
+ if(ten > 0) VMSG_NL(" " << (ten * 10) << "%");
+ for(uint32_t i = iten; i < itenNext && i < len; i++) {
+ uint32_t r = binarySASearch(t, i, _sampleSuffs);
+ if(r == 0xffffffff) continue; // r was one of the samples
+ assert_lt(r, numBuckets);
+ bucketSzs[r]++;
+ assert_lt(bucketSzs[r], len);
+ if(bucketReps[r] == 0xffffffff ||
+ (_randomSrc.nextU32() & 100) == 0)
+ {
+ bucketReps[r] = i; // clobbers previous one, but that's OK
+ }
+ }
+ }
+ VMSG_NL(" 100%");
+ }
+ // Check for large buckets and mergeable pairs of small buckets
+ // and split/merge as necessary
+ int added = 0;
+ int merged = 0;
+ assert_eq(length(bucketSzs), numBuckets);
+ assert_eq(length(bucketReps), numBuckets);
+ {
+ Timer timer(cout, " Splitting and merging time: ", this->verbose());
+ VMSG_NL("Splitting and merging");
+ for(int64_t i = 0; i < numBuckets; i++) {
+ uint32_t mergedSz = bsz + 1;
+ assert(bucketSzs[i] == 0 || bucketReps[i] != 0xffffffff);
+ if(i < (int64_t)numBuckets-1) {
+ mergedSz = bucketSzs[i] + bucketSzs[i+1] + 1;
+ }
+ // Merge?
+ if(mergedSz <= bsz) {
+ bucketSzs[i+1] += (bucketSzs[i]+1);
+ // The following may look strange, but it's necessary
+ // to ensure that the merged bucket has a representative
+ bucketReps[i+1] = _sampleSuffs[i+added];
+ erase(_sampleSuffs, i+added);
+ erase(bucketSzs, i);
+ erase(bucketReps, i);
+ i--; // might go to -1 but ++ will overflow back to 0
+ numBuckets--;
+ merged++;
+ assert_eq(numBuckets, length(_sampleSuffs)+1-added);
+ assert_eq(numBuckets, length(bucketSzs));
+ }
+ // Split?
+ else if(bucketSzs[i] > bsz) {
+ // Add an additional sample from the bucketReps[]
+ // set accumulated in the binarySASearch loop; this
+ // effectively splits the bucket
+ insertValue(_sampleSuffs, i + (added++), bucketReps[i]);
+ }
+ }
+ }
+ if(added == 0) {
+ //if(this->verbose()) {
+ // cout << "Final bucket sizes:" << endl;
+ // cout << " (begin): " << bucketSzs[0] << " (" << (int)(bsz - bucketSzs[0]) << ")" << endl;
+ // for(uint32_t i = 1; i < numBuckets; i++) {
+ // cout << " " << bucketSzs[i] << " (" << (int)(bsz - bucketSzs[i]) << ")" << endl;
+ // }
+ //}
+ break;
+ }
+ // Otherwise, continue until no more buckets need to be
+ // split
+ VMSG_NL("Split " << added << ", merged " << merged << "; iterating...");
+ }
+ // Do *not* force a do-over
+// if(limit == 0) {
+// VMSG_NL("Iterated too many times; trying again...");
+// buildSamples();
+// }
+ VMSG_NL("Avg bucket size: " << ((float)(len-length(_sampleSuffs)) / (length(_sampleSuffs)+1)) << " (target: " << bsz << ")");
+}
+
+/**
+ * Do a simple LCP calculation on two strings.
+ */
+template<typename T> inline
+static uint32_t suffixLcp(const T& t, uint32_t aOff, uint32_t bOff) {
+ uint32_t c = 0;
+ size_t len = length(t);
+ assert_leq(aOff, len);
+ assert_leq(bOff, len);
+ while(aOff + c < len && bOff + c < len && t[aOff + c] == t[bOff + c]) c++;
+ return c;
+}
+
+/**
+ * Calculate the lcp between two suffixes using the difference
+ * cover as a tie-breaker. If the tie-breaker is employed, then
+ * the calculated lcp may be an underestimate. If the tie-breaker is
+ * employed, lcpIsSoft will be set to true (otherwise, false).
+ */
+template<typename TStr> inline
+bool KarkkainenBlockwiseSA<TStr>::tieBreakingLcp(uint32_t aOff,
+ uint32_t bOff,
+ uint32_t& lcp,
+ bool& lcpIsSoft)
+{
+ const TStr& t = this->text();
+ uint32_t c = 0;
+ uint32_t tlen = length(t);
+ assert_leq(aOff, tlen);
+ assert_leq(bOff, tlen);
+ assert(_dc != NULL);
+ uint32_t dcDist = _dc->tieBreakOff(aOff, bOff);
+ lcpIsSoft = false; // hard until proven soft
+ while(c < dcDist && // we haven't hit the tie breaker
+ c < tlen-aOff && // we haven't fallen off of LHS suffix
+ c < tlen-bOff && // we haven't fallen off of RHS suffix
+ t[aOff+c] == t[bOff+c]) // we haven't hit a mismatch
+ c++;
+ lcp = c;
+ if(c == tlen-aOff) {
+ // Fell off LHS (a), a is greater
+ return false;
+ } else if(c == tlen-bOff) {
+ // Fell off RHS (b), b is greater
+ return true;
+ } else if(c == dcDist) {
+ // Hit a tie-breaker element
+ lcpIsSoft = true;
+ assert_neq(dcDist, 0xffffffff);
+ return _dc->breakTie(aOff+c, bOff+c) < 0;
+ } else {
+ assert_neq(t[aOff+c], t[bOff+c]);
+ return t[aOff+c] < t[bOff+c];
+ }
+}
+
+/**
+ * Lookup a suffix LCP in the given z array; if the element is not
+ * filled in then calculate it from scratch.
+ */
+template<typename T>
+static uint32_t lookupSuffixZ(const T& t,
+ uint32_t zOff,
+ uint32_t off,
+ const String<uint32_t>& z)
+{
+ if(zOff < length(z)) {
+ uint32_t ret = z[zOff];
+ assert_eq(ret, suffixLcp(t, off + zOff, off));
+ return ret;
+ }
+ assert_leq(off + zOff, length(t));
+ return suffixLcp(t, off + zOff, off);
+}
+
+/**
+ * true -> i < cmp
+ * false -> i > cmp
+ */
+template<typename TStr> inline
+bool KarkkainenBlockwiseSA<TStr>::suffixCmp(uint32_t cmp,
+ uint32_t i,
+ int64_t& j,
+ int64_t& k,
+ bool& kSoft,
+ const String<uint32_t>& z)
+{
+ const TStr& t = this->text();
+ uint32_t len = length(t);
+ // i is not covered by any previous match
+ uint32_t l;
+ if(i > k) {
+ k = i; // so that i + lHi == kHi
+ l = 0; // erase any previous l
+ kSoft = false;
+ // To be extended
+ }
+ // i is covered by a previous match
+ else /* i <= k */ {
+ assert_gt((int64_t)i, j);
+ uint32_t zIdx = i-j;
+ assert_leq(zIdx, len-cmp);
+ if(zIdx < _dcV || _dc == NULL) {
+ // Go as far as the Z-box says
+ l = lookupSuffixZ(t, zIdx, cmp, z);
+ if(i + l > len) {
+ l = len-i;
+ }
+ assert_leq(i + l, len);
+ // Possibly to be extended
+ } else {
+ // But we're past the point of no-more-Z-boxes
+ bool ret = tieBreakingLcp(i, cmp, l, kSoft);
+ // Sanity-check tie-breaker
+ if(this->sanityCheck()) {
+ if(ret) assert(dollarLt(suffix(t, i), suffix(t, cmp)));
+ else assert(dollarGt(suffix(t, i), suffix(t, cmp)));
+ }
+ j = i;
+ k = i + l;
+ if(this->sanityCheck()) {
+ if(kSoft) { assert_leq(l, suffixLcp(t, i, cmp)); }
+ else { assert_eq (l, suffixLcp(t, i, cmp)); }
+ }
+ return ret;
+ }
+ }
+
+ // Z box extends exactly as far as previous match (or there
+ // is neither a Z box nor a previous match)
+ if(i + l == k) {
+ // Extend
+ while(l < len-cmp && k < len && t[cmp+l] == t[k]) {
+ k++; l++;
+ }
+ j = i; // update furthest-extending LHS
+ kSoft = false;
+ assert_eq(l, suffixLcp(t, i, cmp));
+ }
+ // Z box extends further than previous match
+ else if(i + l > k) {
+ l = k - i; // point to just after previous match
+ j = i; // update furthest-extending LHS
+ if(kSoft) {
+ while(l < len-cmp && k < len && t[cmp+l] == t[k]) {
+ k++; l++;
+ }
+ kSoft = false;
+ assert_eq(l, suffixLcp(t, i, cmp));
+ } else assert_eq(l, suffixLcp(t, i, cmp));
+ }
+
+ // Check that calculated lcp matches actual lcp
+ if(this->sanityCheck()) {
+ if(!kSoft) {
+ // l should exactly match lcp
+ assert_eq(l, suffixLcp(t, i, cmp));
+ } else {
+ // l is an underestimate of LCP
+ assert_leq(l, suffixLcp(t, i, cmp));
+ }
+ }
+ assert_leq(l+i, len);
+ assert_leq(l, len-cmp);
+
+ // i and cmp should not be the same suffix
+ assert(l != len-cmp || i+l != len);
+
+ // Now we're ready to do a comparison on the next char
+ if(l+i != len && (
+ l == len-cmp || // departure from paper algorithm:
+ // falling off pattern implies
+ // pattern is *greater* in our case
+ t[i + l] < t[cmp + l]))
+ {
+ // Case 2: Text suffix is less than upper sample suffix
+ if(this->sanityCheck()) assert(dollarLt(suffix(t, i), suffix(t, cmp)));
+ return true; // suffix at i is less than suffix at cmp
+ }
+ else {
+ // Case 3: Text suffix is greater than upper sample suffix
+ if(this->sanityCheck()) assert(dollarGt(suffix(t, i), suffix(t, cmp)));
+ return false; // suffix at i is less than suffix at cmp
+ }
+}
+
+/**
+ * Retrieve the next block. This is the most performance-critical part
+ * of the blockwise suffix sorting process.
+ */
+template<typename TStr>
+void KarkkainenBlockwiseSA<TStr>::nextBlock() {
+ typedef typename Value<TStr>::Type TAlphabet;
+ String<uint32_t>& bucket = this->_itrBucket;
+ VMSG_NL("Getting block " << (_cur+1) << " of " << length(_sampleSuffs)+1);
+ assert(_built);
+ assert_gt(_dcV, 3);
+ assert_leq(_cur, length(_sampleSuffs));
+ const TStr& t = this->text();
+ uint32_t len = length(t);
+ // Set up the bucket
+ clear(bucket);
+ uint32_t lo = 0xffffffff, hi = 0xffffffff;
+ if(length(_sampleSuffs) == 0) {
+ // Special case: if _sampleSuffs is 0, then multikey-quicksort
+ // everything
+ VMSG_NL(" No samples; assembling all-inclusive block");
+ assert_eq(0, _cur);
+ try {
+ if(capacity(bucket) < this->bucketSz()) {
+ reserve(bucket, len+1, Exact());
+ }
+ for(uint32_t i = 0; i < len; i++) append(bucket, i);
+ } catch(bad_alloc &e) {
+ if(this->_passMemExc) {
+ throw e; // rethrow immediately
+ } else {
+ cerr << "Could not allocate a master suffix-array block of " << ((len+1) * 4) << " bytes" << endl
+ << "Please try using a larger number of blocks by specifying a smaller --bmax or" << endl
+ << "a larger --bmaxdivn" << endl;
+ throw 1;
+ }
+ }
+ } else {
+ try {
+ VMSG_NL(" Reserving size (" << this->bucketSz() << ") for bucket");
+ // BTL: Add a +100 fudge factor; there seem to be instances
+ // where a bucket ends up having one more elt than bucketSz()
+ if(capacity(bucket) < this->bucketSz()+100) {
+ reserve(bucket, this->bucketSz()+100, Exact());
+ }
+ } catch(bad_alloc &e) {
+ if(this->_passMemExc) {
+ throw e; // rethrow immediately
+ } else {
+ cerr << "Could not allocate a suffix-array block of " << ((this->bucketSz()+1) * 4) << " bytes" << endl;
+ cerr << "Please try using a larger number of blocks by specifying a smaller --bmax or" << endl
+ << "a larger --bmaxdivn" << endl;
+ throw 1;
+ }
+ }
+ // Select upper and lower bounds from _sampleSuffs[] and
+ // calculate the Z array up to the difference-cover periodicity
+ // for both. Be careful about first/last buckets.
+ String<uint32_t> zLo, zHi;
+ assert_geq(_cur, 0);
+ assert_leq(_cur, length(_sampleSuffs));
+ bool first = (_cur == 0);
+ bool last = (_cur == length(_sampleSuffs));
+ try {
+ Timer timer(cout, " Calculating Z arrays time: ", this->verbose());
+ VMSG_NL(" Calculating Z arrays");
+ if(!last) {
+ // Not the last bucket
+ assert_lt(_cur, length(_sampleSuffs));
+ hi = _sampleSuffs[_cur];
+ fill(zHi, _dcV, 0, Exact());
+ assert_eq(zHi[0], 0);
+ calcZ(t, hi, zHi, this->verbose(), this->sanityCheck());
+ }
+ if(!first) {
+ // Not the first bucket
+ assert_gt(_cur, 0);
+ assert_leq(_cur, length(_sampleSuffs));
+ lo = _sampleSuffs[_cur-1];
+ fill(zLo, _dcV, 0, Exact());
+ assert_gt(_dcV, 3);
+ assert_eq(zLo[0], 0);
+ calcZ(t, lo, zLo, this->verbose(), this->sanityCheck());
+ }
+ } catch(bad_alloc &e) {
+ if(this->_passMemExc) {
+ throw e; // rethrow immediately
+ } else {
+ cerr << "Could not allocate a z-array of " << (_dcV * 4) << " bytes" << endl;
+ cerr << "Please try using a larger number of blocks by specifying a smaller --bmax or" << endl
+ << "a larger --bmaxdivn" << endl;
+ throw 1;
+ }
+ }
+
+ // This is the most critical loop in the algorithm; this is where
+ // we iterate over all suffixes in the text and pick out those that
+ // fall into the current bucket.
+ //
+ // This loop is based on the SMALLERSUFFIXES function outlined on
+ // p7 of the "Fast BWT" paper
+ //
+ int64_t kHi = -1, kLo = -1;
+ int64_t jHi = -1, jLo = -1;
+ bool kHiSoft = false, kLoSoft = false;
+ assert_eq(0, length(bucket));
+ {
+ Timer timer(cout, " Block accumulator loop time: ", this->verbose());
+ VMSG_NL(" Entering block accumulator loop:");
+ uint32_t lenDiv10 = (len + 9) / 10;
+ for(uint32_t iten = 0, ten = 0; iten < len; iten += lenDiv10, ten++) {
+ uint32_t itenNext = iten + lenDiv10;
+ if(ten > 0) VMSG_NL(" " << (ten * 10) << "%");
+ for(uint32_t i = iten; i < itenNext && i < len; i++) {
+ assert_lt(jLo, i); assert_lt(jHi, i);
+ // Advance the upper-bound comparison by one character
+ if(i == hi || i == lo) continue; // equal to one of the bookends
+ if(hi != 0xffffffff && !suffixCmp(hi, i, jHi, kHi, kHiSoft, zHi)) {
+ continue; // not in the bucket
+ }
+ if(lo != 0xffffffff && suffixCmp(lo, i, jLo, kLo, kLoSoft, zLo)) {
+ continue; // not in the bucket
+ }
+ // In the bucket! - add it
+ assert_lt(i, len);
+ try {
+ appendValue(bucket, i);
+ } catch(bad_alloc &e) {
+ if(this->_passMemExc) {
+ throw e; // rethrow immediately
+ } else {
+ cerr << "Could not append element to block of " << ((length(bucket)) * 4) << " bytes" << endl;
+ cerr << "Please try using a larger number of blocks by specifying a smaller --bmax or" << endl
+ << "a larger --bmaxdivn" << endl;
+ throw 1;
+ }
+ }
+ // Not necessarily true; we allow overflowing buckets
+ // since we can't guarantee that a good set of sample
+ // suffixes can be found in a reasonable amount of time
+ //assert_lt(length(bucket), this->bucketSz());
+ }
+ } // end loop over all suffixes of t
+ VMSG_NL(" 100%");
+ }
+ } // end else clause of if(length(_sampleSuffs) == 0)
+ // Sort the bucket
+ if(length(bucket) > 0) {
+ Timer timer(cout, " Sorting block time: ", this->verbose());
+ VMSG_NL(" Sorting block of length " << length(bucket));
+ this->qsort(bucket);
+ }
+ if(hi != 0xffffffff) {
+ // Not the final bucket; throw in the sample on the RHS
+ appendValue(bucket, hi);
+ } else {
+ // Final bucket; throw in $ suffix
+ appendValue(bucket, len);
+ }
+ VMSG_NL("Returning block of " << length(bucket));
+ _cur++; // advance to next bucket
+}
+
+#endif /*BLOCKWISE_SA_H_*/
diff --git a/src/libSSA/karkkainen_bwt/diff_sample.h b/src/libSSA/karkkainen_bwt/diff_sample.h
new file mode 100644
index 0000000..287cd69
--- /dev/null
+++ b/src/libSSA/karkkainen_bwt/diff_sample.h
@@ -0,0 +1,982 @@
+#ifndef DIFF_SAMPLE_H_
+#define DIFF_SAMPLE_H_
+
+#include <stdint.h>
+#include <seqan/sequence.h>
+#include <seqan/index.h> // for LarssonSadakane
+#include "assert_helpers.h"
+#include "multikey_qsort.h"
+#include "timer.h"
+#include "auto_array.h"
+
+using namespace std;
+using namespace seqan;
+
+#ifndef VMSG_NL
+#define VMSG_NL(args...) \
+if(this->verbose()) { \
+ stringstream tmp; \
+ tmp << args << endl; \
+ this->verbose(tmp.str()); \
+}
+#endif
+
+#ifndef VMSG
+#define VMSG(args...) \
+if(this->verbose()) { \
+ stringstream tmp; \
+ tmp << args; \
+ this->verbose(tmp.str()); \
+}
+#endif
+
+/**
+ * Routines for calculating, sanity-checking, and dispensing difference
+ * cover samples to clients.
+ */
+
+/**
+ *
+ */
+struct sampleEntry {
+ uint32_t maxV;
+ uint32_t numSamples;
+ uint32_t samples[128];
+};
+
+/// Array of Colbourn and Ling calculated difference covers up to
+/// r = 16 (maxV = 5953)
+static struct sampleEntry clDCs[16];
+static bool clDCs_calced = false; /// have clDCs been calculated?
+
+/**
+ * Check that the given difference cover 'ds' actually covers all
+ * differences for a periodicity of v.
+ */
+template<typename T>
+static bool dcRepOk(T v, String<T>& ds) {
+ // diffs[] records all the differences observed
+ bool *covered = new bool[v];
+ for(T i = 1; i < v; i++) {
+ covered[i] = false;
+ }
+ for(T di = T(); di < length(ds); di++) {
+ for(T dj = di+1; dj < length(ds); dj++) {
+ assert_lt(ds[di], ds[dj]);
+ T d1 = (ds[dj] - ds[di]);
+ T d2 = (ds[di] + v - ds[dj]);
+ assert_lt(d1, v);
+ assert_lt(d2, v);
+ covered[d1] = true;
+ covered[d2] = true;
+ }
+ }
+ bool ok = true;
+ for(T i = 1; i < v; i++) {
+ if(covered[i] == false) {
+ ok = false;
+ break;
+ }
+ }
+ delete[] covered;
+ return ok;
+}
+
+/**
+ * Return true iff each element of ts (with length 'limit') is greater
+ * than the last.
+ */
+template<typename T>
+static bool increasing(T* ts, size_t limit) {
+ for(size_t i = 0; i < limit-1; i++) {
+ if(ts[i+1] <= ts[i]) return false;
+ }
+ return true;
+}
+
+/**
+ * Return true iff the given difference cover covers difference 'diff'
+ * mod 'v'.
+ */
+template<typename T>
+static inline bool hasDifference(T *ds, T d, T v, T diff) {
+ // diffs[] records all the differences observed
+ for(T di = T(); di < d; di++) {
+ for(T dj = di+1; dj < d; dj++) {
+ assert_lt(ds[di], ds[dj]);
+ T d1 = (ds[dj] - ds[di]);
+ T d2 = (ds[di] + v - ds[dj]);
+ assert_lt(d1, v);
+ assert_lt(d2, v);
+ if(d1 == diff || d2 == diff) return true;
+ }
+ }
+ return false;
+}
+
+/**
+ * Exhaustively calculate optimal difference cover samples for v = 4,
+ * 8, 16, 32, 64, 128, 256 and store results in p2DCs[]
+ */
+template<typename T>
+void calcExhaustiveDC(T i, bool verbose = false, bool sanityCheck = false) {
+ T v = i;
+ bool *diffs = new bool[v];
+ // v is the target period
+ T ld = (T)ceil(sqrt(v));
+ // ud is the upper bound on |D|
+ T ud = v / 2;
+ // for all possible |D|s
+ bool ok = true;
+ T *ds = NULL;
+ T d;
+ for(d = ld; d <= ud+1; d++) {
+ // for all possible |D| samples
+ ds = new T[d];
+ for(T j = 0; j < d; j++) {
+ ds[j] = j;
+ }
+ assert(increasing(ds, d));
+ while(true) {
+ // reset diffs[]
+ for(T t = 1; t < v; t++) {
+ diffs[t] = false;
+ }
+ T diffCnt = 0;
+ // diffs[] records all the differences observed
+ for(T di = 0; di < d; di++) {
+ for(T dj = di+1; dj < d; dj++) {
+ assert_lt(ds[di], ds[dj]);
+ T d1 = (ds[dj] - ds[di]);
+ T d2 = (ds[di] + v - ds[dj]);
+ assert_lt(d1, v);
+ assert_lt(d2, v);
+ assert_gt(d1, 0);
+ assert_gt(d2, 0);
+ if(!diffs[d1]) diffCnt++; diffs[d1] = true;
+ if(!diffs[d2]) diffCnt++; diffs[d2] = true;
+ }
+ }
+ // Do we observe all possible differences (except 0)
+ ok = diffCnt == v-1;
+ if(ok) {
+ // Yes, all differences are covered
+ break;
+ } else {
+ // Advance ds
+ // (Following is commented out because it turns out
+ // it's slow)
+ // Find a missing difference
+ //uint32_t missing = 0xffffffff;
+ //for(uint32_t t = 1; t < v; t++) {
+ // if(diffs[t] == false) {
+ // missing = diffs[t];
+ // break;
+ // }
+ //}
+ //assert_neq(missing, 0xffffffff);
+ assert(increasing(ds, d));
+ bool advanced = false;
+ bool keepGoing = false;
+ do {
+ keepGoing = false;
+ for(T bd = d-1; bd > 1; bd--) {
+ T dif = (d-1)-bd;
+ if(ds[bd] < v-1-dif) {
+ ds[bd]++;
+ assert_neq(0, ds[bd]);
+ // Reset subsequent ones
+ for(T bdi = bd+1; bdi < d; bdi++) {
+ assert_eq(0, ds[bdi]);
+ ds[bdi] = ds[bdi-1]+1;
+ assert_gt(ds[bdi], ds[bdi-1]);
+ }
+ assert(increasing(ds, d));
+ // (Following is commented out because
+ // it turns out it's slow)
+ // See if the new DC has the missing value
+ //if(!hasDifference(ds, d, v, missing)) {
+ // keepGoing = true;
+ // break;
+ //}
+ advanced = true;
+ break;
+ } else {
+ ds[bd] = 0;
+ // keep going
+ }
+ }
+ } while(keepGoing);
+ // No solution for this |D|
+ if(!advanced) break;
+ assert(increasing(ds, d));
+ }
+ } // next sample assignment
+ if(ok) {
+ break;
+ }
+ delete[] ds;
+ } // next |D|
+ assert(ok);
+ delete[] diffs;
+ cout << "Did exhaustive v=" << v << " |D|=" << d << endl;
+ cout << " ";
+ for(T i = 0; i < d; i++) {
+ cout << ds[i];
+ if(i < d-1) cout << ",";
+ }
+ cout << endl;
+ delete[] ds;
+}
+
+/**
+ * Routune for calculating the elements of clDCs up to r = 16 using the
+ * technique of Colbourn and Ling.
+ *
+ * See http://citeseer.ist.psu.edu/211575.html
+ */
+template <typename T>
+void calcColbournAndLingDCs(bool verbose = false, bool sanityCheck = false) {
+ for(T r = 0; r < 16; r++) {
+ T maxv = 24*r*r + 36*r + 13; // Corollary 2.3
+ T numsamp = 6*r + 4;
+ clDCs[r].maxV = maxv;
+ clDCs[r].numSamples = numsamp;
+ memset(clDCs[r].samples, 0, 4 * 128);
+ T i;
+ // clDCs[r].samples[0] = 0;
+ // Fill in the 1^r part of the B series
+ for(i = 1; i < r+1; i++) {
+ clDCs[r].samples[i] = clDCs[r].samples[i-1] + 1;
+ }
+ // Fill in the (r + 1)^1 part
+ clDCs[r].samples[r+1] = clDCs[r].samples[r] + r + 1;
+ // Fill in the (2r + 1)^r part
+ for(i = r+2; i < r+2+r; i++) {
+ clDCs[r].samples[i] = clDCs[r].samples[i-1] + 2*r + 1;
+ }
+ // Fill in the (4r + 3)^(2r + 1) part
+ for(i = r+2+r; i < r+2+r+2*r+1; i++) {
+ clDCs[r].samples[i] = clDCs[r].samples[i-1] + 4*r + 3;
+ }
+ // Fill in the (2r + 2)^(r + 1) part
+ for(i = r+2+r+2*r+1; i < r+2+r+2*r+1+r+1; i++) {
+ clDCs[r].samples[i] = clDCs[r].samples[i-1] + 2*r + 2;
+ }
+ // Fill in the last 1^r part
+ for(i = r+2+r+2*r+1+r+1; i < r+2+r+2*r+1+r+1+r; i++) {
+ clDCs[r].samples[i] = clDCs[r].samples[i-1] + 1;
+ }
+ assert_eq(i, numsamp);
+ assert_lt(i, 128);
+ if(sanityCheck) {
+ // diffs[] records all the differences observed
+ bool *diffs = new bool[maxv];
+ for(T i = 0; i < numsamp; i++) {
+ for(T j = i+1; j < numsamp; j++) {
+ T d1 = (clDCs[r].samples[j] - clDCs[r].samples[i]);
+ T d2 = (clDCs[r].samples[i] + maxv - clDCs[r].samples[j]);
+ assert_lt(d1, maxv);
+ assert_lt(d2, maxv);
+ diffs[d1] = true;
+ diffs[d2] = true;
+ }
+ }
+ // Should have observed all possible differences (except 0)
+ for(T i = 1; i < maxv; i++) {
+ if(diffs[i] == false) cout << r << ", " << i << endl;
+ assert(diffs[i] == true);
+ }
+ delete[] diffs;
+ }
+ }
+ clDCs_calced = true;
+}
+
+/**
+ * Entries 4-57 are transcribed from page 6 of Luk and Wong's paper
+ * "Two New Quorum Based Algorithms for Distributed Mutual Exclusion",
+ * which is also used and cited in the Burkhardt and Karkkainen's
+ * papers on difference covers for sorting. These samples are optimal
+ * according to Luk and Wong.
+ *
+ * All other entries are generated via the exhaustive algorithm in
+ * calcExhaustiveDC().
+ *
+ * The 0 is stored at the end of the sample as an end-of-list marker,
+ * but 0 is also an element of each.
+ *
+ * Note that every difference cover has a 0 and a 1. Intuitively,
+ * any optimal difference cover sample can be oriented (i.e. rotated)
+ * such that it includes 0 and 1 as elements.
+ *
+ * All samples in this list have been verified to be complete covers.
+ *
+ * A value of 0xffffffff in the first column indicates that there is no
+ * sample for that value of v. We do not keep samples for values of v
+ * less than 3, since they are trivial (and the caller probably didn't
+ * mean to ask for it).
+ */
+static uint32_t dc0to64[65][10] = {
+ {0xffffffff}, // 0
+ {0xffffffff}, // 1
+ {0xffffffff}, // 2
+ {1, 0}, // 3
+ {1, 2, 0}, // 4
+ {1, 2, 0}, // 5
+ {1, 3, 0}, // 6
+ {1, 3, 0}, // 7
+ {1, 2, 4, 0}, // 8
+ {1, 2, 4, 0}, // 9
+ {1, 2, 5, 0}, // 10
+ {1, 2, 5, 0}, // 11
+ {1, 3, 7, 0}, // 12
+ {1, 3, 9, 0}, // 13
+ {1, 2, 3, 7, 0}, // 14
+ {1, 2, 3, 7, 0}, // 15
+ {1, 2, 5, 8, 0}, // 16
+ {1, 2, 4, 12, 0}, // 17
+ {1, 2, 5, 11, 0}, // 18
+ {1, 2, 6, 9, 0}, // 19
+ {1, 2, 3, 6, 10, 0}, // 20
+ {1, 4, 14, 16, 0}, // 21
+ {1, 2, 3, 7, 11, 0}, // 22
+ {1, 2, 3, 7, 11, 0}, // 23
+ {1, 2, 3, 7, 15, 0}, // 24
+ {1, 2, 3, 8, 12, 0}, // 25
+ {1, 2, 5, 9, 15, 0}, // 26
+ {1, 2, 5, 13, 22, 0}, // 27
+ {1, 4, 15, 20, 22, 0}, // 28
+ {1, 2, 3, 4, 9, 14, 0}, // 29
+ {1, 2, 3, 4, 9, 19, 0}, // 30
+ {1, 3, 8, 12, 18, 0}, // 31
+ {1, 2, 3, 7, 11, 19, 0}, // 32
+ {1, 2, 3, 6, 16, 27, 0}, // 33
+ {1, 2, 3, 7, 12, 20, 0}, // 34
+ {1, 2, 3, 8, 12, 21, 0}, // 35
+ {1, 2, 5, 12, 14, 20, 0}, // 36
+ {1, 2, 4, 10, 15, 22, 0}, // 37
+ {1, 2, 3, 4, 8, 14, 23, 0}, // 38
+ {1, 2, 4, 13, 18, 33, 0}, // 39
+ {1, 2, 3, 4, 9, 14, 24, 0}, // 40
+ {1, 2, 3, 4, 9, 15, 25, 0}, // 41
+ {1, 2, 3, 4, 9, 15, 25, 0}, // 42
+ {1, 2, 3, 4, 10, 15, 26, 0}, // 43
+ {1, 2, 3, 6, 16, 27, 38, 0}, // 44
+ {1, 2, 3, 5, 12, 18, 26, 0}, // 45
+ {1, 2, 3, 6, 18, 25, 38, 0}, // 46
+ {1, 2, 3, 5, 16, 22, 40, 0}, // 47
+ {1, 2, 5, 9, 20, 26, 36, 0}, // 48
+ {1, 2, 5, 24, 33, 36, 44, 0}, // 49
+ {1, 3, 8, 17, 28, 32, 38, 0}, // 50
+ {1, 2, 5, 11, 18, 30, 38, 0}, // 51
+ {1, 2, 3, 4, 6, 14, 21, 30, 0}, // 52
+ {1, 2, 3, 4, 7, 21, 29, 44, 0}, // 53
+ {1, 2, 3, 4, 9, 15, 21, 31, 0}, // 54
+ {1, 2, 3, 4, 6, 19, 26, 47, 0}, // 55
+ {1, 2, 3, 4, 11, 16, 33, 39, 0}, // 56
+ {1, 3, 13, 32, 36, 43, 52, 0}, // 57
+
+ // Generated by calcExhaustiveDC()
+ {1, 2, 3, 7, 21, 33, 37, 50, 0}, // 58
+ {1, 2, 3, 6, 13, 21, 35, 44, 0}, // 59
+ {1, 2, 4, 9, 15, 25, 30, 42, 0}, // 60
+ {1, 2, 3, 7, 15, 25, 36, 45, 0}, // 61
+ {1, 2, 4, 10, 32, 39, 46, 51, 0}, // 62
+ {1, 2, 6, 8, 20, 38, 41, 54, 0}, // 63
+ {1, 2, 5, 14, 16, 34, 42, 59, 0} // 64
+};
+
+/**
+ * Get a difference cover for the requested periodicity v.
+ */
+template <typename T>
+static String<T> getDiffCover(T v,
+ bool verbose = false,
+ bool sanityCheck = false)
+{
+ assert_gt(v, 2);
+ String<T> ret;
+
+ // Can we look it up in our hardcoded array?
+ if(v <= 64 && dc0to64[v][0] == 0xffffffff) {
+ if(verbose) cout << "v in hardcoded area, but hardcoded entry was all-fs" << endl;
+ return ret;
+ } else if(v <= 64) {
+ append(ret, 0);
+ for(size_t i = 0; i < 10; i++) {
+ if(dc0to64[v][i] == 0) break;
+ append(ret, dc0to64[v][i]);
+ }
+ if(sanityCheck) assert(dcRepOk(v, ret));
+ return ret;
+ }
+
+ // Can we look it up in our calcColbournAndLingDCs array?
+ if(!clDCs_calced) {
+ calcColbournAndLingDCs<uint32_t>(verbose, sanityCheck);
+ assert(clDCs_calced);
+ }
+ for(size_t i = 0; i < 16; i++) {
+ if(v <= clDCs[i].maxV) {
+ for(size_t j = 0; j < clDCs[i].numSamples; j++) {
+ T s = clDCs[i].samples[j];
+ if(s >= v) {
+ s %= v;
+ for(size_t k = 0; k < length(ret); k++) {
+ if(s == ret[k]) break;
+ if(s < ret[k]) {
+ insertValue(ret, k, s);
+ break;
+ }
+ }
+ } else {
+ append(ret, s % v);
+ }
+ }
+ if(sanityCheck) assert(dcRepOk(v, ret));
+ return ret;
+ }
+ }
+ cerr << "Error: Could not find a difference cover sample for v=" << v << endl;
+ throw 1;
+}
+
+/**
+ * Calculate and return a delta map based on the given difference cover
+ * and periodicity v.
+ */
+template <typename T>
+static String<T> getDeltaMap(T v, const String<T>& dc) {
+ // Declare anchor-map-related items
+ String<T> amap;
+ size_t amapEnts = 1;
+ fill(amap, v, 0xffffffff, Exact());
+ amap[0] = 0;
+ // Print out difference cover (and optionally calculate
+ // anchor map)
+ for(size_t i = 0; i < length(dc); i++) {
+ for(size_t j = i+1; j < length(dc); j++) {
+ assert_gt(dc[j], dc[i]);
+ T diffLeft = dc[j] - dc[i];
+ T diffRight = dc[i] + v - dc[j];
+ assert_lt(diffLeft, v);
+ assert_lt(diffRight, v);
+ if(amap[diffLeft] == 0xffffffff) {
+ amap[diffLeft] = dc[i];
+ amapEnts++;
+ }
+ if(amap[diffRight] == 0xffffffff) {
+ amap[diffRight] = dc[j];
+ amapEnts++;
+ }
+ }
+ }
+ return amap;
+}
+
+/**
+ * Return population count (count of all bits set to 1) of i.
+ */
+template<typename T>
+static unsigned int popCount(T i) {
+ unsigned int cnt = 0;
+ for(size_t j = 0; j < sizeof(T)*8; j++) {
+ if(i & 1) cnt++;
+ i >>= 1;
+ }
+ return cnt;
+}
+
+/**
+ * Calculate log-base-2 of i
+ */
+template<typename T>
+static unsigned int myLog2(T i) {
+ assert_eq(1, popCount(i)); // must be power of 2
+ for(size_t j = 0; j < sizeof(T)*8; j++) {
+ if(i & 1) return j;
+ i >>= 1;
+ }
+ assert(false);
+ return 0xffffffff;
+}
+
+/**
+ *
+ */
+template<typename TStr>
+class DifferenceCoverSample {
+public:
+
+ DifferenceCoverSample(const TStr& __text,
+ uint32_t __v,
+ bool __verbose = false,
+ bool __sanity = false,
+ ostream& __logger = cout) :
+ _text(__text),
+ _v(__v),
+ _verbose(__verbose),
+ _sanity(__sanity),
+ _ds(getDiffCover(_v, _verbose, _sanity)),
+ _dmap(getDeltaMap(_v, _ds)),
+ _d(length(_ds)),
+ _doffs(),
+ _isaPrime(),
+ _dInv(),
+ _log2v(myLog2(_v)),
+ _vmask(0xffffffff << _log2v),
+ _logger(__logger)
+ {
+ assert_gt(_d, 0);
+ assert_eq(1, popCount(_v)); // must be power of 2
+ // Build map from d's to idx's
+ fill(_dInv, _v, 0xffffffff, Exact());
+ for(size_t i = 0; i < length(_ds); i++) _dInv[_ds[i]] = i;
+ }
+
+ /**
+ * Allocate an amount of memory that simulates the peak memory
+ * usage of the DifferenceCoverSample with the given text and v.
+ * Throws bad_alloc if it's not going to fit in memory. Returns
+ * the approximate number of bytes the Cover takes at all times.
+ */
+ static size_t simulateAllocs(const TStr& text, uint32_t v) {
+ String<uint32_t> ds = getDiffCover(v, false /*verbose*/, false /*sanity*/);
+ size_t len = length(text);
+ size_t sPrimeSz = (len / v) * length(ds);
+ // sPrime, sPrimeOrder, _isaPrime all exist in memory at
+ // once and that's the peak
+ AutoArray<uint32_t> aa(sPrimeSz * 3 + (1024 * 1024 /*out of caution*/));
+ return sPrimeSz * 4; // sPrime array
+ }
+
+ uint32_t v() const { return _v; }
+ uint32_t log2v() const { return _log2v; }
+ uint32_t vmask() const { return _vmask; }
+ uint32_t modv(uint32_t i) const { return i & ~_vmask; }
+ uint32_t divv(uint32_t i) const { return i >> _log2v; }
+ uint32_t d() const { return _d; }
+ bool verbose() const { return _verbose; }
+ bool sanityCheck() const { return _sanity; }
+ const TStr& text() const { return _text; }
+ const String<uint32_t>& ds() const { return _ds; }
+ const String<uint32_t>& dmap() const { return _dmap; }
+ ostream& log() const { return _logger; }
+
+ void build();
+ uint32_t tieBreakOff(uint32_t i, uint32_t j) const;
+ int64_t breakTie(uint32_t i, uint32_t j) const;
+ bool isCovered(uint32_t i) const;
+ uint32_t rank(uint32_t i) const;
+
+ /**
+ * Print out the suffix array such that every sample offset has its
+ * rank filled in and every non-sample offset is shown as '-'.
+ */
+ void print(ostream& out) {
+ for(size_t i = 0; i < length(_text); i++) {
+ if(isCovered(i)) {
+ out << rank(i);
+ } else {
+ out << "-";
+ }
+ if(i < length(_text)-1) {
+ out << ",";
+ }
+ }
+ out << endl;
+ }
+
+private:
+
+ void doBuiltSanityCheck() const;
+ void buildSPrime(String<uint32_t>& sPrime);
+
+ bool built() const {
+ return length(_isaPrime) > 0;
+ }
+
+ void verbose(const string& s) const {
+ if(this->verbose()) {
+ this->log() << s;
+ this->log().flush();
+ }
+ }
+
+ const TStr& _text; // text to sample
+ uint32_t _v; // periodicity of sample
+ bool _verbose; //
+ bool _sanity; //
+ String<uint32_t> _ds; // samples: idx -> d
+ String<uint32_t> _dmap; // delta map
+ uint32_t _d; // |D| - size of sample
+ String<uint32_t> _doffs; // offsets into sPrime/isaPrime for each d idx
+ String<uint32_t> _isaPrime; // ISA' array
+ String<uint32_t> _dInv; // Map from d -> idx
+ uint32_t _log2v;
+ uint32_t _vmask;
+ ostream& _logger;
+};
+
+/**
+ * Return true iff suffixes with offsets suf1 and suf2 out of host
+ * string 'host' are identical up to depth 'v'.
+ */
+template <typename TStr>
+static inline bool suffixLt(const TStr& host, uint32_t suf1, uint32_t suf2) {
+ uint32_t hlen = length(host);
+ assert_neq(suf1, suf2);
+ uint32_t i = 0;
+ while(suf1 + i < hlen && suf2 + i < hlen) {
+ if(host[suf1+i] < host[suf2+i]) return true;
+ if(host[suf1+i] > host[suf2+i]) return false;
+ i++;
+ }
+ if(suf1 + i == hlen) {
+ assert_lt(suf2 + i, hlen);
+ return false;
+ }
+ assert_eq(suf2 + i, hlen);
+ return true;
+}
+
+/**
+ * Sanity-check the difference cover by first inverting _isaPrime then
+ * checking that each successive suffix really is less than the next.
+ */
+template <typename TStr>
+void DifferenceCoverSample<TStr>::doBuiltSanityCheck() const {
+ uint32_t v = this->v();
+ assert(built());
+ VMSG_NL(" Doing sanity check");
+ uint32_t added = 0;
+ String<uint32_t> sorted;
+ fill(sorted, length(_isaPrime), 0xffffffff, Exact());
+ for(size_t di = 0; di < this->d(); di++) {
+ uint32_t d = _ds[di];
+ size_t i = 0;
+ for(size_t doi = _doffs[di]; doi < _doffs[di+1]; doi++, i++) {
+ assert_eq(0xffffffff, sorted[_isaPrime[doi]]);
+ // Maps the offset of the suffix to its rank
+ sorted[_isaPrime[doi]] = v*i + d;
+ added++;
+ }
+ }
+ assert_eq(added, length(_isaPrime));
+ for(size_t i = 0; i < length(sorted)-1; i++) {
+ assert(suffixLt(this->text(), sorted[i], sorted[i+1]));
+ }
+}
+
+/**
+ * Build the s' array by sampling suffixes (suffix offsets, actually)
+ * from t according to the difference-cover sample and pack them into
+ * an array of machine words in the order dictated by the "mu" mapping
+ * described in Burkhardt.
+ *
+ * Also builds _doffs map.
+ */
+template <typename TStr>
+void DifferenceCoverSample<TStr>::buildSPrime(String<uint32_t>& sPrime) {
+ const TStr& t = this->text();
+ const String<uint32_t>& ds = this->ds();
+ uint32_t tlen = length(t);
+ uint32_t v = this->v();
+ uint32_t d = this->d();
+ assert_gt(v, 2);
+ assert_lt(d, v);
+ // Record where each d section should begin in sPrime
+ uint32_t tlenDivV = this->divv(tlen);
+ uint32_t tlenModV = this->modv(tlen);
+ uint32_t sPrimeSz = 0;
+ assert(empty(_doffs));
+ reserve(_doffs, d+1, Exact());
+ assert_eq(capacity(_doffs), d+1);
+ for(uint32_t di = 0; di < d; di++) {
+ // mu mapping
+ uint32_t sz = tlenDivV + ((ds[di] <= tlenModV) ? 1 : 0);
+ assert_geq(sz, 0);
+ appendValue(_doffs, sPrimeSz);
+ sPrimeSz += sz;
+ }
+ appendValue(_doffs, sPrimeSz);
+ #ifndef NDEBUG
+ if(tlenDivV > 0) {
+ for(size_t i = 0; i < d; i++) {
+ assert_gt(_doffs[i+1], _doffs[i]);
+ uint32_t diff = _doffs[i+1] - _doffs[i];
+ assert(diff == tlenDivV || diff == tlenDivV+1);
+ }
+ }
+ #endif
+ assert_eq(length(_doffs), d+1);
+ // Size sPrime appropriately
+ reserve(sPrime, sPrimeSz+1, Exact()); // reserve extra slot for LS
+ fill(sPrime, sPrimeSz, 0xffffffff, Exact());
+ // Slot suffixes from text into sPrime according to the mu
+ // mapping; where the mapping would leave a blank, insert a 0
+ uint32_t added = 0;
+ uint32_t i = 0;
+ for(uint32_t ti = 0; ti <= tlen; ti += v) {
+ for(uint32_t di = 0; di < d; di++) {
+ uint32_t tti = ti + ds[di];
+ if(tti > tlen) break;
+ uint32_t spi = _doffs[di] + i;
+ assert_lt(spi, _doffs[di+1]);
+ assert_leq(tti, tlen);
+ assert_lt(spi, sPrimeSz);
+ assert_eq(0xffffffff, sPrime[spi]);
+ sPrime[spi] = tti; added++;
+ }
+ i++;
+ }
+ assert_eq(added, sPrimeSz);
+}
+
+/**
+ * Return true iff suffixes with offsets suf1 and suf2 out of host
+ * string 'host' are identical up to depth 'v'.
+ */
+template <typename TStr>
+static inline bool suffixSameUpTo(const TStr& host,
+ uint32_t suf1,
+ uint32_t suf2,
+ uint32_t v)
+{
+ for(uint32_t i = 0; i < v; i++) {
+ bool endSuf1 = suf1+i >= length(host);
+ bool endSuf2 = suf2+i >= length(host);
+ if((endSuf1 && !endSuf2) || (!endSuf1 && endSuf2)) return false;
+ if(endSuf1 && endSuf2) return true;
+ if(host[suf1+i] != host[suf2+i]) return false;
+ }
+ return true;
+}
+
+/**
+ * Calculates a ranking of all suffixes in the sample and stores them,
+ * packed according to the mu mapping, in _isaPrime.
+ */
+template <typename TStr>
+void DifferenceCoverSample<TStr>::build() {
+ // Local names for relevant types
+ typedef typename Value<TStr>::Type TAlphabet;
+ VMSG_NL("Building DifferenceCoverSample");
+ // Local names for relevant data
+ const TStr& t = this->text();
+ uint32_t v = this->v();
+ assert_gt(v, 2);
+ // Build s'
+ String<uint32_t> sPrime;
+ VMSG_NL(" Building sPrime");
+ buildSPrime(sPrime);
+ assert_gt(length(sPrime), 0);
+ assert_leq(length(sPrime), length(t)+1); // +1 is because of the end-cap
+ uint32_t nextRank = 0;
+ {
+ VMSG_NL(" Building sPrimeOrder");
+ String<uint32_t> sPrimeOrder;
+ reserve(sPrimeOrder, length(sPrime)+1, Exact()); // reserve extra slot for LS
+ resize(sPrimeOrder, length(sPrime), Exact());
+ for(size_t i = 0; i < length(sPrimeOrder); i++) {
+ sPrimeOrder[i] = i;
+ }
+ // sPrime now holds suffix-offsets for DC samples.
+ {
+ Timer timer(cout, " V-Sorting samples time: ", this->verbose());
+ VMSG_NL(" V-Sorting samples");
+ // Extract backing-store array from sPrime and sPrimeOrder;
+ // the mkeyQSortSuf2 routine works on the array for maximum
+ // efficiency
+ uint32_t *sPrimeArr = (uint32_t*)begin(sPrime);
+ size_t slen = length(sPrime);
+ assert_eq(sPrimeArr[0], sPrime[0]);
+ assert_eq(sPrimeArr[slen-1], sPrime[slen-1]);
+ uint32_t *sPrimeOrderArr = (uint32_t*)begin(sPrimeOrder);
+ assert_eq(sPrimeOrderArr[0], sPrimeOrder[0]);
+ assert_eq(sPrimeOrderArr[slen-1], sPrimeOrder[slen-1]);
+ // Sort sample suffixes up to the vth character using a
+ // multikey quicksort. Sort time is proportional to the
+ // number of samples times v. It isn't quadratic.
+ // sPrimeOrder is passed in as a swapping partner for
+ // sPrimeArr, i.e., every time the multikey qsort swaps
+ // elements in sPrime, it swaps the same elements in
+ // sPrimeOrder too. This allows us to easily reconstruct
+ // what the sort did.
+ mkeyQSortSuf2(t, sPrimeArr, slen, sPrimeOrderArr,
+ ValueSize<TAlphabet>::VALUE,
+ this->verbose(), this->sanityCheck(), v);
+ // Make sure sPrime and sPrimeOrder are consistent with
+ // their respective backing-store arrays
+ assert_eq(sPrimeArr[0], sPrime[0]);
+ assert_eq(sPrimeArr[slen-1], sPrime[slen-1]);
+ assert_eq(sPrimeOrderArr[0], sPrimeOrder[0]);
+ assert_eq(sPrimeOrderArr[slen-1], sPrimeOrder[slen-1]);
+ }
+ // Now assign the ranking implied by the sorted sPrime/sPrimeOrder
+ // arrays back into sPrime.
+ VMSG_NL(" Allocating rank array");
+ reserve(_isaPrime, length(sPrime)+1, Exact());
+ fill(_isaPrime, length(sPrime), 0xffffffff, Exact());
+ assert_gt(length(_isaPrime), 0);
+ {
+ Timer timer(cout, " Ranking v-sort output time: ", this->verbose());
+ VMSG_NL(" Ranking v-sort output");
+ for(size_t i = 0; i < length(sPrime)-1; i++) {
+ // Place the appropriate ranking
+ _isaPrime[sPrimeOrder[i]] = nextRank;
+ // If sPrime[i] and sPrime[i+1] are identical up to v, then we
+ // should give the next suffix the same rank
+ if(!suffixSameUpTo(t, sPrime[i], sPrime[i+1], v)) nextRank++;
+ }
+ _isaPrime[sPrimeOrder[length(sPrime)-1]] = nextRank; // finish off
+ }
+ // sPrimeOrder is destroyed
+ // All the information we need is now in _isaPrime
+ }
+ #ifndef NDEBUG
+ // Check that all ranks are sane
+ for(size_t i = 0; i < length(_isaPrime); i++) {
+ assert_neq(_isaPrime[i], 0xffffffff);
+ assert_lt(_isaPrime[i], length(_isaPrime));
+ }
+ #endif
+ // Now pass the sPrimeRanks[] array to LarssonSadakane (in SeqAn).
+ append(_isaPrime, length(_isaPrime));
+ append(sPrime, length(sPrime));
+ {
+ Timer timer(cout, " Invoking Larsson-Sadakane on ranks time: ", this->verbose());
+ VMSG_NL(" Invoking Larsson-Sadakane on ranks");
+ createSuffixArray(sPrime, _isaPrime, LarssonSadakane(), length(_isaPrime));
+ }
+ // sPrime now contains the suffix array (which we ignore)
+ assert_eq(length(_isaPrime), length(sPrime));
+ assert_gt(length(_isaPrime), 0);
+ // chop off final character of _isaPrime
+ resize(_isaPrime, length(_isaPrime)-1);
+ // Subtract 1 from each isaPrime (to adjust for LarssonSadakane
+ // always ranking the final suffix as lexicographically first)
+ for(size_t i = 0; i < length(_isaPrime); i++) {
+ _isaPrime[i]--;
+ }
+ VMSG_NL(" Sanity-checking and returning");
+
+ // done!
+ //if(this->verbose()) print(cout);
+ if(this->sanityCheck()) doBuiltSanityCheck();
+}
+
+/**
+ * Return true iff index i within the text is covered by the difference
+ * cover sample. Allow i to be off the end of the text; simplifies
+ * logic elsewhere.
+ */
+template <typename TStr>
+bool DifferenceCoverSample<TStr>::isCovered(uint32_t i) const {
+ assert(built());
+ uint32_t modi = this->modv(i);
+ assert_lt(modi, length(_dInv));
+ return _dInv[modi] != 0xffffffff;
+}
+
+/**
+ * Given a text offset that's covered, return its lexicographical rank
+ * among the sample suffixes.
+ */
+template <typename TStr>
+uint32_t DifferenceCoverSample<TStr>::rank(uint32_t i) const {
+ assert(built());
+ assert_lt(i, length(this->text()));
+ uint32_t imodv = this->modv(i);
+ assert_neq(0xffffffff, _dInv[imodv]); // must be in the sample
+ uint32_t ioff = this->divv(i);
+ assert_lt(ioff, _doffs[_dInv[imodv]+1] - _doffs[_dInv[imodv]]);
+ uint32_t isaIIdx = _doffs[_dInv[imodv]] + ioff;
+ assert_lt(isaIIdx, length(_isaPrime));
+ uint32_t isaPrimeI = _isaPrime[isaIIdx];
+ assert_leq(isaPrimeI, length(_isaPrime));
+ return isaPrimeI;
+}
+
+/**
+ * Return: < 0 if suffix i is lexicographically less than suffix j; > 0
+ * if suffix j is lexicographically greater.
+ */
+template <typename TStr>
+int64_t DifferenceCoverSample<TStr>::breakTie(uint32_t i, uint32_t j) const {
+ assert(built());
+ assert_neq(i, j);
+ assert_lt(i, length(this->text()));
+ assert_lt(j, length(this->text()));
+ uint32_t imodv = this->modv(i);
+ uint32_t jmodv = this->modv(j);
+ assert_neq(0xffffffff, _dInv[imodv]); // must be in the sample
+ assert_neq(0xffffffff, _dInv[jmodv]); // must be in the sample
+ uint32_t dimodv = _dInv[imodv];
+ uint32_t djmodv = _dInv[jmodv];
+ uint32_t ioff = this->divv(i);
+ uint32_t joff = this->divv(j);
+ assert_lt(dimodv+1, length(_doffs));
+ assert_lt(djmodv+1, length(_doffs));
+ // assert_lt: expected (32024) < (0)
+ assert_lt(ioff, _doffs[dimodv+1] - _doffs[dimodv]);
+ assert_lt(joff, _doffs[djmodv+1] - _doffs[djmodv]);
+ uint32_t isaIIdx = _doffs[dimodv] + ioff;
+ uint32_t isaJIdx = _doffs[djmodv] + joff;
+ assert_lt(isaIIdx, length(_isaPrime));
+ assert_lt(isaJIdx, length(_isaPrime));
+ assert_neq(isaIIdx, isaJIdx); // ranks must be unique
+ uint32_t isaPrimeI = _isaPrime[isaIIdx];
+ uint32_t isaPrimeJ = _isaPrime[isaJIdx];
+ assert_neq(isaPrimeI, isaPrimeJ); // ranks must be unique
+ assert_leq(isaPrimeI, length(_isaPrime));
+ assert_leq(isaPrimeJ, length(_isaPrime));
+ return (int64_t)isaPrimeI - (int64_t)isaPrimeJ;
+}
+
+/**
+ * Given i, j, return the number of additional characters that need to
+ * be compared before the difference cover can break the tie.
+ */
+template <typename TStr>
+uint32_t DifferenceCoverSample<TStr>::tieBreakOff(uint32_t i, uint32_t j) const {
+ const TStr& t = this->text();
+ const String<uint32_t>& dmap = this->dmap();
+ assert(built());
+ // It's actually convenient to allow this, but we're permitted to
+ // return nonsense in that case
+ if(t[i] != t[j]) return 0xffffffff;
+ //assert_eq(t[i], t[j]); // if they're unequal, there's no tie to break
+ uint32_t v = this->v();
+ assert_neq(i, j);
+ assert_lt(i, length(t));
+ assert_lt(j, length(t));
+ uint32_t imod = this->modv(i);
+ uint32_t jmod = this->modv(j);
+ uint32_t diffLeft = (jmod >= imod)? (jmod - imod) : (jmod + v - imod);
+ uint32_t diffRight = (imod >= jmod)? (imod - jmod) : (imod + v - jmod);
+ assert_lt(diffLeft, length(dmap));
+ assert_lt(diffRight, length(dmap));
+ uint32_t destLeft = dmap[diffLeft]; // offset where i needs to be
+ uint32_t destRight = dmap[diffRight]; // offset where i needs to be
+ assert(isCovered(destLeft));
+ assert(isCovered(destLeft+diffLeft));
+ assert(isCovered(destRight));
+ assert(isCovered(destRight+diffRight));
+ assert_lt(destLeft, v);
+ assert_lt(destRight, v);
+ uint32_t deltaLeft = (destLeft >= imod)? (destLeft - imod) : (destLeft + v - imod);
+ if(deltaLeft == v) deltaLeft = 0;
+ uint32_t deltaRight = (destRight >= jmod)? (destRight - jmod) : (destRight + v - jmod);
+ if(deltaRight == v) deltaRight = 0;
+ assert_lt(deltaLeft, v);
+ assert_lt(deltaRight, v);
+ assert(isCovered(i+deltaLeft));
+ assert(isCovered(j+deltaLeft));
+ assert(isCovered(i+deltaRight));
+ assert(isCovered(j+deltaRight));
+ return min(deltaLeft, deltaRight);
+}
+
+#endif /*DIFF_SAMPLE_H_*/
diff --git a/src/libSSA/karkkainen_bwt/multikey_qsort.h b/src/libSSA/karkkainen_bwt/multikey_qsort.h
new file mode 100644
index 0000000..f7837ab
--- /dev/null
+++ b/src/libSSA/karkkainen_bwt/multikey_qsort.h
@@ -0,0 +1,1144 @@
+#ifndef MULTIKEY_QSORT_H_
+#define MULTIKEY_QSORT_H_
+
+#include <iostream>
+#include <seqan/basic.h>
+#include <seqan/file.h>
+#include <seqan/sequence.h>
+#include "alphabet.h"
+#include "assert_helpers.h"
+#include "diff_sample.h"
+
+using namespace std;
+using namespace seqan;
+
+/**
+ * Swap elements a and b in seqan::String s
+ */
+template <typename TStr, typename TPos>
+static inline void swap(TStr& s, size_t slen, TPos a, TPos b) {
+ typedef typename Value<TStr>::Type TAlphabet;
+ assert_lt(a, slen);
+ assert_lt(b, slen);
+ TAlphabet tmp = s[a];
+ s[a] = s[b];
+ s[b] = tmp;
+}
+
+/**
+ * Swap elements a and b in array s
+ */
+template <typename TVal, typename TPos>
+static inline void swap(TVal* s, size_t slen, TPos a, TPos b) {
+ assert_lt(a, slen);
+ assert_lt(b, slen);
+ TVal tmp = s[a];
+ s[a] = s[b];
+ s[b] = tmp;
+}
+
+/**
+ * Helper macro for swapping elements a and b in seqan::String s. Does
+ * some additional sainty checking w/r/t begin and end (which are
+ * parameters to the sorting routines below).
+ */
+#define SWAP(s, a, b) { \
+ assert_geq(a, begin); \
+ assert_geq(b, begin); \
+ assert_lt(a, end); \
+ assert_lt(b, end); \
+ swap(s, slen, a, b); \
+}
+
+/**
+ * Helper macro for swapping the same pair of elements a and b in
+ * two different seqan::Strings s and s2. This is a helpful variant
+ * if, for example, the caller would like to see how their input was
+ * permuted by the sort routine (in that case, the caller would let s2
+ * be an array s2[] where s2 is the same length as s and s2[i] = i).
+ */
+#define SWAP2(s, s2, a, b) { \
+ SWAP(s, a, b); \
+ swap(s2, slen, a, b); \
+}
+
+#define SWAP1(s, s2, a, b) { \
+ SWAP(s, a, b); \
+}
+
+/**
+ * Helper macro that swaps a range of elements [i, i+n) with another
+ * range [j, j+n) in seqan::String s.
+ */
+#define VECSWAP(s, i, j, n) { \
+ if(n > 0) { vecswap(s, slen, i, j, n, begin, end); } \
+}
+
+/**
+ * Helper macro that swaps a range of elements [i, i+n) with another
+ * range [j, j+n) both in seqan::String s and seqan::String s2.
+ */
+#define VECSWAP2(s, s2, i, j, n) { \
+ if(n > 0) { vecswap2(s, slen, s2, i, j, n, begin, end); } \
+}
+
+/**
+ * Helper function that swaps a range of elements [i, i+n) with another
+ * range [j, j+n) in seqan::String s. begin and end represent the
+ * current range under consideration by the caller (one of the
+ * recursive multikey_quicksort routines below).
+ */
+template <typename TStr, typename TPos>
+static inline void vecswap(TStr& s, size_t slen, TPos i, TPos j, TPos n, TPos begin, TPos end) {
+ assert_geq(i, begin);
+ assert_geq(j, begin);
+ assert_lt(i, end);
+ assert_lt(j, end);
+ while(n-- > 0) {
+ assert_geq(n, 0);
+ TPos a = i+n;
+ TPos b = j+n;
+ assert_geq(a, begin);
+ assert_geq(b, begin);
+ assert_lt(a, end);
+ assert_lt(b, end);
+ swap(s, slen, a, b);
+ }
+}
+
+template <typename TVal, typename TPos>
+static inline void vecswap(TVal *s, size_t slen, TPos i, TPos j, TPos n, TPos begin, TPos end) {
+ assert_geq(i, begin);
+ assert_geq(j, begin);
+ assert_lt(i, end);
+ assert_lt(j, end);
+ while(n-- > 0) {
+ assert_geq(n, 0);
+ TPos a = i+n;
+ TPos b = j+n;
+ assert_geq(a, begin);
+ assert_geq(b, begin);
+ assert_lt(a, end);
+ assert_lt(b, end);
+ swap(s, slen, a, b);
+ }
+}
+
+/**
+ * Helper function that swaps a range of elements [i, i+n) with another
+ * range [j, j+n) both in seqan::String s and seqan::String s2. begin
+ * and end represent the current range under consideration by the
+ * caller (one of the recursive multikey_quicksort routines below).
+ */
+template <typename TStr, typename TPos>
+static inline void vecswap2(TStr& s, size_t slen, TStr& s2, TPos i, TPos j, TPos n, TPos begin, TPos end) {
+ assert_geq(i, begin);
+ assert_geq(j, begin);
+ assert_lt(i, end);
+ assert_lt(j, end);
+ while(n-- > 0) {
+ assert_geq(n, 0);
+ TPos a = i+n;
+ TPos b = j+n;
+ assert_geq(a, begin);
+ assert_geq(b, begin);
+ assert_lt(a, end);
+ assert_lt(b, end);
+ swap(s, slen, a, b);
+ swap(s2, slen, a, b);
+ }
+}
+
+template <typename TVal, typename TPos>
+static inline void vecswap2(TVal* s, size_t slen, TVal* s2, TPos i, TPos j, TPos n, TPos begin, TPos end) {
+ assert_geq(i, begin);
+ assert_geq(j, begin);
+ assert_lt(i, end);
+ assert_lt(j, end);
+ while(n-- > 0) {
+ assert_geq(n, 0);
+ TPos a = i+n;
+ TPos b = j+n;
+ assert_geq(a, begin);
+ assert_geq(b, begin);
+ assert_lt(a, end);
+ assert_lt(b, end);
+ swap(s, slen, a, b);
+ swap(s2, slen, a, b);
+ }
+}
+
+/// Retrieve an int-ized version of the ath character of string s, or,
+/// if a goes off the end of s, return a (user-specified) int greater
+/// than any TAlphabet character - 'hi'.
+#define CHAR_AT(ss, aa) ((length(s[ss]) > aa) ? (int)(Dna)(s[ss][aa]) : hi)
+
+/// Retrieve an int-ized version of the ath character of string s, or,
+/// if a goes off the end of s, return a (user-specified) int greater
+/// than any TAlphabet character - 'hi'.
+#define CHAR_AT_SUF(si, off) (((off+s[si]) < hlen) ? ((int)(Dna)(host[off+s[si]])) : (hi))
+
+/// Retrieve an int-ized version of the ath character of string s, or,
+/// if a goes off the end of s, return a (user-specified) int greater
+/// than any TAlphabet character - 'hi'.
+
+#define CHAR_AT_SUF_U8(si, off) char_at_suf_u8(host, hlen, s, si, off, hi)
+
+// Note that CHOOSE_AND_SWAP_RANDOM_PIVOT is unused
+#define CHOOSE_AND_SWAP_RANDOM_PIVOT(sw, ch) { \
+ /* Note: rand() didn't really cut it here; it seemed to run out of */ \
+ /* randomness and, after a time, returned the same thing over and */ \
+ /* over again */ \
+ a = (rand() % n) + begin; /* choose pivot between begin and end */ \
+ assert_lt(a, end); assert_geq(a, begin); \
+ sw(s, s2, begin, a); /* move pivot to beginning */ \
+}
+
+/**
+ * Ad-hoc DNA-centric way of choose a pretty good pivot without using
+ * the pseudo-random number generator. We try to get a 1 or 2 if
+ * possible, since they'll split things more evenly than a 0 or 4. We
+ * also avoid swapping in the event that we choose the first element.
+ */
+#define CHOOSE_AND_SWAP_SMART_PIVOT(sw, ch) { \
+ a = begin; /* choose first elt */ \
+ /* now try to find a better elt */ \
+ if(n >= 5) { /* n is the difference between begin and end */ \
+ if (ch(begin+1, depth) == 1 || ch(begin+1, depth) == 2) a = begin+1; \
+ else if(ch(begin+2, depth) == 1 || ch(begin+2, depth) == 2) a = begin+2; \
+ else if(ch(begin+3, depth) == 1 || ch(begin+3, depth) == 2) a = begin+3; \
+ else if(ch(begin+4, depth) == 1 || ch(begin+4, depth) == 2) a = begin+4; \
+ if(a != begin) sw(s, s2, begin, a); /* move pivot to beginning */ \
+ } \
+ /* the element at [begin] now holds the pivot value */ \
+}
+
+#define CHOOSE_AND_SWAP_PIVOT CHOOSE_AND_SWAP_SMART_PIVOT
+
+#ifndef NDEBUG
+
+/**
+ * Assert that the range of chars at depth 'depth' in strings 'begin'
+ * to 'end' in string-of-suffix-offsets s is parititioned properly
+ * according to the ternary paritioning strategy of Bentley and McIlroy
+ * (*prior to* swapping the = regions to the center)
+ */
+template<typename THost>
+bool assertPartitionedSuf(const THost& host,
+ uint32_t *s,
+ size_t slen,
+ int hi,
+ int pivot,
+ size_t begin,
+ size_t end,
+ size_t depth)
+{
+ size_t hlen = length(host);
+ int state = 0; // 0 -> 1st = section, 1 -> < section, 2 -> > section, 3 -> 2nd = section
+ for(size_t i = begin; i < end; i++) {
+ switch(state) {
+ case 0:
+ if (CHAR_AT_SUF(i, depth) < pivot) { state = 1; break; }
+ else if (CHAR_AT_SUF(i, depth) > pivot) { state = 2; break; }
+ assert_eq(CHAR_AT_SUF(i, depth), pivot); break;
+ case 1:
+ if (CHAR_AT_SUF(i, depth) > pivot) { state = 2; break; }
+ else if (CHAR_AT_SUF(i, depth) == pivot) { state = 3; break; }
+ assert_lt(CHAR_AT_SUF(i, depth), pivot); break;
+ case 2:
+ if (CHAR_AT_SUF(i, depth) == pivot) { state = 3; break; }
+ assert_gt(CHAR_AT_SUF(i, depth), pivot); break;
+ case 3:
+ assert_eq(CHAR_AT_SUF(i, depth), pivot); break;
+ }
+ }
+ return true;
+}
+
+/**
+ * Assert that the range of chars at depth 'depth' in strings 'begin'
+ * to 'end' in string-of-suffix-offsets s is parititioned properly
+ * according to the ternary paritioning strategy of Bentley and McIlroy
+ * (*after* swapping the = regions to the center)
+ */
+template<typename THost>
+bool assertPartitionedSuf2(const THost& host,
+ uint32_t *s,
+ size_t slen,
+ int hi,
+ int pivot,
+ size_t begin,
+ size_t end,
+ size_t depth)
+{
+ size_t hlen = length(host);
+ int state = 0; // 0 -> < section, 1 -> = section, 2 -> > section
+ for(size_t i = begin; i < end; i++) {
+ switch(state) {
+ case 0:
+ if (CHAR_AT_SUF(i, depth) == pivot) { state = 1; break; }
+ else if (CHAR_AT_SUF(i, depth) > pivot) { state = 2; break; }
+ assert_lt(CHAR_AT_SUF(i, depth), pivot); break;
+ case 1:
+ if (CHAR_AT_SUF(i, depth) > pivot) { state = 2; break; }
+ assert_eq(CHAR_AT_SUF(i, depth), pivot); break;
+ case 2:
+ assert_gt(CHAR_AT_SUF(i, depth), pivot); break;
+ }
+ }
+ return true;
+}
+#endif
+
+/**
+ * Assert that the seqan::String s of suffix offsets into seqan::String
+ * 'host' is a seemingly legitimate suffix-offset list (at this time,
+ * we just check that it doesn't list any suffix twice).
+ */
+static void sanityCheckInputSufs(uint32_t *s, size_t slen) {
+ assert_gt(slen, 0);
+ for(size_t i = 0; i < slen; i++) {
+ // Actually, it's convenient to allow the caller to provide
+ // suffix offsets thare are off the end of the host string.
+ // See, e.g., build() in diff_sample.cpp.
+ //assert_lt(s[i], length(host));
+ for(size_t j = i+1; j < slen; j++) {
+ assert_neq(s[i], s[j]);
+ }
+ }
+}
+
+/**
+ * Assert that the seqan::String s of suffix offsets into seqan::String
+ * 'host' really are in lexicographical order up to depth 'upto'.
+ */
+template <typename T>
+void sanityCheckOrderedSufs(const T& host,
+ size_t hlen,
+ uint32_t *s,
+ size_t slen,
+ size_t upto,
+ uint32_t lower = 0,
+ uint32_t upper = 0xffffffff)
+{
+ assert_lt(s[0], hlen);
+ upper = min<uint32_t>(upper, slen-1);
+ for(size_t i = lower; i < upper; i++) {
+ // Allow s[i+t] to point off the end of the string; this is
+ // convenient for some callers
+ if(s[i+1] >= hlen) continue;
+ if(upto == 0xffffffff) {
+ assert(dollarLt(suffix(host, s[i]), suffix(host, s[i+1])));
+ } else {
+#ifndef NDEBUG
+ if(prefix(suffix(host, s[i]), upto) > prefix(suffix(host, s[i+1]), upto)) {
+ // operator > treats shorter strings as
+ // lexicographically smaller, but we want to opposite
+ assert(isPrefix(suffix(host, s[i+1]), suffix(host, s[i])));
+ }
+#endif
+ }
+ }
+}
+
+/**
+ * Main multikey quicksort function for suffixes. Based on Bentley &
+ * Sedgewick's algorithm on p.5 of their paper "Fast Algorithms for
+ * Sorting and Searching Strings". That algorithm has been extended in
+ * three ways:
+ *
+ * 1. Deal with keys of different lengths by checking bounds and
+ * considering off-the-end values to be 'hi' (b/c our goal is the
+ * BWT transform, we're biased toward considring prefixes as
+ * lexicographically *greater* than their extensions).
+ * 2. The multikey_qsort_suffixes version takes a single host string
+ * and a list of suffix offsets as input. This reduces memory
+ * footprint compared to an approach that treats its input
+ * generically as a set of strings (not necessarily suffixes), thus
+ * requiring that we store at least two integers worth of
+ * information for each string.
+ * 3. Sorting functions take an extra "upto" parameter that upper-
+ * bounds the depth to which the function sorts.
+ *
+ * TODO: Consult a tie-breaker (like a difference cover sample) if two
+ * keys share a long prefix.
+ */
+template<typename T>
+void mkeyQSortSuf(const T& host,
+ size_t hlen,
+ uint32_t *s,
+ size_t slen,
+ int hi,
+ size_t begin,
+ size_t end,
+ size_t depth,
+ size_t upto = 0xffffffff)
+{
+ // Helper for making the recursive call; sanity-checks arguments to
+ // make sure that the problem actually got smaller.
+ #define MQS_RECURSE_SUF(nbegin, nend, ndepth) { \
+ assert(nbegin > begin || nend < end || ndepth > depth); \
+ if(ndepth < upto) { /* don't exceed depth of 'upto' */ \
+ mkeyQSortSuf(host, hlen, s, slen, hi, nbegin, nend, ndepth, upto); \
+ } \
+ }
+ assert_leq(begin, slen);
+ assert_leq(end, slen);
+ size_t a, b, c, d, /*e,*/ r;
+ size_t n = end - begin;
+ if(n <= 1) return; // 1-element list already sorted
+ CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF); // pick pivot, swap it into [begin]
+ int v = CHAR_AT_SUF(begin, depth); // v <- randomly-selected pivot value
+ #ifndef NDEBUG
+ {
+ bool stillInBounds = false;
+ for(size_t i = begin; i < end; i++) {
+ if(depth < (hlen-s[i])) {
+ stillInBounds = true;
+ break;
+ } else { /* already fell off this suffix */ }
+ }
+ assert(stillInBounds); // >=1 suffix must still be in bounds
+ }
+ #endif
+ a = b = begin;
+ c = d = end-1;
+ while(true) {
+ // Invariant: everything before a is = pivot, everything
+ // between a and b is <
+ int bc = 0; // shouldn't have to init but gcc on Mac complains
+ while(b <= c && v >= (bc = CHAR_AT_SUF(b, depth))) {
+ if(v == bc) {
+ SWAP(s, a, b); a++;
+ }
+ b++;
+ }
+ // Invariant: everything after d is = pivot, everything
+ // between c and d is >
+ int cc = 0; // shouldn't have to init but gcc on Mac complains
+ while(b <= c && v <= (cc = CHAR_AT_SUF(c, depth))) {
+ if(v == cc) {
+ SWAP(s, c, d); d--;
+ }
+ c--;
+ }
+ if(b > c) break;
+ SWAP(s, b, c);
+ b++;
+ c--;
+ }
+ assert(a > begin || c < end-1); // there was at least one =s
+ assert_lt(d-c, n); // they can't all have been > pivot
+ assert_lt(b-a, n); // they can't all have been < pivot
+ assert(assertPartitionedSuf(host, s, slen, hi, v, begin, end, depth)); // check pre-=-swap invariant
+ r = min(a-begin, b-a); VECSWAP(s, begin, b-r, r); // swap left = to center
+ r = min(d-c, end-d-1); VECSWAP(s, b, end-r, r); // swap right = to center
+ assert(assertPartitionedSuf2(host, s, slen, hi, v, begin, end, depth)); // check post-=-swap invariant
+ r = b-a; // r <- # of <'s
+ if(r > 0) {
+ MQS_RECURSE_SUF(begin, begin + r, depth); // recurse on <'s
+ }
+ // Do not recurse on ='s if the pivot was the off-the-end value;
+ // they're already fully sorted
+ if(v != hi) {
+ MQS_RECURSE_SUF(begin + r, begin + r + (a-begin) + (end-d-1), depth+1); // recurse on ='s
+ }
+ r = d-c; // r <- # of >'s excluding those exhausted
+ if(r > 0 && v < hi-1) {
+ MQS_RECURSE_SUF(end-r, end, depth); // recurse on >'s
+ }
+}
+
+/**
+ * Toplevel function for multikey quicksort over suffixes.
+ */
+template<typename T>
+void mkeyQSortSuf(const T& host,
+ uint32_t *s,
+ size_t slen,
+ int hi,
+ bool verbose = false,
+ bool sanityCheck = false,
+ size_t upto = 0xffffffff)
+{
+ size_t hlen = length(host);
+ assert(!empty(s));
+ if(sanityCheck) sanityCheckInputSufs(s, slen);
+ mkeyQSortSuf(host, hlen, s, slen, hi, (size_t)0, slen, (size_t)0, upto);
+ if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
+}
+
+/**
+ * Just like mkeyQSortSuf but all swaps are applied to s2 as well as s.
+ * This is a helpful variant if, for example, the caller would like to
+ * see how their input was permuted by the sort routine (in that case,
+ * the caller would let s2 be an array s2[] where s2 is the same length
+ * as s and s2[i] = i).
+ */
+template<typename T>
+void mkeyQSortSuf2(const T& host,
+ size_t hlen,
+ uint32_t *s,
+ size_t slen,
+ uint32_t *s2,
+ int hi,
+ size_t begin,
+ size_t end,
+ size_t depth,
+ size_t upto = 0xffffffff)
+{
+ // Helper for making the recursive call; sanity-checks arguments to
+ // make sure that the problem actually got smaller.
+ #define MQS_RECURSE_SUF_DS(nbegin, nend, ndepth) { \
+ assert(nbegin > begin || nend < end || ndepth > depth); \
+ if(ndepth < upto) { /* don't exceed depth of 'upto' */ \
+ mkeyQSortSuf2(host, hlen, s, slen, s2, hi, nbegin, nend, ndepth, upto); \
+ } \
+ }
+ assert_leq(begin, slen);
+ assert_leq(end, slen);
+ size_t a, b, c, d, /*e,*/ r;
+ size_t n = end - begin;
+ if(n <= 1) return; // 1-element list already sorted
+ CHOOSE_AND_SWAP_PIVOT(SWAP2, CHAR_AT_SUF); // pick pivot, swap it into [begin]
+ int v = CHAR_AT_SUF(begin, depth); // v <- randomly-selected pivot value
+ #ifndef NDEBUG
+ {
+ bool stillInBounds = false;
+ for(size_t i = begin; i < end; i++) {
+ if(depth < (hlen-s[i])) {
+ stillInBounds = true;
+ break;
+ } else { /* already fell off this suffix */ }
+ }
+ assert(stillInBounds); // >=1 suffix must still be in bounds
+ }
+ #endif
+ a = b = begin;
+ c = d = /*e =*/ end-1;
+ while(true) {
+ // Invariant: everything before a is = pivot, everything
+ // between a and b is <
+ int bc = 0; // shouldn't have to init but gcc on Mac complains
+ while(b <= c && v >= (bc = CHAR_AT_SUF(b, depth))) {
+ if(v == bc) {
+ SWAP2(s, s2, a, b); a++;
+ }
+ b++;
+ }
+ // Invariant: everything after d is = pivot, everything
+ // between c and d is >
+ int cc = 0; // shouldn't have to init but gcc on Mac complains
+ while(b <= c && v <= (cc = CHAR_AT_SUF(c, depth))) {
+ if(v == cc) {
+ SWAP2(s, s2, c, d); d--; /*e--;*/
+ }
+ //else if(c == e && v == hi) e--;
+ c--;
+ }
+ if(b > c) break;
+ SWAP2(s, s2, b, c);
+ b++;
+ c--;
+ }
+ assert(a > begin || c < end-1); // there was at least one =s
+ assert_lt(/*e*/d-c, n); // they can't all have been > pivot
+ assert_lt(b-a, n); // they can't all have been < pivot
+ assert(assertPartitionedSuf(host, s, slen, hi, v, begin, end, depth)); // check pre-=-swap invariant
+ r = min(a-begin, b-a); VECSWAP2(s, s2, begin, b-r, r); // swap left = to center
+ r = min(d-c, end-d-1); VECSWAP2(s, s2, b, end-r, r); // swap right = to center
+ assert(assertPartitionedSuf2(host, s, slen, hi, v, begin, end, depth)); // check post-=-swap invariant
+ r = b-a; // r <- # of <'s
+ if(r > 0) {
+ MQS_RECURSE_SUF_DS(begin, begin + r, depth); // recurse on <'s
+ }
+ // Do not recurse on ='s if the pivot was the off-the-end value;
+ // they're already fully sorted
+ if(v != hi) {
+ MQS_RECURSE_SUF_DS(begin + r, begin + r + (a-begin) + (end-d-1), depth+1); // recurse on ='s
+ }
+ r = d-c; // r <- # of >'s excluding those exhausted
+ if(r > 0 && v < hi-1) {
+ MQS_RECURSE_SUF_DS(end-r, end, depth); // recurse on >'s
+ }
+}
+
+/**
+ * Toplevel function for multikey quicksort over suffixes with double
+ * swapping.
+ */
+template<typename T>
+void mkeyQSortSuf2(const T& host,
+ uint32_t *s,
+ size_t slen,
+ uint32_t *s2,
+ int hi,
+ bool verbose = false,
+ bool sanityCheck = false,
+ size_t upto = 0xffffffff)
+{
+ size_t hlen = length(host);
+ if(sanityCheck) sanityCheckInputSufs(s, slen);
+ uint32_t *sOrig = NULL;
+ if(sanityCheck) {
+ sOrig = new uint32_t[slen];
+ memcpy(sOrig, s, 4 * slen);
+ }
+ mkeyQSortSuf2(host, hlen, s, slen, s2, hi, (size_t)0, slen, (size_t)0, upto);
+ if(sanityCheck) {
+ sanityCheckOrderedSufs(host, hlen, s, slen, upto);
+ for(size_t i = 0; i < slen; i++) {
+ assert_eq(s[i], sOrig[s2[i]]);
+ }
+ }
+}
+
+// Ugly but necessary; otherwise the compiler chokes dramatically on
+// the DifferenceCoverSample<> template args to the next few functions
+template <typename T>
+class DifferenceCoverSample;
+
+/**
+ * Constant time
+ */
+template<typename T1, typename T2> inline
+bool sufDcLt(const T1& host,
+ const T2& s1,
+ const T2& s2,
+ const DifferenceCoverSample<T1>& dc,
+ bool sanityCheck = false)
+{
+ uint32_t diff = dc.tieBreakOff(s1, s2);
+ assert_lt(diff, dc.v());
+ assert_lt(diff, length(host)-s1);
+ assert_lt(diff, length(host)-s2);
+ if(sanityCheck) {
+ for(uint32_t i = 0; i < diff; i++) {
+ assert_eq(host[s1+i], host[s2+i]);
+ }
+ }
+ bool ret = dc.breakTie(s1+diff, s2+diff) < 0;
+#ifndef NDEBUG
+ if(sanityCheck && ret != dollarLt(suffix(host, s1), suffix(host, s2))) {
+ assert(false);
+ }
+#endif
+ return ret;
+}
+
+/**
+ * k log(k)
+ */
+template<typename T> inline
+void qsortSufDc(const T& host,
+ size_t hlen,
+ uint32_t* s,
+ size_t slen,
+ const DifferenceCoverSample<T>& dc,
+ size_t begin,
+ size_t end,
+ bool sanityCheck = false)
+{
+ assert_leq(end, slen);
+ assert_lt(begin, slen);
+ assert_gt(end, begin);
+ size_t n = end - begin;
+ if(n <= 1) return; // 1-element list already sorted
+ // Note: rand() didn't really cut it here; it seemed to run out of
+ // randomness and, after a time, returned the same thing over and
+ // over again
+ size_t a = (rand() % n) + begin; // choose pivot between begin and end
+ assert_lt(a, end);
+ assert_geq(a, begin);
+ SWAP(s, end-1, a); // move pivot to end
+ size_t cur = 0;
+ for(size_t i = begin; i < end-1; i++) {
+ if(sufDcLt(host, s[i], s[end-1], dc, sanityCheck)) {
+ if(sanityCheck)
+ assert(dollarLt(suffix(host, s[i]), suffix(host, s[end-1])));
+ assert_lt(begin + cur, end-1);
+ SWAP(s, i, begin + cur);
+ cur++;
+ }
+ }
+ // Put pivot into place
+ assert_lt(cur, end-begin);
+ SWAP(s, end-1, begin+cur);
+ if(begin+cur > begin) qsortSufDc(host, hlen, s, slen, dc, begin, begin+cur);
+ if(end > begin+cur+1) qsortSufDc(host, hlen, s, slen, dc, begin+cur+1, end);
+}
+
+/**
+ * Toplevel function for multikey quicksort over suffixes.
+ */
+template<typename T1, typename T2>
+void mkeyQSortSufDcU8(const T1& seqanHost,
+ const T2& host,
+ size_t hlen,
+ uint32_t* s,
+ size_t slen,
+ const DifferenceCoverSample<T1>& dc,
+ int hi,
+ bool verbose = false,
+ bool sanityCheck = false)
+{
+ if(sanityCheck) sanityCheckInputSufs(s, slen);
+ mkeyQSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck);
+ if(sanityCheck) sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff);
+}
+
+/**
+ * Return a boolean indicating whether s1 < s2 using the difference
+ * cover to break the tie.
+ */
+template<typename T1, typename T2> inline
+bool sufDcLtU8(const T1& seqanHost,
+ const T2& host,
+ size_t hlen,
+ uint32_t s1,
+ uint32_t s2,
+ const DifferenceCoverSample<T1>& dc,
+ bool sanityCheck = false)
+{
+ hlen += 0;
+ uint32_t diff = dc.tieBreakOff(s1, s2);
+ assert_lt(diff, dc.v());
+ assert_lt(diff, hlen-s1);
+ assert_lt(diff, hlen-s2);
+ if(sanityCheck) {
+ for(uint32_t i = 0; i < diff; i++) {
+ assert_eq(host[s1+i], host[s2+i]);
+ }
+ }
+ bool ret = dc.breakTie(s1+diff, s2+diff) < 0;
+ // Sanity-check return value using dollarLt
+#ifndef NDEBUG
+ if(sanityCheck &&
+ ret != dollarLt(suffix(seqanHost, s1), suffix(seqanHost, s2)))
+ {
+ assert(false);
+ }
+#endif
+ return ret;
+}
+
+/**
+ * k log(k)
+ */
+template<typename T1, typename T2> inline
+void qsortSufDcU8(const T1& seqanHost,
+ const T2& host,
+ size_t hlen,
+ uint32_t* s,
+ size_t slen,
+ const DifferenceCoverSample<T1>& dc,
+ size_t begin,
+ size_t end,
+ bool sanityCheck = false)
+{
+ assert_leq(end, slen);
+ assert_lt(begin, slen);
+ assert_gt(end, begin);
+ size_t n = end - begin;
+ if(n <= 1) return; // 1-element list already sorted
+ // Note: rand() didn't really cut it here; it seemed to run out of
+ // randomness and, after a time, returned the same thing over and
+ // over again
+ size_t a = (rand() % n) + begin; // choose pivot between begin and end
+ assert_lt(a, end);
+ assert_geq(a, begin);
+ SWAP(s, end-1, a); // move pivot to end
+ size_t cur = 0;
+ for(size_t i = begin; i < end-1; i++) {
+ if(sufDcLtU8(seqanHost, host, hlen, s[i], s[end-1], dc, sanityCheck)) {
+#ifndef NDEBUG
+ if(sanityCheck)
+ assert(dollarLt(suffix(seqanHost, s[i]), suffix(seqanHost, s[end-1])));
+ assert_lt(begin + cur, end-1);
+#endif
+ SWAP(s, i, begin + cur);
+ cur++;
+ }
+ }
+ // Put pivot into place
+ assert_lt(cur, end-begin);
+ SWAP(s, end-1, begin+cur);
+ if(begin+cur > begin) qsortSufDcU8(seqanHost, host, hlen, s, slen, dc, begin, begin+cur);
+ if(end > begin+cur+1) qsortSufDcU8(seqanHost, host, hlen, s, slen, dc, begin+cur+1, end);
+}
+
+#define BUCKET_SORT_CUTOFF (4 * 1024 * 1024)
+#define SELECTION_SORT_CUTOFF 6
+
+// 5 64-element buckets for bucket-sorting A, C, G, T, $
+static uint32_t bkts[4][4 * 1024 * 1024];
+
+/**
+ * Straightforwardly obtain a uint8_t-ized version of t[off]. This
+ * works fine as long as TStr is not packed.
+ */
+template<typename TStr>
+inline uint8_t get_uint8(const TStr& t, uint32_t off) {
+ return t[off];
+}
+
+/**
+ * For incomprehensible generic-programming reasons, getting a uint8_t
+ * version of a character in a packed String<> requires casting first
+ * to Dna then to uint8_t.
+ */
+template<>
+inline uint8_t get_uint8(const String<Dna, Packed<> >& t, uint32_t off) {
+ return (uint8_t)(Dna)t[off];
+}
+
+/**
+ * Return character at offset 'off' from the 'si'th suffix in the array
+ * 's' of suffixes. If the character is out-of-bounds, return hi.
+ */
+template<typename TStr>
+static inline int char_at_suf_u8(const TStr& host,
+ uint32_t hlen,
+ uint32_t* s,
+ uint32_t si,
+ uint32_t off,
+ uint8_t hi)
+{
+ return ((off+s[si]) < hlen) ? get_uint8(host, off+s[si]) : (hi);
+}
+
+template<typename T1, typename T2>
+static void selectionSortSufDcU8(
+ const T1& seqanHost,
+ const T2& host,
+ size_t hlen,
+ uint32_t* s,
+ size_t slen,
+ const DifferenceCoverSample<T1>& dc,
+ uint8_t hi,
+ size_t begin,
+ size_t end,
+ size_t depth,
+ bool sanityCheck = false)
+{
+#define ASSERT_SUF_LT(l, r) \
+ if(sanityCheck && \
+ !dollarLt(suffix(seqanHost, s[l]), \
+ suffix(seqanHost, s[r]))) { \
+ cout << "l: " << suffixStr(seqanHost, s[l]) << endl; \
+ cout << "r: " << suffixStr(seqanHost, s[r]) << endl; \
+ assert(false); \
+ }
+
+ assert_gt(end, begin+1);
+ assert_leq(end-begin, SELECTION_SORT_CUTOFF);
+ assert_eq(hi, 4);
+ uint32_t v = dc.v();
+ if(end == begin+2) {
+ uint32_t off = dc.tieBreakOff(s[begin], s[begin+1]);
+ if(off + s[begin] >= hlen ||
+ off + s[begin+1] >= hlen)
+ {
+ off = 0xffffffff;
+ }
+ if(off != 0xffffffff) {
+ if(off < depth) {
+ qsortSufDcU8<T1,T2>(seqanHost, host, hlen, s, slen, dc,
+ begin, end, sanityCheck);
+ // It's helpful for debugging if we call this here
+ if(sanityCheck) {
+ sanityCheckOrderedSufs(seqanHost, hlen, s, slen,
+ 0xffffffff, begin, end);
+ }
+ return;
+ }
+ v = off - depth + 1;
+ }
+ }
+ assert_leq(v, dc.v());
+ uint32_t lim = v;
+ assert_geq(lim, 0);
+ for(size_t i = begin; i < end-1; i++) {
+ uint32_t targ = i;
+ uint32_t targoff = depth + s[i];
+ for(size_t j = i+1; j < end; j++) {
+ assert_neq(j, targ);
+ uint32_t joff = depth + s[j];
+ uint32_t k;
+ for(k = 0; k <= lim; k++) {
+ assert_neq(j, targ);
+ uint8_t jc = (k + joff < hlen) ? get_uint8(host, k + joff) : hi;
+ uint8_t tc = (k + targoff < hlen) ? get_uint8(host, k + targoff) : hi;
+ assert(jc != hi || tc != hi);
+ if(jc > tc) {
+ // the jth suffix is greater than the current
+ // smallest suffix
+ ASSERT_SUF_LT(targ, j);
+ break;
+ } else if(jc < tc) {
+ // the jth suffix is less than the current smallest
+ // suffix, so update smallest to be j
+ ASSERT_SUF_LT(j, targ);
+ targ = j;
+ targoff = joff;
+ break;
+ } else if(k == lim) {
+ // Check whether either string ends immediately
+ // after this character
+ assert_leq(k + joff + 1, hlen);
+ assert_leq(k + targoff + 1, hlen);
+ if(k + joff + 1 == hlen) {
+ // targ < j
+ assert_neq(k + targoff + 1, hlen);
+ ASSERT_SUF_LT(targ, j);
+ break;
+ } else if(k + targoff + 1 == hlen) {
+ // j < targ
+ ASSERT_SUF_LT(j, targ);
+ targ = j;
+ targoff = joff;
+ break;
+ }
+ } else {
+ // They're equal so far, keep going
+ }
+ }
+ // The jth suffix was equal to the current smallest suffix
+ // up to the difference-cover period, so disambiguate with
+ // difference cover
+ if(k == lim+1) {
+ assert_neq(j, targ);
+ if(sufDcLtU8(seqanHost, host, hlen, s[j], s[targ], dc, sanityCheck)) {
+ // j < targ
+ assert(!sufDcLtU8(seqanHost, host, hlen, s[targ], s[j], dc, sanityCheck));
+ ASSERT_SUF_LT(j, targ);
+ targ = j;
+ targoff = joff;
+ } else {
+ assert(sufDcLtU8(seqanHost, host, hlen, s[targ], s[j], dc, sanityCheck));
+ ASSERT_SUF_LT(targ, j); // !
+ }
+ }
+ }
+ if(i != targ) {
+ ASSERT_SUF_LT(targ, i);
+ // swap i and targ
+ uint32_t tmp = s[i];
+ s[i] = s[targ];
+ s[targ] = tmp;
+ }
+ for(size_t j = i+1; j < end; j++) {
+ ASSERT_SUF_LT(i, j);
+ }
+ }
+ if(sanityCheck) {
+ sanityCheckOrderedSufs(seqanHost, hlen, s, slen,
+ 0xffffffff, begin, end);
+ }
+}
+
+template<typename T1, typename T2>
+static void bucketSortSufDcU8(
+ const T1& seqanHost,
+ const T2& host,
+ size_t hlen,
+ uint32_t* s,
+ size_t slen,
+ const DifferenceCoverSample<T1>& dc,
+ uint8_t hi,
+ size_t begin,
+ size_t end,
+ size_t depth,
+ bool sanityCheck = false)
+{
+ uint32_t cnts[] = { 0, 0, 0, 0, 0 };
+ #define BKT_RECURSE_SUF_DC_U8(nbegin, nend) { \
+ bucketSortSufDcU8<T1,T2>(seqanHost, host, hlen, s, slen, dc, hi, \
+ (nbegin), (nend), depth+1, sanityCheck); \
+ }
+ assert_gt(end, begin);
+ assert_leq(end-begin, BUCKET_SORT_CUTOFF);
+ assert_eq(hi, 4);
+ if(end == begin+1) return; // 1-element list already sorted
+ if(depth > dc.v()) {
+ // Quicksort the remaining suffixes using difference cover
+ // for constant-time comparisons; this is O(k*log(k)) where
+ // k=(end-begin)
+ qsortSufDcU8<T1,T2>(seqanHost, host, hlen, s, slen, dc, begin, end, sanityCheck);
+ return;
+ }
+ if(end-begin <= SELECTION_SORT_CUTOFF) {
+ // Bucket sort remaining items
+ selectionSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi,
+ begin, end, depth, sanityCheck);
+ if(sanityCheck) {
+ sanityCheckOrderedSufs(seqanHost, hlen, s, slen,
+ 0xffffffff, begin, end);
+ }
+ return;
+ }
+ for(size_t i = begin; i < end; i++) {
+ uint32_t off = depth+s[i];
+ uint8_t c = (off < hlen) ? get_uint8(host, off) : hi;
+ assert_leq(c, 4);
+ if(c == 0) {
+ s[begin + cnts[0]++] = s[i];
+ } else {
+ bkts[c-1][cnts[c]++] = s[i];
+ }
+ }
+ assert_eq(cnts[0] + cnts[1] + cnts[2] + cnts[3] + cnts[4], end - begin);
+ uint32_t cur = begin + cnts[0];
+ if(cnts[1] > 0) { memcpy(&s[cur], bkts[0], cnts[1] << 2); cur += cnts[1]; }
+ if(cnts[2] > 0) { memcpy(&s[cur], bkts[1], cnts[2] << 2); cur += cnts[2]; }
+ if(cnts[3] > 0) { memcpy(&s[cur], bkts[2], cnts[3] << 2); cur += cnts[3]; }
+ if(cnts[4] > 0) { memcpy(&s[cur], bkts[3], cnts[4] << 2); }
+ // This frame is now totally finished with bkts[][], so recursive
+ // callees can safely clobber it; we're not done with cnts[], but
+ // that's local to the stack frame.
+ cur = begin;
+ if(cnts[0] > 0) {
+ BKT_RECURSE_SUF_DC_U8(cur, cur + cnts[0]); cur += cnts[0];
+ }
+ if(cnts[1] > 0) {
+ BKT_RECURSE_SUF_DC_U8(cur, cur + cnts[1]); cur += cnts[1];
+ }
+ if(cnts[2] > 0) {
+ BKT_RECURSE_SUF_DC_U8(cur, cur + cnts[2]); cur += cnts[2];
+ }
+ if(cnts[3] > 0) {
+ BKT_RECURSE_SUF_DC_U8(cur, cur + cnts[3]);
+ }
+ // Done
+}
+
+/**
+ * Main multikey quicksort function for suffixes. Based on Bentley &
+ * Sedgewick's algorithm on p.5 of their paper "Fast Algorithms for
+ * Sorting and Searching Strings". That algorithm has been extended in
+ * three ways:
+ *
+ * 1. Deal with keys of different lengths by checking bounds and
+ * considering off-the-end values to be 'hi' (b/c our goal is the
+ * BWT transform, we're biased toward considring prefixes as
+ * lexicographically *greater* than their extensions).
+ * 2. The multikey_qsort_suffixes version takes a single host string
+ * and a list of suffix offsets as input. This reduces memory
+ * footprint compared to an approach that treats its input
+ * generically as a set of strings (not necessarily suffixes), thus
+ * requiring that we store at least two integers worth of
+ * information for each string.
+ * 3. Sorting functions take an extra "upto" parameter that upper-
+ * bounds the depth to which the function sorts.
+ */
+template<typename T1, typename T2>
+void mkeyQSortSufDcU8(const T1& seqanHost,
+ const T2& host,
+ size_t hlen,
+ uint32_t* s,
+ size_t slen,
+ const DifferenceCoverSample<T1>& dc,
+ int hi,
+ size_t begin,
+ size_t end,
+ size_t depth,
+ bool sanityCheck = false)
+{
+ // Helper for making the recursive call; sanity-checks arguments to
+ // make sure that the problem actually got smaller.
+ #define MQS_RECURSE_SUF_DC_U8(nbegin, nend, ndepth) { \
+ assert(nbegin > begin || nend < end || ndepth > depth); \
+ mkeyQSortSufDcU8(seqanHost, host, hlen, s, slen, dc, hi, nbegin, nend, ndepth, sanityCheck); \
+ }
+ assert_leq(begin, slen);
+ assert_leq(end, slen);
+ size_t n = end - begin;
+ if(n <= 1) return; // 1-element list already sorted
+ if(depth > dc.v()) {
+ // Quicksort the remaining suffixes using difference cover
+ // for constant-time comparisons; this is O(k*log(k)) where
+ // k=(end-begin)
+ qsortSufDcU8<T1,T2>(seqanHost, host, hlen, s, slen, dc, begin, end, sanityCheck);
+ if(sanityCheck) {
+ sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff, begin, end);
+ }
+ return;
+ }
+ if(n <= BUCKET_SORT_CUTOFF) {
+ // Bucket sort remaining items
+ bucketSortSufDcU8(seqanHost, host, hlen, s, slen, dc,
+ (uint8_t)hi, begin, end, depth, sanityCheck);
+ if(sanityCheck) {
+ sanityCheckOrderedSufs(seqanHost, hlen, s, slen, 0xffffffff, begin, end);
+ }
+ return;
+ }
+ size_t a, b, c, d, r;
+ CHOOSE_AND_SWAP_PIVOT(SWAP1, CHAR_AT_SUF_U8); // choose pivot, swap to begin
+ int v = CHAR_AT_SUF_U8(begin, depth); // v <- pivot value
+ #ifndef NDEBUG
+ {
+ bool stillInBounds = false;
+ for(size_t i = begin; i < end; i++) {
+ if(depth < (hlen-s[i])) {
+ stillInBounds = true;
+ break;
+ } else { /* already fell off this suffix */ }
+ }
+ assert(stillInBounds); // >=1 suffix must still be in bounds
+ }
+ #endif
+ a = b = begin;
+ c = d = end-1;
+ while(true) {
+ // Invariant: everything before a is = pivot, everything
+ // between a and b is <
+ int bc = 0; // shouldn't have to init but gcc on Mac complains
+ while(b <= c && v >= (bc = CHAR_AT_SUF_U8(b, depth))) {
+ if(v == bc) {
+ SWAP(s, a, b); a++;
+ }
+ b++;
+ }
+ // Invariant: everything after d is = pivot, everything
+ // between c and d is >
+ int cc = 0; // shouldn't have to init but gcc on Mac complains
+ bool hiLatch = true;
+ while(b <= c && v <= (cc = CHAR_AT_SUF_U8(c, depth))) {
+ if(v == cc) {
+ SWAP(s, c, d); d--;
+ }
+ else if(hiLatch && cc == hi) {
+
+ }
+ c--;
+ }
+ if(b > c) break;
+ SWAP(s, b, c);
+ b++;
+ c--;
+ }
+ assert(a > begin || c < end-1); // there was at least one =s
+ assert_lt(d-c, n); // they can't all have been > pivot
+ assert_lt(b-a, n); // they can't all have been < pivot
+ //assert(assertPartitionedSuf(host, s, slen, hi, v, begin, end, depth)); // check pre-=-swap invariant
+ r = min(a-begin, b-a); VECSWAP(s, begin, b-r, r); // swap left = to center
+ r = min(d-c, end-d-1); VECSWAP(s, b, end-r, r); // swap right = to center
+ //assert(assertPartitionedSuf2(host, s, slen, hi, v, begin, end, depth)); // check post-=-swap invariant
+ r = b-a; // r <- # of <'s
+ if(r > 0) {
+ MQS_RECURSE_SUF_DC_U8(begin, begin + r, depth); // recurse on <'s
+ }
+ // Do not recurse on ='s if the pivot was the off-the-end value;
+ // they're already fully sorted
+ if(v != hi) {
+ MQS_RECURSE_SUF_DC_U8(begin + r, begin + r + (a-begin) + (end-d-1), depth+1); // recurse on ='s
+ }
+ r = d-c; // r <- # of >'s excluding those exhausted
+ if(r > 0 && v < hi-1) {
+ MQS_RECURSE_SUF_DC_U8(end-r, end, depth); // recurse on >'s
+ }
+}
+
+
+#endif /*MULTIKEY_QSORT_H_*/
diff --git a/src/libSSA/karkkainen_bwt/random_source.h b/src/libSSA/karkkainen_bwt/random_source.h
new file mode 100644
index 0000000..65ec646
--- /dev/null
+++ b/src/libSSA/karkkainen_bwt/random_source.h
@@ -0,0 +1,61 @@
+#ifndef RANDOM_GEN_H_
+#define RANDOM_GEN_H_
+
+#include "assert_helpers.h"
+
+/**
+ * Simple pseudo-random linear congruential generator, a la Numerical
+ * Recipes.
+ */
+class RandomSource {
+public:
+ static const uint32_t DEFUALT_A = 1664525;
+ static const uint32_t DEFUALT_C = 1013904223;
+
+ RandomSource() :
+ a(DEFUALT_A), c(DEFUALT_C), inited_(false) { }
+ RandomSource(uint32_t _a, uint32_t _c) :
+ a(_a), c(_c), inited_(false) { }
+
+ void init(uint32_t seed = 0) {
+ last = seed;
+ inited_ = true;
+ }
+
+ uint32_t nextU32() {
+ assert(inited_);
+ uint32_t ret;
+ last = a * last + c;
+ ret = last >> 16;
+ last = a * last + c;
+ ret ^= last;
+ lastOff = 0;
+ return ret;
+ }
+
+ uint32_t nextU2() {
+ assert(inited_);
+ if(lastOff > 30) {
+ nextU32();
+ }
+ uint32_t ret = (last >> lastOff) & 3;
+ lastOff += 2;
+ return ret;
+ }
+
+ static uint32_t nextU32(uint32_t last,
+ uint32_t a = DEFUALT_A,
+ uint32_t c = DEFUALT_C)
+ {
+ return (a * last) + c;
+ }
+
+private:
+ uint32_t a;
+ uint32_t c;
+ uint32_t last;
+ uint32_t lastOff;
+ bool inited_;
+};
+
+#endif /*RANDOM_GEN_H_*/
diff --git a/src/libSSA/karkkainen_bwt/timer.h b/src/libSSA/karkkainen_bwt/timer.h
new file mode 100644
index 0000000..c2db053
--- /dev/null
+++ b/src/libSSA/karkkainen_bwt/timer.h
@@ -0,0 +1,63 @@
+#ifndef TIMER_H_
+#define TIMER_H_
+
+#include <ctime>
+#include <iostream>
+#include <iomanip>
+
+using namespace std;
+
+/**
+ * Use time() call to keep track of elapsed time between creation and
+ * destruction. If verbose is true, Timer will print a message showing
+ * elapsed time to the given output stream upon destruction.
+ */
+class Timer {
+public:
+ Timer(ostream& out = cout, const char *msg = "", bool verbose = true) :
+ _t(time(0)), _out(out), _msg(msg), _verbose(verbose) { }
+
+ /// Optionally print message
+ ~Timer() {
+ if(_verbose) write(_out);
+ }
+
+ /// Return elapsed time since Timer object was created
+ time_t elapsed() const {
+ return time(0) - _t;
+ }
+
+ void write(ostream& out) {
+ time_t passed = elapsed();
+ // Print the message supplied at construction time followed
+ // by time elapsed formatted HH:MM:SS
+ unsigned int hours = (passed / 60) / 60;
+ unsigned int minutes = (passed / 60) % 60;
+ unsigned int seconds = (passed % 60);
+ out << _msg << setfill ('0') << setw (2) << hours << ":"
+ << setfill ('0') << setw (2) << minutes << ":"
+ << setfill ('0') << setw (2) << seconds << endl;
+ }
+
+private:
+ time_t _t;
+ ostream& _out;
+ const char *_msg;
+ bool _verbose;
+};
+
+static inline void logTime(std::ostream& os, bool nl = true) {
+ struct tm *current;
+ time_t now;
+ time(&now);
+ current = localtime(&now);
+ os << setfill('0') << setw(2)
+ << current->tm_hour << ":"
+ << setfill('0') << setw(2)
+ << current->tm_min << ":"
+ << setfill('0') << setw(2)
+ << current->tm_sec;
+ if(nl) os << std::endl;
+}
+
+#endif /*TIMER_H_*/
diff --git a/src/libSSA/karkkainen_bwt/zbox.h b/src/libSSA/karkkainen_bwt/zbox.h
new file mode 100644
index 0000000..6f175dd
--- /dev/null
+++ b/src/libSSA/karkkainen_bwt/zbox.h
@@ -0,0 +1,76 @@
+#ifndef ZBOX_H_
+#define ZBOX_H_
+
+/**
+ * Fill z with Z-box information for s. String z will not be resized
+ * and will only be filled up to its size cap. This is the linear-time
+ * algorithm from Gusfield. An optional sanity-check uses a naive
+ * algorithm to double-check results.
+ */
+template<typename T>
+void calcZ(const T& s,
+ uint32_t off,
+ String<uint32_t>& z,
+ bool verbose = false,
+ bool sanityCheck = false)
+{
+ size_t lCur = 0, rCur = 0;
+ size_t zlen = length(z);
+ size_t slen = length(s);
+ assert_gt(zlen, 0);
+ assert_eq(z[0], 0);
+ //assert_leq(zlen, slen);
+ for (size_t k = 1; k < zlen && k+off < slen; k++) {
+ assert_lt(lCur, k);
+ assert(z[lCur] == 0 || z[lCur] == rCur - lCur + 1);
+ if(k > rCur) {
+ // compare starting at k with prefix starting at 0
+ size_t ki = k;
+ while(off+ki < length(s) && s[off+ki] == s[off+ki-k]) ki++;
+ z[k] = ki - k;
+ assert_lt(off+z[k], slen);
+ if(z[k] > 0) {
+ lCur = k;
+ rCur = k + z[k] - 1;
+ }
+ } else {
+ // position k is contained in a Z-box
+ size_t betaLen = rCur - k + 1;
+ size_t kPrime = k - lCur;
+ assert_eq(s[off+k], s[off+kPrime]);
+ if(z[kPrime] < betaLen) {
+ z[k] = z[kPrime];
+ assert_lt(off+z[k], slen);
+ // lCur, rCur unchanged
+ } else if (z[kPrime] > 0) {
+ int q = 0;
+ while (off+q+rCur+1 < length(s) && s[off+q+rCur+1] == s[off+betaLen+q]) q++;
+ z[k] = betaLen + q;
+ assert_lt(off+z[k], slen);
+ rCur = rCur + q;
+ assert_geq(k, lCur);
+ lCur = k;
+ } else {
+ z[k] = 0;
+ assert_lt(off+z[k], slen);
+ // lCur, rCur unchanged
+ }
+ }
+ }
+#ifndef NDEBUG
+ if(sanityCheck) {
+ // Recalculate Z-boxes using naive quadratic-time algorithm and
+ // compare to linear-time result
+ assert_eq(0, z[0]);
+ for(size_t i = 1; i < length(z); i++) {
+ size_t j;
+ for(j = i; off+j < length(s); j++) {
+ if(s[off+j] != s[off+j-i]) break;
+ }
+ assert_eq(j-i, z[i]);
+ }
+ }
+#endif
+}
+
+#endif /*ZBOX_H_*/
diff --git a/src/libSSA/locateOnGenome.cpp b/src/libSSA/locateOnGenome.cpp
new file mode 100644
index 0000000..274fa8d
--- /dev/null
+++ b/src/libSSA/locateOnGenome.cpp
@@ -0,0 +1,462 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <algorithm>
+#include<iostream>
+#include <stdlib.h>
+#include <assert.h>
+#include "locateOnGenome.h"
+#include "utils.h"
+using namespace std;
+
+LocateOnGenome::LocateOnGenome(uchar *file_base): out_uniq(&cout), out_multiple(&cout), out_none(&cout), out_sam(&cout) {
+ // opening index
+ int err = load_index((char *)file_base,(void **)&index);
+ if (err) {
+ cerr << error_index(err) << endl;
+ exit(2);
+ }
+
+ // opening conf file
+ genomeInfo = new GenomeInfo((char *)file_base);
+
+ nb_tags_treated = 0;
+ nb_displayed = 0;
+ display_nb = false;
+}
+
+
+LocateOnGenome::~LocateOnGenome(){
+ free_index(index);
+ delete genomeInfo;
+}
+
+
+ulong LocateOnGenome::getAbsolutePosition(ChrPosition *chrPos) {
+ return genomeInfo->getGenomePosition((uchar *)chrPos->getChrPosition(),
+ chrPos->getRelativePosition());
+}
+
+const uchar *LocateOnGenome::getChromosome(ulong position) {
+ return genomeInfo->getChrNameFromPosition(position).first;
+}
+
+ulong LocateOnGenome::getIdChromosomeFromName(char *chr_name){
+ return genomeInfo->getNumFromName((uchar *)chr_name);
+}
+
+ulong LocateOnGenome::getIdChromosome(ulong position) {
+ return genomeInfo->getNumFromPosition(position).first;
+}
+
+ChrPosition *LocateOnGenome::getChrPos(ulong pos, int strand) {
+ pair<const uchar *, const ulong> infos = genomeInfo->getChrNameFromPosition(pos);
+ return new ChrPosition(infos.second, (char *)infos.first, strand);
+}
+
+float LocateOnGenome::getElapsedTime() {
+ struct timeval t;
+
+ if (gettimeofday(&t,NULL) == -1)
+ return 0;
+ return (t.tv_sec - chrono_sec) + (t.tv_usec-chrono_usec)/1000000.0;
+}
+
+ulong LocateOnGenome::getNbLocations() {
+ return nb_displayed;
+}
+
+pair<uint, uint> LocateOnGenome::getFMIndexRange(uchar *tag, ulong tag_length) {
+ ulong sp, ep;
+ index->getRange(tag, tag_length, sp, ep);
+ return pair<uint, uint>(sp, ep);
+}
+
+pair<uint, uint> LocateOnGenome::getFMIndexReverseRange(uchar *tag, ulong tag_length) {
+ ulong sp, ep;
+ index->getReverseCompRange(tag, tag_length, sp, ep);
+ return pair<uint, uint>(sp, ep);
+}
+
+void LocateOnGenome::getOccurrencesFMIndexRange(ulong sp, ulong ep, ulong **occ, ulong m, ulong nb_disp) {
+ if (nb_disp > 0)
+ index->returnLocate(sp, ep, nb_disp, occ, m);
+ else
+ index->returnLocate(sp, ep, nb_displayed, occ, m);
+}
+
+GenomeInfo * LocateOnGenome::getGenomeInfo() {
+ return genomeInfo;;
+}
+
+uchar *LocateOnGenome::getGenomeSubstring(ulong pos, ulong length, int strand,
+ char *chr_name) {
+ uchar *result;
+ uint num_chr;
+
+ // At this point, both length_chr[num_chr - 1] and total_length[nb_chr] are defined (or should be)
+ if (chr_name) {
+ num_chr = getIdChromosomeFromName(chr_name)+1;
+ if (num_chr > genomeInfo->getNbChr()) { // Discard wrong queries
+ pos = 0;
+ length = 0;
+ num_chr = 0;
+ }
+ if (pos >= genomeInfo->getChrLength(num_chr - 1)) { // Discard wrong queries
+ pos = 0;
+ length = 0;
+ }
+ // At this point, we know that either pos < length_chr[num_chr - 1] or pos = 0
+ if (pos + length > genomeInfo->getChrLength(num_chr - 1)) { // Adjust erroneous queries
+ length = genomeInfo->getChrLength(num_chr - 1) - pos; // No possible unsigned int overflow
+ }
+ pos = genomeInfo->getGenomePosition(num_chr-1, pos);
+ } else {
+ if (! genomeInfo->isValidPosition(pos)) { // Discard wrong queries
+ pos = 0;
+ length = 0;
+ }
+ // At this point, we know that either pos < total_length[nb_chr] or pos = 0
+ if (! genomeInfo->isValidPosition(pos + length - 1)) { // Adjust erroneous queries
+ length = genomeInfo->getGenomeLength() - pos; // No possible unsigned int overflow
+ }
+ }
+ if (!length) { // zero length query is an empty sequence
+ result = (uchar *)malloc(sizeof(uchar));
+ result[0] = 0;
+ } else {
+ // At this point, we know that 1/ pos + length - 1 doesn't produce unsigned int overflow
+ // and that 2/ the subsequence of length 'length' starting at position 'pos' exists.
+ index->extract(pos, pos+length-1, &result);
+ if (strand == -1) {
+ uchar *result2 = (uchar *)malloc((length+1)*sizeof(uchar));
+ for (uint i=0; i < length; i++) {
+ result2[i] = complementDNA(result[length-i-1]);
+ }
+ result2[length]=0;
+ free(result);
+ return result2;
+ }
+// else
+// index->extract(pos-length+1, pos, &result);
+ }
+ return result;
+}
+
+void LocateOnGenome::getLocations(uchar *tag, ulong tag_length, ulong &nb_sens, ulong &nb_antisens, ulong **poccs_sens, ulong **poccs_antisens) {
+ uchar *up_tag = new uchar[tag_length+1];
+ up_tag[tag_length] = 0;
+ for (uint i=0; i < tag_length; i++)
+ up_tag[i] = toupper(tag[i]);
+ nb_sens = index->locate(up_tag, tag_length, poccs_sens,nb_displayed);
+ nb_antisens = 0;
+ if (nb_sens < nb_displayed) {
+ nb_antisens = index->locateReverseComp(up_tag, tag_length, poccs_antisens,nb_displayed-nb_sens);
+ }
+ delete [] up_tag;
+}
+
+pair<ChrPosition **,uint>LocateOnGenome::getLocations(uchar *tag, uint klength, uint tagLength, uint &position_of_locations) {
+ ChrPosition **locations=NULL;
+ uint nb_locs_multiple=0;
+
+ ulong *occs_fwd;
+ uint nb_occs_fwd=0;
+ ulong *occs_rev;
+ uint nb_occs_rev=0;
+ pair<uint,uint> ranges_forward;
+ pair<uint,uint> ranges_reverse;
+
+ uint i = 0;
+ uint nb_occs = 0;
+ position_of_locations=0;
+ // searching the first k-mer located
+ while (i < (tagLength-klength+1) && nb_occs == 0){
+ // multiple is initialized to nb_max_diplayed (--max-locs)
+ nb_locs_multiple=getNbLocations();
+ // get ranges in FM-index
+ ranges_forward = getFMIndexRange((uchar *)&tag[i],klength);
+ ranges_reverse = getFMIndexReverseRange((uchar *)&tag[i],klength);
+
+ // First, on forward strand
+ if (ranges_forward.first <= ranges_forward.second) {
+ getOccurrencesFMIndexRange(ranges_forward.first, ranges_forward.second,&occs_fwd);
+ nb_occs_fwd = ranges_forward.second - ranges_forward.first + 1;
+ }
+ // We check that the number of occurrences is smaller than nb_locs_multiple before the reverse strand treatment
+ if (nb_occs_fwd < nb_locs_multiple) {
+ if (ranges_reverse.first <= ranges_reverse.second) {
+ getOccurrencesFMIndexRange(ranges_reverse.first,
+ ranges_reverse.second,
+ &occs_rev);
+ nb_occs_rev = ranges_reverse.second - ranges_reverse.first + 1;
+ }
+
+ // Again, we check that the total number of occurrences is smaller than nb_locs_multiple
+ // and we adjust the nb_locs_multiple if the limit is not reached
+ if ((nb_occs_fwd+nb_occs_rev) < nb_locs_multiple)
+ nb_locs_multiple=nb_occs_rev+nb_occs_fwd;
+ }
+ nb_occs = nb_locs_multiple;
+ position_of_locations = i;
+ i++;
+ }
+
+ // We save locations
+ if (nb_locs_multiple>0){
+ locations = (ChrPosition **)malloc(sizeof (ChrPosition *)*nb_locs_multiple);
+
+ uint nb_displayed = min(nb_occs_fwd,nb_locs_multiple);
+ for (uint i=0 ; i<nb_displayed ; i++){
+ locations[i] = getChrPos(occs_fwd[i],1);
+ }
+ for (uint i=nb_displayed ; i<nb_locs_multiple ; i++){
+ locations[i] = getChrPos(occs_rev[i-nb_displayed],-1);
+ }
+ }
+
+ // We delete tempory tables
+ if (nb_occs_fwd)
+ free(occs_fwd);
+ if (nb_occs_rev)
+ free(occs_rev);
+
+ return pair<ChrPosition **,uint>(locations,nb_locs_multiple);
+}
+
+ulong LocateOnGenome::getNbOccsLastLocatedTag() {
+ return nbOccs_lastTag;
+}
+
+void LocateOnGenome::getNbOccurrences(uchar *tag, ulong tag_length, ulong &nb_sens, ulong &nb_antisens) {
+ uchar *up_tag = new uchar[tag_length+1];
+ up_tag[tag_length] = 0;
+ for (uint i=0; i < tag_length; i++)
+ up_tag[i] = toupper(tag[i]);
+ nb_sens = index->count(up_tag, tag_length);
+ nb_antisens = index->countReverseComp(up_tag, tag_length);
+ delete [] up_tag;
+}
+
+ulong LocateOnGenome::getNbTagsTreated() {
+ return nb_tags_treated;
+}
+
+
+void LocateOnGenome::locateTag(uchar *tag, ulong tag_length) {
+ ulong *occ_sens;
+ ulong *occ_antisens;
+ ulong n_sens, n_antisens;
+
+ getLocations(tag, tag_length, n_sens, n_antisens, &occ_sens, &occ_antisens);
+
+ nbOccs_lastTag = n_sens + n_antisens;
+ if (nbOccs_lastTag == 1) {
+ displaySingleLocation(tag,tag_length,n_sens, n_antisens, occ_sens, occ_antisens);
+ } else if (nbOccs_lastTag > 1) {
+ displayMultipleLocations(tag,tag_length,n_sens, n_antisens, occ_sens, occ_antisens);
+ } else {
+ displayNoLocation(tag, tag_length);
+ }
+ nb_tags_treated++;
+}
+
+void LocateOnGenome::setDisplayNumbers(bool disp) {
+ display_nb = disp;
+}
+
+void LocateOnGenome::setNbLocations(ulong nb_displayed) {
+ this->nb_displayed=nb_displayed;
+}
+
+void LocateOnGenome::setOutputStreams (ostream *uniq, ostream *multiple, ostream *none) {
+ if (uniq != NULL)
+ out_uniq = uniq;
+ else
+ out_uniq = &cout;
+ if (multiple != NULL)
+ out_multiple = multiple;
+ else
+ out_multiple = &cout;
+ if (none != NULL)
+ out_none = none;
+ else
+ out_none = &cout;
+}
+
+void LocateOnGenome::setOutputUniq(ostream *s) {
+ out_uniq = s;
+}
+void LocateOnGenome::setOutputMultiple(ostream *s) {
+ out_multiple = s;
+}
+void LocateOnGenome::setOutputNone(ostream *s) {
+ out_none = s;
+}
+
+void LocateOnGenome::setOutputSAM(ostream *s) {
+ out_sam = s;
+}
+
+bool LocateOnGenome::startChrono() {
+ struct timeval time;
+
+ if (gettimeofday(&time,NULL) == -1)
+ return false;
+ chrono_sec = time.tv_sec;
+ chrono_usec = time.tv_usec;
+ return true;
+}
+
+void LocateOnGenome::displaySingleLocation(uchar *tag, ulong tag_length, ulong n_sens, ulong n_antisens, ulong *occ_sens, ulong *occ_antisens) {
+ tag[tag_length]=0;
+ if (display_nb)
+ *out_uniq << getNbTagsTreated() << "|";
+ *out_uniq << tag;
+ if (n_sens > 0) {
+ display_occ(out_uniq, occ_sens, n_sens, tag_length, true);
+ free(occ_sens);
+ } else {
+ display_occ(out_uniq, occ_antisens, n_antisens, tag_length, false);
+ free(occ_antisens);
+ }
+ *out_uniq << endl;
+}
+
+void LocateOnGenome::displayMultipleLocations(uchar *tag, ulong tag_length, ulong n_sens, ulong n_antisens, ulong *occ_sens, ulong *occ_antisens) {
+ tag[tag_length]=0;
+ if (display_nb)
+ *out_multiple << getNbTagsTreated() << "|";
+ *out_multiple << tag;
+ if (n_sens > 0) {
+ display_occ(out_multiple, occ_sens, n_sens, tag_length, true);
+ free(occ_sens);
+ }
+ if (n_antisens > 0) {
+ display_occ(out_multiple, occ_antisens, n_antisens, tag_length, false);
+ free(occ_antisens);
+ }
+ *out_multiple << endl;
+}
+
+void LocateOnGenome::displayNoLocation(uchar *tag, ulong tag_length) {
+ tag[tag_length]=0;
+ if (display_nb)
+ *out_none << getNbTagsTreated() << "|";
+ *out_none << tag << endl;
+}
+
+void LocateOnGenome::display_occ(ostream *stream, ulong *occ, ulong n, ulong tag_length, bool sens) {
+ ulong num_chr = 0;
+ ulong old_num_chr = genomeInfo->getNbChr() + 1;
+ int strand = (sens) ? 1 : -1;
+ sort(occ,occ+n);
+ for (ulong i=0; i < n; i++) {
+ pair<const ulong, const ulong> info_pos = genomeInfo->getNumFromPosition(occ[i]);
+ num_chr = info_pos.first;
+ if (num_chr != old_num_chr) {
+ old_num_chr = num_chr;
+ *stream << "|"<< genomeInfo->getChrName(num_chr) << ","<< strand <<"\t";
+ }else{
+ *stream << "," ;
+ }
+ // Positioning according to the chromosomes
+ *stream << info_pos.second ;
+ }
+}
diff --git a/src/libSSA/locateOnGenome.h b/src/libSSA/locateOnGenome.h
new file mode 100644
index 0000000..93718bb
--- /dev/null
+++ b/src/libSSA/locateOnGenome.h
@@ -0,0 +1,237 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef LOCATE_ON_GENOME
+#define LOCATE_ON_GENOME
+
+extern "C" {
+#include <sys/time.h>
+}
+
+#include <ctime>
+#include <fstream>
+#include <iostream>
+#include <utility>
+#include "SSA.h"
+#include "chrPosition.h"
+#include "GenomeInfo.h"
+using namespace std;
+
+
+class LocateOnGenome {
+ private:
+ GenomeInfo *genomeInfo;
+ ostream *out_uniq, *out_multiple, *out_none, *out_sam;
+ TFMindex *index;
+ ulong nb_tags_treated;
+ ulong nb_displayed;
+ ulong nbOccs_lastTag;
+ time_t chrono_sec;
+ suseconds_t chrono_usec;
+ bool display_nb;
+
+ void display_occ(ostream *stream, ulong *occ, ulong n, ulong tag_length, bool sens);
+
+
+ public:
+ /**
+ * @param file_base: Basename of the index file (ie. the common prefix
+ * to the .ssa index and to the .conf file).
+ */
+ LocateOnGenome(uchar *file_base);
+
+ ~LocateOnGenome();
+
+ void displaySingleLocation(uchar *tag, ulong tag_length, ulong n_sens, ulong n_antisens, ulong *occ_sens, ulong *occ_antisens);
+ void displayMultipleLocations(uchar *tag, ulong tag_length, ulong n_sens, ulong n_antisens, ulong *occ_sens, ulong *occ_antisens);
+ void displayNoLocation(uchar *tag, ulong tag_length);
+
+ float getElapsedTime();
+
+
+ void getLocations(uchar *tag, ulong tag_length, ulong &nb_sens, ulong &nb_antisens, ulong **poccs_sens, ulong **poccs_antisens);
+
+ /**
+ * @return all locations of a kmer at position_of_locations and its
+ * number of occurrences. In addition, position_of_locations is set
+ * after pair<ChrPosition **,uint> which determines position of the
+ * k-mer chosen for locations
+ */
+ pair<ChrPosition **,uint>getLocations(uchar *tag, uint klength, uint read_length, uint &position_of_locations);
+
+
+ uint getPositionOfLocations();
+
+ uint getNbLocations();
+
+ /*
+ * @param chrPos : a ChrPosition object
+ * @return the absolute position of chrPos
+ */
+ ulong getAbsolutePosition(ChrPosition *chrPos);
+
+ /**
+ * @param pos: absolute position
+ * @return the chromosome which corresponds to that position
+ */
+ const uchar *getChromosome(ulong position);
+
+ /**
+ * @param chr_name: name of chr
+ * @return an id of the chromosome which corresponds to that name.
+ */
+ ulong getIdChromosomeFromName(char *chr_name);
+
+ /**
+ * @param pos: absolute position
+ * @return an id of the chromosome which corresponds to that position.
+ * This id is mainly useful when one wants to compare two positions
+ * and wants to know if they're on the same chromsome.
+ */
+ ulong getIdChromosome(ulong position);
+
+ /**
+ * @param pos: absolute position
+ * @return the relative position on the genome.
+ */
+ ChrPosition *getChrPos(ulong pos, int strand=0);
+
+ pair<uint, uint> getFMIndexRange(uchar *tag, ulong tag_length);
+
+ pair<uint, uint> getFMIndexReverseRange(uchar *tag, ulong tag_length);
+
+ void getOccurrencesFMIndexRange(ulong sp, ulong ep, ulong **occ, ulong m=0, ulong nb_disp=0);
+
+ /**
+ * @return A pointer to the GenomeInfo object for hvaing all the information
+ * on sequence length, name, IDs, ...
+ */
+ GenomeInfo * getGenomeInfo();
+
+ uchar *getGenomeSubstring(ulong pos, ulong length, int strand=1,
+ char *chr_name = NULL);
+
+
+ ulong getNbTagsTreated();
+ void getNbOccurrences(uchar *tag, ulong tag_length, ulong &nb_sens, ulong &nb_antisens);
+ ulong getNbOccsLastLocatedTag();
+
+ void locateTags(fstream &file, ulong tag_length, ulong nb_threads = 1);
+
+ void locateTag(uchar *tag, ulong tag_length);
+
+
+ /**
+ * @param disp: true iff read number precedes each entry in the output files
+ */
+ void setDisplayNumbers(bool disp);
+
+ void setOutputStreams (ostream *uniq, ostream *multiple, ostream *none);
+ void setOutputUniq(ostream *s);
+ void setOutputMultiple(ostream *s);
+ void setOutputNone(ostream *s);
+ void setOutputSAM(ostream *s);
+
+ void setNbLocations(ulong nb_displayed);
+
+ bool startChrono();
+
+};
+
+#endif
diff --git a/src/libSSA/locateTags.cpp b/src/libSSA/locateTags.cpp
new file mode 100644
index 0000000..3884ff5
--- /dev/null
+++ b/src/libSSA/locateTags.cpp
@@ -0,0 +1,402 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at univ-montp2.fr *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <cstdlib>
+#include "locateTags.h"
+#include "utils.h"
+#include <config.h>
+#include <sstream>
+#include <algorithm>
+#include "../libReadsInfo/samLine.h"
+
+using namespace std;
+
+LocateTags::LocateTags(LocateOnGenome *genome, Parameters *param, char *tags_file, uint threshold):
+ genome(genome),parameters(param),tags_file(tags_file),threshold(threshold)
+{}
+
+void LocateTags::locate(ostream *sam) {
+ // Init stat variables
+ nb_single = 0;
+ nb_multiple = 0;
+ nb_none = 0;
+ nb_tags = 0;
+ sem_init(&stats_mutex,0,1);
+
+ pthread_t threads[parameters->nb_threads];
+ locate_thread_t params[parameters->nb_threads];
+ string **store_samLines[parameters->nb_threads-1];
+ read_t **store_reads[parameters->nb_threads-1];
+ readsReader reads(tags_file,threshold);
+ readIterator *readItForBuffer = reads.begin();
+ readIterator *readIt = reads.begin();
+ sem_t remaining_seats[parameters->nb_threads-1];
+ sem_t processed_reads[parameters->nb_threads-1];
+ uint *positions = NULL;
+ uint nb_samLines;
+ string *samLine;
+
+ if (parameters->nb_threads > 1) {
+ nb_samLines = parameters->nb_tags_info_stored;
+
+ positions = new uint[parameters->nb_threads - 1];
+
+ for (uint j = 0; j < parameters->nb_threads - 1; j++) {
+ positions[j] = 0;
+ params[j].locate = this;
+ sem_init(&processed_reads[j],0,0);
+ params[j].processed_reads = &processed_reads[j];
+ params[j].total_seats = nb_samLines;
+ store_reads[j] = (read_t **)malloc(nb_samLines*sizeof(read_t *));
+ params[j].reads = store_reads[j];
+ store_samLines[j] = (string **)malloc(nb_samLines*sizeof(string *));
+ params[j].seats = store_samLines[j];
+ params[j].keepGoing = true;
+ }
+ } else {
+ nb_samLines = 1;
+ }
+
+ if (parameters->nb_threads > 1) {
+ // add reads data in threads
+ uint i = 0;
+ uint j = 0;
+ uint readCpt = 0;
+ while (!readItForBuffer->isFinished() && i < nb_samLines) {
+ j = 0;
+ while (j < (parameters->nb_threads -1) && !readItForBuffer->isFinished()) {
+ read_t *r = new read_t();
+ setReadInfo(readItForBuffer,r);
+ store_reads[j][i] = r;
+ ++(*readItForBuffer);
+ readCpt++;
+ j++;
+ }
+ i++;
+ }
+ // Init the semaphore according to the number of reads stored
+ // in each thread
+ for (uint k = 0; k < parameters->nb_threads -1; k++) {
+ if (k >= j) {
+ sem_init(&remaining_seats[k],0,i-1);
+ params[k].remaining_seats = &remaining_seats[k];
+ } else {
+ sem_init(&remaining_seats[k],0,i);
+ params[k].remaining_seats = &remaining_seats[k];
+ }
+ }
+
+ // Launching threads
+ for (uint j = 0; j < parameters->nb_threads - 1; j++) {
+ pthread_create(&threads[j], NULL, fillLocations, ¶ms[j]);
+ }
+ }
+
+ uint i = 0;
+ while (!readIt->isFinished()) {
+ if (parameters->nb_threads > 1) {
+ // get the number of the thread we are waiting for
+ uint j = i % (parameters->nb_threads - 1);
+ // wait until the read has been processed
+ sem_wait(&processed_reads[j]);
+ // get the sam line resulting of the read location
+ samLine = store_samLines[j][positions[j]];
+ // delete the read object that has been used to get the location
+ delete store_reads[j][positions[j]];
+ // Add a new read to the thread buffer
+ if (!readItForBuffer->isFinished()) {
+ read_t *r = new read_t();
+ params[j].reads[positions[j]] = r;
+ setReadInfo(readItForBuffer,params[j].reads[positions[j]]);
+ ++(*readItForBuffer);
+ // Tell the tread that it can locate this new read
+ sem_post(&remaining_seats[j]);
+ }
+ // Update the position of the next read to get from
+ // this thread
+ positions[j] = (positions[j] + 1) % nb_samLines;
+ } else {
+ // If we dont use multi-threading we directly compute
+ // sam line for the current read
+ read_t *read = new read_t();
+ setReadInfo(readIt,read);
+ samLine = locateTag(read);
+ delete read;
+ }
+ // Write the sam line in the file
+ *sam << *samLine;
+ delete samLine;
+ ++(*readIt);
+ i++;
+ nb_tags++;
+ }
+
+ // unlock threads
+ for (uint j = 0; j < parameters->nb_threads -1; j++) {
+ params[j].keepGoing = false;
+ sem_post(&remaining_seats[j]);
+ }
+
+ // deleting iterators
+ delete readIt;
+ delete readItForBuffer;
+
+ for (uint j = 0; j < parameters->nb_threads - 1; j++) {
+ free(store_samLines[j]);
+ free(params[j].reads);
+ sem_destroy(&remaining_seats[j]);
+ sem_destroy(&processed_reads[j]);
+ }
+
+ for (uint j = 0; j < parameters->nb_threads - 1; j++) {
+ pthread_join(threads[j], NULL);
+ }
+
+ if (positions)
+ delete [] positions;
+
+}
+
+string *LocateTags::locateTag(read_t *read) {
+ ostringstream os;
+ pair<ChrPosition **,uint>locs;
+ uint pos_locs;
+ string tag_s = read->seq;
+ ulong tag_length = (ulong)tag_s.size();
+ SamLine base_line;
+ // minuscule nucleotide to capital
+ transform(tag_s.begin(), tag_s.end(), tag_s.begin(), static_cast<int(*)(int)>(toupper));
+
+ uchar *tag = (uchar *)tag_s.c_str();
+ string *samLines = new string();
+
+ if (threshold == 0){
+ locs = genome->getLocations((uchar *)&tag[0], tag_length, tag_length, pos_locs);
+ }else{
+ locs = genome->getLocations((uchar *)&tag[0], threshold, tag_length, pos_locs);
+ }
+
+ // write generic SAM features
+ base_line.setQname(read->name);
+ base_line.setSeq(read->seq);
+ base_line.setQual(read->qual);
+
+ // write sam_line, if no loc
+ if (locs.second == 0) {
+ base_line.setSegmentUnmapped();
+ base_line.setMapQ(255);
+ base_line.addOptionalField("NH",locs.second);
+ base_line.writeLine(os);
+ // set mutex for none stats
+ sem_wait(&stats_mutex);
+ nb_none++;
+ sem_post(&stats_mutex);
+ // end mutex zone
+ }
+ // write sam_line for each loc (or a single loc)
+ else{
+ for(ulong i = 0; i < locs.second; i++) {
+ if (i==0 || parameters->treat_multiple){
+ SamLine current_line = base_line;
+ string rname = string(locs.first[i]->getChrPosition());
+ current_line.setRname(rname);
+ current_line.setPos(locs.first[i]->getRelativePosition());
+ current_line.setMapQ(254);
+
+ Cigar cigar;
+ if (threshold > 0){
+ uint soft_size = tag_length-threshold-pos_locs;
+ if (locs.first[i]->getStrand() == 1){
+ if (pos_locs > 0)
+ cigar.append(pos_locs,'S');
+ cigar.append(threshold,'M');
+ if (soft_size > 0)
+ cigar.append(soft_size,'S');
+ }else{
+ if (soft_size > 0)
+ cigar.append(soft_size,'S');
+ cigar.append(threshold,'M');
+ if (pos_locs > 0)
+ cigar.append(pos_locs,'S');
+ }
+ }else
+ cigar.append(tag_length,'M');
+ current_line.setCigar(cigar);
+ if (locs.first[i]->getStrand() == -1){
+ current_line.setSeqReverseComplemented();
+ current_line.reverseComplementeSeq();
+ current_line.reverseQual();
+ }
+ //multiple_alignement.writeLine(cout);
+ // If this is not the primary line
+ if(i>0) {
+ current_line.setSecondaryAlignement();
+ }
+ current_line.addOptionalField("NH",locs.second);
+ // set single and multiple and update stats
+ // use a mutex to protect globa stats update
+ sem_wait(&stats_mutex);
+ if (locs.second == 1)
+ nb_single++;
+ else
+ nb_multiple++;
+ sem_post(&stats_mutex);
+ // end of mutex zone
+ current_line.writeLine(os);
+ }
+ delete locs.first[i];
+ }
+ free(locs.first);
+ }
+ *samLines = os.str();
+ //delete [] tag;
+ return samLines;
+}
+
+uint LocateTags::getNbTags(){
+ return nb_tags;
+}
+
+uint LocateTags::getNbSingle(){
+ return nb_single;
+}
+
+uint LocateTags::getNbMultiple(){
+ return nb_multiple;
+}
+
+uint LocateTags::getNbNone(){
+ return nb_none;
+}
+
+// private methods
+
+void LocateTags::setReadInfo(readIterator *readIt,read_t *read) {
+ if(readIt->getName() != NULL) {
+ read->name = readIt->getName();
+ } else { read->name = "*"; }
+ read->seq = readIt->getSequence();
+ if(readIt->getQuality() != NULL) {
+ read->qual = readIt->getQuality();
+ } else { read->qual = "*";}
+}
+
+void *fillLocations(void *args) {
+ locate_thread_t params = ((locate_thread_t *)args)[0];
+ LocateTags *locate = params.locate;
+ uint current_pos = 0;
+ int semValue;
+ sem_getvalue(params.remaining_seats,&semValue);
+ while(((locate_thread_t *)args)[0].keepGoing || semValue > 0) {
+ // We need one seat for the current read
+ sem_wait(params.remaining_seats);
+ sem_getvalue(params.remaining_seats,&semValue);
+
+ if(((locate_thread_t *)args)[0].keepGoing && semValue >= 0) {
+ params.seats[current_pos] = locate->locateTag(params.reads[current_pos]);
+ sem_post(params.processed_reads);
+ // delete the read
+ //delete params.reads[current_pos];
+ current_pos = (current_pos + 1) % params.total_seats;
+ }
+ }
+ pthread_exit(NULL);
+ return NULL;
+}
diff --git a/src/libSSA/locateTags.h b/src/libSSA/locateTags.h
new file mode 100644
index 0000000..9a67dff
--- /dev/null
+++ b/src/libSSA/locateTags.h
@@ -0,0 +1,211 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at univ-montp2.fr *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef LOCATETAGS_H
+#define LOCATETAGS_H
+
+#include "locateOnGenome.h"
+#include "../Parameters.h"
+#include <ostream>
+#include <string>
+#include <readsReader.h>
+#include <semaphore.h>
+
+using namespace gkarrays;
+
+typedef struct read_s {
+ string name; /* Name of the read in the input file */
+ string seq; /* DNA sequence of the read */
+ string qual; /* Quality of the DNA sequence */
+} read_t;
+
+class LocateTags{
+ private:
+ LocateOnGenome *genome; /* Genome object to locate reads on reference genome */
+ Parameters *parameters; /* Parameters object */
+ char *tags_file;
+ uint nb_single; /* Number of single locations */
+ uint nb_multiple; /* Number of multiple locations */
+ uint nb_none; /* Number of None locations */
+ uint nb_tags; /* Number of tags in the file */
+ uint threshold; /* Threshold to use */
+ sem_t stats_mutex; /* Mutex when thread updates stats values (nb_single, nb_multiple...) */
+
+ public:
+
+ /**
+ * Constructor of locateTags
+ *
+ * @param genome the genome object used for getting locations
+ * @param param the parameters object
+ * @param tags_file the name of the FAST/FASTQ file containing reads to process
+ * @param sam output stream to print the sam file
+ * @param threshold the size of the prefix of the read we are going to use for mapping
+ * if the size equal 0 locateTags will map the whole sequence of the read.
+ */
+ LocateTags(LocateOnGenome *genome, Parameters *param, char *tags_file, uint threshold = 0);
+
+ /**
+ * Destructor of locateTags
+ */
+ ~LocateTags(){};
+
+ /**
+ * Launch location process, and multiple threads if any.
+ */
+ void locate(ostream *sam);
+
+ /**
+ * locate the tag in the genome index and generate the coresponding sam line.
+ *
+ * @param read the read to process
+ * @return a string containing the sam line of the mapping of this read
+ */
+ string *locateTag(read_t *read);
+
+ /**
+ * @return the number of tags that have been processed
+ */
+ uint getNbTags();
+
+ /**
+ * @return the number of single locations
+ */
+ uint getNbSingle();
+
+ /**
+ * @return the number of multiple locations
+ */
+ uint getNbMultiple();
+
+ /**
+ * @return the number of none locations
+ */
+ uint getNbNone();
+
+ private:
+ /**
+ * Set a read_t object with info from iterato
+ *
+ * @readIt the iterator used to fill data of the read object
+ * @read the read to fill
+ */
+ void setReadInfo(readIterator *readIt, read_t *read);
+
+ /**
+ * The function that is call for each thread
+ */
+ friend void *fillLocations(void *);
+
+};
+
+void *fillLocations(void *);
+
+typedef struct locate_thread_s {
+ LocateTags *locate;
+ sem_t *remaining_seats; /* Number of remaining cells containing reads to process */
+ sem_t *processed_reads; /* Number of reads that have been processed and ready to write in the ouput */
+ string **seats; /* Seats where the samLines of the processed reads are stored */
+ read_t **reads; /* Seats where the reads to process are stored */
+ uint total_seats; /* Total number of seats */
+ bool keepGoing; /* Boolean to stop the tread */
+} locate_thread_t;
+
+#endif
diff --git a/src/libSSA/seqan/basic.h b/src/libSSA/seqan/basic.h
new file mode 100644
index 0000000..27beba1
--- /dev/null
+++ b/src/libSSA/seqan/basic.h
@@ -0,0 +1,115 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic.h,v 1.2 2009/05/06 20:32:59 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_H
+#define SEQAN_HEADER_BASIC_H
+
+//____________________________________________________________________________
+// prerequisites
+
+#include <seqan/platform.h>
+
+//#include <cstring>
+#ifdef PLATFORM_WINDOWS
+#include <limits> // limits include file exists only for g++ >= 3.0
+#endif
+
+#include <cstddef> // size_t
+#include <cstdio> // FILE, basic_debug
+#include <ctime>
+#include <iterator>
+#include <algorithm>
+#include <memory.h> // memset
+#include <string> // basic_profile
+
+#define SEQAN_NAMESPACE_MAIN seqan
+
+//____________________________________________________________________________
+
+#include <seqan/basic/basic_forwards.h>
+#ifdef SEQAN_SWITCH_USE_FORWARDS
+#include <seqan/basic/basic_generated_forwards.h>
+#endif
+
+#include <seqan/basic/basic_debug.h>
+#include <seqan/basic/basic_profile.h>
+#include <seqan/basic/basic_definition.h>
+#include <seqan/basic/basic_metaprogramming.h>
+#include <seqan/basic/basic_type.h>
+#include <seqan/basic/basic_tag.h>
+
+//____________________________________________________________________________
+// allocators
+
+#include <seqan/basic/basic_allocator_interface.h>
+#include <seqan/basic/basic_allocator_to_std.h>
+
+#include <seqan/basic/basic_holder.h>
+
+#include <seqan/basic/basic_allocator_simple.h>
+#include <seqan/basic/basic_allocator_singlepool.h>
+#include <seqan/basic/basic_allocator_multipool.h>
+//#include <seqan/basic/basic_allocator_chunkpool.h>
+
+//____________________________________________________________________________
+
+#include <seqan/basic/basic_converter.h>
+#include <seqan/basic/basic_compare.h>
+#include <seqan/basic/basic_operator.h>
+
+#include <seqan/basic/basic_host.h>
+
+//____________________________________________________________________________
+// iterators
+
+#include <seqan/basic/basic_iterator.h>
+#include <seqan/basic/basic_iterator_base.h>
+
+#include <seqan/basic/basic_transport.h>
+
+#include <seqan/basic/basic_iterator_simple.h>
+#include <seqan/basic/basic_iterator_adaptor.h>
+#include <seqan/basic/basic_iterator_position.h>
+#include <seqan/basic/basic_iterator_adapt_std.h>
+//#include <seqan/basic_identifier.h>
+
+#include <seqan/basic/basic_proxy.h>
+
+#include <seqan/basic/basic_pointer.h>
+
+//____________________________________________________________________________
+// alphabets
+
+#include <seqan/basic/basic_alphabet_interface.h>
+#include <seqan/basic/basic_alphabet_trait_basic.h>
+
+#include <seqan/basic/basic_alphabet_interface2.h>
+
+#include <seqan/basic/basic_alphabet_simple_tabs.h>
+#include <seqan/basic/basic_alphabet_simple.h>
+
+//____________________________________________________________________________
+
+//#include <seqan/basic/basic_counted_ptr>
+#include <seqan/basic/basic_volatile_ptr.h>
+
+#include <seqan/basic/basic_aggregates.h>
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_aggregates.h b/src/libSSA/seqan/basic/basic_aggregates.h
new file mode 100644
index 0000000..68e4e70
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_aggregates.h
@@ -0,0 +1,689 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_aggregates.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_AGGREGATES_H
+#define SEQAN_HEADER_BASIC_AGGREGATES_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//____________________________________________________________________________
+
+ struct _Compressed;
+ typedef Tag<_Compressed> Compressed;
+
+ // for Pairs with small i1-values
+ // store i1 and i2 in one word of type i2
+ // use the upper bits for i1 and the lower bits for i2
+ template <unsigned valueSizeI1 = 16>
+ struct CutCompressed {
+ enum { bitSizeI1 = Log2<valueSizeI1>::VALUE };
+ };
+
+/**
+.Class.Pair:
+..cat:Aggregates
+..summary:Stores two arbitrary objects.
+..signature:Pair<T1, T2[, Compression]>
+..param.T1:The type of the first object.
+..param.T2:The type of the second object.
+..param.Compression:If $Compressed$, the pair is stored in a more space efficient way (useful for external storage).
+...note:When compression is enabled, referring to members is not allowed.
+...default:$void$, no compression (faster access).
+.Memfunc.Pair#Pair:
+..class:Class.Pair
+..summary:Constructor
+..signature:Pair<T1, T2> ()
+..signature:Pair<T1, T2> (pair)
+..signature:Pair<T1, T2> (i1, i2)
+..param.pair:Other Pair object. (copy constructor)
+..param.i1:T1 object.
+..param.i2:T2 object.
+.Memvar.Pair#i1:
+..class:Class.Pair
+..summary:T1 object
+.Memvar.Pair#i2:
+..class:Class.Pair
+..summary:T2 object
+*/
+
+ // standard storage
+ template <typename _T1, typename _T2 = _T1, typename TCompression = void>
+ struct Pair {
+ typedef _T1 T1;
+ typedef _T2 T2;
+ _T1 i1;
+ _T2 i2;
+ inline Pair() {}
+ inline Pair(Pair const &_p): i1(_p.i1), i2(_p.i2) {}
+ inline Pair(_T1 const &_i1, _T2 const &_i2): i1(_i1), i2(_i2) {}
+
+ template <typename __T1, typename __T2, typename __TCompression>
+ inline Pair(Pair<__T1, __T2, __TCompression> const &_p):
+ i1(getValueI1(_p)), i2(getValueI2(_p)) {}
+ };
+
+
+
+ // unaligned and unpadded storage (space efficient)
+#ifdef PLATFORM_WINDOWS
+ #pragma pack(push,1)
+#endif
+ template <typename _T1, typename _T2>
+ struct Pair<_T1, _T2, Compressed> {
+ typedef _T1 T1;
+ typedef _T2 T2;
+ _T1 i1;
+ _T2 i2;
+ inline Pair() {}
+ inline Pair(Pair const &_p): i1(_p.i1), i2(_p.i2) {}
+ inline Pair(_T1 const &_i1, _T2 const &_i2): i1(_i1), i2(_i2) {}
+
+ template <typename __T1, typename __T2, typename __TCompression>
+ inline Pair(Pair<__T1, __T2, __TCompression> const &_p):
+ i1(getValueI1(_p)), i2(getValueI2(_p)) {}
+ }
+#ifndef PLATFORM_WINDOWS
+ __attribute__((packed))
+#endif
+ ;
+#ifdef PLATFORM_WINDOWS
+ #pragma pack(pop)
+#endif
+
+
+
+#ifdef PLATFORM_WINDOWS
+ #pragma pack(push,1)
+#endif
+ template <typename _T1, typename _T2, unsigned valueSizeI1>
+ struct Pair<_T1, _T2, CutCompressed<valueSizeI1> > {
+ typedef _T1 T1;
+ typedef _T2 T2;
+
+ typedef _T2 T12;
+
+ T12 i12;
+
+ enum { bitSizeI1 = CutCompressed<valueSizeI1>::bitSizeI1 };
+ enum { bitShiftI1 = BitsPerValue<T12>::VALUE - bitSizeI1 };
+
+ inline Pair() {}
+ inline Pair(Pair const &_p): i12(_p.i12) {}
+ inline Pair(_T1 const &_i1, _T2 const &_i2):
+ i12(((T12)_i1 << bitShiftI1) + (T12)_i2) {}
+
+ template <typename __T1, typename __T2, typename __TCompression>
+ inline Pair(Pair<__T1, __T2, __TCompression> const &_p):
+ i12(((T12)getValueI1(_p) << bitShiftI1) + (T12)getValueI2(_p)) {}
+ }
+#ifndef PLATFORM_WINDOWS
+ __attribute__((packed))
+#endif
+ ;
+#ifdef PLATFORM_WINDOWS
+ #pragma pack(pop)
+#endif
+
+
+
+ template <typename _T1, typename _T2, typename TCompression>
+ std::ostream& operator<<(std::ostream &out, Pair<_T1,_T2,TCompression> const &p) {
+ out << "< " << getValueI1(p) << " , " << getValueI2(p) << " >";
+ return out;
+ }
+
+ template <typename T1, typename T2, typename TCompression>
+ struct Value< Pair<T1, T2, TCompression>, 1 > {
+ typedef T1 Type;
+ };
+
+ template <typename T1, typename T2, typename TCompression>
+ struct Value< Pair<T1, T2, TCompression>, 2 > {
+ typedef T2 Type;
+ };
+
+ template <typename T1, typename T2, typename TCompression>
+ struct Spec< Pair<T1, T2, TCompression> > {
+ typedef TCompression Type;
+ };
+
+
+//____________________________________________________________________________
+
+ template <typename TKey, typename TObject, typename TSpec>
+ struct Key< Pair<TKey, TObject, TSpec> >
+ {
+ typedef TKey Type;
+ };
+
+ template <typename TKey, typename TCargo, typename TSpec>
+ struct Cargo< Pair<TKey, TCargo, TSpec> >
+ {
+ typedef TCargo Type;
+ };
+//____________________________________________________________________________
+
+/**
+.Class.Triple:
+..cat:Aggregates
+..summary:Stores three arbitrary objects.
+..signature:Triple<T1, T2, T3[, Compression]>
+..param.T1:The type of the first object.
+..param.T2:The type of the second object.
+..param.T3:The type of the third object.
+..param.Compression:If $Compressed$, the triple is stored in a more space efficient way (useful for external storage).
+...note:When compression is enabled, referring to members is not allowed.
+...default:$void$, no compression (faster access).
+.Memfunc.Triple#Triple:
+..class:Class.Triple
+..summary:Constructor
+..signature:Triple<T1, T2, T3> ()
+..signature:Triple<T1, T2, T3> (triple)
+..signature:Triple<T1, T2, T3> (i1, i2, i3)
+..param.triple:Other Triple object. (copy constructor)
+..param.i1:T1 object.
+..param.i2:T2 object.
+..param.i3:T3 object.
+.Memvar.Triple#i1:
+..class:Class.Triple
+..summary:T1 object
+.Memvar.Triple#i2:
+..class:Class.Triple
+..summary:T2 object
+.Memvar.Triple#i3:
+..class:Class.Triple
+..summary:T3 object
+*/
+
+ // standard storage
+ template <typename _T1, typename _T2 = _T1, typename _T3 = _T1, typename TCompression = void>
+ struct Triple {
+ typedef _T1 T1;
+ typedef _T2 T2;
+ typedef _T3 T3;
+ _T1 i1;
+ _T2 i2;
+ _T3 i3;
+ inline Triple() {}
+ inline Triple(Triple const &_p):
+ i1(_p.i1), i2(_p.i2), i3(_p.i3) {}
+ inline Triple(_T1 const &_i1, _T2 const &_i2, _T3 const &_i3):
+ i1(_i1), i2(_i2), i3(_i3) {}
+
+ template <typename __T1, typename __T2, typename __T3, typename __TCompression>
+ inline Triple(Triple<__T1, __T2, __T3, __TCompression> const &_p):
+ i1(getValueI1(_p)), i2(getValueI2(_p)), i3(getValueI3(_p)) {}
+ };
+
+ // unaligned and unpadded storage (space efficient)
+#ifdef PLATFORM_WINDOWS
+ #pragma pack(push,1)
+#endif
+ template <typename _T1, typename _T2, typename _T3>
+ struct Triple<_T1, _T2, _T3, Compressed> {
+ typedef _T1 T1;
+ typedef _T2 T2;
+ typedef _T3 T3;
+ _T1 i1;
+ _T2 i2;
+ _T3 i3;
+ inline Triple() {}
+ inline Triple(Triple const &_p):
+ i1(_p.i1), i2(_p.i2), i3(_p.i3) {}
+ inline Triple(_T1 const &_i1, _T2 const &_i2, _T3 const &_i3):
+ i1(_i1), i2(_i2), i3(_i3) {}
+
+ template <typename __T1, typename __T2, typename __T3, typename __TCompression>
+ inline Triple(Triple<__T1, __T2, __T3, __TCompression> const &_p):
+ i1(getValueI1(_p)), i2(getValueI2(_p)), i3(getValueI3(_p)) {}
+ }
+#ifndef PLATFORM_WINDOWS
+ __attribute__((packed))
+#endif
+ ;
+#ifdef PLATFORM_WINDOWS
+ #pragma pack(pop)
+#endif
+
+ template <typename _T1, typename _T2, typename _T3, typename TCompression>
+ std::ostream& operator<<(std::ostream &out, Triple<_T1,_T2,_T3,TCompression> const &t) {
+ out << "< " << getValueI1(t) << " , " << getValueI2(t) << " , " << getValueI3(t) << " >";
+ return out;
+ }
+
+ template <typename T1, typename T2, typename T3, typename TCompression>
+ struct Value< Triple<T1, T2, T3, TCompression>, 1 > {
+ typedef T1 Type;
+ };
+
+ template <typename T1, typename T2, typename T3, typename TCompression>
+ struct Value< Triple<T1, T2, T3, TCompression>, 2 > {
+ typedef T2 Type;
+ };
+
+ template <typename T1, typename T2, typename T3, typename TCompression>
+ struct Value< Triple<T1, T2, T3, TCompression>, 3 > {
+ typedef T3 Type;
+ };
+
+ template <typename T1, typename T2, typename T3, typename TCompression>
+ struct Spec< Triple<T1, T2, T3, TCompression> > {
+ typedef TCompression Type;
+ };
+
+
+//____________________________________________________________________________
+
+/**
+.Class.Tuple:
+..cat:Aggregates
+..summary:A plain fixed-length string.
+..signature:Tuple<T, size[, compress]>
+..param.T:The value type, that is the type of characters stored in the tuple.
+..param.size:The size/length of the tuple.
+...remarks:In contrast to @Class.String@ the length of Tuple is fixed.
+..param.compress:Enable/Disable compression.
+..param.compress:If $void$, no compression is used.
+..param.compress:If $Compressed$, the characters are stored as a bit sequence in an ordinal type (char, ..., __int64)
+...remarks:Only useful for small alphabets and small tuple sizes (|Sigma|^size <= 2^64) as for DNA or protein m-grams)
+...default:void.
+..see:Spec.Sampler
+*/
+
+ // standard storage
+ template <typename _T, unsigned _size, typename TCompression = void>
+ struct Tuple {
+ typedef _T T;
+ enum { size = _size };
+ _T i[_size];
+
+ template <typename TPos>
+ inline _T& operator[](TPos k) {
+ SEQAN_ASSERT(k >= 0 && k < size);
+ return i[k];
+ }
+ template <typename TPos>
+ inline const _T& operator[](TPos k) const {
+ SEQAN_ASSERT(k >= 0 && k < size);
+ return i[k];
+ }
+ inline _T* operator&() { return i; }
+ inline const _T* operator&() const { return i; }
+
+ // has to be inline because elements (like this tuple) of packed structs can't be arguments
+ template <typename TPos, typename SSS>
+ inline SSS const assignValueAt(TPos k, SSS const source) {
+ return i[k] = source;
+ }
+ };
+
+
+ template < unsigned char _size >
+ struct _BitVector {
+ typedef typename _BitVector<_size + 1>::Type Type;
+ };
+
+ template <> struct _BitVector<8> { typedef unsigned char Type; };
+ template <> struct _BitVector<16> { typedef unsigned short Type; };
+ template <> struct _BitVector<32> { typedef unsigned int Type; };
+ template <> struct _BitVector<64> { typedef __int64 Type; };
+ template <> struct _BitVector<255> { typedef __int64 Type; };
+
+ // bit-compressed storage (space efficient)
+#ifdef PLATFORM_WINDOWS
+ #pragma pack(push,1)
+#endif
+ template <typename _T, unsigned _size>
+ struct Tuple<_T, _size, Compressed> {
+ typedef _T T;
+ enum { size = _size };
+ enum { bitSize = BitsPerValue<_T>::VALUE };
+ enum { bitMask = (1 << bitSize) - 1 };
+ enum { mask = (1 << (size * bitSize)) - 1 };
+ typedef typename _BitVector< bitSize * size >::Type CT;
+
+ CT i;
+/*
+ inline Tuple() {
+ SEQAN_ASSERT(bitSize * size <= sizeof(CT) * 8);
+ }
+*/
+ template <typename TPos>
+ inline const _T operator[](TPos k) const {
+ SEQAN_ASSERT(k >= 0 && k < size);
+ return (i >> (size - 1 - k) * bitSize) & bitMask;
+ }
+ template <unsigned __size>
+ inline Tuple operator=(Tuple<_T, __size, Compressed> const &_right) {
+ i = _right.i;
+ return *this;
+ }
+ template <typename TShiftSize>
+ inline CT operator<<=(TShiftSize shift) {
+ return i = (i << (shift * bitSize)) & mask;
+ }
+ template <typename TShiftSize>
+ inline CT operator<<(TShiftSize shift) const {
+ return (i << (shift * bitSize)) & mask;
+ }
+ template <typename TShiftSize>
+ inline CT operator>>=(TShiftSize shift) {
+ return i = (i >> (shift * bitSize));
+ }
+ template <typename TShiftSize>
+ inline CT operator>>(TShiftSize shift) const {
+ return i >> (shift * bitSize);
+ }
+ template <typename T>
+ inline void operator|=(T const &t) {
+ i |= t;
+ }
+ template <typename T, typename TSpec>
+ inline void operator|=(SimpleType<T, TSpec> const &t) {
+ i |= t.value;
+ }
+ inline CT* operator&() { return &i; }
+ inline const CT* operator&() const { return &i; }
+
+ // has to be inline because elements (like this tuple) of packed structs can't be arguments
+ template <typename TPos, typename SSS>
+ inline SSS const assignValueAt(TPos k, SSS const source) {
+ typedef Tuple<_T, _size, Compressed> Tup;
+ typename Tup::CT mask = Tup::bitMask << ((_size - 1 - k) * bitSize);
+ i = (i & ~mask) | ((CT)source << ((_size - 1 - k) * bitSize));
+ return source;
+ }
+ }
+#ifndef PLATFORM_WINDOWS
+ __attribute__((packed))
+#endif
+ ;
+#ifdef PLATFORM_WINDOWS
+ #pragma pack(pop)
+#endif
+
+
+//////////////////////////////////////////////////////////////////////////////
+// length
+
+ template <typename _T, unsigned _size, typename TCompression>
+ inline unsigned length(Tuple<_T, _size, TCompression> const &) { return _size; }
+
+ ///.Metafunction.LENGTH.param.T.type:Class.Tuple
+ template <typename _T, unsigned _size, typename TCompression>
+ struct LENGTH< Tuple<_T, _size, TCompression> >
+ {
+ enum { VALUE = _size };
+ };
+
+//////////////////////////////////////////////////////////////////////////////
+// assignValueAt
+
+ template <typename TObject, typename TPos, typename TSource>
+ inline TSource &
+ assignValueAt(TObject &me, TPos k, TSource &source) {
+ assign(value(me, k), source);
+ return source;
+ }
+
+ template <typename TObject, typename TPos, typename TSource>
+ inline TSource const &
+ assignValueAt(TObject &me, TPos k, TSource const &source) {
+ assign(value(me, k), source);
+ return source;
+ }
+
+ template <typename TTT, unsigned _size, typename SSS, typename TPos>
+ inline SSS const assignValueAt(Tuple<TTT, _size, void> &me, TPos k, SSS const source) {
+ return me.i[k] = source;
+ }
+
+ template <typename TTT, unsigned _size, typename SSS, typename TPos>
+ inline SSS const assignValueAt(Tuple<TTT, _size, Compressed> &me, TPos k, SSS const source) {
+ typedef Tuple<TTT, _size, Compressed> Tup;
+ typename Tup::CT mask = Tup::bitMask << ((_size - 1 - k) * me.bitSize);
+ me.i = (me.i & ~mask) | source << ((_size - 1 - k) * me.bitSize);
+ return source;
+ }
+
+ template <typename TTT, typename SSS, typename SSSpec, unsigned _size, typename TPos>
+ inline SimpleType<SSS, SSSpec> const & assignValueAt(Tuple<TTT, _size, Compressed> &me, TPos k, SimpleType<SSS, SSSpec> const &source) {
+ typedef Tuple<TTT, _size, Compressed> Tup;
+ typename Tup::CT mask = Tup::bitMask << ((_size - 1 - k) * me.bitSize);
+ me.i = (me.i & ~mask) | source.value << ((_size - 1 - k) * me.bitSize);
+ return source;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// clear
+
+ template <typename TTT, unsigned _size, typename TCompression>
+ inline void clear(Tuple<TTT, _size, TCompression> &me) {
+ memset<sizeof(me.i), 0>(&(me.i));
+ }
+ template <typename TTT, unsigned _size>
+ inline void clear(Tuple<TTT, _size, Compressed> &me) {
+ me.i = 0;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// optimized compares
+
+ template <typename TTT, unsigned _sizeL, unsigned _sizeR>
+ inline bool operator<(Tuple<TTT, _sizeL, Compressed> const &_left, Tuple<TTT, _sizeR, Compressed> const &_right) {
+ return _left.i < _right.i;
+ }
+ template <typename TTT, unsigned _sizeL, unsigned _sizeR>
+ inline bool operator>(Tuple<TTT, _sizeL, Compressed> const &_left, Tuple<TTT, _sizeR, Compressed> const &_right) {
+ return _left.i > _right.i;
+ }
+ template <typename TTT, unsigned _sizeL, unsigned _sizeR>
+ inline bool operator==(Tuple<TTT, _sizeL, Compressed> const &_left, Tuple<TTT, _sizeR, Compressed> const &_right) {
+ return _left.i == _right.i;
+ }
+ template <typename TTT, unsigned _sizeL, unsigned _sizeR>
+ inline bool operator!=(Tuple<TTT, _sizeL, Compressed> const &_left, Tuple<TTT, _sizeR, Compressed> const &_right) {
+ return _left.i != _right.i;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// optimized shifts
+
+ struct _TupleShiftLeftWorker {
+ template <typename Arg>
+ static inline void body(Arg &arg, unsigned I) {
+ arg[I-1] = arg[I];
+ }
+ };
+
+ struct _TupleShiftRightWorker {
+ template <typename Arg>
+ static inline void body(Arg &arg, unsigned I) {
+ arg[I] = arg[I-1];
+ }
+ };
+
+ template <typename _T, unsigned _size, typename TCompression>
+ inline void shiftLeft(Tuple<_T, _size, TCompression> &me) {
+ LOOP<_TupleShiftLeftWorker, _size - 1>::run(me);
+ }
+
+ template <typename _T, unsigned _size, typename TCompression>
+ inline void shiftRight(Tuple<_T, _size, TCompression> &me) {
+ LOOP_REVERSE<_TupleShiftRightWorker, _size - 1>::run(me);
+ }
+
+ template <typename _T, unsigned _size>
+ inline void shiftLeft(Tuple<_T, _size, Compressed> &me) {
+ me<<=1;
+ }
+
+ template <typename _T, unsigned _size>
+ inline void shiftRight(Tuple<_T, _size, Compressed> &me) {
+ me>>=1;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// standard output
+
+ template <typename _T, unsigned _size, typename TCompression>
+ std::ostream& operator<<(std::ostream& out, Tuple<_T,_size,TCompression> const &a) {
+ out << "[";
+ if (a.size > 0)
+ out << a[0];
+ for(unsigned j = 1; j < a.size; ++j)
+ out << " " << a[j];
+ out << "]";
+ return out;
+ }
+
+ template <typename _T, unsigned _size, typename TCompression>
+ struct Value< Tuple<_T, _size, TCompression> > {
+ typedef _T Type;
+ };
+
+ template <typename _T, unsigned _size, typename TCompression>
+ struct Spec< Tuple<_T, _size, TCompression> > {
+ typedef TCompression Type;
+ };
+
+//////////////////////////////////////////////////////////////////////////////
+// getValueIx
+
+ template <typename T1, typename T2, typename TCompression>
+ inline T1 getValueI1(Pair<T1, T2, TCompression> const &pair) {
+ return pair.i1;
+ }
+
+ template <typename T1, typename T2, typename TCompression>
+ inline T2 getValueI2(Pair<T1, T2, TCompression> const &pair) {
+ return pair.i2;
+ }
+
+ template <typename T1, typename T2, unsigned valueSizeI1>
+ inline T1 getValueI1(Pair<T1, T2, CutCompressed<valueSizeI1> > const &pair) {
+ typedef Pair<T1, T2, CutCompressed<valueSizeI1> > TPair;
+ return pair.i12 >> TPair::bitShiftI1;
+ }
+
+ template <typename T1, typename T2, unsigned valueSizeI1>
+ inline T2 getValueI2(Pair<T1, T2, CutCompressed<valueSizeI1> > const &pair) {
+ typedef Pair<T1, T2, CutCompressed<valueSizeI1> > TPair;
+ return pair.i12 & (((typename TPair::T12)1 << TPair::bitShiftI1) - 1);
+ }
+//____________________________________________________________________________
+
+ template <typename T1, typename T2, typename T3, typename TCompression>
+ inline T1 getValueI1(Triple<T1, T2, T3, TCompression> const &triple) {
+ return triple.i1;
+ }
+
+ template <typename T1, typename T2, typename T3, typename TCompression>
+ inline T2 getValueI2(Triple<T1, T2, T3, TCompression> const &triple) {
+ return triple.i2;
+ }
+
+ template <typename T1, typename T2, typename T3, typename TCompression>
+ inline T3 getValueI3(Triple<T1, T2, T3, TCompression> const &triple) {
+ return triple.i3;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// assignValueIx
+
+ template <typename T1, typename T2, typename TCompression, typename T>
+ inline void assignValueI1(Pair<T1, T2, TCompression> &pair, T const &_i) {
+ pair.i1 = _i;
+ }
+
+ template <typename T1, typename T2, typename TCompression, typename T>
+ inline void assignValueI2(Pair<T1, T2, TCompression> &pair, T const &_i) {
+ pair.i2 = _i;
+ }
+
+ template <typename T1, typename T2, unsigned valueSizeI1, typename T>
+ inline void assignValueI1(Pair<T1, T2, CutCompressed<valueSizeI1> > &pair, T const &_i)
+ {
+ typedef Pair<T1, T2, CutCompressed<valueSizeI1> > TPair;
+ pair.i12 = ((typename TPair::T12)_i << TPair::bitShiftI1) |
+ (pair.i12 & (((typename TPair::T12)1 << TPair::bitShiftI1) - 1));
+ }
+
+ template <typename T1, typename T2, unsigned valueSizeI1, typename T>
+ inline void assignValueI2(Pair<T1, T2, CutCompressed<valueSizeI1> > &pair, T const &_i) {
+ typedef Pair<T1, T2, CutCompressed<valueSizeI1> > TPair;
+ pair.i12 = (pair.i12 & ~(((typename TPair::T12)1 << TPair::bitShiftI1) - 1)) | _i;
+ }
+//____________________________________________________________________________
+
+ template <typename T1, typename T2, typename T3, typename TCompression, typename T>
+ inline T const assignValueI1(Triple<T1, T2, T3, TCompression> &triple, T const &_i) {
+ return triple.i1 = _i;
+ }
+
+ template <typename T1, typename T2, typename T3, typename TCompression, typename T>
+ inline T const assignValueI2(Triple<T1, T2, T3, TCompression> &triple, T const &_i) {
+ return triple.i2 = _i;
+ }
+
+ template <typename T1, typename T2, typename T3, typename TCompression, typename T>
+ inline T const assignValueI3(Triple<T1, T2, T3, TCompression> &triple, T const &_i) {
+ return triple.i3 = _i;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// operator ==/!= for pairs and triples
+
+ template <typename L1, typename L2, typename LCompression, typename R1, typename R2, typename RCompression>
+ inline bool operator==(Pair<L1, L2, LCompression> const &_left, Pair<R1, R2, RCompression> const &_right) {
+ return _left.i1 == _right.i1 && _left.i2 == _right.i2;
+ }
+ template <typename L1, typename L2, typename LCompression, typename R1, typename R2, typename RCompression>
+ inline bool operator!=(Pair<L1, L2, LCompression> const &_left, Pair<R1, R2, RCompression> const &_right) {
+ return _left.i1 != _right.i1 || _left.i2 != _right.i2;
+ }
+
+ template <typename L1, typename L2, unsigned LSizeI1, typename R1, typename R2, unsigned RSizeI1>
+ inline bool operator==(Pair<L1, L2, CutCompressed<LSizeI1> > const &_left, Pair<R1, R2, CutCompressed<RSizeI1> > const &_right) {
+ return _left.i12 == _right.i12;
+ }
+ template <typename L1, typename L2, unsigned LSizeI1, typename R1, typename R2, unsigned RSizeI1>
+ inline bool operator!=(Pair<L1, L2, CutCompressed<LSizeI1> > const &_left, Pair<R1, R2, CutCompressed<RSizeI1> > const &_right) {
+ return _left.i12 != _right.i12;
+ }
+//____________________________________________________________________________
+
+ template <
+ typename L1, typename L2, typename L3, typename LCompression,
+ typename R1, typename R2, typename R3, typename RCompression>
+ inline bool operator==(Triple<L1, L2, L3, LCompression> const &_left, Triple<R1, R2, R3, RCompression> const &_right) {
+ return _left.i1 == _right.i1 && _left.i2 == _right.i2 && _left.i3 == _right.i3;
+ }
+ template <
+ typename L1, typename L2, typename L3, typename LCompression,
+ typename R1, typename R2, typename R3, typename RCompression>
+ inline bool operator!=(Triple<L1, L2, L3, LCompression> const &_left, Triple<R1, R2, R3, RCompression> const &_right) {
+ return _left.i1 != _right.i1 || _left.i2 != _right.i2 || _left.i3 != _right.i3;
+ }
+
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_allocator_interface.h b/src/libSSA/seqan/basic/basic_allocator_interface.h
new file mode 100644
index 0000000..cc48e0d
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_allocator_interface.h
@@ -0,0 +1,236 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_allocator_interface.h,v 1.1 2008/08/25 16:20:02 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_ALLOCATOR_INTERFACE_H
+#define SEQAN_HEADER_BASIC_ALLOCATOR_INTERFACE_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+//Allocator
+//////////////////////////////////////////////////////////////////////////////
+
+
+/**
+.Class.Allocator:
+..cat:Basic
+..summary:Manager for allocated memory.
+..signature:Allocator<TSpec>
+..param.TSpec:The specializing type.
+...metafunction:Metafunction.Spec
+..implements:Concept.Allocator
+..include:basic.h
+..remarks:There are two reasons for using non-trivial allocators:
+...text:1. Allocators support the function @Function.Allocator#clear@ for a fast deallocation of all
+allocated memory blocks.
+...text:2. Some allocators are faster in allocating an deallocating memory.
+Pool allocators like e.g. @Spec.Single Pool Allocator@ or @Spec.Multi Pool Allocator@
+speed up @Function.allocate@, @Function.deallocate@, and @Function.Allocator#clear@ for
+pooled memory blocks.
+*/
+
+template <typename TSpec>
+struct Allocator;
+
+///.Function.allocate.param.object.type:Class.Allocator
+///.Function.deallocate.param.object.type:Class.Allocator
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Metafunctions
+//////////////////////////////////////////////////////////////////////////////
+
+//.Metafunction.Spec.param.T.type:Class.Allocator
+
+template <typename TSpec>
+struct Spec<Allocator<TSpec> >
+{
+ typedef TSpec Type;
+};
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Tag.Allocator Usage:
+..summary:The purpose of an allocated memory block.
+..tag.TagAllocateTemp:Temporary memory.
+..tag.TagAllocateStorage:Memory for storing container content.
+..see:Function.allocate
+..see:Function.deallocate
+*/
+struct TagAllocateUnspecified_; //< usage not specified
+typedef Tag<TagAllocateUnspecified_> const TagAllocateUnspecified;
+
+struct TagAllocateTemp_; //< allocate temporary memory
+typedef Tag<TagAllocateTemp_> const TagAllocateTemp;
+
+struct TagAllocateStorage_; //< allocate memory for storing member data
+typedef Tag<TagAllocateStorage_> const TagAllocateStorage;
+
+
+//////////////////////////////////////////////////////////////////////////////
+//allocates memory on heap. No c'tors are called.
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.allocate:
+..cat:Memory
+..summary:Allocates memory from heap.
+..signature:allocate(object, data, count [, usage_tag])
+..param.object:Allocator object.
+...remarks:$object$ is conceptually the "owner" of the allocated memory.
+ Objects of all types can be used as allocators. If no special behavior is implemented,
+ default functions allocation/deallocation are applied that uses standard
+ $new$ and $delete$ operators.
+..param.count:Number of items that could be stored in the allocated memory.
+...text:The type of the allocated items is given by the type of $data$.
+..param.usage_tag:A tag the specifies the purpose for the allocated memory.
+...value:@Tag.Allocator Usage@
+..returns.param.data:Pointer to allocated memory.
+...remarks:The value of this pointer is overwritten by the function.
+..remarks:
+...text:The function allocates at least $count*sizeof(data)$ bytes.
+ The allocated memory is large enough
+ to hold $count$ objects of type $T$, where $T *$ is type of $data$.
+...note:These objects are not constructed by $allocate$.
+...text:Use e.g. one of the functions @Function.valueConstruct@, @Function.arrayConstruct@, @Function.arrayConstructCopy@ or @Function.arrayFill@
+to construct the objects.
+A $new$ operator which is part of the C++ standard (defined in $<new>$)
+ can also be used to construct objects at a given memory address.
+..note:All allocated memory blocks should be deallocated by the corresponding function @Function.deallocate at .
+..see:Function.deallocate
+..see:Function.valueConstruct
+..see:Function.arrayFill
+..see:Function.arrayConstruct
+..see:Function.arrayConstructCopy
+*/
+template <typename T, typename TValue, typename TSize>
+inline void
+allocate(T const & me,
+ TValue * & data,
+ TSize count)
+{
+ allocate(me, data, count, TagAllocateUnspecified());
+}
+template <typename T, typename TValue, typename TSize>
+inline void
+allocate(T & me,
+ TValue * & data,
+ TSize count)
+{
+ allocate(me, data, count, TagAllocateUnspecified());
+}
+
+template <typename T, typename TValue, typename TSize, typename TUsage>
+inline void
+allocate(T const &,
+ TValue * & data,
+ TSize count,
+ Tag<TUsage> const)
+{
+ data = (TValue *) operator new(count * sizeof(TValue));
+ if (data)
+ SEQAN_PROADD(SEQAN_PROMEMORY, count * sizeof(TValue));
+}
+template <typename T, typename TValue, typename TSize, typename TUsage>
+inline void
+allocate(T &,
+ TValue * & data,
+ TSize count,
+ Tag<TUsage> const)
+{
+ data = (TValue *) operator new(count * sizeof(TValue));
+ if (data)
+ SEQAN_PROADD(SEQAN_PROMEMORY, count * sizeof(TValue));
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+//deallocates memory that was allocates using allocate(.)
+
+/**
+.Function.deallocate:
+..cat:Memory
+..summary:Deallocates memory.
+..signature:deallocate(object, data, count [, usage_tag])
+..param.object:Allocator object.
+...remarks:$object$ is conceptually the "owner" of the allocated memory.
+ Objects of all types can be used as allocators. If no special behavior is implemented,
+ default functions allocation/deallocation are applied that uses standard
+ $new$ and $delete$ operators.
+..param.data:Pointer to allocated memory that was allocated by $allocate$.
+..param.count:Number of items that could be stored in the allocated memory.
+..param.usage_tag:A tag the specifies the purpose for the allocated memory.
+...value:@Tag.Allocator Usage@
+..remarks:
+...text:The values for $object$, $count$ and $usage_tag$ should be the same that was
+used when $allocate$ was called. The value of $data$ should be the same that was
+returned by $allocate$.
+...note:$deallocate$ does not destruct objects.
+...text:Use e.g. one of the functions @Function.valueDestruct@ or @Function.arrayDestruct@ to destruct the objects.
+$delete$ and $delete []$ operators which are part of the C++ standard (defined in $<new>$)
+ can also be used to destruct objects at a given memory address.
+..see:Function.valueDestruct
+..see:Function.arrayDestruct
+*/
+template <typename T, typename TValue, typename TSize>
+inline void
+deallocate(T const & me,
+ TValue * data,
+ TSize const count)
+{
+ deallocate(me, data, count, TagAllocateUnspecified());
+}
+template <typename T, typename TValue, typename TSize>
+inline void
+deallocate(T & me,
+ TValue * data,
+ TSize const count)
+{
+ deallocate(me, data, count, TagAllocateUnspecified());
+}
+
+template <typename T, typename TValue, typename TSize, typename TUsage>
+inline void
+deallocate(T const & /*me*/,
+ TValue * data,
+ TSize count,
+ Tag<TUsage> const)
+{
+ if (data && count) // .. to use count if SEQAN_PROFILE is not defined
+ SEQAN_PROSUB(SEQAN_PROMEMORY, count * sizeof(TValue));
+ operator delete ((void *) data);
+}
+template <typename T, typename TValue, typename TSize, typename TUsage>
+inline void
+deallocate(T & /*me*/,
+ TValue * data,
+ TSize count,
+ Tag<TUsage> const)
+{
+ if (data && count) // .. to use count if SEQAN_PROFILE is not defined
+ SEQAN_PROSUB(SEQAN_PROMEMORY, count * sizeof(TValue));
+ operator delete ((void *) data);
+}
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_allocator_multipool.h b/src/libSSA/seqan/basic/basic_allocator_multipool.h
new file mode 100644
index 0000000..c637e20
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_allocator_multipool.h
@@ -0,0 +1,230 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_allocator_multipool.h,v 1.2 2009/02/19 01:51:23 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_ALLOCATOR_MULTIPOOL_H
+#define SEQAN_HEADER_BASIC_ALLOCATOR_MULTIPOOL_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+// MultiPool Allocator
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Spec.Multi Pool Allocator:
+..cat:Allocators
+..general:Class.Allocator
+..summary:Allocator that pools memory blocks.
+..signature:Allocator< MultiPool<ParentAllocator, BLOCKING_LIMIT> >
+..param.ParentAllocator:An allocator that is by the pool allocator used to allocate memory.
+...default:@Spec.Simple Allocator@
+...note:The multi pool allocator only supports @Function.clear@ if this function is also implemented for $ParentAllocator$.
+..remarks:A pool allocator allocates several memory blocks at once.
+..param.BLOCKING_LIMIT:The maximum size for memory blocks to be pooled.
+...default:256
+Freed blocks are not immediately deallocated but recycled in subsequential allocations.
+This way, the number of calls to the heap manager is reduced, and that speeds up memory management.
+...text:Note that memory blocks larger than $BLOCKING_LIMIT$ are not pooled
+but immediately allocated and deallocated using $ParentAllocator$.
+*/
+
+
+template <typename TParentAllocator = Allocator<SimpleAlloc<Default> >, unsigned int BLOCKING_LIMIT = 0x100>
+struct MultiPool;
+
+//////////////////////////////////////////////////////////////////////////////
+
+typedef Allocator<MultiPool<Allocator<SimpleAlloc<Default> >, 0x100> > PoolAllocator;
+
+template <typename TParentAllocator, unsigned int BLOCKING_LIMIT_>
+struct Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT_> >
+{
+ enum
+ {
+ BLOCKING_LIMIT = BLOCKING_LIMIT_,
+ GRANULARITY_BITS = 2,
+ BLOCKING_COUNT = BLOCKING_LIMIT >> GRANULARITY_BITS,
+ STORAGE_SIZE = 0xf80
+ };
+
+ char * data_recycled_blocks [BLOCKING_COUNT];
+ char * data_current_begin [BLOCKING_COUNT];
+ char * data_current_free [BLOCKING_COUNT];
+ Holder<TParentAllocator> data_parent_allocator;
+
+ Allocator()
+ {
+SEQAN_CHECKPOINT
+ memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
+ memset(data_current_begin, 0, sizeof(data_current_begin));
+ memset(data_current_free, 0, sizeof(data_current_free));
+ }
+
+ Allocator(TParentAllocator & parent_alloc)
+ {
+SEQAN_CHECKPOINT
+ memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
+ memset(data_current_begin, 0, sizeof(data_current_begin));
+ memset(data_current_free, 0, sizeof(data_current_free));
+
+ setValue(data_parent_allocator, parent_alloc);
+ }
+
+ //Dummy copy
+ Allocator(Allocator const &)
+ {
+ memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
+ memset(data_current_begin, 0, sizeof(data_current_begin));
+ memset(data_current_free, 0, sizeof(data_current_free));
+ }
+ inline Allocator &
+ operator = (Allocator const &)
+ {
+ clear(*this);
+ return *this;
+ }
+
+ ~Allocator()
+ {
+SEQAN_CHECKPOINT
+ clear(*this);
+ }
+};
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TParentAllocator, unsigned int BLOCKING_LIMIT>
+inline TParentAllocator &
+parentAllocator(Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > & me)
+{
+SEQAN_CHECKPOINT
+ return value(me.data_parent_allocator);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TParentAllocator, unsigned int BLOCKING_LIMIT>
+void
+clear(Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > & me)
+{
+SEQAN_CHECKPOINT
+ memset(me.data_recycled_blocks, 0, sizeof(me.data_recycled_blocks));
+ memset(me.data_current_begin, 0, sizeof(me.data_current_begin));
+ memset(me.data_current_free, 0, sizeof(me.data_current_free));
+
+ clear(parentAllocator(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TParentAllocator, unsigned int BLOCKING_LIMIT>
+inline unsigned int
+_allocatorBlockNumber(Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > &,
+ size_t size_)
+{
+SEQAN_CHECKPOINT
+ typedef Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > TAllocator;
+
+ SEQAN_ASSERT(size_)
+
+ if (size_ < BLOCKING_LIMIT)
+ {//blocks
+ return size_ >> TAllocator::GRANULARITY_BITS;
+ }
+ else
+ {//no blocking
+ return TAllocator::BLOCKING_COUNT;
+ }
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TParentAllocator, unsigned int BLOCKING_LIMIT, typename TValue, typename TSize, typename TUsage>
+inline void
+allocate(Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > & me,
+ TValue * & data,
+ TSize count,
+ Tag<TUsage> const tag_)
+{
+SEQAN_CHECKPOINT
+ typedef Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > TAllocator;
+
+ size_t bytes_needed = count * sizeof(TValue);
+ char * ptr;
+
+ unsigned int block_number = _allocatorBlockNumber(me, bytes_needed);
+ if (block_number == TAllocator::BLOCKING_COUNT)
+ {//no blocking
+ return allocate(parentAllocator(me), data, count, tag_);
+ }
+
+ bytes_needed = (block_number + 1) << TAllocator::GRANULARITY_BITS;
+
+ if (me.data_recycled_blocks[block_number])
+ {//use recycled
+ ptr = me.data_recycled_blocks[block_number];
+ me.data_recycled_blocks[block_number] = * reinterpret_cast<char **>(ptr);
+ }
+ else
+ {//use new
+ ptr = me.data_current_free[block_number];
+ if (!ptr || (ptr + bytes_needed > me.data_current_begin[block_number] + TAllocator::STORAGE_SIZE))
+ {//not enough free space in current storage: allocate new
+ allocate(parentAllocator(me), ptr, (size_t) TAllocator::STORAGE_SIZE, tag_);
+ me.data_current_begin[block_number] = ptr;
+ }
+ me.data_current_free[block_number] = ptr + bytes_needed;
+ }
+
+ data = reinterpret_cast<TValue *>(ptr);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TParentAllocator, unsigned int BLOCKING_LIMIT, typename TValue, typename TSize, typename TUsage>
+inline void
+deallocate(Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > & me,
+ TValue * data,
+ TSize count,
+ Tag<TUsage> const tag_)
+{
+SEQAN_CHECKPOINT
+ typedef Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > TAllocator;
+
+ size_t bytes_needed = count * sizeof(TValue);
+
+ unsigned int block_number = _allocatorBlockNumber(me, bytes_needed);
+ if (block_number == TAllocator::BLOCKING_COUNT)
+ {//no blocking
+ return deallocate(parentAllocator(me), data, count, tag_);
+ }
+
+ bytes_needed = (block_number + 1) << TAllocator::GRANULARITY_BITS;
+
+ //link in recycling list
+ *reinterpret_cast<char **>(data) = me.data_recycled_blocks[block_number];
+ me.data_recycled_blocks[block_number] = reinterpret_cast<char *>(data);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_allocator_simple.h b/src/libSSA/seqan/basic/basic_allocator_simple.h
new file mode 100644
index 0000000..6b570cc
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_allocator_simple.h
@@ -0,0 +1,210 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_allocator_simple.h,v 1.1 2008/08/25 16:20:02 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_ALLOCATOR_SIMPLE_H
+#define SEQAN_HEADER_BASIC_ALLOCATOR_SIMPLE_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+
+
+//////////////////////////////////////////////////////////////////////////////
+// SimpleAlloc Allocator
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Spec.Simple Allocator:
+..cat:Allocators
+..general:Class.Allocator
+..summary:General purpose allocator.
+..signature:Allocator< SimpleAlloc<ParentAllocator> >
+..param.ParentAllocator:An allocator that is by the simple allocator used to allocate memory.
+...default:@Tag.Default@
+...remarks:@Tag.Default@ used as allocator means that the default implementations
+of @Function.allocate@ and @Function.deallocate@ are used.
+*/
+
+template <typename TParentAllocator = Default>
+struct SimpleAlloc;
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+typedef Allocator<SimpleAlloc<Default> > SimpleAllocator;
+
+template <typename TParentAllocator>
+struct Allocator<SimpleAlloc<TParentAllocator> >
+{
+ struct Header
+ {
+ Header * left;
+ Header * right;
+ size_t size;
+ };
+
+ Header * data_storages;
+ Holder<TParentAllocator> data_parent_allocator;
+
+ Allocator():
+ data_storages(0)
+ {
+SEQAN_CHECKPOINT
+ }
+
+ Allocator(TParentAllocator & parent_alloc):
+ data_storages(0)
+ {
+SEQAN_CHECKPOINT
+ setValue(data_parent_allocator, parent_alloc);
+ }
+
+ //Dummy copy
+ Allocator(Allocator const &):
+ data_storages(0)
+ {
+ }
+ inline Allocator &
+ operator = (Allocator const &)
+ {
+ clear(*this);
+ return *this;
+ }
+
+ ~Allocator()
+ {
+SEQAN_CHECKPOINT
+ clear(*this);
+ }
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TParentAllocator>
+inline TParentAllocator &
+parentAllocator(Allocator<SimpleAlloc<TParentAllocator> > & me)
+{
+SEQAN_CHECKPOINT
+ return value(me.data_parent_allocator);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.Allocator#clear:
+..cat:Memory
+..summary:Deallocates all memory blocks.
+..signature:clear(allocator)
+..param.allocator:Allocator object.
+...type:Class.Allocator
+...concept:Concept.Allocator
+..remarks:This function deallocates all memory blocks
+that was allocated using @Function.allocate@ for $allocator$.
+The memory is not pooled but directly passed back to the heap manager.
+..see:Function.allocate
+..see:Function.deallocate
+*/
+template <typename TParentAllocator>
+void
+clear(Allocator<SimpleAlloc<TParentAllocator> > & me)
+{
+SEQAN_CHECKPOINT
+ typedef Allocator<SimpleAlloc<TParentAllocator> > TAllocator;
+
+ while (me.data_storages)
+ {
+ typename TAllocator::Header * next_storage = me.data_storages->right;
+ deallocate(parentAllocator(me), reinterpret_cast<char *>(me.data_storages), me.data_storages->size);
+ me.data_storages = next_storage;
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TParentAllocator, typename TValue, typename TSize, typename TUsage>
+inline void
+allocate(Allocator<SimpleAlloc<TParentAllocator> > & me,
+ TValue * & data,
+ TSize count,
+ Tag<TUsage> const)
+{
+SEQAN_CHECKPOINT
+ typedef Allocator<SimpleAlloc<TParentAllocator> > TAllocator;
+ typedef typename TAllocator::Header THeader;
+
+ //compute needed bytes
+ size_t bytes_needed = count * sizeof(TValue) + sizeof(THeader);
+
+ //allocate storage from parent
+ char * ptr;
+ allocate(parentAllocator(me), ptr, bytes_needed, TagAllocateStorage());
+
+ THeader * new_block = reinterpret_cast<THeader *>(ptr);
+ new_block->left = 0;
+ new_block->right = me.data_storages;
+ new_block->size = bytes_needed;
+
+ if (me.data_storages)
+ {
+ me.data_storages->left = new_block;
+ }
+ me.data_storages = new_block;
+
+ //return data
+ data = reinterpret_cast<TValue *>(ptr + sizeof(THeader));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TParentAllocator, typename TValue, typename TSize, typename TUsage>
+inline void
+deallocate(Allocator<SimpleAlloc<TParentAllocator> > & me,
+ TValue * data,
+ TSize,
+ Tag<TUsage> const)
+{
+SEQAN_CHECKPOINT
+ typedef Allocator<SimpleAlloc<TParentAllocator> > TAllocator;
+ typedef typename TAllocator::Header THeader;
+
+ //update links
+ THeader & header = *(reinterpret_cast<THeader *>(data) - 1);
+ if (header.left)
+ {
+ header.left->right = header.right;
+ }
+ else
+ {
+ me.data_storages = header.right;
+ }
+ if (header.right)
+ {
+ header.right->left = header.left;
+ }
+
+ //deallocate storage using parent
+ char * ptr = reinterpret_cast<char *>(& header);
+ deallocate(parentAllocator(me), ptr, header.size);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_allocator_singlepool.h b/src/libSSA/seqan/basic/basic_allocator_singlepool.h
new file mode 100644
index 0000000..88fde00
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_allocator_singlepool.h
@@ -0,0 +1,299 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_allocator_singlepool.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_ALLOCATOR_SINGLE_POOL_H
+#define SEQAN_HEADER_BASIC_ALLOCATOR_SINGLE_POOL_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+// SinglePool Allocator
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Spec.Single Pool Allocator:
+..cat:Allocators
+..general:Class.Allocator
+..summary:Allocator that pools memory blocks of specific size.
+..signature:Allocator< SinglePool<SIZE, ParentAllocator> >
+..param.SIZE:Size of memory blocks that are pooled.
+...value:An unsigned integer with $SIZE >= sizeof(void *)$.
+..param.ParentAllocator:An allocator that is by the pool allocator used to allocate memory.
+...default:@Spec.Simple Allocator@
+...note:The single pool allocator only supports @Function.clear@ if this function is also implemented for $ParentAllocator$.
+..remarks:A pool allocator allocates several memory blocks at once.
+Freed blocks are not immediately deallocated but recycled in subsequential allocations.
+This way, the number of calls to the heap manager is reduced, and that speeds up memory management.
+...text:The single pool allocator only pools memory blocks of size $SIZE$.
+Blocks of other sizes are allocated and deallocated using an allocator of type $ParentAllocator$.
+...text:Using the single pool allocator for blocksizes larger than some KB is not advised.
+*/
+
+template <size_t SIZE, typename TParentAllocator = SimpleAllocator>
+struct SinglePool;
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <size_t SIZE, typename TParentAllocator>
+struct Allocator<SinglePool<SIZE, TParentAllocator> >
+{
+ enum
+ {
+ SIZE_PER_ITEM = SIZE,
+ ITEMS_PER_BLOCK = (SIZE_PER_ITEM < 0x0100) ? 0x01000 / SIZE_PER_ITEM : 16,
+ STORAGE_SIZE = SIZE * ITEMS_PER_BLOCK,
+
+ STORAGE_SIZE_MIN = SIZE
+ };
+
+ char * data_recycled_blocks;
+ char * data_current_begin;
+ char * data_current_end;
+ char * data_current_free;
+ Holder<TParentAllocator> data_parent_allocator;
+
+ Allocator()
+ {
+SEQAN_CHECKPOINT
+ data_recycled_blocks = data_current_end = data_current_free = 0;
+ //dont need to initialize data_current_begin
+ }
+
+ Allocator(size_t reserve_item_count)
+ {
+SEQAN_CHECKPOINT
+ data_recycled_blocks = 0;
+
+ size_t storage_size = (reserve_item_count * SIZE > STORAGE_SIZE_MIN) ? reserve_item_count * SIZE : STORAGE_SIZE_MIN;
+ allocate( parentAllocator( *this ), data_current_begin, storage_size );
+ data_current_end = data_current_begin + storage_size;
+ data_current_free = data_current_begin;
+ }
+
+ Allocator(TParentAllocator & parent_alloc)
+ {
+SEQAN_CHECKPOINT
+ setValue(data_parent_allocator, parent_alloc);
+
+ data_recycled_blocks = data_current_end = data_current_free = 0;
+ //dont need to initialize data_current_begin
+ }
+
+ Allocator(size_t reserve_item_count, TParentAllocator & parent_alloc)
+ {
+SEQAN_CHECKPOINT
+ data_recycled_blocks = 0;
+
+ setValue(data_parent_allocator, parent_alloc);
+
+ size_t storage_size = (reserve_item_count * SIZE > STORAGE_SIZE_MIN) ? reserve_item_count * SIZE : STORAGE_SIZE_MIN;
+ allocate( parentAllocator( *this ), data_current_begin, storage_size );
+ data_current_end = data_current_begin + storage_size;
+ data_current_free = data_current_begin;
+ }
+
+ //Dummy copy
+ Allocator(Allocator const &)
+ {
+ data_recycled_blocks = data_current_end = data_current_free = 0;
+ //dont need to initialize data_current_begin
+ }
+ inline Allocator &
+ operator = (Allocator const &)
+ {
+ clear(*this);
+ return *this;
+ }
+
+ ~Allocator()
+ {
+SEQAN_CHECKPOINT
+ clear(*this);
+ }
+};
+//////////////////////////////////////////////////////////////////////////////
+
+template <size_t SIZE, typename TParentAllocator>
+inline TParentAllocator &
+parentAllocator(Allocator<SinglePool<SIZE, TParentAllocator> > & me)
+{
+SEQAN_CHECKPOINT
+ return value(me.data_parent_allocator);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <size_t SIZE, typename TParentAllocator>
+void
+clear(Allocator<SinglePool<SIZE, TParentAllocator> > & me)
+{
+SEQAN_CHECKPOINT
+
+ me.data_recycled_blocks = me.data_current_end = me.data_current_free = 0;
+
+ clear(parentAllocator(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <size_t SIZE, typename TParentAllocator, typename TValue, typename TSize, typename TUsage>
+inline void
+allocate(Allocator<SinglePool<SIZE, TParentAllocator> > & me,
+ TValue * & data,
+ TSize count,
+ Tag<TUsage> const tag_)
+{
+SEQAN_CHECKPOINT
+ typedef Allocator<SinglePool<SIZE, TParentAllocator> > TAllocator;
+ size_t bytes_needed = count * sizeof(TValue);
+
+ if (bytes_needed != TAllocator::SIZE_PER_ITEM)
+ {//no blocking
+ allocate(parentAllocator(me), data, count, tag_);
+ return;
+ }
+
+ char * ptr;
+ if (me.data_recycled_blocks)
+ {//use recycled
+ ptr = me.data_recycled_blocks;
+ me.data_recycled_blocks = * reinterpret_cast<char **>(ptr);
+ }
+ else
+ {//use new
+ ptr = me.data_current_free;
+ if (ptr + bytes_needed > me.data_current_end)
+ {//not enough free space in current storage: allocate new
+ allocate(parentAllocator(me), ptr, (size_t) TAllocator::STORAGE_SIZE, tag_);
+ me.data_current_begin = ptr;
+ me.data_current_end = ptr + TAllocator::STORAGE_SIZE;
+ }
+ me.data_current_free = ptr + bytes_needed;
+ }
+
+ data = reinterpret_cast<TValue *>(ptr);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <size_t SIZE, typename TParentAllocator, typename TValue, typename TSize, typename TUsage>
+inline void
+deallocate(Allocator<SinglePool<SIZE, TParentAllocator> > & me,
+ TValue * data,
+ TSize count,
+ Tag<TUsage> const tag_)
+{
+SEQAN_CHECKPOINT
+ typedef Allocator<SinglePool<SIZE, TParentAllocator> > TAllocator;
+
+ size_t bytes_needed = count * sizeof(TValue);
+
+ if (bytes_needed != TAllocator::SIZE_PER_ITEM)
+ {//no blocking
+ deallocate(parentAllocator(me), data, count, tag_);
+ return;
+ }
+
+ //link in recycling list
+ *reinterpret_cast<char **>(data) = me.data_recycled_blocks;
+ me.data_recycled_blocks = reinterpret_cast<char *>(data);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+// alternative Interface that takes a Type instead of a SIZE
+//////////////////////////////////////////////////////////////////////////////
+
+
+template <typename TValue, typename TParentAllocator = SimpleAllocator>
+struct SinglePool2;
+
+template <typename TValue, typename TParentAllocator>
+struct Allocator<SinglePool2<TValue, TParentAllocator> >
+{
+ Allocator<SinglePool<sizeof(TValue), TParentAllocator> > data_alloc;
+
+
+ Allocator(size_t reserve_item_count)
+ : data_alloc(reserve_item_count)
+ {
+ }
+
+ Allocator(TParentAllocator & parent_alloc)
+ : data_alloc(parent_alloc)
+ {
+ }
+
+ Allocator(size_t reserve_item_count, TParentAllocator & parent_alloc)
+ : data_alloc(reserve_item_count, parent_alloc)
+
+ {
+ }
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename TParentAllocator>
+inline TParentAllocator &
+parentAllocator(Allocator<SinglePool2<TValue, TParentAllocator> > & me)
+{
+SEQAN_CHECKPOINT
+ return parentAllocator(me.data_alloc);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename TParentAllocator>
+void
+clear(Allocator<SinglePool2<TValue, TParentAllocator> > & me)
+{
+SEQAN_CHECKPOINT
+ clear(me.data_alloc);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename TParentAllocator, typename TValue2, typename TSize, typename TUsage>
+inline void
+allocate(Allocator<SinglePool2<TValue, TParentAllocator> > & me,
+ TValue2 * & data,
+ TSize count,
+ Tag<TUsage> const tag_)
+{
+SEQAN_CHECKPOINT
+ allocate(me.data_alloc, data, count, tag_);
+}
+
+template <typename TValue, typename TParentAllocator, typename TValue2, typename TSize, typename TUsage>
+inline void
+deallocate(Allocator<SinglePool2<TValue, TParentAllocator> > & me,
+ TValue2 * data,
+ TSize count,
+ Tag<TUsage> const tag_)
+{
+SEQAN_CHECKPOINT
+ deallocate(me.data_alloc, data, count, tag_);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_allocator_to_std.h b/src/libSSA/seqan/basic/basic_allocator_to_std.h
new file mode 100644
index 0000000..e54589d
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_allocator_to_std.h
@@ -0,0 +1,178 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_allocator_to_std.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_ALLOCATOR_TO_STD_H
+#define SEQAN_HEADER_BASIC_ALLOCATOR_TO_STD_H
+
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+//helper caller for calling functions that have same name as member functions
+
+template <typename TMe, typename TValue, typename TSize>
+inline void call_allocate(TMe & me, TValue * & data, TSize const count)
+{
+ allocate(me, data, count);
+}
+template <typename TMe, typename TValue, typename TSize>
+inline void call_deallocate(TMe & me, TValue * data, TSize const count)
+{
+ deallocate(me, data, count);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//Filter that adapts seqan allocator zu std allocator
+/**
+.Class.ToStdAllocator:
+..summary:Emulates standard conform allocator.
+..signature:ToStdAllocator<THost, TValue>
+..param.THost:Type of the host allocator object.
+...text:This object is used to call @Function.allocate@ and @Function.deallocate at .
+..param.TValue:Type of allocated items.
+..remarks:The member functions $allocate$ and $deallocate$ of $ToStdAllocator$ call
+the (globale) functions @Function.allocate@ and @Function.deallocate@, respectively. The globale functions
+get an allocator object as their first arguments. This allocator object is not the $ToStdAllocator$ object itself,
+but the host object that was given to the constructor.
+..remarks:
+..see:Function.allocate
+..see:Function.deallocate
+*/
+template <typename THost, typename TValue>
+struct ToStdAllocator
+{
+ typedef TValue value_type;
+ typedef value_type * pointer;
+ typedef value_type & reference;
+ typedef value_type const * const_pointer;
+ typedef value_type const & const_reference;
+
+// typedef typename THost::Size size_type;
+// typedef typename THost::Difference difference_type;
+ typedef size_t size_type;
+ typedef ptrdiff_t difference_type;
+
+/**
+.Memfunc.ToStdAllocator:
+..summary:Constructor
+..signature:ToStdAllocator(host)
+..class:Class.ToStdAllocator
+..param.host:The host object that is used as allocator for @Function.allocate@ and @Function.deallocate at .
+*/
+ ToStdAllocator(THost & host): m_host(& host)
+ {
+ }
+ ToStdAllocator(ToStdAllocator const & alloc): m_host(alloc.m_host)
+ {
+ }
+ ToStdAllocator & operator= (ToStdAllocator const & alloc)
+ {
+ m_host = alloc.m_host;
+ }
+ ~ToStdAllocator()
+ {
+ }
+
+/**
+.Function.host:
+..summary:The object a given object depends on.
+..cat:Dependent Objects
+..signature:host(object)
+..param.object:An object.
+...type:Class.ToStdAllocator
+..returns:The host object.
+*/
+ friend THost & host(ToStdAllocator & me)
+ {
+ return *me.m_host;
+ }
+
+ pointer allocate(size_type count)
+ {
+ value_type * ptr;
+ call_allocate(*m_host, ptr, count);
+ return pointer(ptr);
+ }
+ pointer allocate(size_type count, const void *)
+ {
+ value_type * ptr;
+ call_allocate(*m_host, ptr, count);
+ return pointer(ptr);
+ }
+
+ void deallocate(pointer data, size_type count)
+ {
+ call_deallocate(*m_host, data, count);
+ }
+
+ void construct(pointer ptr, const_reference data)
+ {
+ new(ptr) TValue(data);
+ }
+
+ void destroy(pointer ptr)
+ {
+ ptr->~TValue();
+ }
+
+ pointer address(reference value) const
+ {
+ return (&value);
+ }
+ const_pointer address(const_reference value) const
+ {
+ return (&value);
+ }
+
+ size_type max_size() const
+ {
+ return ~0UL / sizeof(value_type);
+ }
+
+ template<class TValue2>
+ struct rebind
+ {
+ typedef ToStdAllocator<THost, TValue2> other;
+ };
+
+ private:
+ THost * m_host;
+};
+//////////////////////////////////////////////////////////////////////////////
+
+
+
+//returns std-allocator type (for allocators)
+template <typename T, typename TData>
+struct StdAllocator
+{
+ typedef ToStdAllocator<T, TData> Type;
+};
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_alphabet_interface.h b/src/libSSA/seqan/basic/basic_alphabet_interface.h
new file mode 100644
index 0000000..dd9a92f
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_alphabet_interface.h
@@ -0,0 +1,917 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_alphabet_interface.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_ALPHABET_INTERFACE_H
+#define SEQAN_HEADER_BASIC_ALPHABET_INTERFACE_H
+
+#include <new>
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+//IsSimple
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Metafunction.IsSimple:
+..summary:Tests type to be simple.
+..signature:IsSimple<T>::Type
+..param.T:Type that is tested.
+..returns.param.Type:@Tag.Logical Values.True@, if $T$ is a simple type, @Tag.Logical Values.False@ otherwise.
+...default:@Tag.Logical Values.False@
+..remarks:A simple type is a type that does not need constructors to be created,
+a destructor to be destroyed, and copy assignment operators or copy constructors
+to be copied. All POD ("plain old data") types are simple, but some
+non-POD types could be simple too, e.g. some specializations of @Class.SimpleType at .
+..see:Class.SimpleType
+*/
+
+template <typename T>
+struct _IsSimple {
+ typedef False Type;
+};
+
+template <typename T>
+struct IsSimple:
+ public _IsSimple<T> {};
+template <typename T>
+struct IsSimple<T const>:
+ public IsSimple<T> {};
+
+//////////////////////////////////////////////////////////////////////////////
+//very basic Alphabets
+
+typedef char Ascii;
+typedef unsigned char Byte;
+typedef wchar_t Unicode;
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.valueConstruct:
+..cat:Content Manipulation
+..summary:Constructs an object at specified position.
+..signature:valueConstruct(iterator [, param [, move_tag] ])
+..param.iterator:Pointer or iterator to position where the object should be constructed.
+..param.param:Parameter that is forwarded to constructor. (optional)
+..param.move_tag:Instance of the @Tag.Move Switch.move switch tag at . (optional)
+...remarks:If the @Tag.Move Switch.move switch tag@ is specified, it is forwarded to the constructor,
+so the constructed object must support move construction.
+..remarks:The type of the destructed object is the @Metafunction.Value.value type@ of $iterator$.
+*/
+
+struct _ValueConstructor
+{
+ template <typename TIterator>
+ static inline void
+ construct(TIterator it)
+ {
+ typedef typename Value<TIterator>::Type TValue;
+ new( & value(it) ) TValue;
+ }
+
+ template <typename TIterator, typename TParam>
+ static inline void
+ construct(TIterator it,
+ TParam const & param_)
+ {
+ typedef typename Value<TIterator>::Type TValue;
+ new( & value(it) ) TValue(param_);
+ }
+
+ template <typename TIterator, typename TParam>
+ static inline void
+ construct(TIterator it,
+ TParam const & param_,
+ Move tag)
+ {
+ typedef typename Value<TIterator>::Type TValue;
+ new( & value(it) ) TValue(param_, tag);
+ }
+};
+
+struct _ValueConstructorProxy
+{
+ template <typename TIterator>
+ static inline void construct(TIterator) {}
+
+ template <typename TIterator, typename TParam>
+ static inline void construct(TIterator, TParam const &) {}
+
+ template <typename TIterator, typename TParam>
+ static inline void construct(TIterator, TParam const &, Move) {}
+};
+
+//____________________________________________________________________________
+
+struct _ValueDestructor
+{
+ template <typename TIterator>
+ static inline void
+ destruct(TIterator it)
+ {
+ typedef typename Value<TIterator>::Type TValue;
+ value(it).~TValue();
+ }
+};
+struct _ValueDestructorProxy
+{
+ template <typename TIterator>
+ static inline void destruct(TIterator) {}
+};
+
+//____________________________________________________________________________
+
+template <typename TIterator>
+inline void
+valueConstruct(TIterator it)
+{
+SEQAN_CHECKPOINT
+ typedef typename IF<
+ TYPECMP<
+ typename Value<TIterator>::Type &,
+ typename Reference<TIterator>::Type
+ >::VALUE,
+ // THEN
+ _ValueConstructor, // true, types are equal
+ // ELSE
+ _ValueConstructorProxy // false, types differ -> value() returns a proxy
+ >::Type TConstructor;
+
+ TConstructor::construct(it);
+}
+
+template <typename TIterator, typename TParam>
+inline void
+valueConstruct(TIterator it,
+ TParam const & param_)
+{
+SEQAN_CHECKPOINT
+ typedef typename IF<
+ TYPECMP<
+ typename Value<TIterator>::Type &,
+ typename Reference<TIterator>::Type
+ >::VALUE,
+ // THEN
+ _ValueConstructor, // true, types are equal
+ // ELSE
+ _ValueConstructorProxy // false, types differ -> value() returns a proxy
+ >::Type TConstructor;
+
+ TConstructor::construct(it, param_);
+}
+
+template <typename TIterator, typename TParam>
+inline void
+valueConstruct(TIterator it,
+ TParam const & param_,
+ Move tag)
+{
+SEQAN_CHECKPOINT
+ typedef typename IF<
+ TYPECMP<
+ typename Value<TIterator>::Type &,
+ typename Reference<TIterator>::Type
+ >::VALUE,
+ // THEN
+ _ValueConstructor, // true, types are equal
+ // ELSE
+ _ValueConstructorProxy // false, types differ -> value() returns a proxy
+ >::Type TConstructor;
+
+ TConstructor::construct(it, param_, tag);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.valueDestruct:
+..cat:Content Manipulation
+..summary:Destoys an object at specified position.
+..signature:valueDestruct(iterator)
+..param.iterator:Pointer or iterator to position where the object should be constructed.
+..remarks:The type of the constructed object is the @Metafunction.Value.value type@ of $iterator$.
+..see:Function.valueConstruct
+*/
+template <typename TIterator>
+inline void
+valueDestruct(TIterator it)
+{
+SEQAN_CHECKPOINT
+ typedef typename IF<
+ TYPECMP<
+ typename Value<TIterator>::Type &,
+ typename Reference<TIterator>::Type
+ >::VALUE,
+ // THEN
+ _ValueDestructor, // true, types are equal
+ // ELSE
+ _ValueDestructorProxy // false, types differ -> value() returns a proxy
+ >::Type TDestructor;
+
+ TDestructor::destruct(it);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.valueConstructMove:
+..cat:Content Manipulation
+..summary:Move constructs an object at specified position.
+..signature:valueConstructMove(iterator, param)
+..param.iterator:Pointer or iterator to position where the object should be constructed.
+..param.param:Parameter that is moved to the new constructed object.
+..remarks:The type of the destructed object is the @Metafunction.Value.value type@ of $iterator$.
+..remarks:The default implementation just calls @Function.valueConstruct at .
+*/
+template <typename TIterator, typename TValue>
+inline void
+valueConstructMove(TIterator it, TValue const & value)
+{
+ valueConstruct(it, value);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+//arrayConstruct
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.arrayConstruct:
+..cat:Array Handling
+..summary:Construct objects in a given memory buffer.
+..signature:arrayConstruct(begin, end [, value])
+..param.begin:Iterator to the begin of the range that is to be constructed.
+..param.end:Iterator behind the end of the range.
+..param.value:Argument that is forwarded to the constructor. (optional)
+...text:An appropriate constructor is required.
+If $value$ is not specified, the default constructor is used.
+..remarks:The type of the constructed Objects is the @Metafunction.Value.value type@
+of $begin$ and $end$.
+..see:Function.arrayDestruct
+..see:Function.arrayConstructCopy
+..see:Function.arrayFill
+..see:Class.SimpleType
+..see:Function.valueConstruct
+*/
+template<typename TIterator1, typename TIterator2>
+inline void
+_arrayConstruct_Default(TIterator1 begin_,
+ TIterator2 end_)
+{
+SEQAN_CHECKPOINT
+ while (begin_ != end_)
+ {
+ valueConstruct(begin_);
+ ++begin_;
+ }
+}
+template<typename TIterator1, typename TIterator2>
+inline void
+arrayConstruct(TIterator1 begin_,
+ TIterator2 end_)
+{
+SEQAN_CHECKPOINT
+ _arrayConstruct_Default(begin_, end_);
+}
+
+//____________________________________________________________________________
+
+template<typename TIterator1, typename TIterator2, typename TParam>
+inline void
+_arrayConstruct_Default(TIterator1 begin_,
+ TIterator2 end_,
+ TParam const & param_)
+{
+SEQAN_CHECKPOINT
+ while (begin_ != end_)
+ {
+ valueConstruct(begin_, param_);
+ ++begin_;
+ }
+}
+template<typename TIterator1, typename TIterator2, typename TParam>
+inline void
+arrayConstruct(TIterator1 begin_,
+ TIterator2 end_,
+ TParam const & param_)
+{
+SEQAN_CHECKPOINT
+ _arrayConstruct_Default(begin_, end_, param_);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayConstructCopy
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.arrayConstructCopy:
+..cat:Array Handling
+..summary:Copy constructs an array of objects into in a given memory buffer.
+..signature:arrayConstructCopy(source_begin, source_end, target)
+..param.source_begin:Iterator to the first element of the source range.
+..param.source_end:Iterator behind the last element of the source range.
+...text:$source_end$ should have the same type as $source_begin$.
+..param.target:Pointer to the memory block the new objects will be constructed in.
+...text:The type of $target$ specifies the type of the constructed objects:
+If $T*$ is the type of $target$, then the function constructs objects of type $T$.
+...text:The memory buffer should be large enough to store $source_end$ - $source_begin$ objects.
+An appropriate (copy-) constructor that constructs an target objects given a source object is required.
+..see:Function.arrayDestruct
+..see:Function.arrayCopyForward
+..see:Function.arrayCopy
+..see:Function.valueConstruct
+*/
+template<typename TTarget, typename TSource1, typename TSource2>
+inline void
+_arrayConstructCopy_Default(TSource1 source_begin,
+ TSource2 source_end,
+ TTarget target_begin)
+{
+SEQAN_CHECKPOINT
+ while (source_begin != source_end)
+ {
+ valueConstruct(target_begin, *source_begin);
+ ++source_begin;
+ ++target_begin;
+ }
+}
+
+template<typename TTarget, typename TSource1, typename TSource2>
+inline void
+arrayConstructCopy(TSource1 source_begin,
+ TSource2 source_end,
+ TTarget target_begin)
+{
+SEQAN_CHECKPOINT
+ _arrayConstructCopy_Default(source_begin, source_end, target_begin);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayConstructMove
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.arrayConstructMove:
+..cat:Array Handling
+..summary:Move constructs an array of objects into in a given memory buffer.
+..signature:arrayConstructMove(source_begin, source_end, target)
+..param.source_begin:Iterator to the first element of the source range.
+..param.source_end:Iterator behind the last element of the source range.
+...text:$source_end$ should have the same type as $source_begin$.
+..param.target:Pointer to the memory block the new objects will be constructed in.
+...text:The type of $target$ specifies the type of the constructed objects:
+If $T*$ is the type of $target$, then the function constructs objects of type $T$.
+...text:The memory buffer should be large enough to store $source_end$ - $source_begin$ objects.
+An appropriate move constructor that constructs an target objects given a source object is required.
+..see:Function.arrayDestruct
+..see:Function.arrayConstructCopy
+..see:Function.arrayMoveForward
+..see:Function.arrayMove
+..see:Function.valueConstruct
+*/
+template<typename TTarget, typename TSource1, typename TSource2>
+inline void
+_arrayConstructMove_Default(TSource1 source_begin,
+ TSource2 source_end,
+ TTarget target_begin)
+{
+SEQAN_CHECKPOINT
+ while (source_begin < source_end)
+ {
+ valueConstructMove(target_begin, *source_begin);
+ ++source_begin;
+ ++target_begin;
+ }
+}
+
+template<typename TTarget, typename TSource1, typename TSource2>
+inline void
+arrayConstructMove(TSource1 source_begin,
+ TSource2 source_end,
+ TTarget target_begin)
+{
+SEQAN_CHECKPOINT
+ _arrayMoveConstruct_Default(source_begin, source_end, target_begin);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayDestruct
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.arrayDestruct:
+..cat:Array Handling
+..summary:Destroys an array of objects.
+..signature:arrayDestruct(begin, end)
+..param.begin:Iterator to the begin of the range that is to be destructed.
+..param.end:Iterator behind the end of the range.
+..remarks:This function does not deallocates the memory.
+..see:Class.SimpleType
+..see:Function.valueDestruct
+*/
+template<typename TIterator1, typename TIterator2>
+inline void
+_arrayDestruct_Default(TIterator1 begin_,
+ TIterator2 end_)
+{
+SEQAN_CHECKPOINT
+ while (begin_ != end_)
+ {
+ valueDestruct(begin_);
+ ++begin_;
+ }
+}
+template<typename TIterator1, typename TIterator2>
+inline void
+arrayDestruct(TIterator1 begin_,
+ TIterator2 end_)
+{
+SEQAN_CHECKPOINT
+ _arrayDestruct_Default(begin_, end_);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayFill
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.arrayFill:
+..cat:Array Handling
+..summary:Assigns one object to each element of a range.
+..signature:arrayFill(begin, end, value)
+..param.begin:Iterator to the begin of the range that is to be filled.
+..param.end:Iterator behind the end of the range.
+..param.value:Argument that is assigned to all $count$ objects in $array$.
+..remarks:All objects $target_begin[0]$ to $target_begin[count-1]$ are set to $value$.
+..see:Function.arrayCopy
+..see:Function.arrayCopyForward
+*/
+template<typename TIterator1, typename TIterator2, typename TValue>
+inline void
+arrayFill(TIterator1 begin_,
+ TIterator2 end_,
+ TValue const & value)
+{
+SEQAN_CHECKPOINT
+ ::std::fill_n(begin_, end_ - begin_, value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayCopyForward
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.arrayCopyForward:
+..cat:Array Handling
+..summary:Copies a range of objects into another range of objects starting from the first element.
+..signature:arrayCopyForward(source_begin, source_end, target)
+..param.source_begin:Iterator to the first element of the source array.
+..param.source_end:Iterator behind the last element of the source array.
+...text:$source_end$ must have the same type as $source_begin$.
+..param.target:Iterator to the first element of the target array.
+...text:The target capacity should be at least as long as the source range.
+..remarks.note:Be careful if source and target range overlap, because in this case
+ some source elements could be accidently overwritten before they are moved.
+..remarks:If there is no need for the source elements to persist, consider to use
+ at Function.arrayMoveForward@ instead to improve performance.
+..see:Class.SimpleType
+*/
+template<typename TTarget, typename TSource1, typename TSource2>
+inline void
+_arrayCopyForward_Default(TSource1 source_begin,
+ TSource2 source_end,
+ TTarget target_begin)
+{
+SEQAN_CHECKPOINT
+ ::std::copy(source_begin, source_end, target_begin);
+}
+template<typename TTarget, typename TSource1, typename TSource2>
+inline void
+arrayCopyForward(TSource1 source_begin,
+ TSource2 source_end,
+ TTarget target_begin)
+{
+SEQAN_CHECKPOINT
+ _arrayCopyForward_Default(source_begin, source_end, target_begin);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayCopyBackward
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.arrayCopyBackward:
+..cat:Array Handling
+..summary:Copies a range of objects into another range of objects starting from the last element.
+..signature:arrayCopyBackward(source_begin, source_end, target)
+..param.source_begin:Iterator to the first element of the source array.
+..param.source_end:Iterator behind the last element of the source array.
+...text:$source_end$ must have the same type as $source_begin$.
+..param.target:Iterator to the first element of the target array.
+...text:The target capacity should be at least as long as the source range.
+..remarks.note:Be careful if source and target range overlap, because in this case
+ some source elements could be accidently overwritten before they are moved.
+..remarks.text:If source and target do not overlap, consider to use the function
+ at Function.arrayCopyForward@ instead that is faster in some cases.
+..remarks:If there is no need for the source elements to persist, consider to use
+ at Function.arrayMoveBackward@ instead to improve performance.
+..remarks.note:The semantic of this function's argument $target$ differ from the arguments of $::std::copy_backward$.
+..see:Function.arrayCopyForward
+..see:Class.SimpleType
+*/
+template<typename TTarget, typename TSource1, typename TSource2>
+inline void
+_arrayCopyBackward_Default(TSource1 source_begin,
+ TSource2 source_end,
+ TTarget target_begin)
+{
+SEQAN_CHECKPOINT
+ ::std::copy_backward(source_begin, source_end, target_begin + (source_end - source_begin));
+}
+template<typename TTarget, typename TSource1, typename TSource2>
+inline void
+arrayCopyBackward(TSource1 source_begin,
+ TSource2 source_end,
+ TTarget target_begin)
+{
+SEQAN_CHECKPOINT
+ _arrayCopyBackward_Default(source_begin, source_end, target_begin);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayCopy
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.arrayCopy:
+..cat:Array Handling
+..summary:Copies a range of objects into another range of objects.
+..signature:arrayCopy(source_begin, source_end, target)
+..param.source_begin:Iterator to the first element of the source range.
+..param.source_end:Iterator behind the last element of the source range.
+...text:$source_end$ must have the same type as $source_begin$.
+..param.target:Iterator to the first element of the target range.
+...text:The target capacity should be at least as long as the source range.
+..remarks.text:If source and target range do not overlap, consider to use
+ @Function.arrayCopyForward@ instead to improve performance.
+..remarks:If there is no need for the source elements to persist, consider to use
+ @Function.arrayMoveForward@ instead to improve performance.
+..DISABLED.remarks.note:Be careful if source and target range overlap and the size of the
+ source elements differ from the size of target elements, because in this case
+ some source elements could be accidently overwritten before they are moved.
+..see:Function.arrayCopyForward
+..see:Function.arrayCopyBackward
+..see:Class.SimpleType
+*/
+template<typename TTarget, typename TSource1, typename TSource2>
+inline void arrayCopy(TSource1 source_begin,
+ TSource2 source_end,
+ TTarget target_begin)
+{
+ if ((void *) source_begin >= (void *) target_begin)
+ {
+SEQAN_CHECKPOINT
+ arrayCopyForward(source_begin, source_end, target_begin);
+ }
+ else
+ {
+SEQAN_CHECKPOINT
+ arrayCopyBackward(source_begin, source_end, target_begin);
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayMoveForward
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.arrayMoveForward:
+..cat:Array Handling
+..summary:Moves a range of objects into another range of objects starting from the first element.
+..signature:arrayMoveForward(source_begin, source_end, target)
+..param.source_begin:Iterator to the first element of the source array.
+..param.source_end:Iterator behind the last element of the source array.
+...text:$source_end$ must have the same type as $source_begin$.
+..param.target:Iterator to the first element of the target array.
+...text:The target capacity should be at least as long as the source range.
+..remarks:The function possibly clears (but does not destroy) the source elements.
+ If source elements must persist, consider to use @Function.arrayCopyForward@ instead.
+..remarks.note:Be careful if source and target range overlap, because in this case
+ some source elements could be accidently overwritten before they are moved.
+..see:Function.arrayCopyForward
+..see:Class.SimpleType
+*/
+template<typename TTarget, typename TSource1, typename TSource2>
+inline void
+_arrayMoveForward_Default(TSource1 source_begin,
+ TSource2 source_end,
+ TTarget target_begin)
+{
+SEQAN_CHECKPOINT
+ while (source_begin != source_end)
+ {
+ move(*target_begin, *source_begin);
+ ++source_begin;
+ ++target_begin;
+ }
+}
+template<typename TTarget, typename TSource1, typename TSource2>
+inline void
+arrayMoveForward(TSource1 source_begin,
+ TSource2 source_end,
+ TTarget target_begin)
+{
+SEQAN_CHECKPOINT
+ _arrayMoveForward_Default(source_begin, source_end, target_begin);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayMoveBackward
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.arrayMoveBackward:
+..cat:Array Handling
+..summary:Moves a range of objects into another range of objects starting from the last element.
+..signature:arrayMoveBackward(source_begin, source_end, target)
+..param.source_begin:Iterator to the first element of the source array.
+..param.source_end:Iterator behind the last element of the source array.
+...text:$source_end$ must have the same type as $source_begin$.
+..param.target:Iterator to the first element of the target array.
+...text:The target capacity should be at least as long as the source range.
+..remarks:The function possibly clears (but does not destroy) the source elements.
+ If source elements must persist, consider to use @Function.arrayCopyBackward@ instead.
+..remarks.note:Be careful if source and target range overlap, because in this case
+ some source elements could be accidently overwritten before they are moved.
+..remarks.text:If source and target do not overlap, consider to use the function
+ at Function.arrayMoveForward@ instead that is faster in some cases.
+..remarks.note:The semantic of this function's argument $target$ differ from the arguments of $::std::copy_backward$.
+..see:Function.arrayMoveForward
+..see:Function.arrayCopyBackward
+..see:Class.SimpleType
+*/
+template<typename TTarget, typename TSource1, typename TSource2>
+inline void
+_arrayMoveBackward_Default(TSource1 source_begin,
+ TSource2 source_end,
+ TTarget target_begin)
+{
+SEQAN_CHECKPOINT
+ target_begin += (source_end - source_begin);
+ while (source_end != source_begin)
+ {
+ --source_end;
+ --target_begin;
+ move(*target_begin, *source_end);
+ }
+}
+template<typename TTarget, typename TSource1, typename TSource2>
+inline void
+arrayMoveBackward(TSource1 source_begin,
+ TSource2 source_end,
+ TTarget target_begin)
+{
+SEQAN_CHECKPOINT
+ _arrayMoveBackward_Default(source_begin, source_end, target_begin);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayMove
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.arrayMove:
+..cat:Array Handling
+..summary:Moves a range of objects into another range of objects.
+..signature:arrayMove(source_begin, source_end, target)
+..param.source_begin:Iterator to the first element of the source range.
+..param.source_end:Iterator behind the last element of the source range.
+...text:$source_end$ must have the same type as $source_begin$.
+..param.target:Iterator to the first element of the target range.
+...text:The target capacity should be at least as long as the source range.
+..remarks:The function possibly clears (but does not destroy) the source elements.
+ If source elements must persist, consider to use @Function.arrayCopy@ instead.
+..remarks.text:If source and target range do not overlap, consider to use
+ @Function.arrayMoveForward@ instead to improve performance.
+..DISABLED.remarks.note:Be careful if source and target range overlap and the size of the
+ source elements differ from the size of target elements, because in this case
+ some source elements could be accidently overwritten before they are moved.
+..remarks.note:Don't confuse this function with the standard $move$ function that
+resembles @Function.arrayCopy at .
+..see:Function.arrayMoveForward
+..see:Function.arrayMoveBackward
+..see:Function.arrayCopy
+..see:Class.SimpleType
+*/
+template<typename TTarget, typename TSource1, typename TSource2>
+inline void
+arrayMove(TSource1 source_begin,
+ TSource2 source_end,
+ TTarget target_begin)
+{
+ if ((void *) source_begin >= (void *) target_begin)
+ {
+SEQAN_CHECKPOINT
+ arrayMoveForward(source_begin, source_end, target_begin);
+ }
+ else
+ {
+SEQAN_CHECKPOINT
+ arrayMoveBackward(source_begin, source_end, target_begin);
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayClearSpace
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.arrayClearSpace:
+..cat:Array Handling
+..summary:Destroys the begin of an array and keeps the rest.
+..signature:arrayClearSpace(arr_begin, arr_length, keep_from, move_to)
+..param.arr_begin:Pointer to the first element of the array.
+..param.arr_length:Length of the array.
+..param.keep_from:Offset of the first object that will be kept.
+..param.move_to:Offset the first kept object will get at the end of the function.
+..remarks.text:The objects $arr[keep_from]$ to $arr[arr_length-1]$
+are moved to the area beginning at positions $move_to$.
+All objects in $arr[0]$ to $arr[keep_from-1]$ are destroyed.
+After this function, the first $move_to$ positions of the array
+are free and dont contain objects.
+..remarks.text:The array must have at least enough space to store $arr_length + move_to - keep_from$ objects.
+..see:Function.arrayCopy
+..see:Function.arrayDestruct
+..see:Function.arrayCopyForward
+..see:Class.SimpleType
+*/
+template <typename TIterator>
+void _arrayClearSpace_Default(TIterator array_begin,
+ size_t array_length,
+ size_t keep_from,
+ size_t move_to)
+{
+ if (keep_from == array_length)
+ {
+ arrayDestruct(array_begin, array_begin + array_length);
+ return;
+ }
+
+ SEQAN_ASSERT(keep_from < array_length)
+
+ if (keep_from == move_to)
+ {
+ arrayDestruct(array_begin, array_begin + move_to);
+ }
+ else if (keep_from < move_to)
+ {
+ if (array_length > move_to)
+ {
+SEQAN_CHECKPOINT
+ size_t middle = array_length - (move_to - keep_from);
+ arrayConstructMove(array_begin + middle, array_begin + array_length, array_begin + array_length);
+ arrayMove(array_begin + keep_from, array_begin + middle, array_begin + move_to);
+ arrayDestruct(array_begin, array_begin + move_to);
+ }
+ else
+ {
+SEQAN_CHECKPOINT
+ arrayConstructMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to);
+ arrayDestruct(array_begin, array_begin + array_length);
+ }
+ }
+ else
+ {
+SEQAN_CHECKPOINT
+ arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to);
+ arrayDestruct(array_begin, array_begin + move_to);
+ arrayDestruct(array_begin + array_length - (keep_from - move_to), array_begin + array_length);
+ }
+}
+
+template <typename TIterator>
+void arrayClearSpace(TIterator array_begin,
+ size_t array_length,
+ size_t keep_from,
+ size_t move_to)
+{
+ _arrayClearSpace_Default(array_begin, array_length, keep_from, move_to);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+//BitsPerValue
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Metafunction.BitsPerValue:
+..summary:Number of bits needed to store a value.
+..signature:BitsPerValue<T>::VALUE
+..param.T:A class.
+..returns.param.VALUE:Number of bits needed to store $T$.
+...default:$sizeof<T> * 8$
+..see:Metafunction.ValueSize
+*/
+template <typename TValue>
+struct BitsPerValue
+{
+ enum { VALUE = sizeof(TValue) * 8 };
+};
+template <typename TValue>
+struct BitsPerValue<TValue const>:
+ public BitsPerValue<TValue> {};
+
+//////////////////////////////////////////////////////////////////////////////
+//ValueSize
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Metafunction.ValueSize:
+..summary:Number of different values a value type object can have.
+..signature:ValueSize<T>::VALUE
+..param.T:A class.
+..returns.param.VALUE:Value size of $T$.
+..remarks
+...text:This function is only defined for integral types like $unsigned int$, $double$ or @Spec.Dna at .
+..see:Metafunction.Value
+*/
+template <typename T>
+struct ValueSize
+{
+ enum { VALUE = 1 << BitsPerValue<T>::VALUE };
+};
+template <typename TValue>
+struct ValueSize<TValue const>:
+ public ValueSize<TValue> {};
+
+
+
+template < typename T >
+struct _SupremumValueUnsigned { static const T VALUE; };
+template < typename T >
+struct _SupremumValueSigned { static const T VALUE; };
+
+template < typename T >
+struct _InfimumValueUnsigned { static const T VALUE; };
+template < typename T >
+struct _InfimumValueSigned { static const T VALUE; };
+
+
+
+template < typename T >
+const T _SupremumValueUnsigned<T>::VALUE = ~(T)0;
+template < typename T >
+const T _SupremumValueSigned<T>::VALUE = ( (((T)1 << (BitsPerValue<T>::VALUE - 2)) - 1) << 1) + 1;
+
+template < typename T >
+const T _InfimumValueUnsigned<T>::VALUE = 0;
+template < typename T >
+const T _InfimumValueSigned<T>::VALUE = ~(T)_SupremumValueSigned<T>::VALUE;
+
+
+
+template <
+ typename T,
+ typename TParent = typename IF<
+ TYPECMP< typename _MakeSigned<T>::Type, T >::VALUE,
+ _SupremumValueSigned<T>,
+ _SupremumValueUnsigned<T> >::Type >
+struct SupremumValue:
+ public TParent
+{
+};
+
+template <
+ typename T,
+ typename TParent = typename IF<
+ TYPECMP< typename _MakeSigned<T>::Type, T >::VALUE,
+ _InfimumValueSigned<T>,
+ _InfimumValueUnsigned<T> >::Type >
+struct InfimumValue:
+ public TParent
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_alphabet_interface2.h b/src/libSSA/seqan/basic/basic_alphabet_interface2.h
new file mode 100644
index 0000000..d523e2b
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_alphabet_interface2.h
@@ -0,0 +1,178 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_alphabet_interface2.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_ALPHABET_INTERFACE2_H
+#define SEQAN_HEADER_BASIC_ALPHABET_INTERFACE2_H
+
+#include <new>
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// gapValue, gapValueImpl
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.gapValueImpl:
+..hidefromindex
+..cat:Alphabets
+..summary:Implements @Function.gapValue at .
+..signature:gapValueImpl(value_pointer_tag)
+..param.value_pointer_tag:A pointer that is used as a tag to specify the value type.
+...remarks:The pointer needs not to point to a valid object, so it is possible to use a null pointer here.
+..returns:A gap character.
+..remarks.text:This function implements @Function.getValue at .
+It is recommended to use @Function.gapValue@ rather than $gapValueImpl$.
+*/
+
+template <typename T>
+inline T const &
+gapValueImpl(T *)
+{
+SEQAN_CHECKPOINT
+ static T const _gap = T();
+ return _gap;
+}
+
+
+/**
+.Function.gapValue:
+..cat:Alphabets
+..cat:Alignments
+..summary:Returns reference to a value that is used as gap character.
+..signature:gapValue<TValue>()
+..param.TValue:Value type.
+..returns:A gap character.
+..remarks.text:The function is implemented in @Function.gapValueImpl at .
+Do not specialize $gapValue$, specialize @Function.gapValueImpl@ instead!
+..see:Function.gapValueImpl
+*/
+
+template <typename T>
+inline T const &
+gapValue()
+{
+SEQAN_CHECKPOINT
+ T * _tag = 0;
+ return gapValueImpl(_tag);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// supremumValue, supremumValueImpl
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.supremumValueImpl:
+..hidefromindex
+..cat:Alphabets
+..summary:Implements @Function.supremumValue at .
+..signature:supremumValueImpl(value_pointer_tag)
+..param.value_pointer_tag:A pointer that is used as a tag to specify the value type.
+...remarks:The pointer needs not to point to a valid object, so it is possible to use a null pointer here.
+..returns:A value $inf$ that holds: $inf >= i$ for all values $i$.
+..remarks.text:This function implements @Function.supremumValue at .
+It is recommended to use @Function.supremumValue@ rather than $supremumValueImpl$.
+*/
+
+/*
+template <typename T>
+inline T const &
+supremumValueImpl(T *)
+{
+ static T const _value = -1;
+ return _value;
+}
+*/
+
+/**
+.Function.supremumValue:
+..cat:Alphabets
+..summary:Supremum for a given type.
+..signature:supremumValue<T>()
+..param.T:An ordered type.
+..returns:A value $inf$ that holds: $inf >= i$ for all values $i$ of type $T$.
+..remarks.text:The function is implemented in @Function.supremumValueImpl at .
+Do not specialize $supremumValue$, specialize @Function.supremumValueImpl@ instead!
+..see:Function.supremumValueImpl
+*/
+
+template <typename T>
+inline T const &
+supremumValue()
+{
+SEQAN_CHECKPOINT
+ T * _tag = 0;
+ return supremumValueImpl(_tag);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// infimumValue, infimumValueImpl
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.infimumValueImpl:
+..hidefromindex
+..cat:Alphabets
+..summary:Implements @Function.infimumValue at .
+..signature:infimumValueImpl(value_pointer_tag)
+..param.value_pointer_tag:A pointer that is used as a tag to specify the value type.
+...remarks:The pointer needs not to point to a valid object, so it is possible to use a null pointer here.
+..returns:A value $inf$ that holds: $inf <= i$ for all values $i$.
+..remarks.text:This function implements @Function.infimumValue at .
+It is recommended to use @Function.infimumValue@ rather than $infimumValueImpl$.
+*/
+
+/*
+template <typename T>
+inline T const &
+infimumValueImpl(T *)
+{
+ static T const _value = -1;
+ return _value;
+}
+*/
+
+/**
+.Function.infimumValue:
+..cat:Alphabets
+..summary:Infimum for a given type.
+..signature:infimumValue<T>()
+..param.T:An ordered type.
+..returns:A value $inf$ that holds: $inf <= i$ for all values $i$ of type $T$.
+..remarks.text:The function is implemented in @Function.infimumValueImpl at .
+Do not specialize $infimumValue$, specialize @Function.infimumValueImpl@ instead!
+..see:Function.infimumValueImpl
+..see:Function.supremumValue
+*/
+
+template <typename T>
+inline T const &
+infimumValue()
+{
+SEQAN_CHECKPOINT
+ T * _tag = 0;
+ return infimumValueImpl(_tag);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_alphabet_simple.h b/src/libSSA/seqan/basic/basic_alphabet_simple.h
new file mode 100644
index 0000000..9703666
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_alphabet_simple.h
@@ -0,0 +1,1296 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_alphabet_simple.h,v 1.1 2008/08/25 16:20:02 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_ALPHABET_SIMPLE_H
+#define SEQAN_HEADER_BASIC_ALPHABET_SIMPLE_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+//Class that is used for various simple value types
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Class.SimpleType:
+..cat:Basic
+..summary:Implementation for "simple" types.
+..signature:SimpleType<TValue, TSpec>
+..param.TValue:Type that stores the values of an instance.
+...remarks:TValue must be a simple type.
+...metafunction:Metafunction.Value
+..param.TSpec:Specialization tag.
+...metafunction:Metafunction.Spec
+..remarks:
+...text:A "simple type" is a C++ type that can be constructed without constructor,
+destructed without destructor and copied without copy constructor or assignment operator.
+All basic types (like $char$, $int$ or $float$) are simple. Pointers, references and arrays of
+simple types are simple.
+POD types ("plain old data types"), that are - simplified spoken - C++-types that already existed in C,
+are simple too.
+...text:Arrays of simple types can be copied very fast by memory manipulation routines,
+but the default implementation of functions like @Function.arrayCopyForward@ and @Function.arrayCopy@
+are not optimized for simple types this way.
+But for classes derived from $SimpleType$, optimized variants of array manipulation functions are applied.
+...text:Note that simple types need not to be derived or specialized from $SimpleType$, but
+it could be convenient to do so.
+..implements:Concept.Simple Type
+*/
+template <typename TValue, typename TSpec>
+struct SimpleType
+{
+//____________________________________________________________________________
+
+ TValue value;
+
+//____________________________________________________________________________
+
+ SimpleType()
+ {
+SEQAN_CHECKPOINT
+ }
+
+//____________________________________________________________________________
+
+ SimpleType(SimpleType const & other)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, other);
+ }
+
+ template <typename T>
+ SimpleType(T const & other)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, other);
+ }
+
+
+//____________________________________________________________________________
+
+ SimpleType & operator=(SimpleType const & other)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, other);
+ return *this;
+ }
+ template <typename T>
+ SimpleType & operator=(T const & other)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, other);
+ return *this;
+ }
+//____________________________________________________________________________
+
+ ~SimpleType()
+ {
+SEQAN_CHECKPOINT
+ }
+//____________________________________________________________________________
+
+ //this cannot be a template since a template would be in conflict to
+ //the template c'tor
+
+
+ operator long() const
+ {
+SEQAN_CHECKPOINT
+ long c;
+ assign(c, *this);
+ return c;
+ }
+ operator unsigned long() const
+ {
+SEQAN_CHECKPOINT
+ unsigned long c;
+ assign(c, *this);
+ return c;
+ }
+ operator int() const
+ {
+SEQAN_CHECKPOINT
+ int c;
+ assign(c, *this);
+ return c;
+ }
+ operator unsigned int() const
+ {
+SEQAN_CHECKPOINT
+ unsigned int c;
+ assign(c, *this);
+ return c;
+ }
+ operator short() const
+ {
+SEQAN_CHECKPOINT
+ short c;
+ assign(c, *this);
+ return c;
+ }
+ operator unsigned short() const
+ {
+SEQAN_CHECKPOINT
+ unsigned short c;
+ assign(c, *this);
+ return c;
+ }
+ operator char() const
+ {
+SEQAN_CHECKPOINT
+ char c;
+ assign(c, *this);
+ return c;
+ }
+ operator signed char() const
+ {
+SEQAN_CHECKPOINT
+ signed char c;
+ assign(c, *this);
+ return c;
+ }
+ operator unsigned char() const
+ {
+SEQAN_CHECKPOINT
+ unsigned char c;
+ assign(c, *this);
+ return c;
+ }
+
+//____________________________________________________________________________
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// METAFUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.IsSimple.param.T.type:Class.SimpleType
+
+template <typename TValue, typename TSpec>
+struct IsSimple<SimpleType<TValue, TSpec> >
+{
+ typedef True Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Value.param.T.type:Class.SimpleType
+template <typename TValue, typename TSpec>
+struct Value<SimpleType<TValue, TSpec> >
+{
+ typedef TValue Type;
+};
+
+template <typename TValue, typename TSpec>
+struct Value<SimpleType<TValue, TSpec> const >
+{
+ typedef TValue const Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Spec.param.T.type:Class.SimpleType
+template <typename TValue, typename TSpec>
+struct Spec<SimpleType<TValue, TSpec> >
+{
+ typedef TSpec Type;
+};
+
+template <typename TValue, typename TSpec>
+struct Spec<SimpleType<TValue, TSpec> const >
+{
+ typedef TSpec Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename TSpec>
+struct Iterator<SimpleType<TValue, TSpec>, Standard>
+{
+ typedef SimpleType<TValue, TSpec> * Type;
+// typedef Iter<SimpleType<TValue, TSpec>, SimpleIterator> * Type;
+};
+
+template <typename TValue, typename TSpec>
+struct Iterator<SimpleType<TValue, TSpec> const, Standard>
+{
+ typedef SimpleType<TValue, TSpec> const * Type;
+// typedef Iter<SimpleType<TValue, TSpec> const, SimpleIterator> * Type;
+};
+
+
+//////////////////////////////////////////////////////////////////////////////
+// FUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TTarget, typename T, typename TSourceValue, typename TSourceSpec>
+inline typename _RemoveConst<TTarget>::Type
+convertImpl(Convert<TTarget, T> const,
+ SimpleType<TSourceValue, TSourceSpec> const & source_)
+{
+SEQAN_CHECKPOINT
+ typename _RemoveConst<TTarget>::Type target_;
+ assign(target_, source_);
+ return target_;
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TStream, typename TValue, typename TSpec>
+inline TStream &
+operator << (TStream & stream,
+ SimpleType<TValue, TSpec> const & data)
+{
+SEQAN_CHECKPOINT
+ stream << convert<char>(data);
+ return stream;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TStream, typename TValue, typename TSpec>
+inline TStream &
+operator >> (TStream & stream,
+ SimpleType<TValue, TSpec> & data)
+{
+SEQAN_CHECKPOINT
+ char c;
+ stream >> c;
+ assign(data, c);
+ return stream;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// assign
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.assign.param.target.type:Class.SimpleType
+///.Function.assign.param.source.type:Class.SimpleType
+
+
+template <typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TSourceSpec>
+inline void
+assign(SimpleType<TTargetValue, TTargetSpec> & target,
+ SimpleType<TSourceValue, TSourceSpec> & source)
+{
+SEQAN_CHECKPOINT
+ target.value = source.value;
+}
+template <typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TSourceSpec>
+inline void
+assign(SimpleType<TTargetValue, TTargetSpec> & target,
+ SimpleType<TSourceValue, TSourceSpec> const & source)
+{
+SEQAN_CHECKPOINT
+ target.value = source.value;
+}
+
+//____________________________________________________________________________
+
+template <typename TTargetValue, typename TTargetSpec, typename TSource>
+inline void
+assign(SimpleType<TTargetValue, TTargetSpec> & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ target.value = source;
+}
+template <typename TTargetValue, typename TTargetSpec, typename TSource>
+inline void
+assign(SimpleType<TTargetValue, TTargetSpec> & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ target.value = source;
+}
+
+//____________________________________________________________________________
+// Assign Proxy to SimpleType
+//??? Diese Funktionen wurden noetig wegen eines seltsamen VC++-Verhaltens
+
+template <typename TTargetValue, typename TTargetSpec, typename TSourceSpec>
+inline void
+assign(SimpleType<TTargetValue, TTargetSpec> & target,
+ Proxy<TSourceSpec> & source)
+{
+SEQAN_CHECKPOINT
+ target.value = getValue(source);
+}
+
+template <typename TTargetValue, typename TTargetSpec, typename TSourceSpec>
+inline void
+assign(SimpleType<TTargetValue, TTargetSpec> & target,
+ Proxy<TSourceSpec> const & source)
+{
+SEQAN_CHECKPOINT
+ target.value = getValue(source);
+}
+
+//____________________________________________________________________________
+//INTEGRAL TYPES
+//note: it is not possible to write a single function here since "assign"
+//must be specialized for the first argument at the first place
+
+//int
+template <typename TValue, typename TSpec>
+inline void
+assign(int & c_target,
+ SimpleType<TValue, TSpec> & source)
+{
+SEQAN_CHECKPOINT
+ c_target = source.value;
+}
+template <typename TValue, typename TSpec>
+inline void
+assign(int & c_target,
+ SimpleType<TValue, TSpec> const & source)
+{
+SEQAN_CHECKPOINT
+ c_target = source.value;
+}
+
+//unsigned int
+template <typename TValue, typename TSpec>
+inline void
+assign(unsigned int & c_target,
+ SimpleType<TValue, TSpec> & source)
+{
+SEQAN_CHECKPOINT
+ c_target = source.value;
+}
+template <typename TValue, typename TSpec>
+inline void
+assign(unsigned int & c_target,
+ SimpleType<TValue, TSpec> const & source)
+{
+SEQAN_CHECKPOINT
+ c_target = source.value;
+}
+
+//short
+template <typename TValue, typename TSpec>
+inline void
+assign(short & c_target,
+ SimpleType<TValue, TSpec> & source)
+{
+SEQAN_CHECKPOINT
+ c_target = source.value;
+}
+template <typename TValue, typename TSpec>
+inline void
+assign(short & c_target,
+ SimpleType<TValue, TSpec> const & source)
+{
+SEQAN_CHECKPOINT
+ c_target = source.value;
+}
+
+//unsigned short
+template <typename TValue, typename TSpec>
+inline void
+assign(unsigned short & c_target,
+ SimpleType<TValue, TSpec> & source)
+{
+SEQAN_CHECKPOINT
+ c_target = source.value;
+}
+template <typename TValue, typename TSpec>
+inline void
+assign(unsigned short & c_target,
+ SimpleType<TValue, TSpec> const & source)
+{
+SEQAN_CHECKPOINT
+ c_target = source.value;
+}
+
+//char
+template <typename TValue, typename TSpec>
+inline void
+assign(char & c_target,
+ SimpleType<TValue, TSpec> & source)
+{
+SEQAN_CHECKPOINT
+ c_target = source.value;
+}
+template <typename TValue, typename TSpec>
+inline void
+assign(char & c_target,
+ SimpleType<TValue, TSpec> const & source)
+{
+SEQAN_CHECKPOINT
+ c_target = source.value;
+}
+
+//signed char
+template <typename TValue, typename TSpec>
+inline void
+assign(signed char & c_target,
+ SimpleType<TValue, TSpec> & source)
+{
+SEQAN_CHECKPOINT
+ c_target = source.value;
+}
+template <typename TValue, typename TSpec>
+inline void
+assign(signed char & c_target,
+ SimpleType<TValue, TSpec> const & source)
+{
+SEQAN_CHECKPOINT
+ c_target = source.value;
+}
+
+//unsigned char
+template <typename TValue, typename TSpec>
+inline void
+assign(unsigned char & c_target,
+ SimpleType<TValue, TSpec> & source)
+{
+SEQAN_CHECKPOINT
+ c_target = source.value;
+}
+template <typename TValue, typename TSpec>
+inline void
+assign(unsigned char & c_target,
+ SimpleType<TValue, TSpec> const & source)
+{
+SEQAN_CHECKPOINT
+ c_target = source.value;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+// CompareType
+//////////////////////////////////////////////////////////////////////////////
+
+/**.Metafunction.CompareType:
+..summary:Type to convert other types for comparisons.
+..signature:CompareType<TLeft, TRight>::Type
+..param.TLeft:Type of the left operand of a comparison.
+..param.TRight:Type of the right operand of a comparison.
+..return.Type:The Type in which the arguments are converted in order to compare them.
+..remarks:Comparisons are for example operators like $==$ or $<$.
+..remarks.text:Note that there is no rule that guarantees that $CompareType<T1, T2>::Type$
+is the same as $CompareType<T2, T1>::Type$. It is also possible, that only one of these
+two types is defined.
+..remarks.text:This metafunction is used for the implementation of
+comparisons that involve @Class.SimpleType at .
+*/
+//???TODO: muss geprueft werden, ob diese Metafunktion noch ausgeweitet oder aber versteckt wird.
+
+template <typename TLeft, typename TRight>
+struct CompareType;
+
+template <typename T>
+struct CompareType<T, T>
+{
+ typedef T Type;
+};
+
+//____________________________________________________________________________
+
+template <typename TValue, typename TSpec, typename TRight>
+struct CompareType<SimpleType<TValue, TSpec>, TRight>
+{
+ typedef TRight Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// operator ==
+
+template <typename TValue, typename TSpec, typename TRight>
+inline bool
+operator == (SimpleType<TValue, TSpec> const & left_,
+ TRight const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TLeft;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) == convert<TCompareType>(right_);
+}
+
+template <typename TLeft, typename TValue, typename TSpec>
+inline bool
+operator == (TLeft const & left_,
+ SimpleType<TValue, TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TRight;
+ typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+ return convert<TCompareType>(left_) == convert<TCompareType>(right_);
+}
+
+template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec>
+inline bool
+operator == (SimpleType<TLeftValue, TLeftSpec> const & left_,
+ SimpleType<TRightValue, TRightSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TLeftValue, TLeftSpec> TLeft;
+ typedef SimpleType<TRightValue, TRightSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) == convert<TCompareType>(right_);
+}
+
+template <typename TValue, typename TSpec>
+inline bool
+operator == (SimpleType<TValue, TSpec> const & left_,
+ SimpleType<TValue, TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ return convert<TValue>(left_) == convert<TValue>(right_);
+}
+
+
+template <typename TSpec, typename TValue, typename TSpec2>
+inline bool
+operator == (Proxy<TSpec> const & left_,
+ SimpleType<TValue, TSpec2> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TLeft;
+ typedef SimpleType<TValue, TSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) == convert<TCompareType>(right_);
+}
+template <typename TSpec, typename TValue, typename TSpec2>
+inline bool
+operator == (SimpleType<TValue, TSpec2> const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TLeft;
+ typedef Proxy<TSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) == convert<TCompareType>(right_);
+}
+
+
+//____________________________________________________________________________
+// operator !=
+
+template <typename TValue, typename TSpec, typename TRight>
+inline bool
+operator != (SimpleType<TValue, TSpec> const & left_,
+ TRight const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TLeft;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) != convert<TCompareType>(right_);
+}
+
+template <typename TLeft, typename TValue, typename TSpec>
+inline bool
+operator != (TLeft const & left_,
+ SimpleType<TValue, TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TRight;
+ typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+ return convert<TCompareType>(left_) != convert<TCompareType>(right_);
+}
+
+template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec>
+inline bool
+operator != (SimpleType<TLeftValue, TLeftSpec> const & left_,
+ SimpleType<TRightValue, TRightSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TLeftValue, TLeftSpec> TLeft;
+ typedef SimpleType<TRightValue, TRightSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) != convert<TCompareType>(right_);
+}
+
+template <typename TValue, typename TSpec>
+inline bool
+operator != (SimpleType<TValue, TSpec> const & left_,
+ SimpleType<TValue, TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ return convert<TValue>(left_) != convert<TValue>(right_);
+}
+
+
+template <typename TSpec, typename TValue, typename TSpec2>
+inline bool
+operator != (Proxy<TSpec> const & left_,
+ SimpleType<TValue, TSpec2> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TLeft;
+ typedef SimpleType<TValue, TSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) != convert<TCompareType>(right_);
+}
+template <typename TSpec, typename TValue, typename TSpec2>
+inline bool
+operator != (SimpleType<TValue, TSpec2> const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TLeft;
+ typedef Proxy<TSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) != convert<TCompareType>(right_);
+}
+
+
+//____________________________________________________________________________
+// operator <
+
+template <typename TValue, typename TSpec, typename TRight>
+inline bool
+operator < (SimpleType<TValue, TSpec> const & left_,
+ TRight const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TLeft;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) < convert<TCompareType>(right_);
+}
+
+template <typename TLeft, typename TValue, typename TSpec>
+inline bool
+operator < (TLeft const & left_,
+ SimpleType<TValue, TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TRight;
+ typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+ return convert<TCompareType>(left_) < convert<TCompareType>(right_);
+}
+
+template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec>
+inline bool
+operator < (SimpleType<TLeftValue, TLeftSpec> const & left_,
+ SimpleType<TRightValue, TRightSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TLeftValue, TLeftSpec> TLeft;
+ typedef SimpleType<TRightValue, TRightSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) < convert<TCompareType>(right_);
+}
+
+template <typename TValue, typename TSpec>
+inline bool
+operator < (SimpleType<TValue, TSpec> const & left_,
+ SimpleType<TValue, TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ return convert<TValue>(left_) < convert<TValue>(right_);
+}
+
+
+template <typename TSpec, typename TValue, typename TSpec2>
+inline bool
+operator < (Proxy<TSpec> const & left_,
+ SimpleType<TValue, TSpec2> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TLeft;
+ typedef SimpleType<TValue, TSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) < convert<TCompareType>(right_);
+}
+template <typename TSpec, typename TValue, typename TSpec2>
+inline bool
+operator < (SimpleType<TValue, TSpec2> const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TLeft;
+ typedef Proxy<TSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) < convert<TCompareType>(right_);
+}
+
+
+//____________________________________________________________________________
+// operator <=
+
+template <typename TValue, typename TSpec, typename TRight>
+inline bool
+operator <= (SimpleType<TValue, TSpec> const & left_,
+ TRight const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TLeft;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
+}
+
+template <typename TLeft, typename TValue, typename TSpec>
+inline bool
+operator <= (TLeft const & left_,
+ SimpleType<TValue, TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TRight;
+ typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+ return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
+}
+
+template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec>
+inline bool
+operator <= (SimpleType<TLeftValue, TLeftSpec> const & left_,
+ SimpleType<TRightValue, TRightSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TLeftValue, TLeftSpec> TLeft;
+ typedef SimpleType<TRightValue, TRightSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
+}
+
+template <typename TValue, typename TSpec>
+inline bool
+operator <= (SimpleType<TValue, TSpec> const & left_,
+ SimpleType<TValue, TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ return convert<TValue>(left_) <= convert<TValue>(right_);
+}
+
+
+template <typename TSpec, typename TValue, typename TSpec2>
+inline bool
+operator <= (Proxy<TSpec> const & left_,
+ SimpleType<TValue, TSpec2> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TLeft;
+ typedef SimpleType<TValue, TSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
+}
+template <typename TSpec, typename TValue, typename TSpec2>
+inline bool
+operator <= (SimpleType<TValue, TSpec2> const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TLeft;
+ typedef Proxy<TSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
+}
+
+
+
+//____________________________________________________________________________
+// operator >
+
+template <typename TValue, typename TSpec, typename TRight>
+inline bool
+operator > (SimpleType<TValue, TSpec> const & left_,
+ TRight const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TLeft;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) > convert<TCompareType>(right_);
+}
+
+template <typename TLeft, typename TValue, typename TSpec>
+inline bool
+operator > (TLeft const & left_,
+ SimpleType<TValue, TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TRight;
+ typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+ return convert<TCompareType>(left_) > convert<TCompareType>(right_);
+}
+
+template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec>
+inline bool
+operator > (SimpleType<TLeftValue, TLeftSpec> const & left_,
+ SimpleType<TRightValue, TRightSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TLeftValue, TLeftSpec> TLeft;
+ typedef SimpleType<TRightValue, TRightSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) > convert<TCompareType>(right_);
+}
+
+template <typename TValue, typename TSpec>
+inline bool
+operator > (SimpleType<TValue, TSpec> const & left_,
+ SimpleType<TValue, TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ return convert<TValue>(left_) > convert<TValue>(right_);
+}
+
+
+template <typename TSpec, typename TValue, typename TSpec2>
+inline bool
+operator > (Proxy<TSpec> const & left_,
+ SimpleType<TValue, TSpec2> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TLeft;
+ typedef SimpleType<TValue, TSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) > convert<TCompareType>(right_);
+}
+template <typename TSpec, typename TValue, typename TSpec2>
+inline bool
+operator > (SimpleType<TValue, TSpec2> const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TLeft;
+ typedef Proxy<TSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) > convert<TCompareType>(right_);
+}
+
+
+//____________________________________________________________________________
+// operator >=
+
+template <typename TValue, typename TSpec, typename TRight>
+inline bool
+operator >= (SimpleType<TValue, TSpec> const & left_,
+ TRight const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TLeft;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
+}
+
+template <typename TLeft, typename TValue, typename TSpec>
+inline bool
+operator >= (TLeft const & left_,
+ SimpleType<TValue, TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TRight;
+ typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+ return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
+}
+
+template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec>
+inline bool
+operator >= (SimpleType<TLeftValue, TLeftSpec> const & left_,
+ SimpleType<TRightValue, TRightSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TLeftValue, TLeftSpec> TLeft;
+ typedef SimpleType<TRightValue, TRightSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
+}
+
+template <typename TValue, typename TSpec>
+inline bool
+operator >= (SimpleType<TValue, TSpec> const & left_,
+ SimpleType<TValue, TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ return convert<TValue>(left_) >= convert<TValue>(right_);
+}
+
+
+template <typename TSpec, typename TValue, typename TSpec2>
+inline bool
+operator >= (Proxy<TSpec> const & left_,
+ SimpleType<TValue, TSpec2> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TLeft;
+ typedef SimpleType<TValue, TSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
+}
+template <typename TSpec, typename TValue, typename TSpec2>
+inline bool
+operator >= (SimpleType<TValue, TSpec2> const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef SimpleType<TValue, TSpec> TLeft;
+ typedef Proxy<TSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+template<typename _T, typename TSpec>
+inline
+bool lexLess(SimpleType<_T, TSpec> const &_Left, SimpleType<_T, TSpec> const &_Right)
+{ // return lexicographical _Left < _Right
+ typedef typename _MakeUnsigned<_T>::Type TUnsigned;
+ return (TUnsigned)(_Left.value) < (TUnsigned)(_Right.value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename TSpec>
+inline SimpleType<TValue, TSpec> &
+operator ++ (SimpleType<TValue, TSpec> & me)
+{
+ ++me.value;
+ return me;
+}
+template <typename TValue, typename TSpec>
+inline SimpleType<TValue, TSpec>
+operator ++ (SimpleType<TValue, TSpec> & me,
+ int)
+{
+ SimpleType<TValue, TSpec> dummy = me;
+ ++me.value;
+ return dummy;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename TSpec>
+inline SimpleType<TValue, TSpec> &
+operator -- (SimpleType<TValue, TSpec> & me)
+{
+ --me.value;
+ return me;
+}
+template <typename TValue, typename TSpec>
+inline SimpleType<TValue, TSpec>
+operator -- (SimpleType<TValue, TSpec> & me,
+ int)
+{
+ SimpleType<TValue, TSpec> dummy = me;
+ --me.value;
+ return dummy;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Spec.Dna:
+..cat:Alphabets
+..summary:Alphabet for DNA.
+..general:Class.SimpleType
+..signature:Dna
+..remarks:
+...text:The @Metafunction.ValueSize@ of $Dna$ is 4.
+The nucleotides are enumerated this way: $'A' = 0, 'C' = 1, 'G' = 2, 'T' = 3$.
+...text:Objects of type $Dna$ can be converted to various other types and vice versa.
+An object that has a value not in ${'A', 'C', 'G', 'T'}$ is converted to $'A'$.
+...text:$Dna$ is typedef for $SimpleType<char,_Dna>$, while $_Dna$ is a helper
+specialization tag class.
+..see:Metafunction.ValueSize
+..see:Spec.Dna5
+*/
+struct _Dna {};
+typedef SimpleType<unsigned char,_Dna> Dna;
+
+template <> struct ValueSize< Dna > { enum { VALUE = 4 }; };
+template <> struct BitsPerValue< Dna > { enum { VALUE = 2 }; };
+
+//____________________________________________________________________________
+
+/**
+.Spec.Dna5:
+..cat:Alphabets
+..summary:Alphabet for DNA including 'N' character.
+..general:Class.SimpleType
+..signature:Dna5
+..remarks:
+...text:The @Metafunction.ValueSize@ of $Dna5$ is 5.
+The nucleotides are enumerated this way: $'A' = 0, 'C' = 1, 'G' = 2, 'T' = 3$.
+The 'N' character ("unkown nucleotide") is encoded by 4.
+...text:Objects of type $Dna5$ can be converted to various other types and vice versa.
+An object that has a value not in ${'A', 'C', 'G', 'T'}$ is converted to $'N'$.
+...text:$Dna5$ is typedef for $SimpleType<char,_Dna5>$, while $_Dna5$ is a helper
+specialization tag class.
+..see:Metafunction.ValueSize
+*/
+struct _Dna5 {};
+typedef SimpleType<unsigned char, _Dna5> Dna5;
+
+template <> struct ValueSize< Dna5 > { enum { VALUE = 5 }; };
+template <> struct BitsPerValue< Dna5 > { enum { VALUE = 3 }; };
+
+//____________________________________________________________________________
+
+/**
+.Spec.Iupac:
+..cat:Alphabets
+..summary:Iupac code for DNA.
+..general:Class.SimpleType
+..signature:Iupac
+..remarks:
+...text:The @Metafunction.ValueSize@ of $Iupac$ is 16.
+The nucleotides are enumerated from 0 to 15 in this order:
+'U'=0, 'T', 'A', 'W', 'C', 'Y', 'M', 'H', 'G', 'K', 'R', 'D', 'S', 'B', 'V', 'N'=15.
+...text:Objects of type $Iupac$ can be converted to various other types and vice versa.
+Unkown values are converted to $'N'$.
+...text:$Iupac$ is typedef for $SimpleType<char,_Iupac>$, while $_Iupac$ is a helper
+specialization tag class.
+..see:Metafunction.ValueSize
+*/
+struct _Iupac {};
+typedef SimpleType<unsigned char, _Iupac> Iupac;
+
+template <> struct ValueSize< Iupac > { enum { VALUE = 16 }; };
+template <> struct BitsPerValue< Iupac > { enum { VALUE = 4 }; };
+
+
+//____________________________________________________________________________
+
+/**
+.Spec.AminoAcid:
+..cat:Alphabets
+..summary:Iupac code for amino acids.
+..general:Class.SimpleType
+..signature:AminoAcid
+..remarks:
+...text:The @Metafunction.ValueSize@ of $AminoAcid$ is 24.
+...text:The amino acids are enumerated from 0 to 15 in this order:
+...text:'A'=0, 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V'=19.
+...text:The remaining 4 symbols are:
+...text: 'B'=20 (Aspartic Acid, Asparagine), 'Z'=21 (Glutamic Acid, Glutamine), 'X'=22 (unknown), '*'=23 (terminator)
+...text:Objects of type $AminoAcid$ can be converted to $char$ and vice versa.
+Unkown values are converted to $'X'$.
+...text:$AminoAcid$ is typedef for $SimpleType<char,_AminoAcid>$, while $_AminoAcid$ is a helper
+specialization tag class.
+..see:Metafunction.ValueSize
+*/
+struct _AminoAcid {};
+typedef SimpleType<unsigned char, _AminoAcid> AminoAcid;
+
+template <> struct ValueSize< AminoAcid > { enum { VALUE = 24 }; };
+template <> struct BitsPerValue< AminoAcid > { enum { VALUE = 5 }; };
+
+//////////////////////////////////////////////////////////////////////////////
+//ASCII
+
+inline void assign(Ascii & c_target,
+ Dna const & source)
+{
+SEQAN_CHECKPOINT
+ c_target = _Translate_Table_Dna5_2_Ascii<>::VALUE[source.value];
+}
+//____________________________________________________________________________
+
+inline void assign(Ascii & c_target,
+ Dna5 const & source)
+{
+SEQAN_CHECKPOINT
+ c_target = _Translate_Table_Dna5_2_Ascii<>::VALUE[source.value];
+}
+//____________________________________________________________________________
+
+inline void assign(Ascii & c_target, Iupac const & source)
+{
+SEQAN_CHECKPOINT
+ c_target = _Translate_Table_Iupac_2_Ascii<>::VALUE[source.value];
+}
+//____________________________________________________________________________
+
+inline void assign(Ascii & c_target, AminoAcid const & source)
+{
+SEQAN_CHECKPOINT
+ c_target = _Translate_Table_AA_2_Ascii<>::VALUE[source.value];
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//DNA (4 letters)
+
+template <>
+struct CompareType<Dna, Byte> { typedef Dna Type; };
+inline void assign(Dna & target, Byte c_source)
+{
+SEQAN_CHECKPOINT
+ target.value = _Translate_Table_Byte_2_Dna<>::VALUE[c_source];
+}
+//____________________________________________________________________________
+
+template <>
+struct CompareType<Dna, Ascii> { typedef Dna Type; };
+inline void assign(Dna & target, Ascii c_source)
+{
+SEQAN_CHECKPOINT
+ target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char)c_source];
+}
+//____________________________________________________________________________
+
+template <>
+struct CompareType<Dna, Unicode> { typedef Dna Type; };
+inline void assign(Dna & target, Unicode c_source)
+{
+SEQAN_CHECKPOINT
+ target.value = _Translate_Table_Ascii_2_Dna<>::VALUE[(unsigned char) c_source];
+}
+//____________________________________________________________________________
+
+template <>
+struct CompareType<Dna, Dna5> { typedef Dna Type; };
+inline void assign(Dna & target, Dna5 const & c_source)
+{
+SEQAN_CHECKPOINT
+ target.value = c_source.value & 0x03;
+}
+//____________________________________________________________________________
+
+template <>
+struct CompareType<Dna, Iupac> { typedef Dna Type; };
+inline void assign(Dna & target, Iupac const & source)
+{
+SEQAN_CHECKPOINT
+ target.value = _Translate_Table_Iupac_2_Dna<>::VALUE[source.value];
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//DNA (5 letters)
+
+template <>
+struct CompareType<Dna5, Byte> { typedef Dna5 Type; };
+inline void assign(Dna5 & target, Byte c_source)
+{
+SEQAN_CHECKPOINT
+ target.value = _Translate_Table_Byte_2_Dna5<>::VALUE[c_source];
+}
+//____________________________________________________________________________
+
+template <>
+struct CompareType<Dna5, Ascii> { typedef Dna5 Type; };
+inline void assign(Dna5 & target, Ascii c_source)
+{
+SEQAN_CHECKPOINT
+ target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
+}
+//____________________________________________________________________________
+
+template <>
+struct CompareType<Dna5, Unicode> { typedef Dna5 Type; };
+inline void assign(Dna5 & target, Unicode c_source)
+{
+SEQAN_CHECKPOINT
+ target.value = _Translate_Table_Ascii_2_Dna5<>::VALUE[(unsigned char) c_source];
+}
+//____________________________________________________________________________
+
+template <>
+struct CompareType<Dna5, Iupac> { typedef Dna5 Type; };
+inline void assign(Dna5 & target, Iupac const & source)
+{
+SEQAN_CHECKPOINT
+ target.value = _Translate_Table_Iupac_2_Dna5<>::VALUE[source.value];
+}
+
+//____________________________________________________________________________
+
+template <>
+struct CompareType<Dna5, Dna> { typedef Dna Type; };
+inline void assign(Dna5 & target, Dna const & c_source)
+{
+SEQAN_CHECKPOINT
+ target.value = c_source.value;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//IUPAC (4 bits)
+
+template <>
+struct CompareType<Iupac, Byte> { typedef Iupac Type; };
+inline void assign(Iupac & target, Byte c_source)
+{
+SEQAN_CHECKPOINT
+ target.value = _Translate_Table_Byte_2_Iupac<>::VALUE[c_source];
+}
+//____________________________________________________________________________
+
+template <>
+struct CompareType<Iupac, Ascii> { typedef Iupac Type; };
+inline void assign(Iupac & target, Ascii c_source)
+{
+SEQAN_CHECKPOINT
+ target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
+}
+//____________________________________________________________________________
+
+template <>
+struct CompareType<Iupac, Unicode> { typedef Iupac Type; };
+inline void assign(Iupac & target, Unicode c_source)
+{
+SEQAN_CHECKPOINT
+ target.value = _Translate_Table_Ascii_2_Iupac<>::VALUE[(unsigned char) c_source];
+}
+//____________________________________________________________________________
+
+inline void assign(Iupac & target, Dna const & source)
+{
+SEQAN_CHECKPOINT
+ target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
+}
+//____________________________________________________________________________
+
+inline void assign(Iupac & target, Dna5 const & source)
+{
+SEQAN_CHECKPOINT
+ target.value = _Translate_Table_Dna5_2_Iupac<>::VALUE[source.value];
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//Amino Acid (5 bits)
+
+template <>
+struct CompareType<AminoAcid, Byte> { typedef AminoAcid Type; };
+inline void assign(AminoAcid & target, Byte c_source)
+{
+SEQAN_CHECKPOINT
+ target.value = _Translate_Table_Byte_2_AA<>::VALUE[c_source];
+}
+//____________________________________________________________________________
+
+template <>
+struct CompareType<AminoAcid, Ascii> { typedef AminoAcid Type; };
+inline void assign(AminoAcid & target, Ascii c_source)
+{
+SEQAN_CHECKPOINT
+ target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
+}
+//____________________________________________________________________________
+
+template <>
+struct CompareType<AminoAcid, Unicode> { typedef AminoAcid Type; };
+inline void assign(AminoAcid & target, Unicode c_source)
+{
+SEQAN_CHECKPOINT
+ target.value = _Translate_Table_Ascii_2_AA<>::VALUE[(unsigned char) c_source];
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+//////////////////////////////////////////////////////////////////////////////
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_alphabet_simple_tabs.h b/src/libSSA/seqan/basic/basic_alphabet_simple_tabs.h
new file mode 100644
index 0000000..6a82ad9
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_alphabet_simple_tabs.h
@@ -0,0 +1,439 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_alphabet_simple_tabs.h,v 1.1 2008/08/25 16:20:02 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_ALPHABET_SIMPLE_TABS_H
+#define SEQAN_HEADER_BASIC_ALPHABET_SIMPLE_TABS_H
+
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+
+//use same tables for Dna
+
+template <typename T = void>
+struct _Translate_Table_Dna5_2_Ascii
+{
+ static char const VALUE[5];
+};
+template <typename T>
+char const _Translate_Table_Dna5_2_Ascii<T>::VALUE[5] = {'A', 'C', 'G', 'T', 'N'};
+
+//____________________________________________________________________________
+
+template <typename T = void>
+struct _Translate_Table_Dna5_2_Iupac
+{
+ static char const VALUE[5];
+};
+template <typename T>
+char const _Translate_Table_Dna5_2_Iupac<T>::VALUE[5] = {0x02, 0x04, 0x08, 0x01, 0x0f};
+
+//____________________________________________________________________________
+
+template <typename T = void>
+struct _Translate_Table_Iupac_2_Ascii
+{
+ static char const VALUE[16];
+};
+template <typename T>
+char const _Translate_Table_Iupac_2_Ascii<T>::VALUE[16] =
+{
+ 'U', //0000=0
+ 'T', //0001=1 //T=1: change between U and T is just inc/dec
+ 'A', //0010=2
+ 'W', //0011=3 TA
+ 'C', //0100=4
+ 'Y', //0101=5 TC (pyrimidine)
+ 'M', //0110=6 AC
+ 'H', //0111=7 not-G
+ 'G', //1000=8
+ 'K', //1001=9 TG
+ 'R', //1010=A AG (purine)
+ 'D', //1011=B not-C
+ 'S', //1100=C CG
+ 'B', //1101=D non-A
+ 'V', //1110=E non-T
+ 'N' //1111=F any
+};
+
+//____________________________________________________________________________
+
+template <typename T = void>
+struct _Translate_Table_Iupac_2_Dna
+{
+ static char const VALUE[16];
+};
+template <typename T>
+char const _Translate_Table_Iupac_2_Dna<T>::VALUE[16] =
+{
+ 3, //'U'
+ 3, //'T'
+ 0, //'A'
+ 0, //'W' = TA
+ 1, //'C'
+ 1, //'Y' = TC
+ 0, //'M' = AC
+ 0, //'H' = not-G
+ 2, //'G'
+ 2, //'K' = TG
+ 0, //'R' = AG
+ 0, //'D' = not-C
+ 1, //'S' = CG
+ 1, //'B' = non-A
+ 0, //'V' = non-T
+ 0 //'N' = any
+};
+
+//____________________________________________________________________________
+
+
+template <typename T = void>
+struct _Translate_Table_Iupac_2_Dna5
+{
+ static char const VALUE[16];
+};
+template <typename T>
+char const _Translate_Table_Iupac_2_Dna5<T>::VALUE[16] =
+{
+ 3, //'U'
+ 3, //'T'
+ 0, //'A'
+ 4, //'W' = TA
+ 1, //'C'
+ 4, //'Y' = TC
+ 4, //'M' = AC
+ 4, //'H' = not-G
+ 2, //'G'
+ 4, //'K' = TG
+ 4, //'R' = AG
+ 4, //'D' = not-C
+ 4, //'S' = CG
+ 4, //'B' = non-A
+ 4, //'V' = non-T
+ 4 //'N' = any
+};
+
+//____________________________________________________________________________
+
+template <typename T = void>
+struct _Translate_Table_Ascii_2_Dna
+{
+ static char const VALUE[256];
+};
+template <typename T>
+char const _Translate_Table_Ascii_2_Dna<T>::VALUE[256] =
+{
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //0
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //1
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //2
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //3
+
+ 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, //4
+// , A, B, C, D, E, D, G, H, I, J, K, L, M, N, O,
+
+ 0, 0, 0, 0, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //5
+// P, Q, R, S, T, U, V, W, X, Y, Z, , , , ,
+
+ 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, //6
+// , a, b, c, d, e, f, g, h, i, j, k, l, m, n, o,
+
+ 0, 0, 0, 0, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //7
+// p, q, r, s, t, u, v, w, x, y, z, , , , ,
+
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //8
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //9
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //10
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //11
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //12
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //13
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //14
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 //15
+};
+
+//____________________________________________________________________________
+
+
+template <typename T = void>
+struct _Translate_Table_Ascii_2_Dna5
+{
+ static char const VALUE[256];
+};
+template <typename T>
+char const _Translate_Table_Ascii_2_Dna5<T>::VALUE[256] =
+{
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //0
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //1
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //2
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //3
+
+ 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, //4
+// , A, B, C, D, E, D, G, H, I, J, K, L, M, N, O,
+
+ 4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //5
+// P, Q, R, S, T, U, V, W, X, Y, Z, , , , ,
+
+ 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, //6
+// , a, b, c, d, e, f, g, h, i, j, k, l, m, n, o,
+
+ 4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //7
+// p, q, r, s, t, u, v, w, x, y, z, , , , ,
+
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //8
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //9
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //10
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //11
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //12
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //13
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //14
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 //15
+};
+
+//____________________________________________________________________________
+
+
+template <typename T = void>
+struct _Translate_Table_Ascii_2_Iupac
+{
+ static char const VALUE[256];
+};
+template <typename T>
+char const _Translate_Table_Ascii_2_Iupac<T>::VALUE[256] =
+{
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //0
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //1
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //2
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //3
+
+ 15, 2, 13, 4, 11, 15, 15, 8, 7, 15, 15, 9, 15, 6, 15, 15, //4
+ // , A, B, C, D, E, F, G, H, I, J, K, L, M, N, O,
+
+ 15, 15, 10, 12, 1, 0, 14, 3, 15, 5, 15, 15, 15, 15, 15, 15, //5
+ // P, Q, R, S, T, U, V, W, X, Y, Z, , , , ,
+
+ 15, 2, 13, 4, 11, 15, 15, 8, 7, 15, 15, 9, 15, 6, 15, 15, //6
+ // , a, b, c, d, e, f, g, h, i, j, k, l, m, n, o,
+
+ 15, 15, 10, 12, 1, 0, 14, 3, 15, 5, 15, 15, 15, 15, 15, 15, //7
+ // p, q, r, s, t, u, v, w, x, y, z, , , , ,
+
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //8
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //9
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //10
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //11
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //12
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //13
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //14
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15 //15
+};
+
+//____________________________________________________________________________
+
+template <typename T = void>
+struct _Translate_Table_Byte_2_Dna
+{
+ static char const VALUE[256];
+};
+template <typename T>
+char const _Translate_Table_Byte_2_Dna<T>::VALUE[256] =
+{
+ 0, 1, 2, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //0
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //1
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //2
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //3
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //4
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //5
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //6
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //7
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //8
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //9
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //10
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //11
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //12
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //13
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //14
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 //15
+};
+
+//____________________________________________________________________________
+
+
+template <typename T = void>
+struct _Translate_Table_Byte_2_Dna5
+{
+ static char const VALUE[256];
+};
+template <typename T>
+char const _Translate_Table_Byte_2_Dna5<T>::VALUE[256] = {
+ 0, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //0
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //1
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //2
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //3
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //4
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //5
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //6
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //7
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //8
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //9
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //10
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //11
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //12
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //13
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //14
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 //15
+};
+
+//____________________________________________________________________________
+
+
+template <typename T = void>
+struct _Translate_Table_Byte_2_Iupac
+{
+ static char const VALUE[256];
+};
+template <typename T>
+char const _Translate_Table_Byte_2_Iupac<T>::VALUE[256] =
+{
+ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, //0
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //1
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //2
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //3
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //4
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //5
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //6
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //7
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //8
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //9
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //10
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //11
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //12
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //13
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //14
+ 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15 //15
+};
+
+//____________________________________________________________________________
+
+
+template <typename T = void>
+struct _Translate_Table_AA_2_Ascii
+{
+ static char const VALUE[24];
+};
+template <typename T>
+char const _Translate_Table_AA_2_Ascii<T>::VALUE[24] =
+{
+ 'A', // 0 Ala Alanine
+ 'R', // 1 Arg Arginine
+ 'N', // 2 Asn Asparagine
+ 'D', // 3 Asp Aspartic Acid
+ 'C', // 4 Cys Cystine
+ 'Q', // 5 Gln Glutamine
+ 'E', // 6 Glu Glutamic Acid
+ 'G', // 7 Gly Glycine
+ 'H', // 8 His Histidine
+ 'I', // 9 Ile Isoleucine
+ 'L', //10 Leu Leucine
+ 'K', //11 Lys Lysine
+ 'M', //12 Met Methionine
+ 'F', //13 Phe Phenylalanine
+ 'P', //14 Pro Proline
+ 'S', //15 Ser Serine
+ 'T', //16 Thr Threonine
+ 'W', //17 Trp Tryptophan
+ 'Y', //18 Tyr Tyrosine
+ 'V', //19 Val Valine
+ 'B', //20 Aspartic Acid, Asparagine
+ 'Z', //21 Glutamic Acid, Glutamine
+ 'X', //22 Unknown
+ '*' //23 Terminator
+};
+
+//____________________________________________________________________________
+
+
+template <typename T = void>
+struct _Translate_Table_Ascii_2_AA
+{
+ static char const VALUE[256];
+};
+template <typename T>
+char const _Translate_Table_Ascii_2_AA<T>::VALUE[256] =
+{
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //0
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //1
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 22, 22, 22, 22, 22, //2
+// *
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //3
+ 22, 0, 20, 4, 3, 6, 13, 7, 8, 9, 22, 11, 10, 12, 2, 22, //4
+// , A, B, C, D, E, F, G, H, I, J, K, L, M, N, O,
+
+ 14, 5, 1, 15, 16, 22, 19, 17, 22, 18, 21, 22, 22, 22, 22, 22, //5
+// P, Q, R, S, T, U, V, W, X, Y, Z, , , , , ,
+
+ 22, 0, 20, 4, 3, 6, 13, 7, 8, 9, 22, 11, 10, 12, 2, 22, //6
+// , a, b, c, d, e, f, g, h, i, j, k, l, m, n, o,
+
+ 14, 5, 1, 15, 16, 22, 19, 17, 22, 18, 21, 22, 22, 22, 22, 22, //7
+// p, q, r, s, t, u, v, w, x, y, z, , , , , ,
+
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //8
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //9
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //10
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //11
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //12
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //13
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //14
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22 //15
+};
+
+//____________________________________________________________________________
+
+
+template <typename T = void>
+struct _Translate_Table_Byte_2_AA
+{
+ static char const VALUE[256];
+};
+template <typename T>
+char const _Translate_Table_Byte_2_AA<T>::VALUE[256] =
+{
+ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, //0
+ 16, 17, 18, 19, 20, 21, 22, 23, 22, 22, 22, 22, 22, 22, 22, 22, //1
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //2
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //3
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //4
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //5
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //6
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //7
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //8
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //9
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //10
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //11
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //12
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //13
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, //14
+ 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22 //15
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+}//namespace SEQAN_NAMESPACE_MAIN
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_alphabet_trait_basic.h b/src/libSSA/seqan/basic/basic_alphabet_trait_basic.h
new file mode 100644
index 0000000..024bf55
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_alphabet_trait_basic.h
@@ -0,0 +1,733 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_alphabet_trait_basic.h,v 1.2 2009/02/19 01:51:23 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_ALPHABET_TRAIT_BASIC_H
+#define SEQAN_HEADER_BASIC_ALPHABET_TRAIT_BASIC_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayConstruct
+//////////////////////////////////////////////////////////////////////////////
+
+template<typename TIterator>
+inline void
+_arrayConstruct_Pointer(TIterator,
+ TIterator,
+ True)
+{
+SEQAN_CHECKPOINT
+ //nothing to do
+}
+template<typename TIterator>
+inline void
+_arrayConstruct_Pointer(TIterator begin_,
+ TIterator end_,
+ False)
+{
+SEQAN_CHECKPOINT
+ _arrayConstruct_Default(begin_, end_);
+}
+template<typename TValue>
+inline void
+arrayConstruct(TValue * begin_,
+ TValue * end_)
+{
+SEQAN_CHECKPOINT
+ _arrayConstruct_Pointer(begin_, end_, typename IsSimple<TValue>::Type() );
+}
+
+//____________________________________________________________________________
+
+template<typename TIterator, typename TParam>
+inline void
+_arrayConstruct_Pointer(TIterator begin_,
+ TIterator end_,
+ TParam const & param_,
+ True)
+{
+SEQAN_CHECKPOINT
+ arrayFill(begin_, end_, param_);
+}
+template<typename TIterator, typename TParam>
+inline void
+_arrayConstruct_Pointer(TIterator begin_,
+ TIterator end_,
+ TParam const & param_,
+ False)
+{
+SEQAN_CHECKPOINT
+ _arrayConstruct_Default(begin_, end_, param_);
+}
+template<typename TValue, typename TParam>
+inline void
+arrayConstruct(TValue * begin_,
+ TValue * end_,
+ TParam const & param_)
+{
+SEQAN_CHECKPOINT
+ _arrayConstruct_Pointer(begin_, end_, param_, typename IsSimple<TValue>::Type() );
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayConstructCopy
+//////////////////////////////////////////////////////////////////////////////
+
+template<typename TValue>
+inline void
+_arrayConstructCopy_Pointer(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin,
+ True)
+{
+SEQAN_CHECKPOINT
+ arrayCopyForward(source_begin, source_end, target_begin);
+}
+template<typename TValue>
+inline void
+_arrayConstructCopy_Pointer(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin,
+ False)
+{
+SEQAN_CHECKPOINT
+ _arrayConstructCopy_Default(source_begin, source_end, target_begin);
+}
+template<typename TValue>
+inline void
+arrayConstructCopy(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin)
+{
+SEQAN_CHECKPOINT
+ _arrayConstructCopy_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayConstructMove
+//////////////////////////////////////////////////////////////////////////////
+
+template<typename TValue>
+inline void
+_arrayConstructMove_Pointer(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin,
+ True)
+{
+SEQAN_CHECKPOINT
+ arrayMoveForward(source_begin, source_end, target_begin);
+}
+template<typename TValue>
+inline void
+_arrayConstructMove_Pointer(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin,
+ False)
+{
+SEQAN_CHECKPOINT
+ _arrayConstructMove_Default(source_begin, source_end, target_begin);
+}
+template<typename TValue>
+inline void
+arrayConstructMove(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin)
+{
+SEQAN_CHECKPOINT
+ _arrayConstructMove_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayDestruct
+//////////////////////////////////////////////////////////////////////////////
+
+template<typename TValue>
+inline void
+_arrayDestruct_Pointer(TValue * /*begin_*/,
+ TValue * /*end_*/,
+ True)
+{
+SEQAN_CHECKPOINT
+ //do nothing
+}
+template<typename TValue>
+inline void
+_arrayDestruct_Pointer(TValue * begin_,
+ TValue * end_,
+ False)
+{
+SEQAN_CHECKPOINT
+ _arrayDestruct_Default(begin_, end_);
+}
+template<typename TValue>
+inline void
+arrayDestruct(TValue * begin_,
+ TValue * end_)
+{
+SEQAN_CHECKPOINT
+ _arrayDestruct_Pointer(begin_, end_, typename IsSimple<TValue>::Type() );
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayFill
+//////////////////////////////////////////////////////////////////////////////
+
+//no specializiation for pointer to simple
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayCopyForward
+//////////////////////////////////////////////////////////////////////////////
+
+template<typename TValue>
+inline void
+_arrayCopyForward_Pointer(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin,
+ True)
+{
+SEQAN_CHECKPOINT
+ memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
+}
+template<typename TValue>
+inline void
+_arrayCopyForward_Pointer(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin,
+ False)
+{
+SEQAN_CHECKPOINT
+ _arrayCopyForward_Default(source_begin, source_end, target_begin);
+}
+template<typename TValue>
+inline void
+arrayCopyForward(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin)
+{
+SEQAN_CHECKPOINT
+ _arrayCopyForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayCopyBackward
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue>
+inline void
+_arrayCopyBackward_Pointer(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin,
+ True)
+{
+SEQAN_CHECKPOINT
+ memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
+}
+template <typename TValue>
+inline void
+_arrayCopyBackward_Pointer(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin,
+ False)
+{
+SEQAN_CHECKPOINT
+ _arrayCopyBackward_Default(source_begin, source_end, target_begin);
+}
+template<typename TValue>
+inline void
+arrayCopyBackward(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin)
+{
+SEQAN_CHECKPOINT
+ _arrayCopyBackward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayMoveForward
+//////////////////////////////////////////////////////////////////////////////
+
+template<typename TValue>
+inline void
+_arrayMoveForward_Pointer(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin,
+ True)
+{
+SEQAN_CHECKPOINT
+ memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
+}
+template<typename TValue>
+inline void
+_arrayMoveForward_Pointer(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin,
+ False)
+{
+SEQAN_CHECKPOINT
+ _arrayMoveForward_Default(source_begin, source_end, target_begin);
+}
+template<typename TValue>
+inline void
+arrayMoveForward(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin)
+{
+SEQAN_CHECKPOINT
+ _arrayMoveForward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayMoveBackward
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue>
+inline void
+_arrayMoveBackward_Pointer(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin,
+ True)
+{
+SEQAN_CHECKPOINT
+ memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
+}
+template <typename TValue>
+inline void
+_arrayMoveBackward_Pointer(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin,
+ False)
+{
+SEQAN_CHECKPOINT
+ _arrayMoveBackward_Default(source_begin, source_end, target_begin);
+}
+template<typename TValue>
+inline void
+arrayMoveBackward(TValue * source_begin,
+ TValue * source_end,
+ TValue * target_begin)
+{
+SEQAN_CHECKPOINT
+ _arrayMoveBackward_Pointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//arrayClearSpace
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue>
+inline void
+_arrayClearSpace_Pointer(TValue * array_begin,
+ size_t array_length,
+ size_t keep_from,
+ size_t move_to,
+ True)
+{
+ if (keep_from == move_to) return;
+SEQAN_CHECKPOINT
+ arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to);
+}
+template <typename TValue>
+inline void
+_arrayClearSpace_Pointer(TValue * array_begin,
+ size_t array_length,
+ size_t keep_from,
+ size_t move_to,
+ False)
+{
+ _arrayClearSpace_Default(array_begin, array_length, keep_from, move_to);
+}
+template <typename TValue>
+void arrayClearSpace(TValue * array_begin,
+ size_t array_length,
+ size_t keep_from,
+ size_t move_to)
+{
+ _arrayClearSpace_Pointer(array_begin, array_length, keep_from, move_to, typename IsSimple<TValue>::Type() );
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// IsSimple specializations
+//////////////////////////////////////////////////////////////////////////////
+
+// standard types
+template <> struct _IsSimple< bool > { typedef True Type; };
+template <> struct _IsSimple< char > { typedef True Type; };
+
+template <> struct _IsSimple< unsigned char > { typedef True Type; };
+template <> struct _IsSimple< unsigned short > { typedef True Type; };
+template <> struct _IsSimple< unsigned int > { typedef True Type; };
+template <> struct _IsSimple< unsigned long > { typedef True Type; };
+
+template <> struct _IsSimple< signed char > { typedef True Type; };
+template <> struct _IsSimple< signed short > { typedef True Type; };
+template <> struct _IsSimple< signed int > { typedef True Type; };
+template <> struct _IsSimple< signed long > { typedef True Type; };
+
+template <> struct _IsSimple< float > { typedef True Type; };
+template <> struct _IsSimple< double > { typedef True Type; };
+template <> struct _IsSimple< long double > { typedef True Type; };
+
+// user defined types (re-specializations are allowed here)
+template <> struct IsSimple< wchar_t > { typedef True Type; };
+template <> struct IsSimple< __int64 > { typedef True Type; };
+
+//////////////////////////////////////////////////////////////////////////////
+// gapValue
+//////////////////////////////////////////////////////////////////////////////
+
+inline char const &
+gapValueImpl(char *)
+{
+SEQAN_CHECKPOINT
+ static char const _gap = '-';
+ return _gap;
+}
+inline char const &
+gapValueImpl(char const *)
+{
+SEQAN_CHECKPOINT
+ static char const _gap = '-';
+ return _gap;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// generic extreme values
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename T>
+inline T const &
+supremumValueImpl(T *)
+{
+SEQAN_CHECKPOINT
+ return SupremumValue<T>::VALUE;
+}
+template <typename T>
+inline T const &
+infimumValueImpl(T *)
+{
+SEQAN_CHECKPOINT
+ return InfimumValue<T>::VALUE;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// bool
+//////////////////////////////////////////////////////////////////////////////
+
+template <> struct BitsPerValue< bool > { enum { VALUE = 1 }; };
+
+/*
+//////////////////////////////////////////////////////////////////////////////
+// char
+//////////////////////////////////////////////////////////////////////////////
+
+inline char const &
+supremumValueImpl(char *)
+{
+SEQAN_CHECKPOINT
+ static char const _value = (char) 127;
+ return _value;
+}
+inline char const &
+infimumValueImpl(char *)
+{
+SEQAN_CHECKPOINT
+ static char const _value = (char) -128;
+ return _value;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// signed char
+//////////////////////////////////////////////////////////////////////////////
+
+inline signed char const &
+supremumValueImpl(signed char *)
+{
+SEQAN_CHECKPOINT
+ static signed char const _value = 127;
+ return _value;
+}
+inline signed char const &
+infimumValueImpl(signed char *)
+{
+SEQAN_CHECKPOINT
+ static signed char const _value = -128;
+ return _value;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// unsigned char
+//////////////////////////////////////////////////////////////////////////////
+
+inline unsigned char const &
+supremumValueImpl(unsigned char *)
+{
+SEQAN_CHECKPOINT
+ static unsigned char const _value = 255;
+ return _value;
+}
+inline unsigned char const &
+infimumValueImpl(unsigned char *)
+{
+SEQAN_CHECKPOINT
+ static unsigned char const _value = 0;
+ return _value;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// wchar_t
+//////////////////////////////////////////////////////////////////////////////
+
+inline wchar_t const &
+supremumValueImpl(wchar_t *)
+{
+SEQAN_CHECKPOINT
+ static wchar_t const _value = 1UL << (BitsPerValue<wchar_t>::VALUE) - 1;
+ return _value;
+}
+inline wchar_t const &
+infimumValueImpl(wchar_t *)
+{
+SEQAN_CHECKPOINT
+ static wchar_t const _value = 0;
+ return _value;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// signed short
+//////////////////////////////////////////////////////////////////////////////
+
+inline signed short const &
+supremumValueImpl(signed short *)
+{
+SEQAN_CHECKPOINT
+ static signed short const _value = (((1 << (BitsPerValue<signed short>::VALUE - 2)) - 1) << 1) + 1;
+ return _value;
+}
+inline signed short const &
+infimumValueImpl(signed short *dummy)
+{
+SEQAN_CHECKPOINT
+ static signed short const _value = -supremumValueImpl(dummy) - 1;
+ return _value;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// unsigned short
+//////////////////////////////////////////////////////////////////////////////
+
+inline unsigned short const &
+supremumValueImpl(unsigned short *)
+{
+SEQAN_CHECKPOINT
+ static unsigned short const _value = (((1 << (BitsPerValue<unsigned short>::VALUE - 1)) - 1) << 1) + 1;
+ return _value;
+}
+inline unsigned short const &
+infimumValueImpl(unsigned short *)
+{
+SEQAN_CHECKPOINT
+ static unsigned short const _value = 0;
+ return _value;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// signed int
+//////////////////////////////////////////////////////////////////////////////
+
+inline signed int const &
+supremumValueImpl(signed int *)
+{
+SEQAN_CHECKPOINT
+ static signed int const _value = (((1 << (BitsPerValue<signed int>::VALUE - 2)) - 1) << 1) + 1;
+ return _value;
+}
+inline signed int const &
+infimumValueImpl(signed int *dummy)
+{
+SEQAN_CHECKPOINT
+ static signed int const _value = -supremumValueImpl(dummy) - 1;
+ return _value;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// unsigned int
+//////////////////////////////////////////////////////////////////////////////
+
+inline unsigned int const &
+supremumValueImpl(unsigned int *)
+{
+SEQAN_CHECKPOINT
+ static unsigned int const _value = ~0ul;
+ return _value;
+}
+inline unsigned int const &
+infimumValueImpl(unsigned int *)
+{
+SEQAN_CHECKPOINT
+ static unsigned int const _value = 0;
+ return _value;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// signed long
+//////////////////////////////////////////////////////////////////////////////
+
+inline signed long const &
+supremumValueImpl(signed long *)
+{
+SEQAN_CHECKPOINT
+ static signed long const _value = (((1 << (BitsPerValue<signed long>::VALUE - 2)) - 1) << 1) + 1;
+ return _value;
+}
+inline signed long const &
+infimumValueImpl(signed long *dummy)
+{
+SEQAN_CHECKPOINT
+ static signed long const _value = -supremumValueImpl(dummy) - 1;
+ return _value;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// unsigned long
+//////////////////////////////////////////////////////////////////////////////
+
+inline unsigned long const &
+supremumValueImpl(unsigned long *)
+{
+SEQAN_CHECKPOINT
+ static unsigned long const _value = ~0ul;
+ return _value;
+}
+inline unsigned long const &
+infimumValueImpl(unsigned long *)
+{
+SEQAN_CHECKPOINT
+ static unsigned long const _value = 0;
+ return _value;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// signed 64bit int (cannot use long long <- no ISO C++)
+//////////////////////////////////////////////////////////////////////////////
+
+inline __int64 const &
+supremumValueImpl(__int64 *)
+{
+SEQAN_CHECKPOINT
+ static __int64 const _value = ((((__int64)1 << (BitsPerValue<__int64>::VALUE - 2)) - 1) << 1) + 1;
+ return _value;
+}
+inline __int64 const &
+infimumValueImpl(__int64 *dummy)
+{
+SEQAN_CHECKPOINT
+ static __int64 const _value = -supremumValueImpl(dummy) - 1;
+ return _value;
+}
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+// float
+//////////////////////////////////////////////////////////////////////////////
+
+inline float const &
+supremumValueImpl(float *)
+{
+SEQAN_CHECKPOINT
+#ifdef PLATFORM_WINDOWS
+ static float const _value = ::std::numeric_limits<float>::infinity( );
+#else
+ static float const _value = 3.40282347e+38F;
+#endif
+ return _value;
+}
+inline float const &
+infimumValueImpl(float *)
+{
+SEQAN_CHECKPOINT
+#ifdef PLATFORM_WINDOWS
+ static float const _value = -::std::numeric_limits<float>::infinity( );
+#else
+ static float const _value = -3.40282347e+38F;
+#endif
+ return _value;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// double
+//////////////////////////////////////////////////////////////////////////////
+
+inline double const &
+supremumValueImpl(double *)
+{
+SEQAN_CHECKPOINT
+#ifdef PLATFORM_WINDOWS
+ static double const _value = ::std::numeric_limits<double>::infinity( );
+#else
+ static double const _value = 1.7976931348623157e+308;
+#endif
+ return _value;
+}
+inline double const &
+infimumValueImpl(double *)
+{
+SEQAN_CHECKPOINT
+#ifdef PLATFORM_WINDOWS
+ static double const _value = -::std::numeric_limits<double>::infinity( );
+#else
+ static double const _value = -1.7976931348623157e+308;
+#endif
+ return _value;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// long double
+//////////////////////////////////////////////////////////////////////////////
+
+inline long double const &
+supremumValueImpl(long double *)
+{
+SEQAN_CHECKPOINT
+#ifdef PLATFORM_WINDOWS
+ static long double const _value = ::std::numeric_limits<long double>::infinity( );
+#else
+ static long double const _value = 1.7976931348623157e+308;
+#endif
+ return _value;
+}
+inline long double const &
+infimumValueImpl(long double *)
+{
+SEQAN_CHECKPOINT
+#ifdef PLATFORM_WINDOWS
+ static long double const _value = -::std::numeric_limits<long double>::infinity( );
+#else
+ static long double const _value = -1.7976931348623157e+308;
+#endif
+ return _value;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_compare.h b/src/libSSA/seqan/basic/basic_compare.h
new file mode 100644
index 0000000..6499da9
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_compare.h
@@ -0,0 +1,60 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_compare.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_COMPARE_H
+#define SEQAN_HEADER_BASIC_COMPARE_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeft, typename TRight>
+struct CompareType;
+
+template <typename TLeft, typename TRight>
+struct CompareType<TLeft const, TRight>
+{
+ typedef typename CompareType<TLeft, TRight>::Type const Type;
+};
+template <typename TLeft, typename TRight>
+struct CompareType<TLeft, TRight const>
+{
+ typedef typename CompareType<TLeft, TRight>::Type const Type;
+};
+template <typename TLeft, typename TRight>
+struct CompareType<TLeft const, TRight const>
+{
+ typedef typename CompareType<TLeft, TRight>::Type const Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template<typename _T> inline
+bool lexLess(const _T& _Left, const _T& _Right)
+{ // return lexicographical _Left < _Right
+ typedef typename _MakeUnsigned<_T>::Type TUnsigned;
+ return (TUnsigned)_Left < (TUnsigned)_Right;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_converter.h b/src/libSSA/seqan/basic/basic_converter.h
new file mode 100644
index 0000000..966f467
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_converter.h
@@ -0,0 +1,117 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_converter.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_CONVERTER_H
+#define SEQAN_HEADER_BASIC_CONVERTER_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+//Convert
+//////////////////////////////////////////////////////////////////////////////
+
+//gibt den Typ an, in den TSource konvertiert werden kann (TTarget oder TTarget &)
+
+/**
+.Metafunction.Convert:
+..summary:Return type of a conversion.
+..signature:Convert<Target, Source>::Type
+..param.Target:Type the object should be converted to.
+..param.Source:Type of the object that should be converted to $Target$.
+..returns.param.Type:Type that is returned by @Function.convert at .
+...remarks:This is either $Target$ or $Target &$:
+If instances of $Source: /fs/szdevel/src/cvsroot/bowtie/SeqAn-1.1/seqan/basic/basic_converter.h,v $ can be re-interpreted as instances of $Target$,
+than this metafunction returns a reference, otherwise it returns $Target$,
+that is @Function.convert@ returns a temporary.
+..remarks:A constant instance of $Convert$ is (ab)used as tag argument of @Function.convertImpl at .
+*/
+template <typename TTarget, typename TSource = void>
+struct Convert
+{
+ typedef TTarget Type;
+
+};
+
+//////////////////////////////////////////////////////////////////////////////
+//convertImpl
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.convertImpl:
+..hidefromindex
+..cat:Alphabets
+..summary:Implements @Function.convert at .
+..signature:Convert convertImpl(convert, source)
+..param.convert:Object that specifies the conversion.
+...type:Metafunction.Convert
+...remarks:A constant instance of @Metafunction.Convert@ is used to specify the conversion target.
+..param.source:An object that should be converted.
+..returns:$source$ converted to the type specified by convert.
+...metafunction:Metafunction.Convert
+..remarks:This function implements @Function.convert at .
+It is recommended to use @Function.convert@ rather than $convertImpl$.
+*/
+//??? Spezialisiere convertImpl, verwende convert
+//??? Konversion eines einzelnen Zeichens in ein einzelnes Zeichen. Konversion von Sequenzen in Sequenzen finden wo anders statt.
+//??? Kann entweder kopieren oder re-interpretieren, je nach Convert::Type
+template <typename TTarget, typename T, typename TSource>
+inline typename Convert<TTarget, TSource>::Type
+convertImpl(Convert<TTarget, T> const,
+ TSource & source)
+{
+ return source;
+}
+template <typename TTarget, typename T, typename TSource>
+inline typename Convert<TTarget, TSource const>::Type
+convertImpl(Convert<TTarget, T> const,
+ TSource const & source)
+{
+ return source;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//convert
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.convert:
+..cat:Alphabets
+..summary:Converts a value into another value.
+..signature:Convert convert<Target>(source)
+..param.Target:The type $source$ is converted to.
+..param.source:An object that is converted to $Target$.
+..returns:$source$ converted to $Target$.
+...remarks:If $source$ can be re-interpreted as instance of $Target$, then a reference is returned.
+Otherwise the function returns a temporary object.
+...metafunction:Metafunction.Convert
+..remarks:This function is implemented in @Function.convertImpl at .
+Do not specialize $convert$, specialize @Function.convertImpl@ instead.
+..see:Function.convertImpl
+*/
+template <typename TTarget, typename TSource>
+inline typename Convert<TTarget, TSource>::Type
+convert(TSource const & source)
+{
+ return convertImpl(Convert<TTarget, TSource>(), source);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_counted_ptr.h b/src/libSSA/seqan/basic/basic_counted_ptr.h
new file mode 100644
index 0000000..4973a9f
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_counted_ptr.h
@@ -0,0 +1,116 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_counted_ptr.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+// THIS FILE IS CURRENTLY NOT USED IN SEQAN
+
+#ifndef SEQAN_HEADER_BASIC_COUNTED_PTR_H
+#define SEQAN_HEADER_BASIC_COUNTED_PTR_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+ //////////////////////////////////////////////////////////////////////////////
+ // counted pointer
+
+ template < typename Type >
+ struct CountedPtr
+ {
+ typedef CountedPtr _Self;
+ typedef CountedPtr* _SelfPtr;
+ typedef CountedPtr& _SelfRef;
+
+ typedef Type& reference;
+ typedef const Type& const_reference;
+ typedef Type* pointer;
+
+ explicit CountedPtr(pointer p = 0): // allocate a new counter
+ itsCounter(0)
+ {
+ if (p) itsCounter = new counter(p);
+ }
+
+ CountedPtr(const _Self& r) throw() {
+ acquire(r.itsCounter);
+ }
+
+ ~CountedPtr() {
+ release();
+ }
+
+ CountedPtr& operator=(const _Self& r)
+ {
+ if (this != &r) {
+ release();
+ acquire(r.itsCounter);
+ }
+ return *this;
+ }
+
+ reference operator*() const throw() {
+ return *itsCounter->ptr;
+ }
+
+ pointer operator->() const throw() {
+ return itsCounter->ptr;
+ }
+
+ pointer get() const throw() {
+ return itsCounter ? itsCounter->ptr : 0;
+ }
+
+ bool unique() const throw() {
+ return (itsCounter ? itsCounter->count == 1 : true);
+ }
+
+ inline operator pointer () const {
+ return get();
+ }
+
+ private:
+
+ struct counter {
+ pointer ptr;
+ unsigned count;
+ counter(pointer p = 0, unsigned c = 1):
+ ptr(p),
+ count(c) { }
+ }* itsCounter;
+
+ void acquire(counter* c) throw()
+ { // increment the count
+ itsCounter = c;
+ if (c) ++c->count;
+ }
+
+ void release()
+ { // decrement the count, delete if it is 0
+ if (itsCounter) {
+ if (--itsCounter->count == 0) {
+ delete itsCounter->ptr;
+ delete itsCounter;
+ }
+ itsCounter = 0;
+ }
+ }
+ };
+
+}
+
+#endif
diff --git a/src/libSSA/seqan/basic/basic_debug.h b/src/libSSA/seqan/basic/basic_debug.h
new file mode 100644
index 0000000..424b011
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_debug.h
@@ -0,0 +1,385 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_debug.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_DEBUG_H
+#define SEQAN_HEADER_BASIC_DEBUG_H
+
+#ifndef SEQAN_DEBUG_OR_TEST_
+#ifdef SEQAN_DEBUG
+#define SEQAN_DEBUG_OR_TEST_
+#else //#ifdef SEQAN_DEBUG
+#ifdef SEQAN_TEST
+#define SEQAN_DEBUG_OR_TEST_
+#endif //#ifdef SEQAN_TEST
+#endif //#ifdef SEQAN_DEBUG
+#endif //#ifndef SEQAN_DEBUG_OR_TEST_
+
+
+#ifdef SEQAN_DEBUG_OR_TEST_
+#include <cstdio>
+#endif //#ifdef SEQAN_DEBUG_OR_TEST_
+
+#ifdef SEQAN_DEBUG
+
+//throw a fatal debug report if _cond is false
+#define SEQAN_ASSERT(_cond) { if (!(_cond)) ::SEQAN_NAMESPACE_MAIN::debug::Error< ::SEQAN_NAMESPACE_MAIN::debug::Check >(__FILE__, __LINE__, #_cond " is FALSE"); }
+#define SEQAN_ASSERT1(_cond) SEQAN_ASSERT(_cond)
+#define SEQAN_ASSERT2(_cond, _comment) { if (!(_cond)) ::SEQAN_NAMESPACE_MAIN::debug::Error< ::SEQAN_NAMESPACE_MAIN::debug::Check >(__FILE__, __LINE__, _comment); }
+
+//throw a debug report if _cond is false
+#define SEQAN_CHECK(_cond) { if (!(_cond)) ::SEQAN_NAMESPACE_MAIN::debug::Message< ::SEQAN_NAMESPACE_MAIN::debug::Check >(__FILE__, __LINE__, #_cond " is FALSE"); }
+#define SEQAN_CHECK1(_cond) SEQAN_CHECK(_cond)
+#define SEQAN_CHECK2(_cond, _comment) { if (!(_cond)) ::SEQAN_NAMESPACE_MAIN::debug::Message< ::SEQAN_NAMESPACE_MAIN::debug::Check >(__FILE__, __LINE__, _comment); }
+
+#define SEQAN_DO(_cond) { if (!(_cond)) ::SEQAN_NAMESPACE_MAIN::debug::Message< ::SEQAN_NAMESPACE_MAIN::debug::Check >(__FILE__, __LINE__, #_cond " is FALSE"); }
+#define SEQAN_DO1(_cond) SEQAN_DO(_cond)
+#define SEQAN_DO2(_cond, _comment) { if (!(_cond)) ::SEQAN_NAMESPACE_MAIN::debug::Error< ::SEQAN_NAMESPACE_MAIN::debug::Check >(__FILE__, __LINE__, _comment); }
+
+//report a message
+#define SEQAN_ABORT(_comment) { ::SEQAN_NAMESPACE_MAIN::debug::Error< ::SEQAN_NAMESPACE_MAIN::debug::Report >(__FILE__, __LINE__, _comment); }
+#define SEQAN_REPORT(_comment) { ::SEQAN_NAMESPACE_MAIN::debug::Message< ::SEQAN_NAMESPACE_MAIN::debug::Report >(__FILE__, __LINE__, _comment); }
+
+#else //#ifdef SEQAN_DEBUG
+
+//disable debug reports in release built
+#define SEQAN_ASSERT(_cond) {}
+#define SEQAN_ASSERT1(_cond) {}
+#define SEQAN_ASSERT2(_cond, _comment) {}
+
+#define SEQAN_CHECK(_cond) {}
+#define SEQAN_CHECK1(_cond) {}
+#define SEQAN_CHECK2(_cond, _comment) {}
+
+#define SEQAN_DO(_cond) { _cond; }
+#define SEQAN_DO1(_cond) SEQAN_DO(_cond)
+#define SEQAN_DO2(_cond, _comment) { _cond; }
+
+#define SEQAN_ABORT(_comment) {}
+#define SEQAN_REPORT(_comment) {}
+
+#endif //#ifdef SEQAN_DEBUG
+
+#ifdef SEQAN_TEST
+
+//test a condition and report test result
+#define SEQAN_TASSERT(_cond) \
+ { if (!(_cond)) ::SEQAN_NAMESPACE_MAIN::debug::Error< ::SEQAN_NAMESPACE_MAIN::debug::Check >(__FILE__, __LINE__, "(" #_cond ") is FALSE"); }
+#define SEQAN_TASSERT1(_cond) SEQAN_TASSERT(_cond)
+#define SEQAN_TASSERT2(_cond, _comment) \
+ { if (!(_cond)) ::SEQAN_NAMESPACE_MAIN::debug::Error< ::SEQAN_NAMESPACE_MAIN::debug::Check >(__FILE__, __LINE__, _comment); }
+
+#define SEQAN_TCHECK(_cond) \
+ { if (_cond) ::SEQAN_NAMESPACE_MAIN::debug::Result< ::SEQAN_NAMESPACE_MAIN::debug::Check >(__FILE__, __LINE__, "(" #_cond ") is TRUE"); \
+ else ::SEQAN_NAMESPACE_MAIN::debug::Result< ::SEQAN_NAMESPACE_MAIN::debug::Check >(__FILE__, __LINE__, "(" #_cond ") is FALSE"); }
+#define SEQAN_TCHECK1(_cond) SEQAN_TCHECK(_cond)
+#define SEQAN_TCHECK2(_cond, _comment) \
+ { if (_cond) ::SEQAN_NAMESPACE_MAIN::debug::Result< ::SEQAN_NAMESPACE_MAIN::debug::Check >(__FILE__, __LINE__, _comment); }
+
+//report a test result
+#define SEQAN_TABORT(_comment) { ::SEQAN_NAMESPACE_MAIN::debug::Error< ::SEQAN_NAMESPACE_MAIN::debug::Report >(__FILE__, __LINE__, _comment); }
+#define SEQAN_TREPORT(_comment) { ::SEQAN_NAMESPACE_MAIN::debug::Result< ::SEQAN_NAMESPACE_MAIN::debug::Report >(__FILE__, __LINE__, _comment); }
+
+#else //#ifdef SEQAN_TEST
+
+#define SEQAN_TASSERT(_cond) {}
+#define SEQAN_TASSERT1(_cond) {}
+#define SEQAN_TASSERT2(_cond, _comment) {}
+
+#define SEQAN_TCHECK(_cond) {}
+#define SEQAN_TABORT(_comment) {}
+#define SEQAN_TREPORT(_comment) {}
+
+#endif //#ifdef SEQAN_TEST
+//____________________________________________________________________________
+
+#ifdef SEQAN_DEBUG_OR_TEST_
+
+//Test Helper Functions
+
+// compare two files, do not translate linebreaks
+inline bool
+_compareBinaryFiles(char * file1, char * file2)
+{
+ bool ret = false;
+
+ FILE * fl1 = fopen(file1, "rb");
+ if (!fl1) return ret;
+
+ FILE * fl2 = fopen(file2, "rb");
+ if (!fl2)
+ {
+ fclose(fl1);
+ return ret;
+ }
+
+ while (!feof(fl1) && !feof(fl2))
+ {
+ if (fgetc(fl1) != fgetc(fl2)) goto End;
+ }
+
+ ret = feof(fl1) && feof(fl2);
+
+End:
+ fclose(fl2);
+ fclose(fl1);
+
+ return ret;
+
+}
+//____________________________________________________________________________
+
+//one line break is either \r, \n, or \r\n.
+inline void
+_compareTextFiles_readChar(FILE * fl, char & c, bool & is_lb, bool & is_eof)
+{
+ is_lb = false;
+ is_eof = false;
+
+ c = fgetc(fl);
+ if (c == '\r')
+ {
+ is_lb = true;
+ char c_help = fgetc(fl);
+ if (feof(fl)) is_eof = true;
+ else
+ {
+ if (c_help == '\n')
+ {
+ c = fgetc(fl);
+ if (feof(fl)) is_eof = true;
+ }
+ else c = c_help;
+ }
+ }
+ if (c == '\n')
+ {
+ is_lb = true;
+ c = fgetc(fl);
+ if (feof(fl)) is_eof = true;
+ }
+}
+
+// compare two files, translate linebreaks
+inline bool
+_compareTextFiles(char * file1, char * file2)
+{
+ FILE * fl1 = fopen(file1, "rb");
+ if (!fl1) return false;
+
+ FILE * fl2 = fopen(file2, "rb");
+ if (!fl2)
+ {
+ fclose(fl1);
+ return false;
+ }
+
+ bool ret = false;
+
+ bool is_lb1, is_lb2, is_eof1, is_eof2;
+ char c1, c2;
+
+ while (!feof(fl1) && !feof(fl2))
+ {
+ _compareTextFiles_readChar(fl1, c1, is_lb1, is_eof1);
+ _compareTextFiles_readChar(fl2, c2, is_lb2, is_eof2);
+
+ if (is_lb1 ^ is_lb2)
+ {
+ goto End;
+ }
+ if (is_eof1 ^ is_eof2)
+ {
+ goto End;
+ }
+ if (c1 != c2)
+ {
+ goto End;
+ }
+ }
+
+ ret = feof(fl1) && feof(fl2);
+
+End:
+ fclose(fl2);
+ fclose(fl1);
+
+ return ret;
+
+}
+
+
+//____________________________________________________________________________
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+namespace debug
+{
+
+//action of SEQAN_ASSERT, SEQAN_TCHECK and SEQAN_CHECK
+//use as template argument for Error<> and Message<> and Result<>
+class Check {};
+
+//action of SEQAN_ABORT, SEQAN_TREPORT and SEQAN_REPORT
+//use as template argument for Error<> and Message<> and Result<>
+class Report {};
+
+
+//report fatal error
+//template argument TAction is the action (Check or Report)
+//use explicit instatiation for overwriting the default behavior
+template <typename TAction>
+void Error(const char * file, int line, const char * comment="-")
+{
+ std::fprintf(stderr, "%s(%i) : SEQAN: %s\nSEQAN: execution aborted\n", file, line, comment);
+ exit(1);
+}
+
+//report debug message
+//template argument TAction is the action (Check or Report)
+//use explicit instatiation for overwriting the default behavior
+template <typename TAction>
+void Message(const char * file, int line, const char * comment="-")
+{
+ std::fprintf(stderr, "%s(%i) : SEQAN: %s\n", file, line, comment);
+}
+
+//report test result
+//template argument TAction is the action (Check or Report)
+//use explicit instatiation for overwriting the default behavior
+template <typename TAction>
+void Result(const char * file, int line, const char * comment="-")
+{
+ std::fprintf(stdout, "%s(%i) : %s\n", file, line, comment);
+}
+
+} //namespace debug
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifdef SEQAN_DEBUG_OR_TEST_
+
+
+//____________________________________________________________________________
+//Checkpoint Testing
+
+//note: this framework relies on the filenames in the project to be unique
+
+#ifdef SEQAN_TEST
+
+#include <set>
+#include <vector>
+#include <cstring>
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+namespace debug
+{
+struct Checkpoint
+{
+ char const* file;
+ unsigned int line;
+};
+
+struct CheckpointLess : public ::std::binary_function <Checkpoint, Checkpoint, bool>
+{
+ inline bool operator() (Checkpoint const &a, Checkpoint const &b) const
+ {
+ int c = strcmp(a.file, b.file);
+ return c < 0 || (c == 0 && a.line < b.line);
+ }
+};
+
+template <typename T = void>
+struct CheckpointStore
+{
+ static ::std::set<Checkpoint, CheckpointLess> data;
+};
+template <typename T>
+::std::set<Checkpoint, CheckpointLess> CheckpointStore<T>::data;
+
+
+inline bool
+checkpoint(unsigned int line, char const* file)
+{
+ char const* file_name = strrchr(file, '/');
+ char const* file_name_2 = strrchr(file, '\\');
+ if (file_name_2 > file_name) file_name = file_name_2;
+ if (!file_name) file_name = file;
+ else ++file_name;
+
+ Checkpoint cp = {file_name, line};
+ CheckpointStore<>::data.insert(cp);
+ return true;
+}
+#define SEQAN_CHECKPOINT \
+ ::SEQAN_NAMESPACE_MAIN::debug::checkpoint(__LINE__, __FILE__);
+
+
+inline void
+testCheckpoint(char const* file, unsigned int line)
+{
+ Checkpoint cp = {file, line};
+ if (CheckpointStore<>::data.find(cp) == CheckpointStore<>::data.end())
+ Message< Report >(file, line, "Checkpoint lost");
+}
+
+inline void
+verifyCheckpoints(char const* file)
+{
+ char const* file_name = strrchr(file, '/');
+ char const* file_name_2 = strrchr(file, '\\');
+ if (file_name_2 > file_name) file_name = file_name_2;
+ if (!file_name) file_name = file;
+ else ++file_name;
+
+ FILE * fl = ::std::fopen(file, "r");
+ if (!fl)
+ {
+ Error< Report >(file, 0, "verifyCheckpoints could not find this file.");
+ }
+ unsigned int line_number = 1;
+ char buf[1<<16];
+
+ while (::std::fgets(buf, sizeof(buf), fl))
+ {
+ if (::std::strstr(buf, "SEQAN_CHECKPOINT"))
+ {
+ testCheckpoint(file_name, line_number);
+ }
+ ++line_number;
+ }
+
+ ::std::fclose(fl);
+}
+
+} //namespace debug
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#else //#ifdef SEQAN_TEST
+
+#define SEQAN_CHECKPOINT
+
+#endif //#ifdef SEQAN_TEST
+
+//____________________________________________________________________________
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_definition.h b/src/libSSA/seqan/basic/basic_definition.h
new file mode 100644
index 0000000..b12fd4c
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_definition.h
@@ -0,0 +1,405 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_definition.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_DEFINITION_H
+#define SEQAN_HEADER_BASIC_DEFINITION_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename T>
+struct Tag
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Tag.Default:
+..summary:Tag that specifies default behavior.
+..tag.Default:Use default behavior.
+*/
+struct Default_;
+typedef Tag<Default_> const Default;
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Tag.Move Switch:
+..summary:Switch to force move.
+..tag.Move:Move instead of assign.
+..remarks.text:The difference between move constructor and copy constructor
+is that the source object is not copied but moved into the target object.
+The source object can lose its content and will be empty after
+this operation in this case.
+A move constructor can sigificantly faster than a copy constructor.
+..example.code:String source("hello");
+String target(source, Move()); // source is moved to target
+std::cout << source; //nothing printed since source lost content
+std::cout << target; //"hello"
+..see:Function.move
+*/
+
+struct Move_;
+typedef Tag<Move_> const Move;
+
+//////////////////////////////////////////////////////////////////////////////
+
+//Pass to c'tor of iterator to move it to the end
+struct GoEnd_;
+typedef Tag<GoEnd_> const GoEnd;
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+//construct without initializing
+struct MinimalCtor_;
+typedef Tag<MinimalCtor_> const MinimalCtor;
+
+//construct with initializing
+struct NonMinimalCtor_;
+typedef Tag<NonMinimalCtor_> const NonMinimalCtor;
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Tag.Logical Values:
+..summary:Tag that represents true and false.
+..tag.True:The logical value "true".
+..tag.False:The logical value "false".
+*/
+struct True { enum { VALUE = true }; };
+struct False { enum { VALUE = false }; };
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.Nothing:
+..summary:Tag that represents an absent parameter or an absent type.
+..tag.Nothing:Omit parameter.
+*/
+///Empty Data Class.
+struct Nothing {};
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// returns TTo const, if TFrom is const, TTo otherwise
+
+template <typename TFrom, typename TTo>
+struct _CopyConst
+{
+ typedef TTo Type;
+};
+template <typename TFrom, typename TTo>
+struct _CopyConst<TFrom const, TTo>
+{
+ typedef TTo const Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Internal._RemoveConst:
+..signature:_RemoveConst<T>
+..returns:$t$ if $T$ is $t const$, otherwise $T$.
+*/
+template <typename T>
+struct _RemoveConst
+{
+ typedef T Type;
+};
+template <typename T>
+struct _RemoveConst<T const>:
+ public _RemoveConst<T> {};
+
+template <typename T>
+struct _RemoveConst<T &>
+{
+ typedef typename _RemoveConst<T>::Type & Type;
+};
+template <typename T>
+struct _RemoveConst<T *>
+{
+ typedef typename _RemoveConst<T>::Type * Type;
+};
+template <typename T, size_t I>
+struct _RemoveConst<T const [I]>
+{
+ typedef T * Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Internal._MakeUnsigned:
+..signature:_MakeUnsigned<T>
+..returns:$unsigned t$ if $T$ is not $unsigned t$, otherwise $T$.
+*/
+template <typename T>
+struct _MakeUnsigned
+{
+ typedef T Type;
+};
+
+template <typename T>
+struct _MakeUnsigned<T const> {
+ typedef typename _MakeUnsigned<T>::Type const Type;
+};
+
+template <>
+struct _MakeUnsigned<char>
+{
+ typedef unsigned char Type;
+};
+
+template <>
+struct _MakeUnsigned<signed char>
+{
+ typedef unsigned char Type;
+};
+
+template <>
+struct _MakeUnsigned<int>
+{
+ typedef unsigned int Type;
+};
+
+template <>
+struct _MakeUnsigned<short>
+{
+ typedef unsigned short Type;
+};
+
+template <>
+struct _MakeUnsigned<long>
+{
+ typedef unsigned long Type;
+};
+
+/*
+template <>
+struct _MakeUnsigned<long long>
+{
+ typedef unsigned long long Type;
+};
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Internal._MakeSigned:
+..signature:_MakeSigned<T>
+..returns:$signed t$ if $T$ is not $signed t$, otherwise $T$.
+*/
+template <typename T>
+struct _MakeSigned
+{
+ typedef T Type;
+};
+
+template <typename T>
+struct _MakeSigned<T const> {
+ typedef typename _MakeSigned<T>::Type const Type;
+};
+
+template <>
+struct _MakeSigned<char>
+{
+ typedef signed char Type;
+};
+
+template <>
+struct _MakeSigned<unsigned char>
+{
+ typedef signed char Type;
+};
+
+template <>
+struct _MakeSigned<unsigned int>
+{
+ typedef signed int Type;
+};
+
+template <>
+struct _MakeSigned<unsigned short>
+{
+ typedef signed short Type;
+};
+
+template <>
+struct _MakeSigned<unsigned long>
+{
+ typedef signed long Type;
+};
+
+/*
+template <>
+struct _MakeSigned<unsigned long long>
+{
+ typedef signed long long Type;
+};
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Internal._ClassIdentifier:
+..signature:void * _ClassIdentifier<T>::getID()
+..returns:A void * that identifies $T$.
+...text:The returned values of two calls of $getID$ are equal if and only if
+the used type $T$ was the same.
+*/
+template <typename T>
+struct _ClassIdentifier
+{
+ static inline void *
+ getID()
+ {
+SEQAN_CHECKPOINT
+ static bool _id_dummy;
+ return &_id_dummy;
+ }
+};
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.log2:
+..cat:Miscellaneous
+..summary:Computes logarithm of base 2 for integer types
+..signature:unsigned int log2(i)
+..param.i:An integer type.
+..returns:The largest integer smaller or equal than
+the logarithm of $i$.
+*/
+
+#if 0
+template <int BITS_MAX>
+struct _Log2_Impl
+{
+ template <typename T>
+ static inline unsigned int
+ log2(T val, unsigned int offset)
+ {
+ unsigned int val2 = val >> (BITS_MAX / 2);
+ if (val2)
+ {
+ val = val2;
+ offset += BITS_MAX / 2;
+ }
+ return _Log2_Impl<BITS_MAX / 2>::log2(val, offset);
+ }
+};
+
+template <>
+struct _Log2_Impl<1>
+{
+ template <typename T>
+ static inline unsigned int
+ log2(T /*val*/, unsigned int offset)
+ {
+ return offset;
+ }
+};
+
+
+template <typename T>
+inline unsigned int
+log2(T val)
+{
+ enum
+ {
+// BITS_PER_VALUE = BitsPerValue<T>::VALUE //TODO???
+ BITS_PER_VALUE = sizeof(T) * 8
+ };
+
+ return _Log2_Impl<BITS_PER_VALUE>::log2(val, 0);
+}
+#endif
+
+template <typename TValue, typename TExponent>
+inline TValue _intPow(TValue a, TExponent b)
+{
+SEQAN_CHECKPOINT
+ TValue ret = 1;
+ while (b != 0)
+ {
+ if (b & 1) ret *= a;
+ a *= a;
+ b >>= 1;
+ }
+ return ret;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// to avoid conflicts with non-standard macros and namespaces
+// we define our own Min/Max functions
+
+template<typename _Tx> inline
+const _Tx& _min(const _Tx& _Left, const _Tx& _Right)
+{ // return smaller of _Left and _Right
+ if (_Left < _Right)
+ return _Left;
+ else
+ return _Right;
+}
+
+template<typename _Tx, typename _Ty> inline
+_Tx _min(const _Tx& _Left, const _Ty& _Right)
+{ // return smaller of _Left and _Right
+ return (_Right < _Left ? _Right : _Left);
+}
+
+template<typename _Ty> inline
+const _Ty& _max(const _Ty& _Left, const _Ty& _Right)
+{ // return larger of _Left and _Right
+ if (_Left < _Right)
+ return _Right;
+ else
+ return _Left;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename T1, typename T2>
+struct _IsSameType
+{
+ enum {VALUE = false};
+ typedef False Type;
+};
+
+template <typename T>
+struct _IsSameType<T, T>
+{
+ enum {VALUE = true};
+ typedef True Type;
+};
+
+template <typename T1, typename T2>
+inline bool
+_isSameType()
+{
+ return _IsSameType<T1, T2>::VALUE;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
+
+
diff --git a/src/libSSA/seqan/basic/basic_forwards.h b/src/libSSA/seqan/basic/basic_forwards.h
new file mode 100644
index 0000000..13e70fb
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_forwards.h
@@ -0,0 +1,71 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_forwards.h,v 1.1 2008/08/25 16:20:02 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_FORWARD2_H
+#define SEQAN_HEADER_BASIC_FORWARD2_H
+
+//forward declarations (make GCC 4.x happy)
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+// basic_transport.h::assign
+
+template <typename TTarget, typename TSource>
+inline void
+assign(TTarget & target,
+ TSource & source);
+
+template <typename TTarget, typename TSource>
+inline void
+assign(TTarget & target,
+ TSource const & source);
+
+//////////////////////////////////////////////////////////////////////////////
+// string_pointer.h::assignValue
+
+template <typename TValue, typename TPos>
+inline void
+assignValue(TValue * me,
+ TPos pos,
+ TValue const & _value);
+
+//////////////////////////////////////////////////////////////////////////////
+// string_pointer.h::moveValue
+
+template <typename TValue, typename TPos>
+inline void
+moveValue(TValue * me,
+ TPos pos,
+ TValue const & _value);
+
+//////////////////////////////////////////////////////////////////////////////
+// string_pointer.h::value
+
+template <typename TValue, typename TPos>
+inline TValue &
+value(TValue * me,
+ TPos pos);
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_generated_forwards.h b/src/libSSA/seqan/basic/basic_generated_forwards.h
new file mode 100644
index 0000000..55f8ded
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_generated_forwards.h
@@ -0,0 +1,1941 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_GENERATED_FORWARDS_H
+#define SEQAN_HEADER_BASIC_GENERATED_FORWARDS_H
+
+//////////////////////////////////////////////////////////////////////////////
+// NOTE: This file is automatically generated by build_forwards.py
+// Do not edit this file manually!
+//////////////////////////////////////////////////////////////////////////////
+
+
+//////////////////////////////////////////////////////////////////////////////
+// CLASSES
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+namespace debug {
+
+//____________________________________________________________________________
+// Check
+
+class Check; // "projects/library/seqan/basic/basic_debug.h"(238)
+
+//____________________________________________________________________________
+// Checkpoint
+
+struct Checkpoint; // "projects/library/seqan/basic/basic_debug.h"(296)
+
+//____________________________________________________________________________
+// CheckpointLess
+
+struct CheckpointLess; // "projects/library/seqan/basic/basic_debug.h"(302)
+
+//____________________________________________________________________________
+// CheckpointStore
+
+template <typename T > struct CheckpointStore; // "projects/library/seqan/basic/basic_debug.h"(312)
+
+//____________________________________________________________________________
+// Report
+
+class Report; // "projects/library/seqan/basic/basic_debug.h"(242)
+
+} //namespace debug
+} //namespace SEQAN_NAMESPACE_MAIN
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+
+//____________________________________________________________________________
+// AdaptorIterator
+
+template <typename TIterator, typename TSpec > struct AdaptorIterator; // "projects/library/seqan/basic/basic_iterator_adaptor.h"(31)
+
+//____________________________________________________________________________
+// Allocator
+
+template <typename TSpec> struct Allocator; // "projects/library/seqan/basic/basic_allocator_interface.h"(50)
+
+//____________________________________________________________________________
+// BitsPerValue
+
+template <typename TValue> struct BitsPerValue; // "projects/library/seqan/basic/basic_alphabet_interface.h"(837)
+
+//____________________________________________________________________________
+// CASE
+
+template <int tag_,class Type_,class Next_ > struct CASE; // "projects/library/seqan/basic/basic_metaprogramming.h"(76)
+
+//____________________________________________________________________________
+// Cargo
+
+template <typename T> struct Cargo; // "projects/library/seqan/basic/basic_type.h"(290)
+
+//____________________________________________________________________________
+// ChunkPool
+
+#if 0
+template <size_t SIZE, size_t MAX_COUNT , typename TParentAllocator > struct ChunkPool; // "projects/library/seqan/basic/basic_allocator_chunkpool.h"(56)
+#endif
+
+//____________________________________________________________________________
+// ChunkPool2
+
+template <typename TValue, size_t MAX_COUNT , typename TParentAllocator > struct ChunkPool2; // "projects/library/seqan/basic/basic_allocator_chunkpool.h"(248)
+
+//____________________________________________________________________________
+// CompareType
+
+template <typename TLeft, typename TRight> struct CompareType; // "projects/library/seqan/basic/basic_alphabet_simple.h"(500)
+template <typename TLeft, typename TRight> struct CompareType; // "projects/library/seqan/basic/basic_compare.h"(30)
+
+//____________________________________________________________________________
+// Container
+
+template <typename T> struct Container; // "projects/library/seqan/basic/basic_iterator_base.h"(106)
+template <typename T> struct Container; // "projects/library/seqan/basic/basic_iterator.h"(147)
+
+//____________________________________________________________________________
+// Convert
+
+template <typename TTarget, typename TSource > struct Convert; // "projects/library/seqan/basic/basic_converter.h"(48)
+
+//____________________________________________________________________________
+// CountedPtr
+
+template <typename Type > struct CountedPtr; // "projects/library/seqan/basic/basic_counted_ptr.h"(34)
+
+//____________________________________________________________________________
+// CutCompressed
+
+template <unsigned valueSizeI1 > struct CutCompressed; // "projects/library/seqan/basic/basic_aggregates.h"(36)
+
+//____________________________________________________________________________
+// DeepestSpec
+
+template <typename T> struct DeepestSpec; // "projects/library/seqan/basic/basic_type.h"(229)
+
+//____________________________________________________________________________
+// DefaultGetIteratorSpec
+
+template <typename T> struct DefaultGetIteratorSpec; // "projects/library/seqan/basic/basic_iterator.h"(94)
+
+//____________________________________________________________________________
+// DefaultIteratorSpec
+
+template <typename T> struct DefaultIteratorSpec; // "projects/library/seqan/basic/basic_iterator.h"(72)
+
+//____________________________________________________________________________
+// Default_
+
+struct Default_; // "projects/library/seqan/basic/basic_definition.h"(40)
+
+//____________________________________________________________________________
+// Difference
+
+template <typename T> struct Difference; // "projects/library/seqan/basic/basic_type.h"(137)
+
+//____________________________________________________________________________
+// DotDrawing_
+
+struct DotDrawing_; // "projects/library/seqan/basic/basic_tag.h"(36)
+
+//____________________________________________________________________________
+// False
+
+struct False; // "projects/library/seqan/basic/basic_definition.h"(88)
+
+//____________________________________________________________________________
+// GetValue
+
+template <typename T> struct GetValue; // "projects/library/seqan/basic/basic_type.h"(69)
+
+//____________________________________________________________________________
+// GoEnd_
+
+struct GoEnd_; // "projects/library/seqan/basic/basic_definition.h"(66)
+
+//____________________________________________________________________________
+// Gotoh_
+
+struct Gotoh_; // "projects/library/seqan/basic/basic_tag.h"(90)
+
+//____________________________________________________________________________
+// Hirschberg_
+
+struct Hirschberg_; // "projects/library/seqan/basic/basic_tag.h"(118)
+
+//____________________________________________________________________________
+// Holder
+
+template <typename TValue, typename TSpec > struct Holder; // "projects/library/seqan/basic/basic_holder.h"(112)
+
+//____________________________________________________________________________
+// Host
+
+template <typename T> struct Host; // "projects/library/seqan/basic/basic_type.h"(181)
+
+//____________________________________________________________________________
+// IF
+
+template <bool Flag,class Type1, class Type2> struct IF; // "projects/library/seqan/basic/basic_metaprogramming.h"(35)
+
+//____________________________________________________________________________
+// Id
+
+template <typename T> struct Id; // "projects/library/seqan/basic/basic_type.h"(335)
+
+//____________________________________________________________________________
+// InfimumValue
+
+template <typename T, typename TParent > struct InfimumValue; // "projects/library/seqan/basic/basic_alphabet_interface.h"(911)
+
+//____________________________________________________________________________
+// IsSimple
+
+template <typename T> struct IsSimple; // "projects/library/seqan/basic/basic_alphabet_interface.h"(53)
+
+//____________________________________________________________________________
+// Iter
+
+template <typename TContainer, typename TSpec> class Iter; // "projects/library/seqan/basic/basic_iterator_base.h"(41)
+
+//____________________________________________________________________________
+// Iterator
+
+template <typename T, typename TSpec > struct Iterator; // "projects/library/seqan/basic/basic_iterator.h"(129)
+
+//____________________________________________________________________________
+// IteratorProxy
+
+template <typename TIterator> struct IteratorProxy; // "projects/library/seqan/basic/basic_proxy.h"(80)
+
+//____________________________________________________________________________
+// Iterator_Default_Imp
+
+template <typename T, typename TSpec> struct Iterator_Default_Imp; // "projects/library/seqan/basic/basic_iterator.h"(119)
+
+//____________________________________________________________________________
+// Key
+
+template <typename T > struct Key; // "projects/library/seqan/basic/basic_type.h"(358)
+
+//____________________________________________________________________________
+// LENGTH
+
+template <typename T> struct LENGTH; // "projects/library/seqan/basic/basic_type.h"(586)
+
+//____________________________________________________________________________
+// LOOP
+
+template <typename Worker, int I> class LOOP; // "projects/library/seqan/basic/basic_metaprogramming.h"(121)
+
+//____________________________________________________________________________
+// LOOP_REVERSE
+
+template <typename Worker, int I> class LOOP_REVERSE; // "projects/library/seqan/basic/basic_metaprogramming.h"(144)
+
+//____________________________________________________________________________
+// Log2
+
+template <__int64 numerus > struct Log2; // "projects/library/seqan/basic/basic_metaprogramming.h"(166)
+
+//____________________________________________________________________________
+// Log2Floor
+
+template <__int64 numerus > struct Log2Floor; // "projects/library/seqan/basic/basic_metaprogramming.h"(171)
+
+//____________________________________________________________________________
+// MemsetConstValueWorker
+
+template <unsigned SIZE, bool direct, unsigned char c> struct MemsetConstValueWorker; // "projects/library/seqan/basic/basic_metaprogramming.h"(251)
+
+//____________________________________________________________________________
+// MemsetWorker
+
+template <unsigned SIZE, bool direct> struct MemsetWorker; // "projects/library/seqan/basic/basic_metaprogramming.h"(205)
+
+//____________________________________________________________________________
+// MinimalCtor_
+
+struct MinimalCtor_; // "projects/library/seqan/basic/basic_definition.h"(73)
+
+//____________________________________________________________________________
+// Move_
+
+struct Move_; // "projects/library/seqan/basic/basic_definition.h"(60)
+
+//____________________________________________________________________________
+// MultiPool
+
+template <typename TParentAllocator , unsigned int BLOCKING_LIMIT > struct MultiPool; // "projects/library/seqan/basic/basic_allocator_multipool.h"(50)
+
+//____________________________________________________________________________
+// MyersBitVector_
+
+struct MyersBitVector_; // "projects/library/seqan/basic/basic_tag.h"(100)
+
+//____________________________________________________________________________
+// MyersHirschberg_
+
+struct MyersHirschberg_; // "projects/library/seqan/basic/basic_tag.h"(109)
+
+//____________________________________________________________________________
+// NeedlemanWunsch_
+
+struct NeedlemanWunsch_; // "projects/library/seqan/basic/basic_tag.h"(81)
+
+//____________________________________________________________________________
+// NilCase
+
+struct NilCase; // "projects/library/seqan/basic/basic_metaprogramming.h"(72)
+
+//____________________________________________________________________________
+// NonMinimalCtor_
+
+struct NonMinimalCtor_; // "projects/library/seqan/basic/basic_definition.h"(77)
+
+//____________________________________________________________________________
+// Nothing
+
+struct Nothing; // "projects/library/seqan/basic/basic_definition.h"(99)
+
+//____________________________________________________________________________
+// Nussinov_
+
+struct Nussinov_; // "projects/library/seqan/basic/basic_tag.h"(163)
+
+//____________________________________________________________________________
+// Object
+
+template <typename T> struct Object; // "projects/library/seqan/basic/basic_type.h"(377)
+
+//____________________________________________________________________________
+// Pair
+
+template <typename _T1, typename _T2 , typename TCompression > struct Pair; // "projects/library/seqan/basic/basic_aggregates.h"(69)
+
+//____________________________________________________________________________
+// Position
+
+template <typename T> struct Position; // "projects/library/seqan/basic/basic_type.h"(161)
+
+//____________________________________________________________________________
+// PositionIterator
+
+struct PositionIterator; // "projects/library/seqan/basic/basic_iterator_position.h"(29)
+
+//____________________________________________________________________________
+// Power
+
+template <__int64 base, __int64 exponent > struct Power; // "projects/library/seqan/basic/basic_metaprogramming.h"(186)
+
+//____________________________________________________________________________
+// Proxy
+
+template <typename TSpec> struct Proxy; // "projects/library/seqan/basic/basic_transport.h"(67)
+template <typename TSpec> struct Proxy; // "projects/library/seqan/basic/basic_proxy.h"(48)
+
+//____________________________________________________________________________
+// Reference
+
+template <typename T> struct Reference; // "projects/library/seqan/basic/basic_type.h"(91)
+
+//____________________________________________________________________________
+// SWITCH
+
+template <int tag,class Case> class SWITCH; // "projects/library/seqan/basic/basic_metaprogramming.h"(84)
+
+//____________________________________________________________________________
+// Simple
+
+struct Simple; // "projects/library/seqan/basic/basic_holder.h"(86)
+
+//____________________________________________________________________________
+// SimpleAlloc
+
+template <typename TParentAllocator > struct SimpleAlloc; // "projects/library/seqan/basic/basic_allocator_simple.h"(46)
+
+//____________________________________________________________________________
+// SimpleIterator
+
+struct SimpleIterator; // "projects/library/seqan/basic/basic_iterator_simple.h"(30)
+
+//____________________________________________________________________________
+// SimpleType
+
+template <typename TValue, typename TSpec> struct SimpleType; // "projects/library/seqan/basic/basic_alphabet_simple.h"(58)
+
+//____________________________________________________________________________
+// SinglePool
+
+template <size_t SIZE, typename TParentAllocator > struct SinglePool; // "projects/library/seqan/basic/basic_allocator_singlepool.h"(50)
+
+//____________________________________________________________________________
+// SinglePool2
+
+template <typename TValue, typename TParentAllocator > struct SinglePool2; // "projects/library/seqan/basic/basic_allocator_singlepool.h"(226)
+
+//____________________________________________________________________________
+// Size
+
+template <typename T> struct Size; // "projects/library/seqan/basic/basic_type.h"(113)
+
+//____________________________________________________________________________
+// SmithWatermanClump_
+
+struct SmithWatermanClump_; // "projects/library/seqan/basic/basic_tag.h"(145)
+
+//____________________________________________________________________________
+// SmithWatermanIsland_
+
+struct SmithWatermanIsland_; // "projects/library/seqan/basic/basic_tag.h"(154)
+
+//____________________________________________________________________________
+// SmithWaterman_
+
+struct SmithWaterman_; // "projects/library/seqan/basic/basic_tag.h"(136)
+
+//____________________________________________________________________________
+// Source
+
+template <typename TSpec > struct Source; // "projects/library/seqan/basic/basic_type.h"(392)
+
+//____________________________________________________________________________
+// Spec
+
+template <typename T> struct Spec; // "projects/library/seqan/basic/basic_type.h"(200)
+
+//____________________________________________________________________________
+// StdAllocator
+
+template <typename T, typename TData> struct StdAllocator; // "projects/library/seqan/basic/basic_allocator_to_std.h"(166)
+
+//____________________________________________________________________________
+// StdContainerIterator
+
+template <typename TStdContainer> struct StdContainerIterator; // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(68)
+
+//____________________________________________________________________________
+// StdIteratorAdaptor
+
+struct StdIteratorAdaptor; // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(89)
+
+//____________________________________________________________________________
+// SupremumValue
+
+template <typename T, typename TParent > struct SupremumValue; // "projects/library/seqan/basic/basic_alphabet_interface.h"(900)
+
+//____________________________________________________________________________
+// TYPECMP
+
+template <class Type1, class Type2> struct TYPECMP; // "projects/library/seqan/basic/basic_metaprogramming.h"(54)
+
+//____________________________________________________________________________
+// Tag
+
+template <typename T> struct Tag; // "projects/library/seqan/basic/basic_definition.h"(31)
+
+//____________________________________________________________________________
+// TagAllocateStorage_
+
+struct TagAllocateStorage_; // "projects/library/seqan/basic/basic_allocator_interface.h"(84)
+
+//____________________________________________________________________________
+// TagAllocateTemp_
+
+struct TagAllocateTemp_; // "projects/library/seqan/basic/basic_allocator_interface.h"(81)
+
+//____________________________________________________________________________
+// TagAllocateUnspecified_
+
+struct TagAllocateUnspecified_; // "projects/library/seqan/basic/basic_allocator_interface.h"(78)
+
+//____________________________________________________________________________
+// TagRooted_
+
+struct TagRooted_; // "projects/library/seqan/basic/basic_iterator.h"(48)
+
+//____________________________________________________________________________
+// TagStandard_
+
+struct TagStandard_; // "projects/library/seqan/basic/basic_iterator.h"(51)
+
+//____________________________________________________________________________
+// ToStdAllocator
+
+template <typename THost, typename TValue> struct ToStdAllocator; // "projects/library/seqan/basic/basic_allocator_to_std.h"(61)
+
+//____________________________________________________________________________
+// Triple
+
+template <typename _T1, typename _T2 , typename _T3 , typename TCompression > struct Triple; // "projects/library/seqan/basic/basic_aggregates.h"(218)
+
+//____________________________________________________________________________
+// Tristate
+
+struct Tristate; // "projects/library/seqan/basic/basic_holder.h"(87)
+
+//____________________________________________________________________________
+// Tristate2
+
+struct Tristate2; // "projects/library/seqan/basic/basic_holder.h"(790)
+
+//____________________________________________________________________________
+// True
+
+struct True; // "projects/library/seqan/basic/basic_definition.h"(87)
+
+//____________________________________________________________________________
+// Tuple
+
+template <typename _T, unsigned _size, typename TCompression > struct Tuple; // "projects/library/seqan/basic/basic_aggregates.h"(313)
+
+//____________________________________________________________________________
+// Value
+
+template <typename T, const int i > struct Value; // "projects/library/seqan/basic/basic_type.h"(43)
+
+//____________________________________________________________________________
+// ValueSize
+
+template <typename T> struct ValueSize; // "projects/library/seqan/basic/basic_alphabet_interface.h"(859)
+
+//____________________________________________________________________________
+// VertexDescriptor
+
+template <typename T> struct VertexDescriptor; // "projects/library/seqan/basic/basic_type.h"(313)
+
+//____________________________________________________________________________
+// VolatilePtr
+
+template <typename Type > struct VolatilePtr; // "projects/library/seqan/basic/basic_volatile_ptr.h"(40)
+
+//____________________________________________________________________________
+// WEIGHT
+
+template <typename T> struct WEIGHT; // "projects/library/seqan/basic/basic_type.h"(608)
+
+//____________________________________________________________________________
+// WorkerNothing
+
+struct WorkerNothing; // "projects/library/seqan/basic/basic_metaprogramming.h"(115)
+
+//____________________________________________________________________________
+// _AminoAcid
+
+struct _AminoAcid; // "projects/library/seqan/basic/basic_alphabet_simple.h"(1085)
+
+//____________________________________________________________________________
+// _BitVector
+
+template <unsigned char _size > struct _BitVector; // "projects/library/seqan/basic/basic_aggregates.h"(340)
+
+//____________________________________________________________________________
+// _ClassIdentifier
+
+template <typename T> struct _ClassIdentifier; // "projects/library/seqan/basic/basic_definition.h"(269)
+
+//____________________________________________________________________________
+// _Compressed
+
+struct _Compressed; // "projects/library/seqan/basic/basic_aggregates.h"(29)
+
+//____________________________________________________________________________
+// _ConstParameter
+
+template <typename T> struct _ConstParameter; // "projects/library/seqan/basic/basic_type.h"(474)
+
+//____________________________________________________________________________
+// _CopyConst
+
+template <typename TFrom, typename TTo> struct _CopyConst; // "projects/library/seqan/basic/basic_definition.h"(108)
+
+//____________________________________________________________________________
+// _Dna
+
+struct _Dna; // "projects/library/seqan/basic/basic_alphabet_simple.h"(1010)
+
+//____________________________________________________________________________
+// _Dna5
+
+struct _Dna5; // "projects/library/seqan/basic/basic_alphabet_simple.h"(1034)
+
+//____________________________________________________________________________
+// _HammingDistance
+
+struct _HammingDistance; // "projects/library/seqan/basic/basic_tag.h"(50)
+
+//____________________________________________________________________________
+// _InfimumValueSigned
+
+template <typename T > struct _InfimumValueSigned; // "projects/library/seqan/basic/basic_alphabet_interface.h"(876)
+
+//____________________________________________________________________________
+// _InfimumValueUnsigned
+
+template <typename T > struct _InfimumValueUnsigned; // "projects/library/seqan/basic/basic_alphabet_interface.h"(874)
+
+//____________________________________________________________________________
+// _IsSameType
+
+template <typename T1, typename T2> struct _IsSameType; // "projects/library/seqan/basic/basic_definition.h"(378)
+
+//____________________________________________________________________________
+// _IsSimple
+
+template <typename T> struct _IsSimple; // "projects/library/seqan/basic/basic_alphabet_interface.h"(47)
+
+//____________________________________________________________________________
+// _Iupac
+
+struct _Iupac; // "projects/library/seqan/basic/basic_alphabet_simple.h"(1058)
+
+//____________________________________________________________________________
+// _LevenshteinDistance
+
+struct _LevenshteinDistance; // "projects/library/seqan/basic/basic_tag.h"(51)
+
+//____________________________________________________________________________
+// _Log2_Impl
+
+template <int BITS_MAX> struct _Log2_Impl; // "projects/library/seqan/basic/basic_definition.h"(292)
+
+//____________________________________________________________________________
+// _MakeSigned
+
+template <typename T> struct _MakeSigned; // "projects/library/seqan/basic/basic_definition.h"(212)
+
+//____________________________________________________________________________
+// _MakeUnsigned
+
+template <typename T> struct _MakeUnsigned; // "projects/library/seqan/basic/basic_definition.h"(157)
+
+//____________________________________________________________________________
+// _Parameter
+
+template <typename T> struct _Parameter; // "projects/library/seqan/basic/basic_type.h"(416)
+
+//____________________________________________________________________________
+// _Pointer
+
+template <typename T> struct _Pointer; // "projects/library/seqan/basic/basic_type.h"(519)
+
+//____________________________________________________________________________
+// _RemoveConst
+
+template <typename T> struct _RemoveConst; // "projects/library/seqan/basic/basic_definition.h"(126)
+
+//____________________________________________________________________________
+// _SupremumValueSigned
+
+template <typename T > struct _SupremumValueSigned; // "projects/library/seqan/basic/basic_alphabet_interface.h"(871)
+
+//____________________________________________________________________________
+// _SupremumValueUnsigned
+
+template <typename T > struct _SupremumValueUnsigned; // "projects/library/seqan/basic/basic_alphabet_interface.h"(869)
+
+//____________________________________________________________________________
+// _Translate_Table_AA_2_Ascii
+
+template <typename T > struct _Translate_Table_AA_2_Ascii; // "projects/library/seqan/basic/basic_alphabet_simple_tabs.h"(337)
+
+//____________________________________________________________________________
+// _Translate_Table_Ascii_2_AA
+
+template <typename T > struct _Translate_Table_Ascii_2_AA; // "projects/library/seqan/basic/basic_alphabet_simple_tabs.h"(374)
+
+//____________________________________________________________________________
+// _Translate_Table_Ascii_2_Dna
+
+template <typename T > struct _Translate_Table_Ascii_2_Dna; // "projects/library/seqan/basic/basic_alphabet_simple_tabs.h"(138)
+
+//____________________________________________________________________________
+// _Translate_Table_Ascii_2_Dna5
+
+template <typename T > struct _Translate_Table_Ascii_2_Dna5; // "projects/library/seqan/basic/basic_alphabet_simple_tabs.h"(176)
+
+//____________________________________________________________________________
+// _Translate_Table_Ascii_2_Iupac
+
+template <typename T > struct _Translate_Table_Ascii_2_Iupac; // "projects/library/seqan/basic/basic_alphabet_simple_tabs.h"(214)
+
+//____________________________________________________________________________
+// _Translate_Table_Byte_2_AA
+
+template <typename T > struct _Translate_Table_Byte_2_AA; // "projects/library/seqan/basic/basic_alphabet_simple_tabs.h"(412)
+
+//____________________________________________________________________________
+// _Translate_Table_Byte_2_Dna
+
+template <typename T > struct _Translate_Table_Byte_2_Dna; // "projects/library/seqan/basic/basic_alphabet_simple_tabs.h"(251)
+
+//____________________________________________________________________________
+// _Translate_Table_Byte_2_Dna5
+
+template <typename T > struct _Translate_Table_Byte_2_Dna5; // "projects/library/seqan/basic/basic_alphabet_simple_tabs.h"(280)
+
+//____________________________________________________________________________
+// _Translate_Table_Byte_2_Iupac
+
+template <typename T > struct _Translate_Table_Byte_2_Iupac; // "projects/library/seqan/basic/basic_alphabet_simple_tabs.h"(308)
+
+//____________________________________________________________________________
+// _Translate_Table_Dna5_2_Ascii
+
+template <typename T > struct _Translate_Table_Dna5_2_Ascii; // "projects/library/seqan/basic/basic_alphabet_simple_tabs.h"(33)
+
+//____________________________________________________________________________
+// _Translate_Table_Dna5_2_Iupac
+
+template <typename T > struct _Translate_Table_Dna5_2_Iupac; // "projects/library/seqan/basic/basic_alphabet_simple_tabs.h"(43)
+
+//____________________________________________________________________________
+// _Translate_Table_Iupac_2_Ascii
+
+template <typename T > struct _Translate_Table_Iupac_2_Ascii; // "projects/library/seqan/basic/basic_alphabet_simple_tabs.h"(53)
+
+//____________________________________________________________________________
+// _Translate_Table_Iupac_2_Dna
+
+template <typename T > struct _Translate_Table_Iupac_2_Dna; // "projects/library/seqan/basic/basic_alphabet_simple_tabs.h"(81)
+
+//____________________________________________________________________________
+// _Translate_Table_Iupac_2_Dna5
+
+template <typename T > struct _Translate_Table_Iupac_2_Dna5; // "projects/library/seqan/basic/basic_alphabet_simple_tabs.h"(110)
+
+//____________________________________________________________________________
+// _TupleShiftLeftWorker
+
+struct _TupleShiftLeftWorker; // "projects/library/seqan/basic/basic_aggregates.h"(510)
+
+//____________________________________________________________________________
+// _TupleShiftRightWorker
+
+struct _TupleShiftRightWorker; // "projects/library/seqan/basic/basic_aggregates.h"(517)
+
+//____________________________________________________________________________
+// _ValueConstructor
+
+struct _ValueConstructor; // "projects/library/seqan/basic/basic_alphabet_interface.h"(81)
+
+//____________________________________________________________________________
+// _ValueConstructorProxy
+
+struct _ValueConstructorProxy; // "projects/library/seqan/basic/basic_alphabet_interface.h"(111)
+
+//____________________________________________________________________________
+// _ValueDestructor
+
+struct _ValueDestructor; // "projects/library/seqan/basic/basic_alphabet_interface.h"(125)
+
+//____________________________________________________________________________
+// _ValueDestructorProxy
+
+struct _ValueDestructorProxy; // "projects/library/seqan/basic/basic_alphabet_interface.h"(135)
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+
+//////////////////////////////////////////////////////////////////////////////
+// TYPEDEFS
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+
+//____________________________________________________________________________
+// AminoAcid
+
+typedef SimpleType<unsigned char, _AminoAcid> AminoAcid; // "projects/library/seqan/basic/basic_alphabet_simple.h"(1086)
+
+//____________________________________________________________________________
+// Ascii
+
+typedef char Ascii; // "projects/library/seqan/basic/basic_alphabet_interface.h"(61)
+
+//____________________________________________________________________________
+// Byte
+
+typedef unsigned char Byte; // "projects/library/seqan/basic/basic_alphabet_interface.h"(62)
+
+//____________________________________________________________________________
+// Compressed
+
+typedef Tag<_Compressed> Compressed; // "projects/library/seqan/basic/basic_aggregates.h"(30)
+
+//____________________________________________________________________________
+// Default
+
+typedef Tag<Default_> const Default; // "projects/library/seqan/basic/basic_definition.h"(41)
+
+//____________________________________________________________________________
+// Dna
+
+typedef SimpleType<unsigned char,_Dna> Dna; // "projects/library/seqan/basic/basic_alphabet_simple.h"(1011)
+
+//____________________________________________________________________________
+// Dna5
+
+typedef SimpleType<unsigned char, _Dna5> Dna5; // "projects/library/seqan/basic/basic_alphabet_simple.h"(1035)
+
+//____________________________________________________________________________
+// DotDrawing
+
+typedef Tag<DotDrawing_> const DotDrawing; // "projects/library/seqan/basic/basic_tag.h"(37)
+
+//____________________________________________________________________________
+// EditDistance
+
+typedef Tag<_LevenshteinDistance> EditDistance; // "projects/library/seqan/basic/basic_tag.h"(55)
+
+//____________________________________________________________________________
+// GoEnd
+
+typedef Tag<GoEnd_> const GoEnd; // "projects/library/seqan/basic/basic_definition.h"(67)
+
+//____________________________________________________________________________
+// Gotoh
+
+typedef Tag<Gotoh_> const Gotoh; // "projects/library/seqan/basic/basic_tag.h"(91)
+
+//____________________________________________________________________________
+// HammingDistance
+
+typedef Tag<_HammingDistance> HammingDistance; // "projects/library/seqan/basic/basic_tag.h"(53)
+
+//____________________________________________________________________________
+// Hirschberg
+
+typedef Tag<Hirschberg_> const Hirschberg; // "projects/library/seqan/basic/basic_tag.h"(119)
+
+//____________________________________________________________________________
+// Iupac
+
+typedef SimpleType<unsigned char, _Iupac> Iupac; // "projects/library/seqan/basic/basic_alphabet_simple.h"(1059)
+
+//____________________________________________________________________________
+// LevenshteinDistance
+
+typedef Tag<_LevenshteinDistance> LevenshteinDistance; // "projects/library/seqan/basic/basic_tag.h"(54)
+
+//____________________________________________________________________________
+// MinimalCtor
+
+typedef Tag<MinimalCtor_> const MinimalCtor; // "projects/library/seqan/basic/basic_definition.h"(74)
+
+//____________________________________________________________________________
+// Move
+
+typedef Tag<Move_> const Move; // "projects/library/seqan/basic/basic_definition.h"(61)
+
+//____________________________________________________________________________
+// MyersBitVector
+
+typedef Tag<MyersBitVector_> const MyersBitVector; // "projects/library/seqan/basic/basic_tag.h"(101)
+
+//____________________________________________________________________________
+// MyersHirschberg
+
+typedef Tag<MyersHirschberg_> const MyersHirschberg; // "projects/library/seqan/basic/basic_tag.h"(110)
+
+//____________________________________________________________________________
+// NeedlemanWunsch
+
+typedef Tag<NeedlemanWunsch_> const NeedlemanWunsch; // "projects/library/seqan/basic/basic_tag.h"(82)
+
+//____________________________________________________________________________
+// NonMinimalCtor
+
+typedef Tag<NonMinimalCtor_> const NonMinimalCtor; // "projects/library/seqan/basic/basic_definition.h"(78)
+
+//____________________________________________________________________________
+// Nussinov
+
+typedef Tag<Nussinov_> const Nussinov; // "projects/library/seqan/basic/basic_tag.h"(164)
+
+//____________________________________________________________________________
+// PoolAllocator
+
+typedef Allocator<MultiPool<Allocator<SimpleAlloc<Default> >, 0x100> > PoolAllocator; // "projects/library/seqan/basic/basic_allocator_multipool.h"(54)
+
+//____________________________________________________________________________
+// Rooted
+
+typedef Tag<TagRooted_> const Rooted; // "projects/library/seqan/basic/basic_iterator.h"(49)
+
+//____________________________________________________________________________
+// SimpleAllocator
+
+typedef Allocator<SimpleAlloc<Default> > SimpleAllocator; // "projects/library/seqan/basic/basic_allocator_simple.h"(51)
+
+//____________________________________________________________________________
+// SmithWaterman
+
+typedef Tag<SmithWaterman_> const SmithWaterman; // "projects/library/seqan/basic/basic_tag.h"(137)
+
+//____________________________________________________________________________
+// SmithWatermanClump
+
+typedef Tag<SmithWatermanClump_> const SmithWatermanClump; // "projects/library/seqan/basic/basic_tag.h"(146)
+
+//____________________________________________________________________________
+// SmithWatermanIsland
+
+typedef Tag<SmithWatermanIsland_> const SmithWatermanIsland; // "projects/library/seqan/basic/basic_tag.h"(155)
+
+//____________________________________________________________________________
+// Standard
+
+typedef Tag<TagStandard_> const Standard; // "projects/library/seqan/basic/basic_iterator.h"(52)
+
+//____________________________________________________________________________
+// TagAllocateStorage
+
+typedef Tag<TagAllocateStorage_> const TagAllocateStorage; // "projects/library/seqan/basic/basic_allocator_interface.h"(85)
+
+//____________________________________________________________________________
+// TagAllocateTemp
+
+typedef Tag<TagAllocateTemp_> const TagAllocateTemp; // "projects/library/seqan/basic/basic_allocator_interface.h"(82)
+
+//____________________________________________________________________________
+// TagAllocateUnspecified
+
+typedef Tag<TagAllocateUnspecified_> const TagAllocateUnspecified; // "projects/library/seqan/basic/basic_allocator_interface.h"(79)
+
+//____________________________________________________________________________
+// Unicode
+
+typedef wchar_t Unicode; // "projects/library/seqan/basic/basic_alphabet_interface.h"(63)
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+
+//////////////////////////////////////////////////////////////////////////////
+// FUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+namespace debug {
+
+//____________________________________________________________________________
+// Error
+
+template <typename TAction> void Error(const char * file, int line, const char * comment); // "projects/library/seqan/basic/basic_debug.h"(250)
+
+//____________________________________________________________________________
+// Message
+
+template <typename TAction> void Message(const char * file, int line, const char * comment); // "projects/library/seqan/basic/basic_debug.h"(260)
+
+//____________________________________________________________________________
+// Result
+
+template <typename TAction> void Result(const char * file, int line, const char * comment); // "projects/library/seqan/basic/basic_debug.h"(269)
+
+//____________________________________________________________________________
+// checkpoint
+
+inline bool checkpoint(unsigned int line, char const* file); // "projects/library/seqan/basic/basic_debug.h"(321)
+
+//____________________________________________________________________________
+// testCheckpoint
+
+inline void testCheckpoint(char const* file, unsigned int line); // "projects/library/seqan/basic/basic_debug.h"(338)
+
+//____________________________________________________________________________
+// verifyCheckpoints
+
+inline void verifyCheckpoints(char const* file); // "projects/library/seqan/basic/basic_debug.h"(346)
+
+} //namespace debug
+} //namespace SEQAN_NAMESPACE_MAIN
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+
+//____________________________________________________________________________
+// _allocatorBlockNumber
+
+template <typename TParentAllocator, unsigned int BLOCKING_LIMIT> inline unsigned int _allocatorBlockNumber(Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > &, size_t size_); // "projects/library/seqan/basic/basic_allocator_multipool.h"(140)
+
+//____________________________________________________________________________
+// _arrayClearSpace_Default
+
+template <typename TIterator> void _arrayClearSpace_Default(TIterator array_begin, size_t array_length, size_t keep_from, size_t move_to); // "projects/library/seqan/basic/basic_alphabet_interface.h"(774)
+
+//____________________________________________________________________________
+// _arrayClearSpace_Pointer
+
+template <typename TValue> inline void _arrayClearSpace_Pointer(TValue * array_begin, size_t array_length, size_t keep_from, size_t move_to, True); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(342)
+template <typename TValue> inline void _arrayClearSpace_Pointer(TValue * array_begin, size_t array_length, size_t keep_from, size_t move_to, False); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(354)
+
+//____________________________________________________________________________
+// _arrayConstructCopy_Default
+
+template <typename TTarget, typename TSource1, typename TSource2> inline void _arrayConstructCopy_Default(TSource1 source_begin, TSource2 source_end, TTarget target_begin); // "projects/library/seqan/basic/basic_alphabet_interface.h"(349)
+
+//____________________________________________________________________________
+// _arrayConstructCopy_Pointer
+
+template <typename TValue> inline void _arrayConstructCopy_Pointer(TValue * source_begin, TValue * source_end, TValue * target_begin, True); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(100)
+template <typename TValue> inline void _arrayConstructCopy_Pointer(TValue * source_begin, TValue * source_end, TValue * target_begin, False); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(110)
+
+//____________________________________________________________________________
+// _arrayConstructMove_Default
+
+template <typename TTarget, typename TSource1, typename TSource2> inline void _arrayConstructMove_Default(TSource1 source_begin, TSource2 source_end, TTarget target_begin); // "projects/library/seqan/basic/basic_alphabet_interface.h"(397)
+
+//____________________________________________________________________________
+// _arrayConstructMove_Pointer
+
+template <typename TValue> inline void _arrayConstructMove_Pointer(TValue * source_begin, TValue * source_end, TValue * target_begin, True); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(134)
+template <typename TValue> inline void _arrayConstructMove_Pointer(TValue * source_begin, TValue * source_end, TValue * target_begin, False); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(144)
+
+//____________________________________________________________________________
+// _arrayConstruct_Default
+
+template <typename TIterator1, typename TIterator2> inline void _arrayConstruct_Default(TIterator1 begin_, TIterator2 end_); // "projects/library/seqan/basic/basic_alphabet_interface.h"(280)
+template <typename TIterator1, typename TIterator2, typename TParam> inline void _arrayConstruct_Default(TIterator1 begin_, TIterator2 end_, TParam const & param_); // "projects/library/seqan/basic/basic_alphabet_interface.h"(304)
+
+//____________________________________________________________________________
+// _arrayConstruct_Pointer
+
+template <typename TIterator> inline void _arrayConstruct_Pointer(TIterator, TIterator, True); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(36)
+template <typename TIterator> inline void _arrayConstruct_Pointer(TIterator begin_, TIterator end_, False); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(45)
+template <typename TIterator, typename TParam> inline void _arrayConstruct_Pointer(TIterator begin_, TIterator end_, TParam const & param_, True); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(66)
+template <typename TIterator, typename TParam> inline void _arrayConstruct_Pointer(TIterator begin_, TIterator end_, TParam const & param_, False); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(76)
+
+//____________________________________________________________________________
+// _arrayCopyBackward_Default
+
+template <typename TTarget, typename TSource1, typename TSource2> inline void _arrayCopyBackward_Default(TSource1 source_begin, TSource2 source_end, TTarget target_begin); // "projects/library/seqan/basic/basic_alphabet_interface.h"(547)
+
+//____________________________________________________________________________
+// _arrayCopyBackward_Pointer
+
+template <typename TValue> inline void _arrayCopyBackward_Pointer(TValue * source_begin, TValue * source_end, TValue * target_begin, True); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(239)
+template <typename TValue> inline void _arrayCopyBackward_Pointer(TValue * source_begin, TValue * source_end, TValue * target_begin, False); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(249)
+
+//____________________________________________________________________________
+// _arrayCopyForward_Default
+
+template <typename TTarget, typename TSource1, typename TSource2> inline void _arrayCopyForward_Default(TSource1 source_begin, TSource2 source_end, TTarget target_begin); // "projects/library/seqan/basic/basic_alphabet_interface.h"(504)
+
+//____________________________________________________________________________
+// _arrayCopyForward_Pointer
+
+template <typename TValue> inline void _arrayCopyForward_Pointer(TValue * source_begin, TValue * source_end, TValue * target_begin, True); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(205)
+template <typename TValue> inline void _arrayCopyForward_Pointer(TValue * source_begin, TValue * source_end, TValue * target_begin, False); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(215)
+
+//____________________________________________________________________________
+// _arrayDestruct_Default
+
+template <typename TIterator1, typename TIterator2> inline void _arrayDestruct_Default(TIterator1 begin_, TIterator2 end_); // "projects/library/seqan/basic/basic_alphabet_interface.h"(436)
+
+//____________________________________________________________________________
+// _arrayDestruct_Pointer
+
+template <typename TValue> inline void _arrayDestruct_Pointer(TValue * , TValue * , True); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(167)
+template <typename TValue> inline void _arrayDestruct_Pointer(TValue * begin_, TValue * end_, False); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(176)
+
+//____________________________________________________________________________
+// _arrayMoveBackward_Default
+
+template <typename TTarget, typename TSource1, typename TSource2> inline void _arrayMoveBackward_Default(TSource1 source_begin, TSource2 source_end, TTarget target_begin); // "projects/library/seqan/basic/basic_alphabet_interface.h"(679)
+
+//____________________________________________________________________________
+// _arrayMoveBackward_Pointer
+
+template <typename TValue> inline void _arrayMoveBackward_Pointer(TValue * source_begin, TValue * source_end, TValue * target_begin, True); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(307)
+template <typename TValue> inline void _arrayMoveBackward_Pointer(TValue * source_begin, TValue * source_end, TValue * target_begin, False); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(317)
+
+//____________________________________________________________________________
+// _arrayMoveForward_Default
+
+template <typename TTarget, typename TSource1, typename TSource2> inline void _arrayMoveForward_Default(TSource1 source_begin, TSource2 source_end, TTarget target_begin); // "projects/library/seqan/basic/basic_alphabet_interface.h"(630)
+
+//____________________________________________________________________________
+// _arrayMoveForward_Pointer
+
+template <typename TValue> inline void _arrayMoveForward_Pointer(TValue * source_begin, TValue * source_end, TValue * target_begin, True); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(273)
+template <typename TValue> inline void _arrayMoveForward_Pointer(TValue * source_begin, TValue * source_end, TValue * target_begin, False); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(283)
+
+//____________________________________________________________________________
+// _intPow
+
+template <typename TValue, typename TExponent> inline TValue _intPow(TValue a, TExponent b); // "projects/library/seqan/basic/basic_definition.h"(334)
+
+//____________________________________________________________________________
+// _isSameType
+
+template <typename T1, typename T2> inline bool _isSameType(); // "projects/library/seqan/basic/basic_definition.h"(393)
+
+//____________________________________________________________________________
+// _max
+
+template <typename _Ty> inline const _Ty& _max(const _Ty& _Left, const _Ty& _Right); // "projects/library/seqan/basic/basic_definition.h"(367)
+
+//____________________________________________________________________________
+// _min
+
+template <typename _Tx> inline const _Tx& _min(const _Tx& _Left, const _Tx& _Right); // "projects/library/seqan/basic/basic_definition.h"(352)
+template <typename _Tx, typename _Ty> inline _Tx _min(const _Tx& _Left, const _Ty& _Right); // "projects/library/seqan/basic/basic_definition.h"(361)
+
+//____________________________________________________________________________
+// _toParameter
+
+template <typename T> typename _Parameter<T>::Type _toParameter(T * _object); // "projects/library/seqan/basic/basic_type.h"(447)
+template <typename T> typename _Parameter<T>::Type _toParameter(T _object); // "projects/library/seqan/basic/basic_type.h"(454)
+
+//____________________________________________________________________________
+// _toPointer
+
+template <typename T> typename _Pointer<T>::Type _toPointer(T & _object); // "projects/library/seqan/basic/basic_type.h"(553)
+template <typename T> typename _Pointer<T const>::Type _toPointer(T const & _object); // "projects/library/seqan/basic/basic_type.h"(560)
+template <typename T> typename _Pointer<T *>::Type _toPointer(T * _object); // "projects/library/seqan/basic/basic_type.h"(568)
+
+//____________________________________________________________________________
+// addRef
+
+template <typename T> inline void addRef(T & ); // "projects/library/seqan/basic/basic_holder.h"(45)
+template <typename T> inline void addRef(T const & ); // "projects/library/seqan/basic/basic_holder.h"(51)
+
+//____________________________________________________________________________
+// allocate
+
+template <size_t SIZE, typename TParentAllocator, typename TValue, typename TSize, typename TUsage> inline void allocate(Allocator<SinglePool<SIZE, TParentAllocator> > & me, TValue * & data, TSize count, Tag<TUsage> const tag_); // "projects/library/seqan/basic/basic_allocator_singlepool.h"(162)
+template <typename TValue, typename TParentAllocator, typename TValue2, typename TSize, typename TUsage> inline void allocate(Allocator<SinglePool2<TValue, TParentAllocator> > & me, TValue2 * & data, TSize count, Tag<TUsage> const tag_); // "projects/library/seqan/basic/basic_allocator_singlepool.h"(279)
+template <typename TParentAllocator, unsigned int BLOCKING_LIMIT, typename TValue, typename TSize, typename TUsage> inline void allocate(Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > & me, TValue * & data, TSize count, Tag<TUsage> const tag_); // "projects/library/seqan/basic/basic_allocator_multipool.h"(165)
+template <typename TParentAllocator, typename TValue, typename TSize, typename TUsage> inline void allocate(Allocator<SimpleAlloc<TParentAllocator> > & me, TValue * & data, TSize count, Tag<TUsage> const); // "projects/library/seqan/basic/basic_allocator_simple.h"(146)
+template <typename T, typename TValue, typename TSize> inline void allocate(T const & me, TValue * & data, TSize count); // "projects/library/seqan/basic/basic_allocator_interface.h"(129)
+template <typename T, typename TValue, typename TSize> inline void allocate(T & me, TValue * & data, TSize count); // "projects/library/seqan/basic/basic_allocator_interface.h"(137)
+template <typename T, typename TValue, typename TSize, typename TUsage> inline void allocate(T const &, TValue * & data, TSize count, Tag<TUsage> const); // "projects/library/seqan/basic/basic_allocator_interface.h"(147)
+template <typename T, typename TValue, typename TSize, typename TUsage> inline void allocate(T &, TValue * & data, TSize count, Tag<TUsage> const); // "projects/library/seqan/basic/basic_allocator_interface.h"(158)
+//template <size_t SIZE, size_t MAX_COUNT, typename TParentAllocator, typename TValue, typename TSize, typename TUsage> inline void allocate(Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > & me, TValue * & data, TSize count, Tag<TUsage> const tag_); // "projects/library/seqan/basic/basic_allocator_chunkpool.h"(173)
+template <typename TValue, size_t MAX_COUNT, typename TParentAllocator, typename TValue2, typename TSize, typename TUsage> inline void allocate(Allocator<ChunkPool2<TValue, MAX_COUNT, TParentAllocator> > & me, TValue2 * & data, TSize count, Tag<TUsage> const tag_); // "projects/library/seqan/basic/basic_allocator_chunkpool.h"(302)
+
+//____________________________________________________________________________
+// arrayClearSpace
+
+template <typename TIterator> void arrayClearSpace(TIterator array_begin, size_t array_length, size_t keep_from, size_t move_to); // "projects/library/seqan/basic/basic_alphabet_interface.h"(818)
+template <typename TValue> void arrayClearSpace(TValue * array_begin, size_t array_length, size_t keep_from, size_t move_to); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(362)
+
+//____________________________________________________________________________
+// arrayConstruct
+
+template <typename TIterator1, typename TIterator2> inline void arrayConstruct(TIterator1 begin_, TIterator2 end_); // "projects/library/seqan/basic/basic_alphabet_interface.h"(292)
+template <typename TIterator1, typename TIterator2, typename TParam> inline void arrayConstruct(TIterator1 begin_, TIterator2 end_, TParam const & param_); // "projects/library/seqan/basic/basic_alphabet_interface.h"(317)
+template <typename TValue> inline void arrayConstruct(TValue * begin_, TValue * end_); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(53)
+template <typename TValue, typename TParam> inline void arrayConstruct(TValue * begin_, TValue * end_, TParam const & param_); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(85)
+
+//____________________________________________________________________________
+// arrayConstructCopy
+
+template <typename TTarget, typename TSource1, typename TSource2> inline void arrayConstructCopy(TSource1 source_begin, TSource2 source_end, TTarget target_begin); // "projects/library/seqan/basic/basic_alphabet_interface.h"(364)
+template <typename TValue> inline void arrayConstructCopy(TValue * source_begin, TValue * source_end, TValue * target_begin); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(119)
+
+//____________________________________________________________________________
+// arrayConstructMove
+
+template <typename TTarget, typename TSource1, typename TSource2> inline void arrayConstructMove(TSource1 source_begin, TSource2 source_end, TTarget target_begin); // "projects/library/seqan/basic/basic_alphabet_interface.h"(412)
+template <typename TValue> inline void arrayConstructMove(TValue * source_begin, TValue * source_end, TValue * target_begin); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(153)
+
+//____________________________________________________________________________
+// arrayCopy
+
+template <typename TTarget, typename TSource1, typename TSource2> inline void arrayCopy(TSource1 source_begin, TSource2 source_end, TTarget target_begin); // "projects/library/seqan/basic/basic_alphabet_interface.h"(591)
+
+//____________________________________________________________________________
+// arrayCopyBackward
+
+template <typename TTarget, typename TSource1, typename TSource2> inline void arrayCopyBackward(TSource1 source_begin, TSource2 source_end, TTarget target_begin); // "projects/library/seqan/basic/basic_alphabet_interface.h"(556)
+template <typename TValue> inline void arrayCopyBackward(TValue * source_begin, TValue * source_end, TValue * target_begin); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(258)
+
+//____________________________________________________________________________
+// arrayCopyForward
+
+template <typename TTarget, typename TSource1, typename TSource2> inline void arrayCopyForward(TSource1 source_begin, TSource2 source_end, TTarget target_begin); // "projects/library/seqan/basic/basic_alphabet_interface.h"(513)
+template <typename TValue> inline void arrayCopyForward(TValue * source_begin, TValue * source_end, TValue * target_begin); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(224)
+
+//____________________________________________________________________________
+// arrayDestruct
+
+template <typename TIterator1, typename TIterator2> inline void arrayDestruct(TIterator1 begin_, TIterator2 end_); // "projects/library/seqan/basic/basic_alphabet_interface.h"(448)
+template <typename TValue> inline void arrayDestruct(TValue * begin_, TValue * end_); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(184)
+
+//____________________________________________________________________________
+// arrayFill
+
+template <typename TIterator1, typename TIterator2, typename TValue> inline void arrayFill(TIterator1 begin_, TIterator2 end_, TValue const & value); // "projects/library/seqan/basic/basic_alphabet_interface.h"(474)
+
+//____________________________________________________________________________
+// arrayMove
+
+template <typename TTarget, typename TSource1, typename TSource2> inline void arrayMove(TSource1 source_begin, TSource2 source_end, TTarget target_begin); // "projects/library/seqan/basic/basic_alphabet_interface.h"(732)
+
+//____________________________________________________________________________
+// arrayMoveBackward
+
+template <typename TTarget, typename TSource1, typename TSource2> inline void arrayMoveBackward(TSource1 source_begin, TSource2 source_end, TTarget target_begin); // "projects/library/seqan/basic/basic_alphabet_interface.h"(694)
+template <typename TValue> inline void arrayMoveBackward(TValue * source_begin, TValue * source_end, TValue * target_begin); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(326)
+
+//____________________________________________________________________________
+// arrayMoveForward
+
+template <typename TTarget, typename TSource1, typename TSource2> inline void arrayMoveForward(TSource1 source_begin, TSource2 source_end, TTarget target_begin); // "projects/library/seqan/basic/basic_alphabet_interface.h"(644)
+template <typename TValue> inline void arrayMoveForward(TValue * source_begin, TValue * source_end, TValue * target_begin); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(292)
+
+//____________________________________________________________________________
+// assign
+
+template <typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TSourceSpec> inline void assign(SimpleType<TTargetValue, TTargetSpec> & target, SimpleType<TSourceValue, TSourceSpec> & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(294)
+template <typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TSourceSpec> inline void assign(SimpleType<TTargetValue, TTargetSpec> & target, SimpleType<TSourceValue, TSourceSpec> const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(302)
+template <typename TTargetValue, typename TTargetSpec, typename TSource> inline void assign(SimpleType<TTargetValue, TTargetSpec> & target, TSource & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(313)
+template <typename TTargetValue, typename TTargetSpec, typename TSource> inline void assign(SimpleType<TTargetValue, TTargetSpec> & target, TSource const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(321)
+template <typename TTargetValue, typename TTargetSpec, typename TSourceSpec> inline void assign(SimpleType<TTargetValue, TTargetSpec> & target, Proxy<TSourceSpec> & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(334)
+template <typename TTargetValue, typename TTargetSpec, typename TSourceSpec> inline void assign(SimpleType<TTargetValue, TTargetSpec> & target, Proxy<TSourceSpec> const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(343)
+template <typename TValue, typename TSpec> inline void assign(int & c_target, SimpleType<TValue, TSpec> & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(358)
+template <typename TValue, typename TSpec> inline void assign(int & c_target, SimpleType<TValue, TSpec> const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(366)
+template <typename TValue, typename TSpec> inline void assign(unsigned int & c_target, SimpleType<TValue, TSpec> & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(376)
+template <typename TValue, typename TSpec> inline void assign(unsigned int & c_target, SimpleType<TValue, TSpec> const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(384)
+template <typename TValue, typename TSpec> inline void assign(short & c_target, SimpleType<TValue, TSpec> & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(394)
+template <typename TValue, typename TSpec> inline void assign(short & c_target, SimpleType<TValue, TSpec> const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(402)
+template <typename TValue, typename TSpec> inline void assign(unsigned short & c_target, SimpleType<TValue, TSpec> & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(412)
+template <typename TValue, typename TSpec> inline void assign(unsigned short & c_target, SimpleType<TValue, TSpec> const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(420)
+template <typename TValue, typename TSpec> inline void assign(char & c_target, SimpleType<TValue, TSpec> & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(430)
+template <typename TValue, typename TSpec> inline void assign(char & c_target, SimpleType<TValue, TSpec> const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(438)
+template <typename TValue, typename TSpec> inline void assign(signed char & c_target, SimpleType<TValue, TSpec> & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(448)
+template <typename TValue, typename TSpec> inline void assign(signed char & c_target, SimpleType<TValue, TSpec> const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(456)
+template <typename TValue, typename TSpec> inline void assign(unsigned char & c_target, SimpleType<TValue, TSpec> & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(466)
+template <typename TValue, typename TSpec> inline void assign(unsigned char & c_target, SimpleType<TValue, TSpec> const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(474)
+inline void assign(Ascii & c_target, Dna const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1096)
+inline void assign(Ascii & c_target, Dna5 const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1104)
+inline void assign(Ascii & c_target, Iupac const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1111)
+inline void assign(Ascii & c_target, AminoAcid const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1118)
+inline void assign(Dna & target, Byte c_source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1129)
+inline void assign(Dna & target, Ascii c_source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1138)
+inline void assign(Dna & target, Unicode c_source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1147)
+inline void assign(Dna & target, Dna5 const & c_source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1156)
+inline void assign(Dna & target, Iupac const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1165)
+inline void assign(Dna5 & target, Byte c_source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1176)
+inline void assign(Dna5 & target, Ascii c_source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1185)
+inline void assign(Dna5 & target, Unicode c_source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1194)
+inline void assign(Dna5 & target, Iupac const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1203)
+inline void assign(Dna5 & target, Dna const & c_source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1213)
+inline void assign(Iupac & target, Byte c_source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1224)
+inline void assign(Iupac & target, Ascii c_source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1233)
+inline void assign(Iupac & target, Unicode c_source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1242)
+inline void assign(Iupac & target, Dna const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1249)
+inline void assign(Iupac & target, Dna5 const & source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1256)
+inline void assign(AminoAcid & target, Byte c_source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1267)
+inline void assign(AminoAcid & target, Ascii c_source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1276)
+inline void assign(AminoAcid & target, Unicode c_source); // "projects/library/seqan/basic/basic_alphabet_simple.h"(1285)
+template <typename TTarget, typename TSource> inline void assign(TTarget & target, TSource & source); // "projects/library/seqan/basic/basic_transport.h"(52)
+template <typename TTarget, typename TSource> inline void assign(TTarget & target, TSource const & source); // "projects/library/seqan/basic/basic_transport.h"(60)
+template <typename TTargetSpec, typename TSource> inline void assign(Proxy<TTargetSpec> & target, TSource & source); // "projects/library/seqan/basic/basic_transport.h"(73)
+template <typename TTargetSpec, typename TSource> inline void assign(Proxy<TTargetSpec> & target, TSource const & source); // "projects/library/seqan/basic/basic_transport.h"(82)
+template <typename TTargetContainer, typename TSource> inline void assign(Iter<TTargetContainer, PositionIterator> & target, TSource const & source); // "projects/library/seqan/basic/basic_iterator_position.h"(440)
+template <typename TValue> inline void assign(Holder<TValue, Tristate> & target_, Holder<TValue, Tristate> const & source_); // "projects/library/seqan/basic/basic_holder.h"(554)
+template <typename TValue> inline void assign(Holder<TValue, Simple> & target_, Holder<TValue, Simple> const & source_); // "projects/library/seqan/basic/basic_holder.h"(774)
+template <typename TValue> inline void assign(Holder<TValue, Tristate2> & target_, Holder<TValue, Tristate2> const & source_); // "projects/library/seqan/basic/basic_holder.h"(1091)
+template <typename TTargetContainer, typename TIterator, typename TSpec, typename TSource> inline void assign(Iter<TTargetContainer, AdaptorIterator<TIterator, TSpec> > & target, TSource const & source); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(514)
+template <typename TTargetContainer, typename TSource> inline void assign(Iter<TTargetContainer, StdIteratorAdaptor> & target, TSource const & source); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(427)
+
+//____________________________________________________________________________
+// assignHost
+
+template <typename T, typename THost> inline void assignHost(T & me, THost & host_); // "projects/library/seqan/basic/basic_host.h"(135)
+template <typename T, typename THost> inline void assignHost(T & me, THost const & host_); // "projects/library/seqan/basic/basic_host.h"(143)
+
+//____________________________________________________________________________
+// assignValue
+
+template <typename TContainer, typename TValue> inline void assignValue(Iter<TContainer, PositionIterator> & me, TValue _value); // "projects/library/seqan/basic/basic_iterator_position.h"(184)
+template <typename TContainer, typename TValue> inline void assignValue(Iter<TContainer, PositionIterator> const & me, TValue _value); // "projects/library/seqan/basic/basic_iterator_position.h"(192)
+template <typename TValue, typename TSource> inline void assignValue(Holder<TValue, Tristate> & me, TSource const & value_); // "projects/library/seqan/basic/basic_holder.h"(512)
+template <typename TValue, typename TSource> inline void assignValue(Holder<TValue, Simple> & me, TSource const & value_); // "projects/library/seqan/basic/basic_holder.h"(752)
+template <typename TValue, typename TSource> inline void assignValue(Holder<TValue, Tristate2> & me, TSource const & value_); // "projects/library/seqan/basic/basic_holder.h"(1049)
+template <typename T, typename TValue> inline void assignValue(T & me, TValue const & _value); // "projects/library/seqan/basic/basic_iterator.h"(258)
+template <typename T, typename TValue> inline void assignValue(T const & me, TValue const & _value); // "projects/library/seqan/basic/basic_iterator.h"(268)
+template <typename TContainer, typename TIterator, typename TSpec, typename TValue> inline void assignValue(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me, TValue const & _value); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(288)
+template <typename TContainer, typename TIterator, typename TSpec, typename TValue> inline void assignValue(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me, TValue const & _value); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(296)
+template <typename TContainer, typename TValue> inline void assignValue(Iter<TContainer, StdIteratorAdaptor> & me, TValue & val); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(165)
+template <typename TContainer, typename TValue> inline void assignValue(Iter<TContainer, StdIteratorAdaptor> & me, TValue const & val); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(172)
+
+//____________________________________________________________________________
+// assignValueAt
+
+template <typename TObject, typename TPos, typename TSource> inline TSource & assignValueAt(TObject &me, TPos k, TSource &source); // "projects/library/seqan/basic/basic_aggregates.h"(442)
+template <typename TObject, typename TPos, typename TSource> inline TSource const & assignValueAt(TObject &me, TPos k, TSource const &source); // "projects/library/seqan/basic/basic_aggregates.h"(449)
+template <typename TTT, unsigned _size, typename SSS, typename TPos> inline SSS const assignValueAt(Tuple<TTT, _size, void> &me, TPos k, SSS const source); // "projects/library/seqan/basic/basic_aggregates.h"(455)
+template <typename TTT, unsigned _size, typename SSS, typename TPos> inline SSS const assignValueAt(Tuple<TTT, _size, Compressed> &me, TPos k, SSS const source); // "projects/library/seqan/basic/basic_aggregates.h"(460)
+template <typename TTT, typename SSS, typename SSSpec, unsigned _size, typename TPos> inline SimpleType<SSS, SSSpec> const & assignValueAt(Tuple<TTT, _size, Compressed> &me, TPos k, SimpleType<SSS, SSSpec> const &source); // "projects/library/seqan/basic/basic_aggregates.h"(468)
+
+//____________________________________________________________________________
+// assignValueI1
+
+template <typename T1, typename T2, typename TCompression, typename T> inline void assignValueI1(Pair<T1, T2, TCompression> &pair, T const &_i); // "projects/library/seqan/basic/basic_aggregates.h"(613)
+template <typename T1, typename T2, unsigned valueSizeI1, typename T> inline void assignValueI1(Pair<T1, T2, CutCompressed<valueSizeI1> > &pair, T const &_i); // "projects/library/seqan/basic/basic_aggregates.h"(624)
+template <typename T1, typename T2, typename T3, typename TCompression, typename T> inline T const assignValueI1(Triple<T1, T2, T3, TCompression> &triple, T const &_i); // "projects/library/seqan/basic/basic_aggregates.h"(638)
+
+//____________________________________________________________________________
+// assignValueI2
+
+template <typename T1, typename T2, typename TCompression, typename T> inline void assignValueI2(Pair<T1, T2, TCompression> &pair, T const &_i); // "projects/library/seqan/basic/basic_aggregates.h"(618)
+template <typename T1, typename T2, unsigned valueSizeI1, typename T> inline void assignValueI2(Pair<T1, T2, CutCompressed<valueSizeI1> > &pair, T const &_i); // "projects/library/seqan/basic/basic_aggregates.h"(631)
+template <typename T1, typename T2, typename T3, typename TCompression, typename T> inline T const assignValueI2(Triple<T1, T2, T3, TCompression> &triple, T const &_i); // "projects/library/seqan/basic/basic_aggregates.h"(643)
+
+//____________________________________________________________________________
+// assignValueI3
+
+template <typename T1, typename T2, typename T3, typename TCompression, typename T> inline T const assignValueI3(Triple<T1, T2, T3, TCompression> &triple, T const &_i); // "projects/library/seqan/basic/basic_aggregates.h"(648)
+
+//____________________________________________________________________________
+// atBegin
+
+template <typename T, typename TContainer> inline bool atBegin(T const & it, TContainer const & cont); // "projects/library/seqan/basic/basic_iterator.h"(394)
+template <typename T> inline bool atBegin(T const & it); // "projects/library/seqan/basic/basic_iterator.h"(404)
+
+//____________________________________________________________________________
+// atEnd
+
+template <typename T, typename TContainer> inline bool atEnd(T & it, TContainer const & cont); // "projects/library/seqan/basic/basic_iterator.h"(435)
+template <typename T, typename TContainer> inline bool atEnd(T const & it, TContainer const & cont); // "projects/library/seqan/basic/basic_iterator.h"(443)
+template <typename T> inline bool atEnd(T & it); // "projects/library/seqan/basic/basic_iterator.h"(452)
+template <typename T> inline bool atEnd(T const & it); // "projects/library/seqan/basic/basic_iterator.h"(459)
+template <typename TContainer, typename TIterator, typename TSpec> inline bool atEnd(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(501)
+
+//____________________________________________________________________________
+// atNil
+
+template <typename TIterator> inline bool atNil(TIterator & me); // "projects/library/seqan/basic/basic_iterator.h"(714)
+template <typename TIterator> inline bool atNil(TIterator * me); // "projects/library/seqan/basic/basic_iterator.h"(723)
+
+//____________________________________________________________________________
+// call_allocate
+
+template <typename TMe, typename TValue, typename TSize> inline void call_allocate(TMe & me, TValue * & data, TSize const count); // "projects/library/seqan/basic/basic_allocator_to_std.h"(33)
+
+//____________________________________________________________________________
+// call_deallocate
+
+template <typename TMe, typename TValue, typename TSize> inline void call_deallocate(TMe & me, TValue * data, TSize const count); // "projects/library/seqan/basic/basic_allocator_to_std.h"(38)
+
+//____________________________________________________________________________
+// clear
+
+template <size_t SIZE, typename TParentAllocator> void clear(Allocator<SinglePool<SIZE, TParentAllocator> > & me); // "projects/library/seqan/basic/basic_allocator_singlepool.h"(146)
+template <typename TValue, typename TParentAllocator> void clear(Allocator<SinglePool2<TValue, TParentAllocator> > & me); // "projects/library/seqan/basic/basic_allocator_singlepool.h"(266)
+template <typename TValue> inline void clear(Holder<TValue, Tristate> & me); // "projects/library/seqan/basic/basic_holder.h"(314)
+template <typename TValue> inline void clear(Holder<TValue, Simple> & me); // "projects/library/seqan/basic/basic_holder.h"(685)
+template <typename TValue> inline void clear(Holder<TValue, Tristate2> & me); // "projects/library/seqan/basic/basic_holder.h"(901)
+template <typename TParentAllocator, unsigned int BLOCKING_LIMIT> void clear(Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > & me); // "projects/library/seqan/basic/basic_allocator_multipool.h"(125)
+template <typename TParentAllocator> void clear(Allocator<SimpleAlloc<TParentAllocator> > & me); // "projects/library/seqan/basic/basic_allocator_simple.h"(126)
+//template <size_t SIZE, size_t MAX_COUNT, typename TParentAllocator> void clear(Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > & me); // "projects/library/seqan/basic/basic_allocator_chunkpool.h"(157)
+template <typename TValue, size_t MAX_COUNT, typename TParentAllocator> void clear(Allocator<ChunkPool2<TValue, MAX_COUNT, TParentAllocator> > & me); // "projects/library/seqan/basic/basic_allocator_chunkpool.h"(289)
+template <typename TTT, unsigned _size, typename TCompression> inline void clear(Tuple<TTT, _size, TCompression> &me); // "projects/library/seqan/basic/basic_aggregates.h"(479)
+template <typename TTT, unsigned _size> inline void clear(Tuple<TTT, _size, Compressed> &me); // "projects/library/seqan/basic/basic_aggregates.h"(483)
+
+//____________________________________________________________________________
+// clearHost
+
+template <typename T> inline void clearHost(T & me); // "projects/library/seqan/basic/basic_host.h"(59)
+
+//____________________________________________________________________________
+// container
+
+template <typename T> inline typename Container<T>::Type container(T me); // "projects/library/seqan/basic/basic_iterator.h"(328)
+
+//____________________________________________________________________________
+// convert
+
+template <typename TTarget, typename TSource> inline typename Convert<TTarget, TSource>::Type convert(TSource const & source); // "projects/library/seqan/basic/basic_converter.h"(110)
+
+//____________________________________________________________________________
+// convertImpl
+
+template <typename TTarget, typename T, typename TSourceValue, typename TSourceSpec> inline typename _RemoveConst<TTarget>::Type convertImpl(Convert<TTarget, T> const, SimpleType<TSourceValue, TSourceSpec> const & source_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(247)
+template <typename TTarget, typename T, typename TSpec> inline typename Convert<TTarget, Proxy<TSpec> >::Type convertImpl(Convert<TTarget, T> const, Proxy<TSpec> & source); // "projects/library/seqan/basic/basic_proxy.h"(264)
+template <typename TTarget, typename T, typename TSpec> inline typename Convert<TTarget, Proxy<TSpec> const>::Type convertImpl(Convert<TTarget, T> const, Proxy<TSpec> const & source); // "projects/library/seqan/basic/basic_proxy.h"(271)
+template <typename TTarget, typename T, typename TSource> inline typename Convert<TTarget, TSource>::Type convertImpl(Convert<TTarget, T> const, TSource & source); // "projects/library/seqan/basic/basic_converter.h"(78)
+template <typename TTarget, typename T, typename TSource> inline typename Convert<TTarget, TSource const>::Type convertImpl(Convert<TTarget, T> const, TSource const & source); // "projects/library/seqan/basic/basic_converter.h"(85)
+
+//____________________________________________________________________________
+// create
+
+template <typename TValue> inline void create(Holder<TValue, Tristate> & me); // "projects/library/seqan/basic/basic_holder.h"(361)
+template <typename TValue> inline void create(Holder<TValue, Tristate> & me, typename _Parameter<TValue const>::Type value_); // "projects/library/seqan/basic/basic_holder.h"(395)
+template <typename TValue> inline void create(Holder<TValue, Simple> & me); // "projects/library/seqan/basic/basic_holder.h"(694)
+template <typename TValue> inline void create(Holder<TValue, Simple> & me, TValue const & value_); // "projects/library/seqan/basic/basic_holder.h"(704)
+template <typename TValue> inline void create(Holder<TValue, Tristate2> & me); // "projects/library/seqan/basic/basic_holder.h"(932)
+template <typename TValue> inline void create(Holder<TValue, Tristate2> & me, TValue const & value_); // "projects/library/seqan/basic/basic_holder.h"(966)
+
+//____________________________________________________________________________
+// createHost
+
+template <typename T> inline void createHost(T & me); // "projects/library/seqan/basic/basic_host.h"(69)
+template <typename T, typename THost> inline void createHost(T & me, THost & host_); // "projects/library/seqan/basic/basic_host.h"(80)
+template <typename T, typename THost> inline void createHost(T & me, THost const & host_); // "projects/library/seqan/basic/basic_host.h"(88)
+
+//____________________________________________________________________________
+// deallocate
+
+template <size_t SIZE, typename TParentAllocator, typename TValue, typename TSize, typename TUsage> inline void deallocate(Allocator<SinglePool<SIZE, TParentAllocator> > & me, TValue * data, TSize count, Tag<TUsage> const tag_); // "projects/library/seqan/basic/basic_allocator_singlepool.h"(202)
+template <typename TValue, typename TParentAllocator, typename TValue2, typename TSize, typename TUsage> inline void deallocate(Allocator<SinglePool2<TValue, TParentAllocator> > & me, TValue2 * data, TSize count, Tag<TUsage> const tag_); // "projects/library/seqan/basic/basic_allocator_singlepool.h"(290)
+template <typename TParentAllocator, unsigned int BLOCKING_LIMIT, typename TValue, typename TSize, typename TUsage> inline void deallocate(Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > & me, TValue * data, TSize count, Tag<TUsage> const tag_); // "projects/library/seqan/basic/basic_allocator_multipool.h"(207)
+template <typename TParentAllocator, typename TValue, typename TSize, typename TUsage> inline void deallocate(Allocator<SimpleAlloc<TParentAllocator> > & me, TValue * data, TSize, Tag<TUsage> const); // "projects/library/seqan/basic/basic_allocator_simple.h"(181)
+template <typename T, typename TValue, typename TSize> inline void deallocate(T const & me, TValue * data, TSize const count); // "projects/library/seqan/basic/basic_allocator_interface.h"(198)
+template <typename T, typename TValue, typename TSize> inline void deallocate(T & me, TValue * data, TSize const count); // "projects/library/seqan/basic/basic_allocator_interface.h"(206)
+template <typename T, typename TValue, typename TSize, typename TUsage> inline void deallocate(T const & , TValue * data, TSize count, Tag<TUsage> const); // "projects/library/seqan/basic/basic_allocator_interface.h"(216)
+template <typename T, typename TValue, typename TSize, typename TUsage> inline void deallocate(T & , TValue * data, TSize count, Tag<TUsage> const); // "projects/library/seqan/basic/basic_allocator_interface.h"(227)
+//template <size_t SIZE, size_t MAX_COUNT, typename TParentAllocator, typename TValue, typename TSize, typename TUsage> inline void deallocate(Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > & me, TValue * data, TSize count, Tag<TUsage> const tag_); // "projects/library/seqan/basic/basic_allocator_chunkpool.h"(222)
+template <typename TValue, size_t MAX_COUNT, typename TParentAllocator, typename TValue2, typename TSize, typename TUsage> inline void deallocate(Allocator<ChunkPool2<TValue, MAX_COUNT, TParentAllocator> > & me, TValue2 * data, TSize count, Tag<TUsage> const tag_); // "projects/library/seqan/basic/basic_allocator_chunkpool.h"(313)
+
+//____________________________________________________________________________
+// dependent
+
+template <typename TValue> inline bool dependent(Holder<TValue, Tristate> const & me); // "projects/library/seqan/basic/basic_holder.h"(300)
+template <typename TValue> inline bool dependent(Holder<TValue, Simple> const & me); // "projects/library/seqan/basic/basic_holder.h"(675)
+template <typename TValue> inline bool dependent(Holder<TValue, Tristate2> const & me); // "projects/library/seqan/basic/basic_holder.h"(887)
+
+//____________________________________________________________________________
+// dependentHost
+
+template <typename T> inline bool dependentHost(T const & me); // "projects/library/seqan/basic/basic_host.h"(49)
+
+//____________________________________________________________________________
+// detach
+
+template <typename TValue> inline void detach(Holder<TValue, Tristate> & me); // "projects/library/seqan/basic/basic_holder.h"(430)
+template <typename TValue> inline void detach(Holder<TValue, Simple> & me); // "projects/library/seqan/basic/basic_holder.h"(714)
+template <typename TValue> inline void detach(Holder<TValue, Tristate2> & me); // "projects/library/seqan/basic/basic_holder.h"(987)
+
+//____________________________________________________________________________
+// difference
+
+template <typename TIterator> inline typename Difference<TIterator>::Type difference( TIterator const & begin, TIterator const & end); // "projects/library/seqan/basic/basic_iterator.h"(657)
+
+//____________________________________________________________________________
+// empty
+
+template <typename TValue> inline bool empty(Holder<TValue, Tristate> const & me); // "projects/library/seqan/basic/basic_holder.h"(288)
+template <typename TValue> inline bool empty(Holder<TValue, Simple> const & me); // "projects/library/seqan/basic/basic_holder.h"(665)
+template <typename TValue> inline bool empty(Holder<TValue, Tristate2> const & me); // "projects/library/seqan/basic/basic_holder.h"(875)
+
+//____________________________________________________________________________
+// emptyHost
+
+template <typename T> inline bool emptyHost(T const & me); // "projects/library/seqan/basic/basic_host.h"(39)
+
+//____________________________________________________________________________
+// gapValue
+
+template <typename T> inline T const & gapValue(); // "projects/library/seqan/basic/basic_alphabet_interface2.h"(71)
+
+//____________________________________________________________________________
+// gapValueImpl
+
+inline char const & gapValueImpl(char *); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(400)
+inline char const & gapValueImpl(char const *); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(407)
+template <typename T> inline T const & gapValueImpl(T *); // "projects/library/seqan/basic/basic_alphabet_interface2.h"(48)
+
+//____________________________________________________________________________
+// getValue
+
+template <typename TSpec> typename GetValue<Proxy<TSpec> >::Type getValue(Proxy<TSpec> & me); // "projects/library/seqan/basic/basic_proxy.h"(235)
+template <typename TSpec> typename GetValue<Proxy<TSpec> const>::Type getValue(Proxy<TSpec> const & me); // "projects/library/seqan/basic/basic_proxy.h"(241)
+template <typename T> inline typename GetValue<T>::Type getValue(T & me); // "projects/library/seqan/basic/basic_iterator.h"(210)
+template <typename T> inline typename GetValue<T const>::Type getValue(T const & me); // "projects/library/seqan/basic/basic_iterator.h"(217)
+template <typename T> inline T & getValue(T * me); // "projects/library/seqan/basic/basic_iterator.h"(225)
+
+//____________________________________________________________________________
+// getValueI1
+
+template <typename T1, typename T2, typename TCompression> inline T1 getValueI1(Pair<T1, T2, TCompression> const &pair); // "projects/library/seqan/basic/basic_aggregates.h"(572)
+template <typename T1, typename T2, unsigned valueSizeI1> inline T1 getValueI1(Pair<T1, T2, CutCompressed<valueSizeI1> > const &pair); // "projects/library/seqan/basic/basic_aggregates.h"(582)
+template <typename T1, typename T2, typename T3, typename TCompression> inline T1 getValueI1(Triple<T1, T2, T3, TCompression> const &triple); // "projects/library/seqan/basic/basic_aggregates.h"(595)
+
+//____________________________________________________________________________
+// getValueI2
+
+template <typename T1, typename T2, typename TCompression> inline T2 getValueI2(Pair<T1, T2, TCompression> const &pair); // "projects/library/seqan/basic/basic_aggregates.h"(577)
+template <typename T1, typename T2, unsigned valueSizeI1> inline T2 getValueI2(Pair<T1, T2, CutCompressed<valueSizeI1> > const &pair); // "projects/library/seqan/basic/basic_aggregates.h"(588)
+template <typename T1, typename T2, typename T3, typename TCompression> inline T2 getValueI2(Triple<T1, T2, T3, TCompression> const &triple); // "projects/library/seqan/basic/basic_aggregates.h"(600)
+
+//____________________________________________________________________________
+// getValueI3
+
+template <typename T1, typename T2, typename T3, typename TCompression> inline T3 getValueI3(Triple<T1, T2, T3, TCompression> const &triple); // "projects/library/seqan/basic/basic_aggregates.h"(605)
+
+//____________________________________________________________________________
+// goBegin
+
+template <typename TIterator, typename TContainer> inline void goBegin(TIterator & it, TContainer & container); // "projects/library/seqan/basic/basic_iterator.h"(488)
+template <typename TIterator> inline void goBegin(TIterator & it); // "projects/library/seqan/basic/basic_iterator.h"(506)
+
+//____________________________________________________________________________
+// goEnd
+
+template <typename TIterator, typename TContainer> inline void goEnd(TIterator & it, TContainer & container); // "projects/library/seqan/basic/basic_iterator.h"(536)
+template <typename TIterator, typename TContainer> inline void goEnd(TIterator & it, TContainer const & container); // "projects/library/seqan/basic/basic_iterator.h"(544)
+template <typename TIterator> inline void goEnd(TIterator & it); // "projects/library/seqan/basic/basic_iterator.h"(552)
+
+//____________________________________________________________________________
+// goFurther
+
+template <typename TIterator, typename TDiff> inline void goFurther(TIterator & it, TDiff steps); // "projects/library/seqan/basic/basic_iterator.h"(602)
+
+//____________________________________________________________________________
+// goNext
+
+template <typename TContainer> inline void goNext(Iter<TContainer, PositionIterator> & me); // "projects/library/seqan/basic/basic_iterator_position.h"(295)
+template <typename TIterator> inline void goNext(TIterator & it); // "projects/library/seqan/basic/basic_iterator.h"(576)
+template <typename TContainer, typename TIterator, typename TSpec> inline void goNext(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(355)
+template <typename TContainer> inline void goNext(Iter<TContainer, StdIteratorAdaptor> & me); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(280)
+
+//____________________________________________________________________________
+// goNil
+
+template <typename TIterator> inline void goNil(TIterator & me); // "projects/library/seqan/basic/basic_iterator.h"(681)
+template <typename TIterator> inline void goNil(TIterator * & me); // "projects/library/seqan/basic/basic_iterator.h"(689)
+
+//____________________________________________________________________________
+// goPrevious
+
+template <typename TContainer> inline void goPrevious(Iter<TContainer, PositionIterator> & me); // "projects/library/seqan/basic/basic_iterator_position.h"(307)
+template <typename TIterator> inline void goPrevious(TIterator & it); // "projects/library/seqan/basic/basic_iterator.h"(626)
+template <typename TContainer, typename TIterator, typename TSpec> inline void goPrevious(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(367)
+template <typename TContainer> inline void goPrevious(Iter<TContainer, StdIteratorAdaptor> & me); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(292)
+
+//____________________________________________________________________________
+// host
+
+template <typename T> inline typename Host<T>::Type & host(T & me); // "projects/library/seqan/basic/basic_host.h"(117)
+template <typename T> inline typename Host<T const>::Type & host(T const & me); // "projects/library/seqan/basic/basic_host.h"(124)
+
+//____________________________________________________________________________
+// hostIterator
+
+template <typename TContainer> inline typename StdContainerIterator<TContainer>::Type & hostIterator(Iter<TContainer, StdIteratorAdaptor> & me); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(129)
+template <typename TContainer> inline typename StdContainerIterator<TContainer>::Type const & hostIterator(Iter<TContainer, StdIteratorAdaptor> const & me); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(135)
+
+//____________________________________________________________________________
+// infimumValue
+
+template <typename T> inline T const & infimumValue(); // "projects/library/seqan/basic/basic_alphabet_interface2.h"(169)
+
+//____________________________________________________________________________
+// infimumValueImpl
+
+template <typename T> inline T const & infimumValueImpl(T *); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(427)
+inline float const & infimumValueImpl(float *); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(666)
+inline double const & infimumValueImpl(double *); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(693)
+inline long double const & infimumValueImpl(long double *); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(720)
+
+//____________________________________________________________________________
+// length
+
+template <typename TTT, unsigned _size, typename TCompression> inline unsigned length(Tuple<TTT, _size, TCompression> const &); // "projects/library/seqan/basic/basic_aggregates.h"(428)
+
+//____________________________________________________________________________
+// lexLess
+
+template <typename TTT, typename TSpec> inline bool lexLess(SimpleType<TTT, TSpec> const &Left, SimpleType<TTT, TSpec> const &Right); // "projects/library/seqan/basic/basic_alphabet_simple.h"(948)
+template <typename TTT> inline bool lexLess(const TTT& Left, const TTT& Right); // "projects/library/seqan/basic/basic_compare.h"(52)
+
+//____________________________________________________________________________
+// log2
+
+// projects/library/seqan/basic/basic_definition.h(322)
+//template <typename TTT> inline unsigned int log2(TTT v);
+
+//____________________________________________________________________________
+// memset
+
+template <unsigned SIZE> finline void memset(void* ptr, unsigned char c); // "projects/library/seqan/basic/basic_metaprogramming.h"(241)
+template <unsigned SIZE, unsigned char c> finline void memset(void* ptr); // "projects/library/seqan/basic/basic_metaprogramming.h"(287)
+
+//____________________________________________________________________________
+// move
+
+template <typename TTarget, typename TSource> inline void move(TTarget & target, TSource & source); // "projects/library/seqan/basic/basic_transport.h"(108)
+template <typename TTarget, typename TSource> inline void move(TTarget const & target, TSource & source); // "projects/library/seqan/basic/basic_transport.h"(116)
+template <typename TTarget, typename TSource> inline void move(TTarget & target, TSource const & source); // "projects/library/seqan/basic/basic_transport.h"(124)
+template <typename TTarget, typename TSource> inline void move(TTarget const & target, TSource const & source); // "projects/library/seqan/basic/basic_transport.h"(132)
+
+//____________________________________________________________________________
+// moveHost
+
+template <typename T, typename THost> inline void moveHost(T & me, THost & host_); // "projects/library/seqan/basic/basic_host.h"(153)
+template <typename T, typename THost> inline void moveHost(T & me, THost const & host_); // "projects/library/seqan/basic/basic_host.h"(161)
+
+//____________________________________________________________________________
+// moveValue
+
+template <typename TContainer, typename TValue> inline void moveValue(Iter<TContainer, PositionIterator> & me, TValue _value); // "projects/library/seqan/basic/basic_iterator_position.h"(205)
+template <typename TContainer, typename TValue> inline void moveValue(Iter<TContainer, PositionIterator> const & me, TValue _value); // "projects/library/seqan/basic/basic_iterator_position.h"(213)
+template <typename TValue, typename TSource> inline void moveValue(Holder<TValue, Tristate> & me, TSource const & value_); // "projects/library/seqan/basic/basic_holder.h"(533)
+template <typename TValue, typename TSource> inline void moveValue(Holder<TValue, Simple> & me, TSource const & value_); // "projects/library/seqan/basic/basic_holder.h"(763)
+template <typename TValue, typename TSource> inline void moveValue(Holder<TValue, Tristate2> & me, TSource const & value_); // "projects/library/seqan/basic/basic_holder.h"(1070)
+template <typename T, typename TValue> inline void moveValue(T & me, TValue const & _value); // "projects/library/seqan/basic/basic_iterator.h"(297)
+template <typename T, typename TValue> inline void moveValue(T const & me, TValue const & _value); // "projects/library/seqan/basic/basic_iterator.h"(306)
+template <typename TContainer, typename TIterator, typename TSpec, typename TValue> inline void moveValue(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me, TValue const & _value); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(309)
+template <typename TContainer, typename TIterator, typename TSpec, typename TValue> inline void moveValue(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me, TValue const & _value); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(317)
+template <typename TContainer, typename TValue> inline void moveValue(Iter<TContainer, StdIteratorAdaptor> & me, TValue & val); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(184)
+template <typename TContainer, typename TValue> inline void moveValue(Iter<TContainer, StdIteratorAdaptor> & me, TValue const & val); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(191)
+
+//____________________________________________________________________________
+// nukeCopies
+
+template <typename TValue> inline void nukeCopies(TValue* &); // "projects/library/seqan/basic/basic_volatile_ptr.h"(152)
+template <typename TValue> inline void nukeCopies(VolatilePtr<TValue> &ptr); // "projects/library/seqan/basic/basic_volatile_ptr.h"(155)
+
+//____________________________________________________________________________
+// operator!=
+
+template <typename TValue, typename TSpec, typename TRight> inline bool operator!= (SimpleType<TValue, TSpec> const & left_, TRight const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(594)
+template <typename TLeft, typename TValue, typename TSpec> inline bool operator!= (TLeft const & left_, SimpleType<TValue, TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(605)
+template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec> inline bool operator!= (SimpleType<TLeftValue, TLeftSpec> const & left_, SimpleType<TRightValue, TRightSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(616)
+template <typename TValue, typename TSpec> inline bool operator!= (SimpleType<TValue, TSpec> const & left_, SimpleType<TValue, TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(628)
+template <typename TSpec, typename TValue, typename TSpec2> inline bool operator!= (Proxy<TSpec> const & left_, SimpleType<TValue, TSpec2> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(638)
+template <typename TSpec, typename TValue, typename TSpec2> inline bool operator!= (SimpleType<TValue, TSpec2> const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(649)
+template <typename TContainer> inline bool operator!= (Iter<TContainer, PositionIterator> const & left, Iter<TContainer, PositionIterator> const & right); // "projects/library/seqan/basic/basic_iterator_position.h"(239)
+template <typename TSpec, typename TRight> inline bool operator!= (Proxy<TSpec> const & left_, TRight const & right_); // "projects/library/seqan/basic/basic_proxy.h"(328)
+template <typename TLeft, typename TSpec> inline bool operator!= (TLeft const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(339)
+template <typename TLeftSpec, typename TRightSpec> inline bool operator!= (Proxy<TLeftSpec> const & left_, Proxy<TRightSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(350)
+template <typename TSpec> inline bool operator!= (Proxy<TSpec> const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(362)
+template <typename TContainer, typename TIterator, typename TSpec> inline bool operator!= (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & left, Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & right); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(343)
+template <typename TTT, unsigned _sizeL, unsigned _sizeR> inline bool operator!=(Tuple<TTT, _sizeL, Compressed> const &_left, Tuple<TTT, _sizeR, Compressed> const &_right); // "projects/library/seqan/basic/basic_aggregates.h"(503)
+template <typename L1, typename L2, typename LCompression, typename R1, typename R2, typename RCompression> inline bool operator!=(Pair<L1, L2, LCompression> const &_left, Pair<R1, R2, RCompression> const &_right); // "projects/library/seqan/basic/basic_aggregates.h"(660)
+template <typename L1, typename L2, unsigned LSizeI1, typename R1, typename R2, unsigned RSizeI1> inline bool operator!=(Pair<L1, L2, CutCompressed<LSizeI1> > const &_left, Pair<R1, R2, CutCompressed<RSizeI1> > const &_right); // "projects/library/seqan/basic/basic_aggregates.h"(669)
+template <typename L1, typename L2, typename L3, typename LCompression, typename R1, typename R2, typename R3, typename RCompression> inline bool operator!=(Triple<L1, L2, L3, LCompression> const &_left, Triple<R1, R2, R3, RCompression> const &_right); // "projects/library/seqan/basic/basic_aggregates.h"(683)
+template <typename TContainer> inline bool operator!= (Iter<TContainer, StdIteratorAdaptor> const & left, Iter<TContainer, StdIteratorAdaptor> const & right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(216)
+
+//____________________________________________________________________________
+// operator*
+
+template <typename TContainer, typename TSpec> inline typename Reference<Iter<TContainer, TSpec> >::Type operator* (Iter<TContainer, TSpec> & me); // "projects/library/seqan/basic/basic_iterator_base.h"(143)
+template <typename TContainer, typename TSpec> inline typename Reference<Iter<TContainer, TSpec> const>::Type operator* (Iter<TContainer, TSpec> const & me); // "projects/library/seqan/basic/basic_iterator_base.h"(150)
+
+//____________________________________________________________________________
+// operator+
+
+template <typename TContainer, typename TIntegral> inline Iter<TContainer, PositionIterator> operator+ (Iter<TContainer, PositionIterator> const & left, TIntegral right); // "projects/library/seqan/basic/basic_iterator_position.h"(319)
+template <typename TContainer> inline Iter<TContainer, PositionIterator> operator+ (Iter<TContainer, PositionIterator> const & left, int right); // "projects/library/seqan/basic/basic_iterator_position.h"(328)
+template <typename TContainer, typename TIntegral> inline Iter<TContainer, PositionIterator> operator+ (TIntegral left, Iter<TContainer, PositionIterator> const & right); // "projects/library/seqan/basic/basic_iterator_position.h"(337)
+template <typename TContainer> inline Iter<TContainer, PositionIterator> operator+ (int left, Iter<TContainer, PositionIterator> const & right); // "projects/library/seqan/basic/basic_iterator_position.h"(346)
+template <typename TContainer, typename TIterator, typename TSpec, typename TIntegral> inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> > operator+ (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & left, TIntegral right); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(380)
+template <typename TContainer, typename TIterator, typename TSpec> inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> > operator+ (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & left, int right); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(389)
+template <typename TContainer, typename TIterator, typename TSpec, typename TIntegral> inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> > operator+ (TIntegral left, Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & right); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(398)
+template <typename TContainer, typename TIterator, typename TSpec> inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> > operator+ (int left, Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & right); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(407)
+template <typename TContainer, typename TIntegral> inline Iter<TContainer, StdIteratorAdaptor> operator+ (Iter<TContainer, StdIteratorAdaptor> const & left, TIntegral right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(305)
+template <typename TContainer> inline Iter<TContainer, StdIteratorAdaptor> operator+ (Iter<TContainer, StdIteratorAdaptor> const & left, int right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(314)
+template <typename TContainer, typename TIntegral> inline Iter<TContainer, StdIteratorAdaptor> operator+ (TIntegral left, Iter<TContainer, StdIteratorAdaptor> const & right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(323)
+template <typename TContainer> inline Iter<TContainer, StdIteratorAdaptor> operator+ (int left, Iter<TContainer, StdIteratorAdaptor> const & right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(332)
+
+//____________________________________________________________________________
+// operator++
+
+template <typename TValue, typename TSpec> inline SimpleType<TValue, TSpec> & operator++ (SimpleType<TValue, TSpec> & me); // "projects/library/seqan/basic/basic_alphabet_simple.h"(958)
+template <typename TValue, typename TSpec> inline SimpleType<TValue, TSpec> operator++ (SimpleType<TValue, TSpec> & me, int); // "projects/library/seqan/basic/basic_alphabet_simple.h"(966)
+template <typename TContainer, typename TSpec> inline Iter<TContainer, TSpec> const & operator++ (Iter<TContainer, TSpec> & me); // "projects/library/seqan/basic/basic_iterator_base.h"(162)
+template <typename TContainer, typename TSpec> inline Iter<TContainer, TSpec> const operator++ (Iter<TContainer, TSpec> & me, int); // "projects/library/seqan/basic/basic_iterator_base.h"(171)
+
+//____________________________________________________________________________
+// operator+=
+
+template <typename TContainer, typename TIntegral> inline Iter<TContainer, PositionIterator> & operator+= (Iter<TContainer, PositionIterator> & left, TIntegral right); // "projects/library/seqan/basic/basic_iterator_position.h"(359)
+template <typename TContainer> inline Iter<TContainer, PositionIterator> & operator+= (Iter<TContainer, PositionIterator> & left, int right); // "projects/library/seqan/basic/basic_iterator_position.h"(369)
+template <typename TContainer, typename TIterator, typename TSpec, typename TIntegral> inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & operator+= (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & left, TIntegral right); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(420)
+template <typename TContainer, typename TIterator, typename TSpec> inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & operator+= (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & left, int right); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(430)
+template <typename TContainer, typename TIntegral> inline Iter<TContainer, StdIteratorAdaptor> & operator+= (Iter<TContainer, StdIteratorAdaptor> & left, TIntegral right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(345)
+template <typename TContainer> inline Iter<TContainer, StdIteratorAdaptor> & operator+= (Iter<TContainer, StdIteratorAdaptor> & left, int right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(355)
+
+//____________________________________________________________________________
+// operator-
+
+template <typename TContainer, typename TIntegral> inline Iter<TContainer, PositionIterator> operator- (Iter<TContainer, PositionIterator> const & left, TIntegral right); // "projects/library/seqan/basic/basic_iterator_position.h"(383)
+template <typename TContainer> inline Iter<TContainer, PositionIterator> operator- (Iter<TContainer, PositionIterator> const & left, int right); // "projects/library/seqan/basic/basic_iterator_position.h"(392)
+template <typename TContainer> inline typename Difference<TContainer>::Type operator- (Iter<TContainer, PositionIterator> const & left, Iter<TContainer, PositionIterator> const & right); // "projects/library/seqan/basic/basic_iterator_position.h"(403)
+template <typename TContainer, typename TIterator, typename TSpec, typename TIntegral> inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> > operator- (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & left, TIntegral right); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(444)
+template <typename TContainer, typename TIterator, typename TSpec> inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> > operator- (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & left, int right); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(453)
+template <typename TContainer, typename TIterator, typename TSpec> inline typename Difference<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > >::Type operator- (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & left, Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & right); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(464)
+template <typename TContainer, typename TIntegral> inline Iter<TContainer, StdIteratorAdaptor> operator- (Iter<TContainer, StdIteratorAdaptor> const & left, TIntegral right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(369)
+template <typename TContainer> inline Iter<TContainer, StdIteratorAdaptor> operator- (Iter<TContainer, StdIteratorAdaptor> const & left, int right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(378)
+template <typename TContainer> inline typename Difference<Iter<TContainer, StdIteratorAdaptor> >::Type operator- (Iter<TContainer, StdIteratorAdaptor> const & left, Iter<TContainer, StdIteratorAdaptor> const & right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(389)
+
+//____________________________________________________________________________
+// operator--
+
+template <typename TValue, typename TSpec> inline SimpleType<TValue, TSpec> & operator-- (SimpleType<TValue, TSpec> & me); // "projects/library/seqan/basic/basic_alphabet_simple.h"(977)
+template <typename TValue, typename TSpec> inline SimpleType<TValue, TSpec> operator-- (SimpleType<TValue, TSpec> & me, int); // "projects/library/seqan/basic/basic_alphabet_simple.h"(985)
+template <typename TContainer, typename TSpec> inline Iter<TContainer, TSpec> const & operator-- (Iter<TContainer, TSpec> & me); // "projects/library/seqan/basic/basic_iterator_base.h"(185)
+template <typename TContainer, typename TSpec> inline Iter<TContainer, TSpec> const operator-- (Iter<TContainer, TSpec> & me, int); // "projects/library/seqan/basic/basic_iterator_base.h"(194)
+
+//____________________________________________________________________________
+// operator-=
+
+template <typename TContainer, typename TIntegral> inline Iter<TContainer, PositionIterator> & operator-= (Iter<TContainer, PositionIterator> & left, TIntegral right); // "projects/library/seqan/basic/basic_iterator_position.h"(416)
+template <typename TContainer> inline Iter<TContainer, PositionIterator> & operator-= (Iter<TContainer, PositionIterator> & left, int right); // "projects/library/seqan/basic/basic_iterator_position.h"(426)
+template <typename TContainer, typename TIterator, typename TSpec, typename TIntegral> inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & operator-= (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & left, TIntegral right); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(477)
+template <typename TContainer, typename TIterator, typename TSpec> inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & operator-= (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & left, int right); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(487)
+template <typename TContainer, typename TIntegral> inline Iter<TContainer, StdIteratorAdaptor> & operator-= (Iter<TContainer, StdIteratorAdaptor> & left, TIntegral right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(402)
+template <typename TContainer> inline Iter<TContainer, StdIteratorAdaptor> & operator-= (Iter<TContainer, StdIteratorAdaptor> & left, int right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(412)
+
+//____________________________________________________________________________
+// operator<
+
+template <typename TValue, typename TSpec, typename TRight> inline bool operator< (SimpleType<TValue, TSpec> const & left_, TRight const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(665)
+template <typename TLeft, typename TValue, typename TSpec> inline bool operator< (TLeft const & left_, SimpleType<TValue, TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(676)
+template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec> inline bool operator< (SimpleType<TLeftValue, TLeftSpec> const & left_, SimpleType<TRightValue, TRightSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(687)
+template <typename TValue, typename TSpec> inline bool operator< (SimpleType<TValue, TSpec> const & left_, SimpleType<TValue, TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(699)
+template <typename TSpec, typename TValue, typename TSpec2> inline bool operator< (Proxy<TSpec> const & left_, SimpleType<TValue, TSpec2> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(709)
+template <typename TSpec, typename TValue, typename TSpec2> inline bool operator< (SimpleType<TValue, TSpec2> const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(720)
+template <typename TContainer> inline bool operator< (Iter<TContainer, PositionIterator> const & left, Iter<TContainer, PositionIterator> const & right); // "projects/library/seqan/basic/basic_iterator_position.h"(252)
+template <typename TSpec, typename TRight> inline bool operator< (Proxy<TSpec> const & left_, TRight const & right_); // "projects/library/seqan/basic/basic_proxy.h"(376)
+template <typename TLeft, typename TSpec> inline bool operator< (TLeft const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(387)
+template <typename TLeftSpec, typename TRightSpec> inline bool operator< (Proxy<TLeftSpec> const & left_, Proxy<TRightSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(398)
+template <typename TSpec> inline bool operator< (Proxy<TSpec> const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(410)
+template <typename TTT, unsigned _sizeL, unsigned _sizeR> inline bool operator<(Tuple<TTT, _sizeL, Compressed> const &_left, Tuple<TTT, _sizeR, Compressed> const &_right); // "projects/library/seqan/basic/basic_aggregates.h"(491)
+template <typename TContainer> inline bool operator< (Iter<TContainer, StdIteratorAdaptor> const & left, Iter<TContainer, StdIteratorAdaptor> const & right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(229)
+
+//____________________________________________________________________________
+// operator<<
+
+template <typename TStream, typename TValue, typename TSpec> inline TStream & operator<< (TStream & stream, SimpleType<TValue, TSpec> const & data); // "projects/library/seqan/basic/basic_alphabet_simple.h"(262)
+template <typename TStream, typename TSpec> inline TStream & operator<< (TStream & strm, Proxy<TSpec> & proxy); // "projects/library/seqan/basic/basic_proxy.h"(591)
+template <typename TStream, typename TSpec> inline TStream & operator<< (TStream & strm, Proxy<TSpec> const & proxy); // "projects/library/seqan/basic/basic_proxy.h"(598)
+template <typename TTT1, typename TTT2, typename TCompression> std::ostream& operator<<(std::ostream &out, Pair<TTT1,TTT2,TCompression> const &p); // "projects/library/seqan/basic/basic_aggregates.h"(148)
+template <typename TTT1, typename TTT2, typename TTT3, typename TCompression> std::ostream& operator<<(std::ostream &out, Triple<TTT1,TTT2,TTT3,TCompression> const &t); // "projects/library/seqan/basic/basic_aggregates.h"(267)
+template <typename TTT, unsigned _size, typename TCompression> std::ostream& operator<<(std::ostream& out, Tuple<TTT,_size,TCompression> const &a); // "projects/library/seqan/basic/basic_aggregates.h"(548)
+
+//____________________________________________________________________________
+// operator<=
+
+template <typename TValue, typename TSpec, typename TRight> inline bool operator<= (SimpleType<TValue, TSpec> const & left_, TRight const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(736)
+template <typename TLeft, typename TValue, typename TSpec> inline bool operator<= (TLeft const & left_, SimpleType<TValue, TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(747)
+template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec> inline bool operator<= (SimpleType<TLeftValue, TLeftSpec> const & left_, SimpleType<TRightValue, TRightSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(758)
+template <typename TValue, typename TSpec> inline bool operator<= (SimpleType<TValue, TSpec> const & left_, SimpleType<TValue, TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(770)
+template <typename TSpec, typename TValue, typename TSpec2> inline bool operator<= (Proxy<TSpec> const & left_, SimpleType<TValue, TSpec2> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(780)
+template <typename TSpec, typename TValue, typename TSpec2> inline bool operator<= (SimpleType<TValue, TSpec2> const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(791)
+template <typename TContainer> inline bool operator<= (Iter<TContainer, PositionIterator> const & left, Iter<TContainer, PositionIterator> const & right); // "projects/library/seqan/basic/basic_iterator_position.h"(274)
+template <typename TSpec, typename TRight> inline bool operator<= (Proxy<TSpec> const & left_, TRight const & right_); // "projects/library/seqan/basic/basic_proxy.h"(423)
+template <typename TLeft, typename TSpec> inline bool operator<= (TLeft const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(434)
+template <typename TLeftSpec, typename TRightSpec> inline bool operator<= (Proxy<TLeftSpec> const & left_, Proxy<TRightSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(445)
+template <typename TSpec> inline bool operator<= (Proxy<TSpec> const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(457)
+template <typename TContainer> inline bool operator<= (Iter<TContainer, StdIteratorAdaptor> const & left, Iter<TContainer, StdIteratorAdaptor> const & right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(255)
+
+//____________________________________________________________________________
+// operator==
+
+template <typename TValue, typename TSpec, typename TRight> inline bool operator== (SimpleType<TValue, TSpec> const & left_, TRight const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(523)
+template <typename TLeft, typename TValue, typename TSpec> inline bool operator== (TLeft const & left_, SimpleType<TValue, TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(534)
+template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec> inline bool operator== (SimpleType<TLeftValue, TLeftSpec> const & left_, SimpleType<TRightValue, TRightSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(545)
+template <typename TValue, typename TSpec> inline bool operator== (SimpleType<TValue, TSpec> const & left_, SimpleType<TValue, TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(557)
+template <typename TSpec, typename TValue, typename TSpec2> inline bool operator== (Proxy<TSpec> const & left_, SimpleType<TValue, TSpec2> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(567)
+template <typename TSpec, typename TValue, typename TSpec2> inline bool operator== (SimpleType<TValue, TSpec2> const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(578)
+template <typename TContainer> inline bool operator== (Iter<TContainer, PositionIterator> const & left, Iter<TContainer, PositionIterator> const & right); // "projects/library/seqan/basic/basic_iterator_position.h"(226)
+template <typename TSpec, typename TRight> inline bool operator== (Proxy<TSpec> const & left_, TRight const & right_); // "projects/library/seqan/basic/basic_proxy.h"(281)
+template <typename TLeft, typename TSpec> inline bool operator== (TLeft const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(292)
+template <typename TLeftSpec, typename TRightSpec> inline bool operator== (Proxy<TLeftSpec> const & left_, Proxy<TRightSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(303)
+template <typename TSpec> inline bool operator== (Proxy<TSpec> const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(315)
+template <typename TContainer, typename TIterator, typename TSpec> inline bool operator== (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & left, Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & right); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(330)
+template <typename TTT, unsigned _sizeL, unsigned _sizeR> inline bool operator==(Tuple<TTT, _sizeL, Compressed> const &_left, Tuple<TTT, _sizeR, Compressed> const &_right); // "projects/library/seqan/basic/basic_aggregates.h"(499)
+template <typename L1, typename L2, typename LCompression, typename R1, typename R2, typename RCompression> inline bool operator==(Pair<L1, L2, LCompression> const &_left, Pair<R1, R2, RCompression> const &_right); // "projects/library/seqan/basic/basic_aggregates.h"(656)
+template <typename L1, typename L2, unsigned LSizeI1, typename R1, typename R2, unsigned RSizeI1> inline bool operator==(Pair<L1, L2, CutCompressed<LSizeI1> > const &_left, Pair<R1, R2, CutCompressed<RSizeI1> > const &_right); // "projects/library/seqan/basic/basic_aggregates.h"(665)
+template <typename L1, typename L2, typename L3, typename LCompression, typename R1, typename R2, typename R3, typename RCompression> inline bool operator==(Triple<L1, L2, L3, LCompression> const &_left, Triple<R1, R2, R3, RCompression> const &_right); // "projects/library/seqan/basic/basic_aggregates.h"(677)
+template <typename TContainer> inline bool operator== (Iter<TContainer, StdIteratorAdaptor> const & left, Iter<TContainer, StdIteratorAdaptor> const & right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(203)
+
+//____________________________________________________________________________
+// operator>
+
+template <typename TValue, typename TSpec, typename TRight> inline bool operator> (SimpleType<TValue, TSpec> const & left_, TRight const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(808)
+template <typename TLeft, typename TValue, typename TSpec> inline bool operator> (TLeft const & left_, SimpleType<TValue, TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(819)
+template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec> inline bool operator> (SimpleType<TLeftValue, TLeftSpec> const & left_, SimpleType<TRightValue, TRightSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(830)
+template <typename TValue, typename TSpec> inline bool operator> (SimpleType<TValue, TSpec> const & left_, SimpleType<TValue, TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(842)
+template <typename TSpec, typename TValue, typename TSpec2> inline bool operator> (Proxy<TSpec> const & left_, SimpleType<TValue, TSpec2> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(852)
+template <typename TSpec, typename TValue, typename TSpec2> inline bool operator> (SimpleType<TValue, TSpec2> const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(863)
+template <typename TContainer> inline bool operator> (Iter<TContainer, PositionIterator> const & left, Iter<TContainer, PositionIterator> const & right); // "projects/library/seqan/basic/basic_iterator_position.h"(261)
+template <typename TSpec, typename TRight> inline bool operator> (Proxy<TSpec> const & left_, TRight const & right_); // "projects/library/seqan/basic/basic_proxy.h"(471)
+template <typename TLeft, typename TSpec> inline bool operator> (TLeft const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(482)
+template <typename TLeftSpec, typename TRightSpec> inline bool operator> (Proxy<TLeftSpec> const & left_, Proxy<TRightSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(493)
+template <typename TSpec> inline bool operator> (Proxy<TSpec> const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(505)
+template <typename TTT, unsigned _sizeL, unsigned _sizeR> inline bool operator>(Tuple<TTT, _sizeL, Compressed> const &_left, Tuple<TTT, _sizeR, Compressed> const &_right); // "projects/library/seqan/basic/basic_aggregates.h"(495)
+template <typename TContainer> inline bool operator> (Iter<TContainer, StdIteratorAdaptor> const & left, Iter<TContainer, StdIteratorAdaptor> const & right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(242)
+
+//____________________________________________________________________________
+// operator>=
+
+template <typename TValue, typename TSpec, typename TRight> inline bool operator>= (SimpleType<TValue, TSpec> const & left_, TRight const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(879)
+template <typename TLeft, typename TValue, typename TSpec> inline bool operator>= (TLeft const & left_, SimpleType<TValue, TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(890)
+template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec> inline bool operator>= (SimpleType<TLeftValue, TLeftSpec> const & left_, SimpleType<TRightValue, TRightSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(901)
+template <typename TValue, typename TSpec> inline bool operator>= (SimpleType<TValue, TSpec> const & left_, SimpleType<TValue, TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(913)
+template <typename TSpec, typename TValue, typename TSpec2> inline bool operator>= (Proxy<TSpec> const & left_, SimpleType<TValue, TSpec2> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(923)
+template <typename TSpec, typename TValue, typename TSpec2> inline bool operator>= (SimpleType<TValue, TSpec2> const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_alphabet_simple.h"(934)
+template <typename TContainer> inline bool operator>= (Iter<TContainer, PositionIterator> const & left, Iter<TContainer, PositionIterator> const & right); // "projects/library/seqan/basic/basic_iterator_position.h"(283)
+template <typename TSpec, typename TRight> inline bool operator>= (Proxy<TSpec> const & left_, TRight const & right_); // "projects/library/seqan/basic/basic_proxy.h"(519)
+template <typename TLeft, typename TSpec> inline bool operator>= (TLeft const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(530)
+template <typename TLeftSpec, typename TRightSpec> inline bool operator>= (Proxy<TLeftSpec> const & left_, Proxy<TRightSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(541)
+template <typename TSpec> inline bool operator>= (Proxy<TSpec> const & left_, Proxy<TSpec> const & right_); // "projects/library/seqan/basic/basic_proxy.h"(553)
+template <typename TContainer> inline bool operator>= (Iter<TContainer, StdIteratorAdaptor> const & left, Iter<TContainer, StdIteratorAdaptor> const & right); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(268)
+
+//____________________________________________________________________________
+// operator>>
+
+template <typename TStream, typename TValue, typename TSpec> inline TStream & operator>> (TStream & stream, SimpleType<TValue, TSpec> & data); // "projects/library/seqan/basic/basic_alphabet_simple.h"(274)
+template <typename TStream, typename TSpec> inline TStream & operator>> (TStream & strm, Proxy<TSpec> & proxy); // "projects/library/seqan/basic/basic_proxy.h"(565)
+template <typename TStream, typename TSpec> inline TStream & operator>> (TStream & strm, Proxy<TSpec> const& proxy); // "projects/library/seqan/basic/basic_proxy.h"(577)
+
+//____________________________________________________________________________
+// parentAllocator
+
+template <size_t SIZE, typename TParentAllocator> inline TParentAllocator & parentAllocator(Allocator<SinglePool<SIZE, TParentAllocator> > & me); // "projects/library/seqan/basic/basic_allocator_singlepool.h"(136)
+template <typename TValue, typename TParentAllocator> inline TParentAllocator & parentAllocator(Allocator<SinglePool2<TValue, TParentAllocator> > & me); // "projects/library/seqan/basic/basic_allocator_singlepool.h"(256)
+template <typename TParentAllocator, unsigned int BLOCKING_LIMIT> inline TParentAllocator & parentAllocator(Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > & me); // "projects/library/seqan/basic/basic_allocator_multipool.h"(115)
+template <typename TParentAllocator> inline TParentAllocator & parentAllocator(Allocator<SimpleAlloc<TParentAllocator> > & me); // "projects/library/seqan/basic/basic_allocator_simple.h"(103)
+//template <size_t SIZE, size_t MAX_COUNT, typename TParentAllocator> inline TParentAllocator & parentAllocator(Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > & me); // "projects/library/seqan/basic/basic_allocator_chunkpool.h"(147)
+template <typename TValue, size_t MAX_COUNT, typename TParentAllocator> inline TParentAllocator & parentAllocator(Allocator<ChunkPool2<TValue, MAX_COUNT, TParentAllocator> > & me); // "projects/library/seqan/basic/basic_allocator_chunkpool.h"(279)
+
+//____________________________________________________________________________
+// position
+
+template <typename TContainer, typename TSpec, typename TContainer2> inline typename Position<Iter<TContainer, TSpec> const>::Type position(Iter<TContainer, TSpec> const & me, TContainer2 const &); // "projects/library/seqan/basic/basic_iterator_base.h"(211)
+template <typename T> inline typename Position<T>::Type position(T * me); // "projects/library/seqan/basic/basic_iterator.h"(354)
+template <typename TContainer, typename TIterator> inline typename Position<TContainer>::Type position(TIterator const & it, TContainer const & me); // "projects/library/seqan/basic/basic_iterator.h"(363)
+template <typename TContainer, typename TContainer2> inline typename Position<Iter<TContainer, SimpleIterator> const>::Type position(Iter<TContainer, SimpleIterator> const & me, TContainer2 const & cont); // "projects/library/seqan/basic/basic_iterator_simple.h"(108)
+template <typename TContainer, typename TIterator, typename TSpec> inline typename Position<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const>::Type position(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(232)
+template <typename TContainer, typename TIterator, typename TSpec, typename TContainer2> inline typename Position<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const>::Type position(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me, TContainer2 const &); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(243)
+
+//____________________________________________________________________________
+// releaseRef
+
+template <typename T> inline void releaseRef(T & ); // "projects/library/seqan/basic/basic_holder.h"(73)
+template <typename T> inline void releaseRef(T const & ); // "projects/library/seqan/basic/basic_holder.h"(79)
+
+//____________________________________________________________________________
+// set
+
+template <typename TTarget, typename TSource> inline void set(TTarget & target, TSource & source); // "projects/library/seqan/basic/basic_transport.h"(160)
+template <typename TTarget, typename TSource> inline void set(TTarget const & target, TSource & source); // "projects/library/seqan/basic/basic_transport.h"(168)
+template <typename TTarget, typename TSource> inline void set(TTarget & target, TSource const & source); // "projects/library/seqan/basic/basic_transport.h"(176)
+template <typename TTarget, typename TSource> inline void set(TTarget const & target, TSource const & source); // "projects/library/seqan/basic/basic_transport.h"(184)
+
+//____________________________________________________________________________
+// setHost
+
+template <typename T, typename THost> inline void setHost(T & me, THost & host_); // "projects/library/seqan/basic/basic_host.h"(99)
+template <typename T, typename THost> inline void setHost(T & me, THost const & host_); // "projects/library/seqan/basic/basic_host.h"(107)
+
+//____________________________________________________________________________
+// setPosition
+
+template <typename TContainer, typename TIterator, typename TSpec, typename TPosition> inline void setPosition(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me, TPosition pos_); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(256)
+
+//____________________________________________________________________________
+// setValue
+
+template <typename TValue> inline void setValue(Holder<TValue, Tristate> & me, typename _Parameter<TValue>::Type value_); // "projects/library/seqan/basic/basic_holder.h"(453)
+template <typename TValue, typename TValue2> inline void setValue(Holder<TValue, Tristate> & me, TValue2 const & value_); // "projects/library/seqan/basic/basic_holder.h"(467)
+template <typename TValue> inline void setValue(Holder<TValue, Simple> & me, TValue const & value_); // "projects/library/seqan/basic/basic_holder.h"(724)
+template <typename TValue> inline void setValue(Holder<TValue, Tristate2> & me, TValue & value_); // "projects/library/seqan/basic/basic_holder.h"(999)
+
+//____________________________________________________________________________
+// shiftLeft
+
+template <typename TTT, unsigned _size, typename TCompression> inline void shiftLeft(Tuple<TTT, _size, TCompression> &me); // "projects/library/seqan/basic/basic_aggregates.h"(525)
+template <typename TTT, unsigned _size> inline void shiftLeft(Tuple<TTT, _size, Compressed> &me); // "projects/library/seqan/basic/basic_aggregates.h"(535)
+
+//____________________________________________________________________________
+// shiftRight
+
+template <typename TTT, unsigned _size, typename TCompression> inline void shiftRight(Tuple<TTT, _size, TCompression> &me); // "projects/library/seqan/basic/basic_aggregates.h"(530)
+template <typename TTT, unsigned _size> inline void shiftRight(Tuple<TTT, _size, Compressed> &me); // "projects/library/seqan/basic/basic_aggregates.h"(540)
+
+//____________________________________________________________________________
+// supremumValue
+
+template <typename T> inline T const & supremumValue(); // "projects/library/seqan/basic/basic_alphabet_interface2.h"(120)
+
+//____________________________________________________________________________
+// supremumValueImpl
+
+template <typename T> inline T const & supremumValueImpl(T *); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(420)
+inline float const & supremumValueImpl(float *); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(655)
+inline double const & supremumValueImpl(double *); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(682)
+inline long double const & supremumValueImpl(long double *); // "projects/library/seqan/basic/basic_alphabet_trait_basic.h"(709)
+
+//____________________________________________________________________________
+// value
+
+template <typename TContainer> inline typename Reference<Iter<TContainer, PositionIterator> >::Type value(Iter<TContainer, PositionIterator> & me); // "projects/library/seqan/basic/basic_iterator_position.h"(164)
+template <typename TContainer> inline typename Reference<Iter<TContainer, PositionIterator> >::Type value(Iter<TContainer, PositionIterator> const & me); // "projects/library/seqan/basic/basic_iterator_position.h"(171)
+template <typename TValue> inline typename Reference<Holder<TValue, Tristate> >::Type value(Holder<TValue, Tristate> & me); // "projects/library/seqan/basic/basic_holder.h"(479)
+template <typename TValue> inline typename Reference<Holder<TValue, Tristate> const>::Type value(Holder<TValue, Tristate> const & me); // "projects/library/seqan/basic/basic_holder.h"(496)
+template <typename TValue> inline typename Reference<Holder<TValue, Simple> >::Type value(Holder<TValue, Simple> & me); // "projects/library/seqan/basic/basic_holder.h"(734)
+template <typename TValue> inline typename Reference<Holder<TValue, Simple> const>::Type value(Holder<TValue, Simple> const & me); // "projects/library/seqan/basic/basic_holder.h"(741)
+template <typename TValue> inline typename Reference<Holder<TValue, Tristate2> >::Type value(Holder<TValue, Tristate2> & me); // "projects/library/seqan/basic/basic_holder.h"(1016)
+template <typename TValue> inline typename Reference<Holder<TValue, Tristate2> const>::Type value(Holder<TValue, Tristate2> const & me); // "projects/library/seqan/basic/basic_holder.h"(1033)
+template <typename T> inline typename Reference<T>::Type value(T & me); // "projects/library/seqan/basic/basic_iterator.h"(171)
+template <typename T> inline typename Reference<T const>::Type value(T const & me); // "projects/library/seqan/basic/basic_iterator.h"(178)
+template <typename T> inline T & value(T * me); // "projects/library/seqan/basic/basic_iterator.h"(187)
+template <typename TContainer, typename TIterator, typename TSpec> inline typename Reference<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > >::Type value(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(268)
+template <typename TContainer, typename TIterator, typename TSpec> inline typename Reference<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const>::Type value(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me); // "projects/library/seqan/basic/basic_iterator_adaptor.h"(275)
+template <typename TContainer> inline typename Reference<Iter<TContainer, StdIteratorAdaptor> >::Type value(Iter<TContainer, StdIteratorAdaptor> & me); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(146)
+template <typename TContainer> inline typename Reference<Iter<TContainer, StdIteratorAdaptor> const>::Type value(Iter<TContainer, StdIteratorAdaptor> const & me); // "projects/library/seqan/basic/basic_iterator_adapt_std.h"(152)
+
+//____________________________________________________________________________
+// valueConstruct
+
+template <typename TIterator> inline void valueConstruct(TIterator it); // "projects/library/seqan/basic/basic_alphabet_interface.h"(145)
+template <typename TIterator, typename TParam> inline void valueConstruct(TIterator it, TParam const & param_); // "projects/library/seqan/basic/basic_alphabet_interface.h"(165)
+template <typename TIterator, typename TParam> inline void valueConstruct(TIterator it, TParam const & param_, Move tag); // "projects/library/seqan/basic/basic_alphabet_interface.h"(186)
+
+//____________________________________________________________________________
+// valueConstructMove
+
+template <typename TIterator, typename TValue> inline void valueConstructMove(TIterator it, TValue const & value); // "projects/library/seqan/basic/basic_alphabet_interface.h"(248)
+
+//____________________________________________________________________________
+// valueDestruct
+
+template <typename TIterator> inline void valueDestruct(TIterator it); // "projects/library/seqan/basic/basic_alphabet_interface.h"(216)
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+//____________________________________________________________________________
+// _compareBinaryFiles
+
+inline bool _compareBinaryFiles(char * file1, char * file2); // "projects/library/seqan/basic/basic_debug.h"(119)
+
+//____________________________________________________________________________
+// _compareTextFiles
+
+inline bool _compareTextFiles(char * file1, char * file2); // "projects/library/seqan/basic/basic_debug.h"(182)
+
+//____________________________________________________________________________
+// _compareTextFiles_readChar
+
+inline void _compareTextFiles_readChar(FILE * fl, char & c, bool & is_lb, bool & is_eof); // "projects/library/seqan/basic/basic_debug.h"(151)
+
+#endif
+
diff --git a/src/libSSA/seqan/basic/basic_holder.h b/src/libSSA/seqan/basic/basic_holder.h
new file mode 100644
index 0000000..df5a791
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_holder.h
@@ -0,0 +1,1120 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_holder.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_HOLDER_H
+#define SEQAN_HEADER_BASIC_HOLDER_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// addRef
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.addRef:
+..summary:Called when dependency is added.
+..cat:Dependent Objects
+..signature:addRef(host)
+..param.host:The host object.
+..remarks.text:A call of this function denotes that a client object is about to become
+dependent on $host$.
+..remarks.text:The default behavior is: Do nothing.
+..see:Class.Holder
+*/
+
+template <typename T>
+inline void
+addRef(T & /*me*/)
+{// general: do nothing
+SEQAN_CHECKPOINT
+}
+template <typename T>
+inline void
+addRef(T const & /*me*/)
+{// general: do nothing
+SEQAN_CHECKPOINT
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// releaseRef
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.releaseRef:
+..summary:Called when dependency is released.
+..cat:Dependent Objects
+..signature:releaseRef(host)
+..param.host:The host object.
+..remarks.text:A call of this function denotes that a former dependent client object
+ceases to be dependent on $host$.
+..remarks.text:The default behavior is: Do nothing.
+..see:Class.Holder
+..see:Function.addRef
+*/
+template <typename T>
+inline void
+releaseRef(T & /*me*/)
+{// general: do nothing
+SEQAN_CHECKPOINT
+}
+template <typename T>
+inline void
+releaseRef(T const & /*me*/)
+{// general: do nothing
+SEQAN_CHECKPOINT
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Tags
+
+struct Simple;
+struct Tristate;
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Holder
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Class.Holder:
+..cat:Basic
+..summary:Manages relationship to another object.
+..signature:Holder<TValue, TSpec>
+..param.TValue:Type of the managed object.
+...metafunction:Metafunction.Value
+..param.TSpec:The specializing type.
+...metafunction:Metafunction.Spec
+...default:$Tristate$
+..remarks.text:The main purpose of this class is to facilitate the handling of
+member objects. If we want class $A$ to be dependent on or the owner of another object of class $B$,
+then we add a data member of type $Holder<B>$ to $A$.
+$Holder$ offers some useful access functions, stores the kind of relationship between $A$ and $B$,
+and executes all needed @Function.addRef@ and @Function.releaseRef@ calls.
+*/
+
+template <typename TValue, typename TSpec = Tristate>
+struct Holder;
+
+
+//////////////////////////////////////////////////////////////////////////////
+// METAFUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Value.param.T.type:Class.Holder
+
+template <typename TValue, typename TSpec>
+struct Value< Holder<TValue, TSpec> >
+{
+ typedef typename _RemoveConst<TValue>::Type Type;
+};
+template <typename TValue, typename TSpec>
+struct Value< Holder<TValue, TSpec> const>
+{
+ typedef typename _RemoveConst<TValue>::Type Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Spec.param.T.type:Class.Holder
+
+template <typename TValue, typename TSpec>
+struct Spec< Holder<TValue, TSpec> >
+{
+ typedef TSpec Type;
+};
+template <typename TValue, typename TSpec>
+struct Spec< Holder<TValue, TSpec> const>
+{
+ typedef TSpec Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Reference.param.T.type:Class.Holder
+
+template <typename TValue, typename TSpec>
+struct Reference< Holder<TValue, TSpec> >
+{
+ typedef typename Value< Holder<TValue, TSpec> >::Type & Type;
+};
+template <typename TValue, typename TSpec>
+struct Reference< Holder<TValue, TSpec> const>
+{
+ typedef typename Value< Holder<TValue, TSpec> const>::Type & Type;
+};
+
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+// Tristate Holder
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Spec.Tristate Holder
+..cat:Holders
+..summary:Holder that can be empty, dependent, or owner.
+..signature:Holder<TValue, Tristate>
+..param.TValue:Type of the managed object.
+..general:Class.Holder
+..remarks.text:A tristate holder $A$ that holds an object $B$ has one of the following states:
+..remarks.text:- owner: $A$ is the owner of $B$. If $A$ is destroyed, $B$ will be destroyed automatically.
+..remarks.text:- dependent: $A$ depends on $B$. $B$ should not be destroyed as long as $A$ is used.
+..remarks.text:- empty: there is currently no object reference stored in the holder $A$.
+..remarks.text:The state of the holder can be determined by @Function.empty@ and @Function.dependent at .
+*/
+
+template <typename TValue>
+struct Holder<TValue, Tristate>
+{
+public:
+ enum EHolderState
+ {
+ EMPTY = 0,
+ OWNER = 1,
+ DEPENDENT = ~0
+ };
+
+// typedef typename _RemoveConst<TValue>::Type TValue_NotConst;
+ typedef typename Value<Holder>::Type THostValue;
+
+ typename _Pointer<THostValue>::Type data_value;
+ EHolderState data_state;
+
+//____________________________________________________________________________
+
+/**
+.Memfunc.Holder:
+..class:Class.Holder
+..summary:Constructor
+..signature:Holder<TValue, TInfix> ()
+..signature:Holder<TValue, TInfix> (holder)
+..signature:Holder<TValue, TInfix> (value)
+..param.holder:Another holder object.
+..param.value:An object of type $TValue$.
+..remarks.text:
+The default constructor creates a holder that is in state 'empty'.
+If a $value$ is passed to the constructor, the holder will be in state 'dependent'.
+*/
+
+ Holder():
+ data_state(EMPTY)
+ {
+SEQAN_CHECKPOINT
+ }
+ Holder(Holder const & source_):
+ data_state(EMPTY)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source_);
+ }
+ Holder(typename _Parameter<THostValue>::Type value_):
+ data_state(EMPTY)
+ {
+SEQAN_CHECKPOINT
+ setValue(*this, value_);
+ }
+ Holder(typename _ConstParameter<THostValue>::Type value_):
+ data_state(EMPTY)
+ {
+SEQAN_CHECKPOINT
+ assignValue(*this, value_);
+ }
+
+/**
+.Memfunc.~Holder:
+..class:Class.Holder
+..summary:Destructor
+..signature:~Holder()
+..remarks.text:
+If the holder is in state 'owner', the holded object will be destoyed too.
+*/
+ ~Holder()
+ {
+SEQAN_CHECKPOINT
+ clear(*this);
+ }
+
+//____________________________________________________________________________
+
+ Holder const &
+ operator = (Holder const & source_)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source_);
+ return *this;
+ }
+
+ Holder const &
+ operator = (typename _ConstParameter<THostValue>::Type value_)
+ {
+SEQAN_CHECKPOINT
+ assignValue(*this, value_);
+ return *this;
+ }
+
+ operator typename _Parameter<THostValue>::Type()
+ {
+SEQAN_CHECKPOINT
+ return *data_value;
+ }
+//____________________________________________________________________________
+
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// FUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.empty.param.object.type:Class.Holder
+
+template <typename TValue>
+inline bool
+empty(Holder<TValue, Tristate> const & me)
+{
+SEQAN_CHECKPOINT
+ return (me.data_state == Holder<TValue, Tristate>::EMPTY);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.dependent.param.object.type:Class.Holder
+
+template <typename TValue>
+inline bool
+dependent(Holder<TValue, Tristate> const & me)
+{
+SEQAN_CHECKPOINT
+ return (me.data_state == Holder<TValue, Tristate>::DEPENDENT);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.clear.param.object.type:Class.Holder
+///.Function.clear.remarks.text:If $clear$ is applied on a @Class.Holder@ object,
+///the state of this object is set to 'empty'.
+
+template <typename TValue>
+inline void
+clear(Holder<TValue, Tristate> & me)
+{
+ switch (me.data_state)
+ {
+ case Holder<TValue, Tristate>::EMPTY:
+ break;
+
+ case Holder<TValue, Tristate>::DEPENDENT:
+ {
+SEQAN_CHECKPOINT
+ releaseRef(_toParameter<TValue>(me.data_value));
+ me.data_state = Holder<TValue, Tristate>::EMPTY;
+ }
+ break;
+
+ default: /*Holder<TValue, TSpec>::OWNER*/
+ {
+SEQAN_CHECKPOINT
+ valueDestruct(me.data_value);
+ deallocate(me, me.data_value, 1);
+ me.data_state = Holder<TValue, Tristate>::EMPTY;
+ }
+ break;
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.create:
+..summary:Makes an object to owner of its content.
+..cat:Dependent Objects
+..signature:create(holder [, object])
+..param.holder:A holder object.
+...type:Class.Holder
+..param.object:Object from which a copy is made and stored in $holder$. (optional)
+...type:Metafunction.Value.Value<Holder>::Type
+..remarks.text:After this operation, $holder$ will be in state 'owner'.
+If $object$ is specified, $holder$ will hold a copy of $object$ at the end of this function.
+If $object$ is not specified, the action depends on the former state of $holder$:
+..remarks.text:- If the state of $holder$ was 'empty', a new object is default constructed and stored into $holder$.
+..remarks.text:- If the state of $holder$ was 'dependent', a copy of the former object is made and stored into $holder$.
+..remarks.text:- If the state of $holder$ was already 'owner', nothing happens.
+..see:Class.Holder
+*/
+
+template <typename TValue>
+inline void
+create(Holder<TValue, Tristate> & me)
+{
+ typedef Holder<TValue, Tristate> THolder;
+
+ switch (me.data_state)
+ {
+ case Holder<TValue, Tristate>::EMPTY:
+ {
+SEQAN_CHECKPOINT
+ allocate(me, me.data_value, 1);
+ valueConstruct(me.data_value);
+ me.data_state = THolder::OWNER;
+ }
+ break;
+
+ case THolder::DEPENDENT:
+ {
+SEQAN_CHECKPOINT
+ typename _Parameter<TValue>::Type old_value = value(me);
+ allocate(me, me.data_value, 1);
+ valueConstruct(me.data_value, old_value);
+ me.data_state = THolder::OWNER;
+ releaseRef(old_value);
+ }
+ break;
+ default:;
+ }
+}
+
+//____________________________________________________________________________
+
+template <typename TValue>
+inline void
+create(Holder<TValue, Tristate> & me,
+ typename _Parameter<TValue const>::Type value_)
+{
+SEQAN_CHECKPOINT
+
+ if (me.data_state == Holder<TValue, Tristate>::OWNER)
+ {
+ assign(_toParameter(me.data_value), value_);
+ return;
+ }
+
+ clear(me);
+ allocate(me, me.data_value, 1);
+ valueConstruct(me.data_value, value_);
+ me.data_state = Holder<TValue, Tristate>::OWNER;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.detach:
+..summary:Makes an object independent from other objects.
+..cat:Dependent Objects
+..signature:detach(object)
+..param.object:An object.
+...type:Class.Holder
+..remarks:
+After this function, $object$ does not depends from any other entity outside of $object$,
+like a @Function.source@ or a @Function.host@, and @Function.dependent.dependent(object)@ returns $false$
+..see:Function.source
+..see:Function.host
+..see:Function.createSource
+..see:Function.create
+*/
+
+template <typename TValue>
+inline void
+detach(Holder<TValue, Tristate> & me)
+{
+SEQAN_CHECKPOINT
+ create(me);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.setValue:
+..cat:Content Manipulation
+..summary:Makes holder dependent.
+..signature:setValue(holder, object)
+..param.holder:A holder object.
+...type:Class.Holder
+..param.object:Object from which $holder$ will be dependent.
+...type:Metafunction.Value.Value<Holder>::Type
+..remarks.text:After this operation, $holder$ will be dependent in state 'dependent'.
+..see:Class.Holder
+*/
+
+template <typename TValue>
+inline void
+setValue(Holder<TValue, Tristate> & me,
+ typename _Parameter<TValue>::Type value_)
+{
+SEQAN_CHECKPOINT
+ typedef typename Value<Holder<TValue, Tristate> >::Type THolderType;
+
+ clear(me);
+ me.data_value = _toPointer(value_);
+ me.data_state = Holder<TValue, Tristate>::DEPENDENT;
+ addRef(_toParameter<THolderType>(me.data_value));
+}
+
+template <typename TValue, typename TValue2>
+inline void
+setValue(Holder<TValue, Tristate> & me,
+ TValue2 const & value_)
+{
+SEQAN_CHECKPOINT
+ set(value(me), value_);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.value.param.object.type:Class.Holder
+
+template <typename TValue>
+inline typename Reference<Holder<TValue, Tristate> >::Type
+value(Holder<TValue, Tristate> & me)
+{
+SEQAN_CHECKPOINT
+ typedef Holder<TValue, Tristate> THolder;
+
+ if (empty(me))
+ {
+ allocate(me, me.data_value, 1);
+ valueConstruct(me.data_value);
+ me.data_state = THolder::OWNER;
+ }
+
+ typedef typename Value<Holder<TValue, Tristate> >::Type THolderType;
+ return _toParameter<THolderType>(me.data_value);
+}
+template <typename TValue>
+inline typename Reference<Holder<TValue, Tristate> const>::Type
+value(Holder<TValue, Tristate> const & me)
+{
+SEQAN_CHECKPOINT
+ SEQAN_ASSERT(!empty(me));
+
+ typedef typename Value<Holder<TValue, Tristate> >::Type THolderType;
+ return _toParameter<THolderType>(me.data_value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.assignValue.param.object.type:Class.Holder
+
+template <typename TValue, typename TSource>
+inline void
+assignValue(Holder<TValue, Tristate> & me,
+ TSource const & value_)
+{
+SEQAN_CHECKPOINT
+ typedef typename Value<Holder<TValue, Tristate> >::Type THostValue;
+ if (empty(me))
+ {
+ create(me, value_);
+ }
+ else
+ {
+ assign(_toParameter<THostValue>(me.data_value), value_);
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.moveValue.param.object.type:Class.Holder
+
+template <typename TValue, typename TSource>
+inline void
+moveValue(Holder<TValue, Tristate> & me,
+ TSource const & value_)
+{
+SEQAN_CHECKPOINT
+ if (empty(me))
+ {
+ create(me, value_);
+ }
+ else
+ {
+ move(value(me), value_);
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.assign.param.target.type:Class.Holder
+///.Function.assign.param.source.type:Class.Holder
+
+template <typename TValue>
+inline void
+assign(Holder<TValue, Tristate> & target_,
+ Holder<TValue, Tristate> const & source_)
+{
+SEQAN_CHECKPOINT
+ switch(source_.data_state)
+ {
+ case Holder<TValue, Tristate>::EMPTY:
+ {
+ clear(target_);
+ }
+ break;
+
+ case Holder<TValue, Tristate>::OWNER:
+ {
+ assignValue(target_, value(source_));
+ }
+ break;
+
+ default: /*case Holder<TValue, Tristate>::DEPENDENT*/
+ {
+ setValue(target_, value(source_));
+ }
+ break;
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+// Simple Holder
+//////////////////////////////////////////////////////////////////////////////
+//??? TODO: Documentation of Simple Holder
+
+template <typename TValue>
+struct Holder<TValue, Simple>
+{
+ typedef typename Value<Holder>::Type THolderValue;
+ typedef typename _Parameter<THolderValue>::Type THolderParameter;
+
+ mutable THolderValue data_value;
+//____________________________________________________________________________
+
+ Holder()
+ {
+SEQAN_CHECKPOINT
+ }
+ Holder(Holder & source_):
+ data_value(source_.data_value)
+ {
+SEQAN_CHECKPOINT
+ }
+ Holder(Holder const & source_):
+ data_value(source_.data_value)
+ {
+SEQAN_CHECKPOINT
+ }
+ template <typename TSource>
+ Holder(TSource & value_):
+ data_value(value_)
+ {
+SEQAN_CHECKPOINT
+ }
+ template <typename TSource>
+ Holder(TSource const & value_):
+ data_value(value_)
+ {
+SEQAN_CHECKPOINT
+ }
+/*
+ Holder(TValue const & value_):
+ data_value(value_)
+ {
+SEQAN_CHECKPOINT
+ }
+*/
+ ~Holder()
+ {
+SEQAN_CHECKPOINT
+ }
+
+//____________________________________________________________________________
+
+ Holder const &
+ operator = (Holder const & source_)
+ {
+SEQAN_CHECKPOINT
+ data_value = source_.data_value;
+ return *this;
+ }
+
+ Holder const &
+ operator = (THolderValue const & value_)
+ {
+SEQAN_CHECKPOINT
+ data_value = value_;
+ return *this;
+ }
+
+ operator THolderParameter()
+ {
+SEQAN_CHECKPOINT
+ return *data_value;
+ }
+//____________________________________________________________________________
+};
+
+
+//////////////////////////////////////////////////////////////////////////////
+// FUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue>
+inline bool
+empty(Holder<TValue, Simple> const & me)
+{
+SEQAN_CHECKPOINT
+ return false;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue>
+inline bool
+dependent(Holder<TValue, Simple> const & me)
+{
+SEQAN_CHECKPOINT
+ return false;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue>
+inline void
+clear(Holder<TValue, Simple> & me)
+{
+SEQAN_CHECKPOINT
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue>
+inline void
+create(Holder<TValue, Simple> & me)
+{
+SEQAN_CHECKPOINT
+}
+
+//____________________________________________________________________________
+
+template <typename TValue>
+inline void
+create(Holder<TValue, Simple> & me,
+ TValue const & value_)
+{
+SEQAN_CHECKPOINT
+ me.data_value = value_;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue>
+inline void
+detach(Holder<TValue, Simple> & me)
+{
+SEQAN_CHECKPOINT
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue>
+inline void
+setValue(Holder<TValue, Simple> & me,
+ TValue const & value_)
+{
+SEQAN_CHECKPOINT
+ me.data_value = value_;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue>
+inline typename Reference<Holder<TValue, Simple> >::Type
+value(Holder<TValue, Simple> & me)
+{
+SEQAN_CHECKPOINT
+ return me.data_value;
+}
+template <typename TValue>
+inline typename Reference<Holder<TValue, Simple> const>::Type
+value(Holder<TValue, Simple> const & me)
+{
+SEQAN_CHECKPOINT
+ return me.data_value;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename TSource>
+inline void
+assignValue(Holder<TValue, Simple> & me,
+ TSource const & value_)
+{
+SEQAN_CHECKPOINT
+ assignValue(me.data_value, value_);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename TSource>
+inline void
+moveValue(Holder<TValue, Simple> & me,
+ TSource const & value_)
+{
+SEQAN_CHECKPOINT
+ move(me.data_value, value_);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue>
+inline void
+assign(Holder<TValue, Simple> & target_,
+ Holder<TValue, Simple> const & source_)
+{
+SEQAN_CHECKPOINT
+ assignValue(target_, source_);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// New Tristate Holder that works also on pointers
+//////////////////////////////////////////////////////////////////////////////
+
+struct Tristate2;
+
+template <typename TValue>
+struct Holder<TValue, Tristate2>
+{
+public:
+ enum EHolderState
+ {
+ EMPTY = 0,
+ OWNER = 1,
+ DEPENDENT = ~0
+ };
+
+ typedef typename Value<Holder>::Type THostValue;
+
+ TValue * data_value;
+ EHolderState data_state;
+
+//____________________________________________________________________________
+
+ Holder():
+ data_state(EMPTY)
+ {
+SEQAN_CHECKPOINT
+ }
+ Holder(Holder const & source_):
+ data_state(EMPTY)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source_);
+ }
+ Holder(typename _Parameter<THostValue>::Type value_):
+ data_state(EMPTY)
+ {
+SEQAN_CHECKPOINT
+ setValue(*this, value_);
+ }
+ Holder(typename _ConstParameter<THostValue>::Type value_):
+ data_state(EMPTY)
+ {
+SEQAN_CHECKPOINT
+ assignValue(*this, value_);
+ }
+ ~Holder()
+ {
+SEQAN_CHECKPOINT
+ clear(*this);
+ }
+
+//____________________________________________________________________________
+
+ Holder const &
+ operator = (Holder const & source_)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source_);
+ return *this;
+ }
+
+ Holder const &
+ operator = (TValue const & value_)
+ {
+SEQAN_CHECKPOINT
+ assignValue(*this, value_);
+ return *this;
+ }
+
+ operator TValue &()
+ {
+SEQAN_CHECKPOINT
+ return *data_value;
+ }
+//____________________________________________________________________________
+
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// FUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.empty.param.object.type:Class.Holder
+
+template <typename TValue>
+inline bool
+empty(Holder<TValue, Tristate2> const & me)
+{
+SEQAN_CHECKPOINT
+ return (me.data_state == Holder<TValue, Tristate2>::EMPTY);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.dependent.param.object.type:Class.Holder
+
+template <typename TValue>
+inline bool
+dependent(Holder<TValue, Tristate2> const & me)
+{
+SEQAN_CHECKPOINT
+ return (me.data_state == Holder<TValue, Tristate2>::DEPENDENT);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.clear.param.object.type:Class.Holder
+///.Function.clear.remarks.text:If $clear$ is applied on a @Class.Holder@ object,
+///the state of this object is set to 'empty'.
+
+template <typename TValue>
+inline void
+clear(Holder<TValue, Tristate2> & me)
+{
+ switch (me.data_state)
+ {
+ case Holder<TValue, Tristate2>::EMPTY:
+ break;
+
+ case Holder<TValue, Tristate2>::DEPENDENT:
+ {
+SEQAN_CHECKPOINT
+ releaseRef(*(me.data_value));
+ me.data_state = Holder<TValue, Tristate2>::EMPTY;
+ }
+ break;
+
+ default: /*Holder<TValue, TSpec>::OWNER*/
+ {
+SEQAN_CHECKPOINT
+ valueDestruct(me.data_value);
+ deallocate(me, me.data_value, 1);
+ me.data_state = Holder<TValue, Tristate2>::EMPTY;
+ }
+ break;
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+template <typename TValue>
+inline void
+create(Holder<TValue, Tristate2> & me)
+{
+ typedef Holder<TValue, Tristate2> THolder;
+
+ switch (me.data_state)
+ {
+ case Holder<TValue, Tristate2>::EMPTY:
+ {
+SEQAN_CHECKPOINT
+ allocate(me, me.data_value, 1);
+ valueConstruct(me.data_value);
+ me.data_state = THolder::OWNER;
+ }
+ break;
+
+ case THolder::DEPENDENT:
+ {
+SEQAN_CHECKPOINT
+ TValue & old_value = value(me);
+ allocate(me, me.data_value, 1);
+ valueConstruct(me.data_value, old_value);
+ me.data_state = THolder::OWNER;
+ releaseRef(old_value);
+ }
+ break;
+ default:;
+ }
+}
+
+//____________________________________________________________________________
+
+template <typename TValue>
+inline void
+create(Holder<TValue, Tristate2> & me,
+ TValue const & value_)
+{
+SEQAN_CHECKPOINT
+
+ if (me.data_state == Holder<TValue, Tristate2>::OWNER)
+ {
+ assign(*(me.data_value), value_);
+ return;
+ }
+
+ clear(me);
+ allocate(me, me.data_value, 1);
+ valueConstruct(me.data_value, value_);
+ me.data_state = Holder<TValue, Tristate2>::OWNER;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+template <typename TValue>
+inline void
+detach(Holder<TValue, Tristate2> & me)
+{
+SEQAN_CHECKPOINT
+ create(me);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+template <typename TValue>
+inline void
+setValue(Holder<TValue, Tristate2> & me,
+ TValue & value_)
+{
+SEQAN_CHECKPOINT
+ typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
+
+ clear(me);
+ me.data_value = & value_;
+ me.data_state = Holder<TValue, Tristate2>::DEPENDENT;
+ addRef(value_);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.value.param.object.type:Class.Holder
+
+template <typename TValue>
+inline typename Reference<Holder<TValue, Tristate2> >::Type
+value(Holder<TValue, Tristate2> & me)
+{
+SEQAN_CHECKPOINT
+ typedef Holder<TValue, Tristate2> THolder;
+
+ if (empty(me))
+ {
+ allocate(me, me.data_value, 1);
+ valueConstruct(me.data_value);
+ me.data_state = THolder::OWNER;
+ }
+
+ typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
+ return *(me.data_value);
+}
+template <typename TValue>
+inline typename Reference<Holder<TValue, Tristate2> const>::Type
+value(Holder<TValue, Tristate2> const & me)
+{
+SEQAN_CHECKPOINT
+ SEQAN_ASSERT(!empty(me));
+
+ return *(me.data_value);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.assignValue.param.object.type:Class.Holder
+
+template <typename TValue, typename TSource>
+inline void
+assignValue(Holder<TValue, Tristate2> & me,
+ TSource const & value_)
+{
+SEQAN_CHECKPOINT
+ typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
+ if (empty(me))
+ {
+ create(me, value_);
+ }
+ else
+ {
+ assign(*(me.data_value), value_);
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.moveValue.param.object.type:Class.Holder
+
+template <typename TValue, typename TSource>
+inline void
+moveValue(Holder<TValue, Tristate2> & me,
+ TSource const & value_)
+{
+SEQAN_CHECKPOINT
+ if (empty(me))
+ {
+ create(me, value_);
+ }
+ else
+ {
+ move(value(me), value_);
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.assign.param.target.type:Class.Holder
+///.Function.assign.param.source.type:Class.Holder
+
+template <typename TValue>
+inline void
+assign(Holder<TValue, Tristate2> & target_,
+ Holder<TValue, Tristate2> const & source_)
+{
+SEQAN_CHECKPOINT
+ switch(source_.data_state)
+ {
+ case Holder<TValue, Tristate2>::EMPTY:
+ {
+ clear(target_);
+ }
+ break;
+
+ case Holder<TValue, Tristate2>::OWNER:
+ {
+ assignValue(target_, value(source_));
+ }
+ break;
+
+ default: /*case Holder<TValue, Tristate2>::DEPENDENT*/
+ {
+ setValue(target_, value(source_));
+ }
+ break;
+ }
+}
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
+
+
diff --git a/src/libSSA/seqan/basic/basic_host.h b/src/libSSA/seqan/basic/basic_host.h
new file mode 100644
index 0000000..a1a7231
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_host.h
@@ -0,0 +1,171 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_host.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_HOST_H
+#define SEQAN_HEADER_BASIC_HOST_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+
+//////////////////////////////////////////////////////////////////////////////
+// Host Functions
+//////////////////////////////////////////////////////////////////////////////
+//these functions assume that the hosted object exports a function "_dataHost"
+//that returns a reference to a holder type of Host<T>::Type &
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename T>
+inline bool
+emptyHost(T const & me)
+{
+SEQAN_CHECKPOINT
+ return empty(_dataHost(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename T>
+inline bool
+dependentHost(T const & me)
+{
+SEQAN_CHECKPOINT
+ return dependent(_dataHost(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename T>
+inline void
+clearHost(T & me)
+{
+SEQAN_CHECKPOINT
+ clear(_dataHost(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename T>
+inline void
+createHost(T & me)
+{
+SEQAN_CHECKPOINT
+ create(_dataHost(me));
+}
+
+//____________________________________________________________________________
+
+template <typename T, typename THost>
+inline void
+createHost(T & me,
+ THost & host_)
+{
+SEQAN_CHECKPOINT
+ create(_dataHost(me), host_);
+}
+template <typename T, typename THost>
+inline void
+createHost(T & me,
+ THost const & host_)
+{
+SEQAN_CHECKPOINT
+ create(_dataHost(me), host_);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename T, typename THost>
+inline void
+setHost(T & me,
+ THost & host_)
+{
+SEQAN_CHECKPOINT
+ setValue(_dataHost(me), host_);
+}
+template <typename T, typename THost>
+inline void
+setHost(T & me,
+ THost const & host_)
+{
+SEQAN_CHECKPOINT
+ setValue(_dataHost(me), host_);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename T>
+inline typename Host<T>::Type &
+host(T & me)
+{
+SEQAN_CHECKPOINT
+ return value(_dataHost(me));
+}
+template <typename T>
+inline typename Host<T const>::Type &
+host(T const & me)
+{
+SEQAN_CHECKPOINT
+ return value(_dataHost(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename T, typename THost>
+inline void
+assignHost(T & me,
+ THost & host_)
+{
+SEQAN_CHECKPOINT
+ assignValue(_dataHost(me), host_);
+}
+template <typename T, typename THost>
+inline void
+assignHost(T & me,
+ THost const & host_)
+{
+SEQAN_CHECKPOINT
+ assignValue(_dataHost(me), host_);
+}
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename T, typename THost>
+inline void
+moveHost(T & me,
+ THost & host_)
+{
+SEQAN_CHECKPOINT
+ moveValue(_dataHost(me), host_);
+}
+template <typename T, typename THost>
+inline void
+moveHost(T & me,
+ THost const & host_)
+{
+SEQAN_CHECKPOINT
+ moveValue(_dataHost(me), host_);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
+
+
diff --git a/src/libSSA/seqan/basic/basic_iterator.h b/src/libSSA/seqan/basic/basic_iterator.h
new file mode 100644
index 0000000..9ccc0dd
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_iterator.h
@@ -0,0 +1,732 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_iterator.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_ITERATOR_H
+#define SEQAN_HEADER_BASIC_ITERATOR_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+// TAGS
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.Iterator Spec:
+..summary:Specifies the kind of an iterator.
+..tag.Rooted:Rooted iterator.
+...remarks
+....text:This iterator implements some more advanced functions like
+ at Function.container@ and @Function.position at .
+....concept:Concept.Rooted Iterator
+..tag.Standard:Standard conform iterator.
+...remarks
+....text:Note that standard iterators need not to implement all functions
+that are available for rooted iterators.
+....concept:Concept.Iterator
+..remarks.text:The default iterator spec is given by @Metafunction.DefaultIteratorSpec at .
+..see:Metafunction.DefaultIteratorSpec
+..see:Concept.Iterator
+*/
+
+struct TagRooted_;
+typedef Tag<TagRooted_> const Rooted;
+
+struct TagStandard_;
+typedef Tag<TagStandard_> const Standard;
+
+
+//////////////////////////////////////////////////////////////////////////////
+// METAFUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Metafunction.DefaultIteratorSpec:
+..hidefromindex
+..summary:Specifies default kind of iterator.
+..signature:DefaultIteratorSpec<T>::Type
+..param.T:Container type for which the default iterator spec is determined.
+...concept:Concept.Container
+..returns.param.Type:Iterator spec of $T$.
+..see:Metafunction.Iterator
+*/
+
+template <typename T>
+struct DefaultIteratorSpec
+{
+ typedef Standard Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Metafunction.DefaultGetIteratorSpec:
+..hidefromindex
+..summary:Specifies default kind of iterator returned by functions.
+..signature:DefaultGetIteratorSpec<T>::Type
+..param.T:Container type for which the spec is determined.
+...concept:Concept.Container
+..returns.param.Type:Iterator spec of $T$.
+..remarks:This metafunction returns the iterator spec of iterators that are returned by functions like
+ at Function.begin@, @Function.end@, or @Function.iter at .
+..see:Metafunction.Iterator
+..see:Metafunction.DefaultIteratorSpec
+*/
+
+template <typename T>
+struct DefaultGetIteratorSpec
+{
+ typedef Rooted Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Metafunction.Iterator:
+..summary:Type of iterator objects that are used to traverse the container.
+..signature:Iterator<T, TSpec>::Type
+..param.T:Type for which the iterator type is determined.
+...concept:Concept.Container
+...type:Class.Iter
+..param.TSpec:Specifies an @Tag.Iterator Spec.iterator spec at .
+...default:The default iterator spec is given by @Metafunction.DefaultIteratorSpec at .
+..returns.param.Type:Iterator type of $T$.
+..remarks.text:Iterators behave like pointers in some respects.
+ For example, you can use $*it$ to access the value object the iterator $it$ points to.
+ But note that $Iterator<T>::Type$ can differ from $T *$, depending on $T$.
+..see:Metafunction.Position
+*/
+
+//____________________________________________________________________________
+
+template <typename T, typename TSpec>
+struct Iterator_Default_Imp;
+
+//Iterator_Default_Imp<T, Standard> is implemented in basic_iterator_simple.h
+//Iterator_Default_Imp<T, Rooted> is implemented in basic_iterator_adaptor.h
+
+//____________________________________________________________________________
+
+template <typename T, typename TSpec = typename DefaultIteratorSpec<T>::Type>
+struct Iterator:
+ Iterator_Default_Imp<T, TSpec>
+{
+};
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Metafunction.Container:
+..summary:Type of the container given an iterator.
+..signature:Container<T>::Type
+..param.T:Iterator type.
+...type:Class.Iter
+...concept:Concept.Iterator
+..returns.param.Type:The container type to $T$.
+*/
+
+template <typename T>
+struct Container
+{
+ typedef T Type;
+};
+
+
+//////////////////////////////////////////////////////////////////////////////
+// GENERAL FUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+
+//////////////////////////////////////////////////////////////////////////////
+// value
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.value:
+..signature:Reference value(object)
+..param.object:An object that holds a value or an iterator that points to a value.
+...type:Class.Iter
+...concept:Concept.Iterator
+*/
+
+template <typename T>
+inline typename Reference<T>::Type
+value(T & me)
+{
+SEQAN_CHECKPOINT
+ return *me;
+}
+template <typename T>
+inline typename Reference<T const>::Type
+value(T const & me)
+{
+SEQAN_CHECKPOINT
+ return *me;
+}
+
+
+template <typename T>
+inline T &
+value(T * me)
+{
+SEQAN_CHECKPOINT
+ return *me;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// getValue
+//////////////////////////////////////////////////////////////////////////////
+
+//unary getValue
+/**
+.Function.getValue:
+..cat:Iteration
+..signature:GetValue getValue(object)
+..param.object:An object that holds a value or points to a value.
+...type:Class.Iter
+...concept:Concept.Iterator
+..see:Metafunction.GetValue
+*/
+
+template <typename T>
+inline typename GetValue<T>::Type
+getValue(T & me)
+{
+SEQAN_CHECKPOINT
+ return value(me);
+}
+template <typename T>
+inline typename GetValue<T const>::Type
+getValue(T const & me)
+{
+SEQAN_CHECKPOINT
+ return value(me);
+}
+
+template <typename T>
+inline T &
+getValue(T * me)
+{
+SEQAN_CHECKPOINT
+ return value(me);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//toGetValue
+//////////////////////////////////////////////////////////////////////////////
+//Nimmt eine Reference und macht daraus einen GetValue
+//???TODO toGetValue()
+
+//////////////////////////////////////////////////////////////////////////////
+// assignValue
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.assignValue:
+..cat:Iteration
+..summary:Assigns value to item.
+..signature:assignValue(object, value)
+..param.object:An object that holds a value or points to a value.
+...type:Class.Iter
+...concept:Concept.Iterator
+..param.value:A value that is assigned to the item $object$ holds or points to.
+..remarks.text:This function is similar to @Function.assign at .
+The difference is, that $assignValue$ just changes a value stored in $object$ or the value $object$ points to,
+while @Function.assign@ changes the whole object.
+..see:Function.assign
+*/
+
+template <typename T, typename TValue>
+inline void
+assignValue(T & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ assign(value(me), _value);
+}
+
+//const version for iterators as targets
+template <typename T, typename TValue>
+inline void
+assignValue(T const & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ assign(value(me), _value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// moveValue
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.moveValue:
+..cat:Iteration
+..summary:Assigns value to item.
+..signature:moveValue(object, value)
+..param.object:An object that holds a value or points to a value.
+...type:Class.Iter
+...concept:Concept.Iterator
+..param.value:A value that is handed over to the item $object$ holds or points to.
+..remarks.text:This function is similar to @Function.move at .
+The difference is, that $moveValue$ just changes a value stored in $object$ or the value $object$ points to,
+while @Function.move@ changes the whole object.
+..see:Function.move
+..see:Function.assignValue
+*/
+
+template <typename T, typename TValue>
+inline void
+moveValue(T & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ move(value(me), _value);
+}
+//const version for iterators as targets
+template <typename T, typename TValue>
+inline void
+moveValue(T const & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ move(value(me), _value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.container:
+..cat:Iteration
+..summary:Container of an iterator.
+..signature:Container container(iterator)
+..param.iterator:An iterator.
+...type:Class.Iter
+...concept:Concept.Rooted Iterator
+..returns:The container that $iterator$ traverses.
+...metafunction:Metafunction.Container
+*/
+
+template <typename T>
+inline typename Container<T>::Type
+container(T me)
+{
+SEQAN_CHECKPOINT
+ return me;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.position:
+..summary:Position of an iterator.
+..cat:Iteration
+..signature:Position position(iterator [, container])
+..param.iterator:An iterator.
+...type:Class.Iter
+...concept:Concept.Iterator
+..param.container:A container.
+...concept:Concept.Container
+...remarks:If $iterator$ implements @Concept.Rooted Iterator@, then $container$ is optional.
+...remarks:If $container$ is specified, $iterator$ must be a container of $container$.
+..returns:The position of the value in the container $iterator$ points to.
+...metafunction:Metafunction.Position
+*/
+
+template <typename T>
+inline typename Position<T>::Type
+position(T * me)
+{
+SEQAN_CHECKPOINT
+ return 0;
+}
+
+template <typename TContainer, typename TIterator>
+inline typename Position<TContainer>::Type
+position(TIterator const & it,
+ TContainer const & me)
+{
+SEQAN_CHECKPOINT
+ return it - begin(me, Standard());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+//////////////////////////////////////////////////////////////////////////////
+// atBegin
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.atBegin:
+..cat:Iteration
+..summary:Determines whether an iterator is at the beginning position.
+..signature:bool atBegin(iterator [, container])
+..param.iterator:An iterator.
+...type:Class.Iter
+...concept:Concept.Iterator
+..param.container:Container of $iterator$. (optional)
+...remarks.text:If $iterator$ implements @Concept.Rooted Iterator@ then $container$ is optional otherwise $container$ is required.
+..returns:$true$ if $iterator$ points to the fist item of the container, otherwise $false$.
+..see:Function.begin
+*/
+
+//TODO???: Was, wenn der Container leer ist?
+
+template <typename T, typename TContainer>
+inline bool
+atBegin(T const & it, TContainer const & cont)
+{
+SEQAN_CHECKPOINT
+ return it == begin(cont, Standard());
+}
+
+//____________________________________________________________________________
+
+template <typename T>
+inline bool
+atBegin(T const & it)
+{
+SEQAN_CHECKPOINT
+ return atBegin(it, container(it));
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// atEnd
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.atEnd:
+..cat:Iteration
+..summary:Determines whether an iterator is at the end position.
+..signature:bool atEnd(iterator [, container])
+..param.iterator:An iterator.
+...type:Class.Iter
+...concept:Concept.Iterator
+..param.container:Container of $iterator$.
+...remarks.text:If $iterator$ implements @Concept.Rooted Iterator@ then $container$ is optional.
+....text:$container$ is also optional for iterators to @Adaption.char array.char arrays at .
+....text:Otherwise, $container$ is required.
+..returns:$true$ if $iterator$ points behind the last item of the container, otherwise $false$.
+..see:Function.atBegin
+..see:Function.end
+*/
+
+template <typename T, typename TContainer>
+inline bool
+atEnd(T & it,
+ TContainer const & cont)
+{
+SEQAN_CHECKPOINT
+ return it == end(cont, Standard());
+}
+template <typename T, typename TContainer>
+inline bool
+atEnd(T const & it,
+ TContainer const & cont)
+{
+SEQAN_CHECKPOINT
+ return it == end(cont, Standard());
+}
+//____________________________________________________________________________
+
+template <typename T>
+inline bool
+atEnd(T & it)
+{
+SEQAN_CHECKPOINT
+ return atEnd(it, container(it));
+}
+template <typename T>
+inline bool
+atEnd(T const & it)
+{
+SEQAN_CHECKPOINT
+ return atEnd(it, container(it));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// goBegin
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.goBegin:
+..cat:Iteration
+..summary:Iterates to the first position of a container.
+..signature:goBegin(iterator [, container])
+..param.iterator:Object that iterates through $container$.
+...type:Class.Iter
+...concept:Concept.Iterator
+...text:$iterator$ is set to the position of the first item in $container$.
+..param.container:Container of $iterator$.
+...remarks.text:If $iterator$ implements @Concept.Rooted Iterator@ then $container$ is optional,
+otherwise $container$ is required.
+..remarks:This function is equivalent to $iterator = begin(container)$.
+..see:Function.begin
+..see:Function.atBegin
+..see:Function.goEnd
+*/
+template <typename TIterator, typename TContainer>
+inline void
+goBegin(TIterator & it,
+ TContainer & container)
+{
+SEQAN_CHECKPOINT
+ it = begin(container);
+}
+/*
+template <typename TIterator, typename TContainer>
+inline void
+goBegin(TIterator & it,
+ TContainer const & container)
+{
+SEQAN_CHECKPOINT
+ it = begin(container);
+}
+*/
+
+template <typename TIterator>
+inline void
+goBegin(TIterator & it)
+{
+SEQAN_CHECKPOINT
+ goBegin(it, container(it));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// goEnd
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.goEnd:
+..cat:Iteration
+..summary:Iterates to the last position of a container.
+..signature:goEnd(iterator [, container])
+..param.iterator:Object that iterates through $container$.
+...type:Class.Iter
+...concept:Concept.Iterator
+...text:$iterator$ is set to the position behin the last item in $container$.
+..param.container:Container of $iterator$.
+...remarks.text:If $iterator$ implements @Concept.Rooted Iterator@ then $container$ is optional,
+otherwise $container$ is required.
+..remarks:This function is equivalent to $iterator = end(container)$.
+..see:Function.end
+..see:Function.atEnd
+..see:Function.goBegin
+..see:Function.goEnd
+*/
+template <typename TIterator, typename TContainer>
+inline void
+goEnd(TIterator & it,
+ TContainer & container)
+{
+SEQAN_CHECKPOINT
+ it = end(container);
+}
+template <typename TIterator, typename TContainer>
+inline void
+goEnd(TIterator & it,
+ TContainer const & container)
+{
+SEQAN_CHECKPOINT
+ it = end(container);
+}
+
+template <typename TIterator>
+inline void
+goEnd(TIterator & it)
+{
+SEQAN_CHECKPOINT
+ goEnd(it, container(it));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// goNext
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.goNext:
+..cat:Iteration
+..summary:Iterates to next position.
+..signature:goNext(iterator)
+..param.iterator:An iterator.
+...type:Class.Iter
+...concept:Concept.Iterator
+...text:$iterator$ is set to the next position of an iteration through its container.
+..remarks:This function is equivalent to $++iterator$.
+..see:Function.goBegin
+..see:Function.goEnd
+*/
+template <typename TIterator>
+inline void
+goNext(TIterator & it)
+{
+SEQAN_CHECKPOINT
+ ++it;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// goFurther
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.goFurther:
+..cat:Iteration
+..summary:Iterates some steps further.
+..signature:goFurther(iterator, steps)
+..param.iterator:An iterator.
+...type:Class.Iter
+...concept:Concept.Iterator
+...text:$iterator$ is set $steps$ positions further in the iteration through the container.
+..param.steps:Number of steps $iterator$ should be moved further.
+...remarks:If $iterator$ supports bidirectional iteration, $steps$ could also be negativ.
+..remarks:This function is equivalent to $iterator += steps$ for random access iterators.
+..see:Function.goNext
+..see:Function.goPrevious
+*/
+
+template <typename TIterator, typename TDiff> inline
+void goFurther(TIterator & it, TDiff steps)
+{ // return distance type from arbitrary argument
+ it += steps;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// goPrevious
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.goPrevious:
+..cat:Iteration
+..summary:Iterates to pevious position.
+..signature:goPrevious(iterator)
+..param.iterator:An iterator.
+...type:Class.Iter
+...concept:Concept.Iterator
+...text:$iterator$ is set to the pevious position of an iteration through its container.
+..remarks:This function is equivalent to $--iterator$.
+..see:Function.goBegin
+..see:Function.goEnd
+..see:Function.goNext
+*/
+template <typename TIterator>
+inline void
+goPrevious(TIterator & it)
+{
+SEQAN_CHECKPOINT
+ --it;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// difference
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.difference:
+..cat:Iteration
+..summary:The difference between two iterators.
+..signature:difference(begin, end)
+..param.begin:Iterator to the first position of a range.
+...type:Class.Iter
+...Concept.Iterator
+..param.end:Iterator behind the last position of a range.
+...type:Class.Iter
+...Concept.Iterator
+..returns:Length of the range between $begin$ and $end$.
+..remarks:This function is equivalent to $begin - end$.
+...text:Usually, $begin$ and $end$ have the same type.
+..see:Function.begin
+..see:Function.end
+..see:Function.length
+*/
+
+template <typename TIterator> inline
+typename Difference<TIterator>::Type difference(
+ TIterator const & begin,
+ TIterator const & end)
+{ // return distance type from arbitrary argument
+SEQAN_CHECKPOINT
+ return end - begin;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// goNil
+//////////////////////////////////////////////////////////////////////////////
+
+
+/**
+.Function.goNil:
+..cat:Iteration
+..summary:Moves iterator to nil position.
+..signature:goNil(iterator)
+..param.iterator:The iterator that will be moved.
+...type:Class.String
+..remarks:$iterator$ is set to an invalid position, e.g. $NULL$ for pointer types.
+..see:Function.clear
+*/
+
+template <typename TIterator>
+inline void
+goNil(TIterator & me)
+{
+SEQAN_CHECKPOINT
+ me = TIterator();
+}
+
+template <typename TIterator>
+inline void
+goNil(TIterator * & me)
+{
+SEQAN_CHECKPOINT
+ me = 0;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// atNil
+//////////////////////////////////////////////////////////////////////////////
+
+
+/**
+.Function.atNil:
+..cat:Iteration
+..summary:Tests whether iterator is at nil position.
+..signature:bool atNil(iterator)
+..param.iterator:An iterator.
+...type:Class.String
+..returns:$true$ if $iterator$ points to an ivalid position, e.g. $iterator$ is a $NULL$ pointer.
+$false$ otherwise.
+..see:Function.goNil
+*/
+
+template <typename TIterator>
+inline bool
+atNil(TIterator & me)
+{
+SEQAN_CHECKPOINT
+ return me == TIterator();
+}
+
+
+template <typename TIterator>
+inline bool
+atNil(TIterator * me)
+{
+SEQAN_CHECKPOINT
+ return me == 0;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_iterator_adapt_std.h b/src/libSSA/seqan/basic/basic_iterator_adapt_std.h
new file mode 100644
index 0000000..a39f23b
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_iterator_adapt_std.h
@@ -0,0 +1,436 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_iterator_adapt_std.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_ITERATOR_ADAPT_STD_H
+#define SEQAN_HEADER_BASIC_ITERATOR_ADAPT_STD_H
+
+//////////////////////////////////////////////////////////////////////////////
+
+//adapt SeqAn iterator to std
+namespace std
+{
+ template<typename TContainer, typename TSpec>
+ struct iterator_traits<seqan::Iter<TContainer, TSpec> >
+ {
+ typedef ::seqan::Iter<TContainer, TSpec> TIter;
+
+ typedef random_access_iterator_tag iterator_category;
+ typedef typename ::seqan::Value<TIter>::Type value_type;
+ typedef typename ::seqan::Difference<TIter>::Type difference_type;
+ typedef typename ::seqan::Value<TIter>::Type * pointer;
+ typedef typename ::seqan::Reference<TIter>::Type reference;
+ };
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//helper Metafunction
+
+/* This simple, general implementation cannot be used due to strange VC++ 2003 behavior
+
+template <typename TStdContainer>
+struct StdContainerIterator
+{
+ typedef typename TStdContainer::iterator Type;
+};
+
+template <typename TStdContainer>
+struct StdContainerIterator<TStdContainer const>
+{
+ typedef typename TStdContainer::const_iterator Type;
+};
+*/
+
+//we use this instead: specialize StdContainerIterator for each std-container
+template <typename TStdContainer>
+struct StdContainerIterator
+{
+ typedef void * Type; //dummy, just to make VC++ 2003 happy
+};
+
+template <typename TChar, typename TCharTraits, typename TAlloc>
+struct StdContainerIterator< ::std::basic_string<TChar, TCharTraits, TAlloc> >
+{
+ typedef ::std::basic_string<TChar, TCharTraits, TAlloc> TContainer;
+ typedef typename TContainer::iterator Type;
+};
+template <typename TChar, typename TCharTraits, typename TAlloc>
+struct StdContainerIterator< ::std::basic_string<TChar, TCharTraits, TAlloc> const>
+{
+ typedef ::std::basic_string<TChar, TCharTraits, TAlloc> TContainer;
+ typedef typename TContainer::const_iterator Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+//adapt std iterator to SeqAn
+
+
+struct StdIteratorAdaptor;
+
+template <typename TContainer>
+class Iter<TContainer, StdIteratorAdaptor>
+{
+public:
+ typedef typename StdContainerIterator<TContainer>::Type TIterator;
+ TIterator data_iterator;
+
+ Iter() {}
+ Iter(Iter const & other_): data_iterator(other_.data_iterator) {}
+ Iter(TIterator const & iter_): data_iterator(iter_) {}
+ Iter(TContainer const & cont_): data_iterator(begin(cont_)) {}
+
+ Iter const & operator = (Iter const & other_)
+ {
+ data_iterator = other_.data_iterator;
+ return *this;
+ }
+ Iter const & operator = (TIterator const & iter_)
+ {
+ data_iterator = iter_;
+ return *this;
+ }
+
+ operator TIterator &()
+ {
+ return data_iterator;
+ }
+
+ ~Iter() {}
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// hostIterator
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline typename StdContainerIterator<TContainer>::Type &
+hostIterator(Iter<TContainer, StdIteratorAdaptor> & me)
+{
+ return me.data_iterator;
+}
+template <typename TContainer>
+inline typename StdContainerIterator<TContainer>::Type const &
+hostIterator(Iter<TContainer, StdIteratorAdaptor> const & me)
+{
+ return me.data_iterator;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// value
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline typename Reference<Iter<TContainer, StdIteratorAdaptor> >::Type
+value(Iter<TContainer, StdIteratorAdaptor> & me)
+{
+ return *(me.data_iterator);
+}
+template <typename TContainer>
+inline typename Reference<Iter<TContainer, StdIteratorAdaptor> const>::Type
+value(Iter<TContainer, StdIteratorAdaptor> const & me)
+{
+ return *(me.data_iterator);
+}
+
+
+/////////////////////////////////////////////////////////////////////////////
+// assignValue
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TValue>
+inline void
+assignValue(Iter<TContainer, StdIteratorAdaptor> & me,
+ TValue & val)
+{
+ *(me.data_iterator) = val;
+}
+template <typename TContainer, typename TValue>
+inline void
+assignValue(Iter<TContainer, StdIteratorAdaptor> & me,
+ TValue const & val)
+{
+ *(me.data_iterator) = val;
+}
+
+/////////////////////////////////////////////////////////////////////////////
+// moveValue
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TValue>
+inline void
+moveValue(Iter<TContainer, StdIteratorAdaptor> & me,
+ TValue & val)
+{
+ move(*(me.data_iterator), val);
+}
+template <typename TContainer, typename TValue>
+inline void
+moveValue(Iter<TContainer, StdIteratorAdaptor> & me,
+ TValue const & val)
+{
+ move(*(me.data_iterator), val);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator ==
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline bool
+operator == (Iter<TContainer, StdIteratorAdaptor> const & left,
+ Iter<TContainer, StdIteratorAdaptor> const & right)
+{
+SEQAN_CHECKPOINT
+ return hostIterator(left) == hostIterator(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator !=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline bool
+operator != (Iter<TContainer, StdIteratorAdaptor> const & left,
+ Iter<TContainer, StdIteratorAdaptor> const & right)
+{
+SEQAN_CHECKPOINT
+ return hostIterator(left) != hostIterator(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator <
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline bool
+operator < (Iter<TContainer, StdIteratorAdaptor> const & left,
+ Iter<TContainer, StdIteratorAdaptor> const & right)
+{
+SEQAN_CHECKPOINT
+ return hostIterator(left) < hostIterator(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator >
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline bool
+operator > (Iter<TContainer, StdIteratorAdaptor> const & left,
+ Iter<TContainer, StdIteratorAdaptor> const & right)
+{
+SEQAN_CHECKPOINT
+ return hostIterator(left) > hostIterator(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator <=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline bool
+operator <= (Iter<TContainer, StdIteratorAdaptor> const & left,
+ Iter<TContainer, StdIteratorAdaptor> const & right)
+{
+SEQAN_CHECKPOINT
+ return hostIterator(left) <= hostIterator(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator >=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline bool
+operator >= (Iter<TContainer, StdIteratorAdaptor> const & left,
+ Iter<TContainer, StdIteratorAdaptor> const & right)
+{
+SEQAN_CHECKPOINT
+ return hostIterator(left) >= hostIterator(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// goNext
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline void
+goNext(Iter<TContainer, StdIteratorAdaptor> & me)
+{
+SEQAN_CHECKPOINT
+ goNext(hostIterator(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// goPrevious
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline void
+goPrevious(Iter<TContainer, StdIteratorAdaptor> & me)
+{
+SEQAN_CHECKPOINT
+ goPrevious(hostIterator(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator +
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIntegral>
+inline Iter<TContainer, StdIteratorAdaptor>
+operator + (Iter<TContainer, StdIteratorAdaptor> const & left,
+ TIntegral right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, StdIteratorAdaptor>(hostIterator(left) + right);
+}
+// for <anonymous enum> types
+template <typename TContainer>
+inline Iter<TContainer, StdIteratorAdaptor>
+operator + (Iter<TContainer, StdIteratorAdaptor> const & left,
+ int right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, StdIteratorAdaptor>(hostIterator(left) + right);
+}
+
+template <typename TContainer, typename TIntegral>
+inline Iter<TContainer, StdIteratorAdaptor>
+operator + (TIntegral left,
+ Iter<TContainer, StdIteratorAdaptor> const & right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, StdIteratorAdaptor>(hostIterator(right) + left);
+}
+// for <anonymous enum> types
+template <typename TContainer>
+inline Iter<TContainer, StdIteratorAdaptor>
+operator + (int left,
+ Iter<TContainer, StdIteratorAdaptor> const & right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, StdIteratorAdaptor>(hostIterator(right) + left);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator +=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIntegral>
+inline Iter<TContainer, StdIteratorAdaptor> &
+operator += (Iter<TContainer, StdIteratorAdaptor> & left,
+ TIntegral right)
+{
+SEQAN_CHECKPOINT
+ hostIterator(left) += right;
+ return left;
+}
+// for <anonymous enum> types
+template <typename TContainer>
+inline Iter<TContainer, StdIteratorAdaptor> &
+operator += (Iter<TContainer, StdIteratorAdaptor> & left,
+ int right)
+{
+SEQAN_CHECKPOINT
+ hostIterator(left) += right;
+ return left;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator -
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIntegral>
+inline Iter<TContainer, StdIteratorAdaptor>
+operator - (Iter<TContainer, StdIteratorAdaptor> const & left,
+ TIntegral right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, StdIteratorAdaptor>(hostIterator(left) - right);
+}
+// for <anonymous enum> types
+template <typename TContainer>
+inline Iter<TContainer, StdIteratorAdaptor>
+operator - (Iter<TContainer, StdIteratorAdaptor> const & left,
+ int right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, StdIteratorAdaptor>(hostIterator(left) - right);
+}
+
+//____________________________________________________________________________
+
+template <typename TContainer>
+inline typename Difference<Iter<TContainer, StdIteratorAdaptor> >::Type
+operator - (Iter<TContainer, StdIteratorAdaptor> const & left,
+ Iter<TContainer, StdIteratorAdaptor> const & right)
+{
+SEQAN_CHECKPOINT
+ return hostIterator(left) - hostIterator(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator -=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIntegral>
+inline Iter<TContainer, StdIteratorAdaptor> &
+operator -= (Iter<TContainer, StdIteratorAdaptor> & left,
+ TIntegral right)
+{
+SEQAN_CHECKPOINT
+ hostIterator(left) -= right;
+ return left;
+}
+// for <anonymous enum> types
+template <typename TContainer>
+inline Iter<TContainer, StdIteratorAdaptor> &
+operator -= (Iter<TContainer, StdIteratorAdaptor> & left,
+ int right)
+{
+SEQAN_CHECKPOINT
+ hostIterator(left) -= right;
+ return left;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+// assign (Conversion)
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TTargetContainer, typename TSource>
+inline void
+assign(Iter<TTargetContainer, StdIteratorAdaptor> & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ target.data_iterator = begin(container(source)) + position(source);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_iterator_adaptor.h b/src/libSSA/seqan/basic/basic_iterator_adaptor.h
new file mode 100644
index 0000000..9a68a98
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_iterator_adaptor.h
@@ -0,0 +1,524 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_iterator_adaptor.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_ITERATOR_ADAPTOR_H
+#define SEQAN_HEADER_BASIC_ITERATOR_ADAPTOR_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+// Tag
+
+//An iterator that adapts a std iterator to a default seqan iterator
+template <typename TIterator, typename TSpec = Default>
+struct AdaptorIterator;
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename T>
+struct Iterator_Default_Imp<T, Rooted>
+{
+ typedef typename Iterator<T, Standard>::Type TStandardIterator;
+ typedef Iter<T, AdaptorIterator<TStandardIterator> > Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// Adaptor Iterator
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Spec.Adaptor Iterator:
+..cat:Iterators
+..general:Class.Iter
+..summary:Adapts iterators to @Concept.Rooted Iterator at .
+..signature:Iter<TContainer, AdaptorIterator<TIterator [, TSpec]> >
+..param.TContainer:Type of the container that can be iterated by $TIterator$.
+...remarks:Use @Metafunction.Container@ to get the container type for a given iterator.
+..param.TIterator:Type of the iterator that is adapted to @Concept.Rooted Iterator at .
+..remarks.text:Adaptor iterators can implicitly converted to $TIterator$.
+*/
+
+template <typename TContainer, typename TIterator, typename TSpec>
+class Iter<TContainer, AdaptorIterator<TIterator, TSpec> >
+{
+private:
+ typename _Pointer<TContainer>::Type data_container;
+ TIterator data_iterator;
+//____________________________________________________________________________
+
+/**
+.Memfunc.AdaptorIterator#Iter:
+..class:Spec.Adaptor Iterator
+..summary:Constructor
+..signature:Iter()
+..signature:Iter(iter)
+..signature:Iter(container [, iterator])
+..param.iter:Another adaptor iterator object.
+..param.container:The corresponding container object.
+..param.iterator:A iterator of $container$. (optional)
+...remarks.text:If this argument is omitted, the adaptor iterator is initialized to the @Function.begin.begin iterator@ of $container$.
+*/
+
+public:
+ Iter():
+ data_container(0)
+ {
+SEQAN_CHECKPOINT
+ data_iterator = TIterator();
+ }
+/*//TODO: welches "begin" zur initialisierung von "data_iterator" aufrufen?
+ Iter(typename _Parameter<TContainer>::Type container_):
+ data_container(_toPointer(container_)),
+ data_iterator(begin(container_))
+ {
+SEQAN_CHECKPOINT
+ }
+*/
+ Iter(typename _Parameter<TContainer>::Type container_, TIterator it_):
+ data_container(_toPointer(container_)),
+ data_iterator(it_)
+ {
+SEQAN_CHECKPOINT
+ }
+ Iter(Iter const & other_):
+ data_container(other_.data_container),
+ data_iterator(other_.data_iterator)
+ {
+SEQAN_CHECKPOINT
+ }
+/*
+ template <typename TSource>
+ Iter(TSource & source)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source);
+ }
+ template <typename TSource>
+ Iter(TSource const & source)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source);
+ }
+*/
+
+ ~Iter()
+ {
+SEQAN_CHECKPOINT
+ }
+
+ Iter const &
+ operator = (Iter const & other_)
+ {
+SEQAN_CHECKPOINT
+ data_container = other_.data_container;
+ data_iterator = other_.data_iterator;
+ return *this;
+ }
+/*
+ template <typename TSource>
+ Iter const &
+ operator = (TSource & source)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source);
+ return *this;
+ }
+ template <typename TSource>
+ Iter const &
+ operator = (TSource const & source)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source);
+ return *this;
+ }
+*/
+//____________________________________________________________________________
+
+ friend inline typename _Parameter<TContainer>::Type
+ container(Iter & me)
+ {
+SEQAN_CHECKPOINT
+ return _toParameter<TContainer>(me.data_container);
+ }
+ friend inline typename _Parameter<TContainer>::Type
+ container(Iter const & me)
+ {
+SEQAN_CHECKPOINT
+ return _toParameter<TContainer>(me.data_container);
+ }
+//____________________________________________________________________________
+
+ friend inline void
+ setContainer(Iter & me, typename _Parameter<TContainer>::Type container_)
+ {
+SEQAN_CHECKPOINT
+ if (me.data_container && me.data_iterator != TIterator())
+ {
+ typename Position<Iter>::Type pos = position(me);
+ me.data_container = _toPointer(container_);
+ setPosition(me, pos);
+ }
+ else
+ {
+ me.data_container = _toPointer(container_);
+ }
+ }
+
+//____________________________________________________________________________
+
+ friend inline TIterator &
+ hostIterator(Iter & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_iterator;
+ }
+ friend inline TIterator const &
+ hostIterator(Iter const & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_iterator;
+ }
+
+//____________________________________________________________________________
+
+ operator TIterator () const
+ {
+SEQAN_CHECKPOINT
+ return data_iterator;
+ }
+
+//____________________________________________________________________________
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// METAFUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+/*
+template <typename TContainer, typename TIterator, typename TSpec>
+struct Reference<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const>:
+ Reference<TIterator const>
+{
+};
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+// FUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+
+//////////////////////////////////////////////////////////////////////////////
+// position
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIterator, typename TSpec>
+inline typename Position<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const>::Type
+position(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me)
+{
+SEQAN_CHECKPOINT
+ return hostIterator(me) - begin(container(me), Standard());
+}
+
+//____________________________________________________________________________
+
+template <typename TContainer, typename TIterator, typename TSpec, typename TContainer2>
+inline typename Position<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const>::Type
+position(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me,
+ TContainer2 const &)
+{
+SEQAN_CHECKPOINT
+ return hostIterator(me) - begin(container(me), Standard());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// setPosition
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIterator, typename TSpec, typename TPosition>
+inline void
+setPosition(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me,
+ TPosition pos_)
+{
+SEQAN_CHECKPOINT
+ hostIterator(me) = begin(container(me), Standard()) + pos_;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// value
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIterator, typename TSpec>
+inline typename Reference<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > >::Type
+value(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me)
+{
+SEQAN_CHECKPOINT
+ return value(hostIterator(me));
+}
+template <typename TContainer, typename TIterator, typename TSpec>
+inline typename Reference<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const>::Type
+value(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me)
+{
+SEQAN_CHECKPOINT
+ return value(hostIterator(me));
+}
+
+/////////////////////////////////////////////////////////////////////////////
+// assignValue
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIterator, typename TSpec, typename TValue>
+inline void
+assignValue(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ assignValue(hostIterator(me), _value);
+}
+template <typename TContainer, typename TIterator, typename TSpec, typename TValue>
+inline void
+assignValue(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ assignValue(hostIterator(me), _value);
+}
+
+/////////////////////////////////////////////////////////////////////////////
+// moveValue
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIterator, typename TSpec, typename TValue>
+inline void
+moveValue(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ moveValue(hostIterator(me), _value);
+}
+template <typename TContainer, typename TIterator, typename TSpec, typename TValue>
+inline void
+moveValue(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ moveValue(hostIterator(me), _value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator ==
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIterator, typename TSpec>
+inline bool
+operator == (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & left,
+ Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & right)
+{
+SEQAN_CHECKPOINT
+ return hostIterator(left) == hostIterator(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator !=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIterator, typename TSpec>
+inline bool
+operator != (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & left,
+ Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & right)
+{
+SEQAN_CHECKPOINT
+ return hostIterator(left) != hostIterator(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// goNext
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIterator, typename TSpec>
+inline void
+goNext(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me)
+{
+SEQAN_CHECKPOINT
+ goNext(hostIterator(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// goPrevious
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIterator, typename TSpec>
+inline void
+goPrevious(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me)
+{
+SEQAN_CHECKPOINT
+ goPrevious(hostIterator(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator +
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIterator, typename TSpec, typename TIntegral>
+inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> >
+operator + (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & left,
+ TIntegral right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(left), hostIterator(left) + right);
+}
+// for <anonymous enum> types
+template <typename TContainer, typename TIterator, typename TSpec>
+inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> >
+operator + (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & left,
+ int right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(left), hostIterator(left) + right);
+}
+
+template <typename TContainer, typename TIterator, typename TSpec, typename TIntegral>
+inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> >
+operator + (TIntegral left,
+ Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(right), hostIterator(right) + left);
+}
+// for <anonymous enum> types
+template <typename TContainer, typename TIterator, typename TSpec>
+inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> >
+operator + (int left,
+ Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(right), hostIterator(right) + left);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator +=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIterator, typename TSpec, typename TIntegral>
+inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> > &
+operator += (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & left,
+ TIntegral right)
+{
+SEQAN_CHECKPOINT
+ hostIterator(left) += right;
+ return left;
+}
+// for <anonymous enum> types
+template <typename TContainer, typename TIterator, typename TSpec>
+inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> > &
+operator += (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & left,
+ int right)
+{
+SEQAN_CHECKPOINT
+ hostIterator(left) += right;
+ return left;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator -
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIterator, typename TSpec, typename TIntegral>
+inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> >
+operator - (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & left,
+ TIntegral right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(left), hostIterator(left) - right);
+}
+// for <anonymous enum> types
+template <typename TContainer, typename TIterator, typename TSpec>
+inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> >
+operator - (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & left,
+ int right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(left), hostIterator(left) - right);
+}
+
+//____________________________________________________________________________
+
+template <typename TContainer, typename TIterator, typename TSpec>
+inline typename Difference<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > >::Type
+operator - (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & left,
+ Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & right)
+{
+SEQAN_CHECKPOINT
+ return hostIterator(left) - hostIterator(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator -=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIterator, typename TSpec, typename TIntegral>
+inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> > &
+operator -= (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & left,
+ TIntegral right)
+{
+SEQAN_CHECKPOINT
+ hostIterator(left) -= right;
+ return left;
+}
+// for <anonymous enum> types
+template <typename TContainer, typename TIterator, typename TSpec>
+inline Iter<TContainer, AdaptorIterator<TIterator, TSpec> > &
+operator -= (Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & left,
+ int right)
+{
+SEQAN_CHECKPOINT
+ hostIterator(left) -= right;
+ return left;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+// atEnd
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIterator, typename TSpec>
+inline bool
+atEnd(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me)
+{
+SEQAN_CHECKPOINT
+ return atEnd(me, container(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// assign (Conversion)
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TTargetContainer, typename TIterator, typename TSpec, typename TSource>
+inline void
+assign(Iter<TTargetContainer, AdaptorIterator<TIterator, TSpec> > & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ target.data_container = container(source);
+ target.data_iterator = begin(container(source)) + position(source);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_iterator_base.h b/src/libSSA/seqan/basic/basic_iterator_base.h
new file mode 100644
index 0000000..4c3049a
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_iterator_base.h
@@ -0,0 +1,221 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_iterator_base.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_ITERATOR_BASE_H
+#define SEQAN_HEADER_BASIC_ITERATOR_BASE_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+// Iter
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Class.Iter:
+..cat:Basic
+..summary:Iterator that is used to traverse containers.
+..signature:Iter<TContainer, TSpec>
+..param.TContainer:Type of the container that can be iterated by $Iter$.
+...metafunction:Metafunction.Container
+..param.TSpec:The specializing type.
+...metafunction:Metafunction.Spec
+..implements:Concept.Iterator
+*/
+template <typename TContainer, typename TSpec>
+class Iter;
+
+//////////////////////////////////////////////////////////////////////////////
+///.Metafunction.Spec.param.T.type:Class.Iter
+
+template <typename TContainer, typename TSpec>
+struct Spec<Iter<TContainer, TSpec> >
+{
+ typedef TSpec Type;
+};
+template <typename TContainer, typename TSpec>
+struct Spec<Iter<TContainer, TSpec> const>
+{
+ typedef TSpec Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Value.param.T.type:Class.Iter
+
+template <typename TContainer, typename TSpec>
+struct Value<Iter<TContainer, TSpec> >:
+ Value<TContainer>
+{
+};
+template <typename TContainer, typename TSpec>
+struct Value<Iter<TContainer, TSpec> const>:
+ Value<TContainer>
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.GetValue.param.T.type:Class.Iter
+
+template <typename TContainer, typename TSpec>
+struct GetValue<Iter<TContainer, TSpec> >:
+ GetValue<TContainer>
+{
+};
+template <typename TContainer, typename TSpec>
+struct GetValue<Iter<TContainer, TSpec> const>:
+ GetValue<TContainer>
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Reference.param.T.type:Class.Iter
+
+template <typename TContainer, typename TSpec>
+struct Reference<Iter<TContainer, TSpec> >:
+ Reference<TContainer>
+{
+};
+template <typename TContainer, typename TSpec>
+struct Reference<Iter<TContainer, TSpec> const>:
+ Reference<TContainer>
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Container.param.T.type:Class.Iter
+
+template <typename T> struct Container;
+
+template <typename TContainer, typename TSpec>
+struct Container<Iter<TContainer, TSpec> >
+{
+ typedef TContainer Type;
+};
+template <typename TContainer, typename TSpec>
+struct Container<Iter<TContainer, TSpec> const>
+{
+ typedef TContainer Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+/*
+///.Metafunction.Host.param.T.type:Class.Iter
+
+template <typename TContainer, typename TSpec>
+struct Host<Iter<TContainer, TSpec> >:
+ Container<Iter<TContainer, TSpec> >
+{
+};
+template <typename TContainer, typename TSpec>
+struct Host<Iter<TContainer, TSpec> const>:
+ Container<Iter<TContainer, TSpec> const>
+{
+};
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+// operator *
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TSpec>
+inline typename Reference<Iter<TContainer, TSpec> >::Type
+operator * (Iter<TContainer, TSpec> & me)
+{
+SEQAN_CHECKPOINT
+ return value(me);
+}
+template <typename TContainer, typename TSpec>
+inline typename Reference<Iter<TContainer, TSpec> const>::Type
+operator * (Iter<TContainer, TSpec> const & me)
+{
+SEQAN_CHECKPOINT
+ return value(me);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator ++
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TSpec>
+inline Iter<TContainer, TSpec> const &
+operator ++ (Iter<TContainer, TSpec> & me)
+{
+SEQAN_CHECKPOINT
+ goNext(me);
+ return me;
+}
+
+template <typename TContainer, typename TSpec>
+inline Iter<TContainer, TSpec> const
+operator ++ (Iter<TContainer, TSpec> & me, int)
+{
+SEQAN_CHECKPOINT
+ Iter<TContainer, TSpec> temp_(me);
+ goNext(me);
+ return temp_;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator --
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TSpec>
+inline Iter<TContainer, TSpec> const &
+operator -- (Iter<TContainer, TSpec> & me)
+{
+SEQAN_CHECKPOINT
+ goPrevious(me);
+ return me;
+}
+
+template <typename TContainer, typename TSpec>
+inline Iter<TContainer, TSpec> const
+operator -- (Iter<TContainer, TSpec> & me, int)
+{
+SEQAN_CHECKPOINT
+ Iter<TContainer, TSpec> temp_(me);
+ goPrevious(me);
+ return temp_;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// position
+//////////////////////////////////////////////////////////////////////////////
+
+//most Iter classes are rooted strings
+
+template <typename TContainer, typename TSpec, typename TContainer2>
+inline typename Position<Iter<TContainer, TSpec> const>::Type
+position(Iter<TContainer, TSpec> const & me,
+ TContainer2 const &)
+{
+SEQAN_CHECKPOINT
+ return position(me);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_iterator_position.h b/src/libSSA/seqan/basic/basic_iterator_position.h
new file mode 100644
index 0000000..adc4222
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_iterator_position.h
@@ -0,0 +1,450 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_iterator_position.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_ITERATOR_POSITION_H
+#define SEQAN_HEADER_BASIC_ITERATOR_POSITION_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+// Tag
+
+struct PositionIterator;
+
+//////////////////////////////////////////////////////////////////////////////
+// Position Iterator
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Spec.Position Iterator:
+..cat:Iterators
+..general:Class.Iter
+..summary:Adapts @Metafunction.Position.position@ to @Concept.Rooted Iterator.iterator at .
+..signature:Iter<TContainer, PositionIterator>
+..param.TContainer:Type of the container.
+...metafunction:Metafunction.Container
+..remarks
+...text:Position Iterators provide the concept @Concept.Rooted Iterator at .
+..see:Metafunction.Position
+*/
+
+template <typename TContainer>
+class Iter<TContainer, PositionIterator>
+{
+public:
+ typedef typename Position<TContainer>::Type TPosition;
+
+ typename _Pointer<TContainer>::Type data_container;
+ TPosition data_position;
+//____________________________________________________________________________
+
+public:
+/**
+.Memfunc.PositionIterator#Iter:
+..class:Spec.Position Iterator
+..summary:Constructor
+..signature:Iter()
+..signature:Iter(iter)
+..signature:Iter(container [, position])
+..param.iter:Another position iterator object.
+..param.container:The corresponding container object.
+...metafunction:Metafunction.Container
+..param.position:A position in $container$. (optional)
+...metafunction:Metafunction.Position
+...remarks.text:If this argument is omitted, the adaptor iterator is initialized to the @Function.beginPosition.begin position@ of $container$.
+*/
+ Iter()
+ {
+SEQAN_CHECKPOINT
+ }
+ Iter(typename _Parameter<TContainer>::Type container_, TPosition position_ = 0):
+ data_container(_toPointer(container_)),
+ data_position(position_)
+ {
+SEQAN_CHECKPOINT
+ }
+ Iter(Iter const & other_):
+ data_container(other_.data_container),
+ data_position(other_.data_position)
+ {
+SEQAN_CHECKPOINT
+ }
+ template <typename TContainer2, typename TSpec2>
+ Iter(Iter<TContainer2, TSpec2> const & other_)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, other_);
+ }
+ ~Iter()
+ {
+SEQAN_CHECKPOINT
+ }
+ Iter const &
+ operator = (Iter const & other_)
+ {
+SEQAN_CHECKPOINT
+ data_container = other_.data_container;
+ data_position = other_.data_position;
+ return *this;
+ }
+//____________________________________________________________________________
+
+ friend inline typename _Parameter<TContainer>::Type
+ container(Iter & me)
+ {
+SEQAN_CHECKPOINT
+ return _toParameter<TContainer>(me.data_container);
+ }
+ friend inline typename _Parameter<TContainer>::Type
+ container(Iter const & me)
+ {
+SEQAN_CHECKPOINT
+ return _toParameter<TContainer>(me.data_container);
+ }
+//____________________________________________________________________________
+
+ friend inline void
+ setContainer(Iter & me, typename _Parameter<TContainer>::Type container_)
+ {
+SEQAN_CHECKPOINT
+ typename Position<Iter>::Type pos = position(me);
+ me.data_container = _toPointer(container_);
+ setPosition(me, pos);
+ }
+
+//____________________________________________________________________________
+
+ friend inline TPosition &
+ position(Iter & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_position;
+ }
+ friend inline TPosition const &
+ position(Iter const & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_position;
+ }
+//____________________________________________________________________________
+
+ friend inline void
+ setPosition(Iter & me, TPosition position_)
+ {
+SEQAN_CHECKPOINT
+ me.data_position = position_;
+ }
+//____________________________________________________________________________
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// value
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline typename Reference<Iter<TContainer, PositionIterator> >::Type
+value(Iter<TContainer, PositionIterator> & me)
+{
+SEQAN_CHECKPOINT
+ return value(container(me), position(me));
+}
+template <typename TContainer>
+inline typename Reference<Iter<TContainer, PositionIterator> >::Type
+value(Iter<TContainer, PositionIterator> const & me)
+{
+SEQAN_CHECKPOINT
+ return value(container(me), position(me));
+}
+
+/////////////////////////////////////////////////////////////////////////////
+// assignValue
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TValue>
+inline void
+assignValue(Iter<TContainer, PositionIterator> & me,
+ TValue _value)
+{
+SEQAN_CHECKPOINT
+ assignValue(container(me), position(me), _value);
+}
+template <typename TContainer, typename TValue>
+inline void
+assignValue(Iter<TContainer, PositionIterator> const & me,
+ TValue _value)
+{
+SEQAN_CHECKPOINT
+ assignValue(container(me), position(me), _value);
+}
+
+/////////////////////////////////////////////////////////////////////////////
+// moveValue
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TValue>
+inline void
+moveValue(Iter<TContainer, PositionIterator> & me,
+ TValue _value)
+{
+SEQAN_CHECKPOINT
+ moveValue(container(me), position(me), _value);
+}
+template <typename TContainer, typename TValue>
+inline void
+moveValue(Iter<TContainer, PositionIterator> const & me,
+ TValue _value)
+{
+SEQAN_CHECKPOINT
+ moveValue(container(me), position(me), _value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator ==
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline bool
+operator == (Iter<TContainer, PositionIterator> const & left,
+ Iter<TContainer, PositionIterator> const & right)
+{
+SEQAN_CHECKPOINT
+ return position(left) == position(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator !=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline bool
+operator != (Iter<TContainer, PositionIterator> const & left,
+ Iter<TContainer, PositionIterator> const & right)
+{
+SEQAN_CHECKPOINT
+ return position(left) != position(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator < / >
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline bool
+operator < (Iter<TContainer, PositionIterator> const & left,
+ Iter<TContainer, PositionIterator> const & right)
+{
+SEQAN_CHECKPOINT
+ return position(left) < position(right);
+}
+
+template <typename TContainer>
+inline bool
+operator > (Iter<TContainer, PositionIterator> const & left,
+ Iter<TContainer, PositionIterator> const & right)
+{
+SEQAN_CHECKPOINT
+ return position(left) > position(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator <= / >=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline bool
+operator <= (Iter<TContainer, PositionIterator> const & left,
+ Iter<TContainer, PositionIterator> const & right)
+{
+SEQAN_CHECKPOINT
+ return position(left) <= position(right);
+}
+
+template <typename TContainer>
+inline bool
+operator >= (Iter<TContainer, PositionIterator> const & left,
+ Iter<TContainer, PositionIterator> const & right)
+{
+SEQAN_CHECKPOINT
+ return position(left) >= position(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// goNext
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline void
+goNext(Iter<TContainer, PositionIterator> & me)
+{
+SEQAN_CHECKPOINT
+ setPosition(me, position(me) + 1);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// goPrevious
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer>
+inline void
+goPrevious(Iter<TContainer, PositionIterator> & me)
+{
+SEQAN_CHECKPOINT
+ setPosition(me, position(me) - 1);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator +
+//////////////////////////////////////////////////////////////////////////////
+template <typename TContainer, typename TIntegral>
+inline Iter<TContainer, PositionIterator>
+operator + (Iter<TContainer, PositionIterator> const & left,
+ TIntegral right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, PositionIterator>(container(left), position(left) + right);
+}
+// for <anonymous enum> types
+template <typename TContainer>
+inline Iter<TContainer, PositionIterator>
+operator + (Iter<TContainer, PositionIterator> const & left,
+ int right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, PositionIterator>(container(left), position(left) + right);
+}
+
+template <typename TContainer, typename TIntegral>
+inline Iter<TContainer, PositionIterator>
+operator + (TIntegral left,
+ Iter<TContainer, PositionIterator> const & right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, PositionIterator>(container(right), position(right) + left);
+}
+// for <anonymous enum> types
+template <typename TContainer>
+inline Iter<TContainer, PositionIterator>
+operator + (int left,
+ Iter<TContainer, PositionIterator> const & right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, PositionIterator>(container(right), position(right) + left);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator +=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIntegral>
+inline Iter<TContainer, PositionIterator> &
+operator += (Iter<TContainer, PositionIterator> & left,
+ TIntegral right)
+{
+SEQAN_CHECKPOINT
+ setPosition(left, position(left) + right);
+ return left;
+}
+// for <anonymous enum> types
+template <typename TContainer>
+inline Iter<TContainer, PositionIterator> &
+operator += (Iter<TContainer, PositionIterator> & left,
+ int right)
+{
+SEQAN_CHECKPOINT
+ setPosition(left, position(left) + right);
+ return left;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator -
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIntegral>
+inline Iter<TContainer, PositionIterator>
+operator - (Iter<TContainer, PositionIterator> const & left,
+ TIntegral right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, PositionIterator>(container(left), position(left) - right);
+}
+// for <anonymous enum> types
+template <typename TContainer>
+inline Iter<TContainer, PositionIterator>
+operator - (Iter<TContainer, PositionIterator> const & left,
+ int right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, PositionIterator>(container(left), position(left) - right);
+}
+
+//____________________________________________________________________________
+
+template <typename TContainer>
+inline typename Difference<TContainer>::Type
+operator - (Iter<TContainer, PositionIterator> const & left,
+ Iter<TContainer, PositionIterator> const & right)
+{
+SEQAN_CHECKPOINT
+ return position(left) - position(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator -=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIntegral>
+inline Iter<TContainer, PositionIterator> &
+operator -= (Iter<TContainer, PositionIterator> & left,
+ TIntegral right)
+{
+SEQAN_CHECKPOINT
+ setPosition(left, position(left) - right);
+ return left;
+}
+// for <anonymous enum> types
+template <typename TContainer>
+inline Iter<TContainer, PositionIterator> &
+operator -= (Iter<TContainer, PositionIterator> & left,
+ int right)
+{
+SEQAN_CHECKPOINT
+ setPosition(left, position(left) - right);
+ return left;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// assign (Conversion)
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TTargetContainer, typename TSource>
+inline void
+assign(Iter<TTargetContainer, PositionIterator> & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ target.data_container = container(source);
+ target.data_position = position(source);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_iterator_simple.h b/src/libSSA/seqan/basic/basic_iterator_simple.h
new file mode 100644
index 0000000..8bfe78f
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_iterator_simple.h
@@ -0,0 +1,117 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_iterator_simple.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_ITERATOR_SIMPLE_H
+#define SEQAN_HEADER_BASIC_ITERATOR_SIMPLE_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+// Iter
+//////////////////////////////////////////////////////////////////////////////
+
+struct SimpleIterator;
+
+/**
+.Spec.SimpleIterator:
+..cat:Iterators
+..summary:A simple iterator.
+..signature:Iter<TContainer, SimpleIterator>
+..param.TContainer:Type of the container that can be iterated.
+...metafunction:Metafunction.Container
+..general:Class.Iter
+*/
+template <typename TContainer>
+class Iter<TContainer, SimpleIterator>
+{
+public:
+ typedef typename Value<TContainer>::Type TValue;
+ TValue * data_ptr;
+
+ Iter()
+ {
+ }
+ Iter(Iter const & other_):
+ data_ptr(other_.data_ptr)
+ {
+ }
+ Iter(TValue * other_data_ptr):
+ data_ptr(other_data_ptr)
+ {
+ }
+ template <typename TContainer2>
+ Iter(Iter<TContainer2, SimpleIterator> const & other_):
+ data_ptr(other_.data_ptr)
+ {
+ }
+ ~Iter()
+ {
+ }
+ Iter const &
+ operator = (Iter const & other_)
+ {
+ this->data_ptr = other_.data_ptr;
+ return *this;
+ }
+ Iter const &
+ operator = (TValue * other_data_ptr)
+ {
+ data_ptr = other_data_ptr;
+ return *this;
+ }
+ template <typename TContainer2>
+ Iter const &
+ operator = (Iter<TContainer2, SimpleIterator> const & other_)
+ {
+ this->data_ptr = other_.data_ptr;
+ return *this;
+ }
+
+ operator TValue * ()
+ {
+ return data_ptr;
+ }
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename T>
+struct Iterator_Default_Imp<T, Standard>
+{
+ typedef typename Value<T>::Type * Type;
+// typedef Iter<T, SimpleIterator> Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TContainer2>
+inline typename Position<Iter<TContainer, SimpleIterator> const>::Type
+position(Iter<TContainer, SimpleIterator> const & me,
+ TContainer2 const & cont)
+{
+SEQAN_CHECKPOINT
+ return me.data_ptr - begin(cont);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_metaprogramming.h b/src/libSSA/seqan/basic/basic_metaprogramming.h
new file mode 100644
index 0000000..fffe660
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_metaprogramming.h
@@ -0,0 +1,293 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_metaprogramming.h,v 1.2 2009/02/19 01:51:23 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_BASIC_METAPROGRAMMING_H
+#define SEQAN_BASIC_METAPROGRAMMING_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+ //////////////////////////////////////////////////////////////////////////////
+ // generic "if" (using meta-programming)
+ // if Flag is true, the resulting type is Type1
+ // if Flag is false, the resulting type is Type2
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <bool Flag,class Type1, class Type2>
+ struct IF
+ {
+ typedef Type1 Type;
+ };
+
+ template <class Type1, class Type2>
+ struct IF<false,Type1,Type2>
+ {
+ typedef Type2 Type;
+ };
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // generic type comparison (using meta-programming)
+ // if Type1 equals Type2, VALUE is true
+ // if Type1 differs from Type2, VALUE is false
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <class Type1, class Type2>
+ struct TYPECMP
+ {
+ typedef False Type;
+ enum { VALUE = false };
+ };
+
+ template <class Type1>
+ struct TYPECMP<Type1, Type1>
+ {
+ typedef True Type;
+ enum { VALUE = true };
+ };
+
+ //////////////////////////////////////////////////////////////////////////////
+ // generic "switch" (using meta-programming)
+ //////////////////////////////////////////////////////////////////////////////
+
+ const int DEFAULT = ~(~0u >> 1); // initialize with the smallest int
+
+ struct NilCase {};
+
+ template <int tag_,class Type_,class Next_ = NilCase>
+ struct CASE
+ {
+ enum { tag = tag_ };
+ typedef Type_ Type;
+ typedef Next_ Next;
+ };
+
+ template <int tag,class Case>
+ class SWITCH
+ {
+ typedef typename Case::Next NextCase;
+ enum
+ {
+ caseTag = Case::tag,
+ found = (caseTag == tag || caseTag == DEFAULT)
+ };
+ public:
+ typedef typename
+ IF<
+ found,
+ typename Case::Type,
+ typename SWITCH<tag,NextCase>::Type
+ >::Type Type;
+ };
+
+ template <int tag>
+ class SWITCH<tag,NilCase>
+ {
+ public:
+ typedef NilCase Type;
+ };
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // generic loops (using meta-programming)
+ // corresponds to for(i=1; i<=I; ++i) ...
+ //////////////////////////////////////////////////////////////////////////////
+
+ // example of a loop Worker class
+ struct WorkerNothing
+ {
+ template <typename Arg>
+ static inline void body(Arg &arg, int I) {}
+ };
+
+ template <typename Worker, int I>
+ class LOOP {
+ public:
+ template <typename Arg>
+ static inline void run(Arg &arg) {
+ LOOP<Worker, I - 1>::run(arg);
+ Worker::body(arg, I);
+ }
+ };
+
+ template <typename Worker>
+ class LOOP<Worker, 0> {
+ public:
+ // end of loop
+ template <typename Arg>
+ static inline void run(Arg &) {}
+ };
+
+ //////////////////////////////////////////////////////////////////////////////
+ // generic reverse loops (using meta-programming)
+ // corresponds to for(i=I; i>0; --i) ...
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename Worker, int I>
+ class LOOP_REVERSE {
+ public:
+ template <typename Arg>
+ static inline void run(Arg &arg) {
+ Worker::body(arg, I);
+ LOOP_REVERSE<Worker, I - 1>::run(arg);
+ }
+ };
+
+ template <typename Worker>
+ class LOOP_REVERSE<Worker, 0> {
+ public:
+ // end of loop
+ template <typename Arg>
+ static inline void run(Arg &) {}
+ };
+
+ //////////////////////////////////////////////////////////////////////////////
+ // logarithmus dualis (using meta-programming)
+ //////////////////////////////////////////////////////////////////////////////
+
+ template < __int64 numerus >
+ struct Log2 {
+ enum { VALUE = Log2<(numerus + 1) / 2>::VALUE + 1 }; // ceil(log_2(n))
+ };
+
+ template < __int64 numerus >
+ struct Log2Floor {
+ enum { VALUE = Log2Floor<numerus / 2>::VALUE + 1 }; // floor(log_2(n))
+ };
+
+ template <> struct Log2<1> { enum { VALUE = 0 }; };
+ template <> struct Log2<0> { enum { VALUE = 0 }; };
+ template <> struct Log2Floor<1> { enum { VALUE = 0 }; };
+ template <> struct Log2Floor<0> { enum { VALUE = 0 }; };
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // exponentiation (using meta-programming)
+ //////////////////////////////////////////////////////////////////////////////
+
+ template < __int64 base, __int64 exponent >
+ struct Power {
+ enum {
+ VALUE =
+ Power<base, exponent / 2>::VALUE *
+ Power<base, exponent - (exponent / 2)>::VALUE
+ };
+ };
+
+ template < __int64 base > struct Power<base, 1> { enum { VALUE = base }; };
+ template < __int64 base > struct Power<base, 0> { enum { VALUE = 1 }; };
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // memset with fill size (using meta-programming)
+ //////////////////////////////////////////////////////////////////////////////
+
+ using ::memset;
+
+ template <unsigned SIZE, bool direct>
+ struct MemsetWorker {
+ finline static void run(unsigned char* ptr, unsigned char c) { memset(ptr, c, SIZE); }
+ };
+
+ template <unsigned SIZE>
+ struct MemsetWorker<SIZE, true> {
+ finline static void run(unsigned char* ptr, unsigned char c) {
+ *((unsigned*)ptr) = ((unsigned)c << 24) + ((unsigned)c << 16) + ((unsigned)c << 8) + (unsigned)c;
+ MemsetWorker<SIZE - 4, true>::run(ptr + 4, c);
+ }
+ };
+
+ template <>
+ struct MemsetWorker<0, true> {
+ finline static void run(unsigned char*, unsigned char) {}
+ };
+
+ template <>
+ struct MemsetWorker<1, true> {
+ finline static void run(unsigned char* ptr, unsigned char c) { *ptr = c; }
+ };
+
+ template <>
+ struct MemsetWorker<2, true> {
+ finline static void run(unsigned char* ptr, unsigned char c) { *(unsigned short *)ptr = ((unsigned short)c << 8) + (unsigned short)c; }
+ };
+
+ template <>
+ struct MemsetWorker<3, true> {
+ finline static void run(unsigned char* ptr, unsigned char c) {
+ MemsetWorker<2, true>::run(ptr, c);
+ MemsetWorker<1, true>::run(ptr + 2, c);
+ }
+ };
+
+ template <unsigned SIZE>
+ finline void memset(void* ptr, unsigned char c) {
+ MemsetWorker<SIZE, SIZE <= 32>::run((unsigned char*)ptr, c);
+ }
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // memset with fill value (using meta-programming)
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <unsigned SIZE, bool direct, unsigned char c>
+ struct MemsetConstValueWorker {
+ finline static void run(unsigned char* ptr) { memset(ptr, c, SIZE); }
+ };
+
+ template <unsigned SIZE, unsigned char c>
+ struct MemsetConstValueWorker<SIZE, true, c> {
+ finline static void run(unsigned char* ptr) {
+ *((unsigned*)ptr) = ((unsigned)c << 24) + ((unsigned)c << 16) + ((unsigned)c << 8) + (unsigned)c;
+ MemsetConstValueWorker<SIZE - 4, true, c>::run(ptr + 4);
+ }
+ };
+
+ template <unsigned char c>
+ struct MemsetConstValueWorker<0, true, c> {
+ finline static void run(unsigned char* ptr) {}
+ };
+
+ template <unsigned char c>
+ struct MemsetConstValueWorker<1, true, c> {
+ finline static void run(unsigned char* ptr) { *ptr = c; }
+ };
+
+ template <unsigned char c>
+ struct MemsetConstValueWorker<2, true, c> {
+ finline static void run(unsigned char* ptr) { *(unsigned short *)ptr = ((unsigned short)c << 8) + (unsigned short)c; }
+ };
+
+ template <unsigned char c>
+ struct MemsetConstValueWorker<3, true, c> {
+ finline static void run(unsigned char* ptr) {
+ MemsetConstValueWorker<2, true, c>::run(ptr);
+ MemsetConstValueWorker<1, true, c>::run(ptr + 2);
+ }
+ };
+
+ template <unsigned SIZE, unsigned char c>
+ finline void memset(void* ptr) {
+ MemsetConstValueWorker<SIZE, SIZE <= 32, c>::run((unsigned char*)ptr);
+ }
+
+}
+
+#endif
diff --git a/src/libSSA/seqan/basic/basic_operator.h b/src/libSSA/seqan/basic/basic_operator.h
new file mode 100644
index 0000000..2bd48d9
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_operator.h
@@ -0,0 +1,32 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_operator.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_OPERATOR_H
+#define SEQAN_HEADER_BASIC_OPERATOR_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
+
+
diff --git a/src/libSSA/seqan/basic/basic_pointer.h b/src/libSSA/seqan/basic/basic_pointer.h
new file mode 100644
index 0000000..83825c0
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_pointer.h
@@ -0,0 +1,103 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_pointer.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_POINTER_H
+#define SEQAN_HEADER_BASIC_POINTER_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Value.param.T.type:Adaption.char array
+
+template <typename TValue>
+struct Value< TValue * >
+{
+ typedef TValue Type;
+};
+template <typename TValue>
+struct Value< TValue * const>
+{
+ typedef TValue Type;
+};
+
+//The next two metafunctions dont work in VC++ due to a compiler bug.
+//(the default implementation in common_type.h is called instead)
+//work-around: convert arrays to pointers.
+template <typename TValue, size_t SIZE>
+struct Value< TValue [SIZE] >
+{
+ typedef TValue Type;
+};
+template <typename TValue, size_t SIZE>
+struct Value< TValue const [SIZE] >
+{
+ typedef TValue const Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Iterator.param.T.type:Adaption.char array
+
+template <typename TValue>
+struct Iterator< TValue *, Standard>
+{
+ typedef TValue * Type;
+};
+template <typename TValue>
+struct Iterator< TValue * const, Standard>
+{
+ typedef TValue * Type;
+};
+
+//____________________________________________________________________________
+
+template <typename TValue, size_t SIZE>
+struct Iterator< TValue [SIZE], Standard>:
+ Iterator<TValue *, Standard>
+{
+};
+template <typename TValue, size_t SIZE>
+struct Iterator< TValue const [SIZE], Standard>:
+ Iterator<TValue const *, Standard>
+{
+};
+
+template <typename TValue, size_t SIZE>
+struct Iterator< TValue [SIZE], Rooted>:
+ Iterator<TValue *, Rooted>
+{
+};
+template <typename TValue, size_t SIZE>
+struct Iterator< TValue const [SIZE], Rooted>:
+ Iterator<TValue const *, Rooted>
+{
+};
+
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_profile.h b/src/libSSA/seqan/basic/basic_profile.h
new file mode 100644
index 0000000..edcf42b
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_profile.h
@@ -0,0 +1,503 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_profile.h,v 1.1 2008/08/25 16:20:02 langmead Exp $
+ ==========================================================================*/
+
+//SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
+
+#ifndef SEQAN_HEADER_BASIC_PROFILE_H
+#define SEQAN_HEADER_BASIC_PROFILE_H
+
+// todo: substitute defines with inlines
+#ifndef SEQAN_PROFILE
+
+ #define SEQAN_PROSET(i,v)
+ #define SEQAN_PROADD(i,v)
+ #define SEQAN_PROSUB(i,v)
+ #define SEQAN_PROVAL(i) 0
+ #define SEQAN_PROEXTRAS(i)
+ #define SEQAN_PROMARK(m)
+ #define SEQAN_PROENDMARK(m)
+ #define SEQAN_PRORESET
+ #define SEQAN_PROGETTIME 0
+ #define SEQAN_PROTIMESTART(a)
+ #define SEQAN_PROTIMEDIFF(a) 0
+ // replace malloc and free in external tools
+ // with SEQAN_PROMALLOC and SEQAN_PROFREE to profile
+ // their memory usage
+ #define SEQAN_PROMALLOC(s) malloc(s)
+ #define SEQAN_PROFREE(p) free(p)
+
+#else
+
+ #define SEQAN_PROSET(i,v) _proSet(i,v)
+ #define SEQAN_PROADD(i,v) _proAdd(i,v)
+ #define SEQAN_PROSUB(i,v) _proSub(i,v)
+ #define SEQAN_PROVAL(i) (_proData<>::_proValue[i])
+ #define SEQAN_PROEXTRAS(i) {_proData<>::_proExtraCount = i;}
+ #define SEQAN_PROMARK(m) _proMark(m)
+ #define SEQAN_PROENDMARK(m) _proEndMark(m)
+ #define SEQAN_PRORESET _proReset()
+ #define SEQAN_PROGETTIME sysTime()
+ #define SEQAN_PROTIMESTART(a) _proFloat a = sysTime()
+ #define SEQAN_PROTIMEDIFF(a) (sysTime() - a)
+ #define SEQAN_PROMALLOC(s) _proMalloc(s)
+ #define SEQAN_PROFREE(p) _proFree(p)
+
+#endif
+
+#ifdef PLATFORM_WINDOWS
+ typedef __int64 _proInt;
+#else
+ typedef int64_t _proInt;
+#endif
+
+ typedef double _proFloat;
+
+
+ typedef _proFloat _proTValue;
+
+ enum _proConsts {
+ SEQAN_PROPAGESIZE = 4096, // B in byte
+ SEQAN_PROFLOAT = 0,
+ SEQAN_PROINT = 1,
+ SEQAN_PROTIME = 2,
+ SEQAN_PROTYPEMASK = 3,
+ SEQAN_PROSTATE = 4
+ };
+
+ enum _proValueIndex {
+ SEQAN_PROSYSTIME = 0,
+ SEQAN_PROCPUTIME = 1,
+ SEQAN_PROMEMORY = 2, // current memory usage (state value)
+ SEQAN_PROIO = 3, // IOs done (measured in Blocks of size B)
+ SEQAN_PROIORANDOM = 4, // IOs calls done (read/write calls done)
+ SEQAN_PROIOVOLUME = 5, // current disk usage (state value)
+ SEQAN_PRODEPTH = 6, // algorithmic rec. depth or loop count
+ SEQAN_PROOPENFILES = 7, // currently opened files
+ SEQAN_PROIWAIT = 8, // waiting time (initiating)
+ SEQAN_PROCWAIT = 9, // waiting time (completing)
+ SEQAN_PROEXTRA1 = 10,
+ SEQAN_PROEXTRA2 = 11,
+ SEQAN_PROEXTRA3 = 12,
+ SEQAN_PROINDEXCOUNT = 13,
+ SEQAN_PROEXTRACOUNT = 3
+ };
+
+ const char _proValueType[] = {
+ SEQAN_PROTIME,
+ SEQAN_PROTIME,
+ SEQAN_PROINT + SEQAN_PROSTATE,
+ SEQAN_PROINT,
+ SEQAN_PROINT,
+ SEQAN_PROINT + SEQAN_PROSTATE,
+ SEQAN_PROINT + SEQAN_PROSTATE,
+ SEQAN_PROINT + SEQAN_PROSTATE,
+ SEQAN_PROFLOAT,
+ SEQAN_PROFLOAT,
+ SEQAN_PROFLOAT + SEQAN_PROSTATE,
+ SEQAN_PROFLOAT + SEQAN_PROSTATE,
+ SEQAN_PROFLOAT + SEQAN_PROSTATE
+ };
+
+ typedef _proTValue _proTStates[SEQAN_PROINDEXCOUNT];
+ typedef _proFloat _proTTimes[SEQAN_PROINDEXCOUNT];
+
+
+
+ struct _proFile;
+
+ template <typename T = void>
+ struct _proData
+ {
+ static _proTStates _proValue;
+ static _proTTimes _proLastUpdate;
+ static int _proExtraCount;
+
+ static clock_t _proCpuTimeLast; // clock_t wraps around every 72mins
+ static _proInt _proCpuTimeOffset; // we have to work around this
+
+ static _proFile* _proPFile;
+ static _proFile* _proPFileStream;
+ };
+
+ template <typename T> _proTStates _proData<T>::_proValue = {};
+ template <typename T> _proTStates _proData<T>::_proLastUpdate = {};
+ template <typename T> int _proData<T>::_proExtraCount = 0;
+ template <typename T> clock_t _proData<T>::_proCpuTimeLast = 0;
+ template <typename T> _proInt _proData<T>::_proCpuTimeOffset = 0;
+ template <typename T> _proFile* _proData<T>::_proPFile = NULL;
+ template <typename T> _proFile* _proData<T>::_proPFileStream = NULL;
+
+
+ inline _proFile* & _proPFile() { return _proData<>::_proPFile; }
+ inline _proFile* & _proPFileStream() { return _proData<>::_proPFileStream; }
+
+
+// HINT: The unit of all time functions is second.
+ inline _proFloat cpuTime() {
+ clock_t now = clock();
+ if (_proData<>::_proCpuTimeLast > now) { // test for time wrap
+ _proData<>::_proCpuTimeOffset += (~0u); // got one
+ _proData<>::_proCpuTimeOffset ++;
+// printf("\n!!WRAP!! old:%d, now:%d ofs:%d\n",_proData<>::_proCpuTimeLast,now,_proData<>::_proCpuTimeOffset);
+ }
+ _proData<>::_proCpuTimeLast = now;
+ return (_proData<>::_proCpuTimeOffset + now) / (_proFloat)CLOCKS_PER_SEC;
+ }
+
+ #ifdef PLATFORM_WINDOWS
+// inline _proFloat sysTime() { return GetTickCount() * 1e-3; }
+ inline _proFloat sysTime() { return ( (_proFloat) clock() ) / CLOCKS_PER_SEC; }
+ #else
+
+ #include <unistd.h>
+ #if _POSIX_TIMERS > 0
+ #ifndef SEQAN_USE_CLOCKGETTIME
+ #define SEQAN_USE_CLOCKGETTIME
+ #endif
+ #endif
+
+ #ifndef SEQAN_USE_CLOCKGETTIME
+ /* some systems e.g. darwin have no clock_gettime */
+
+ #include <sys/time.h>
+
+ inline _proFloat sysTime() {
+ struct timeval tp;
+ gettimeofday(&tp, NULL);
+ return tp.tv_sec + tp.tv_usec * 1e-6;
+ }
+
+ #else
+
+ inline _proFloat sysTime() {
+ /*struct timespec tp;
+ clock_gettime(CLOCK_MONOTONIC, &tp);
+ return tp.tv_sec + tp.tv_nsec * 1e-9;*/
+ return 0; // BTL: to compile under cygwin
+ }
+
+ #endif
+
+ #endif
+
+
+ struct _proFile {
+
+ FILE *out;
+ bool running;
+
+ _proFloat dumpStep; // 0 .. manual dump mode, >0 .. live stream
+ _proFloat dumpNext;
+
+ _proTStates all, last;
+ ::std::string mark;
+ unsigned lines;
+
+ _proFile() {
+ running = false;
+ }
+
+ _proFile(char const *fname, _proFloat _dumpStep = 300.0) { // five minutes default dump interval
+ running = false;
+ start(fname, _dumpStep);
+ }
+
+ ~_proFile() {
+ if (running) stop();
+ }
+
+ inline void start(char const *fname, _proFloat _dumpStep = 300.0, bool append = false) {
+ if (append)
+ out = fopen(fname, "a");
+ else {
+ out = fopen(fname, "w");
+ dumpHeader();
+ }
+
+ if (!out) printf("WARNING: proFile could not be opened.\n");
+
+ setTime(_proData<>::_proValue);
+ syncAll(all);
+ syncAll(last);
+ running = true;
+ lines = 0;
+ dumpStep = _dumpStep;
+ dumpNext = sysTime();
+ dump(last);
+ }
+
+ inline void stop() {
+ dump(last);
+ maximize(all, last);
+ if (dumpStep == 0) {
+ mark = "Zusammenfassung";
+ dump(all);
+ }
+ fclose(out);
+ running = false;
+ }
+
+ inline void syncTime(_proTStates &dst) {
+ memcpy(dst, _proData<>::_proValue, 2 * sizeof(_proTValue));
+ }
+
+ inline void sync(_proTStates &dst) {
+ memcpy(&(dst[2]), &(_proData<>::_proValue[2]), sizeof(_proTStates) - 2 * sizeof(_proTValue));
+ }
+
+ inline void syncAll(_proTStates &dst) {
+ memcpy(dst, _proData<>::_proValue, sizeof(_proTStates));
+ }
+
+ inline static void setTime(_proTStates &dst) {
+ dst[0] = sysTime();
+ dst[1] = cpuTime();
+ }
+
+ inline void maximize(_proTStates &dst, _proTStates const &src) {
+ for(int i = 0; i < SEQAN_PROINDEXCOUNT; ++i)
+ if (((_proValueType[i] & SEQAN_PROSTATE) != 0))
+ if (dst[i] < src[i])
+ dst[i] = src[i];
+ }
+
+ inline void dumpTab() {
+ if (!bol)
+ fprintf(out, " \t");
+ bol = false;
+ }
+
+ inline void dumpEndl() { fprintf(out, "\n"); }
+
+ inline void dumpHeader() {
+ fprintf(out, "\"Echtzeit\"\t\"CPU-Zeit\"\t\"Speicher\"\t\"I/O-Zugriffe\"\t\"wahlfreie I/Os\"\t\"I/O-Volumen\"\t\"Rekursionstiefe\"\t\"Offene Dateien\"\t\"Idle-Zeit vor I/O\"\t\"Idle-Zeit nach I/O\"\n");
+ }
+
+ inline void dumpTime(_proFloat seconds) {
+ if (seconds < 0) {
+ fputc('-', out);
+ seconds = -seconds;
+ }
+ int secs = (int)seconds;
+ int mins = secs/60; secs -= 60*mins;
+ int hours = mins/60; mins -= 60*hours;
+ fprintf(out, "%d:%02d:%02d", hours, mins, secs);
+ }
+
+ inline void dumpTimeEx(_proFloat seconds) {
+ int milli = (int)(seconds * 1000.0);
+ int secs = (int)seconds;
+ int mins = secs/60; secs -= 60*mins;
+ int hours = mins/60; mins -= 60*hours;
+ fprintf(out, "%d:%02d:%02d.%03d", hours, mins, secs, milli);
+ }
+
+ inline void dumpValue(_proTStates &stat, int valNum) {
+ _proFloat f = stat[valNum];
+ if ((_proValueType[valNum] & SEQAN_PROSTATE) == 0)
+ f = _proData<>::_proValue[valNum] - f;
+
+ switch (_proValueType[valNum] & SEQAN_PROTYPEMASK) {
+ case SEQAN_PROINT: // state value -> print last seen maximum
+ fprintf(out, "%.0f", f);
+ break;
+
+ case SEQAN_PROFLOAT:
+ fprintf(out, "%f", f);
+ break;
+
+ case SEQAN_PROTIME:
+ dumpTimeEx(f);
+ }
+ }
+
+ inline void dumpSysValues(_proTStates &stat) {
+ for(int i = 0; i < SEQAN_PROINDEXCOUNT - SEQAN_PROEXTRACOUNT; ++i) {
+ dumpTab();
+ dumpValue(stat, i);
+ }
+ }
+
+ inline void dumpExtraValues(_proTStates &stat) {
+ for(int i = 0; i < _proData<>::_proExtraCount; ++i) {
+ dumpTab();
+ dumpValue(stat, SEQAN_PROINDEXCOUNT - SEQAN_PROEXTRACOUNT + i);
+ }
+ }
+
+ inline void dumpMark() {
+ if (!mark.empty()) {
+ dumpTab();
+ fprintf(out, "\"%s\"", mark.c_str());
+ mark.erase();
+ }
+ }
+
+ inline void dump(_proTStates &stat) {
+ setTime(_proData<>::_proValue);
+ dumpNext += dumpStep;
+ bol = true;
+ bool _flush = ((dumpStep == 0.0)) || ((lines & 16) == 0);
+
+ dumpSysValues(stat);
+ dumpExtraValues(stat);
+ dumpMark();
+ dumpEndl();
+ if (_flush) fflush(out);
+ ++lines;
+ }
+
+ inline void signalDumpTest(_proFloat now) {
+ if (dumpStep > 0 && now > dumpNext && running) {
+ dump(last);
+ maximize(all, last);
+ sync(last);
+ }
+ }
+
+ inline void signalNewMax(int valNum) {
+ if (running)
+ if (last[valNum] < _proData<>::_proValue[valNum])
+ last[valNum] = _proData<>::_proValue[valNum];
+ }
+
+ inline void setMark(const char *text) {
+ if (running) {
+ mark = text;
+ if (dumpStep == 0.0) {
+ dump(last); // manual dump;
+ maximize(all, last);
+ sync(last);
+ }
+ }
+ }
+
+ inline void reset() {
+ syncTime(last);
+ }
+
+ inline void setEndMark(const char *text) {
+ if (running) {
+ setMark(text);
+ reset();
+ }
+ }
+
+ private:
+
+ bool bol; // begin of line
+ };
+
+
+
+/*
+ inline void _proSignalDumpTest(_proFloat now);
+ inline void _proSignalNewMax(int valNum);
+ inline void _proMark(const char *text);
+ inline void _proEndMark(const char *text);
+ inline void _proReset();
+
+ inline void _proSet(int valNum, _proFloat value);
+ inline void _proAdd(int valNum, _proFloat value);
+ inline void _proSub(int valNum, _proFloat value);
+
+ // simple interface for external programs
+ inline void *_proMalloc(size_t size);
+ inline void _proFree(void *_ptr);
+*/
+
+ inline void _proSignalDumpTest(_proFloat now) {
+ if (_proData<>::_proPFileStream) _proData<>::_proPFileStream->signalDumpTest(now);
+ }
+
+ inline void _proSignalNewMax(int valNum) {
+ if (((_proValueType[valNum] & SEQAN_PROSTATE) != 0)) {
+ if (_proData<>::_proPFileStream) _proData<>::_proPFileStream->signalNewMax(valNum);
+ if (_proData<>::_proPFile) _proData<>::_proPFile->signalNewMax(valNum);
+ }
+ }
+
+ inline void _proMark(const char *text) {
+ if (_proData<>::_proPFileStream) _proData<>::_proPFileStream->setMark(text);
+ if (_proData<>::_proPFile) _proData<>::_proPFile->setMark(text);
+ }
+
+ inline void _proEndMark(const char *text) {
+ if (_proData<>::_proPFileStream) { _proData<>::_proPFileStream->setEndMark(text); }
+ if (_proData<>::_proPFile) { _proData<>::_proPFile->setEndMark(text); }
+ }
+
+ inline void _proReset() {
+ if (_proData<>::_proPFileStream) { _proData<>::_proPFileStream->reset(); }
+ if (_proData<>::_proPFile) { _proData<>::_proPFile->reset(); }
+ }
+
+
+
+
+ inline void _proSet(_proValueIndex valNum, _proFloat value) {
+ _proFloat now = sysTime();
+ _proData<>::_proLastUpdate[valNum] = now;
+ if (_proData<>::_proValue[valNum] < value) {
+ _proData<>::_proValue[valNum] = value;
+ _proSignalNewMax(valNum);
+ } else
+ _proData<>::_proValue[valNum] = value;
+ _proSignalDumpTest(now);
+ }
+
+ inline void _proAdd(_proValueIndex valNum, _proFloat value) {
+ _proFloat now = sysTime();
+ _proData<>::_proValue[valNum] += value;
+ _proData<>::_proLastUpdate[valNum] = now;
+ if (valNum == SEQAN_PROIO) _proAdd(SEQAN_PROIORANDOM, 1);
+ _proSignalNewMax(valNum);
+ _proSignalDumpTest(now);
+ }
+
+ inline void _proSub(_proValueIndex valNum, _proFloat value) {
+ _proFloat now = sysTime();
+ _proData<>::_proValue[valNum] -= value;
+ _proData<>::_proLastUpdate[valNum] = now;
+ _proSignalDumpTest(now);
+ }
+
+ // simple interface for external programs
+ inline void *_proMalloc(size_t size) {
+ size_t *ptr = reinterpret_cast<size_t*>(malloc(size + sizeof(size_t)));
+ if (ptr) {
+ _proAdd(SEQAN_PROMEMORY, *ptr = size);
+// printf("_proMalloc %x size %d\n", ptr, size);
+ ++ptr;
+ }
+ return ptr;
+ }
+
+ inline void _proFree(void *_ptr) {
+ size_t *ptr = reinterpret_cast<size_t*>(_ptr);
+ if (ptr) {
+ --ptr;
+// printf("_proFree %x size %d\n", _ptr, *ptr);
+ _proSub(SEQAN_PROMEMORY, *ptr);
+ }
+ free(ptr);
+ }
+
+#endif
diff --git a/src/libSSA/seqan/basic/basic_proxy.h b/src/libSSA/seqan/basic/basic_proxy.h
new file mode 100644
index 0000000..c384e05
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_proxy.h
@@ -0,0 +1,606 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_proxy.h,v 1.1 2008/08/25 16:20:02 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_PROXY_H
+#define SEQAN_HEADER_BASIC_PROXY_H
+
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Proxy
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Class.Proxy:
+..cat:Basic
+..summary:Emulates object of another class.
+..signature:Proxy<TSpec>
+..param.TSpec:The specializing type.
+...metafunction:Metafunction.Spec
+..remarks.text:Use @Metafunction.Value@ to get the emulated type.
+An instance of $Proxy$ behaves like an object of its value type.
+$Proxy$ can be used as reference type (see @Metafunction.Reference@).
+..remarks.text:Note that functions that are both general and specialized for
+the value type should be specialized for $Proxy<TSpec>$ too,
+since otherwise the general version will be called.
+*/
+
+template <typename TSpec>
+struct Proxy;
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Spec.param.T.type:Class.Proxy
+
+template <typename TSpec>
+struct Spec< Proxy<TSpec> >
+{
+ typedef TSpec Type;
+};
+template <typename TSpec>
+struct Spec< Proxy<TSpec> const>
+{
+ typedef TSpec Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// Iterator Proxy
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Spec.Iterator Proxy:
+..cat:Proxies
+..general:Class.Proxy
+..summary:Proxy that is implemented by an iterator.
+..signature:Proxy<IteratorProxy<TIterator> >
+..param.TIterator:Iterator type.
+..remarks.text:The value type of an iterator proxy is the value type of the
+iterator $TIterator$.
+*/
+
+template <typename TIterator>
+struct IteratorProxy;
+
+//____________________________________________________________________________
+
+template <typename TIterator>
+struct Proxy<IteratorProxy<TIterator> >
+{
+public:
+ typedef typename Value<Proxy>::Type TValue;
+ typedef typename GetValue<Proxy>::Type TAccessor;
+
+ typedef typename _RemoveConst<TAccessor>::Type TAccessor_NotConst;
+
+private:
+ TIterator data_iterator;
+
+public:
+ Proxy(TIterator const _it):
+ data_iterator(_it)
+ {
+SEQAN_CHECKPOINT
+ }
+ Proxy(Proxy const & _other):
+ data_iterator(_other.data_iterator)
+ {
+SEQAN_CHECKPOINT
+ }
+
+ ~Proxy()
+ {
+SEQAN_CHECKPOINT
+ }
+
+ Proxy const &
+ operator = (Proxy const & _other)
+ {
+SEQAN_CHECKPOINT
+ assignValue(data_iterator, getValue(_other.data_iterator));
+ return *this;
+ }
+
+ Proxy const &
+ operator = (TValue const & _value)
+ {
+SEQAN_CHECKPOINT
+ assignValue(data_iterator, _value);
+ return *this;
+ }
+
+ operator TAccessor_NotConst()
+ {
+SEQAN_CHECKPOINT
+ return getValue(data_iterator);
+ }
+
+//____________________________________________________________________________
+
+ //not documented
+ friend inline TIterator &
+ iter(Proxy & me)
+ {
+ return me.data_iterator;
+ }
+ friend inline TIterator const &
+ iter(Proxy const & me)
+ {
+ return me.data_iterator;
+ }
+
+//____________________________________________________________________________
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// Metafunctions
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Value.param.T.type:Class.Proxy
+
+template <typename TIterator>
+struct Value< Proxy<IteratorProxy<TIterator> > >:
+ Value<TIterator>
+{
+};
+template <typename TIterator>
+struct Value< Proxy<IteratorProxy<TIterator> > const>
+{
+ typedef typename Value<TIterator>::Type const Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.GetValue.param.T.type:Class.Proxy
+
+template <typename TIterator>
+struct GetValue< Proxy<IteratorProxy<TIterator> > >:
+ GetValue<TIterator>
+{
+};
+template <typename TIterator>
+struct GetValue< Proxy<IteratorProxy<TIterator> > const>
+{
+ typedef typename GetValue<TIterator const>::Type Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Reference.param.T.type:Class.Proxy
+
+template <typename TIterator>
+struct Reference< Proxy<IteratorProxy<TIterator> > >
+{
+ typedef Proxy<IteratorProxy<TIterator> > Type;
+};
+template <typename TIterator>
+struct Reference< Proxy<IteratorProxy<TIterator> > const >
+{
+ typedef Proxy<IteratorProxy<TIterator> > const Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Size.param.T.type:Class.Proxy
+
+template <typename TIterator>
+struct Size< Proxy<IteratorProxy<TIterator> > >:
+ Size<TIterator>
+{
+};
+template <typename TIterator>
+struct Size< Proxy<IteratorProxy<TIterator> > const>:
+ Size<TIterator>
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Difference.param.T.type:Class.Proxy
+
+template <typename TIterator>
+struct Difference< Proxy<IteratorProxy<TIterator> > >:
+ Difference<TIterator>
+{
+};
+template <typename TIterator>
+struct Difference< Proxy<IteratorProxy<TIterator> > const>:
+ Difference<TIterator>
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TSpec>
+typename GetValue<Proxy<TSpec> >::Type
+getValue(Proxy<TSpec> & me)
+{
+ return getValue(iter(me));
+}
+template <typename TSpec>
+typename GetValue<Proxy<TSpec> const>::Type
+getValue(Proxy<TSpec> const & me)
+{
+ return getValue(iter(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Comparison
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TSpec, typename T>
+struct CompareType <Proxy<TSpec>, T>
+{
+ typedef typename Value<Proxy<TSpec> >::Type TValue;
+ typedef typename _RemoveConst<TValue>::Type TValue_NoConst;
+ typedef typename CompareType<TValue_NoConst, T>::Type Type;
+};
+
+//???TODO: Symmetrie von CompareType herstellen
+//____________________________________________________________________________
+
+template <typename TTarget, typename T, typename TSpec>
+inline typename Convert<TTarget, Proxy<TSpec> >::Type
+convertImpl(Convert<TTarget, T> const,
+ Proxy<TSpec> & source)
+{
+ return convert<TTarget>(getValue(source));
+}
+template <typename TTarget, typename T, typename TSpec>
+inline typename Convert<TTarget, Proxy<TSpec> const>::Type
+convertImpl(Convert<TTarget, T> const,
+ Proxy<TSpec> const & source)
+{
+ return convert<TTarget>(getValue(source));
+}
+//////////////////////////////////////////////////////////////////////////////
+// operator ==
+
+template <typename TSpec, typename TRight>
+inline bool
+operator == (Proxy<TSpec> const & left_,
+ TRight const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TLeft;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) == convert<TCompareType>(right_);
+}
+
+template <typename TLeft, typename TSpec>
+inline bool
+operator == (TLeft const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TRight;
+ typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+ return convert<TCompareType>(left_) == convert<TCompareType>(right_);
+}
+
+template <typename TLeftSpec, typename TRightSpec>
+inline bool
+operator == (Proxy<TLeftSpec> const & left_,
+ Proxy<TRightSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TLeftSpec> TLeft;
+ typedef Proxy<TRightSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) == convert<TCompareType>(right_);
+}
+
+template <typename TSpec>
+inline bool
+operator == (Proxy<TSpec> const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef typename GetValue<Proxy<TSpec> >::Type TAccessor;
+ return convert<TAccessor>(left_) == convert<TAccessor>(right_);
+}
+
+//____________________________________________________________________________
+// operator !=
+
+template <typename TSpec, typename TRight>
+inline bool
+operator != (Proxy<TSpec> const & left_,
+ TRight const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TLeft;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) != convert<TCompareType>(right_);
+}
+
+template <typename TLeft, typename TSpec>
+inline bool
+operator != (TLeft const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TRight;
+ typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+ return convert<TCompareType>(left_) != convert<TCompareType>(right_);
+}
+
+template <typename TLeftSpec, typename TRightSpec>
+inline bool
+operator != (Proxy<TLeftSpec> const & left_,
+ Proxy<TRightSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TLeftSpec> TLeft;
+ typedef Proxy<TRightSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) != convert<TCompareType>(right_);
+}
+
+template <typename TSpec>
+inline bool
+operator != (Proxy<TSpec> const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef typename GetValue<Proxy<TSpec> >::Type TAccessor;
+ return convert<TAccessor>(left_) != convert<TAccessor>(right_);
+}
+
+
+//____________________________________________________________________________
+// operator <
+
+template <typename TSpec, typename TRight>
+inline bool
+operator < (Proxy<TSpec> const & left_,
+ TRight const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TLeft;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) < convert<TCompareType>(right_);
+}
+
+template <typename TLeft, typename TSpec>
+inline bool
+operator < (TLeft const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TRight;
+ typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+ return convert<TCompareType>(left_) < convert<TCompareType>(right_);
+}
+
+template <typename TLeftSpec, typename TRightSpec>
+inline bool
+operator < (Proxy<TLeftSpec> const & left_,
+ Proxy<TRightSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TLeftSpec> TLeft;
+ typedef Proxy<TRightSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) < convert<TCompareType>(right_);
+}
+
+template <typename TSpec>
+inline bool
+operator < (Proxy<TSpec> const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef typename GetValue<Proxy<TSpec> >::Type TAccessor;
+ return convert<TAccessor>(left_) < convert<TAccessor>(right_);
+}
+
+//____________________________________________________________________________
+// operator <=
+
+template <typename TSpec, typename TRight>
+inline bool
+operator <= (Proxy<TSpec> const & left_,
+ TRight const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TLeft;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
+}
+
+template <typename TLeft, typename TSpec>
+inline bool
+operator <= (TLeft const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TRight;
+ typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+ return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
+}
+
+template <typename TLeftSpec, typename TRightSpec>
+inline bool
+operator <= (Proxy<TLeftSpec> const & left_,
+ Proxy<TRightSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TLeftSpec> TLeft;
+ typedef Proxy<TRightSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
+}
+
+template <typename TSpec>
+inline bool
+operator <= (Proxy<TSpec> const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef typename GetValue<Proxy<TSpec> >::Type TAccessor;
+ return convert<TAccessor>(left_) <= convert<TAccessor>(right_);
+}
+
+
+//____________________________________________________________________________
+// operator >
+
+template <typename TSpec, typename TRight>
+inline bool
+operator > (Proxy<TSpec> const & left_,
+ TRight const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TLeft;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) > convert<TCompareType>(right_);
+}
+
+template <typename TLeft, typename TSpec>
+inline bool
+operator > (TLeft const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TRight;
+ typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+ return convert<TCompareType>(left_) > convert<TCompareType>(right_);
+}
+
+template <typename TLeftSpec, typename TRightSpec>
+inline bool
+operator > (Proxy<TLeftSpec> const & left_,
+ Proxy<TRightSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TLeftSpec> TLeft;
+ typedef Proxy<TRightSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) > convert<TCompareType>(right_);
+}
+
+template <typename TSpec>
+inline bool
+operator > (Proxy<TSpec> const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef typename GetValue<Proxy<TSpec> >::Type TAccessor;
+ return convert<TAccessor>(left_) > convert<TAccessor>(right_);
+}
+
+
+//____________________________________________________________________________
+// operator >=
+
+template <typename TSpec, typename TRight>
+inline bool
+operator >= (Proxy<TSpec> const & left_,
+ TRight const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TLeft;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
+}
+
+template <typename TLeft, typename TSpec>
+inline bool
+operator >= (TLeft const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TSpec> TRight;
+ typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+ return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
+}
+
+template <typename TLeftSpec, typename TRightSpec>
+inline bool
+operator >= (Proxy<TLeftSpec> const & left_,
+ Proxy<TRightSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef Proxy<TLeftSpec> TLeft;
+ typedef Proxy<TRightSpec> TRight;
+ typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+ return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
+}
+
+template <typename TSpec>
+inline bool
+operator >= (Proxy<TSpec> const & left_,
+ Proxy<TSpec> const & right_)
+{
+SEQAN_CHECKPOINT
+ typedef typename GetValue<Proxy<TSpec> >::Type TAccessor;
+ return convert<TAccessor>(left_) >= convert<TAccessor>(right_);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TStream, typename TSpec>
+inline TStream &
+operator >> (TStream & strm,
+ Proxy<TSpec> & proxy)
+{
+ typedef Proxy<TSpec> TProxy;
+ typedef typename Value<TProxy>::Type TValue;
+ TValue temp;
+ strm >> temp;
+ assignValue(iter(proxy), temp);
+ return strm;
+}
+template <typename TStream, typename TSpec>
+inline TStream &
+operator >> (TStream & strm,
+ Proxy<TSpec> const& proxy)
+{
+ typedef Proxy<TSpec> TProxy;
+ typedef typename Value<TProxy>::Type TValue;
+ TValue temp;
+ strm >> temp;
+ assignValue(iter(proxy), temp);
+ return strm;
+}
+
+
+template <typename TStream, typename TSpec>
+inline TStream &
+operator << (TStream & strm,
+ Proxy<TSpec> & proxy)
+{
+ return strm << getValue(proxy);
+}
+template <typename TStream, typename TSpec>
+inline TStream &
+operator << (TStream & strm,
+ Proxy<TSpec> const & proxy)
+{
+ return strm << getValue(proxy);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_tag.h b/src/libSSA/seqan/basic/basic_tag.h
new file mode 100644
index 0000000..3035cba
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_tag.h
@@ -0,0 +1,173 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_tag.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_TAG_H
+#define SEQAN_HEADER_BASIC_TAG_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.DotDrawing
+..summary:Switch to trigger drawing in dot format.
+..value.DotDrawing:Graphs in dot format.
+*/
+
+struct DotDrawing_;
+typedef Tag<DotDrawing_> const DotDrawing;
+
+
+/**
+.Tag.HammingDistance
+..summary:Switch to trigger Hamming distance, which is a measure of character substitutions.
+*/
+
+/**
+.Tag.LevenshteinDistance
+..summary:Switch to trigger Levenshtein distance, which is a measure of edit operations (character substitutions, deletions or insertions).
+*/
+
+struct _HammingDistance;
+struct _LevenshteinDistance;
+
+typedef Tag<_HammingDistance> HammingDistance;
+typedef Tag<_LevenshteinDistance> LevenshteinDistance;
+typedef Tag<_LevenshteinDistance> EditDistance;
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Alignment: Tags
+//////////////////////////////////////////////////////////////////////////////
+//Sollte eigentlich nach align/, aber da jetzt ja so viele
+//alignment algorithmen in graph/ gelandet sind...
+
+/**
+.Tag.Global Alignment Algorithms:
+..summary:Global alignment algorithm used by globalAlignment.
+..see:Function.globalAlignment
+..see:Tag.Local Alignment Algorithms
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.Global Alignment Algorithms.value.NeedlemanWunsch:
+ Dynamic programming algorithm for alignments by Needleman and Wunsch.
+*/
+
+struct NeedlemanWunsch_;
+typedef Tag<NeedlemanWunsch_> const NeedlemanWunsch;
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.Global Alignment Algorithms.value.Gotoh:
+ Gotoh's affine gap cost alignment algorithm.
+*/
+struct Gotoh_;
+typedef Tag<Gotoh_> const Gotoh;
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.Global Alignment Algorithms.value.MyersBitVector:
+ Myers' bit vector alignment algorithm for edit distance.
+ Note that this algorithm does not returns the alignment itself, but only computes the score.
+*/
+struct MyersBitVector_;
+typedef Tag<MyersBitVector_> const MyersBitVector;
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.Global Alignment Algorithms.value.MyersHirschberg:
+ Myers' bit vector algorithm for edit distance combined with Hirschberg's linear space alignment algorithm.
+*/
+struct MyersHirschberg_;
+typedef Tag<MyersHirschberg_> const MyersHirschberg;
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.Global Alignment Algorithms.value.Hirschberg:
+ Hirschberg's linear space global alignment algorithm.
+*/
+struct Hirschberg_;
+typedef Tag<Hirschberg_> const Hirschberg;
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.Local Alignment Algorithms:
+..summary:Local alignment algorithm used by localAlignment.
+..see:Function.localAlignment
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.Local Alignment Algorithms.value.SmithWaterman:
+ Triggers a Smith Waterman local alignment algorithm.
+*/
+struct SmithWaterman_;
+typedef Tag<SmithWaterman_> const SmithWaterman;
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.Local Alignment Algorithms.value.SmithWatermanClump:
+ Local alignment algorithm with "declumping" by Waterman and Eggert.
+*/
+struct SmithWatermanClump_;
+typedef Tag<SmithWatermanClump_> const SmithWatermanClump;
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.Local Alignment Algorithms.value.SmithWatermanIsland:
+ Local alignment algorithm finding all "islands".
+*/
+struct SmithWatermanIsland_;
+typedef Tag<SmithWatermanIsland_> const SmithWatermanIsland;
+
+//////////////////////////////////////////////////////////////////////////////
+
+/*DISABLED
+.Tag.RNA Folding Algorithms.value.Nussinov:
+ Nussinov style RNA folding algorithm
+*/
+struct Nussinov_;
+typedef Tag<Nussinov_> const Nussinov;
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_transport.h b/src/libSSA/seqan/basic/basic_transport.h
new file mode 100644
index 0000000..4757d87
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_transport.h
@@ -0,0 +1,196 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_transport.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_TRANSPORT_H
+#define SEQAN_HEADER_BASIC_TRANSPORT_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+//assign
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.assign:
+..summary:Assigns one object to another object.
+..cat:Content Manipulation
+..signature:assign(target, source)
+..signature:assign(target, source [, limit] [,resize_tag])
+..param.target: Gets the content of $source$.
+..param.source: Is copied to $target$.
+..param.limit: The maximal length of $target$ after the operation. (optional)
+...remarks:This arguments can be applied if $target$ is a container.
+..param.resize_tag: Specifies the strategy that is applied if $target$ has not enough capacity to store the complete content. (optional)
+...type:Tag.Overflow Strategy
+...default:Specified by @Metafunction.DefaultOverflowImplicit@ of the $target$ type.
+...remarks:This arguments can be applied if $target$ is a container.
+..remarks:$assign(target, source)$ is semantically equivalent to $target = source$.
+*/
+
+template <typename TTarget, typename TSource>
+inline void
+assign(TTarget & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ target = source;
+}
+template <typename TTarget, typename TSource>
+inline void
+assign(TTarget & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ target = source;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TSpec> struct Proxy;
+
+template<typename TTargetSpec, typename TSource>
+inline void
+assign(Proxy<TTargetSpec> & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ assignValue(iter(target), source);
+}
+
+template<typename TTargetSpec, typename TSource>
+inline void
+assign(Proxy<TTargetSpec> & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ assignValue(iter(target), source);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// move
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.move:
+..summary:Hands over content from one container to another container.
+..cat:Content Manipulation
+..signature:move(target, source)
+..param.target:A container $source$ is moved to.
+..param.source:A container that is moved to $target$.
+..remarks:The function tries to hand over the contents of $source$ to $target$.
+If this is possible, $source$ losts its content and will therefore be empty after this operation.
+Otherwise, the function behaves like @Function.assign@ and $source$ is copied to $target$.
+..see:Function.assign
+*/
+
+template<typename TTarget, typename TSource>
+inline void
+move(TTarget & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ assign(target, source);
+}
+template<typename TTarget, typename TSource>
+inline void
+move(TTarget const & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ assign(target, source);
+}
+template<typename TTarget, typename TSource>
+inline void
+move(TTarget & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ assign(target, source);
+}
+template<typename TTarget, typename TSource>
+inline void
+move(TTarget const & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ assign(target, source);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// set
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.set:
+..summary:Assigns one object to another object avoiding to copy contents.
+..cat:Content Manipulation
+..signature:assign(target, source)
+..signature:assign(target, source)
+..param.target: Gets the content of $source$.
+..param.source: Content source.
+..remarks:$set(target, source)$ is semantically equivalent to $target = source$.
+If possible, $set$ copies content references instead of the content itself.
+*/
+
+//TODO: rename set to ...
+
+template<typename TTarget, typename TSource>
+inline void
+set(TTarget & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ assign(target, source);
+}
+template<typename TTarget, typename TSource>
+inline void
+set(TTarget const & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ assign(target, source);
+}
+template<typename TTarget, typename TSource>
+inline void
+set(TTarget & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ assign(target, source);
+}
+template<typename TTarget, typename TSource>
+inline void
+set(TTarget const & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ assign(target, source);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
+
+
diff --git a/src/libSSA/seqan/basic/basic_type.h b/src/libSSA/seqan/basic/basic_type.h
new file mode 100644
index 0000000..320fa99
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_type.h
@@ -0,0 +1,624 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_type.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_TYPE_H
+#define SEQAN_HEADER_BASIC_TYPE_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Metafunction.Value:
+..summary:Type of the items in the container.
+..signature:Value<T>::Type
+..param.T:Type for which the value type is determined.
+..returns.param.Type:Value type of $T$.
+..remarks.text:The value type of a container $T$ is the type of the elements in $T$.
+ For example, the value type of a sequence of $int$ is $int$.
+..example.code:Value<String<char> >::Type c; //c has type char
+*/
+
+template <typename T, const int i = 0>
+struct Value
+{
+ typedef T Type;
+};
+/*
+template <typename T>
+struct Value<T const>
+{
+ typedef T Type;
+};
+*/
+//____________________________________________________________________________
+
+/**
+.Metafunction.GetValue:
+..summary:Type for reading values.
+..signature:GetValue<T>::Type
+..param.T:Type of container that holds a value.
+..returns.param.Type:GetValue type of $T$.
+..remarks.text:Depending on $T$, the $GetValue$-type can either be $Value<T>::Type &$ or $Value<T>::Type$.
+..text:$GetValue$ is the return type of @Function.getValue@ that allows a (read-only) access to objects.
+Do not confuse it with @Function.value@ that returns a @Metafunction.Reference.reference@ to the value.
+..see:Metafunction.Value
+..see:Function.getValue
+*/
+template <typename T>
+struct GetValue
+{
+ typedef typename Value<T>::Type const & Type;
+};
+template <typename T>
+struct GetValue<T const>:
+ public GetValue<T>
+{
+};
+
+//____________________________________________________________________________
+
+/**
+.Metafunction.Reference:
+..summary:Reference type.
+..signature:Reference<T>::Type
+..param.T:A Type.
+..returns.param.Type:Either $T &$ or a proxy object @Class.Proxy@ for $T$.
+..see:Metafunction.Value
+..see:Metafunction.GetValue
+*/
+template <typename T>
+struct Reference
+{
+ typedef typename Value<T>::Type & Type;
+};
+template <typename T>
+struct Reference<T const>
+{
+ typedef typename Value<T>::Type const & Type;
+};
+
+//____________________________________________________________________________
+
+
+/**
+.Metafunction.Size:
+..summary:Type of an object that is suitable to hold size information.
+..signature:Size<T>::Type
+..param.T:Type for which the size type is determined.
+..returns.param.Type:Size type of $T$.
+..remarks.text:In most cases this type is $size_t$.
+*/
+template <typename T>
+struct Size
+{
+ typedef size_t Type;
+};
+template <typename T>
+struct Size<T const>:
+ Size<T>
+{
+};
+
+//____________________________________________________________________________
+
+
+/**
+.Metafunction.Difference:
+..summary:Type of an object that stores the difference between two iterators.
+..signature:Difference<T>::Type
+..param.T:Type for which the difference type is determined.
+...type:Class.Iter
+..returns.param.Type:Difference type of $T$.
+..remarks.text:In most cases this type is $ptrdiff_t$.
+..see:Metafunction.Size
+*/
+template <typename T>
+struct Difference
+{
+ typedef ptrdiff_t Type;
+};
+template <typename T>
+struct Difference<T const>:
+ Difference<T>
+{
+};
+
+//____________________________________________________________________________
+
+
+/**
+.Metafunction.Position:
+..summary:Type of an object that represents a position in a container.
+..signature:Position<T>::Type
+..param.T:Type for which the position type is determined.
+...type:Class.Iter
+...type:Class.String
+..returns.param.Type:Position type of $T$.
+..see:Metafunction.Iterator
+*/
+template <typename T>
+struct Position
+{
+ typedef typename Size<T>::Type Type;
+};
+template <typename T>
+struct Position<T const>:
+ Position<T>
+{
+};
+
+//____________________________________________________________________________
+
+/**
+.Metafunction.Host:
+..summary:Type of the object a given object depends on.
+..signature:Host<T>::Type
+..param.T:Type for which the host type is determined.
+..returns.param.Type:Host type of $T$.
+*/
+template <typename T>
+struct Host
+{
+ typedef T Type;
+};
+
+//____________________________________________________________________________
+
+/**
+.Metafunction.Spec:
+..summary:The spec of a class.
+..signature:Spec<T>::Type
+..param.T:Type for which the spec is determined.
+..returns.param.Type:Spec of $T$.
+..remarks:The spec of a SeqAn type is the class that is used in template subclassing
+ to specify the specialization.
+ For example, the spec of $String<char, Alloc<> >$ is $Alloc<>$.
+*/
+
+// default case
+template <typename T>
+struct Spec {
+ typedef void Type;
+};
+
+
+// one argument case
+template <template <typename> class T, typename TSpec>
+struct Spec< T<TSpec> > {
+ typedef TSpec Type;
+};
+
+template <typename T>
+struct Spec<T const>:
+ public Spec<T> {};
+
+//____________________________________________________________________________
+
+/**
+.Metafunction.DeepestSpec:
+..summary:The deepest spec of a class with nested template arguments.
+..signature:DeepestSpec<T>::Type
+..param.T:Type for which the deepest spec is determined.
+..returns.param.Type:Deepest spec of $T$.
+..remarks:The spec of a SeqAn type is the innermost class that is used in nested subclassing.
+ For example, the deepest spec of $Iter<..., VSTree<BottomUp<MUMs> > >$ is $MUMs$.
+*/
+
+// default case
+template <typename T>
+struct DeepestSpec {
+ typedef T Type;
+};
+
+// recursion for 1 argument
+template <
+ template <typename> class T,
+ typename T1 >
+struct DeepestSpec< T<T1> > {
+ typedef typename
+ IF<
+ TYPECMP<T1, void>::VALUE, // is T1 void?
+ T<T1>, // yes, end of recursion
+ typename DeepestSpec< typename Spec< T<T1> >::Type >::Type // no, recurse
+ >::Type Type;
+};
+
+// recursion for 2 arguments
+template <
+ template <typename, typename> class T,
+ typename T1, typename T2 >
+struct DeepestSpec< T<T1,T2> >:
+ DeepestSpec< typename Spec< T<T1,T2> >::Type > {};
+
+// recursion for 3 arguments
+template <
+ template <typename, typename, typename> class T,
+ typename T1, typename T2, typename T3 >
+struct DeepestSpec< T<T1,T2,T3> >:
+ DeepestSpec< typename Spec< T<T1,T2,T3> >::Type > {};
+
+// recursion for 4 arguments
+template <
+ template <typename, typename, typename, typename> class T,
+ typename T1, typename T2, typename T3, typename T4 >
+struct DeepestSpec< T<T1,T2,T3,T4> >:
+ DeepestSpec< typename Spec< T<T1,T2,T3,T4> >::Type > {};
+
+// recursion for 5 arguments
+template <
+ template <typename, typename, typename, typename, typename> class T,
+ typename T1, typename T2, typename T3, typename T4, typename T5 >
+struct DeepestSpec< T<T1,T2,T3,T4,T5> >:
+ DeepestSpec< typename Spec< T<T1,T2,T3,T4,T5> >::Type > {};
+
+template <typename T>
+struct DeepestSpec<T const>:
+ public DeepestSpec<T> {};
+
+//____________________________________________________________________________
+
+/**
+.Metafunction.Cargo:
+..summary:Type of additional data stored in an object.
+..signature:Cargo<T>::Type
+..param.T:Type for which the cargo tyoe is determined.
+..returns.param.Type:Cargo of $T$.
+..remarks:The definition of Cargo allows the addition of user specific data to existing data structures.
+*/
+
+template <typename T>
+struct Cargo {
+ typedef Nothing Type;
+};
+template <typename T>
+struct Cargo<T const> {
+ typedef typename Cargo<T>::Type const Type;
+};
+
+//____________________________________________________________________________
+
+/**
+.Metafunction.VertexDescriptor:
+..summary:Type of an object that represents a vertex descriptor.
+..signature:VertexDescriptor<T>::Type
+..param.T:Type T must be a graph. All graphs currently use ids as vertex descriptors.
+..returns.param.Type:VertexDescriptor type.
+..remarks.text:The vertex descriptor is a unique handle to a vertex in a graph.
+It is used in various graph functions, e.g., to add edges, to create OutEdge Iterators or to remove a vertex.
+It is also used to attach properties to vertices.
+..example.code:VertexDescriptor<Graph<> >::Type vD; //vD is a vertex descriptor
+*/
+
+template <typename T>
+struct VertexDescriptor {
+ typedef void* Type;
+};
+template <typename T>
+struct VertexDescriptor<T const>:
+ public VertexDescriptor<T> {};
+
+
+//____________________________________________________________________________
+
+
+/**
+.Metafunction.Id:
+..summary:Type of an object that represents an id.
+..signature:Id<T>::Type
+..param.T:Type for which a suitable id type is determined.
+..returns.param.Type:Id type.
+..remarks.text:The id type of a container is the type that is used to uniquely identify its elements.
+In most cases this type is unsigned int.
+..example.code:Id<Graph<> >::Type id; //id has type unsigned int
+*/
+template<typename T>
+struct Id {
+ typedef unsigned int Type;
+};
+
+//____________________________________________________________________________
+
+template<typename T>
+struct Id<T const> {
+ typedef unsigned int Type;
+};
+
+//____________________________________________________________________________
+
+/**
+.Metafunction.Key:
+..summary:Key type of a key to cargo mapping.
+..signature:Key<T>::Type
+..param.T:Type for which a key type is determined.
+..returns.param.Type:Key type.
+...default:The type $T$ itself.
+*/
+template< typename T >
+struct Key
+{
+ typedef T Type;
+};
+
+template <typename T>
+struct Key<T const>:
+ Key<T> {};
+
+//____________________________________________________________________________
+
+/*VERALTET
+.Metafunction.Object:
+..summary:Object type of a key to object mapping.
+..signature:Object<T>::Type
+..param.T:Type for which a object type is determined.
+..returns.param.Type:Object type.
+*/
+
+template<typename T>
+struct Object;
+
+template <typename T>
+struct Object<T const>:
+ Object<T> {};
+
+
+//____________________________________________________________________________
+
+/**
+.Metafunction.Source
+*/
+
+template < typename TSpec = void >
+struct Source
+{
+ typedef TSpec Type;
+};
+
+template <typename T>
+struct Source<T const>:
+ Source<T>
+{
+};
+
+//____________________________________________________________________________
+
+/**
+.Internal._Parameter:
+..cat:Metafunctions
+..summary:Type for function parameters and return values.
+..signature:_Parameter<T>::Type
+..param.T:A type.
+..returns.param.Type:The parameter type for arguments of type $T$.
+...text:If $T$ is a pointer or array type, then $_Parameter<T>::Type$ is $T$,
+otherwise $_Parameter<T>::Type$ is $T &$.
+*/
+template <typename T>
+struct _Parameter
+{
+ typedef T & Type;
+};
+
+template <typename T>
+struct _Parameter<T *>
+{
+ typedef T * Type;
+};
+template <typename T, size_t I>
+struct _Parameter<T [I]>
+{
+ typedef T * Type;
+};
+
+
+/**
+.Internal._toParameter:
+..cat:Functions
+..summary:Transforms pointers to parameter types.
+..signature:_toParameter<T>(pointer)
+..param.pointer:A pointer.
+..param.T:A Type.
+...text:$object$ is transformed into the parameter type of $T$ that is given by @Internal._Parameter at .
+...note:This type must be explicitely specified.
+..returns:To $TParameter$ transformed $object$.
+..see:Internal._Parameter
+*/
+template <typename T>
+typename _Parameter<T>::Type
+_toParameter(T * _object)
+{
+SEQAN_CHECKPOINT
+ return * _object;
+}
+template <typename T>
+typename _Parameter<T>::Type
+_toParameter(T _object)
+{
+SEQAN_CHECKPOINT
+ return _object;
+}
+
+//____________________________________________________________________________
+
+/**
+.Internal._ConstParameter:
+..cat:Metafunctions
+..summary:Type for constant function parameters and return values.
+..signature:_ConstParameter<T>::Type
+..param.T:A type.
+..returns.param.Type:The const parameter type for arguments of type $T$.
+...text:If $T$ is a pointer or array type, then $_Parameter<T>::Type$ is a pointer to a const array,
+otherwise $_Parameter<T>::Type$ is $T const &$.
+..see:Internal._Parameter
+*/
+template <typename T>
+struct _ConstParameter
+{
+ typedef T const & Type;
+};
+template <typename T>
+struct _ConstParameter<T const>:
+ public _ConstParameter<T> {};
+
+template <typename T>
+struct _ConstParameter<T *>
+{
+ typedef T const * Type;
+};
+template <typename T>
+struct _ConstParameter<T const *>
+{
+ typedef T const * Type;
+};
+
+template <typename T, size_t I>
+struct _ConstParameter<T [I]>
+{
+ typedef T const * Type;
+};
+template <typename T, size_t I>
+struct _ConstParameter<T const [I]>
+{
+ typedef T const * Type;
+};
+
+//____________________________________________________________________________
+
+/**
+.Internal._Pointer:
+..cat:Metafunctions
+..summary:The associated pointer type.
+..signature:_Pointer<T>::Type
+..param.T:A type.
+..returns.param.Type:A pointer type for $T$.
+...text:if $T$ is already a pointer type, then $_Pointer<T>::Type$ is $T$,
+otherwise $_Pointer<T>::Type$ is $T *$.
+..see:Internal._Parameter
+..see:Internal._toParameter
+*/
+template <typename T>
+struct _Pointer
+{
+ typedef T * Type;
+};
+
+template <typename T>
+struct _Pointer<T *>
+{
+ typedef T * Type;
+};
+template <typename T>
+struct _Pointer<T * const>
+{
+ typedef T * const Type;
+};
+
+template <typename T, size_t I>
+struct _Pointer<T [I]>
+{
+ typedef T * Type;
+};
+
+/**
+.Internal._toPointer:
+..cat:Functions
+..summary:Transforms types into pointers.
+..signature:_toPointer(object)
+..param.object:An object.
+..returns:$object$, transformed to a pointer.
+...text:The type of the returned pointer is given by @Internal._Pointer at .
+..see:Internal._Pointer
+*/
+template <typename T>
+typename _Pointer<T>::Type
+_toPointer(T & _object)
+{
+SEQAN_CHECKPOINT
+ return & _object;
+}
+template <typename T>
+typename _Pointer<T const>::Type
+_toPointer(T const & _object)
+{
+SEQAN_CHECKPOINT
+ return & _object;
+}
+
+template <typename T>
+typename _Pointer<T *>::Type
+_toPointer(T * _object)
+{
+SEQAN_CHECKPOINT
+ return _object;
+}
+
+//____________________________________________________________________________
+
+
+/**
+.Metafunction.LENGTH:
+..summary:Number of elements in a fixed-size container.
+..signature:LENGTH<T>::Type
+..param.T:Type for which the number of elements is determined.
+..returns.param.VALUE:Number of elements.
+..remarks.text:The default return value is 1 for dynamic-size containers.
+*/
+template <typename T>
+struct LENGTH
+{
+ enum { VALUE = 1 };
+};
+template <typename T>
+struct LENGTH<T const>:
+ LENGTH<T>
+{
+};
+
+/**
+.Metafunction.WEIGHT:
+..summary:Number of relevant positions in a shape.
+..signature:WEIGHT<T>::Type
+..param.T:Shape type for which the number of relevant positions is determined.
+...type:Class.Shape
+..returns.param.VALUE:Number of relevant positions.
+..remarks.text:The default return value is the result of the @Metafunction.LENGTH@ function.
+For gapped shapes this is the number of '1's.
+*/
+template <typename T>
+struct WEIGHT:
+ LENGTH<T>
+{
+};
+template <typename T>
+struct WEIGHT<T const>:
+ WEIGHT<T>
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+//Iterator: see basic_iterator.h
+
+//////////////////////////////////////////////////////////////////////////////
+
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/basic/basic_volatile_ptr.h b/src/libSSA/seqan/basic/basic_volatile_ptr.h
new file mode 100644
index 0000000..6a6bdd5
--- /dev/null
+++ b/src/libSSA/seqan/basic/basic_volatile_ptr.h
@@ -0,0 +1,159 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: basic_volatile_ptr.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_BASIC_VOLATILE_PTR_H
+#define SEQAN_HEADER_BASIC_VOLATILE_PTR_H
+
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+ //////////////////////////////////////////////////////////////////////////////
+ // volatile pointer
+ // allows you to handle volatile data (used by ext. string during swapping)
+ //
+ // imagine volatile pointers as nodes in an undirected graph
+ // when you assign one to another then they are connected
+ // all pointers in a connection component points to the same value
+ // by calling nukeCopies you can destroy the component and set all pointers to NULL
+
+ template < typename Type >
+ struct VolatilePtr
+ {
+ typedef VolatilePtr _Self;
+ typedef VolatilePtr* _SelfPtr;
+ typedef VolatilePtr& _SelfRef;
+
+ typedef Type& reference;
+ typedef const Type& const_reference;
+ typedef Type* pointer;
+
+ pointer ptr;
+ _SelfPtr next; // prev == NULL means this is the master node
+ _SelfPtr prev; // prev == NULL means this is the master node
+
+ VolatilePtr() { // volatile pinters behave like normal pointers
+ prev = this; // and are not initialized (ptr) per default
+ next = this;
+ };
+
+ VolatilePtr(const pointer _p) {
+ ptr = _p;
+ prev = this;
+ next = this;
+ }
+
+ VolatilePtr(const _Self& _vp) {
+ ptr = _vp.ptr;
+ prev = this;
+ next = this;
+ }
+
+ VolatilePtr(_SelfRef _vp) {
+ ptr = _vp.ptr;
+ prev = this;
+ next = this;
+ if (ptr) hangOn(_vp);
+ }
+
+ ~VolatilePtr() {
+ hangOff();
+ }
+
+ template <typename size_type>
+ inline reference operator[] (size_type offset) {
+ return ptr[offset];
+ }
+
+ template <typename size_type>
+ inline const_reference operator[] (size_type offset) const {
+ return ptr[offset];
+ }
+
+ inline _Self& operator=(_Self const &_Right) {
+ hangOff();
+ ptr = _Right.ptr;
+ if (ptr) hangOn(const_cast<_Self&>(_Right));
+ return *this;
+ }
+
+ inline _Self& operator=(pointer const _Right) {
+ hangOff();
+ ptr = _Right;
+ return *this;
+ }
+
+ inline bool isLonely() {
+ return next == this;
+ }
+
+ inline void nukeCopies() {
+ _SelfPtr p = next;
+ while (p != this) {
+ _SelfPtr tmp = p->next;
+ p->ptr = NULL;
+ p->prev = p;
+ p->next = p;
+ p = tmp;
+ }
+ prev = this;
+ next = this;
+ }
+
+ inline bool operator== (const _Self &I) const {
+ return ptr == I.ptr;
+ }
+
+ inline bool operator!= (const _Self &I) const {
+ return ptr != I.ptr;
+ }
+
+ inline operator pointer () const {
+ return ptr;
+ }
+
+ private:
+
+ inline void hangOn(_SelfRef _prev) {
+ // hang on between _prev and _prev.next
+ prev = &_prev;
+ next = _prev.next;
+ _prev.next = this;
+ next->prev = this;
+ }
+
+ inline void hangOff() {
+ next->prev = prev;
+ prev->next = next;
+ next = this;
+ prev = this;
+ }
+ };
+
+ template <typename TValue>
+ inline void nukeCopies(TValue* &) {}
+
+ template <typename TValue>
+ inline void nukeCopies(VolatilePtr<TValue> &ptr) { ptr.nukeCopies(); }
+
+}
+
+#endif
diff --git a/src/libSSA/seqan/file.h b/src/libSSA/seqan/file.h
new file mode 100644
index 0000000..034a8e0
--- /dev/null
+++ b/src/libSSA/seqan/file.h
@@ -0,0 +1,89 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: file.h,v 1.4 2009/03/13 14:51:00 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FILE_H
+#define SEQAN_HEADER_FILE_H
+
+//____________________________________________________________________________
+// prerequisites
+
+#include <iostream>
+#include <climits>
+#include <cstdio>
+#include <list>
+#include <vector>
+#include <map>
+#include <cmath>
+
+#include <seqan/sequence.h>
+
+
+//____________________________________________________________________________
+
+#include <seqan/file/file_forwards.h>
+
+#ifdef SEQAN_SWITCH_USE_FORWARDS
+#include <seqan/file/file_generated_forwards.h>
+#endif
+
+#include <seqan/file/cstream.h>
+#include <seqan/file/stream.h>
+
+#include <seqan/file/chunk_collector.h>
+#include <seqan/file/meta.h>
+
+//____________________________________________________________________________
+// file formats
+
+#include <seqan/file/file_format.h>
+
+#include <seqan/file/stream_algorithms.h>
+
+//file formats for sequences
+#include <seqan/file/file_format_raw.h>
+#include <seqan/file/file_format_fasta.h>
+//#include <seqan/file/file_format_embl.h>
+//#include <seqan/file/file_format_genbank.h>
+
+//file formats for alignments
+#include <seqan/file/file_format_fasta_align.h>
+
+//others
+#include <seqan/file/file_format_cgviz.h>
+
+//____________________________________________________________________________
+
+//#include <seqan/file/file_format_guess.h>
+
+//____________________________________________________________________________
+// files
+
+#include <seqan/file/file_base.h>
+#include <seqan/file/file_array.h>
+
+//#include <seqan/system.h> // async file (default file type of File<>)
+/*#include <seqan/system/file_sync.h>
+#include <seqan/system/system_event.h>
+#include <seqan/system/file_async.h>
+*/
+//____________________________________________________________________________
+// external string
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/file/chunk_collector.h b/src/libSSA/seqan/file/chunk_collector.h
new file mode 100644
index 0000000..c4515d1
--- /dev/null
+++ b/src/libSSA/seqan/file/chunk_collector.h
@@ -0,0 +1,534 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: chunk_collector.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_CHUNK_COLLECTOR_H
+#define SEQAN_HEADER_CHUNK_COLLECTOR_H
+
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Internal._ChunkCollector:
+..cat:Classes
+..summary:Reads piecewise from stream, collects pieces (chunks) in a vector.
+..signature:_ChunkCollector<Host>
+..param.Host:Type of host object that is used as allocator.
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename T>
+struct ChunkLength
+{
+ enum { VALUE = 1024 };
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// _StreamChunkCollector class: collects content of a stream in chunks
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+class _ChunkCollector
+{
+protected:
+ THost * data_host;
+ typename Size<THost>::Type data_length;
+
+ typedef ::std::vector<typename Value<THost>::Type *, ToStdAllocator<THost, typename Value<THost>::Type *> > Chunk_Holder;
+ Chunk_Holder data_chunks;
+
+public:
+ static int const CHUNK_LENGTH = ChunkLength<_ChunkCollector>::VALUE;
+
+public:
+ _ChunkCollector(THost & _host):
+ data_host(& _host),
+ data_length(0),
+ data_chunks(typename Chunk_Holder::allocator_type(_host))
+ {
+ }
+
+ ~_ChunkCollector()
+ {
+ clear(*this);
+ }
+
+public:
+
+ friend inline void
+ clear(_ChunkCollector & me)
+ {
+ typename Chunk_Holder::iterator it = me.data_chunks.begin();
+ typename Chunk_Holder::iterator it_end = me.data_chunks.end();
+
+ for (; it != it_end; ++it)
+ {
+ deallocate(me.data_host, *it, CHUNK_LENGTH);
+ }
+
+ me.data_chunks.clear();
+ me.data_length = 0;
+ }
+
+ friend inline typename Size<THost>::Type
+ length(_ChunkCollector const & me)
+ {
+ return me.data_length;
+ }
+
+ friend inline void
+ _setLength(_ChunkCollector & me, typename Size<THost>::Type new_length)
+ {
+ me.data_length = new_length;
+ }
+
+ friend inline int
+ chunkCount(_ChunkCollector const & me)
+ {
+ return me.data_chunks.size();
+ }
+
+ friend inline typename Value<THost>::Type *
+ getChunk(_ChunkCollector const & me, int chunk_number)
+ {
+ return me.data_chunks[chunk_number];
+ }
+
+ friend inline typename Value<THost>::Type *
+ createChunk(_ChunkCollector & me)
+ {
+ typename Value<THost>::Type * new_chunk;
+ allocate(me.data_host, new_chunk, CHUNK_LENGTH);
+ me.data_chunks.push_back(new_chunk);
+ return new_chunk;
+ }
+};
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+struct Host<_ChunkCollector<THost> >
+{
+ typedef THost Type;
+};
+
+template <typename THost>
+struct Host<_ChunkCollector<THost> const >
+{
+ typedef THost Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+struct Value<_ChunkCollector<THost> >
+{
+ typedef typename Value<THost>::Type Type;
+};
+
+template <typename THost>
+struct Value<_ChunkCollector<THost> const >
+{
+ typedef typename Value<THost>::Type Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+struct GetValue<_ChunkCollector<THost> >
+{
+ typedef typename GetValue<THost>::Type Type;
+};
+
+template <typename THost>
+struct GetValue<_ChunkCollector<THost> const >
+{
+ typedef typename GetValue<THost>::Type Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+struct Size<_ChunkCollector<THost> >
+{
+ typedef typename Size<THost>::Type Type;
+};
+
+template <typename THost>
+struct Size<_ChunkCollector<THost> const >
+{
+ typedef typename Size<THost>::Type Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+struct _Assign_Stream_2_ChunkCollector
+{
+ template <typename THost, typename TSource>
+ static inline void
+ assign_(_ChunkCollector<THost> & target,
+ TSource & source)
+ {
+ clear(target);
+
+ while (!_streamEOF(source))
+ {
+ typename Value<THost>::Type * chunk = createChunk(target);
+ typename Size<THost>::Type count = _streamRead(chunk, source, ChunkLength< _ChunkCollector<THost> >::VALUE);
+ _setLength(target, length(target) + count);
+ }
+ }
+
+ template <typename THost, typename TSource>
+ static inline void
+ assign_(_ChunkCollector<THost> & target,
+ TSource & source,
+ typename Size< _ChunkCollector<THost> >::Type limit)
+ {
+ clear(target);
+
+ while (!_streamEOF(source))
+ {
+ typename Value<THost>::Type * chunk = createChunk(target);
+ typename Size<THost>::Type count = _streamRead(chunk, source, ChunkLength< _ChunkCollector<THost> >::VALUE);
+ _setLength(target, length(target) + count);
+
+ if (length(target) >= limit)
+ {
+ _setLength(target, limit);
+ break;
+ }
+ }
+ }
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost, typename TSource>
+inline void
+assign(_ChunkCollector<THost> & target,
+ TSource & source)
+{
+ _Assign_Stream_2_ChunkCollector::assign_(target, source);
+}
+template <typename THost, typename TSource>
+inline void
+assign(_ChunkCollector<THost> & target,
+ TSource const & source)
+{
+ _Assign_Stream_2_ChunkCollector::assign_(target, source);
+}
+
+template <typename THost, typename TSource, typename TSize>
+inline void
+assign(_ChunkCollector<THost> & target,
+ TSource & source,
+ TSize limit)
+{
+ _Assign_Stream_2_ChunkCollector::assign_(target, source, limit);
+}
+template <typename THost, typename TSource, typename TSize>
+inline void
+assign(_ChunkCollector<THost> & target,
+ TSource const & source,
+ TSize limit)
+{
+ _Assign_Stream_2_ChunkCollector::assign_(target, source, limit);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TExpand>
+struct _Assign_ChunkCollector_2_String
+{
+ template <typename TTarget, typename TSource>
+ static void assign_(
+ TTarget & target,
+ TSource & source)
+ {
+ typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), TExpand());
+
+ int i_end = chunkCount(source);
+ typename Value<TTarget>::Type * pos = begin(target);
+ for (int i = 0; i < i_end; ++i)
+ {
+ bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
+ typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : ChunkLength<TSource>::VALUE;
+ typename Value<TSource>::Type * chunk = getChunk(source, i);
+
+ arrayConstructCopy(chunk, chunk + chunk_length, pos);
+ if (is_last_chunk) break;
+ pos += chunk_length;
+ }
+ }
+
+ template <typename TTarget, typename TSource>
+ static void assign_(
+ TTarget & target,
+ TSource & source,
+ typename Size<TTarget>::Type limit)
+ {
+ typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), limit, TExpand());
+
+ int i_end = chunkCount(source);
+ typename Value<TTarget>::Type * pos = begin(target);
+ for (int i = 0; i < i_end; ++i)
+ {
+ bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
+ typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : ChunkLength<TSource>::VALUE;
+ typename Value<TSource>::Type * chunk = getChunk(source, i);
+
+ arrayConstructCopy(chunk, chunk + chunk_length, pos);
+ if (is_last_chunk) break;
+ pos += chunk_length;
+ }
+ }
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
+inline void
+assign(String<TTargetValue, TTargetSpec> & target,
+ _ChunkCollector<TSourceHost> const & source,
+ Tag<TExpand> const tag)
+{
+ _Assign_ChunkCollector_2_String<Tag<TExpand> const>::assign_(target, source);
+}
+template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
+inline void
+assign(String<TTargetValue, TTargetSpec> & target,
+ _ChunkCollector<TSourceHost> const & source,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
+ Tag<TExpand> const tag)
+{
+ _Assign_ChunkCollector_2_String<Tag<TExpand> const>::assign_(target, source, limit);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TExpand>
+struct _Append_ChunkCollector_2_String
+{
+ template <typename TTarget, typename TSource>
+ static void append_(
+ TTarget & target,
+ TSource & source)
+ {
+ typedef typename Size<TTarget>::Type TSize;
+ TSize target_length_old = length(target);
+ TSize part_length = _clearSpace(target, length(source), target_length_old, target_length_old, TExpand());
+
+ int i_end = chunkCount(source);
+ typename Value<TTarget>::Type * pos = begin(target) + target_length_old; //begin(target) was possibly changed by _clearSpace
+ for (int i = 0; i < i_end; ++i)
+ {
+ bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
+ typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : (TSize) ChunkLength<TSource>::VALUE;
+ typename Value<TSource>::Type * chunk = getChunk(source, i);
+
+ arrayConstructCopy(chunk, chunk + chunk_length, pos);
+ if (is_last_chunk) break;
+ pos += chunk_length;
+ }
+ }
+
+ template <typename TTarget, typename TSource>
+ static void append_(
+ TTarget & target,
+ TSource & source,
+ typename Size<TTarget>::Type limit)
+ {
+ typedef typename Size<TTarget>::Type TSize;
+ TSize target_length_old = length(target);
+ TSize part_length = _clearSpace(target, length(source), target_length_old, target_length_old, limit, TExpand());
+
+ int i_end = chunkCount(source);
+ typename Value<TTarget>::Type * pos = begin(target) + target_length_old; //begin(target) was possibly changed by _clearSpace
+ for (int i = 0; i < i_end; ++i)
+ {
+ bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
+ typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : (TSize) ChunkLength<TSource>::VALUE;
+ typename Value<TSource>::Type * chunk = getChunk(source, i);
+
+ arrayConstructCopy(chunk, chunk + chunk_length, pos);
+ if (is_last_chunk) break;
+ pos += chunk_length;
+ }
+ }
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
+inline void
+append(String<TTargetValue, TTargetSpec> & target,
+ _ChunkCollector<TSourceHost> const & source,
+ Tag<TExpand> const )
+{
+ _Append_ChunkCollector_2_String<Tag<TExpand> const>::append_(target, source);
+}
+template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
+inline void
+append(String<TTargetValue, TTargetSpec> & target,
+ _ChunkCollector<TSourceHost> const & source,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
+ Tag<TExpand> const )
+{
+ _Append_ChunkCollector_2_String<Tag<TExpand> const>::append_(target, source, limit);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TExpand>
+struct _Replace_ChunkCollector_2_String
+{
+ template <typename TTarget, typename TSource>
+ static void replace_(
+ TTarget & target,
+ typename Size<TTarget>::Type pos_begin,
+ typename Size<TTarget>::Type pos_end,
+ TSource & source)
+ {
+ typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), pos_begin, pos_end, TExpand());
+
+ int i_end = chunkCount(source);
+ typename Value<TTarget>::Type * pos = begin(target) + pos_begin;
+ for (int i = 0; i < i_end; ++i)
+ {
+ bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
+ typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : ChunkLength<TSource>::VALUE;
+ typename Value<TSource>::Type * chunk = getChunk(source, i);
+
+ arrayConstructCopy(chunk, chunk + chunk_length, pos);
+ if (is_last_chunk) break;
+ pos += chunk_length;
+ }
+ }
+
+ template <typename TTarget, typename TSource>
+ static void replace_(
+ TTarget & target,
+ typename Size<TTarget>::Type pos_begin,
+ typename Size<TTarget>::Type pos_end,
+ TSource & source,
+ typename Size<TTarget>::Type limit)
+ {
+ typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), pos_begin, pos_end, limit, TExpand());
+
+ int i_end = chunkCount(source);
+ typename Value<TTarget>::Type * pos = begin(target) + pos_begin;
+ for (int i = 0; i < i_end; ++i)
+ {
+ bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
+ typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : ChunkLength<TSource>::VALUE;
+ typename Value<TSource>::Type * chunk = getChunk(source, i);
+
+ arrayConstructCopy(chunk, chunk + chunk_length, pos);
+ if (is_last_chunk) break;
+ pos += chunk_length;
+ }
+ }
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
+inline void
+replace(String<TTargetValue, TTargetSpec> & target,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end,
+ _ChunkCollector<TSourceHost> const & source,
+ Tag<TExpand> const tag)
+{
+ _Replace_ChunkCollector_2_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source);
+}
+
+template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
+inline void
+replace(String<TTargetValue, TTargetSpec> & target,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end,
+ _ChunkCollector<TSourceHost> const & source,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
+ Tag<TExpand> const tag)
+{
+ _Replace_ChunkCollector_2_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source, limit);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TTargetValue, typename TSourceHost, typename TExpand>
+inline void
+replace(TTargetValue * target,
+ size_t pos_begin,
+ size_t pos_end,
+ _ChunkCollector<TSourceHost> const & source,
+ Tag<TExpand> const tag)
+{
+ _Replace_ChunkCollector_2_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source);
+}
+
+template <typename TTargetValue, typename TSourceHost, typename TExpand>
+inline void
+replace(TTargetValue * target,
+ size_t pos_begin,
+ size_t pos_end,
+ _ChunkCollector<TSourceHost> const & source,
+ size_t limit,
+ Tag<TExpand> const tag)
+{
+ _Replace_ChunkCollector_2_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source, limit);
+}
+//____________________________________________________________________________
+/*
+template <typename TTargetValue, typename TSourceHost, typename TExpand>
+inline void
+replace(TTargetValue * target,
+ size_t pos_begin,
+ size_t pos_end,
+ _ChunkCollector<TSourceHost> const & source,
+ Tag<TExpand> const tag)
+{
+ _Replace_ChunkCollector_2_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source);
+}
+
+template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
+inline void
+replace(String<TTargetValue, TTargetSpec> & target,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end,
+ _ChunkCollector<TSourceHost> const & source,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
+ Tag<TExpand> const tag)
+{
+ _Replace_ChunkCollector_2_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source, limit);
+}
+*/
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/file/cstream.h b/src/libSSA/seqan/file/cstream.h
new file mode 100644
index 0000000..56f4315
--- /dev/null
+++ b/src/libSSA/seqan/file/cstream.h
@@ -0,0 +1,283 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: cstream.h,v 1.2 2009/03/03 18:47:37 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_CSTREAM_H
+#define SEQAN_HEADER_CSTREAM_H
+
+#include <cstdio>
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Adaption."std::FILE *":
+..summary:Standard library C style streams.
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+// Position is now defined in file/file_cstyle.h
+/*
+template <>
+struct Position<FILE *>
+{
+ typedef long Type;
+};
+*/
+//////////////////////////////////////////////////////////////////////////////
+
+template <>
+struct Value<FILE *>
+{
+ typedef char Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+/*
+template <>
+struct Position<FILE *>
+{
+ typedef ::std::fpos_t Type;
+};
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename T>
+struct _IsTellSeekStream;
+
+template <>
+struct _IsTellSeekStream<FILE *>
+{
+ typedef True Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+inline bool
+_streamOpen(::std::FILE * & me, String<char> path, bool for_read = true)
+{
+SEQAN_CHECKPOINT
+ size_t plen = length(path);
+ char *s = new char[plen + 1];
+ for(size_t i = 0; i < plen; i++) {
+ s[i] = path[i];
+ }
+ s[plen] = '\0';
+ if (for_read)
+ {
+ me = fopen(s, "rb");
+ }
+ else
+ {
+ me = fopen(s, "wb");
+ }
+ delete[] s;
+ return (me != 0);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+inline void
+_streamClose(::std::FILE * & me)
+{
+SEQAN_CHECKPOINT
+ if (me)
+ {
+ fclose(me);
+ me = 0;
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Internal._streamEOF.param.stream.type:Adaption."std::FILE *"
+
+inline bool
+_streamEOF(::std::FILE * me)
+{
+SEQAN_CHECKPOINT
+ return feof(me) || ferror(me);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Internal._streamRead.param.stream.type:Adaption."std::FILE *"
+
+template <typename TValue>
+inline size_t
+_streamRead(TValue * target,
+ ::std::FILE * source,
+ size_t limit)
+{
+SEQAN_CHECKPOINT
+ return ::std::fread(target, sizeof(TValue), limit, source);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Internal._streamGet.param.stream.type:Adaption."std::FILE *"
+
+inline char
+_streamGet(::std::FILE * source)
+{
+SEQAN_CHECKPOINT
+ return getc(source);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Internal._streamPut.param.stream.type:Adaption."std::FILE *"
+
+inline void
+_streamPut(::std::FILE * target,
+ char character)
+{
+SEQAN_CHECKPOINT
+ putc(character, target);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Internal._streamPut.param.stream.type:Adaption."std::FILE *"
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Internal._streamTellG.param.stream.type:Adaption."std::FILE *"
+
+inline Position<FILE *>::Type
+_streamTellG(FILE * me)
+{
+SEQAN_CHECKPOINT
+ return ::std::ftell(me);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Internal._streamTellP.param.stream.type:Adaption."std::FILE *"
+
+inline Position<FILE *>::Type
+_streamTellP(FILE * me)
+{
+SEQAN_CHECKPOINT
+ return ::std::ftell(me);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Internal._streamSeekG.param.stream.type:Adaption."std::FILE *"
+
+inline void
+_streamSeekG(FILE * me,
+ Position<FILE *>::Type pos)
+{
+SEQAN_CHECKPOINT
+ ::std::fseek(me, pos, SEEK_SET);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Internal._streamSeekP.param.stream.type:Adaption."std::FILE *"
+
+inline void
+_streamSeekP(FILE * me,
+ Position<FILE *>::Type pos)
+{
+SEQAN_CHECKPOINT
+ ::std::fseek(me, pos, SEEK_SET);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Internal._streamSeek2G.param.stream.type:Adaption."std::FILE *"
+
+inline void
+_streamSeek2G(FILE * me,
+ int off)
+{
+SEQAN_CHECKPOINT
+ ::std::fseek(me, off, SEEK_CUR);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Internal._streamUnget.param.stream.type:Adaption."std::FILE *"
+
+inline void
+_streamUnget(::std::FILE * stream)
+{
+SEQAN_CHECKPOINT
+ _streamSeek2G(stream, -1);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Stream operators for FILE *
+//////////////////////////////////////////////////////////////////////////////
+
+// ISO C++ operators are only allowed for classes, not for pointers
+
+/*
+template <typename TSource>
+inline FILE *
+operator << (FILE * target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ write(target, source);
+ return target;
+}
+template <typename TSource>
+inline FILE *
+operator << (FILE * target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ write(target, source);
+ return target;
+}
+
+//____________________________________________________________________________
+
+template <typename TTarget>
+inline FILE *
+operator >> (FILE * source,
+ TTarget & target)
+{
+SEQAN_CHECKPOINT
+ read(source, target);
+ return source;
+}
+template <typename TTarget>
+inline FILE *
+operator >> (FILE * source,
+ TTarget const & target)
+{
+SEQAN_CHECKPOINT
+ read(source, target);
+ return source;
+}
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/file/file_array.h b/src/libSSA/seqan/file/file_array.h
new file mode 100644
index 0000000..52f5855
--- /dev/null
+++ b/src/libSSA/seqan/file/file_array.h
@@ -0,0 +1,427 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: file_array.h,v 1.1 2008/08/25 16:20:03 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FILE_ARRAY_H
+#define SEQAN_HEADER_FILE_ARRAY_H
+
+#include <sstream>
+#include <iomanip>
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+ //template < __int64 _FileSize = 2*1024*1024*1024-1, typename TFile = File<> >
+ //struct Chained;
+
+ //template < unsigned _FileCount = 2, typename TFile = File<> >
+ //struct Striped;
+
+
+ template < __int64 _FileSize, typename TFile >
+ struct Size< File< Chained<_FileSize, TFile> > >
+ {
+ typedef __int64 Type;
+ };
+
+ template < __int64 _FileSize, typename TFile >
+ struct Position< File< Chained<_FileSize, TFile> > >
+ {
+ typedef __int64 Type;
+ };
+
+ template < __int64 _FileSize, typename TFile >
+ struct Difference< File< Chained<_FileSize, TFile> > >
+ {
+ typedef __int64 Type;
+ };
+
+ template < __int64 _FileSize, typename TFile >
+ struct aRequest< File< Chained<_FileSize, TFile> > >
+ {
+ typedef typename aRequest<TFile>::Type Type;
+ };
+
+
+ template < unsigned _FileCount, typename TFile >
+ struct Size< File< Striped<_FileCount, TFile> > >
+ {
+ typedef __int64 Type;
+ };
+
+ template < unsigned _FileCount, typename TFile >
+ struct Position< File< Striped<_FileCount, TFile> > >
+ {
+ typedef __int64 Type;
+ };
+
+ template < unsigned _FileCount, typename TFile >
+ struct Difference< File< Striped<_FileCount, TFile> > >
+ {
+ typedef __int64 Type;
+ };
+
+ template < unsigned _FileCount, typename TFile >
+ struct aRequest< File< Striped<_FileCount, TFile> > >
+ {
+ typedef typename aRequest<TFile>::Type Type;
+ };
+
+
+ template < unsigned _FileCount, typename TFile >
+ class File< Striped<_FileCount, TFile> >: public Tuple< TFile, _FileCount > {
+ File(void *dummy = NULL) {} // to be compatible with the FILE*(NULL) constructor
+ operator bool() const { return (*this)[0]; }
+ };
+
+ template < __int64 _FileSize, typename TFile >
+ class File< Chained<_FileSize, TFile> >: public String< TFile > {
+ typedef String< TFile > Base;
+
+ ::std::string baseName;
+ int openMode;
+ __int64 fileSize;
+ bool temporary;
+
+ File(void *dummy = NULL) : // to be compatible with the FILE*(NULL) constructor
+ fileSize(0),
+ _realign(false) {}
+
+ private:
+
+ bool _realign;
+
+ template < typename TSize, typename TValue >
+ inline void _alignFloor(TSize _size, TValue const *) {
+ __int64 alignment = sizeof(TValue) * sectorSize(TFile());
+ fileSize = (_size / alignment) * alignment;
+ }
+
+ template < typename TSize, typename TValue >
+ inline void _alignCeil(TSize _size, TValue const *) {
+ __int64 alignment = sizeof(TValue) * sectorSize(TFile());
+ fileSize = ((_size + alignment - 1) / alignment) * alignment;
+ }
+
+ public:
+
+ inline ::std::string getFileName(int i) const {
+ ::std::stringstream strm;
+ strm << baseName << '.' << ::std::setfill('0') << ::std::setw(3) << i;
+ return strm.str();
+ }
+
+ inline operator bool() const {
+ return (*this)[0];
+ }
+
+ inline unsigned fileCount() const {
+ return length(*(Base*)this);
+ }
+
+ inline TFile& getFile(int fileNo) {
+ unsigned _oldFileCount = fileCount();
+ if (fileNo >= _oldFileCount) {
+ resize(*(Base*)this, fileNo + 1);
+ for(unsigned i = _oldFileCount; i <= fileNo; ++i)
+ if (temporary)
+ openTemp((*this)[i], openMode);
+ else
+ open((*this)[i], getFileName(i).c_str(), openMode);
+ }
+ return (*this)[fileNo];
+ }
+
+ inline void tryOpen() {
+ unsigned fileCount = 0;
+ while (fileExists(getFileName(fileCount).c_str())) ++fileCount;
+ if (fileCount) {
+ fileSize = size(getFile(0));
+ _realign = (fileCount == 1);
+ getFile(fileCount - 1);
+ }
+ }
+
+ // fileSize dependent functions
+
+ template < typename TValue >
+ inline void adjustFileSize(TValue const *dummy) {
+ if (_realign) {
+ _alignCeil(fileSize, dummy);
+ _realign = false;
+ if (fileSize < _FileSize)
+ fileSize = 0;
+ }
+ if (!fileSize)
+ _alignFloor(_FileSize, dummy);
+ }
+
+ template < typename TPos, typename TOffset, typename TValue >
+ inline TFile& getFileAndOffset(TPos offset, TOffset &fileOffset, TValue const *dummy) {
+ adjustFileSize(dummy);
+ offset *= sizeof(TValue);
+ fileOffset = (offset % fileSize) / sizeof(TValue);
+ return getFile(offset / fileSize);
+ }
+
+ template < typename TOffset, typename TValue >
+ inline __int64 restAt(TOffset fileOffset, TValue const *dummy) {
+ adjustFileSize(dummy);
+ __int64 restBytes = fileSize;
+ restBytes -= fileOffset * sizeof(TValue);
+ return restBytes / sizeof(TValue);
+ }
+
+ inline void resizeArray(__int64 _newSize) {
+ if (fileSize) {
+ unsigned _oldFileCount = fileCount();
+ unsigned _newFileCount = enclosingBlocks(_newSize, fileSize);
+ for(unsigned i = _newFileCount; i < _oldFileCount; ++i) {
+ close((*this)[i]);
+ if (!temporary) fileUnlink(getFileName(i).c_str());
+ }
+ resize(*(Base*)this, _newFileCount);
+ if (_newFileCount) {
+ typename Size<TFile>::Type lastFileSize = _newSize % fileSize;
+ if (fileSize) resize((*this)[_newFileCount - 1], lastFileSize);
+ }
+ }
+ }
+
+ inline void clearInternals() {
+ clear(*(Base*)this);
+ fileSize = 0;
+ _realign = false;
+ }
+ };
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // generic open/close interface
+ template < typename TFileArray >
+ inline bool _openTempFArray(TFileArray &me, int openMode) {
+ bool result = true;
+ for(int i = 0; i < length(me); ++i)
+ result &= openTemp(me[i], openMode);
+ return result;
+ }
+
+ template < typename TFileArray >
+ inline bool _openTempFArray(TFileArray &me) {
+ return _openTempFArray(me, DefaultOpenTempMode<TFileArray>::VALUE);
+ }
+
+ template < typename TFileArray >
+ inline bool _reopenFArray(TFileArray &me, int openMode) {
+ bool result = true;
+ for(int i = 0; i < length(me); ++i)
+ result &= reopen(me[i], openMode);
+ return result;
+ }
+
+ template < typename TFileArray >
+ inline bool _closeFArray(TFileArray &me) {
+ bool result = true;
+ for(int i = 0; i < length(me); ++i)
+ if (me[i]) result &= close(me[i]);
+ return result;
+ }
+
+ template < typename TFileArray >
+ inline unsigned _sectorSizeFArray(TFileArray &me, int openMode) {
+ return sectorSize(me[0]);
+ }
+
+ template < typename TFileArray >
+ inline typename Size<TFileArray>::Type
+ _sizeFArray(TFileArray &me) {
+ typename Size<TFileArray>::Type sum = 0;
+ for(int i = 0; i < length(me); ++i)
+ sum += size(me[i]);
+ return sum;
+ }
+
+ template < typename TFileArray >
+ inline bool _flushFArray(TFileArray &me) {
+ bool result = true;
+ for(int i = 0; i < length(me); ++i)
+ result &= flush(me[i]);
+ return result;
+ }
+
+ template < typename TFileArray, typename TRequest >
+ inline bool _cancelFArray(TFileArray &me, TRequest &request) {
+ bool result = true;
+ for(int i = 0; i < length(me); ++i)
+ result &= cancel(me[i], &request);
+ return result;
+ }
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // standard file array wrappers
+
+ template < __int64 _FileSize, typename TFile >
+ inline unsigned length(File< Chained<_FileSize, TFile> > const &me) {
+ return me.fileCount();
+ }
+
+ template < unsigned _FileCount, typename TFile >
+ inline unsigned length(File< Striped<_FileCount, TFile> > const &me) {
+ return _FileCount;
+ }
+
+ template < __int64 _FileSize, typename TFile >
+ inline bool open(File< Chained<_FileSize, TFile> > &me, const char *fileName, int openMode) {
+ me.baseName = fileName;
+ me.openMode = openMode;
+ me.temporary = false;
+ me.tryOpen();
+ return true;
+ }
+
+ template < __int64 _FileSize, typename TFile >
+ inline bool openTemp(File< Chained<_FileSize, TFile> > &me, int openMode) {
+ me.openMode = openMode;
+ me.temporary = true;
+ return true;
+ }
+
+ template < unsigned _FileCount, typename TFile >
+ inline bool openTemp(File< Striped<_FileCount, TFile> > &me, int openMode) {
+ return _openTempFArray(me, openMode);
+ }
+
+ template < __int64 _FileSize, typename TFile >
+ inline bool close(File< Chained<_FileSize, TFile> > &me) {
+ _closeFArray(me);
+ me.clearInternals();
+ return true;
+ }
+
+ template < unsigned _FileCount, typename TFile >
+ inline bool close(File< Striped<_FileCount, TFile> > &me) { return _closeFArray(me); }
+
+ template < __int64 _FileSize, typename TFile >
+ __int64 size(File< Chained<_FileSize, TFile> > &me) {
+ return _sizeFArray(me);
+ }
+
+ template < unsigned _FileCount, typename TFile >
+ __int64 size(File< Striped<_FileCount, TFile> > &me) {
+ return _sizeFArray(me);
+ }
+
+ template < __int64 _FileSize, typename TFile, typename TSize >
+ inline void resize(File< Chained<_FileSize, TFile> > &me, TSize new_length) {
+ me.resizeArray(new_length);
+ }
+
+ template < __int64 _FileSize, typename TFile, typename TValue, typename TSize >
+ inline void allocate(File< Chained<_FileSize, TFile> > const &me, TValue* &data, TSize count) {
+ allocate(me[0], data, count);
+ }
+
+ template < __int64 _FileSize, typename TFile, typename TValue, typename TSize >
+ inline void deallocate(File< Chained<_FileSize, TFile> > const &me, TValue* &data, TSize count) {
+ deallocate(me[0], data, count);
+ }
+
+ template < unsigned _FileCount, typename TFile, typename TValue, typename TSize >
+ inline void allocate(File< Striped<_FileCount, TFile> > const &me, TValue* &data, TSize count) {
+ allocate(me[0], data, count);
+ }
+
+ template < unsigned _FileCount, typename TFile, typename TValue, typename TSize >
+ inline void deallocate(File< Striped<_FileCount, TFile> > const &me, TValue* &data, TSize count) {
+ deallocate(me[0], data, count);
+ }
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // read/write wrappers
+
+ template < __int64 _FileSize, typename TFile, typename TValue, typename TSize, typename TOffset >
+ inline bool readAt(File< Chained<_FileSize, TFile> > &me, TValue *memPtr, TSize count, TOffset offset) {
+ TOffset fileOfs = 0;
+ while (count) {
+ TFile &file = me.getFileAndOffset(offset, fileOfs, memPtr);
+ TSize xmitSize = _min(me.restAt(fileOfs, memPtr), (__int64)count);
+ if (!readAt(file, memPtr, xmitSize, fileOfs)) return false;
+ count -= xmitSize;
+ offset += xmitSize;
+ memPtr += xmitSize;
+ }
+ return true;
+ }
+
+ template < __int64 _FileSize, typename TFile, typename TValue, typename TSize, typename TOffset >
+ inline bool writeAt(File< Chained<_FileSize, TFile> > &me, TValue const *memPtr, TSize count, TOffset offset) {
+ TOffset fileOfs = 0;
+ while (count) {
+ TFile &file = me.getFileAndOffset(offset, fileOfs, memPtr);
+ TSize xmitSize = _min(me.restAt(fileOfs, memPtr), (__int64)count);
+ if (!writeAt(file, memPtr, xmitSize, fileOfs)) return false;
+ count -= xmitSize;
+ offset += xmitSize;
+ memPtr += xmitSize;
+ }
+ return true;
+ }
+
+ template < __int64 _FileSize, typename TFile, typename TValue, typename TSize, typename TOffset, typename TRequest >
+ inline bool areadAt(File< Chained<_FileSize, TFile> > &me, TValue *memPtr, TSize count, TOffset offset, TRequest &req) {
+ TOffset fileOfs = 0;
+ while (count) {
+ TFile &file = me.getFileAndOffset(offset, fileOfs, memPtr);
+ TSize xmitSize = _min(me.restAt(fileOfs, memPtr), (__int64)count);
+ if (count != xmitSize) {
+ if (!readAt(file, memPtr, xmitSize, fileOfs)) return false;
+ } else
+ if (!areadAt(file, memPtr, xmitSize, fileOfs, req)) return false;
+ count -= xmitSize;
+ offset += xmitSize;
+ memPtr += xmitSize;
+ }
+ return true;
+ }
+
+ template < __int64 _FileSize, typename TFile, typename TValue, typename TSize, typename TOffset, typename TRequest >
+ inline bool awriteAt(File< Chained<_FileSize, TFile> > &me, TValue const *memPtr, TSize count, TOffset offset, TRequest &req) {
+ TOffset fileOfs = 0;
+ while (count) {
+ TFile &file = me.getFileAndOffset(offset, fileOfs, memPtr);
+ TSize xmitSize = _min(me.restAt(fileOfs, memPtr), (__int64)count);
+ if (count != xmitSize) {
+ if (!writeAt(file, memPtr, xmitSize, fileOfs)) return false;
+ } else
+ if (!awriteAt(file, memPtr, xmitSize, fileOfs, req)) return false;
+ count -= xmitSize;
+ offset += xmitSize;
+ memPtr += xmitSize;
+ }
+ return true;
+ }
+
+}
+
+#endif
diff --git a/src/libSSA/seqan/file/file_base.h b/src/libSSA/seqan/file/file_base.h
new file mode 100644
index 0000000..40d8d22
--- /dev/null
+++ b/src/libSSA/seqan/file/file_base.h
@@ -0,0 +1,697 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: file_base.h,v 1.2 2009/02/19 01:51:23 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FILE_BASE_H
+#define SEQAN_HEADER_FILE_BASE_H
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+ // To override the system's default temporary directory use the following:
+ //#define SEQAN_DEFAULT_TMPDIR "/var/tmp"
+
+ // To use direct I/O access define SEQAN_DIRECTIO (not completely tested yet)
+ //#define SEQAN_DIRECTIO
+
+
+/**
+.Spec.Sync:
+..cat:Files
+..general:Class.File
+..summary:File structure supporting synchronous input/output access.
+..signature:File<Sync<> >
+..remarks:This class suports pseudo-asynchronous access methods, i.e. the methods to initiate a I/O request return after request completion.
+*/
+
+ template <typename TSpec = void>
+ struct Sync;
+
+/**
+.Spec.Async:
+..cat:Files
+..general:Class.File
+..summary:File structure supporting synchronous and asynchronous input/output access.
+..signature:File<Async<> >
+*/
+
+ template <typename TSpec = void>
+ struct Async;
+
+
+/**
+.Class.File:
+..cat:Input/Output
+..summary:Represents a file.
+..signature:File<TSpec>
+..param.TSpec:The specializing type.
+...default:$Async<>$, see @Spec.Async at .
+*/
+
+ template <typename TSpec = Async<> >
+ class File;
+
+/**
+.Spec.Chained:
+..cat:Files
+..general:Class.File
+..summary:Splits a large file into a chain of smaller files.
+..signature:File<Chained<FileSize, TFile> >
+..param.FileSize:The maximal split file size in byte.
+...default:2^31-1 (~2GB)
+..param.TFile:Underlying @Class.File@ type.
+...default:$File<>$, see @Class.File at .
+..remarks:This file type uses a chain of $TFile$ files, whose file sizes are at most $FileSize$ bytes.
+Chained Files should be used for file systems or $TFile$ types that don't support large files (e.g. FAT32, C-style FILE*).
+..remarks:The chain can be used as if it were one contiguous file.
+*/
+
+ // chained file's default filesize is 2gb-1byte (fat16 filesize limitation)
+ template < __int64 _FileSize = ~(((__int64)1) << 63), typename TFile = File<> >
+ struct Chained;
+
+/**
+.Spec.Striped:
+..cat:Files
+..general:Class.File
+..summary:Stripes a file across multiple files.
+..signature:File<Chained<FileCount, TFile> >
+..param.FileCount:The number of files used for striping.
+...default:2
+..param.TFile:Underlying @Class.File@ type.
+...default:$File<>$, see @Class.File at .
+..remarks:This file type uses a software striping without redundance (see RAID0) to accelerate I/O access when using more than one disks.
+..remarks:Striped files should only be used in @Class.Pool at s or external Strings as they only support block operations and no random accesses.
+*/
+
+ template < unsigned _FileCount = 2, typename TFile = File<> >
+ struct Striped;
+
+ enum FileOpenMode {
+ OPEN_RDONLY = 1,
+ OPEN_WRONLY = 2,
+ OPEN_RDWR = 3,
+ OPEN_MASK = 3,
+ OPEN_CREATE = 4,
+ OPEN_APPEND = 8,
+ OPEN_ASYNC = 16,
+ OPEN_TEMPORARY = 32,
+ OPEN_QUIET = 128
+ };
+
+ template <typename T>
+ struct DefaultOpenMode {
+ enum { VALUE = (OPEN_RDWR + OPEN_CREATE) | OPEN_APPEND };
+ };
+
+ template <typename T>
+ struct DefaultOpenTempMode {
+ enum { VALUE = OPEN_RDWR + OPEN_CREATE };
+ };
+
+ enum FileSeekMode {
+ SEEK_BEGIN = 0,
+ SEEK_CURRENT = 1
+#ifndef SEEK_END
+ , SEEK_END = 2
+#endif
+ };
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // result type of asynch. functions
+ // you have to call release(aRequest<T>) after a finished *event based* transfer
+ struct aDummyRequest {};
+
+/**
+.Class.aRequest:
+..cat:Input/Output
+..summary:Associated with an asynchronous I/O request.
+..signature:aRequest<TFile>
+..param.TFile:A File type.
+..remarks:This structure is used to identify asynchronous requests after their initiation.
+*/
+
+ template < typename T >
+ struct aRequest
+ {
+ typedef aDummyRequest Type;
+ };
+/*
+ //////////////////////////////////////////////////////////////////////////////
+ // event to represent asynchronous transfers
+ // you can wait for it or test it
+ template < typename T >
+ struct aEvent
+ {
+ typedef DummyEvent Type;
+ };
+
+ ////////////////////////////////////////////////////////////////////////////////
+ // callback hint parameter type
+ // hint lets you recognize the finished asynch. transfer in your own callback routine
+ template < typename T >
+ struct aHint
+ {
+ typedef void Type;
+ };
+
+ //////////////////////////////////////////////////////////////////////////////
+ // callback function interface
+ template < typename T >
+ struct aCallback
+ {
+ typedef void Type(aHint<T> *);
+ };
+
+ //////////////////////////////////////////////////////////////////////////////
+ // file queue interface
+ template < typename T >
+ struct aQueue
+ {
+ typedef Nothing Type;
+ };
+*/
+
+ //////////////////////////////////////////////////////////////////////////////
+ // generic open/close interface
+
+/**
+.Function.open:
+..summary:Opens a file.
+..cat:Input/Output
+..signature:open(file, fileName[, openMode])
+..param.file:A File object.
+...type:Class.File
+..param.fileName:C-style character string containing the file name.
+..param.openMode:The combination of flags defining how the file should be opened.
+...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
+...remarks:To create or overwrite a file add $OPEN_CREATE$.
+...remarks:To append a file if existing add $OPEN_APPEND$.
+...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
+..returns:A $bool$ which is $true$ on success.
+*/
+
+ template < typename TSpec >
+ inline bool open(File<TSpec> &me, const char *fileName, int openMode) {
+ return me.open(fileName, openMode);
+ }
+
+ template < typename TSpec >
+ inline bool open(File<TSpec> &me, const char *fileName) {
+ return open(me, fileName, DefaultOpenMode<File<TSpec> >::VALUE);
+ }
+
+/**
+.Function.openTemp:
+..summary:Opens a temporary file.
+..cat:Input/Output
+..signature:openTemp(file)
+..param.file:A File object.
+...type:Class.File
+..remarks:After closing this file will automatically be deleted.
+..remarks:The openmode (see @Function.open@) is $OPEN_RDWR | OPEN_CREATE$.
+..returns:A $bool$ which is $true$ on success.
+*/
+
+ template < typename TSpec >
+ inline bool openTemp(File<TSpec> &me) {
+ return me.openTemp();
+ }
+
+ template < typename TSpec >
+ inline bool openTemp(File<TSpec> &me, int openMode) {
+ return me.openTemp(openMode);
+ }
+
+ template < typename File >
+ inline void reopen(File &, int) {
+ }
+
+/**
+.Function.close:
+..cat:Input/Output
+..summary:Closes a file.
+..signature:close(file)
+..param.file:A File object.
+...type:Class.File
+..returns:A $bool$ which is $true$ on success.
+*/
+
+ template < typename TSpec >
+ inline bool close(File<TSpec> & me) {
+ return me.close();
+ }
+
+ template < typename TSpec >
+ inline unsigned sectorSize(File<TSpec> const & /*me*/) {
+ return 4096;
+ }
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // generic read(At)/write(At) interface
+
+/**
+.Function.read:
+..cat:Input/Output
+..summary:Loads records from a file.
+..signature:read(file, memPtr, count)
+..param.file:A File object.
+...type:Class.File
+..param.memPtr:A pointer to the first destination record in memory.
+..param.count:The amount of records to be read.
+..returns:A $bool$ which is $true$ on success.
+..remarks:The records are read from the position pointed by the current file pointer (see @Function.seek@).
+*/
+
+ template < typename TSpec, typename TValue, typename TSize >
+ inline bool read(File<TSpec> & me, TValue *memPtr, TSize const count) {
+ return me.read(memPtr, count * sizeof(TValue));
+ }
+
+/**
+.Function.write:
+..cat:Input/Output
+..summary:Saves records to a file.
+..signature:write(file, memPtr, count)
+..param.file:A File object.
+...type:Class.File
+..param.memPtr:A pointer to the first source record in memory.
+..param.count:The amount of records to be written.
+..returns:A $bool$ which is $true$ on success.
+..remarks:The records are written at the position pointed by the current file pointer (see @Function.seek@).
+*/
+
+ template < typename TSpec, typename TValue, typename TSize >
+ inline bool write(File<TSpec> & me, TValue const *memPtr, TSize const count) {
+ return me.write(memPtr, count * sizeof(TValue));
+ }
+
+/**
+.Function.readAt:
+..summary:Loads records from a specific position in a file.
+..cat:Input/Output
+..signature:readAt(file, memPtr, count, fileOfs)
+..param.file:A File object.
+...type:Class.File
+..param.memPtr:A pointer to the first destination record in memory.
+..param.count:The amount of records to be read.
+..param.fileOfs:The absolute file position in bytes measured from the beginning.
+..returns:A $bool$ which is $true$ on success.
+*/
+
+ template < typename TFile, typename TValue, typename TSize, typename TPos >
+ inline bool readAt(TFile & me, TValue *memPtr, TSize const count, TPos const fileOfs) {
+ typedef typename Position<TFile>::Type pos_t;
+ seek(me, (pos_t)fileOfs * (pos_t)sizeof(TValue));
+ return read(me, memPtr, count);
+ }
+
+/**
+.Function.writeAt:
+..summary:Saves records to a specific position in a file.
+..cat:Input/Output
+..signature:writeAt(file, memPtr, count, fileOfs)
+..param.file:A File object.
+...type:Class.File
+..param.memPtr:A pointer to the first source record in memory.
+..param.count:The amount of records to be written.
+..param.fileOfs:The absolute file position in bytes measured from the beginning.
+..returns:A $bool$ which is $true$ on success.
+*/
+
+ template < typename TFile, typename TValue, typename TSize, typename TPos >
+ inline bool writeAt(TFile & me, TValue const *memPtr, TSize const count, TPos const fileOfs) {
+ typedef typename Position<TFile>::Type pos_t;
+ seek(me, (pos_t)fileOfs * (pos_t)sizeof(TValue));
+ return write(me, memPtr, count);
+ }
+
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // generic seek/tell/size/resize interface
+
+/**
+.Function.seek:
+..summary:Changes the current file pointer.
+..cat:Input/Output
+..signature:seek(file, fileOfs[, origin])
+..param.file:A File object.
+...type:Class.File
+..param.fileOfs:A file offset measured in bytes relative to $origin$.
+..param.origin:Selects the origin from where to calculate the new position.
+...default:$SEEK_BEGIN$
+...remarks:For $SEEK_BEGIN$, $SEEK_CURRENT$, or $SEEK_END$ the origin is the beginning, the current pointer, or the end of the file.
+..returns:The new file position measured in bytes from the beginning.
+*/
+
+ template < typename TSpec, typename TPos >
+ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const fileOfs, int origin) {
+ typedef typename Position< File<TSpec> >::Type TFilePos;
+ TFilePos newOfs = me.seek(fileOfs, origin);
+ #ifdef SEQAN_DEBUG_OR_TEST_
+ if (origin == SEEK_BEGIN && newOfs != (TFilePos)fileOfs) {
+ ::std::cerr << "seek returned " << ::std::hex << newOfs << " instead of " << fileOfs << ::std::dec << ::std::endl;
+ }
+ #endif
+ return newOfs;
+ }
+
+ template < typename TSpec, typename TPos >
+ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const fileOfs) {
+ return seek(me, fileOfs, SEEK_BEGIN);
+ }
+/**
+.Function.tell:
+..summary:Gets the current file pointer.
+..cat:Input/Output
+..signature:tell(file)
+..param.file:A File object.
+...type:Class.File
+..returns:The current file position measured in bytes from the beginning.
+*/
+
+ template < typename TSpec >
+ inline typename Position< File<TSpec> >::Type tell(File<TSpec> &me) {
+ return me.tell();
+ }
+
+/**
+.Function.rewind:
+..summary:Sets the current file pointer to the beginning.
+..cat:Input/Output
+..signature:rewind(file)
+..param.file:A File object.
+...type:Class.File
+..remarks:Calls @Function.seek@$(file, 0)$ by default.
+*/
+
+ template < typename File >
+ inline void rewind(File &me) {
+ seek(me, 0);
+ }
+
+/**
+.Function.size:
+..summary:Gets the file size.
+..cat:Input/Output
+..signature:size(file)
+..param.file:A File object.
+...type:Class.File
+..returns:The file size measured in bytes.
+*/
+
+ template < typename TSpec >
+ inline typename Size<File<TSpec> >::Type size(File<TSpec> &me) {
+ typename Size<File<TSpec> >::Type old_pos = tell(me);
+ typename Size<File<TSpec> >::Type result = seek(me, 0, SEEK_END);
+ seek(me, old_pos, SEEK_BEGIN);
+ return result;
+ }
+
+/**
+.Function.resize:
+..cat:Input/Output
+..signature:resize(file, new_length)
+..param.file:A File object.
+...type:Class.File
+..param.new_length:The new file size measured in bytes.
+*/
+
+ template < typename TSpec, typename TSize >
+ inline void resize(File<TSpec> &me, TSize new_length) {
+ typename Size<File<TSpec> >::Type old_pos = tell(me);
+ seek(me, new_length, SEEK_BEGIN);
+ setEOF(me);
+ seek(me, old_pos, SEEK_BEGIN);
+ }
+
+/**
+.Function.setEOF:
+..summary:Sets the file end to the current pointer.
+..cat:Input/Output
+..signature:setEOF(file)
+..param.file:A File object.
+...type:Class.File
+*/
+
+ template < typename TSpec >
+ inline bool setEOF(File<TSpec> &/*me*/) {
+ return true;
+ }
+
+
+ //////////////////////////////////////////////////////////////////////
+ // Pseudo asynchronous Methods
+ //////////////////////////////////////////////////////////////////////
+
+ //////////////////////////////////////////////////////////////////////
+ // callback based read/write
+/*
+ template < typename File, typename TValue, typename TSize,
+ typename aCallback, typename aHint >
+ inline typename aRequest<File>::Type
+ aread(File & me, TValue *memPtr, TSize const count,
+ aCallback* cb, aHint* hint)
+ {
+ result = read(me, memPtr, count);
+ cb(hint);
+ return NULL;
+ }
+
+ template < typename File, typename TValue, typename TSize,
+ typename aCallback, typename aHint >
+ inline typename aRequest<File>::Type
+ awrite(File & me, TValue const *memPtr, TSize const count,
+ aCallback* cb, aHint* hint)
+ {
+ write(me, memPtr, count);
+ cb(hint);
+ return NULL;
+ }
+
+ template < typename File, typename TValue, typename TSize, typename TPos,
+ typename aCallback, typename aHint >
+ inline typename aRequest<File>::Type
+ areadAt(File & me, TValue *memPtr, TSize const count, TPos const fileOfs,
+ aCallback* cb, aHint* hint)
+ {
+ readAt(me, memPtr, count, fileOfs);
+ cb(hint);
+ return NULL;
+ }
+
+ template < typename File, typename TValue, typename TSize, typename TPos,
+ typename aCallback, typename aHint >
+ inline typename aRequest<File>::Type
+ awriteAt(File & me, TValue const *memPtr, TSize const count, TPos const fileOfs,
+ aCallback* cb, aHint* hint)
+ {
+ result = writeAt(me, memPtr, count, fileOfs);
+ cb(hint);
+ return NULL;
+ }
+
+
+ //////////////////////////////////////////////////////////////////////
+ // event based read/write
+
+ template < typename File, typename TValue, typename TSize,
+ typename aEvent >
+ inline typename aRequest<File>::Type
+ aread(File & me, TValue *memPtr, TSize const count,
+ aEvent &event)
+ {
+ read(me, memPtr, count);
+ event.signal();
+ return NULL;
+ }
+
+ template < typename File, typename TValue, typename TSize,
+ typename aEvent >
+ inline typename aRequest<File>::Type
+ awrite(File & me, TValue const *memPtr, TSize const count,
+ aEvent &event)
+ {
+ write(me, memPtr, count);
+ event.signal();
+ return NULL;
+ }
+
+ template < typename File, typename TValue, typename TSize, typename TPos,
+ typename aEvent >
+ inline typename aRequest<File>::Type
+ areadAt(File & me, TValue *memPtr, TSize const count, TPos const fileOfs,
+ aEvent &event)
+ {
+ readAt(me, memPtr, count, fileOfs);
+ event.signal();
+ return NULL;
+ }
+
+ template < typename File, typename TValue, typename TSize, typename TPos,
+ typename aEvent >
+ inline typename aRequest<File>::Type
+ awriteAt(File & me, TValue const *memPtr, TSize const count, TPos const fileOfs,
+ aEvent &event)
+ {
+ writeAt(me, memPtr, count, fileOfs);
+ event.signal();
+ return NULL;
+ }
+*/
+
+ //////////////////////////////////////////////////////////////////////
+ // queue-less request based pseudo asychronous read/write
+
+/**
+.Function.areadAt:
+..summary:Asynchronously loads records from a specific position in a file.
+..cat:Input/Output
+..signature:areadAt(file, memPtr, count, fileOfs, request)
+..param.file:A File object.
+...type:Class.File
+..param.memPtr:A pointer to the first destination record in memory.
+..param.count:The amount of records to be read.
+..param.fileOfs:The absolute file position in bytes measured from the beginning.
+..param.request:Reference to a structure that will be associated with this asynchronous request.
+...type:Class.aRequest
+..returns:A $bool$ which is $true$ on success.
+*/
+
+ template < typename File, typename TValue, typename TSize, typename TPos,
+ typename aRequest >
+ inline bool
+ areadAt(File & me, TValue *memPtr, TSize const count, TPos const fileOfs,
+ aRequest &request)
+ {
+ return readAt(me, memPtr, count, fileOfs);
+ }
+
+/**
+.Function.awriteAt:
+..summary:Asynchronously saves records to a specific position in a file.
+..cat:Input/Output
+..signature:awriteAt(file, memPtr, count, fileOfs, request)
+..param.file:A File object.
+...type:Class.File
+..param.memPtr:A pointer to the first source record in memory.
+..param.count:The amount of records to be written.
+..param.fileOfs:The absolute file position in bytes measured from the beginning.
+..param.request:Reference to a structure that will be associated with this asynchronous request.
+...type:Class.aRequest
+..returns:A $bool$ which is $true$ on success.
+*/
+
+ template < typename File, typename TValue, typename TSize, typename TPos,
+ typename aRequest >
+ inline bool
+ awriteAt(File & me, TValue const *memPtr, TSize const count, TPos const fileOfs,
+ aRequest &request)
+ {
+ return writeAt(me, memPtr, count, fileOfs);
+ }
+
+
+ //////////////////////////////////////////////////////////////////////
+ // pseudo queue specific functions
+
+/**
+.Function.flush:
+..summary:Waits for all open requests to complete.
+..cat:Input/Output
+..signature:flush(file)
+..param.file:A File object.
+...type:Class.File
+..remarks:$flush$ returns after all pending requests are completed.
+*/
+
+ template < typename TSpec >
+ inline void flush(File<TSpec> &) {
+ }
+
+/**
+.Function.waitFor:
+..summary:Waits for an asynchronous request to complete.
+..cat:Input/Output
+..signature:waitFor(request[, timeout_millis])
+..param.request:Reference to an aRequest object.
+...type:Class.aRequest
+..param.timeout_millis:Timout value in milliseconds.
+...remarks:A value of 0 can be used to test for completion without waiting.
+...default:Infinity.
+..returns:A $bool$ which is $true$ on completion and $false$ on timeout.
+..remarks:$waitFor$ suspends the calling process until $request$ is completed or after $timeout_millis$ milliseconds.
+*/
+
+ inline bool waitFor(aDummyRequest &) {
+ return true;
+ }
+
+ template < typename TTime >
+ inline bool waitFor(aDummyRequest &, TTime) {
+ return true;
+ }
+
+ // deprecated
+ template < typename TSpec, typename aRequest >
+ inline void release(File<TSpec> &, aRequest &) {
+ }
+
+/**
+.Function.cancel:
+..summary:Cancels an asynchronous request.
+..cat:Input/Output
+..signature:cancel(file, request)
+..param.file:A File object.
+...type:Class.File
+..param.request:Reference to an aRequest object.
+...type:Class.aRequest
+..returns:A $bool$ which is $true$ on success.
+*/
+
+ template < typename TSpec, typename aRequest >
+ inline bool cancel(File<TSpec> &, aRequest &) {
+ return true;
+ }
+
+
+ // little helpers
+
+ template <typename T1, typename T2> inline
+ T1 enclosingBlocks(T1 _size, T2 _blockSize) {
+ return (_size + _blockSize - 1) / _blockSize;
+ }
+
+ template <typename T1, typename T2> inline
+ T1 alignSize(T1 _size, T2 _aligning) {
+ if (_size < _aligning)
+ return _aligning;
+ else
+ return (_size / _aligning) * (T1)_aligning;
+ }
+
+}
+
+#endif
diff --git a/src/libSSA/seqan/file/file_format.h b/src/libSSA/seqan/file/file_format.h
new file mode 100644
index 0000000..93336df
--- /dev/null
+++ b/src/libSSA/seqan/file/file_format.h
@@ -0,0 +1,686 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: file_format.h,v 1.1 2008/08/25 16:20:03 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FILE_FORMAT_H
+#define SEQAN_HEADER_FILE_FORMAT_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.File Format:
+..summary:A file format.
+*/
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Metafunctions
+//////////////////////////////////////////////////////////////////////////////
+
+//////////////////////////////////////////////////////////////////////////////
+
+//////////////////////////////////////////////////////////////////////////////
+//Base Class for all FileFormat classes
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Class.FileFormat:
+..cat:Input/Output
+..summary:Object that stores a file format.
+..signature:FileFormat<File, Data [, Format [, Meta] ]>
+..see:Tag.File Format
+*/
+
+template <
+ typename TFile,
+ typename TData,
+ typename TMeta,
+ typename TFormat = void >
+struct FileFormat:
+ public FileFormat<TFile, TData, TMeta, void>
+{
+public:
+ typedef typename Size<TData>::Type TSize;
+
+ FileFormat() {}
+ FileFormat(FileFormat const &) {}
+ ~FileFormat() {}
+ FileFormat const & operator =(FileFormat const &) {}
+
+ inline void *
+ formatID_() const
+ {
+SEQAN_CHECKPOINT
+ return _ClassIdentifier<TFormat>::getID();
+ }
+
+ virtual void
+ read_(TFile & file, TData & data) const
+ {
+SEQAN_CHECKPOINT
+ read(file, data, TFormat());
+ }
+ virtual void
+ read_(TFile & file, TData & data, TSize limit) const
+ {
+SEQAN_CHECKPOINT
+ read(file, data, limit, TFormat());
+ }
+
+ virtual void
+ readMeta_(TFile & file, TMeta & meta) const
+ {
+SEQAN_CHECKPOINT
+ readMeta(file, meta, TFormat());
+ }
+
+ virtual void
+ goNext_(TFile & file) const
+ {
+SEQAN_CHECKPOINT
+ goNext(file, TFormat());
+ }
+
+ virtual TSize
+ length_(TFile & file) const
+ {
+SEQAN_CHECKPOINT
+ length(file, TFormat());
+ }
+
+ virtual void
+ write_(TFile & file, TData & data) const
+ {
+SEQAN_CHECKPOINT
+ write(file, data, TFormat());
+ }
+ virtual void
+ write_(TFile & file, TData & data, TMeta & meta) const
+ {
+SEQAN_CHECKPOINT
+ write(file, data, meta, TFormat());
+ }
+};
+
+//____________________________________________________________________________
+
+//base class for all file format classes
+
+template <typename TFile, typename TData, typename TMeta>
+struct FileFormat<TFile, TData, TMeta, void>
+{
+public:
+ typedef typename Size<TData>::Type TSize;
+
+ FileFormat() {}
+ FileFormat(FileFormat const &) {}
+ ~FileFormat() {};
+ FileFormat const & operator =(FileFormat const &) {}
+
+ virtual void *
+ formatID_() const = 0;
+
+ virtual void
+ read_(TFile & file, TData & data) const = 0;
+ virtual void
+ read_(TFile & file, TData & data, TSize limit) const = 0;
+
+ virtual void
+ readMeta_(TFile & file, TMeta & meta) const = 0;
+
+ virtual void
+ goNext_(TFile & file) const = 0;
+
+ virtual TSize
+ length_(TFile & file) const = 0;
+
+ virtual void
+ write_(TFile & file, TData & data) const = 0;
+ virtual void
+ write_(TFile & file, TData & data, TMeta & meta) const = 0;
+
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// Wrapper for functions to virtuals
+//////////////////////////////////////////////////////////////////////////////
+
+
+template <typename TFile, typename TData, typename TMeta, typename TFormat>
+inline void *
+formatID(FileFormat<TFile, TData, TMeta, TFormat> const & file_format)
+{
+SEQAN_CHECKPOINT
+ return file_format.formatID_();
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.Fileformat#read:
+..cat:Input/Output
+..summary:Loads a record from file.
+..signature:read(file, data [, meta], format)
+..signature:read(file, data [, meta], tag)
+..param.file:An input file.
+..param.data:A container that gets the data read from $file$.
+..param.meta:A container that gets meta data from $file$. (optional)
+..param.format:A file format object.
+...type:Class.FileFormat.File Format object
+..param.tag:A file format tag.
+...type:Tag.File Format.File Format tag
+..remarks:The result of this operation is stored in $data$.
+..remarks:The function leaves $file$ at the position for reading the next record.
+..see:Function.assign
+*/
+template <typename TFile, typename TData, typename TMeta, typename TFormat>
+inline void
+read(TFile & file,
+ TData & data,
+ FileFormat<TFile, TData, TMeta, TFormat> const & file_format)
+{
+SEQAN_CHECKPOINT
+ file_format.read_(file, data);
+}
+
+template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TSize>
+inline void
+read(TFile & file,
+ TData & data,
+ TSize limit,
+ FileFormat<TFile, TData, TMeta, TFormat> const & file_format)
+{
+SEQAN_CHECKPOINT
+ file_format.read_(file, data, limit);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.readMeta:
+..cat:Input/Output
+..summary:Read meta information from file.
+..signature:readMeta(file, meta, file_format)
+..param.file:A file that contains data in the format specified by $file_format$.
+..param.meta:A data structure that is able to store meta informations stored in $file$.
+..param.file_format:A file format.
+..returns.param.meta:The meta data read from $file$.
+...type:Tag.File Format
+*/
+
+template <typename TFile, typename TData, typename TMeta, typename TFormat>
+inline void
+readMeta(TFile & file,
+ TMeta & meta,
+ FileFormat<TFile, TData, TMeta, TFormat> const & file_format)
+{
+SEQAN_CHECKPOINT
+ file_format.readMeta_(file, meta);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.goNext:
+..cat:Input/Output
+*/
+
+template <typename TFile, typename TData, typename TMeta, typename TFormat>
+inline void
+goNext(TFile & file,
+ FileFormat<TFile, TData, TMeta, TFormat> const & file_format)
+{
+SEQAN_CHECKPOINT
+ file_format.goNext_(file);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.length:
+..cat:Input/Output
+*/
+
+template <typename TFile, typename TData, typename TMeta, typename TFormat>
+inline void
+length(TFile & file,
+ FileFormat<TFile, TData, TMeta, TFormat> const & file_format)
+{
+SEQAN_CHECKPOINT
+ file_format.length_(file);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.Fileformat#write:
+..cat:Input/Output
+..summary:Writes to stream.
+..signature:write(stream, source)
+..signature:write(stream, begin, end)
+..param.stream: A stream object.
+...type:Adaption."std::iostream"
+..param.source: Container that is written to $stream$.
+..param.begin: Iterator to the first character of the range.
+..param.end: Iterator behind the last character of the range.
+..remarks:The content of $source$ is written 'as-is' to $stream$.
+*/
+
+template <typename TFile, typename TData, typename TMeta, typename TFormat>
+inline void
+write(TFile & file,
+ TData & data,
+ FileFormat<TFile, TData, TMeta, TFormat> const & file_format)
+{
+SEQAN_CHECKPOINT
+ file_format.write_(file, data);
+}
+template <typename TFile, typename TData, typename TMeta, typename TFormat>
+inline void
+write(TFile & file,
+ TData & data,
+ TMeta & meta,
+ FileFormat<TFile, TData, TMeta, TFormat> const & file_format)
+{
+SEQAN_CHECKPOINT
+ file_format.write_(file, data, meta);
+}
+
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Comparison of two FileFormat objects
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TFileLeft, typename TDataLeft, typename TMetaLeft, typename TFormatLeft, typename TFileRight, typename TDataRight, typename TMetaRight, typename TFormatRight>
+inline bool
+operator == (FileFormat<TFileLeft, TDataLeft, TMetaLeft, TFormatLeft> const & left,
+ FileFormat<TFileRight, TDataRight, TMetaRight, TFormatRight> const & right)
+{
+SEQAN_CHECKPOINT
+ return formatID(left) == formatID(right);
+}
+
+template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TFormat2>
+inline bool
+operator == (FileFormat<TFile, TData, TMeta, TFormat> const & left,
+ Tag<TFormat2> const)
+{
+SEQAN_CHECKPOINT
+ return formatID(left) == _ClassIdentifier<Tag<TFormat2> const>::getID();
+}
+
+template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TFormat2>
+inline bool
+operator == (Tag<TFormat2> const,
+ FileFormat<TFile, TData, TMeta, TFormat> const & right)
+{
+SEQAN_CHECKPOINT
+ return _ClassIdentifier<Tag<TFormat2> const>::getID() == formatID(right);
+}
+
+//____________________________________________________________________________
+
+template <typename TFileLeft, typename TDataLeft, typename TMetaLeft, typename TFormatLeft, typename TFileRight, typename TDataRight, typename TMetaRight, typename TFormatRight>
+inline bool
+operator != (FileFormat<TFileLeft, TDataLeft, TMetaLeft, TFormatLeft> const & left,
+ FileFormat<TFileRight, TDataRight, TMetaRight, TFormatRight> const & right)
+{
+SEQAN_CHECKPOINT
+ return formatID(left) != formatID(right);
+}
+
+template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TFormat2>
+inline bool
+operator != (FileFormat<TFile, TData, TMeta, TFormat> const & left,
+ Tag<TFormat2> const)
+{
+SEQAN_CHECKPOINT
+ return formatID(left) != _ClassIdentifier<Tag<TFormat2> const>::getID();
+}
+
+template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TFormat2>
+inline bool
+operator != (Tag<TFormat2> const,
+ FileFormat<TFile, TData, TMeta, TFormat> const & right)
+{
+SEQAN_CHECKPOINT
+ return _ClassIdentifier<Tag<TFormat2> const>::getID() != formatID(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// allgemeine Funktionen fuer Streams
+//////////////////////////////////////////////////////////////////////////////
+//TODO??? Das muss in eine extra Datei
+
+
+/*
+template <typename TStream, typename TIterator>
+inline void
+write(TStream & target,
+ TIterator begin_,
+ TIterator end_)
+{
+ while (begin_ != end_)
+ {
+ _streamPut(target, convert<char>(*begin_));
+ ++begin_;
+ }
+}
+
+//____________________________________________________________________________
+
+template <typename TStream, typename TSource>
+inline void
+write(TStream & target,
+ TSource const & source)
+{
+ write(target, begin(source), end(source));
+}
+//TODO???: Spezialisierungen zum blockweise schreiben bei contiguous strings von char
+//Anmerkungen: write wird nach dem zweiten Argument (source) spezialisiert!
+
+//____________________________________________________________________________
+
+template <typename TStream, typename TSource>
+inline void
+write(TStream & target,
+ TSource const & source,
+ typename Size<TSource>::Type limit_)
+{
+ if (length(source) > limit_)
+ {
+ write(target, begin(source), begin(source) + limit_);
+ }
+ else
+ {
+ write(target, begin(source), end(source));
+ }
+}
+
+*/
+//////////////////////////////////////////////////////////////////////////////
+
+// Helper function for scanning a stream
+// c = next character, pass it to the next call of the function
+
+template <typename TFile, typename TString, typename TChar>
+inline void
+_stream_appendLine(TFile & file,
+ TString & str,
+ TChar & c)
+{
+ while (true)
+ {
+ if (_streamEOF(file)) break;
+
+ if (c == '\r')
+ {
+ c = _streamGet(file);
+ if (c == '\n')
+ {
+ c = _streamGet(file);
+ }
+ break;
+ }
+ if (c == '\n')
+ {
+ c = _streamGet(file);
+ break;
+ }
+
+ appendValue(str, c);
+
+ c = _streamGet(file);
+ }
+}
+//____________________________________________________________________________
+
+template <typename TFile, typename TChar>
+inline void
+_stream_countLine(TFile & file,
+ TChar & c)
+
+{
+ while (true)
+ {
+ if (_streamEOF(file)) break;
+
+ if (c == '\r')
+ {
+ c = _streamGet(file);
+ if (c == '\n')
+ {
+ c = _streamGet(file);
+ }
+ break;
+ }
+ if (c == '\n')
+ {
+ c = _streamGet(file);
+ break;
+ }
+
+ c = _streamGet(file);
+ }
+}
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TChar>
+inline typename Size<TFile>::Type
+_stream_skipLine(TFile & file,
+ TChar & c)
+
+{
+ typename Size<TFile>::Type count = 0;
+ while (true)
+ {
+ if (_streamEOF(file)) break;
+
+ if (c == '\r')
+ {
+ c = _streamGet(file);
+ if (c == '\n')
+ {
+ c = _streamGet(file);
+ }
+ break;
+ }
+ if (c == '\n')
+ {
+ c = _streamGet(file);
+ break;
+ }
+
+ ++count;
+
+ c = _streamGet(file);
+ }
+
+ return count;
+}
+
+
+
+
+////////////////////////////////////////////////////////////////////////////
+//new ones
+
+//new ones for streams
+template<typename TFile, typename TChar>
+inline void
+_stream_skipWhitespace(TFile& file, TChar& c)
+{
+ if ((c!=' ') && (c != '\t')) return;
+ while (!_streamEOF(file)) {
+ c = _streamGet(file);
+ if ((c!=' ') && (c != '\t')) break;
+ }
+}
+
+////////////////////////////////////////////////////////////////////////////
+
+
+template<typename TFile, typename TChar>
+inline String<char>
+_stream_readWord(TFile & file, TChar& c)
+{
+ // Read word
+ String<char> str(c);
+ while (!_streamEOF(file)) {
+ c = _streamGet(file);
+ if (!_stream_isLetter(c)) break;
+ append(str, c);
+ }
+ return str;
+}
+
+////////////////////////////////////////////////////////////////////////////
+
+template<typename TChar>
+inline bool
+_stream_isLetter(TChar const c)
+{
+ return ((c == 'a') || (c == 'b') || (c == 'c') || (c == 'd') || (c == 'e') ||
+ (c == 'f') || (c == 'g') || (c == 'h') || (c == 'i') || (c == 'j') ||
+ (c == 'k') || (c == 'l') || (c == 'm') || (c == 'n') || (c == 'o') ||
+ (c == 'p') || (c == 'q') || (c == 'r') || (c == 's') || (c == 't') ||
+ (c == 'u') || (c == 'v') || (c == 'w') || (c == 'x') || (c == 'y') ||
+ (c == 'z') || (c == 'A') || (c == 'B') || (c == 'C') || (c == 'D') ||
+ (c == 'E') || (c == 'F') || (c == 'G') || (c == 'H') || (c == 'I') ||
+ (c == 'J') || (c == 'K') || (c == 'L') || (c == 'M') || (c == 'N') ||
+ (c == 'O') || (c == 'P') || (c == 'Q') || (c == 'R') || (c == 'S') ||
+ (c == 'T') || (c == 'U') || (c == 'V') || (c == 'W') || (c == 'X') ||
+ (c == 'Y') || (c == 'Z'));
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+//new ones for strings
+
+template <typename TString, typename TIter>
+inline typename Size<TString>::Type
+_string_skipLine(TString & str,
+ TIter & it)
+
+{
+ typename Size<TString>::Type count = 0;
+ typename Iterator<TString,Standard>::Type end_it = end(str,Standard());
+ while (true)
+ {
+ if (it == end_it) break;
+
+ if (*it == '\r')
+ {
+ ++it;
+ if (*it == '\n')
+ {
+ ++it;
+ }
+ break;
+ }
+ if (*it == '\n')
+ {
+ ++it;
+ break;
+ }
+
+ ++count;
+ ++it;
+ }
+
+ return count;
+}
+
+/////////////////////////////////////////////////////////////////////////
+
+template <typename TString1, typename TString2, typename TIter>
+inline void
+_string_appendLine(TString1 & str,
+ TString2 & a_str,
+ TIter & it)
+{
+ typename Iterator<TString1,Standard>::Type end_it = end(str,Standard());
+ while (true)
+ {
+ if (it == end_it) break;
+
+ if (*it == '\r')
+ {
+ ++it;
+ if (*it == '\n')
+ {
+ ++it;
+ }
+ break;
+ }
+ if (*it == '\n')
+ {
+ ++it;
+ break;
+ }
+
+ appendValue(a_str, getValue(it));
+ ++it;
+ }
+}
+
+////////////////////////////////////////////////////////////////////////////
+
+template<typename TString, typename TIter>
+inline void
+_string_skipWhitespace(TString& str, TIter& it)
+{
+ typename Iterator<TString,Standard>::Type end_it = end(str,Standard())-1;
+ while (it != end_it) {
+ if ((*it!=' ') && (*it != '\t')) break;
+ ++it;
+ }
+}
+
+////////////////////////////////////////////////////////////////////////////
+
+template<typename TString, typename TIter>
+inline int
+_string_readNumber(TString & str, TIter& it)
+{
+ // Read number
+ typename Iterator<TString,Standard>::Type end_it = end(str,Standard())-1;
+ String<char> numstr(getValue(it));
+ while (it != end_it) {
+ ++it;
+ if (!_parse_isDigit(*it)) break;
+ append(numstr, getValue(it));
+ }
+ return atoi(toCString(numstr));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+//////////////////////////////////////////////////////////////////////////////
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/file/file_format_cgviz.h b/src/libSSA/seqan/file/file_format_cgviz.h
new file mode 100644
index 0000000..9cd11f0
--- /dev/null
+++ b/src/libSSA/seqan/file/file_format_cgviz.h
@@ -0,0 +1,226 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: file_format_cgviz.h,v 1.1 2008/08/25 16:20:03 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FILE_CGVIZ_H
+#define SEQAN_HEADER_FILE_CGVIZ_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// File Formats - CGViz
+//////////////////////////////////////////////////////////////////////////////
+
+
+/**
+.Tag.File Format.tag.CGViz:
+ CGViz file format for sequences. Only output.
+*/
+struct TagCGViz_;
+typedef Tag<TagCGViz_> const CGViz;
+
+/////////////////////////////////////////////////////////////////////////
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// goNext
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TFile>
+void goNext(TFile & file, CGViz) {
+ SEQAN_CHECKPOINT
+ SEQAN_ASSERT(!_streamEOF(file))
+
+ return;
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// write
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TFile, typename TStringContainer, typename TSource, typename TSpec>
+void _write_impl(TFile& target, Align<TSource, TSpec>& align, TStringContainer& ids, CGViz) {
+ SEQAN_CHECKPOINT
+
+ typedef Align<TSource, TSpec> const TAlign;
+ typedef typename Row<TAlign>::Type TRow;
+ typedef typename Position<typename Rows<TAlign>::Type>::Type TRowsPosition;
+ typedef typename Position<TAlign>::Type TPosition;
+ TRowsPosition row_count = length(rows(align));
+ if (row_count < 2) return;
+
+ unsigned int pair=1;
+ unsigned int count=0;
+ for(TRowsPosition i=0;i<row_count-1;++i) {
+ for(TRowsPosition j=i+1;j<row_count;++j) {
+
+ // Print header
+ _streamWrite(target, "{DATA dat");
+ _streamPutInt(target, pair);
+ _streamPut(target, '\n');
+ _streamWrite(target, "[__GLOBAL__] dimension=2:\n");
+
+ TPosition begin_ = beginPosition(cols(align));
+ TPosition end_ = endPosition(cols(align));
+
+ bool match = false;
+ while(begin_ < end_) {
+ if ((row(align, i)[begin_]==row(align, j)[begin_]) && (row(align, i)[begin_]!='-')) {
+ if (!match) {
+ match=true;
+ _streamPutInt(target, toSourcePosition(row(align,i),begin_+1));
+ _streamPut(target, ' ');
+ _streamPutInt(target, toSourcePosition(row(align,j),begin_+1));
+ _streamPut(target, ' ');
+ }
+ }
+ if ((row(align, i)[begin_]!=row(align, j)[begin_]) || (row(align, i)[begin_]=='-') || (row(align, j)[begin_]=='-')) {
+ if (match) {
+ _streamPutInt(target, toSourcePosition(row(align,i),begin_));
+ _streamPut(target, ' ');
+ _streamPutInt(target, toSourcePosition(row(align,j),begin_));
+ _streamPut(target, '\n');
+ match=false;
+ }
+ }
+ begin_++;
+ }
+ if (match) {
+ _streamPutInt(target, toSourcePosition(row(align,i),begin_));
+ _streamPut(target, ' ');
+ _streamPutInt(target, toSourcePosition(row(align,j),begin_));
+ _streamPut(target, '\n');
+ match=false;
+ }
+ _streamPut(target, '}');
+ _streamPut(target, '\n');
+
+ // Write footer
+ _streamWrite(target, "{GLYPH Glyph");
+ _streamPutInt(target, pair);
+ _streamPut(target, '\n');
+ _streamWrite(target, "drawerName=Lines\n");
+ _streamWrite(target, "lineWidth=3\n");
+ _streamPut(target, '}');
+ _streamPut(target, '\n');
+ _streamWrite(target, "{PANE Pane");
+ _streamPutInt(target, pair);
+ _streamPut(target, '\n');
+ _streamWrite(target, "uLabel=");
+ _streamWrite(target, getValue(ids,i));
+ _streamPut(target, '\n');
+ _streamWrite(target, "uStop=");
+ _streamPutInt(target, length(source(row(align,i))));
+ _streamPut(target, '\n');
+ _streamWrite(target, "vLabel=");
+ _streamWrite(target, getValue(ids,j));
+ _streamPut(target, '\n');
+ _streamWrite(target, "vStop=");
+ _streamPutInt(target, length(source(row(align,j))));
+ _streamPut(target, '\n');
+ _streamPut(target, '}');
+ _streamPut(target, '\n');
+ _streamWrite(target, "{WINDOW Window");
+ _streamPutInt(target, pair);
+ _streamPut(target, '\n');
+ _streamPut(target, '}');
+ _streamPut(target, '\n');
+ _streamWrite(target, "{FEEDER Feeder<");
+ _streamPutInt(target, pair);
+ _streamPut(target, '>');
+ _streamPut(target, ' ');
+ _streamPutInt(target, count);
+ _streamPut(target, ' ');
+ _streamPutInt(target, count+1);
+ _streamPut(target, '\n');
+ _streamPut(target, '}');
+ _streamPut(target, '\n');
+ ++count;
+ _streamWrite(target, "{THREADER Threader<");
+ _streamPutInt(target, pair);
+ _streamPut(target, '>');
+ _streamPut(target, ' ');
+ _streamPutInt(target, count);
+ _streamPut(target, ' ');
+ _streamPutInt(target, count+1);
+ _streamPut(target, '\n');
+ _streamPut(target, '}');
+ _streamPut(target, '\n');
+ ++count;
+ _streamWrite(target, "{ANCHOR Anchor<");
+ _streamPutInt(target, pair);
+ _streamPut(target, '>');
+ _streamPut(target, ' ');
+ _streamPutInt(target, count);
+ _streamPut(target, ' ');
+ _streamPutInt(target, count+1);
+ _streamPut(target, '\n');
+ _streamPut(target, '}');
+ _streamPut(target, '\n');
+ count+=2;
+ ++pair;
+ }
+ }
+}
+
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TSource, typename TSpec>
+void write(TFile & file, Align<TSource, TSpec>& align, CGViz) {
+ SEQAN_CHECKPOINT
+ _write_impl(file, align, String<String<char> >(), CGViz());
+}
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TStringContainer, typename TSource, typename TSpec>
+void write(TFile & file, Align<TSource, TSpec> & align, TStringContainer& ids, CGViz) {
+ SEQAN_CHECKPOINT
+ _write_impl(file, align, ids, CGViz());
+}
+
+
+//VisualC++ const array bug workaround
+template <typename TFile, typename TStringContainer, typename TSource, typename TSpec>
+void write(TFile & file, Align<TSource, TSpec>* align, TStringContainer & ids, CGViz) {
+ SEQAN_CHECKPOINT
+ _write_impl(file, align, ids, CGViz());
+}
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TStringContainer, typename TSource, typename TSpec, typename TMeta>
+void write(TFile & file, Align<TSource, TSpec> & align, TStringContainer& ids, TMeta &, CGViz) {
+ SEQAN_CHECKPOINT
+ _write_impl(file, align, ids, CGViz());
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+} //namespace SEQAN_NAMESPACE_MAIN
+
+//////////////////////////////////////////////////////////////////////////////
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/file/file_format_fasta.h b/src/libSSA/seqan/file/file_format_fasta.h
new file mode 100644
index 0000000..5676b1b
--- /dev/null
+++ b/src/libSSA/seqan/file/file_format_fasta.h
@@ -0,0 +1,520 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: file_format_fasta.h,v 1.1 2008/08/25 16:20:03 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FILE_FASTA_H
+#define SEQAN_HEADER_FILE_FASTA_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// File Formats - Fasta
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.File Format.tag.Fasta:
+ FASTA file format for sequences.
+*/
+struct TagFasta_;
+typedef Tag<TagFasta_> const Fasta;
+
+//////////////////////////////////////////////////////////////////////////////
+// Filereader
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TFile, typename TFile2, typename TSpec>
+inline void
+goBegin(Iter<TFile, FileReader<Fasta, TFile2, TSpec> > & it, bool skip_meta)
+{
+ if (_streamEOF(host(it)))
+ {
+ it.data_eof = true;
+ return;
+ }
+
+ if (skip_meta && (it.data_char == '>'))
+ {
+ //skip meta line
+ _stream_skipLine(host(it), it.data_char);
+ }
+
+ //eliminate linebreaks
+ while ((it.data_char == '\n') || (it.data_char == '\r'))
+ {
+ if (_streamEOF(host(it)))
+ {
+ it.data_eof = true;
+ return;
+ }
+ it.data_char = _streamGet(host(it));
+ }
+
+ if (it.data_char == '>')
+ {//end of record
+ it.data_eof = true;
+ _streamUnget(host(it));
+ return;
+ }
+
+ it.data_file_pos = _streamTellG(host(it)) - 1;
+ it.data_eof = _streamEOF(host(it));
+}
+template <typename TFile, typename TFile2, typename TSpec>
+inline void
+goBegin(Iter<TFile, FileReader<Fasta, TFile2, TSpec> > & it)
+{
+ goBegin(it, true);
+}
+
+
+template <typename TFile, typename TFile2, typename TSpec>
+inline void
+goNext(Iter<TFile, FileReader<Fasta, TFile2, TSpec> > & it)
+{
+/*
+ if (_streamEOF(host(it)))
+ {
+ it.data_eof = true;
+ return;
+ }
+*/
+ it.data_char = _streamGet(host(it));
+ ++it.data_file_pos;
+
+ if (_streamEOF(host(it)))
+ {
+ it.data_eof = true;
+ return;
+ }
+
+ if ((it.data_char == '\n') || (it.data_char == '\r'))
+ {//linebreak detected: find begin of next line
+ do
+ {
+ it.data_char = _streamGet(host(it));
+ if (_streamEOF(host(it)))
+ {
+ it.data_eof = true;
+ return;
+ }
+ ++it.data_file_pos;
+ } while ((it.data_char == '\n') || (it.data_char == '\r'));
+
+ if (it.data_char == '>')
+ {//end of record
+ _streamUnget(host(it));
+ it.data_eof = true;
+ }
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// FileFormat Interface
+//////////////////////////////////////////////////////////////////////////////
+
+
+
+/////////////////////////////////////////////////////////////////////////
+//count_valid: zaehlt die nicht-Zeilenumbrueche (input/output)
+//count_all: zaehlt alle Zeichen incl. Zeilenumbrueche (input/output)
+//returns: zuletzt gelesenes Zeichen = das erste hinter dem Zeilenumbruch bzw. eof
+//the last read char is not counted!
+//count_valid and count_all are not resetted but counted up
+template <typename TFile, typename TSize>
+inline typename Value<TFile>::Type
+_fasta_scan_line(TFile & file,
+ TSize & count_valid,
+ TSize & count_all)
+{
+SEQAN_CHECKPOINT
+ SEQAN_ASSERT(!_streamEOF(file))
+
+ TSize count = 0;
+
+ while (true)
+ {
+ typename Value<TFile>::Type c = _streamGet(file);
+
+ if (_streamEOF(file))
+ {
+ count_valid += count;
+ count_all += count;
+ return c;
+ }
+
+ if ((c == '\n') || (c == '\r'))
+ {
+ do
+ {
+ ++count_all;
+ c = _streamGet(file);
+ } while ((c == '\n') || (c == '\r'));
+
+ count_valid += count;
+ count_all += count;
+ return c;
+ }
+
+ if (c != '\r')
+ {
+ ++count;
+ }
+ }
+}
+
+
+/////////////////////////////////////////////////////////////////////////
+template <typename TFile, typename TSize>
+inline void
+_read_n_chars_from_file(TFile & file, TSize count)
+{
+SEQAN_CHECKPOINT
+ for (TSize i = 0; i < count; ++i)
+ {
+ _streamGet(file);
+ }
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// read
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TFile, typename TData, typename TSize>
+void
+read(TFile & file,
+ TData & data,
+ TSize limit,
+ Fasta)
+{
+SEQAN_CHECKPOINT
+
+ SEQAN_ASSERT(!_streamEOF(file))
+ clear(data);
+
+ //determine begin position
+ typename Value<TFile>::Type c_first = _streamGet(file);
+ SEQAN_ASSERT(!_streamEOF(file))
+
+ typename Position<TFile>::Type begin_pos = _streamTellG(file);
+ typename Size<TData>::Type count_valid = 1; //"valid" characters read (without line breaks)
+ typename Size<TData>::Type count_all = 1; //all characters read (with line breaks)
+
+ if (_streamEOF(file))
+ {
+ return;
+ }
+
+ if (c_first == '>')
+ {//there is an id line: skip it
+ c_first = _fasta_scan_line(file, count_valid, count_all);
+ }
+
+ if ((c_first == '>') || _streamEOF(file))
+ {//another id line = empty entry
+ _streamSeekG(file, begin_pos);
+ _read_n_chars_from_file(file, count_all);
+ return;
+ }
+
+ begin_pos = _streamTellG(file);
+
+ count_valid = 1;
+ count_all = 1;
+ typename Value<TFile>::Type c;
+ bool eof_reached = false;
+ //determine length
+ while (true)
+ {
+ c = _fasta_scan_line(file, count_valid, count_all);
+ if (_streamEOF(file))
+ {//end of file: stop searching
+ eof_reached = true;
+ break;
+ }
+ if (c == '>')
+ {//next entry found: stop seaching
+ break;
+ }
+ if ((c != '\n') && (c != '\r'))
+ {
+ ++count_valid; //count c
+ }
+ ++count_all;
+ }
+
+ //reserve space
+ typename Size<TData>::Type count = count_valid;
+ if (count > limit)
+ {
+ count = limit;
+ }
+ resize(data, count);
+ if (length(data) < count)
+ {
+ count = length(data);
+ }
+
+ //read sequence
+ _streamSeekG(file, begin_pos);
+
+ typename Position<TData>::Type pos = 0;
+ c = c_first;
+ while (true)
+ {
+ if ((c != '\n') && (c != '\r'))
+ {
+ data[pos] = c;
+ ++pos;
+ }
+ if (pos >= count) break;
+
+ c = _streamGet(file);
+ --count_all;
+ }
+
+ //move file ptr to next entry
+ _read_n_chars_from_file(file, count_all - 1);
+ if(eof_reached)
+ _streamGet(file);
+}
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TData>
+void
+read(TFile & file,
+ TData & data,
+ Fasta tag)
+{
+SEQAN_CHECKPOINT
+ typedef typename Size<TData>::Type TSize;
+ read(file, data, supremumValue<TSize>(), tag);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// readID
+//////////////////////////////////////////////////////////////////////////////
+
+//the ID is the complete first line (without the leading '>'-sign)
+
+template <typename TFile, typename TString>
+void
+readID(TFile & file,
+ TString & id,
+ Fasta)
+{
+SEQAN_CHECKPOINT
+ SEQAN_ASSERT(!_streamEOF(file))
+
+ typename Position<TFile>::Type start_pos = _streamTellG(file);
+
+ typename Value<TFile>::Type c = _streamGet(file);
+ if (c != '>')
+ {
+ clear(id);
+ }
+ else
+ {
+ typename Size<TString>::Type count_valid = 0;
+ typename Size<TString>::Type count_all = 0;
+ _fasta_scan_line(file, count_valid, count_all);
+
+ if (! count_valid)
+ {
+ clear(id);
+ }
+ else
+ {
+ resize(id, count_valid);
+ if (length(id) < count_valid)
+ {
+ count_valid = length(id);
+ }
+
+ _streamSeekG(file, start_pos);
+ c = _streamGet(file); //pop the '>' character
+ for (typename Position<TString>::Type pos = 0; count_valid; --count_valid)
+ {
+ id[pos] = _streamGet(file);
+ ++pos;
+ }
+ }
+ }
+ _streamSeekG(file, start_pos);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// readMeta
+//////////////////////////////////////////////////////////////////////////////
+
+//Fasta file records have no meta data
+
+template <typename TFile, typename TMeta>
+void
+readMeta(TFile & file,
+ TMeta & meta,
+ Fasta)
+{
+SEQAN_CHECKPOINT
+ readID(file, meta, Fasta());
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// goNext
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TFile>
+void
+goNext(TFile & file,
+ Fasta)
+{
+SEQAN_CHECKPOINT
+ SEQAN_ASSERT(!_streamEOF(file))
+
+ bool found_data = false;
+ while (true)
+ {
+ typename Value<TFile>::Type c = _streamGet(file);
+
+ if (_streamEOF(file)) return;
+
+ if (c == '\n' || c == '\r')
+ {
+ do {
+ c = _streamGet(file);
+ if (_streamEOF(file)) return;
+ } while (c == '\n' || c == '\r');
+
+ if (c != '>')
+ {
+ found_data = true;
+ }
+ else if (found_data)
+ {
+ _streamUnget(file);
+ return;
+ }
+ }
+ }
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// write
+//////////////////////////////////////////////////////////////////////////////
+
+
+template <typename TFile, typename TString, typename TData>
+void
+_write_impl(TFile & file,
+ TData & data,
+ TString & id,
+ Fasta)
+{
+SEQAN_CHECKPOINT
+ _streamPut(file, '>');
+ _streamWrite(file, id);
+ _streamPut(file, '\n');
+
+ //typename Iterator<TData, Standard>::Type it = begin(data, Standard());
+ //typename Iterator<TData, Standard>::Type it_end = end(data, Standard());
+ typename Iterator<TData>::Type it = begin(data);
+ typename Iterator<TData>::Type it_end = end(data);
+
+ int i = 0;
+
+ for (; it < it_end; ++it)
+ {
+ if (i == 60)
+ {
+ _streamPut(file, '\n');
+ i = 0;
+ }
+ ++i;
+
+ _streamPut(file, *it);
+ }
+ _streamPut(file, '\n');
+}
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TString, typename TData, typename TMeta>
+void
+write(TFile & file,
+ TData & data,
+ Fasta)
+{
+SEQAN_CHECKPOINT
+ _write_impl(file, data, "", Fasta());
+}
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TString, typename TData>
+void
+write(TFile & file,
+ TData & data,
+ TString & id,
+ Fasta)
+{
+SEQAN_CHECKPOINT
+ _write_impl(file, data, id, Fasta());
+}
+
+
+//VisualC++ const array bug workaround
+template <typename TFile, typename TString, typename TDataValue>
+void
+write(TFile & file,
+ TDataValue * data,
+ TString & id,
+ Fasta)
+{
+SEQAN_CHECKPOINT
+ _write_impl(file, data, id, Fasta());
+
+}
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TString, typename TData, typename TMeta>
+void
+write(TFile & file,
+ TData & data,
+ TString & id,
+ TMeta &,
+ Fasta)
+{
+SEQAN_CHECKPOINT
+ _write_impl(file, data, id, Fasta());
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+} //namespace SEQAN_NAMESPACE_MAIN
+
+//////////////////////////////////////////////////////////////////////////////
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/file/file_format_fasta_align.h b/src/libSSA/seqan/file/file_format_fasta_align.h
new file mode 100644
index 0000000..6790f4b
--- /dev/null
+++ b/src/libSSA/seqan/file/file_format_fasta_align.h
@@ -0,0 +1,320 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: file_format_fasta_align.h,v 1.1 2008/08/25 16:20:03 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FILE_FASTA_ALIGN_H
+#define SEQAN_HEADER_FILE_FASTA_ALIGN_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// File Formats - Fasta alignment format
+//////////////////////////////////////////////////////////////////////////////
+
+//forward declarations
+template <typename T>
+struct Row;
+
+template <typename T>
+struct Rows;
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.File Format.tag.Fasta alignment:
+ FASTA alignment file format for sequences.
+*/
+struct TagFastaAlign_;
+typedef Tag<TagFastaAlign_> const FastaAlign;
+
+
+/////////////////////////////////////////////////////////////////////////
+
+template <typename TFile, typename TSize>
+void _fasta_align_scan_line(TFile & file, TSize & count) {
+
+ SEQAN_CHECKPOINT
+ SEQAN_ASSERT(!_streamEOF(file))
+
+ while (true) {
+ typename Value<TFile>::Type c = _streamGet(file);
+
+ if (_streamEOF(file)) return;
+ if (c == '\n') return;
+
+ if ((c != '\r') && (c!='-')) {
+ ++count;
+ }
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// read
+//////////////////////////////////////////////////////////////////////////////
+template <typename TFile, typename TSource, typename TSpec>
+void read(TFile & file, Align<TSource, TSpec> & align, FastaAlign) {
+SEQAN_CHECKPOINT
+
+ SEQAN_ASSERT(!_streamEOF(file))
+
+ typedef typename Value<TSource>::Type TSourceValue;
+ typedef typename Size<TSourceValue>::Type TSize;
+ TSize limit = supremumValue<TSize>();
+
+ //Determine begin position, end position and length of each sequence
+ String<TSize> beg_end_length;
+
+ typename Position<TFile>::Type begin_pos;
+ typename Position<TFile>::Type end_pos;
+ typename Value<TFile>::Type c;
+ TSize count;
+
+ while (!_streamEOF(file)) {
+ begin_pos = _streamTellG(file);
+ count = 0;
+ SEQAN_ASSERT(!_streamEOF(file))
+
+
+ c = _streamGet(file);
+
+ // Skip id
+ if (c == '>') {
+ _fasta_align_scan_line(file, count);
+ begin_pos = _streamTellG(file);
+ count = 0;
+ } else { //If no id first letter belongs to sequence
+ count = 1;
+ }
+
+ // Count letters
+ while (true) {
+ _fasta_align_scan_line(file, count);
+
+ typename Value<TFile>::Type c = _streamGet(file);
+ if (c == '>') {
+ _streamSeek2G(file, -1);
+ end_pos = _streamTellG(file);
+ break;
+ }
+ if (_streamEOF(file)) {
+ end_pos = _streamTellG(file);
+ break;
+ }
+ if ((c != '\n') && (c != '\r') && (c!='-')) {
+ ++count;
+ }
+ }
+ if (count > limit) {
+ count = limit;
+ }
+
+ append(beg_end_length, begin_pos);
+ append(beg_end_length, end_pos);
+ append(beg_end_length, count);
+ }
+
+ // Resize alignment data structure
+ TSize numRows=length(beg_end_length) / 3;
+ resize(rows(align), numRows); //rows
+
+ typedef Align<TSource, TSpec> TAlign;
+ typedef typename Row<TAlign>::Type TRow;
+
+ for(TSize i=0;i<numRows;++i) {
+ TSize begin = beg_end_length[i*3];
+// TSize end = beg_end_length[i*3+1];
+ count = beg_end_length[i*3+2];
+
+ //Reserve space
+ clear(row(align,i));
+ createSource(row(align,i));
+ resize(source(row(align,i)),count);
+ if (length(source(row(align,i))) < count) {
+ count = length(source(row(align,i)));
+ }
+ setSourceEndPosition(row(align,i),count);
+
+ //Read sequence
+ _streamSeekG(file, begin);
+
+ typename Position<TSource>::Type pos;
+ for (pos = 0; pos < count; ) {
+ c = _streamGet(file);
+ if ((c != '\n') && (c != '\r') && (c != '-')) {
+ source(row(align,i))[pos] = c;
+ ++pos;
+ }
+ if (c=='-') {
+ insertGap(row(align,i), toViewPosition(row(align,i), pos));
+ }
+ }
+ }
+
+ _streamSeekG(file, 0);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// readIDs
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TFile, typename TStringContainer>
+void readIDs(TFile& file, TStringContainer& ids, FastaAlign) {
+
+ SEQAN_CHECKPOINT
+
+ SEQAN_ASSERT(!_streamEOF(file))
+
+ typedef typename Value<TStringContainer>::Type TString;
+ typename Position<TFile>::Type start_pos;
+ typename Value<TFile>::Type c;
+
+
+ TString id;
+ while(true) {
+ c = _streamGet(file);
+ while ((!_streamEOF(file)) && (c != '>')) c = _streamGet(file);
+ if (!_streamEOF(file)) {
+ start_pos = _streamTellG(file);
+ typename Size<TString>::Type count = 0;
+ _fasta_align_scan_line(file, count);
+ if (! count) clear(id);
+ else {
+ resize(id, count);
+ if (length(id) < count) {
+ count = length(id);
+ }
+ _streamSeekG(file, start_pos);
+ for (typename Position<TString>::Type pos = 0; pos<count; ++pos) {
+ id[pos] = _streamGet(file);
+ }
+ }
+ appendValue(ids, id);
+ } else {
+ break;
+ }
+ }
+ _streamSeekG(file, 0);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// readMeta
+//////////////////////////////////////////////////////////////////////////////
+
+//Fasta file records have no meta data
+
+template <typename TFile, typename TMeta>
+void readMeta(TFile & file, TMeta & meta, FastaAlign) {
+ SEQAN_CHECKPOINT
+ clear(meta);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// goNext
+//////////////////////////////////////////////////////////////////////////////
+template <typename TFile>
+void goNext(TFile & file, FastaAlign) {
+ SEQAN_CHECKPOINT
+ SEQAN_ASSERT(!_streamEOF(file))
+
+ return;
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// write
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TFile, typename TStringContainer, typename TSource, typename TSpec>
+void _write_impl(TFile& file, Align<TSource, TSpec>& align, TStringContainer& ids, FastaAlign) {
+ SEQAN_CHECKPOINT
+
+ typedef Align<TSource, TSpec> const TAlign;
+ typedef typename Row<TAlign>::Type TRow;
+ typedef typename Position<typename Rows<TAlign>::Type>::Type TRowsPosition;
+ typedef typename Position<TAlign>::Type TPosition;
+ TRowsPosition row_count = length(rows(align));
+
+ for(TRowsPosition i=0;i<row_count;++i) {
+ TRow & row_ = row(align, i);
+
+ typedef typename Iterator<typename Row<TAlign>::Type const, Standard>::Type TIter;
+ TIter begin_ = iter(row_, beginPosition(cols(align)));
+ TIter end_ = iter(row_, endPosition(cols(align)));
+
+ _streamPut(file, '>');
+ _streamWrite(file, getValue(ids,i));
+ _streamPut(file, '\n');
+
+ int chars=0;
+ while(begin_ != end_) {
+ if (chars == 60) {
+ _streamPut(file, '\n');
+ chars = 0;
+ }
+ if (isGap(begin_)) _streamPut(file, gapValue<char>());
+ else _streamPut(file, getValue(source(begin_)));
+ chars++;
+ ++begin_;
+ }
+ _streamPut(file, '\n');
+ }
+}
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TSource, typename TSpec>
+void write(TFile & file, Align<TSource, TSpec>& align, FastaAlign) {
+ SEQAN_CHECKPOINT
+ _write_impl(file, align, String<String<char> >(), FastaAlign());
+}
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TStringContainer, typename TSource, typename TSpec>
+void write(TFile & file, Align<TSource, TSpec> & align, TStringContainer& ids, FastaAlign) {
+ SEQAN_CHECKPOINT
+ _write_impl(file, align, ids, FastaAlign());
+}
+
+
+//VisualC++ const array bug workaround
+template <typename TFile, typename TStringContainer, typename TSource, typename TSpec>
+void write(TFile & file, Align<TSource, TSpec>* align, TStringContainer & ids, FastaAlign) {
+ SEQAN_CHECKPOINT
+ _write_impl(file, align, ids, FastaAlign());
+}
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TStringContainer, typename TSource, typename TSpec, typename TMeta>
+void write(TFile & file, Align<TSource, TSpec> & align, TStringContainer& ids, TMeta &, FastaAlign) {
+ SEQAN_CHECKPOINT
+ _write_impl(file, align, ids, FastaAlign());
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+} //namespace SEQAN_NAMESPACE_MAIN
+
+//////////////////////////////////////////////////////////////////////////////
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/file/file_format_guess.h b/src/libSSA/seqan/file/file_format_guess.h
new file mode 100644
index 0000000..a4c5287
--- /dev/null
+++ b/src/libSSA/seqan/file/file_format_guess.h
@@ -0,0 +1,103 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: file_format_guess.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FILE_GUESS_H
+#define SEQAN_HEADER_FILE_GUESS_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// guessFileFormat
+//////////////////////////////////////////////////////////////////////////////
+
+//guessFileFormat braucht auch data, weil die FileFormat-Klasse von TData
+//abhaengig, und das ist so, weil sonst die Kombination von Templates mit
+//virtuellen Funktionen nicht funktionieren wuerde.
+/**
+.Function.guessFileFormat:
+..cat:Input/Output
+..summary:Tries to determine the format of a file.
+..signature:guessFileFormat(file, data)
+..param.file: An input file.
+..param.data: The target container.
+...remarks:This container is not modified by this function.
+..returns:A file format object instance that represents the determined file format.
+...type:Class.FileFormat
+..remarks:The $data$-argument is used here as a tag to determine the type of the target.
+..see:Function.Fileformat#read
+..see:Tag.File Format
+*/
+template <typename TFile, typename TData, typename TMeta>
+inline FileFormat<TFile, TData, TMeta, void> &
+guessFileFormat(TFile & file,
+ TData & data)
+{
+SEQAN_CHECKPOINT
+ typename Position<TFile>::Type old_pos = _streamTellG(file);
+ typename Value<TFile>::Type c;
+
+ _streamSeekG(file, 0); /// move to beginning of file
+ c = _streamGet(file);
+
+ if (c=='>')
+ {
+ _streamSeekG(file, old_pos);
+ return getFileFormatInstance<TFile, TData, Fasta, TMeta>();
+ }
+
+ if (c=='L')
+ {
+ _streamSeekG(file, old_pos);
+ return getFileFormatInstance<TFile, TData, Genbank, TMeta>();
+ }
+
+ if (c=='I')
+ {
+ _streamSeekG(file, old_pos);
+ return getFileFormatInstance<TFile, TData, Embl, TMeta>();
+ }
+
+ else
+ {
+ _streamSeekG(file, old_pos);
+ return getFileFormatInstance<TFile, TData, Raw, TMeta>();
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/* DOCH NICHT:
+template <typename TTarget, typename TSource>
+inline void
+read(TTarget & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ read(target, source, guessFileFormat(target, source));
+}
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+} //namespace SEQAN_NAMESPACE_MAIN
+
+//////////////////////////////////////////////////////////////////////////////
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/file/file_format_raw.h b/src/libSSA/seqan/file/file_format_raw.h
new file mode 100644
index 0000000..3b905db
--- /dev/null
+++ b/src/libSSA/seqan/file/file_format_raw.h
@@ -0,0 +1,345 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: file_format_raw.h,v 1.1 2008/08/25 16:20:03 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FILE_RAW_H
+#define SEQAN_HEADER_FILE_RAW_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// File Formats - Raw
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Tag.File Format.tag.Raw:
+ The file contains data in a raw format.
+..remark:It is supposed that the file contains one single piece of data,
+that is the file cannot store multiple records.
+*/
+
+struct TagRaw_;
+typedef Tag<TagRaw_> const Raw;
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// read
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TFile, typename TData, typename TTag>
+struct _Read_Raw;
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TData>
+struct _Read_Raw<TFile, TData, True>
+{
+ static void
+ read_(TFile & file,
+ TData & data)
+ {
+SEQAN_CHECKPOINT
+ SEQAN_ASSERT(!_streamEOF(file))
+
+ //determine length
+ typename Position<TFile>::Type begin_pos = _streamTellG(file);
+ typename Size<TData>::Type count = 0;
+ typename Value<TFile>::Type c = _streamGet(file);
+
+ while (!_streamEOF(file))
+ {
+ c = _streamGet(file);
+ ++count;
+ }
+
+ //reserve space
+ resize(data, count);
+
+ if (!count) return;
+
+ if (length(data) < count)
+ {
+ count = length(data);
+ }
+
+ //read sequence
+ _streamSeekG(file, begin_pos);
+
+ typename Position<TData>::Type pos;
+ for (pos = 0; pos < count; )
+ {
+ c = _streamGet(file);
+ assignValue(data, pos, c);
+ ++pos;
+ }
+ }
+//____________________________________________________________________________
+
+ template <typename TSize>
+ static void
+ read_(TFile & file,
+ TData & data,
+ TSize _limit)
+ {
+SEQAN_CHECKPOINT
+ SEQAN_ASSERT(!_streamEOF(file))
+
+ typename Size<TData>::Type limit = _limit;
+
+ //determine length
+ typename Position<TFile>::Type begin_pos = _streamTellG(file);
+ typename Size<TData>::Type count = 0;
+ typename Value<TFile>::Type c = _streamGet(file);
+
+ while (!_streamEOF(file))
+ {
+ c = _streamGet(file);
+ ++count;
+ if (count == limit) break;
+ }
+
+ //reserve space
+ resize(data, count);
+
+ if (!count) return;
+
+ if (length(data) < count)
+ {
+ count = length(data);
+ }
+
+ //read sequence
+ _streamSeekG(file, begin_pos);
+
+ typename Position<TData>::Type pos;
+ for (pos = 0; pos < count; )
+ {
+ c = _streamGet(file);
+ assignValue(data, pos, c);
+ ++pos;
+ }
+ }
+};
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TData>
+struct _Read_Raw<TFile, TData, False>
+{
+ static void
+ read_(TFile & file,
+ TData & data)
+ {
+SEQAN_CHECKPOINT
+
+ clear(data);
+ if (!_streamEOF(file))
+ {
+SEQAN_CHECKPOINT
+ _ChunkCollector<TData> chunk_collector(data);
+ assign(chunk_collector, file);
+ append(data, chunk_collector);
+ }
+ }
+
+//____________________________________________________________________________
+
+ template <typename TSize>
+ static void
+ read_(TFile & file,
+ TData & data,
+ TSize limit)
+ {
+SEQAN_CHECKPOINT
+
+ clear(data);
+ if (!_streamEOF(file))
+ {
+SEQAN_CHECKPOINT
+ _ChunkCollector<TData> chunk_collector(data);
+ assign(chunk_collector, file, limit);
+ append(data, chunk_collector, limit);
+ }
+ }
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+template <typename TFile, typename TData>
+void
+read(TFile & file,
+ TData & data,
+ Raw)
+{
+SEQAN_CHECKPOINT
+ _Read_Raw<TFile, TData, typename _IsTellSeekStream<TFile>::Type>::read_(file, data);
+}
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TData, typename TSize>
+void
+read(TFile & file,
+ TData & data,
+ TSize limit,
+ Raw)
+{
+SEQAN_CHECKPOINT
+ _Read_Raw<TFile, TData, typename _IsTellSeekStream<TFile>::Type>::read_(file, data, limit);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// readID
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TFile, typename TString>
+void
+readID(TFile & /*file*/,
+ TString & id,
+ Raw)
+{
+SEQAN_CHECKPOINT
+ clear(id);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// readMeta
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TFile, typename TMeta>
+void
+readMeta(TFile & file,
+ TMeta & meta,
+ Raw)
+{
+SEQAN_CHECKPOINT
+ clear(meta);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// goNext
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TFile>
+void
+goNext(TFile & file,
+ Raw)
+{
+SEQAN_CHECKPOINT
+ SEQAN_ASSERT(!_streamEOF(file))
+
+//??? TODO: set file to eof
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// write
+//////////////////////////////////////////////////////////////////////////////
+
+
+template <typename TFile, typename TString, typename TData>
+void
+write(TFile & file,
+ TData const & data,
+ Raw)
+{
+SEQAN_CHECKPOINT
+ _streamWrite(file, data);
+}
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TData, typename TString>
+void
+write(TFile & file,
+ TData const & data,
+ TString const &,
+ Raw)
+{
+SEQAN_CHECKPOINT
+ _streamWrite(file, data);
+}
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TString, typename TData, typename TMeta>
+void
+write(TFile & file,
+ TData const & data,
+ TString const &,
+ TMeta const &,
+ Raw)
+{
+SEQAN_CHECKPOINT
+ _streamWrite(file, data);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// default functions
+//////////////////////////////////////////////////////////////////////////////
+
+
+template <typename TFile, typename TData>
+void
+read(TFile & file,
+ TData & data)
+{
+ read(file, data, Raw());
+}
+
+template <typename TFile, typename TData, typename TSize>
+void
+read(TFile & file,
+ TData & data,
+ TSize limit)
+{
+SEQAN_CHECKPOINT
+ read(file, data, limit, Raw());
+}
+
+//____________________________________________________________________________
+
+template <typename TFile, typename TData>
+void
+write(TFile & file,
+ TData & data)
+{
+SEQAN_CHECKPOINT
+ write(file, data, "", Raw());
+}
+template <typename TFile, typename TData>
+void
+write(TFile & file,
+ TData const & data)
+{
+SEQAN_CHECKPOINT
+ write(file, data, "", Raw());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+} //namespace SEQAN_NAMESPACE_MAIN
+
+//////////////////////////////////////////////////////////////////////////////
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/file/file_forwards.h b/src/libSSA/seqan/file/file_forwards.h
new file mode 100644
index 0000000..987c820
--- /dev/null
+++ b/src/libSSA/seqan/file/file_forwards.h
@@ -0,0 +1,44 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: file_forwards.h,v 1.1 2008/08/25 16:20:03 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FILE_FORWARDS_H
+#define SEQAN_HEADER_FILE_FORWARDS_H
+
+//SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
+
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TSource, typename TSpec>
+class Align;
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+//////////////////////////////////////////////////////////////////////////////
+
+#endif
+
diff --git a/src/libSSA/seqan/file/file_generated_forwards.h b/src/libSSA/seqan/file/file_generated_forwards.h
new file mode 100644
index 0000000..61dd531
--- /dev/null
+++ b/src/libSSA/seqan/file/file_generated_forwards.h
@@ -0,0 +1,1155 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FILE_GENERATED_FORWARDS_H
+#define SEQAN_HEADER_FILE_GENERATED_FORWARDS_H
+
+//////////////////////////////////////////////////////////////////////////////
+// NOTE: This file is automatically generated by build_forwards.py
+// Do not edit this file manually!
+//////////////////////////////////////////////////////////////////////////////
+
+
+//////////////////////////////////////////////////////////////////////////////
+// CLASSES
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+
+//____________________________________________________________________________
+// Async
+
+template <typename TSpec > struct Async; // "projects/library/seqan/file/file_base.h"(58)
+
+//____________________________________________________________________________
+// Chained
+
+template <__int64 _FileSize , typename TFile > struct Chained; // "projects/library/seqan/file/file_base.h"(90)
+
+//____________________________________________________________________________
+// ChunkLength
+
+template <typename T> struct ChunkLength; // "projects/library/seqan/file/chunk_collector.h"(41)
+
+//____________________________________________________________________________
+// DefaultOpenMode
+
+template <typename T> struct DefaultOpenMode; // "projects/library/seqan/file/file_base.h"(122)
+
+//____________________________________________________________________________
+// DefaultOpenTempMode
+
+template <typename T> struct DefaultOpenTempMode; // "projects/library/seqan/file/file_base.h"(127)
+
+//____________________________________________________________________________
+// Dynamic
+
+template <typename TSpec > struct Dynamic; // "projects/library/seqan/file/file_page.h"(185)
+
+//____________________________________________________________________________
+// External
+
+template <typename TConfig > struct External; // "projects/library/seqan/file/string_external.h"(158)
+
+//____________________________________________________________________________
+// ExternalConfig
+
+template <typename _TFile , unsigned _PageSize , unsigned _Frames > struct ExternalConfig; // "projects/library/seqan/file/string_external.h"(83)
+
+//____________________________________________________________________________
+// ExternalConfigLarge
+
+template <typename _TFile , unsigned _PageSize , unsigned _Frames > struct ExternalConfigLarge; // "projects/library/seqan/file/string_external.h"(118)
+
+//____________________________________________________________________________
+// ExternalConfigSize
+
+template <typename TSize, typename _TFile , unsigned _PageSize , unsigned _Frames > struct ExternalConfigSize; // "projects/library/seqan/file/string_external.h"(150)
+
+//____________________________________________________________________________
+// File
+
+template <typename TSpec > class File; // "projects/library/seqan/file/file_base.h"(71)
+
+//____________________________________________________________________________
+// FileFormat
+
+template <typename TFile, typename TData, typename TMeta, typename TFormat > struct FileFormat; // "projects/library/seqan/file/file_format.h"(60)
+
+//____________________________________________________________________________
+// FileReader
+
+ template <typename TFormat, typename TFile , typename TSpec > struct FileReader; // "projects/library/seqan/file/file_filereaderiterator.h"(30)
+
+//____________________________________________________________________________
+// FileReaderIterator
+
+struct FileReaderIterator; // "projects/library/seqan/file/file_filereader.h"(402)
+
+//____________________________________________________________________________
+// Fixed
+
+template <unsigned _PageSize > struct Fixed; // "projects/library/seqan/file/file_page.h"(228)
+
+//____________________________________________________________________________
+// PageBucket
+
+template <typename TValue > struct PageBucket; // "projects/library/seqan/file/file_page.h"(159)
+
+//____________________________________________________________________________
+// PageBucketExtended
+
+template <typename TValue > struct PageBucketExtended; // "projects/library/seqan/file/file_page.h"(165)
+
+//____________________________________________________________________________
+// PageChain
+
+template <typename TPageFrame > struct PageChain; // "projects/library/seqan/file/file_page.h"(189)
+template <typename TPageFrame > struct PageChain; // "projects/library/seqan/file/file_page.h"(509)
+
+//____________________________________________________________________________
+// PageContainer
+
+template <typename TPageFrame, unsigned _Frames, unsigned _PriorityLevels > struct PageContainer; // "projects/library/seqan/file/file_page.h"(723)
+
+//____________________________________________________________________________
+// PageFrame
+
+template <typename TValue, typename TFile, typename TSpec > struct PageFrame; // "projects/library/seqan/file/file_page.h"(178)
+
+//____________________________________________________________________________
+// Row
+
+template <typename T> struct Row; // "projects/library/seqan/file/file_format_fasta_align.h"(33)
+
+//____________________________________________________________________________
+// Rows
+
+template <typename T> struct Rows; // "projects/library/seqan/file/file_format_fasta_align.h"(36)
+
+//____________________________________________________________________________
+// SimpleBuffer
+
+template <typename TValue > struct SimpleBuffer; // "projects/library/seqan/file/file_page.h"(35)
+
+//____________________________________________________________________________
+// Striped
+
+template <unsigned _FileCount , typename TFile > struct Striped; // "projects/library/seqan/file/file_base.h"(107)
+
+//____________________________________________________________________________
+// Sync
+
+template <typename TSpec > struct Sync; // "projects/library/seqan/file/file_base.h"(47)
+
+//____________________________________________________________________________
+// TagCGViz_
+
+struct TagCGViz_; // "projects/library/seqan/file/file_format_cgviz.h"(36)
+
+//____________________________________________________________________________
+// TagEmbl_
+
+struct TagEmbl_; // "projects/library/seqan/file/file_format_embl.h"(34)
+
+//____________________________________________________________________________
+// TagFastaAlign_
+
+struct TagFastaAlign_; // "projects/library/seqan/file/file_format_fasta_align.h"(44)
+
+//____________________________________________________________________________
+// TagFasta_
+
+struct TagFasta_; // "projects/library/seqan/file/file_format_fasta.h"(35)
+
+//____________________________________________________________________________
+// TagGenbank_
+
+struct TagGenbank_; // "projects/library/seqan/file/file_format_genbank.h"(35)
+
+//____________________________________________________________________________
+// TagRaw_
+
+struct TagRaw_; // "projects/library/seqan/file/file_format_raw.h"(37)
+
+//____________________________________________________________________________
+// VectorConstIterator
+
+template <typename _Vector > struct VectorConstIterator; // "projects/library/seqan/file/string_external.h"(275)
+
+//____________________________________________________________________________
+// VectorFwdConstIterator
+
+template <typename _Vector > struct VectorFwdConstIterator; // "projects/library/seqan/file/string_external.h"(641)
+
+//____________________________________________________________________________
+// VectorFwdIterator
+
+template <typename _Vector > struct VectorFwdIterator; // "projects/library/seqan/file/string_external.h"(392)
+
+//____________________________________________________________________________
+// VectorIterator
+
+template <typename _Vector > struct VectorIterator; // "projects/library/seqan/file/string_external.h"(165)
+
+//____________________________________________________________________________
+// _Append_ChunkCollector_2_String
+
+template <typename TExpand> struct _Append_ChunkCollector_2_String; // "projects/library/seqan/file/chunk_collector.h"(334)
+
+//____________________________________________________________________________
+// _Assign_ChunkCollector_2_String
+
+template <typename TExpand> struct _Assign_ChunkCollector_2_String; // "projects/library/seqan/file/chunk_collector.h"(264)
+
+//____________________________________________________________________________
+// _Assign_Stream_2_ChunkCollector
+
+struct _Assign_Stream_2_ChunkCollector; // "projects/library/seqan/file/chunk_collector.h"(186)
+
+//____________________________________________________________________________
+// _ChunkCollector
+
+template <typename THost> class _ChunkCollector; // "projects/library/seqan/file/chunk_collector.h"(51)
+
+//____________________________________________________________________________
+// _FileReader_Types
+
+template <typename T> struct _FileReader_Types; // "projects/library/seqan/file/file_filereader.h"(410)
+
+//____________________________________________________________________________
+// _IsTellSeekStream
+
+template <typename T> struct _IsTellSeekStream; // "projects/library/seqan/file/stream.h"(179)
+template <typename T> struct _IsTellSeekStream; // "projects/library/seqan/file/cstream.h"(63)
+
+//____________________________________________________________________________
+// _Read_Raw
+
+template <typename TFile, typename TData, typename TTag> struct _Read_Raw; // "projects/library/seqan/file/file_format_raw.h"(47)
+
+//____________________________________________________________________________
+// _Replace_ChunkCollector_2_String
+
+template <typename TExpand> struct _Replace_ChunkCollector_2_String; // "projects/library/seqan/file/chunk_collector.h"(407)
+
+//____________________________________________________________________________
+// aDummyRequest
+
+struct aDummyRequest; // "projects/library/seqan/file/file_base.h"(143)
+
+//____________________________________________________________________________
+// aRequest
+
+template <typename T > struct aRequest; // "projects/library/seqan/file/file_base.h"(156)
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+
+//////////////////////////////////////////////////////////////////////////////
+// TYPEDEFS
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+
+//____________________________________________________________________________
+// CGViz
+
+typedef Tag<TagCGViz_> const CGViz; // "projects/library/seqan/file/file_format_cgviz.h"(37)
+
+//____________________________________________________________________________
+// Embl
+
+typedef Tag<TagEmbl_> const Embl; // "projects/library/seqan/file/file_format_embl.h"(35)
+
+//____________________________________________________________________________
+// Fasta
+
+typedef Tag<TagFasta_> const Fasta; // "projects/library/seqan/file/file_format_fasta.h"(36)
+
+//____________________________________________________________________________
+// FastaAlign
+
+typedef Tag<TagFastaAlign_> const FastaAlign; // "projects/library/seqan/file/file_format_fasta_align.h"(45)
+
+//____________________________________________________________________________
+// Genbank
+
+typedef Tag<TagGenbank_> const Genbank; // "projects/library/seqan/file/file_format_genbank.h"(36)
+
+//____________________________________________________________________________
+// Raw
+
+typedef Tag<TagRaw_> const Raw; // "projects/library/seqan/file/file_format_raw.h"(38)
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+
+//////////////////////////////////////////////////////////////////////////////
+// FUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+
+//____________________________________________________________________________
+// _FileReaderString_construct
+
+template <typename TValue, typename TFormat, typename TFile, typename TSpec> inline void _FileReaderString_construct(String<TValue, FileReader<TFormat, TFile, TSpec> > & me); // "projects/library/seqan/file/file_filereader.h"(254)
+
+//____________________________________________________________________________
+// _FileReaderString_findblock
+
+template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TPosition> inline unsigned int _FileReaderString_findblock(String<TValue, FileReader<TFormat, TFile, TSpec> > & me, TPosition pos); // "projects/library/seqan/file/file_filereader.h"(233)
+
+//____________________________________________________________________________
+// _FileReaderString_isValidBlock
+
+template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TUint> inline bool _FileReaderString_isValidBlock(String<TValue, FileReader<TFormat, TFile, TSpec> > & me, TUint block_number); // "projects/library/seqan/file/file_filereader.h"(271)
+
+//____________________________________________________________________________
+// _FileReaderString_loadComplete
+
+template <typename TValue, typename TFormat, typename TFile, typename TSpec> inline void _FileReaderString_loadComplete(String<TValue, FileReader<TFormat, TFile, TSpec> > & me); // "projects/library/seqan/file/file_filereader.h"(288)
+
+//____________________________________________________________________________
+// _FileReaderString_loadblock
+
+template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TPosition> inline void _FileReaderString_loadblock(String<TValue, FileReader<TFormat, TFile, TSpec> > & me, TPosition blocknum); // "projects/library/seqan/file/file_filereader.h"(167)
+
+//____________________________________________________________________________
+// _cancelFArray
+
+template <typename TFileArray, typename TRequest > inline bool _cancelFArray(TFileArray &me, TRequest &request); // "projects/library/seqan/file/file_array.h"(272)
+
+//____________________________________________________________________________
+// _closeFArray
+
+template <typename TFileArray > inline bool _closeFArray(TFileArray &me); // "projects/library/seqan/file/file_array.h"(242)
+
+//____________________________________________________________________________
+// _dataFile
+
+template <typename TValue, typename TFormat, typename TFile, typename TSpec> inline TFile & _dataFile(String<TValue, FileReader<TFormat, TFile, TSpec> > & me); // "projects/library/seqan/file/file_filereader.h"(156)
+
+//____________________________________________________________________________
+// _fasta_align_scan_line
+
+template <typename TFile, typename TSize> void _fasta_align_scan_line(TFile & file, TSize & count); // "projects/library/seqan/file/file_format_fasta_align.h"(51)
+
+//____________________________________________________________________________
+// _fasta_scan_line
+
+template <typename TFile, typename TSize> inline typename Value<TFile>::Type _fasta_scan_line(TFile & file, TSize & count_valid, TSize & count_all); // "projects/library/seqan/file/file_format_fasta.h"(145)
+
+//____________________________________________________________________________
+// _flushFArray
+
+template <typename TFileArray > inline bool _flushFArray(TFileArray &me); // "projects/library/seqan/file/file_array.h"(264)
+
+//____________________________________________________________________________
+// _getCStyleOpenMode
+
+inline const char * _getCStyleOpenMode(int openMode); // "projects/library/seqan/file/file_cstyle.h"(66)
+
+//____________________________________________________________________________
+// _openTempFArray
+
+template <typename TFileArray > inline bool _openTempFArray(TFileArray &me, int openMode); // "projects/library/seqan/file/file_array.h"(221)
+template <typename TFileArray > inline bool _openTempFArray(TFileArray &me); // "projects/library/seqan/file/file_array.h"(229)
+
+//____________________________________________________________________________
+// _read_n_chars_from_file
+
+template <typename TFile, typename TSize> inline void _read_n_chars_from_file(TFile & file, TSize count); // "projects/library/seqan/file/file_format_fasta.h"(187)
+
+//____________________________________________________________________________
+// _reopenFArray
+
+template <typename TFileArray > inline bool _reopenFArray(TFileArray &me, int openMode); // "projects/library/seqan/file/file_array.h"(234)
+
+//____________________________________________________________________________
+// _sectorSizeFArray
+
+template <typename TFileArray > inline unsigned _sectorSizeFArray(TFileArray &me, int openMode); // "projects/library/seqan/file/file_array.h"(250)
+
+//____________________________________________________________________________
+// _sizeFArray
+
+template <typename TFileArray > inline typename Size<TFileArray>::Type _sizeFArray(TFileArray &me); // "projects/library/seqan/file/file_array.h"(256)
+
+//____________________________________________________________________________
+// _streamClose
+
+inline void _streamClose(::std::FILE * & me); // "projects/library/seqan/file/cstream.h"(93)
+
+//____________________________________________________________________________
+// _streamEOF
+
+template <typename TValue, typename TTraits> inline bool _streamEOF(::std::basic_ios<TValue, TTraits> const & me); // "projects/library/seqan/file/stream.h"(209)
+inline bool _streamEOF(::std::FILE * me); // "projects/library/seqan/file/cstream.h"(108)
+
+//____________________________________________________________________________
+// _streamGet
+
+template <typename TValue, typename TTraits> inline TValue _streamGet(::std::basic_istream<TValue, TTraits> & source); // "projects/library/seqan/file/stream.h"(253)
+inline char _streamGet(::std::FILE * source); // "projects/library/seqan/file/cstream.h"(133)
+
+//____________________________________________________________________________
+// _streamOpen
+
+inline bool _streamOpen(::std::FILE * & me, String<char> path, bool for_read ); // "projects/library/seqan/file/cstream.h"(75)
+
+//____________________________________________________________________________
+// _streamPeek
+
+template <typename TValue, typename TTraits> inline TValue _streamPeek(::std::basic_istream<TValue, TTraits> & source); // "projects/library/seqan/file/stream.h"(273)
+
+//____________________________________________________________________________
+// _streamPut
+
+template <typename TValue, typename TTraits, typename TChar> inline void _streamPut(::std::basic_ostream<TValue, TTraits> & target, TChar character); // "projects/library/seqan/file/stream.h"(313)
+inline void _streamPut(::std::FILE * target, char character); // "projects/library/seqan/file/cstream.h"(145)
+
+//____________________________________________________________________________
+// _streamPutFloat
+
+template <typename TStream> inline void _streamPutFloat(TStream & target, float number, char const * format_string); // "projects/library/seqan/file/stream_algorithms.h"(73)
+template <typename TStream> inline void _streamPutFloat(TStream & target, float number); // "projects/library/seqan/file/stream_algorithms.h"(83)
+
+//____________________________________________________________________________
+// _streamPutInt
+
+template <typename TStream> inline void _streamPutInt(TStream & target, int number, char const * format_string); // "projects/library/seqan/file/stream_algorithms.h"(44)
+template <typename TStream> inline void _streamPutInt(TStream & target, int number); // "projects/library/seqan/file/stream_algorithms.h"(54)
+
+//____________________________________________________________________________
+// _streamRead
+
+template <typename TValue, typename TTraits> inline ::std::streamsize _streamRead(TValue * target, ::std::basic_istream<TValue, TTraits> & source, ::std::streamsize limit); // "projects/library/seqan/file/stream.h"(232)
+template <typename TValue> inline size_t _streamRead(TValue * target, ::std::FILE * source, size_t limit); // "projects/library/seqan/file/cstream.h"(122)
+
+//____________________________________________________________________________
+// _streamSeek2G
+
+template <typename TValue, typename TTraits> inline void _streamSeek2G(::std::basic_istream<TValue, TTraits> & me, int off); // "projects/library/seqan/file/stream.h"(420)
+inline void _streamSeek2G(FILE * me, int off); // "projects/library/seqan/file/cstream.h"(208)
+
+//____________________________________________________________________________
+// _streamSeekG
+
+template <typename TValue, typename TTraits> inline void _streamSeekG(::std::basic_istream<TValue, TTraits> & me, typename Position< ::std::basic_istream<TValue, TTraits> >::Type pos); // "projects/library/seqan/file/stream.h"(373)
+inline void _streamSeekG(FILE * me, Position<FILE *>::Type pos); // "projects/library/seqan/file/cstream.h"(184)
+
+//____________________________________________________________________________
+// _streamSeekP
+
+template <typename TValue, typename TTraits> inline void _streamSeekP(::std::basic_ostream<TValue, TTraits> & me, typename Position< ::std::basic_ostream<TValue, TTraits> >::Type pos); // "projects/library/seqan/file/stream.h"(397)
+inline void _streamSeekP(FILE * me, Position<FILE *>::Type pos); // "projects/library/seqan/file/cstream.h"(196)
+
+//____________________________________________________________________________
+// _streamTellG
+
+template <typename TValue, typename TTraits> inline typename Position< ::std::basic_istream<TValue, TTraits> >::Type _streamTellG(::std::basic_istream<TValue, TTraits> & me); // "projects/library/seqan/file/stream.h"(332)
+inline Position<FILE *>::Type _streamTellG(FILE * me); // "projects/library/seqan/file/cstream.h"(161)
+
+//____________________________________________________________________________
+// _streamTellP
+
+template <typename TValue, typename TTraits> inline typename Position< ::std::basic_ostream<TValue, TTraits> >::Type _streamTellP(::std::basic_ostream<TValue, TTraits> & me); // "projects/library/seqan/file/stream.h"(351)
+inline Position<FILE *>::Type _streamTellP(FILE * me); // "projects/library/seqan/file/cstream.h"(172)
+
+//____________________________________________________________________________
+// _streamUnget
+
+template <typename TValue, typename TTraits> inline void _streamUnget(::std::basic_istream<TValue, TTraits> & source); // "projects/library/seqan/file/stream.h"(292)
+inline void _streamUnget(::std::FILE * stream); // "projects/library/seqan/file/cstream.h"(219)
+
+//____________________________________________________________________________
+// _streamWrite
+
+template <typename TTarget, typename T1, typename T2, typename TCompression> inline void _streamWrite(TTarget & target, Pair<T1, T2, TCompression> const & source); // "projects/library/seqan/file/stream_algorithms.h"(94)
+template <typename TTarget, typename T1, typename T2, typename T3, typename TCompression> inline void _streamWrite(TTarget & target, Triple<T1, T2, T3, TCompression> const & source); // "projects/library/seqan/file/stream_algorithms.h"(104)
+template <typename TTarget, typename TSource> inline void _streamWrite(TTarget & target, TSource const & source); // "projects/library/seqan/file/stream_algorithms.h"(128)
+
+//____________________________________________________________________________
+// _streamWriteRange
+
+template <typename TTarget, typename TIterator> inline void _streamWriteRange(TTarget & target, TIterator begin_, TIterator end_); // "projects/library/seqan/file/stream_algorithms.h"(193)
+
+//____________________________________________________________________________
+// _streamWriteSeq
+
+template <typename TTarget, typename TSource> inline void _streamWriteSeq(TTarget & target, TSource const & source, False const); // "projects/library/seqan/file/stream_algorithms.h"(140)
+template <typename TTarget, typename TSource> inline void _streamWriteSeq(TTarget & target, TSource const & source, True const); // "projects/library/seqan/file/stream_algorithms.h"(151)
+template <typename TTarget, typename TSourceValue> inline void _streamWriteSeq(TTarget & target, TSourceValue const * source, True const); // "projects/library/seqan/file/stream_algorithms.h"(168)
+
+//____________________________________________________________________________
+// _stream_appendLine
+
+template <typename TFile, typename TString, typename TChar> inline void _stream_appendLine(TFile & file, TString & str, TChar & c); // "projects/library/seqan/file/file_format.h"(432)
+
+//____________________________________________________________________________
+// _stream_countLine
+
+template <typename TFile, typename TChar> inline void _stream_countLine(TFile & file, TChar & c); // "projects/library/seqan/file/file_format.h"(464)
+
+//____________________________________________________________________________
+// _stream_isLetter
+
+template <typename TChar> inline bool _stream_isLetter(TChar const c); // "projects/library/seqan/file/file_format.h"(564)
+
+//____________________________________________________________________________
+// _stream_readWord
+
+template <typename TFile, typename TChar> inline String<char> _stream_readWord(TFile & file, TChar& c); // "projects/library/seqan/file/file_format.h"(548)
+
+//____________________________________________________________________________
+// _stream_skipLine
+
+template <typename TFile, typename TChar> inline typename Size<TFile>::Type _stream_skipLine(TFile & file, TChar & c); // "projects/library/seqan/file/file_format.h"(495)
+
+//____________________________________________________________________________
+// _stream_skipWhitespace
+
+template <typename TFile, typename TChar> inline void _stream_skipWhitespace(TFile& file, TChar& c); // "projects/library/seqan/file/file_format.h"(534)
+
+//____________________________________________________________________________
+// _string_appendLine
+
+template <typename TString1, typename TString2, typename TIter> inline void _string_appendLine(TString1 & str, TString2 & a_str, TIter & it); // "projects/library/seqan/file/file_format.h"(624)
+
+//____________________________________________________________________________
+// _string_readNumber
+
+template <typename TString, typename TIter> inline int _string_readNumber(TString & str, TIter& it); // "projects/library/seqan/file/file_format.h"(668)
+
+//____________________________________________________________________________
+// _string_skipLine
+
+template <typename TString, typename TIter> inline typename Size<TString>::Type _string_skipLine(TString & str, TIter & it); // "projects/library/seqan/file/file_format.h"(588)
+
+//____________________________________________________________________________
+// _string_skipWhitespace
+
+template <typename TString, typename TIter> inline void _string_skipWhitespace(TString& str, TIter& it); // "projects/library/seqan/file/file_format.h"(655)
+
+//____________________________________________________________________________
+// _write_impl
+
+template <typename TFile, typename TStringContainer, typename TSource, typename TSpec> void _write_impl(TFile& target, Align<TSource, TSpec>& align, TStringContainer& ids, CGViz); // "projects/library/seqan/file/file_format_cgviz.h"(62)
+template <typename TFile, typename TString, typename TData> void _write_impl(TFile & file, TData & data, TString & id, Fasta); // "projects/library/seqan/file/file_format_fasta.h"(434)
+template <typename TFile, typename TStringContainer, typename TSource, typename TSpec> void _write_impl(TFile& file, Align<TSource, TSpec>& align, TStringContainer& ids, FastaAlign); // "projects/library/seqan/file/file_format_fasta_align.h"(246)
+
+//____________________________________________________________________________
+// alignSize
+
+template <typename T1, typename T2> inline T1 alignSize(T1 _size, T2 _aligning); // "projects/library/seqan/file/file_base.h"(688)
+
+//____________________________________________________________________________
+// allocPage
+
+template <typename TValue, typename TSize, typename T > inline void allocPage(SimpleBuffer<TValue> &pf, TSize size, T const & me); // "projects/library/seqan/file/file_page.h"(119)
+template <typename TValue, typename TFile, typename TSpec, typename T > inline void allocPage(PageFrame<TValue, TFile, TSpec> &pf, T const & me); // "projects/library/seqan/file/file_page.h"(334)
+
+//____________________________________________________________________________
+// allocate
+
+template <__int64 _FileSize, typename TFile, typename TValue, typename TSize > inline void allocate(File< Chained<_FileSize, TFile> > const &me, TValue* &data, TSize count); // "projects/library/seqan/file/file_array.h"(340)
+template <unsigned _FileCount, typename TFile, typename TValue, typename TSize > inline void allocate(File< Striped<_FileCount, TFile> > const &me, TValue* &data, TSize count); // "projects/library/seqan/file/file_array.h"(350)
+
+//____________________________________________________________________________
+// append
+
+template <typename TValue, typename TConfig, typename TString, typename TExpand > inline void append(String<TValue, External<TConfig> > &me, TString const &string, Tag<TExpand> const expand); // "projects/library/seqan/file/string_external.h"(1895)
+template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand> inline void append(String<TTargetValue, TTargetSpec> & target, _ChunkCollector<TSourceHost> const & source, Tag<TExpand> const ); // "projects/library/seqan/file/chunk_collector.h"(390)
+template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand> inline void append(String<TTargetValue, TTargetSpec> & target, _ChunkCollector<TSourceHost> const & source, typename Size< String<TTargetValue, TTargetSpec> >::Type limit, Tag<TExpand> const ); // "projects/library/seqan/file/chunk_collector.h"(399)
+
+//____________________________________________________________________________
+// appendValue
+
+template <typename TValue, typename TConfig, typename TExpand > inline void appendValue(String<TValue, External<TConfig> > &me, TValue const &_Val, Tag<TExpand> const); // "projects/library/seqan/file/string_external.h"(1886)
+
+//____________________________________________________________________________
+// areadAt
+
+template <typename File, typename TValue, typename TSize, typename TPos, typename aRequest > inline bool areadAt(File & me, TValue *memPtr, TSize const count, TPos const fileOfs, aRequest &request); // "projects/library/seqan/file/file_base.h"(588)
+template <__int64 _FileSize, typename TFile, typename TValue, typename TSize, typename TOffset, typename TRequest > inline bool areadAt(File< Chained<_FileSize, TFile> > &me, TValue *memPtr, TSize count, TOffset offset, TRequest &req); // "projects/library/seqan/file/file_array.h"(392)
+
+//____________________________________________________________________________
+// assign
+
+template <typename TValue, typename TConfig, typename TSource, typename TExpand > inline void assign( String<TValue, External<TConfig> > &target, TSource const &source, Tag<TExpand> const); // "projects/library/seqan/file/string_external.h"(1937)
+template <typename THost, typename TSource> inline void assign(_ChunkCollector<THost> & target, TSource & source); // "projects/library/seqan/file/chunk_collector.h"(231)
+template <typename THost, typename TSource> inline void assign(_ChunkCollector<THost> & target, TSource const & source); // "projects/library/seqan/file/chunk_collector.h"(238)
+template <typename THost, typename TSource, typename TSize> inline void assign(_ChunkCollector<THost> & target, TSource & source, TSize limit); // "projects/library/seqan/file/chunk_collector.h"(247)
+template <typename THost, typename TSource, typename TSize> inline void assign(_ChunkCollector<THost> & target, TSource const & source, TSize limit); // "projects/library/seqan/file/chunk_collector.h"(255)
+template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand> inline void assign(String<TTargetValue, TTargetSpec> & target, _ChunkCollector<TSourceHost> const & source, Tag<TExpand> const tag); // "projects/library/seqan/file/chunk_collector.h"(316)
+template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand> inline void assign(String<TTargetValue, TTargetSpec> & target, _ChunkCollector<TSourceHost> const & source, typename Size< String<TTargetValue, TTargetSpec> >::Type limit, Tag<TExpand> const tag); // "projects/library/seqan/file/chunk_collector.h"(325)
+
+//____________________________________________________________________________
+// atBegin
+
+template <typename TContainer> inline bool atBegin(Iter<TContainer, FileReaderIterator> & it); // "projects/library/seqan/file/file_filereader.h"(760)
+template <typename TContainer> inline bool atBegin(Iter<TContainer, FileReaderIterator> const & it); // "projects/library/seqan/file/file_filereader.h"(766)
+template <typename TExtString> inline bool atBegin(VectorIterator<TExtString> &it); // "projects/library/seqan/file/string_external.h"(1650)
+template <typename TExtString> inline bool atBegin(VectorIterator<TExtString> const &it); // "projects/library/seqan/file/string_external.h"(1652)
+template <typename TExtString> inline bool atBegin(VectorConstIterator<TExtString> &it); // "projects/library/seqan/file/string_external.h"(1655)
+template <typename TExtString> inline bool atBegin(VectorConstIterator<TExtString> const &it); // "projects/library/seqan/file/string_external.h"(1657)
+template <typename TExtString> inline bool atBegin(VectorFwdIterator<TExtString> &it); // "projects/library/seqan/file/string_external.h"(1660)
+template <typename TExtString> inline bool atBegin(VectorFwdIterator<TExtString> const &it); // "projects/library/seqan/file/string_external.h"(1664)
+template <typename TExtString> inline bool atBegin(VectorFwdConstIterator<TExtString> &it); // "projects/library/seqan/file/string_external.h"(1669)
+template <typename TExtString> inline bool atBegin(VectorFwdConstIterator<TExtString> const &it); // "projects/library/seqan/file/string_external.h"(1673)
+
+//____________________________________________________________________________
+// atEnd
+
+template <typename TContainer> inline bool atEnd(Iter<TContainer, FileReaderIterator> & it); // "projects/library/seqan/file/file_filereader.h"(745)
+template <typename TContainer> inline bool atEnd(Iter<TContainer, FileReaderIterator> const & it); // "projects/library/seqan/file/file_filereader.h"(751)
+template <typename TExtString> inline bool atEnd(VectorIterator<TExtString> &it); // "projects/library/seqan/file/string_external.h"(1679)
+template <typename TExtString> inline bool atEnd(VectorIterator<TExtString> const &it); // "projects/library/seqan/file/string_external.h"(1681)
+template <typename TExtString> inline bool atEnd(VectorConstIterator<TExtString> &it); // "projects/library/seqan/file/string_external.h"(1684)
+template <typename TExtString> inline bool atEnd(VectorConstIterator<TExtString> const &it); // "projects/library/seqan/file/string_external.h"(1686)
+template <typename TExtString> inline bool atEnd(VectorFwdIterator<TExtString> &it); // "projects/library/seqan/file/string_external.h"(1689)
+template <typename TExtString> inline bool atEnd(VectorFwdIterator<TExtString> const &it); // "projects/library/seqan/file/string_external.h"(1693)
+template <typename TExtString> inline bool atEnd(VectorFwdConstIterator<TExtString> &it); // "projects/library/seqan/file/string_external.h"(1698)
+template <typename TExtString> inline bool atEnd(VectorFwdConstIterator<TExtString> const &it); // "projects/library/seqan/file/string_external.h"(1702)
+template <typename TFile, typename TFormat, typename TFile2, typename TSpec> inline bool atEnd(Iter<TFile, FileReader<TFormat, TFile2, TSpec> > & it); // "projects/library/seqan/file/file_filereaderiterator.h"(127)
+
+//____________________________________________________________________________
+// awriteAt
+
+template <typename File, typename TValue, typename TSize, typename TPos, typename aRequest > inline bool awriteAt(File & me, TValue const *memPtr, TSize const count, TPos const fileOfs, aRequest &request); // "projects/library/seqan/file/file_base.h"(612)
+template <__int64 _FileSize, typename TFile, typename TValue, typename TSize, typename TOffset, typename TRequest > inline bool awriteAt(File< Chained<_FileSize, TFile> > &me, TValue const *memPtr, TSize count, TOffset offset, TRequest &req); // "projects/library/seqan/file/file_array.h"(409)
+
+//____________________________________________________________________________
+// begin
+
+template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TIteratorSpec> inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> >, TIteratorSpec >::Type begin(String<TValue, FileReader<TFormat, TFile, TSpec> > & me, Tag<TIteratorSpec> const); // "projects/library/seqan/file/file_filereader.h"(340)
+template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TIteratorSpec> inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> > const, TIteratorSpec >::Type begin(String<TValue, FileReader<TFormat, TFile, TSpec> > const & me, Tag<TIteratorSpec> const); // "projects/library/seqan/file/file_filereader.h"(348)
+template <typename TValue, typename TConfig, typename TSpec > inline typename Iterator<String<TValue, External<TConfig> >, Tag<TSpec> const>::Type begin(String<TValue, External<TConfig> > &me, Tag<TSpec> const); // "projects/library/seqan/file/string_external.h"(1834)
+template <typename TValue, typename TConfig, typename TSpec > inline typename Iterator<String<TValue, External<TConfig> > const, Tag<TSpec> const>::Type begin(String<TValue, External<TConfig> > const &me, Tag<TSpec> const); // "projects/library/seqan/file/string_external.h"(1840)
+template <typename TValue > inline TValue* begin(SimpleBuffer<TValue> &pf, Standard); // "projects/library/seqan/file/file_page.h"(134)
+template <typename TValue > inline TValue const * begin(SimpleBuffer<TValue> const &pf, Standard); // "projects/library/seqan/file/file_page.h"(139)
+
+//____________________________________________________________________________
+// cancel
+
+template <typename TSpec, typename aRequest > inline bool cancel(File<TSpec> &, aRequest &); // "projects/library/seqan/file/file_base.h"(675)
+template <typename TValue, typename TFile, typename TSpec > inline bool cancel(PageFrame<TValue, TFile, TSpec> &pf, TFile &file); // "projects/library/seqan/file/file_page.h"(427)
+
+//____________________________________________________________________________
+// clear
+
+template <typename TValue, typename TConfig > inline void clear(String<TValue, External<TConfig> > &me); // "projects/library/seqan/file/string_external.h"(1710)
+
+//____________________________________________________________________________
+// close
+
+inline bool close(FILE* me); // "projects/library/seqan/file/file_cstyle.h"(103)
+template <typename TValue, typename TConfig > inline bool close(String<TValue, External<TConfig> > &me); // "projects/library/seqan/file/string_external.h"(1795)
+template <typename TSpec > inline bool close(File<TSpec> & me); // "projects/library/seqan/file/file_base.h"(261)
+template <__int64 _FileSize, typename TFile > inline bool close(File< Chained<_FileSize, TFile> > &me); // "projects/library/seqan/file/file_array.h"(315)
+template <unsigned _FileCount, typename TFile > inline bool close(File< Striped<_FileCount, TFile> > &me); // "projects/library/seqan/file/file_array.h"(322)
+
+//____________________________________________________________________________
+// container
+
+template <typename TContainer> inline TContainer & container(Iter<TContainer, FileReaderIterator> & it); // "projects/library/seqan/file/file_filereader.h"(573)
+template <typename TContainer> inline TContainer & container(Iter<TContainer, FileReaderIterator> const & it); // "projects/library/seqan/file/file_filereader.h"(579)
+template <typename TExtString> inline TExtString & container(VectorIterator<TExtString> &it); // "projects/library/seqan/file/string_external.h"(1629)
+template <typename TExtString> inline TExtString & container(VectorIterator<TExtString> const &it); // "projects/library/seqan/file/string_external.h"(1631)
+template <typename TExtString> inline TExtString & container(VectorConstIterator<TExtString> &it); // "projects/library/seqan/file/string_external.h"(1634)
+template <typename TExtString> inline TExtString & container(VectorConstIterator<TExtString> const &it); // "projects/library/seqan/file/string_external.h"(1636)
+template <typename TExtString> inline TExtString & container(VectorFwdIterator<TExtString> &it); // "projects/library/seqan/file/string_external.h"(1639)
+template <typename TExtString> inline TExtString & container(VectorFwdIterator<TExtString> const &it); // "projects/library/seqan/file/string_external.h"(1641)
+template <typename TExtString> inline TExtString & container(VectorFwdConstIterator<TExtString> &it); // "projects/library/seqan/file/string_external.h"(1644)
+template <typename TExtString> inline TExtString & container(VectorFwdConstIterator<TExtString> const &it); // "projects/library/seqan/file/string_external.h"(1646)
+
+//____________________________________________________________________________
+// deallocate
+
+template <__int64 _FileSize, typename TFile, typename TValue, typename TSize > inline void deallocate(File< Chained<_FileSize, TFile> > const &me, TValue* &data, TSize count); // "projects/library/seqan/file/file_array.h"(345)
+template <unsigned _FileCount, typename TFile, typename TValue, typename TSize > inline void deallocate(File< Striped<_FileCount, TFile> > const &me, TValue* &data, TSize count); // "projects/library/seqan/file/file_array.h"(355)
+
+//____________________________________________________________________________
+// enclosingBlocks
+
+template <typename T1, typename T2> inline T1 enclosingBlocks(T1 _size, T2 _blockSize); // "projects/library/seqan/file/file_base.h"(683)
+
+//____________________________________________________________________________
+// end
+
+template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TIteratorSpec> inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> >, TIteratorSpec >::Type end(String<TValue, FileReader<TFormat, TFile, TSpec> > & me, Tag<TIteratorSpec> const); // "projects/library/seqan/file/file_filereader.h"(360)
+template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TIteratorSpec> inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> > const, TIteratorSpec >::Type end(String<TValue, FileReader<TFormat, TFile, TSpec> > const & me, Tag<TIteratorSpec> const); // "projects/library/seqan/file/file_filereader.h"(368)
+template <typename TValue, typename TConfig, typename TSpec > inline typename Iterator<String<TValue, External<TConfig> >, Tag<TSpec> const>::Type end(String<TValue, External<TConfig> > &me, Tag<TSpec> const); // "projects/library/seqan/file/string_external.h"(1846)
+template <typename TValue, typename TConfig, typename TSpec > inline typename Iterator<String<TValue, External<TConfig> > const, Tag<TSpec> const>::Type end(String<TValue, External<TConfig> > const &me, Tag<TSpec> const); // "projects/library/seqan/file/string_external.h"(1853)
+template <typename TValue > inline TValue * end(SimpleBuffer<TValue> &pf, Standard); // "projects/library/seqan/file/file_page.h"(144)
+template <typename TValue > inline TValue const * end(SimpleBuffer<TValue> const &pf, Standard); // "projects/library/seqan/file/file_page.h"(149)
+
+//____________________________________________________________________________
+// equiDistantAlignedDistribution
+
+template <typename TValue, typename TSize, typename T, class Function > inline unsigned equiDistantAlignedDistribution( SimpleBuffer<TValue> &_clusterBuffer, unsigned aligning, unsigned _bufferSize, T const &me, TSize _size, unsigned _pageSize, Function const &_Func); // "projects/library/seqan/file/file_page.h"(934)
+
+//____________________________________________________________________________
+// equiDistantDistribution
+
+template <typename TValue, typename TSize, typename T, class Function > inline bool equiDistantDistribution( SimpleBuffer<TValue> &_clusterBuffer, unsigned _bufferSize, T const &me, TSize _size, unsigned _pageSize, Function const &_Func); // "projects/library/seqan/file/file_page.h"(872)
+
+//____________________________________________________________________________
+// flush
+
+inline bool flush(FILE*); // "projects/library/seqan/file/file_cstyle.h"(182)
+template <typename TValue, typename TConfig > inline void flush(String<TValue, External<TConfig> > &me); // "projects/library/seqan/file/string_external.h"(1722)
+template <typename TSpec > inline void flush(File<TSpec> &); // "projects/library/seqan/file/file_base.h"(631)
+
+//____________________________________________________________________________
+// formatID
+
+template <typename TFile, typename TData, typename TMeta, typename TFormat> inline void * formatID(FileFormat<TFile, TData, TMeta, TFormat> const & file_format); // "projects/library/seqan/file/file_format.h"(171)
+
+//____________________________________________________________________________
+// freePage
+
+template <typename TValue, typename T > inline void freePage(SimpleBuffer<TValue> &pf, T const & me); // "projects/library/seqan/file/file_page.h"(126)
+template <typename TValue, typename TFile, typename TSpec, typename T > inline void freePage(PageFrame<TValue, TFile, TSpec> &pf, T const & me); // "projects/library/seqan/file/file_page.h"(344)
+
+//____________________________________________________________________________
+// getValue
+
+template <typename TContainer> inline typename GetValue<Iter<TContainer, FileReaderIterator> >::Type getValue(Iter<TContainer, FileReaderIterator> & it); // "projects/library/seqan/file/file_filereader.h"(533)
+template <typename TContainer> inline typename GetValue<Iter<TContainer, FileReaderIterator> >::Type getValue(Iter<TContainer, FileReaderIterator> const & it); // "projects/library/seqan/file/file_filereader.h"(544)
+template <typename TFile, typename TFormat, typename TFile2, typename TSpec> inline typename GetValue<Iter<TFile, FileReader<TFormat, TFile2, TSpec> > >::Type getValue(Iter<TFile, FileReader<TFormat, TFile2, TSpec> > & it); // "projects/library/seqan/file/file_filereaderiterator.h"(120)
+
+//____________________________________________________________________________
+// goBegin
+
+template <typename TContainer> inline void goBegin(Iter<TContainer, FileReaderIterator> & it); // "projects/library/seqan/file/file_filereader.h"(711)
+template <typename TFile, typename TFile2, typename TSpec> inline void goBegin(Iter<TFile, FileReader<Fasta, TFile2, TSpec> > & it, bool skip_meta); // "projects/library/seqan/file/file_format_fasta.h"(45)
+template <typename TFile, typename TFile2, typename TSpec> inline void goBegin(Iter<TFile, FileReader<Fasta, TFile2, TSpec> > & it); // "projects/library/seqan/file/file_format_fasta.h"(82)
+template <typename TFile, typename TFile2, typename TSpec> inline void goBegin(Iter<TFile, FileReader<Genbank, TFile2, TSpec> > & it, bool skip_meta ); // "projects/library/seqan/file/file_format_genbank.h"(46)
+template <typename TFile, typename TFile2, typename TSpec> inline void goBegin(Iter<TFile, FileReader<Embl, TFile2, TSpec> > & it, bool skip_meta ); // "projects/library/seqan/file/file_format_embl.h"(47)
+
+//____________________________________________________________________________
+// goEnd
+
+template <typename TContainer> inline void goEnd(Iter<TContainer, FileReaderIterator> & it); // "projects/library/seqan/file/file_filereader.h"(733)
+
+//____________________________________________________________________________
+// goNext
+
+template <typename TFile> void goNext(TFile & file, CGViz); // "projects/library/seqan/file/file_format_cgviz.h"(48)
+template <typename TFile> void goNext(TFile & file, Raw); // "projects/library/seqan/file/file_format_raw.h"(247)
+template <typename TContainer> inline void goNext(Iter<TContainer, FileReaderIterator> & it); // "projects/library/seqan/file/file_filereader.h"(645)
+template <typename TFile, typename TFile2, typename TSpec> inline void goNext(Iter<TFile, FileReader<Fasta, TFile2, TSpec> > & it); // "projects/library/seqan/file/file_format_fasta.h"(90)
+template <typename TFile> void goNext(TFile & file, Fasta); // "projects/library/seqan/file/file_format_fasta.h"(390)
+template <typename TFile, typename TFile2, typename TSpec> inline void goNext(Iter<TFile, FileReader<Genbank, TFile2, TSpec> > & it); // "projects/library/seqan/file/file_format_genbank.h"(124)
+template <typename TFile> inline void goNext(TFile & file, Genbank); // "projects/library/seqan/file/file_format_genbank.h"(254)
+template <typename TFile> void goNext(TFile & file, FastaAlign); // "projects/library/seqan/file/file_format_fasta_align.h"(233)
+template <typename TFile, typename TData, typename TMeta, typename TFormat> inline void goNext(TFile & file, FileFormat<TFile, TData, TMeta, TFormat> const & file_format); // "projects/library/seqan/file/file_format.h"(251)
+template <typename TFile, typename TFile2, typename TSpec> inline void goNext(Iter<TFile, FileReader<Embl, TFile2, TSpec> > & it); // "projects/library/seqan/file/file_format_embl.h"(108)
+template <typename TFile> inline void goNext(TFile & file, Embl); // "projects/library/seqan/file/file_format_embl.h"(427)
+
+//____________________________________________________________________________
+// goPrevious
+
+template <typename TContainer> inline void goPrevious(Iter<TContainer, FileReaderIterator> & it); // "projects/library/seqan/file/file_filereader.h"(677)
+
+//____________________________________________________________________________
+// guessFileFormat
+
+template <typename TFile, typename TData, typename TMeta> inline FileFormat<TFile, TData, TMeta, void> & guessFileFormat(TFile & file, TData & data); // "projects/library/seqan/file/file_format_guess.h"(52)
+
+//____________________________________________________________________________
+// host
+
+template <typename TFile, typename TFormat, typename TFile2, typename TSpec> inline TFile & host(Iter<TFile, FileReader<TFormat, TFile2, TSpec> > & it); // "projects/library/seqan/file/file_filereaderiterator.h"(105)
+
+//____________________________________________________________________________
+// id
+
+template <typename TValue, typename TFormat, typename TFile, typename TSpec> inline void const * id(String<TValue, FileReader<TFormat, TFile, TSpec> > const & me); // "projects/library/seqan/file/file_filereader.h"(301)
+template <typename TValue, typename TConfig > inline void const * id(String<TValue, External<TConfig> > const &me); // "projects/library/seqan/file/string_external.h"(1958)
+
+//____________________________________________________________________________
+// iterator
+
+template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TPosition, typename TIteratorSpec> inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> >, TIteratorSpec >::Type iterator(String<TValue, FileReader<TFormat, TFile, TSpec> > & me, TPosition pos, Tag<TIteratorSpec> const); // "projects/library/seqan/file/file_filereader.h"(381)
+template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TPosition, typename TIteratorSpec> inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> > const, TIteratorSpec >::Type iterator(String<TValue, FileReader<TFormat, TFile, TSpec> > const & me, TPosition pos, Tag<TIteratorSpec> const); // "projects/library/seqan/file/file_filereader.h"(390)
+
+//____________________________________________________________________________
+// length
+
+template <typename TValue, typename TFormat, typename TFile, typename TSpec> inline typename Size< String<TValue, FileReader<TFormat, TFile, TSpec> > >::Type length(String<TValue, FileReader<TFormat, TFile, TSpec> > & me); // "projects/library/seqan/file/file_filereader.h"(328)
+template <typename TValue, typename TConfig > inline typename Size< String<TValue, External<TConfig> > >::Type length(String<TValue, External<TConfig> > const &me); // "projects/library/seqan/file/string_external.h"(1803)
+template <typename TValue > inline typename Size<SimpleBuffer<TValue> >::Type length(SimpleBuffer<TValue> const &me); // "projects/library/seqan/file/file_page.h"(109)
+template <typename TValue, typename TFile, unsigned _PageSize > inline typename Size<PageFrame<TValue, TFile, Fixed<_PageSize> > >::Type length(PageFrame<TValue, TFile, Fixed<_PageSize> > const & ); // "projects/library/seqan/file/file_page.h"(286)
+template <__int64 _FileSize, typename TFile > inline unsigned length(File< Chained<_FileSize, TFile> > const &me); // "projects/library/seqan/file/file_array.h"(284)
+template <unsigned _FileCount, typename TFile > inline unsigned length(File< Striped<_FileCount, TFile> > const &me); // "projects/library/seqan/file/file_array.h"(289)
+template <typename TFile, typename TData, typename TMeta, typename TFormat> inline void length(TFile & file, FileFormat<TFile, TData, TMeta, TFormat> const & file_format); // "projects/library/seqan/file/file_format.h"(267)
+
+//____________________________________________________________________________
+// open
+
+inline bool open(FILE* &me, const char *fileName, int openMode); // "projects/library/seqan/file/file_cstyle.h"(89)
+inline bool open(FILE* &me, const char *fileName); // "projects/library/seqan/file/file_cstyle.h"(94)
+template <typename TValue, typename TConfig > inline bool open(String<TValue, External<TConfig> > &me, const char *fileName, int openMode); // "projects/library/seqan/file/string_external.h"(1734)
+template <typename TValue, typename TConfig > inline bool open(String<TValue, External<TConfig> > &me, const char *fileName); // "projects/library/seqan/file/string_external.h"(1740)
+template <typename TValue, typename TConfig > inline bool open(String<TValue, External<TConfig> > &me, typename TConfig::TFile file); // "projects/library/seqan/file/string_external.h"(1746)
+template <typename TSpec > inline bool open(File<TSpec> &me, const char *fileName, int openMode); // "projects/library/seqan/file/file_base.h"(215)
+template <typename TSpec > inline bool open(File<TSpec> &me, const char *fileName); // "projects/library/seqan/file/file_base.h"(220)
+template <__int64 _FileSize, typename TFile > inline bool open(File< Chained<_FileSize, TFile> > &me, const char *fileName, int openMode); // "projects/library/seqan/file/file_array.h"(294)
+
+//____________________________________________________________________________
+// openTemp
+
+inline bool openTemp(FILE* &me); // "projects/library/seqan/file/file_cstyle.h"(98)
+template <typename TValue, typename TConfig > inline bool openTemp(String<TValue, External<TConfig> > &me); // "projects/library/seqan/file/string_external.h"(1758)
+template <typename TSpec > inline bool openTemp(File<TSpec> &me); // "projects/library/seqan/file/file_base.h"(237)
+template <typename TSpec > inline bool openTemp(File<TSpec> &me, int openMode); // "projects/library/seqan/file/file_base.h"(242)
+template <__int64 _FileSize, typename TFile > inline bool openTemp(File< Chained<_FileSize, TFile> > &me, int openMode); // "projects/library/seqan/file/file_array.h"(303)
+template <unsigned _FileCount, typename TFile > inline bool openTemp(File< Striped<_FileCount, TFile> > &me, int openMode); // "projects/library/seqan/file/file_array.h"(310)
+
+//____________________________________________________________________________
+// operator!=
+
+template <typename TContainer> inline bool operator!= (Iter<TContainer, FileReaderIterator> const & left, Iter<TContainer, FileReaderIterator> const & right); // "projects/library/seqan/file/file_filereader.h"(791)
+template <typename TFileLeft, typename TDataLeft, typename TMetaLeft, typename TFormatLeft, typename TFileRight, typename TDataRight, typename TMetaRight, typename TFormatRight> inline bool operator!= (FileFormat<TFileLeft, TDataLeft, TMetaLeft, TFormatLeft> const & left, FileFormat<TFileRight, TDataRight, TMetaRight, TFormatRight> const & right); // "projects/library/seqan/file/file_format.h"(348)
+template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TFormat2> inline bool operator!= (FileFormat<TFile, TData, TMeta, TFormat> const & left, Tag<TFormat2> const); // "projects/library/seqan/file/file_format.h"(357)
+template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TFormat2> inline bool operator!= (Tag<TFormat2> const, FileFormat<TFile, TData, TMeta, TFormat> const & right); // "projects/library/seqan/file/file_format.h"(366)
+
+//____________________________________________________________________________
+// operator+
+
+template <typename TContainer, typename TIntegral> inline Iter<TContainer, FileReaderIterator> operator+ (Iter<TContainer, FileReaderIterator> const & left, TIntegral right); // "projects/library/seqan/file/file_filereader.h"(848)
+template <typename TContainer, typename TIntegral> inline Iter<TContainer, FileReaderIterator> operator+ (TIntegral left, Iter<TContainer, FileReaderIterator> const & right); // "projects/library/seqan/file/file_filereader.h"(856)
+
+//____________________________________________________________________________
+// operator+=
+
+template <typename TContainer, typename TIntegral> inline Iter<TContainer, FileReaderIterator> & operator+= (Iter<TContainer, FileReaderIterator> & left, TIntegral right); // "projects/library/seqan/file/file_filereader.h"(869)
+
+//____________________________________________________________________________
+// operator-
+
+template <typename TContainer, typename TIntegral> inline Iter<TContainer, FileReaderIterator> operator- (Iter<TContainer, FileReaderIterator> const & left, TIntegral right); // "projects/library/seqan/file/file_filereader.h"(887)
+template <typename TContainer> inline typename Difference<Iter<TContainer, FileReaderIterator> >::Type operator- (Iter<TContainer, FileReaderIterator> const & left, Iter<TContainer, FileReaderIterator> const & right); // "projects/library/seqan/file/file_filereader.h"(898)
+
+//____________________________________________________________________________
+// operator-=
+
+template <typename TContainer, typename TIntegral> inline Iter<TContainer, FileReaderIterator> & operator-= (Iter<TContainer, FileReaderIterator> & left, TIntegral right); // "projects/library/seqan/file/file_filereader.h"(911)
+
+//____________________________________________________________________________
+// operator<
+
+template <typename TContainer> inline bool operator< (Iter<TContainer, FileReaderIterator> const & left, Iter<TContainer, FileReaderIterator> const & right); // "projects/library/seqan/file/file_filereader.h"(804)
+
+//____________________________________________________________________________
+// operator<<
+
+template <typename TValue > ::std::ostream& operator<<(::std::ostream &out, const PageBucketExtended<TValue> &pb); // "projects/library/seqan/file/file_page.h"(170)
+template <typename TValue, typename TFile, typename TSpec > ::std::ostream& operator<<(::std::ostream &out, const PageFrame<TValue, TFile, TSpec > &pf); // "projects/library/seqan/file/file_page.h"(304)
+
+//____________________________________________________________________________
+// operator<=
+
+template <typename TContainer> inline bool operator<= (Iter<TContainer, FileReaderIterator> const & left, Iter<TContainer, FileReaderIterator> const & right); // "projects/library/seqan/file/file_filereader.h"(826)
+
+//____________________________________________________________________________
+// operator==
+
+template <typename TContainer> inline bool operator== (Iter<TContainer, FileReaderIterator> const & left, Iter<TContainer, FileReaderIterator> const & right); // "projects/library/seqan/file/file_filereader.h"(778)
+template <typename TFileLeft, typename TDataLeft, typename TMetaLeft, typename TFormatLeft, typename TFileRight, typename TDataRight, typename TMetaRight, typename TFormatRight> inline bool operator== (FileFormat<TFileLeft, TDataLeft, TMetaLeft, TFormatLeft> const & left, FileFormat<TFileRight, TDataRight, TMetaRight, TFormatRight> const & right); // "projects/library/seqan/file/file_format.h"(319)
+template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TFormat2> inline bool operator== (FileFormat<TFile, TData, TMeta, TFormat> const & left, Tag<TFormat2> const); // "projects/library/seqan/file/file_format.h"(328)
+template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TFormat2> inline bool operator== (Tag<TFormat2> const, FileFormat<TFile, TData, TMeta, TFormat> const & right); // "projects/library/seqan/file/file_format.h"(337)
+
+//____________________________________________________________________________
+// operator>
+
+template <typename TContainer> inline bool operator> (Iter<TContainer, FileReaderIterator> const & left, Iter<TContainer, FileReaderIterator> const & right); // "projects/library/seqan/file/file_filereader.h"(813)
+
+//____________________________________________________________________________
+// operator>=
+
+template <typename TContainer> inline bool operator>= (Iter<TContainer, FileReaderIterator> const & left, Iter<TContainer, FileReaderIterator> const & right); // "projects/library/seqan/file/file_filereader.h"(835)
+
+//____________________________________________________________________________
+// pageSize
+
+template <typename TValue > inline typename Size<SimpleBuffer<TValue> >::Type pageSize(SimpleBuffer<TValue> &me); // "projects/library/seqan/file/file_page.h"(92)
+template <typename TValue, typename TFile, unsigned _PageSize > inline typename Size<PageFrame<TValue, TFile, Fixed<_PageSize> > >::Type pageSize(PageFrame<TValue, TFile, Fixed<_PageSize> > & ); // "projects/library/seqan/file/file_page.h"(292)
+
+//____________________________________________________________________________
+// position
+
+template <typename TContainer> inline typename Position<Iter<TContainer, FileReaderIterator> >::Type position(Iter<TContainer, FileReaderIterator> const & it); // "projects/library/seqan/file/file_filereader.h"(588)
+
+//____________________________________________________________________________
+// push_back
+
+template <typename TValue, typename TConfig > inline void push_back(String<TValue, External<TConfig> > &me, TValue const &_Val); // "projects/library/seqan/file/string_external.h"(1877)
+
+//____________________________________________________________________________
+// read
+
+template <typename TFile, typename TData> void read(TFile & file, TData & data, Raw); // "projects/library/seqan/file/file_format_raw.h"(191)
+template <typename TFile, typename TData, typename TSize> void read(TFile & file, TData & data, TSize limit, Raw); // "projects/library/seqan/file/file_format_raw.h"(204)
+template <typename TFile, typename TData> void read(TFile & file, TData & data); // "projects/library/seqan/file/file_format_raw.h"(307)
+template <typename TFile, typename TData, typename TSize> void read(TFile & file, TData & data, TSize limit); // "projects/library/seqan/file/file_format_raw.h"(316)
+template <typename TValue, typename TSize > inline bool read(FILE* me, TValue *memPtr, TSize const count); // "projects/library/seqan/file/file_cstyle.h"(127)
+template <typename TFile, typename TData, typename TSize> void read(TFile & file, TData & data, TSize limit, Fasta); // "projects/library/seqan/file/file_format_fasta.h"(206)
+template <typename TFile, typename TData> void read(TFile & file, TData & data, Fasta tag); // "projects/library/seqan/file/file_format_fasta.h"(306)
+template <typename TSpec, typename TValue, typename TSize > inline bool read(File<TSpec> & me, TValue *memPtr, TSize const count); // "projects/library/seqan/file/file_base.h"(288)
+template <typename TFile, typename TData> inline void read(TFile & file, TData & data, Genbank); // "projects/library/seqan/file/file_format_genbank.h"(170)
+template <typename TFile, typename TData, typename TSize> inline void read(TFile & file, TData & data, TSize limit, Genbank); // "projects/library/seqan/file/file_format_genbank.h"(188)
+template <typename TFile, typename TSource, typename TSpec> void read(TFile & file, Align<TSource, TSpec> & align, FastaAlign); // "projects/library/seqan/file/file_format_fasta_align.h"(72)
+template <typename TFile, typename TData, typename TMeta, typename TFormat> inline void read(TFile & file, TData & data, FileFormat<TFile, TData, TMeta, TFormat> const & file_format); // "projects/library/seqan/file/file_format.h"(200)
+template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TSize> inline void read(TFile & file, TData & data, TSize limit, FileFormat<TFile, TData, TMeta, TFormat> const & file_format); // "projects/library/seqan/file/file_format.h"(211)
+template <typename TFile, typename TData> inline void read(TFile & file, TData & data, Embl); // "projects/library/seqan/file/file_format_embl.h"(153)
+template <typename TFile, typename TData, typename TSize> inline void read(TFile & file, TData & data, TSize limit, Embl); // "projects/library/seqan/file/file_format_embl.h"(171)
+
+//____________________________________________________________________________
+// readAt
+
+template <typename TValue, typename TSize, typename TPos > inline bool readAt(FILE* me, TValue *memPtr, TSize const count, TPos const fileOfs); // "projects/library/seqan/file/file_cstyle.h"(145)
+template <typename TFile, typename TValue, typename TSize, typename TPos > inline bool readAt(TFile & me, TValue *memPtr, TSize const count, TPos const fileOfs); // "projects/library/seqan/file/file_base.h"(324)
+template <__int64 _FileSize, typename TFile, typename TValue, typename TSize, typename TOffset > inline bool readAt(File< Chained<_FileSize, TFile> > &me, TValue *memPtr, TSize count, TOffset offset); // "projects/library/seqan/file/file_array.h"(364)
+
+//____________________________________________________________________________
+// readBucket
+
+template <typename TValue, unsigned _FileCount, typename TFile > inline unsigned readBucket( PageBucket<TValue> &b, int pageNo, unsigned pageSize, unsigned dataSize, File< Striped<_FileCount, TFile> > &file); // "projects/library/seqan/file/file_page_raid0.h"(134)
+template <typename TValue, typename TFile > inline unsigned readBucket(PageBucket<TValue> &b, int pageNo, unsigned pageSize, unsigned dataSize, TFile &file); // "projects/library/seqan/file/file_page.h"(456)
+
+//____________________________________________________________________________
+// readFeature
+
+template <typename TData, typename TKey, typename TString> inline typename Position<TString>::Type readFeature(TString & str, typename Position<TString>::Type start_pos, TData & data, TKey key, Embl); // "projects/library/seqan/file/file_format_embl.h"(372)
+
+//____________________________________________________________________________
+// readID
+
+template <typename TFile, typename TString> void readID(TFile & , TString & id, Raw); // "projects/library/seqan/file/file_format_raw.h"(219)
+template <typename TFile, typename TString> void readID(TFile & file, TString & id, Fasta); // "projects/library/seqan/file/file_format_fasta.h"(324)
+
+//____________________________________________________________________________
+// readIDs
+
+template <typename TFile, typename TStringContainer> void readIDs(TFile& file, TStringContainer& ids, FastaAlign); // "projects/library/seqan/file/file_format_fasta_align.h"(178)
+
+//____________________________________________________________________________
+// readLastPage
+
+template <typename TValue, unsigned _FileCount, typename TFile, typename TSpec, typename TSize > inline bool readLastPage( int pageNo, PageFrame<TValue, File< Striped<_FileCount, TFile> >, TSpec> &pf, File< Striped<_FileCount, TFile> > &file, TSize size); // "projects/library/seqan/file/file_page_raid0.h"(84)
+template <typename TValue, typename TFile, typename TSpec, typename TSize> inline bool readLastPage(int pageNo, PageFrame<TValue, TFile, TSpec> &pf, TFile &file, TSize size); // "projects/library/seqan/file/file_page.h"(381)
+
+//____________________________________________________________________________
+// readLineType
+
+template <typename TFile, typename TData, typename TKey> inline void readLineType(TFile & file, TData & data, TKey key, Embl); // "projects/library/seqan/file/file_format_embl.h"(248)
+template <typename TData, typename TValue, typename TSpec, typename TKey> inline void readLineType(String<TValue,TSpec> & meta, TData & data, TKey key, Embl); // "projects/library/seqan/file/file_format_embl.h"(305)
+
+//____________________________________________________________________________
+// readMeta
+
+template <typename TFile, typename TMeta> void readMeta(TFile & file, TMeta & meta, Raw); // "projects/library/seqan/file/file_format_raw.h"(233)
+template <typename TFile, typename TMeta> void readMeta(TFile & file, TMeta & meta, Fasta); // "projects/library/seqan/file/file_format_fasta.h"(376)
+template <typename TFile, typename TMeta> inline void readMeta(TFile & file, TMeta & meta, Genbank); // "projects/library/seqan/file/file_format_genbank.h"(212)
+template <typename TFile, typename TMeta> void readMeta(TFile & file, TMeta & meta, FastaAlign); // "projects/library/seqan/file/file_format_fasta_align.h"(223)
+template <typename TFile, typename TData, typename TMeta, typename TFormat> inline void readMeta(TFile & file, TMeta & meta, FileFormat<TFile, TData, TMeta, TFormat> const & file_format); // "projects/library/seqan/file/file_format.h"(235)
+template <typename TFile, typename TMeta> inline void readMeta(TFile & file, TMeta & meta, Embl); // "projects/library/seqan/file/file_format_embl.h"(194)
+
+//____________________________________________________________________________
+// readPage
+
+template <typename TValue, unsigned _FileCount, typename TFile, typename TSpec > inline bool readPage( int pageNo, PageFrame<TValue, File< Striped<_FileCount, TFile> >, TSpec> &pf, File< Striped<_FileCount, TFile> > &file); // "projects/library/seqan/file/file_page_raid0.h"(40)
+template <typename TValue, typename TFile, typename TSpec > inline bool readPage(int pageNo, PageFrame<TValue, TFile, TSpec> &pf, TFile &file); // "projects/library/seqan/file/file_page.h"(356)
+template <typename TValue, typename TFile, typename TSpec > inline bool readPage(PageFrame<TValue, TFile, Dynamic<TSpec> > &pf, TFile &file); // "projects/library/seqan/file/file_page.h"(440)
+
+//____________________________________________________________________________
+// release
+
+template <typename aRequest > inline void release(FILE*, aRequest &); // "projects/library/seqan/file/file_cstyle.h"(187)
+template <typename TSpec, typename aRequest > inline void release(File<TSpec> &, aRequest &); // "projects/library/seqan/file/file_base.h"(659)
+
+//____________________________________________________________________________
+// reopen
+
+template <typename File > inline void reopen(File &, int); // "projects/library/seqan/file/file_base.h"(247)
+
+//____________________________________________________________________________
+// replace
+
+template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand> inline void replace(String<TTargetValue, TTargetSpec> & target, typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin, typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end, _ChunkCollector<TSourceHost> const & source, Tag<TExpand> const tag); // "projects/library/seqan/file/chunk_collector.h"(465)
+template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand> inline void replace(String<TTargetValue, TTargetSpec> & target, typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin, typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end, _ChunkCollector<TSourceHost> const & source, typename Size< String<TTargetValue, TTargetSpec> >::Type limit, Tag<TExpand> const tag); // "projects/library/seqan/file/chunk_collector.h"(477)
+template <typename TTargetValue, typename TSourceHost, typename TExpand> inline void replace(TTargetValue * target, size_t pos_begin, size_t pos_end, _ChunkCollector<TSourceHost> const & source, Tag<TExpand> const tag); // "projects/library/seqan/file/chunk_collector.h"(490)
+template <typename TTargetValue, typename TSourceHost, typename TExpand> inline void replace(TTargetValue * target, size_t pos_begin, size_t pos_end, _ChunkCollector<TSourceHost> const & source, size_t limit, Tag<TExpand> const tag); // "projects/library/seqan/file/chunk_collector.h"(502)
+
+//____________________________________________________________________________
+// reserve
+
+template <typename TValue, typename TConfig, typename TSize, typename TExpand > inline typename Size< String<TValue, External<TConfig> > >::Type reserve( String<TValue, External<TConfig> > &me, TSize new_capacity, Tag<TExpand> const); // "projects/library/seqan/file/string_external.h"(1826)
+
+//____________________________________________________________________________
+// resize
+
+template <typename TSize > inline void resize(FILE* me, TSize new_length); // "projects/library/seqan/file/file_cstyle.h"(176)
+template <typename TValue, typename TConfig, typename TSize, typename TExpand > inline typename Size< String<TValue, External<TConfig> > >::Type resize( String<TValue, External<TConfig> > &me, TSize new_length, Tag<TExpand> const); // "projects/library/seqan/file/string_external.h"(1814)
+template <typename TSpec, typename TSize > inline void resize(File<TSpec> &me, TSize new_length); // "projects/library/seqan/file/file_base.h"(443)
+template <typename TValue, typename TSize > inline void resize(SimpleBuffer<TValue> &me, TSize size); // "projects/library/seqan/file/file_page.h"(114)
+template <typename TValue, typename TFile, typename TSpec, typename TSize > inline void resize(PageFrame<TValue, TFile, Dynamic<TSpec> > &me, TSize size); // "projects/library/seqan/file/file_page.h"(274)
+template <typename TValue, typename TFile, unsigned _PageSize, typename TSize > inline void resize(PageFrame<TValue, TFile, Fixed<_PageSize> > & , TSize ); // "projects/library/seqan/file/file_page.h"(297)
+template <__int64 _FileSize, typename TFile, typename TSize > inline void resize(File< Chained<_FileSize, TFile> > &me, TSize new_length); // "projects/library/seqan/file/file_array.h"(335)
+
+//____________________________________________________________________________
+// rewind
+
+template <typename File > inline void rewind(File &me); // "projects/library/seqan/file/file_base.h"(411)
+
+//____________________________________________________________________________
+// save
+
+template <typename TValue, typename TConfig > inline bool save(String<TValue, External<TConfig> > const &me, const char *fileName, int openMode); // "projects/library/seqan/file/string_external.h"(1765)
+template <typename TValue, typename TConfig > inline bool save(String<TValue, External<TConfig> > const &me, const char *fileName); // "projects/library/seqan/file/string_external.h"(1773)
+template <typename TValue, typename TConfig > inline bool save(String<TValue, External<TConfig> > const &me, typename TConfig::TFile file); // "projects/library/seqan/file/string_external.h"(1781)
+
+//____________________________________________________________________________
+// sectorSize
+
+inline unsigned sectorSize(FILE* const &); // "projects/library/seqan/file/file_cstyle.h"(108)
+template <typename TSpec > inline unsigned sectorSize(File<TSpec> const & ); // "projects/library/seqan/file/file_base.h"(266)
+
+//____________________________________________________________________________
+// seek
+
+template <typename TPos > inline Size<FILE*>::Type seek(FILE* me, TPos const fileOfs, int origin); // "projects/library/seqan/file/file_cstyle.h"(113)
+template <typename TPos > inline Size<FILE*>::Type seek(FILE* me, TPos const fileOfs); // "projects/library/seqan/file/file_cstyle.h"(118)
+template <typename TSpec, typename TPos > inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const fileOfs, int origin); // "projects/library/seqan/file/file_base.h"(370)
+template <typename TSpec, typename TPos > inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const fileOfs); // "projects/library/seqan/file/file_base.h"(382)
+
+//____________________________________________________________________________
+// setEOF
+
+template <typename TSpec > inline bool setEOF(File<TSpec> & ); // "projects/library/seqan/file/file_base.h"(460)
+
+//____________________________________________________________________________
+// setPageSize
+
+template <typename TValue, typename TSize > inline void setPageSize(SimpleBuffer<TValue> &me, TSize size); // "projects/library/seqan/file/file_page.h"(97)
+
+//____________________________________________________________________________
+// setPosition
+
+template <typename TContainer, typename TPos> inline void setPosition(Iter<TContainer, FileReaderIterator> & it, TPos pos); // "projects/library/seqan/file/file_filereader.h"(613)
+
+//____________________________________________________________________________
+// size
+
+inline Size<FILE*>::Type size(FILE* me); // "projects/library/seqan/file/file_cstyle.h"(166)
+template <typename TSpec > inline typename Size<File<TSpec> >::Type size(File<TSpec> &me); // "projects/library/seqan/file/file_base.h"(426)
+template <typename TValue > inline typename Size<SimpleBuffer<TValue> >::Type size(SimpleBuffer<TValue> const &me); // "projects/library/seqan/file/file_page.h"(103)
+template <typename TValue, typename TFile, unsigned _PageSize > inline typename Size<PageFrame<TValue, TFile, Fixed<_PageSize> > >::Type size(PageFrame<TValue, TFile, Fixed<_PageSize> > & ); // "projects/library/seqan/file/file_page.h"(280)
+template <__int64 _FileSize, typename TFile > __int64 size(File< Chained<_FileSize, TFile> > &me); // "projects/library/seqan/file/file_array.h"(325)
+template <unsigned _FileCount, typename TFile > __int64 size(File< Striped<_FileCount, TFile> > &me); // "projects/library/seqan/file/file_array.h"(330)
+
+//____________________________________________________________________________
+// tell
+
+inline Size<FILE*>::Type tell(FILE* me); // "projects/library/seqan/file/file_cstyle.h"(122)
+template <typename TSpec > inline typename Position< File<TSpec> >::Type tell(File<TSpec> &me); // "projects/library/seqan/file/file_base.h"(396)
+
+//____________________________________________________________________________
+// value
+
+template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TPos> inline TValue value(String<TValue, FileReader<TFormat, TFile, TSpec> > & me, TPos pos); // "projects/library/seqan/file/file_filereader.h"(312)
+template <typename TContainer> inline typename Reference<Iter<TContainer, FileReaderIterator> >::Type value(Iter<TContainer, FileReaderIterator> & it); // "projects/library/seqan/file/file_filereader.h"(558)
+template <typename TContainer> inline typename Reference<Iter<TContainer, FileReaderIterator> >::Type value(Iter<TContainer, FileReaderIterator> const & it); // "projects/library/seqan/file/file_filereader.h"(564)
+template <typename TValue, typename TConfig, typename TPos > inline typename Reference<String<TValue, External<TConfig> > >::Type value(String<TValue, External<TConfig> > &me, TPos pos); // "projects/library/seqan/file/string_external.h"(1861)
+template <typename TValue, typename TConfig, typename TPos > inline typename Reference<String<TValue, External<TConfig> > const>::Type value(String<TValue, External<TConfig> > const &me, TPos pos); // "projects/library/seqan/file/string_external.h"(1868)
+template <typename TFile, typename TFormat, typename TFile2, typename TSpec> inline typename Reference<Iter<TFile, FileReader<TFormat, TFile2, TSpec> > >::Type value(Iter<TFile, FileReader<TFormat, TFile2, TSpec> > & it); // "projects/library/seqan/file/file_filereaderiterator.h"(113)
+
+//____________________________________________________________________________
+// waitFor
+
+inline bool waitFor(aDummyRequest &); // "projects/library/seqan/file/file_base.h"(648)
+template <typename TTime > inline bool waitFor(aDummyRequest &, TTime); // "projects/library/seqan/file/file_base.h"(653)
+template <typename TValue, typename TFile, typename TSpec > inline bool waitFor(PageFrame<TValue, TFile, TSpec> &pf); // "projects/library/seqan/file/file_page.h"(407)
+template <typename TValue, typename TFile, typename TSpec, typename TTime > inline bool waitFor(PageFrame<TValue, TFile, TSpec> &pf, TTime timeOut); // "projects/library/seqan/file/file_page.h"(417)
+
+//____________________________________________________________________________
+// write
+
+template <typename TFile, typename TSource, typename TSpec> void write(TFile & file, Align<TSource, TSpec>& align, CGViz); // "projects/library/seqan/file/file_format_cgviz.h"(190)
+template <typename TFile, typename TStringContainer, typename TSource, typename TSpec> void write(TFile & file, Align<TSource, TSpec> & align, TStringContainer& ids, CGViz); // "projects/library/seqan/file/file_format_cgviz.h"(198)
+template <typename TFile, typename TStringContainer, typename TSource, typename TSpec> void write(TFile & file, Align<TSource, TSpec>* align, TStringContainer & ids, CGViz); // "projects/library/seqan/file/file_format_cgviz.h"(206)
+template <typename TFile, typename TStringContainer, typename TSource, typename TSpec, typename TMeta> void write(TFile & file, Align<TSource, TSpec> & align, TStringContainer& ids, TMeta &, CGViz); // "projects/library/seqan/file/file_format_cgviz.h"(214)
+template <typename TFile, typename TString, typename TData> void write(TFile & file, TData const & data, Raw); // "projects/library/seqan/file/file_format_raw.h"(266)
+template <typename TFile, typename TData, typename TString> void write(TFile & file, TData const & data, TString const &, Raw); // "projects/library/seqan/file/file_format_raw.h"(279)
+template <typename TFile, typename TString, typename TData, typename TMeta> void write(TFile & file, TData const & data, TString const &, TMeta const &, Raw); // "projects/library/seqan/file/file_format_raw.h"(293)
+template <typename TFile, typename TData> void write(TFile & file, TData & data); // "projects/library/seqan/file/file_format_raw.h"(327)
+template <typename TFile, typename TData> void write(TFile & file, TData const & data); // "projects/library/seqan/file/file_format_raw.h"(335)
+template <typename TValue, typename TSize > inline bool write(FILE* me, TValue const *memPtr, TSize const count); // "projects/library/seqan/file/file_cstyle.h"(136)
+template <typename TFile, typename TString, typename TData, typename TMeta> void write(TFile & file, TData & data, Fasta); // "projects/library/seqan/file/file_format_fasta.h"(468)
+template <typename TFile, typename TString, typename TData> void write(TFile & file, TData & data, TString & id, Fasta); // "projects/library/seqan/file/file_format_fasta.h"(481)
+template <typename TFile, typename TString, typename TDataValue> void write(TFile & file, TDataValue * data, TString & id, Fasta); // "projects/library/seqan/file/file_format_fasta.h"(494)
+template <typename TFile, typename TString, typename TData, typename TMeta> void write(TFile & file, TData & data, TString & id, TMeta &, Fasta); // "projects/library/seqan/file/file_format_fasta.h"(509)
+template <typename TSpec, typename TValue, typename TSize > inline bool write(File<TSpec> & me, TValue const *memPtr, TSize const count); // "projects/library/seqan/file/file_base.h"(306)
+template <typename TFile, typename TData> inline void write(TFile & file, TData & data, Genbank); // "projects/library/seqan/file/file_format_genbank.h"(292)
+template <typename TFile, typename TData, typename TMeta> inline void write(TFile & file, TData & data, TMeta & meta, Genbank); // "projects/library/seqan/file/file_format_genbank.h"(348)
+template <typename TFile, typename TSource, typename TSpec> void write(TFile & file, Align<TSource, TSpec>& align, FastaAlign); // "projects/library/seqan/file/file_format_fasta_align.h"(284)
+template <typename TFile, typename TStringContainer, typename TSource, typename TSpec> void write(TFile & file, Align<TSource, TSpec> & align, TStringContainer& ids, FastaAlign); // "projects/library/seqan/file/file_format_fasta_align.h"(292)
+template <typename TFile, typename TStringContainer, typename TSource, typename TSpec> void write(TFile & file, Align<TSource, TSpec>* align, TStringContainer & ids, FastaAlign); // "projects/library/seqan/file/file_format_fasta_align.h"(300)
+template <typename TFile, typename TStringContainer, typename TSource, typename TSpec, typename TMeta> void write(TFile & file, Align<TSource, TSpec> & align, TStringContainer& ids, TMeta &, FastaAlign); // "projects/library/seqan/file/file_format_fasta_align.h"(308)
+template <typename TFile, typename TData, typename TMeta, typename TFormat> inline void write(TFile & file, TData & data, FileFormat<TFile, TData, TMeta, TFormat> const & file_format); // "projects/library/seqan/file/file_format.h"(293)
+template <typename TFile, typename TData, typename TMeta, typename TFormat> inline void write(TFile & file, TData & data, TMeta & meta, FileFormat<TFile, TData, TMeta, TFormat> const & file_format); // "projects/library/seqan/file/file_format.h"(303)
+template <typename TFile, typename TData> inline void write(TFile & file, TData & data, Embl); // "projects/library/seqan/file/file_format_embl.h"(465)
+template <typename TFile, typename TData, typename TMeta> inline void write(TFile & file, TData & data, TMeta & meta, Embl); // "projects/library/seqan/file/file_format_embl.h"(531)
+
+//____________________________________________________________________________
+// writeAt
+
+template <typename TValue, typename TSize, typename TPos > inline bool writeAt(FILE* me, TValue const *memPtr, TSize const count, TPos const fileOfs); // "projects/library/seqan/file/file_cstyle.h"(156)
+template <typename TFile, typename TValue, typename TSize, typename TPos > inline bool writeAt(TFile & me, TValue const *memPtr, TSize const count, TPos const fileOfs); // "projects/library/seqan/file/file_base.h"(344)
+template <__int64 _FileSize, typename TFile, typename TValue, typename TSize, typename TOffset > inline bool writeAt(File< Chained<_FileSize, TFile> > &me, TValue const *memPtr, TSize count, TOffset offset); // "projects/library/seqan/file/file_array.h"(378)
+
+//____________________________________________________________________________
+// writeBucket
+
+template <typename TValue, unsigned _FileCount, typename TFile > inline bool writeBucket( PageBucket<TValue> &b, int pageNo, unsigned pageSize, File< Striped<_FileCount, TFile> > &file); // "projects/library/seqan/file/file_page_raid0.h"(158)
+template <typename TValue, unsigned _FileCount, typename TFile, typename TSpec > inline bool writeBucket( PageFrame<TValue, File< Striped<_FileCount, TFile> >, Dynamic<TSpec> > &pf, unsigned &pageOfs, File< Striped<_FileCount, TFile> > &file); // "projects/library/seqan/file/file_page_raid0.h"(179)
+template <typename TValue, typename TFile > inline bool writeBucket(PageBucket<TValue> &b, int pageNo, unsigned pageSize, TFile &file); // "projects/library/seqan/file/file_page.h"(474)
+template <typename TValue, typename TFile, typename TSpec > inline bool writeBucket(PageFrame<TValue, TFile, Dynamic<TSpec> > &pf, unsigned &pageOfs, TFile &file); // "projects/library/seqan/file/file_page.h"(490)
+
+//____________________________________________________________________________
+// writeLastPage
+
+template <typename TValue, unsigned _FileCount, typename TFile, typename TSpec, typename TSize > inline bool writeLastPage( PageFrame<TValue, File< Striped<_FileCount, TFile> >, TSpec> &pf, int pageNo, File< Striped<_FileCount, TFile> > &file, TSize size); // "projects/library/seqan/file/file_page_raid0.h"(106)
+template <typename TValue, typename TFile, typename TSpec, typename TSize > inline bool writeLastPage(PageFrame<TValue, TFile, TSpec> &pf, int pageNo, TFile &file, TSize size); // "projects/library/seqan/file/file_page.h"(394)
+
+//____________________________________________________________________________
+// writePage
+
+template <typename TValue, unsigned _FileCount, typename TFile, typename TSpec > inline bool writePage( PageFrame<TValue, File< Striped<_FileCount, TFile> >, TSpec> &pf, int pageNo, File< Striped<_FileCount, TFile> > &file); // "projects/library/seqan/file/file_page_raid0.h"(62)
+template <typename TValue, typename TFile, typename TSpec > inline bool writePage(PageFrame<TValue, TFile, TSpec> &pf, int pageNo, TFile &file); // "projects/library/seqan/file/file_page.h"(369)
+template <typename TValue, typename TFile, typename TSpec > inline bool writePage(PageFrame<TValue, TFile, Dynamic<TSpec> > &pf, TFile &file); // "projects/library/seqan/file/file_page.h"(448)
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif
+
diff --git a/src/libSSA/seqan/file/meta.h b/src/libSSA/seqan/file/meta.h
new file mode 100644
index 0000000..c130fd4
--- /dev/null
+++ b/src/libSSA/seqan/file/meta.h
@@ -0,0 +1,36 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: meta.h,v 1.1 2008/08/25 16:20:03 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FILE_META_H
+#define SEQAN_HEADER_FILE_META_H
+
+
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/file/stream.h b/src/libSSA/seqan/file/stream.h
new file mode 100644
index 0000000..62c10b5
--- /dev/null
+++ b/src/libSSA/seqan/file/stream.h
@@ -0,0 +1,430 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: stream.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_STREAM_H
+#define SEQAN_HEADER_STREAM_H
+
+#include <iosfwd>
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Adaption."std::iostream":
+..summary:Standard library stream classes.
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename TTraits>
+struct Position< ::std::basic_ios<TValue, TTraits> >
+{
+ typedef typename ::std::basic_ios<TValue, TTraits>::pos_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Position< ::std::basic_streambuf<TValue, TTraits> >
+{
+ typedef typename ::std::basic_streambuf<TValue, TTraits>::pos_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Position< ::std::basic_istream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_istream<TValue, TTraits>::pos_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Position< ::std::basic_ostream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_ostream<TValue, TTraits>::pos_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Position< ::std::basic_iostream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_iostream<TValue, TTraits>::pos_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Position< ::std::basic_stringbuf<TValue, TTraits> >
+{
+ typedef typename ::std::basic_stringbuf<TValue, TTraits>::pos_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Position< ::std::basic_istringstream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_istringstream<TValue, TTraits>::pos_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Position< ::std::basic_ostringstream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_ostringstream<TValue, TTraits>::pos_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Position< ::std::basic_stringstream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_stringstream<TValue, TTraits>::pos_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Position< ::std::basic_filebuf<TValue, TTraits> >
+{
+ typedef typename ::std::basic_filebuf<TValue, TTraits>::pos_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Position< ::std::basic_ifstream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_ifstream<TValue, TTraits>::pos_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Position< ::std::basic_ofstream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_ofstream<TValue, TTraits>::pos_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Position< ::std::basic_fstream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_fstream<TValue, TTraits>::pos_type Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename TTraits>
+struct Value< ::std::basic_ios<TValue, TTraits> >
+{
+ typedef typename ::std::basic_ios<TValue, TTraits>::char_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Value< ::std::basic_streambuf<TValue, TTraits> >
+{
+ typedef typename ::std::basic_streambuf<TValue, TTraits>::char_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Value< ::std::basic_istream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_istream<TValue, TTraits>::char_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Value< ::std::basic_ostream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_ostream<TValue, TTraits>::char_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Value< ::std::basic_iostream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_iostream<TValue, TTraits>::char_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Value< ::std::basic_stringbuf<TValue, TTraits> >
+{
+ typedef typename ::std::basic_stringbuf<TValue, TTraits>::char_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Value< ::std::basic_istringstream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_istringstream<TValue, TTraits>::char_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Value< ::std::basic_ostringstream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_ostringstream<TValue, TTraits>::char_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Value< ::std::basic_stringstream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_stringstream<TValue, TTraits>::char_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Value< ::std::basic_filebuf<TValue, TTraits> >
+{
+ typedef typename ::std::basic_filebuf<TValue, TTraits>::char_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Value< ::std::basic_ifstream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_ifstream<TValue, TTraits>::char_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Value< ::std::basic_ofstream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_ofstream<TValue, TTraits>::char_type Type;
+};
+template <typename TValue, typename TTraits>
+struct Value< ::std::basic_fstream<TValue, TTraits> >
+{
+ typedef typename ::std::basic_fstream<TValue, TTraits>::char_type Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**.interal._IsTellSeekStream:
+..summary:Determines whether stream supports tell and seek functions.
+..cat:Metafunction
+*/
+
+template <typename T>
+struct _IsTellSeekStream
+{
+ typedef False Type;
+};
+
+
+template <typename TValue, typename TTraits>
+struct _IsTellSeekStream< ::std::basic_ifstream<TValue, TTraits> >
+{
+ typedef True Type;
+};
+template <typename TValue, typename TTraits>
+struct _IsTellSeekStream< ::std::basic_fstream<TValue, TTraits> >
+{
+ typedef True Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Internal._streamEOF:
+..summary:Test stream for being in eof or error state.
+..cat:Streams
+..signature:_streamEOF(stream)
+..param.stream:A stream object.
+...type:Adaption."std::iostream"
+..returns:$true$, if stream is at end of file or was set to error state, $false$ otherwise.
+*/
+template <typename TValue, typename TTraits>
+inline bool
+_streamEOF(::std::basic_ios<TValue, TTraits> const & me)
+{
+SEQAN_CHECKPOINT
+ return me.eof() || me.fail();
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Internal._streamRead:
+..summary:Read some characters from stream into a buffer.
+..cat:Streams
+..signature:_streamRead(target, stream, limit)
+..param.target:A buffer that is filled.
+..param.stream:An input stream.
+...type:Adaption."std::iostream"
+..param.limit:The maximal number of characters that is read from $stream$.
+..returns:The number of characters read from $stream$.
+*/
+template <typename TValue, typename TTraits>
+inline ::std::streamsize
+_streamRead(TValue * target,
+ ::std::basic_istream<TValue, TTraits> & source,
+ ::std::streamsize limit)
+{
+SEQAN_CHECKPOINT
+ source.read(target, limit);
+ return source.gcount();
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Internal._streamGet:
+..summary:Read one character from stream.
+..cat:Streams
+..signature:_streamGet(stream)
+..param.stream:An input stream.
+...type:Adaption."std::iostream"
+..returns:The character read.
+*/
+
+template <typename TValue, typename TTraits>
+inline TValue
+_streamGet(::std::basic_istream<TValue, TTraits> & source)
+{
+SEQAN_CHECKPOINT
+ return source.get();
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Internal._streamPeek:
+..summary:Return the next character to be read from stream.
+..cat:Streams
+..signature:_streamPeek(stream)
+..param.stream:An input stream.
+...type:Adaption."std::iostream"
+..returns:The character to be read.
+*/
+
+template <typename TValue, typename TTraits>
+inline TValue
+_streamPeek(::std::basic_istream<TValue, TTraits> & source)
+{
+SEQAN_CHECKPOINT
+ return source.peek();
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Internal._streamUnget:
+..summary:Put the last read character back into stream.
+..cat:Streams
+..signature:_streamUnget(stream)
+..param.stream:An input stream.
+...type:Adaption."std::iostream"
+*/
+
+template <typename TValue, typename TTraits>
+inline void
+_streamUnget(::std::basic_istream<TValue, TTraits> & source)
+{
+SEQAN_CHECKPOINT
+ source.unget();
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Internal._streamPut:
+..summary:Writes one character to stream.
+..cat:Streams
+..signature:_streamPut(stream, character)
+..param.stream:An input stream.
+...type:Adaption."std::iostream"
+..param.character:A character that is written to $stream$.
+*/
+
+template <typename TValue, typename TTraits, typename TChar>
+inline void
+_streamPut(::std::basic_ostream<TValue, TTraits> & target,
+ TChar character)
+{
+SEQAN_CHECKPOINT
+ target.put(convert<TValue>(character));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Internal._streamTellG:
+..cat:Streams
+..summary:Gets current position of input stream.
+..signature:_streamTellG(stream)
+..param.stream:An input stream.
+...type:Adaption."std::iostream"
+..returns:The current position in $stream$.
+*/
+template <typename TValue, typename TTraits>
+inline typename Position< ::std::basic_istream<TValue, TTraits> >::Type
+_streamTellG(::std::basic_istream<TValue, TTraits> & me)
+{
+SEQAN_CHECKPOINT
+ return me.tellg();
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Internal._streamTellP:
+..cat:Streams
+..summary:Gets current position of output stream.
+..signature:_streamTellP(stream)
+..param.stream:An ouput stream.
+...type:Adaption."std::iostream"
+..returns:The current position in $stream$.
+..see:Internal._streamTellG
+*/
+template <typename TValue, typename TTraits>
+inline typename Position< ::std::basic_ostream<TValue, TTraits> >::Type
+_streamTellP(::std::basic_ostream<TValue, TTraits> & me)
+{
+SEQAN_CHECKPOINT
+ return me.tellp();
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Internal._streamSeekG:
+..summary:Moves input stream to a position.
+..cat:Streams
+..signature:_streamSeekG(stream, position)
+..param.stream:An input stream.
+...type:Adaption."std::iostream"
+..param.position:A position within the stream.
+...remarks:Use @Function._streamTellG@ to get valid stream positions.
+..see:Internal._streamTellG
+*/
+template <typename TValue, typename TTraits>
+inline void
+_streamSeekG(::std::basic_istream<TValue, TTraits> & me,
+ typename Position< ::std::basic_istream<TValue, TTraits> >::Type pos)
+{
+SEQAN_CHECKPOINT
+ me.clear();
+ me.seekg(pos);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Internal._streamSeekP:
+..summary:Moves output stream to a position.
+..cat:Streams
+..signature:_streamSeekP(stream, position)
+..param.stream:An output stream.
+...type:Adaption."std::iostream"
+..param.position:A position within the stream.
+...remarks:Use @Function._streamTellP@ to get valid stream positions.
+..see:Internal._streamTellP
+..see:Internal._streamSeekG
+*/
+template <typename TValue, typename TTraits>
+inline void
+_streamSeekP(::std::basic_ostream<TValue, TTraits> & me,
+ typename Position< ::std::basic_ostream<TValue, TTraits> >::Type pos)
+{
+SEQAN_CHECKPOINT
+ me.clear();
+ me.seekp(pos);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Internal._streamSeek2G:
+..summary:Moves input stream position relative to current position.
+..cat:Streams
+..signature:_streamSeek2G(stream, offset)
+..param.stream:An input stream.
+...type:Adaption."std::iostream"
+..param.offset:The amout the position is changed.
+...remarks:If this value is negative.
+..see:Internal._streamSeekG
+*/
+template <typename TValue, typename TTraits>
+inline void
+_streamSeek2G(::std::basic_istream<TValue, TTraits> & me,
+ int off)
+{
+SEQAN_CHECKPOINT
+ me.seekg(off, ::std::ios_base::cur);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/file/stream_algorithms.h b/src/libSSA/seqan/file/stream_algorithms.h
new file mode 100644
index 0000000..6f5a188
--- /dev/null
+++ b/src/libSSA/seqan/file/stream_algorithms.h
@@ -0,0 +1,208 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: stream_algorithms.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_STREAM_ALGORITHMS_H
+#define SEQAN_HEADER_STREAM_ALGORITHMS_H
+
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+
+
+/**
+.Internal._streamPutInt:
+..summary:Converts an integer to a character and writes it to stream.
+..cat:Streams
+..signature:_streamPutInt(stream, number [, format_string])
+..param.target:An output stream.
+...type:Adaption."std::iostream"
+..param.number:A number that is written to $stream$.
+*/
+template <typename TStream>
+inline void
+_streamPutInt(TStream & target,
+ int number,
+ char const * format_string)
+{
+SEQAN_CHECKPOINT
+ char str[BitsPerValue<int>::VALUE];
+ sprintf(str, format_string, number);
+ _streamWrite(target, str);
+}
+template <typename TStream>
+inline void
+_streamPutInt(TStream & target,
+ int number)
+{
+SEQAN_CHECKPOINT
+ _streamPutInt(target, number, "%d");
+}
+
+/**
+.Internal._streamPutFloat:
+..summary:Converts a float to a character and writes it to stream.
+..cat:Streams
+..signature:_streamPutFloat(stream, number [, format_string])
+..param.target:An output stream.
+...type:Adaption."std::iostream"
+..param.number:A number that is written to $stream$.
+*/
+template <typename TStream>
+inline void
+_streamPutFloat(TStream & target,
+ float number,
+ char const * format_string)
+{
+SEQAN_CHECKPOINT
+ char str[BitsPerValue<float>::VALUE];
+ sprintf(str, format_string, number);
+ _streamWrite(target, str);
+}
+template <typename TStream>
+inline void
+_streamPutFloat(TStream & target,
+ float number)
+{
+SEQAN_CHECKPOINT
+ _streamPutFloat(target, number, "%f");
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TTarget, typename T1, typename T2, typename TCompression>
+inline void
+_streamWrite(TTarget & target,
+ Pair<T1, T2, TCompression> const & source)
+{
+SEQAN_CHECKPOINT
+ _streamWrite(target, getValueI1(source));
+ _streamWrite(target, getValueI2(source));
+}
+
+template <typename TTarget, typename T1, typename T2, typename T3, typename TCompression>
+inline void
+_streamWrite(TTarget & target,
+ Triple<T1, T2, T3, TCompression> const & source)
+{
+SEQAN_CHECKPOINT
+ _streamWrite(target, getValueI1(source));
+ _streamWrite(target, getValueI2(source));
+ _streamWrite(target, getValueI3(source));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+
+/**
+.Internal._streamWrite:
+..summary:Writes a sequence to stream.
+..cat:Streams
+..signature:_streamWrite(stream, sequence)
+..param.stream:An input stream.
+..param.sequence:A sequence that is written to $stream$.
+*/
+
+template <typename TTarget, typename TSource>
+inline void
+_streamWrite(TTarget & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ _streamWriteSeq(target, source, typename IsSequence<TSource const>::Type());
+}
+
+//____________________________________________________________________________
+
+template <typename TTarget, typename TSource>
+inline void
+_streamWriteSeq(TTarget & target,
+ TSource const & source,
+ False const)
+{
+ _streamPut(target, source);
+}
+
+//____________________________________________________________________________
+
+template <typename TTarget, typename TSource>
+inline void
+_streamWriteSeq(TTarget & target,
+ TSource const & source,
+ True const)
+{
+SEQAN_CHECKPOINT
+ typename Iterator<TSource const, Standard>::Type it = begin(source, Standard());
+ typename Iterator<TSource const, Standard>::Type it_end = end(source, Standard());
+
+ for (; it < it_end; ++it)
+ {
+ typename GetValue<TSource const>::Type val_ = getValue(it);
+ _streamWrite(target, val_);
+ }
+}
+
+template <typename TTarget, typename TSourceValue>
+inline void
+_streamWriteSeq(TTarget & target,
+ TSourceValue const * source,
+ True const)
+{
+SEQAN_CHECKPOINT
+
+ for (; !atEnd(source); ++source)
+ {
+ _streamWrite(target, *source);
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Internal._streamWriteRange:
+..summary:Writes a range to stream.
+..cat:Streams
+..signature:_streamWriteRange(stream, begin_iterator, end_iterator)
+..param.stream:An input stream.
+..param.sequence:A sequence that is written to $stream$.
+*/
+
+template <typename TTarget, typename TIterator>
+inline void
+_streamWriteRange(TTarget & target,
+ TIterator begin_,
+ TIterator end_)
+{
+SEQAN_CHECKPOINT
+ for (; begin_ != end_; ++begin_)
+ {
+ _streamPut(target, *begin_);
+ }
+}
+
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/find.h b/src/libSSA/seqan/find.h
new file mode 100644
index 0000000..fd50b22
--- /dev/null
+++ b/src/libSSA/seqan/find.h
@@ -0,0 +1,78 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: find.h,v 1.2 2009/03/13 14:44:34 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FIND_H
+#define SEQAN_HEADER_FIND_H
+
+//____________________________________________________________________________
+// prerequisites
+
+#include <cmath>
+
+#include <deque>
+
+#include <seqan/sequence.h>
+//#include <seqan/score.h>
+//#include <seqan/graph_types.h>
+//#include <seqan/graph_algorithms.h>
+//#include <seqan/map.h>
+
+//____________________________________________________________________________
+
+#ifdef SEQAN_SWITCH_USE_FORWARDS
+#include <seqan/find/find_generated_forwards.h>
+#endif
+
+#include <seqan/find/find_base.h>
+
+//____________________________________________________________________________
+// exact pattern matching
+
+#include <seqan/find/find_horspool.h>
+//#include <seqan/find/find_shiftand.h>
+//#include <seqan/find/find_shiftor.h>
+//#include <seqan/find/find_bndm.h>
+//#include <seqan/find/find_quasar.h>
+
+//____________________________________________________________________________
+// exact pattern matching
+//#include <seqan/find/find_wild_shiftand.h>
+
+//____________________________________________________________________________
+//multiple pattern search
+
+//#include <seqan/find/find_ahocorasick.h>
+#include <seqan/find/find_multiple_shiftand.h>
+//#include <seqan/find/find_set_horspool.h>
+
+//#include <seqan/find/find_multi.h> //wegwerfen
+//#include <seqan/find/find_wumanber.h> //todo
+
+//____________________________________________________________________________
+// approximate pattern matching
+
+#include <seqan/find/find_score.h>
+//#include <seqan/find/find_myers_ukkonen.h>
+//#include <seqan/find/find_abndm.h>
+//#include <seqan/find/find_pex.h>
+
+//#include <seqan/find/find_bom.h>
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/find/find_base.h b/src/libSSA/seqan/find/find_base.h
new file mode 100644
index 0000000..5f7e206
--- /dev/null
+++ b/src/libSSA/seqan/find/find_base.h
@@ -0,0 +1,806 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: find_base.h,v 1.1 2008/08/25 16:20:07 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FIND_BASE_H
+#define SEQAN_HEADER_FIND_BASE_H
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Metafunction.DefaultFinder:
+..cat:Searching
+..summary:Default @Class.Finder@ specialization type.
+..signature:DefaultFinder<THaystack>::Type
+..param.THaystack:The given haystack type.
+..returns:Is $void$ by default and @Tag.Index Find Algorithm.ESA_FIND_MLR@ if $THaystack$ is an @Class.Index at .
+*/
+ template < typename TObject >
+ struct DefaultFinder {
+ typedef void Type;
+ };
+
+/**
+.Metafunction.DefaultPattern:
+..cat:Searching
+..summary:Default @Class.Pattern@ specialization type.
+..signature:DefaultPattern<TNeedle>::Type
+..param.TNeedle:The given needle type.
+..returns:Is $void$ by default.
+*/
+ template < typename TObject >
+ struct DefaultPattern {
+ typedef void Type;
+ };
+
+/**
+.Metafunction.Haystack:
+..summary:Returns the haystack type of a @Class.Finder@ type.
+..cat:Searching
+..signature:Haystack<TFinder>::Type
+..param.TFinder:A @Class.Finder@ type.
+...type:Class.Finder
+..returns:The haystack type of $TFinder$, i.e. $THaystack$ for $Finder<THaystack, TSpec>$.
+*/
+
+ template <typename TFinder>
+ struct Haystack {
+ typedef typename Container<TFinder>::Type Type;
+ };
+
+/**
+.Metafunction.Needle:
+..summary:Returns the needle type of a @Class.Pattern@ type.
+..cat:Searching
+..signature:Needle<TPattern>::Type
+..param.TPattern:A @Class.Pattern@ type.
+...type:Class.Pattern
+..returns:The needle type of $TPattern$, i.e. $TNeedle$ for $Pattern<TNeedle, TSpec>$.
+*/
+
+ template <typename TPattern>
+ struct Needle {
+ typedef typename Host<TPattern>::Type Type;
+ };
+
+ template <typename THost, typename TSpec>
+ struct Needle<Segment<THost, TSpec> > {
+ typedef Segment<THost, TSpec> Type;
+ };
+
+ template <typename THost, typename TSpec>
+ struct Needle<Segment<THost, TSpec> const> {
+ typedef Segment<THost, TSpec> const Type;
+ };
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Class.Pattern:
+..summary:Holds the needle and preprocessing data (depends on algorithm).
+..cat:Searching
+..signature:Pattern<TNeedle[, TSpec]>
+..param.TNeedle:The needle type.
+...type:Class.String
+..param.TSpec:The online-algorithm to search with.
+...remarks:Leave empty for index-based pattern matching (see @Class.Index@).
+...default:The result of @Metafunction.DefaultPattern@
+..remarks:If $TNeedle$ is a set of strings, then $position(pattern)$ returns the index of the currently matching needle.
+*/
+
+template < typename TNeedle, typename TSpec = typename DefaultPattern<TNeedle>::Type >
+class Pattern;
+
+//default implementation
+template < typename TNeedle >
+class Pattern<TNeedle, void>
+{
+public:
+ typedef typename Position<TNeedle>::Type TNeedlePosition;
+
+ Holder<TNeedle> data_host;
+ TNeedlePosition data_begin_position;
+ TNeedlePosition data_end_position;
+
+ Pattern() {}
+
+ template <typename _TNeedle>
+ Pattern(_TNeedle & ndl):
+ data_host(ndl) {}
+
+ template <typename _TNeedle>
+ Pattern(_TNeedle const & ndl):
+ data_host(ndl) {}
+
+};
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TNeedle, typename TSpec>
+inline Holder<TNeedle> &
+_dataHost(Pattern<TNeedle, TSpec> & me)
+{
+ return me.data_host;
+}
+template <typename TNeedle, typename TSpec>
+inline Holder<TNeedle> &
+_dataHost(Pattern<TNeedle, TSpec> const & me)
+{
+ return const_cast<Holder<TNeedle> &>(me.data_host);
+}
+
+//host access: see basic_host.h
+
+
+//???TODO: Diese Funktion entfernen! (sobald setHost bei anderen pattern nicht mehr eine Art "assignHost" ist)
+template <typename TNeedle, typename TSpec, typename TNeedle2>
+inline void
+setHost(Pattern<TNeedle, TSpec> & me,
+ TNeedle2 const & ndl)
+{
+ me.data_host = ndl; //assign => Pattern haelt eine Kopie => doof!
+}
+template <typename TNeedle, typename TSpec, typename TNeedle2>
+inline void
+setHost(Pattern<TNeedle, TSpec> & me,
+ TNeedle2 & ndl)
+{
+ me.data_host = ndl; //assign => Pattern haelt eine Kopie => doof!
+}
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TNeedle, typename TSpec>
+inline typename Position<Pattern<TNeedle, TSpec> >::Type &
+beginPosition(Pattern<TNeedle, TSpec> & me)
+{
+ return me.data_begin_position;
+}
+template <typename TNeedle, typename TSpec>
+inline typename Position<Pattern<TNeedle, TSpec> const >::Type &
+beginPosition(Pattern<TNeedle, TSpec> const & me)
+{
+ return me.data_begin_position;
+}
+
+
+template <typename TNeedle, typename TSpec, typename TPosition>
+inline void
+setBeginPosition(Pattern<TNeedle, TSpec> & me,
+ TPosition _pos)
+{
+ me.data_begin_position = _pos;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TNeedle, typename TSpec>
+inline typename Position<Pattern<TNeedle, TSpec> >::Type &
+endPosition(Pattern<TNeedle, TSpec> & me)
+{
+ return me.data_end_position;
+}
+template <typename TNeedle, typename TSpec>
+inline typename Position<Pattern<TNeedle, TSpec> const >::Type &
+endPosition(Pattern<TNeedle, TSpec> const & me)
+{
+ return me.data_end_position;
+}
+
+template <typename TNeedle, typename TSpec, typename TPosition>
+inline void
+setEndPosition(Pattern<TNeedle, TSpec> & me,
+ TPosition _pos)
+{
+ me.data_end_position = _pos;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TNeedle, typename TSpec>
+inline typename Infix<TNeedle>::Type
+segment(Pattern<TNeedle, TSpec> & me)
+{
+ typedef typename Infix<TNeedle>::Type TInfix;
+ return TInfix(host(me), me.data_begin_position, me.data_end_position);
+}
+template <typename TNeedle, typename TSpec>
+inline typename Infix<TNeedle>::Type
+segment(Pattern<TNeedle, TSpec> const & me)
+{
+ typedef typename Infix<TNeedle>::Type TInfix;
+ return TInfix(host(me), me.data_begin_position, me.data_end_position);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+/**
+.Function.needle:
+..summary:Returns the needle of a @Class.Pattern@ object (not implemented for some online-algorithms).
+..cat:Searching
+..signature:needle(pattern)
+..param.pattern:The @Class.Pattern@ object to search with.
+...type:Class.Pattern
+..returns:The needle object to search for.
+..remarks:The result type is @Metafunction.Needle@$<TPattern>::Type$ for pattern of type $TPattern$.
+*/
+
+template < typename TObject >
+inline typename Needle<TObject>::Type &
+needle(TObject &obj)
+{
+ return obj;
+}
+
+template < typename TObject >
+inline typename Needle<TObject const>::Type &
+needle(TObject const &obj)
+{
+ return obj;
+}
+
+
+///.Function.position.param.iterator.type:Class.Pattern
+
+template < typename TNeedle, typename TSpec >
+inline typename Needle< Pattern<TNeedle, TSpec> >::Type &
+needle(Pattern<TNeedle, TSpec> & obj)
+{
+ return host(obj);
+}
+
+template < typename TNeedle, typename TSpec >
+inline typename Needle< Pattern<TNeedle, TSpec> const>::Type &
+needle(Pattern<TNeedle, TSpec> const & obj)
+{
+ return host(obj);
+}
+
+/**
+.Function.setNeedle:
+..summary:Sets the needle of a @Class.Pattern@ object and optionally induces preprocessing.
+..cat:Searching
+..signature:setNeedle(pattern, needle)
+..param.pattern:The @Class.Pattern@ object to search with.
+...type:Class.Pattern
+..param.needle:The needle object to search for.
+...type:Class.String
+*/
+
+ template < typename TNeedle, typename TSpec >
+ inline void
+ setNeedle(Pattern<TNeedle, TSpec> &obj, TNeedle const &ndl) {
+ setHost(obj, ndl);
+ }
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.find:
+..summary:Search for a @Class.Pattern@ in a @Class.Finder@ object.
+..cat:Searching
+..signature:find(finder, pattern)
+..signature:find(finder, pattern, k)
+..param.finder:The @Class.Finder@ object to search through.
+...remarks:For online-algorithm $patterns$, finder can also be an arbitrary @Concept.Rooted Iterator at .
+...type:Class.Finder
+...type:Concept.Rooted Iterator
+..param.pattern:The @Class.Pattern@ object to search for.
+...remarks:For index $finders$, pattern can also be a Sequence.
+...type:Class.Pattern
+..param.k:Desired minimal score (for approximate matching).
+...remarks:$k$ has to be a number <= 0.
+...remarks:Differences are deletions, insertions and substitutions.
+..returns:$boolean$ that indicates whether an occurence of $pattern$ was found or not.
+..remarks:Repeated calls of this function iterate through all occurences of $pattern$.
+*/
+
+/**
+.Class.Finder:
+..summary:Holds the haystack and a current search context.
+..cat:Searching
+..signature:Finder<THaystack[, TSpec]>
+..param.THaystack:The haystack type.
+...type:Class.String
+...type:Class.Index
+..param.TSpec:The index-algorithm to search with (Optional).
+...default:The result of @Metafunction.DefaultFinder@
+...remarks:Leave empty for online pattern matching (see @Class.Pattern@).
+...remarks:If $THaystack$ is an @Class.Index@, then $TSpec$ specifies the index search algorithm.
+..remarks:$position(finder)$ returns the position of the current hit in the haystack.
+If $THaystack$ is a set of strings or an index of a set of strings, then $position(finder)$ returns a @Class.Pair@ $(hayNo, pos)$,
+in which $hayNo$ is the haystack index and $pos$ the local position of the hit.
+..remarks:Use $clear(finder)$ to reset a finder object and search from the beginning.
+*/
+
+///.Function.clear.param.object.type:Class.Finder
+///.Function.position.param.iterator.type:Class.Finder
+
+ template < typename THaystack, typename TSpec = typename DefaultFinder<THaystack>::Type >
+ class Finder
+ {
+ typedef typename Iterator<THaystack, Rooted>::Type TIterator;
+
+ public:
+ TIterator data_iterator;
+ bool _needReinit; // if true, the Pattern needs to be reinitialized
+
+ Finder():
+ _needReinit(true) {}
+
+ Finder(THaystack &haystack):
+ data_iterator(begin(haystack, Rooted())),
+ _needReinit(true) {}
+
+ Finder(TIterator &iter):
+ data_iterator(iter),
+ _needReinit(true) {}
+
+ Finder(TIterator const &iter):
+ data_iterator(iter),
+ _needReinit(true) {}
+
+ Finder(Finder const &orig):
+ data_iterator(orig.data_iterator),
+ _needReinit(orig._needReinit) {};
+
+//____________________________________________________________________________
+
+ inline typename Reference<TIterator>::Type
+ operator* ()
+ {
+SEQAN_CHECKPOINT
+ return value(hostIterator(*this));
+ }
+
+ inline typename Reference<TIterator const>::Type
+ operator* () const
+ {
+SEQAN_CHECKPOINT
+ return value(hostIterator(*this));
+ }
+
+//____________________________________________________________________________
+
+ operator TIterator () const
+ {
+SEQAN_CHECKPOINT
+ return data_iterator;
+ }
+
+//____________________________________________________________________________
+
+ };
+
+
+
+//____________________________________________________________________________
+
+ template <typename THaystack, typename TSpec>
+ inline typename _Parameter<THaystack>::Type
+ host(Finder<THaystack, TSpec> & me)
+ {
+SEQAN_CHECKPOINT
+ return container(hostIterator(me));
+ }
+
+ template <typename THaystack, typename TSpec>
+ inline typename _Parameter<THaystack>::Type
+ host(Finder<THaystack, TSpec> const & me)
+ {
+SEQAN_CHECKPOINT
+ return container(hostIterator(me));
+ }
+
+ template <typename THaystack, typename TSpec>
+ inline typename _Parameter<THaystack>::Type
+ container(Finder<THaystack, TSpec> & me)
+ {
+SEQAN_CHECKPOINT
+ return container(hostIterator(me));
+ }
+
+ template <typename THaystack, typename TSpec>
+ inline typename _Parameter<THaystack>::Type
+ container(Finder<THaystack, TSpec> const & me)
+ {
+SEQAN_CHECKPOINT
+ return container(hostIterator(me));
+ }
+
+//____________________________________________________________________________
+
+ template <typename THaystack, typename TSpec>
+ inline void
+ setHost(Finder<THaystack, TSpec> & me, typename _Parameter<THaystack>::Type container_)
+ {
+SEQAN_CHECKPOINT
+ setContainer(hostIterator(me), container_);
+ goBegin(me);
+ }
+
+ template <typename THaystack, typename TSpec>
+ inline void
+ setContainer(Finder<THaystack, TSpec> & me, typename _Parameter<THaystack>::Type container_)
+ {
+SEQAN_CHECKPOINT
+ setContainer(hostIterator(me), container_);
+ goBegin(me);
+ }
+
+//____________________________________________________________________________
+
+ template <typename THaystack, typename TSpec>
+ inline typename Iterator<THaystack, Rooted>::Type &
+ hostIterator(Finder<THaystack, TSpec> & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_iterator;
+ }
+
+ template <typename THaystack, typename TSpec>
+ inline typename Iterator<THaystack, Rooted>::Type const &
+ hostIterator(Finder<THaystack, TSpec> const & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_iterator;
+ }
+
+//____________________________________________________________________________
+
+ template <typename THaystack, typename TSpec>
+ inline bool
+ empty(Finder<THaystack, TSpec> & me)
+ {
+SEQAN_CHECKPOINT
+ return me._needReinit;
+ }
+
+ template <typename THaystack, typename TSpec>
+ inline void
+ clear(Finder<THaystack, TSpec> & me)
+ {
+SEQAN_CHECKPOINT
+ me._needReinit = true;
+ }
+
+//____________________________________________________________________________
+
+ template <typename T>
+ inline void
+ _finderSetNonEmpty(T & me)
+ {
+SEQAN_CHECKPOINT
+ goBegin(me);
+ }
+
+
+ template <typename THaystack, typename TSpec>
+ inline void
+ _finderSetNonEmpty(Finder<THaystack, TSpec> & me)
+ {
+SEQAN_CHECKPOINT
+ me._needReinit = false;
+ }
+
+//____________________________________________________________________________
+
+ template <typename THaystack, typename TSpec>
+ inline bool
+ atBegin(Finder<THaystack, TSpec> & me)
+ {
+SEQAN_CHECKPOINT
+ return (!empty(me) && atBegin(hostIterator(me)));
+ }
+
+ template <typename THaystack, typename TSpec>
+ inline bool
+ atEnd(Finder<THaystack, TSpec> & me)
+ {
+SEQAN_CHECKPOINT
+ return (!empty(me) && atEnd(hostIterator(me)));
+ }
+
+//____________________________________________________________________________
+
+ template <typename THaystack, typename TSpec>
+ inline void
+ goBegin(Finder<THaystack, TSpec> & me)
+ {
+SEQAN_CHECKPOINT
+ //_finderSetNonEmpty(me);
+ goBegin(hostIterator(me));
+ }
+
+ template <typename THaystack, typename TSpec>
+ inline void
+ goEnd(Finder<THaystack, TSpec> & me)
+ {
+SEQAN_CHECKPOINT
+ //_finderSetNonEmpty(me);
+ goEnd(hostIterator(me));
+ }
+
+//____________________________________________________________________________
+
+ template <typename THaystack, typename TSpec>
+ inline typename Position<Finder<THaystack, TSpec> >::Type
+ position(Finder<THaystack, TSpec> & me)
+ {
+SEQAN_CHECKPOINT
+ if (empty(me)) return 0;
+ return position(hostIterator(me));
+ }
+
+ template <typename THaystack, typename TSpec>
+ inline typename Position<Finder<THaystack, TSpec> >::Type
+ position(Finder<THaystack, TSpec> const & me)
+ {
+SEQAN_CHECKPOINT
+ if (empty(me)) return 0;
+ return position(hostIterator(me));
+ }
+
+//____________________________________________________________________________
+/**
+.Function.setPosition:
+..cat:Searching
+..summary:Sets the position of a finder.
+..signature:setPosition(finder, pos)
+..param.finder:A finder.
+...class:Class.Finder
+..param.pos:A position.
+...metafunction:Metafunction.Position
+..see:Function.position
+*/
+
+ template <typename THaystack, typename TSpec, typename TPosition>
+ inline void
+ setPosition(Finder<THaystack, TSpec> & me, TPosition pos_)
+ {
+SEQAN_CHECKPOINT
+ setPosition(hostIterator(me), pos_);
+ }
+
+//____________________________________________________________________________
+
+ template <typename THaystack, typename TSpec>
+ inline Finder<THaystack, TSpec> &
+ operator--(Finder<THaystack, TSpec> & me)
+ {
+SEQAN_CHECKPOINT
+ --hostIterator(me);
+ return me;
+ }
+
+ template <typename THaystack, typename TSpec>
+ inline Finder<THaystack, TSpec> &
+ operator++(Finder<THaystack, TSpec> & me)
+ {
+SEQAN_CHECKPOINT
+/* if (beforeBegin()) {
+ goBegin(hostIterator(me));
+ } else*/
+ ++hostIterator(me);
+ return me;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// operator +
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename THaystack, typename TSpec, typename TIntegral>
+ inline Finder<THaystack, TSpec> const
+ operator + (Finder<THaystack, TSpec> const & left, TIntegral right)
+ {
+SEQAN_CHECKPOINT
+ return Finder<THaystack, TSpec>(hostIterator(left) + right);
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// operator +=
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename THaystack, typename TSpec, typename TIntegral>
+ inline Finder<THaystack, TSpec> &
+ operator += (Finder<THaystack, TSpec> & left,
+ TIntegral right)
+ {
+SEQAN_CHECKPOINT
+ hostIterator(left) += right;
+ return left;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// operator -
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename THaystack, typename TSpec, typename TIntegral>
+ inline Finder<THaystack, TSpec> const
+ operator - (Finder<THaystack, TSpec> const & left, TIntegral right)
+ {
+SEQAN_CHECKPOINT
+ return Finder<THaystack, TSpec>(hostIterator(left) - right);
+ }
+
+ template <typename THaystack, typename TSpec, typename TIntegral>
+ inline typename Difference<Finder<THaystack, TSpec> const>::Type
+ operator - (Finder<THaystack, TSpec> const & left, Finder<THaystack, TSpec> const & right)
+ {
+SEQAN_CHECKPOINT
+ return hostIterator(left) - hostIterator(right);
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// operator -=
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename THaystack, typename TSpec, typename TIntegral>
+ inline Finder<THaystack, TSpec> &
+ operator -= (Finder<THaystack, TSpec> & left,
+ TIntegral right)
+ {
+SEQAN_CHECKPOINT
+ hostIterator(left) -= right;
+ return left;
+ }
+
+//____________________________________________________________________________
+
+
+/**
+.Function.setHaystack:
+..summary:Sets the haystack of a @Class.Finder@ object.
+..cat:Searching
+..signature:setHaystack(finder, haystack)
+..param.finder:The @Class.Finder@ object to search with.
+...type:Class.Finder
+..param.haystack:The haystack object the finder searches through.
+...type:Class.String
+*/
+
+ template < typename THaystack, typename TSpec >
+ inline void
+ setHaystack(Finder<THaystack, TSpec> &obj, THaystack const &hstk) {
+ setHost(obj, hstk);
+ }
+
+/**
+.Function.haystack:
+..summary:Returns the haystack of a @Class.Finder@ object.
+..cat:Searching
+..signature:haystack(finder)
+..param.finder:The @Class.Finder@ object to search through.
+...type:Class.Finder
+..returns:The haystack object.
+..remarks:The result type is @Metafunction.Haystack@$<TFinder>::Type$ for finder of type $TFinder$.
+*/
+
+ template < typename TObject >
+ inline typename Haystack<TObject>::Type &
+ haystack(TObject &obj) {
+ return container(obj);
+ }
+
+ template < typename TObject >
+ inline typename Haystack<TObject const>::Type &
+ haystack(TObject const &obj) {
+ return container(obj);
+ }
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+ template <typename THaystack, typename TSpec>
+ struct Container< Finder<THaystack, TSpec> > {
+ typedef THaystack Type;
+ };
+
+ template <typename THaystack, typename TSpec>
+ struct Container< Finder<THaystack, TSpec> const> {
+ typedef THaystack const Type;
+ };
+
+ template <typename THaystack, typename TSpec>
+ struct Host< Finder<THaystack, TSpec> > {
+ typedef THaystack Type;
+ };
+
+ template <typename THaystack, typename TSpec>
+ struct Host< Finder<THaystack, TSpec> const> {
+ typedef THaystack const Type;
+ };
+
+
+ template <typename THaystack, typename TSpec>
+ struct Value< Finder<THaystack, TSpec> > {
+ typedef typename Value<THaystack>::Type Type;
+ };
+
+ template <typename THaystack, typename TSpec>
+ struct Position< Finder<THaystack, TSpec> >:
+ Position<THaystack> {};
+
+ template <typename THaystack, typename TSpec>
+ struct Difference< Finder<THaystack, TSpec> > {
+ typedef typename Difference<THaystack>::Type Type;
+ };
+
+ template <typename THaystack, typename TSpec>
+ struct Size< Finder<THaystack, TSpec> > {
+ typedef typename Size<THaystack>::Type Type;
+ };
+
+//____________________________________________________________________________
+
+
+ template <typename TNeedle, typename TSpec>
+ struct Container< Pattern<TNeedle, TSpec> > {
+ typedef TNeedle Type;
+ };
+
+ template <typename TNeedle, typename TSpec>
+ struct Container< Pattern<TNeedle, TSpec> const > {
+ typedef TNeedle const Type;
+ };
+
+ template <typename TNeedle, typename TSpec>
+ struct Host< Pattern<TNeedle, TSpec> > {
+ typedef TNeedle Type;
+ };
+
+ template <typename TNeedle, typename TSpec>
+ struct Host< Pattern<TNeedle, TSpec> const > {
+ typedef TNeedle const Type;
+ };
+
+
+ template <typename TPattern, typename TSpec>
+ struct Value< Pattern<TPattern, TSpec> > {
+ typedef typename Value<TPattern>::Type Type;
+ };
+
+ template <typename TPattern, typename TSpec>
+ struct Position< Pattern<TPattern, TSpec> > {
+ typedef typename Position<TPattern>::Type Type;
+ };
+
+ template <typename TPattern, typename TSpec>
+ struct Difference< Pattern<TPattern, TSpec> > {
+ typedef typename Difference<TPattern>::Type Type;
+ };
+
+ template <typename TPattern, typename TSpec>
+ struct Size< Pattern<TPattern, TSpec> > {
+ typedef typename Size<TPattern>::Type Type;
+ };
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/find/find_generated_forwards.h b/src/libSSA/seqan/find/find_generated_forwards.h
new file mode 100644
index 0000000..e1709ee
--- /dev/null
+++ b/src/libSSA/seqan/find/find_generated_forwards.h
@@ -0,0 +1,838 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FIND_GENERATED_FORWARDS_H
+#define SEQAN_HEADER_FIND_GENERATED_FORWARDS_H
+
+//////////////////////////////////////////////////////////////////////////////
+// NOTE: This file is automatically generated by build_forwards.py
+// Do not edit this file manually!
+//////////////////////////////////////////////////////////////////////////////
+
+
+//////////////////////////////////////////////////////////////////////////////
+// CLASSES
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+
+//____________________________________________________________________________
+// AbndmAlgo
+
+struct AbndmAlgo; // "projects/library/seqan/find/find_abndm.h"(76)
+
+//____________________________________________________________________________
+// AlignTextBanded
+
+struct AlignTextBanded; // "projects/library/seqan/find/find_myers_ukkonen.h"(46)
+
+//____________________________________________________________________________
+// AlignTextGlobal
+
+struct AlignTextGlobal; // "projects/library/seqan/find/find_myers_ukkonen.h"(45)
+
+//____________________________________________________________________________
+// AlignTextLocal
+
+struct AlignTextLocal; // "projects/library/seqan/find/find_myers_ukkonen.h"(44)
+
+//____________________________________________________________________________
+// DPSearch
+
+template <typename TScore> struct DPSearch; // "projects/library/seqan/find/find_score.h"(32)
+
+//____________________________________________________________________________
+// DefaultFinder
+
+template <typename TObject > struct DefaultFinder; // "projects/library/seqan/find/find_base.h"(41)
+
+//____________________________________________________________________________
+// DefaultHash
+
+class DefaultHash; // "projects/library/seqan/find/find_wumanber.h"(63)
+
+//____________________________________________________________________________
+// DefaultPattern
+
+template <typename TObject > struct DefaultPattern; // "projects/library/seqan/find/find_base.h"(54)
+
+//____________________________________________________________________________
+// FileReader
+
+template <typename TFormat, typename TFile, typename TSpec> struct FileReader; // "projects/library/seqan/find/find_horspool.h"(308)
+
+//____________________________________________________________________________
+// Finder
+
+template <typename THaystack, typename TSpec > class Finder; // "projects/library/seqan/find/find_base.h"(343)
+
+//____________________________________________________________________________
+// Haystack
+
+template <typename TFinder> struct Haystack; // "projects/library/seqan/find/find_base.h"(69)
+
+//____________________________________________________________________________
+// Hierarchical
+
+struct Hierarchical; // "projects/library/seqan/find/find_pex.h"(30)
+
+//____________________________________________________________________________
+// Index
+
+template <typename TObject, typename TSpec > class Index; // "projects/library/seqan/find/find_swift.h"(34)
+
+//____________________________________________________________________________
+// Needle
+
+template <typename TPattern> struct Needle; // "projects/library/seqan/find/find_base.h"(84)
+
+//____________________________________________________________________________
+// NonHierarchical
+
+struct NonHierarchical; // "projects/library/seqan/find/find_pex.h"(31)
+
+//____________________________________________________________________________
+// Pattern
+
+template <typename TNeedle, typename TSpec > class Pattern; // "projects/library/seqan/find/find_base.h"(114)
+
+//____________________________________________________________________________
+// Pex
+
+template <typename TVerification, typename TMultiFinder > struct Pex; // "projects/library/seqan/find/find_pex.h"(34)
+
+//____________________________________________________________________________
+// PexMultiFinder
+
+template <typename T> struct PexMultiFinder; // "projects/library/seqan/find/find_pex.h"(53)
+
+//____________________________________________________________________________
+// Pipe
+
+//template <typename TInput, typename TSpec > struct Pipe; // "projects/library/seqan/find/find_swift.h"(179)
+
+//____________________________________________________________________________
+// Swift
+
+template <typename TSpec > struct Swift; // "projects/library/seqan/find/find_swift.h"(44)
+
+//____________________________________________________________________________
+// SwiftParameters
+
+struct SwiftParameters; // "projects/library/seqan/find/find_swift.h"(65)
+
+//____________________________________________________________________________
+// WuManber
+
+template <typename THash > class WuManber; // "projects/library/seqan/find/find_wumanber.h"(238)
+
+//____________________________________________________________________________
+// _AhoCorasick
+
+struct _AhoCorasick; // "projects/library/seqan/find/find_ahocorasick.h"(46)
+
+//____________________________________________________________________________
+// _BndmAlgo
+
+struct _BndmAlgo; // "projects/library/seqan/find/find_bndm.h"(44)
+
+//____________________________________________________________________________
+// _BomAlgo
+
+struct _BomAlgo; // "projects/library/seqan/find/find_bom.h"(44)
+
+//____________________________________________________________________________
+// _Horspool
+
+struct _Horspool; // "projects/library/seqan/find/find_horspool.h"(43)
+
+//____________________________________________________________________________
+// _MultipatternFinder
+
+struct _MultipatternFinder; // "projects/library/seqan/find/find_multi.h"(29)
+
+//____________________________________________________________________________
+// _MultipleShiftAnd
+
+struct _MultipleShiftAnd; // "projects/library/seqan/find/find_multiple_shiftand.h"(44)
+
+//____________________________________________________________________________
+// _MyersUkkonen
+
+template <typename TSpec> struct _MyersUkkonen; // "projects/library/seqan/find/find_myers_ukkonen.h"(49)
+
+//____________________________________________________________________________
+// _MyersUkkonenHP0
+
+template <typename T> struct _MyersUkkonenHP0; // "projects/library/seqan/find/find_myers_ukkonen.h"(62)
+
+//____________________________________________________________________________
+// _PexRange
+
+template <typename TPosition,typename TScore,typename TVerifier,typename TNeedle> struct _PexRange; // "projects/library/seqan/find/find_pex.h"(64)
+
+//____________________________________________________________________________
+// _Quasar
+
+struct _Quasar; // "projects/library/seqan/find/find_quasar.h"(33)
+
+//____________________________________________________________________________
+// _SetHorspool
+
+struct _SetHorspool; // "projects/library/seqan/find/find_set_horspool.h"(44)
+
+//____________________________________________________________________________
+// _ShiftAnd
+
+struct _ShiftAnd; // "projects/library/seqan/find/find_shiftand.h"(44)
+
+//____________________________________________________________________________
+// _ShiftOr
+
+struct _ShiftOr; // "projects/library/seqan/find/find_shiftor.h"(44)
+
+//____________________________________________________________________________
+// _SwiftBucket
+
+template <typename TSpec, typename TSize, typename TShortSize > struct _SwiftBucket; // "projects/library/seqan/find/find_swift.h"(79)
+
+//____________________________________________________________________________
+// _SwiftBucketParams
+
+template <typename TSpec, typename TSize, typename TShortSize > struct _SwiftBucketParams; // "projects/library/seqan/find/find_swift.h"(98)
+
+//____________________________________________________________________________
+// _SwiftHit
+
+template <typename THstkPos> struct _SwiftHit; // "projects/library/seqan/find/find_swift.h"(113)
+
+//____________________________________________________________________________
+// _SwiftLocal
+
+struct _SwiftLocal; // "projects/library/seqan/find/find_swift.h"(36)
+
+//____________________________________________________________________________
+// _SwiftSemiGlobal
+
+struct _SwiftSemiGlobal; // "projects/library/seqan/find/find_swift.h"(39)
+
+//____________________________________________________________________________
+// _WildShiftAnd
+
+struct _WildShiftAnd; // "projects/library/seqan/find/find_wild_shiftand.h"(31)
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+
+//////////////////////////////////////////////////////////////////////////////
+// TYPEDEFS
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+
+//____________________________________________________________________________
+// AhoCorasick
+
+typedef Tag<_AhoCorasick> AhoCorasick; // "projects/library/seqan/find/find_ahocorasick.h"(47)
+
+//____________________________________________________________________________
+// BndmAlgo
+
+typedef Tag<_BndmAlgo> BndmAlgo; // "projects/library/seqan/find/find_bndm.h"(45)
+
+//____________________________________________________________________________
+// BomAlgo
+
+typedef Tag<_BomAlgo> BomAlgo; // "projects/library/seqan/find/find_bom.h"(45)
+
+//____________________________________________________________________________
+// Horspool
+
+typedef Tag<_Horspool> Horspool; // "projects/library/seqan/find/find_horspool.h"(44)
+
+//____________________________________________________________________________
+// MultipatternFinder
+
+typedef Tag<_MultipatternFinder> MultipatternFinder; // "projects/library/seqan/find/find_multi.h"(30)
+
+//____________________________________________________________________________
+// MultipleShiftAnd
+
+typedef Tag<_MultipleShiftAnd> MultipleShiftAnd; // "projects/library/seqan/find/find_multiple_shiftand.h"(45)
+
+//____________________________________________________________________________
+// MyersUkkonen
+
+typedef Tag<_MyersUkkonen<AlignTextLocal> > MyersUkkonen; // "projects/library/seqan/find/find_myers_ukkonen.h"(51)
+
+//____________________________________________________________________________
+// MyersUkkonenBanded
+
+typedef Tag<_MyersUkkonen<AlignTextBanded> > MyersUkkonenBanded; // "projects/library/seqan/find/find_myers_ukkonen.h"(53)
+
+//____________________________________________________________________________
+// MyersUkkonenGlobal
+
+typedef Tag<_MyersUkkonen<AlignTextGlobal> > MyersUkkonenGlobal; // "projects/library/seqan/find/find_myers_ukkonen.h"(52)
+
+//____________________________________________________________________________
+// PexHierarchical
+
+typedef Pex<Hierarchical,AhoCorasick> PexHierarchical; // "projects/library/seqan/find/find_pex.h"(36)
+
+//____________________________________________________________________________
+// PexNonHierarchical
+
+typedef Pex<NonHierarchical,AhoCorasick> PexNonHierarchical; // "projects/library/seqan/find/find_pex.h"(37)
+
+//____________________________________________________________________________
+// Quasar
+
+typedef Tag<_Quasar> Quasar; // "projects/library/seqan/find/find_quasar.h"(34)
+
+//____________________________________________________________________________
+// SetHorspool
+
+typedef Tag<_SetHorspool> SetHorspool; // "projects/library/seqan/find/find_set_horspool.h"(45)
+
+//____________________________________________________________________________
+// ShiftAnd
+
+typedef Tag<_ShiftAnd> ShiftAnd; // "projects/library/seqan/find/find_shiftand.h"(45)
+
+//____________________________________________________________________________
+// ShiftOr
+
+typedef Tag<_ShiftOr> ShiftOr; // "projects/library/seqan/find/find_shiftor.h"(45)
+
+//____________________________________________________________________________
+// SwiftLocal
+
+typedef Tag<_SwiftLocal> SwiftLocal; // "projects/library/seqan/find/find_swift.h"(37)
+
+//____________________________________________________________________________
+// SwiftSemiGlobal
+
+typedef Tag<_SwiftSemiGlobal> SwiftSemiGlobal; // "projects/library/seqan/find/find_swift.h"(40)
+
+//____________________________________________________________________________
+// WildShiftAnd
+
+typedef Tag<_WildShiftAnd> WildShiftAnd; // "projects/library/seqan/find/find_wild_shiftand.h"(32)
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+
+//////////////////////////////////////////////////////////////////////////////
+// FUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+
+//____________________________________________________________________________
+// _createAcTrie
+
+template <typename TNeedle> inline void _createAcTrie(Pattern<TNeedle, AhoCorasick> & me); // "projects/library/seqan/find/find_ahocorasick.h"(120)
+
+//____________________________________________________________________________
+// _createTree
+
+template <typename TNeedle, typename TMultiFinder> void _createTree(Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > &me, unsigned start, unsigned end, unsigned k, unsigned parent, unsigned direction ,unsigned idx, unsigned plen); // "projects/library/seqan/find/find_pex.h"(424)
+
+//____________________________________________________________________________
+// _dataHost
+
+template <typename TNeedle, typename TSpec> inline Holder<TNeedle> & _dataHost(Pattern<TNeedle, TSpec> & me); // "projects/library/seqan/find/find_base.h"(143)
+template <typename TNeedle, typename TSpec> inline Holder<TNeedle> & _dataHost(Pattern<TNeedle, TSpec> const & me); // "projects/library/seqan/find/find_base.h"(149)
+
+//____________________________________________________________________________
+// _findAbndm_LargeNeedle
+
+template <typename TFinder, typename TNeedle> inline bool _findAbndm_LargeNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo> & me); // "projects/library/seqan/find/find_abndm.h"(371)
+
+//____________________________________________________________________________
+// _findAbndm_SmallNeedle
+
+template <typename TFinder, typename TNeedle> inline bool _findAbndm_SmallNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo> & me); // "projects/library/seqan/find/find_abndm.h"(237)
+
+//____________________________________________________________________________
+// _findBndm_LargeNeedle
+
+template <typename TFinder, typename TNeedle> inline bool _findBndm_LargeNeedle(TFinder & finder, Pattern<TNeedle, BndmAlgo> & me); // "projects/library/seqan/find/find_bndm.h"(184)
+
+//____________________________________________________________________________
+// _findBndm_SmallNeedle
+
+template <typename TFinder, typename TNeedle> inline bool _findBndm_SmallNeedle(TFinder & finder, Pattern<TNeedle, BndmAlgo> & me); // "projects/library/seqan/find/find_bndm.h"(160)
+
+//____________________________________________________________________________
+// _findMyersLargePatterns
+
+template <typename TFinder, typename TNeedle, typename TSpec> inline bool _findMyersLargePatterns (TFinder & finder, Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me); // "projects/library/seqan/find/find_myers_ukkonen.h"(362)
+template <typename TFinder, typename TNeedle, typename TSpec> inline bool _findMyersLargePatterns( TFinder & finder, Pattern<TNeedle, Tag<_MyersUkkonen<AlignTextBanded> > > & me); // "projects/library/seqan/find/find_myers_ukkonen.h"(505)
+
+//____________________________________________________________________________
+// _findMyersSmallPatterns
+
+template <typename TFinder, typename TNeedle, typename TSpec> inline bool _findMyersSmallPatterns (TFinder & finder, Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me); // "projects/library/seqan/find/find_myers_ukkonen.h"(457)
+template <typename TFinder, typename TNeedle> inline bool _findMyersSmallPatterns( TFinder & finder, Pattern<TNeedle, Tag<_MyersUkkonen<AlignTextBanded> > > & me); // "projects/library/seqan/find/find_myers_ukkonen.h"(775)
+
+//____________________________________________________________________________
+// _findShiftAnd_LargeNeedle
+
+template <typename TFinder, typename TNeedle> inline bool _findShiftAnd_LargeNeedle(TFinder & finder, Pattern<TNeedle, ShiftAnd> & me); // "projects/library/seqan/find/find_shiftand.h"(180)
+template <typename TFinder, typename TNeedle> bool _findShiftAnd_LargeNeedle(TFinder & finder, Pattern<TNeedle, MultipleShiftAnd> & me); // "projects/library/seqan/find/find_multiple_shiftand.h"(313)
+template <typename TFinder, typename TNeedle> inline bool _findShiftAnd_LargeNeedle(TFinder & finder, Pattern<TNeedle, WildShiftAnd> & me); // "projects/library/seqan/find/find_wild_shiftand.h"(590)
+
+//____________________________________________________________________________
+// _findShiftAnd_SmallNeedle
+
+template <typename TFinder, typename TNeedle> inline bool _findShiftAnd_SmallNeedle(TFinder & finder, Pattern<TNeedle, ShiftAnd> & me); // "projects/library/seqan/find/find_shiftand.h"(160)
+template <typename TFinder, typename TNeedle> bool _findShiftAnd_SmallNeedle(TFinder & finder, Pattern<TNeedle, MultipleShiftAnd> & me); // "projects/library/seqan/find/find_multiple_shiftand.h"(261)
+template <typename TFinder, typename TNeedle> inline bool _findShiftAnd_SmallNeedle(TFinder & finder, Pattern<TNeedle, WildShiftAnd> & me); // "projects/library/seqan/find/find_wild_shiftand.h"(567)
+
+//____________________________________________________________________________
+// _findShiftOr_LargeNeedle
+
+template <typename TFinder, typename TNeedle> bool _findShiftOr_LargeNeedle(TFinder & finder, Pattern<TNeedle, ShiftOr> & me); // "projects/library/seqan/find/find_shiftor.h"(212)
+
+//____________________________________________________________________________
+// _findShiftOr_SmallNeedle
+
+template <typename TFinder, typename TNeedle> bool _findShiftOr_SmallNeedle(TFinder & finder, Pattern<TNeedle, ShiftOr> & me); // "projects/library/seqan/find/find_shiftor.h"(178)
+
+//____________________________________________________________________________
+// _find_score_simple_proportional
+
+template <typename TFinder, typename TNeedle, typename TScore> bool _find_score_simple_proportional(TFinder & finder, Pattern<TNeedle, DPSearch<TScore> > & me); // "projects/library/seqan/find/find_score.h"(350)
+
+//____________________________________________________________________________
+// _finderSetNonEmpty
+
+template <typename T> inline void _finderSetNonEmpty(T & me); // "projects/library/seqan/find/find_base.h"(494)
+template <typename THaystack, typename TSpec> inline void _finderSetNonEmpty(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(503)
+
+//____________________________________________________________________________
+// _getCharacterClass
+
+template <typename TValue,typename TNeedle2> String <unsigned> _getCharacterClass(TNeedle2 const & host,unsigned start,unsigned end); // "projects/library/seqan/find/find_wild_shiftand.h"(261)
+
+//____________________________________________________________________________
+// _getRoot
+
+template <typename TNeedle, typename TMultiFinder> int _getRoot(Pattern<TNeedle, Pex<NonHierarchical, TMultiFinder > > & me); // "projects/library/seqan/find/find_pex.h"(213)
+template <typename TNeedle, typename TMultiFinder> int _getRoot(Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > &); // "projects/library/seqan/find/find_pex.h"(220)
+
+//____________________________________________________________________________
+// _isInt
+
+inline bool _isInt(String<char> const & number); // "projects/library/seqan/find/find_wild_shiftand.h"(99)
+
+//____________________________________________________________________________
+// _length_wo_wild
+
+template <typename TNeedle> unsigned _length_wo_wild(TNeedle const & needle); // "projects/library/seqan/find/find_wild_shiftand.h"(189)
+
+//____________________________________________________________________________
+// _myersCoreSmall
+
+template <typename TWord, typename TAlignSpec> inline int _myersCoreSmall(TWord &VP, TWord &VN, TWord const &bitmap, int scoreBit, Tag<_MyersUkkonen<TAlignSpec> >); // "projects/library/seqan/find/find_myers_ukkonen.h"(743)
+
+//____________________________________________________________________________
+// _myersCoreSmallDiag
+
+template <typename TWord, typename TAlignSpec> inline int _myersCoreSmallDiag(TWord &VP, TWord &VN, TWord const &bitmap, int scoreBit, Tag<_MyersUkkonen<TAlignSpec> >); // "projects/library/seqan/find/find_myers_ukkonen.h"(758)
+
+//____________________________________________________________________________
+// _patternFirstInit
+
+template <typename TNeedle, typename TSpec, typename TNeedle2> inline void _patternFirstInit(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me, TNeedle2 & needle); // "projects/library/seqan/find/find_myers_ukkonen.h"(174)
+template <typename TNeedle, typename TNeedle2> inline void _patternFirstInit(Pattern<TNeedle, Tag<_MyersUkkonen<AlignTextBanded> > > & me, TNeedle2 & ndl); // "projects/library/seqan/find/find_myers_ukkonen.h"(199)
+
+//____________________________________________________________________________
+// _patternInit
+
+template <typename TNeedle, typename TSpec, typename TFinder> void _patternInit(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > &me, TFinder &); // "projects/library/seqan/find/find_myers_ukkonen.h"(284)
+template <typename TNeedle, typename TFinder> void _patternInit(Pattern<TNeedle, Tag<_MyersUkkonen<AlignTextBanded> > > &me, TFinder &finder); // "projects/library/seqan/find/find_myers_ukkonen.h"(312)
+template <typename TIndex, typename TFloat, typename _TSize, typename TSpec> inline void _patternInit(Pattern<TIndex, Swift<TSpec> > &pattern, TFloat errorRate, _TSize minLengthForAll); // "projects/library/seqan/find/find_swift.h"(333)
+template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, Quasar> & me); // "projects/library/seqan/find/find_quasar.h"(109)
+template <typename TNeedle, typename TFinder, typename TMultiFinder> void _patternInit(Pattern<TNeedle, Pex<NonHierarchical, TMultiFinder > > &me, TFinder &); // "projects/library/seqan/find/find_pex.h"(266)
+template <typename TNeedle, typename TFinder, typename TMultiFinder> void _patternInit(Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > &me, TFinder &); // "projects/library/seqan/find/find_pex.h"(479)
+template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, ShiftAnd> & me); // "projects/library/seqan/find/find_shiftand.h"(130)
+template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, Horspool> &); // "projects/library/seqan/find/find_horspool.h"(125)
+template <typename TNeedle, typename TScore> inline void _patternInit (Pattern<TNeedle, DPSearch<TScore> > & me); // "projects/library/seqan/find/find_score.h"(299)
+template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, MultipleShiftAnd> & me); // "projects/library/seqan/find/find_multiple_shiftand.h"(218)
+template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, BomAlgo> & me); // "projects/library/seqan/find/find_bom.h"(129)
+template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, ShiftOr> & me); // "projects/library/seqan/find/find_shiftor.h"(129)
+template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, WildShiftAnd> & me); // "projects/library/seqan/find/find_wild_shiftand.h"(518)
+template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, SetHorspool> & me); // "projects/library/seqan/find/find_set_horspool.h"(175)
+template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, BndmAlgo> & me); // "projects/library/seqan/find/find_bndm.h"(131)
+template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, AhoCorasick> & me); // "projects/library/seqan/find/find_ahocorasick.h"(225)
+template <typename TNeedle> inline void _patternInit (Pattern<TNeedle, AbndmAlgo> & me); // "projects/library/seqan/find/find_abndm.h"(196)
+
+//____________________________________________________________________________
+// _printMask
+
+inline void _printMask(String <unsigned> const & mask,String <char> name); // "projects/library/seqan/find/find_abndm.h"(33)
+inline void _printMask(String <unsigned> const & mask,unsigned start, unsigned len,String <char> name); // "projects/library/seqan/find/find_abndm.h"(46)
+
+//____________________________________________________________________________
+// _printR
+
+template <typename TNeedle> void _printR(Pattern<TNeedle, AbndmAlgo> & me); // "projects/library/seqan/find/find_abndm.h"(127)
+
+//____________________________________________________________________________
+// _printSwiftBuckets
+
+template <typename TNeedle, typename TIndexSpec, typename TSpec > inline void _printSwiftBuckets(Pattern< Index<TNeedle, TIndexSpec>, Swift<TSpec> > &p); // "projects/library/seqan/find/find_swift.h"(288)
+
+//____________________________________________________________________________
+// _printSwiftParams
+
+template <typename TParams> inline void _printSwiftParams(TParams &bucketParams); // "projects/library/seqan/find/find_swift.h"(276)
+
+//____________________________________________________________________________
+// _swiftBucketNo
+
+template <typename TIndex, typename TSpec, typename TParams, typename TSize> inline unsigned _swiftBucketNo(Pattern<TIndex, Swift<TSpec> > const &, TParams &bucketParams, TSize seqNo); // "projects/library/seqan/find/find_swift.h"(324)
+
+//____________________________________________________________________________
+// _swiftBucketParams
+
+template <typename TIndex, typename TSpec, typename TSize> inline typename Pattern<TIndex, Swift<TSpec> >::TBucketParams & _swiftBucketParams(Pattern<TIndex, Swift<TSpec> > & pattern, TSize seqNo); // "projects/library/seqan/find/find_swift.h"(314)
+
+//____________________________________________________________________________
+// _swiftMultiFlushBuckets
+
+template <typename THaystack, typename TIndex, typename TSpec > inline bool _swiftMultiFlushBuckets( Finder<THaystack, Swift<TSpec> > &finder, Pattern<TIndex, Swift<TSpec> > &pattern); // "projects/library/seqan/find/find_swift.h"(612)
+
+//____________________________________________________________________________
+// _swiftMultiProcessQGram
+
+template <typename THaystack, typename TIndex, typename TSpec, typename THValue > inline bool _swiftMultiProcessQGram( Finder<THaystack, Swift<TSpec> > &finder, Pattern<TIndex, Swift<TSpec> > &pattern, THValue hash); // "projects/library/seqan/find/find_swift.h"(491)
+
+//____________________________________________________________________________
+// _validate
+
+template <typename TNeedle2> bool _validate(TNeedle2 const & needle); // "projects/library/seqan/find/find_wild_shiftand.h"(111)
+
+//____________________________________________________________________________
+// atBegin
+
+template <typename THaystack, typename TSpec> inline bool atBegin(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(513)
+
+//____________________________________________________________________________
+// atEnd
+
+template <typename THaystack, typename TSpec> inline bool atEnd(Finder<THaystack, Swift<TSpec> > & me); // "projects/library/seqan/find/find_swift.h"(218)
+template <typename THaystack, typename TSpec> inline bool atEnd(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(521)
+
+//____________________________________________________________________________
+// beginPosition
+
+template <typename THaystack, typename TSpec> inline typename Position<Finder<THaystack, Swift<TSpec> > >::Type beginPosition(Finder<THaystack, Swift<TSpec> > & finder); // "projects/library/seqan/find/find_swift.h"(720)
+template <typename THaystack, typename TSpec> inline typename Position<Finder<THaystack, Swift<TSpec> > >::Type beginPosition(Finder<THaystack, Swift<TSpec> > const & finder); // "projects/library/seqan/find/find_swift.h"(728)
+template <typename TNeedle, typename TSpec> inline typename Position<Pattern<TNeedle, TSpec> >::Type & beginPosition(Pattern<TNeedle, TSpec> & me); // "projects/library/seqan/find/find_base.h"(176)
+template <typename TNeedle, typename TSpec> inline typename Position<Pattern<TNeedle, TSpec> const >::Type & beginPosition(Pattern<TNeedle, TSpec> const & me); // "projects/library/seqan/find/find_base.h"(182)
+
+//____________________________________________________________________________
+// clear
+
+template <typename TNeedle, typename TIndexSpec, typename TSpec> inline void clear(Pattern<Index<TNeedle, TIndexSpec>, Swift<TSpec> > & me); // "projects/library/seqan/find/find_swift.h"(692)
+template <typename THaystack, typename TSpec> inline void clear(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(484)
+
+//____________________________________________________________________________
+// container
+
+template <typename THaystack, typename TSpec> inline typename _Parameter<THaystack>::Type container(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(420)
+template <typename THaystack, typename TSpec> inline typename _Parameter<THaystack>::Type container(Finder<THaystack, TSpec> const & me); // "projects/library/seqan/find/find_base.h"(428)
+
+//____________________________________________________________________________
+// empty
+
+template <typename TNeedle, typename TIndexSpec, typename TSpec> inline bool empty(Pattern<Index<TNeedle, TIndexSpec>, Swift<TSpec> > & me); // "projects/library/seqan/find/find_swift.h"(685)
+template <typename THaystack, typename TSpec> inline bool empty(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(476)
+
+//____________________________________________________________________________
+// endPosition
+
+template <typename THaystack, typename TSpec> inline typename Position<Finder<THaystack, Swift<TSpec> > >::Type endPosition(Finder<THaystack, Swift<TSpec> > & finder); // "projects/library/seqan/find/find_swift.h"(738)
+template <typename THaystack, typename TSpec> inline typename Position<Finder<THaystack, Swift<TSpec> > >::Type endPosition(Finder<THaystack, Swift<TSpec> > const & finder); // "projects/library/seqan/find/find_swift.h"(746)
+template <typename TNeedle, typename TSpec> inline typename Position<Pattern<TNeedle, TSpec> >::Type & endPosition(Pattern<TNeedle, TSpec> & me); // "projects/library/seqan/find/find_base.h"(200)
+template <typename TNeedle, typename TSpec> inline typename Position<Pattern<TNeedle, TSpec> const >::Type & endPosition(Pattern<TNeedle, TSpec> const & me); // "projects/library/seqan/find/find_base.h"(206)
+
+//____________________________________________________________________________
+// find
+
+template <typename TFinder, typename TNeedle, typename TSpec> inline bool find (TFinder & finder, Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me); // "projects/library/seqan/find/find_myers_ukkonen.h"(961)
+template <typename TFinder, typename TNeedle, typename TSpec> inline bool find (TFinder & finder, Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me, int const k); // "projects/library/seqan/find/find_myers_ukkonen.h"(997)
+template <typename THaystack, typename TNeedle, typename TIndexSpec, typename TSpec> inline bool find( Finder<THaystack, Swift<TSpec> > &finder, Pattern<Index<TNeedle, TIndexSpec>, Swift<TSpec> > &pattern, double errorRate); // "projects/library/seqan/find/find_swift.h"(799)
+//template <typename THashes, typename TPipeSpec, typename TNeedle, typename TIndexSpec, typename TSpec> inline bool find( Finder<Pipe<THashes, TPipeSpec>, Swift<TSpec> > &finder, Pattern<Index<TNeedle, TIndexSpec>, Swift<TSpec> > &pattern, double errorRate, bool printDots); // "projects/library/seqan/find/find_swift.h"(843)
+template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, Quasar> & me); // "projects/library/seqan/find/find_quasar.h"(138)
+template <typename TFinder, typename TNeedle, typename TMultiFinder> inline bool find (TFinder & finder, Pattern<TNeedle, Pex<NonHierarchical, TMultiFinder > > & me); // "projects/library/seqan/find/find_pex.h"(335)
+template <typename TFinder, typename TNeedle, typename TMultiFinder> inline bool find (TFinder & finder, Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > & me); // "projects/library/seqan/find/find_pex.h"(520)
+template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, ShiftAnd> & me); // "projects/library/seqan/find/find_shiftand.h"(217)
+template <typename TFinder, typename TNeedle2> bool find(TFinder & finder, Pattern<TNeedle2, Horspool> & me); // "projects/library/seqan/find/find_horspool.h"(448)
+template <typename TFinder, typename TNeedle, typename TScore> inline bool find(TFinder & finder, Pattern<TNeedle, DPSearch<TScore> > & me); // "projects/library/seqan/find/find_score.h"(430)
+template <typename TFinder, typename TNeedle, typename TScore> inline bool find(TFinder & finder, Pattern<TNeedle, DPSearch<TScore> > & me, int const limit_); // "projects/library/seqan/find/find_score.h"(440)
+template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, MultipleShiftAnd> & me); // "projects/library/seqan/find/find_multiple_shiftand.h"(386)
+template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, BomAlgo> & me); // "projects/library/seqan/find/find_bom.h"(159)
+template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, ShiftOr> & me); // "projects/library/seqan/find/find_shiftor.h"(248)
+template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, WildShiftAnd> & me); // "projects/library/seqan/find/find_wild_shiftand.h"(631)
+template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, SetHorspool> & me); // "projects/library/seqan/find/find_set_horspool.h"(213)
+template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, BndmAlgo> & me); // "projects/library/seqan/find/find_bndm.h"(229)
+template <typename TFinder, typename TNeedle> inline bool find(TFinder & finder, Pattern<TNeedle, AhoCorasick> & me); // "projects/library/seqan/find/find_ahocorasick.h"(263)
+template <typename TFinder, typename TNeedle> inline bool find (TFinder & finder, Pattern<TNeedle, AbndmAlgo > & me); // "projects/library/seqan/find/find_abndm.h"(575)
+template <typename TFinder, typename TNeedle> inline bool find (TFinder & finder, Pattern<TNeedle, AbndmAlgo > & me, int const k); // "projects/library/seqan/find/find_abndm.h"(594)
+
+//____________________________________________________________________________
+// find_horspool
+
+template <typename TFinder, typename TNeedle2> bool find_horspool(TFinder & finder, Pattern<TNeedle2, Horspool> & me, bool find_first); // "projects/library/seqan/find/find_horspool.h"(152)
+template <typename TValue, typename TFormat, typename TFile, typename FileReaderTSpec, typename TFinderSpec, typename TNeedle2> bool find_horspool(Finder<String<TValue, FileReader<TFormat, TFile, FileReaderTSpec> >, TFinderSpec > & finder, Pattern<TNeedle2, Horspool> & me, bool find_first); // "projects/library/seqan/find/find_horspool.h"(315)
+
+//____________________________________________________________________________
+// getScore
+
+template <typename TNeedle, typename TSpec> int getScore(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me); // "projects/library/seqan/find/find_myers_ukkonen.h"(271)
+template <typename TNeedle, typename TVerification, typename TMultiFinder> int getScore(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me); // "projects/library/seqan/find/find_pex.h"(230)
+template <typename TNeedle, typename TScore> inline typename Value<TScore>::Type getScore(Pattern<TNeedle, DPSearch<TScore> > & me); // "projects/library/seqan/find/find_score.h"(290)
+template <typename TNeedle> int getScore(Pattern<TNeedle, AbndmAlgo > & me); // "projects/library/seqan/find/find_abndm.h"(228)
+
+//____________________________________________________________________________
+// goBegin
+
+template <typename THaystack, typename TSpec> inline void goBegin(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(531)
+
+//____________________________________________________________________________
+// goEnd
+
+template <typename THaystack, typename TSpec> inline void goEnd(Finder<THaystack, Swift<TSpec> > & me); // "projects/library/seqan/find/find_swift.h"(225)
+template <typename THaystack, typename TSpec> inline void goEnd(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(540)
+
+//____________________________________________________________________________
+// haystack
+
+template <typename TObject > inline typename Haystack<TObject>::Type & haystack(TObject &obj); // "projects/library/seqan/find/find_base.h"(703)
+template <typename TObject > inline typename Haystack<TObject const>::Type & haystack(TObject const &obj); // "projects/library/seqan/find/find_base.h"(709)
+
+//____________________________________________________________________________
+// host
+
+template <typename TNeedle, typename TSpec> inline typename Host<Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > >::Type & host(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me); // "projects/library/seqan/find/find_myers_ukkonen.h"(227)
+template <typename TNeedle, typename TSpec> inline typename Host<Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > const>::Type & host(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > const & me); // "projects/library/seqan/find/find_myers_ukkonen.h"(235)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, Quasar>const>::Type & host(Pattern<TNeedle, Quasar> & me); // "projects/library/seqan/find/find_quasar.h"(119)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, Quasar>const>::Type & host(Pattern<TNeedle, Quasar> const & me); // "projects/library/seqan/find/find_quasar.h"(127)
+template <typename TNeedle, typename TVerification, typename TMultiFinder> inline typename Host<Pattern<TNeedle, Pex<TVerification,TMultiFinder > > const>::Type & host(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me); // "projects/library/seqan/find/find_pex.h"(196)
+template <typename TNeedle, typename TVerification, typename TMultiFinder> inline typename Host<Pattern<TNeedle, Pex<TVerification,TMultiFinder > > const>::Type & host(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > const & me); // "projects/library/seqan/find/find_pex.h"(204)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, ShiftAnd>const>::Type & host(Pattern<TNeedle, ShiftAnd> & me); // "projects/library/seqan/find/find_shiftand.h"(142)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, ShiftAnd>const>::Type & host(Pattern<TNeedle, ShiftAnd> const & me); // "projects/library/seqan/find/find_shiftand.h"(150)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, Horspool> >::Type & host(Pattern<TNeedle, Horspool> & me); // "projects/library/seqan/find/find_horspool.h"(132)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, Horspool> const>::Type & host(Pattern<TNeedle, Horspool> const & me); // "projects/library/seqan/find/find_horspool.h"(140)
+template <typename THaystack, typename TSpec> inline typename _Parameter<THaystack>::Type host(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(404)
+template <typename THaystack, typename TSpec> inline typename _Parameter<THaystack>::Type host(Finder<THaystack, TSpec> const & me); // "projects/library/seqan/find/find_base.h"(412)
+template <typename TNeedle, typename TScore> inline typename Host<Pattern<TNeedle, DPSearch<TScore> > >::Type & host(Pattern<TNeedle, DPSearch<TScore> > & me); // "projects/library/seqan/find/find_score.h"(144)
+template <typename TNeedle, typename TScore> inline typename Host<Pattern<TNeedle, DPSearch<TScore> > const>::Type & host(Pattern<TNeedle, DPSearch<TScore> > const & me); // "projects/library/seqan/find/find_score.h"(152)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, MultipleShiftAnd>const>::Type & host(Pattern<TNeedle, MultipleShiftAnd> & me); // "projects/library/seqan/find/find_multiple_shiftand.h"(236)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, MultipleShiftAnd>const>::Type & host(Pattern<TNeedle, MultipleShiftAnd> const & me); // "projects/library/seqan/find/find_multiple_shiftand.h"(244)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, BomAlgo>const>::Type & host(Pattern<TNeedle, BomAlgo> & me); // "projects/library/seqan/find/find_bom.h"(140)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, BomAlgo>const>::Type & host(Pattern<TNeedle, BomAlgo> const & me); // "projects/library/seqan/find/find_bom.h"(148)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, ShiftOr>const>::Type & host(Pattern<TNeedle, ShiftOr> & me); // "projects/library/seqan/find/find_shiftor.h"(143)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, ShiftOr>const>::Type & host(Pattern<TNeedle, ShiftOr> const & me); // "projects/library/seqan/find/find_shiftor.h"(151)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, WildShiftAnd>const>::Type & host(Pattern<TNeedle, WildShiftAnd> & me); // "projects/library/seqan/find/find_wild_shiftand.h"(550)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, WildShiftAnd>const>::Type & host(Pattern<TNeedle, WildShiftAnd> const & me); // "projects/library/seqan/find/find_wild_shiftand.h"(558)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, SetHorspool>const>::Type & host(Pattern<TNeedle, SetHorspool> & me); // "projects/library/seqan/find/find_set_horspool.h"(188)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, SetHorspool>const>::Type & host(Pattern<TNeedle, SetHorspool> const & me); // "projects/library/seqan/find/find_set_horspool.h"(196)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, BndmAlgo>const>::Type & host(Pattern<TNeedle, BndmAlgo> & me); // "projects/library/seqan/find/find_bndm.h"(143)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, BndmAlgo>const>::Type & host(Pattern<TNeedle, BndmAlgo> const & me); // "projects/library/seqan/find/find_bndm.h"(151)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, AhoCorasick>const>::Type & host(Pattern<TNeedle, AhoCorasick> & me); // "projects/library/seqan/find/find_ahocorasick.h"(238)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, AhoCorasick>const>::Type & host(Pattern<TNeedle, AhoCorasick> const & me); // "projects/library/seqan/find/find_ahocorasick.h"(246)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, AbndmAlgo>const>::Type & host(Pattern<TNeedle, AbndmAlgo> & me); // "projects/library/seqan/find/find_abndm.h"(209)
+template <typename TNeedle> inline typename Host<Pattern<TNeedle, AbndmAlgo>const>::Type & host(Pattern<TNeedle, AbndmAlgo> const & me); // "projects/library/seqan/find/find_abndm.h"(217)
+
+//____________________________________________________________________________
+// hostIterator
+
+template <typename THaystack, typename TSpec> inline typename Iterator<THaystack, Rooted>::Type & hostIterator(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(458)
+template <typename THaystack, typename TSpec> inline typename Iterator<THaystack, Rooted>::Type const & hostIterator(Finder<THaystack, TSpec> const & me); // "projects/library/seqan/find/find_base.h"(466)
+
+//____________________________________________________________________________
+// needle
+
+template <typename TObject > inline typename Needle<TObject>::Type & needle(TObject &obj); // "projects/library/seqan/find/find_base.h"(252)
+template <typename TObject > inline typename Needle<TObject const>::Type & needle(TObject const &obj); // "projects/library/seqan/find/find_base.h"(259)
+template <typename TNeedle, typename TSpec > inline typename Needle< Pattern<TNeedle, TSpec> >::Type & needle(Pattern<TNeedle, TSpec> & obj); // "projects/library/seqan/find/find_base.h"(269)
+template <typename TNeedle, typename TSpec > inline typename Needle< Pattern<TNeedle, TSpec> const>::Type & needle(Pattern<TNeedle, TSpec> const & obj); // "projects/library/seqan/find/find_base.h"(276)
+
+//____________________________________________________________________________
+// operator+
+
+template <typename THaystack, typename TSpec, typename TIntegral> inline Finder<THaystack, TSpec> const operator+ (Finder<THaystack, TSpec> const & left, TIntegral right); // "projects/library/seqan/find/find_base.h"(617)
+
+//____________________________________________________________________________
+// operator++
+
+template <typename THaystack, typename TSpec> inline Finder<THaystack, TSpec> & operator++(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(601)
+
+//____________________________________________________________________________
+// operator+=
+
+template <typename THaystack, typename TSpec, typename TIntegral> inline Finder<THaystack, TSpec> & operator+= (Finder<THaystack, TSpec> & left, TIntegral right); // "projects/library/seqan/find/find_base.h"(630)
+
+//____________________________________________________________________________
+// operator-
+
+template <typename THaystack, typename TSpec, typename TIntegral> inline Finder<THaystack, TSpec> const operator- (Finder<THaystack, TSpec> const & left, TIntegral right); // "projects/library/seqan/find/find_base.h"(643)
+template <typename THaystack, typename TSpec, typename TIntegral> inline typename Difference<Finder<THaystack, TSpec> const>::Type operator- (Finder<THaystack, TSpec> const & left, Finder<THaystack, TSpec> const & right); // "projects/library/seqan/find/find_base.h"(651)
+
+//____________________________________________________________________________
+// operator--
+
+template <typename THaystack, typename TSpec> inline Finder<THaystack, TSpec> & operator--(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(592)
+
+//____________________________________________________________________________
+// operator-=
+
+template <typename THaystack, typename TSpec, typename TIntegral> inline Finder<THaystack, TSpec> & operator-= (Finder<THaystack, TSpec> & left, TIntegral right); // "projects/library/seqan/find/find_base.h"(664)
+
+//____________________________________________________________________________
+// position
+
+template <typename THaystack, typename TSpec> inline typename Position<Finder<THaystack, Swift<TSpec> > >::Type position(Finder<THaystack, Swift<TSpec> > & finder); // "projects/library/seqan/find/find_swift.h"(702)
+template <typename THaystack, typename TSpec> inline typename Position<Finder<THaystack, Swift<TSpec> > >::Type position(Finder<THaystack, Swift<TSpec> > const & finder); // "projects/library/seqan/find/find_swift.h"(710)
+template <typename THaystack, typename TSpec> inline typename Position<Finder<THaystack, TSpec> >::Type position(Finder<THaystack, TSpec> & me); // "projects/library/seqan/find/find_base.h"(551)
+template <typename THaystack, typename TSpec> inline typename Position<Finder<THaystack, TSpec> >::Type position(Finder<THaystack, TSpec> const & me); // "projects/library/seqan/find/find_base.h"(560)
+template <typename TNeedle> inline typename Size<TNeedle>::Type position(Pattern<TNeedle, MultipleShiftAnd> & me); // "projects/library/seqan/find/find_multiple_shiftand.h"(255)
+template <typename TNeedle> inline typename Size<TNeedle>::Type position(Pattern<TNeedle, SetHorspool> & me); // "projects/library/seqan/find/find_set_horspool.h"(207)
+template <typename TNeedle> inline typename Size<TNeedle>::Type position(Pattern<TNeedle, AhoCorasick> & me); // "projects/library/seqan/find/find_ahocorasick.h"(257)
+
+//____________________________________________________________________________
+// range
+
+template <typename THaystack, typename TSpec> inline typename Infix<THaystack>::Type range(Finder<THaystack, Swift<TSpec> > &finder); // "projects/library/seqan/find/find_swift.h"(756)
+template <typename THaystack, typename TSpec, typename TText> inline typename Infix<TText>::Type range(Finder<THaystack, Swift<TSpec> > &finder, TText &text); // "projects/library/seqan/find/find_swift.h"(772)
+template <typename TNeedle, typename TIndexSpec, typename TSpec> inline typename Value<TNeedle>::Type & range(Pattern<Index<TNeedle, TIndexSpec>, Swift<TSpec> > &pattern); // "projects/library/seqan/find/find_swift.h"(788)
+
+//____________________________________________________________________________
+// scoreLimit
+
+template <typename TNeedle, typename TSpec> inline int scoreLimit(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > const & me); // "projects/library/seqan/find/find_myers_ukkonen.h"(247)
+template <typename TNeedle, typename TVerification, typename TMultiFinder> inline int scoreLimit(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > const & me); // "projects/library/seqan/find/find_pex.h"(241)
+template <typename TNeedle, typename TScore> inline typename Value<TScore>::Type scoreLimit(Pattern<TNeedle, DPSearch<TScore> > const & me); // "projects/library/seqan/find/find_score.h"(245)
+template <typename TNeedle> inline int scoreLimit(Pattern<TNeedle, AbndmAlgo > const & me); // "projects/library/seqan/find/find_abndm.h"(551)
+
+//____________________________________________________________________________
+// scoringScheme
+
+template <typename TNeedle, typename TScore> inline TScore const & scoringScheme(Pattern<TNeedle, DPSearch<TScore> > & me); // "projects/library/seqan/find/find_score.h"(193)
+
+//____________________________________________________________________________
+// segment
+
+template <typename TNeedle, typename TSpec> inline typename Infix<TNeedle>::Type segment(Pattern<TNeedle, TSpec> & me); // "projects/library/seqan/find/find_base.h"(223)
+template <typename TNeedle, typename TSpec> inline typename Infix<TNeedle>::Type segment(Pattern<TNeedle, TSpec> const & me); // "projects/library/seqan/find/find_base.h"(230)
+
+//____________________________________________________________________________
+// setBeginPosition
+
+template <typename TNeedle, typename TSpec, typename TPosition> inline void setBeginPosition(Pattern<TNeedle, TSpec> & me, TPosition _pos); // "projects/library/seqan/find/find_base.h"(191)
+
+//____________________________________________________________________________
+// setContainer
+
+template <typename THaystack, typename TSpec> inline void setContainer(Finder<THaystack, TSpec> & me, typename _Parameter<THaystack>::Type container_); // "projects/library/seqan/find/find_base.h"(447)
+
+//____________________________________________________________________________
+// setEndPosition
+
+template <typename TNeedle, typename TSpec, typename TPosition> inline void setEndPosition(Pattern<TNeedle, TSpec> & me, TPosition _pos); // "projects/library/seqan/find/find_base.h"(214)
+
+//____________________________________________________________________________
+// setHaystack
+
+template <typename THaystack, typename TSpec > inline void setHaystack(Finder<THaystack, TSpec> &obj, THaystack const &hstk); // "projects/library/seqan/find/find_base.h"(686)
+
+//____________________________________________________________________________
+// setHost
+
+template <typename TNeedle, typename TSpec, typename TNeedle2> void setHost(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me, TNeedle2 & ndl); // "projects/library/seqan/find/find_myers_ukkonen.h"(209)
+template <typename TNeedle, typename TSpec, typename TNeedle2> void setHost(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me, TNeedle2 const & ndl); // "projects/library/seqan/find/find_myers_ukkonen.h"(217)
+template <typename TNeedle, typename TNeedle2> inline void setHost (Pattern<TNeedle, Quasar> & me, TNeedle2 const& needle); // "projects/library/seqan/find/find_quasar.h"(92)
+template <typename TNeedle, typename TNeedle2> inline void setHost (Pattern<TNeedle, Quasar> & me, TNeedle2 & needle); // "projects/library/seqan/find/find_quasar.h"(100)
+template <typename TNeedle, typename TNeedle2, typename TVerification, typename TMultiFinder> void setHost (Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me, TNeedle2 const & needle); // "projects/library/seqan/find/find_pex.h"(176)
+template <typename TNeedle, typename TNeedle2, typename TVerification, typename TMultiFinder> void setHost (Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me, TNeedle2 & needle); // "projects/library/seqan/find/find_pex.h"(187)
+template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, ShiftAnd> & me, TNeedle2 const & needle); // "projects/library/seqan/find/find_shiftand.h"(80)
+template <typename TNeedle, typename TNeedle2> inline void setHost (Pattern<TNeedle, ShiftAnd> & me, TNeedle2 & needle); // "projects/library/seqan/find/find_shiftand.h"(121)
+template <typename TNeedle, typename TNeedle2> void setHost(Pattern<TNeedle, Horspool> & me, TNeedle2 const & ndl); // "projects/library/seqan/find/find_horspool.h"(86)
+template <typename TNeedle, typename TNeedle2> void setHost(Pattern<TNeedle, Horspool> & horsp, TNeedle2 & ndl); // "projects/library/seqan/find/find_horspool.h"(117)
+template <typename TNeedle, typename TSpec, typename TNeedle2> inline void setHost(Pattern<TNeedle, TSpec> & me, TNeedle2 const & ndl); // "projects/library/seqan/find/find_base.h"(161)
+template <typename TNeedle, typename TSpec, typename TNeedle2> inline void setHost(Pattern<TNeedle, TSpec> & me, TNeedle2 & ndl); // "projects/library/seqan/find/find_base.h"(168)
+template <typename THaystack, typename TSpec> inline void setHost(Finder<THaystack, TSpec> & me, typename _Parameter<THaystack>::Type container_); // "projects/library/seqan/find/find_base.h"(438)
+template <typename TNeedle, typename TScore, typename TNeedle2> void setHost(Pattern<TNeedle, DPSearch<TScore> > & me, TNeedle2 & ndl); // "projects/library/seqan/find/find_score.h"(164)
+template <typename TNeedle, typename TScore, typename TNeedle2> void setHost(Pattern<TNeedle, DPSearch<TScore> > & me, TNeedle2 const & ndl); // "projects/library/seqan/find/find_score.h"(172)
+template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, MultipleShiftAnd> & me, TNeedle2 const & needle); // "projects/library/seqan/find/find_multiple_shiftand.h"(124)
+template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, MultipleShiftAnd> & me, TNeedle2 & needle); // "projects/library/seqan/find/find_multiple_shiftand.h"(209)
+template <typename TNeedle, typename TNeedle2> inline void setHost (Pattern<TNeedle, BomAlgo> & me, TNeedle2 const& needle); // "projects/library/seqan/find/find_bom.h"(108)
+template <typename TNeedle, typename TNeedle2> inline void setHost (Pattern<TNeedle, BomAlgo> & me, TNeedle2 & needle); // "projects/library/seqan/find/find_bom.h"(120)
+template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, ShiftOr> & me, TNeedle2 const & needle); // "projects/library/seqan/find/find_shiftor.h"(79)
+template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, ShiftOr> & me, TNeedle2 & needle); // "projects/library/seqan/find/find_shiftor.h"(120)
+template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, WildShiftAnd> & me, TNeedle2 const & needle); // "projects/library/seqan/find/find_wild_shiftand.h"(289)
+template <typename TNeedle, typename TNeedle2> inline void setHost (Pattern<TNeedle, WildShiftAnd> & me, TNeedle2 & needle); // "projects/library/seqan/find/find_wild_shiftand.h"(509)
+template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, SetHorspool> & me, TNeedle2 const & needle); // "projects/library/seqan/find/find_set_horspool.h"(112)
+template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, SetHorspool> & me, TNeedle2 & needle); // "projects/library/seqan/find/find_set_horspool.h"(166)
+template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, BndmAlgo> & me, TNeedle2 const& needle); // "projects/library/seqan/find/find_bndm.h"(82)
+template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, BndmAlgo> & me, TNeedle2 & needle); // "projects/library/seqan/find/find_bndm.h"(122)
+template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, AhoCorasick> & me, TNeedle2 const & needle); // "projects/library/seqan/find/find_ahocorasick.h"(187)
+template <typename TNeedle, typename TNeedle2> inline void setHost (Pattern<TNeedle, AhoCorasick> & me, TNeedle2 & needle); // "projects/library/seqan/find/find_ahocorasick.h"(216)
+template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, AbndmAlgo> & me, TNeedle2 const& needle); // "projects/library/seqan/find/find_abndm.h"(140)
+template <typename TNeedle, typename TNeedle2> void setHost (Pattern<TNeedle, AbndmAlgo> & me, TNeedle2 & needle); // "projects/library/seqan/find/find_abndm.h"(188)
+
+//____________________________________________________________________________
+// setNeedle
+
+template <typename TNeedle, typename TSpec > inline void setNeedle(Pattern<TNeedle, TSpec> &obj, TNeedle const &ndl); // "projects/library/seqan/find/find_base.h"(293)
+
+//____________________________________________________________________________
+// setPosition
+
+template <typename THaystack, typename TSpec, typename TPosition> inline void setPosition(Finder<THaystack, TSpec> & me, TPosition pos_); // "projects/library/seqan/find/find_base.h"(582)
+
+//____________________________________________________________________________
+// setScoreLimit
+
+template <typename TNeedle, typename TSpec, typename TScoreValue> inline void setScoreLimit(Pattern<TNeedle, Tag<_MyersUkkonen<TSpec> > > & me, TScoreValue _limit); // "projects/library/seqan/find/find_myers_ukkonen.h"(260)
+template <typename TNeedle, typename TScoreValue,typename TVerification, typename TMultiFinder> inline void setScoreLimit(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me, TScoreValue _limit); // "projects/library/seqan/find/find_pex.h"(254)
+template <typename TNeedle, typename TScore, typename TScoreValue> inline void setScoreLimit(Pattern<TNeedle, DPSearch<TScore> > & me, TScoreValue _limit); // "projects/library/seqan/find/find_score.h"(266)
+template <typename TNeedle, typename TScoreValue> inline void setScoreLimit(Pattern<TNeedle, AbndmAlgo > & me, TScoreValue _limit); // "projects/library/seqan/find/find_abndm.h"(564)
+
+//____________________________________________________________________________
+// setScoringScheme
+
+template <typename TNeedle, typename TScore, typename TScore2> inline void setScoringScheme(Pattern<TNeedle, DPSearch<TScore> > & me, TScore2 & score); // "projects/library/seqan/find/find_score.h"(215)
+template <typename TNeedle, typename TScore, typename TScore2> inline void setScoringScheme(Pattern<TNeedle, DPSearch<TScore> > & me, TScore2 const & score); // "projects/library/seqan/find/find_score.h"(224)
+
+//____________________________________________________________________________
+// valid
+
+template <typename TNeedle> inline bool valid(Pattern <TNeedle,WildShiftAnd> & me); // "projects/library/seqan/find/find_wild_shiftand.h"(531)
+template <typename TNeedle> inline bool valid(Pattern <TNeedle,WildShiftAnd> const & me); // "projects/library/seqan/find/find_wild_shiftand.h"(539)
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif
+
diff --git a/src/libSSA/seqan/find/find_horspool.h b/src/libSSA/seqan/find/find_horspool.h
new file mode 100644
index 0000000..5733163
--- /dev/null
+++ b/src/libSSA/seqan/find/find_horspool.h
@@ -0,0 +1,483 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: find_horspool.h,v 1.1 2008/08/25 16:20:06 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FIND_HORSPOOL_H
+#define SEQAN_HEADER_FIND_HORSPOOL_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// Horspool
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Spec.Horspool:
+..summary: Exact string matching using Horspool's algorithm (1980).
+..general:Class.Pattern
+..cat:Searching
+..signature:Pattern<TNeedle, Horspool>
+..param.TNeedle:The needle type.
+...type:Class.String
+*/
+
+///.Class.Pattern.param.TSpec.type:Spec.Horspool
+
+struct _Horspool;
+typedef Tag<_Horspool> Horspool;
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TNeedle>
+class Pattern<TNeedle, Horspool>
+{
+//____________________________________________________________________________
+
+public:
+ typedef typename Size<TNeedle>::Type TSize;
+
+ Holder<TNeedle> data_needle;
+ String<TSize> data_map;
+
+//____________________________________________________________________________
+
+public:
+ Pattern() {}
+
+ Pattern(Pattern const & other_):
+ data_map(other_.data_map) {}
+
+ template <typename TNeedle2>
+ Pattern(TNeedle2 const & ndl)
+ {
+ setHost(*this, ndl);
+ }
+
+ Pattern const &
+ operator = (Pattern const & other_)
+ {
+ data_map = other_.data_map;
+ return *this;
+ }
+//____________________________________________________________________________
+};
+
+
+template <typename TNeedle, typename TNeedle2>
+void
+setHost(Pattern<TNeedle, Horspool> & me, TNeedle2 const & ndl)
+{
+ typedef typename Value<TNeedle>::Type TValue;
+ typedef typename Size<TNeedle>::Type TSize;
+
+ SEQAN_ASSERT(!empty(ndl));
+
+ TSize value_size = ValueSize<TValue>::VALUE;
+
+ //make room for map
+ resize(me.data_map, value_size);
+
+ //fill map
+ typename Value<String<TSize> >::Type jump_width = length(ndl); //das ist so umstaendlich wegen VC++ 2003
+ arrayFill(begin(me.data_map, Standard()), begin(me.data_map, Standard()) + value_size, jump_width);
+
+ typename Iterator<TNeedle2 const, Standard>::Type it;
+ it = begin(ndl, Standard());
+ while (jump_width > 1)
+ {
+ --jump_width;
+ unsigned int pos_ = *it; //conversion value type to unsigned int
+ me.data_map[pos_] = jump_width;
+ ++it;
+ }
+
+ me.data_needle = ndl;
+}
+
+template <typename TNeedle, typename TNeedle2>
+void
+setHost(Pattern<TNeedle, Horspool> & horsp, TNeedle2 & ndl)
+{
+ setHost(horsp, reinterpret_cast<TNeedle2 const &>(ndl));
+}
+
+//____________________________________________________________________________
+
+
+template <typename TNeedle>
+inline void _patternInit (Pattern<TNeedle, Horspool> &) {}
+
+//____________________________________________________________________________
+
+template <typename TNeedle>
+inline typename Host<Pattern<TNeedle, Horspool> >::Type &
+host(Pattern<TNeedle, Horspool> & me)
+{
+SEQAN_CHECKPOINT
+ return value(me.data_needle);
+}
+
+template <typename TNeedle>
+inline typename Host<Pattern<TNeedle, Horspool> const>::Type &
+host(Pattern<TNeedle, Horspool> const & me)
+{
+SEQAN_CHECKPOINT
+ return value(me.data_needle);
+}
+
+//____________________________________________________________________________
+
+template <typename TFinder, typename TNeedle2>
+bool
+find_horspool(TFinder & finder,
+ Pattern<TNeedle2, Horspool> & me,
+ bool find_first)
+{
+SEQAN_CHECKPOINT
+ typedef typename Haystack<TFinder>::Type THaystack;
+ THaystack & hayst = haystack(finder);
+
+ typedef Pattern<TNeedle2, Horspool> TPattern;
+ typedef typename Needle<TPattern>::Type TNeedle;
+ TNeedle & ndl = needle(me);
+
+ typedef typename Size<TNeedle>::Type TNeedleSize;
+ TNeedleSize ndl_size = length(ndl);
+
+ typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
+ THaystackIterator haystack_end = end(hayst, Standard());
+ THaystackIterator it = begin(hayst, Standard());
+ it += position(finder) + ndl_size - 1; //it points to the last character
+ THaystackIterator it_next = it;
+
+ typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
+ TNeedleIterator nit; //needle iterator
+ TNeedleIterator nit_begin = begin(ndl, Standard());
+ TNeedleIterator nit_end = end(ndl, Standard()) - 1; //here the verification begins
+
+ unsigned int char_i;
+
+ if (find_first)
+ {
+ goto VALIDATE;
+ }
+
+MOVE_FURTHER:
+ //move to next position
+ char_i = *it; //conversion to unsigned integer
+ it_next = it + me.data_map[char_i];
+ if (it_next >= haystack_end)
+ {//found nothing
+ return false;
+ }
+
+ it = it_next;
+
+VALIDATE:
+ //validate current position
+ for (nit = nit_end; nit >= nit_begin; --nit)
+ {
+ if (*nit != *it_next)
+ {//invalid!
+ goto MOVE_FURTHER;
+ }
+ --it_next;
+ }
+
+ //valid! return hit
+ setPosition(finder, it - begin(hayst, Standard()) - ndl_size + 1);
+ return true;
+}
+
+//____________________________________________________________________________
+// Sentinel variant (not used at the moment)
+//TODO: if not enough space at the end of the haystack: call non-sentinel search
+/*
+template <typename TFinder, typename TNeedle2>
+bool
+find_horspool_sentinel(TFinder & finder,
+ Pattern<TNeedle2, Horspool> & me,
+ bool find_first)
+{
+SEQAN_CHECKPOINT
+ typedef typename Haystack<TFinder>::Type THaystack;
+ THaystack & hayst = haystack(finder);
+
+
+ typedef Pattern<TNeedle2, Horspool> TPattern;
+ typedef typename Needle<TPattern>::Type TNeedle;
+ TNeedle & ndl = needle(me);
+
+ //implant sentinel
+ typename Size<THaystack>::Type old_haystack_size = length(hayst);
+ if (find_first)
+ {
+ typedef typename Position<TFinder>::Type TFinderPosition;
+ TFinderPosition finder_pos = position(finder);
+
+ append(hayst, ndl, Exact());
+ if (length(hayst) != old_haystack_size + length(ndl))
+ {//not enough place in haystack
+//TODO!!!
+printf("error!");
+return false;
+ }
+ setPosition(finder, finder_pos);
+ }
+ else
+ {
+ _setLength(hayst, old_haystack_size + length(ndl));
+ }
+
+ typedef typename Size<TNeedle>::Type TNeedleSize;
+ TNeedleSize ndl_size = length(ndl);
+
+ typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
+ THaystackIterator it = begin(hayst, Standard());
+ THaystackIterator haystack_end = it + old_haystack_size;
+ it += position(finder) + ndl_size - 1; //it points to the last character
+
+ typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
+ TNeedleIterator nit; //needle iterator
+ TNeedleIterator nit_begin = begin(ndl, Standard());
+ TNeedleIterator nit_end = end(ndl, Standard()) - 1; //here the verification begins
+
+ typedef typename Value<TNeedle>::Type TNeedleValue;
+ TNeedleValue char_needle_last = *nit_end;
+ TNeedleValue char_haystack_last;
+
+ char_haystack_last = *it;
+
+ if (find_first)
+ {
+ goto VALIDATE;
+ }
+
+ //main loop
+MOVE_FURTHER:
+ it += me.data_map[_ord(char_haystack_last)];
+ char_haystack_last = *it;
+ if (char_haystack_last != char_needle_last) goto MOVE_FURTHER;
+
+
+ if (it >= haystack_end)
+ {//found nothing
+ resize(hayst, old_haystack_size);
+ return false;
+ }
+
+VALIDATE:
+ //validate current position
+ THaystackIterator it_back = it;
+ for (nit = nit_end; nit >= nit_begin; --nit)
+ {
+ if (*nit != *it_back)
+ {//invalid!
+ goto MOVE_FURTHER;
+ }
+ --it_back;
+ }
+
+ //valid! return hit
+ setPosition(finder, it - begin(hayst, Standard()) - ndl_size + 1);
+ resize(hayst, old_haystack_size);
+ return true;
+}
+*/
+//____________________________________________________________________________
+//spec for file reader haystacks
+
+template <typename TFormat, typename TFile, typename TSpec>
+struct FileReader;
+
+template <typename TValue, typename TFormat, typename TFile, typename FileReaderTSpec, typename TFinderSpec, typename TNeedle2>
+bool
+find_horspool(Finder<String<TValue, FileReader<TFormat, TFile, FileReaderTSpec> >, TFinderSpec > & finder,
+ Pattern<TNeedle2, Horspool> & me,
+ bool find_first)
+{
+SEQAN_CHECKPOINT
+ typedef Finder<String<TValue, FileReader<TFormat, TFile, FileReaderTSpec> >, TFinderSpec > TFinder;
+ typedef typename Haystack<TFinder>::Type THaystack;
+ THaystack & hayst = haystack(finder);
+
+ typedef Pattern<TNeedle2, Horspool> TPattern;
+ typedef typename Needle<TPattern>::Type TNeedle;
+ TNeedle & ndl = needle(me);
+
+ typedef typename Size<TNeedle>::Type TNeedleSize;
+ TNeedleSize ndl_size = length(ndl);
+
+ typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
+ THaystackIterator it(hayst, position(finder) + ndl_size - 1); //it points to the last character
+
+ typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
+ TNeedleIterator nit; //needle iterator
+ TNeedleIterator nit_begin = begin(ndl, Standard());
+ TNeedleIterator nit_end = end(ndl, Standard()) - 1; //here the verification begins
+
+ unsigned int char_i;
+
+ if (find_first)
+ {
+ goto VALIDATE;
+ }
+
+MOVE_FURTHER:
+ //move to next position
+ char_i = *it; //conversion to unsigned integer
+ it += me.data_map[char_i];
+ if (atEnd(it))
+ {//found nothing
+ return false;
+ }
+
+VALIDATE:
+ //validate current position
+ for (nit = nit_end; nit >= nit_begin; --nit)
+ {
+ if (*nit != *it)
+ {//invalid!
+ it += (nit_end - nit);
+ goto MOVE_FURTHER;
+ }
+ --it;
+ }
+
+ //valid! return hit
+ setPosition(finder, it - begin(hayst, Standard()) + 1);
+ return true;
+
+}
+
+//____________________________________________________________________________
+/* groepl variante
+
+template <typename TFinder, typename TNeedle2>
+bool
+find_horspool(TFinder & finder,
+ Pattern<TNeedle2, Horspool> & me,
+ bool find_first)
+{
+SEQAN_CHECKPOINT
+ typedef typename Haystack<TFinder>::Type THaystack;
+ THaystack & hayst = haystack(finder);
+
+ typedef Pattern<TNeedle2, Horspool> TPattern;
+ typedef typename Needle<TPattern>::Type TNeedle;
+ TNeedle & ndl = needle(me);
+
+ typename Size<TNeedle>::Type ndl_size = length(ndl);
+
+ typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
+ THaystackIterator haystack_end = end(hayst, Standard());
+ THaystackIterator it = begin(hayst, Standard());
+ it += position(finder) + ndl_size - 1; //it points to the last character
+ THaystackIterator it2;
+
+ typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
+ TNeedleIterator nit; //needle iterator
+ TNeedleIterator nit_begin = begin(ndl, Standard());
+ TNeedleIterator nit_end = end(ndl, Standard()) - 2; //here the verification begins
+
+ typedef typename Value<TNeedle>::Type TNeedleValue;
+ TNeedleValue last_needle_char = value(ndl, ndl_size - 1);
+
+ unsigned int char_i;
+
+ if (!find_first)
+ {
+ ++it;
+ }
+
+MOVE_FURTHER:
+ //scan for the last character
+ while (true)
+ {
+ if (it >= haystack_end)
+ {//found nothing
+ return false;
+ }
+ if (*it == last_needle_char)
+ {
+ break;
+ }
+ ++it;
+ }
+
+VALIDATE:
+ it2 = it;
+ //validate current position
+ for (nit = nit_end; nit >= nit_begin; --nit)
+ {
+ --it2;
+ if (*nit != *it2)
+ {//invalid! skip!
+ char_i = *it; //conversion to unsigned integer
+ it += me.data_map[char_i];
+ goto MOVE_FURTHER;
+ }
+ }
+
+ //valid! return hit
+ setPosition(finder, it - begin(hayst, Standard()) - ndl_size + 1);
+ return true;
+}
+*/
+
+template <typename TFinder, typename TNeedle2>
+bool
+find(TFinder & finder, Pattern<TNeedle2, Horspool> & me)
+{
+SEQAN_CHECKPOINT
+ bool find_first = empty(finder);
+ if (find_first)
+ {
+ _patternInit(me);
+ _finderSetNonEmpty(finder);
+ }
+
+ SEQAN_ASSERT(length(needle(me)) > 0)
+
+ return find_horspool(finder, me, find_first);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Host
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TNeedle>
+struct Host< Pattern<TNeedle, Horspool> >
+{
+ typedef TNeedle Type;
+};
+
+template <typename TNeedle>
+struct Host< Pattern<TNeedle, Horspool> const>
+{
+ typedef TNeedle const Type;
+};
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/find/find_multi.h b/src/libSSA/seqan/find/find_multi.h
new file mode 100644
index 0000000..261b822
--- /dev/null
+++ b/src/libSSA/seqan/find/find_multi.h
@@ -0,0 +1,143 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: find_multi.h,v 1.1 2008/08/25 16:20:06 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FIND_MULTI_H
+#define SEQAN_HEADER_FIND_MULTI_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+
+struct _MultipatternFinder;
+typedef Tag<_MultipatternFinder> MultipatternFinder;
+
+//____________________________________________________________________________
+
+template <typename THaystack>
+class Finder<THaystack, MultipatternFinder>
+{
+//____________________________________________________________________________
+private:
+ unsigned int data_pattern;
+
+public:
+ Finder():
+ data_pattern(0)
+ {
+SEQAN_CHECKPOINT
+ }
+
+ Finder(Finder const & other_):
+ data_pattern(other_.data_pattern)
+ {
+SEQAN_CHECKPOINT
+ }
+
+ ~Finder()
+ {
+SEQAN_CHECKPOINT
+ }
+//____________________________________________________________________________
+
+ Finder &
+ operator = (Finder const & other_)
+ {
+SEQAN_CHECKPOINT
+ data_pattern = other_.data_pattern;
+ return *this;
+ }
+//____________________________________________________________________________
+
+ friend inline unsigned int &
+ needle(Finder & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_pattern;
+ }
+ friend inline unsigned int const &
+ needle(Finder const & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_pattern;
+ }
+//____________________________________________________________________________
+
+ friend inline void
+ setNeedle(Finder & me, unsigned int const needleIndex_)
+ {
+SEQAN_CHECKPOINT
+ me.data_pattern = needleIndex_;
+ }
+
+//____________________________________________________________________________
+
+ friend inline void
+ init(Finder & me)
+ {
+SEQAN_CHECKPOINT
+ me.data_pattern = 0;
+ }
+//____________________________________________________________________________
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THaystack, typename TNeedle>
+friend inline bool
+find(Finder & me,
+ THaystack & hstk,
+ TNeedle const & ndl)
+{
+SEQAN_CHECKPOINT
+ while ( needle(me) < length(ndl) )
+ {
+ Finder<THaystack, Horspool> horspool(ndl[needle(me)]);
+ bool found = find(horspool, hstk, ndl[needle(me)]);
+ if (found)
+ {
+ return true;
+ }
+ setPosition(hstk, 0);
+ ++needle(me);
+ }
+ return false;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/*
+template <typename THaystack, typename TNeedle>
+bool
+findNext(Finder & me,
+ THaystack & hstk,
+ TNeedle const & ndl)
+{
+SEQAN_CHECKPOINT
+ ++hstk;
+ return find(me, hstk, ndl);
+}*/
+
+//////////////////////////////////////////////////////////////////////////////
+
+};
+
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/find/find_multiple_shiftand.h b/src/libSSA/seqan/find/find_multiple_shiftand.h
new file mode 100644
index 0000000..7371403
--- /dev/null
+++ b/src/libSSA/seqan/find/find_multiple_shiftand.h
@@ -0,0 +1,418 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: find_multiple_shiftand.h,v 1.1 2008/08/25 16:20:07 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FIND_MULTIPLESHIFTAND_H
+#define SEQAN_HEADER_FIND_MULTIPLESHIFTAND_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// Multiple ShiftAnd
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Spec.MultipleShiftAnd:
+..summary: Multiple exact string matching using bit parallelism. The total size of the patterns should fit into a computer word.
+..general:Class.Pattern
+..cat:Searching
+..signature:Pattern<TNeedle, MultipleShiftAnd>
+..param.TNeedle:The needle type, a string of keywords.
+...type:Class.String
+..remarks.text:The types of all keywords in the needle and the haystack have to match.
+*/
+
+///.Class.Pattern.param.TSpec.type:Spec.MultipleShiftAnd
+
+struct _MultipleShiftAnd;
+typedef Tag<_MultipleShiftAnd> MultipleShiftAnd;
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TNeedle>
+class Pattern<TNeedle, MultipleShiftAnd> {
+//____________________________________________________________________________
+private:
+ Pattern(Pattern const& other);
+ Pattern const& operator=(Pattern const & other);
+
+//____________________________________________________________________________
+public:
+ typedef unsigned int TWord;
+ typedef typename Size<TNeedle>::Type TSize;
+ Holder<TNeedle> data_needle;
+ TWord* table; // Look up table for each character in the alphabet (called B in "Navarro")
+ TWord* prefSufMatch; // Set of all the prefixes of needle that match a suffix of haystack (called D in "Navarro")
+ TWord* di; // Initialization word
+ TWord* df; // Final test word
+ TWord alphabetSize; // e.g., char --> 256
+ TWord totalLength; // Lenght of concatenated keywords
+ TWord blockCount; // #unsigned ints required to store needle
+ std::deque<Pair<TSize, TSize> > data_keyword; // All keywords that produced a hit here
+ TSize data_keywordIndex; // Last keyword index
+ TSize data_needleLength; // Last needle length
+
+//____________________________________________________________________________
+
+ Pattern() {
+ table = 0;
+ prefSufMatch=0;
+ di = 0;
+ df = 0;
+ }
+
+ template <typename TNeedle2>
+ Pattern(TNeedle2 const & ndl)
+ {
+ table = 0;
+ prefSufMatch=0;
+ di = 0;
+ df = 0;
+ setHost(*this, ndl);
+ }
+
+ ~Pattern() {
+ SEQAN_CHECKPOINT
+ if (table != 0) {
+ deallocate(this, table, alphabetSize * blockCount);
+ deallocate(this, prefSufMatch, blockCount);
+ deallocate(this, di, blockCount);
+ deallocate(this, df, blockCount);
+ }
+ }
+//____________________________________________________________________________
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// Host Metafunctions
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TNeedle>
+struct Host< Pattern<TNeedle, MultipleShiftAnd> >
+{
+ typedef TNeedle Type;
+};
+
+template <typename TNeedle>
+struct Host< Pattern<TNeedle, MultipleShiftAnd> const>
+{
+ typedef TNeedle const Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// Functions
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TNeedle, typename TNeedle2>
+void setHost (Pattern<TNeedle, MultipleShiftAnd> & me, TNeedle2 const & needle) {
+ SEQAN_CHECKPOINT
+ typedef unsigned int TWord;
+ typedef typename Value<TNeedle>::Type TKeyword;
+ typedef typename Value<TKeyword>::Type TAlphabet;
+ if (me.table != 0) {
+ deallocate(me, me.table, me.alphabetSize * me.blockCount);
+ deallocate(me, me.di, me.blockCount);
+ deallocate(me, me.df, me.blockCount);
+ }
+
+ typename Iterator<TNeedle2 const, Rooted>::Type it = begin(needle);
+ me.totalLength = 0;
+ for(;!atEnd(it);goNext(it)) {
+ me.totalLength += length(*it);
+ }
+ me.alphabetSize = ValueSize<TAlphabet>::VALUE;
+ if (me.totalLength<1) me.blockCount=1;
+ else me.blockCount=((me.totalLength-1) / BitsPerValue<TWord>::VALUE)+1;
+
+ allocate (me, me.table, me.blockCount * me.alphabetSize);
+ arrayFill (me.table, me.table + me.blockCount * me.alphabetSize, 0);
+
+ allocate (me, me.di, me.blockCount);
+ arrayFill (me.di, me.di + me.blockCount, 0);
+
+ allocate (me, me.df, me.blockCount);
+ arrayFill (me.df, me.df + me.blockCount, 0);
+
+ goBegin(it);
+ TWord j = 0;
+ for(;!atEnd(it);goNext(it)) {
+ me.di[j / BitsPerValue<TWord>::VALUE] |= (1<<(j%BitsPerValue<TWord>::VALUE));
+ for (TWord posInKeyword = 0; posInKeyword < length(*it); ++posInKeyword) {
+ // Determine character position in array table
+ TWord index = convert<TWord>(getValue(*it,posInKeyword));
+ me.table[me.blockCount*index + j / BitsPerValue<TWord>::VALUE] |= (1<<(j%BitsPerValue<TWord>::VALUE));
+ ++j;
+ }
+ me.df[(j - 1) / BitsPerValue<TWord>::VALUE] |= (1<<((j-1)%BitsPerValue<TWord>::VALUE));
+ }
+ setValue(me.data_needle, needle);
+
+ /*
+ // Debug code
+ std::cout << "Alphabet size: " << me.alphabetSize << ::std::endl;
+ std::cout << "Needle length: " << me.totalLength << ::std::endl;
+ std::cout << "Block count: " << me.blockCount << ::std::endl;
+ std::cout << "K: ";
+ goBegin(it);
+ for(;!atEnd(it);goNext(it)) {
+ std::cout << *it;
+ }
+ std::cout << ::std::endl;
+ std::cout << "Table: " << ::std::endl;
+ for(unsigned int i=0;i<me.alphabetSize;++i) {
+ //if ((i<97) || (i>122)) continue;
+ std::cout << TAlphabet(i) << ": ";
+ for(int j=0;j<me.blockCount;++j) {
+ for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+ std::cout << ((me.table[me.blockCount*i+j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+ }
+ }
+ std::cout << ::std::endl;
+ }
+ std::cout << "DI and DF: " << ::std::endl;
+ std::cout << "I: ";
+ for(int j=0;j<me.blockCount;++j) {
+ for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+ std::cout << ((me.di[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+ }
+ }
+ std::cout << ::std::endl;
+ std::cout << "F: ";
+ for(int j=0;j<me.blockCount;++j) {
+ for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+ std::cout << ((me.df[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+ }
+ }
+ std::cout << ::std::endl;
+ */
+}
+
+template <typename TNeedle, typename TNeedle2>
+void setHost (Pattern<TNeedle, MultipleShiftAnd> & me, TNeedle2 & needle)
+{
+ setHost(me, reinterpret_cast<TNeedle2 const &>(needle));
+}
+
+//____________________________________________________________________________
+
+
+template <typename TNeedle>
+inline void _patternInit (Pattern<TNeedle, MultipleShiftAnd> & me)
+{
+SEQAN_CHECKPOINT
+ typedef unsigned int TWord;
+
+ if (me.prefSufMatch != 0) {
+ deallocate(me, me.prefSufMatch, me.blockCount);
+ }
+ allocate (me, me.prefSufMatch, me.blockCount);
+ arrayFill (me.prefSufMatch, me.prefSufMatch + me.blockCount, 0);
+ me.data_keyword.clear();
+ me.data_keywordIndex = 0;
+}
+
+//____________________________________________________________________________
+
+template <typename TNeedle>
+inline typename Host<Pattern<TNeedle, MultipleShiftAnd>const>::Type &
+host(Pattern<TNeedle, MultipleShiftAnd> & me)
+{
+SEQAN_CHECKPOINT
+ return value(me.data_needle);
+}
+
+template <typename TNeedle>
+inline typename Host<Pattern<TNeedle, MultipleShiftAnd>const>::Type &
+host(Pattern<TNeedle, MultipleShiftAnd> const & me)
+{
+SEQAN_CHECKPOINT
+ return value(me.data_needle);
+}
+
+//____________________________________________________________________________
+
+
+template <typename TNeedle>
+inline typename Size<TNeedle>::Type
+position(Pattern<TNeedle, MultipleShiftAnd> & me)
+{
+ return me.data_keywordIndex;
+}
+
+
+template <typename TFinder, typename TNeedle>
+bool _findShiftAnd_SmallNeedle(TFinder & finder, Pattern<TNeedle, MultipleShiftAnd> & me) {
+ SEQAN_CHECKPOINT
+ typedef unsigned int TWord;
+ typedef typename Size<TNeedle>::Type TSize;
+ while (!atEnd(finder)) {
+ TWord pos = convert<TWord>(*finder);
+ me.prefSufMatch[0] = ((me.prefSufMatch[0] << 1) | me.di[0]) & me.table[me.blockCount*pos];
+
+ /*
+ // Debug code
+ std::cout << " ";
+ for(int j=0;j<me.blockCount;++j) {
+ for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+ std::cout << ((me.prefSufMatch[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+ }
+ }
+ std::cout << ::std::endl;
+ */
+
+ if ((me.prefSufMatch[0] & me.df[0]) != 0) {
+ // Check which pattern has matched
+ typename Iterator<TNeedle, Rooted>::Type it = begin(value(me.data_needle));
+ TWord j = 0;
+ for(;!atEnd(it);goNext(it)) {
+ j += length(*it);
+ TWord test = (1<<((j-1)%BitsPerValue<TWord>::VALUE));
+ /*
+ // Debug code
+ std::cout << "Tes";
+ for(int j=0;j<me.blockCount;++j) {
+ for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+ std::cout << ((test & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+ }
+ }
+ std::cout << ::std::endl;
+ */
+ if ((me.prefSufMatch[0] & test) != 0) {
+ me.data_keyword.push_back(Pair<TSize,TSize>(position(it),length(*it)));
+ }
+ }
+ me.data_keywordIndex = (me.data_keyword.front()).i1;
+ me.data_needleLength = (me.data_keyword.front()).i2;
+ me.data_keyword.pop_front();
+ finder -= (me.data_needleLength - 1);
+ return true;
+ }
+ goNext(finder);
+ }
+ return false;
+}
+
+template <typename TFinder, typename TNeedle>
+bool _findShiftAnd_LargeNeedle(TFinder & finder, Pattern<TNeedle, MultipleShiftAnd> & me) {
+ SEQAN_CHECKPOINT
+ typedef typename Size<TNeedle>::Type TSize;
+ typedef unsigned int TWord;
+ while (!atEnd(finder)) {
+ TWord pos = convert<TWord>(*finder);
+ TWord carry = 1;
+ for(TWord block=0;block<me.blockCount;++block) {
+ bool newCarry = ((me.prefSufMatch[block] & (1<< (BitsPerValue<TWord>::VALUE - 1)))!=0);
+ me.prefSufMatch[block]<<=1;
+ me.prefSufMatch[block]|=carry;
+ carry = newCarry;
+ }
+ for(TWord block=0;block<me.blockCount;++block) me.prefSufMatch[block] |= me.di[block];
+ for(TWord block=0;block<me.blockCount;++block) me.prefSufMatch[block] &= me.table[me.blockCount*pos+block];
+
+ /*
+ // Debug code
+ std::cout << " ";
+ for(int j=0;j<me.blockCount;++j) {
+ for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+ std::cout << ((me.prefSufMatch[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+ }
+ }
+ std::cout << ::std::endl;
+ */
+
+ bool match = false;
+ for(TWord block=0;block<me.blockCount;++block) {
+ if ((me.prefSufMatch[block] & me.df[block]) != 0) {
+ match = true;
+ break;
+ }
+ }
+ if (match) {
+ // Check which pattern has matched
+ typename Iterator<TNeedle, Rooted>::Type it = begin(value(me.data_needle));
+ TWord j = 0;
+ for(;!atEnd(it);goNext(it)) {
+ j += length(*it);
+ TWord* test;
+ allocate (me, test, me.blockCount);
+ arrayFill (test, test + me.blockCount, 0);
+ test[(j - 1) / BitsPerValue<TWord>::VALUE] |= (1<<((j-1)%BitsPerValue<TWord>::VALUE));
+
+ /*
+ // Debug code
+ std::cout << "Tes";
+ for(int i=0;i<me.blockCount;++i) {
+ for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+ std::cout << ((test[i] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+ }
+ }
+ std::cout << ::std::endl;
+ */
+
+ if ((me.prefSufMatch[(j - 1) / BitsPerValue<TWord>::VALUE] & test[(j - 1) / BitsPerValue<TWord>::VALUE]) != 0) {
+ me.data_keyword.push_back(Pair<TSize,TSize>(position(it),length(*it)));
+ }
+ deallocate(me, test, me.blockCount);
+ }
+ me.data_keywordIndex = (me.data_keyword.front()).i1;
+ me.data_needleLength = (me.data_keyword.front()).i2;
+ me.data_keyword.pop_front();
+ finder -= (me.data_needleLength - 1);
+ return true;
+ }
+ goNext(finder);
+ }
+ return false;
+}
+
+template <typename TFinder, typename TNeedle>
+inline bool find(TFinder & finder, Pattern<TNeedle, MultipleShiftAnd> & me) {
+ SEQAN_CHECKPOINT
+
+ // Check for left-over keywords
+ if ((!empty(finder)) &&
+ (!me.data_keyword.empty())) {
+ finder += me.data_needleLength - 1;
+ me.data_keywordIndex = (me.data_keyword.front()).i1;
+ me.data_needleLength = (me.data_keyword.front()).i2;
+ me.data_keyword.pop_front();
+ finder -= (me.data_needleLength - 1);
+ return true;
+ }
+
+
+ if (empty(finder)) {
+ _patternInit(me);
+ _finderSetNonEmpty(finder);
+ } else
+ finder += me.data_needleLength;
+
+ // Fast algorithm for needles < machine word?
+ if (me.blockCount == 1) {
+ return _findShiftAnd_SmallNeedle(finder, me);
+ } else {
+ return _findShiftAnd_LargeNeedle(finder, me);
+ }
+ return false;
+}
+
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_FIND_MULTIPLESHIFTAND_H
diff --git a/src/libSSA/seqan/find/find_score.h b/src/libSSA/seqan/find/find_score.h
new file mode 100644
index 0000000..871e918
--- /dev/null
+++ b/src/libSSA/seqan/find/find_score.h
@@ -0,0 +1,451 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: find_score.h,v 1.1 2008/08/25 16:20:07 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FIND_SCORE_H
+#define SEQAN_HEADER_FIND_SCORE_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// DPSearch
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TScore>
+struct DPSearch;
+
+
+/**
+.Spec.DPSearch:
+..cat:Searching
+..general:Class.Pattern
+..summary:A dynamic programming algorithm for approximate string-matching with a user-definable scoring function.
+..signature:Pattern<TNeedle, DPSearch<TScore> >
+..param.TNeedle:The needle type.
+...type:Class.String
+..param.TScore:The scoring function.
+...type:Class.Score
+..remarks.text:The algorithm is based on the Sellers/Needleman-Wunsch dynamic progamming algorithm.
+The $Pattern$ object only contains the right-most column of the dynamic programming matrix.
+...note:At the moment, the algorithm only works on linear gap costs.
+*/
+
+///.Class.Pattern.param.TSpec.type:Class.Score
+
+
+template <typename TNeedle, typename TScore>
+class Pattern<TNeedle, DPSearch<TScore> >
+{
+public:
+ typedef typename Value<TScore>::Type TScoreValue;
+
+ Holder<TNeedle> data_needle;
+ TScore data_score;
+ TScoreValue data_limit;
+ String<TScoreValue> data_tab;
+
+public:
+ Pattern():
+ data_limit(0)
+ {
+SEQAN_CHECKPOINT
+ }
+
+ Pattern(TNeedle & _needle,
+ TScore & _score_func,
+ TScoreValue _limit = 0):
+ data_score(_score_func),
+ data_limit(_limit)
+ {
+SEQAN_CHECKPOINT
+ setHost(*this, _needle);
+ }
+
+ Pattern(TNeedle & _needle,
+ TScoreValue _limit = 0):
+ data_limit(_limit)
+ {
+SEQAN_CHECKPOINT
+ setHost(*this, _needle);
+ }
+
+ Pattern(TScoreValue _limit):
+ data_limit(_limit)
+ {
+SEQAN_CHECKPOINT
+ create(data_score);
+ }
+
+ Pattern(Pattern const & other):
+ data_needle( other.data_needle ),
+ data_score( other.data_score ),
+ data_limit( other.data_limit ),
+ data_tab( other.data_tab )
+ {
+SEQAN_CHECKPOINT
+ }
+
+ inline Pattern &
+ operator = (Pattern const & other)
+ {
+SEQAN_CHECKPOINT
+ this->data_needle = other.data_needle;
+ this->data_score = other.data_score;
+ this->data_limit = other.data_limit;
+ this->data_tab = other.data_tab;
+
+ return *this;
+ }
+};
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Host
+//////////////////////////////////////////////////////////////////////////////
+
+/* //see find_base.h
+
+template <typename TNeedle, typename TScore>
+struct Host< Pattern<TNeedle, DPSearch<TScore> > >
+{
+ typedef TNeedle Type;
+};
+
+template <typename TNeedle, typename TScore>
+struct Host< Pattern<TNeedle, DPSearch<TScore> > const>
+{
+ typedef TNeedle const Type;
+};
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+template <typename TNeedle, typename TScore>
+inline typename Host<Pattern<TNeedle, DPSearch<TScore> > >::Type &
+host(Pattern<TNeedle, DPSearch<TScore> > & me)
+{
+SEQAN_CHECKPOINT
+ return value(me.data_needle);
+}
+
+template <typename TNeedle, typename TScore>
+inline typename Host<Pattern<TNeedle, DPSearch<TScore> > const>::Type &
+host(Pattern<TNeedle, DPSearch<TScore> > const & me)
+{
+SEQAN_CHECKPOINT
+ return value(me.data_needle);
+}
+
+
+//____________________________________________________________________________
+
+template <typename TNeedle, typename TScore, typename TNeedle2>
+void
+setHost(Pattern<TNeedle, DPSearch<TScore> > & me,
+ TNeedle2 & ndl)
+{
+ me.data_needle = ndl;
+ clear(me.data_tab);
+}
+template <typename TNeedle, typename TScore, typename TNeedle2>
+void
+setHost(Pattern<TNeedle, DPSearch<TScore> > & me,
+ TNeedle2 const & ndl)
+{
+ me.data_needle = ndl;
+ clear(me.data_tab);
+}
+
+
+//____________________________________________________________________________
+
+/**.Function.scoringScheme
+..cat:Searching
+..summary:The @glos:scoring scheme@ used for finding or aligning.
+..signature:scoringScheme(obj)
+..param.obj:Object that holds a @glos:scoring scheme@
+...type:Spec.DPSearch
+..returns:The @glos:scoring scheme@ used in $obj$
+..see:glos:scoring scheme
+*/
+
+template <typename TNeedle, typename TScore>
+inline TScore const &
+scoringScheme(Pattern<TNeedle, DPSearch<TScore> > & me)
+{
+SEQAN_CHECKPOINT
+ return me.data_score;
+}
+
+//____________________________________________________________________________
+
+/**.Function.setScoringScheme
+..cat:Searching
+..summary:Sets the @glos:scoring scheme@ used for finding or aligning.
+..signature:setScoringScheme(obj, score)
+..param.obj:Object that holds a @glos:scoring scheme at .
+...type:Spec.DPSearch
+..param.score:The new @glos:scoring scheme@ used by $obj$.
+..see:glos:scoring scheme
+..see:Function.scoringScheme
+*/
+
+template <typename TNeedle, typename TScore, typename TScore2>
+inline void
+setScoringScheme(Pattern<TNeedle, DPSearch<TScore> > & me,
+ TScore2 & score)
+{
+SEQAN_CHECKPOINT
+ me.data_score = score;
+ clear(me.data_tab);
+}
+template <typename TNeedle, typename TScore, typename TScore2>
+inline void
+setScoringScheme(Pattern<TNeedle, DPSearch<TScore> > & me,
+ TScore2 const & score)
+{
+SEQAN_CHECKPOINT
+ me.data_score = score;
+ clear(me.data_tab);
+}
+
+//____________________________________________________________________________
+
+
+/**.Function.scoreLimit
+..cat:Searching
+..summary:The minimal score a match must reach in approximate searching.
+..signature:scoreLimit(pattern)
+..param.pattern:A @Concept.Pattern|pattern@ that can be used for approximate searching.
+...type:Spec.DPSearch
+..returns:The current score limit of $pattern$.
+*/
+
+template <typename TNeedle, typename TScore>
+inline typename Value<TScore>::Type
+scoreLimit(Pattern<TNeedle, DPSearch<TScore> > const & me)
+{
+SEQAN_CHECKPOINT
+ return me.data_limit;
+}
+
+//____________________________________________________________________________
+
+/**.Function.setScoreLimit
+..cat:Searching
+..summary:Sets the minimal score a match must reach in approximate searching.
+..signature:setScoreLimit(pattern, limit)
+..param.pattern:A @Concept.Pattern|pattern@ that can be used for approximate searching.
+...type:Spec.DPSearch
+..param.limit:The new score limit.
+..see:Function.scoreLimit
+*/
+
+template <typename TNeedle, typename TScore, typename TScoreValue>
+inline void
+setScoreLimit(Pattern<TNeedle, DPSearch<TScore> > & me,
+ TScoreValue _limit)
+{
+SEQAN_CHECKPOINT
+ me.data_limit = _limit;
+}
+
+//____________________________________________________________________________
+// returns the score of the last hit position found (note:position = end of occurrence in haystack)
+
+/**.Function.getScore
+..cat:Searching
+..summary:Score of the last found match in approximate searching.
+..signature:getScore(pattern)
+..param.pattern:A @Concept.Pattern|pattern@ that can be used for approximate searching.
+...type:Spec.DPSearch
+..returns:The score of the last match found using $pattern$.
+...remarks:If no match was found, the value is undefined.
+..see:Function.scoreLimit
+..see:Function.setScoreLimit
+..see:Function.find
+*/
+
+template <typename TNeedle, typename TScore>
+inline typename Value<TScore>::Type
+getScore(Pattern<TNeedle, DPSearch<TScore> > & me)
+{
+ return front(me.data_tab);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+template <typename TNeedle, typename TScore>
+inline void _patternInit (Pattern<TNeedle, DPSearch<TScore> > & me)
+{
+ typedef Pattern<TNeedle, DPSearch<TScore> > TPattern;
+ typedef typename Value<TScore>::Type TScoreValue;
+
+ typedef typename Size<TPattern>::Type TSize;
+
+ typedef String<TScoreValue> TTab;
+ typedef typename Iterator<TTab, Standard>::Type TIterator;
+
+ TScoreValue score_gap = scoreGapExtend(scoringScheme(me));
+
+ TTab & string_tab = me.data_tab;
+
+ //allocate enough memory for one column of DP matrix
+ TSize need_length = length(needle(me));
+ SEQAN_ASSERT(need_length);
+
+ TSize got_length = resize(string_tab, need_length);
+ SEQAN_ASSERT(got_length >= need_length);
+
+// if (length(_dataNeedle(me)) < got_length) throw(0); //???TODO: Throw "not enough memory" exception
+
+ //init matrix
+ //note: The column is stored in reverse order
+ TIterator tab_end = begin(string_tab, Standard());
+ TIterator tab = end(string_tab, Standard());
+
+ TScoreValue x = score_gap;
+
+ while (tab > tab_end)
+ {
+ --tab;
+ *tab = x;
+ x += score_gap;
+ }
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// find, findNext
+//////////////////////////////////////////////////////////////////////////////
+
+//proportional gap cost: Needleman-Wunsch
+
+//???TODO: Ukkonen trick?
+//???TODO: Finder for affine gap costs?
+
+template <typename TFinder, typename TNeedle, typename TScore>
+bool
+_find_score_simple_proportional(TFinder & finder, Pattern<TNeedle, DPSearch<TScore> > & me)
+{
+ typedef typename Value<TScore>::Type TScoreValue;
+ typedef String<TScoreValue> TTab;
+ typedef typename Iterator<TTab, Standard>::Type TTabIterator;
+ typedef typename Iterator<TNeedle const, Standard>::Type TNeedleIterator;
+ typedef typename Value<typename Haystack<TFinder>::Type>::Type THaystackValue;
+
+ String<TScoreValue> & string_tab = me.data_tab;
+
+ TScoreValue score_gap = scoreGapExtend(scoringScheme(me));
+ TScoreValue score_match = scoreMatch(scoringScheme(me));
+ TScoreValue score_mismatch = scoreMismatch(scoringScheme(me));
+
+ //init table
+
+ if (empty(finder))
+ {
+ clear(me.data_tab);
+ _finderSetNonEmpty(finder);
+ }
+ else
+ {
+ goNext(finder);
+ }
+
+ if (! length(me.data_tab))
+ {
+ _patternInit(me);
+ }
+ //start searching
+
+ TTabIterator tab_begin = end(string_tab, Standard());
+
+ TNeedleIterator it_begin = begin(host(me), Standard());
+ TNeedleIterator it_end = end(host(me), Standard());
+
+ //for each character in haystack, do...
+ for (; !atEnd(finder); ++finder)
+ {
+ //get character
+ THaystackValue c = *finder;
+
+ //init some variables
+ TNeedleIterator it = it_begin;
+ TScoreValue * tab = tab_begin;
+ TScoreValue h = 0;
+ TScoreValue v = 0;
+
+ //fill the column
+ while (it < it_end)
+ {
+ --tab; //note: the column is stored in "reverse order"
+
+ TScoreValue m2 = (c == *it) ? h + score_match : h + score_mismatch;
+ h = *tab;
+ TScoreValue m1 = (h > v) ? h + score_gap : v + score_gap;
+
+ v = (m1 > m2) ? m1 : m2;
+ *tab = v;
+
+ ++it;
+ }
+
+ if (*tab >= scoreLimit(me) )
+ {//found a hit
+ return true;
+ }
+
+ }
+
+ //found nothing
+ return false;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TFinder, typename TNeedle, typename TScore>
+inline bool
+find(TFinder & finder,
+ Pattern<TNeedle, DPSearch<TScore> > & me)
+{
+ SEQAN_ASSERT(scoreGapOpen(scoringScheme(me)) == scoreGapExtend(scoringScheme(me))) //this finder is only defined for linear gap costs
+ return _find_score_simple_proportional(finder, me);
+}
+
+template <typename TFinder, typename TNeedle, typename TScore>
+inline bool
+find(TFinder & finder,
+ Pattern<TNeedle, DPSearch<TScore> > & me,
+ int const limit_)
+{
+ SEQAN_ASSERT(scoreGapOpen(scoringScheme(me)) == scoreGapExtend(scoringScheme(me))) //this finder is only defined for linear gap costs
+ setScoreLimit(me, limit_);
+ return _find_score_simple_proportional(finder, me);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/find/find_set_horspool.h b/src/libSSA/seqan/find/find_set_horspool.h
new file mode 100644
index 0000000..b9a72d1
--- /dev/null
+++ b/src/libSSA/seqan/find/find_set_horspool.h
@@ -0,0 +1,286 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: find_set_horspool.h,v 1.1 2008/08/25 16:20:07 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_FIND_SETHORSPOOL_H
+#define SEQAN_HEADER_FIND_SETHORSPOOL_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// Set Horspool Algorithm
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Spec.SetHorspool:
+..summary: Multiple exact string matching using set horspool algorithm.
+..general:Class.Pattern
+..cat:Searching
+..signature:Pattern<TNeedle, SetHorspool>
+..param.TNeedle:The needle type, a string of keywords.
+...type:Class.String
+..remarks.text:The types of all keywords in the needle and the haystack have to match.
+*/
+
+///.Class.Pattern.param.TSpec.type:Spec.SetHorspool
+
+struct _SetHorspool;
+typedef Tag<_SetHorspool> SetHorspool;
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TNeedle>
+class Pattern<TNeedle, SetHorspool> {
+//____________________________________________________________________________
+private:
+ Pattern(Pattern const& other);
+ Pattern const& operator=(Pattern const & other);
+
+//____________________________________________________________________________
+public:
+ typedef typename Size<TNeedle>::Type TSize;
+ typedef typename Value<TNeedle>::Type TValue;
+ typedef typename Value<TValue>::Type TAlphabet;
+ typedef Graph<Automaton<TAlphabet> > TGraph;
+ typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+
+ Holder<TNeedle> data_needle;
+ Graph<Automaton<TAlphabet> > data_reverseTrie; // Search trie
+ String<String<TSize> > data_terminalStateMap;
+ String<TSize> data_dMap; // Jump table
+ TSize data_lmin;
+ String<TSize> data_endPositions; // All remaining keyword indices
+ TSize data_keywordIndex; // Current keyword that produced a hit
+ TSize data_needleLength; // Last length of needle to reposition finder
+ TVertexDescriptor data_lastState; // Last state in the trie
+
+//____________________________________________________________________________
+
+ Pattern() {
+ }
+
+ template <typename TNeedle2>
+ Pattern(TNeedle2 const & ndl)
+ {
+ setHost(*this, ndl);
+ }
+
+ ~Pattern() {
+ SEQAN_CHECKPOINT
+ }
+//____________________________________________________________________________
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// Host Metafunctions
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TNeedle>
+struct Host< Pattern<TNeedle, SetHorspool> >
+{
+ typedef TNeedle Type;
+};
+
+template <typename TNeedle>
+struct Host< Pattern<TNeedle, SetHorspool> const>
+{
+ typedef TNeedle const Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// Functions
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TNeedle, typename TNeedle2>
+void setHost (Pattern<TNeedle, SetHorspool> & me, TNeedle2 const & needle) {
+ SEQAN_CHECKPOINT
+ typedef typename Value<TNeedle>::Type TKeyword;
+ typedef typename Size<TKeyword>::Type TSize;
+ typedef typename Value<TKeyword>::Type TAlphabet;
+
+ // clean-up
+ clear(me.data_reverseTrie);
+ clear(me.data_terminalStateMap);
+ clear(me.data_endPositions);
+ clear(me.data_dMap);
+ me.data_lmin=0;
+
+ // Create Trie
+ createTrieOnReverse(me.data_reverseTrie,me.data_terminalStateMap,needle);
+ assignRoot(me.data_reverseTrie,0);
+ setValue(me.data_needle, needle);
+
+ // Create jump map
+ TSize alphabet_size = ValueSize<TAlphabet>::VALUE;
+ resize(me.data_dMap, alphabet_size);
+ me.data_lmin = _getInfinity<TSize>();
+ typename Iterator<TNeedle2 const, Rooted>::Type it = begin(needle);
+ for(;!atEnd(it);goNext(it)) {
+ TSize tmp = length(*it);
+ if (tmp<me.data_lmin) me.data_lmin = tmp;
+ }
+ for(TSize i=0;i<alphabet_size;++i) {
+ me.data_dMap[i]=me.data_lmin;
+ }
+ goBegin(it);
+ for(;!atEnd(it);goNext(it)) {
+ for(TSize pos = 0;pos < length(*it) - 1; ++pos) {
+ TSize ind = ordValue((TAlphabet)(*it)[pos]);
+ if ((length(*it)- 1 - pos) < me.data_dMap[ind]) {
+ me.data_dMap[ind] = (length(*it) - 1 - pos);
+ }
+ }
+ }
+
+ /*
+ fstream strm;
+ strm.open(TEST_PATH "my_trie.dot", ios_base::out | ios_base::trunc);
+ String<String<char> > nodeMap;
+ _createTrieNodeNames(me.data_reverseTrie, me.data_terminalStateMap, nodeMap);
+ String<String<char> > edgeMap;
+ _createEdgeNames(me.data_reverseTrie,edgeMap);
+ write(strm,me.data_reverseTrie,nodeMap,edgeMap,DotDrawing());
+ strm.close();
+ */
+}
+
+template <typename TNeedle, typename TNeedle2>
+void setHost (Pattern<TNeedle, SetHorspool> & me, TNeedle2 & needle)
+{
+ setHost(me, reinterpret_cast<TNeedle2 const &>(needle));
+}
+
+//____________________________________________________________________________
+
+
+template <typename TNeedle>
+inline void _patternInit (Pattern<TNeedle, SetHorspool> & me)
+{
+SEQAN_CHECKPOINT
+ clear(me.data_endPositions);
+ me.data_keywordIndex = 0;
+ me.data_lastState = getRoot(me.data_reverseTrie);
+}
+
+
+//____________________________________________________________________________
+
+template <typename TNeedle>
+inline typename Host<Pattern<TNeedle, SetHorspool>const>::Type &
+host(Pattern<TNeedle, SetHorspool> & me)
+{
+SEQAN_CHECKPOINT
+ return value(me.data_needle);
+}
+
+template <typename TNeedle>
+inline typename Host<Pattern<TNeedle, SetHorspool>const>::Type &
+host(Pattern<TNeedle, SetHorspool> const & me)
+{
+SEQAN_CHECKPOINT
+ return value(me.data_needle);
+}
+
+//____________________________________________________________________________
+
+
+template <typename TNeedle>
+inline typename Size<TNeedle>::Type
+position(Pattern<TNeedle, SetHorspool> & me)
+{
+ return me.data_keywordIndex;
+}
+
+
+template <typename TFinder, typename TNeedle>
+inline bool find(TFinder & finder, Pattern<TNeedle, SetHorspool> & me) {
+ SEQAN_CHECKPOINT
+ typedef typename Value<TNeedle>::Type TKeyword;
+ typedef typename Size<TKeyword>::Type TSize;
+ typedef typename Value<TKeyword>::Type TAlphabet;
+ typedef Graph<Automaton<TAlphabet> > TGraph;
+ typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+
+ TVertexDescriptor current = getRoot(me.data_reverseTrie);
+
+ // Process left-over hits
+ if ((!empty(finder)) &&
+ (!empty(me.data_endPositions))) {
+ finder += me.data_needleLength;
+ current = me.data_lastState;
+ me.data_keywordIndex = me.data_endPositions[length(me.data_endPositions)-1];
+ me.data_needleLength = length(getValue(host(me), me.data_keywordIndex))-1;
+ if (length(me.data_endPositions) > 1) resize(me.data_endPositions, (length(me.data_endPositions)-1));
+ else clear(me.data_endPositions);
+ me.data_lastState = current;
+ finder -= me.data_needleLength;
+ return true;
+ }
+
+ TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+ TSize j = 0;
+ if (empty(finder)) {
+ _patternInit(me);
+ _finderSetNonEmpty(finder);
+ finder += me.data_lmin - 1;
+ } else {
+ finder += me.data_needleLength;
+ j = me.data_needleLength + 1;
+ current = me.data_lastState;
+ }
+
+ TSize haystackLength = length(container(finder));
+ bool oldMatch = true;
+ // Do not change to !atEnd(finder) because of jump map!
+ while(position(finder) < haystackLength) {
+ while ((position(finder)>=j) &&
+ (getSuccessor(me.data_reverseTrie, current, *(finder-j))!= nilVal))
+ {
+ me.data_endPositions = getProperty(me.data_terminalStateMap,current);
+ if ((!oldMatch) && (!empty(me.data_endPositions))) break;
+ current = getSuccessor(me.data_reverseTrie, current, *(finder-j));
+ if (current == nilVal) break;
+ ++j;
+ oldMatch = false;
+ }
+ me.data_endPositions = getProperty(me.data_terminalStateMap,current);
+ if ((!oldMatch) &&
+ (!empty(me.data_endPositions)))
+ {
+ me.data_keywordIndex = me.data_endPositions[length(me.data_endPositions)-1];
+ me.data_needleLength = length(getValue(host(me), me.data_keywordIndex))-1;
+ if (length(me.data_endPositions) > 1) resize(me.data_endPositions, length(me.data_endPositions)-1);
+ else clear(me.data_endPositions);
+ me.data_lastState = current;
+ finder -= me.data_needleLength;
+ return true;
+ }
+ oldMatch = false;
+ TSize ind = ordValue(*finder);
+ setPosition(finder, position(finder) + getValue(me.data_dMap, ind));
+ j = 0;
+ current = getRoot(me.data_reverseTrie);
+ }
+ return false;
+}
+
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_FIND_SETHORSPOOL_H
diff --git a/src/libSSA/seqan/index.h b/src/libSSA/seqan/index.h
new file mode 100644
index 0000000..ddb3eac
--- /dev/null
+++ b/src/libSSA/seqan/index.h
@@ -0,0 +1,113 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: index.h,v 1.6 2009/03/13 14:46:42 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_INDEX_H
+#define SEQAN_HEADER_INDEX_H
+
+//____________________________________________________________________________
+// prerequisites
+
+#include <seqan/sequence.h>
+//#include <seqan/pipe.h>
+//#include <seqan/modifier.h>
+
+#include <seqan/find/find_base.h>
+//#include <seqan/misc/misc_set.h>
+
+#include <climits>
+#include <functional>
+#include <vector>
+#include <stack>
+#include <queue>
+#include <algorithm>
+#include <iterator>
+#include <utility>
+#include <string.h> // memset
+
+
+//////////////////////////////////////////////////////////////////////////////
+// INDEX CONSTRUCTION
+//////////////////////////////////////////////////////////////////////////////
+
+
+#ifdef SEQAN_SWITCH_USE_FORWARDS
+#include <seqan/index/index_manual_forwards.h>
+#include <seqan/index/index_generated_forwards.h>
+#endif
+
+#include <seqan/index/index_base.h>
+
+//____________________________________________________________________________
+// suffix array creators
+
+//#include <seqan/index/radix.h>
+//#include <seqan/index/index_sa_btree.h>
+#include <seqan/index/index_sa_lss.h>
+//#include <seqan/index/index_sa_mm.h>
+//#include <seqan/index/index_sa_qsort.h>
+//
+//#include <seqan/index/pump_extender3.h>
+//#include <seqan/index/pipe_merger3.h>
+//
+//#include <seqan/index/pump_extender7.h>
+//#include <seqan/index/pipe_merger7.h>
+
+//#include <seqan/index/pump_separator7.h>
+
+//____________________________________________________________________________
+// enhanced table creators
+
+//#include <seqan/index/pump_lcp_core.h>
+
+//____________________________________________________________________________
+// q-gram index creator
+
+#include <seqan/index/shape_base.h>
+#include <seqan/index/shape_gapped.h>
+#include <seqan/index/shape_predefined.h>
+//#include <seqan/index/index_qgram.h>
+//#include <seqan/index/index_qgram_nested.h>
+
+
+//////////////////////////////////////////////////////////////////////////////
+// INDEX USAGE
+//////////////////////////////////////////////////////////////////////////////
+
+#include <seqan/index/index_qgram_find.h>
+#include <seqan/index/index_find.h>
+
+//____________________________________________________________________________
+// (virtual) suffix trees
+
+//____________________________________________________________________________
+// suffix tree algorithms
+
+//____________________________________________________________________________
+// Pizza & Chili interface (compressed indices)
+
+//#include <seqan/index/index_pizzachili.h>
+//#include <seqan/index/index_pizzachili_find.h>
+
+//____________________________________________________________________________
+// Shawarma interface (suffix array creators)
+
+//#include <seqan/index/index_shawarma.h>
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/index/index_base.h b/src/libSSA/seqan/index/index_base.h
new file mode 100644
index 0000000..12d89ad
--- /dev/null
+++ b/src/libSSA/seqan/index/index_base.h
@@ -0,0 +1,954 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: index_base.h,v 1.3 2009/03/13 14:34:32 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_INDEX_BASE_H
+#define SEQAN_HEADER_INDEX_BASE_H
+
+//#define SEQAN_TEST_INDEX
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// needful forward declarations
+
+ // suffix array construction specs
+ struct Skew3;
+ struct Skew7;
+ struct LarssonSadakane;
+ struct ManberMyers;
+ struct SAQSort;
+ struct QGram_Alg;
+
+ // lcp table construction algorithms
+ struct Kasai;
+ struct KasaiOriginal; // original, but more space-consuming algorithm
+
+ // enhanced suffix array construction algorithms
+ struct ChildTab;
+ struct BWT;
+
+ template <typename TSpec = void>
+ struct Index_ESA;
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Metafunction.DefaultIndexSpec:
+..cat:Index
+..summary:Default @Class.Index@ specialization type.
+..signature:DefaultIndexSpec<TText>::Type
+..param.TText:The given text type.
+..returns:Can be @Spec.Index_ESA@ or $Index_QGram$, etc.
+..remarks:Currently @Spec.Index_ESA@ is default if $TText$ is a @Class.String at .
+*/
+ template < typename TObject >
+ struct DefaultIndexSpec {
+ typedef Index_ESA<> Type;
+ };
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Metafunction.DefaultIndexStringSpec:
+..cat:Index
+..summary:Default @Class.String@ specialization type of the @Metafunction.Fibre@ of an @Class.Index at .
+..signature:DefaultIndexStringSpec<TIndex>::Type
+..param.TIndex:An @Class.Index@ Type.
+..returns:If the underlying text is a @Class.String@ or a set of Strings (see @Class.StringSet@) the String's spec. type is returned.
+..remarks:Most of the @Class.Index@ fibres are strings. The @Class.String@ specialization type is chosen by this meta-function.
+*/
+ template < typename TIndex >
+ struct DefaultIndexStringSpec {
+ typedef Alloc<> Type;
+ };
+
+// template < typename TValue, typename TSpec >
+// struct DefaultIndexStringSpec< String<TValue, External<TSpec> > > {
+// typedef External<TSpec> Type;
+// };
+
+ template < typename TString, typename TSpec >
+ struct DefaultIndexStringSpec< StringSet<TString, TSpec> >:
+ DefaultIndexStringSpec<TString> {};
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Class.Index:
+..summary:Contains preprocessing data of a fixed text. Allows fast dictionary look-up and advanced computations.
+..cat:Index
+..signature:Index<TText[, TSpec]>
+..param.TText:The text type.
+...type:Class.String
+...metafunction:Metafunction.Host
+..param.TSpec:The index type.
+...default:The result of @Metafunction.DefaultIndexSpec@
+...metafunction:Metafunction.Spec
+..remarks:An index contains various arrays or objects, also called fibres (see @Metafunction.Fibre@).
+..remarks:These fibres are created on demand depending on the requirements of an algorithm.
+*/
+
+///.Function.setHaystack.param.haystack.type:Class.Index
+
+ // index as a haystack
+ template <
+ typename TObject,
+ typename TSpec = typename DefaultIndexSpec<TObject>::Type >
+ class Index;
+
+ template <typename TObject, typename TSpec>
+ struct Host< Index<TObject, TSpec> > {
+ typedef TObject Type;
+ };
+
+ template <typename TObject, typename TSpec>
+ struct Spec< Index<TObject, TSpec> > {
+ typedef TSpec Type;
+ };
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Metafunction.Fibre:
+..summary:Type of a specific bundle member (fibre).
+..signature:Fibre<TIndex, TSpec>::Type
+..cat:Index
+..param.TIndex:The fibre container type.
+..param.TSpec:Type to specify the fibre.
+..returns:Fibre type.
+..remarks:An @Class.Index@ can be seen as a bundle consisting of various fibres. In most cases this type is $String<Size<TIndex>::Type>$.
+..remarks:A @Metafunction.Fibre@ need not to be a real container. It can also be view (see @Tag.ESA Index Fibres.ESA_RawText@).
+*/
+ // meta function to get the type of a bundle fibre
+ template < typename TIndex, typename TSpec >
+ struct Fibre {
+ typedef String< typename Size<TIndex>::Type > Type;
+ };
+
+ template < typename TIndex, typename TSpec >
+ struct Fibre<TIndex const, TSpec> {
+ typedef typename Fibre<TIndex, TSpec>::Type const Type;
+ };
+
+ struct FibreRecord {
+ unsigned id;
+ void* ptr;
+ bool owner;
+ };
+
+ // less function to search in sorted list for fibre id
+ struct FibreLess: public ::std::binary_function<FibreRecord, unsigned, bool>
+ { // functor for operator>
+ inline bool operator()(FibreRecord const & _Left, unsigned const _Right) const
+ { // apply operator> to operands
+ return (_Left.id < _Right);
+ }
+ };
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Metafunction.DefaultIndexCreator:
+..cat:Index
+..summary:Default algorithm to create a demanded and not yet existing @Metafunction.Fibre at .
+..signature:DefaultIndexCreator<TIndex, TFibre>::Type
+..param.TIndex:An @Class.Index@ Type.
+..param.TFibre:A tag specifying the fibre (e.g. @Tag.ESA Index Fibres.ESA_SA@).
+..returns:A tag specifying the default algorithm to create the fibre with.
+*/
+ // standard algorithm for indices creation
+ template < typename TIndex, typename TFibre >
+ struct DefaultIndexCreator {
+ typedef Default Type;
+ };
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ .Class.Bundle:
+ ..summary:General purpose container of various members.
+ ..signature:Bundle<TValue, TSize>
+ ..param.TValue:The value type, that is the type of the items/characters stored in the string.
+ ...remarks:Use @Metafunction.Value@ to get the value type for a given class.
+ ..param.TSpec:The specializing type.
+ ...default:$Alloc<>$, see @Spec.Alloc String at .
+*/
+/*
+ template < typename TSpec = void >
+ struct Bundle {
+ typedef ::std::vector<FibreRecord> TFibreRecords;
+ TFibreRecords fibres;
+ };
+
+ template < typename TBundleSpec, typename TFibreSpec >
+ inline FibreRecord& getRecord(Bundle<TBundleSpec> &bundle, TFibreSpec const) {
+ unsigned id = (unsigned)_ClassIdentifier<TFibreSpec>::getID();
+
+ typename Bundle<TBundleSpec>::TFibreRecords::iterator first = lower_bound(bundle.fibres.begin(), bundle.fibres.end(), id, FibreLess());
+ if (!first->id != id) {
+ FibreRecord rec;
+ rec.id = id;
+ rec.ptr = NULL;
+ rec.owner = true;
+ bundle.fibres.insert(first, rec);
+ } else
+ return *first;
+ }
+
+ template < typename TBundleSpec, typename TFibreSpec >
+ inline typename Fibre<Bundle<TBundleSpec>, TFibreSpec>::Type & getFibre(Bundle<TBundleSpec> &bundle, TFibreSpec const) {
+ typedef typename Fibre<Bundle<TBundleSpec>, TFibreSpec>::Type Type;
+ unsigned id = (unsigned)_ClassIdentifier<TFibreSpec>::getID();
+
+ FibreRecord &rec = getRecord(bundle, TFibreSpec());
+ if (!rec.ptr)
+ rec.ptr = new Type();
+ return *reinterpret_cast<Type*>(rec.ptr);
+ }
+
+ template < typename TBundleSpec, typename TFibreSpec >
+ inline typename Fibre<Bundle<TBundleSpec>, TFibreSpec>::Type const & getFibre(Bundle<TBundleSpec> const &bundle, TFibreSpec const) {
+ typedef typename Fibre<Bundle<TBundleSpec>, TFibreSpec>::Type Type;
+ unsigned id = (unsigned)_ClassIdentifier<TFibreSpec>::getID();
+
+ FibreRecord &rec = getRecord(bundle, TFibreSpec());
+ return *reinterpret_cast<Type*>(rec.ptr);
+ }
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+// various fibre specs for enhanced suffix arrays
+
+ struct _Fibre_Text; // Original text. Can be a String or a StringSet
+ struct _Fibre_RawText; // Concatenation of the strings above
+ struct _Fibre_SA; // suffix array (of raw text with virtual $-delimiters) with Pair entries
+ struct _Fibre_RawSA; // suffix array with integer entries
+ struct _Fibre_SAE; // suffix array reordered in a b-tree
+ struct _Fibre_LCP; // lcp table of raw text
+ struct _Fibre_LCPE; // lcp interval tree
+ struct _Fibre_ChildTab; // childtab (Kurtz et al.) of raw text
+ struct _Fibre_BWT; // burrows wheeler table of raw text
+
+ typedef Tag<_Fibre_Text> const Fibre_Text;
+ typedef Tag<_Fibre_RawText> const Fibre_RawText;
+ typedef Tag<_Fibre_SA> const Fibre_SA;
+ typedef Tag<_Fibre_RawSA> const Fibre_RawSA;
+ typedef Tag<_Fibre_SAE> const Fibre_SAE;
+ typedef Tag<_Fibre_LCP> const Fibre_LCP;
+ typedef Tag<_Fibre_LCPE> const Fibre_LCPE;
+ typedef Tag<_Fibre_ChildTab> const Fibre_ChildTab;
+ typedef Tag<_Fibre_BWT> const Fibre_BWT;
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Metafunction.SAValue:
+..cat:Index
+..summary:The default alphabet type of a suffix array, i.e. the type to store a position of a string or string set.
+..signature:SAValue<TObject>::Type
+..param.TObject:A string, string set, or index type.
+...type:Class.String
+...type:Class.StringSet
+...type:Class.Index
+..returns:A type to store a position.
+...text:If $TObject$ is a @Class.String@, it is a single integer value. By default this is the @Metafunction.Size@ type of $TObject$.
+...text:If $TObject$ is a @Class.StringSet@, it could be a single integer too (called global position, see @Spec.ConcatDirect@) or a @Class.Pair@ (called local position, see @Spec.Owner@).
+Currently SeqAn defaults to a local position for @Class.StringSet@ classes (index_base.h):
+...code:template < typename TString, typename TSpec >
+struct SAValue< StringSet<TString, TSpec> > {
+ typedef Pair<
+ typename Size< StringSet<TString, TSpec> >::Type,
+ typename SAValue<TString>::Type,
+ Compressed
+ > Type;
+};
+..note:SAValue is the return type of various function, e.g. @Function.position@ for the @Class.Index@ @Class.Finder@ class, @Function.getOccurrence@, @Function.getOccurrences@ etc.
+You should always use the type of this meta-function to store the return values.
+If you want to write algorithms for both variants (local and global positions) you
+should use the functions @Function.posLocalize@, @Function.posGlobalize@, @Function.getSeqNo@ and @Function.getSeqOffset at .
+..note:If $TObject$ is an @Class.Index@, @Metafunction.Position@ returns the same value as $SAValue$. You can change the position type of an index by overloading $SAValue$, not @Metafunction.Position at .
+*/
+ template <typename TObject>
+ struct SAValue:
+ Size<TObject> {};
+
+ template <typename TObject>
+ struct SAValue<TObject const>:
+ SAValue<TObject> {};
+
+ // to speed up sequence number computation
+ // we use a pair of seqNo and localPosition
+ template < typename TString, typename TSpec >
+ struct SAValue< StringSet<TString, TSpec> > {
+ typedef Pair<
+ typename Size< StringSet<TString, TSpec> >::Type,
+ typename SAValue<TString>::Type,
+ Compressed
+ > Type;
+ };
+
+/*
+ template < typename TString, typename TSpec >
+ struct SAValue< StringSet<TString, TSpec> > {
+ typedef Pair<
+ typename Size< StringSet<TString, TSpec> >::Type,
+ typename SAValue<TString>::Type,
+ CutCompressed<4> // max. 4 sequences
+ > Type; // max. 2^30 characters each
+ };
+*/
+ template < typename TText, typename TSpec >
+ struct SAValue< Index<TText, TSpec> >:
+ SAValue<TText> {};
+
+ template < typename TObject, typename TSpec >
+ struct DefaultIndexStringSpec< Index<TObject, TSpec> >:
+ DefaultIndexStringSpec<TObject> {};
+
+//////////////////////////////////////////////////////////////////////////////
+// value and size type of an index
+
+ template < typename TText, typename TSpec >
+ struct Value< Index<TText, TSpec> > {
+ typedef typename Value<
+ typename Fibre< Index<TText, TSpec>, Fibre_RawText>::Type
+ >::Type Type;
+ };
+
+ template < typename TText, typename TSpec >
+ struct Size< Index<TText, TSpec> > {
+ typedef typename Size<
+ typename Fibre< Index<TText, TSpec>, Fibre_RawText>::Type
+ >::Type Type;
+ };
+
+ template < typename TText, typename TSpec >
+ struct Position< Index<TText, TSpec> >:
+ SAValue< Index<TText, TSpec> > {};
+
+//////////////////////////////////////////////////////////////////////////////
+// default table type
+
+ template < typename TObject, typename TSpec, typename TFibre >
+ struct Fibre< Index<TObject, TSpec>, Tag<TFibre> const > {
+ typedef String<
+ typename Size< Index<TObject, TSpec> >::Type,
+ typename DefaultIndexStringSpec< Index<TObject, TSpec> >::Type
+ > Type;
+ };
+
+//////////////////////////////////////////////////////////////////////////////
+// original text
+
+ template < typename TText, typename TSpec >
+ struct Fibre< Index<TText, TSpec>, Fibre_Text> {
+ typedef TText Type;
+ };
+
+//////////////////////////////////////////////////////////////////////////////
+// concatenated text
+
+ template < typename TText, typename TSpec >
+ struct Fibre< Index<TText, TSpec>, Fibre_RawText> {
+ typedef typename Concatenator<TText>::Type Type;
+ };
+
+//////////////////////////////////////////////////////////////////////////////
+// suffix array type
+
+ template < typename TText, typename TSpec >
+ struct Fibre< Index<TText, TSpec>, Fibre_SA> {
+ typedef String<
+ typename SAValue< Index<TText, TSpec> >::Type,
+ typename DefaultIndexStringSpec< Index<TText, TSpec> >::Type
+ > Type;
+ };
+
+//////////////////////////////////////////////////////////////////////////////
+// globalize functor
+
+ template <typename InType, typename TLimitsString, typename Result = typename Value<TLimitsString>::Type>
+ struct FunctorGlobalize : public ::std::unary_function<InType,Result> {
+ TLimitsString const *limits;
+
+ FunctorGlobalize() {}
+ FunctorGlobalize(TLimitsString const &_limits) : limits(&_limits) {}
+ inline Result operator()(const InType& x) const
+ {
+ return posGlobalize(x, *limits);
+ }
+ };
+
+//////////////////////////////////////////////////////////////////////////////
+// raw suffix array contains integer offsets relative to raw text
+
+ template < typename TString, typename TSSetSpec, typename TSpec >
+ struct Fibre< Index<StringSet<TString, TSSetSpec>, TSpec>, Fibre_RawSA>
+ {
+ typedef Index< StringSet<TString, TSSetSpec>, TSpec> TIndex;
+// typedef ModifiedString<
+// typename Fibre<TIndex, Fibre_SA>::Type,
+// ModView< FunctorGlobalize<
+// typename Value< typename Fibre<TIndex, Fibre_SA>::Type >::Type,
+// typename StringSetLimits<StringSet<TString, TSSetSpec> >::Type >
+// >
+// > Type;
+ };
+
+//////////////////////////////////////////////////////////////////////////////
+// default burrows-wheeler table
+
+ template < typename TText, typename TSpec >
+ struct Fibre< Index<TText, TSpec>, Fibre_BWT> {
+ typedef String <
+ typename Value< Index<TText, TSpec> >::Type,
+ typename DefaultIndexStringSpec< Index<TText, TSpec> >::Type
+ > Type;
+ };
+
+
+//////////////////////////////////////////////////////////////////////////////
+// default fibre creators
+
+ template < typename TText, typename TSpec >
+ struct DefaultIndexCreator<Index<TText, TSpec>, Fibre_SA> {
+ typedef Skew7 Type; // standard suffix array creator is skew7
+ };
+
+ template < typename TText, typename TSpec >
+ struct DefaultIndexCreator<Index<TText, TSpec>, Fibre_LCP> {
+ typedef Kasai Type;
+ };
+
+ template < typename TText, typename TSpec >
+ struct DefaultIndexCreator<Index<TText, TSpec>, Fibre_BWT> {
+ typedef BWT Type;
+ };
+
+ template < typename TText, typename TSpec >
+ struct DefaultIndexCreator<Index<TText, TSpec>, Fibre_ChildTab> {
+ typedef ChildTab Type;
+ };
+
+
+//////////////////////////////////////////////////////////////////////////////
+// fibre interface to access the enhanced suffix array tables
+
+/**
+.Function.getFibre:
+..summary:Returns a specific @Metafunction.Fibre@ of an @Class.Index@ object.
+..cat:Index
+..signature:getFibre(index, fibre_tag)
+..param.index:The @Class.Index@ object holding the fibre.
+...type:Class.Index
+..param.fibre_tag:A tag that identifies the @Metafunction.Fibre@ (e.g. @Tag.ESA Index Fibres.ESA_SA@).
+..returns:A reference to the @Metafunction.Fibre@ object.
+*/
+
+ template <typename TText, typename TSpec>
+ inline Holder<TText> & _dataHost(Index<TText, TSpec> &index) {
+ return index.text;
+ }
+ template <typename TText, typename TSpec>
+ inline Holder<TText> const & _dataHost(Index<TText, TSpec> const &index) {
+ return index.text;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec>, Fibre_Text>::Type &
+ getFibre(Index<TText, TSpec> &index, Fibre_Text) {
+ return value(index.text);
+ }
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_Text>::Type &
+ getFibre(Index<TText, TSpec> const &index, Fibre_Text) {
+ return value(index.text);
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec>, Fibre_RawText>::Type &
+ getFibre(Index<TText, TSpec> &index, Fibre_RawText) {
+ return concat(value(index.text));
+ }
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_RawText>::Type &
+ getFibre(Index<TText, TSpec> const &index, Fibre_RawText) {
+ return concat(value(index.text));
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec>, Fibre_SA>::Type &
+ getFibre(Index<TText, TSpec> &index, Fibre_SA) {
+ return index.sa;
+ }
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_SA>::Type &
+ getFibre(Index<TText, TSpec> const &index, Fibre_SA) {
+ return index.sa;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_SA>::Type &
+ getFibre(Index<TText, TSpec> &index, Fibre_RawSA) {
+ return indexSA(index);
+ }
+/*
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_SA>::Type &
+ getFibre(Index<TText, TSpec> const &index, Fibre_RawSA) {
+ return indexSA(index);
+ }
+*/
+ template <typename TString, typename TSSetSpec, typename TSpec>
+ inline typename Fibre<Index<StringSet<TString, TSSetSpec>, TSpec>, Fibre_RawSA>::Type
+ getFibre(Index<StringSet<TString, TSSetSpec>, TSpec> &index, Fibre_RawSA)
+ {
+ typedef Index< StringSet<TString, TSSetSpec>, TSpec> TIndex;
+
+ typedef FunctorGlobalize<
+ typename Value< typename Fibre<TIndex, Fibre_SA>::Type >::Type,
+ typename StringSetLimits<StringSet<TString, TSSetSpec> >::Type
+ > TFunctor;
+
+// typedef ModifiedString<
+// typename Fibre<Index<StringSet<TString, TSSetSpec>, TSpec>, Fibre_SA>::Type,
+// ModView< TFunctor >
+// > ModString;
+
+ return ModString(indexSA(index), TFunctor(stringSetLimits(indexText(index))));
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec>, Fibre_LCP>::Type &
+ getFibre(Index<TText, TSpec> &index, Fibre_LCP) {
+ return index.lcp;
+ }
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_LCP>::Type &
+ getFibre(Index<TText, TSpec> const &index, Fibre_LCP) {
+ return index.lcp;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec>, Fibre_LCPE>::Type &
+ getFibre(Index<TText, TSpec> &index, Fibre_LCPE) {
+ return index.lcpe;
+ }
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_LCPE>::Type &
+ getFibre(Index<TText, TSpec> const &index, Fibre_LCPE) {
+ return index.lcpe;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec>, Fibre_ChildTab>::Type &
+ getFibre(Index<TText, TSpec> &index, Fibre_ChildTab) {
+ return index.childtab;
+ }
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_ChildTab>::Type &
+ getFibre(Index<TText, TSpec> const &index, Fibre_ChildTab) {
+ return index.childtab;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec>, Fibre_BWT>::Type &
+ getFibre(Index<TText, TSpec> &index, Fibre_BWT) {
+ return index.bwt;
+ }
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_BWT>::Type &
+ getFibre(Index<TText, TSpec> const &index, Fibre_BWT) {
+ return index.bwt;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+///.Function.length.param.object.type:Class.Index
+
+ template <typename TText, typename TSpec>
+ inline typename Size<Index<TText, TSpec> >::Type
+ length(Index<TText, TSpec> const &index) {
+ return length(indexRawText(index));
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename TText, typename TSpec>
+ inline typename Size<TText>::Type
+ countSequences(Index<TText, TSpec> const &index) {
+ return countSequences(indexText(index));
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename TSeqNo, typename TText, typename TSpec>
+ inline typename Size<Index<TText, TSpec> >::Type
+ sequenceLength(TSeqNo seqNo, Index<TText, TSpec> const &index) {
+ return sequenceLength(seqNo, indexText(index));
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename TPos, typename TText, typename TSpec>
+ inline typename Size<Index<TText, TSpec> >::Type
+ suffixLength(TPos pos, Index<TText, TSpec> const &index) {
+ return sequenceLength(getSeqNo(pos, stringSetLimits(index)), index) - getSeqOffset(pos, stringSetLimits(index));
+ }
+
+
+//////////////////////////////////////////////////////////////////////////////
+// unified textAt interface
+
+ template <typename TPos, typename TIndex>
+ inline typename Reference<typename Fibre<TIndex, Fibre_RawText>::Type>::Type
+ textAt(TPos i, TIndex &index) {
+ return value(getFibre(index, Fibre_RawText()), i);
+ }
+ template <typename TPos, typename TString, typename TSSetSpec, typename TSpec>
+ inline typename Reference<typename Fibre< Index< StringSet<TString, TSSetSpec>, TSpec>, Fibre_RawText>::Type>::Type
+ textAt(TPos i, Index< StringSet<TString, TSSetSpec>, TSpec> &index) {
+ return value(getFibre(index, Fibre_RawText()), posGlobalize(i, stringSetLimits(index)));
+ }
+ template <typename TPos, typename TString, typename TSpec>
+ inline typename Reference<typename Fibre< Index< StringSet<TString, Owner<Default> >, TSpec>, Fibre_RawText>::Type>::Type
+ textAt(TPos i, Index< StringSet<TString, Owner<Default> >, TSpec> &index) {
+ Pair <
+ typename Size< StringSet<TString, Owner<Default> > >::Type,
+ typename Size< TString >::Type > locPos;
+ posLocalize(locPos, i, stringSetLimits(index));
+ return value(value(getFibre(index, Fibre_Text()), getValueI1(locPos)), getValueI2(locPos));
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.rawtextAt:
+..summary:Shortcut for $value(indexRawText(..), ..)$.
+..cat:Index
+..signature:rawtextAt(position, index)
+..param.position:A position in the array on which the value should be accessed.
+..param.index:The @Class.Index@ object holding the fibre.
+...type:Spec.Index_ESA
+..returns:A reference or proxy to the value.
+*/
+
+ template <typename TPos, typename TIndex>
+ inline typename Reference<typename Fibre<TIndex, Fibre_RawText>::Type>::Type rawtextAt(TPos i, TIndex &index) {
+ return value(getFibre(index, Fibre_RawText()), i);
+ }
+ template <typename TPos, typename TIndex>
+ inline typename Reference<typename Fibre<TIndex const, Fibre_RawText>::Type>::Type rawtextAt(TPos i, TIndex const &index) {
+ return value(getFibre(index, Fibre_RawText()), i);
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.saAt:
+..summary:Shortcut for $value(indexSA(..), ..)$.
+..cat:Index
+..signature:saAt(position, index)
+..param.position:A position in the array on which the value should be accessed.
+..param.index:The @Class.Index@ object holding the fibre.
+...type:Spec.Index_ESA
+..returns:A reference or proxy to the value.
+*/
+
+ template <typename TPos, typename TIndex>
+ inline typename Reference<typename Fibre<TIndex, Fibre_SA>::Type>::Type saAt(TPos i, TIndex &index) {
+ return value(getFibre(index, Fibre_SA()), i);
+ }
+ template <typename TPos, typename TIndex>
+ inline typename Reference<typename Fibre<TIndex const, Fibre_SA>::Type>::Type saAt(TPos i, TIndex const &index) {
+ return value(getFibre(index, Fibre_SA()), i);
+ }
+
+ template <typename TPos, typename TIndex>
+ inline typename Value<typename Fibre<TIndex const, Fibre_RawSA>::Type>::Type rawsaAt(TPos i, TIndex const &index) {
+ return posGlobalize(saAt(i, index), stringSetLimits(indexText(index)));
+ }
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.lcpAt:
+..summary:Shortcut for $value(indexLCP(..), ..)$.
+..cat:Index
+..signature:lcpAt(position, index)
+..param.position:A position in the array on which the value should be accessed.
+..param.index:The @Class.Index@ object holding the fibre.
+...type:Spec.Index_ESA
+..returns:A reference or proxy to the value.
+*/
+
+ template <typename TPos, typename TIndex>
+ inline typename Reference<typename Fibre<TIndex, Fibre_LCP>::Type>::Type lcpAt(TPos i, TIndex &index) {
+ return value(getFibre(index, Fibre_LCP()), i);
+ }
+ template <typename TPos, typename TIndex>
+ inline typename Reference<typename Fibre<TIndex const, Fibre_LCP>::Type>::Type lcpAt(TPos i, TIndex const &index) {
+ return value(getFibre(index, Fibre_LCP()), i);
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.lcpeAt:
+..summary:Shortcut for $value(indexLCPE(..), ..)$.
+..cat:Index
+..signature:lcpeAt(position, index)
+..param.position:A position in the array on which the value should be accessed.
+..param.index:The @Class.Index@ object holding the fibre.
+...type:Spec.Index_ESA
+..returns:A reference or proxy to the value.
+*/
+
+ template <typename TPos, typename TIndex>
+ inline typename Reference<typename Fibre<TIndex, Fibre_LCPE>::Type>::Type lcpeAt(TPos i, TIndex &index) {
+ return value(getFibre(index, Fibre_LCPE()), i);
+ }
+ template <typename TPos, typename TIndex>
+ inline typename Reference<typename Fibre<TIndex const, Fibre_LCPE>::Type>::Type lcpeAt(TPos i, TIndex const &index) {
+ return value(getFibre(index, Fibre_LCPE()), i);
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.childAt:
+..summary:Shortcut for $value(indexChildTab(..), ..)$.
+..cat:Index
+..signature:childAt(position, index)
+..param.position:A position in the array on which the value should be accessed.
+..param.index:The @Class.Index@ object holding the fibre.
+...type:Spec.Index_ESA
+..returns:A reference or proxy to the value.
+*/
+
+ template <typename TPos, typename TIndex>
+ inline typename Reference<typename Fibre<TIndex, Fibre_ChildTab>::Type>::Type childAt(TPos i, TIndex &index) {
+ return value(getFibre(index, Fibre_ChildTab()), i);
+ }
+ template <typename TPos, typename TIndex>
+ inline typename Reference<typename Fibre<TIndex const, Fibre_ChildTab>::Type>::Type childAt(TPos i, TIndex const &index) {
+ return value(getFibre(index, Fibre_ChildTab()), i);
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.bwtAt:
+..summary:Shortcut for $value(indexBWT(..), ..)$.
+..cat:Index
+..signature:bwtAt(position, index)
+..param.position:A position in the array on which the value should be accessed.
+..param.index:The @Class.Index@ object holding the fibre.
+...type:Spec.Index_ESA
+..returns:A reference or proxy to the value.
+*/
+
+ template <typename TPos, typename TIndex>
+ inline typename Reference<typename Fibre<TIndex, Fibre_BWT>::Type>::Type bwtAt(TPos i, TIndex &index) {
+ return value(getFibre(index, Fibre_BWT()), i);
+ }
+ template <typename TPos, typename TIndex>
+ inline typename Reference<typename Fibre<TIndex const, Fibre_BWT>::Type>::Type bwtAt(TPos i, TIndex const &index) {
+ return value(getFibre(index, Fibre_BWT()), i);
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// interface for infinity/invalid values
+
+ template <typename TValue>
+ inline void _setSizeInval(TValue &v) {
+ v = SupremumValue<TValue>::VALUE;
+ }
+
+ template <typename TValue>
+ inline bool _isSizeInval(TValue const &v) {
+ return v == SupremumValue<TValue>::VALUE;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.indexText:
+..summary:Shortcut for $getFibre(.., ESA_Text)$.
+..cat:Index
+..signature:indexText(index)
+..param.index:The @Class.Index@ object holding the fibre.
+...type:Spec.Index_ESA
+..returns:A reference to the @Tag.ESA Index Fibres.ESA_Text@ fibre (original text).
+*/
+
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec>, Fibre_Text>::Type & indexText(Index<TText, TSpec> &index) { return getFibre(index, Fibre_Text()); }
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_Text>::Type & indexText(Index<TText, TSpec> const &index) { return getFibre(index, Fibre_Text()); }
+
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename TText, typename TSpec>
+ inline typename StringSetLimits<TText const>::Type
+ stringSetLimits(Index<TText, TSpec> &) {
+ return Nothing();
+ }
+
+ template <typename TText, typename TSpec>
+ inline typename StringSetLimits<TText const>::Type
+ stringSetLimits(Index<TText, TSpec> const &) {
+ return Nothing();
+ }
+
+ template <typename TString, typename TSSetSpec, typename TSpec>
+ inline typename StringSetLimits< StringSet<TString, TSSetSpec> const >::Type &
+ stringSetLimits(Index<StringSet<TString, TSSetSpec>, TSpec> &index) {
+ return stringSetLimits(indexText(index));
+ }
+
+ template <typename TString, typename TSSetSpec, typename TSpec>
+ inline typename StringSetLimits< StringSet<TString, TSSetSpec> const >::Type &
+ stringSetLimits(Index<StringSet<TString, TSSetSpec>, TSpec> const &index) {
+ return stringSetLimits(indexText(index));
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.indexRawText:
+..summary:Shortcut for $getFibre(.., ESA_RawText)$.
+..cat:Index
+..signature:indexRawText(index)
+..param.index:The @Class.Index@ object holding the fibre.
+...type:Spec.Index_ESA
+..returns:A reference to the @Tag.ESA Index Fibres.ESA_RawText@ fibre (concatenated input text).
+*/
+
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec>, Fibre_RawText>::Type & indexRawText(Index<TText, TSpec> &index) { return getFibre(index, Fibre_RawText()); }
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_RawText>::Type & indexRawText(Index<TText, TSpec> const &index) { return getFibre(index, Fibre_RawText()); }
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.indexSA:
+..summary:Shortcut for $getFibre(.., ESA_SA)$.
+..cat:Index
+..signature:indexSA(index)
+..param.index:The @Class.Index@ object holding the fibre.
+...type:Spec.Index_ESA
+..returns:A reference to the @Tag.ESA Index Fibres.ESA_SA@ fibre (suffix array).
+*/
+
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec>, Fibre_SA>::Type & indexSA(Index<TText, TSpec> &index) { return getFibre(index, Fibre_SA()); }
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_SA>::Type & indexSA(Index<TText, TSpec> const &index) { return getFibre(index, Fibre_SA()); }
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.indexRawSA:
+..summary:Shortcut for $getFibre(.., ESA_RawSA)$.
+..cat:Index
+..signature:indexRawSA(index)
+..param.index:The @Class.Index@ object holding the fibre.
+...type:Spec.Index_ESA
+..returns:A reference to the @Tag.ESA Index Fibres.ESA_RawSA@ fibre (suffix array).
+*/
+
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec>, Fibre_RawSA>::Type indexRawSA(Index<TText, TSpec> &index) { return getFibre(index, Fibre_RawSA()); }
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_RawSA>::Type indexRawSA(Index<TText, TSpec> const &index) { return getFibre(index, Fibre_RawSA()); }
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.indexLCP:
+..summary:Shortcut for $getFibre(.., ESA_LCP)$.
+..cat:Index
+..signature:indexLCP(index)
+..param.index:The @Class.Index@ object holding the fibre.
+...type:Spec.Index_ESA
+..returns:A reference to the @Tag.ESA Index Fibres.ESA_LCP@ fibre (lcp table).
+*/
+
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec>, Fibre_LCP>::Type & indexLCP(Index<TText, TSpec> &index) { return getFibre(index, Fibre_LCP()); }
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_LCP>::Type & indexLCP(Index<TText, TSpec> const &index) { return getFibre(index, Fibre_LCP()); }
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.indexLCPE:
+..summary:Shortcut for $getFibre(.., ESA_LCPE)$.
+..cat:Index
+..signature:indexLCPE(index)
+..param.index:The @Class.Index@ object holding the fibre.
+...type:Spec.Index_ESA
+..returns:A reference to the @Tag.ESA Index Fibres.ESA_LCPE@ fibre (enhanced lcp table).
+*/
+
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec>, Fibre_LCPE>::Type & indexLCPE(Index<TText, TSpec> &index) { return getFibre(index, Fibre_LCPE()); }
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_LCPE>::Type & indexLCPE(Index<TText, TSpec> const &index) { return getFibre(index, Fibre_LCPE()); }
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.indexBWT:
+..summary:Shortcut for $getFibre(.., ESA_BWT)$.
+..cat:Index
+..signature:indexBWT(index)
+..param.index:The @Class.Index@ object holding the fibre.
+...type:Spec.Index_ESA
+..returns:A reference to the @Tag.ESA Index Fibres.ESA_BWT@ fibre (Burrows-Wheeler table).
+*/
+
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec>, Fibre_BWT>::Type & indexBWT(Index<TText, TSpec> &index) { return getFibre(index, Fibre_BWT()); }
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_BWT>::Type & indexBWT(Index<TText, TSpec> const &index) { return getFibre(index, Fibre_BWT()); }
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.indexChildTab:
+..summary:Shortcut for $getFibre(.., ESA_ChildTab)$.
+..cat:Index
+..signature:indexChildTab(index)
+..param.index:The @Class.Index@ object holding the fibre.
+...type:Spec.Index_ESA
+..returns:A reference to the @Tag.ESA Index Fibres.ESA_ChildTab@ fibre (child table).
+*/
+
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec>, Fibre_ChildTab>::Type & indexChildTab(Index<TText, TSpec> &index) { return getFibre(index, Fibre_ChildTab()); }
+ template <typename TText, typename TSpec>
+ inline typename Fibre<Index<TText, TSpec> const, Fibre_ChildTab>::Type & indexChildTab(Index<TText, TSpec> const &index) { return getFibre(index, Fibre_ChildTab()); }
+
+}
+
+#endif
diff --git a/src/libSSA/seqan/index/index_find.h b/src/libSSA/seqan/index/index_find.h
new file mode 100644
index 0000000..a734c78
--- /dev/null
+++ b/src/libSSA/seqan/index/index_find.h
@@ -0,0 +1,268 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: index_find.h,v 1.1 2008/08/25 16:20:05 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_INDEX_FIND_H
+#define SEQAN_HEADER_INDEX_FIND_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ struct Position< Finder< Index<TText, TSpec>, TSpecFinder > >:
+ SAValue< Index<TText, TSpec> > {};
+
+
+//////////////////////////////////////////////////////////////////////////////
+// generic Finder class for all indices containing a suffix array or
+// similar table, where a query result is an interval in this table
+//
+// your index must specialize the function _findFirstIndex and set
+// finder.range to the interval containing the query hits. See:
+//
+// template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
+// inline void _findFirstIndex(
+// Finder< Index<TText, TSpec>, TSpecFinder > &finder,
+// TPattern const &pattern,
+// ESA_FIND_MLR const)
+// {
+// Index<TText, TSpec> &index = haystack(finder);
+// indexRequire(index, ESA_SA());
+// finder.range = equalRangeSAIterator(indexText(index), indexSA(index), pattern);
+// }
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ class Finder< Index<TText, TSpec>, TSpecFinder >
+ {
+ protected:
+ typedef Index<TText, TSpec> TIndex;
+ typedef typename Fibre<TIndex, Fibre_SA>::Type TSA;
+ typedef typename Iterator<TSA const, Standard>::Type TIterator;
+
+ public:
+ Holder<TIndex> index;
+ Pair<TIterator> range;
+ TIterator data_iterator;
+
+ Finder()
+ {
+ clear(*this);
+ }
+ Finder(TIndex &_index): index(_index)
+ {
+ clear(*this);
+ }
+ Finder(TIndex const &_index): index(_index)
+ {
+ clear(*this);
+ }
+ };
+
+//____________________________________________________________________________
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline typename _Parameter< Index<TText, TSpec> >::Type
+ host(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+ {
+SEQAN_CHECKPOINT
+ return value(me.index);
+ }
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline typename _Parameter< Index<TText, TSpec> >::Type
+ host(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
+ {
+SEQAN_CHECKPOINT
+ return value(me.index);
+ }
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline typename _Parameter< Index<TText, TSpec> >::Type
+ container(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+ {
+SEQAN_CHECKPOINT
+ return value(me.index);
+ }
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline typename _Parameter< Index<TText, TSpec> >::Type
+ container(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
+ {
+SEQAN_CHECKPOINT
+ return value(me.index);
+ }
+
+//____________________________________________________________________________
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline void
+ setHost(
+ Finder< Index<TText, TSpec>, TSpecFinder > & me,
+ typename _Parameter<Index<TText, TSpec> >::Type container_)
+ {
+SEQAN_CHECKPOINT
+ me.index = container;
+ }
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline void
+ setContainer(
+ Finder< Index<TText, TSpec>, TSpecFinder > & me,
+ typename _Parameter<Index<TText, TSpec> >::Type container_)
+ {
+SEQAN_CHECKPOINT
+ me.index = container;
+ }
+
+//____________________________________________________________________________
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline typename Iterator< typename Fibre<Index<TText, TSpec>, Fibre_SA>::Type, Standard>::Type &
+ hostIterator(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_iterator;
+ }
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline typename Iterator< typename Fibre<Index<TText, TSpec>, Fibre_SA>::Type, Standard>::Type const &
+ hostIterator(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_iterator;
+ }
+
+
+//____________________________________________________________________________
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline bool
+ empty(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+ {
+SEQAN_CHECKPOINT
+ return me.range.i1 == me.range.i2;
+ }
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline void
+ clear(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+ {
+SEQAN_CHECKPOINT
+ typedef Index<TText, TSpec> TIndex;
+ typedef typename Fibre<TIndex, Fibre_SA>::Type TSA;
+ typedef typename Iterator<TSA, Standard>::Type TIterator;
+ me.range.i1 = me.range.i2 = TIterator();
+ }
+
+//____________________________________________________________________________
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline bool
+ atBegin(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+ {
+SEQAN_CHECKPOINT
+ return (empty(me) || hostIterator(me) == me.range.i1);
+ }
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline bool
+ atEnd(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+ {
+SEQAN_CHECKPOINT
+ return (empty(me) || hostIterator(me) == me.range.i2);
+ }
+
+//____________________________________________________________________________
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline void
+ goBegin(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+ {
+SEQAN_CHECKPOINT
+ hostIterator(me) = me.range.i1;
+ }
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline void
+ goEnd(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+ {
+SEQAN_CHECKPOINT
+ hostIterator(me) = me.range.i2;
+ }
+
+//____________________________________________________________________________
+/*
+ template < typename TText, typename TSpec, typename TSpecFinder, typename TPosition >
+ inline void
+ setPosition(Finder< Index<TText, TSpec>, TSpecFinder > & me, TPosition pos_)
+ {
+SEQAN_CHECKPOINT
+ hostIterator(me) = me.range.i1 + pos_;
+ }
+*/
+//____________________________________________________________________________
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
+ position(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+ {
+SEQAN_CHECKPOINT
+ SEQAN_ASSERT(!empty(me))
+ return *me.data_iterator;
+ }
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
+ position(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
+ {
+SEQAN_CHECKPOINT
+ SEQAN_ASSERT(!empty(me))
+ return hostIterator(me) - begin(container(me), Rooted());
+ }
+
+
+//////////////////////////////////////////////////////////////////////////////
+// find
+
+ template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
+ inline bool find(
+ Finder<Index<TText, TSpec>, TSpecFinder> &finder,
+ TPattern const &pattern)
+ {
+ if (empty(finder)) {
+ _findFirstIndex(finder, needle(pattern), TSpecFinder());
+ hostIterator(finder) = finder.range.i1;
+ } else
+ ++hostIterator(finder);
+ return !atEnd(finder);
+ }
+
+ template < typename TText, typename TSpec, typename TSpecFinder >
+ inline bool find(Finder<Index<TText, TSpec>, TSpecFinder> &finder)
+ {
+ if (empty(finder)) return false;
+ ++hostIterator(finder);
+ return !atEnd(finder);
+ }
+
+}
+
+#endif
diff --git a/src/libSSA/seqan/index/index_generated_forwards.h b/src/libSSA/seqan/index/index_generated_forwards.h
new file mode 100644
index 0000000..d5b4560
--- /dev/null
+++ b/src/libSSA/seqan/index/index_generated_forwards.h
@@ -0,0 +1,2648 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_INDEX_GENERATED_FORWARDS_H
+#define SEQAN_HEADER_INDEX_GENERATED_FORWARDS_H
+
+//////////////////////////////////////////////////////////////////////////////
+// NOTE: This file is automatically generated by build_forwards.py
+// Do not edit this file manually!
+//////////////////////////////////////////////////////////////////////////////
+
+
+//////////////////////////////////////////////////////////////////////////////
+// CLASSES
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+namespace impl {
+
+//____________________________________________________________________________
+// substringHelperPizzaChili
+
+template <typename TValue, typename TSpec, typename TPos> struct substringHelperPizzaChili; // "projects/library/seqan/index/index_pizzachili_string.h"(520)
+
+} //namespace impl
+} //namespace SEQAN_NAMESPACE_MAIN
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+
+//____________________________________________________________________________
+// Align
+
+template <typename TSource, typename TSpec> class Align; // "projects/library/seqan/index/index_esa_base.h"(189)
+
+//____________________________________________________________________________
+// ArrayGaps
+
+struct ArrayGaps; // "projects/library/seqan/index/index_esa_base.h"(186)
+
+//____________________________________________________________________________
+// BTree
+
+template <unsigned BlockSize > struct BTree; // "projects/library/seqan/index/index_esa_find.h"(70)
+
+//____________________________________________________________________________
+// BWT
+
+struct BWT; // "projects/library/seqan/index/index_base.h"(46)
+struct BWT; // "projects/library/seqan/index/index_bwt.h"(30)
+
+//____________________________________________________________________________
+// BottomUp
+
+template <typename TSpec > struct BottomUp; // "projects/library/seqan/index/index_esa_base.h"(125)
+
+//____________________________________________________________________________
+// ChildTab
+
+struct ChildTab; // "projects/library/seqan/index/index_childtab.h"(30)
+struct ChildTab; // "projects/library/seqan/index/index_base.h"(45)
+
+//____________________________________________________________________________
+// CompareSkewDCStream
+
+template <typename TValue> struct CompareSkewDCStream; // "projects/library/seqan/index/pipe_merger7.h"(95)
+
+//____________________________________________________________________________
+// DeepShallow
+
+struct DeepShallow; // "projects/library/seqan/index/index_shawarma.h"(42)
+
+//____________________________________________________________________________
+// DefaultIndexCreator
+
+template <typename TIndex, typename TFibre > struct DefaultIndexCreator; // "projects/library/seqan/index/index_base.h"(177)
+
+//____________________________________________________________________________
+// DefaultIndexSpec
+
+template <typename TObject > struct DefaultIndexSpec; // "projects/library/seqan/index/index_base.h"(63)
+
+//____________________________________________________________________________
+// DefaultIndexStringSpec
+
+template <typename TIndex > struct DefaultIndexStringSpec; // "projects/library/seqan/index/index_base.h"(78)
+
+//____________________________________________________________________________
+// DivSufSort
+
+struct DivSufSort; // "projects/library/seqan/index/index_shawarma.h"(41)
+
+//____________________________________________________________________________
+// EmptyEdges
+
+struct EmptyEdges; // "projects/library/seqan/index/index_esa_base.h"(102)
+
+//____________________________________________________________________________
+// Extender3
+
+struct Extender3; // "projects/library/seqan/index/pump_extender3.h"(30)
+
+//____________________________________________________________________________
+// Extender7
+
+template <typename TCompression > struct Extender7; // "projects/library/seqan/index/pump_extender7.h"(33)
+
+//____________________________________________________________________________
+// Extender7Multi
+
+template <typename TPair, typename TCompression > struct Extender7Multi; // "projects/library/seqan/index/pump_extender7.h"(228)
+
+//____________________________________________________________________________
+// Fibre
+
+template <typename TIndex, typename TSpec > struct Fibre; // "projects/library/seqan/index/index_base.h"(141)
+
+//____________________________________________________________________________
+// FibreLess
+
+struct FibreLess; // "projects/library/seqan/index/index_base.h"(158)
+
+//____________________________________________________________________________
+// FibreRecord
+
+struct FibreRecord; // "projects/library/seqan/index/index_base.h"(150)
+
+//____________________________________________________________________________
+// FixedGappedShape
+
+template <typename TSpec> struct FixedGappedShape; // "projects/library/seqan/index/shape_base.h"(32)
+
+//____________________________________________________________________________
+// FixedShape
+
+template <unsigned q> struct FixedShape; // "projects/library/seqan/index/shape_base.h"(28)
+
+//____________________________________________________________________________
+// FunctorGlobalize
+
+template <typename InType, typename TLimitsString, typename Result > struct FunctorGlobalize; // "projects/library/seqan/index/index_base.h"(386)
+
+//____________________________________________________________________________
+// GetVSTreeIteratorTraits
+
+template <typename TIterator> struct GetVSTreeIteratorTraits; // "projects/library/seqan/index/index_esa_base.h"(148)
+
+//____________________________________________________________________________
+// HardwiredShape
+
+template <int P00 , int P01 , int P02 , int P03 , int P04 , int P05 , int P06 , int P07 , int P08 , int P09 , int P10 , int P11 , int P12 , int P13 , int P14 , int P15 , int P16 , int P17 , int P18 , int P19 > struct HardwiredShape; // "projects/library/seqan/index/shape_gapped.h"(50)
+
+//____________________________________________________________________________
+// HideEmptyEdges
+
+struct HideEmptyEdges; // "projects/library/seqan/index/index_esa_base.h"(101)
+
+//____________________________________________________________________________
+// Index
+
+template <typename TObject, typename TSpec > class Index; // "projects/library/seqan/index/index_base.h"(114)
+
+//____________________________________________________________________________
+// Index_ESA
+
+template <typename TSpec > struct Index_ESA; // "projects/library/seqan/index/index_base.h"(49)
+
+//____________________________________________________________________________
+// Index_QGram
+
+template <typename TShapeSpec, typename TSpec > struct Index_QGram; // "projects/library/seqan/index/index_qgram.h"(100)
+
+//____________________________________________________________________________
+// Index_Wotd
+
+template <typename TSpec > struct Index_Wotd; // "projects/library/seqan/index/index_wotd.h"(56)
+
+//____________________________________________________________________________
+// InvalidPizzaChiliSpec
+
+struct InvalidPizzaChiliSpec; // "projects/library/seqan/index/pizzachili_api.h"(37)
+
+//____________________________________________________________________________
+// Kasai
+
+struct Kasai; // "projects/library/seqan/index/index_base.h"(41)
+struct Kasai; // "projects/library/seqan/index/index_lcp.h"(30)
+
+//____________________________________________________________________________
+// KasaiOriginal
+
+struct KasaiOriginal; // "projects/library/seqan/index/index_base.h"(42)
+struct KasaiOriginal; // "projects/library/seqan/index/index_lcp.h"(31)
+
+//____________________________________________________________________________
+// LarssonSadakane
+
+struct LarssonSadakane; // "projects/library/seqan/index/index_sa_lss.h"(336)
+struct LarssonSadakane; // "projects/library/seqan/index/index_base.h"(35)
+
+//____________________________________________________________________________
+// LcpConfig
+
+struct LcpConfig; // "projects/library/seqan/index/pump_lcp_core.h"(31)
+
+//____________________________________________________________________________
+// LeftCompleteTree
+
+struct LeftCompleteTree; // "projects/library/seqan/index/index_esa_find.h"(67)
+
+//____________________________________________________________________________
+// MSufSort
+
+struct MSufSort; // "projects/library/seqan/index/index_shawarma.h"(40)
+
+//____________________________________________________________________________
+// MUMs
+
+struct MUMs; // "projects/library/seqan/index/index_esa_base.h"(129)
+
+//____________________________________________________________________________
+// ManberMyers
+
+struct ManberMyers; // "projects/library/seqan/index/index_sa_mm.h"(27)
+struct ManberMyers; // "projects/library/seqan/index/index_base.h"(36)
+
+//____________________________________________________________________________
+// MaxRepeat
+
+template <typename TSTree> struct MaxRepeat; // "projects/library/seqan/index/index_esa_algs.h"(602)
+
+//____________________________________________________________________________
+// MaxRepeatOccurrences
+
+struct MaxRepeatOccurrences; // "projects/library/seqan/index/index_esa_base.h"(132)
+
+//____________________________________________________________________________
+// Merger3
+
+struct Merger3; // "projects/library/seqan/index/pipe_merger3.h"(30)
+
+//____________________________________________________________________________
+// Merger7
+
+struct Merger7; // "projects/library/seqan/index/pipe_merger7.h"(178)
+
+//____________________________________________________________________________
+// Merger7Multi
+
+template <typename TLimitsString> struct Merger7Multi; // "projects/library/seqan/index/pipe_merger7.h"(187)
+
+//____________________________________________________________________________
+// MultiMEM
+
+template <typename TSTree> struct MultiMEM; // "projects/library/seqan/index/index_esa_algs_multi.h"(385)
+
+//____________________________________________________________________________
+// MultiMEMOccurences
+
+struct MultiMEMOccurences; // "projects/library/seqan/index/index_esa_base.h"(134)
+
+//____________________________________________________________________________
+// ParentLinks
+
+template <typename TSpec > struct ParentLinks; // "projects/library/seqan/index/index_esa_base.h"(121)
+
+//____________________________________________________________________________
+// PizzaChili
+
+template <typename TSpec> struct PizzaChili; // "projects/library/seqan/index/index_pizzachili_string.h"(47)
+
+//____________________________________________________________________________
+// PizzaChiliCodeProvider
+
+template <typename TSpec> struct PizzaChiliCodeProvider; // "projects/library/seqan/index/pizzachili_api.h"(40)
+
+//____________________________________________________________________________
+// Postorder
+
+struct Postorder; // "projects/library/seqan/index/index_esa_base.h"(96)
+
+//____________________________________________________________________________
+// PostorderEmptyEdges
+
+struct PostorderEmptyEdges; // "projects/library/seqan/index/index_esa_base.h"(98)
+
+//____________________________________________________________________________
+// Preorder
+
+struct Preorder; // "projects/library/seqan/index/index_esa_base.h"(95)
+
+//____________________________________________________________________________
+// PreorderEmptyEdges
+
+struct PreorderEmptyEdges; // "projects/library/seqan/index/index_esa_base.h"(97)
+
+//____________________________________________________________________________
+// QGram_Alg
+
+struct QGram_Alg; // "projects/library/seqan/index/index_base.h"(38)
+
+//____________________________________________________________________________
+// QSufSort
+
+struct QSufSort; // "projects/library/seqan/index/index_shawarma.h"(43)
+
+//____________________________________________________________________________
+// Repeat
+
+template <typename TPos, typename TPeriod> struct Repeat; // "projects/library/seqan/index/repeat_base.h"(28)
+
+//____________________________________________________________________________
+// RepeatFinderParams
+
+template <typename TSize> struct RepeatFinderParams; // "projects/library/seqan/index/repeat_base.h"(47)
+
+//____________________________________________________________________________
+// SAQSort
+
+struct SAQSort; // "projects/library/seqan/index/index_base.h"(37)
+struct SAQSort; // "projects/library/seqan/index/index_sa_qsort.h"(27)
+
+//____________________________________________________________________________
+// SAValue
+
+template <typename TObject> struct SAValue; // "projects/library/seqan/index/index_base.h"(288)
+
+//____________________________________________________________________________
+// SearchTreeIterator
+
+template <typename TString, typename TSpec > class SearchTreeIterator; // "projects/library/seqan/index/index_esa_find.h"(73)
+
+//____________________________________________________________________________
+// Shape
+
+template <typename TValue , typename TSpec > class Shape; // "projects/library/seqan/index/shape_base.h"(54)
+
+//____________________________________________________________________________
+// Shawarma
+
+template <typename TSpec> struct Shawarma; // "projects/library/seqan/index/index_shawarma.h"(38)
+
+//____________________________________________________________________________
+// Skew3
+
+struct Skew3; // "projects/library/seqan/index/index_base.h"(33)
+struct Skew3; // "projects/library/seqan/index/index_skew3.h"(30)
+
+//____________________________________________________________________________
+// Skew7
+
+struct Skew7; // "projects/library/seqan/index/index_base.h"(34)
+struct Skew7; // "projects/library/seqan/index/index_skew7.h"(30)
+
+//____________________________________________________________________________
+// SkewDCStream
+
+template <typename TValue> struct SkewDCStream; // "projects/library/seqan/index/pipe_merger7.h"(71)
+
+//____________________________________________________________________________
+// SortedList
+
+struct SortedList; // "projects/library/seqan/index/index_esa_find.h"(66)
+
+//____________________________________________________________________________
+// SuperMaxRepeats
+
+struct SuperMaxRepeats; // "projects/library/seqan/index/index_esa_base.h"(127)
+
+//____________________________________________________________________________
+// SuperMaxRepeatsFast
+
+struct SuperMaxRepeatsFast; // "projects/library/seqan/index/index_esa_base.h"(128)
+
+//____________________________________________________________________________
+// TRepeatFinder
+
+struct TRepeatFinder; // "projects/library/seqan/index/repeat_base.h"(53)
+
+//____________________________________________________________________________
+// TopDown
+
+template <typename TSpec > struct TopDown; // "projects/library/seqan/index/index_esa_base.h"(117)
+
+//____________________________________________________________________________
+// VSTree
+
+template <typename TSpec > struct VSTree; // "projects/library/seqan/index/index_esa_base.h"(113)
+
+//____________________________________________________________________________
+// VSTreeIteratorTraits
+
+template <typename TDFSOrder , typename THideEmptyEdges > struct VSTreeIteratorTraits; // "projects/library/seqan/index/index_esa_base.h"(32)
+
+//____________________________________________________________________________
+// VertexESA
+
+template <typename TSize> struct VertexESA; // "projects/library/seqan/index/index_esa_base.h"(153)
+
+//____________________________________________________________________________
+// WotdDFI
+
+template <typename TPredHull , typename TPred > struct WotdDFI; // "projects/library/seqan/index/index_dfi.h"(74)
+
+//____________________________________________________________________________
+// WotdOriginal_
+
+struct WotdOriginal_; // "projects/library/seqan/index/index_wotd.h"(52)
+
+//____________________________________________________________________________
+// _AllocHelper
+
+template <typename TValue, typename TSpec> struct _AllocHelper; // "projects/library/seqan/index/index_pizzachili_string.h"(283)
+
+//____________________________________________________________________________
+// _Context_LSS
+
+template <typename TValue> struct _Context_LSS; // "projects/library/seqan/index/index_sa_lss.h"(40)
+
+//____________________________________________________________________________
+// _DFIEntry
+
+struct _DFIEntry; // "projects/library/seqan/index/index_dfi.h"(32)
+
+//____________________________________________________________________________
+// _DFIPredDefault
+
+template <bool RESULT> struct _DFIPredDefault; // "projects/library/seqan/index/index_dfi.h"(44)
+
+//____________________________________________________________________________
+// _Fibre_BWT
+
+struct _Fibre_BWT; // "projects/library/seqan/index/index_base.h"(245)
+
+//____________________________________________________________________________
+// _Fibre_ChildTab
+
+struct _Fibre_ChildTab; // "projects/library/seqan/index/index_base.h"(244)
+
+//____________________________________________________________________________
+// _Fibre_Counts
+
+struct _Fibre_Counts; // "projects/library/seqan/index/index_qgram.h"(64)
+
+//____________________________________________________________________________
+// _Fibre_CountsDir
+
+struct _Fibre_CountsDir; // "projects/library/seqan/index/index_qgram.h"(65)
+
+//____________________________________________________________________________
+// _Fibre_Dir
+
+struct _Fibre_Dir; // "projects/library/seqan/index/index_qgram.h"(61)
+
+//____________________________________________________________________________
+// _Fibre_LCP
+
+struct _Fibre_LCP; // "projects/library/seqan/index/index_base.h"(242)
+
+//____________________________________________________________________________
+// _Fibre_LCPE
+
+struct _Fibre_LCPE; // "projects/library/seqan/index/index_base.h"(243)
+
+//____________________________________________________________________________
+// _Fibre_PizzaChili_Compressed
+
+struct _Fibre_PizzaChili_Compressed; // "projects/library/seqan/index/index_pizzachili.h"(41)
+
+//____________________________________________________________________________
+// _Fibre_RawSA
+
+struct _Fibre_RawSA; // "projects/library/seqan/index/index_base.h"(240)
+
+//____________________________________________________________________________
+// _Fibre_RawText
+
+struct _Fibre_RawText; // "projects/library/seqan/index/index_base.h"(238)
+
+//____________________________________________________________________________
+// _Fibre_SA
+
+struct _Fibre_SA; // "projects/library/seqan/index/index_base.h"(239)
+
+//____________________________________________________________________________
+// _Fibre_SADir
+
+struct _Fibre_SADir; // "projects/library/seqan/index/index_qgram.h"(62)
+
+//____________________________________________________________________________
+// _Fibre_SAE
+
+struct _Fibre_SAE; // "projects/library/seqan/index/index_base.h"(241)
+
+//____________________________________________________________________________
+// _Fibre_Shape
+
+struct _Fibre_Shape; // "projects/library/seqan/index/index_qgram.h"(63)
+
+//____________________________________________________________________________
+// _Fibre_Text
+
+struct _Fibre_Text; // "projects/library/seqan/index/index_base.h"(237)
+
+//____________________________________________________________________________
+// _Finder_LCPE
+
+struct _Finder_LCPE; // "projects/library/seqan/index/index_esa_find.h"(49)
+
+//____________________________________________________________________________
+// _Finder_MLR
+
+struct _Finder_MLR; // "projects/library/seqan/index/index_esa_find.h"(48)
+
+//____________________________________________________________________________
+// _Finder_QGramLookup
+
+struct _Finder_QGramLookup; // "projects/library/seqan/index/index_qgram_find.h"(30)
+
+//____________________________________________________________________________
+// _FractionCompound
+
+template <typename TValue, typename TSize> struct _FractionCompound; // "projects/library/seqan/index/index_esa_algs.h"(250)
+
+//____________________________________________________________________________
+// _FractionHeader
+
+template <typename TSize> struct _FractionHeader; // "projects/library/seqan/index/index_esa_algs.h"(239)
+
+//____________________________________________________________________________
+// _FractionMultiCompound
+
+template <typename TValue, typename TSize> struct _FractionMultiCompound; // "projects/library/seqan/index/index_esa_algs_multi.h"(132)
+
+//____________________________________________________________________________
+// _HistoryStackEntry
+
+template <typename TVSTreeIter > struct _HistoryStackEntry; // "projects/library/seqan/index/index_esa_stree.h"(125)
+
+//____________________________________________________________________________
+// _HistoryStackWotdModified
+
+template <typename TSize> struct _HistoryStackWotdModified; // "projects/library/seqan/index/index_wotd.h"(209)
+
+//____________________________________________________________________________
+// _HistoryStackWotdOriginal
+
+template <typename TSize> struct _HistoryStackWotdOriginal; // "projects/library/seqan/index/index_wotd.h"(202)
+
+//____________________________________________________________________________
+// _MaxRepeats
+
+template <typename TSpec > struct _MaxRepeats; // "projects/library/seqan/index/index_esa_base.h"(106)
+
+//____________________________________________________________________________
+// _MultiMEMs
+
+struct _MultiMEMs; // "projects/library/seqan/index/index_esa_base.h"(107)
+
+//____________________________________________________________________________
+// _PizzaChiliFinder
+
+struct _PizzaChiliFinder; // "projects/library/seqan/index/index_pizzachili_find.h"(26)
+
+//____________________________________________________________________________
+// _PizzaChili_AF
+
+struct _PizzaChili_AF; // "projects/library/seqan/index/pizzachili_api.h"(67)
+
+//____________________________________________________________________________
+// _PizzaChili_CCSA
+
+struct _PizzaChili_CCSA; // "projects/library/seqan/index/pizzachili_api.h"(70)
+
+//____________________________________________________________________________
+// _PizzaChili_FM
+
+struct _PizzaChili_FM; // "projects/library/seqan/index/pizzachili_api.h"(73)
+
+//____________________________________________________________________________
+// _PizzaChili_LZ
+
+struct _PizzaChili_LZ; // "projects/library/seqan/index/pizzachili_api.h"(76)
+
+//____________________________________________________________________________
+// _PizzaChili_RLFM
+
+struct _PizzaChili_RLFM; // "projects/library/seqan/index/pizzachili_api.h"(82)
+
+//____________________________________________________________________________
+// _PizzaChili_RSA
+
+struct _PizzaChili_RSA; // "projects/library/seqan/index/pizzachili_api.h"(79)
+
+//____________________________________________________________________________
+// _PizzaChili_SA
+
+struct _PizzaChili_SA; // "projects/library/seqan/index/pizzachili_api.h"(85)
+
+//____________________________________________________________________________
+// _PizzaChili_SADA
+
+struct _PizzaChili_SADA; // "projects/library/seqan/index/pizzachili_api.h"(88)
+
+//____________________________________________________________________________
+// _PizzaChili_SSA
+
+struct _PizzaChili_SSA; // "projects/library/seqan/index/pizzachili_api.h"(91)
+
+//____________________________________________________________________________
+// _PizzaChili_Test
+
+struct _PizzaChili_Test; // "projects/library/seqan/index/pizzachili_api.h"(94)
+
+//____________________________________________________________________________
+// _Postorder
+
+struct _Postorder; // "projects/library/seqan/index/index_esa_base.h"(29)
+
+//____________________________________________________________________________
+// _Preorder
+
+struct _Preorder; // "projects/library/seqan/index/index_esa_base.h"(28)
+
+//____________________________________________________________________________
+// _QGramLess
+
+template <typename TSAValue, typename TText > struct _QGramLess; // "projects/library/seqan/index/index_qgram.h"(347)
+
+//____________________________________________________________________________
+// _QGramLessNoCheck
+
+template <typename TSAValue, typename TText > struct _QGramLessNoCheck; // "projects/library/seqan/index/index_qgram.h"(506)
+
+//____________________________________________________________________________
+// _QGramLessNoCheckOffset
+
+template <typename TSAValue, typename TText > struct _QGramLessNoCheckOffset; // "projects/library/seqan/index/index_qgram.h"(588)
+
+//____________________________________________________________________________
+// _QGramLessOffset
+
+template <typename TSAValue, typename TText > struct _QGramLessOffset; // "projects/library/seqan/index/index_qgram.h"(442)
+
+//____________________________________________________________________________
+// _RepeatLess
+
+template <typename TPos> struct _RepeatLess; // "projects/library/seqan/index/repeat_base.h"(82)
+
+//____________________________________________________________________________
+// _SAValueLess
+
+template <typename TOccValue> struct _SAValueLess; // "projects/library/seqan/index/index_shims.h"(449)
+
+//____________________________________________________________________________
+// _SkewNIndx
+
+template <int I, typename T > struct _SkewNIndx; // "projects/library/seqan/index/pipe_merger7.h"(34)
+
+//____________________________________________________________________________
+// _SkewShift
+
+template <int I, typename T > struct _SkewShift; // "projects/library/seqan/index/pipe_merger7.h"(31)
+
+//____________________________________________________________________________
+// _SuffixLess
+
+template <typename TSAValue, typename TText > struct _SuffixLess; // "projects/library/seqan/index/index_sa_qsort.h"(33)
+
+//____________________________________________________________________________
+// _SuffixLessOffset
+
+template <typename TSAValue, typename TText > struct _SuffixLessOffset; // "projects/library/seqan/index/index_sa_qsort.h"(71)
+
+//____________________________________________________________________________
+// _VertexWotdModified
+
+template <typename TSize> struct _VertexWotdModified; // "projects/library/seqan/index/index_wotd.h"(163)
+
+//____________________________________________________________________________
+// _VertexWotdOriginal
+
+template <typename TSize> struct _VertexWotdOriginal; // "projects/library/seqan/index/index_wotd.h"(148)
+
+//____________________________________________________________________________
+// _qgram_comp
+
+template <typename InType, typename Result > struct _qgram_comp; // "projects/library/seqan/index/index_qgram.h"(1227)
+
+//____________________________________________________________________________
+// _qgram_hash
+
+template <typename TValue, typename TResult > struct _qgram_hash; // "projects/library/seqan/index/index_qgram.h"(1262)
+
+//____________________________________________________________________________
+// filter_globalizer
+
+template <typename InType, typename TLimitsString, typename Result > struct filter_globalizer; // "projects/library/seqan/index/index_bwt.h"(130)
+
+//____________________________________________________________________________
+// map_inverse
+
+template <typename InType, typename Result > struct map_inverse; // "projects/library/seqan/index/index_lcp.h"(45)
+
+//____________________________________________________________________________
+// map_inverse_multi
+
+template <typename InType, typename TLimitsString, typename Result > struct map_inverse_multi; // "projects/library/seqan/index/index_lcp.h"(148)
+
+//____________________________________________________________________________
+// skew3_extend_comp
+
+template <typename InType, typename Result > struct skew3_extend_comp; // "projects/library/seqan/index/index_skew3.h"(107)
+
+//____________________________________________________________________________
+// skew3_ncomp
+
+template <typename InType, typename Result > struct skew3_ncomp; // "projects/library/seqan/index/index_skew3.h"(49)
+
+//____________________________________________________________________________
+// skew3_nmap_extended
+
+template <typename InType, typename Result > struct skew3_nmap_extended; // "projects/library/seqan/index/index_skew3.h"(101)
+
+//____________________________________________________________________________
+// skew3_nmap_linear
+
+template <typename InType, typename Result > struct skew3_nmap_linear; // "projects/library/seqan/index/index_skew3.h"(72)
+
+//____________________________________________________________________________
+// skew3_nmap_sliced
+
+template <typename InType, typename Result > struct skew3_nmap_sliced; // "projects/library/seqan/index/index_skew3.h"(80)
+
+//____________________________________________________________________________
+// skew3_unslicer_func
+
+template <typename InType, typename Result > struct skew3_unslicer_func; // "projects/library/seqan/index/index_skew3.h"(89)
+
+//____________________________________________________________________________
+// skew7_extend_comp
+
+template <typename InType, const int EXT_LENGTH, typename Result > struct skew7_extend_comp; // "projects/library/seqan/index/index_skew7.h"(137)
+
+//____________________________________________________________________________
+// skew7_global_sliced_multi
+
+template <typename InType, typename TLimitsString, typename TResultSize , typename Result > struct skew7_global_sliced_multi; // "projects/library/seqan/index/index_skew7_multi.h"(109)
+
+//____________________________________________________________________________
+// skew7_ncomp
+
+template <typename InType, typename Result > struct skew7_ncomp; // "projects/library/seqan/index/index_skew7.h"(49)
+
+//____________________________________________________________________________
+// skew7_ncomp_multi
+
+template <typename InType, typename Result > struct skew7_ncomp_multi; // "projects/library/seqan/index/index_skew7_multi.h"(42)
+
+//____________________________________________________________________________
+// skew7_nmap_extended
+
+template <typename InType, typename Result > struct skew7_nmap_extended; // "projects/library/seqan/index/index_skew7.h"(131)
+
+//____________________________________________________________________________
+// skew7_nmap_linear
+
+template <typename InType, typename Result > struct skew7_nmap_linear; // "projects/library/seqan/index/index_skew7.h"(91)
+
+//____________________________________________________________________________
+// skew7_nmap_sliced
+
+template <typename InType, typename Result > struct skew7_nmap_sliced; // "projects/library/seqan/index/index_skew7.h"(99)
+
+//____________________________________________________________________________
+// skew7_unslicer_func
+
+template <typename InType, typename Result > struct skew7_unslicer_func; // "projects/library/seqan/index/index_skew7.h"(115)
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+
+//////////////////////////////////////////////////////////////////////////////
+// TYPEDEFS
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+namespace impl {
+
+//____________________________________________________________________________
+// error_t
+
+typedef int error_t; // "projects/library/seqan/index/pizzachili_api.h"(34)
+
+//____________________________________________________________________________
+// index_t
+
+typedef void* index_t; // "projects/library/seqan/index/pizzachili_api.h"(33)
+
+//____________________________________________________________________________
+// uchar_t
+
+typedef unsigned char uchar_t; // "projects/library/seqan/index/pizzachili_api.h"(31)
+
+//____________________________________________________________________________
+// ulong_t
+
+typedef unsigned long ulong_t; // "projects/library/seqan/index/pizzachili_api.h"(32)
+
+} //namespace impl
+} //namespace SEQAN_NAMESPACE_MAIN
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+
+//____________________________________________________________________________
+// ESA_BWT
+
+typedef Fibre_BWT ESA_BWT; // "projects/library/seqan/index/index_esa_base.h"(239)
+
+//____________________________________________________________________________
+// ESA_ChildTab
+
+typedef Fibre_ChildTab ESA_ChildTab; // "projects/library/seqan/index/index_esa_base.h"(238)
+
+//____________________________________________________________________________
+// ESA_FIND_LCPE
+
+typedef Tag<_Finder_LCPE> const ESA_FIND_LCPE; // "projects/library/seqan/index/index_esa_find.h"(52)
+
+//____________________________________________________________________________
+// ESA_FIND_MLR
+
+typedef Tag<_Finder_MLR> const ESA_FIND_MLR; // "projects/library/seqan/index/index_esa_find.h"(51)
+
+//____________________________________________________________________________
+// ESA_LCP
+
+typedef Fibre_LCP ESA_LCP; // "projects/library/seqan/index/index_esa_base.h"(236)
+
+//____________________________________________________________________________
+// ESA_LCPE
+
+typedef Fibre_LCPE ESA_LCPE; // "projects/library/seqan/index/index_esa_base.h"(237)
+
+//____________________________________________________________________________
+// ESA_RawSA
+
+typedef Fibre_RawSA ESA_RawSA; // "projects/library/seqan/index/index_esa_base.h"(234)
+
+//____________________________________________________________________________
+// ESA_RawText
+
+typedef Fibre_RawText ESA_RawText; // "projects/library/seqan/index/index_esa_base.h"(232)
+
+//____________________________________________________________________________
+// ESA_SA
+
+typedef Fibre_SA ESA_SA; // "projects/library/seqan/index/index_esa_base.h"(233)
+
+//____________________________________________________________________________
+// ESA_SAE
+
+typedef Fibre_SAE ESA_SAE; // "projects/library/seqan/index/index_esa_base.h"(235)
+
+//____________________________________________________________________________
+// ESA_Text
+
+typedef Fibre_Text ESA_Text; // "projects/library/seqan/index/index_esa_base.h"(231)
+
+//____________________________________________________________________________
+// Fibre_BWT
+
+typedef Tag<_Fibre_BWT> const Fibre_BWT; // "projects/library/seqan/index/index_base.h"(255)
+
+//____________________________________________________________________________
+// Fibre_ChildTab
+
+typedef Tag<_Fibre_ChildTab> const Fibre_ChildTab; // "projects/library/seqan/index/index_base.h"(254)
+
+//____________________________________________________________________________
+// Fibre_Counts
+
+typedef Tag<_Fibre_Counts> const Fibre_Counts; // "projects/library/seqan/index/index_qgram.h"(70)
+
+//____________________________________________________________________________
+// Fibre_CountsDir
+
+typedef Tag<_Fibre_CountsDir> const Fibre_CountsDir; // "projects/library/seqan/index/index_qgram.h"(71)
+
+//____________________________________________________________________________
+// Fibre_Dir
+
+typedef Tag<_Fibre_Dir> const Fibre_Dir; // "projects/library/seqan/index/index_qgram.h"(67)
+
+//____________________________________________________________________________
+// Fibre_LCP
+
+typedef Tag<_Fibre_LCP> const Fibre_LCP; // "projects/library/seqan/index/index_base.h"(252)
+
+//____________________________________________________________________________
+// Fibre_LCPE
+
+typedef Tag<_Fibre_LCPE> const Fibre_LCPE; // "projects/library/seqan/index/index_base.h"(253)
+
+//____________________________________________________________________________
+// Fibre_PizzaChili_Compressed
+
+typedef Tag<_Fibre_PizzaChili_Compressed> const Fibre_PizzaChili_Compressed; // "projects/library/seqan/index/index_pizzachili.h"(44)
+
+//____________________________________________________________________________
+// Fibre_PizzaChili_Text
+
+typedef Tag<_Fibre_Text> const Fibre_PizzaChili_Text; // "projects/library/seqan/index/index_pizzachili.h"(43)
+
+//____________________________________________________________________________
+// Fibre_RawSA
+
+typedef Tag<_Fibre_RawSA> const Fibre_RawSA; // "projects/library/seqan/index/index_base.h"(250)
+
+//____________________________________________________________________________
+// Fibre_RawText
+
+typedef Tag<_Fibre_RawText> const Fibre_RawText; // "projects/library/seqan/index/index_base.h"(248)
+
+//____________________________________________________________________________
+// Fibre_SA
+
+typedef Tag<_Fibre_SA> const Fibre_SA; // "projects/library/seqan/index/index_base.h"(249)
+
+//____________________________________________________________________________
+// Fibre_SADir
+
+typedef Tag<_Fibre_SADir> const Fibre_SADir; // "projects/library/seqan/index/index_qgram.h"(68)
+
+//____________________________________________________________________________
+// Fibre_SAE
+
+typedef Tag<_Fibre_SAE> const Fibre_SAE; // "projects/library/seqan/index/index_base.h"(251)
+
+//____________________________________________________________________________
+// Fibre_Shape
+
+typedef Tag<_Fibre_Shape> const Fibre_Shape; // "projects/library/seqan/index/index_qgram.h"(69)
+
+//____________________________________________________________________________
+// Fibre_Text
+
+typedef Tag<_Fibre_Text> const Fibre_Text; // "projects/library/seqan/index/index_base.h"(247)
+
+//____________________________________________________________________________
+// GappedShape
+
+typedef FixedGappedShape<Default> GappedShape; // "projects/library/seqan/index/shape_base.h"(33)
+
+//____________________________________________________________________________
+// MaxRepeats
+
+typedef _MaxRepeats<void> MaxRepeats; // "projects/library/seqan/index/index_esa_base.h"(131)
+
+//____________________________________________________________________________
+// MultiMEMs
+
+typedef _MaxRepeats<_MultiMEMs> MultiMEMs; // "projects/library/seqan/index/index_esa_base.h"(133)
+
+//____________________________________________________________________________
+// PizzaChiliFinder
+
+typedef Tag<_PizzaChiliFinder> const PizzaChiliFinder; // "projects/library/seqan/index/index_pizzachili_find.h"(36)
+
+//____________________________________________________________________________
+// PizzaChili_AF
+
+typedef Tag<_PizzaChili_AF> const PizzaChili_AF; // "projects/library/seqan/index/pizzachili_api.h"(68)
+
+//____________________________________________________________________________
+// PizzaChili_CCSA
+
+typedef Tag<_PizzaChili_CCSA> const PizzaChili_CCSA; // "projects/library/seqan/index/pizzachili_api.h"(71)
+
+//____________________________________________________________________________
+// PizzaChili_Compressed
+
+typedef Fibre_PizzaChili_Compressed PizzaChili_Compressed; // "projects/library/seqan/index/index_pizzachili.h"(47)
+
+//____________________________________________________________________________
+// PizzaChili_FM
+
+typedef Tag<_PizzaChili_FM> const PizzaChili_FM; // "projects/library/seqan/index/pizzachili_api.h"(74)
+
+//____________________________________________________________________________
+// PizzaChili_LZ
+
+typedef Tag<_PizzaChili_LZ> const PizzaChili_LZ; // "projects/library/seqan/index/pizzachili_api.h"(77)
+
+//____________________________________________________________________________
+// PizzaChili_RLFM
+
+typedef Tag<_PizzaChili_RLFM> const PizzaChili_RLFM; // "projects/library/seqan/index/pizzachili_api.h"(83)
+
+//____________________________________________________________________________
+// PizzaChili_RSA
+
+typedef Tag<_PizzaChili_RSA> const PizzaChili_RSA; // "projects/library/seqan/index/pizzachili_api.h"(80)
+
+//____________________________________________________________________________
+// PizzaChili_SA
+
+typedef Tag<_PizzaChili_SA> const PizzaChili_SA; // "projects/library/seqan/index/pizzachili_api.h"(86)
+
+//____________________________________________________________________________
+// PizzaChili_SADA
+
+typedef Tag<_PizzaChili_SADA> const PizzaChili_SADA; // "projects/library/seqan/index/pizzachili_api.h"(89)
+
+//____________________________________________________________________________
+// PizzaChili_SSA
+
+typedef Tag<_PizzaChili_SSA> const PizzaChili_SSA; // "projects/library/seqan/index/pizzachili_api.h"(92)
+
+//____________________________________________________________________________
+// PizzaChili_Test
+
+typedef Tag<_PizzaChili_Test> const PizzaChili_Test; // "projects/library/seqan/index/pizzachili_api.h"(95)
+
+//____________________________________________________________________________
+// PizzaChili_Text
+
+typedef Fibre_PizzaChili_Text PizzaChili_Text; // "projects/library/seqan/index/index_pizzachili.h"(46)
+
+//____________________________________________________________________________
+// QGram_Counts
+
+typedef Fibre_Counts QGram_Counts; // "projects/library/seqan/index/index_qgram.h"(82)
+
+//____________________________________________________________________________
+// QGram_CountsDir
+
+typedef Fibre_CountsDir QGram_CountsDir; // "projects/library/seqan/index/index_qgram.h"(83)
+
+//____________________________________________________________________________
+// QGram_Dir
+
+typedef Fibre_Dir QGram_Dir; // "projects/library/seqan/index/index_qgram.h"(79)
+
+//____________________________________________________________________________
+// QGram_FIND_Lookup
+
+typedef Tag<_Finder_QGramLookup> const QGram_FIND_Lookup; // "projects/library/seqan/index/index_qgram_find.h"(38)
+
+//____________________________________________________________________________
+// QGram_RawSA
+
+typedef Fibre_RawSA QGram_RawSA; // "projects/library/seqan/index/index_qgram.h"(78)
+
+//____________________________________________________________________________
+// QGram_RawText
+
+typedef Fibre_RawText QGram_RawText; // "projects/library/seqan/index/index_qgram.h"(76)
+
+//____________________________________________________________________________
+// QGram_SA
+
+typedef Fibre_SA QGram_SA; // "projects/library/seqan/index/index_qgram.h"(77)
+
+//____________________________________________________________________________
+// QGram_SADir
+
+typedef Fibre_SADir QGram_SADir; // "projects/library/seqan/index/index_qgram.h"(80)
+
+//____________________________________________________________________________
+// QGram_Shape
+
+typedef Fibre_Shape QGram_Shape; // "projects/library/seqan/index/index_qgram.h"(81)
+
+//____________________________________________________________________________
+// QGram_Text
+
+typedef Fibre_Text QGram_Text; // "projects/library/seqan/index/index_qgram.h"(75)
+
+//____________________________________________________________________________
+// SimpleShape
+
+typedef FixedShape<0> SimpleShape; // "projects/library/seqan/index/shape_base.h"(29)
+
+//____________________________________________________________________________
+// WotdOriginal
+
+typedef Tag<WotdOriginal_> const WotdOriginal; // "projects/library/seqan/index/index_wotd.h"(53)
+
+//____________________________________________________________________________
+// Wotd_Dir
+
+typedef Fibre_Dir Wotd_Dir; // "projects/library/seqan/index/index_wotd.h"(35)
+
+//____________________________________________________________________________
+// Wotd_RawSA
+
+typedef Fibre_RawSA Wotd_RawSA; // "projects/library/seqan/index/index_wotd.h"(34)
+
+//____________________________________________________________________________
+// Wotd_RawText
+
+typedef Fibre_RawText Wotd_RawText; // "projects/library/seqan/index/index_wotd.h"(32)
+
+//____________________________________________________________________________
+// Wotd_SA
+
+typedef Fibre_SA Wotd_SA; // "projects/library/seqan/index/index_wotd.h"(33)
+
+//____________________________________________________________________________
+// Wotd_Text
+
+typedef Fibre_Text Wotd_Text; // "projects/library/seqan/index/index_wotd.h"(31)
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+
+//////////////////////////////////////////////////////////////////////////////
+// FUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+namespace impl {
+
+//____________________________________________________________________________
+// clearIndex
+
+template <typename TText, typename TSpec> inline void clearIndex(Index<TText, PizzaChili<TSpec> >& me); // "projects/library/seqan/index/index_pizzachili.h"(132)
+
+//____________________________________________________________________________
+// createPizzaChiliIndex
+
+template <typename TText, typename TSpec> inline bool createPizzaChiliIndex( Index<TText, PizzaChili<TSpec> >& me, uchar_t* textstart, ulong_t textlength ); // "projects/library/seqan/index/index_pizzachili.h"(256)
+
+//____________________________________________________________________________
+// getOptionsString
+
+template <typename TText, typename TSpec> inline char const* getOptionsString(Index<TText, PizzaChili<TSpec> >& ); // "projects/library/seqan/index/index_pizzachili.h"(162)
+template <typename TText> inline char const* getOptionsString(Index<TText, PizzaChili<PizzaChili_SA> >& ); // "projects/library/seqan/index/index_pizzachili.h"(169)
+template <typename TText> inline char const* getOptionsString(Index<TText, PizzaChili<PizzaChili_FM> >& ); // "projects/library/seqan/index/index_pizzachili.h"(176)
+template <typename TText> inline char const* getOptionsString(Index<TText, PizzaChili<PizzaChili_RSA> >& ); // "projects/library/seqan/index/index_pizzachili.h"(183)
+
+//____________________________________________________________________________
+// getPizzaChiliString
+
+template <typename TPattern> inline uchar_t* getPizzaChiliString(TPattern const& pattern); // "projects/library/seqan/index/index_pizzachili_find.h"(92)
+inline uchar_t* getPizzaChiliString(char const* pattern); // "projects/library/seqan/index/index_pizzachili_find.h"(110)
+
+//____________________________________________________________________________
+// queryText
+
+template <typename TValue, typename TSpec> inline void queryText(String<TValue, PizzaChili<TSpec> > const& me); // "projects/library/seqan/index/index_pizzachili_string.h"(419)
+
+} //namespace impl
+} //namespace SEQAN_NAMESPACE_MAIN
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+
+//____________________________________________________________________________
+// __cp_
+
+template <typename Dest, typename Ofs, typename Src> static finline Src const __cp_(Dest &dst, Ofs const ofs, Src const src); // "projects/library/seqan/index/pump_extender7.h"(67)
+
+//____________________________________________________________________________
+// _adjustRightBorder
+
+template <typename TText, typename TSpec > inline void _adjustRightBorder( Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &); // "projects/library/seqan/index/index_wotd.h"(493)
+template <typename TText, typename TIndexSpec, typename TSpec > inline void _adjustRightBorder( Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it); // "projects/library/seqan/index/index_wotd.h"(499)
+
+//____________________________________________________________________________
+// _bucketLCP
+
+template <typename TSA, typename TText > typename Size<TText>::Type _bucketLCP(TSA const &sa, TText const &text); // "projects/library/seqan/index/index_wotd.h"(1249)
+template <typename TSA, typename TText, typename TSize > typename Size<TText>::Type _bucketLCP(TSA const &sa, TText const &text, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(1283)
+template <typename TSA, typename TText, typename TSpec, typename TSize > typename Size<TText>::Type _bucketLCP(TSA const &sa, StringSet<TText, TSpec> const &stringSet, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(1315)
+
+//____________________________________________________________________________
+// _createBWTableWrapper
+
+template <typename TBWT, typename TText, typename TSA, typename _TTextRandom > inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa, _TTextRandom const); // "projects/library/seqan/index/index_shims.h"(424)
+template <typename TBWT, typename TText, typename TSA > inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa, True const); // "projects/library/seqan/index/index_shims.h"(432)
+
+//____________________________________________________________________________
+// _dataHost
+
+template <typename TText, typename TSpec> inline Holder<TText> & _dataHost(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(464)
+template <typename TText, typename TSpec> inline Holder<TText> const & _dataHost(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(468)
+
+//____________________________________________________________________________
+// _deallocateStorage
+
+template <typename TValue, typename TSpec> inline void _deallocateStorage( String<TValue, PizzaChili<TSpec> >& , TValue* begin, typename Size<String<TValue, PizzaChili<TSpec> > >::Type ); // "projects/library/seqan/index/index_pizzachili_string.h"(370)
+
+//____________________________________________________________________________
+// _dfsClear
+
+template <typename TIndex, class TSpec > inline void _dfsClear(Iter<TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(1393)
+
+//____________________________________________________________________________
+// _dfsLCP
+
+template <typename TIndex, class TSpec > inline typename Size<TIndex>::Type & _dfsLCP(Iter< TIndex, VSTree< BottomUp<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1860)
+template <typename TIndex, class TSpec > inline typename Size<TIndex>::Type _dfsLCP(Iter< TIndex, VSTree< BottomUp<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1866)
+
+//____________________________________________________________________________
+// _dfsOnLeaf
+
+template <typename TIndex, typename TSpec > inline void _dfsOnLeaf(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(274)
+template <typename TSTree, typename TSpec > inline void _dfsOnLeaf(Iter<TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > &it); // "projects/library/seqan/index/index_esa_algs.h"(496)
+template <typename TSTree > inline void _dfsOnLeaf(Iter<TSTree, VSTree< BottomUp<MultiMEMs> > > &it); // "projects/library/seqan/index/index_esa_algs_multi.h"(338)
+
+//____________________________________________________________________________
+// _dfsOnPop
+
+template <typename TIndex, typename TSpec, typename TSize > inline void _dfsOnPop(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it, TSize const); // "projects/library/seqan/index/index_esa_stree.h"(262)
+
+//____________________________________________________________________________
+// _dfsOnPush
+
+template <typename TIndex, typename TSpec, typename TElement > inline void _dfsOnPush(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it, TElement const &e); // "projects/library/seqan/index/index_esa_stree.h"(269)
+template <typename TSTree, typename TElement, typename TSpec > inline void _dfsOnPush(Iter<TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > &it, TElement const &e); // "projects/library/seqan/index/index_esa_algs.h"(482)
+
+//____________________________________________________________________________
+// _dfsRange
+
+template <typename TIndex, class TSpec > inline Pair<typename Size<TIndex>::Type> & _dfsRange(Iter< TIndex, VSTree< BottomUp<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1847)
+template <typename TIndex, class TSpec > inline Pair<typename Size<TIndex>::Type> const & _dfsRange(Iter< TIndex, VSTree< BottomUp<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1854)
+
+//____________________________________________________________________________
+// _dfsReversedOrder
+
+template <typename TIndex, typename TSpec > inline bool _dfsReversedOrder(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(256)
+
+//____________________________________________________________________________
+// _dump
+
+template <typename TText, typename TPredHull, typename TPred> inline void _dump(Index<TText, Index_Wotd< WotdDFI<TPredHull, TPred> > > &index); // "projects/library/seqan/index/index_dfi.h"(470)
+template <typename TText, typename TSpec> inline void _dump(Index<TText, Index_Wotd<TSpec> > &index); // "projects/library/seqan/index/index_wotd.h"(1580)
+template <typename TText, typename TSpec> inline void _dump(Index<TText, Index_ESA<TSpec> > &index); // "projects/library/seqan/index/index_esa_stree.h"(238)
+
+//____________________________________________________________________________
+// _dumpFreq
+
+template <typename TText, typename TPredHull, typename TPred> inline void _dumpFreq(Index<TText, Index_Wotd< WotdDFI<TPredHull, TPred> > > &index); // "projects/library/seqan/index/index_dfi.h"(497)
+
+//____________________________________________________________________________
+// _dumpHistoryStack
+
+template <typename TIndex, typename TSpec > inline void _dumpHistoryStack(Iter<TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(229)
+
+//____________________________________________________________________________
+// _equalRangeLCPE
+
+template <typename TText, typename TSA, typename TLCP, typename TSpec, typename TQuery > inline Pair< typename Iterator<TSA, Standard>::Type > _equalRangeLCPE( TText &text, TSA &sa, SearchTreeIterator< TLCP, TSpec > treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(1362)
+template <typename TText, typename TSA, typename TLCP, typename TQuery > inline Pair< typename Iterator<TSA, Standard>::Type > _equalRangeLCPE( TText &text, TSA &sa, TLCP &lcp, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(1514)
+
+//____________________________________________________________________________
+// _equalRangeSA
+
+template <typename TText, typename TSA, typename TSpec, typename TQuery > inline Pair< typename Iterator<TSA, Standard>::Type > _equalRangeSA( TText &text, SearchTreeIterator< TSA, TSpec > treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(632)
+
+//____________________________________________________________________________
+// _findFirstIndex
+
+template <typename TText, typename TSpec, typename TSpecFinder, typename TPattern> inline void _findFirstIndex( Finder<Index<TText, PizzaChili<TSpec> >, TSpecFinder>& finder, TPattern const& pattern, PizzaChiliFinder const ); // "projects/library/seqan/index/index_pizzachili_find.h"(123)
+template <typename TText, typename TSpec, typename TSpecFinder, typename TPattern > inline void _findFirstIndex( Finder< Index<TText, TSpec>, TSpecFinder > &finder, TPattern const &pattern, QGram_FIND_Lookup const); // "projects/library/seqan/index/index_qgram_find.h"(57)
+template <typename TText, typename TSpec, typename TSpecFinder, typename TPattern > inline void _findFirstIndex( Finder< Index<TText, TSpec>, TSpecFinder > &finder, TPattern const &pattern, ESA_FIND_MLR const); // "projects/library/seqan/index/index_esa_find.h"(1742)
+template <typename TText, typename TSpec, typename TSpecFinder, typename TPattern > inline void _findFirstIndex( Finder< Index<TText, TSpec>, TSpecFinder > &finder, TPattern const &pattern, ESA_FIND_LCPE const); // "projects/library/seqan/index/index_esa_find.h"(1754)
+
+//____________________________________________________________________________
+// _fractionMerge
+
+template <typename TSTree, typename TSpec, typename TValue, typename TSize > inline void _fractionMerge( Iter<TSTree, VSTree< BottomUp<TSpec> > > &it, _FractionCompound<TValue, TSize> &parent, _FractionCompound<TValue, TSize> &child); // "projects/library/seqan/index/index_esa_algs.h"(451)
+template <typename TSTree, typename TSpec, typename TValue, typename TSize > inline void _fractionMerge( Iter<TSTree, VSTree< BottomUp<TSpec> > > &it, _FractionMultiCompound<TValue, TSize> &parent, _FractionMultiCompound<TValue, TSize> &child); // "projects/library/seqan/index/index_esa_algs_multi.h"(317)
+
+//____________________________________________________________________________
+// _fullDir2Length
+
+template <typename TIndex> inline int _fullDir2Length(TIndex const &index); // "projects/library/seqan/index/index_qgram.h"(330)
+
+//____________________________________________________________________________
+// _fullDirLength
+
+template <typename TIndex> inline int _fullDirLength(TIndex const &index); // "projects/library/seqan/index/index_qgram.h"(322)
+
+//____________________________________________________________________________
+// _getDown
+
+template <typename TSize, typename TIndex > inline TSize _getDown(TSize i, TIndex const &index); // "projects/library/seqan/index/index_esa_stree.h"(1836)
+
+//____________________________________________________________________________
+// _getNextl
+
+template <typename TSize, typename TIndex > inline TSize _getNextl(TSize i, TIndex const &index); // "projects/library/seqan/index/index_esa_stree.h"(1821)
+
+//____________________________________________________________________________
+// _getNodeByChar
+
+template <typename TText, class TSpec, typename TValue > inline bool _getNodeByChar( Iter< Index<TText, Index_ESA<TSpec> >, VSTree<TSpec> > const &it, TValue c, typename VertexDescriptor< Index<TText, Index_ESA<TSpec> > >::Type &childDesc); // "projects/library/seqan/index/index_esa_stree.h"(787)
+
+//____________________________________________________________________________
+// _getNodeLP
+
+template <typename TText, typename TSpec, typename TPos> inline TPos _getNodeLP( Index<TText, Index_Wotd<TSpec> > const &index, TPos pos); // "projects/library/seqan/index/index_wotd.h"(1366)
+
+//____________________________________________________________________________
+// _getUp
+
+template <typename TSize, typename TIndex > inline TSize _getUp(TSize i, TIndex const &index); // "projects/library/seqan/index/index_esa_stree.h"(1827)
+
+//____________________________________________________________________________
+// _goDown
+
+template <typename TText, typename TSpec, typename TDFSOrder, typename THideEmptyEdges > inline bool _goDown( Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &it, VSTreeIteratorTraits<TDFSOrder, THideEmptyEdges> const); // "projects/library/seqan/index/index_wotd.h"(524)
+template <typename TText, typename TIndexSpec, typename TSpec, typename TDFSOrder, typename THideEmptyEdges > inline bool _goDown( Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it, VSTreeIteratorTraits<TDFSOrder, THideEmptyEdges> const); // "projects/library/seqan/index/index_wotd.h"(560)
+template <typename TText, class TIndexSpec, class TSpec, typename TDFSOrder > inline bool _goDown( Iter< Index<TText, Index_ESA<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it, VSTreeIteratorTraits<TDFSOrder, False> const); // "projects/library/seqan/index/index_esa_stree.h"(1035)
+template <typename TText, class TIndexSpec, class TSpec, typename TDFSOrder > inline bool _goDown( Iter< Index<TText, Index_ESA<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it, VSTreeIteratorTraits<TDFSOrder, True> const); // "projects/library/seqan/index/index_esa_stree.h"(1055)
+
+//____________________________________________________________________________
+// _goDownChar
+
+template <typename TText, class TSpec, typename TValue > inline bool _goDownChar( Iter<Index<TText, Index_Wotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &it, TValue c); // "projects/library/seqan/index/index_wotd.h"(1609)
+template <typename TText, class TIndexSpec, class TSpec, typename TValue > inline bool _goDownChar( Iter<Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it, TValue c); // "projects/library/seqan/index/index_wotd.h"(1631)
+template <typename TIndex, class TSpec, typename TValue > inline bool _goDownChar(Iter< TIndex, VSTree< TopDown<TSpec> > > &it, TValue c); // "projects/library/seqan/index/index_esa_stree.h"(1100)
+
+//____________________________________________________________________________
+// _goDownObject
+
+template <typename TIndex, typename TSpec, typename TObject > inline bool _goDownObject( Iter< TIndex, VSTree< TopDown<TSpec> > > &it, TObject const &obj, False); // "projects/library/seqan/index/index_esa_stree.h"(1168)
+template <typename TIndex, typename TSpec, typename TObject > inline bool _goDownObject( Iter< TIndex, VSTree< TopDown<TSpec> > > &it, TObject const &obj, True); // "projects/library/seqan/index/index_esa_stree.h"(1178)
+
+//____________________________________________________________________________
+// _goDownString
+
+template <typename TIndex, typename TSpec, typename TString, typename TSize > inline bool _goDownString( Iter< TIndex, VSTree< TopDown<TSpec> > > &node, TString const &pattern, TSize &lcp); // "projects/library/seqan/index/index_esa_stree.h"(1118)
+
+//____________________________________________________________________________
+// _goRight
+
+template <typename TText, typename TSpec, typename TDFSOrder, typename THideEmptyEdges > inline bool _goRight( Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &it, VSTreeIteratorTraits<TDFSOrder, THideEmptyEdges> const); // "projects/library/seqan/index/index_wotd.h"(596)
+template <typename TText, typename TIndexSpec, typename TSpec, typename TDFSOrder, typename THideEmptyEdges > inline bool _goRight( Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it, VSTreeIteratorTraits<TDFSOrder, THideEmptyEdges> const); // "projects/library/seqan/index/index_wotd.h"(620)
+template <typename TText, class TIndexSpec, class TSpec, typename TDFSOrder, typename THideEmptyEdges > inline bool _goRight( Iter< Index<TText, Index_ESA<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it, VSTreeIteratorTraits<TDFSOrder, THideEmptyEdges> const); // "projects/library/seqan/index/index_esa_stree.h"(1289)
+
+//____________________________________________________________________________
+// _goUp
+
+template <typename TText, typename TWotdSpec, typename TSpec > inline bool _goUp(Iter< Index<TText, Index_Wotd<TWotdSpec> >, VSTree< TopDown<TSpec> > > &it); // "projects/library/seqan/index/index_wotd.h"(645)
+template <typename TText, typename TSpec > inline bool _goUp(Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it); // "projects/library/seqan/index/index_wotd.h"(657)
+template <typename TText, typename TIndexSpec, typename TSpec > inline bool _goUp(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it); // "projects/library/seqan/index/index_wotd.h"(674)
+template <typename TIndex, class TSpec > inline bool _goUp(Iter< TIndex, VSTree< TopDown<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1219)
+template <typename TIndex, class TSpec > inline bool _goUp(Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1231)
+
+//____________________________________________________________________________
+// _hashFixedShape
+
+template <typename THValue, typename TValue, typename TIter> inline THValue _hashFixedShape(THValue hash, TIter &, TValue const, FixedShape<1> const); // "projects/library/seqan/index/shape_base.h"(290)
+template <typename THValue, typename TValue, typename TIter, unsigned q> inline THValue _hashFixedShape(THValue hash, TIter &it, TValue const, FixedShape<q> const); // "projects/library/seqan/index/shape_base.h"(296)
+
+//____________________________________________________________________________
+// _hashHardwiredShape
+
+template <typename THValue, typename TValue, typename TIter> inline THValue _hashHardwiredShape(THValue hash, TIter &, TValue const, HardwiredShape< 0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0 > const); // "projects/library/seqan/index/shape_gapped.h"(448)
+template <int P01, int P02, int P03, int P04, int P05, int P06, int P07, int P08, int P09, int P10, int P11, int P12, int P13, int P14, int P15, int P16, int P17, int P18, int P19, typename THValue, typename TValue, typename TIter > inline THValue _hashHardwiredShape(THValue hash, TIter &it, TValue const, HardwiredShape< 1 ,P01,P02,P03,P04, P05,P06,P07,P08,P09, P10,P11,P12,P13,P14, P15,P16,P17,P18,P19 > const); // "projects/library/seqan/index/shape_gapped.h"(465)
+template <int P00, int P01, int P02, int P03, int P04, int P05, int P06, int P07, int P08, int P09, int P10, int P11, int P12, int P13, int P14, int P15, int P16, int P17, int P18, int P19, typename THValue, typename TValue, typename TIter > inline THValue _hashHardwiredShape(THValue hash, TIter &it, TValue const, HardwiredShape< P00,P01,P02,P03,P04, P05,P06,P07,P08,P09, P10,P11,P12,P13,P14, P15,P16,P17,P18,P19 > const); // "projects/library/seqan/index/shape_gapped.h"(488)
+
+//____________________________________________________________________________
+// _hashTuple2FixedShape
+
+template <typename THValue, typename TValue, typename TTValue, unsigned SIZE, typename TCompressed> inline THValue _hashTuple2FixedShape( THValue const, Tuple<TTValue, SIZE, TCompressed> const &tuple, TValue const, FixedShape<1> const); // "projects/library/seqan/index/shape_base.h"(353)
+template <typename THValue, typename TValue, typename TTValue, unsigned SIZE, typename TCompressed, unsigned q> inline THValue _hashTuple2FixedShape( THValue const, Tuple<TTValue, SIZE, TCompressed> const &tuple, TValue const, FixedShape<q> const); // "projects/library/seqan/index/shape_base.h"(364)
+
+//____________________________________________________________________________
+// _haveMaximalRepeats
+
+template <typename TValue, typename TSize> int _haveMaximalRepeats( _FractionCompound<TValue, TSize> const &a, _FractionCompound<TValue, TSize> const &b); // "projects/library/seqan/index/index_esa_algs.h"(268)
+template <typename TValue, typename TSize> int _haveMaximalRepeats( _FractionCompound<TValue, TSize> const &a, _FractionCompound<TValue, TSize> const &b, TValue &equalKey); // "projects/library/seqan/index/index_esa_algs.h"(289)
+
+//____________________________________________________________________________
+// _historyClear
+
+template <typename TIndex, class TSpec > inline void _historyClear(Iter< TIndex, VSTree<TSpec> > &); // "projects/library/seqan/index/index_esa_stree.h"(989)
+template <typename TIndex, class TSpec > inline void _historyClear(Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it); // "projects/library/seqan/index/index_esa_stree.h"(993)
+
+//____________________________________________________________________________
+// _historyPush
+
+template <typename TText, typename TIndexSpec, typename TSpec > inline void _historyPush(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it); // "projects/library/seqan/index/index_wotd.h"(235)
+template <typename TText, typename TSpec > inline void _historyPush(Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it); // "projects/library/seqan/index/index_wotd.h"(244)
+template <typename TText, typename TIndexSpec, typename TSpec > inline void _historyPush(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it); // "projects/library/seqan/index/index_wotd.h"(255)
+template <typename TText, class TIndexSpec, class TSpec > inline void _historyPush(Iter< Index<TText, Index_ESA<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1004)
+template <typename TText, class TIndexSpec, class TSpec > inline void _historyPush(Iter< Index<TText, Index_ESA<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1010)
+
+//____________________________________________________________________________
+// _indexRequireBottomUpIteration
+
+template <typename TText, typename TSpec > void _indexRequireBottomUpIteration(Index<TText, Index_ESA<TSpec> > &index); // "projects/library/seqan/index/index_esa_base.h"(298)
+
+//____________________________________________________________________________
+// _indexRequireTopDownIteration
+
+template <typename TText, typename TSpec > void _indexRequireTopDownIteration(Index<TText, Index_ESA<TSpec> > &index); // "projects/library/seqan/index/index_esa_base.h"(290)
+template <typename TText, typename TSpec > void _indexRequireTopDownIteration(Index<TText, Index_Wotd<TSpec> > &index); // "projects/library/seqan/index/index_wotd.h"(193)
+
+//____________________________________________________________________________
+// _isLeaf
+
+template <typename TText, typename TIndexSpec, typename TSpec, typename TDFSOrder > inline bool _isLeaf( Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree<TSpec> > const &it, VSTreeIteratorTraits<TDFSOrder, False> const); // "projects/library/seqan/index/index_wotd.h"(281)
+template <typename TText, typename TIndexSpec, typename TSpec, typename TDFSOrder > inline bool _isLeaf( Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree<TSpec> > const &it, VSTreeIteratorTraits<TDFSOrder, True> const); // "projects/library/seqan/index/index_wotd.h"(292)
+template <typename TSize > inline bool _isLeaf(VertexESA<TSize> const &vDesc); // "projects/library/seqan/index/index_esa_stree.h"(1750)
+template <typename TIndex, class TSpec, typename TDFSOrder > inline bool _isLeaf( Iter<TIndex, VSTree<TSpec> > const &it, VSTreeIteratorTraits<TDFSOrder, False> const); // "projects/library/seqan/index/index_esa_stree.h"(1760)
+template <typename TIndex, class TSpec, typename TDFSOrder > inline bool _isLeaf( Iter<TIndex, VSTree<TSpec> > const &it, VSTreeIteratorTraits<TDFSOrder, True> const); // "projects/library/seqan/index/index_esa_stree.h"(1769)
+
+//____________________________________________________________________________
+// _isNextl
+
+template <typename TSize, typename TIndex > inline bool _isNextl(TSize i, TIndex const &index); // "projects/library/seqan/index/index_esa_stree.h"(1805)
+
+//____________________________________________________________________________
+// _isRoot
+
+template <typename TSize > inline bool _isRoot(_VertexWotdOriginal<TSize> const &value); // "projects/library/seqan/index/index_wotd.h"(267)
+template <typename TSize > inline bool _isRoot(_VertexWotdModified<TSize> const &value); // "projects/library/seqan/index/index_wotd.h"(272)
+template <typename TSize > inline bool _isRoot(VertexESA<TSize> const &value); // "projects/library/seqan/index/index_esa_stree.h"(1501)
+
+//____________________________________________________________________________
+// _isSizeInval
+
+template <typename TValue> inline bool _isSizeInval(TValue const &v); // "projects/library/seqan/index/index_base.h"(794)
+
+//____________________________________________________________________________
+// _isUp
+
+template <typename TSize, typename TIndex > inline bool _isUp(TSize i, TIndex const &index); // "projects/library/seqan/index/index_esa_stree.h"(1813)
+
+//____________________________________________________________________________
+// _leqSkew3
+
+template <typename T, typename ST> inline bool _leqSkew3(T a1, ST a2, T b1, ST b2); // "projects/library/seqan/index/index_skew3.h"(313)
+template <typename T, typename ST> inline bool _leqSkew3(T a1, T a2, ST a3, T b1, T b2, ST b3); // "projects/library/seqan/index/index_skew3.h"(319)
+
+//____________________________________________________________________________
+// _leqSkew7
+
+template <typename TTextIter, typename TSize> inline bool _leqSkew7(TTextIter a1, TSize a2, TTextIter b1, TSize b2, TSize n); // "projects/library/seqan/index/index_skew7.h"(414)
+template <typename TTextIter, typename TSize> inline bool _leqSkew7(TTextIter a, TTextIter b, TSize n); // "projects/library/seqan/index/index_skew7.h"(425)
+template <typename TTextIter, typename TSize, typename TString> inline bool _leqSkew7(unsigned a, unsigned b, TTextIter spos[], const TSize tpos[], const bool islast[], const TString &s124, const long adjust[7][7]); // "projects/library/seqan/index/index_skew7.h"(436)
+
+//____________________________________________________________________________
+// _lowerBoundLCPE
+
+template <typename TText, typename TSA, typename TLCP, typename TSpec, typename TQuery, typename TDiff_ > inline typename Iterator<TSA, Standard>::Type _lowerBoundLCPE( TText &text, TSA &sa, SearchTreeIterator< TLCP, TSpec > treeIter, TQuery &query, TDiff_ lcpLower, TDiff_ lcpUpper); // "projects/library/seqan/index/index_esa_find.h"(992)
+template <typename TText, typename TSA, typename TLCP, typename TSpec, typename TQuery > inline typename Iterator<TSA, Standard>::Type _lowerBoundLCPE( TText &text, TSA &sa, SearchTreeIterator< TLCP, TSpec > &treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(1169)
+
+//____________________________________________________________________________
+// _lowerBoundSA
+
+template <typename TText, typename TSA, typename TSpec, typename TQuery > inline typename Iterator<TSA, Standard>::Type _lowerBoundSA( TText &text, SearchTreeIterator< TSA, TSpec > treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(524)
+
+//____________________________________________________________________________
+// _onGoDown
+
+template <typename TIndex, typename TSpec > inline void _onGoDown(Iter<TIndex, VSTree< TopDown<TSpec> > > &); // "projects/library/seqan/index/index_esa_stree.h"(1018)
+
+//____________________________________________________________________________
+// _onGoRight
+
+template <typename TIndex, typename TSpec > inline void _onGoRight(Iter<TIndex, VSTree< TopDown<TSpec> > > &); // "projects/library/seqan/index/index_esa_stree.h"(1021)
+
+//____________________________________________________________________________
+// _onGoUp
+
+template <typename TIndex, typename TSpec > inline void _onGoUp(Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &); // "projects/library/seqan/index/index_esa_stree.h"(1024)
+
+//____________________________________________________________________________
+// _pizzaChiliDeallocate
+
+template <typename TValue> inline void _pizzaChiliDeallocate(TValue* begin); // "projects/library/seqan/index/index_pizzachili_string.h"(276)
+
+//____________________________________________________________________________
+// _pizzaChiliReallocate
+
+template <typename TValue, typename TSpec> inline typename Value<String<TValue, PizzaChili<TSpec> > >::Type* _pizzaChiliReallocate( String<TValue, PizzaChili<TSpec> >& me, typename Size<String<TValue, PizzaChili<TSpec> > >::Type new_capacity ); // "projects/library/seqan/index/index_pizzachili_string.h"(259)
+
+//____________________________________________________________________________
+// _qgramCountQGrams
+
+template <typename TDir, typename TText, typename TShape > inline void _qgramCountQGrams(TDir &dir, TText const &text, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(640)
+template <typename TDir, typename TString, typename TSpec, typename TShape > inline void _qgramCountQGrams(TDir &dir, StringSet<TString, TSpec> const &stringSet, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(660)
+
+//____________________________________________________________________________
+// _qgramCummulativeSum
+
+template <typename TDir, typename TWithConstraints > inline typename Value<TDir>::Type _qgramCummulativeSum(TDir &dir, TWithConstraints); // "projects/library/seqan/index/index_qgram.h"(690)
+
+//____________________________________________________________________________
+// _qgramCummulativeSumAlt
+
+template <typename TDir, typename TWithConstraints > inline typename Value<TDir>::Type _qgramCummulativeSumAlt(TDir &dir, TWithConstraints const); // "projects/library/seqan/index/index_qgram.h"(722)
+
+//____________________________________________________________________________
+// _qgramDisableBuckets
+
+template <typename TIndex > inline bool _qgramDisableBuckets(TIndex &); // "projects/library/seqan/index/index_qgram.h"(863)
+
+//____________________________________________________________________________
+// _qgramFillSuffixArray
+
+template <typename TSA, typename TText, typename TShape, typename TDir, typename TWithConstraints > inline void _qgramFillSuffixArray(TSA &sa, TText const &text, TShape &shape, TDir &dir, TWithConstraints const); // "projects/library/seqan/index/index_qgram.h"(748)
+template <typename TSA, typename TString, typename TSpec, typename TShape, typename TDir, typename TWithConstraints > inline void _qgramFillSuffixArray( TSA &sa, StringSet<TString, TSpec> const &stringSet, TShape &shape, TDir &dir, TWithConstraints const); // "projects/library/seqan/index/index_qgram.h"(790)
+
+//____________________________________________________________________________
+// _qgramPostprocessBuckets
+
+template <typename TDir > inline void _qgramPostprocessBuckets(TDir &dir); // "projects/library/seqan/index/index_qgram.h"(831)
+
+//____________________________________________________________________________
+// _reallocateStorage
+
+template <typename TValue, typename TSpec> inline typename Value<String<TValue, PizzaChili<TSpec> > >::Type* _reallocateStorage( String<TValue, PizzaChili<TSpec> >& me, typename Size<String<TValue, PizzaChili<TSpec> > >::Type new_capacity, Exact ); // "projects/library/seqan/index/index_pizzachili_string.h"(359)
+
+//____________________________________________________________________________
+// _refineQGramIndex
+
+template <typename TSA, typename TDir, typename TText, typename TSize1, typename TSize2 > void _refineQGramIndex( TSA &sa, TDir &dir, TText const &text, TSize1 oldQ, TSize2 newQ); // "projects/library/seqan/index/index_qgram.h"(1033)
+
+//____________________________________________________________________________
+// _setLength
+
+template <typename TValue, typename TSpec> inline void _setLength( String<TValue, PizzaChili<TSpec> >& me, size_t new_length ); // "projects/library/seqan/index/index_pizzachili_string.h"(409)
+
+//____________________________________________________________________________
+// _setSizeInval
+
+template <typename TValue> inline void _setSizeInval(TValue &v); // "projects/library/seqan/index/index_base.h"(789)
+
+//____________________________________________________________________________
+// _sortBucketQuickSort
+
+template <typename TSA, typename TText, typename TSize> void _sortBucketQuickSort( TSA &sa, TText &text, TSize lcp); // "projects/library/seqan/index/index_sa_qsort.h"(87)
+
+//____________________________________________________________________________
+// _sortFirstWotdBucket
+
+template <typename TText, typename TSpec, typename TPredHull, typename TPred > typename Size< Index<StringSet<TText, TSpec>, Index_Wotd<WotdDFI<TPredHull, TPred> > > >::Type _sortFirstWotdBucket(Index<StringSet<TText, TSpec>, Index_Wotd<WotdDFI<TPredHull, TPred> > > &index); // "projects/library/seqan/index/index_dfi.h"(171)
+template <typename TIndex > typename Size<TIndex>::Type _sortFirstWotdBucket(TIndex &index); // "projects/library/seqan/index/index_wotd.h"(890)
+template <typename TText, typename TSpec, typename TIndexSpec > typename Size< Index<StringSet<TText, TSpec>, TIndexSpec> >::Type _sortFirstWotdBucket(Index<StringSet<TText, TSpec>, TIndexSpec> &index); // "projects/library/seqan/index/index_wotd.h"(935)
+
+//____________________________________________________________________________
+// _sortWotdBucket
+
+template <typename TText, typename TSpec, typename TPredHull, typename TPred, typename TSize > TSize _sortWotdBucket( Index<StringSet<TText, TSpec>, Index_Wotd<WotdDFI<TPredHull, TPred> > > &index, TSize left, TSize right, TSize prefixLen); // "projects/library/seqan/index/index_dfi.h"(260)
+template <typename TText, typename TSize > TSize _sortWotdBucket( Index<TText, Index_Wotd<WotdOriginal> > &index, TSize left, TSize right, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(999)
+template <typename TIndex, typename TSize > TSize _sortWotdBucket( TIndex &index, TSize left, TSize right, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(1108)
+template <typename TText, typename TSpec, typename TIndexSpec, typename TSize > TSize _sortWotdBucket( Index<StringSet<TText, TSpec>, TIndexSpec> &index, TSize left, TSize right, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(1171)
+
+//____________________________________________________________________________
+// _storeWotdChildren
+
+template <typename TText, typename TPredHull, typename TPred, typename TSize> inline void _storeWotdChildren( Index<TText, Index_Wotd<WotdDFI<TPredHull, TPred> > > &index, TSize dirOfs, TSize lcp); // "projects/library/seqan/index/index_dfi.h"(397)
+template <typename TText, typename TPos> inline void _storeWotdChildren( Index<TText, Index_Wotd<WotdOriginal> > &index, TPos dirOfs); // "projects/library/seqan/index/index_wotd.h"(1385)
+template <typename TText, typename TSpec, typename TSize> inline void _storeWotdChildren( Index<TText, Index_Wotd<TSpec> > &index, TSize dirOfs, TSize lcp); // "projects/library/seqan/index/index_wotd.h"(1441)
+
+//____________________________________________________________________________
+// _treeLevels
+
+template <typename TSize > inline unsigned _treeLevels(TSize lcpSize); // "projects/library/seqan/index/index_lcp_tree.h"(146)
+
+//____________________________________________________________________________
+// _upperBoundLCPE
+
+template <typename TText, typename TSA, typename TLCP, typename TSpec, typename TQuery, typename TDiff_ > inline typename Iterator<TSA, Standard>::Type _upperBoundLCPE( TText &text, TSA &sa, SearchTreeIterator< TLCP, TSpec > treeIter, TQuery &query, TDiff_ lcpLower, TDiff_ lcpUpper); // "projects/library/seqan/index/index_esa_find.h"(1192)
+template <typename TText, typename TSA, typename TLCP, typename TSpec, typename TQuery > inline typename Iterator<TSA, Standard>::Type _upperBoundLCPE( TText &text, TSA &sa, SearchTreeIterator< TLCP, TSpec > &treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(1342)
+
+//____________________________________________________________________________
+// _upperBoundSA
+
+template <typename TText, typename TSA, typename TSpec, typename TQuery > inline typename Iterator<TSA, Standard>::Type _upperBoundSA( TText &text, SearchTreeIterator< TSA, TSpec > treeIter, TQuery &query); // "projects/library/seqan/index/index_esa_find.h"(578)
+
+//____________________________________________________________________________
+// _wotdCountChars
+
+template <typename TBuckets, typename TText > inline void _wotdCountChars(TBuckets &buckets, TText const &text); // "projects/library/seqan/index/index_wotd.h"(700)
+template <typename TBuckets, typename TText, typename TSpec > inline void _wotdCountChars(TBuckets &buckets, StringSet<TText, TSpec> const &stringSet); // "projects/library/seqan/index/index_wotd.h"(714)
+template <typename TBuckets, typename TText, typename TSA, typename TSize > inline typename Size<TText>::Type _wotdCountChars( TBuckets &buckets, TText const &text, TSA const &sa, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(767)
+template <typename TBuckets, typename TText, typename TSpec, typename TSA, typename TSize > inline typename Size<TText>::Type _wotdCountChars( TBuckets &buckets, StringSet<TText, TSpec> const &stringSet, TSA const &sa, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(803)
+
+//____________________________________________________________________________
+// _wotdCountCharsWotdOriginal
+
+template <typename TBuckets, typename TText, typename TSA, typename TSize > inline typename Size<TText>::Type _wotdCountCharsWotdOriginal( TBuckets &buckets, TText const &text, TSA &sa, TSize prefixLen); // "projects/library/seqan/index/index_wotd.h"(736)
+
+//____________________________________________________________________________
+// _wotdCreateFirstLevel
+
+template <typename TText, typename TSpec> inline void _wotdCreateFirstLevel(Index<TText, Index_Wotd<TSpec> > &index); // "projects/library/seqan/index/index_wotd.h"(1681)
+
+//____________________________________________________________________________
+// _wotdCummulativeSum
+
+template <typename TBounds, typename TBuckets, typename TSize > inline typename Size<TBuckets>::Type _wotdCummulativeSum(TBounds &bounds, TBuckets const &buckets, TSize offset); // "projects/library/seqan/index/index_wotd.h"(844)
+template <typename TBounds, typename TBuckets > inline typename Size<TBuckets>::Type _wotdCummulativeSum(TBounds &bounds, TBuckets const &buckets); // "projects/library/seqan/index/index_wotd.h"(870)
+
+//____________________________________________________________________________
+// _wotdEvaluate
+
+template <typename TText, typename TSpec > inline typename Size< Index<TText, Index_Wotd<WotdOriginal> > >::Type _wotdEvaluate(Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_wotd.h"(1497)
+template <typename TText, typename TIndexSpec, typename TSpec > inline typename Size< Index<TText, Index_Wotd<TIndexSpec> > >::Type _wotdEvaluate(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_wotd.h"(1538)
+
+//____________________________________________________________________________
+// alignment
+
+template <typename TString, typename TSSetSpec, typename TIndexSpec, class TSpec > inline Align<TString, ArrayGaps> alignment(Iter< Index< StringSet<TString, TSSetSpec>, TIndexSpec >, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(643)
+template <typename TString, typename TConcSpec, typename TIndexSpec, class TSpec > inline Align<TString, ArrayGaps> alignment(Iter< Index< StringSet<TString, Owner<ConcatDirect<TConcSpec> > >, TIndexSpec >, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(689)
+
+//____________________________________________________________________________
+// assign
+
+template <typename TValue, typename TSpec, typename TSource, typename TExpand> inline void assign( String<TValue, PizzaChili<TSpec> >& target, TSource const& source, Tag<TExpand> const ); // "projects/library/seqan/index/index_pizzachili_string.h"(196)
+template <typename TValue, typename TSpec, typename TSource, typename TExpand> inline void assign( String<TValue, PizzaChili<TSpec> >& target, TSource const* source, Tag<TExpand> const ); // "projects/library/seqan/index/index_pizzachili_string.h"(210)
+template <typename TValue, typename TSpec, typename TExpand> inline void assign( String<TValue, PizzaChili<TSpec> >& target, String<TValue, PizzaChili<TSpec> > const& source, Tag<TExpand> const ); // "projects/library/seqan/index/index_pizzachili_string.h"(224)
+
+//____________________________________________________________________________
+// atBegin
+
+template <typename TText, typename TSpec, typename TSpecFinder > inline bool atBegin(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(180)
+
+//____________________________________________________________________________
+// atEnd
+
+template <typename TText, typename TSpec > inline bool atEnd(Iter<Index<TText, Index_Wotd<WotdOriginal> >, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_wotd.h"(477)
+template <typename TText, typename TSpec > inline bool atEnd(Iter<Index<TText, Index_Wotd<WotdOriginal> >, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_wotd.h"(483)
+template <typename TText, typename TSpec, typename TSpecFinder > inline bool atEnd(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(188)
+template <typename TIndex, class TSpec > inline bool atEnd(Iter<TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(1467)
+template <typename TIndex, class TSpec > inline bool atEnd(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1473)
+template <typename TRepeat > inline bool atEnd(Iter<TRepeat, MaxRepeatOccurrences> const &it); // "projects/library/seqan/index/index_esa_algs.h"(824)
+template <typename TRepeat > inline bool atEnd(Iter<TRepeat, MaxRepeatOccurrences> &it); // "projects/library/seqan/index/index_esa_algs.h"(829)
+template <typename TRepeat > inline bool atEnd(Iter<TRepeat, MultiMEMOccurences> const &it); // "projects/library/seqan/index/index_esa_algs_multi.h"(644)
+template <typename TRepeat > inline bool atEnd(Iter<TRepeat, MultiMEMOccurences> &it); // "projects/library/seqan/index/index_esa_algs_multi.h"(649)
+
+//____________________________________________________________________________
+// begin
+
+template <typename TValue, typename TSpec, typename TTag> inline typename Iterator<String<TValue, PizzaChili<TSpec> >, Tag<TSpec> const>::Type begin( String<TValue, PizzaChili<TSpec> >& me, Tag<TTag> const ); // "projects/library/seqan/index/index_pizzachili_string.h"(464)
+template <typename TValue, typename TSpec, typename TTag> inline typename Iterator<String<TValue, PizzaChili<TSpec> > const, Tag<TSpec> const>::Type begin( String<TValue, PizzaChili<TSpec> > const& me, Tag<TTag> const ); // "projects/library/seqan/index/index_pizzachili_string.h"(475)
+template <typename TText, typename TIndexSpec, class TSpec > inline typename Iterator<Index<TText, TIndexSpec>, TSpec >::Type begin(Index<TText, TIndexSpec> &index, TSpec const); // "projects/library/seqan/index/index_esa_stree.h"(877)
+template <typename TSTree, class TSpec > inline typename Iterator< Iter< TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > >::Type begin(Iter< TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > &it); // "projects/library/seqan/index/index_esa_algs.h"(579)
+
+//____________________________________________________________________________
+// bwtAt
+
+template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex, Fibre_BWT>::Type>::Type bwtAt(TPos i, TIndex &index); // "projects/library/seqan/index/index_base.h"(777)
+template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex const, Fibre_BWT>::Type>::Type bwtAt(TPos i, TIndex const &index); // "projects/library/seqan/index/index_base.h"(781)
+
+//____________________________________________________________________________
+// cargo
+
+template <typename TText, typename TSpec> inline typename Reference< typename Cargo<Index<TText, TSpec> >::Type >::Type cargo(Index<TText, TSpec> & me); // "projects/library/seqan/index/index_shims.h"(595)
+template <typename TText, typename TSpec> inline typename Reference< typename Cargo<Index<TText, TSpec> const>::Type >::Type cargo(Index<TText, TSpec> const & me); // "projects/library/seqan/index/index_shims.h"(603)
+
+//____________________________________________________________________________
+// childAt
+
+template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex, Fibre_ChildTab>::Type>::Type childAt(TPos i, TIndex &index); // "projects/library/seqan/index/index_base.h"(756)
+template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex const, Fibre_ChildTab>::Type>::Type childAt(TPos i, TIndex const &index); // "projects/library/seqan/index/index_base.h"(760)
+
+//____________________________________________________________________________
+// childrenAreLeaves
+
+template <typename TIndex, class TSpec > inline bool childrenAreLeaves(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1734)
+
+//____________________________________________________________________________
+// childtab_process
+
+template <typename TLCPInput, typename TDest > inline void childtab_process(TLCPInput &lcpIn, TDest &dest); // "projects/library/seqan/index/index_childtab.h"(44)
+
+//____________________________________________________________________________
+// clear
+
+template <typename TText, typename TSpec> inline void clear(Index<TText, Index_ESA<TSpec> > &index); // "projects/library/seqan/index/index_esa_base.h"(307)
+template <typename TText, typename TSpec> inline void clear(Index<TText, PizzaChili<TSpec> >& me); // "projects/library/seqan/index/index_pizzachili.h"(150)
+template <typename TText, typename TSpec, typename TSpecFinder > inline void clear(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(167)
+template <typename TValue, typename TSpec> inline void clear(String<TValue, PizzaChili<TSpec> >& me); // "projects/library/seqan/index/index_pizzachili_string.h"(178)
+template <typename TIndex, class TSpec > inline void clear(Iter<TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(1387)
+
+//____________________________________________________________________________
+// container
+
+template <typename TText, typename TSpec, typename TSpecFinder > inline typename _Parameter< Index<TText, TSpec> >::Type container(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(100)
+template <typename TText, typename TSpec, typename TSpecFinder > inline typename _Parameter< Index<TText, TSpec> >::Type container(Finder< Index<TText, TSpec>, TSpecFinder > const & me); // "projects/library/seqan/index/index_find.h"(108)
+template <typename TIndex, class TSpec > inline TIndex const & container(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(543)
+template <typename TIndex, class TSpec > inline TIndex & container(Iter< TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(548)
+
+//____________________________________________________________________________
+// control
+
+//template <typename TInput > inline bool control(Pipe< TInput, LarssonSadakane > &me, ControlBeginRead const &command); // "projects/library/seqan/index/index_sa_lss.h"(413)
+//template <typename TInput > inline bool control(Pipe< TInput, Merger3 > &me, ControlBeginRead const &command); // "projects/library/seqan/index/pipe_merger3.h"(134)
+//template <typename TInput > inline bool control(Pipe< TInput, Merger7 > &me, ControlBeginRead const &command); // "projects/library/seqan/index/pipe_merger7.h"(475)
+//template <typename TInput > inline bool control(Pipe< TInput, Merger7 > &me, ControlEof const &); // "projects/library/seqan/index/pipe_merger7.h"(483)
+//template <typename TInput > inline bool control(Pipe< TInput, Merger7 > &me, ControlEos const &); // "projects/library/seqan/index/pipe_merger7.h"(488)
+//template <typename TInput, typename TLimitsString > inline bool control(Pipe< TInput, Merger7Multi<TLimitsString> > &me, ControlBeginRead const &command); // "projects/library/seqan/index/pipe_merger7.h"(506)
+//template <typename TInput, typename TLimitsString > inline bool control(Pipe< TInput, Merger7Multi<TLimitsString> > &me, ControlEof const &); // "projects/library/seqan/index/pipe_merger7.h"(513)
+//template <typename TInput, typename TLimitsString > inline bool control(Pipe< TInput, Merger7Multi<TLimitsString> > &me, ControlEos const &); // "projects/library/seqan/index/pipe_merger7.h"(518)
+
+//____________________________________________________________________________
+// countChildren
+
+template <typename TIndex, class TSpec > inline typename Size<TIndex>::Type countChildren(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(763)
+
+//____________________________________________________________________________
+// countOccurrences
+
+template <typename TIndex, class TSpec > inline typename Size<TIndex>::Type countOccurrences(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(600)
+
+//____________________________________________________________________________
+// countSequences
+
+template <typename TText, typename TSpec> inline typename Size<TText>::Type countSequences(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(609)
+
+//____________________________________________________________________________
+// createBWTable
+
+template <typename TBWT, typename TText, typename TSA > inline void createBWTable(TBWT &bwt, TText const &s, TSA const &sa); // "projects/library/seqan/index/index_shims.h"(439)
+
+//____________________________________________________________________________
+// createBWTableExt
+
+template <typename TBWT, typename TText, typename TSA > void createBWTableExt( TBWT &bwt, TText const &s, TSA const &SA); // "projects/library/seqan/index/index_shims.h"(394)
+
+//____________________________________________________________________________
+// createBWTableInt
+
+template <typename TBWT, typename TText, typename TSA > void createBWTableInt( TBWT &bwt, TText const &s, TSA const &SA); // "projects/library/seqan/index/index_bwt.h"(247)
+template <typename TBWT, typename TString, typename TSpec, typename TSA > void createBWTableInt( TBWT &bwt, StringSet<TString, TSpec> const &s, TSA const &SA); // "projects/library/seqan/index/index_bwt.h"(275)
+
+//____________________________________________________________________________
+// createChildTable
+
+//template <typename TLCPTable, typename TValue, typename TConfig > inline void createChildTable( String<TValue, External<TConfig> > &childtab, TLCPTable &lcp); // "projects/library/seqan/index/index_childtab.h"(197)
+template <typename TLCPInput, typename TDest > inline void createChildTable(TDest &dest, TLCPInput const &lcpIn); // "projects/library/seqan/index/index_childtab.h"(209)
+
+//____________________________________________________________________________
+// createChildTableExt
+
+template <typename TLCPTable, typename TChildTable > void createChildTableExt( TChildTable &childtab, TLCPTable &lcp); // "projects/library/seqan/index/index_childtab.h"(171)
+
+//____________________________________________________________________________
+// createCountsArray
+
+template <typename TCounts, typename TDir, typename TString, typename TSpec, typename TShape > void createCountsArray( TCounts &counts, TDir &dir, StringSet<TString, TSpec> const &stringSet, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(1150)
+
+//____________________________________________________________________________
+// createLCPBinTree
+
+template <class LCPFwdIt, class FlatOutIt > inline FlatOutIt createLCPBinTree( LCPFwdIt _First, LCPFwdIt _Last, FlatOutIt _Dest); // "projects/library/seqan/index/index_lcp_tree.h"(33)
+template <typename TLCPE, typename TLCP > inline void createLCPBinTree(TLCPE &lcp_enhanced, TLCP &lcp); // "projects/library/seqan/index/index_lcp_tree.h"(139)
+//template <typename TValue, typename TConfig, typename TLCP > inline void createLCPBinTree(String<TValue, External<TConfig> > &lcp_enhanced, TLCP &lcp); // "projects/library/seqan/index/index_lcp_tree.h"(155)
+
+//____________________________________________________________________________
+// createLCPETable
+
+template <typename TValue, typename TSpec, typename TText, typename TSA, typename TAlgSpec > void createLCPETable( String< TValue, TSpec > &LCPE, TText const &s, TSA const &SA, TAlgSpec const alg); // "projects/library/seqan/index/index_shims.h"(334)
+//template <typename TValue, typename TConfig, typename TText, typename TSA, typename TAlgSpec > void createLCPETable( String< TValue, External<TConfig> > &LCPE, TText const &s, TSA const &SA, TAlgSpec const alg); // "projects/library/seqan/index/index_shims.h"(359)
+template <typename TValue, typename TSpec, typename TText, typename TSA> inline void createLCPETable( String< TValue, TSpec > &LCPE, TText &s, TSA &SA); // "projects/library/seqan/index/index_shims.h"(373)
+
+//____________________________________________________________________________
+// createLCPETableExt
+
+template <typename TValue, typename TSpec, typename TObject, typename TSA, typename TAlgSpec > void createLCPETableExt( String< TValue, TSpec > &LCPE, TObject const &text, TSA const &suffixArray, TAlgSpec const); // "projects/library/seqan/index/index_shims.h"(301)
+
+//____________________________________________________________________________
+// createLCPTable
+
+//template <typename TLCPTable, typename TText, typename TSA > void createLCPTable( TLCPTable &LCP, TText const &s, TSA const &SA, KasaiOriginal const); // "projects/library/seqan/index/index_lcp.h"(253)
+//template <typename TLCPTable, typename TText, typename TSA > void createLCPTable( TLCPTable &LCP, TText const &s, TSA const &SA, Kasai const); // "projects/library/seqan/index/index_lcp.h"(315)
+template <typename TLCPTable, typename TString, typename TSpec, typename TSA > void createLCPTable( TLCPTable &LCP, StringSet<TString, TSpec> const &sset, TSA const &SA, Kasai const); // "projects/library/seqan/index/index_lcp.h"(398)
+
+//____________________________________________________________________________
+// createLCPTableExt
+
+template <typename TLCPTable, typename TObject, typename TSA, typename TAlgSpec > void createLCPTableExt( TLCPTable &LCP, TObject const &text, TSA const &suffixArray, TAlgSpec const); // "projects/library/seqan/index/index_shims.h"(179)
+template <typename TLCPTable, typename TString, typename TSpec, typename TSA, typename TAlgSpec > void createLCPTableExt( TLCPTable &LCP, StringSet<TString, TSpec> const &stringSet, TSA const &suffixArray, TAlgSpec const); // "projects/library/seqan/index/index_shims.h"(210)
+
+//____________________________________________________________________________
+// createQGramIndex
+
+template <typename TIndex > void createQGramIndex(TIndex &index); // "projects/library/seqan/index/index_qgram.h"(869)
+template <typename TSA, typename TDir, typename TText, typename TShape > void createQGramIndex( TSA &sa, TDir &dir, TText const &text, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(915)
+
+//____________________________________________________________________________
+// createQGramIndexDirOnly
+
+template <typename TDir, typename TText, typename TShape > void createQGramIndexDirOnly( TDir &dir, TText const &text, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(1089)
+template <typename TDir, typename TString, typename TSpec, typename TShape > void createQGramIndexDirOnly( TDir &dir, StringSet<TString, TSpec> const &stringSet, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(1111)
+
+//____________________________________________________________________________
+// createQGramIndexExt
+
+template <typename TSA, typename TDir, typename TText, typename TShape > void createQGramIndexExt( TSA &suffixArray, TDir &dir, TText &text, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(1287)
+template <typename TSA, typename TDir, typename TString, typename TSpec, typename TShape, typename TLimitsString > void createQGramIndexExt( TSA &suffixArray, TDir &dir, StringSet<TString, TSpec> const &stringSet, TShape &shape, TLimitsString &limits); // "projects/library/seqan/index/index_qgram.h"(1374)
+
+//____________________________________________________________________________
+// createQGramIndexSAOnly
+
+template <typename TSA, typename TText, typename TShape > void createQGramIndexSAOnly( TSA &sa, TText const &text, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(951)
+template <typename TSA, typename TString, typename TSpec, typename TShape > void createQGramIndexSAOnly( TSA &sa, StringSet<TString, TSpec> const &stringSet, TShape &shape); // "projects/library/seqan/index/index_qgram.h"(986)
+
+//____________________________________________________________________________
+// createSABTree
+
+template <class SAFwdIt, class FlatOutIt > inline FlatOutIt createSABTree( SAFwdIt _First, SAFwdIt _Last, FlatOutIt _Dest, unsigned BlockSize); // "projects/library/seqan/index/index_sa_btree.h"(33)
+template <typename TSAB, typename TSA > inline void createSABTree(TSAB &sa_btree, TSA &sa, unsigned BlockSize); // "projects/library/seqan/index/index_sa_btree.h"(96)
+//template <typename TValue, typename TConfig, typename TSA > inline void createSABTree(String<TValue, External<TConfig> > &sa_btree, TSA &sa, unsigned BlockSize); // "projects/library/seqan/index/index_sa_btree.h"(110)
+
+//____________________________________________________________________________
+// createSuffixArray
+
+template <typename TSA, typename TText > void createSuffixArray( TSA &SA, TText &s, Shawarma<DeepShallow> const); // "projects/library/seqan/index/index_shawarma.h"(58)
+template <typename TSA, typename TText, typename TAlgSpec > inline void createSuffixArray( TSA &SA, TText const &s, TAlgSpec const &alg); // "projects/library/seqan/index/index_shims.h"(121)
+//template <typename TSA, typename TValue, typename TConfig, typename TAlgSpec > inline void createSuffixArray( TSA &SA, String< TValue, External<TConfig> > const &s, TAlgSpec const alg); // "projects/library/seqan/index/index_shims.h"(139)
+template <typename TSA, typename TValue, typename TSpec, typename TSSetSpec, typename TAlgSpec > inline void createSuffixArray( TSA &SA, StringSet< String<TValue, TSpec>, TSSetSpec > const &s, TAlgSpec const); // "projects/library/seqan/index/index_shims.h"(155)
+template <typename TSA, typename TText > void createSuffixArray( TSA &SA, TText &s, LarssonSadakane const &, unsigned K); // "projects/library/seqan/index/index_sa_lss.h"(352)
+template <typename TSA, typename TText > void createSuffixArray( TSA &SA, TText &s, ManberMyers const &, unsigned K, unsigned maxdepth); // "projects/library/seqan/index/index_sa_mm.h"(42)
+template <typename TSA, typename TText > inline void createSuffixArray( TSA &SA, TText &s, SAQSort const &); // "projects/library/seqan/index/index_sa_qsort.h"(102)
+//template <typename TSA, typename TValue, typename TConfig > inline void createSuffixArray( TSA &SA, String< TValue, External<TConfig> > &s, Skew3 const &spec, unsigned K, unsigned maxdepth); // "projects/library/seqan/index/index_skew3.h"(299)
+template <typename TSA, typename TText > void createSuffixArray( TSA &SA, TText &s, Skew3 const &, unsigned K, unsigned maxdepth, unsigned depth); // "projects/library/seqan/index/index_skew3.h"(342)
+template <typename TSA, typename TText > inline void createSuffixArray( TSA &SA, TText &s, Skew3 const &alg, unsigned K, unsigned maxdepth); // "projects/library/seqan/index/index_skew3.h"(494)
+//template <typename TSA, typename TValue, typename TConfig > inline void createSuffixArray( TSA &SA, String< TValue, External<TConfig> > &s, Skew7 const &spec, unsigned K, unsigned maxdepth); // "projects/library/seqan/index/index_skew7.h"(399)
+template <typename TSA, typename TText > void createSuffixArray( TSA &SA, TText &s, Skew7 const &, unsigned K, unsigned maxdepth, unsigned depth); // "projects/library/seqan/index/index_skew7.h"(472)
+template <typename TSA, typename TText > inline void createSuffixArray( TSA &SA, TText &s, Skew7 const &alg, unsigned K, unsigned maxdepth); // "projects/library/seqan/index/index_skew7.h"(795)
+
+//____________________________________________________________________________
+// createSuffixArrayExt
+
+template <typename TSA, typename TObject, typename TAlgSpec > void createSuffixArrayExt( TSA &suffixArray, TObject const &text, TAlgSpec const); // "projects/library/seqan/index/index_shims.h"(40)
+template <typename TSA, typename TString, typename TSpec, typename TAlgSpec > void createSuffixArrayExt( TSA &suffixArray, StringSet<TString, TSpec> const &stringSet, TAlgSpec const); // "projects/library/seqan/index/index_shims.h"(74)
+
+//____________________________________________________________________________
+// createSuffixArrayPart
+
+template <typename TSA, typename TText, typename TSize > inline void createSuffixArrayPart( TSA &SA, TText &s, ManberMyers const &alg, TSize maxLCP, unsigned K ); // "projects/library/seqan/index/index_sa_mm.h"(167)
+template <typename TSA, typename TText, typename TSize > inline void createSuffixArrayPart( TSA &SA, TText &s, Skew3 const &_dummy, TSize maxLCP, unsigned K ); // "projects/library/seqan/index/index_skew3.h"(508)
+template <typename TSA, typename TText, typename TSize > inline void createSuffixArrayPart( TSA &SA, TText &s, Skew7 const &_dummy, TSize maxLCP, unsigned K ); // "projects/library/seqan/index/index_skew7.h"(809)
+
+//____________________________________________________________________________
+// dirAt
+
+template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex, Fibre_Dir>::Type>::Type dirAt(TPos i, TIndex &index); // "projects/library/seqan/index/index_qgram.h"(265)
+template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex const, Fibre_Dir>::Type>::Type dirAt(TPos i, TIndex const &index); // "projects/library/seqan/index/index_qgram.h"(269)
+
+//____________________________________________________________________________
+// empty
+
+template <typename TText, typename TSpec, typename TSpecFinder > inline bool empty(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(159)
+template <typename TIndex, class TSpec > inline bool empty(Iter<TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(1452)
+template <typename TIndex, class TSpec > inline bool empty(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1458)
+
+//____________________________________________________________________________
+// emptyParentEdge
+
+template <typename TText, typename TIndexSpec, typename TSpec > inline bool emptyParentEdge(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree<TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_wotd.h"(425)
+template <typename TText, typename TIndexSpec, typename TSpec > inline bool emptyParentEdge(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree<TopDown<ParentLinks<TSpec> > > > const &it); // "projects/library/seqan/index/index_wotd.h"(438)
+template <typename TIndex, typename TSpec > inline bool emptyParentEdge(Iter< TIndex, VSTree<TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(427)
+
+//____________________________________________________________________________
+// end
+
+template <typename TValue, typename TSpec, typename TTag> inline typename Iterator<String<TValue, PizzaChili<TSpec> >, Tag<TSpec> const>::Type end( String<TValue, PizzaChili<TSpec> >& me, Tag<TTag> const ); // "projects/library/seqan/index/index_pizzachili_string.h"(486)
+template <typename TValue, typename TSpec, typename TTag> inline typename Iterator<String<TValue, PizzaChili<TSpec> > const, Tag<TSpec> const>::Type end( String<TValue, PizzaChili<TSpec> > const& me, Tag<TTag> const ); // "projects/library/seqan/index/index_pizzachili_string.h"(497)
+template <typename TText, typename TIndexSpec, class TSpec > inline typename Iterator<Index<TText, TIndexSpec>, TSpec >::Type end(Index<TText, TIndexSpec> &index, TSpec const); // "projects/library/seqan/index/index_esa_stree.h"(927)
+template <typename TSTree, class TSpec > inline typename Iterator< Iter< TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > >::Type end(Iter< TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > &it); // "projects/library/seqan/index/index_esa_algs.h"(589)
+
+//____________________________________________________________________________
+// eof
+
+template <typename TIndex, class TSpec > inline bool eof(Iter<TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(1440)
+template <typename TIndex, class TSpec > inline bool eof(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1446)
+
+//____________________________________________________________________________
+// equalRangeLCPE
+
+template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline Pair< typename Position<TSA>::Type > equalRangeLCPE( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(1586)
+template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline Pair< typename Position<TSA>::Type > equalRangeLCPE( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(1688)
+
+//____________________________________________________________________________
+// equalRangeLCPEIterator
+
+template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline Pair< typename Iterator<TSA, Standard>::Type > equalRangeLCPEIterator( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(1637)
+template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline Pair< typename Iterator<TSA, Standard>::Type > equalRangeLCPEIterator( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(1707)
+
+//____________________________________________________________________________
+// equalRangeSA
+
+template <typename TText, typename TSA, typename TQuery, typename TFlatTreeSpec > inline Pair< typename Position<TSA>::Type > equalRangeSA( TText const &text, TSA const &sa, TQuery const &query, TFlatTreeSpec const); // "projects/library/seqan/index/index_esa_find.h"(853)
+template <typename TText, typename TSA, typename TQuery > inline Pair< typename Position<TSA>::Type > equalRangeSA( TText const &text, TSA const &sa, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(870)
+template <typename TText, typename TSA, typename TQuery, typename TFlatTreeSpec > inline Pair< typename Position<TSA>::Type > equalRangeSA( TText const &text, TSA const &sa, TQuery *query, TFlatTreeSpec const); // "projects/library/seqan/index/index_esa_find.h"(950)
+template <typename TText, typename TSA, typename TQuery > inline Pair< typename Position<TSA>::Type > equalRangeSA( TText const &text, TSA const &sa, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(967)
+
+//____________________________________________________________________________
+// equalRangeSAIterator
+
+template <typename TText, typename TSA, typename TQuery > inline Pair< typename Iterator<TSA const, Standard>::Type > equalRangeSAIterator( TText const &text, TSA const &sa, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(727)
+template <typename TText, typename TSA, typename TQuery > inline Pair< typename Iterator<TSA const, Standard>::Type > equalRangeSAIterator( TText const &text, TSA const &sa, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(773)
+
+//____________________________________________________________________________
+// find
+
+template <typename TText, typename TSpec, typename TSpecFinder, typename TPattern > inline bool find( Finder<Index<TText, TSpec>, TSpecFinder> &finder, TPattern const &pattern); // "projects/library/seqan/index/index_find.h"(249)
+template <typename TText, typename TSpec, typename TSpecFinder > inline bool find(Finder<Index<TText, TSpec>, TSpecFinder> &finder); // "projects/library/seqan/index/index_find.h"(260)
+
+//____________________________________________________________________________
+// findRepeats
+
+template <typename TRepeatStore, typename TText, typename TRepeatSize, typename TPeriodSize> void findRepeats(TRepeatStore &repString, TText const &text, TRepeatSize minRepeatLen, TPeriodSize maxPeriod); // "projects/library/seqan/index/repeat_base.h"(92)
+template <typename TRepeatStore, typename TString, typename TSpec, typename TRepeatSize> void findRepeats(TRepeatStore &repString, StringSet<TString, TSpec> const &text, TRepeatSize minRepeatLen); // "projects/library/seqan/index/repeat_base.h"(189)
+
+//____________________________________________________________________________
+// getFibre
+
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, PizzaChili<TSpec> > const, PizzaChili_Text>::Type getFibre(Index<TText, PizzaChili<TSpec> > const& me, PizzaChili_Text const); // "projects/library/seqan/index/index_pizzachili.h"(210)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, PizzaChili<TSpec> >, PizzaChili_Text>::Type getFibre(Index<TText, PizzaChili<TSpec> >& me, PizzaChili_Text const); // "projects/library/seqan/index/index_pizzachili.h"(217)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_Dir>::Type & getFibre(Index<TText, TSpec> &index, Fibre_Dir); // "projects/library/seqan/index/index_qgram.h"(188)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_Dir>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_Dir); // "projects/library/seqan/index/index_qgram.h"(193)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_Counts>::Type & getFibre(Index<TText, TSpec> &index, Fibre_Counts); // "projects/library/seqan/index/index_qgram.h"(199)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_Counts>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_Counts); // "projects/library/seqan/index/index_qgram.h"(204)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_CountsDir>::Type & getFibre(Index<TText, TSpec> &index, Fibre_CountsDir); // "projects/library/seqan/index/index_qgram.h"(210)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_CountsDir>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_CountsDir); // "projects/library/seqan/index/index_qgram.h"(215)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_Shape>::Type & getFibre(Index<TText, TSpec> &index, Fibre_Shape); // "projects/library/seqan/index/index_qgram.h"(221)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_Shape>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_Shape); // "projects/library/seqan/index/index_qgram.h"(226)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_Text>::Type & getFibre(Index<TText, TSpec> &index, Fibre_Text); // "projects/library/seqan/index/index_base.h"(476)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_Text>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_Text); // "projects/library/seqan/index/index_base.h"(481)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_RawText>::Type & getFibre(Index<TText, TSpec> &index, Fibre_RawText); // "projects/library/seqan/index/index_base.h"(489)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_RawText>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_RawText); // "projects/library/seqan/index/index_base.h"(494)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_SA>::Type & getFibre(Index<TText, TSpec> &index, Fibre_SA); // "projects/library/seqan/index/index_base.h"(502)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_SA>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_SA); // "projects/library/seqan/index/index_base.h"(507)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_SA>::Type & getFibre(Index<TText, TSpec> &index, Fibre_RawSA); // "projects/library/seqan/index/index_base.h"(515)
+template <typename TString, typename TSSetSpec, typename TSpec> inline typename Fibre<Index<StringSet<TString, TSSetSpec>, TSpec>, Fibre_RawSA>::Type getFibre(Index<StringSet<TString, TSSetSpec>, TSpec> &index, Fibre_RawSA); // "projects/library/seqan/index/index_base.h"(528)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_LCP>::Type & getFibre(Index<TText, TSpec> &index, Fibre_LCP); // "projects/library/seqan/index/index_base.h"(548)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_LCP>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_LCP); // "projects/library/seqan/index/index_base.h"(553)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_LCPE>::Type & getFibre(Index<TText, TSpec> &index, Fibre_LCPE); // "projects/library/seqan/index/index_base.h"(561)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_LCPE>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_LCPE); // "projects/library/seqan/index/index_base.h"(566)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_ChildTab>::Type & getFibre(Index<TText, TSpec> &index, Fibre_ChildTab); // "projects/library/seqan/index/index_base.h"(574)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_ChildTab>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_ChildTab); // "projects/library/seqan/index/index_base.h"(579)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_BWT>::Type & getFibre(Index<TText, TSpec> &index, Fibre_BWT); // "projects/library/seqan/index/index_base.h"(587)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_BWT>::Type & getFibre(Index<TText, TSpec> const &index, Fibre_BWT); // "projects/library/seqan/index/index_base.h"(592)
+
+//____________________________________________________________________________
+// getFrequency
+
+template <typename TIndex, class TSpec, typename TSet > inline typename Size<TIndex>::Type getFrequency(Iter<TIndex, VSTree<TSpec> > const &it, TSet &set); // "projects/library/seqan/index/index_esa_stree.h"(1686)
+template <typename TIndex, class TSpec > inline typename Size<TIndex>::Type getFrequency(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1714)
+
+//____________________________________________________________________________
+// getKmerSimilarityMatrix
+
+template <typename TObject, typename TShapeSpec, typename TSpec, typename TDistMatrix > inline void getKmerSimilarityMatrix( Index< TObject, Index_QGram<TShapeSpec, TSpec> > &index, TDistMatrix &distMat); // "projects/library/seqan/index/index_qgram.h"(1538)
+template <typename TObject, typename TShapeSpec, typename TSpec, typename TDistMatrix, typename TSeqNoString > inline void getKmerSimilarityMatrix( Index< TObject, Index_QGram<TShapeSpec, TSpec> > &index, TDistMatrix &distMat, TSeqNoString const &seqNo); // "projects/library/seqan/index/index_qgram.h"(1638)
+
+//____________________________________________________________________________
+// getOccurrence
+
+template <typename TText, typename TSpec > inline typename SAValue<Index<TText, Index_Wotd<WotdOriginal> > >::Type getOccurrence(Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_wotd.h"(418)
+template <typename TIndex, class TSpec > inline typename SAValue<TIndex>::Type getOccurrence(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(581)
+
+//____________________________________________________________________________
+// getOccurrences
+
+template <typename TIndex, class TSpec > inline typename Infix< typename Fibre<TIndex, Fibre_SA>::Type const >::Type getOccurrences(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(621)
+
+//____________________________________________________________________________
+// getOccurrencesBWT
+
+template <typename TIndex, class TSpec > inline typename Infix< typename Fibre<TIndex, ESA_BWT>::Type const >::Type getOccurrencesBWT(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(723)
+
+//____________________________________________________________________________
+// goBegin
+
+template <typename TText, typename TSpec, typename TSpecFinder > inline void goBegin(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(198)
+template <typename TText, typename TIndexSpec, class TSpec > inline void goBegin(Iter<Index<TText, TIndexSpec>, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(887)
+template <typename TText, typename TIndexSpec, class TSpec > inline void goBegin(Iter<Index<TText, Index_ESA<TIndexSpec> >, VSTree< BottomUp<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(906)
+template <typename TRepeat > inline Iter<TRepeat, MaxRepeatOccurrences> & goBegin(Iter<TRepeat, MaxRepeatOccurrences> &it); // "projects/library/seqan/index/index_esa_algs.h"(810)
+
+//____________________________________________________________________________
+// goDown
+
+template <typename TIndex, class TSpec > inline bool goDown(Iter< TIndex, VSTree< TopDown<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1085)
+template <typename TIndex, typename TSpec, typename TObject > inline bool goDown( Iter< TIndex, VSTree< TopDown<TSpec> > > &it, TObject const &obj); // "projects/library/seqan/index/index_esa_stree.h"(1190)
+template <typename TIndex, typename TSpec, typename TString, typename TSize > inline bool goDown( Iter< TIndex, VSTree< TopDown<TSpec> > > &it, TString const &pattern, TSize &lcp); // "projects/library/seqan/index/index_esa_stree.h"(1200)
+
+//____________________________________________________________________________
+// goEnd
+
+template <typename TText, typename TSpec, typename TSpecFinder > inline void goEnd(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(206)
+template <typename TText, typename TIndexSpec, class TSpec > inline void goEnd(Iter<Index<TText, Index_ESA<TIndexSpec> >, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(938)
+template <typename TText, typename TIndexSpec, class TSpec > inline void goEnd(Iter<Index<TText, Index_ESA<TIndexSpec> >, VSTree< BottomUp<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(945)
+template <typename TRepeat > inline Iter<TRepeat, MaxRepeatOccurrences> & goEnd(Iter<TRepeat, MaxRepeatOccurrences> &it); // "projects/library/seqan/index/index_esa_algs.h"(819)
+
+//____________________________________________________________________________
+// goNext
+
+template <typename TIndex, typename TSpec > inline void goNext(Iter<TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(956)
+template <typename TIndex, typename TSpec, typename TTraits > inline void goNext(Iter<TIndex, VSTree<TSpec> > &it, TTraits const traits); // "projects/library/seqan/index/index_esa_stree.h"(961)
+template <typename TSTree > inline void goNext(Iter< TSTree, VSTree< BottomUp<SuperMaxRepeats> > > &it); // "projects/library/seqan/index/index_esa_algs.h"(96)
+template <typename TText, typename TSpec > inline void goNext(Iter< Index<TText, Index_ESA<TSpec> >, VSTree< BottomUp<SuperMaxRepeatsFast> > > &it); // "projects/library/seqan/index/index_esa_algs.h"(187)
+template <typename TSTree, typename TSpec > inline void goNext(Iter< TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > &it); // "projects/library/seqan/index/index_esa_algs.h"(533)
+template <typename TRepeat > inline Iter<TRepeat, MaxRepeatOccurrences> & goNext(Iter<TRepeat, MaxRepeatOccurrences> &it); // "projects/library/seqan/index/index_esa_algs.h"(793)
+template <typename TSTree > inline void goNext(Iter< TSTree, VSTree< BottomUp<MUMs> > > &it); // "projects/library/seqan/index/index_esa_algs_multi.h"(100)
+template <typename TRepeat > inline Iter<TRepeat, MultiMEMOccurences> & goNext(Iter<TRepeat, MultiMEMOccurences> &it); // "projects/library/seqan/index/index_esa_algs_multi.h"(630)
+
+//____________________________________________________________________________
+// goNextImpl
+
+template <typename TIndex, typename TSpec, typename THideEmptyEdges > inline void goNextImpl( Iter<TIndex, VSTree< BottomUp<TSpec> > > &it, VSTreeIteratorTraits<_Postorder, THideEmptyEdges> const); // "projects/library/seqan/index/index_esa_stree.h"(284)
+template <typename TIndex, typename TSpec, typename THideEmptyEdges > inline void goNextImpl( Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it, VSTreeIteratorTraits<_Preorder, THideEmptyEdges> const); // "projects/library/seqan/index/index_esa_stree.h"(1405)
+template <typename TIndex, typename TSpec, typename THideEmptyEdges > inline void goNextImpl( Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it, VSTreeIteratorTraits<_Postorder, THideEmptyEdges> const); // "projects/library/seqan/index/index_esa_stree.h"(1421)
+
+//____________________________________________________________________________
+// goRight
+
+template <typename TIndex, class TSpec > inline bool goRight(Iter< TIndex, VSTree< TopDown<TSpec> > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1316)
+
+//____________________________________________________________________________
+// goRoot
+
+template <typename TText, typename TSpec > inline void goRoot(Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_wotd.h"(454)
+template <typename TText, typename TIndexSpec, typename TSpec > inline void goRoot(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_wotd.h"(466)
+template <typename TText, typename TIndexSpec, class TSpec > inline void goRoot(Iter<Index<TText, TIndexSpec>, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(865)
+
+//____________________________________________________________________________
+// goUp
+
+template <typename TIndex, class TSpec > inline bool goUp(Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it); // "projects/library/seqan/index/index_esa_stree.h"(1244)
+
+//____________________________________________________________________________
+// hash
+
+template <typename TValue, typename TIter> inline typename Value< Shape<TValue, GappedShape> >::Type hash(Shape<TValue, GappedShape> &me, TIter it); // "projects/library/seqan/index/shape_gapped.h"(368)
+template <typename TValue, typename TSpec, typename TIter, typename TSize> inline typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type hash(Shape<TValue, FixedGappedShape<TSpec> > &me, TIter it, TSize charsLeft); // "projects/library/seqan/index/shape_gapped.h"(385)
+template <int P00, int P01, int P02, int P03, int P04, int P05, int P06, int P07, int P08, int P09, int P10, int P11, int P12, int P13, int P14, int P15, int P16, int P17, int P18, int P19, typename TValue, typename TIter > inline typename Value< Shape<TValue, FixedGappedShape< HardwiredShape< P00,P01,P02,P03,P04, P05,P06,P07,P08,P09, P10,P11,P12,P13,P14, P15,P16,P17,P18,P19 > > > >::Type hash(Shape<TValue, FixedGappedShape< HardwiredShape< P00,P01,P02,P03,P04, P05,P06,P07,P08,P09, P10,P [...]
+template <typename TValue, typename TIter> typename Value< Shape<TValue, SimpleShape> >::Type hash(Shape<TValue, SimpleShape> &me, TIter it); // "projects/library/seqan/index/shape_base.h"(271)
+template <typename TValue, unsigned q, typename TIter> inline typename Value< Shape<TValue, FixedShape<q> > >::Type hash(Shape<TValue, FixedShape<q> > &me, TIter it); // "projects/library/seqan/index/shape_base.h"(307)
+template <typename TValue, typename TSpec, typename TIter, typename TSize> inline typename Value< Shape<TValue, TSpec> >::Type hash(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft); // "projects/library/seqan/index/shape_base.h"(320)
+template <typename TValue, typename TTValue, unsigned SIZE, unsigned q> typename Value< Shape<TValue, FixedShape<q> > >::Type hash( Shape<TValue, FixedShape<q> > &me, Tuple<TTValue, SIZE, Compressed> const &tuple); // "projects/library/seqan/index/shape_base.h"(379)
+template <typename TValue, typename TTValue, unsigned SIZE, typename TCompressed, unsigned q> typename Value< Shape<TValue, FixedShape<q> > >::Type hash( Shape<TValue, FixedShape<q> > &me, Tuple<TTValue, SIZE, TCompressed> const &tuple); // "projects/library/seqan/index/shape_base.h"(400)
+
+//____________________________________________________________________________
+// hash2
+
+template <typename TValue, typename TSpec, typename TIter, typename TSize> inline typename Value< Shape<TValue, TSpec> >::Type hash2(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft); // "projects/library/seqan/index/shape_base.h"(490)
+
+//____________________________________________________________________________
+// hash2Next
+
+template <typename TValue, typename TSpec, typename TIter, typename TSize> inline typename Value< Shape<TValue, TSpec> >::Type hash2Next(Shape<TValue, TSpec> &me, TIter &it, TSize charsLeft); // "projects/library/seqan/index/shape_base.h"(568)
+
+//____________________________________________________________________________
+// hash2Upper
+
+template <typename TValue, typename TSpec, typename TIter, typename TSize> inline typename Value< Shape<TValue, TSpec> >::Type hash2Upper(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft); // "projects/library/seqan/index/shape_base.h"(519)
+
+//____________________________________________________________________________
+// hashNext
+
+template <typename TValue, typename TSpec, typename TIter> inline typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type hashNext(Shape<TValue, FixedGappedShape<TSpec> > &me, TIter it); // "projects/library/seqan/index/shape_gapped.h"(536)
+template <typename TValue, typename TSpec, typename TIter> inline typename Value< Shape<TValue, TSpec> >::Type hashNext(Shape<TValue, TSpec> &me, TIter &it); // "projects/library/seqan/index/shape_base.h"(463)
+
+//____________________________________________________________________________
+// hashUpper
+
+template <typename TValue, typename TSpec, typename TIter, typename TSize> inline typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type hashUpper(Shape<TValue, FixedGappedShape<TSpec> > &me, TIter it, TSize charsLeft); // "projects/library/seqan/index/shape_gapped.h"(413)
+template <typename TValue, typename TSpec, typename TIter, typename TSize> inline typename Value< Shape<TValue, TSpec> >::Type hashUpper(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft); // "projects/library/seqan/index/shape_base.h"(422)
+
+//____________________________________________________________________________
+// host
+
+template <typename TText, typename TSpec, typename TSpecFinder > inline typename _Parameter< Index<TText, TSpec> >::Type host(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(84)
+template <typename TText, typename TSpec, typename TSpecFinder > inline typename _Parameter< Index<TText, TSpec> >::Type host(Finder< Index<TText, TSpec>, TSpecFinder > const & me); // "projects/library/seqan/index/index_find.h"(92)
+
+//____________________________________________________________________________
+// hostIterator
+
+template <typename TText, typename TSpec, typename TSpecFinder > inline typename Iterator< typename Fibre<Index<TText, TSpec>, Fibre_SA>::Type, Standard>::Type & hostIterator(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(140)
+template <typename TText, typename TSpec, typename TSpecFinder > inline typename Iterator< typename Fibre<Index<TText, TSpec>, Fibre_SA>::Type, Standard>::Type const & hostIterator(Finder< Index<TText, TSpec>, TSpecFinder > const & me); // "projects/library/seqan/index/index_find.h"(148)
+
+//____________________________________________________________________________
+// indexBWT
+
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_BWT>::Type & indexBWT(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(932)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_BWT>::Type & indexBWT(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(934)
+
+//____________________________________________________________________________
+// indexChildTab
+
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_ChildTab>::Type & indexChildTab(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(948)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_ChildTab>::Type & indexChildTab(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(950)
+
+//____________________________________________________________________________
+// indexCounts
+
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_Counts>::Type & indexCounts(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_qgram.h"(289)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_Counts>::Type & indexCounts(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_qgram.h"(294)
+
+//____________________________________________________________________________
+// indexCountsDir
+
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_CountsDir>::Type & indexCountsDir(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_qgram.h"(300)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_CountsDir>::Type & indexCountsDir(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_qgram.h"(305)
+
+//____________________________________________________________________________
+// indexCreate
+
+template <typename TText, typename TPredHull, typename TPred> inline bool indexCreate(Index<TText, Index_Wotd<WotdDFI<TPredHull, TPred> > > &index, Wotd_SA const, Default const); // "projects/library/seqan/index/index_dfi.h"(518)
+template <typename TText, typename TSpec> inline bool indexCreate(Index<TText, PizzaChili<TSpec> >& me, PizzaChili_Compressed const); // "projects/library/seqan/index/index_pizzachili.h"(278)
+template <typename TText, typename TSpec> inline bool indexCreate(Index<TText, Index_Wotd<TSpec> > &index, Wotd_SA const, Default const); // "projects/library/seqan/index/index_wotd.h"(1712)
+template <typename TText, typename TSpec, typename TSpecAlg> inline bool indexCreate(Index<TText, TSpec> &index, Fibre_SA, TSpecAlg const alg); // "projects/library/seqan/index/index_shims.h"(498)
+template <typename TText, typename TSpec, typename TSpecAlg> inline bool indexCreate(Index<TText, TSpec> &index, Fibre_LCP, TSpecAlg const alg); // "projects/library/seqan/index/index_shims.h"(506)
+template <typename TText, typename TSpec, typename TSpecAlg> inline bool indexCreate(Index<TText, TSpec> &index, Fibre_LCPE, TSpecAlg const alg); // "projects/library/seqan/index/index_shims.h"(514)
+template <typename TText, typename TSpec> inline bool indexCreate(Index<TText, TSpec> &index, Fibre_BWT, BWT const); // "projects/library/seqan/index/index_shims.h"(523)
+template <typename TText, typename TSpec> inline bool indexCreate(Index<TText, TSpec> &index, Fibre_ChildTab, ChildTab const); // "projects/library/seqan/index/index_shims.h"(531)
+template <typename TText, typename TSpec, typename TFibre> inline bool indexCreate(Index<TText, TSpec> &index, Tag<TFibre> const fibre); // "projects/library/seqan/index/index_shims.h"(539)
+template <typename TText, typename TShapeSpec, typename TSpec> inline bool indexCreate( Index<TText, Index_QGram<TShapeSpec, TSpec> > &index, Fibre_SADir, Default const); // "projects/library/seqan/index/index_qgram.h"(1459)
+template <typename TText, typename TShapeSpec, typename TSpec> inline bool indexCreate( Index<TText, Index_QGram<TShapeSpec, TSpec> > &index, Fibre_SA, Default const alg); // "projects/library/seqan/index/index_qgram.h"(1487)
+template <typename TText, typename TShapeSpec, typename TSpec> inline bool indexCreate( Index<TText, Index_QGram<TShapeSpec, TSpec> > &index, Fibre_Counts, Default const); // "projects/library/seqan/index/index_qgram.h"(1509)
+
+//____________________________________________________________________________
+// indexDir
+
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_Dir>::Type & indexDir(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_qgram.h"(243)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_Dir>::Type & indexDir(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_qgram.h"(248)
+
+//____________________________________________________________________________
+// indexLCP
+
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_LCP>::Type & indexLCP(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(900)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_LCP>::Type & indexLCP(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(902)
+
+//____________________________________________________________________________
+// indexLCPE
+
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_LCPE>::Type & indexLCPE(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(916)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_LCPE>::Type & indexLCPE(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(918)
+
+//____________________________________________________________________________
+// indexRawSA
+
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_RawSA>::Type indexRawSA(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(884)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_RawSA>::Type indexRawSA(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(886)
+
+//____________________________________________________________________________
+// indexRawText
+
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_RawText>::Type & indexRawText(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(852)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_RawText>::Type & indexRawText(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(854)
+
+//____________________________________________________________________________
+// indexRequire
+
+template <typename TText, typename TSpec, typename TFibre> inline bool indexRequire(Index<TText, TSpec> &index, Tag<TFibre> const fibre); // "projects/library/seqan/index/index_shims.h"(581)
+
+//____________________________________________________________________________
+// indexSA
+
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_SA>::Type & indexSA(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(868)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_SA>::Type & indexSA(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(870)
+
+//____________________________________________________________________________
+// indexShape
+
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_Shape>::Type & indexShape(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_qgram.h"(311)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_Shape>::Type & indexShape(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_qgram.h"(316)
+
+//____________________________________________________________________________
+// indexSolveDependencies
+
+template <typename TText, typename TSpec> inline bool indexSolveDependencies(Index<TText, PizzaChili<TSpec> >& me, PizzaChili_Compressed const); // "projects/library/seqan/index/index_pizzachili.h"(242)
+template <typename TText, typename TSpec, typename TFibre> inline bool indexSolveDependencies(Index<TText, TSpec> &, Tag<TFibre> const); // "projects/library/seqan/index/index_shims.h"(612)
+template <typename TText, typename TSpec> inline bool indexSolveDependencies(Index<TText, TSpec> &index, Fibre_LCP); // "projects/library/seqan/index/index_shims.h"(618)
+template <typename TText, typename TSpec> inline bool indexSolveDependencies(Index<TText, TSpec> &index, Fibre_LCPE); // "projects/library/seqan/index/index_shims.h"(624)
+template <typename TText, typename TSpec> inline bool indexSolveDependencies(Index<TText, TSpec> &index, Fibre_ChildTab); // "projects/library/seqan/index/index_shims.h"(630)
+template <typename TText, typename TSpec> inline bool indexSolveDependencies(Index<TText, TSpec> &index, Fibre_BWT); // "projects/library/seqan/index/index_shims.h"(636)
+
+//____________________________________________________________________________
+// indexSupplied
+
+template <typename TText, typename TSpec> inline bool indexSupplied(Index<TText, PizzaChili<TSpec> >& me, PizzaChili_Compressed const); // "projects/library/seqan/index/index_pizzachili.h"(226)
+template <typename TText, typename TSpec> inline bool indexSupplied(Index<TText, PizzaChili<TSpec> >& me, PizzaChili_Text const); // "projects/library/seqan/index/index_pizzachili.h"(233)
+template <typename TText, typename TSpec, typename TFibre> inline bool indexSupplied(Index<TText, TSpec> &index, Tag<TFibre> const fibre); // "projects/library/seqan/index/index_shims.h"(560)
+template <typename TText, typename TSpec> inline bool indexSupplied(Index<TText, TSpec> &index, Fibre_SADir); // "projects/library/seqan/index/index_qgram.h"(1478)
+
+//____________________________________________________________________________
+// indexText
+
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, PizzaChili<TSpec> >, PizzaChili_Text>::Type indexText(Index<TText, PizzaChili<TSpec> >& me); // "projects/library/seqan/index/index_pizzachili.h"(194)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, PizzaChili<TSpec> > const, PizzaChili_Text>::Type indexText(Index<TText, PizzaChili<TSpec> > const& me); // "projects/library/seqan/index/index_pizzachili.h"(201)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec>, Fibre_Text>::Type & indexText(Index<TText, TSpec> &index); // "projects/library/seqan/index/index_base.h"(810)
+template <typename TText, typename TSpec> inline typename Fibre<Index<TText, TSpec> const, Fibre_Text>::Type & indexText(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(812)
+
+//____________________________________________________________________________
+// infix
+
+template <typename TValue, typename TSpec, typename TPosBegin, typename TPosEnd> inline typename Infix<String<TValue, PizzaChili<TSpec> > >::Type infix( String<TValue, PizzaChili<TSpec> > const& me, TPosBegin begin, TPosEnd end ); // "projects/library/seqan/index/index_pizzachili_string.h"(724)
+template <typename TValue, typename TSpec, typename TPosBegin, typename TPosEnd> inline typename Infix<String<TValue, PizzaChili<TSpec> > >::Type infix( String<TValue, PizzaChili<TSpec> >& me, TPosBegin begin, TPosEnd end ); // "projects/library/seqan/index/index_pizzachili_string.h"(735)
+
+//____________________________________________________________________________
+// isLeaf
+
+template <typename TIndex, class TSpec > inline bool isLeaf(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1795)
+
+//____________________________________________________________________________
+// isLeftMaximal
+
+template <typename TIndex, class TSpec > inline bool isLeftMaximal(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1541)
+
+//____________________________________________________________________________
+// isPartiallyLeftExtensible
+
+template <typename TIndex, class TSpec, typename TSet > inline bool isPartiallyLeftExtensible(Iter<TIndex, VSTree<TSpec> > const &it, TSet &charSet); // "projects/library/seqan/index/index_esa_stree.h"(1589)
+template <typename TIndex, class TSpec > inline bool isPartiallyLeftExtensible(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1623)
+
+//____________________________________________________________________________
+// isRightTerminal
+
+template <typename TIndex, class TSpec > inline bool isRightTerminal(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1518)
+
+//____________________________________________________________________________
+// isRoot
+
+template <typename TIndex, class TSpec > inline bool isRoot(Iter<TIndex, VSTree< BottomUp<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1489)
+template <typename TIndex, class TSpec > inline bool isRoot(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1495)
+
+//____________________________________________________________________________
+// isUnique
+
+template <typename TIndex, class TSpec, typename TSet > inline bool isUnique(Iter<TIndex, VSTree<TSpec> > const &it, TSet &set); // "projects/library/seqan/index/index_esa_stree.h"(1641)
+template <typename TIndex, class TSpec > inline bool isUnique(Iter<TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1664)
+
+//____________________________________________________________________________
+// lca
+
+template <typename TIndex, class TSpec1, class TSpec2 > inline bool lca( Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec1> > > > &a, Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec2> > > > &b, Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec1> > > > &_lca); // "projects/library/seqan/index/index_esa_stree.h"(456)
+
+//____________________________________________________________________________
+// lcp
+
+template <typename TIndex, class TSpec1, class TSpec2 > inline typename Size<TIndex>::Type lcp( Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec1> > > > &a, Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec2> > > > &b); // "projects/library/seqan/index/index_esa_stree.h"(507)
+
+//____________________________________________________________________________
+// lcpAt
+
+template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex, Fibre_LCP>::Type>::Type lcpAt(TPos i, TIndex &index); // "projects/library/seqan/index/index_base.h"(714)
+template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex const, Fibre_LCP>::Type>::Type lcpAt(TPos i, TIndex const &index); // "projects/library/seqan/index/index_base.h"(718)
+
+//____________________________________________________________________________
+// lcp_process
+
+template <typename TTextInput, typename TInvertedSAInput, typename TDest > static void lcp_process(TTextInput &textIn, TInvertedSAInput &invertedSAIn, TDest &dest, LcpConfig conf); // "projects/library/seqan/index/pump_lcp_core.h"(56)
+template <typename TTextInput, typename TInvertedSAInput, typename TDest > static inline void lcp_process(TTextInput &textIn, TInvertedSAInput &invertedSAIn, TDest &dest); // "projects/library/seqan/index/pump_lcp_core.h"(196)
+
+//____________________________________________________________________________
+// lcp_process_multi
+
+template <typename TTextInput, typename TLimitsString, typename TInvertedSAInput, typename TDest > static void lcp_process_multi( TTextInput &textIn, TLimitsString const &limits, TInvertedSAInput &invertedSAIn, TDest &dest, LcpConfig conf); // "projects/library/seqan/index/pump_lcp_core.h"(208)
+template <typename TTextInput, typename TLimitsString, typename TInvertedSAInput, typename TDest > static void lcp_process_multi( TTextInput &textIn, TLimitsString const &limits, TInvertedSAInput &invertedSAIn, TDest &dest); // "projects/library/seqan/index/pump_lcp_core.h"(367)
+
+//____________________________________________________________________________
+// lcpeAt
+
+template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex, Fibre_LCPE>::Type>::Type lcpeAt(TPos i, TIndex &index); // "projects/library/seqan/index/index_base.h"(735)
+template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex const, Fibre_LCPE>::Type>::Type lcpeAt(TPos i, TIndex const &index); // "projects/library/seqan/index/index_base.h"(739)
+
+//____________________________________________________________________________
+// length
+
+//template <typename TInput > inline typename Size< Pipe< TInput, LarssonSadakane > >::Type length(Pipe< TInput, LarssonSadakane > const &me); // "projects/library/seqan/index/index_sa_lss.h"(421)
+template <typename TValue, typename TSpec> inline typename Size<String<TValue, PizzaChili<TSpec> > >::Type length(String<TValue, PizzaChili<TSpec> > const& me); // "projects/library/seqan/index/index_pizzachili_string.h"(379)
+template <typename TValue, typename TSpec> inline typename Size< Shape<TValue, TSpec> >::Type length(Shape<TValue, TSpec> const &me); // "projects/library/seqan/index/shape_base.h"(215)
+template <typename TText, typename TSpec> inline typename Size<Index<TText, TSpec> >::Type length(Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(601)
+template <typename TSTree, typename TSpec > inline typename Size<TSTree>::Type length(Iter< TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > const &it); // "projects/library/seqan/index/index_esa_algs.h"(570)
+template <typename TSTree> inline typename Size< MaxRepeat<TSTree> >::Type length(MaxRepeat<TSTree> const &repeat); // "projects/library/seqan/index/index_esa_algs.h"(619)
+template <typename TSTree> inline typename Size< MultiMEM<TSTree> >::Type length(MultiMEM<TSTree> const &repeat); // "projects/library/seqan/index/index_esa_algs_multi.h"(402)
+//template <typename TInput > inline typename Size< Pipe< TInput, Merger3 > >::Type length(Pipe< TInput, Merger3 > const &me); // "projects/library/seqan/index/pipe_merger3.h"(145)
+//template <typename TInput > inline typename Size< Pipe< TInput, Merger7 > >::Type length(Pipe< TInput, Merger7 > const &me); // "projects/library/seqan/index/pipe_merger7.h"(494)
+//template <typename TInput, typename TLimitsString > inline typename Size< Pipe< TInput, Merger7Multi<TLimitsString> > >::Type length(Pipe< TInput, Merger7Multi<TLimitsString> > const &me); // "projects/library/seqan/index/pipe_merger7.h"(524)
+
+//____________________________________________________________________________
+// lowerBoundLCPE
+
+template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline typename Position<TLCPE>::Type lowerBoundLCPE( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(1554)
+template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline typename Position<TLCPE>::Type lowerBoundLCPE( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(1656)
+
+//____________________________________________________________________________
+// lowerBoundLCPEIterator
+
+template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline typename Iterator<TSA, Standard>::Type lowerBoundLCPEIterator( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(1605)
+
+//____________________________________________________________________________
+// lowerBoundSA
+
+template <typename TText, typename TSA, typename TQuery, typename TFlatTreeSpec > inline typename Position<TSA>::Type lowerBoundSA( TText const &text, TSA const &sa, TQuery const &query, TFlatTreeSpec const); // "projects/library/seqan/index/index_esa_find.h"(793)
+template <typename TText, typename TSA, typename TQuery > inline typename Position<TSA>::Type lowerBoundSA( TText const &text, TSA const &sa, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(807)
+template <typename TText, typename TSA, typename TQuery, typename TFlatTreeSpec > inline typename Position<TSA>::Type lowerBoundSA( TText const &text, TSA const &sa, TQuery *query, TFlatTreeSpec const); // "projects/library/seqan/index/index_esa_find.h"(890)
+template <typename TText, typename TSA, typename TQuery > inline typename Position<TSA>::Type lowerBoundSA( TText const &text, TSA const &sa, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(904)
+
+//____________________________________________________________________________
+// lowerBoundSAIterator
+
+template <typename TText, typename TSA, typename TQuery > inline typename Iterator<TSA const, Standard>::Type lowerBoundSAIterator( TText const &text, TSA const &sa, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(699)
+template <typename TText, typename TSA, typename TQuery > inline typename Iterator<TSA const, Standard>::Type lowerBoundSAIterator( TText const &text, TSA const &sa, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(745)
+
+//____________________________________________________________________________
+// nodeDepth
+
+template <typename TIndex, typename TSpec > inline typename Size<TIndex>::Type nodeDepth(Iter< TIndex, VSTree<TopDown<ParentLinks<TSpec> > > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(390)
+
+//____________________________________________________________________________
+// nodeHullPredicate
+
+template <typename TText, typename TPredHull, typename TPred, typename TSpec > inline bool nodeHullPredicate( Iter<Index<TText, Index_Wotd< WotdDFI<TPredHull, TPred> > >, TSpec> const &it); // "projects/library/seqan/index/index_dfi.h"(158)
+template <typename TIndex, class TSpec > inline bool nodeHullPredicate(Iter<TIndex, TSpec> &); // "projects/library/seqan/index/index_esa_stree.h"(857)
+template <typename TText, typename TSpec> bool nodeHullPredicate(Iter<Index<TText, Index_Wotd<TRepeatFinder> >, TSpec> &it); // "projects/library/seqan/index/repeat_base.h"(75)
+
+//____________________________________________________________________________
+// nodePredicate
+
+template <typename TText, typename TPredHull, typename TPred, typename TSpec > inline bool nodePredicate( Iter<Index<TText, Index_Wotd< WotdDFI<TPredHull, TPred> > >, TSpec> const &it); // "projects/library/seqan/index/index_dfi.h"(145)
+template <typename TIndex, class TSpec > inline bool nodePredicate(Iter<TIndex, TSpec> &); // "projects/library/seqan/index/index_esa_stree.h"(839)
+template <typename TText, typename TSpec> bool nodePredicate(Iter<Index<TText, Index_Wotd<TRepeatFinder> >, TSpec> &it); // "projects/library/seqan/index/repeat_base.h"(67)
+
+//____________________________________________________________________________
+// nodeUp
+
+template <typename TIndex, class TSpec > inline typename VertexDescriptor<TIndex>::Type nodeUp(Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1256)
+template <typename TIndex, class TSpec > inline typename VertexDescriptor<TIndex>::Type const & nodeUp(Iter< TIndex, VSTree< TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1271)
+
+//____________________________________________________________________________
+// open
+
+template <typename TObject, typename TSpec > inline bool open( Index< TObject, Index_ESA<TSpec> > &index, const char *fileName, int openMode); // "projects/library/seqan/index/index_esa_base.h"(324)
+template <typename TObject, typename TSpec > inline bool open( Index< TObject, Index_ESA<TSpec> > &index, const char *fileName); // "projects/library/seqan/index/index_esa_base.h"(340)
+template <typename TText, typename TSpec> inline bool open( Index<TText, PizzaChili<TSpec> >& me, char const* filename ); // "projects/library/seqan/index/index_pizzachili.h"(334)
+template <typename TValue, typename TSpec > inline bool open(String<TValue, TSpec> &string, const char *fileName, int openMode); // "projects/library/seqan/index/index_shims.h"(646)
+template <typename TValue, typename TSpec > inline bool open(String<TValue, TSpec> &string, const char *fileName); // "projects/library/seqan/index/index_shims.h"(654)
+template <typename THost, typename TSpec > inline bool open(Segment<THost, TSpec> &string, const char *fileName, int openMode); // "projects/library/seqan/index/index_shims.h"(660)
+template <typename THost, typename TSpec > inline bool open(Segment<THost, TSpec> &string, const char *fileName); // "projects/library/seqan/index/index_shims.h"(668)
+template <typename TValue, typename TSpec, typename TSSSpec > inline bool open(StringSet<String<TValue, TSpec>, TSSSpec> &multi, const char *fileName, int openMode); // "projects/library/seqan/index/index_shims.h"(674)
+template <typename TValue, typename TSpec, typename TSSSpec> inline bool open(StringSet<String<TValue, TSpec>, TSSSpec> &multi, const char *fileName); // "projects/library/seqan/index/index_shims.h"(694)
+template <typename TObject, typename TShapeSpec, typename TSpec > inline bool open( Index< TObject, Index_QGram<TShapeSpec, TSpec> > &index, const char *fileName, int openMode); // "projects/library/seqan/index/index_qgram.h"(1755)
+template <typename TObject, typename TShapeSpec, typename TSpec > inline bool open( Index< TObject, Index_QGram<TShapeSpec, TSpec> > &index, const char *fileName); // "projects/library/seqan/index/index_qgram.h"(1769)
+
+//____________________________________________________________________________
+// operator!=
+
+template <typename TRepeat > inline bool operator!= ( Iter<TRepeat, MaxRepeatOccurrences> const &itA, Iter<TRepeat, MaxRepeatOccurrences> const &itB); // "projects/library/seqan/index/index_esa_algs.h"(851)
+
+//____________________________________________________________________________
+// operator<<
+
+//template <typename TInput, typename TObject, typename TPair, typename TLimitsString > inline bool operator<<(Pipe< TInput, Multi<Skew7, TPair, TLimitsString> > &me, TObject &textIn); // "projects/library/seqan/index/index_skew7_multi.h"(404)
+//template <typename TInput, typename _TLCPInput > inline bool operator<<(Pipe< TInput, ChildTab > &me, _TLCPInput const &in); // "projects/library/seqan/index/index_childtab.h"(162)
+//template <typename TInput, typename _TTextInput, typename _TSuffixArrayInput > inline bool operator<<(Pipe< TInput, Kasai > &me, Bundle2< _TTextInput, _TSuffixArrayInput > const &bundleIn); // "projects/library/seqan/index/index_lcp.h"(131)
+//template <typename TInput, typename _TTextInput, typename _TSuffixArrayInput, typename TPair, typename TLimitsString > inline bool operator<<(Pipe< TInput, Multi<Kasai, TPair, TLimitsString> > &me, Bundle2< _TTextInput, _TSuffixArrayInput > const &bundleIn); // "projects/library/seqan/index/index_lcp.h"(234)
+//template <typename TInput, typename TObject > inline bool operator<<(Pipe< TInput, Skew3 > &me, TObject &textIn); // "projects/library/seqan/index/index_skew3.h"(285)
+//template <typename TInput, typename _TTextInput, typename _TSuffixArrayInput > inline bool operator<<(Pipe< TInput, BWT > &me, Bundle2< _TTextInput, _TSuffixArrayInput > const &bundleIn); // "projects/library/seqan/index/index_bwt.h"(113)
+//template <typename TInput, typename _TTextInput, typename _TSuffixArrayInput, typename TPair, typename TLimitsString > inline bool operator<<(Pipe< TInput, Multi<BWT, TPair, TLimitsString> > &me, Bundle2< _TTextInput, _TSuffixArrayInput > const &bundleIn); // "projects/library/seqan/index/index_bwt.h"(229)
+//template <typename TValue> std::ostream& operator<<(std::ostream &out, const SkewDCStream<TValue> &s); // "projects/library/seqan/index/pipe_merger7.h"(77)
+//template <typename TInput, typename TObject > inline bool operator<<(Pipe< TInput, Skew7 > &me, TObject &textIn); // "projects/library/seqan/index/index_skew7.h"(385)
+
+//____________________________________________________________________________
+// operator==
+
+template <typename TRepeat > inline bool operator== ( Iter<TRepeat, MaxRepeatOccurrences> const &itA, Iter<TRepeat, MaxRepeatOccurrences> const &itB); // "projects/library/seqan/index/index_esa_algs.h"(840)
+
+//____________________________________________________________________________
+// orderOccurrences
+
+template <typename TValue, typename TSpec> inline void orderOccurrences(String<TValue, TSpec> &occString); // "projects/library/seqan/index/index_shims.h"(474)
+
+//____________________________________________________________________________
+// parentEdgeFirstChar
+
+template <typename TIndex, class TSpec > inline typename Value<TIndex>::Type parentEdgeFirstChar(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1377)
+
+//____________________________________________________________________________
+// parentEdgeLabel
+
+template <typename TText, typename TSpec > inline typename Infix< typename Fibre<Index<TText, Index_Wotd<WotdOriginal> >, ESA_RawText>::Type const >::Type parentEdgeLabel(Iter< Index<TText, Index_Wotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_wotd.h"(401)
+template <typename TIndex, class TSpec > inline typename Infix< typename Fibre<TIndex, Fibre_Text>::Type const >::Type parentEdgeLabel(Iter< TIndex, VSTree< TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1357)
+
+//____________________________________________________________________________
+// parentEdgeLength
+
+template <typename TIndex, typename TSize > inline typename Size<TIndex>::Type parentEdgeLength(TIndex const &index, _VertexWotdOriginal<TSize> &vDesc); // "projects/library/seqan/index/index_wotd.h"(309)
+template <typename TIndex, typename TSize > inline typename Size<TIndex>::Type parentEdgeLength(TIndex const &index, _VertexWotdModified<TSize> &vDesc); // "projects/library/seqan/index/index_wotd.h"(332)
+template <typename TText, typename TIndexSpec, typename TSpec > inline typename Size< Index<TText, Index_Wotd<TIndexSpec> > >::Type parentEdgeLength(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_wotd.h"(364)
+template <typename TText, class TIndexSpec, class TSpec > inline typename Size< Index<TText, Index_ESA<TIndexSpec> > >::Type parentEdgeLength(Iter< Index<TText, Index_ESA<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(1339)
+
+//____________________________________________________________________________
+// parentRepLength
+
+template <typename TText, typename TIndexSpec, typename TSpec > inline typename Size< Index<TText, Index_Wotd<TIndexSpec> > >::Type parentRepLength(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_wotd.h"(374)
+template <typename TText, typename TIndexSpec, typename TSpec > inline typename Size< Index<TText, Index_Wotd<TIndexSpec> > >::Type parentRepLength(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > const &it); // "projects/library/seqan/index/index_wotd.h"(383)
+template <typename TIndex, typename TSpec > inline typename Size<TIndex>::Type parentRepLength(Iter< TIndex, VSTree<TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(408)
+
+//____________________________________________________________________________
+// position
+
+template <typename TText, typename TSpec, typename TSpecFinder > inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type position(Finder< Index<TText, TSpec>, TSpecFinder > & me); // "projects/library/seqan/index/index_find.h"(226)
+template <typename TText, typename TSpec, typename TSpecFinder > inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type position(Finder< Index<TText, TSpec>, TSpecFinder > const & me); // "projects/library/seqan/index/index_find.h"(235)
+
+//____________________________________________________________________________
+// prefix
+
+template <typename TValue, typename TSpec, typename TPos> inline typename Prefix<String<TValue, PizzaChili<TSpec> > >::Type prefix( String<TValue, PizzaChili<TSpec> > const& me, TPos end ); // "projects/library/seqan/index/index_pizzachili_string.h"(747)
+template <typename TValue, typename TSpec, typename TPos> inline typename Prefix<String<TValue, PizzaChili<TSpec> > >::Type prefix( String<TValue, PizzaChili<TSpec> >& me, TPos end ); // "projects/library/seqan/index/index_pizzachili_string.h"(757)
+
+//____________________________________________________________________________
+// radixExtend
+
+template <typename TSortedArray, typename TUnsortedArray, typename TCountArray, typename TText > void radixExtend( TSortedArray &b, TUnsortedArray const &a, TText const &r, TCountArray &c, unsigned K); // "projects/library/seqan/index/radix.h"(118)
+
+//____________________________________________________________________________
+// radixExtendClip
+
+template <typename TSortedArray, typename TUnsortedArray, typename TCountArray, typename TText > void radixExtendClip( TSortedArray &b, TUnsortedArray const &a, TText const &r, TCountArray &c, unsigned K); // "projects/library/seqan/index/radix.h"(153)
+
+//____________________________________________________________________________
+// radixPass
+
+template <typename TSortedArray, typename TUnsortedArray, typename TCountArray, typename TText > void radixPass( TSortedArray &b, TUnsortedArray const &a, TText const &r, TCountArray &c, unsigned K); // "projects/library/seqan/index/radix.h"(39)
+template <typename TSortedArray, typename TUnsortedArray, typename TCountArray, typename TText, typename TShift > void radixPass( TSortedArray &b, TUnsortedArray const &a, TText const &r, TCountArray &c, unsigned K, TShift shift); // "projects/library/seqan/index/radix.h"(75)
+
+//____________________________________________________________________________
+// rawsaAt
+
+template <typename TPos, typename TIndex> inline typename Value<typename Fibre<TIndex const, Fibre_RawSA>::Type>::Type rawsaAt(TPos i, TIndex const &index); // "projects/library/seqan/index/index_base.h"(696)
+
+//____________________________________________________________________________
+// rawtextAt
+
+template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex, Fibre_RawText>::Type>::Type rawtextAt(TPos i, TIndex &index); // "projects/library/seqan/index/index_base.h"(666)
+template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex const, Fibre_RawText>::Type>::Type rawtextAt(TPos i, TIndex const &index); // "projects/library/seqan/index/index_base.h"(670)
+
+//____________________________________________________________________________
+// repLength
+
+template <typename TText, typename TIndexSpec, typename TSpec > inline typename Size< Index<TText, Index_Wotd<TIndexSpec> > >::Type repLength(Iter< Index<TText, Index_Wotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_wotd.h"(392)
+template <typename TIndex, typename TSpec > inline typename Size<TIndex>::Type repLength(Iter< TIndex, VSTree<BottomUp<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(355)
+template <typename TIndex, typename TSize > inline typename Size<TIndex>::Type repLength(TIndex const &index, VertexESA<TSize> const &vDesc); // "projects/library/seqan/index/index_esa_stree.h"(367)
+template <typename TIndex, typename TSpec > inline typename Size<TIndex>::Type repLength(Iter< TIndex, VSTree<TopDown<TSpec> > > const &it); // "projects/library/seqan/index/index_esa_stree.h"(383)
+template <typename TSTree, typename TSpec > inline typename Size<TSTree>::Type repLength(Iter< TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > const &it); // "projects/library/seqan/index/index_esa_algs.h"(562)
+
+//____________________________________________________________________________
+// representative
+
+template <typename TIndex, class TSpec > inline typename Infix< typename Fibre<TIndex, Fibre_Text>::Type const >::Type representative(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(744)
+
+//____________________________________________________________________________
+// resize
+
+template <typename TValue, typename TSize> inline typename Size< Shape<TValue, SimpleShape> >::Type resize(Shape<TValue, SimpleShape> & me, TSize new_length); // "projects/library/seqan/index/shape_base.h"(246)
+
+//____________________________________________________________________________
+// saAt
+
+template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex, Fibre_SA>::Type>::Type saAt(TPos i, TIndex &index); // "projects/library/seqan/index/index_base.h"(687)
+template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex const, Fibre_SA>::Type>::Type saAt(TPos i, TIndex const &index); // "projects/library/seqan/index/index_base.h"(691)
+
+//____________________________________________________________________________
+// save
+
+template <typename TObject, typename TSpec > inline bool save( Index< TObject, Index_ESA<TSpec> > &index, const char *fileName, int openMode); // "projects/library/seqan/index/index_esa_base.h"(353)
+template <typename TObject, typename TSpec > inline bool save( Index< TObject, Index_ESA<TSpec> > &index, const char *fileName); // "projects/library/seqan/index/index_esa_base.h"(369)
+template <typename TText, typename TSpec> inline bool save( Index<TText, PizzaChili<TSpec> >& me, char const* filename ); // "projects/library/seqan/index/index_pizzachili.h"(352)
+template <typename TValue, typename TSpec > inline bool save(String<TValue, TSpec> const &string, const char *fileName, int openMode); // "projects/library/seqan/index/index_shims.h"(704)
+template <typename TValue, typename TSpec > inline bool save(String<TValue, TSpec> &string, const char *fileName); // "projects/library/seqan/index/index_shims.h"(714)
+template <typename THost, typename TSpec > inline bool save(Segment<THost, TSpec> const &string, const char *fileName, int openMode); // "projects/library/seqan/index/index_shims.h"(720)
+template <typename THost, typename TSpec > inline bool save(Segment<THost, TSpec> const &string, const char *fileName); // "projects/library/seqan/index/index_shims.h"(729)
+template <typename TValue, typename TSpec, typename TSSSpec> inline bool save(StringSet<String<TValue, TSpec>, TSSSpec> const &multi, const char *fileName, int openMode); // "projects/library/seqan/index/index_shims.h"(735)
+template <typename TValue, typename TSpec, typename TSSSpec> inline bool save(StringSet<String<TValue, TSpec>, TSSSpec> const &multi, const char *fileName); // "projects/library/seqan/index/index_shims.h"(750)
+template <typename TObject, typename TShapeSpec, typename TSpec > inline bool save( Index< TObject, Index_QGram<TShapeSpec, TSpec> > &index, const char *fileName, int openMode); // "projects/library/seqan/index/index_qgram.h"(1782)
+template <typename TObject, typename TShapeSpec, typename TSpec > inline bool save( Index< TObject, Index_QGram<TShapeSpec, TSpec> > &index, const char *fileName); // "projects/library/seqan/index/index_qgram.h"(1796)
+
+//____________________________________________________________________________
+// sequenceLength
+
+template <typename TSeqNo, typename TText, typename TSpec> inline typename Size<Index<TText, TSpec> >::Type sequenceLength(TSeqNo seqNo, Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(617)
+
+//____________________________________________________________________________
+// setContainer
+
+template <typename TText, typename TSpec, typename TSpecFinder > inline void setContainer( Finder< Index<TText, TSpec>, TSpecFinder > & me, typename _Parameter<Index<TText, TSpec> >::Type container_); // "projects/library/seqan/index/index_find.h"(130)
+
+//____________________________________________________________________________
+// setHost
+
+template <typename TText, typename TSpec, typename TSpecFinder > inline void setHost( Finder< Index<TText, TSpec>, TSpecFinder > & me, typename _Parameter<Index<TText, TSpec> >::Type container_); // "projects/library/seqan/index/index_find.h"(120)
+
+//____________________________________________________________________________
+// setIndexText
+
+template <typename TText, typename TSpec, typename TOtherText> inline void setIndexText(Index<TText, PizzaChili<TSpec> >& me, TOtherText& text); // "projects/library/seqan/index/index_pizzachili.h"(303)
+
+//____________________________________________________________________________
+// sizeofLCPE
+
+template <typename TSize > inline TSize sizeofLCPE(TSize n); // "projects/library/seqan/index/index_lcp_tree.h"(105)
+template <class LCPFwdIt, typename TSize > inline void sizeofLCPE(LCPFwdIt _First, LCPFwdIt _Last, TSize &_Size); // "projects/library/seqan/index/index_lcp_tree.h"(124)
+
+//____________________________________________________________________________
+// sizeofLCPH
+
+template <typename TSize > inline TSize sizeofLCPH(TSize n); // "projects/library/seqan/index/index_lcp_tree.h"(116)
+template <class LCPFwdIt, typename TSize > inline void sizeofLCPH(LCPFwdIt _First, LCPFwdIt _Last, TSize &_Size); // "projects/library/seqan/index/index_lcp_tree.h"(132)
+
+//____________________________________________________________________________
+// sizeofSAB
+
+template <typename TSize > inline TSize sizeofSAB(TSize n, unsigned BlockSize); // "projects/library/seqan/index/index_sa_btree.h"(79)
+template <class SAFwdIt, typename TSize > inline void sizeofSAB(SAFwdIt _First, SAFwdIt _Last, TSize &_Size, unsigned BlockSize); // "projects/library/seqan/index/index_sa_btree.h"(90)
+
+//____________________________________________________________________________
+// skew3_extend
+
+template <typename TTextInput, typename TNameInput, typename TOut0, typename TOut12 > static bool skew3_extend(TTextInput &textIn, TNameInput &nameIn, TOut0 &out0, TOut12 &out12); // "projects/library/seqan/index/pump_extender3.h"(54)
+
+//____________________________________________________________________________
+// skew7_extend
+
+template <typename TTextInput, typename TNameInput, typename TOut0, typename TOut3, typename TOut5, typename TOut6, typename TOut124 > static bool skew7_extend(TTextInput &textIn, TNameInput &nameIn, TOut0 &out0, TOut3 &out3, TOut5 &out5, TOut6 &out6, TOut124 &out124); // "projects/library/seqan/index/pump_extender7.h"(75)
+
+//____________________________________________________________________________
+// skew7_extend_multi
+
+template <typename TTextInput, typename TLimitsString, typename TNameInput, typename TOut0, typename TOut3, typename TOut5, typename TOut6, typename TOut124 > static bool skew7_extend_multi( TTextInput &textIn, TLimitsString const &limits, TNameInput &nameIn1, TNameInput &nameIn2, TNameInput &nameIn4, TOut0 &out0, TOut3 &out3, TOut5 &out5, TOut6 &out6, TOut124 &out124); // "projects/library/seqan/index/pump_extender7.h"(265)
+
+//____________________________________________________________________________
+// skew7_separate_slices
+
+template <typename TInput, typename TFunctor, typename TOut1, typename TOut2, typename TOut4 > static void skew7_separate_slices( TInput &in, TFunctor const &funcSlice, TOut1 &out1, TOut2 &out2, TOut4 &out4); // "projects/library/seqan/index/pump_separator7.h"(35)
+
+//____________________________________________________________________________
+// stringSetLimits
+
+template <typename TText, typename TSpec> inline typename StringSetLimits<TText const>::Type stringSetLimits(Index<TText, TSpec> &); // "projects/library/seqan/index/index_base.h"(818)
+template <typename TText, typename TSpec> inline typename StringSetLimits<TText const>::Type stringSetLimits(Index<TText, TSpec> const &); // "projects/library/seqan/index/index_base.h"(824)
+template <typename TString, typename TSSetSpec, typename TSpec> inline typename StringSetLimits< StringSet<TString, TSSetSpec> const >::Type & stringSetLimits(Index<StringSet<TString, TSSetSpec>, TSpec> &index); // "projects/library/seqan/index/index_base.h"(830)
+template <typename TString, typename TSSetSpec, typename TSpec> inline typename StringSetLimits< StringSet<TString, TSSetSpec> const >::Type & stringSetLimits(Index<StringSet<TString, TSSetSpec>, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(836)
+
+//____________________________________________________________________________
+// stringToShape
+
+template <typename TValue, typename TSpec, typename TShapeString> inline void stringToShape( Shape<TValue, FixedGappedShape<TSpec> > &me, TShapeString const &bitmap); // "projects/library/seqan/index/shape_gapped.h"(561)
+
+//____________________________________________________________________________
+// suffix
+
+template <typename TValue, typename TSpec, typename TPos> inline typename Suffix<String<TValue, PizzaChili<TSpec> > >::Type suffix( String<TValue, PizzaChili<TSpec> > const& me, TPos begin ); // "projects/library/seqan/index/index_pizzachili_string.h"(769)
+template <typename TValue, typename TSpec, typename TPos> inline typename Suffix<String<TValue, PizzaChili<TSpec> > >::Type suffix( String<TValue, PizzaChili<TSpec> >& me, TPos begin ); // "projects/library/seqan/index/index_pizzachili_string.h"(779)
+
+//____________________________________________________________________________
+// suffixLength
+
+template <typename TPos, typename TText, typename TSpec> inline typename Size<Index<TText, TSpec> >::Type suffixLength(TPos pos, Index<TText, TSpec> const &index); // "projects/library/seqan/index/index_base.h"(625)
+
+//____________________________________________________________________________
+// textAt
+
+template <typename TPos, typename TIndex> inline typename Reference<typename Fibre<TIndex, Fibre_RawText>::Type>::Type textAt(TPos i, TIndex &index); // "projects/library/seqan/index/index_base.h"(635)
+template <typename TPos, typename TString, typename TSSetSpec, typename TSpec> inline typename Reference<typename Fibre< Index< StringSet<TString, TSSetSpec>, TSpec>, Fibre_RawText>::Type>::Type textAt(TPos i, Index< StringSet<TString, TSSetSpec>, TSpec> &index); // "projects/library/seqan/index/index_base.h"(640)
+template <typename TPos, typename TString, typename TSpec> inline typename Reference<typename Fibre< Index< StringSet<TString, Owner<Default> >, TSpec>, Fibre_RawText>::Type>::Type textAt(TPos i, Index< StringSet<TString, Owner<Default> >, TSpec> &index); // "projects/library/seqan/index/index_base.h"(645)
+
+//____________________________________________________________________________
+// treeLevelsSAB
+
+template <typename TSize > inline unsigned treeLevelsSAB(TSize saSize, unsigned BlockSize); // "projects/library/seqan/index/index_sa_btree.h"(103)
+
+//____________________________________________________________________________
+// unhash
+
+template <typename TString, typename THash> inline void unhash(TString &result, THash hash, unsigned q); // "projects/library/seqan/index/shape_base.h"(593)
+
+//____________________________________________________________________________
+// upperBoundLCPE
+
+template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline typename Position<TLCPE>::Type upperBoundLCPE( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(1570)
+template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline typename Position<TLCPE>::Type upperBoundLCPE( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(1672)
+
+//____________________________________________________________________________
+// upperBoundLCPEIterator
+
+template <typename TText, typename TSA, typename TLCPE, typename TQuery > inline typename Iterator<TSA, Standard>::Type upperBoundLCPEIterator( TText const &text, TSA const &sa, TLCPE const &lcpe, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(1621)
+
+//____________________________________________________________________________
+// upperBoundSA
+
+template <typename TText, typename TSA, typename TQuery, typename TFlatTreeSpec > inline typename Position<TSA>::Type upperBoundSA( TText const &text, TSA const &sa, TQuery const &query, TFlatTreeSpec const); // "projects/library/seqan/index/index_esa_find.h"(823)
+template <typename TText, typename TSA, typename TQuery > inline typename Position<TSA>::Type upperBoundSA( TText const &text, TSA const &sa, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(837)
+template <typename TText, typename TSA, typename TQuery, typename TFlatTreeSpec > inline typename Position<TSA>::Type upperBoundSA( TText const &text, TSA const &sa, TQuery *query, TFlatTreeSpec const); // "projects/library/seqan/index/index_esa_find.h"(920)
+template <typename TText, typename TSA, typename TQuery > inline typename Position<TSA>::Type upperBoundSA( TText const &text, TSA const &sa, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(934)
+
+//____________________________________________________________________________
+// upperBoundSAIterator
+
+template <typename TText, typename TSA, typename TQuery > inline typename Iterator<TSA const, Standard>::Type upperBoundSAIterator( TText const &text, TSA const &sa, TQuery const &query); // "projects/library/seqan/index/index_esa_find.h"(713)
+template <typename TText, typename TSA, typename TQuery > inline typename Iterator<TSA const, Standard>::Type upperBoundSAIterator( TText const &text, TSA const &sa, TQuery *query); // "projects/library/seqan/index/index_esa_find.h"(759)
+
+//____________________________________________________________________________
+// value
+
+template <typename TValue, typename TSpec> inline typename Value< Shape<TValue, TSpec> >::Type value(Shape<TValue, TSpec> &me); // "projects/library/seqan/index/shape_base.h"(205)
+template <typename TIndex, class TSpec > inline typename VertexDescriptor<TIndex>::Type & value(Iter< TIndex, VSTree<TSpec> > &it); // "projects/library/seqan/index/index_esa_stree.h"(557)
+template <typename TIndex, class TSpec > inline typename VertexDescriptor<TIndex>::Type const & value(Iter< TIndex, VSTree<TSpec> > const &it); // "projects/library/seqan/index/index_esa_stree.h"(563)
+template <typename TSTree, typename TSpec > inline typename VertexDescriptor<TSTree>::Type value(Iter< TSTree, VSTree< BottomUp<_MaxRepeats<TSpec> > > > const &it); // "projects/library/seqan/index/index_esa_algs.h"(551)
+template <typename TRepeat > inline typename Value< Iter<TRepeat, MaxRepeatOccurrences> >::Type & value(Iter<TRepeat, MaxRepeatOccurrences> const &it); // "projects/library/seqan/index/index_esa_algs.h"(780)
+template <typename TRepeat > inline typename Value< Iter<TRepeat, MaxRepeatOccurrences> >::Type & value(Iter<TRepeat, MaxRepeatOccurrences> &it); // "projects/library/seqan/index/index_esa_algs.h"(786)
+
+//____________________________________________________________________________
+// weight
+
+template <typename TValue, typename TSpec> inline typename Size< Shape<TValue, FixedGappedShape<TSpec> > >::Type weight(Shape<TValue, FixedGappedShape<TSpec> > const & me); // "projects/library/seqan/index/shape_gapped.h"(358)
+template <typename TValue, typename TSpec> inline typename Size< Shape<TValue, TSpec> >::Type weight(Shape<TValue, TSpec> const &me); // "projects/library/seqan/index/shape_base.h"(235)
+
+//____________________________________________________________________________
+// write
+
+template <typename TFile, typename TText, typename TESASpec> void write(TFile & file, Index<TText, Index_ESA<TESASpec> > & stree, DotDrawing); // "projects/library/seqan/index/index_esa_drawing.h"(31)
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif
+
diff --git a/src/libSSA/seqan/index/index_manual_forwards.h b/src/libSSA/seqan/index/index_manual_forwards.h
new file mode 100644
index 0000000..1ef3d7f
--- /dev/null
+++ b/src/libSSA/seqan/index/index_manual_forwards.h
@@ -0,0 +1,55 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: index_manual_forwards.h,v 1.1 2008/08/25 16:20:05 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_INDEX_MANUAL_FORWARDS_H
+#define SEQAN_HEADER_INDEX_MANUAL_FORWARDS_H
+
+//SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
+
+//////////////////////////////////////////////////////////////////////////////
+// CLASSES
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+
+ struct _Fibre_Text; // Original text. Can be a String or a StringSet
+ struct _Fibre_RawText; // Concatenation of the strings above
+ struct _Fibre_SA; // suffix array (of raw text with virtual $-delimiters) with Pair entries
+ struct _Fibre_RawSA; // suffix array with integer entries
+ struct _Fibre_SAE; // suffix array reordered in a b-tree
+ struct _Fibre_LCP; // lcp table of raw text
+ struct _Fibre_LCPE; // lcp interval tree
+ struct _Fibre_ChildTab; // childtab (Kurtz et al.) of raw text
+ struct _Fibre_BWT; // burrows wheeler table of raw text
+
+ typedef Tag<_Fibre_Text> const Fibre_Text;
+ typedef Tag<_Fibre_RawText> const Fibre_RawText;
+ typedef Tag<_Fibre_SA> const Fibre_SA;
+ typedef Tag<_Fibre_RawSA> const Fibre_RawSA;
+ typedef Tag<_Fibre_SAE> const Fibre_SAE;
+ typedef Tag<_Fibre_LCP> const Fibre_LCP;
+ typedef Tag<_Fibre_LCPE> const Fibre_LCPE;
+ typedef Tag<_Fibre_ChildTab> const Fibre_ChildTab;
+ typedef Tag<_Fibre_BWT> const Fibre_BWT;
+
+}
+
+#endif
+
diff --git a/src/libSSA/seqan/index/index_qgram_find.h b/src/libSSA/seqan/index/index_qgram_find.h
new file mode 100644
index 0000000..7d33301
--- /dev/null
+++ b/src/libSSA/seqan/index/index_qgram_find.h
@@ -0,0 +1,82 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: index_qgram_find.h,v 1.1 2008/08/25 16:20:05 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_INDEX_QGRAM_FIND_H
+#define SEQAN_HEADER_INDEX_QGRAM_FIND_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// QGram finders
+
+ struct _Finder_QGramLookup; //Finder that simply looks up the q-gram in the hash table
+
+/**
+.Tag.Index Find Algorithm
+..tag.QGram_FIND_Lookup:q-gram search.
+Finds q-grams in a @Spec.Index_QGram@ index using the hash table.
+*/
+
+ typedef Tag<_Finder_QGramLookup> const QGram_FIND_Lookup;
+
+//____________________________________________________________________________
+
+
+ template < typename TText, typename TShapeSpec, typename TSpec >
+ struct DefaultFinder<Index<TText, Index_QGram<TShapeSpec, TSpec> > > {
+ typedef QGram_FIND_Lookup Type;
+ };
+
+
+//////////////////////////////////////////////////////////////////////////////
+// _findFirstIndex implementation
+
+ template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
+ inline void _findFirstIndex(
+ Finder< Index<TText, TSpec>, TSpecFinder > &finder,
+ TPattern const &pattern,
+ QGram_FIND_Lookup const)
+ {
+ typedef Index<TText, TSpec> TIndex;
+ typedef typename Fibre<TIndex, QGram_SA>::Type TSA;
+ typedef typename Fibre<TIndex, QGram_Shape>::Type TShape;
+ typedef typename Fibre<TIndex, QGram_Dir>::Type TDir;
+ typedef typename Iterator<TSA const, Standard>::Type TSAIterator;
+ typedef typename Iterator<TPattern const, Standard>::Type TPatternIterator;
+
+ TIndex &index = haystack(finder);
+ indexRequire(index, QGram_SADir());
+
+ TSAIterator saIt = begin(indexSA(index), Standard());
+ TPatternIterator pIt = begin(pattern, Standard());
+ TDir const &dir = indexDir(index);
+ TShape &shape = indexShape(index);
+
+ finder.range.i1 = saIt + dir[hash(shape, pIt, length(pattern))];
+ finder.range.i2 = saIt + dir[hashUpper(shape, pIt, length(pattern))];
+ }
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_
diff --git a/src/libSSA/seqan/index/index_sa_lss.h b/src/libSSA/seqan/index/index_sa_lss.h
new file mode 100644
index 0000000..df23b8c
--- /dev/null
+++ b/src/libSSA/seqan/index/index_sa_lss.h
@@ -0,0 +1,427 @@
+/*
+ * index_sa_lss.h
+ * SeqAn
+ *
+ * Created by David Weese on 18.04.07.
+ *
+ * This file contains the suffix array algorithm implementation
+ * by Larsson and Sadakane with the following modifications.
+ *
+ * MODIFICATIONS:
+ * - a context is used for reentrance
+ * - a generic TValue is used instead of int
+ * - functions are surrounded by SeqAn's namespace to omit namespace pollution
+ *
+ * David Weese, 2007
+ *
+ */
+
+/* qsufsort.c
+ Copyright 1999, N. Jesper Larsson, all rights reserved.
+
+ This file contains an implementation of the algorithm presented in "Faster
+ Suffix Sorting" by N. Jesper Larsson (jesper at cs.lth.se) and Kunihiko
+ Sadakane (sada at is.s.u-tokyo.ac.jp).
+
+ This software may be used freely for any purpose. However, when distributed,
+ the original source must be clearly stated, and, when the source code is
+ distributed, the copyright notice must be retained and any alterations in
+ the code must be clearly marked. No warranty is given regarding the quality
+ of this software.*/
+
+#ifndef SEQAN_HEADER_INDEX_SA_LSS_H
+#define SEQAN_HEADER_INDEX_SA_LSS_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+template <typename TValue>
+struct _Context_LSS
+{
+ TValue *I, /* group array, ultimately suffix array.*/
+ *V, /* inverse array, ultimately inverse of I.*/
+ r, /* number of symbols aggregated by transform.*/
+ h; /* length of already-sorted prefixes.*/
+
+ // MODIFIED: renamed defines according to SeqAn's naming conventions
+ #define SEQAN_LSSKEY(p) (V[*(p)+(h)])
+ #define SEQAN_LSSSWAP(p, q) (tmp=*(p), *(p)=*(q), *(q)=tmp)
+ #define SEQAN_LSSMED3(a, b, c) (SEQAN_LSSKEY(a)<SEQAN_LSSKEY(b) ? \
+ (SEQAN_LSSKEY(b)<SEQAN_LSSKEY(c) ? (b) : SEQAN_LSSKEY(a)<SEQAN_LSSKEY(c) ? (c) : (a)) \
+ : (SEQAN_LSSKEY(b)>SEQAN_LSSKEY(c) ? (b) : SEQAN_LSSKEY(a)>SEQAN_LSSKEY(c) ? (c) : (a)))
+
+ /* Subroutine for select_sort_split and sort_split. Sets group numbers for a
+ group whose lowest position in I is pl and highest position is pm.*/
+
+ inline void update_group(TValue *pl, TValue *pm)
+ {
+ TValue g;
+
+ g=pm-I; /* group number.*/
+ V[*pl]=g; /* update group number of first position.*/
+ if (pl==pm)
+ *pl=-1; /* one element, sorted group.*/
+ else
+ do /* more than one element, unsorted group.*/
+ V[*++pl]=g; /* update group numbers.*/
+ while (pl<pm);
+ }
+
+ /* Quadratic sorting method to use for small subarrays. To be able to update
+ group numbers consistently, a variant of selection sorting is used.*/
+
+ inline void select_sort_split(TValue *p, TValue n) {
+ TValue *pa, *pb, *pi, *pn;
+ TValue f, v, tmp;
+
+ pa=p; /* pa is start of group being picked out.*/
+ pn=p+n-1; /* pn is last position of subarray.*/
+ while (pa<pn) {
+ for (pi=pb=pa+1, f=SEQAN_LSSKEY(pa); pi<=pn; ++pi)
+ if ((v=SEQAN_LSSKEY(pi))<f) {
+ f=v; /* f is smallest key found.*/
+ SEQAN_LSSSWAP(pi, pa); /* place smallest element at beginning.*/
+ pb=pa+1; /* pb is position for elements equal to f.*/
+ } else if (v==f) { /* if equal to smallest key.*/
+ SEQAN_LSSSWAP(pi, pb); /* place next to other smallest elements.*/
+ ++pb;
+ }
+ update_group(pa, pb-1); /* update group values for new group.*/
+ pa=pb; /* continue sorting rest of the subarray.*/
+ }
+ if (pa==pn) { /* check if last part is single element.*/
+ V[*pa]=pa-I;
+ *pa=-1; /* sorted group.*/
+ }
+ }
+
+ /* Subroutine for sort_split, algorithm by Bentley & McIlroy.*/
+
+ inline TValue choose_pivot(TValue *p, TValue n) {
+ TValue *pl, *pm, *pn;
+ TValue s;
+
+ pm=p+(n>>1); /* small arrays, middle element.*/
+ if (n>7) {
+ pl=p;
+ pn=p+n-1;
+ if (n>40) { /* big arrays, pseudomedian of 9.*/
+ s=n>>3;
+ pl=SEQAN_LSSMED3(pl, pl+s, pl+s+s);
+ pm=SEQAN_LSSMED3(pm-s, pm, pm+s);
+ pn=SEQAN_LSSMED3(pn-s-s, pn-s, pn);
+ }
+ pm=SEQAN_LSSMED3(pl, pm, pn); /* midsize arrays, median of 3.*/
+ }
+ return SEQAN_LSSKEY(pm);
+ }
+
+ /* Sorting routine called for each unsorted group. Sorts the array of integers
+ (suffix numbers) of length n starting at p. The algorithm is a ternary-split
+ quicksort taken from Bentley & McIlroy, "Engineering a Sort Function",
+ Software -- Practice and Experience 23(11), 1249-1265 (November 1993). This
+ function is based on Program 7.*/
+
+ inline void sort_split(TValue *p, TValue n)
+ {
+ TValue *pa, *pb, *pc, *pd, *pl, *pm, *pn;
+ TValue f, v, s, t, tmp;
+
+ if (n<7) { /* multi-selection sort smallest arrays.*/
+ select_sort_split(p, n);
+ return;
+ }
+
+ v=choose_pivot(p, n);
+ pa=pb=p;
+ pc=pd=p+n-1;
+ while (1) { /* split-end partition.*/
+ while (pb<=pc && (f=SEQAN_LSSKEY(pb))<=v) {
+ if (f==v) {
+ SEQAN_LSSSWAP(pa, pb);
+ ++pa;
+ }
+ ++pb;
+ }
+ while (pc>=pb && (f=SEQAN_LSSKEY(pc))>=v) {
+ if (f==v) {
+ SEQAN_LSSSWAP(pc, pd);
+ --pd;
+ }
+ --pc;
+ }
+ if (pb>pc)
+ break;
+ SEQAN_LSSSWAP(pb, pc);
+ ++pb;
+ --pc;
+ }
+ pn=p+n;
+ if ((s=pa-p)>(t=pb-pa))
+ s=t;
+ for (pl=p, pm=pb-s; s; --s, ++pl, ++pm)
+ SEQAN_LSSSWAP(pl, pm);
+ if ((s=pd-pc)>(t=pn-pd-1))
+ s=t;
+ for (pl=pb, pm=pn-s; s; --s, ++pl, ++pm)
+ SEQAN_LSSSWAP(pl, pm);
+
+ s=pb-pa;
+ t=pd-pc;
+ if (s>0)
+ sort_split(p, s);
+ update_group(p+s, p+n-t-1);
+ if (t>0)
+ sort_split(p+n-t, t);
+ }
+
+ /* Bucketsort for first iteration.
+
+ Input: x[0...n-1] holds integers in the range 1...k-1, all of which appear
+ at least once. x[n] is 0. (This is the corresponding output of transform.) k
+ must be at most n+1. p is array of size n+1 whose contents are disregarded.
+
+ Output: x is V and p is I after the initial sorting stage of the refined
+ suffix sorting algorithm.*/
+
+ inline void bucketsort(TValue *x, TValue *p, TValue n, TValue k)
+ {
+ TValue *pi, i, c, d, g;
+
+ for (pi=p; pi<p+k; ++pi)
+ *pi=-1; /* mark linked lists empty.*/
+ for (i=0; i<=n; ++i) {
+ x[i]=p[c=x[i]]; /* insert in linked list.*/
+ p[c]=i;
+ }
+ for (pi=p+k-1, i=n; pi>=p; --pi) {
+ d=x[c=*pi]; /* c is position, d is next in list.*/
+ x[c]=g=i; /* last position equals group number.*/
+ if (d>=0) { /* if more than one element in group.*/
+ p[i--]=c; /* p is permutation for the sorted x.*/
+ do {
+ d=x[c=d]; /* next in linked list.*/
+ x[c]=g; /* group number in x.*/
+ p[i--]=c; /* permutation in p.*/
+ } while (d>=0);
+ } else
+ p[i--]=-1; /* one element, sorted group.*/
+ }
+ }
+
+ /* Transforms the alphabet of x by attempting to aggregate several symbols into
+ one, while preserving the suffix order of x. The alphabet may also be
+ compacted, so that x on output comprises all integers of the new alphabet
+ with no skipped numbers.
+
+ Input: x is an array of size n+1 whose first n elements are positive
+ integers in the range l...k-1. p is array of size n+1, used for temporary
+ storage. q controls aggregation and compaction by defining the maximum value
+ for any symbol during transformation: q must be at least k-l; if q<=n,
+ compaction is guaranteed; if k-l>n, compaction is never done; if q is
+ INT_MAX, the maximum number of symbols are aggregated into one.
+
+ Output: Returns an integer j in the range 1...q representing the size of the
+ new alphabet. If j<=n+1, the alphabet is compacted. The global variable r is
+ set to the number of old symbols grouped into one. Only x[n] is 0.*/
+
+ inline TValue transform(TValue *x, TValue *p, TValue n, TValue k, TValue l, TValue q)
+ {
+ TValue b, c, d, e, i, j, m, s;
+ TValue *pi, *pj;
+
+ for (s=0, i=k-l; i; i>>=1)
+ ++s; /* s is number of bits in old symbol.*/
+ e=SupremumValue<TValue>::VALUE>>s; /* e is for overflow checking.*/
+ for (b=d=r=0; r<n && d<=e && (c=d<<s|(k-l))<=q; ++r) {
+ b=b<<s|(x[r]-l+1); /* b is start of x in chunk alphabet.*/
+ d=c; /* d is max symbol in chunk alphabet.*/
+ }
+ m=(1<<(r-1)*s)-1; /* m masks off top old symbol from chunk.*/
+ x[n]=l-1; /* emulate zero terminator.*/
+ if (d<=n) { /* if bucketing possible, compact alphabet.*/
+ for (pi=p; pi<=p+d; ++pi)
+ *pi=0; /* zero transformation table.*/
+ for (pi=x+r, c=b; pi<=x+n; ++pi) {
+ p[c]=1; /* mark used chunk symbol.*/
+ c=(c&m)<<s|(*pi-l+1); /* shift in next old symbol in chunk.*/
+ }
+ for (i=1; i<r; ++i) { /* handle last r-1 positions.*/
+ p[c]=1; /* mark used chunk symbol.*/
+ c=(c&m)<<s; /* shift in next old symbol in chunk.*/
+ }
+ for (pi=p, j=1; pi<=p+d; ++pi)
+ if (*pi)
+ *pi=j++; /* j is new alphabet size.*/
+ for (pi=x, pj=x+r, c=b; pj<=x+n; ++pi, ++pj) {
+ *pi=p[c]; /* transform to new alphabet.*/
+ c=(c&m)<<s|(*pj-l+1); /* shift in next old symbol in chunk.*/
+ }
+ while (pi<x+n) { /* handle last r-1 positions.*/
+ *pi++=p[c]; /* transform to new alphabet.*/
+ c=(c&m)<<s; /* shift right-end zero in chunk.*/
+ }
+ } else { /* bucketing not possible, don't compact.*/
+ for (pi=x, pj=x+r, c=b; pj<=x+n; ++pi, ++pj) {
+ *pi=c; /* transform to new alphabet.*/
+ c=(c&m)<<s|(*pj-l+1); /* shift in next old symbol in chunk.*/
+ }
+ while (pi<x+n) { /* handle last r-1 positions.*/
+ *pi++=c; /* transform to new alphabet.*/
+ c=(c&m)<<s; /* shift right-end zero in chunk.*/
+ }
+ j=d+1; /* new alphabet size.*/
+ }
+ x[n]=0; /* end-of-string symbol is zero.*/
+ return j; /* return new alphabet size.*/
+ }
+
+ /* Makes suffix array p of x. x becomes inverse of p. p and x are both of size
+ n+1. Contents of x[0...n-1] are integers in the range l...k-1. Original
+ contents of x[n] is disregarded, the n-th symbol being regarded as
+ end-of-string smaller than all other symbols.*/
+
+ void suffixsort(TValue *x, TValue *p, TValue n, TValue k, TValue l)
+ {
+ TValue *pi, *pk;
+ TValue i, j, s, sl;
+
+ V=x; /* set global values.*/
+ I=p;
+
+ if (n>=k-l) { /* if bucketing possible,*/
+ j=transform(V, I, n, k, l, n);
+ bucketsort(V, I, n, j); /* bucketsort on first r positions.*/
+ } else {
+ transform(V, I, n, k, l, SupremumValue<TValue>::VALUE);
+ for (i=0; i<=n; ++i)
+ I[i]=i; /* initialize I with suffix numbers.*/
+ h=0;
+ sort_split(I, n+1); /* quicksort on first r positions.*/
+ }
+ h=r; /* number of symbols aggregated by transform.*/
+
+ while (*I>=-n) {
+ pi=I; /* pi is first position of group.*/
+ sl=0; /* sl is negated length of sorted groups.*/
+ do {
+ if ((s=*pi)<0) {
+ pi-=s; /* skip over sorted group.*/
+ sl+=s; /* add negated length to sl.*/
+ } else {
+ if (sl) {
+ *(pi+sl)=sl; /* combine sorted groups before pi.*/
+ sl=0;
+ }
+ pk=I+V[s]+1; /* pk-1 is last position of unsorted group.*/
+ sort_split(pi, pk-pi);
+ pi=pk; /* next group.*/
+ }
+ } while (pi<=I+n);
+ if (sl) /* if the array ends with a sorted group.*/
+ *(pi+sl)=sl; /* combine sorted groups at end of I.*/
+ h=2*h; /* double sorted-depth.*/
+ }
+
+ for (i=0; i<=n; ++i) /* reconstruct suffix array from inverse.*/
+ I[V[i]]=i;
+ }
+};
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// SeqAn interface
+
+ struct LarssonSadakane {};
+
+ // WARNING:
+ // 1. the content of s will be destroyed
+ // 2. s and SA have to have size n+1
+ // 3. s[n] must be unique and less than any other character in s
+ //
+ // better use LarssonSadakane as a pipe (look down)
+
+ template < typename TSA,
+ typename TText >
+ void createSuffixArray(
+ TSA &SA,
+ TText &s,
+ LarssonSadakane const &,
+ unsigned K)
+ {
+ typedef typename Value<TSA>::Type TValue;
+ typedef typename _MakeSigned<TValue>::Type TSValue; // LarssonSadakane expects signed values
+ _Context_LSS<TSValue> c;
+ c.suffixsort(
+ (TSValue*)begin(s, Standard()), // text
+ (TSValue*)begin(SA, Standard()), // SA
+ length(s) - 1, // n
+ K, // text[i] < K
+ 0); // text[i] >= 0
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // qsufsort pipe
+// template < typename TInput >
+// struct Pipe< TInput, LarssonSadakane >
+// {
+// typedef typename SAValue<TInput>::Type TValue;
+// typedef String<TValue, Alloc<> > TText;
+// typedef String<TValue, Alloc<> > TSA;
+// typedef Pipe<TSA, Source<> > TSource;
+//
+// TSA sa;
+// TSource in;
+//
+// Pipe(TInput &_textIn):
+// in(sa)
+// {
+// typedef typename Iterator<TText, Standard>::Type TIter;
+//
+// TValue len = length(_textIn);
+// TText text;
+// resize(text, len + 1, Exact());
+//
+// TIter it = begin(text);
+// TIter itEnd = begin(text) + len;
+// TValue maxChar = 0;
+//
+// beginRead(_textIn);
+// for(; it != itEnd; ++it, ++_textIn) {
+// TValue val = (*it = 1 + (TValue)*_textIn);
+// if (val > maxChar)
+// maxChar = val;
+// }
+// endRead(_textIn);
+//
+// resize(sa, len + 1, Exact());
+// createSuffixArray(sa, text, LarssonSadakane(), maxChar + 1);
+// }
+//
+// inline typename Value<TSource>::Type const & operator*() {
+// return *in;
+// }
+//
+// inline Pipe& operator++() {
+// ++in;
+// return *this;
+// }
+// };
+
+// template < typename TInput >
+// inline bool control(Pipe< TInput, LarssonSadakane > &me, ControlBeginRead const &command) {
+// control(me.in, command);
+// ++me.in;
+// return true;
+// }
+
+// template < typename TInput >
+// inline typename Size< Pipe< TInput, LarssonSadakane > >::Type
+// length(Pipe< TInput, LarssonSadakane > const &me) {
+// return length(me.in) - 1;
+// }
+
+}
+
+#endif
diff --git a/src/libSSA/seqan/index/shape_base.h b/src/libSSA/seqan/index/shape_base.h
new file mode 100644
index 0000000..6e66f79
--- /dev/null
+++ b/src/libSSA/seqan/index/shape_base.h
@@ -0,0 +1,607 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: shape_base.h,v 1.1 2008/08/25 16:20:05 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SHAPE_BASE_H
+#define SEQAN_HEADER_SHAPE_BASE_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+ template <unsigned q>
+ struct FixedShape {};
+ typedef FixedShape<0> SimpleShape;
+
+ template <typename TSpec>
+ struct FixedGappedShape {};
+ typedef FixedGappedShape<Default> GappedShape;
+
+
+/**
+.Class.Shape:
+..cat:Index
+..summary:Stores hash value and shape for an ungapped or gapped q-gram.
+..signature:Shape<TValue, TSpec>
+..param.TValue:The @Metafunction.Value@ type of the string the shape is applied to (e.g. $Dna$).
+..param.TSpec:The specializing type.
+...default:@Spec.SimpleShape@, for ungapped q-grams.
+..remarks:The @Metafunction.ValueSize@ of Shape is the ValueSize of TValue which is the alphabet size.
+..remarks:To get the span or the weight of a shape call @Function.length@ or @Function.weight at .
+.Memfunc.Shape#Shape:
+..class:Class.Shape
+..summary:Constructor
+..signature:Shape<TValue, TSpec> ()
+..signature:Shape<TValue, TSpec> (shape)
+..param.shape:Other Shape object. (copy constructor)
+*/
+ template <typename TValue = Dna, typename TSpec = SimpleShape>
+ class Shape;
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Value.param.T.type:Class.Shape
+ template <typename TValue, typename TSpec>
+ struct Value<Shape<TValue,TSpec> >
+ {
+ typedef unsigned Type;
+ };
+
+///.Metafunction.Size.param.T.type:Class.Shape
+ template <typename TValue, typename TSpec>
+ struct Size<Shape<TValue,TSpec> >
+ {
+ typedef unsigned Type;
+ };
+
+///.Metafunction.LENGTH.param.T.type:Class.Shape
+ template <typename TValue, unsigned q>
+ struct LENGTH< Shape<TValue, FixedShape<q> > >
+ {
+ enum { VALUE = q };
+ };
+
+///.Metafunction.WEIGHT.param.T.type:Class.Shape
+ template <typename TValue, unsigned q>
+ struct WEIGHT< Shape<TValue, FixedShape<q> > >
+ {
+ enum { VALUE = q };
+ };
+
+///.Metafunction.ValueSize.param.T.type:Class.Shape
+ template <typename TValue, typename TSpec>
+ struct ValueSize< Shape<TValue, TSpec> > {
+ enum { VALUE = Power<
+ ValueSize<TValue>::VALUE,
+ WEIGHT< Shape<TValue, TSpec> >::VALUE >::VALUE };
+ };
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Spec.SimpleShape:
+..cat:Index
+..summary:A variable length ungapped shape (also called q-gram or k-mer).
+..general:Class.Shape
+..signature:Shape<TValue, SimpleShape>
+..param.TValue:The @Metafunction.Value@ type of the string the shape is applied to (e.g. $Dna$).
+..remarks:A SimpleShape must be resized first to a valid length. To do so, call @Function.resize at .
+..see:Spec.FixedShape
+*/
+
+ //////////////////////////////////////////////////////////////////////////////
+ // ungapped shape with variable length
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TValue>
+ class Shape<TValue, SimpleShape>
+ {
+ public:
+//____________________________________________________________________________
+
+ unsigned span;
+ typename Value<Shape>::Type hValue;
+ typename Value<Shape>::Type XValue;
+ typename Value<Shape>::Type leftFactor;
+ typename Value<Shape>::Type leftFactor2;
+ TValue leftChar;
+//____________________________________________________________________________
+
+/**
+.Memfunc.SimpleShape#Shape:
+..class:Spec.SimpleShape
+..summary:Constructor
+..signature:Shape<TValue, SimpleShape> ()
+..signature:Shape<TValue, SimpleShape> (shape)
+..signature:Shape<TValue, SimpleShape> (q)
+..param.shape:Other Shape object. (copy constructor)
+..param.q:Length of the ungapped q-gram.
+*/
+ Shape() {}
+
+ Shape(unsigned _span)
+ {
+ resize(*this, _span);
+ }
+
+ template <unsigned q>
+ Shape(Shape<TValue, FixedShape<q> > const &other)
+ {
+ *this = other;
+ }
+
+//____________________________________________________________________________
+
+ template <unsigned q>
+ inline Shape &
+ operator=(Shape<TValue, FixedShape<q> > const &other)
+ {
+ span = other.span;
+ hValue = other.hValue;
+ XValue = other.XValue;
+ leftFactor = other.leftFactor;
+ leftFactor2 = other.leftFactor2;
+ leftChar = other.leftChar;
+ return *this;
+ }
+ };
+
+ //////////////////////////////////////////////////////////////////////////////
+ // ungapped shape with fixed length q
+ //////////////////////////////////////////////////////////////////////////////
+
+/**
+.Spec.FixedShape:
+..cat:Index
+..summary:A fixed length ungapped shape (also called q-gram or k-mer).
+..general:Class.Shape
+..signature:Shape<TValue, FixedShape<q> >
+..param.TValue:The @Metafunction.Value@ type of the sequence the shape is applied to (e.g. $Dna$).
+..param.q:The length of the shape.
+*/
+
+ template <typename TValue, unsigned q>
+ class Shape<TValue, FixedShape<q> >
+ {
+ public:
+//____________________________________________________________________________
+
+ enum { span = q };
+ enum { leftFactor = Power<ValueSize<TValue>::VALUE, q - 1>::VALUE };
+ enum { leftFactor2 = (Power<ValueSize<TValue>::VALUE, q>::VALUE - 1) / (ValueSize<TValue>::VALUE - 1) };
+ // Sigma^(q-1) + Sigma^(q-2) + ... + Sigma + 1
+
+ typename Value<Shape>::Type hValue; // current hash value
+ typename Value<Shape>::Type XValue; // Sum_{i=0..q-1} (x_i + 1)
+ TValue leftChar; // left-most character
+//____________________________________________________________________________
+
+ };
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.value.param.object.type:Class.Shape
+ template <typename TValue, typename TSpec>
+ inline typename Value< Shape<TValue, TSpec> >::Type
+ value(Shape<TValue, TSpec> &me)
+ {
+ return me.hValue;
+ }
+
+//____________________________________________________________________________
+
+///.Function.length.param.object.type:Class.Shape
+ template <typename TValue, typename TSpec>
+ inline typename Size< Shape<TValue, TSpec> >::Type
+ length(Shape<TValue, TSpec> const &me)
+ {
+ SEQAN_CHECKPOINT
+ return me.span;
+ }
+
+//____________________________________________________________________________
+
+/**.Function.weight:
+..cat:Index
+..summary:Number of relevant positions in a shape.
+..signature:weight(shape)
+..param.shape:Shape object for which the number of relevant positions is determined.
+...type:Class.Shape
+..returns:Number of relevant positions.
+..remarks.text:For ungapped shapes the return value is the result of the @Function.length@ function.
+For gapped shapes this is the number of '1's.
+*/
+ template <typename TValue, typename TSpec>
+ inline typename Size< Shape<TValue, TSpec> >::Type
+ weight(Shape<TValue, TSpec> const &me)
+ {
+ SEQAN_CHECKPOINT
+ return length(me);
+ }
+
+//____________________________________________________________________________
+
+///.Function.resize.param.object.type:Spec.SimpleShape
+ template <typename TValue, typename TSize>
+ inline typename Size< Shape<TValue, SimpleShape> >::Type
+ resize(Shape<TValue, SimpleShape> & me, TSize new_length)
+ {
+ SEQAN_CHECKPOINT
+ me.leftFactor = _intPow((unsigned)ValueSize<TValue>::VALUE, new_length - 1);
+ me.leftFactor2 = (_intPow((unsigned)ValueSize<TValue>::VALUE, new_length) - 1) / (ValueSize<TValue>::VALUE - 1);
+ return me.span = new_length;
+ }
+
+//____________________________________________________________________________
+
+/**.Function.hash:
+..cat:Index
+..summary:Computes a (lower) hash value for a shape applied to a sequence.
+..signature:hash(shape, it)
+..signature:hash(shape, it, charsLeft)
+..param.shape:Shape to be used for hashing.
+...type:Class.Shape
+..param.it:Sequence iterator pointing to the first character of the shape.
+..param.charsLeft:The distance of $it$ to the string end.
+If $charsLeft$ is smaller than the shape's span, the hash value corresponds to the smallest shape beginning with $charsLeft$ characters.
+..returns:Hash value of the shape.
+*/
+
+ template <typename TValue, typename TIter>
+ typename Value< Shape<TValue, SimpleShape> >::Type
+ hash(Shape<TValue, SimpleShape> &me, TIter it)
+ {
+ SEQAN_CHECKPOINT
+ typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
+ typedef typename Size< Shape<TValue, SimpleShape> >::Type TSize;
+
+ me.hValue = ordValue(me.leftChar = *it);
+ for(TSize i = 1; i < me.span; ++i) {
+ ++it;
+ me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+ }
+ return me.hValue;
+ }
+
+//____________________________________________________________________________
+// fixed ungapped shapes
+
+ // loop unrolling ...
+ template <typename THValue, typename TValue, typename TIter>
+ inline THValue
+ _hashFixedShape(THValue hash, TIter &, TValue const, FixedShape<1> const) {
+ return hash;
+ }
+
+ template <typename THValue, typename TValue, typename TIter, unsigned q>
+ inline THValue
+ _hashFixedShape(THValue hash, TIter &it, TValue const, FixedShape<q> const) {
+ ++it;
+ return _hashFixedShape(
+ hash * ValueSize<TValue>::VALUE + ordValue((TValue)*it),
+ it, TValue(), FixedShape<q - 1>());
+ }
+
+ // ... for fixed ungapped shapes
+ template <typename TValue, unsigned q, typename TIter>
+ inline typename Value< Shape<TValue, FixedShape<q> > >::Type
+ hash(Shape<TValue, FixedShape<q> > &me, TIter it)
+ {
+ SEQAN_CHECKPOINT
+ typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
+ typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
+
+ me.hValue = ordValue(me.leftChar = *it);
+ return me.hValue = _hashFixedShape(me.hValue, it, TValue(), FixedShape<q>());
+ }
+
+
+ template <typename TValue, typename TSpec, typename TIter, typename TSize>
+ inline typename Value< Shape<TValue, TSpec> >::Type
+ hash(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft)
+ {
+ SEQAN_CHECKPOINT
+ typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
+
+ TSize iEnd = me.span;
+ if (iEnd > charsLeft) iEnd = charsLeft;
+
+ TSize i = 0;
+ if (iEnd > 0) {
+ me.hValue = ordValue(me.leftChar = *it);
+ for(i = 1; i < iEnd; ++i) {
+ ++it;
+ me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+ }
+ } else
+ return me.hValue = 0;
+
+ // fill shape with zeros
+ for(; i < (TSize)me.span; ++i)
+ me.hValue *= ValueSize<TValue>::VALUE;
+ return me.hValue;
+ }
+
+//____________________________________________________________________________
+// Tuple -> fixed ungapped shapes
+
+ template <typename THValue, typename TValue, typename TTValue, unsigned SIZE, typename TCompressed>
+ inline THValue
+ _hashTuple2FixedShape(
+ THValue const,
+ Tuple<TTValue, SIZE, TCompressed> const &tuple,
+ TValue const,
+ FixedShape<1> const)
+ {
+ return ordValue(tuple[0]);
+ }
+
+ template <typename THValue, typename TValue, typename TTValue, unsigned SIZE, typename TCompressed, unsigned q>
+ inline THValue
+ _hashTuple2FixedShape(
+ THValue const,
+ Tuple<TTValue, SIZE, TCompressed> const &tuple,
+ TValue const,
+ FixedShape<q> const)
+ {
+ return _hashTuple2FixedShape(THValue(), tuple, TValue(), FixedShape<q - 1>())
+ * ValueSize<TValue>::VALUE + ordValue(tuple[q-1]);
+ }
+
+ // ... for fixed ungapped shapes
+ template <
+ typename TValue,
+ typename TTValue,
+ unsigned SIZE,
+ unsigned q>
+ typename Value< Shape<TValue, FixedShape<q> > >::Type
+ hash(
+ Shape<TValue, FixedShape<q> > &me,
+ Tuple<TTValue, SIZE, Compressed> const &tuple)
+ {
+ SEQAN_CHECKPOINT
+ if (ValueSize<TValue>::VALUE == (1 << BitsPerValue<TTValue>::VALUE))
+ if (q == SIZE)
+ return tuple.i;
+ else
+ return tuple >> (q - SIZE);
+ else
+ return me.hValue = _hashTuple2FixedShape(me.hValue, tuple, TValue(), FixedShape<q>());
+ }
+
+ template <
+ typename TValue,
+ typename TTValue,
+ unsigned SIZE,
+ typename TCompressed,
+ unsigned q>
+ typename Value< Shape<TValue, FixedShape<q> > >::Type
+ hash(
+ Shape<TValue, FixedShape<q> > &me,
+ Tuple<TTValue, SIZE, TCompressed> const &tuple)
+ {
+ SEQAN_CHECKPOINT
+ return me.hValue = _hashTuple2FixedShape(me.hValue, tuple, TValue(), FixedShape<q>());
+ }
+
+//____________________________________________________________________________
+
+/**.Function.hashUpper:
+..cat:Index
+..summary:Computes an upper hash value for a shape applied to a sequence.
+..signature:hashUpper(shape, it, charsLeft)
+..param.shape:Shape to be used for hashing.
+...type:Class.Shape
+..param.it:Sequence iterator pointing to the first character of the shape.
+..param.charsLeft:The distance of $it$ to the string end.
+If $charsLeft$ is smaller than the shape's span, the hash value corresponds to the biggest shape beginning with $charsLeft$ characters + 1.
+..returns:Upper hash value of the shape.
+*/
+
+ template <typename TValue, typename TSpec, typename TIter, typename TSize>
+ inline typename Value< Shape<TValue, TSpec> >::Type
+ hashUpper(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft)
+ {
+ SEQAN_CHECKPOINT
+ typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
+
+ TSize iEnd = me.span;
+ if (iEnd > charsLeft) iEnd = charsLeft;
+
+ TSize i = 0;
+ if (iEnd > 0) {
+ me.hValue = ordValue(me.leftChar = *it);
+ for(i = 1; i < iEnd; ++i) {
+ ++it;
+ me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+ }
+ ++me.hValue;
+ } else
+ me.hValue = 1;
+
+ // fill shape with zeros
+ for(; i < (TSize)me.span; ++i)
+ me.hValue *= ValueSize<TValue>::VALUE;
+ return me.hValue;
+ }
+
+//____________________________________________________________________________
+
+/**
+.Function.hashNext:
+..cat:Index
+..summary:Computes the hash value for the adjacent shape.
+..signature:hashNext(shape, it)
+..param.shape:Shape to be used for hashing.
+...type:Class.Shape
+..param.it:Sequence iterator pointing to the first character of the adjacent shape.
+..returns:Hash value of the q-gram.
+..remarks:@Function.hash@ has to be called before.
+*/
+
+ template <typename TValue, typename TSpec, typename TIter>
+ inline typename Value< Shape<TValue, TSpec> >::Type
+ hashNext(Shape<TValue, TSpec> &me, TIter &it)
+ {
+ SEQAN_CHECKPOINT
+ // remove first, shift left, and add next character
+ typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
+ me.hValue =
+ (me.hValue - ordValue(me.leftChar) * (THValue)me.leftFactor) * ValueSize<TValue>::VALUE
+ + ordValue((TValue)*(it + (THValue)me.span - 1));
+ me.leftChar = *it;
+ return me.hValue;
+ }
+
+//____________________________________________________________________________
+
+/**.Function.hash2:
+..cat:Index
+..summary:Computes a unique hash value of a shape, even if it is shorter than its span.
+..signature:hash2(shape, it, charsLeft)
+..param.shape:Shape to be used for hashing.
+...type:Class.Shape
+..param.it:Sequence iterator pointing to the first character of the shape.
+..param.charsLeft:The distance of $it$ to the string end.
+..returns:Hash value of the shape.
+*/
+
+ template <typename TValue, typename TSpec, typename TIter, typename TSize>
+ inline typename Value< Shape<TValue, TSpec> >::Type
+ hash2(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft)
+ {
+ SEQAN_CHECKPOINT
+ typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
+
+ TSize iEnd = me.span;
+ if (iEnd > charsLeft) iEnd = charsLeft;
+
+ TSize i = 0;
+ if (iEnd > 0) {
+ me.hValue = me.XValue = ordValue(me.leftChar = *it);
+ for(i = 1; i < iEnd; ++i) {
+ ++it;
+ // update sum of x_i
+ me.XValue += ordValue((TValue)*it);
+ // shift hash
+ me.hValue = me.hValue * ValueSize<TValue>::VALUE + me.XValue;
+ }
+ } else
+ return me.hValue = me.XValue = 0;
+
+ // fill shape with zeros
+ for(; i < (TSize)me.span; ++i)
+ me.hValue = me.hValue * ValueSize<TValue>::VALUE + me.XValue;
+ return me.hValue += iEnd;
+ }
+
+ template <typename TValue, typename TSpec, typename TIter, typename TSize>
+ inline typename Value< Shape<TValue, TSpec> >::Type
+ hash2Upper(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft)
+ {
+ SEQAN_CHECKPOINT
+ typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
+
+ TSize iEnd = me.span;
+ if (iEnd > charsLeft) iEnd = charsLeft;
+
+ THValue hValue, XValue;
+ TSize i = 0;
+ if (iEnd > 0) {
+ hValue = XValue = ordValue((TValue)*it);
+ for(i = 1; i < iEnd; ++i) {
+ ++it;
+ // update sum of x_i
+ XValue += ordValue((TValue)*it);
+ // shift hash
+ hValue = hValue * ValueSize<TValue>::VALUE + XValue;
+ }
+ } else
+ hValue = XValue = 0;
+
+ if (charsLeft <= me.span) {
+ ++XValue;
+ ++hValue;
+ }
+
+ // fill shape with zeros
+ for(; i < (TSize)me.span; ++i)
+ hValue = hValue * ValueSize<TValue>::VALUE + XValue;
+ return hValue += iEnd;
+ }
+
+//____________________________________________________________________________
+
+/**
+.Function.hash2Next:
+..cat:Index
+..summary:Computes a unique hash value for the adjacent shape, even if it is shorter than q.
+..signature:hash2Next(shape, it)
+..param.shape:Shape to be used for hashing the q-gram.
+...type:Class.Shape
+..param.it:Sequence iterator pointing to the first character of the adjacent shape.
+..returns:Hash value of the shape.
+..remarks:@Function.hash@ has to be called before with $shape$ on the left adjacent q-gram.
+*/
+
+ template <typename TValue, typename TSpec, typename TIter, typename TSize>
+ inline typename Value< Shape<TValue, TSpec> >::Type
+ hash2Next(Shape<TValue, TSpec> &me, TIter &it, TSize charsLeft)
+ {
+ SEQAN_CHECKPOINT
+ // remove first, shift left, and add next character
+ typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
+
+ if (charsLeft >= me.span) {
+ // update sum of x_i
+ me.XValue = me.XValue + ordValue((TValue)*(it + me.span - 1)) - ordValue(me.leftChar);
+ // shift hash
+ me.hValue = (me.hValue - ordValue(me.leftChar) * (THValue)me.leftFactor2) * ValueSize<TValue>::VALUE + me.XValue
+ - me.span * (ValueSize<TValue>::VALUE - 1);
+ } else {
+ // update sum of x_i
+ me.XValue -= ordValue(me.leftChar);
+ // shift hash
+ me.hValue = (me.hValue - ordValue(me.leftChar) * (THValue)me.leftFactor2) * ValueSize<TValue>::VALUE + me.XValue
+ - charsLeft * (ValueSize<TValue>::VALUE - 1) - ValueSize<TValue>::VALUE;
+ }
+
+ me.leftChar = *it;
+ return me.hValue;
+ }
+
+ template <typename TString, typename THash>
+ inline void unhash(TString &result, THash hash, unsigned q)
+ {
+ SEQAN_CHECKPOINT
+ typedef typename Value<TString>::Type TValue;
+
+ resize(result, q);
+ for (unsigned i = q; i > 0; )
+ {
+ result[--i] = (TValue)(hash % ValueSize<TValue>::VALUE);
+ hash /= ValueSize<TValue>::VALUE;
+ }
+ }
+
+} // namespace seqan
+
+#endif
diff --git a/src/libSSA/seqan/index/shape_gapped.h b/src/libSSA/seqan/index/shape_gapped.h
new file mode 100644
index 0000000..8a9d724
--- /dev/null
+++ b/src/libSSA/seqan/index/shape_gapped.h
@@ -0,0 +1,593 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: shape_gapped.h,v 1.1 2008/08/25 16:20:05 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SHAPE_GAPPED_H
+#define SEQAN_HEADER_SHAPE_GAPPED_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// HardwiredShape allows compiler-time defined gapped shape
+
+/**
+.Class.HardwiredShape:
+..cat:Index
+..summary:A structure to define a fixed gapped shape.
+..signature:HardwiredShape<P1, P2, ..., Pn>
+..param.P1, P2, ..., Pn:Px is the distance of the x'th '1' to the next '1' in the shape.
+...remarks:At most 20 parameters are allowed, so the maximal shape weight is 21.
+..remarks:You can use this structure to define your one gapped shapes in conjunction with @Spec.FixedGappedShape at .
+..note:The shape $1100101$ corresponds to $HardwiredShape<1,3,2>$.
+..note:The following predefined shapes are already available in $seqan/index/shape_predefined.h$:
+..file:../projects/library/seqan/index/shape_predefined.h
+*/
+
+ // Pxx = spaces between '1's
+ template <
+ int P00 = 0, int P01 = 0, int P02 = 0, int P03 = 0, int P04 = 0,
+ int P05 = 0, int P06 = 0, int P07 = 0, int P08 = 0, int P09 = 0,
+ int P10 = 0, int P11 = 0, int P12 = 0, int P13 = 0, int P14 = 0,
+ int P15 = 0, int P16 = 0, int P17 = 0, int P18 = 0, int P19 = 0
+ >
+ struct HardwiredShape {
+ static const int DIFFS[];
+ };
+
+ template <
+ int P00, int P01, int P02, int P03, int P04,
+ int P05, int P06, int P07, int P08, int P09,
+ int P10, int P11, int P12, int P13, int P14,
+ int P15, int P16, int P17, int P18, int P19
+ >
+ const int HardwiredShape<
+ P00,P01,P02,P03,P04,
+ P05,P06,P07,P08,P09,
+ P10,P11,P12,P13,P14,
+ P15,P16,P17,P18,P19
+ >::DIFFS[] = {
+ P00,P01,P02,P03,P04,
+ P05,P06,P07,P08,P09,
+ P10,P11,P12,P13,P14,
+ P15,P16,P17,P18,P19, 0
+ };
+
+
+//////////////////////////////////////////////////////////////////////////////
+// LENGTH meta-function for fixed gapped shapes
+
+ template <>
+ struct LENGTH< HardwiredShape<
+ 0,0,0,0,0,
+ 0,0,0,0,0,
+ 0,0,0,0,0,
+ 0,0,0,0,0> >
+ {
+ enum { VALUE = 1 };
+ };
+
+ template <
+ int P00, int P01, int P02, int P03, int P04,
+ int P05, int P06, int P07, int P08, int P09,
+ int P10, int P11, int P12, int P13, int P14,
+ int P15, int P16, int P17, int P18, int P19
+ >
+ struct LENGTH< HardwiredShape<
+ P00,P01,P02,P03,P04,
+ P05,P06,P07,P08,P09,
+ P10,P11,P12,P13,P14,
+ P15,P16,P17,P18,P19> >
+ {
+ enum { VALUE = LENGTH< HardwiredShape<
+ P01,P02,P03,P04,P05,
+ P06,P07,P08,P09,P10,
+ P11,P12,P13,P14,P15,
+ P16,P17,P18,P19, 0 > >::VALUE + P00 };
+ };
+
+ template <
+ typename TValue,
+ int P00, int P01, int P02, int P03, int P04,
+ int P05, int P06, int P07, int P08, int P09,
+ int P10, int P11, int P12, int P13, int P14,
+ int P15, int P16, int P17, int P18, int P19
+ >
+ struct LENGTH< Shape<TValue, FixedGappedShape< HardwiredShape<
+ P00,P01,P02,P03,P04,
+ P05,P06,P07,P08,P09,
+ P10,P11,P12,P13,P14,
+ P15,P16,P17,P18,P19
+ > > > >:
+ LENGTH< HardwiredShape<
+ P00,P01,P02,P03,P04,
+ P05,P06,P07,P08,P09,
+ P10,P11,P12,P13,P14,
+ P15,P16,P17,P18,P19
+ > > {};
+
+
+//////////////////////////////////////////////////////////////////////////////
+// WEIGHT meta-function for fixed gapped shapes
+
+ template <>
+ struct WEIGHT< HardwiredShape<
+ 0,0,0,0,0,
+ 0,0,0,0,0,
+ 0,0,0,0,0,
+ 0,0,0,0,0> >
+ {
+ enum { VALUE = 1 };
+ };
+
+ template <
+ int P00, int P01, int P02, int P03, int P04,
+ int P05, int P06, int P07, int P08, int P09,
+ int P10, int P11, int P12, int P13, int P14,
+ int P15, int P16, int P17, int P18, int P19
+ >
+ struct WEIGHT< HardwiredShape<
+ P00,P01,P02,P03,P04,
+ P05,P06,P07,P08,P09,
+ P10,P11,P12,P13,P14,
+ P15,P16,P17,P18,P19> >
+ {
+ enum { VALUE = WEIGHT< HardwiredShape<
+ P01,P02,P03,P04,P05,
+ P06,P07,P08,P09,P10,
+ P11,P12,P13,P14,P15,
+ P16,P17,P18,P19, 0 > >::VALUE + 1 };
+ };
+
+ template <
+ typename TValue,
+ int P00, int P01, int P02, int P03, int P04,
+ int P05, int P06, int P07, int P08, int P09,
+ int P10, int P11, int P12, int P13, int P14,
+ int P15, int P16, int P17, int P18, int P19
+ >
+ struct WEIGHT< Shape<TValue, FixedGappedShape< HardwiredShape<
+ P00,P01,P02,P03,P04,
+ P05,P06,P07,P08,P09,
+ P10,P11,P12,P13,P14,
+ P15,P16,P17,P18,P19
+ > > > >:
+ WEIGHT< HardwiredShape<
+ P00,P01,P02,P03,P04,
+ P05,P06,P07,P08,P09,
+ P10,P11,P12,P13,P14,
+ P15,P16,P17,P18,P19
+ > > {};
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Spec.GappedShape:
+..cat:Index
+..summary:A variable gapped shape.
+..general:Class.Shape
+..signature:Shape<TValue, GappedShape>
+..param.TValue:The @Metafunction.Value@ type of the string the shape is applied to (e.g. $Dna$).
+..remarks:A GappedShape must be initialized first with a valid shape. To do so, call @Function.stringToShape at .
+..see:Spec.FixedGappedShape
+*/
+
+ //////////////////////////////////////////////////////////////////////////////
+ // variable gapped shape
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TValue>
+ class Shape<TValue, GappedShape>
+ {
+ public:
+//____________________________________________________________________________
+
+ unsigned span;
+ unsigned weight;
+ String<int> diffs;
+
+ typename Value<Shape>::Type hValue; // current hash value
+//____________________________________________________________________________
+
+/**
+.Memfunc.GappedShape#Shape:
+..class:Spec.GappedShape
+..summary:Constructor
+..signature:Shape<TValue, GappedShape> ()
+..signature:Shape<TValue, GappedShape> (q)
+..signature:Shape<TValue, GappedShape> (shape)
+..signature:Shape<TValue, GappedShape> (predefined)
+..param.q:Creates an ungapped q-gram.
+..param.shape:Any other gapped/ungapped shape.
+..param.predefined:Any instance of a predefined shape spec (e.g. $ShapePatternHunter$).
+..see:Class.HardwiredShape
+*/
+ Shape() {}
+
+ // c'tor for ungapped shapes
+ Shape(unsigned _span):
+ span(_span),
+ weight(_span)
+ {
+ SEQAN_CHECKPOINT
+ resize(diffs, _span);
+ for(unsigned i = 0; i < _span; ++i)
+ diffs[i] = 1;
+ }
+
+ Shape(Shape const &other):
+ span(other.span),
+ weight(other.weight),
+ diffs(other.diffs),
+ hValue(other.hValue) {}
+
+ template <typename TSpec>
+ Shape(Shape<TValue, TSpec> const &other)
+ {
+ *this = other;
+ }
+
+ template <typename TSpec>
+ Shape(FixedGappedShape<TSpec> const &other)
+ {
+ *this = other;
+ }
+
+ template <typename TStringValue, typename TSpec>
+ Shape(String<TStringValue, TSpec> const &bitmap)
+ {
+ *this = bitmap;
+ }
+
+//____________________________________________________________________________
+
+ template <unsigned q>
+ inline Shape &
+ operator=(Shape<TValue, FixedShape<q> > const &other)
+ {
+ span = length(other);
+ weight = weight(other);
+ resize(diffs, weight);
+ for(unsigned i = 1; i < weight; ++i)
+ diffs[i] = 1;
+ hValue = other.hValue;
+ return *this;
+ }
+
+ template <typename TSpec>
+ inline Shape &
+ operator=(Shape<TValue, FixedGappedShape<TSpec> > const &other)
+ {
+ span = other.span;
+ weight = other.weight;
+ diffs = other.diffs;
+ hValue = other.hValue;
+ return *this;
+ }
+
+ template <typename TSpec>
+ inline Shape &
+ operator=(FixedGappedShape<TSpec> const)
+ {
+ typedef Shape<TValue, FixedGappedShape<TSpec> > TShape;
+ return *this = TShape();
+ }
+
+ template <typename TStringValue, typename TSpec>
+ inline Shape &
+ operator=(String<TStringValue, TSpec> const &bitmap)
+ {
+ stringToShape(*this, bitmap);
+ return *this;
+ }
+ };
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Spec.FixedGappedShape:
+..cat:Index
+..summary:A fixed gapped shape.
+..general:Class.Shape
+..signature:Shape<TValue, FixedGappedShape<TSpec> >
+..param.TValue:The @Metafunction.Value@ type of the string the shape is applied to (e.g. $Dna$).
+..param.TSpec:A structure to store the shape at compile-time.
+...type:Class.HardwiredShape
+..remarks:There are predefined shapes in $index/shape_predefined.h$.
+You can simply use them with $Shape<TValue, ShapePatternHunter>$ for example.
+..see:Class.HardwiredShape
+*/
+
+ //////////////////////////////////////////////////////////////////////////////
+ // fixed gapped shape
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TValue, typename TSpec>
+ class Shape<TValue, FixedGappedShape<TSpec> >
+ {
+ public:
+//____________________________________________________________________________
+
+ typedef FixedGappedShape<TSpec> TShapeSpec;
+
+ enum { span = LENGTH<Shape>::VALUE };
+ enum { weight = WEIGHT<Shape>::VALUE };
+ const int *diffs;
+
+ typename Value<Shape>::Type hValue; // current hash value
+//____________________________________________________________________________
+
+ Shape():
+ diffs(TSpec::DIFFS) {}
+
+ Shape(Shape const &other):
+ diffs(other.diffs),
+ hValue(other.hValue) {}
+//____________________________________________________________________________
+
+ inline Shape &
+ operator=(Shape const &other)
+ {
+ hValue = other.hValue;
+ }
+ };
+
+//////////////////////////////////////////////////////////////////////////////
+
+ template <typename TValue, typename TSpec>
+ inline typename Size< Shape<TValue, FixedGappedShape<TSpec> > >::Type
+ weight(Shape<TValue, FixedGappedShape<TSpec> > const & me)
+ {
+ SEQAN_CHECKPOINT
+ return me.weight;
+ }
+
+//____________________________________________________________________________
+
+ template <typename TValue, typename TIter>
+ inline typename Value< Shape<TValue, GappedShape> >::Type
+ hash(Shape<TValue, GappedShape> &me, TIter it)
+ {
+ SEQAN_CHECKPOINT
+ typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
+ typedef typename Size< Shape<TValue, GappedShape> >::Type TSize;
+
+ me.hValue = ordValue((TValue)*it);
+ TSize iEnd = me.weight - 1;
+ for(TSize i = 0; i < iEnd; ++i) {
+ goFurther(it, me.diffs[i]);
+ me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+ }
+ return me.hValue;
+ }
+
+ template <typename TValue, typename TSpec, typename TIter, typename TSize>
+ inline typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type
+ hash(Shape<TValue, FixedGappedShape<TSpec> > &me, TIter it, TSize charsLeft)
+ {
+ SEQAN_CHECKPOINT
+ typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
+
+ TSize iEnd = me.weight;
+ if (iEnd > charsLeft) iEnd = charsLeft;
+
+ TSize i = 0;
+ if (iEnd > 0) {
+ me.hValue = ordValue((TValue)*it);
+ --iEnd;
+ for(; i < iEnd; ++i) {
+ goFurther(it, me.diffs[i]);
+ me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+ }
+ ++i;
+ } else
+ return me.hValue = 0;
+
+ // fill shape with zeros
+ for(; i < (TSize)me.weight; ++i)
+ me.hValue *= ValueSize<TValue>::VALUE;
+ return me.hValue;
+ }
+
+ template <typename TValue, typename TSpec, typename TIter, typename TSize>
+ inline typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type
+ hashUpper(Shape<TValue, FixedGappedShape<TSpec> > &me, TIter it, TSize charsLeft)
+ {
+ SEQAN_CHECKPOINT
+ typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
+
+ TSize iEnd = me.weight;
+ if (iEnd > charsLeft) iEnd = charsLeft;
+
+ TSize i = 0;
+ if (iEnd > 0) {
+ me.hValue = ordValue((TValue)*it);
+ --iEnd;
+ for(; i < iEnd; ++i) {
+ goFurther(it, me.diffs[i]);
+ me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+ }
+ ++i;
+ ++me.hValue;
+ } else
+ return me.hValue = 1;
+
+ // fill shape with zeros
+ for(; i < (TSize)me.weight; ++i)
+ me.hValue *= ValueSize<TValue>::VALUE;
+ return me.hValue;
+ }
+
+//____________________________________________________________________________
+
+ template <typename THValue, typename TValue, typename TIter>
+ inline THValue
+ _hashHardwiredShape(THValue hash, TIter &, TValue const, HardwiredShape<
+ 0,0,0,0,0,
+ 0,0,0,0,0,
+ 0,0,0,0,0,
+ 0,0,0,0,0 > const)
+ {
+ return hash;
+ }
+
+ template <
+ int P01, int P02, int P03, int P04,
+ int P05, int P06, int P07, int P08, int P09,
+ int P10, int P11, int P12, int P13, int P14,
+ int P15, int P16, int P17, int P18, int P19,
+ typename THValue, typename TValue, typename TIter
+ >
+ inline THValue
+ _hashHardwiredShape(THValue hash, TIter &it, TValue const, HardwiredShape<
+ 1 ,P01,P02,P03,P04,
+ P05,P06,P07,P08,P09,
+ P10,P11,P12,P13,P14,
+ P15,P16,P17,P18,P19 > const)
+ {
+ ++it;
+ return _hashHardwiredShape(hash * ValueSize<TValue>::VALUE + ordValue((TValue)*it),
+ it, TValue(), HardwiredShape<
+ P01,P02,P03,P04,P05,
+ P06,P07,P08,P09,P10,
+ P11,P12,P13,P14,P15,
+ P16,P17,P18,P19, 0 >());
+ }
+
+ template <
+ int P00, int P01, int P02, int P03, int P04,
+ int P05, int P06, int P07, int P08, int P09,
+ int P10, int P11, int P12, int P13, int P14,
+ int P15, int P16, int P17, int P18, int P19,
+ typename THValue, typename TValue, typename TIter
+ >
+ inline THValue
+ _hashHardwiredShape(THValue hash, TIter &it, TValue const, HardwiredShape<
+ P00,P01,P02,P03,P04,
+ P05,P06,P07,P08,P09,
+ P10,P11,P12,P13,P14,
+ P15,P16,P17,P18,P19 > const)
+ {
+ it += P00;
+ return _hashHardwiredShape(hash * ValueSize<TValue>::VALUE + ordValue((TValue)*it),
+ it, TValue(), HardwiredShape<
+ P01,P02,P03,P04,P05,
+ P06,P07,P08,P09,P10,
+ P11,P12,P13,P14,P15,
+ P16,P17,P18,P19, 0 >());
+ }
+
+ template <
+ int P00, int P01, int P02, int P03, int P04,
+ int P05, int P06, int P07, int P08, int P09,
+ int P10, int P11, int P12, int P13, int P14,
+ int P15, int P16, int P17, int P18, int P19,
+ typename TValue, typename TIter
+ >
+ inline typename Value< Shape<TValue, FixedGappedShape< HardwiredShape<
+ P00,P01,P02,P03,P04,
+ P05,P06,P07,P08,P09,
+ P10,P11,P12,P13,P14,
+ P15,P16,P17,P18,P19
+ > > > >::Type
+ hash(Shape<TValue, FixedGappedShape< HardwiredShape<
+ P00,P01,P02,P03,P04,
+ P05,P06,P07,P08,P09,
+ P10,P11,P12,P13,P14,
+ P15,P16,P17,P18,P19
+ > > > &me, TIter it)
+ {
+ SEQAN_CHECKPOINT
+ typedef HardwiredShape<
+ P00,P01,P02,P03,P04,
+ P05,P06,P07,P08,P09,
+ P10,P11,P12,P13,P14,
+ P15,P16,P17,P18,P19 > TSpec;
+ typedef FixedGappedShape<TSpec> TShape;
+ typedef typename Value< Shape<TValue, TShape> >::Type THValue;
+
+ me.hValue = (THValue)ordValue((TValue)*it);
+ return me.hValue = _hashHardwiredShape(me.hValue, it, TValue(), TSpec());
+ }
+
+//____________________________________________________________________________
+
+ template <typename TValue, typename TSpec, typename TIter>
+ inline typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type
+ hashNext(Shape<TValue, FixedGappedShape<TSpec> > &me, TIter it)
+ {
+ SEQAN_CHECKPOINT
+ return hash(me, it);
+ }
+
+
+//____________________________________________________________________________
+
+/**.Function.stringToShape:
+..cat:Index
+..summary:Takes a shape given as a string of '1' (relevant position) and '0'
+(irrelevant position) and converts it into a Shape object.
+..signature:stringToShape(shape, bitmap)
+..param.shape:Shape object that is manipulated.
+...type:Spec.GappedShape
+..param.bitmap:A character string of '1' and '0' representing relevant and irrelevant positions (blanks) respectively.
+...remarks:This string must begin with a '1'.
+...type:Class.String
+*/
+
+ template <typename TValue, typename TSpec, typename TShapeString>
+ inline void
+ stringToShape(
+ Shape<TValue, FixedGappedShape<TSpec> > &me,
+ TShapeString const &bitmap)
+ {
+ SEQAN_CHECKPOINT
+ typedef typename Iterator<TShapeString const>::Type TIter;
+ typedef typename Iterator<String<int> >::Type TShapeIter;
+
+ me.span = length(bitmap);
+
+ unsigned oneCount = 0;
+ TIter it = begin(bitmap, Standard());
+ TIter itEnd = end(bitmap, Standard());
+ for(; it != itEnd; ++it)
+ if (*it == '1')
+ ++oneCount;
+
+ me.weight = oneCount;
+ resize(me.diffs, oneCount);
+
+ unsigned diff = 0;
+ it = begin(bitmap, Standard());
+ TShapeIter itS = begin(me.diffs, Standard());
+ for(; it != itEnd; ++it) {
+ if (*it == '1') {
+ *itS = diff;
+ ++itS;
+ diff = 0;
+ }
+ ++diff;
+ }
+ }
+
+} // namespace seqan
+
+#endif
diff --git a/src/libSSA/seqan/index/shape_predefined.h b/src/libSSA/seqan/index/shape_predefined.h
new file mode 100644
index 0000000..a46da60
--- /dev/null
+++ b/src/libSSA/seqan/index/shape_predefined.h
@@ -0,0 +1,114 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: shape_predefined.h,v 1.1 2008/08/25 16:20:05 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SHAPE_PREDEFINED_H
+#define SEQAN_HEADER_SHAPE_PREDEFINED_H
+
+//SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+ //////////////////////////////////////////////////////////////////////////////
+ // some predefined gapped shapes
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // Single seed of
+ // B.Ma and J.Tromp and M.Li,
+ // "PatternHunter: faster and more sensitive homology search"
+ // Bioinformatics 18, 2002
+ //
+ // weight:11
+ // length:18
+ //
+ // shape:
+ // 111010010100110111
+
+ typedef FixedGappedShape<
+ HardwiredShape< 1, 1, 2, 3, 2, 3, 1, 2, 1, 1 >
+ > ShapePatternHunter;
+
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // Multiple seeds of
+ // L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
+ // WABI, 2007
+ //
+ // weight:9
+ // length:15
+ //
+ // shapes:
+ // 111010100100111
+ // 110100110011101
+ // 111010001011011
+ //
+ // sensitivity:
+ // 65% 0.747975 70% 0.897741
+ // 75% 0.973134 80% 0.996226
+
+ typedef FixedGappedShape<
+ HardwiredShape< 1, 1, 2, 2, 3, 3, 1, 1 >
+ > ShapeIlie_9_15_1;
+
+ typedef FixedGappedShape<
+ HardwiredShape< 1, 2, 3, 1, 3, 1, 1, 2 >
+ > ShapeIlie_9_15_2;
+
+ typedef FixedGappedShape<
+ HardwiredShape< 1, 1, 2, 4, 2, 1, 2, 1 >
+ > ShapeIlie_9_15_3;
+
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // Multiple seeds of
+ // L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
+ // WABI 2007
+ //
+ // weight:9
+ // length:13..23
+ //
+ // shapes:
+ // 1110110100111
+ // 11010000110010111
+ // 11100010010000101011
+ //
+ // sensitivity:
+ // 65% 0.767413 70% 0.910949
+ // 75% 0.978558 80% 0.997357
+
+ typedef FixedGappedShape<
+ HardwiredShape< 1, 1, 2, 1, 2, 3, 1, 1 >
+ > ShapeIlie_9_1323_1;
+
+ typedef FixedGappedShape<
+ HardwiredShape< 1, 2, 5, 1, 3, 2, 1, 1 >
+ > ShapeIlie_9_1323_2;
+
+ typedef FixedGappedShape<
+ HardwiredShape< 1, 1, 4, 3, 5, 2, 2, 1 >
+ > ShapeIlie_9_1323_3;
+
+
+} // namespace seqan
+
+#endif
diff --git a/src/libSSA/seqan/platform.h b/src/libSSA/seqan/platform.h
new file mode 100644
index 0000000..7f7b0bc
--- /dev/null
+++ b/src/libSSA/seqan/platform.h
@@ -0,0 +1,27 @@
+#define PLATFORM "gcc"
+
+#ifndef PLATFORM_GCC
+ #define PLATFORM_GCC
+#endif
+
+// should be set before including anything
+#ifndef _FILE_OFFSET_BITS
+ #define _FILE_OFFSET_BITS 64
+#endif
+
+#ifndef _LARGEFILE_SOURCE
+ #define _LARGEFILE_SOURCE
+#endif
+
+//#include <unistd.h>
+#include <inttypes.h>
+
+#define finline __inline__
+
+// default 64bit type
+#if defined(__GNUC__) && !defined(__INTEL_COMPILER) && !defined(__int64)
+typedef int64_t __int64;
+#endif
+
+//define SEQAN_SWITCH_USE_FORWARDS to use generated forwards
+#define SEQAN_SWITCH_USE_FORWARDS
diff --git a/src/libSSA/seqan/sequence.h b/src/libSSA/seqan/sequence.h
new file mode 100644
index 0000000..99c4a4f
--- /dev/null
+++ b/src/libSSA/seqan/sequence.h
@@ -0,0 +1,65 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: sequence.h,v 1.1 2008/08/25 16:20:06 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SEQUENCE_H
+#define SEQAN_HEADER_SEQUENCE_H
+
+//____________________________________________________________________________
+// prerequisites
+
+#include <seqan/basic.h>
+
+//____________________________________________________________________________
+
+#include <seqan/sequence/sequence_forwards.h>
+
+#ifdef SEQAN_SWITCH_USE_FORWARDS
+#include <seqan/sequence/sequence_generated_forwards.h>
+#endif
+
+#include <seqan/sequence/sequence_interface.h>
+#include <seqan/sequence/lexical.h>
+
+//____________________________________________________________________________
+// segments (suffix, ...)
+
+#include <seqan/sequence/segment_base.h>
+#include <seqan/sequence/segment_infix.h>
+#include <seqan/sequence/segment_suffix.h>
+#include <seqan/sequence/segment_prefix.h>
+
+//____________________________________________________________________________
+// strings
+
+#include <seqan/sequence/string_base.h>
+#include <seqan/sequence/string_pointer.h>
+#include <seqan/sequence/string_alloc.h>
+#include <seqan/sequence/string_array.h>
+#include <seqan/sequence/string_cstyle.h>
+#include <seqan/sequence/string_stack.h>
+#include <seqan/sequence/string_packed.h>
+#include <seqan/sequence/string_value_expand.h>
+
+#include <seqan/sequence/std_string.h>
+
+#include <seqan/sequence/sequence_multiple.h>
+#include <seqan/sequence/sequence_shortcuts.h>
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/sequence/lexical.h b/src/libSSA/seqan/sequence/lexical.h
new file mode 100644
index 0000000..f73cc97
--- /dev/null
+++ b/src/libSSA/seqan/sequence/lexical.h
@@ -0,0 +1,787 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: lexical.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_LEXICAL_H
+#define SEQAN_HEADER_LEXICAL_H
+
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+// Switches for prefix ordering mode
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.Prefix Order:
+..summary:Specify whether a prefix is smaller or greater.
+..tag.TagPrefixLess:A prefix is smaller.
+...text:For example: $"abc" < "abcde"$.
+..tag.TagPrefixGreater:A prefix is greater.
+...text:For example: $"abc" > "abcde"$.
+..remarks:The default for all comparison functions is $TagPrefixLess$.
+*/
+struct TagPrefixLess_ {};
+typedef Tag<TagPrefixLess_> const TagPrefixLess;
+
+struct TagPrefixGreater_ {};
+typedef Tag<TagPrefixGreater_> const TagPrefixGreater;
+
+
+/**
+.Metafunction.DefaultPrefixOrder:
+..hidefromindex
+..summary:The default prefix order.
+..signature:DefaultPrefixOrder<T>::Type
+..param.T:Type for which the prefix order is determined.
+..returns.param.Type:Prefix order tag for type of $T$.
+..see:Tag.Prefix Order
+*/
+template <typename T>
+struct DefaultPrefixOrder
+{
+ typedef TagPrefixLess Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// Lexical
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Class.Lexical:
+..cat:Basic
+..summary:Comparator for lexical comparison.
+..signature:Lexical<TSpec>
+..param.TSpec:The specializing type.
+...metafunction:Metafunction.Spec
+...text:This type can be used for specializations of $Lexical$.
+...remarks:$TSpec$ is by default interpreted as size-type.
+...default:$size_t$
+..remarks:
+...text:This class implement comparator objects that perform (lexical) comparisons between two sequences.
+The result of the comparison is stored in the data members of the instance an can be
+accessed by some functions, for example @Function.isLess@ or @Function.isEqual at .
+...text:In most cases, there is no need for an explicite use of comparators,
+but sometimes this concept provide the opportunity to speed up the code.
+..example:
+...text:This program compares the strings $str1$ and $str2$:
+...code:if (isLess(str1, str2)) //first comparison
+{
+ //str1 < str2
+}
+else if (isGreater(str1, str2)) //second comparison
+{
+ //str1 > str2
+}
+else
+{
+ //str == str2
+}
+...text:Using a comparator, the same program only needs one comparison instead of two:
+...code:Lexical <> comparator(str1, str2); //comparison is executed here
+if (isLess(comparator))
+{
+ //str1 < str2
+}
+else if (lexGreater(comparator))
+{
+ //str1 > str2
+}
+else
+{
+ //str == str2
+}
+...text:The state of a default constructed $Lexical$ instance is undefined until
+it is set by a call of @Function.compare at .
+..see:Metafunction.Comparator
+*/
+
+template <typename TSpec = size_t>
+struct Lexical
+{
+public:
+ typename Size<Lexical>::Type data_lcp;
+ char data_compare;
+
+public:
+ Lexical()
+ {
+SEQAN_CHECKPOINT
+ }
+
+ template <typename TLeft, typename TRight>
+ Lexical(TLeft const & left, TRight const & right)
+ {
+SEQAN_CHECKPOINT
+ compare(*this, left, right);
+ }
+
+ Lexical(Lexical const & other):
+ data_lcp(other.data_lcp),
+ data_compare(other.data_compare)
+ {
+SEQAN_CHECKPOINT
+ };
+
+ Lexical & operator=(Lexical const & other)
+ {
+SEQAN_CHECKPOINT
+ data_compare = other.data_compare;
+ data_lcp = other.data_lcp;
+ return *this;
+ }
+
+ ~Lexical() {}
+//____________________________________________________________________________
+
+ enum
+ {
+ EQUAL = 1,
+ LESS = 2,
+ GREATER = 4,
+ LEFT_IS_PREFIX = 8,
+ RIGHT_IS_PREFIX = 16
+ };
+};
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Metafunctions
+//////////////////////////////////////////////////////////////////////////////
+// Comparator: returns object that can compare objects of type T
+
+/**
+.Metafunction.Comparator:
+..summary:Type of comparator object
+..signature:Comparator<T>::Type
+..param.T:Type for which the comparator type is to be determined.
+..returns.param.Type:Comparator type
+..remarks:Comparators are objects that can be used to compare other objects and store the
+result of comparisons.
+*/
+template <typename T>
+struct Comparator
+{
+ typedef Lexical<typename Size<T>::Type> Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// Size
+
+template <typename TSpec>
+struct Size<Lexical<TSpec> >
+{
+ typedef TSpec Type;
+};
+
+template <typename TSpec>
+struct Size<Lexical<TSpec> const>
+{
+ typedef TSpec Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// Spec
+
+template <typename TSpec>
+struct Spec<Lexical<TSpec> >
+{
+ typedef TSpec Type;
+};
+
+template <typename TSpec>
+struct Spec<Lexical<TSpec> const>
+{
+ typedef TSpec Type;
+};
+
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+// compare
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.compare:
+..cat:Comparisons
+..summary:Compares two objects.
+..signature:compare(comparator, left, right)
+..param.left:The first objects.
+..param.right:The second objects that is compared to $left$.
+..param.comparator:Object that stores the results.
+...type:Class.Lexical
+..see:Metafunction.Comparator
+*/
+
+template <typename TSpec, typename TLeft, typename TRight>
+inline void
+compare_(Lexical<TSpec> & lexical,
+ TLeft & left,
+ TRight & right)
+{
+SEQAN_CHECKPOINT
+ typedef typename Value<TLeft>::Type TLeftValue;
+
+ typename Iterator<TLeft, Standard>::Type left_it = begin(left, Standard());
+ typename Size<TLeft>::Type left_length = length(left);
+ typename Iterator<TRight, Standard>::Type right_it = begin(right, Standard());
+ typename Size<TRight>::Type right_length = length(right);
+
+ if (left_length == right_length) lexical.data_compare = Lexical<TSpec>::EQUAL;
+ else if (left_length < right_length) lexical.data_compare = Lexical<TSpec>::LEFT_IS_PREFIX;
+ else
+ {
+ lexical.data_compare = Lexical<TSpec>::RIGHT_IS_PREFIX;
+ left_length = right_length;
+ }
+
+ lexical.data_lcp = 0;
+ for (lexical.data_lcp = 0; lexical.data_lcp < left_length; ++lexical.data_lcp)
+ {
+ if (*left_it < *right_it)
+ {
+ lexical.data_compare = Lexical<TSpec>::LESS;
+ break;
+ }
+ if (*left_it > *right_it)
+ {
+ lexical.data_compare = Lexical<TSpec>::GREATER;
+ break;
+ }
+ ++left_it;
+ ++right_it;
+ }
+}
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TSpec, typename TLeft, typename TRight>
+inline void
+compare(Lexical<TSpec> & lexical,
+ TLeft const & left,
+ TRight const & right)
+{
+ compare_(lexical, left, right);
+}
+
+//workaround for VC++ "const arrays" bug
+template <typename TSpec, typename TLeftValue, typename TRight>
+inline void
+compare(Lexical<TSpec> & lexical,
+ TLeftValue const * left,
+ TRight const & right)
+{
+ compare_(lexical, left, right);
+}
+template <typename TSpec, typename TLeftValue, typename TRightValue>
+inline void
+compare(Lexical<TSpec> & lexical,
+ TLeftValue const * left,
+ TRightValue const * right)
+{
+ compare_(lexical, left, right);
+}
+template <typename TSpec, typename TLeft, typename TRightValue>
+inline void
+compare(Lexical<TSpec> & lexical,
+ TLeft const & left,
+ TRightValue const * right)
+{
+ compare_(lexical, left, right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// isEqual
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.isEqual:
+..cat:Comparisons
+..summary:Operator "==".
+..signature:isEqual(left, right)
+..signature:isEqual(comparator)
+..param.left:The first parameter.
+..param.right:The second parameter that is compared to $left$.
+..param.comparator:A comparator.
+...type:Class.Lexical
+..returns:$true$ if $left$ equals $right$, $false$ otherwise.
+..see:Metafunction.Comparator
+*/
+template <typename TLeft, typename TRight >
+inline bool
+isEqual(TLeft const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return left == right;
+}
+
+template <typename TSpec>
+inline bool
+isEqual(Lexical<TSpec> const & _lex)
+{
+SEQAN_CHECKPOINT
+ return (_lex.data_compare & Lexical<TSpec>::EQUAL);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// isNotEqual
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.isNotEqual:
+..cat:Comparisons
+..summary:Operator "!=".
+..signature:isNotEqual(left, right)
+..signature:isNotEqual(comparator)
+..param.left:The first parameter.
+..param.right:The second parameter that is compared to $left$.
+..param.comparator:A comparator.
+...type:Class.Lexical
+..returns:$true$ if $left$ is not equal to $right$, $false$ otherwise.
+..see:Metafunction.Comparator
+*/
+template <typename TLeft, typename TRight >
+inline bool
+isNotEqual(TLeft const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return left != right;
+}
+
+template <typename TSpec>
+inline bool
+isNotEqual(Lexical<TSpec> const & _lex)
+{
+SEQAN_CHECKPOINT
+ return !(_lex.data_compare & Lexical<TSpec>::EQUAL);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// isLess
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.isLess:
+..cat:Comparisons
+..summary:Operator "<".
+..signature:isLess(left, right [, prefix_order_tag])
+..signature:isLess(comparator)
+..param.left:The first parameter.
+..param.right:The second parameter that is compared to $left$.
+..param.prefix_order_tag:Tag that specify whether prefixes are less or greater. (optional)
+...text:If omitted, the default tag is determined by @Metafunction.DefaultPrefixOrder@ for the type of $left$.
+...see:Tag.Prefix Order
+..param.comparator:A comparator.
+...type:Class.Lexical
+..returns:$true$ if $left$ is less than $right$, $false$ otherwise.
+..see:Metafunction.Comparator
+..remarks:
+...text:Sequences are compared in lexicographical order.
+..see:Tag.Prefix Order
+..see:Metafunction.DefaultPrefixOrder
+*/
+template <typename TLeft, typename TRight, typename TPrefixOrder >
+inline bool
+isLess(TLeft const & left,
+ TRight const & right,
+ Tag<TPrefixOrder> const tag)
+{
+SEQAN_CHECKPOINT
+ typename Comparator<TLeft>::Type _lex(left, right);
+ return isLess(_lex, tag);
+}
+template <typename TLeft, typename TRight>
+inline bool
+isLess(TLeft const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return left < right;
+}
+
+template <typename TSpec>
+inline bool
+isLess(Lexical<TSpec> const & _lex,
+ TagPrefixLess)
+{
+SEQAN_CHECKPOINT
+ return (_lex.data_compare & (Lexical<TSpec>::LESS | Lexical<TSpec>::LEFT_IS_PREFIX));
+}
+template <typename TSpec>
+inline bool
+isLess(Lexical<TSpec> const & _lex,
+ TagPrefixGreater)
+{
+SEQAN_CHECKPOINT
+ return (_lex.data_compare & (Lexical<TSpec>::LESS | Lexical<TSpec>::RIGHT_IS_PREFIX));
+}
+template <typename TSpec>
+inline bool
+isLess(Lexical<TSpec> const & _lex)
+{
+SEQAN_CHECKPOINT
+ return isLess(_lex, typename DefaultPrefixOrder< Lexical<TSpec> >::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// isLessOrEqual
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.isLessOrEqual:
+..cat:Comparisons
+..summary:Operator "<=".
+..signature:isLessOrEqual(left, right [, prefix_order_tag])
+..signature:isLessOrEqual(comparator)
+..param.left:The first parameter.
+..param.right:The second parameter that is compared to $left$.
+..param.prefix_order_tag:Tag that specify whether prefixes are less or greater. (optional)
+...text:If omitted, the default tag is determined by @Metafunction.DefaultPrefixOrder@ for the type of $left$.
+...see:Tag.Prefix Order
+..param.comparator:A comparator.
+...type:Class.Lexical
+..returns:$true$ if $left$ is less than or equal to $right$, $false$ otherwise.
+..see:Metafunction.Comparator
+..remarks:
+...text:Sequences are compared in lexicographical order.
+..see:Tag.Prefix Order
+..see:Metafunction.DefaultPrefixOrder
+*/
+
+template <typename TLeft, typename TRight, typename TPrefixOrder >
+inline bool
+isLessOrEqual(TLeft const & left,
+ TRight const & right,
+ Tag<TPrefixOrder> const tag)
+{
+SEQAN_CHECKPOINT
+ typename Comparator<TLeft>::Type _lex(left, right);
+ return isLessOrEqual(_lex, tag);
+}
+template <typename TLeft, typename TRight>
+inline bool
+isLessOrEqual(TLeft const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return left <= right;
+}
+
+template <typename TSpec>
+inline bool
+isLessOrEqual(Lexical<TSpec> const & _lex,
+ TagPrefixLess)
+{
+SEQAN_CHECKPOINT
+ return (_lex.data_compare & (Lexical<TSpec>::LESS | Lexical<TSpec>::EQUAL | Lexical<TSpec>::LEFT_IS_PREFIX));
+}
+template <typename TSpec>
+inline bool
+isLessOrEqual(Lexical<TSpec> const & _lex,
+ TagPrefixGreater)
+{
+SEQAN_CHECKPOINT
+ return (_lex.data_compare & (Lexical<TSpec>::LESS | Lexical<TSpec>::EQUAL | Lexical<TSpec>::RIGHT_IS_PREFIX));
+}
+template <typename TSpec>
+inline bool
+isLessOrEqual(Lexical<TSpec> const & _lex)
+{
+SEQAN_CHECKPOINT
+ return isLessOrEqual(_lex, typename DefaultPrefixOrder< Lexical<TSpec> >::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// isGreater
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.isGreater:
+..cat:Comparisons
+..summary:Operator ">".
+..signature:isGreater(left, right [, prefix_order_tag])
+..signature:isGreater(comparator)
+..param.left:The first parameter.
+..param.right:The second parameter that is compared to $left$.
+..param.prefix_order_tag:Tag that specify whether prefixes are less or greater. (optional)
+...text:If omitted, the default tag is determined by @Metafunction.DefaultPrefixOrder@ for the type of $left$.
+...see:Tag.Prefix Order
+..param.comparator:A comparator.
+...type:Class.Lexical
+..returns:$true$ if $left$ is greater than $right$, $false$ otherwise.
+..see:Metafunction.Comparator
+..remarks:
+...text:Sequences are compared in lexicographical order.
+..see:Tag.Prefix Order
+..see:Metafunction.DefaultPrefixOrder
+*/
+template <typename TLeft, typename TRight, typename TPrefixOrder >
+inline bool
+isGreater(TLeft const & left,
+ TRight const & right,
+ Tag<TPrefixOrder> const tag)
+{
+SEQAN_CHECKPOINT
+ typename Comparator<TLeft>::Type _lex(left, right);
+ return isGreater(_lex, tag);
+}
+template <typename TLeft, typename TRight>
+inline bool
+isGreater(TLeft const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return left > right;
+}
+
+template <typename TSpec>
+inline bool
+isGreater(Lexical<TSpec> const & _lex,
+ TagPrefixLess)
+{
+SEQAN_CHECKPOINT
+ return (_lex.data_compare & (Lexical<TSpec>::GREATER | Lexical<TSpec>::RIGHT_IS_PREFIX));
+}
+template <typename TSpec>
+inline bool
+isGreater(Lexical<TSpec> const & _lex,
+ TagPrefixGreater)
+{
+SEQAN_CHECKPOINT
+ return (_lex.data_compare & (Lexical<TSpec>::GREATER | Lexical<TSpec>::LEFT_IS_PREFIX));
+}
+template <typename TSpec>
+inline bool
+isGreater(Lexical<TSpec> const & _lex)
+{
+SEQAN_CHECKPOINT
+ return isGreater(_lex, typename DefaultPrefixOrder< Lexical<TSpec> >::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// isGreaterOrEqual
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.isGreaterOrEqual:
+..cat:Comparisons
+..summary:Operator ">=".
+..signature:isGreaterOrEqual(left, right [, prefix_order_tag])
+..signature:isGreaterOrEqual(comparator)
+..param.left:The first parameter.
+..param.right:The second parameter that is compared to $left$.
+..param.prefix_order_tag:Tag that specify whether prefixes are less or greater. (optional)
+...text:If omitted, the default tag is determined by @Metafunction.DefaultPrefixOrder@ for the type of $left$.
+...see:Tag.Prefix Order
+..param.comparator:A comparator.
+...type:Class.Lexical
+..returns:$true$ if $left$ is greater than or equal to $right$, $false$ otherwise.
+..see:Metafunction.Comparator
+..remarks:
+...text:Sequences are compared in lexicographical order.
+..see:Tag.Prefix Order
+..see:Metafunction.DefaultPrefixOrder
+*/
+
+template <typename TLeft, typename TRight, typename TPrefixOrder >
+inline bool
+isGreaterOrEqual(TLeft const & left,
+ TRight const & right,
+ Tag<TPrefixOrder> const tag)
+{
+SEQAN_CHECKPOINT
+ typename Comparator<TLeft>::Type _lex(left, right);
+ return isGreaterOrEqual(_lex, tag);
+}
+template <typename TLeft, typename TRight>
+inline bool
+isGreaterOrEqual(TLeft const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return left >= right;
+}
+
+template <typename TSpec>
+inline bool
+isGreaterOrEqual(Lexical<TSpec> const & _lex,
+ TagPrefixLess)
+{
+SEQAN_CHECKPOINT
+ return (_lex.data_compare & (Lexical<TSpec>::GREATER | Lexical<TSpec>::EQUAL | Lexical<TSpec>::RIGHT_IS_PREFIX));
+}
+template <typename TSpec>
+inline bool
+isGreaterOrEqual(Lexical<TSpec> const & _lex,
+ TagPrefixGreater)
+{
+SEQAN_CHECKPOINT
+ return (_lex.data_compare & (Lexical<TSpec>::GREATER | Lexical<TSpec>::EQUAL | Lexical<TSpec>::LEFT_IS_PREFIX));
+}
+template <typename TSpec>
+inline bool
+isGreaterOrEqual(Lexical<TSpec> const & _lex)
+{
+SEQAN_CHECKPOINT
+ return isGreaterOrEqual(_lex, typename DefaultPrefixOrder< Lexical<TSpec> >::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// isPrefix
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.isPrefix:
+..cat:Comparisons
+..summary:Test whether a sequence is prefix of another sequence.
+..signature:isPrefix(left, right)
+..signature:isPrefix(comparator)
+..param.left:The first sequence, the putative prefix.
+..param.right:The second sequence.
+..param.comparator:A comparator.
+...type:Class.Lexical
+..returns:$true$ if $left$ is a prefix of $right$, $false$ otherwise.
+..see:Metafunction.Comparator
+..remarks:By definition, the whole sequence is a prefix of itself too: $isPrefix("abc", "abc") == true$.
+*/
+
+template <typename TLeft, typename TRight >
+inline bool
+isPrefix(TLeft const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ typename Comparator<TLeft>::Type _lex(left, right);
+ return isPrefix(_lex);
+}
+template <typename TSpec>
+inline bool
+isPrefix(Lexical<TSpec> const & _lex)
+{
+SEQAN_CHECKPOINT
+ return (_lex.data_compare & (Lexical<TSpec>::LEFT_IS_PREFIX | Lexical<TSpec>::EQUAL));
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// hasPrefix
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.hasPrefix:
+..cat:Comparisons
+..summary:Test whether a sequence is prefix of another sequence.
+..signature:hasPrefix(left, right)
+..signature:hasPrefix(comparator)
+..param.left:The first sequence.
+..param.right:The second sequence, the putative prefix.
+..param.comparator:A comparator.
+...type:Class.Lexical
+..returns:$true$ if $right$ is a prefix of $left$, $false$ otherwise.
+..see:Metafunction.Comparator
+..see:Function.isPrefix
+..remarks:By definition, the whole sequence is a prefix of itself too: $hasPrefix("abc", "abc") == true$.
+*/
+
+template <typename TLeft, typename TRight >
+inline bool
+hasPrefix(TLeft const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ typename Comparator<TLeft>::Type _lex(left, right);
+ return hasPrefix(_lex);
+}
+template <typename TSpec>
+inline bool
+hasPrefix(Lexical<TSpec> const & _lex)
+{
+SEQAN_CHECKPOINT
+ return (_lex.data_compare & (Lexical<TSpec>::RIGHT_IS_PREFIX | Lexical<TSpec>::EQUAL));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// lcpLength
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.lcpLength:
+..summary:Length of longest common prefix.
+..cat:Comparisons
+..signature:lcpLength(left, right)
+..signature:lcpLength(comparator)
+..param.left:The first sequence.
+..param.right:The second sequence that is compared to $left$.
+..param.comparator:A comparator.
+...type:Class.Lexical
+..returns:The length of the longest common prefix of $left$ and $right$.
+..see:Metafunction.Comparator
+*/
+template <typename TLeft, typename TRight >
+inline typename Size<TLeft>::Type
+lcpLength(TLeft const & left, TRight const & right)
+{
+SEQAN_CHECKPOINT
+ typename Comparator<TLeft>::Type _lex(left, right);
+ return lcpLength(_lex);
+}
+
+template <typename TSpec>
+inline typename Size< Lexical<TSpec> >::Type
+lcpLength(Lexical<TSpec> const & _lex)
+{
+SEQAN_CHECKPOINT
+ return _lex.data_lcp;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// lcpLength
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.ordValue:
+..summary:Maps an alphabet 1-to-1 to the interval [0..ValueSize).
+..cat:Alphabets
+..signature:ordValue(value)
+..param.value:Arbitrary character value.
+...type:Class.SimpleType
+..returns:An $unsigned int$ between 0 and @Metafunction.ValueSize@ of the type of value.
+..note:This function first converts value to its unsigned value type and after that to an $unsigned int$.
+You can't use $(unsigned int)c$ for a character $c$ as on some systems $char$ is signed and a $-1$ would be mapped to $0xffffffff$ instead of $0x000000ff$.
+*/
+
+template <typename TValue>
+inline unsigned ordValue(TValue const &c)
+{
+ return (typename _MakeUnsigned<TValue>::Type const &)c;
+}
+
+template <typename TValue, typename TSpec>
+inline unsigned ordValue(SimpleType<TValue,TSpec> const &c)
+{
+ return c;
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/sequence/segment_base.h b/src/libSSA/seqan/sequence/segment_base.h
new file mode 100644
index 0000000..af45a2e
--- /dev/null
+++ b/src/libSSA/seqan/sequence/segment_base.h
@@ -0,0 +1,1181 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: segment_base.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SEGMENT_BASE_H
+#define SEQAN_HEADER_SEGMENT_BASE_H
+
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// Segment
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Class.Segment:
+..cat:Sequences
+..summary:A contiguous part of a sequence.
+..signature:Segment<THost, TSpec>
+..param.THost:Type of the whole sequence.
+...metafunction:Metafunction.Host
+...text:Instances of $Segment<THost, TSpec>$ are subsequences of $THost$ objects.
+..param.TSpec:The specializing type.
+...metafunction:Metafunction.Spec
+...default:@Spec.InfixSegment at .
+*/
+
+struct InfixSegment;
+
+template <typename THost, typename TSpec = InfixSegment>
+class Segment
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Host.param.T.type:Class.Segment
+
+template <typename THost, typename TSpec>
+struct Host<Segment<THost, TSpec> >
+{
+ typedef THost Type;
+};
+
+template <typename THost, typename TSpec>
+struct Host<Segment<THost, TSpec> const >
+{
+ typedef THost Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Spec.param.T.type:Class.Segment
+
+template <typename THost, typename TSpec>
+struct Spec<Segment<THost, TSpec> >
+{
+ typedef TSpec Type;
+};
+template <typename THost, typename TSpec>
+struct Spec<Segment<THost, TSpec> const>
+{
+ typedef TSpec Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Value.param.T.type:Class.Segment
+
+template <typename THost, typename TSpec>
+struct Value<Segment<THost, TSpec> >
+{
+ typedef typename Value<THost>::Type Type;
+};
+
+template <typename THost, typename TSpec>
+struct Value<Segment<THost, TSpec> const >
+{
+ typedef typename Value<THost const>::Type Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.GetValue.param.T.type:Class.Segment
+
+template <typename THost, typename TSpec>
+struct GetValue<Segment<THost, TSpec> >
+{
+ typedef typename GetValue<THost>::Type Type;
+};
+
+template <typename THost, typename TSpec>
+struct GetValue<Segment<THost, TSpec> const >
+{
+ typedef typename GetValue<THost const>::Type Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Iterator.param.T.type:Class.Segment
+
+template <typename THost, typename TSpec>
+struct Iterator<Segment<THost, TSpec>, Rooted>
+{
+ typedef Segment<THost, TSpec> TSequence;
+ typedef typename Iterator<THost, Standard>::Type TIterator;
+ typedef Iter<TSequence, AdaptorIterator<TIterator> > Type;
+};
+template <typename THost, typename TSpec>
+struct Iterator<Segment<THost, TSpec> const, Rooted>
+{
+ typedef Segment<THost, TSpec> const TSequence;
+ typedef typename Iterator<THost const, Standard>::Type TIterator;
+ typedef Iter<TSequence, AdaptorIterator<TIterator> > Type;
+};
+
+template <typename THost, typename TSpec>
+struct Iterator<Segment<THost, TSpec>, Standard>:
+ Iterator<THost, Standard>
+{
+};
+template <typename THost, typename TSpec>
+struct Iterator<Segment<THost, TSpec> const, Standard>:
+ Iterator<THost, Standard>
+{
+};
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Size.param.T.type:Class.Segment
+
+template <typename THost, typename TSpec>
+struct Size<Segment<THost, TSpec> >
+{
+ typedef typename Size<THost>::Type Type;
+};
+
+template <typename THost, typename TSpec>
+struct Size<Segment<THost, TSpec> const >
+{
+ typedef typename Size<THost>::Type Type;
+};
+
+template <typename THost, typename TSpec>
+struct Position<Segment<THost, TSpec> >
+{
+ typedef typename Position<THost>::Type Type;
+};
+
+template <typename THost, typename TSpec>
+struct Position<Segment<THost, TSpec> const >
+{
+ typedef typename Position<THost>::Type Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.DefaultOverflowImplicit.param.T.type:Class.Segment
+
+template <typename THost, typename TSpec>
+struct DefaultOverflowImplicit<Segment<THost, TSpec > >:
+ DefaultOverflowImplicit<THost>
+{
+};
+
+template <typename THost, typename TSpec>
+struct DefaultOverflowImplicit<Segment<THost, TSpec > const >:
+ DefaultOverflowImplicit<THost>
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.DefaultOverflowExplicit.param.T.type:Class.Segment
+
+template <typename THost, typename TSpec>
+struct DefaultOverflowExplicit<Segment<THost, TSpec > >:
+ DefaultOverflowExplicit<THost>
+{
+};
+
+template <typename THost, typename TSpec>
+struct DefaultOverflowExplicit<Segment<THost, TSpec > const >:
+ DefaultOverflowExplicit<THost>
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.IsContiguous.param.T.type:Class.Segment
+
+template <typename THost, typename TSpec>
+struct IsContiguous< Segment<THost, TSpec> >:
+ public IsContiguous<THost> {};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.IsSequence.param.T.type:Class.Segment
+
+template <typename THost, typename TSpec>
+struct IsSequence< Segment<THost, TSpec> > {
+ typedef True Type;
+ enum { VALUE = true };
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.atBegin.param.iterator.type:Class.Segment
+///.Function.atEnd.param.iterator.type:Class.Segment
+///.Function.goBegin.param.iterator.type:Class.Segment
+///.Function.goEnd.param.iterator.type:Class.Segment
+///.Function.goNext.param.iterator.type:Class.Segment
+///.Function.goPrevious.param.iterator.type:Class.Segment
+///.Function.value.param.container.type:Class.Segment
+
+///.Function.shareResources.param.sequence1, sequence2.type:Class.Segment
+
+//////////////////////////////////////////////////////////////////////////////
+// functions for all Segment classes
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.id.param.object.type:Class.Segment
+
+template <typename THost, typename TSpec>
+inline void const *
+id(Segment<THost, TSpec> const & me)
+{
+SEQAN_CHECKPOINT
+ return id(host(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.length.param.object.type:Class.Segment
+
+template <typename THost, typename TSpec>
+inline typename Size<Segment<THost, TSpec> const>::Type
+length(Segment<THost, TSpec> const & me)
+{
+SEQAN_CHECKPOINT
+ return endPosition(me) - beginPosition(me);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.capacity.param.object.type:Class.Segment
+
+template <typename THost, typename TSpec>
+inline typename Size< Segment<THost, TSpec> const>::Type
+capacity(Segment<THost, TSpec> const & me)
+{
+SEQAN_CHECKPOINT
+ return capacity(host(me)) + length(me) - length(host(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// assign
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.assign:
+..remarks:If $target$ is a @Class.Segment@ object, then
+$limit$ denotes the maximal length of @Function.host.$host(target)$@ after the operation.
+..param.target.type:Class.Segment
+..param.source.type:Class.Segment
+*/
+
+//overload of binary version for strings:
+
+template<typename THost, typename TSpec, typename TSource>
+inline void
+assign(Segment<THost, TSpec> & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ typedef Segment<THost, TSpec> TTarget;
+ assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template<typename THost, typename TSpec, typename TSource>
+inline void
+assign(Segment<THost, TSpec> & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ typedef Segment<THost, TSpec> TTarget;
+ assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+
+//(for temporary targets)
+
+template<typename THost, typename TSpec, typename TSource>
+inline void
+assign(Segment<THost, TSpec> const & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ typedef Segment<THost, TSpec> const TTarget;
+ assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template<typename THost, typename TSpec, typename TSource>
+inline void
+assign(Segment<THost, TSpec> const & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ typedef Segment<THost, TSpec> const TTarget;
+ assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TExpand>
+struct _Assign_Segment
+{
+ template <typename THost, typename TSpec, typename TSource>
+ static inline void
+ assign_(
+ Segment<THost, TSpec> & target,
+ TSource & source)
+ {
+SEQAN_CHECKPOINT
+ if ((void *) &target == (void *) &source) return;
+
+ typedef Segment<THost, TSpec> Target;
+
+ replace(host(target), beginPosition(target), endPosition(target), source, TExpand());
+
+ typename Iterator<Target, Standard>::Type new_end = begin(target, Standard()) + length(source);
+ typename Iterator<THost, Standard>::Type host_end = end(host(target), Standard());
+ if (new_end > host_end) new_end = host_end;
+ setEnd(target, new_end);
+ }
+
+ template <typename THost, typename TSpec, typename TSource>
+ static inline void
+ assign_(
+ Segment<THost, TSpec> & target,
+ TSource & source,
+ typename Size< Segment<THost, TSpec> >::Type limit)
+ {
+SEQAN_CHECKPOINT
+ if ((void *) &target == (void *) &source) return;
+
+ typedef Segment<THost, TSpec> Target;
+
+ replace(host(target), beginPosition(target), endPosition(target), source, limit, TExpand());
+
+ typename Iterator<Target, Standard>::Type new_end = begin(target, Standard()) + length(source);
+ typename Iterator<THost, Standard>::Type host_end = end(host(target), Standard());
+ if (begin(target, Standard()) > host_end) setBegin(target, host_end);
+ if (new_end > host_end) new_end = host_end;
+ setEnd(target, new_end);
+ }
+
+ template <typename THost, typename TSpec, typename TSource>
+ static inline void
+ assign_(
+ Segment<THost, TSpec> const & target,
+ TSource & source)
+ {
+SEQAN_CHECKPOINT
+ replace(host(target), beginPosition(target), endPosition(target), source, TExpand());
+ }
+
+ template <typename THost, typename TSpec, typename TSource>
+ static inline void
+ assign_(
+ Segment<THost, TSpec> const & target,
+ TSource & source,
+ typename Size< Segment<THost, TSpec> >::Type limit)
+ {
+SEQAN_CHECKPOINT
+ replace(host(target), beginPosition(target), endPosition(target), source, limit, TExpand());
+ }
+};
+
+//____________________________________________________________________________
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+assign(Segment<THost, TSpec> & target,
+ TSource & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Assign_Segment<Tag<TExpand> const>::assign_(target, source);
+}
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+assign(Segment<THost, TSpec> & target,
+ TSource const & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Assign_Segment<Tag<TExpand> const>::assign_(target, source);
+}
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+assign(Segment<THost, TSpec> & target,
+ TSource & source,
+ typename Size< Segment<THost, TSpec> >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Assign_Segment<Tag<TExpand> const>::assign_(target, source, limit);
+}
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+assign(Segment<THost, TSpec> & target,
+ TSource const & source,
+ typename Size< Segment<THost, TSpec> >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Assign_Segment<Tag<TExpand> const>::assign_(target, source, limit);
+}
+
+//(for temporary targets)
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+assign(Segment<THost, TSpec> const & target,
+ TSource & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Assign_Segment<Tag<TExpand> const>::assign_(target, source);
+}
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+assign(Segment<THost, TSpec> const & target,
+ TSource const & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Assign_Segment<Tag<TExpand> const>::assign_(target, source);
+}
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+assign(Segment<THost, TSpec> const & target,
+ TSource & source,
+ typename Size< Segment<THost, TSpec> >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Assign_Segment<Tag<TExpand> const>::assign_(target, source, limit);
+}
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+assign(Segment<THost, TSpec> const & target,
+ TSource const & source,
+ typename Size< Segment<THost, TSpec> >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Assign_Segment<Tag<TExpand> const>::assign_(target, source, limit);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// move
+//////////////////////////////////////////////////////////////////////////////
+
+//overload of binary version:
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+move(Segment<THost, TSpec> & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ typedef Segment<THost, TSpec> TTarget;
+ move(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+move(Segment<THost, TSpec> & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ typedef Segment<THost, TSpec> TTarget;
+ move(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+
+//(for temporary targets)
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+move(Segment<THost, TSpec> const & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ typedef Segment<THost, TSpec> const TTarget;
+ move(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+move(Segment<THost, TSpec> const & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ typedef Segment<THost, TSpec> const TTarget;
+ move(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// append
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.append:
+..remarks:If $target$ is a @Class.Segment@ object, then
+$limit$ denotes the maximal length of @Function.host.$host(target)$@ after the operation.
+..param.target.type:Class.Segment
+..param.source.type:Class.Segment
+*/
+
+
+template <typename TExpand>
+struct _Append_Sequence_2_Segment
+{
+ template <typename THost, typename TSpec, typename TSource>
+ static inline void
+ append_(
+ Segment<THost, TSpec> & target,
+ TSource & source)
+ {
+SEQAN_CHECKPOINT
+ typedef Segment<THost, TSpec> Target;
+
+ replace(host(target), endPosition(target), endPosition(target), source, TExpand());
+
+ typename Iterator<Target, Standard>::Type new_end = end(target, Standard()) + length(source);
+ typename Iterator<THost, Standard>::Type host_end = end(host(target), Standard());
+ if (new_end > host_end) new_end = host_end;
+ setEnd(target, new_end);
+ }
+
+ template <typename THost, typename TSpec, typename TSource>
+ static inline void
+ append_(
+ Segment<THost, TSpec> & target,
+ TSource const & source,
+ typename Size< Segment<THost, TSpec> >::Type limit)
+ {
+SEQAN_CHECKPOINT
+ typedef Segment<THost, TSpec> Target;
+
+ replace(host(target), endPosition(target), endPosition(target), source, limit, TExpand());
+ typename Iterator<Target, Standard>::Type new_end = end(target, Standard()) + length(source);
+ typename Iterator<THost, Standard>::Type host_end = end(host(target), Standard());
+ if (begin(target) > host_end) setBegin(target, host_end);
+ if (new_end > host_end) new_end = host_end;
+ setEnd(target, new_end);
+ }
+
+ template <typename THost, typename TSpec, typename TSource>
+ static inline void
+ append_(
+ Segment<THost, TSpec> const & target,
+ TSource & source)
+ {
+SEQAN_CHECKPOINT
+ replace(host(target), endPosition(target), endPosition(target), source, TExpand());
+ }
+
+ template <typename THost, typename TSpec, typename TSource>
+ static inline void
+ append_(
+ Segment<THost, TSpec> const & target,
+ TSource const & source,
+ typename Size< Segment<THost, TSpec> >::Type limit)
+ {
+SEQAN_CHECKPOINT
+ replace(host(target), endPosition(target), endPosition(target), source, limit, TExpand()); //??? INSERT
+ }
+};
+//____________________________________________________________________________
+
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+append(
+ Segment<THost, TSpec> & target,
+ TSource & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Append_Sequence_2_Segment<Tag<TExpand> const>::append_(target, source);
+}
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+append(
+ Segment<THost, TSpec> & target,
+ TSource const & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Append_Sequence_2_Segment<Tag<TExpand> const>::append_(target, source);
+}
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+append(
+ Segment<THost, TSpec> & target,
+ TSource & source,
+ typename Size< Segment<THost, TSpec> >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Append_Sequence_2_Segment<Tag<TExpand> const>::append_(target, source, limit);
+}
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+append(
+ Segment<THost, TSpec> & target,
+ TSource const & source,
+ typename Size< Segment<THost, TSpec> >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Append_Sequence_2_Segment<Tag<TExpand> const>::append_(target, source, limit);
+}
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+append(
+ Segment<THost, TSpec> const & target,
+ TSource & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Append_Sequence_2_Segment<Tag<TExpand> const>::append_(target, source);
+}
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+append(
+ Segment<THost, TSpec> const & target,
+ TSource const & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Append_Sequence_2_Segment<Tag<TExpand> const>::append_(target, source);
+}
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+append(
+ Segment<THost, TSpec> const & target,
+ TSource & source,
+ typename Size< Segment<THost, TSpec> >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Append_Sequence_2_Segment<Tag<TExpand> const>::append_(target, source, limit);
+}
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+append(
+ Segment<THost, TSpec> const & target,
+ TSource const & source,
+ typename Size< Segment<THost, TSpec> >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Append_Sequence_2_Segment<Tag<TExpand> const>::append_(target, source, limit);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// appendValue
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TExpand>
+struct _Append_Value_2_Segment
+{
+ template <typename T, typename TValue>
+ static inline void
+ appendValue_(T & me,
+ TValue & _value)
+ {
+SEQAN_CHECKPOINT
+ insertValue(host(me), endPosition(me), TExpand());
+ if (endPosition(me) < length(host(me)) ) //this could be false for some TExpand
+ {
+ setEndPosition(me, endPosition(me) + 1);
+ }
+ }
+};
+
+//____________________________________________________________________________
+
+template <typename THost, typename TSpec, typename TValue, typename TExpand>
+inline void
+appendValue(Segment<THost, TSpec> & me,
+ TValue const & _value,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Append_Value_2_Segment<Tag<TExpand> const>::appendValue_(me, _value);
+}
+template <typename THost, typename TSpec, typename TValue, typename TExpand>
+inline void
+appendValue(Segment<THost, TSpec> const & me,
+ TValue const & _value,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Append_Value_2_Segment<Tag<TExpand> const>::appendValue_(me, _value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// insertValue
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TExpand>
+struct _Insert_Value_2_Segment
+{
+ template <typename T, typename TPosition, typename TValue>
+ static inline void
+ insertValue_(T & me,
+ TPosition pos,
+ TValue & _value)
+ {
+SEQAN_CHECKPOINT
+ insertValue(host(me), beginPosition(me) + pos, TExpand());
+ if (endPosition(me) < length(host(me)) ) //this could be false for some TExpand
+ {
+ setEndPosition(me, endPosition(me) + 1);
+ }
+ }
+};
+
+//____________________________________________________________________________
+
+template <typename THost, typename TSpec, typename TPosition, typename TValue, typename TExpand>
+inline void
+insertValue(Segment<THost, TSpec> & me,
+ TPosition pos,
+ TValue const & _value,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Insert_Value_2_Segment<Tag<TExpand> const>::insertValue_(me, pos, _value);
+}
+template <typename THost, typename TSpec, typename TPosition, typename TValue, typename TExpand>
+inline void
+insertValue(Segment<THost, TSpec> const & me,
+ TPosition pos,
+ TValue const & _value,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Insert_Value_2_Segment<Tag<TExpand> const>::insertValue_(me, pos, _value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// replace
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.replace:
+..remarks:If $target$ is a @Class.Segment@ object, then
+$limit$ denotes the maximal length of @Function.host.$host(target)$@ after the operation.
+..param.target.type:Class.Segment
+..param.source.type:Class.Segment
+*/
+
+template <typename TExpand>
+struct _Replace_Sequence_2_Segment
+{
+ template <typename THost, typename TSpec, typename TSource>
+ static inline void
+ replace_(
+ Segment<THost, TSpec> & target,
+ typename Position< Segment<THost, TSpec> >::Type pos_begin,
+ typename Position< Segment<THost, TSpec> >::Type pos_end,
+ TSource & source)
+ {
+SEQAN_CHECKPOINT
+ typedef Segment<THost, TSpec> Target;
+
+ replace(host(target), beginPosition(target) + pos_begin, beginPosition(target) + pos_end, source, TExpand());
+
+ typename Iterator<Target, Standard>::Type new_end = begin(target, Standard()) + length(target) - pos_end + pos_begin + length(source);
+ typename Iterator<THost, Standard>::Type host_end = end(host(target), Standard());
+ if (new_end > host_end) new_end = host_end;
+ setEnd(target, new_end);
+ }
+
+ template <typename THost, typename TSpec, typename TSource>
+ static inline void
+ replace_(
+ Segment<THost, TSpec> & target,
+ typename Position< Segment<THost, TSpec> >::Type pos_begin,
+ typename Position< Segment<THost, TSpec> >::Type pos_end,
+ TSource & source,
+ typename Size< Segment<THost, TSpec> >::Type limit)
+ {
+SEQAN_CHECKPOINT
+ typedef Segment<THost, TSpec> Target;
+
+ replace(host(target), beginPosition(target) + pos_begin, beginPosition(target) + pos_end, source, limit, TExpand());
+
+ typename Iterator<Target, Standard>::Type new_end = begin(target, Standard()) + length(target) - pos_end + pos_begin + length(source);
+ typename Iterator<THost, Standard>::Type host_end = end(host(target), Standard());
+ if (begin(target, Standard()) > host_end) setBegin(target, host_end);
+ if (new_end > host_end) new_end = host_end;
+ setEnd(target, new_end);
+ }
+
+ template <typename THost, typename TSpec, typename TSource>
+ static inline void
+ replace_(
+ Segment<THost, TSpec> const & target,
+ typename Position< Segment<THost, TSpec> const>::Type pos_begin,
+ typename Position< Segment<THost, TSpec> const>::Type pos_end,
+ TSource & source)
+ {
+SEQAN_CHECKPOINT
+ replace(host(target), beginPosition(target) + pos_begin, beginPosition(target) + pos_end, source, TExpand());
+ }
+
+ template <typename THost, typename TSpec, typename TSource>
+ static inline void
+ replace_(
+ Segment<THost, TSpec> const & target,
+ typename Position< Segment<THost, TSpec> const>::Type pos_begin,
+ typename Position< Segment<THost, TSpec> const>::Type pos_end,
+ TSource & source,
+ typename Size< Segment<THost, TSpec> >::Type limit)
+ {
+SEQAN_CHECKPOINT
+ replace(host(target), beginPosition(target) + pos_begin, beginPosition(target) + pos_end, source, limit, TExpand()); //??? INSERT
+ }
+};
+//____________________________________________________________________________
+
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+replace(
+ Segment<THost, TSpec> & target,
+ typename Position< Segment<THost, TSpec> >::Type pos_begin,
+ typename Position< Segment<THost, TSpec> >::Type pos_end,
+ TSource & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Replace_Sequence_2_Segment<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source);
+}
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+replace(
+ Segment<THost, TSpec> & target,
+ typename Position< Segment<THost, TSpec> >::Type pos_begin,
+ typename Position< Segment<THost, TSpec> >::Type pos_end,
+ TSource const & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Replace_Sequence_2_Segment<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source);
+}
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+replace(
+ Segment<THost, TSpec> & target,
+ typename Position< Segment<THost, TSpec> >::Type pos_begin,
+ typename Position< Segment<THost, TSpec> >::Type pos_end,
+ TSource & source,
+ typename Size< Segment<THost, TSpec> >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Replace_Sequence_2_Segment<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source, limit);
+}
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+replace(
+ Segment<THost, TSpec> & target,
+ typename Position< Segment<THost, TSpec> >::Type pos_begin,
+ typename Position< Segment<THost, TSpec> >::Type pos_end,
+ TSource const & source,
+ typename Size< Segment<THost, TSpec> >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Replace_Sequence_2_Segment<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source, limit);
+}
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+replace(
+ Segment<THost, TSpec> const & target,
+ typename Position< Segment<THost, TSpec> const>::Type pos_begin,
+ typename Position< Segment<THost, TSpec> const>::Type pos_end,
+ TSource & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Replace_Sequence_2_Segment<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source);
+}
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+replace(
+ Segment<THost, TSpec> const & target,
+ typename Position< Segment<THost, TSpec> const>::Type pos_begin,
+ typename Position< Segment<THost, TSpec> const>::Type pos_end,
+ TSource const & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Replace_Sequence_2_Segment<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source);
+}
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+replace(
+ Segment<THost, TSpec> const & target,
+ typename Position< Segment<THost, TSpec> const>::Type pos_begin,
+ typename Position< Segment<THost, TSpec> const>::Type pos_end,
+ TSource & source,
+ typename Size< Segment<THost, TSpec> >::Type limit,
+ Tag<TExpand> const )
+{
+SEQAN_CHECKPOINT
+ _Replace_Sequence_2_Segment<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source, limit);
+}
+template <typename THost, typename TSpec, typename TSource, typename TExpand>
+inline void
+replace(
+ Segment<THost, TSpec> const & target,
+ typename Position< Segment<THost, TSpec> const>::Type pos_begin,
+ typename Position< Segment<THost, TSpec> const>::Type pos_end,
+ TSource const & source,
+ typename Size< Segment<THost, TSpec> >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Replace_Sequence_2_Segment<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source, limit);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// handling of iterators as begin and end
+
+/*
+template<typename THost, typename TTargetSpec, typename TSource, typename TExpand>
+inline void
+replace(Segment<THost, TTargetSpec> & target,
+ typename Iterator< Segment<THost, TTargetSpec>, Rooted>::Type pos_begin,
+ typename Iterator< Segment<THost, TTargetSpec>, Rooted>::Type pos_end,
+ TSource & source,
+ Tag<TExpand> const tag)
+{
+SEQAN_CHECKPOINT
+ replace(target, position(pos_begin), position(pos_end), source, tag);
+}
+
+template<typename THost, typename TTargetSpec, typename TSource, typename TExpand>
+inline void
+replace(Segment<THost, TTargetSpec> & target,
+ typename Iterator< Segment<THost, TTargetSpec>, Rooted>::Type pos_begin,
+ typename Iterator< Segment<THost, TTargetSpec>, Rooted>::Type pos_end,
+ TSource & source,
+ typename Size< Segment<THost, TTargetSpec> >::Type limit,
+ Tag<TExpand> const tag)
+{
+SEQAN_CHECKPOINT
+ replace(target, position(pos_begin), position(pos_end), source, limit, tag);
+}
+
+template<typename THost, typename TTargetSpec, typename TSource, typename TExpand>
+inline void
+replace(Segment<THost, TTargetSpec> const & target,
+ typename Iterator< Segment<THost, TTargetSpec> const, Rooted>::Type pos_begin,
+ typename Iterator< Segment<THost, TTargetSpec> const, Rooted>::Type pos_end,
+ TSource & source,
+ Tag<TExpand> const tag)
+{
+SEQAN_CHECKPOINT
+ replace(target, position(pos_begin), position(pos_end), source, tag);
+}
+
+template<typename THost, typename TTargetSpec, typename TSource, typename TExpand>
+inline void
+replace(Segment<THost, TTargetSpec> const & target,
+ typename Iterator< Segment<THost, TTargetSpec> const, Rooted>::Type pos_begin,
+ typename Iterator< Segment<THost, TTargetSpec> const, Rooted>::Type pos_end,
+ TSource & source,
+ typename Size< Segment<THost, TTargetSpec> >::Type limit,
+ Tag<TExpand> const tag)
+{
+SEQAN_CHECKPOINT
+ replace(target, position(pos_begin), position(pos_end), source, limit, tag);
+}
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+///.Function.resize.param.object.type:Class.Segment
+
+template <typename THost, typename TSpec, typename TExpand>
+inline typename Size< Segment<THost, TSpec> >::Type
+resize(
+ Segment<THost, TSpec> & me,
+ typename Size< Segment<THost, TSpec> >::Type new_length,
+ Tag<TExpand> const tag)
+{
+SEQAN_CHECKPOINT
+
+ typename Size<Segment<THost, TSpec> >::Type me_length = length(me);
+ typename Position<THost>::Type me_end_pos = endPosition(me);
+ if (new_length > me_length)
+ {
+ new_length = me_length + resizeSpace(host(me), new_length - me_length, me_end_pos, me_end_pos, tag);
+ }
+ else if (new_length < me_length)
+ {
+ new_length = resizeSpace(host(me), 0, me_end_pos - (me_length - new_length), me_end_pos, tag);
+ }
+ _setLength(me, new_length);
+ return new_length;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//??? TODO: fill (kopie von resize anpassen)
+
+//////////////////////////////////////////////////////////////////////////////
+///.Function.clear.param.object.type:Class.Segment
+
+template <typename THost, typename TSpec>
+inline void
+clear(Segment<THost, TSpec> & target)
+{
+SEQAN_CHECKPOINT
+ assign(target, "");
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftValue, typename TLeftSpec, typename TRight>
+Segment<TLeftValue, TLeftSpec> const &
+operator += (Segment<TLeftValue, TLeftSpec> & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ append(left, right);
+ return left;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftHost, typename TLeftSpec, typename TRight >
+inline bool
+operator == (Segment<TLeftHost, TLeftSpec> const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ typename Comparator<Segment<TLeftHost, TLeftSpec> >::Type _lex(left, right);
+ return isEqual(_lex);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftHost, typename TLeftSpec, typename TRight >
+inline bool
+operator != (Segment<TLeftHost, TLeftSpec> const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ typename Comparator<Segment<TLeftHost, TLeftSpec> >::Type _lex(left, right);
+ return isNotEqual(_lex);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftHost, typename TLeftSpec, typename TRight>
+inline bool
+operator < (Segment<TLeftHost, TLeftSpec> const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return isLess(left, right, typename DefaultPrefixOrder<Segment<TLeftHost, TLeftSpec> >::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftHost, typename TLeftSpec, typename TRight>
+inline bool
+operator <= (Segment<TLeftHost, TLeftSpec> const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return isLessOrEqual(left, right, typename DefaultPrefixOrder<Segment<TLeftHost, TLeftSpec> >::Type());
+}
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftHost, typename TLeftSpec, typename TRight>
+inline bool
+operator > (Segment<TLeftHost, TLeftSpec> const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return isGreater(left, right, typename DefaultPrefixOrder<Segment<TLeftHost, TLeftSpec> >::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftHost, typename TLeftSpec, typename TRight>
+inline bool
+operator >= (Segment<TLeftHost, TLeftSpec> const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return isGreaterOrEqual(left, right, typename DefaultPrefixOrder<Segment<TLeftHost, TLeftSpec> >::Type());
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// stream operators
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TStream, typename THost, typename TSpec>
+inline TStream &
+operator << (TStream & target,
+ Segment<THost, TSpec> const & source)
+{
+SEQAN_CHECKPOINT
+ write(target, source);
+ return target;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TStream, typename THost, typename TSpec>
+inline TStream &
+operator >> (TStream & source,
+ Segment<THost, TSpec> & target)
+{
+SEQAN_CHECKPOINT
+ read(source, target);
+ return source;
+}
+template <typename TStream, typename THost, typename TSpec>
+inline TStream &
+operator >> (TStream & source,
+ Segment<THost, TSpec> const & target)
+{
+SEQAN_CHECKPOINT
+ read(source, target);
+ return source;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/sequence/segment_infix.h b/src/libSSA/seqan/sequence/segment_infix.h
new file mode 100644
index 0000000..e1daaf4
--- /dev/null
+++ b/src/libSSA/seqan/sequence/segment_infix.h
@@ -0,0 +1,794 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: segment_infix.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SEGMENT_INFIX_H
+#define SEQAN_HEADER_SEGMENT_INFIX_H
+
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// InfixSegment
+//////////////////////////////////////////////////////////////////////////////
+
+
+/**
+.Spec.InfixSegment:
+..cat:Segments
+..summary:An arbitrary segment.
+..general:Class.Segment
+..signature:Segment<THost, InfixSegment>
+..param.THost:Type of the whole sequence.
+...text:Instances of $Segment<THost, InfixSegment>$ are infixes of $THost$ objects.
+...remarks:Use @Metafunction.Host@ to get the host type for a given class.
+..remarks.note:Since the appropriate segment type depends on the host sequence type,
+ it is recommended to use the metafunction @Metafunction.Infix@ instead of explicitely
+ choose a specialization of @Class.Segment at .
+..see:Metafunction.Infix
+*/
+
+template <typename THost_>
+class Segment<THost_, InfixSegment>
+{
+protected:
+ typedef typename Host<Segment>::Type THost;
+
+ typename _Pointer<THost>::Type data_host;
+ typename Position<THost>::Type data_begin_position;
+ typename Position<THost>::Type data_end_position;
+
+
+//____________________________________________________________________________
+
+public:
+
+/**
+.Memfunc.InfixSegment#Segment:
+..class:Spec.InfixSegment
+..summary:Constructor
+..signature:Segment<THost, InfixSegment> ()
+..signature:Segment<THost, InfixSegment> (infix)
+..signature:Segment<THost, InfixSegment> (host [, begin, end])
+..param.infix:Other infix object. (copy constructor)
+..param.host:The whole sequence.
+..param.begin:Position/iterator in $host$ of the first item in segment.
+...type:Metafunction.Position.$Position<THost>::Type$
+...type:Metafunction.Iterator.$Iterator<THost>::Type$
+..param.end:Position/iterator behind the end of the segment.
+...type:Metafunction.Position.$Position<THost>::Type$
+...type:Metafunction.Iterator.$Iterator<THost>::Type$
+..remarks:
+...text:A Segment object cannot work without a host. If the object is default constructed,
+the host must be set by @Function.setHost@ before the segment can be used.
+...text:If a segment object is constructed by the copy constructor, the
+members of the new constructed object are set to the same values as the members in the
+source object; the host object is not modified.
+Note that this is a special case, since all other copy operations result in changes
+of the host object.
+...text:$begin$ and $end$ must be valid positions/iterators in $host$.
+If $begin$ und $end$ are omitted, the infix segment corresponding to
+the first character of $host$ is constructed.
+This is the same segment that is returned by @Function.goBegin at .
+*/
+ Segment():
+ data_begin_position(0),
+ data_end_position(0)
+ {
+SEQAN_CHECKPOINT
+ }
+
+ Segment(typename _Parameter<THost>::Type _host):
+ data_host(_toPointer(_host)),
+ data_begin_position(0),
+ data_end_position(1)
+ {
+SEQAN_CHECKPOINT
+ }
+
+ Segment(typename _Parameter<THost>::Type _host, typename Position<THost>::Type _begin_index, typename Position<THost>::Type _end_index):
+ data_host(_toPointer(_host)),
+ data_begin_position(_begin_index),
+ data_end_position(_end_index)
+ {
+SEQAN_CHECKPOINT
+ }
+/*
+ Segment(typename _Parameter<THost>::Type _host, typename Iterator<THost, Rooted>::Type _begin, typename Iterator<THost, Rooted>::Type _end):
+ data_host(_toPointer(_host)),
+ data_begin_position(position(_begin)),
+ data_end_position(position(_end))
+ {
+SEQAN_CHECKPOINT
+ }
+*/
+ Segment(typename _Parameter<THost>::Type _host, typename Iterator<THost, Standard>::Type _begin, typename Iterator<THost, Standard>::Type _end):
+ data_host(_toPointer(_host)),
+ data_begin_position(position(_begin, _host)),
+ data_end_position(position(_end, _host))
+ {
+SEQAN_CHECKPOINT
+ }
+ template <typename THost2, typename TSpec2>
+ Segment(Segment<THost2, TSpec2> const & _other):
+ data_host(_toPointer(host(_other))),
+ data_begin_position(beginPosition(_other)),
+ data_end_position(endPosition(_other))
+ {
+SEQAN_CHECKPOINT
+ }
+
+ ~ Segment()
+ {
+SEQAN_CHECKPOINT
+ }
+
+ template <typename TSource>
+ inline Segment &
+ operator = (TSource const & source)
+ {
+ assign(*this, source);
+ return *this;
+ }
+ inline Segment &
+ operator = (Segment const & source)
+ {
+ assign(*this, source);
+ return *this;
+ }
+//____________________________________________________________________________
+
+public:
+
+///Function.host.param.object.type:Class.Segment
+
+ friend inline typename _Parameter<THost>::Type
+ host(Segment & me)
+ {
+SEQAN_CHECKPOINT
+ return _toParameter<THost>(me.data_host);
+ }
+
+ friend inline typename _Parameter<THost>::Type
+ host(Segment const & me)
+ {
+SEQAN_CHECKPOINT
+ return _toParameter<THost>(me.data_host);
+ }
+
+//____________________________________________________________________________
+
+/**
+.Function.setHost:
+..summary:Sets the host of an object.
+..cat:Dependent Objects
+..signature:setHost(object, host)
+..param.object:The object that will get a new host.
+...type:Class.Segment
+..param.host:The new host.
+..remarks:After this operation, $object$ depends on $host$.
+...text:Note that setting the host can invalidate $object$.
+For example, if one changes the host of a @Class.Segment@ object, it is possible
+that begin- and end-position of the segment does not fit into the new host sequence.
+..see:Function.host
+*/
+ friend inline void
+ setHost(Segment & me, typename _Parameter<THost>::Type _host)
+ {
+SEQAN_CHECKPOINT
+ me.data_host = _toPointer(_host);
+ }
+
+//____________________________________________________________________________
+
+ template <typename TPos>
+ inline typename Reference<Segment>::Type
+ operator [] (TPos pos)
+ {
+SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+
+ template <typename TPos>
+ inline typename Reference<Segment const>::Type
+ operator [] (TPos pos) const
+ {
+SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+
+//____________________________________________________________________________
+
+///.Function.begin.param.object.type:Class.Segment
+
+ friend inline typename Iterator<Segment, Standard>::Type
+ begin(Segment & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return begin(host(me), Standard()) + me.data_begin_position;
+ }
+ friend inline typename Iterator<Segment const, Standard>::Type
+ begin(Segment const & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return begin(host(me), Standard()) + me.data_begin_position;
+ }
+
+//____________________________________________________________________________
+
+///.Function.beginPosition.param.object.type:Class.Segment
+
+ friend inline typename Position<Segment>::Type
+ beginPosition(Segment & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_begin_position;
+ }
+ friend inline typename Position<Segment const>::Type
+ beginPosition(Segment const & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_begin_position;
+ }
+
+//____________________________________________________________________________
+
+/**
+.Function.setBegin:
+..summary:Sets begin of object in host.
+..cat:Dependent Objects
+..signature:setBegin(object, new_begin)
+..param.object:An object.
+...type:Spec.InfixSegment
+...type:Spec.SuffixSegment
+..param.new_begin:iterator to the new first item in $host(object)$ that belongs of $object$.
+...type:Metafunction.Iterator
+..see:Function.begin
+..see:Function.beginPosition
+*/
+ template <typename TIterator>
+ friend inline void
+ setBegin(Segment & me, TIterator new_begin)
+ {
+SEQAN_CHECKPOINT
+ me.data_begin_position = new_begin - begin(host(me));//, Standard());
+ }
+
+
+//____________________________________________________________________________
+
+/**
+.Function.setBeginPosition:
+..summary:Sets begin position of object in host.
+..cat:Dependent Objects
+..signature:setBeginPosition(object, new_begin)
+..param.object:An object.
+...type:Spec.InfixSegment
+...type:Spec.SuffixSegment
+..param.new_begin:position of the new first item in $host(object)$ that belongs of $object$.
+...type:Metafunction.Position
+..see:Function.begin
+..see:Function.beginPosition
+..see:Function.setBegin
+*/
+
+ template <typename TPosition>
+ friend inline void
+ setBeginPosition(Segment & me, TPosition new_begin)
+ {
+SEQAN_CHECKPOINT
+ me.data_begin_position = new_begin;
+ }
+
+//____________________________________________________________________________
+
+///.Function.begin.param.object.type:Class.Segment
+
+ friend inline typename Iterator<Segment, Standard>::Type
+ end(Segment & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return begin(host(me), Standard()) + me.data_end_position;
+ }
+ friend inline typename Iterator<Segment const, Standard>::Type
+ end(Segment const & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return begin(host(me), Standard()) + me.data_end_position;
+ }
+
+//____________________________________________________________________________
+
+///.Function.endPosition.param.object.type:Class.Segment
+
+ friend inline typename Position<Segment>::Type
+ endPosition(Segment & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_end_position;
+ }
+ friend inline typename Position<Segment>::Type
+ endPosition(Segment const & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_end_position;
+ }
+
+//____________________________________________________________________________
+
+/**
+.Function.setEnd:
+..summary:Sets end of object in host.
+..cat:Dependent Objects
+..signature:setEnd(object, new_end)
+..param.object:An object.
+...type:Spec.InfixSegment
+...type:Spec.PrefixSegment
+..param.new_end:Iterator behind the last item in $host(object)$ belongs of $object$.
+...type:Metafunction.Iterator
+..see:Function.end
+..see:Function.endPosition
+..see:Function.setBegin
+*/
+
+ template <typename TIterator>
+ friend inline void
+ setEnd(Segment & me, TIterator new_end)
+ {
+SEQAN_CHECKPOINT
+ me.data_end_position = new_end - begin(host(me));//, Standard());
+ }
+
+/* //unnoetig
+ friend inline void
+ setEnd(Segment & me)
+ {
+SEQAN_CHECKPOINT
+ setEnd(me, end(host(me)));
+ }
+*/
+//____________________________________________________________________________
+
+
+/**
+.Function.setEndPosition:
+..summary:Sets begin position of object in host.
+..cat:Dependent Objects
+..signature:setEndPosition(object, new_end)
+..param.object:An object.
+...type:Spec.InfixSegment
+...type:Spec.PrefixSegment
+..param.new_end:position behind the last item in $host(object)$ that belongs of $object$.
+...type:Metafunction.Position
+..see:Function.end
+..see:Function.endPosition
+..see:Function.setBeginPosition
+..see:Function.setEnd
+*/
+
+ template <typename TPosition>
+ friend inline void
+ setEndPosition(Segment & me, TPosition new_end)
+ {
+SEQAN_CHECKPOINT
+ me.data_end_position = new_end;
+ }
+
+//____________________________________________________________________________
+
+ friend inline void
+ _setLength(
+ Segment & me,
+ typename Size<THost>::Type new_length)
+ {
+SEQAN_CHECKPOINT
+ me.data_end_position = me.data_begin_position + new_length;
+ }
+
+//____________________________________________________________________________
+
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Metafunction.Infix:
+..summary:Infix sequence type.
+..signature:Infix<T>::Type
+..param.T:A sequence type.
+...type:Class.String
+..returns.param.Type:The infix type.
+..see:Spec.InfixSegment
+*/
+
+template <typename THost>
+struct Infix
+{
+ typedef Segment<THost, InfixSegment> Type;
+};
+
+template <typename THost, typename TSpec>
+struct Infix< Segment<THost, TSpec> >
+{
+ typedef Segment<THost, InfixSegment> Type;
+};
+
+template <typename THost, typename TSpec>
+struct Infix< Segment<THost, TSpec> const >:
+ Infix< Segment<THost, TSpec> > {};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost, typename TPosition1, typename TPosition2>
+inline void
+set(Segment<THost, InfixSegment> & me,
+ THost & host_,
+ TPosition1 begin_,
+ TPosition2 end_)
+{
+SEQAN_CHECKPOINT
+ setHost(me, host_);
+ setBegin(me, begin_);
+ setEnd(me, end_);
+}
+//____________________________________________________________________________
+
+template <typename THost>
+inline void
+set(Segment<THost, InfixSegment> & me,
+ THost & host_)
+{
+SEQAN_CHECKPOINT
+ setHost(me, host_);
+ setBegin(me, begin(host_, Standard()));
+ setEnd(me, end(host_, Standard()));
+}
+template <typename THost>
+inline void
+set(Segment<THost, InfixSegment> & me,
+ THost const & host_)
+{
+SEQAN_CHECKPOINT
+ setHost(me, host_);
+ setBegin(me, begin(host_, Standard()));
+ setEnd(me, end(host_, Standard()));
+}
+
+//____________________________________________________________________________
+
+template <typename THost, typename TSpec>
+inline void
+set(Segment<THost, InfixSegment> & me,
+ Segment<THost, TSpec> & source)
+{
+SEQAN_CHECKPOINT
+ setHost(me, host(source));
+ setBeginPosition(me, beginPosition(source));
+ setEndPosition(me, endPosition(source));
+}
+template <typename THost, typename TSpec>
+inline void
+set(Segment<THost, InfixSegment> & me,
+ Segment<THost, TSpec> const & source)
+{
+SEQAN_CHECKPOINT
+ setHost(me, host(source));
+ setBeginPosition(me, beginPosition(source));
+ setEndPosition(me, endPosition(source));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline bool
+atBegin(Segment<THost, InfixSegment> & segment)
+{
+SEQAN_CHECKPOINT
+ return (beginPosition(segment) == endPosition(segment));
+}
+template <typename THost>
+inline bool
+atBegin(Segment<THost, InfixSegment> const & segment)
+{
+SEQAN_CHECKPOINT
+ return (beginPosition(segment) == endPosition(segment));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline bool
+atEnd(Segment<THost, InfixSegment> & segment)
+{
+SEQAN_CHECKPOINT
+ return (endPosition(segment) - beginPosition(segment)) > length(host(segment));
+}
+template <typename THost>
+inline bool
+atEnd(Segment<THost, InfixSegment> const & segment)
+{
+SEQAN_CHECKPOINT
+ return (endPosition(segment) - beginPosition(segment)) > length(host(segment));
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline void
+goBegin(Segment<THost, InfixSegment> & segment)
+{
+SEQAN_CHECKPOINT
+ setBeginPosition(segment, 0);
+ setEndPosition(segment, 1);
+}
+template <typename THost, typename THost2>
+inline void
+goBegin(Segment<THost, InfixSegment> & segment,
+ THost2 &)
+{
+ goBegin(segment);
+}
+template <typename THost, typename THost2>
+inline void
+goBegin(Segment<THost, InfixSegment> & segment,
+ THost2 const &)
+{
+ goBegin(segment);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+template <typename THost>
+inline void
+goEnd(Segment<THost, InfixSegment> & segment)
+{
+SEQAN_CHECKPOINT
+ setBeginPosition(segment, 0);
+ setEndPosition(segment, length(host(segment)));
+}
+template <typename THost, typename THost2>
+inline void
+goEnd(Segment<THost, InfixSegment> & segment,
+ THost2 &)
+{
+ goEnd(segment);
+}
+template <typename THost, typename THost2>
+inline void
+goEnd(Segment<THost, InfixSegment> & segment,
+ THost2 const &)
+{
+ goEnd(segment);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline Segment<THost, InfixSegment> &
+operator ++(Segment<THost, InfixSegment> & segment)
+{
+SEQAN_CHECKPOINT
+ if (endPosition(segment) == length(host(segment)))
+ {
+ setEndPosition(segment, endPosition(segment) - beginPosition(segment) + 1);
+ setBeginPosition(segment, 0);
+ }
+ else
+ {
+ setBeginPosition(segment, beginPosition(segment) + 1);
+ setEndPosition(segment, endPosition(segment) + 1);
+ }
+ return segment;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline Segment<THost, InfixSegment> &
+operator --(Segment<THost, InfixSegment> & segment)
+{
+SEQAN_CHECKPOINT
+ if (!beginPosition(segment))
+ {
+ typename Size<THost>::Type host_length = length(host(segment));
+
+ setBeginPosition(segment, host_length - endPosition(segment) + beginPosition(segment) + 1);
+ setEndPosition(segment, host_length);
+ }
+ else
+ {
+ setBeginPosition(segment, beginPosition(segment) - 1);
+ setEndPosition(segment, endPosition(segment) - 1);
+ }
+ return segment;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost, typename TSpec, typename TPos>
+inline typename Reference< Segment<THost, TSpec> >::Type
+value(Segment<THost, TSpec> & me,
+ TPos pos)
+{
+SEQAN_CHECKPOINT
+ return *(begin(me, Standard()) + pos);
+}
+
+template <typename THost, typename TSpec, typename TPos>
+inline typename Reference< Segment<THost, TSpec> const >::Type
+value(Segment<THost, TSpec> const & me,
+ TPos pos)
+{
+SEQAN_CHECKPOINT
+ return *(begin(me, Standard()) + pos);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.infix:
+..cat:Containers
+..summary:Creates infix object.
+..signature:infix(host, begin, end)
+..param.host:The complete sequence.
+...type:Class.String
+...type:Adaption.char array
+..param.begin:Position or iterator of the first element of the segment.
+...type:Metafunction.Position
+...type:Metafunction.Iterator
+..param.end:Position or iterator behind the last element of the segment.
+...remarks:$end$ must have the same type as $begin$.
+..returns:The infix of $host$ between $begin$ and $end-1$.
+...remarks:The type of the infix is given by @Metafunction.Infix at .
+..remarks:Notational sugar.
+..see:Spec.InfixSegment
+*/
+
+template <typename T, typename TPosBegin, typename TPosEnd>
+inline typename Infix<T>::Type
+infix(T & t, TPosBegin pos_begin, TPosEnd pos_end)
+{
+SEQAN_CHECKPOINT
+ return typename Infix<T>::Type(t, pos_begin, pos_end);
+}
+
+template <typename T, typename TPosBegin, typename TPosEnd>
+inline typename Infix<T *>::Type
+infix(T * t, TPosBegin pos_begin, TPosEnd pos_end)
+{
+SEQAN_CHECKPOINT
+ return typename Infix<T *>::Type (t, pos_begin, pos_end);
+}
+
+template <typename T, typename TSpec, typename TPosBegin, typename TPosEnd>
+inline typename Infix<Segment<T, TSpec> >::Type
+infix(Segment<T, TSpec> & t, TPosBegin pos_begin, TPosEnd pos_end)
+{
+SEQAN_CHECKPOINT
+ return typename Infix<Segment<T, TSpec> >::Type (
+ host(t),
+ beginPosition(t) + pos_begin,
+ beginPosition(t) + pos_end);
+}
+
+template <typename T, typename TSpec, typename TPosBegin, typename TPosEnd>
+inline typename Infix<Segment<T, TSpec> const>::Type
+infix(Segment<T, TSpec> const & t, TPosBegin pos_begin, TPosEnd pos_end)
+{
+SEQAN_CHECKPOINT
+ return typename Infix<Segment<T, TSpec> const>::Type (
+ host(t),
+ beginPosition(t) + pos_begin,
+ beginPosition(t) + pos_end);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.infixWithLength:
+..cat:Containers
+..summary:Creates infix object.
+..signature:infixWithLength(host, begin, length)
+..param.host:The complete sequence.
+...type:Class.String
+...type:Adaption.char array
+..param.begin:Position or iterator of the first element of the segment.
+...type:Metafunction.Position
+...type:Metafunction.Iterator
+..param.length:Length of the returned infix.
+..returns:The infix of $host$ between $begin$ and $begin+length-1$.
+...remarks:The type of the infix is given by @Metafunction.Infix at .
+..remarks:Notational sugar.
+..see:Spec.InfixSegment
+*/
+
+template <typename T, typename TPosBegin, typename TSize>
+inline typename Infix<T>::Type
+infixWithLength(T & t, TPosBegin pos_begin, TSize length)
+{
+SEQAN_CHECKPOINT
+ return typename Infix<T>::Type(t, pos_begin, pos_begin + length);
+}
+
+template <typename T, typename TPosBegin, typename TSize>
+inline typename Infix<T *>::Type
+infixWithLength(T * t, TPosBegin pos_begin, TSize length)
+{
+SEQAN_CHECKPOINT
+ return typename Infix<T *>::Type (t, pos_begin, pos_begin + length);
+}
+
+template <typename T, typename TSpec, typename TPosBegin, typename TSize>
+inline typename Infix<Segment<T, TSpec> >::Type
+infixWithLength(Segment<T, TSpec> & t, TPosBegin pos_begin, TSize length)
+{
+SEQAN_CHECKPOINT
+ return typename Infix<Segment<T, TSpec> >::Type (
+ host(t),
+ beginPosition(t) + pos_begin,
+ beginPosition(t) + pos_begin + length);
+}
+
+template <typename T, typename TSpec, typename TPosBegin, typename TSize>
+inline typename Infix<Segment<T, TSpec> const>::Type
+infixWithLength(Segment<T, TSpec> const & t, TPosBegin pos_begin, TSize length)
+{
+SEQAN_CHECKPOINT
+ return typename Infix<Segment<T, TSpec> const>::Type (
+ host(t),
+ beginPosition(t) + pos_begin,
+ beginPosition(t) + pos_begin + length);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//setBegin
+
+
+template <typename TIterator>
+inline void
+setBegin(TIterator new_begin)
+{
+SEQAN_CHECKPOINT
+ setBegin(container(new_begin), hostIterator(new_begin));
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+//setEnd
+
+template <typename TIterator>
+inline void
+setEnd(TIterator new_end)
+{
+SEQAN_CHECKPOINT
+ setEnd(container(new_end), new_end);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/sequence/segment_prefix.h b/src/libSSA/seqan/sequence/segment_prefix.h
new file mode 100644
index 0000000..edf6ad9
--- /dev/null
+++ b/src/libSSA/seqan/sequence/segment_prefix.h
@@ -0,0 +1,595 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: segment_prefix.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SEGMENT_PREFIX_H
+#define SEQAN_HEADER_SEGMENT_PREFIX_H
+
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// PrefixSegment
+//////////////////////////////////////////////////////////////////////////////
+
+
+/**
+.Spec.PrefixSegment:
+..cat:Segments
+..summary:First part of a sequence.
+..general:Class.Segment
+..signature:Segment<THost, PrefixSegment>
+..param.THost:Type of the whole sequence.
+...text:Instances of $Segment<THost, PrefixSegment>$ are prefixes of $THost$ objects.
+...remarks:Use @Metafunction.Host@ to get the host type for a given class.
+..remarks.note:Since the appropriate segment type depends on the host sequence type,
+ it is recommended to use the metafunction @Metafunction.Prefix@ instead of explicitely
+ choose a specialization of @Class.Segment at .
+..see:Spec.InfixSegment
+..see:Spec.SuffixSegment
+..see:Metafunction.Prefix
+*/
+
+struct PrefixSegment;
+
+template <typename THost_>
+class Segment<THost_, PrefixSegment>
+{
+protected:
+ typedef typename Host<Segment>::Type THost;
+
+ typename _Pointer<THost>::Type data_host;
+ typename Position<THost>::Type data_end_position;
+
+//____________________________________________________________________________
+
+public:
+
+/**
+.Memfunc.PrefixSegment#Segment:
+..class:Spec.PrefixSegment
+..summary:Constructor
+..signature:Segment<THost, PrefixSegment> ()
+..signature:Segment<THost, PrefixSegment> (prefix)
+..signature:Segment<THost, PrefixSegment> (host [, end])
+..param.prefix:Other prefix object. (copy constructor)
+..param.host:The whole sequence.
+..param.end:Position in $host$ behind the last item in segment. (optional)
+...default:$length(host)$
+...type:Metafunction.Position.$Position<THost>::Type$
+...type:Metafunction.Iterator.$Iterator<THost>::Type$
+..remarks:
+...text:A Segment object cannot work without a host. If the object is default constructed,
+the host must be set by @Function.setHost@ before the segment can be used.
+...text:If a segment object is constructed by the copy constructor, the
+members of the new constructed object are set to the same values as the members in the
+source object; the host object is not modified.
+Note that this is a special case, since all other copy operations result in changes
+of the host object.
+...text:$begin$ must be a valid position/iterator in $host$.
+If $begin$ is omitted, the prefix segment corresponding to
+the whole sequence $host$ is constructed.
+This is the same segment that is returned by @Function.goBegin at .
+*/
+ Segment():
+ data_end_position(0)
+ {
+SEQAN_CHECKPOINT
+ }
+
+ Segment(THost & _host):
+ data_host(& _host),
+ data_end_position(length(_host))
+ {
+SEQAN_CHECKPOINT
+ }
+
+ Segment(typename _Parameter<THost>::Type _host, typename Position<THost>::Type _end_index):
+ data_host(_toPointer(_host)),
+ data_end_position(_end_index)
+ {
+SEQAN_CHECKPOINT
+ }
+/*
+ Segment(typename _Parameter<THost>::Type _host, typename Iterator<THost, Rooted>::Type _end):
+ data_host(_toPointer(_host)),
+ data_end_position(position(_end))
+ {
+SEQAN_CHECKPOINT
+ }
+*/
+ Segment(typename _Parameter<THost>::Type _host, typename Iterator<THost, Standard>::Type _end):
+ data_host(_toPointer(_host)),
+ data_end_position(position(_end, _host))
+ {
+SEQAN_CHECKPOINT
+ }
+
+/*
+ Segment(Segment const & _other):
+ data_host(_other.data_host),
+ data_end_position(_other.data_end_position)
+ {
+SEQAN_CHECKPOINT
+ }
+*/
+ template <typename THost2, typename TSpec2>
+ Segment(Segment<THost2, TSpec2> const & _other):
+ data_host(_toPointer(host(_other))),
+ data_end_position(endPosition(_other))
+ {
+SEQAN_CHECKPOINT
+ }
+
+ ~ Segment()
+ {
+SEQAN_CHECKPOINT
+ }
+
+ template <typename TSource>
+ inline Segment &
+ operator = (TSource const & source)
+ {
+ assign(*this, source);
+ return *this;
+ }
+ inline Segment &
+ operator = (Segment const & source)
+ {
+ assign(*this, source);
+ return *this;
+ }
+//____________________________________________________________________________
+
+public:
+
+ friend inline typename _Parameter<THost>::Type
+ host(Segment & me)
+ {
+SEQAN_CHECKPOINT
+ return _toParameter<THost>(me.data_host);
+ }
+
+ friend inline typename _Parameter<THost>::Type
+ host(Segment const & me)
+ {
+SEQAN_CHECKPOINT
+ return _toParameter<THost>(me.data_host);
+ }
+
+//____________________________________________________________________________
+
+ friend inline void
+ setHost(Segment & me, typename _Parameter<THost>::Type _host)
+ {
+SEQAN_CHECKPOINT
+ me.data_host = _toPointer(_host);
+ }
+
+//____________________________________________________________________________
+
+ template <typename TPos>
+ inline typename Reference<Segment>::Type
+ operator [] (TPos pos)
+ {
+SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+
+ template <typename TPos>
+ inline typename Reference<Segment const>::Type
+ operator [] (TPos pos) const
+ {
+SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+
+//____________________________________________________________________________
+
+ friend inline typename Iterator<Segment, Standard>::Type
+ begin(Segment & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return begin(host(me), Standard());
+ }
+ friend inline typename Iterator<Segment const, Standard>::Type
+ begin(Segment const & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return begin(host(me), Standard());
+ }
+
+//____________________________________________________________________________
+
+ friend inline typename Position<Segment const>::Type
+ beginPosition(Segment const & /*me*/)
+ {
+SEQAN_CHECKPOINT
+ return 0;
+ }
+ friend inline typename Position<Segment>::Type
+ beginPosition(Segment & /*me*/)
+ {
+SEQAN_CHECKPOINT
+ return 0;
+ }
+
+//____________________________________________________________________________
+
+ template <typename TIterator>
+ friend inline void
+ setBegin(Segment &, TIterator)
+ {
+ }
+
+//____________________________________________________________________________
+
+ friend inline typename Iterator<Segment, Standard>::Type
+ end(Segment & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return begin(host(me), Standard()) + me.data_end_position;
+ }
+ friend inline typename Iterator<Segment const, Standard>::Type
+ end(Segment const & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return begin(host(me), Standard()) + me.data_end_position;
+ }
+
+//____________________________________________________________________________
+
+/* //unnoetig
+ friend inline void
+ setEnd(Segment & me)
+ {
+SEQAN_CHECKPOINT
+ me.data_end_position = length(host(me));
+ }
+*/
+ friend inline void
+ setEndPosition(Segment & me, typename Position<Segment>::Type new_end)
+ {
+SEQAN_CHECKPOINT
+ me.data_end_position = new_end;
+ }
+
+ friend inline void
+ setEnd(Segment & me, typename Iterator<Segment, Standard>::Type new_end)
+ {
+SEQAN_CHECKPOINT
+ me.data_end_position = new_end - begin(host(me));//, Standard());
+ }
+
+ friend inline void
+ setEnd(typename Iterator<Segment, Rooted>::Type new_end)
+ {
+SEQAN_CHECKPOINT
+ container(new_end).data_end_position = hostIterator(new_end) - begin(host(container(new_end)));//, Standard());
+ }
+
+//____________________________________________________________________________
+
+ friend inline void
+ _setLength(
+ Segment & me,
+ typename Size<THost>::Type new_length)
+ {
+SEQAN_CHECKPOINT
+ me.data_end_position = new_length;
+ }
+
+//____________________________________________________________________________
+
+ friend inline typename Position<Segment>::Type
+ endPosition(Segment & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_end_position;
+ }
+ friend inline typename Position<Segment const>::Type
+ endPosition(Segment const & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_end_position;
+ }
+
+//____________________________________________________________________________
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Metafunction.Prefix:
+..summary:Prefix sequence type.
+..signature:Prefix<T>::Type
+..param.T:A sequence type.
+...type:Class.String
+..returns.param.Type:The prefix type.
+..see:Spec.PrefixSegment
+..see:Metafunction.Infix
+*/
+
+struct InfixSegment;
+struct SuffixSegment;
+
+template <typename THost>
+struct Prefix
+{
+ typedef Segment<THost, PrefixSegment> Type;
+};
+
+template <typename THost>
+struct Prefix< Segment<THost, InfixSegment> >
+{
+ typedef Segment<THost, InfixSegment> Type;
+};
+template <typename THost>
+struct Prefix< Segment<THost, SuffixSegment> >
+{
+ typedef Segment<THost, InfixSegment> Type;
+};
+template <typename THost>
+struct Prefix< Segment<THost, PrefixSegment> >
+{
+ typedef Segment<THost, PrefixSegment> Type;
+};
+
+template <typename THost, typename TSpec>
+struct Prefix< Segment<THost, TSpec> const >:
+ Prefix< Segment<THost, TSpec> > {};
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost, typename TPosition>
+inline void
+set(Segment<THost, PrefixSegment> & me,
+ THost & host_,
+ TPosition end_)
+{
+SEQAN_CHECKPOINT
+ setHost(me, host_);
+ setEnd(me, end_);
+}
+//____________________________________________________________________________
+
+template <typename THost>
+inline void
+set(Segment<THost, PrefixSegment> & me,
+ THost & host_)
+{
+SEQAN_CHECKPOINT
+ setHost(me, host_);
+ setEnd(me, end(host_));
+}
+
+//____________________________________________________________________________
+
+template <typename THost, typename TSpec>
+inline void
+set(Segment<THost, PrefixSegment> & me,
+ Segment<THost, TSpec> & source)
+{
+SEQAN_CHECKPOINT
+ setHost(me, host(source));
+ setEndPosition(me, endPosition(source));
+}
+
+template <typename THost, typename TSpec>
+inline void
+set(Segment<THost, PrefixSegment> & me,
+ Segment<THost, TSpec> const & source)
+{
+SEQAN_CHECKPOINT
+ setHost(me, host(source));
+ setEndPosition(me, endPosition(source));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline bool
+atBegin(Segment<THost, PrefixSegment> const & segment)
+{
+SEQAN_CHECKPOINT
+ return (endPosition(segment) == length(host(segment)));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline bool
+atEnd(Segment<THost, PrefixSegment> const & segment)
+{
+SEQAN_CHECKPOINT
+ return (endPosition(segment) == 0);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline void
+goBegin(Segment<THost, PrefixSegment> & segment,
+ THost &)
+{
+SEQAN_CHECKPOINT
+ goBegin(segment);
+}
+
+template <typename THost>
+inline void
+goBegin(Segment<THost, PrefixSegment> & segment)
+{
+ setEnd(segment);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline void
+goEnd(Segment<THost, PrefixSegment> & segment,
+ THost &)
+{
+SEQAN_CHECKPOINT
+ goEnd(segment);
+}
+
+template <typename THost>
+inline void
+goEnd(Segment<THost, PrefixSegment> & segment)
+{
+ setEnd(segment, 0);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline Segment<THost, PrefixSegment> &
+operator ++(Segment<THost, PrefixSegment> & segment)
+{
+ setEnd(segment, endPosition(segment) - 1);
+ return segment;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline Segment<THost, PrefixSegment> &
+operator --(Segment<THost, PrefixSegment> & segment)
+{
+ setEnd(segment, endPosition(segment) + 1);
+ return segment;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.prefix:
+..cat:Containers
+..summary:Creates prefix object.
+..signature:prefix(host, end)
+..param.host:The complete sequence.
+...type:Class.String
+...type:Adaption.char array
+..param.end:Position or iterator behind the last element of the segment.
+...type:Metafunction.Position
+...type:Metafunction.Iterator
+..returns:The prefix of $host that begins at $begin$.
+...remarks:The type of the prefix is given by @Metafunction.Prefix at .
+..remarks:Notational sugar.
+..see:Spec.PrefixSegment
+..see:Function.suffix
+..see:Function.infix
+*/
+
+template <typename T, typename TPosEnd>
+inline typename Prefix<T>::Type
+prefix(T & t, TPosEnd pos_end)
+{
+SEQAN_CHECKPOINT
+ return typename Prefix<T>::Type(t, pos_end);
+}
+
+template <typename T, typename TPosEnd>
+inline typename Prefix<T *>::Type
+prefix(T * t, TPosEnd pos_end)
+{
+SEQAN_CHECKPOINT
+ return typename Prefix<T *>::Type (t, pos_end);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// A prefix of a prefix -> is a prefix
+template <typename T, typename TPosEnd>
+inline typename Prefix<Segment<T, PrefixSegment> >::Type
+prefix(Segment<T, PrefixSegment> & t, TPosEnd pos_end)
+{
+SEQAN_CHECKPOINT
+ return typename Prefix<Segment<T, PrefixSegment> >::Type (
+ host(t),
+ beginPosition(t) + pos_end);
+}
+template <typename T, typename TPosEnd>
+inline typename Prefix<Segment<T, PrefixSegment> const>::Type
+prefix(Segment<T, PrefixSegment> const & t, TPosEnd pos_end)
+{
+SEQAN_CHECKPOINT
+ return typename Prefix<Segment<T, PrefixSegment> const>::Type (
+ host(t),
+ beginPosition(t) + pos_end);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// A prefix of an infix -> is an infix
+template <typename T, typename TPosEnd>
+inline typename Prefix<Segment<T, InfixSegment> >::Type
+prefix(Segment<T, InfixSegment> & t, TPosEnd pos_end)
+{
+SEQAN_CHECKPOINT
+ return typename Prefix<Segment<T, InfixSegment> >::Type (
+ host(t),
+ beginPosition(t),
+ beginPosition(t) + pos_end);
+}
+template <typename T, typename TPosEnd>
+inline typename Prefix<Segment<T, InfixSegment> const>::Type
+prefix(Segment<T, InfixSegment> const & t, TPosEnd pos_end)
+{
+SEQAN_CHECKPOINT
+ return typename Prefix<Segment<T, InfixSegment> const>::Type (
+ host(t),
+ beginPosition(t),
+ beginPosition(t) + pos_end);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// A prefix of an suffix -> is an infix
+template <typename T, typename TPosEnd>
+inline typename Prefix<Segment<T, SuffixSegment> >::Type
+prefix(Segment<T, SuffixSegment> & t, TPosEnd pos_end)
+{
+SEQAN_CHECKPOINT
+ return typename Prefix<Segment<T, SuffixSegment> >::Type (
+ host(t),
+ beginPosition(t),
+ beginPosition(t) + pos_end);
+}
+template <typename T, typename TPosEnd>
+inline typename Prefix<Segment<T, SuffixSegment> const>::Type
+prefix(Segment<T, SuffixSegment> const & t, TPosEnd pos_end)
+{
+SEQAN_CHECKPOINT
+ return typename Prefix<Segment<T, SuffixSegment> const>::Type (
+ host(t),
+ beginPosition(t),
+ beginPosition(t) + pos_end);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/sequence/segment_suffix.h b/src/libSSA/seqan/sequence/segment_suffix.h
new file mode 100644
index 0000000..36d360b
--- /dev/null
+++ b/src/libSSA/seqan/sequence/segment_suffix.h
@@ -0,0 +1,583 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: segment_suffix.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SEGMENT_SUFFIX_H
+#define SEQAN_HEADER_SEGMENT_SUFFIX_H
+
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// SuffixSegment
+//////////////////////////////////////////////////////////////////////////////
+
+
+/**
+.Spec.SuffixSegment:
+..cat:Segments
+..summary:End part segment of a sequence.
+..general:Class.Segment
+..signature:Segment<THost, SuffixSegment>
+..param.THost:Type of the whole sequence.
+...text:Instances of $Segment<THost, SuffixSegment>$ are suffixes of $THost$ objects.
+...remarks:Use @Metafunction.Host@ to get the host type for a given class.
+..remarks.note:Since the appropriate segment type depends on the host sequence type,
+ it is recommended to use the metafunction @Metafunction.Suffix@ instead of explicitely
+ choose a specialization of @Class.Segment at .
+..see:Spec.InfixSegment
+..see:Metafunction.Suffix
+*/
+
+struct SuffixSegment;
+
+template <typename THost_>
+class Segment<THost_, SuffixSegment>
+{
+protected:
+ typedef typename Host<Segment>::Type THost;
+
+ typename _Pointer<THost>::Type data_host;
+ typename Position<THost>::Type data_begin_position;
+
+//____________________________________________________________________________
+
+public:
+
+/**
+.Memfunc.SuffixSegment#Segment:
+..class:Spec.SuffixSegment
+..summary:Constructor
+..signature:Segment<THost, SuffixSegment> ()
+..signature:Segment<THost, SuffixSegment> (suffix)
+..signature:Segment<THost, SuffixSegment> (host [, begin])
+..param.suffix:Other suffix object. (copy constructor)
+..param.host:The whole sequence.
+..param.begin:Position in $host$ of the first item in segment. (optional)
+...default:$0$
+...type:Metafunction.Position.$Position<THost>::Type$
+...type:Metafunction.Iterator.$Iterator<THost>::Type$
+..remarks:
+...text:A Segment object cannot work without a host. If the object is default constructed,
+the host must be set by @Function.setHost@ before the segment can be used.
+...text:If a segment object is constructed by the copy constructor, the
+members of the new constructed object are set to the same values as the members in the
+source object; the host object is not modified.
+Note that this is a special case, since all other copy operations result in changes
+of the host object.
+...text:$begin$ must be a valid position/iterator in $host$.
+If $begin$ is omitted, the suffix segment corresponding to
+the whole sequence $host$ is constructed.
+This is the same segment that is returned by @Function.goBegin at .
+*/
+ Segment():
+ data_begin_position(0)
+ {
+SEQAN_CHECKPOINT
+ }
+
+ Segment(THost & _host):
+ data_host(& _host),
+ data_begin_position(0)
+ {
+SEQAN_CHECKPOINT
+ }
+
+ Segment(typename _Parameter<THost>::Type _host, typename Position<THost>::Type _begin_index):
+ data_host(_toPointer(_host)),
+ data_begin_position(_begin_index)
+ {
+SEQAN_CHECKPOINT
+ }
+/*
+ Segment(typename _Parameter<THost>::Type _host, typename Iterator<THost, Rooted>::Type _begin):
+ data_host(_toPointer(_host)),
+ data_begin_position(position(_begin))
+ {
+SEQAN_CHECKPOINT
+ }
+*/
+ Segment(typename _Parameter<THost>::Type _host, typename Iterator<THost, Standard>::Type _begin):
+ data_host(_toPointer(_host)),
+ data_begin_position(position(_begin, _host))
+ {
+SEQAN_CHECKPOINT
+ }
+/*
+ Segment(Segment const & _other):
+ data_host(_other.data_host),
+ data_begin_position(_other.data_begin_position)
+ {
+SEQAN_CHECKPOINT
+ }
+*/
+ template <typename THost2, typename TSpec2>
+ Segment(Segment<THost2, TSpec2> const & _other):
+ data_host(_toPointer(host(_other))),
+ data_begin_position(beginPosition(_other))
+ {
+SEQAN_CHECKPOINT
+ }
+
+ ~ Segment()
+ {
+SEQAN_CHECKPOINT
+ }
+
+ template <typename TSource>
+ inline Segment &
+ operator = (TSource const & source)
+ {
+ assign(*this, source);
+ return *this;
+ }
+ inline Segment &
+ operator = (Segment const & source)
+ {
+ assign(*this, source);
+ return *this;
+ }
+//____________________________________________________________________________
+
+public:
+
+ friend inline typename _Parameter<THost>::Type
+ host(Segment & me)
+ {
+SEQAN_CHECKPOINT
+ return _toParameter<THost>(me.data_host);
+ }
+
+ friend inline typename _Parameter<THost>::Type
+ host(Segment const & me)
+ {
+SEQAN_CHECKPOINT
+ return _toParameter<THost>(me.data_host);
+ }
+
+//____________________________________________________________________________
+
+ friend inline void
+ setHost(Segment & me, typename _Parameter<THost>::Type _host)
+ {
+SEQAN_CHECKPOINT
+ me.data_host = _toPointer(_host);
+ }
+
+//____________________________________________________________________________
+
+ template <typename TPos>
+ inline typename Reference<Segment>::Type
+ operator [] (TPos pos)
+ {
+SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+
+ template <typename TPos>
+ inline typename Reference<Segment const>::Type
+ operator [] (TPos pos) const
+ {
+SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+
+//____________________________________________________________________________
+
+ friend inline typename Iterator<Segment, Standard>::Type
+ begin(Segment & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return begin(host(me), Standard()) + me.data_begin_position;
+ }
+ friend inline typename Iterator<Segment const, Standard>::Type
+ begin(Segment const & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return begin(host(me), Standard()) + me.data_begin_position;
+ }
+
+//____________________________________________________________________________
+
+ friend inline typename Position<Segment const>::Type
+ beginPosition(Segment const & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_begin_position;
+ }
+ friend inline typename Position<Segment>::Type
+ beginPosition(Segment & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_begin_position;
+ }
+//____________________________________________________________________________
+
+ template <typename TIterator>
+ friend inline void
+ setBegin(Segment & me, TIterator new_begin)
+ {
+SEQAN_CHECKPOINT
+ me.data_begin_position = new_begin - begin(host(me));//, Standard());
+ }
+
+ friend inline void
+ setBegin(typename Iterator<Segment, Rooted>::Type new_begin)
+ {
+SEQAN_CHECKPOINT
+ container(new_begin).data_begin_position = hostIterator(new_begin) - begin(host(container(new_begin)));//, Standard());
+ }
+
+//____________________________________________________________________________
+
+ template <typename TPosition>
+ friend inline void
+ setBeginPosition(Segment & me, TPosition new_begin)
+ {
+SEQAN_CHECKPOINT
+ me.data_begin_position = new_begin;
+ }
+
+//____________________________________________________________________________
+
+ friend inline typename Iterator<Segment, Standard>::Type
+ end(Segment & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return end(host(me), Standard());
+ }
+ friend inline typename Iterator<Segment const, Standard>::Type
+ end(Segment const & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return end(host(me), Standard());
+ }
+
+//____________________________________________________________________________
+
+
+ friend inline typename Position<Segment>::Type
+ endPosition(Segment & me)
+ {
+SEQAN_CHECKPOINT
+ return length(host(me));
+ }
+
+ friend inline typename Position<Segment const>::Type
+ endPosition(Segment const & me)
+ {
+SEQAN_CHECKPOINT
+ return length(host(me));
+ }
+
+//____________________________________________________________________________
+
+ template <typename TIterator>
+ friend inline void
+ setEnd(Segment &, TIterator)
+ {
+ }
+
+ friend inline void
+ _setLength(Segment &, typename Size<THost>::Type)
+ {
+ }
+
+//____________________________________________________________________________
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Metafunction.Suffix:
+..summary:Suffix sequence type.
+..signature:Suffix<T>::Type
+..param.T:A sequence type.
+...type:Class.String
+..returns.param.Type:The suffix type.
+..see:Spec.SuffixSegment
+..see:Metafunction.Infix
+..see:Metafunction.Prefix
+*/
+
+struct PrefixSegment;
+struct InfixSegment;
+
+template <typename THost>
+struct Suffix
+{
+ typedef Segment<THost, SuffixSegment> Type;
+};
+
+template <typename THost>
+struct Suffix< Segment<THost, InfixSegment> >
+{
+ typedef Segment<THost, InfixSegment> Type;
+};
+template <typename THost>
+struct Suffix< Segment<THost, SuffixSegment> >
+{
+ typedef Segment<THost, SuffixSegment> Type;
+};
+template <typename THost>
+struct Suffix< Segment<THost, PrefixSegment> >
+{
+ typedef Segment<THost, InfixSegment> Type;
+};
+
+template <typename THost, typename TSpec>
+struct Suffix< Segment<THost, TSpec> const >:
+ Suffix< Segment<THost, TSpec> > {};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost, typename TPosition>
+inline void
+set(Segment<THost, SuffixSegment> & me,
+ THost & host_,
+ TPosition begin_)
+{
+SEQAN_CHECKPOINT
+ setHost(me, host_);
+ setBegin(me, begin_);
+}
+//____________________________________________________________________________
+
+template <typename THost>
+inline void
+set(Segment<THost, SuffixSegment> & me,
+ THost & host_)
+{
+SEQAN_CHECKPOINT
+ setHost(me, host_);
+ setBegin(me, begin(host_, Standard()));
+}
+
+//____________________________________________________________________________
+
+template <typename THost, typename TSpec>
+inline void
+set(Segment<THost, SuffixSegment> & me,
+ Segment<THost, TSpec> & source)
+{
+SEQAN_CHECKPOINT
+ setHost(me, host(source));
+ setBeginPosition(me, beginPosition(source));
+}
+
+template <typename THost, typename TSpec>
+inline void
+set(Segment<THost, SuffixSegment> & me,
+ Segment<THost, TSpec> const & source)
+{
+SEQAN_CHECKPOINT
+ setHost(me, host(source));
+ setBeginPosition(me, beginPosition(source));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline bool
+atBegin(Segment<THost, SuffixSegment> const & segment)
+{
+SEQAN_CHECKPOINT
+ return (beginPosition(segment) == 0);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline bool
+atEnd(Segment<THost, SuffixSegment> const & segment)
+{
+SEQAN_CHECKPOINT
+ return (beginPosition(segment) == length(host(segment)));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline void
+goBegin(Segment<THost, SuffixSegment> & segment,
+ THost &)
+{
+SEQAN_CHECKPOINT
+ goBegin(segment);
+}
+
+template <typename THost>
+inline void
+goBegin(Segment<THost, SuffixSegment> & segment)
+{
+ setBegin(segment);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline void
+goEnd(Segment<THost, SuffixSegment> & segment,
+ THost &)
+{
+SEQAN_CHECKPOINT
+ goEnd(segment);
+}
+
+template <typename THost>
+inline void
+goEnd(Segment<THost, SuffixSegment> & segment)
+{
+ setBegin(segment, length(host(segment))-1);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline Segment<THost, SuffixSegment> &
+operator ++(Segment<THost, SuffixSegment> & segment)
+{
+ setBegin(segment, beginPosition(segment) + 1);
+ return segment;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THost>
+inline Segment<THost, SuffixSegment> &
+operator --(Segment<THost, SuffixSegment> & segment)
+{
+ setBegin(segment, beginPosition(segment) - 1);
+ return segment;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.suffix:
+..cat:Containers
+..summary:Creates suffix object.
+..signature:suffix(host, begin)
+..param.host:The complete sequence.
+...type:Class.String
+...type:Adaption.char array
+..param.begin:Position or iterator of the first element of the segment.
+...type:Metafunction.Position
+...type:Metafunction.Iterator
+..returns:The suffix of $host that begins at $begin$.
+...remarks:The type of the suffix is given by @Metafunction.Suffix at .
+..remarks:Notational sugar.
+..see:Spec.SuffixSegment
+..see:Function.infix
+*/
+
+template <typename T, typename TPosBegin>
+inline typename Suffix<T>::Type
+suffix(T & t, TPosBegin pos_begin)
+{
+SEQAN_CHECKPOINT
+ return typename Suffix<T>::Type(t, pos_begin);
+}
+
+template <typename T, typename TPosBegin>
+inline typename Suffix<T *>::Type
+suffix(T * t, TPosBegin pos_begin)
+{
+SEQAN_CHECKPOINT
+ return typename Suffix<T *>::Type (t, pos_begin);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// A suffix of a prefix -> is an infix
+template <typename T, typename TPosBegin>
+inline typename Suffix<Segment<T, PrefixSegment> >::Type
+suffix(Segment<T, PrefixSegment> & t, TPosBegin pos_begin)
+{
+SEQAN_CHECKPOINT
+ return typename Suffix<Segment<T, PrefixSegment> >::Type (
+ host(t),
+ beginPosition(t) + pos_begin,
+ endPosition(t));
+}
+template <typename T, typename TPosBegin>
+inline typename Suffix<Segment<T, PrefixSegment> const>::Type
+suffix(Segment<T, PrefixSegment> const & t, TPosBegin pos_begin)
+{
+SEQAN_CHECKPOINT
+ return typename Suffix<Segment<T, PrefixSegment> const>::Type (
+ host(t),
+ beginPosition(t) + pos_begin,
+ endPosition(t));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// A suffix of a infix -> is an infix
+template <typename T, typename TPosBegin>
+inline typename Suffix<Segment<T, InfixSegment> >::Type
+suffix(Segment<T, InfixSegment> & t, TPosBegin pos_begin)
+{
+SEQAN_CHECKPOINT
+ return typename Suffix<Segment<T, InfixSegment> >::Type (
+ host(t),
+ beginPosition(t) + pos_begin,
+ endPosition(t));
+}
+template <typename T, typename TPosBegin>
+inline typename Suffix<Segment<T, InfixSegment> const>::Type
+suffix(Segment<T, InfixSegment> const & t, TPosBegin pos_begin)
+{
+SEQAN_CHECKPOINT
+ return typename Suffix<Segment<T, InfixSegment> const>::Type (
+ host(t),
+ beginPosition(t) + pos_begin,
+ endPosition(t));
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// A suffix of a suffix -> is a suffix
+template <typename T, typename TPosBegin>
+inline typename Suffix<Segment<T, SuffixSegment> >::Type
+suffix(Segment<T, SuffixSegment> & t, TPosBegin pos_begin)
+{
+SEQAN_CHECKPOINT
+ return typename Suffix<Segment<T, SuffixSegment> >::Type (
+ host(t),
+ beginPosition(t) + pos_begin);
+}
+template <typename T, typename TPosBegin>
+inline typename Suffix<Segment<T, SuffixSegment> const>::Type
+suffix(Segment<T, SuffixSegment> const & t, TPosBegin pos_begin)
+{
+SEQAN_CHECKPOINT
+ return typename Suffix<Segment<T, SuffixSegment> const>::Type (
+ host(t),
+ beginPosition(t) + pos_begin);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/sequence/sequence_forwards.h b/src/libSSA/seqan/sequence/sequence_forwards.h
new file mode 100644
index 0000000..411aed3
--- /dev/null
+++ b/src/libSSA/seqan/sequence/sequence_forwards.h
@@ -0,0 +1,52 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: sequence_forwards.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SEQUENCE_FORWARDS_H
+#define SEQAN_HEADER_SEQUENCE_FORWARDS_H
+
+//SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
+
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TFile, typename TData>
+void read(TFile & file, TData & data); // "projects/library/seqan/file/file_format_raw.h"(307)
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TFile, typename TData>
+void write(TFile & file, TData & data); // "projects/library/seqan/file/file_format_raw.h"(327)
+
+template <typename TFile, typename TData>
+void write(TFile & file, TData const & data); // "projects/library/seqan/file/file_format_raw.h"(335)
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+//////////////////////////////////////////////////////////////////////////////
+
+#endif
+
diff --git a/src/libSSA/seqan/sequence/sequence_generated_forwards.h b/src/libSSA/seqan/sequence/sequence_generated_forwards.h
new file mode 100644
index 0000000..3edea41
--- /dev/null
+++ b/src/libSSA/seqan/sequence/sequence_generated_forwards.h
@@ -0,0 +1,1557 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SEQUENCE_GENERATED_FORWARDS_H
+#define SEQAN_HEADER_SEQUENCE_GENERATED_FORWARDS_H
+
+//////////////////////////////////////////////////////////////////////////////
+// NOTE: This file is automatically generated by build_forwards.py
+// Do not edit this file manually!
+//////////////////////////////////////////////////////////////////////////////
+
+
+//////////////////////////////////////////////////////////////////////////////
+// CLASSES
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+
+//____________________________________________________________________________
+// Alloc
+
+template <typename TSpec > struct Alloc; // "projects/library/seqan/sequence/string_base.h"(34)
+
+//____________________________________________________________________________
+// AllowsFastRandomAccess
+
+template <typename T> struct AllowsFastRandomAccess; // "projects/library/seqan/sequence/sequence_interface.h"(172)
+
+//____________________________________________________________________________
+// Array
+
+template <unsigned int ISize> struct Array; // "projects/library/seqan/sequence/string_array.h"(42)
+
+//____________________________________________________________________________
+// Block
+
+template <unsigned int SPACE > struct Block; // "projects/library/seqan/sequence/string_stack.h"(47)
+
+//____________________________________________________________________________
+// CStyle
+
+struct CStyle; // "projects/library/seqan/sequence/string_cstyle.h"(67)
+
+//____________________________________________________________________________
+// Comparator
+
+template <typename T> struct Comparator; // "projects/library/seqan/sequence/lexical.h"(180)
+
+//____________________________________________________________________________
+// ConcatDirect
+
+template <typename TDelimiter > struct ConcatDirect; // "projects/library/seqan/sequence/sequence_multiple.h"(67)
+
+//____________________________________________________________________________
+// ConcatVirtual
+
+template <typename TDelimiter > struct ConcatVirtual; // "projects/library/seqan/sequence/sequence_multiple.h"(1871)
+
+//____________________________________________________________________________
+// Concatenator
+
+template <typename TObject> struct Concatenator; // "projects/library/seqan/sequence/sequence_multiple.h"(95)
+
+//____________________________________________________________________________
+// ConcatenatorNto1
+
+template <typename TStringSet> struct ConcatenatorNto1; // "projects/library/seqan/sequence/sequence_multiple.h"(1711)
+
+//____________________________________________________________________________
+// DefaultOverflowExplicit
+
+template <typename TValue> struct DefaultOverflowExplicit; // "projects/library/seqan/sequence/string_pointer.h"(69)
+template <typename T> struct DefaultOverflowExplicit; // "projects/library/seqan/sequence/sequence_interface.h"(109)
+
+//____________________________________________________________________________
+// DefaultOverflowImplicit
+
+template <typename TValue> struct DefaultOverflowImplicit; // "projects/library/seqan/sequence/string_pointer.h"(44)
+template <typename T> struct DefaultOverflowImplicit; // "projects/library/seqan/sequence/sequence_interface.h"(89)
+
+//____________________________________________________________________________
+// DefaultPrefixOrder
+
+template <typename T> struct DefaultPrefixOrder; // "projects/library/seqan/sequence/lexical.h"(58)
+
+//____________________________________________________________________________
+// Dependent
+
+template <typename TSpec > struct Dependent; // "projects/library/seqan/sequence/sequence_multiple.h"(50)
+
+//____________________________________________________________________________
+// Infix
+
+template <typename THost> struct Infix; // "projects/library/seqan/sequence/segment_infix.h"(427)
+
+//____________________________________________________________________________
+// InfixSegment
+
+struct InfixSegment; // "projects/library/seqan/sequence/segment_base.h"(45)
+struct InfixSegment; // "projects/library/seqan/sequence/segment_prefix.h"(334)
+struct InfixSegment; // "projects/library/seqan/sequence/segment_suffix.h"(325)
+
+//____________________________________________________________________________
+// IsContiguous
+
+template <typename TValue> struct IsContiguous; // "projects/library/seqan/sequence/string_pointer.h"(97)
+template <typename T> struct IsContiguous; // "projects/library/seqan/sequence/sequence_interface.h"(130)
+
+//____________________________________________________________________________
+// IsSequence
+
+template <typename T> struct IsSequence; // "projects/library/seqan/sequence/sequence_interface.h"(151)
+
+//____________________________________________________________________________
+// Lexical
+
+template <typename TSpec > struct Lexical; // "projects/library/seqan/sequence/lexical.h"(117)
+
+//____________________________________________________________________________
+// MapType
+
+template <typename T> struct MapType; // "projects/library/seqan/sequence/string_value_expand.h"(211)
+
+//____________________________________________________________________________
+// Owner
+
+template <typename TSpec > struct Owner; // "projects/library/seqan/sequence/sequence_multiple.h"(84)
+
+//____________________________________________________________________________
+// Packed
+
+template <typename THostspec > struct Packed; // "projects/library/seqan/sequence/string_packed.h"(33)
+
+//____________________________________________________________________________
+// Prefix
+
+template <typename THost> struct Prefix; // "projects/library/seqan/sequence/segment_prefix.h"(339)
+
+//____________________________________________________________________________
+// PrefixSegment
+
+struct PrefixSegment; // "projects/library/seqan/sequence/segment_prefix.h"(50)
+struct PrefixSegment; // "projects/library/seqan/sequence/segment_suffix.h"(324)
+
+//____________________________________________________________________________
+// Segment
+
+template <typename THost, typename TSpec > class Segment; // "projects/library/seqan/sequence/segment_base.h"(49)
+
+//____________________________________________________________________________
+// String
+
+template <typename TValue, typename TSpec > class String; // "projects/library/seqan/sequence/string_base.h"(54)
+
+//____________________________________________________________________________
+// StringSet
+
+template <typename TString, typename TSpec > class StringSet; // "projects/library/seqan/sequence/sequence_multiple.h"(92)
+
+//____________________________________________________________________________
+// StringSetLimits
+
+template <typename TString> struct StringSetLimits; // "projects/library/seqan/sequence/sequence_multiple.h"(110)
+
+//____________________________________________________________________________
+// StringSetPosition
+
+template <typename TString> struct StringSetPosition; // "projects/library/seqan/sequence/sequence_multiple.h"(120)
+
+//____________________________________________________________________________
+// Suffix
+
+template <typename THost> struct Suffix; // "projects/library/seqan/sequence/segment_suffix.h"(329)
+
+//____________________________________________________________________________
+// SuffixSegment
+
+struct SuffixSegment; // "projects/library/seqan/sequence/segment_prefix.h"(335)
+struct SuffixSegment; // "projects/library/seqan/sequence/segment_suffix.h"(49)
+
+//____________________________________________________________________________
+// TagExact_
+
+struct TagExact_; // "projects/library/seqan/sequence/sequence_interface.h"(69)
+
+//____________________________________________________________________________
+// TagGenerous_
+
+struct TagGenerous_; // "projects/library/seqan/sequence/sequence_interface.h"(65)
+
+//____________________________________________________________________________
+// TagInsist_
+
+struct TagInsist_; // "projects/library/seqan/sequence/sequence_interface.h"(56)
+
+//____________________________________________________________________________
+// TagLimit_
+
+struct TagLimit_; // "projects/library/seqan/sequence/sequence_interface.h"(61)
+
+//____________________________________________________________________________
+// TagPrefixGreater_
+
+struct TagPrefixGreater_; // "projects/library/seqan/sequence/lexical.h"(43)
+
+//____________________________________________________________________________
+// TagPrefixLess_
+
+struct TagPrefixLess_; // "projects/library/seqan/sequence/lexical.h"(40)
+
+//____________________________________________________________________________
+// ValueExpand
+
+template <typename THost, typename TMap, typename TSpec > struct ValueExpand; // "projects/library/seqan/sequence/string_value_expand.h"(31)
+
+//____________________________________________________________________________
+// ValueExpandIter
+
+struct ValueExpandIter; // "projects/library/seqan/sequence/string_value_expand.h"(33)
+
+//____________________________________________________________________________
+// _Append_Sequence_2_Segment
+
+template <typename TExpand> struct _Append_Sequence_2_Segment; // "projects/library/seqan/sequence/segment_base.h"(543)
+
+//____________________________________________________________________________
+// _Append_String
+
+template <typename TExpand> struct _Append_String; // "projects/library/seqan/sequence/string_base.h"(977)
+
+//____________________________________________________________________________
+// _Append_Value_2_Segment
+
+template <typename TExpand> struct _Append_Value_2_Segment; // "projects/library/seqan/sequence/segment_base.h"(697)
+
+//____________________________________________________________________________
+// _Append_Value_2_String
+
+template <typename TExpand> struct _Append_Value_2_String; // "projects/library/seqan/sequence/string_base.h"(1094)
+
+//____________________________________________________________________________
+// _Assign_Segment
+
+template <typename TExpand> struct _Assign_Segment; // "projects/library/seqan/sequence/segment_base.h"(333)
+
+//____________________________________________________________________________
+// _Assign_String
+
+template <typename TExpand> struct _Assign_String; // "projects/library/seqan/sequence/string_base.h"(753)
+
+//____________________________________________________________________________
+// _Assign_String_2_StringArray
+
+template <typename TExpand, bool IS_CONTIGUOUS> struct _Assign_String_2_StringArray; // "projects/library/seqan/sequence/string_cstyle.h"(457)
+
+//____________________________________________________________________________
+// _ClearSpace_Expand_String_Base_
+
+template <typename TExpand> struct _ClearSpace_Expand_String_Base_; // "projects/library/seqan/sequence/string_base.h"(426)
+
+//____________________________________________________________________________
+// _ClearSpace_String_Base_
+
+template <typename TExpand> struct _ClearSpace_String_Base_; // "projects/library/seqan/sequence/string_base.h"(214)
+
+//____________________________________________________________________________
+// _ClearSpace_String_Packed_
+
+template <typename TExpand> struct _ClearSpace_String_Packed_; // "projects/library/seqan/sequence/string_packed.h"(533)
+
+//____________________________________________________________________________
+// _Create_ArrayString
+
+template <typename TExpand> struct _Create_ArrayString; // "projects/library/seqan/sequence/string_cstyle.h"(600)
+
+//____________________________________________________________________________
+// _Create_ArrayString_Expand
+
+template <typename TExpand> struct _Create_ArrayString_Expand; // "projects/library/seqan/sequence/string_cstyle.h"(547)
+
+//____________________________________________________________________________
+// _Fill_String
+
+template <typename TExpand> struct _Fill_String; // "projects/library/seqan/sequence/string_base.h"(1468)
+
+//____________________________________________________________________________
+// _Insert_Value_2_Segment
+
+template <typename TExpand> struct _Insert_Value_2_Segment; // "projects/library/seqan/sequence/segment_base.h"(739)
+
+//____________________________________________________________________________
+// _Insert_Value_2_String
+
+template <typename TExpand> struct _Insert_Value_2_String; // "projects/library/seqan/sequence/string_base.h"(1140)
+
+//____________________________________________________________________________
+// _PackedConsts
+
+template <typename TPackedContainer> struct _PackedConsts; // "projects/library/seqan/sequence/string_packed.h"(285)
+
+//____________________________________________________________________________
+// _Replace_Sequence_2_Segment
+
+template <typename TExpand> struct _Replace_Sequence_2_Segment; // "projects/library/seqan/sequence/segment_base.h"(792)
+
+//____________________________________________________________________________
+// _Replace_String
+
+template <typename TExpand> struct _Replace_String; // "projects/library/seqan/sequence/string_base.h"(1179)
+
+//____________________________________________________________________________
+// _Resize_String
+
+template <typename TExpand> struct _Resize_String; // "projects/library/seqan/sequence/string_base.h"(1413)
+
+//____________________________________________________________________________
+// _TempCopy
+
+template <typename T> struct _TempCopy; // "projects/library/seqan/sequence/string_base.h"(108)
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+
+//////////////////////////////////////////////////////////////////////////////
+// TYPEDEFS
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+
+//____________________________________________________________________________
+// CharString
+
+typedef String<char, Alloc<void> > CharString; // "projects/library/seqan/sequence/sequence_shortcuts.h"(37)
+
+//____________________________________________________________________________
+// Dna5String
+
+typedef String<Dna5, Alloc<void> > Dna5String; // "projects/library/seqan/sequence/sequence_shortcuts.h"(119)
+
+//____________________________________________________________________________
+// DnaString
+
+typedef String<Dna, Alloc<void> > DnaString; // "projects/library/seqan/sequence/sequence_shortcuts.h"(90)
+
+//____________________________________________________________________________
+// Exact
+
+typedef Tag<TagExact_> const Exact; // "projects/library/seqan/sequence/sequence_interface.h"(70)
+
+//____________________________________________________________________________
+// Generous
+
+typedef Tag<TagGenerous_> const Generous; // "projects/library/seqan/sequence/sequence_interface.h"(66)
+
+//____________________________________________________________________________
+// Insist
+
+typedef Tag<TagInsist_> const Insist; // "projects/library/seqan/sequence/sequence_interface.h"(57)
+
+//____________________________________________________________________________
+// IupacString
+
+typedef String<Iupac, Alloc<void> > IupacString; // "projects/library/seqan/sequence/sequence_shortcuts.h"(148)
+
+//____________________________________________________________________________
+// Limit
+
+typedef Tag<TagLimit_> const Limit; // "projects/library/seqan/sequence/sequence_interface.h"(62)
+
+//____________________________________________________________________________
+// Peptide
+
+typedef String<AminoAcid, Alloc<void> > Peptide; // "projects/library/seqan/sequence/sequence_shortcuts.h"(176)
+
+//____________________________________________________________________________
+// TagPrefixGreater
+
+typedef Tag<TagPrefixGreater_> const TagPrefixGreater; // "projects/library/seqan/sequence/lexical.h"(44)
+
+//____________________________________________________________________________
+// TagPrefixLess
+
+typedef Tag<TagPrefixLess_> const TagPrefixLess; // "projects/library/seqan/sequence/lexical.h"(41)
+
+//____________________________________________________________________________
+// Tight
+
+typedef Tag<TagInsist_> const Tight; // "projects/library/seqan/sequence/sequence_interface.h"(58)
+
+//____________________________________________________________________________
+// UnicodeString
+
+typedef String<wchar_t, Alloc<void> > UnicodeString; // "projects/library/seqan/sequence/sequence_shortcuts.h"(63)
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+
+//////////////////////////////////////////////////////////////////////////////
+// FUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN {
+
+//____________________________________________________________________________
+// _assignValue_packed_string_iterator
+
+template <typename TIter, typename TValue> inline void _assignValue_packed_string_iterator(TIter & me, TValue & _value); // "projects/library/seqan/sequence/string_packed.h"(969)
+
+//____________________________________________________________________________
+// _assign_copy_packed_string
+
+template <typename TTarget, typename TSource, typename TTag> inline void _assign_copy_packed_string(TTarget & target, TSource & source, Tag<TTag> const tag); // "projects/library/seqan/sequence/string_packed.h"(327)
+template <typename TTarget, typename TSource, typename TSize, typename TTag> inline void _assign_copy_packed_string(TTarget & target, TSource & source, TSize limit, Tag<TTag> const tag); // "projects/library/seqan/sequence/string_packed.h"(345)
+
+//____________________________________________________________________________
+// _begin_default
+
+template <typename T> inline typename Iterator<T, Standard>::Type _begin_default(T & me, Standard); // "projects/library/seqan/sequence/sequence_interface.h"(278)
+template <typename T> inline typename Iterator<T const, Standard>::Type _begin_default(T const & me, Standard); // "projects/library/seqan/sequence/sequence_interface.h"(286)
+template <typename T> inline typename Iterator<T, Rooted>::Type _begin_default(T & me, Rooted); // "projects/library/seqan/sequence/sequence_interface.h"(298)
+template <typename T> inline typename Iterator<T const, Rooted>::Type _begin_default(T const & me, Rooted); // "projects/library/seqan/sequence/sequence_interface.h"(307)
+
+//____________________________________________________________________________
+// _clearSpace
+
+template <typename TValue, typename TExpand> inline size_t _clearSpace(TValue * me, size_t size, Tag<TExpand> const); // "projects/library/seqan/sequence/string_pointer.h"(390)
+template <typename TValue, typename TExpand> inline size_t _clearSpace(TValue * me, size_t size, size_t limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_pointer.h"(401)
+template <typename TValue, typename TPosition, typename TExpand> inline size_t _clearSpace(TValue * me, size_t size, TPosition pos_begin, TPosition pos_end, Tag<TExpand> const); // "projects/library/seqan/sequence/string_pointer.h"(413)
+template <typename TValue, typename TPosition, typename TExpand> inline size_t _clearSpace(TValue * me, size_t size, TPosition pos_begin, TPosition pos_end, size_t limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_pointer.h"(426)
+template <typename TValue, typename THostspec, typename TExpand> inline typename Size< String<TValue, Packed<THostspec> > >::Type _clearSpace(String<TValue, Packed<THostspec> > & me, typename Size< String<TValue, Packed<THostspec> > >::Type size, Tag<TExpand> const); // "projects/library/seqan/sequence/string_packed.h"(673)
+template <typename TValue, typename THostspec, typename TExpand> inline typename Size< String<TValue, Packed<THostspec> > >::Type _clearSpace(String<TValue, Packed<THostspec> > & me, typename Size< String<TValue, Packed<THostspec> > >::Type size, typename Size< String<TValue, Packed<THostspec> > >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_packed.h"(684)
+template <typename TValue, typename THostspec, typename TPosition, typename TExpand> inline typename Size< String<TValue, Packed<THostspec> > >::Type _clearSpace(String<TValue, Packed<THostspec> > & me, typename Size< String<TValue, Packed<THostspec> > >::Type size, TPosition pos_begin, TPosition pos_end, Tag<TExpand> const); // "projects/library/seqan/sequence/string_packed.h"(696)
+template <typename TValue, typename THostspec, typename TPosition, typename TExpand> inline typename Size< String<TValue, Packed<THostspec> > >::Type _clearSpace(String<TValue, Packed<THostspec> > & me, typename Size< String<TValue, Packed<THostspec> > >::Type size, TPosition pos_begin, TPosition pos_end, typename Size< String<TValue, Packed<THostspec> > >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_packed.h"(709)
+template <typename TValue, typename TSpec, typename TSize, typename TExpand> inline typename Size< String<TValue, TSpec> >::Type _clearSpace(String<TValue, TSpec> & me, TSize size, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(631)
+template <typename TValue, typename TSpec, typename TSize, typename TExpand> inline typename Size< String<TValue, TSpec> >::Type _clearSpace(String<TValue, TSpec> & me, TSize size, TSize limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(642)
+template <typename TValue, typename TSpec, typename TSize, typename TPosition, typename TExpand> inline typename Size< String<TValue, TSpec> >::Type _clearSpace(String<TValue, TSpec> & me, TSize size, TPosition pos_begin, TPosition pos_end, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(654)
+template <typename TValue, typename TSpec, typename TSize, typename TPosition, typename TExpand> inline typename Size< String<TValue, TSpec> >::Type _clearSpace(String<TValue, TSpec> & me, TSize size, TPosition pos_begin, TPosition pos_end, TSize limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(667)
+
+//____________________________________________________________________________
+// _computeSize4Capacity
+
+template <typename T, typename TSize> inline TSize _computeSize4Capacity(T const & , TSize capacity); // "projects/library/seqan/sequence/sequence_interface.h"(900)
+
+//____________________________________________________________________________
+// _countNonZeroValues
+
+template <typename TValue, typename TSpec, typename TPos > inline typename Size< String<TValue, TSpec> >::Type _countNonZeroValues(String<TValue, TSpec> const &me, TPos i); // "projects/library/seqan/sequence/sequence_multiple.h"(1009)
+
+//____________________________________________________________________________
+// _end_default
+
+template <typename T> inline typename Iterator<T, Standard>::Type _end_default(T & me, Standard); // "projects/library/seqan/sequence/sequence_interface.h"(461)
+template <typename T> inline typename Iterator<T const, Standard>::Type _end_default(T const & me, Standard); // "projects/library/seqan/sequence/sequence_interface.h"(469)
+template <typename T> inline typename Iterator<T, Rooted>::Type _end_default(T & me, Rooted); // "projects/library/seqan/sequence/sequence_interface.h"(481)
+template <typename T> inline typename Iterator<T const, Rooted>::Type _end_default(T const & me, Rooted); // "projects/library/seqan/sequence/sequence_interface.h"(490)
+
+//____________________________________________________________________________
+// _findIthNonZeroValue
+
+template <typename TValue, typename TSpec, typename TPos > inline typename Size< String<TValue, TSpec> >::Type _findIthNonZeroValue(String<TValue, TSpec> const &me, TPos i); // "projects/library/seqan/sequence/sequence_multiple.h"(990)
+
+//____________________________________________________________________________
+// _getMap
+
+template <typename TValue, typename THost, typename TMap, typename TSpec> inline TMap & _getMap(String< TValue, ValueExpand<THost, TMap, TSpec> > & me); // "projects/library/seqan/sequence/string_value_expand.h"(230)
+template <typename TValue, typename THost, typename TMap, typename TSpec> inline TMap & _getMap(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me); // "projects/library/seqan/sequence/string_value_expand.h"(236)
+
+//____________________________________________________________________________
+// _getValueExpandFlagValue
+
+template <typename TValue, typename THost, typename TMap, typename TSpec> inline typename Value<THost>::Type _getValueExpandFlagValue(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me); // "projects/library/seqan/sequence/string_value_expand.h"(245)
+
+//____________________________________________________________________________
+// _moveContiguous
+
+template <typename TTarget, typename TSource> void _moveContiguous(TTarget & target, TSource & source); // "projects/library/seqan/sequence/string_base.h"(862)
+
+//____________________________________________________________________________
+// _reallocateStorage
+
+template <typename TValue, typename TSpec> inline typename Value<String<TValue, TSpec> >::Type * _reallocateStorage( String<TValue, TSpec> & me, typename Size< String<TValue, TSpec> >::Type new_capacity, Exact); // "projects/library/seqan/sequence/string_base.h"(1348)
+template <typename TValue, typename TSpec> inline typename Value<String<TValue, TSpec> >::Type * _reallocateStorage( String<TValue, TSpec> & me, typename Size< String<TValue, TSpec> >::Type new_capacity, typename Size< String<TValue, TSpec> >::Type limit, Exact); // "projects/library/seqan/sequence/string_base.h"(1364)
+template <typename TValue, typename TSpec> inline typename Value<String<TValue, TSpec> >::Type * _reallocateStorage( String<TValue, TSpec> & me, typename Size< String<TValue, TSpec> >::Type new_capacity, Generous); // "projects/library/seqan/sequence/string_base.h"(1380)
+template <typename TValue, typename TSpec> inline typename Value<String<TValue, TSpec> >::Type * _reallocateStorage( String<TValue, TSpec> & me, typename Size< String<TValue, TSpec> >::Type new_capacity, typename Size< String<TValue, TSpec> >::Type limit, Generous); // "projects/library/seqan/sequence/string_base.h"(1397)
+
+//____________________________________________________________________________
+// _refreshStringSetLimits
+
+template <typename T > inline void _refreshStringSetLimits(T &); // "projects/library/seqan/sequence/sequence_multiple.h"(959)
+template <typename TString, typename TSpec > inline void _refreshStringSetLimits(StringSet< TString, Owner<ConcatDirect<TSpec> > > &); // "projects/library/seqan/sequence/sequence_multiple.h"(962)
+template <typename TString, typename TSpec > inline void _refreshStringSetLimits(StringSet< TString, TSpec > &me); // "projects/library/seqan/sequence/sequence_multiple.h"(966)
+
+//____________________________________________________________________________
+// _setLength
+
+template <typename TValue> inline void _setLength(TValue * me, size_t new_length); // "projects/library/seqan/sequence/string_pointer.h"(352)
+
+//____________________________________________________________________________
+// _validStringSetLimits
+
+template <typename T > inline bool _validStringSetLimits(T const &); // "projects/library/seqan/sequence/sequence_multiple.h"(941)
+template <typename TString, typename TSpec > inline bool _validStringSetLimits(StringSet< TString, TSpec > const &me); // "projects/library/seqan/sequence/sequence_multiple.h"(946)
+template <typename TString, typename TSpec > inline bool _validStringSetLimits(StringSet< TString, Owner<ConcatDirect<TSpec> > > const &); // "projects/library/seqan/sequence/sequence_multiple.h"(951)
+
+//____________________________________________________________________________
+// append
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void append( Segment<THost, TSpec> & target, TSource & source, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(609)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void append( Segment<THost, TSpec> & target, TSource const & source, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(619)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void append( Segment<THost, TSpec> & target, TSource & source, typename Size< Segment<THost, TSpec> >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(631)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void append( Segment<THost, TSpec> & target, TSource const & source, typename Size< Segment<THost, TSpec> >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(642)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void append( Segment<THost, TSpec> const & target, TSource & source, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(653)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void append( Segment<THost, TSpec> const & target, TSource const & source, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(663)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void append( Segment<THost, TSpec> const & target, TSource & source, typename Size< Segment<THost, TSpec> >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(675)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void append( Segment<THost, TSpec> const & target, TSource const & source, typename Size< Segment<THost, TSpec> >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(686)
+template <typename TTargetValue, typename TSource, typename TExpand> inline void append(TTargetValue * target, TSource const & source, Tag<TExpand> const); // "projects/library/seqan/sequence/string_pointer.h"(542)
+template <typename TTargetValue, typename TSource, typename TExpand> inline void append(TTargetValue * target, TSource const & source, size_t limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_pointer.h"(553)
+template <typename TTargetValue, typename TSourceValue, typename TExpand> inline void append(TTargetValue * target, TSourceValue const * source, Tag<TExpand> const); // "projects/library/seqan/sequence/string_pointer.h"(566)
+template <typename TTargetValue, typename TSourceValue, typename TExpand> inline void append(TTargetValue * target, TSourceValue const * source, size_t limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_pointer.h"(577)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void append(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, Generous); // "projects/library/seqan/sequence/std_string.h"(425)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void append(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit, Generous); // "projects/library/seqan/sequence/std_string.h"(436)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void append(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, Limit); // "projects/library/seqan/sequence/std_string.h"(463)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void append(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit, Limit); // "projects/library/seqan/sequence/std_string.h"(474)
+template <typename TTarget, typename TSource> inline void append(TTarget & target, TSource & source); // "projects/library/seqan/sequence/sequence_interface.h"(1025)
+template <typename TTarget, typename TSource> inline void append(TTarget const & target, TSource & source); // "projects/library/seqan/sequence/sequence_interface.h"(1033)
+template <typename TTarget, typename TSource> inline void append(TTarget & target, TSource const & source); // "projects/library/seqan/sequence/sequence_interface.h"(1041)
+template <typename TTarget, typename TSource> inline void append(TTarget const & target, TSource const & source); // "projects/library/seqan/sequence/sequence_interface.h"(1049)
+template <typename TTarget, typename TSource> inline void append(TTarget & target, TSource & source, typename Size<TTarget>::Type limit); // "projects/library/seqan/sequence/sequence_interface.h"(1061)
+template <typename TTarget, typename TSource> inline void append(TTarget const & target, TSource & source, typename Size<TTarget>::Type limit); // "projects/library/seqan/sequence/sequence_interface.h"(1070)
+template <typename TTarget, typename TSource> inline void append(TTarget & target, TSource const & source, typename Size<TTarget>::Type limit); // "projects/library/seqan/sequence/sequence_interface.h"(1079)
+template <typename TTarget, typename TSource> inline void append(TTarget const & target, TSource const & source, typename Size<TTarget>::Type limit); // "projects/library/seqan/sequence/sequence_interface.h"(1088)
+template <typename TValue, unsigned int SPACE, typename TSource, typename TExpand> inline void append( String<TValue, Block<SPACE> >& me, TSource const& source, Tag<TExpand> const tag); // "projects/library/seqan/sequence/string_stack.h"(368)
+template <typename TTargetValue, typename TTargetSpec, typename TSource, typename TExpand> inline void append(String<TTargetValue, TTargetSpec> & target, TSource const & source, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(1042)
+template <typename TTargetValue, typename TTargetSpec, typename TSource, typename TExpand> inline void append(String<TTargetValue, TTargetSpec> & target, TSource const & source, typename Size< String<TTargetValue, TTargetSpec> >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(1054)
+template <typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TExpand> inline void append(String<TTargetValue, TTargetSpec> & target, TSourceValue * source, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(1068)
+template <typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TExpand> inline void append(String<TTargetValue, TTargetSpec> & target, TSourceValue * source, typename Size< String<TTargetValue, TTargetSpec> >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(1080)
+
+//____________________________________________________________________________
+// appendValue
+
+template <typename THost, typename TSpec, typename TValue, typename TExpand> inline void appendValue(Segment<THost, TSpec> & me, TValue const & _value, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(719)
+template <typename THost, typename TSpec, typename TValue, typename TExpand> inline void appendValue(Segment<THost, TSpec> const & me, TValue const & _value, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(728)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TValue, typename TTag> inline void appendValue(::std::basic_string<TChar, TCharTraits, TAlloc> & me, TValue const & _value, TTag); // "projects/library/seqan/sequence/std_string.h"(492)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TValue> inline void appendValue(::std::basic_string<TChar, TCharTraits, TAlloc> & me, TValue const & _value, Limit); // "projects/library/seqan/sequence/std_string.h"(502)
+template <typename TString, typename TString2, typename TExpand > inline void appendValue( StringSet< TString, Owner<Default> > &me, TString2 const &obj, Tag<TExpand> const); // "projects/library/seqan/sequence/sequence_multiple.h"(1042)
+template <typename TString, typename TString2, typename TExpand > inline void appendValue( StringSet< TString, Owner<ConcatDirect<void> > > &me, TString2 const &obj, Tag<TExpand> const); // "projects/library/seqan/sequence/sequence_multiple.h"(1053)
+template <typename TString, typename TDelimiter, typename TString2, typename TExpand > inline void appendValue( StringSet< TString, Owner<ConcatDirect<TDelimiter> > > &me, TString2 const &obj, Tag<TExpand> const); // "projects/library/seqan/sequence/sequence_multiple.h"(1063)
+template <typename TString, typename TExpand > inline void appendValue( StringSet<TString, Dependent<Generous> > &me, TString const &obj, Tag<TExpand> const); // "projects/library/seqan/sequence/sequence_multiple.h"(1075)
+template <typename TString, typename TExpand > inline void appendValue( StringSet<TString, Dependent<Tight> > &me, TString const &obj, Tag<TExpand> const); // "projects/library/seqan/sequence/sequence_multiple.h"(1087)
+template <typename T, typename TValue> inline void appendValue(T & me, TValue const & _value); // "projects/library/seqan/sequence/sequence_interface.h"(1114)
+template <typename T, typename TValue> inline void appendValue(T const & me, TValue const & _value); // "projects/library/seqan/sequence/sequence_interface.h"(1122)
+template <typename TValue, unsigned int SPACE, typename TVal, typename TExpand> inline void appendValue( String<TValue, Block<SPACE> >& me, TVal const& source, Tag<TExpand> const tag); // "projects/library/seqan/sequence/string_stack.h"(384)
+template <typename TTargetValue, typename TTargetSpec, typename TValue, typename TExpand> inline void appendValue(String<TTargetValue, TTargetSpec> & me, TValue const & _value, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(1126)
+
+//____________________________________________________________________________
+// assign
+
+template <typename TTargetValue, typename TSource, typename TExpand> inline void assign(String<TTargetValue, CStyle> & target, TSource & source, Tag<TExpand> const tag); // "projects/library/seqan/sequence/string_cstyle.h"(389)
+template <typename TTargetValue, typename TSource, typename TExpand> inline void assign(String<TTargetValue, CStyle> & target, TSource const & source, Tag<TExpand> const tag); // "projects/library/seqan/sequence/string_cstyle.h"(399)
+template <typename TTargetValue, typename TSource, typename TSize, typename TExpand> inline void assign(String<TTargetValue, CStyle> & target, TSource & source, TSize limit, Tag<TExpand> const tag); // "projects/library/seqan/sequence/string_cstyle.h"(410)
+template <typename TTargetValue, typename TSource, typename TSize, typename TExpand> inline void assign(String<TTargetValue, CStyle> & target, TSource const & source, TSize limit, Tag<TExpand> const tag); // "projects/library/seqan/sequence/string_cstyle.h"(421)
+template <typename TTargetValue, typename TSourceValue, typename TExpand> inline void assign(String<TTargetValue, CStyle> & target, TSourceValue const * source, Tag<TExpand> const tag); // "projects/library/seqan/sequence/string_cstyle.h"(435)
+template <typename TTargetValue, typename TSourceValue, typename TSize, typename TExpand> inline void assign(String<TTargetValue, CStyle> & target, TSourceValue const * source, TSize limit, Tag<TExpand> const tag); // "projects/library/seqan/sequence/string_cstyle.h"(446)
+template <typename TValue, typename TSourceSpec, typename TExpand> inline void assign(String<TValue, CStyle> & target, String<TValue, TSourceSpec> & source, Tag<TExpand> const); // "projects/library/seqan/sequence/string_cstyle.h"(520)
+template <typename THost, typename TSpec, typename TSource> inline void assign(Segment<THost, TSpec> & target, TSource & source); // "projects/library/seqan/sequence/segment_base.h"(293)
+template <typename THost, typename TSpec, typename TSource> inline void assign(Segment<THost, TSpec> & target, TSource const & source); // "projects/library/seqan/sequence/segment_base.h"(302)
+template <typename THost, typename TSpec, typename TSource> inline void assign(Segment<THost, TSpec> const & target, TSource & source); // "projects/library/seqan/sequence/segment_base.h"(314)
+template <typename THost, typename TSpec, typename TSource> inline void assign(Segment<THost, TSpec> const & target, TSource const & source); // "projects/library/seqan/sequence/segment_base.h"(323)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void assign(Segment<THost, TSpec> & target, TSource & source, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(403)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void assign(Segment<THost, TSpec> & target, TSource const & source, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(412)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void assign(Segment<THost, TSpec> & target, TSource & source, typename Size< Segment<THost, TSpec> >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(423)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void assign(Segment<THost, TSpec> & target, TSource const & source, typename Size< Segment<THost, TSpec> >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(433)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void assign(Segment<THost, TSpec> const & target, TSource & source, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(445)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void assign(Segment<THost, TSpec> const & target, TSource const & source, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(454)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void assign(Segment<THost, TSpec> const & target, TSource & source, typename Size< Segment<THost, TSpec> >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(465)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void assign(Segment<THost, TSpec> const & target, TSource const & source, typename Size< Segment<THost, TSpec> >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(475)
+template <typename TTargetValue, typename TSource> inline void assign(TTargetValue * target, TSource & source); // "projects/library/seqan/sequence/string_pointer.h"(444)
+template <typename TTargetValue, typename TSource> inline void assign(TTargetValue * target, TSource const & source); // "projects/library/seqan/sequence/string_pointer.h"(453)
+template <typename TTargetValue, typename TSource, typename TExpand> inline void assign(TTargetValue * target, TSource const & source, Tag<TExpand> const); // "projects/library/seqan/sequence/string_pointer.h"(466)
+template <typename TTargetValue, typename TSource, typename TExpand> inline void assign(TTargetValue * target, TSource const & source, size_t limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_pointer.h"(477)
+template <typename TTargetValue, typename TSourceValue, typename TExpand> inline void assign(TTargetValue * target, TSourceValue const * source, Tag<TExpand> const); // "projects/library/seqan/sequence/string_pointer.h"(490)
+template <typename TTargetValue, typename TSourceValue, typename TExpand> inline void assign(TTargetValue * target, TSourceValue const * source, size_t limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_pointer.h"(501)
+template <typename TValue, typename THostspec, typename TTag> inline void assign(String<TValue, Packed<THostspec> > & target, String<TValue, Packed<THostspec> > & source, Tag<TTag> const tag); // "projects/library/seqan/sequence/string_packed.h"(369)
+template <typename TValue, typename THostspec, typename TTag> inline void assign(String<TValue, Packed<THostspec> > & target, String<TValue, Packed<THostspec> > const & source, Tag<TTag> const tag); // "projects/library/seqan/sequence/string_packed.h"(377)
+template <typename TValue, typename THostspec, typename TSize, typename TTag> void assign(String<TValue, Packed<THostspec> > & target, String<TValue, Packed<THostspec> > & source, TSize limit, Tag<TTag> const tag); // "projects/library/seqan/sequence/string_packed.h"(386)
+template <typename TValue, typename THostspec, typename TSize, typename TTag> void assign(String<TValue, Packed<THostspec> > & target, String<TValue, Packed<THostspec> > const & source, TSize limit, Tag<TTag> const tag); // "projects/library/seqan/sequence/string_packed.h"(394)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource & source); // "projects/library/seqan/sequence/std_string.h"(272)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source); // "projects/library/seqan/sequence/std_string.h"(280)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource, typename TSize> inline void assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource & source, TSize limit); // "projects/library/seqan/sequence/std_string.h"(290)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource, typename TSize> inline void assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, TSize limit); // "projects/library/seqan/sequence/std_string.h"(299)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource & source, Generous); // "projects/library/seqan/sequence/std_string.h"(311)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, Generous); // "projects/library/seqan/sequence/std_string.h"(320)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource & source, typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit, Generous); // "projects/library/seqan/sequence/std_string.h"(347)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit, Generous); // "projects/library/seqan/sequence/std_string.h"(357)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource & source, Limit); // "projects/library/seqan/sequence/std_string.h"(369)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, Limit); // "projects/library/seqan/sequence/std_string.h"(378)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource & source, typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit, Limit); // "projects/library/seqan/sequence/std_string.h"(389)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit, Limit); // "projects/library/seqan/sequence/std_string.h"(404)
+template <typename TTarget, typename TSource> inline void assign(TTarget & target, TSource & source, typename Size<TTarget>::Type limit); // "projects/library/seqan/sequence/sequence_interface.h"(970)
+template <typename TTarget, typename TSource> inline void assign(TTarget const & target, TSource & source, typename Size<TTarget>::Type limit); // "projects/library/seqan/sequence/sequence_interface.h"(979)
+template <typename TTarget, typename TSource> inline void assign(TTarget & target, TSource const & source, typename Size<TTarget>::Type limit); // "projects/library/seqan/sequence/sequence_interface.h"(988)
+template <typename TTarget, typename TSource> inline void assign(TTarget const & target, TSource const & source, typename Size<TTarget>::Type limit); // "projects/library/seqan/sequence/sequence_interface.h"(997)
+template <typename TValue, unsigned int SPACE, typename TSource> inline void assign( String<TValue, Block<SPACE> >& target, TSource const& source); // "projects/library/seqan/sequence/string_stack.h"(226)
+template <typename TTargetValue, typename TTargetSpec, typename TSource> inline void assign(String<TTargetValue, TTargetSpec> & target, TSource & source); // "projects/library/seqan/sequence/string_base.h"(734)
+template <typename TTargetValue, typename TTargetSpec, typename TSource> inline void assign(String<TTargetValue, TTargetSpec> & target, TSource const & source); // "projects/library/seqan/sequence/string_base.h"(743)
+template <typename TTargetValue, typename TTargetSpec, typename TSource, typename TExpand> inline void assign(String<TTargetValue, TTargetSpec> & target, TSource const & source, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(810)
+template <typename TTargetValue, typename TTargetSpec, typename TSource, typename TSize, typename TExpand> inline void assign(String<TTargetValue, TTargetSpec> & target, TSource const & source, TSize limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(820)
+template <typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TExpand> inline void assign(String<TTargetValue, TTargetSpec> & target, TSourceValue const * source, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(833)
+template <typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TSize, typename TExpand> inline void assign(String<TTargetValue, TTargetSpec> & target, TSourceValue const * source, TSize limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(843)
+
+//____________________________________________________________________________
+// assignValue
+
+template <typename TContainer, typename TIterator, typename TValue> inline void assignValue(Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > & me, TValue const & _value); // "projects/library/seqan/sequence/string_value_expand.h"(453)
+template <typename TContainer, typename TIterator, typename TValue> inline void assignValue(Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > const & me, TValue const & _value); // "projects/library/seqan/sequence/string_value_expand.h"(473)
+template <typename TValue, typename TPos> inline void assignValue(TValue * me, TPos pos, TValue const & _value); // "projects/library/seqan/sequence/string_pointer.h"(266)
+template <typename TContainer, typename THostspec, typename TValue> inline void assignValue(Iter<TContainer, Packed<THostspec> > & me, TValue const & _value); // "projects/library/seqan/sequence/string_packed.h"(985)
+template <typename TContainer, typename THostspec, typename TValue> inline void assignValue(Iter<TContainer, Packed<THostspec> > const & me, TValue const & _value); // "projects/library/seqan/sequence/string_packed.h"(995)
+template <typename T, typename TValue, typename TPos> inline void assignValue(T & me, TPos pos, TValue const & _value); // "projects/library/seqan/sequence/sequence_interface.h"(775)
+template <typename TValue, typename TSpec, typename TValue2> inline void assignValue(String<TValue, TSpec> & me, TValue2 const & _value); // "projects/library/seqan/sequence/string_base.h"(715)
+
+//____________________________________________________________________________
+// assignValueById
+
+template <typename TString, typename TSpec, typename TString2> inline typename Id<StringSet<TString, TSpec> >::Type assignValueById(StringSet<TString, TSpec>& me, TString2& obj); // "projects/library/seqan/sequence/sequence_multiple.h"(1366)
+template <typename TString, typename TSpec, typename TId> inline typename Id<StringSet<TString, Owner<TSpec> > >::Type assignValueById(StringSet<TString, Owner<TSpec> >& me, TString& obj, TId id); // "projects/library/seqan/sequence/sequence_multiple.h"(1378)
+template <typename TString, typename TId> inline typename Id<StringSet<TString, Dependent<Generous> > >::Type assignValueById(StringSet<TString, Dependent<Generous> >& me, TString& obj, TId id); // "projects/library/seqan/sequence/sequence_multiple.h"(1394)
+template <typename TString, typename TId> inline typename Id<StringSet<TString, Dependent<Tight> > >::Type assignValueById(StringSet<TString, Dependent<Tight> >& me, TString& obj, TId id); // "projects/library/seqan/sequence/sequence_multiple.h"(1413)
+template <typename TString, typename TSpec1, typename TSpec2, typename TId> inline typename Id<StringSet<TString, TSpec1> >::Type assignValueById(StringSet<TString, TSpec1>& dest, StringSet<TString, TSpec2>& source, TId id); // "projects/library/seqan/sequence/sequence_multiple.h"(1434)
+
+//____________________________________________________________________________
+// assign_std_string_Generous_impl
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign_std_string_Generous_impl(::std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource & source, typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit); // "projects/library/seqan/sequence/std_string.h"(331)
+
+//____________________________________________________________________________
+// atBegin
+
+template <typename THost> inline bool atBegin(Segment<THost, InfixSegment> & segment); // "projects/library/seqan/sequence/segment_infix.h"(506)
+template <typename THost> inline bool atBegin(Segment<THost, InfixSegment> const & segment); // "projects/library/seqan/sequence/segment_infix.h"(513)
+template <typename THost> inline bool atBegin(Segment<THost, PrefixSegment> const & segment); // "projects/library/seqan/sequence/segment_prefix.h"(415)
+template <typename TSSet, typename TSpec> inline bool atBegin(Iter<TSSet, ConcatVirtual<TSpec> > &me); // "projects/library/seqan/sequence/sequence_multiple.h"(2227)
+template <typename TSSet, typename TSpec> inline bool atBegin(Iter<TSSet, ConcatVirtual<TSpec> > const &me); // "projects/library/seqan/sequence/sequence_multiple.h"(2234)
+template <typename THost> inline bool atBegin(Segment<THost, SuffixSegment> const & segment); // "projects/library/seqan/sequence/segment_suffix.h"(404)
+
+//____________________________________________________________________________
+// atEnd
+
+template <typename THost> inline bool atEnd(Segment<THost, InfixSegment> & segment); // "projects/library/seqan/sequence/segment_infix.h"(523)
+template <typename THost> inline bool atEnd(Segment<THost, InfixSegment> const & segment); // "projects/library/seqan/sequence/segment_infix.h"(530)
+template <typename TValue> inline bool atEnd(TValue * pos); // "projects/library/seqan/sequence/string_pointer.h"(290)
+template <typename TValue> inline bool atEnd(TValue * pos, TValue const * container); // "projects/library/seqan/sequence/string_pointer.h"(301)
+template <typename THost> inline bool atEnd(Segment<THost, PrefixSegment> const & segment); // "projects/library/seqan/sequence/segment_prefix.h"(425)
+template <typename TSSet, typename TSpec> inline bool atEnd(Iter<TSSet, ConcatVirtual<TSpec> > &me); // "projects/library/seqan/sequence/sequence_multiple.h"(2245)
+template <typename TSSet, typename TSpec> inline bool atEnd(Iter<TSSet, ConcatVirtual<TSpec> > const &me); // "projects/library/seqan/sequence/sequence_multiple.h"(2252)
+template <typename THost> inline bool atEnd(Segment<THost, SuffixSegment> const & segment); // "projects/library/seqan/sequence/segment_suffix.h"(414)
+template <typename TValue, unsigned int SPACE, typename TIteratorSpec> inline bool atEnd( Iter<String<TValue, Block<SPACE> >, TIteratorSpec>& it, String<TValue, Block<SPACE> >& container); // "projects/library/seqan/sequence/string_stack.h"(260)
+
+//____________________________________________________________________________
+// atEndOfSequence
+
+template <typename TIterator> inline bool atEndOfSequence(TIterator const &me); // "projects/library/seqan/sequence/sequence_multiple.h"(2263)
+template <typename TSSet, typename TSpec> inline bool atEndOfSequence(Iter<TSSet, ConcatVirtual<TSpec> > const &me); // "projects/library/seqan/sequence/sequence_multiple.h"(2270)
+template <typename TIterator> inline bool atEndOfSequence(TIterator &me); // "projects/library/seqan/sequence/sequence_multiple.h"(2277)
+
+//____________________________________________________________________________
+// back
+
+template <typename T> inline typename Reference<T const>::Type back(T const & me); // "projects/library/seqan/sequence/sequence_interface.h"(679)
+template <typename T> inline typename Reference<T>::Type back(T & me); // "projects/library/seqan/sequence/sequence_interface.h"(687)
+
+//____________________________________________________________________________
+// begin
+
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TTag> inline typename Iterator<String< TValue, ValueExpand<THost, TMap, TSpec> >, Tag<TTag> const>::Type begin(String< TValue, ValueExpand<THost, TMap, TSpec> > & me, Tag<TTag> const tag_); // "projects/library/seqan/sequence/string_value_expand.h"(293)
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TTag> inline typename Iterator<String< TValue, ValueExpand<THost, TMap, TSpec> > const, Tag<TTag> const>::Type begin(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me, Tag<TTag> const tag_); // "projects/library/seqan/sequence/string_value_expand.h"(301)
+template <typename T> inline typename Iterator<T *, typename DefaultGetIteratorSpec<T>::Type>::Type begin(T * me); // "projects/library/seqan/sequence/string_pointer.h"(147)
+template <typename TValue> inline typename Iterator<TValue *, Standard>::Type begin(TValue * me, Standard); // "projects/library/seqan/sequence/string_pointer.h"(158)
+template <typename TValue> inline typename Iterator<TValue const *, Standard>::Type begin(TValue const * me, Standard); // "projects/library/seqan/sequence/string_pointer.h"(168)
+template <typename TValue, typename TSpec> inline typename Iterator<TValue *, Tag<TSpec> const>::Type begin(TValue * me, Tag<TSpec> const); // "projects/library/seqan/sequence/string_pointer.h"(177)
+template <typename TValue, typename TSpec> inline typename Iterator<TValue const *, Tag<TSpec> const>::Type begin(TValue const * me, Tag<TSpec> const); // "projects/library/seqan/sequence/string_pointer.h"(187)
+template <typename TValue, typename THostspec, typename TTag> inline typename Iterator<String<TValue, Packed<THostspec> >, Tag<TTag> const>::Type begin(String<TValue, Packed<THostspec> > & me, Tag<TTag> const tag_); // "projects/library/seqan/sequence/string_packed.h"(440)
+template <typename TValue, typename THostspec, typename TTag> inline typename Iterator<String<TValue, Packed<THostspec> > const, Tag<TTag> const>::Type begin(String<TValue, Packed<THostspec> > const & me, Tag<TTag> const tag_); // "projects/library/seqan/sequence/string_packed.h"(448)
+template <typename TChar, typename TCharTraits, typename TAlloc> inline typename Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc>, Standard>::Type begin(::std::basic_string<TChar, TCharTraits, TAlloc> & me, Standard); // "projects/library/seqan/sequence/std_string.h"(159)
+template <typename TChar, typename TCharTraits, typename TAlloc> inline typename Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc> const, Standard>::Type begin(::std::basic_string<TChar, TCharTraits, TAlloc> const & me, Standard); // "projects/library/seqan/sequence/std_string.h"(167)
+template <typename TStringSet, typename TSpec > inline typename Iterator< ConcatenatorNto1<TStringSet const>, Tag<TSpec> const >::Type begin(ConcatenatorNto1<TStringSet const> concat, Tag<TSpec> const); // "projects/library/seqan/sequence/sequence_multiple.h"(1800)
+template <typename TStringSet, typename TSpec > inline typename Iterator< ConcatenatorNto1<TStringSet>, Tag<TSpec> const >::Type begin(ConcatenatorNto1<TStringSet> concat, Tag<TSpec> const); // "projects/library/seqan/sequence/sequence_multiple.h"(1807)
+template <typename T> inline typename Iterator<T, typename DefaultGetIteratorSpec<T>::Type>::Type begin(T & me); // "projects/library/seqan/sequence/sequence_interface.h"(259)
+template <typename T> inline typename Iterator<T const, typename DefaultGetIteratorSpec<T>::Type>::Type begin(T const & me); // "projects/library/seqan/sequence/sequence_interface.h"(266)
+template <typename T, typename TSpec> inline typename Iterator<T, Tag<TSpec> const>::Type begin(T & me, Tag<TSpec> const tag_); // "projects/library/seqan/sequence/sequence_interface.h"(327)
+template <typename T, typename TSpec> inline typename Iterator<T const, Tag<TSpec> const>::Type begin(T const & me, Tag<TSpec> const tag_); // "projects/library/seqan/sequence/sequence_interface.h"(335)
+template <typename TValue, unsigned int SPACE, typename TSpec> inline typename Iterator<String<TValue, Block<SPACE> >, Tag<TSpec> const >::Type begin(String<TValue, Block<SPACE> > &me, Tag<TSpec> const); // "projects/library/seqan/sequence/string_stack.h"(191)
+template <typename TValue, unsigned int SPACE, typename TSpec> inline typename Iterator<String<TValue, Block<SPACE> > const, Tag<TSpec> const>::Type begin(String<TValue, Block<SPACE> > const &me, Tag<TSpec> const); // "projects/library/seqan/sequence/string_stack.h"(199)
+
+//____________________________________________________________________________
+// beginPosition
+
+template <typename T> inline typename Position<T>::Type beginPosition(T &); // "projects/library/seqan/sequence/sequence_interface.h"(406)
+template <typename T> inline typename Position<T>::Type beginPosition(T const &); // "projects/library/seqan/sequence/sequence_interface.h"(413)
+
+//____________________________________________________________________________
+// capacity
+
+template <typename THost, typename TSpec> inline typename Size< Segment<THost, TSpec> const>::Type capacity(Segment<THost, TSpec> const & me); // "projects/library/seqan/sequence/segment_base.h"(270)
+template <typename TValue, typename THost, typename TMap, typename TSpec> inline typename Size<String< TValue, ValueExpand<THost, TMap, TSpec> > const>::Type capacity(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me); // "projects/library/seqan/sequence/string_value_expand.h"(361)
+template <typename TValue, typename THostspec> inline typename Size<String<TValue, Packed<THostspec> > const>::Type capacity(String<TValue, Packed<THostspec> > const & me); // "projects/library/seqan/sequence/string_packed.h"(505)
+template <typename TChar, typename TCharTraits, typename TAlloc> inline typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type capacity(::std::basic_string<TChar, TCharTraits, TAlloc> const & me); // "projects/library/seqan/sequence/std_string.h"(233)
+template <typename T> inline typename Size<T const>::Type capacity(T const & me); // "projects/library/seqan/sequence/sequence_interface.h"(856)
+template <typename TValue, unsigned int SPACE> inline typename Size<String<TValue, Block<SPACE> > >::Type capacity(String<TValue, Block<SPACE> > const & me); // "projects/library/seqan/sequence/string_stack.h"(522)
+
+//____________________________________________________________________________
+// clear
+
+template <typename THost, typename TSpec> inline void clear(Segment<THost, TSpec> & target); // "projects/library/seqan/sequence/segment_base.h"(1055)
+template <typename TValue> inline void clear(TValue * me); // "projects/library/seqan/sequence/string_pointer.h"(364)
+template <typename TValue, typename THostspec> inline void clear(String<TValue, Packed<THostspec> > & me); // "projects/library/seqan/sequence/string_packed.h"(520)
+template <typename TChar, typename TCharTraits, typename TAlloc> inline void clear(::std::basic_string<TChar, TCharTraits, TAlloc> & me); // "projects/library/seqan/sequence/std_string.h"(257)
+template <typename TString > inline void clear(StringSet< TString, Owner<Default> > &me); // "projects/library/seqan/sequence/sequence_multiple.h"(1107)
+template <typename TString, typename TDelimiter > inline void clear(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > &me); // "projects/library/seqan/sequence/sequence_multiple.h"(1116)
+template <typename TString > inline void clear(StringSet< TString, Dependent<Generous> > & me); // "projects/library/seqan/sequence/sequence_multiple.h"(1124)
+template <typename TString > inline void clear(StringSet<TString, Dependent<Tight> >& me); // "projects/library/seqan/sequence/sequence_multiple.h"(1133)
+template <typename TValue, unsigned int SPACE> inline void clear(String<TValue, Block<SPACE> >& me); // "projects/library/seqan/sequence/string_stack.h"(271)
+template <typename TValue, typename TSpec> inline void clear(String<TValue, TSpec> & me); // "projects/library/seqan/sequence/string_base.h"(204)
+
+//____________________________________________________________________________
+// compare
+
+template <typename TSpec, typename TLeft, typename TRight> inline void compare(Lexical<TSpec> & lexical, TLeft const & left, TRight const & right); // "projects/library/seqan/sequence/lexical.h"(278)
+template <typename TSpec, typename TLeftValue, typename TRight> inline void compare(Lexical<TSpec> & lexical, TLeftValue const * left, TRight const & right); // "projects/library/seqan/sequence/lexical.h"(288)
+template <typename TSpec, typename TLeftValue, typename TRightValue> inline void compare(Lexical<TSpec> & lexical, TLeftValue const * left, TRightValue const * right); // "projects/library/seqan/sequence/lexical.h"(296)
+template <typename TSpec, typename TLeft, typename TRightValue> inline void compare(Lexical<TSpec> & lexical, TLeft const & left, TRightValue const * right); // "projects/library/seqan/sequence/lexical.h"(304)
+
+//____________________________________________________________________________
+// compare_
+
+template <typename TSpec, typename TLeft, typename TRight> inline void compare_(Lexical<TSpec> & lexical, TLeft & left, TRight & right); // "projects/library/seqan/sequence/lexical.h"(237)
+
+//____________________________________________________________________________
+// computeGenerousCapacity
+
+template <typename T, typename TSize> inline TSize computeGenerousCapacity(T const & , TSize capacity); // "projects/library/seqan/sequence/sequence_interface.h"(927)
+
+//____________________________________________________________________________
+// concat
+
+template <typename TString> inline typename Concatenator<TString>::Type & concat(TString &string); // "projects/library/seqan/sequence/sequence_multiple.h"(1848)
+template <typename TString, typename TSpec> inline typename Concatenator< StringSet<TString, TSpec> >::Type & concat(StringSet<TString, TSpec> &set); // "projects/library/seqan/sequence/sequence_multiple.h"(1854)
+template <typename TString, typename TSpec> inline typename Concatenator< StringSet<TString, TSpec> const>::Type & concat(StringSet<TString, TSpec> const &set); // "projects/library/seqan/sequence/sequence_multiple.h"(1860)
+
+//____________________________________________________________________________
+// container
+
+template <typename TSSet, typename TSpec> inline typename Concatenator<TSSet>::Type container(Iter<TSSet, ConcatVirtual<TSpec> > &me); // "projects/library/seqan/sequence/sequence_multiple.h"(2209)
+template <typename TSSet, typename TSpec> inline typename Concatenator<TSSet>::Type container(Iter<TSSet, ConcatVirtual<TSpec> > const &me); // "projects/library/seqan/sequence/sequence_multiple.h"(2216)
+
+//____________________________________________________________________________
+// countSequences
+
+template <typename TString> inline unsigned countSequences(TString const &); // "projects/library/seqan/sequence/sequence_multiple.h"(620)
+template <typename TString, typename TSpec> inline typename Size<StringSet<TString, TSpec> >::Type countSequences(StringSet<TString, TSpec> const &stringSet); // "projects/library/seqan/sequence/sequence_multiple.h"(626)
+
+//____________________________________________________________________________
+// create
+
+template <typename TTargetValue, typename TSource> inline void create(String<TTargetValue, CStyle> & target, TSource & source); // "projects/library/seqan/sequence/string_cstyle.h"(693)
+template <typename TTargetValue, typename TSource, typename TSize> inline void create(String<TTargetValue, CStyle> & target, TSource & source, TSize limit); // "projects/library/seqan/sequence/string_cstyle.h"(704)
+template <typename TTargetValue, typename TSource, typename TExpand> inline void create(String<TTargetValue, CStyle> & target, TSource & source, Tag<TExpand> const); // "projects/library/seqan/sequence/string_cstyle.h"(717)
+template <typename TTargetValue, typename TSource, typename TSize, typename TExpand> inline void create(String<TTargetValue, CStyle> & target, TSource & source, TSize limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_cstyle.h"(728)
+template <typename TTargetValue, typename TSource, typename TExpand> inline void create(String<TTargetValue, CStyle> & target, TSource const & source, Tag<TExpand> const); // "projects/library/seqan/sequence/string_cstyle.h"(738)
+template <typename TTargetValue, typename TSource, typename TSize, typename TExpand> inline void create(String<TTargetValue, CStyle> & target, TSource const & source, TSize limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_cstyle.h"(749)
+template <typename TTargetValue, typename TSourceValue, typename TExpand> inline void create(String<TTargetValue, CStyle> & target, TSourceValue const * source, Tag<TExpand> const); // "projects/library/seqan/sequence/string_cstyle.h"(762)
+template <typename TTargetValue, typename TSourceValue, typename TSize, typename TExpand> inline void create(String<TTargetValue, CStyle> & target, TSourceValue const * source, TSize limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_cstyle.h"(773)
+
+//____________________________________________________________________________
+// empty
+
+template <typename TValue> inline bool empty(TValue * me); // "projects/library/seqan/sequence/string_pointer.h"(377)
+template <typename TChar, typename TCharTraits, typename TAlloc> inline bool empty(::std::basic_string<TChar, TCharTraits, TAlloc> const & me); // "projects/library/seqan/sequence/std_string.h"(245)
+template <typename T> inline bool empty(T const & me); // "projects/library/seqan/sequence/sequence_interface.h"(879)
+template <typename TValue, unsigned int SPACE> inline bool empty(String<TValue, Block<SPACE> > const& me); // "projects/library/seqan/sequence/string_stack.h"(503)
+
+//____________________________________________________________________________
+// end
+
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TTag> inline typename Iterator<String< TValue, ValueExpand<THost, TMap, TSpec> >, Tag<TTag> const>::Type end(String< TValue, ValueExpand<THost, TMap, TSpec> > & me, Tag<TTag> const tag_); // "projects/library/seqan/sequence/string_value_expand.h"(312)
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TTag> inline typename Iterator<String< TValue, ValueExpand<THost, TMap, TSpec> > const, Tag<TTag> const>::Type end(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me, Tag<TTag> const tag_); // "projects/library/seqan/sequence/string_value_expand.h"(320)
+template <typename TValue> inline typename Iterator<TValue *, Standard>::Type end(TValue * me, Standard); // "projects/library/seqan/sequence/string_pointer.h"(201)
+template <typename TValue> inline typename Iterator<TValue const *, Standard>::Type end(TValue const * me, Standard); // "projects/library/seqan/sequence/string_pointer.h"(211)
+template <typename TValue, typename TSpec> inline typename Iterator<TValue *, Tag<TSpec> const>::Type end(TValue * me, Tag<TSpec> const tag_); // "projects/library/seqan/sequence/string_pointer.h"(220)
+template <typename TValue, typename TSpec> inline typename Iterator<TValue const *, Tag<TSpec> const>::Type end(TValue const * me, Tag<TSpec> const tag_); // "projects/library/seqan/sequence/string_pointer.h"(229)
+template <typename TValue, typename THostspec, typename TTag> inline typename Iterator<String<TValue, Packed<THostspec> >, Tag<TTag> const>::Type end(String<TValue, Packed<THostspec> > & me, Tag<TTag> const tag_); // "projects/library/seqan/sequence/string_packed.h"(461)
+template <typename TValue, typename THostspec, typename TTag> inline typename Iterator<String<TValue, Packed<THostspec> > const, Tag<TTag> const>::Type end(String<TValue, Packed<THostspec> > const & me, Tag<TTag> const tag_); // "projects/library/seqan/sequence/string_packed.h"(469)
+template <typename TChar, typename TCharTraits, typename TAlloc> inline typename Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc>, Standard>::Type end(::std::basic_string<TChar, TCharTraits, TAlloc> & me, Standard); // "projects/library/seqan/sequence/std_string.h"(180)
+template <typename TChar, typename TCharTraits, typename TAlloc> inline typename Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc> const, Standard>::Type end(::std::basic_string<TChar, TCharTraits, TAlloc> const & me, Standard); // "projects/library/seqan/sequence/std_string.h"(188)
+template <typename TStringSet, typename TSpec > inline typename Iterator< ConcatenatorNto1<TStringSet const>, Tag<TSpec> const >::Type end(ConcatenatorNto1<TStringSet const> concat, Tag<TSpec> const); // "projects/library/seqan/sequence/sequence_multiple.h"(1817)
+template <typename TStringSet, typename TSpec > inline typename Iterator< ConcatenatorNto1<TStringSet>, Tag<TSpec> const >::Type end(ConcatenatorNto1<TStringSet> concat, Tag<TSpec> const); // "projects/library/seqan/sequence/sequence_multiple.h"(1825)
+template <typename T> inline typename Iterator<T, typename DefaultGetIteratorSpec<T>::Type>::Type end(T & me); // "projects/library/seqan/sequence/sequence_interface.h"(442)
+template <typename T> inline typename Iterator<T const, typename DefaultGetIteratorSpec<T>::Type>::Type end(T const & me); // "projects/library/seqan/sequence/sequence_interface.h"(449)
+template <typename T, typename TSpec> inline typename Iterator<T, Tag<TSpec> const>::Type end(T & me, Tag<TSpec> const tag_); // "projects/library/seqan/sequence/sequence_interface.h"(502)
+template <typename T, typename TSpec> inline typename Iterator<T const, Tag<TSpec> const>::Type end(T const & me, Tag<TSpec> const tag_); // "projects/library/seqan/sequence/sequence_interface.h"(510)
+template <typename TValue, unsigned int SPACE, typename TSpec> inline typename Iterator<String<TValue, Block<SPACE> >, Tag<TSpec> const >::Type end(String<TValue, Block<SPACE> > &me, Tag<TSpec> const); // "projects/library/seqan/sequence/string_stack.h"(208)
+template <typename TValue, unsigned int SPACE, typename TSpec> inline typename Iterator<String<TValue, Block<SPACE> > const, Tag<TSpec> const>::Type end(String<TValue, Block<SPACE> > const &me, Tag<TSpec> const); // "projects/library/seqan/sequence/string_stack.h"(216)
+
+//____________________________________________________________________________
+// endPosition
+
+template <typename T> inline typename Position<T>::Type endPosition(T & me); // "projects/library/seqan/sequence/sequence_interface.h"(535)
+template <typename T> inline typename Position<T>::Type endPosition(T const & me); // "projects/library/seqan/sequence/sequence_interface.h"(542)
+
+//____________________________________________________________________________
+// erase
+
+template <typename T, typename TPosition> inline void erase(T & me, TPosition pos, TPosition pos_end); // "projects/library/seqan/sequence/sequence_interface.h"(1433)
+template <typename T, typename TPosition> inline void erase(T & me, TPosition pos); // "projects/library/seqan/sequence/sequence_interface.h"(1442)
+
+//____________________________________________________________________________
+// fill
+
+template <typename TValue, typename TExpand> inline size_t fill( TValue * me, size_t new_length, TValue const & val, Tag<TExpand> const &); // "projects/library/seqan/sequence/string_pointer.h"(690)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSize, typename TExpand> inline typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type fill( ::std::basic_string<TChar, TCharTraits, TAlloc> & me, TSize new_length, TChar const & val, Tag<TExpand> const &); // "projects/library/seqan/sequence/std_string.h"(667)
+template <typename T, typename TSize, typename TValue> inline typename Size<T>::Type fill( T & me, TSize new_length, TValue const & val); // "projects/library/seqan/sequence/sequence_interface.h"(1483)
+template <typename TValue, typename TSpec, typename TSize, typename TValue2, typename TExpand> inline TSize fill(String<TValue, TSpec> & me, TSize new_length, TValue2 const & val, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(1508)
+
+//____________________________________________________________________________
+// front
+
+template <typename T> inline typename Reference<T>::Type front(T & me); // "projects/library/seqan/sequence/sequence_interface.h"(645)
+template <typename T> inline typename Reference<T const>::Type front(T const & me); // "projects/library/seqan/sequence/sequence_interface.h"(652)
+
+//____________________________________________________________________________
+// getSeqNo
+
+template <typename TPosition> inline TPosition getSeqNo(TPosition const &, Nothing const &); // "projects/library/seqan/sequence/sequence_multiple.h"(214)
+template <typename TPosition> inline TPosition getSeqNo(TPosition const &); // "projects/library/seqan/sequence/sequence_multiple.h"(225)
+template <typename T1, typename T2, typename TCompression, typename TLimitsString> inline T1 getSeqNo(Pair<T1, T2, TCompression> const &pos, TLimitsString const &); // "projects/library/seqan/sequence/sequence_multiple.h"(239)
+template <typename T1, typename T2, typename TCompression> inline T1 getSeqNo(Pair<T1, T2, TCompression> const &pos); // "projects/library/seqan/sequence/sequence_multiple.h"(244)
+template <typename TPos, typename TLimitsString> inline TPos getSeqNo(TPos const &pos, TLimitsString const &limits); // "projects/library/seqan/sequence/sequence_multiple.h"(264)
+
+//____________________________________________________________________________
+// getSeqOffset
+
+template <typename TPosition> inline TPosition getSeqOffset(TPosition const &pos, Nothing const &); // "projects/library/seqan/sequence/sequence_multiple.h"(219)
+template <typename TPosition> inline TPosition getSeqOffset(TPosition const &pos); // "projects/library/seqan/sequence/sequence_multiple.h"(230)
+template <typename T1, typename T2, typename TCompression, typename TLimitsString> inline T2 getSeqOffset(Pair<T1, T2, TCompression> const &pos, TLimitsString const &); // "projects/library/seqan/sequence/sequence_multiple.h"(250)
+template <typename T1, typename T2, typename TCompression> inline T1 getSeqOffset(Pair<T1, T2, TCompression> const &pos); // "projects/library/seqan/sequence/sequence_multiple.h"(255)
+template <typename TPos, typename TLimitsString> inline TPos getSeqOffset(TPos const &pos, TLimitsString const &limits); // "projects/library/seqan/sequence/sequence_multiple.h"(273)
+
+//____________________________________________________________________________
+// getValue
+
+template <typename TContainer, typename TIterator> inline typename Value<TContainer>::Type getValue(Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > & me); // "projects/library/seqan/sequence/string_value_expand.h"(396)
+template <typename TContainer, typename TIterator> inline void getValue(Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > const & me); // "projects/library/seqan/sequence/string_value_expand.h"(413)
+template <typename TContainer, typename THostspec> inline typename GetValue<Iter<TContainer, Packed<THostspec> > >::Type getValue(Iter<TContainer, Packed<THostspec> > & me); // "projects/library/seqan/sequence/string_packed.h"(949)
+template <typename TContainer, typename THostspec> inline typename GetValue<Iter<TContainer, Packed<THostspec> > const>::Type getValue(Iter<TContainer, Packed<THostspec> > const & me); // "projects/library/seqan/sequence/string_packed.h"(956)
+template <typename T, typename TPos> inline typename GetValue<T>::Type getValue(T & me, TPos pos); // "projects/library/seqan/sequence/sequence_interface.h"(610)
+template <typename T, typename TPos> inline typename GetValue<T const>::Type getValue(T const & me, TPos pos); // "projects/library/seqan/sequence/sequence_interface.h"(618)
+
+//____________________________________________________________________________
+// getValueById
+
+template <typename TString, typename TSpec, typename TId> inline typename Reference<StringSet<TString, Owner<TSpec> > >::Type getValueById(StringSet<TString, Owner<TSpec> >& me, TId const id); // "projects/library/seqan/sequence/sequence_multiple.h"(1279)
+template <typename TString, typename TId> inline typename Reference<StringSet<TString, Dependent<Generous> > >::Type getValueById(StringSet<TString, Dependent<Generous> >& me, TId const id); // "projects/library/seqan/sequence/sequence_multiple.h"(1290)
+template <typename TString, typename TId> inline typename Reference<StringSet<TString, Dependent<Tight> > >::Type getValueById(StringSet<TString, Dependent<Tight> >&me, TId const id); // "projects/library/seqan/sequence/sequence_multiple.h"(1302)
+
+//____________________________________________________________________________
+// goBegin
+
+template <typename THost> inline void goBegin(Segment<THost, InfixSegment> & segment); // "projects/library/seqan/sequence/segment_infix.h"(541)
+template <typename THost, typename THost2> inline void goBegin(Segment<THost, InfixSegment> & segment, THost2 &); // "projects/library/seqan/sequence/segment_infix.h"(550)
+template <typename THost, typename THost2> inline void goBegin(Segment<THost, InfixSegment> & segment, THost2 const &); // "projects/library/seqan/sequence/segment_infix.h"(557)
+template <typename THost> inline void goBegin(Segment<THost, PrefixSegment> & segment, THost &); // "projects/library/seqan/sequence/segment_prefix.h"(436)
+template <typename THost> inline void goBegin(Segment<THost, PrefixSegment> & segment); // "projects/library/seqan/sequence/segment_prefix.h"(444)
+template <typename THost> inline void goBegin(Segment<THost, SuffixSegment> & segment, THost &); // "projects/library/seqan/sequence/segment_suffix.h"(425)
+template <typename THost> inline void goBegin(Segment<THost, SuffixSegment> & segment); // "projects/library/seqan/sequence/segment_suffix.h"(433)
+
+//____________________________________________________________________________
+// goEnd
+
+template <typename THost> inline void goEnd(Segment<THost, InfixSegment> & segment); // "projects/library/seqan/sequence/segment_infix.h"(567)
+template <typename THost, typename THost2> inline void goEnd(Segment<THost, InfixSegment> & segment, THost2 &); // "projects/library/seqan/sequence/segment_infix.h"(576)
+template <typename THost, typename THost2> inline void goEnd(Segment<THost, InfixSegment> & segment, THost2 const &); // "projects/library/seqan/sequence/segment_infix.h"(583)
+template <typename THost> inline void goEnd(Segment<THost, PrefixSegment> & segment, THost &); // "projects/library/seqan/sequence/segment_prefix.h"(454)
+template <typename THost> inline void goEnd(Segment<THost, PrefixSegment> & segment); // "projects/library/seqan/sequence/segment_prefix.h"(462)
+template <typename THost> inline void goEnd(Segment<THost, SuffixSegment> & segment, THost &); // "projects/library/seqan/sequence/segment_suffix.h"(443)
+template <typename THost> inline void goEnd(Segment<THost, SuffixSegment> & segment); // "projects/library/seqan/sequence/segment_suffix.h"(451)
+
+//____________________________________________________________________________
+// goNext
+
+template <typename TContainer, typename THostspec> inline void goNext(Iter<TContainer, Packed<THostspec> > & me); // "projects/library/seqan/sequence/string_packed.h"(1144)
+template <typename TStringSet, typename TSpec> inline void goNext(Iter<TStringSet, ConcatVirtual<TSpec> > & me); // "projects/library/seqan/sequence/sequence_multiple.h"(2067)
+
+//____________________________________________________________________________
+// goPrevious
+
+template <typename TContainer, typename THostspec> inline void goPrevious(Iter<TContainer, Packed<THostspec> > & me); // "projects/library/seqan/sequence/string_packed.h"(1165)
+template <typename TStringSet, typename TSpec> inline void goPrevious(Iter<TStringSet, ConcatVirtual<TSpec> > & me); // "projects/library/seqan/sequence/sequence_multiple.h"(2093)
+
+//____________________________________________________________________________
+// hasPrefix
+
+template <typename TLeft, typename TRight > inline bool hasPrefix(TLeft const & left, TRight const & right); // "projects/library/seqan/sequence/lexical.h"(707)
+template <typename TSpec> inline bool hasPrefix(Lexical<TSpec> const & _lex); // "projects/library/seqan/sequence/lexical.h"(715)
+
+//____________________________________________________________________________
+// id
+
+template <typename THost, typename TSpec> inline void const * id(Segment<THost, TSpec> const & me); // "projects/library/seqan/sequence/segment_base.h"(246)
+template <typename TValue, typename THost, typename TMap, typename TSpec> inline void const * id(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me); // "projects/library/seqan/sequence/string_value_expand.h"(257)
+template <typename TValue, typename THostspec> inline void const * id(String<TValue, Packed<THostspec> > const & me); // "projects/library/seqan/sequence/string_packed.h"(406)
+template <typename TChar, typename TCharTraits, typename TAlloc> inline void const * id(::std::basic_string<TChar, TCharTraits, TAlloc> const & me); // "projects/library/seqan/sequence/std_string.h"(147)
+template <typename T> inline void const * id(T const & me); // "projects/library/seqan/sequence/sequence_interface.h"(208)
+
+//____________________________________________________________________________
+// idToPosition
+
+template <typename TString, typename TSpec, typename TId> inline typename Id<StringSet<TString, Owner<TSpec> > >::Type idToPosition(StringSet<TString, Owner<TSpec> >&, TId const id); // "projects/library/seqan/sequence/sequence_multiple.h"(1578)
+template <typename TString, typename TId> inline typename Id<StringSet<TString, Dependent<Generous> > >::Type idToPosition(StringSet<TString, Dependent<Generous> >& me, TId const id); // "projects/library/seqan/sequence/sequence_multiple.h"(1587)
+template <typename TString, typename TId> inline typename Id<StringSet<TString, Dependent<Tight> > >::Type idToPosition(StringSet<TString, Dependent<Tight> >&me, TId const id); // "projects/library/seqan/sequence/sequence_multiple.h"(1596)
+
+//____________________________________________________________________________
+// infix
+
+template <typename T, typename TPosBegin, typename TPosEnd> inline typename Infix<T>::Type infix(T & t, TPosBegin pos_begin, TPosEnd pos_end); // "projects/library/seqan/sequence/segment_infix.h"(673)
+template <typename T, typename TPosBegin, typename TPosEnd> inline typename Infix<T *>::Type infix(T * t, TPosBegin pos_begin, TPosEnd pos_end); // "projects/library/seqan/sequence/segment_infix.h"(681)
+template <typename T, typename TSpec, typename TPosBegin, typename TPosEnd> inline typename Infix<Segment<T, TSpec> >::Type infix(Segment<T, TSpec> & t, TPosBegin pos_begin, TPosEnd pos_end); // "projects/library/seqan/sequence/segment_infix.h"(689)
+template <typename T, typename TSpec, typename TPosBegin, typename TPosEnd> inline typename Infix<Segment<T, TSpec> const>::Type infix(Segment<T, TSpec> const & t, TPosBegin pos_begin, TPosEnd pos_end); // "projects/library/seqan/sequence/segment_infix.h"(700)
+
+//____________________________________________________________________________
+// infixWithLength
+
+template <typename T, typename TPosBegin, typename TSize> inline typename Infix<T>::Type infixWithLength(T & t, TPosBegin pos_begin, TSize length); // "projects/library/seqan/sequence/segment_infix.h"(731)
+template <typename T, typename TPosBegin, typename TSize> inline typename Infix<T *>::Type infixWithLength(T * t, TPosBegin pos_begin, TSize length); // "projects/library/seqan/sequence/segment_infix.h"(739)
+template <typename T, typename TSpec, typename TPosBegin, typename TSize> inline typename Infix<Segment<T, TSpec> >::Type infixWithLength(Segment<T, TSpec> & t, TPosBegin pos_begin, TSize length); // "projects/library/seqan/sequence/segment_infix.h"(747)
+template <typename T, typename TSpec, typename TPosBegin, typename TSize> inline typename Infix<Segment<T, TSpec> const>::Type infixWithLength(Segment<T, TSpec> const & t, TPosBegin pos_begin, TSize length); // "projects/library/seqan/sequence/segment_infix.h"(758)
+template <typename TString, typename TSpec, typename TPosition, typename TSize > inline typename Infix<TString>::Type infixWithLength(StringSet< TString, TSpec > &me, TPosition pos, TSize length); // "projects/library/seqan/sequence/sequence_multiple.h"(468)
+template <typename TString, typename TSpec, typename TPosition, typename TSize > inline typename Infix<TString const>::Type infixWithLength(StringSet< TString, TSpec > const &me, TPosition pos, TSize length); // "projects/library/seqan/sequence/sequence_multiple.h"(482)
+template <typename TString, typename TDelimiter, typename TPosition, typename TSize > inline typename Infix<TString>::Type infixWithLength(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > &me, TPosition pos, TSize length); // "projects/library/seqan/sequence/sequence_multiple.h"(496)
+template <typename TString, typename TDelimiter, typename TPosition, typename TSize > inline typename Infix<TString const>::Type infixWithLength(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > const &me, TPosition pos, TSize length); // "projects/library/seqan/sequence/sequence_multiple.h"(503)
+
+//____________________________________________________________________________
+// insertValue
+
+template <typename THost, typename TSpec, typename TPosition, typename TValue, typename TExpand> inline void insertValue(Segment<THost, TSpec> & me, TPosition pos, TValue const & _value, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(763)
+template <typename THost, typename TSpec, typename TPosition, typename TValue, typename TExpand> inline void insertValue(Segment<THost, TSpec> const & me, TPosition pos, TValue const & _value, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(773)
+template <typename T, typename TPosition, typename TValue> inline void insertValue(T & me, TPosition pos, TValue const & _value); // "projects/library/seqan/sequence/sequence_interface.h"(1149)
+template <typename T, typename TPosition, typename TValue> inline void insertValue(T const & me, TPosition pos, TValue const & _value); // "projects/library/seqan/sequence/sequence_interface.h"(1158)
+template <typename TTargetValue, typename TTargetSpec, typename TPosition, typename TValue, typename TExpand> inline void insertValue(String<TTargetValue, TTargetSpec> & me, TPosition pos, TValue const & _value, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(1165)
+
+//____________________________________________________________________________
+// isEqual
+
+template <typename TLeftValue, typename TRight > inline bool isEqual(TLeftValue * left, TRight const & right); // "projects/library/seqan/sequence/string_pointer.h"(715)
+template <typename TLeft, typename TRight > inline bool isEqual(TLeft const & left, TRight const & right); // "projects/library/seqan/sequence/lexical.h"(329)
+template <typename TSpec> inline bool isEqual(Lexical<TSpec> const & _lex); // "projects/library/seqan/sequence/lexical.h"(337)
+
+//____________________________________________________________________________
+// isGreater
+
+template <typename TLeftValue, typename TRight> inline bool isGreater(TLeftValue * left, TRight const & right); // "projects/library/seqan/sequence/string_pointer.h"(800)
+template <typename TLeft, typename TRight, typename TPrefixOrder > inline bool isGreater(TLeft const & left, TRight const & right, Tag<TPrefixOrder> const tag); // "projects/library/seqan/sequence/lexical.h"(540)
+template <typename TLeft, typename TRight> inline bool isGreater(TLeft const & left, TRight const & right); // "projects/library/seqan/sequence/lexical.h"(549)
+template <typename TSpec> inline bool isGreater(Lexical<TSpec> const & _lex, TagPrefixLess); // "projects/library/seqan/sequence/lexical.h"(558)
+template <typename TSpec> inline bool isGreater(Lexical<TSpec> const & _lex, TagPrefixGreater); // "projects/library/seqan/sequence/lexical.h"(566)
+template <typename TSpec> inline bool isGreater(Lexical<TSpec> const & _lex); // "projects/library/seqan/sequence/lexical.h"(573)
+
+//____________________________________________________________________________
+// isGreaterOrEqual
+
+template <typename TLeftValue, typename TRight> inline bool isGreaterOrEqual(TLeftValue * left, TRight const & right); // "projects/library/seqan/sequence/string_pointer.h"(820)
+template <typename TLeft, typename TRight, typename TPrefixOrder > inline bool isGreaterOrEqual(TLeft const & left, TRight const & right, Tag<TPrefixOrder> const tag); // "projects/library/seqan/sequence/lexical.h"(608)
+template <typename TLeft, typename TRight> inline bool isGreaterOrEqual(TLeft const & left, TRight const & right); // "projects/library/seqan/sequence/lexical.h"(617)
+template <typename TSpec> inline bool isGreaterOrEqual(Lexical<TSpec> const & _lex, TagPrefixLess); // "projects/library/seqan/sequence/lexical.h"(626)
+template <typename TSpec> inline bool isGreaterOrEqual(Lexical<TSpec> const & _lex, TagPrefixGreater); // "projects/library/seqan/sequence/lexical.h"(634)
+template <typename TSpec> inline bool isGreaterOrEqual(Lexical<TSpec> const & _lex); // "projects/library/seqan/sequence/lexical.h"(641)
+
+//____________________________________________________________________________
+// isLess
+
+template <typename TLeftValue, typename TRight> inline bool isLess(TLeftValue * left, TRight const & right); // "projects/library/seqan/sequence/string_pointer.h"(760)
+template <typename TLeft, typename TRight, typename TPrefixOrder > inline bool isLess(TLeft const & left, TRight const & right, Tag<TPrefixOrder> const tag); // "projects/library/seqan/sequence/lexical.h"(405)
+template <typename TLeft, typename TRight> inline bool isLess(TLeft const & left, TRight const & right); // "projects/library/seqan/sequence/lexical.h"(414)
+template <typename TSpec> inline bool isLess(Lexical<TSpec> const & _lex, TagPrefixLess); // "projects/library/seqan/sequence/lexical.h"(423)
+template <typename TSpec> inline bool isLess(Lexical<TSpec> const & _lex, TagPrefixGreater); // "projects/library/seqan/sequence/lexical.h"(431)
+template <typename TSpec> inline bool isLess(Lexical<TSpec> const & _lex); // "projects/library/seqan/sequence/lexical.h"(438)
+
+//____________________________________________________________________________
+// isLessOrEqual
+
+template <typename TLeftValue, typename TRight> inline bool isLessOrEqual(TLeftValue * left, TRight const & right); // "projects/library/seqan/sequence/string_pointer.h"(780)
+template <typename TLeft, typename TRight, typename TPrefixOrder > inline bool isLessOrEqual(TLeft const & left, TRight const & right, Tag<TPrefixOrder> const tag); // "projects/library/seqan/sequence/lexical.h"(473)
+template <typename TLeft, typename TRight> inline bool isLessOrEqual(TLeft const & left, TRight const & right); // "projects/library/seqan/sequence/lexical.h"(482)
+template <typename TSpec> inline bool isLessOrEqual(Lexical<TSpec> const & _lex, TagPrefixLess); // "projects/library/seqan/sequence/lexical.h"(491)
+template <typename TSpec> inline bool isLessOrEqual(Lexical<TSpec> const & _lex, TagPrefixGreater); // "projects/library/seqan/sequence/lexical.h"(499)
+template <typename TSpec> inline bool isLessOrEqual(Lexical<TSpec> const & _lex); // "projects/library/seqan/sequence/lexical.h"(506)
+
+//____________________________________________________________________________
+// isNotEqual
+
+template <typename TLeftValue, typename TRight > inline bool isNotEqual(TLeftValue * left, TRight const & right); // "projects/library/seqan/sequence/string_pointer.h"(737)
+template <typename TLeft, typename TRight > inline bool isNotEqual(TLeft const & left, TRight const & right); // "projects/library/seqan/sequence/lexical.h"(363)
+template <typename TSpec> inline bool isNotEqual(Lexical<TSpec> const & _lex); // "projects/library/seqan/sequence/lexical.h"(371)
+
+//____________________________________________________________________________
+// isPrefix
+
+template <typename TLeft, typename TRight > inline bool isPrefix(TLeft const & left, TRight const & right); // "projects/library/seqan/sequence/lexical.h"(669)
+template <typename TSpec> inline bool isPrefix(Lexical<TSpec> const & _lex); // "projects/library/seqan/sequence/lexical.h"(677)
+
+//____________________________________________________________________________
+// iter
+
+template <typename TValue, typename THost, typename TMap, typename TPos, typename TSpec, typename TTag> inline typename Iterator<String< TValue, ValueExpand<THost, TMap, TSpec> >, Tag<TTag> const>::Type iter(String< TValue, ValueExpand<THost, TMap, TSpec> > & me, TPos pos_, Tag<TTag> const tag_); // "projects/library/seqan/sequence/string_value_expand.h"(269)
+template <typename TValue, typename THost, typename TMap, typename TPos, typename TSpec, typename TTag> inline typename Iterator<String< TValue, ValueExpand<THost, TMap, TSpec> > const, Tag<TTag> const>::Type iter(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me, TPos pos_, Tag<TTag> const tag_ ); // "projects/library/seqan/sequence/string_value_expand.h"(280)
+template <typename TValue, typename THostspec, typename TPos, typename TTag> inline typename Iterator<String<TValue, Packed<THostspec> >, Tag<TTag> const>::Type iter(String<TValue, Packed<THostspec> > & me, TPos pos_, Tag<TTag> const); // "projects/library/seqan/sequence/string_packed.h"(418)
+template <typename TValue, typename THostspec, typename TPos, typename TTag> inline typename Iterator<String<TValue, Packed<THostspec> > const, Tag<TTag> const>::Type iter(String<TValue, Packed<THostspec> > const & me, TPos pos_, Tag<TTag> const); // "projects/library/seqan/sequence/string_packed.h"(428)
+template <typename T, typename TPos> inline typename Iterator<T, typename DefaultGetIteratorSpec<T>::Type>::Type iter(T & me, TPos pos); // "projects/library/seqan/sequence/sequence_interface.h"(720)
+template <typename T, typename TPos> inline typename Iterator<T const, typename DefaultGetIteratorSpec<T>::Type>::Type iter(T const & me, TPos pos); // "projects/library/seqan/sequence/sequence_interface.h"(728)
+template <typename T, typename TPos, typename TTag> inline typename Iterator<T, Tag<TTag> const>::Type iter(T & me, TPos pos, Tag<TTag> const tag_); // "projects/library/seqan/sequence/sequence_interface.h"(739)
+template <typename T, typename TPos, typename TTag> inline typename Iterator<T const, Tag<TTag> const>::Type iter(T const & me, TPos pos, Tag<TTag> const tag_); // "projects/library/seqan/sequence/sequence_interface.h"(748)
+
+//____________________________________________________________________________
+// lcpLength
+
+template <typename TLeft, typename TRight > inline typename Size<TLeft>::Type lcpLength(TLeft const & left, TRight const & right); // "projects/library/seqan/sequence/lexical.h"(739)
+template <typename TSpec> inline typename Size< Lexical<TSpec> >::Type lcpLength(Lexical<TSpec> const & _lex); // "projects/library/seqan/sequence/lexical.h"(748)
+
+//____________________________________________________________________________
+// length
+
+template <typename THost, typename TSpec> inline typename Size<Segment<THost, TSpec> const>::Type length(Segment<THost, TSpec> const & me); // "projects/library/seqan/sequence/segment_base.h"(258)
+template <typename TValue, typename THost, typename TMap, typename TSpec> inline typename Size<String< TValue, ValueExpand<THost, TMap, TSpec> > const>::Type length(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me); // "projects/library/seqan/sequence/string_value_expand.h"(351)
+template <typename TValue> inline size_t length(TValue * me); // "projects/library/seqan/sequence/string_pointer.h"(313)
+template <typename TValue> inline size_t length(TValue const * me); // "projects/library/seqan/sequence/string_pointer.h"(324)
+inline size_t length(char * me); // "projects/library/seqan/sequence/string_pointer.h"(334)
+inline size_t length(char const * me); // "projects/library/seqan/sequence/string_pointer.h"(341)
+template <typename TChar, typename TCharTraits, typename TAlloc> inline typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type length(::std::basic_string<TChar, TCharTraits, TAlloc> const & me); // "projects/library/seqan/sequence/std_string.h"(221)
+template <typename TString, typename TSpec > inline typename Size< StringSet< TString, TSpec > >::Type length(StringSet< TString, TSpec > const &me); // "projects/library/seqan/sequence/sequence_multiple.h"(1148)
+template <typename TString> inline typename Size<StringSet<TString, Dependent<Tight> > >::Type length(StringSet<TString, Dependent<Tight> > const &me); // "projects/library/seqan/sequence/sequence_multiple.h"(1155)
+template <typename TStringSet > inline typename Size< ConcatenatorNto1<TStringSet> >::Type length(ConcatenatorNto1<TStringSet> const &me); // "projects/library/seqan/sequence/sequence_multiple.h"(1790)
+template <typename T> inline typename Size<T const>::Type length(T const & ); // "projects/library/seqan/sequence/sequence_interface.h"(829)
+template <typename TValue, unsigned int SPACE> inline typename Size<String<TValue, Block<SPACE> > >::Type length(String<TValue, Block<SPACE> > const & me); // "projects/library/seqan/sequence/string_stack.h"(511)
+template <typename TValue, typename TSpec> inline typename Size< String<TValue, TSpec> const>::Type length(String<TValue, TSpec> const & me); // "projects/library/seqan/sequence/string_base.h"(179)
+
+//____________________________________________________________________________
+// lengthSum
+
+template <typename TString > inline typename Size<TString>::Type lengthSum(TString const &me); // "projects/library/seqan/sequence/sequence_multiple.h"(1023)
+template <typename TString, typename TSpec > inline typename Size<TString>::Type lengthSum(StringSet< TString, TSpec > const &me); // "projects/library/seqan/sequence/sequence_multiple.h"(1028)
+
+//____________________________________________________________________________
+// move
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void move(Segment<THost, TSpec> & target, TSource & source); // "projects/library/seqan/sequence/segment_base.h"(490)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void move(Segment<THost, TSpec> & target, TSource const & source); // "projects/library/seqan/sequence/segment_base.h"(499)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void move(Segment<THost, TSpec> const & target, TSource & source); // "projects/library/seqan/sequence/segment_base.h"(511)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void move(Segment<THost, TSpec> const & target, TSource const & source); // "projects/library/seqan/sequence/segment_base.h"(520)
+template <typename TTargetValue, typename TSource> inline void move(TTargetValue * & target, TSource & source); // "projects/library/seqan/sequence/string_pointer.h"(516)
+template <typename TTargetValue, typename TSource> inline void move(TTargetValue * & target, TSource const & source); // "projects/library/seqan/sequence/string_pointer.h"(524)
+template <typename TTargetValue, typename TSourceValue, typename TSpec> inline void move(String<TTargetValue, Alloc<TSpec> > & target, String<TSourceValue, Alloc<TSpec> > & source); // "projects/library/seqan/sequence/string_alloc.h"(360)
+template <typename TTargetValue, typename TSourceValue, typename TSpec> inline void move(String<TTargetValue, Alloc<TSpec> > & target, String<TSourceValue, Alloc<TSpec> > const & source); // "projects/library/seqan/sequence/string_alloc.h"(367)
+template <typename TValue, typename TSpec> inline void move(String<TValue, Alloc<TSpec> > & target, String<TValue, Alloc<TSpec> > & source); // "projects/library/seqan/sequence/string_alloc.h"(375)
+template <typename TValue, typename TSpec> inline void move(String<TValue, Alloc<TSpec> > & target, String<TValue, Alloc<TSpec> > const & source); // "projects/library/seqan/sequence/string_alloc.h"(389)
+template <typename TTargetValue, typename TTargetSpec, typename TSource> inline void move(String<TTargetValue, TTargetSpec> & target, TSource & source); // "projects/library/seqan/sequence/string_base.h"(915)
+template <typename TTargetValue, typename TTargetSpec, typename TSource> inline void move(String<TTargetValue, TTargetSpec> & target, TSource const & source); // "projects/library/seqan/sequence/string_base.h"(924)
+template <typename TTargetValue, typename TTargetSpec, typename TSource, typename TTag> inline void move(String<TTargetValue, TTargetSpec> & target, TSource & source, Tag<TTag> const tag); // "projects/library/seqan/sequence/string_base.h"(937)
+template <typename TTargetValue, typename TTargetSpec, typename TSource, typename TTag> inline void move(String<TTargetValue, TTargetSpec> & target, TSource const & source, Tag<TTag> const tag); // "projects/library/seqan/sequence/string_base.h"(947)
+
+//____________________________________________________________________________
+// moveValue
+
+template <typename TContainer, typename TIterator, typename TValue> inline void moveValue(Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > & me, TValue const & _value); // "projects/library/seqan/sequence/string_value_expand.h"(496)
+template <typename TContainer, typename TIterator, typename TValue> inline void moveValue(Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > const & me, TValue const & _value); // "projects/library/seqan/sequence/string_value_expand.h"(504)
+template <typename TValue, typename TPos> inline void moveValue(TValue * me, TPos pos, TValue const & _value); // "projects/library/seqan/sequence/string_pointer.h"(280)
+template <typename TContainer, typename THostspec, typename TValue> inline void moveValue(Iter<TContainer, Packed<THostspec> > & me, TValue const & _value); // "projects/library/seqan/sequence/string_packed.h"(1010)
+template <typename TContainer, typename THostspec, typename TValue> inline void moveValue(Iter<TContainer, Packed<THostspec> > const & me, TValue const & _value); // "projects/library/seqan/sequence/string_packed.h"(1018)
+template <typename T, typename TValue, typename TPos> inline void moveValue(T & me, TPos pos, TValue const & _value); // "projects/library/seqan/sequence/sequence_interface.h"(804)
+
+//____________________________________________________________________________
+// operator!=
+
+template <typename TLeftHost, typename TLeftSpec, typename TRight > inline bool operator!= (Segment<TLeftHost, TLeftSpec> const & left, TRight const & right); // "projects/library/seqan/sequence/segment_base.h"(1091)
+template <typename TContainer, typename THostspec> inline bool operator!= (Iter<TContainer, Packed<THostspec> > const & left, Iter<TContainer, Packed<THostspec> > const & right); // "projects/library/seqan/sequence/string_packed.h"(1080)
+template <typename TSSetL, typename TSpecL, typename TSSetR, typename TSpecR> inline bool operator!= ( Iter<TSSetL, ConcatVirtual<TSpecL> > const &L, Iter<TSSetR, ConcatVirtual<TSpecR> > const &R); // "projects/library/seqan/sequence/sequence_multiple.h"(2173)
+template <typename TLeftValue, typename TLeftSpec, typename TRight > inline bool operator!=(String<TLeftValue, TLeftSpec> const & left, TRight const & right); // "projects/library/seqan/sequence/string_base.h"(1572)
+
+//____________________________________________________________________________
+// operator*
+
+template <typename TStringSet, typename TSpec> inline typename Reference< Iter< TStringSet, ConcatVirtual<TSpec> > const>::Type operator* (Iter<TStringSet, ConcatVirtual<TSpec> > const & me); // "projects/library/seqan/sequence/sequence_multiple.h"(2051)
+template <typename TStringSet, typename TSpec> inline typename Reference< Iter< TStringSet, ConcatVirtual<TSpec> > >::Type operator* (Iter<TStringSet, ConcatVirtual<TSpec> > & me); // "projects/library/seqan/sequence/sequence_multiple.h"(2057)
+
+//____________________________________________________________________________
+// operator+
+
+template <typename TContainer, typename THostspec, typename TIntegral> inline Iter<TContainer, Packed<THostspec> > operator+ (Iter<TContainer, Packed<THostspec> > const & left, TIntegral right); // "projects/library/seqan/sequence/string_packed.h"(1189)
+template <typename TContainer, typename THostspec, typename TIntegral> inline Iter<TContainer, Packed<THostspec> > operator+ (TIntegral left, Iter<TContainer, Packed<THostspec> > const & right); // "projects/library/seqan/sequence/string_packed.h"(1197)
+template <typename TStringSet, typename TSpec, typename TDelta> inline Iter<TStringSet, ConcatVirtual<TSpec> > operator+ (Iter<TStringSet, ConcatVirtual<TSpec> > const & me, TDelta delta); // "projects/library/seqan/sequence/sequence_multiple.h"(2119)
+template <typename TStringSet, typename TSpec, typename T1, typename T2, typename TCompression> inline Iter<TStringSet, ConcatVirtual<TSpec> > operator+ (Iter<TStringSet, ConcatVirtual<TSpec> > const & me, Pair<T1, T2, TCompression> delta); // "projects/library/seqan/sequence/sequence_multiple.h"(2127)
+
+//____________________________________________________________________________
+// operator++
+
+template <typename THost> inline Segment<THost, InfixSegment> & operator++(Segment<THost, InfixSegment> & segment); // "projects/library/seqan/sequence/segment_infix.h"(592)
+template <typename THost> inline Segment<THost, PrefixSegment> & operator++(Segment<THost, PrefixSegment> & segment); // "projects/library/seqan/sequence/segment_prefix.h"(471)
+template <typename TStringSet, typename TSpec> inline Iter<TStringSet, ConcatVirtual<TSpec> > const & operator++ (Iter<TStringSet, ConcatVirtual<TSpec> > & me); // "projects/library/seqan/sequence/sequence_multiple.h"(2074)
+template <typename TStringSet, typename TSpec> inline Iter<TStringSet, ConcatVirtual<TSpec> > const & operator++ (Iter<TStringSet, ConcatVirtual<TSpec> > & me, int); // "projects/library/seqan/sequence/sequence_multiple.h"(2081)
+template <typename THost> inline Segment<THost, SuffixSegment> & operator++(Segment<THost, SuffixSegment> & segment); // "projects/library/seqan/sequence/segment_suffix.h"(460)
+
+//____________________________________________________________________________
+// operator+=
+
+template <typename TLeftValue, typename TLeftSpec, typename TRight> Segment<TLeftValue, TLeftSpec> const & operator+= (Segment<TLeftValue, TLeftSpec> & left, TRight const & right); // "projects/library/seqan/sequence/segment_base.h"(1066)
+template <typename TContainer, typename THostspec, typename TIntegral> inline Iter<TContainer, Packed<THostspec> > & operator+= (Iter<TContainer, Packed<THostspec> > & left, TIntegral right); // "projects/library/seqan/sequence/string_packed.h"(1210)
+template <typename TLeftValue, typename TLeftSpec, typename TRight > String<TLeftValue, TLeftSpec> const & operator+= (String<TLeftValue, TLeftSpec> & left, TRight const & right); // "projects/library/seqan/sequence/string_base.h"(1548)
+
+//____________________________________________________________________________
+// operator-
+
+template <typename TContainer, typename THostspec, typename TIntegral> inline Iter<TContainer, Packed<THostspec> > operator- (Iter<TContainer, Packed<THostspec> > const & left, TIntegral right); // "projects/library/seqan/sequence/string_packed.h"(1224)
+template <typename TContainer, typename THostspec> inline typename Difference<Iter<TContainer, Packed<THostspec> > >::Type operator- (Iter<TContainer, Packed<THostspec> > const & left, Iter<TContainer, Packed<THostspec> > const & right); // "projects/library/seqan/sequence/string_packed.h"(1235)
+template <typename TSSetL, typename TSpecL, typename TSSetR, typename TSpecR> typename Difference<Iter<TSSetL, ConcatVirtual<TSpecL> > >::Type operator- ( Iter<TSSetL, ConcatVirtual<TSpecL> > const &L, Iter<TSSetR, ConcatVirtual<TSpecR> > const &R); // "projects/library/seqan/sequence/sequence_multiple.h"(2142)
+template <typename TStringSet, typename TSpec, typename TDelta> inline Iter<TStringSet, ConcatVirtual<TSpec> > operator- (Iter<TStringSet, ConcatVirtual<TSpec> > const & me, TDelta delta); // "projects/library/seqan/sequence/sequence_multiple.h"(2148)
+
+//____________________________________________________________________________
+// operator--
+
+template <typename THost> inline Segment<THost, InfixSegment> & operator--(Segment<THost, InfixSegment> & segment); // "projects/library/seqan/sequence/segment_infix.h"(612)
+template <typename THost> inline Segment<THost, PrefixSegment> & operator--(Segment<THost, PrefixSegment> & segment); // "projects/library/seqan/sequence/segment_prefix.h"(481)
+template <typename TStringSet, typename TSpec> inline Iter<TStringSet, ConcatVirtual<TSpec> > const & operator-- (Iter<TStringSet, ConcatVirtual<TSpec> > & me); // "projects/library/seqan/sequence/sequence_multiple.h"(2100)
+template <typename TStringSet, typename TSpec> inline Iter<TStringSet, ConcatVirtual<TSpec> > const & operator-- (Iter<TStringSet, ConcatVirtual<TSpec> > & me, int); // "projects/library/seqan/sequence/sequence_multiple.h"(2107)
+template <typename THost> inline Segment<THost, SuffixSegment> & operator--(Segment<THost, SuffixSegment> & segment); // "projects/library/seqan/sequence/segment_suffix.h"(470)
+
+//____________________________________________________________________________
+// operator-=
+
+template <typename TContainer, typename THostspec, typename TIntegral> inline Iter<TContainer, Packed<THostspec> > & operator-= (Iter<TContainer, Packed<THostspec> > & left, TIntegral right); // "projects/library/seqan/sequence/string_packed.h"(1248)
+
+//____________________________________________________________________________
+// operator<
+
+template <typename TLeftHost, typename TLeftSpec, typename TRight> inline bool operator< (Segment<TLeftHost, TLeftSpec> const & left, TRight const & right); // "projects/library/seqan/sequence/segment_base.h"(1103)
+template <typename TContainer, typename THostspec> inline bool operator< (Iter<TContainer, Packed<THostspec> > const & left, Iter<TContainer, Packed<THostspec> > const & right); // "projects/library/seqan/sequence/string_packed.h"(1119)
+template <typename TSSetL, typename TSpecL, typename TSSetR, typename TSpecR> inline bool operator< ( Iter<TSSetL, ConcatVirtual<TSpecL> > const &L, Iter<TSSetR, ConcatVirtual<TSpecR> > const &R); // "projects/library/seqan/sequence/sequence_multiple.h"(2187)
+template <typename TLeftValue, typename TLeftSpec, typename TRight> inline bool operator< (String<TLeftValue, TLeftSpec> const & left, TRight const & right); // "projects/library/seqan/sequence/string_base.h"(1584)
+
+//____________________________________________________________________________
+// operator<<
+
+template <typename TStream, typename THost, typename TSpec> inline TStream & operator<< (TStream & target, Segment<THost, TSpec> const & source); // "projects/library/seqan/sequence/segment_base.h"(1149)
+template <typename TStream, typename TValue, typename TSpec> inline TStream & operator<< (TStream & target, String<TValue, TSpec> const & source); // "projects/library/seqan/sequence/string_base.h"(1629)
+
+//____________________________________________________________________________
+// operator<=
+
+template <typename TLeftHost, typename TLeftSpec, typename TRight> inline bool operator<= (Segment<TLeftHost, TLeftSpec> const & left, TRight const & right); // "projects/library/seqan/sequence/segment_base.h"(1114)
+template <typename TContainer, typename THostspec> inline bool operator<= (Iter<TContainer, Packed<THostspec> > const & left, Iter<TContainer, Packed<THostspec> > const & right); // "projects/library/seqan/sequence/string_packed.h"(1132)
+template <typename TLeftValue, typename TLeftSpec, typename TRight> inline bool operator<= (String<TLeftValue, TLeftSpec> const & left, TRight const & right); // "projects/library/seqan/sequence/string_base.h"(1595)
+
+//____________________________________________________________________________
+// operator==
+
+template <typename TLeftHost, typename TLeftSpec, typename TRight > inline bool operator== (Segment<TLeftHost, TLeftSpec> const & left, TRight const & right); // "projects/library/seqan/sequence/segment_base.h"(1079)
+template <typename TContainer, typename THostspec> inline bool operator== (Iter<TContainer, Packed<THostspec> > const & left, Iter<TContainer, Packed<THostspec> > const & right); // "projects/library/seqan/sequence/string_packed.h"(1067)
+template <typename TSSetL, typename TSpecL, typename TSSetR, typename TSpecR> inline bool operator== ( Iter<TSSetL, ConcatVirtual<TSpecL> > const &L, Iter<TSSetR, ConcatVirtual<TSpecR> > const &R); // "projects/library/seqan/sequence/sequence_multiple.h"(2163)
+template <typename TLeftValue, typename TLeftSpec, typename TRight > inline bool operator== (String<TLeftValue, TLeftSpec> const & left, TRight const & right); // "projects/library/seqan/sequence/string_base.h"(1560)
+
+//____________________________________________________________________________
+// operator>
+
+template <typename TLeftHost, typename TLeftSpec, typename TRight> inline bool operator> (Segment<TLeftHost, TLeftSpec> const & left, TRight const & right); // "projects/library/seqan/sequence/segment_base.h"(1124)
+template <typename TContainer, typename THostspec> inline bool operator> (Iter<TContainer, Packed<THostspec> > const & left, Iter<TContainer, Packed<THostspec> > const & right); // "projects/library/seqan/sequence/string_packed.h"(1093)
+template <typename TSSetL, typename TSpecL, typename TSSetR, typename TSpecR> inline bool operator> ( Iter<TSSetL, ConcatVirtual<TSpecL> > const &L, Iter<TSSetR, ConcatVirtual<TSpecR> > const &R); // "projects/library/seqan/sequence/sequence_multiple.h"(2197)
+template <typename TLeftValue, typename TLeftSpec, typename TRight> inline bool operator> (String<TLeftValue, TLeftSpec> const & left, TRight const & right); // "projects/library/seqan/sequence/string_base.h"(1605)
+
+//____________________________________________________________________________
+// operator>=
+
+template <typename TLeftHost, typename TLeftSpec, typename TRight> inline bool operator>= (Segment<TLeftHost, TLeftSpec> const & left, TRight const & right); // "projects/library/seqan/sequence/segment_base.h"(1135)
+template <typename TContainer, typename THostspec> inline bool operator>= (Iter<TContainer, Packed<THostspec> > const & left, Iter<TContainer, Packed<THostspec> > const & right); // "projects/library/seqan/sequence/string_packed.h"(1106)
+template <typename TLeftValue, typename TLeftSpec, typename TRight> inline bool operator>= (String<TLeftValue, TLeftSpec> const & left, TRight const & right); // "projects/library/seqan/sequence/string_base.h"(1616)
+
+//____________________________________________________________________________
+// operator>>
+
+template <typename TStream, typename THost, typename TSpec> inline TStream & operator>> (TStream & source, Segment<THost, TSpec> & target); // "projects/library/seqan/sequence/segment_base.h"(1161)
+template <typename TStream, typename THost, typename TSpec> inline TStream & operator>> (TStream & source, Segment<THost, TSpec> const & target); // "projects/library/seqan/sequence/segment_base.h"(1170)
+template <typename TStream, typename TValue, typename TSpec> inline TStream & operator>> (TStream & source, String<TValue, TSpec> & target); // "projects/library/seqan/sequence/string_base.h"(1641)
+
+//____________________________________________________________________________
+// ordValue
+
+template <typename TValue> inline unsigned ordValue(TValue const &c); // "projects/library/seqan/sequence/lexical.h"(770)
+template <typename TValue, typename TSpec> inline unsigned ordValue(SimpleType<TValue,TSpec> const &c); // "projects/library/seqan/sequence/lexical.h"(776)
+
+//____________________________________________________________________________
+// pop
+
+template <typename TValue, unsigned int SPACE> inline void pop(String<TValue, Block<SPACE> >& me); // "projects/library/seqan/sequence/string_stack.h"(474)
+
+//____________________________________________________________________________
+// pop_back
+
+template <typename TValue, unsigned int SPACE> inline void pop_back(String<TValue, Block<SPACE> >& me); // "projects/library/seqan/sequence/string_stack.h"(496)
+
+//____________________________________________________________________________
+// posAdd
+
+template <typename TPos, typename TDelta> inline TPos posAdd(TPos pos, TDelta delta); // "projects/library/seqan/sequence/sequence_multiple.h"(547)
+template <typename T1, typename T2, typename TCompression, typename TDelta> inline Pair<T1, T2, TCompression> posAdd(Pair<T1, T2, TCompression> const &pos, TDelta delta); // "projects/library/seqan/sequence/sequence_multiple.h"(553)
+
+//____________________________________________________________________________
+// posAtFirstLocal
+
+template <typename TPos, typename TLimitsString> inline bool posAtFirstLocal(TPos pos, TLimitsString const &limits); // "projects/library/seqan/sequence/sequence_multiple.h"(513)
+template <typename TPos> inline bool posAtFirstLocal(TPos pos); // "projects/library/seqan/sequence/sequence_multiple.h"(517)
+
+//____________________________________________________________________________
+// posCompare
+
+template <typename TPos> inline int posCompare(TPos const &a, TPos const &b); // "projects/library/seqan/sequence/sequence_multiple.h"(589)
+template <typename T1, typename T2, typename TCompression> inline int posCompare(Pair<T1, T2, TCompression> const &a, Pair<T1, T2, TCompression> const &b); // "projects/library/seqan/sequence/sequence_multiple.h"(596)
+
+//____________________________________________________________________________
+// posGlobalize
+
+template <typename TPosition> inline TPosition posGlobalize(TPosition const &pos, Nothing const &); // "projects/library/seqan/sequence/sequence_multiple.h"(300)
+template <typename T1, typename T2, typename TCompression> inline T2 posGlobalize(Pair<T1, T2, TCompression> const &pos, Nothing const &); // "projects/library/seqan/sequence/sequence_multiple.h"(306)
+template <typename TLimitsString, typename TPosition> inline TPosition posGlobalize(TPosition const &pos, TLimitsString const &); // "projects/library/seqan/sequence/sequence_multiple.h"(312)
+template <typename TLimitsString, typename T1, typename T2, typename TCompression> inline typename Value<TLimitsString>::Type posGlobalize(Pair<T1, T2, TCompression> const &pos, TLimitsString const &limits); // "projects/library/seqan/sequence/sequence_multiple.h"(319)
+
+//____________________________________________________________________________
+// posLess
+
+template <typename TPos> inline bool posLess(TPos const &a, TPos const &b); // "projects/library/seqan/sequence/sequence_multiple.h"(577)
+template <typename T1, typename T2, typename TCompression> inline bool posLess(Pair<T1, T2, TCompression> const &a, Pair<T1, T2, TCompression> const &b); // "projects/library/seqan/sequence/sequence_multiple.h"(582)
+
+//____________________________________________________________________________
+// posLocalize
+
+template <typename TResult, typename TPosition> inline void posLocalize(TResult &result, TPosition const &pos, Nothing const &); // "projects/library/seqan/sequence/sequence_multiple.h"(343)
+template <typename T1, typename T2, typename TCompression, typename TPosition> inline void posLocalize(Pair<T1, T2, TCompression> &result, TPosition const &pos, Nothing const &); // "projects/library/seqan/sequence/sequence_multiple.h"(348)
+template <typename TResult, typename TSize, typename TSpec, typename TPosition> inline void posLocalize(TResult &result, TPosition const &pos, String<TSize, TSpec> const &limits); // "projects/library/seqan/sequence/sequence_multiple.h"(355)
+template <typename TResult, typename TSize, typename TSpec, typename T1, typename T2, typename TCompression> inline void posLocalize(TResult &result, Pair<T1, T2, TCompression> const &pos, String<TSize, TSpec> const & ); // "projects/library/seqan/sequence/sequence_multiple.h"(365)
+
+//____________________________________________________________________________
+// posNext
+
+template <typename TPos> inline TPos posNext(TPos pos); // "projects/library/seqan/sequence/sequence_multiple.h"(535)
+template <typename T1, typename T2, typename TCompression> inline Pair<T1, T2, TCompression> posNext(Pair<T1, T2, TCompression> const &pos); // "projects/library/seqan/sequence/sequence_multiple.h"(541)
+
+//____________________________________________________________________________
+// posPrev
+
+template <typename TPos> inline TPos posPrev(TPos pos); // "projects/library/seqan/sequence/sequence_multiple.h"(524)
+template <typename T1, typename T2, typename TCompression> inline Pair<T1, T2, TCompression> posPrev(Pair<T1, T2, TCompression> const &pos); // "projects/library/seqan/sequence/sequence_multiple.h"(529)
+
+//____________________________________________________________________________
+// posSub
+
+template <typename TA, typename TB> inline TA posSub(TA a, TB b); // "projects/library/seqan/sequence/sequence_multiple.h"(559)
+template <typename TA1, typename TA2, typename TACompression, typename TB1, typename TB2, typename TBCompression > inline TA2 posSub(Pair<TA1, TA2, TACompression> const &a, Pair<TB1, TB2, TBCompression> const &b); // "projects/library/seqan/sequence/sequence_multiple.h"(568)
+
+//____________________________________________________________________________
+// position
+
+template <typename TContainer, typename THostspec> inline typename Position<Iter<TContainer, Packed<THostspec> > const>::Type position(Iter<TContainer, Packed<THostspec> > const & me); // "projects/library/seqan/sequence/string_packed.h"(902)
+
+//____________________________________________________________________________
+// positionToId
+
+template <typename TString, typename TSpec, typename TPos> inline typename Id<StringSet<TString, Owner<TSpec> > >::Type positionToId(StringSet<TString, Owner<TSpec> >&, TPos const pos); // "projects/library/seqan/sequence/sequence_multiple.h"(1518)
+template <typename TString, typename TPos> inline typename Id<StringSet<TString, Dependent<Generous> > >::Type positionToId(StringSet<TString, Dependent<Generous> >& me, TPos const pos); // "projects/library/seqan/sequence/sequence_multiple.h"(1527)
+template <typename TString, typename TPos> inline typename Id<StringSet<TString, Dependent<Generous> > >::Type positionToId(StringSet<TString, Dependent<Generous> > const& me, TPos const pos); // "projects/library/seqan/sequence/sequence_multiple.h"(1536)
+template <typename TString, typename TPos> inline typename Id<StringSet<TString, Dependent<Tight> > >::Type positionToId(StringSet<TString, Dependent<Tight> >&me, TPos const pos); // "projects/library/seqan/sequence/sequence_multiple.h"(1545)
+template <typename TString, typename TPos> inline typename Id<StringSet<TString, Dependent<Tight> > >::Type positionToId(StringSet<TString, Dependent<Tight> > const&me, TPos const pos); // "projects/library/seqan/sequence/sequence_multiple.h"(1554)
+
+//____________________________________________________________________________
+// prefix
+
+template <typename T, typename TPosEnd> inline typename Prefix<T>::Type prefix(T & t, TPosEnd pos_end); // "projects/library/seqan/sequence/segment_prefix.h"(510)
+template <typename T, typename TPosEnd> inline typename Prefix<T *>::Type prefix(T * t, TPosEnd pos_end); // "projects/library/seqan/sequence/segment_prefix.h"(518)
+template <typename T, typename TPosEnd> inline typename Prefix<Segment<T, PrefixSegment> >::Type prefix(Segment<T, PrefixSegment> & t, TPosEnd pos_end); // "projects/library/seqan/sequence/segment_prefix.h"(528)
+template <typename T, typename TPosEnd> inline typename Prefix<Segment<T, PrefixSegment> const>::Type prefix(Segment<T, PrefixSegment> const & t, TPosEnd pos_end); // "projects/library/seqan/sequence/segment_prefix.h"(537)
+template <typename T, typename TPosEnd> inline typename Prefix<Segment<T, InfixSegment> >::Type prefix(Segment<T, InfixSegment> & t, TPosEnd pos_end); // "projects/library/seqan/sequence/segment_prefix.h"(549)
+template <typename T, typename TPosEnd> inline typename Prefix<Segment<T, InfixSegment> const>::Type prefix(Segment<T, InfixSegment> const & t, TPosEnd pos_end); // "projects/library/seqan/sequence/segment_prefix.h"(559)
+template <typename T, typename TPosEnd> inline typename Prefix<Segment<T, SuffixSegment> >::Type prefix(Segment<T, SuffixSegment> & t, TPosEnd pos_end); // "projects/library/seqan/sequence/segment_prefix.h"(573)
+template <typename T, typename TPosEnd> inline typename Prefix<Segment<T, SuffixSegment> const>::Type prefix(Segment<T, SuffixSegment> const & t, TPosEnd pos_end); // "projects/library/seqan/sequence/segment_prefix.h"(583)
+template <typename TString, typename TSpec, typename TPosition > inline typename Prefix<TString>::Type prefix(StringSet< TString, TSpec > &me, TPosition pos); // "projects/library/seqan/sequence/sequence_multiple.h"(376)
+template <typename TString, typename TSpec, typename TPosition > inline typename Prefix<TString const>::Type prefix(StringSet< TString, TSpec > const &me, TPosition pos); // "projects/library/seqan/sequence/sequence_multiple.h"(390)
+template <typename TString, typename TDelimiter, typename TPosition > inline typename Infix<TString>::Type prefix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > &me, TPosition pos); // "projects/library/seqan/sequence/sequence_multiple.h"(404)
+template <typename TString, typename TDelimiter, typename TPosition > inline typename Infix<TString const>::Type prefix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > const &me, TPosition pos); // "projects/library/seqan/sequence/sequence_multiple.h"(411)
+
+//____________________________________________________________________________
+// push
+
+template <typename TValue, unsigned int SPACE, typename TVal> inline void push( String<TValue, Block<SPACE> >& me, TVal const& source); // "projects/library/seqan/sequence/string_stack.h"(403)
+template <typename TValue, unsigned int SPACE> inline void push(String<TValue, Block<SPACE> >& me); // "projects/library/seqan/sequence/string_stack.h"(410)
+
+//____________________________________________________________________________
+// push_back
+
+template <typename TValue, unsigned int SPACE, typename TVal> inline void push_back( String<TValue, Block<SPACE> >& me, TVal const& source); // "projects/library/seqan/sequence/string_stack.h"(429)
+
+//____________________________________________________________________________
+// removeValueById
+
+template <typename TString, typename TSpec, typename TId> inline void removeValueById(StringSet<TString, Owner<TSpec> >& me, TId const id); // "projects/library/seqan/sequence/sequence_multiple.h"(1458)
+template <typename TString, typename TId> inline void removeValueById(StringSet<TString, Dependent<Generous> >& me, TId const id); // "projects/library/seqan/sequence/sequence_multiple.h"(1468)
+template <typename TString, typename TId> inline void removeValueById(StringSet<TString, Dependent<Tight> >& me, TId const id); // "projects/library/seqan/sequence/sequence_multiple.h"(1482)
+
+//____________________________________________________________________________
+// replace
+
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void replace( Segment<THost, TSpec> & target, typename Position< Segment<THost, TSpec> >::Type pos_begin, typename Position< Segment<THost, TSpec> >::Type pos_end, TSource & source, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(869)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void replace( Segment<THost, TSpec> & target, typename Position< Segment<THost, TSpec> >::Type pos_begin, typename Position< Segment<THost, TSpec> >::Type pos_end, TSource const & source, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(881)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void replace( Segment<THost, TSpec> & target, typename Position< Segment<THost, TSpec> >::Type pos_begin, typename Position< Segment<THost, TSpec> >::Type pos_end, TSource & source, typename Size< Segment<THost, TSpec> >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(895)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void replace( Segment<THost, TSpec> & target, typename Position< Segment<THost, TSpec> >::Type pos_begin, typename Position< Segment<THost, TSpec> >::Type pos_end, TSource const & source, typename Size< Segment<THost, TSpec> >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(908)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void replace( Segment<THost, TSpec> const & target, typename Position< Segment<THost, TSpec> const>::Type pos_begin, typename Position< Segment<THost, TSpec> const>::Type pos_end, TSource & source, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(921)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void replace( Segment<THost, TSpec> const & target, typename Position< Segment<THost, TSpec> const>::Type pos_begin, typename Position< Segment<THost, TSpec> const>::Type pos_end, TSource const & source, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(933)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void replace( Segment<THost, TSpec> const & target, typename Position< Segment<THost, TSpec> const>::Type pos_begin, typename Position< Segment<THost, TSpec> const>::Type pos_end, TSource & source, typename Size< Segment<THost, TSpec> >::Type limit, Tag<TExpand> const ); // "projects/library/seqan/sequence/segment_base.h"(947)
+template <typename THost, typename TSpec, typename TSource, typename TExpand> inline void replace( Segment<THost, TSpec> const & target, typename Position< Segment<THost, TSpec> const>::Type pos_begin, typename Position< Segment<THost, TSpec> const>::Type pos_end, TSource const & source, typename Size< Segment<THost, TSpec> >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/segment_base.h"(960)
+template <typename TTargetValue, typename TSource, typename TExpand> inline void replace(TTargetValue * target, size_t pos_begin, size_t pos_end, TSource const & source, Tag<TExpand> const); // "projects/library/seqan/sequence/string_pointer.h"(596)
+template <typename TTargetValue, typename TSource, typename TExpand> inline void replace(TTargetValue * target, size_t pos_begin, size_t pos_end, TSource const & source, size_t limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_pointer.h"(609)
+template <typename TTargetValue, typename TSourceValue, typename TExpand> inline void replace(TTargetValue * target, size_t pos_begin, size_t pos_end, TSourceValue const * source, Tag<TExpand> const); // "projects/library/seqan/sequence/string_pointer.h"(623)
+template <typename TTargetValue, typename TSourceValue, typename TExpand> inline void replace(TTargetValue * target, size_t pos_begin, size_t pos_end, TSourceValue const * source, size_t limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_pointer.h"(636)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void replace(::std::basic_string<TChar, TCharTraits, TAlloc> & target, typename Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_begin, typename Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_end, TSource const & source, Generous); // "projects/library/seqan/sequence/std_string.h"(520)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void replace(::std::basic_string<TChar, TCharTraits, TAlloc> & target, typename Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_begin, typename Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_end, TSource const & source, typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit, Generous); // "projects/library/seqan/sequence/std_s [...]
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void replace(::std::basic_string<TChar, TCharTraits, TAlloc> & target, typename Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_begin, typename Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_end, TSource const & source, Limit); // "projects/library/seqan/sequence/std_string.h"(569)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void replace(::std::basic_string<TChar, TCharTraits, TAlloc> & target, typename Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_begin, typename Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_end, TSource const & source, typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit, Limit); // "projects/library/seqan/sequence/std_stri [...]
+template <typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource> inline void replace(TTarget & target, TPositionBegin pos_begin, TPositionEnd pos_end, TSource & source); // "projects/library/seqan/sequence/sequence_interface.h"(1195)
+template <typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource> inline void replace(TTarget const & target, TPositionBegin pos_begin, TPositionEnd pos_end, TSource & source); // "projects/library/seqan/sequence/sequence_interface.h"(1204)
+template <typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource> inline void replace(TTarget & target, TPositionBegin pos_begin, TPositionEnd pos_end, TSource const & source); // "projects/library/seqan/sequence/sequence_interface.h"(1213)
+template <typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource> inline void replace(TTarget const & target, TPositionBegin pos_begin, TPositionEnd pos_end, TSource const & source); // "projects/library/seqan/sequence/sequence_interface.h"(1222)
+template <typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource> inline void replace(TTarget & target, TPositionBegin pos_begin, TPositionEnd pos_end, TSource & source, typename Size<TTarget>::Type limit); // "projects/library/seqan/sequence/sequence_interface.h"(1235)
+template <typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource> inline void replace(TTarget const & target, TPositionBegin pos_begin, TPositionEnd pos_end, TSource & source, typename Size<TTarget>::Type limit); // "projects/library/seqan/sequence/sequence_interface.h"(1245)
+template <typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource> inline void replace(TTarget & target, TPositionBegin pos_begin, TPositionEnd pos_end, TSource const & source, typename Size<TTarget>::Type limit); // "projects/library/seqan/sequence/sequence_interface.h"(1255)
+template <typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource> inline void replace(TTarget const & target, TPositionBegin pos_begin, TPositionEnd pos_end, TSource const & source, typename Size<TTarget>::Type limit); // "projects/library/seqan/sequence/sequence_interface.h"(1265)
+template <typename TTargetValue, typename TTargetSpec, typename TSource, typename TExpand> inline void replace(String<TTargetValue, TTargetSpec> & target, typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin, typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end, TSource const & source, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(1247)
+template <typename TTargetValue, typename TTargetSpec, typename TSource, typename TExpand> inline void replace(String<TTargetValue, TTargetSpec> & target, typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin, typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end, TSource const & source, typename Size< String<TTargetValue, TTargetSpec> >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(1261)
+template <typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TExpand> inline void replace(String<TTargetValue, TTargetSpec> & target, typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin, typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end, TSourceValue const * source, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(1277)
+template <typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TExpand> inline void replace(String<TTargetValue, TTargetSpec> & target, typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin, typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end, TSourceValue const * source, typename Size< String<TTargetValue, TTargetSpec> >::Type limit, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(1291)
+
+//____________________________________________________________________________
+// reserve
+
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TSize, typename TExpand> inline TSize reserve(String< TValue, ValueExpand<THost, TMap, TSpec> > & me, TSize new_length, Tag<TExpand> const tag); // "projects/library/seqan/sequence/string_value_expand.h"(384)
+template <typename TValue, typename TSpec, typename _TSize, typename TExpand> inline typename Size< String<TValue, Packed<TSpec> > >::Type reserve( String<TValue, Packed<TSpec> > & seq, _TSize new_capacity, Tag<TExpand> const tag); // "projects/library/seqan/sequence/string_packed.h"(726)
+template <typename TValue, typename TSpec, typename _TSize> inline typename Size< String<TValue, Alloc<TSpec> > >::Type reserve( String<TValue, Packed<TSpec> > & me, _TSize new_capacity, Limit); // "projects/library/seqan/sequence/string_packed.h"(741)
+template <typename TValue, typename TSpec, typename _TSize> inline typename Size< String<TValue, Alloc<TSpec> > >::Type reserve( String<TValue, Packed<TSpec> > & me, _TSize new_capacity, Insist); // "projects/library/seqan/sequence/string_packed.h"(756)
+template <typename TValue, typename TSpec, typename _TSize, typename TExpand> inline typename Size< String<TValue, Alloc<TSpec> > >::Type reserve( String<TValue, Alloc<TSpec> > & seq, _TSize new_capacity, Tag<TExpand> const tag); // "projects/library/seqan/sequence/string_alloc.h"(410)
+template <typename TValue, typename TSpec, typename _TSize> inline typename Size< String<TValue, Alloc<TSpec> > >::Type reserve( String<TValue, Alloc<TSpec> > & me, _TSize new_capacity, Limit); // "projects/library/seqan/sequence/string_alloc.h"(439)
+template <typename TValue, typename TSpec, typename _TSize> inline typename Size< String<TValue, Alloc<TSpec> > >::Type reserve( String<TValue, Alloc<TSpec> > & , _TSize new_capacity, Insist); // "projects/library/seqan/sequence/string_alloc.h"(454)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TExpand> inline typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type reserve( ::std::basic_string<TChar, TCharTraits, TAlloc> & seq, typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type new_capacity, Tag<TExpand> const &); // "projects/library/seqan/sequence/std_string.h"(630)
+template <typename T, typename TSize> inline typename Size<T>::Type reserve( T & , TSize new_capacity, Insist); // "projects/library/seqan/sequence/sequence_interface.h"(1300)
+template <typename T, typename TSize> inline typename Size<T>::Type reserve( T & me, TSize new_capacity, Limit); // "projects/library/seqan/sequence/sequence_interface.h"(1311)
+template <typename T, typename TSize> inline typename Size<T>::Type reserve( T & me, TSize new_capacity); // "projects/library/seqan/sequence/sequence_interface.h"(1323)
+template <typename TValue, unsigned int SPACE, typename TSize, typename TExpand> inline typename Size< String<TValue, Block<SPACE> > >::Type reserve(String<TValue, Block<SPACE> > & me, TSize new_capacity, Tag<TExpand> const); // "projects/library/seqan/sequence/string_stack.h"(356)
+
+//____________________________________________________________________________
+// resize
+
+template <typename THost, typename TSpec, typename TExpand> inline typename Size< Segment<THost, TSpec> >::Type resize( Segment<THost, TSpec> & me, typename Size< Segment<THost, TSpec> >::Type new_length, Tag<TExpand> const tag); // "projects/library/seqan/sequence/segment_base.h"(1029)
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TSize> inline TSize resize(String< TValue, ValueExpand<THost, TMap, TSpec> > & me, TSize new_length); // "projects/library/seqan/sequence/string_value_expand.h"(372)
+template <typename TValue, typename TExpand> inline size_t resize( TValue * me, size_t new_length, Tag<TExpand> const &); // "projects/library/seqan/sequence/string_pointer.h"(675)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSize, typename TExpand> inline typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type resize( ::std::basic_string<TChar, TCharTraits, TAlloc> & me, TSize new_length, Tag<TExpand> const &); // "projects/library/seqan/sequence/std_string.h"(650)
+template <typename TString, typename TSpec, typename TSize > inline typename Size< StringSet< TString, TSpec > >::Type resize(StringSet< TString, TSpec > &me, TSize new_size); // "projects/library/seqan/sequence/sequence_multiple.h"(1165)
+template <typename TString, typename TSpec, typename TSize > inline typename Size< StringSet< TString, Owner<ConcatDirect<TSpec> > > >::Type resize(StringSet< TString, Owner<ConcatDirect<TSpec> > > &me, TSize new_size); // "projects/library/seqan/sequence/sequence_multiple.h"(1173)
+template <typename T, typename TSize> inline typename Size<T>::Type resize( T & me, TSize new_length); // "projects/library/seqan/sequence/sequence_interface.h"(1358)
+template <typename TValue, unsigned int SPACE, typename TSize2, typename TExpand> inline typename Size< String<TValue, Block<SPACE> > >::Type resize(String<TValue, Block<SPACE> > & me, TSize2 new_length, Tag<TExpand> const); // "projects/library/seqan/sequence/string_stack.h"(308)
+template <typename TValue, unsigned int SPACE, typename TSize2> inline typename Size< String<TValue, Block<SPACE> > >::Type resize(String<TValue, Block<SPACE> > & me, TSize2 new_length, Limit); // "projects/library/seqan/sequence/string_stack.h"(329)
+template <typename TValue, typename TSpec, typename TSize, typename TExpand> inline typename Size< String<TValue, TSpec> >::Type resize( String<TValue, TSpec> & me, TSize new_length, Tag<TExpand> const); // "projects/library/seqan/sequence/string_base.h"(1457)
+
+//____________________________________________________________________________
+// resizeSpace
+
+template <typename T, typename TSize, typename TPosition> inline TSize resizeSpace(T & me, TSize size, TPosition pos_begin, TPosition pos_end); // "projects/library/seqan/sequence/sequence_interface.h"(1393)
+template <typename T, typename TSize, typename TPosition> inline TSize resizeSpace(T & me, TSize size, TPosition pos_begin, TPosition pos_end, TSize limit); // "projects/library/seqan/sequence/sequence_interface.h"(1405)
+template <typename TValue, typename TSpec, typename TPosition, typename TExpand> inline typename Size< String<TValue, TSpec> >::Type resizeSpace(String<TValue, TSpec> & me, typename Size< String<TValue, TSpec> >::Type size, TPosition pos_begin, TPosition pos_end, Tag<TExpand> const tag); // "projects/library/seqan/sequence/string_base.h"(685)
+template <typename TValue, typename TSpec, typename TPosition, typename TExpand> inline typename Size< String<TValue, TSpec> >::Type resizeSpace(String<TValue, TSpec> & me, typename Size< String<TValue, TSpec> >::Type size, TPosition pos_begin, TPosition pos_end, typename Size< String<TValue, TSpec> >::Type limit, Tag<TExpand> const tag); // "projects/library/seqan/sequence/string_base.h"(700)
+
+//____________________________________________________________________________
+// sequenceLength
+
+template <typename TSeqNo, typename TString> inline typename Size<TString>::Type sequenceLength(TSeqNo , TString const &string); // "projects/library/seqan/sequence/sequence_multiple.h"(634)
+template <typename TSeqNo, typename TString, typename TSpec> inline typename Size<StringSet<TString, TSpec> >::Type sequenceLength(TSeqNo seqNo, StringSet<TString, TSpec> const &stringSet); // "projects/library/seqan/sequence/sequence_multiple.h"(640)
+
+//____________________________________________________________________________
+// set
+
+template <typename THost, typename TPosition1, typename TPosition2> inline void set(Segment<THost, InfixSegment> & me, THost & host_, TPosition1 begin_, TPosition2 end_); // "projects/library/seqan/sequence/segment_infix.h"(449)
+template <typename THost> inline void set(Segment<THost, InfixSegment> & me, THost & host_); // "projects/library/seqan/sequence/segment_infix.h"(461)
+template <typename THost> inline void set(Segment<THost, InfixSegment> & me, THost const & host_); // "projects/library/seqan/sequence/segment_infix.h"(471)
+template <typename THost, typename TSpec> inline void set(Segment<THost, InfixSegment> & me, Segment<THost, TSpec> & source); // "projects/library/seqan/sequence/segment_infix.h"(484)
+template <typename THost, typename TSpec> inline void set(Segment<THost, InfixSegment> & me, Segment<THost, TSpec> const & source); // "projects/library/seqan/sequence/segment_infix.h"(494)
+template <typename THost, typename TPosition> inline void set(Segment<THost, PrefixSegment> & me, THost & host_, TPosition end_); // "projects/library/seqan/sequence/segment_prefix.h"(371)
+template <typename THost> inline void set(Segment<THost, PrefixSegment> & me, THost & host_); // "projects/library/seqan/sequence/segment_prefix.h"(382)
+template <typename THost, typename TSpec> inline void set(Segment<THost, PrefixSegment> & me, Segment<THost, TSpec> & source); // "projects/library/seqan/sequence/segment_prefix.h"(394)
+template <typename THost, typename TSpec> inline void set(Segment<THost, PrefixSegment> & me, Segment<THost, TSpec> const & source); // "projects/library/seqan/sequence/segment_prefix.h"(404)
+template <typename THost, typename TPosition> inline void set(Segment<THost, SuffixSegment> & me, THost & host_, TPosition begin_); // "projects/library/seqan/sequence/segment_suffix.h"(360)
+template <typename THost> inline void set(Segment<THost, SuffixSegment> & me, THost & host_); // "projects/library/seqan/sequence/segment_suffix.h"(371)
+template <typename THost, typename TSpec> inline void set(Segment<THost, SuffixSegment> & me, Segment<THost, TSpec> & source); // "projects/library/seqan/sequence/segment_suffix.h"(383)
+template <typename THost, typename TSpec> inline void set(Segment<THost, SuffixSegment> & me, Segment<THost, TSpec> const & source); // "projects/library/seqan/sequence/segment_suffix.h"(393)
+
+//____________________________________________________________________________
+// setBegin
+
+template <typename TIterator> inline void setBegin(TIterator new_begin); // "projects/library/seqan/sequence/segment_infix.h"(773)
+
+//____________________________________________________________________________
+// setEnd
+
+template <typename TIterator> inline void setEnd(TIterator new_end); // "projects/library/seqan/sequence/segment_infix.h"(785)
+
+//____________________________________________________________________________
+// setPosition
+
+template <typename TContainer, typename THostspec, typename TPosition> inline void setPosition(Iter<TContainer, Packed<THostspec> > & me, TPosition pos_); // "projects/library/seqan/sequence/string_packed.h"(917)
+
+//____________________________________________________________________________
+// shareResources
+
+template <typename T1, typename T2> inline bool shareResources(T1 const & obj1, T2 const & obj2); // "projects/library/seqan/sequence/sequence_interface.h"(230)
+template <typename TValue, typename TSpec> inline bool shareResources(String<TValue, TSpec> const & obj1, TValue const & obj2); // "projects/library/seqan/sequence/string_base.h"(132)
+template <typename TValue, typename TSpec> inline bool shareResources(TValue const & obj1, String<TValue, TSpec> const & obj2); // "projects/library/seqan/sequence/string_base.h"(141)
+
+//____________________________________________________________________________
+// shrinkToFit
+
+template <typename T, typename TSize, typename TValue> inline void shrinkToFit(T & me); // "projects/library/seqan/sequence/sequence_interface.h"(1508)
+
+//____________________________________________________________________________
+// stringSetLimits
+
+template <typename TStringSet> inline typename StringSetLimits<TStringSet>::Type stringSetLimits(TStringSet &); // "projects/library/seqan/sequence/sequence_multiple.h"(157)
+template <typename TString, typename TSpec> inline typename StringSetLimits< StringSet<TString, TSpec> >::Type & stringSetLimits(StringSet<TString, TSpec> &stringSet); // "projects/library/seqan/sequence/sequence_multiple.h"(163)
+template <typename TString, typename TSpec> inline typename StringSetLimits< StringSet<TString, TSpec> const>::Type & stringSetLimits(StringSet<TString, TSpec> const &stringSet); // "projects/library/seqan/sequence/sequence_multiple.h"(171)
+
+//____________________________________________________________________________
+// subset
+
+template <typename TString, typename TSpec, typename TDestSpec, typename TIds, typename TLength> inline void subset(StringSet<TString, Owner<TSpec> >& source, StringSet<TString, TDestSpec>& dest, TIds ids, TLength len); // "projects/library/seqan/sequence/sequence_multiple.h"(1631)
+template <typename TString, typename TIds, typename TLength> inline void subset(StringSet<TString, Dependent<Generous> >& source, StringSet<TString, Dependent<Generous> >& dest, TIds ids, TLength len); // "projects/library/seqan/sequence/sequence_multiple.h"(1641)
+template <typename TString, typename TIds, typename TLength> inline void subset(StringSet<TString, Dependent<Tight> >& source, StringSet<TString, Dependent<Tight> >& dest, TIds ids, TLength len); // "projects/library/seqan/sequence/sequence_multiple.h"(1661)
+template <typename TString, typename TSpec, typename TIds> inline void subset(StringSet<TString, TSpec>& source, StringSet<TString, TSpec>& dest, TIds ids); // "projects/library/seqan/sequence/sequence_multiple.h"(1696)
+
+//____________________________________________________________________________
+// suffix
+
+template <typename TString, typename TSpec, typename TPosition > inline typename Suffix<TString>::Type suffix(StringSet< TString, TSpec > &me, TPosition pos); // "projects/library/seqan/sequence/sequence_multiple.h"(422)
+template <typename TString, typename TSpec, typename TPosition > inline typename Suffix<TString const>::Type suffix(StringSet< TString, TSpec > const &me, TPosition pos); // "projects/library/seqan/sequence/sequence_multiple.h"(436)
+template <typename TString, typename TDelimiter, typename TPosition > inline typename Infix<TString>::Type suffix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > &me, TPosition pos); // "projects/library/seqan/sequence/sequence_multiple.h"(450)
+template <typename TString, typename TDelimiter, typename TPosition > inline typename Infix<TString const>::Type suffix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > const &me, TPosition pos); // "projects/library/seqan/sequence/sequence_multiple.h"(457)
+template <typename T, typename TPosBegin> inline typename Suffix<T>::Type suffix(T & t, TPosBegin pos_begin); // "projects/library/seqan/sequence/segment_suffix.h"(498)
+template <typename T, typename TPosBegin> inline typename Suffix<T *>::Type suffix(T * t, TPosBegin pos_begin); // "projects/library/seqan/sequence/segment_suffix.h"(506)
+template <typename T, typename TPosBegin> inline typename Suffix<Segment<T, PrefixSegment> >::Type suffix(Segment<T, PrefixSegment> & t, TPosBegin pos_begin); // "projects/library/seqan/sequence/segment_suffix.h"(516)
+template <typename T, typename TPosBegin> inline typename Suffix<Segment<T, PrefixSegment> const>::Type suffix(Segment<T, PrefixSegment> const & t, TPosBegin pos_begin); // "projects/library/seqan/sequence/segment_suffix.h"(526)
+template <typename T, typename TPosBegin> inline typename Suffix<Segment<T, InfixSegment> >::Type suffix(Segment<T, InfixSegment> & t, TPosBegin pos_begin); // "projects/library/seqan/sequence/segment_suffix.h"(539)
+template <typename T, typename TPosBegin> inline typename Suffix<Segment<T, InfixSegment> const>::Type suffix(Segment<T, InfixSegment> const & t, TPosBegin pos_begin); // "projects/library/seqan/sequence/segment_suffix.h"(549)
+template <typename T, typename TPosBegin> inline typename Suffix<Segment<T, SuffixSegment> >::Type suffix(Segment<T, SuffixSegment> & t, TPosBegin pos_begin); // "projects/library/seqan/sequence/segment_suffix.h"(563)
+template <typename T, typename TPosBegin> inline typename Suffix<Segment<T, SuffixSegment> const>::Type suffix(Segment<T, SuffixSegment> const & t, TPosBegin pos_begin); // "projects/library/seqan/sequence/segment_suffix.h"(572)
+
+//____________________________________________________________________________
+// suffixLength
+
+template <typename TPos, typename TString> inline typename Size<TString>::Type suffixLength(TPos pos, TString const &string); // "projects/library/seqan/sequence/sequence_multiple.h"(606)
+template <typename TPos, typename TString, typename TSpec> inline typename Size<TString>::Type suffixLength(TPos pos, StringSet<TString, TSpec> const &stringSet); // "projects/library/seqan/sequence/sequence_multiple.h"(612)
+
+//____________________________________________________________________________
+// toCString
+
+template <typename T> inline typename Value<T>::Type * toCString(T & me); // "projects/library/seqan/sequence/string_cstyle.h"(796)
+
+//____________________________________________________________________________
+// top
+
+template <typename TValue, unsigned int SPACE> inline TValue & top(String<TValue, Block<SPACE> > & me); // "projects/library/seqan/sequence/string_stack.h"(436)
+template <typename TValue, unsigned int SPACE> inline TValue const & top(String<TValue, Block<SPACE> > const& me); // "projects/library/seqan/sequence/string_stack.h"(444)
+
+//____________________________________________________________________________
+// topPrev
+
+template <typename TValue, unsigned int SPACE> inline TValue & topPrev(String<TValue, Block<SPACE> > & me); // "projects/library/seqan/sequence/string_stack.h"(452)
+template <typename TValue, unsigned int SPACE> inline TValue const & topPrev(String<TValue, Block<SPACE> > const& me); // "projects/library/seqan/sequence/string_stack.h"(463)
+
+//____________________________________________________________________________
+// value
+
+template <typename THost, typename TSpec, typename TPos> inline typename Reference< Segment<THost, TSpec> >::Type value(Segment<THost, TSpec> & me, TPos pos); // "projects/library/seqan/sequence/segment_infix.h"(635)
+template <typename THost, typename TSpec, typename TPos> inline typename Reference< Segment<THost, TSpec> const >::Type value(Segment<THost, TSpec> const & me, TPos pos); // "projects/library/seqan/sequence/segment_infix.h"(644)
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TPos> inline typename Reference<String< TValue, ValueExpand<THost, TMap, TSpec> > >::Type value(String< TValue, ValueExpand<THost, TMap, TSpec> > & me, TPos pos); // "projects/library/seqan/sequence/string_value_expand.h"(331)
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TPos> inline typename Reference<String< TValue, ValueExpand<THost, TMap, TSpec> > const>::Type value(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me, TPos pos); // "projects/library/seqan/sequence/string_value_expand.h"(340)
+template <typename TContainer, typename TIterator> inline typename Reference<Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > >::Type value(Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > & me); // "projects/library/seqan/sequence/string_value_expand.h"(433)
+template <typename TContainer, typename TIterator> inline typename Reference<Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > >::Type value(Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > const & me); // "projects/library/seqan/sequence/string_value_expand.h"(441)
+template <typename TValue, typename TPos> inline TValue & value(TValue * me, TPos pos); // "projects/library/seqan/sequence/string_pointer.h"(243)
+template <typename TValue, typename TPos> inline TValue const & value(TValue const * me, TPos pos); // "projects/library/seqan/sequence/string_pointer.h"(252)
+template <typename TValue, typename THostspec, typename TPos> inline typename Reference<String<TValue, Packed<THostspec> > >::Type value(String<TValue, Packed<THostspec> > & me, TPos pos); // "projects/library/seqan/sequence/string_packed.h"(482)
+template <typename TValue, typename THostspec, typename TPos> inline typename Reference<String<TValue, Packed<THostspec> > const>::Type value(String<TValue, Packed<THostspec> > const & me, TPos pos); // "projects/library/seqan/sequence/string_packed.h"(491)
+template <typename TContainer, typename THostspec> inline typename Reference<Iter<TContainer, Packed<THostspec> > >::Type value(Iter<TContainer, Packed<THostspec> > & me); // "projects/library/seqan/sequence/string_packed.h"(930)
+template <typename TContainer, typename THostspec> inline typename Reference<Iter<TContainer, Packed<THostspec> > const>::Type value(Iter<TContainer, Packed<THostspec> > const & me); // "projects/library/seqan/sequence/string_packed.h"(937)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TPos> inline typename GetValue< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type value(::std::basic_string<TChar, TCharTraits, TAlloc> & me, TPos pos); // "projects/library/seqan/sequence/std_string.h"(201)
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TPos> inline typename GetValue< ::std::basic_string<TChar, TCharTraits, TAlloc> const>::Type value(::std::basic_string<TChar, TCharTraits, TAlloc> const & me, TPos pos); // "projects/library/seqan/sequence/std_string.h"(209)
+template <typename TString, typename TPos > inline typename Reference< StringSet< TString, Owner<Default> > >::Type value(StringSet< TString, Owner<Default> > & me, TPos pos); // "projects/library/seqan/sequence/sequence_multiple.h"(1185)
+template <typename TString, typename TPos > inline typename Reference< StringSet< TString, Owner<Default> > const >::Type value(StringSet< TString, Owner<Default> > const & me, TPos pos); // "projects/library/seqan/sequence/sequence_multiple.h"(1192)
+template <typename TString, typename TSpec, typename TPos > inline typename Infix<TString>::Type value(StringSet< TString, Owner<ConcatDirect<TSpec> > > & me, TPos pos); // "projects/library/seqan/sequence/sequence_multiple.h"(1200)
+template <typename TString, typename TSpec, typename TPos > inline typename Infix<TString const>::Type value(StringSet< TString, Owner<ConcatDirect<TSpec> > > const & me, TPos pos); // "projects/library/seqan/sequence/sequence_multiple.h"(1207)
+template <typename TString, typename TPos > inline typename Reference<StringSet< TString, Dependent<Tight> > >::Type value(StringSet< TString, Dependent<Tight> >& me, TPos pos); // "projects/library/seqan/sequence/sequence_multiple.h"(1215)
+template <typename TString, typename TPos > inline typename Reference<StringSet< TString, Dependent<Tight> > const >::Type value(StringSet< TString, Dependent<Tight> >const & me, TPos pos); // "projects/library/seqan/sequence/sequence_multiple.h"(1226)
+template <typename TString, typename TPos > inline typename Reference<StringSet< TString, Dependent<Generous> > >::Type value(StringSet< TString, Dependent<Generous> >& me, TPos pos); // "projects/library/seqan/sequence/sequence_multiple.h"(1237)
+template <typename TString, typename TPos > inline typename Reference< StringSet< TString, Dependent<Generous> > const >::Type value(StringSet< TString, Dependent<Generous> > const & me, TPos pos); // "projects/library/seqan/sequence/sequence_multiple.h"(1249)
+template <typename TStringSet, typename TPos > inline typename Reference< ConcatenatorNto1<TStringSet> >::Type value(ConcatenatorNto1<TStringSet> &me, TPos globalPos); // "projects/library/seqan/sequence/sequence_multiple.h"(1769)
+template <typename TStringSet, typename TPos > inline typename Reference< ConcatenatorNto1<TStringSet> const >::Type value(ConcatenatorNto1<TStringSet> const &me, TPos globalPos); // "projects/library/seqan/sequence/sequence_multiple.h"(1778)
+template <typename TStringSet, typename TSpec> inline typename Reference< Iter< TStringSet, ConcatVirtual<TSpec> > const>::Type value(Iter<TStringSet, ConcatVirtual<TSpec> > const & me); // "projects/library/seqan/sequence/sequence_multiple.h"(2039)
+template <typename TStringSet, typename TSpec> inline typename Reference< Iter< TStringSet, ConcatVirtual<TSpec> > >::Type value(Iter<TStringSet, ConcatVirtual<TSpec> > & me); // "projects/library/seqan/sequence/sequence_multiple.h"(2045)
+template <typename T, typename TPos> inline typename Reference<T>::Type value(T & me, TPos ); // "projects/library/seqan/sequence/sequence_interface.h"(568)
+template <typename T, typename TPos> inline typename Reference<T const>::Type value(T const & me, TPos ); // "projects/library/seqan/sequence/sequence_interface.h"(576)
+template <typename TValue, unsigned int SPACE, typename TPos> inline typename Reference<String<TValue, Block<SPACE> > >::Type value( String<TValue, Block<SPACE> >& stack, TPos const pos); // "projects/library/seqan/sequence/string_stack.h"(240)
+template <typename TValue, unsigned int SPACE, typename TPos> inline typename Reference<String<TValue, Block<SPACE> > >::Type value( String<TValue, Block<SPACE> > const& stack, TPos const pos); // "projects/library/seqan/sequence/string_stack.h"(250)
+template <typename TValue, typename TSpec, typename TPos> inline typename Reference< String<TValue, TSpec> >::Type value(String<TValue, TSpec> & me, TPos pos); // "projects/library/seqan/sequence/string_base.h"(158)
+template <typename TValue, typename TSpec, typename TPos> inline typename Reference< String<TValue, TSpec> const >::Type value(String<TValue, TSpec> const & me, TPos pos); // "projects/library/seqan/sequence/string_base.h"(167)
+
+//____________________________________________________________________________
+// valueById
+
+template <typename TString, typename TSpec, typename TId> inline typename Reference<StringSet<TString, TSpec> >::Type valueById(StringSet<TString, TSpec>& me, TId const id); // "projects/library/seqan/sequence/sequence_multiple.h"(1333)
+
+//____________________________________________________________________________
+// valueConstruct
+
+template <typename TContainer, typename THostspec> inline void valueConstruct(Iter<TContainer, Packed<THostspec> > const & ); // "projects/library/seqan/sequence/string_packed.h"(1031)
+template <typename TContainer, typename THostspec, typename TParam> inline void valueConstruct(Iter<TContainer, Packed<THostspec> > const & it, TParam const & param_); // "projects/library/seqan/sequence/string_packed.h"(1037)
+template <typename TContainer, typename THostspec, typename TParam> inline void valueConstruct(Iter<TContainer, Packed<THostspec> > const & it, TParam const & param_, Move tag); // "projects/library/seqan/sequence/string_packed.h"(1045)
+
+//____________________________________________________________________________
+// valueDestruct
+
+template <typename TContainer, typename THostspec> inline void valueDestruct(Iter<TContainer, Packed<THostspec> > const & ); // "projects/library/seqan/sequence/string_packed.h"(1056)
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif
+
diff --git a/src/libSSA/seqan/sequence/sequence_interface.h b/src/libSSA/seqan/sequence/sequence_interface.h
new file mode 100644
index 0000000..7806fd1
--- /dev/null
+++ b/src/libSSA/seqan/sequence/sequence_interface.h
@@ -0,0 +1,1516 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: sequence_interface.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SEQUENCE_INTERFACE_H
+#define SEQAN_HEADER_SEQUENCE_INTERFACE_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// Expand
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Tag.Overflow Strategy:
+..summary:The strategy for resizing containers.
+..tag.Insist:No capacity check.
+...remarks:The user has to ensure that the container's capacity is large enough.
+..tag.Limit:Limit the contents to current capacity.
+...remarks: All entries that exceed the capacity are lost.
+..tag.Exact:Expand as far as needed.
+...remarks: The capacity is only changed if the current capacity is not large enough.
+ If the capacity can only be expanded up to a certain ammount, it will be increased as far as possible
+ and the contents are limited to the new capacity.
+...remarks:Note that the capacity will never be shrinked.
+ Use @Function.shrinkToFit@ to resize the capacity down to the current length.
+..tag.Generous:Expand if needed, get precautionary extra space.
+...remarks:Whenever the capacity has to be increased, the new capacity is choosen somewhat large than actually needed.
+ This strategy limits the number of capacity changes, so that resizing takes armotized constant time.
+ Use this strategy if the total amount of storage is unkown at first.
+...remarks:The new capacity is computed by @Function.computeGenerousCapacity at .
+By default, it is guaranteed not to exceed about
+ tree halfs of the space that is used to store the data.
+ The user can overload @Function.computeGenerousCapacity@ in order to change this behavior.
+..remarks:Changing the capacity of a container can invalidate the iterators of this container.
+..remarks:If no overflow tag is specified, most operations use the default overflow strategy given by @Metafunction.DefaultOverflowImplicit@
+or @Metafunction.DefaultOverflowExplicit@, depending on the kind of operation.
+*/
+struct TagInsist_;
+typedef Tag<TagInsist_> const Insist;
+typedef Tag<TagInsist_> const Tight;
+//Insist INSIST;
+
+struct TagLimit_;
+typedef Tag<TagLimit_> const Limit;
+//Limit LIMIT;
+
+struct TagGenerous_;
+typedef Tag<TagGenerous_> const Generous;
+//Generous GENEROUS;
+
+struct TagExact_;
+typedef Tag<TagExact_> const Exact;
+//Exact EXACT;
+
+//____________________________________________________________________________
+
+/**
+.Metafunction.DefaultOverflowImplicit:
+..hidefromindex
+..summary:The default overflow strategy for implicit resize.
+..signature:DefaultOverflowImplicit<T>::Type
+..param.T:Type for which the overflow strategy is determined.
+...type:Class.String
+..returns.param.Type:Expansion tag for type of $T$.
+..remarks:This function is used for functions that cause an implicit change of a container's size, like
+e.g. @Function.assign@, @Function.append@, and @Function.replace at .
+..see:Tag.Overflow Strategy
+*/
+template <typename T>
+struct DefaultOverflowImplicit
+{
+ typedef Insist Type;
+};
+
+//____________________________________________________________________________
+
+/**
+.Metafunction.DefaultOverflowExplicit:
+..hidefromindex
+..summary:The default overflow strategy for explicit resize.
+..signature:DefaultOverflowExplicit<T>::Type
+..param.T:Type for which the overflow strategy is determined.
+...type:Class.String
+..returns.param.Type:Expansion tag for type of $T$.
+..remarks:This function is used for functions that change a container's size explicit, like e.g. @Function.resize at .
+..see:Tag.Overflow Strategy
+..see:Metafunction.DefaultOverflowImplicit
+*/
+template <typename T>
+struct DefaultOverflowExplicit
+{
+ typedef Exact Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// IsContiguous
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Metafunction.IsContiguous:
+..summary:Determines whether a container stores its elements in a contiguous array.
+..signature:IsContiguous<T>::VALUE
+..param.T:Type that is tested for being a string.
+..returns.param.VALUE:$true$ if $T$ is a string, $false$ otherwise.
+..remarks:Definition: A sequence container is "contiguous", if its elements
+ are stored in a single contiguous array.
+ Examples for contiguous sequences are @Spec.Alloc String@ or @Adaption.char array at .
+..remarks:If an object $obj$ is a contiguous sequence, then $begin(obj)$ can be
+ converted to a pointer to the first element of the content array.
+*/
+template <typename T>
+struct IsContiguous
+{
+ typedef False Type;
+ enum { VALUE = false };
+};
+template <typename T>
+struct IsContiguous<T const>:
+ public IsContiguous<T> {};
+
+//////////////////////////////////////////////////////////////////////////////
+// IsSequence
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Metafunction.IsSequence:
+..summary:Determines whether a container stores its elements in sequential order.
+..signature:IsSequence<T>::VALUE
+..param.T:Type that is tested for being a sequence.
+..returns.param.VALUE:$true$ if $T$ is a sequence, $false$ otherwise.
+..remarks:For example @Class.String@ and @Class.Segment@ return $true$.
+*/
+template <typename T>
+struct IsSequence
+{
+ typedef False Type;
+ enum { VALUE = false };
+};
+template <typename T>
+struct IsSequence<T const>:
+ public IsSequence<T> {};
+
+//////////////////////////////////////////////////////////////////////////////
+// AllowsFastRandomAccess
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Metafunction.AllowsFastRandomAccess:
+..summary:Determines whether a sequence efficiently supports random access.
+..signature:AllowsFastRandomAccess<T>::VALUE
+..param.T:Type that is tested for fast random access.
+..returns.param.VALUE:$true$ if $T$ supports fast random access, $false$ otherwise.
+..remarks:For example @Spec.Alloc String@, @Class.Segment@, and @Spec.Block String@ return $true$.
+*/
+template <typename T>
+struct AllowsFastRandomAccess
+{
+ typedef True Type;
+ enum { VALUE = true };
+};
+template <typename T>
+struct AllowsFastRandomAccess<T const>:
+ public AllowsFastRandomAccess<T> {};
+
+//////////////////////////////////////////////////////////////////////////////
+// identification
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.id:
+..cat:Miscellaneous
+..summary:A value that identifies the underlying sequence.
+..signature:void const * id(object)
+..param.object:The object for which the id will be determined.
+..returns:The id of $sequence$.
+..remarks.text:Two sequences should have the same id, if they share the same resource, e.g. the same memory buffer.
+..remarks.text:The exact semantic of the returned id can vary for different classes.
+Typically, the id of a string is a $void const *$ to the end of the string.
+..remarks.note:The id of a single character need not to be the id of its container.
+..example.code:String<char> str = "hallo seqan";
+bool b1 = (id(str) == id(infix(str, 3, 7)); //true
+bool b2 = (id(str) == id(String<char>(str))); //false
+bool b3 = (id(str) == id(toCString(str)));
+..example.text:In this example, $b1$ is $true$, since the segment object returned by $infix()$
+is just a filter and uses the buffer of it's host object $str$.
+..example.text:$String<char>(str)$ constructs a temporary copy of $str$, so these two
+strings have different id values.
+..example.text:The result of the last comparison depends on the implementation of $toCString$
+and cannot be predicted at compile time.
+*/
+template <typename T>
+inline void const *
+id(T const & me)
+{
+SEQAN_CHECKPOINT
+ return end(me, Standard());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.shareResources:
+..cat:Miscellaneous
+..summary:Determines whether two sequences share the same resource.
+..signature:bool shareResources(sequence1, sequence2)
+..param.sequence1, sequence2:Two sequences.
+..returns:$false$ if it can be guaranteed that $sequence1$ and $sequence2$ can be modified without changing each other, $true$ otherwise.
+..remarks:Non-sequences are interpreted as sequences of size 1.
+..remarks:Note that this function may not work properly for argument types that are not listed here.
+*/
+
+template <typename T1, typename T2>
+inline bool
+shareResources(T1 const & obj1,
+ T2 const & obj2)
+{
+SEQAN_CHECKPOINT
+ return id(obj1) == id(obj2);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// begin
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.begin:
+..cat:Iteration
+..cat:Containers
+..summary:The begin of a container.
+..signature:Iterator begin(object [, tag])
+..param.object:A container.
+...type:Class.String
+...concept:Concept.Container
+..param.tag:An @Tag.Iterator Spec.iterator spec@ tag that specifies the kind of the iterator returned. (optional)
+...default:Given by @Metafunction.DefaultGetIteratorSpec at .
+..returns:An iterator to the first item in $object$.
+...metafunction:Metafunction.Iterator
+..remarks.text:If the container does not contain any items at all, the function may return 0.
+..see:Function.end
+..see:Metafunction.Iterator
+*/
+template <typename T>
+inline typename Iterator<T, typename DefaultGetIteratorSpec<T>::Type>::Type
+begin(T & me)
+{
+SEQAN_CHECKPOINT
+ return begin(me, typename DefaultGetIteratorSpec<T>::Type()) ;
+}
+template <typename T>
+inline typename Iterator<T const, typename DefaultGetIteratorSpec<T>::Type>::Type
+begin(T const & me)
+{
+SEQAN_CHECKPOINT
+ return begin(me, typename DefaultGetIteratorSpec<T>::Type()) ;
+}
+
+//____________________________________________________________________________
+
+//* ???Anti Default Sequences
+template <typename T>
+inline typename Iterator<T, Standard>::Type
+_begin_default(T & me,
+ Standard)
+{
+SEQAN_CHECKPOINT
+ return & me;
+}
+template <typename T>
+inline typename Iterator<T const, Standard>::Type
+_begin_default(T const & me,
+ Standard)
+{
+SEQAN_CHECKPOINT
+ return & me;
+}
+//*/
+
+//____________________________________________________________________________
+
+template <typename T>
+inline typename Iterator<T, Rooted>::Type
+_begin_default(T & me,
+ Rooted)
+{
+SEQAN_CHECKPOINT
+ typedef typename Iterator<T, Rooted>::Type TIterator;
+ return TIterator(me, begin(me, Standard()));
+}
+template <typename T>
+inline typename Iterator<T const, Rooted>::Type
+_begin_default(T const & me,
+ Rooted)
+{
+SEQAN_CHECKPOINT
+ typedef typename Iterator<T const, Rooted>::Type TIterator;
+ return TIterator(me, begin(me, Standard()));
+}
+//____________________________________________________________________________
+
+//folgende forward Deklaration wurde wegen Phaenomene bei VC++ 2003 hinzugenommen
+//implemented in string_pointer.h
+template <typename TValue>
+inline typename Iterator<TValue const *, Standard>::Type
+begin(TValue const * me,
+ Standard);
+
+//____________________________________________________________________________
+
+template <typename T, typename TSpec>
+inline typename Iterator<T, Tag<TSpec> const>::Type
+begin(T & me,
+ Tag<TSpec> const tag_)
+{
+SEQAN_CHECKPOINT
+ return _begin_default(me, tag_);
+}
+template <typename T, typename TSpec>
+inline typename Iterator<T const, Tag<TSpec> const>::Type
+begin(T const & me,
+ Tag<TSpec> const tag_)
+{
+SEQAN_CHECKPOINT
+ return _begin_default(me, tag_);
+}
+
+
+/*
+template <typename TValue>
+inline typename Iterator<TValue *, Standard>::Type
+begin(TValue * me,
+ Standard)
+{
+SEQAN_CHECKPOINT
+ return me;
+}
+
+//folgende Version wurde wegen eines seltsamen Phaenomens bei VC++ hinzugenommen
+template <typename TValue>
+inline typename Iterator<TValue const *, Standard>::Type
+begin(TValue const * me,
+ Standard)
+{
+SEQAN_CHECKPOINT
+ return me;
+}
+
+template <typename TValue, typename TSpec>
+inline typename Iterator<TValue *, Standard>::Type
+begin(TValue * me,
+ Tag<TSpec> const tag_)
+// Standard)
+{
+SEQAN_CHECKPOINT
+ return me;
+}
+
+//folgende Version wurde wegen eines seltsamen Phaenomens bei VC++ hinzugenommen
+template <typename TValue, typename TSpec>
+inline typename Iterator<TValue const *, Standard>::Type
+begin(TValue const * me,
+ Tag<TSpec> const tag_)
+// Standard)
+{
+SEQAN_CHECKPOINT
+ return me;
+}
+
+*/
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// beginPosition
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.beginPosition:
+..cat:Containers
+..summary:Begin position of object in host.
+..signature:Position beginPosition(object)
+..param.object:An object.
+...type:Class.String
+...concept:Concept.Container
+..returns:The position of the first item in $host(object)$ that belongs of $object$.
+...metafunction:Metafunction.Position
+..remarks
+...text:For most classes $beginPosition$ always returns 0. Exceptions are e.g. @Spec.InfixSegment@ and @Spec.SuffixSegment at .
+..see:Function.begin
+*/
+template <typename T>
+inline typename Position<T>::Type
+beginPosition(T &)
+{
+SEQAN_CHECKPOINT
+ return 0;
+}
+template <typename T>
+inline typename Position<T>::Type
+beginPosition(T const &)
+{
+SEQAN_CHECKPOINT
+ return 0;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// end
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.end:
+..cat:Iteration
+..cat:Containers
+..summary:The end of a container.
+..signature:Iterator end(object [, tag])
+..param.object:A container.
+...type:Class.String
+...concept:Concept.Container
+..param.tag:An @Tag.Iterator Spec.iterator spec@ tag that specifies the kind of the iterator returned. (optional)
+...default:Given by @Metafunction.DefaultGetIteratorSpec at .
+..returns:An iterator that points behind the last item in $object$.
+...metafunction:Metafunction.Iterator
+..remarks.text:If the container does not contain any items at all, the function may return 0.
+..see:Function.begin
+..see:Metafunction.Iterator
+*/
+template <typename T>
+inline typename Iterator<T, typename DefaultGetIteratorSpec<T>::Type>::Type
+end(T & me)
+{
+SEQAN_CHECKPOINT
+ return end(me, typename DefaultGetIteratorSpec<T>::Type()) ;
+}
+template <typename T>
+inline typename Iterator<T const, typename DefaultGetIteratorSpec<T>::Type>::Type
+end(T const & me)
+{
+SEQAN_CHECKPOINT
+ return end(me, typename DefaultGetIteratorSpec<T>::Type()) ;
+}
+
+//____________________________________________________________________________
+
+//* ???Anti Default Sequences
+template <typename T>
+inline typename Iterator<T, Standard>::Type
+_end_default(T & me,
+ Standard)
+{
+SEQAN_CHECKPOINT
+ return (& me) + 1;
+}
+template <typename T>
+inline typename Iterator<T const, Standard>::Type
+_end_default(T const & me,
+ Standard)
+{
+SEQAN_CHECKPOINT
+ return (& me) + 1;
+}
+//*/
+
+//____________________________________________________________________________
+
+template <typename T>
+inline typename Iterator<T, Rooted>::Type
+_end_default(T & me,
+ Rooted)
+{
+SEQAN_CHECKPOINT
+ typedef typename Iterator<T, Rooted>::Type TIterator;
+ return TIterator(me, end(me, Standard()));
+}
+template <typename T>
+inline typename Iterator<T const, Rooted>::Type
+_end_default(T const & me,
+ Rooted)
+{
+SEQAN_CHECKPOINT
+ typedef typename Iterator<T const, Rooted>::Type TIterator;
+ return TIterator(me, end(me, Standard()));
+}
+
+//____________________________________________________________________________
+
+template <typename T, typename TSpec>
+inline typename Iterator<T, Tag<TSpec> const>::Type
+end(T & me,
+ Tag<TSpec> const tag_)
+{
+SEQAN_CHECKPOINT
+ return _end_default(me, tag_);
+}
+template <typename T, typename TSpec>
+inline typename Iterator<T const, Tag<TSpec> const>::Type
+end(T const & me,
+ Tag<TSpec> const tag_)
+{
+SEQAN_CHECKPOINT
+ return _end_default(me, tag_);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// endPosition
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.endPosition:
+..cat:Containers
+..summary:End position of object in host.
+..signature:Position endPosition(object)
+..param.object:An object.
+...concept:Concept.Container
+...type:Class.String
+..returns:The position behind the last item in $host(object)$ that belongs of $object$.
+...metafunction:Metafunction.Position
+..see:Function.end
+..see:Function.beginPosition
+*/
+template <typename T>
+inline typename Position<T>::Type
+endPosition(T & me)
+{
+SEQAN_CHECKPOINT
+ return length(me);
+}
+template <typename T>
+inline typename Position<T>::Type
+endPosition(T const & me)
+{
+SEQAN_CHECKPOINT
+ return length(me);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// value
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.value:
+..cat:Iteration
+..cat:Containers
+..summary:Reference to the value.
+..signature:Reference value(container, position)
+..param.container:A container of values.
+..param.position:A position in $container$ on which the value should be accessed.
+..returns:A reference or proxy to the value.
+...metafunction:Metafunction.Reference
+*/
+
+//* ???Anti Default Sequences
+template <typename T, typename TPos>
+inline typename Reference<T>::Type
+value(T & me,
+ TPos /*pos*/)
+{
+SEQAN_CHECKPOINT
+ return me;
+}
+template <typename T, typename TPos>
+inline typename Reference<T const>::Type
+value(T const & me,
+ TPos /*pos*/)
+{
+SEQAN_CHECKPOINT
+ return me;
+}
+//*/
+
+//////////////////////////////////////////////////////////////////////////////
+// getValue
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.getValue:
+..summary:Access to the value.
+..cat:Containers
+..cat:Content Manipulation
+..signature:GetValue getValue(container, pos)
+..param.container:A container.
+...concept:Concept.Container
+..param.pos:The position of an item in $object$.
+...remarks:$pos$ should be convertible to $Position<T>::Type$ for $container$-type $T$.
+..returns:The item at position $pos$ in $container$.
+This can either be a reference to the item or a temporary copy of the item.
+...metafunction:Metafunction.GetValue
+..remarks:
+...text:If $pos$ is out of range, then the behavior of the function is undefined.
+..see:Metafunction.GetValue
+..see:Metafunction.Position
+..see:Function.value
+*/
+
+template <typename T, typename TPos>
+inline typename GetValue<T>::Type
+getValue(T & me,
+ TPos pos)
+{
+SEQAN_CHECKPOINT
+ return (typename GetValue<T>::Type) value(me, pos);
+}
+template <typename T, typename TPos>
+inline typename GetValue<T const>::Type
+getValue(T const & me,
+ TPos pos)
+{
+SEQAN_CHECKPOINT
+ return value(me, pos);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// front
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.Container#front:
+..cat:Containers
+..summary:The first item in container.
+..signature:Iterator front(container)
+..param.container:A container.
+...concept:Concept.Container
+..returns:A @Metafunction.Reference.reference@ of the first item in $container$.
+...metafunction:Metafunction.Reference
+..remarks:This function is equivalent to $value(me, beginPosition(me))$.
+..see:Function.value
+..see:Function.begin
+*/
+
+
+template <typename T>
+inline typename Reference<T>::Type
+front(T & me)
+{
+SEQAN_CHECKPOINT
+ return value(me, beginPosition(me));
+}
+template <typename T>
+inline typename Reference<T const>::Type
+front(T const & me)
+{
+SEQAN_CHECKPOINT
+ return value(me, beginPosition(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// back
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.back:
+..cat:Containers
+..summary:The last item in container.
+..signature:Iterator back(container)
+..param.container:A container.
+...concept:Concept.Container
+..returns:A @Metafunction.Reference.reference@ of the last item in $container$.
+...metafunction:Metafunction.Reference
+..remarks:This function is equivalent to $value(me, endPosition(me) - 1)$.
+..see:Function.value
+..see:Function.end
+..see:Function.Container#front
+*/
+
+template <typename T>
+inline typename Reference<T const>::Type
+back(T const & me)
+{
+SEQAN_CHECKPOINT
+ return value(me, endPosition(me) - 1);
+}
+
+template <typename T>
+inline typename Reference<T>::Type
+back(T & me)
+{
+SEQAN_CHECKPOINT
+ return value(me, endPosition(me) - 1);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// iter
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.iter:
+..cat:Containers
+..summary:Iterator to item at given position.
+..signature:Iterator iter(object, pos [, tag])
+..param.object:A container.
+...type:Class.String
+..param.pos:The position of an item in $object$.
+...metafunction:Metafunction.Position
+..param.tag:An @Tag.Iterator Spec.iterator spec@ tag that specifies the kind of the iterator returned. (optional)
+...default:Given by @Metafunction.DefaultGetIteratorSpec at .
+..returns:An iterator to the item at position $pos$ in $object$.
+...metafunction:Metafunction.Iterator
+..remarks:
+...text:If $pos$ is out of range, then the behavior of the function is undefined.
+..see:Function.value
+..see:Metafunction.Iterator
+..see:Metafunction.Position
+*/
+
+template <typename T, typename TPos>
+inline typename Iterator<T, typename DefaultGetIteratorSpec<T>::Type>::Type
+iter(T & me,
+ TPos pos)
+{
+SEQAN_CHECKPOINT
+ return iter(me, pos, typename DefaultGetIteratorSpec<T>::Type());
+}
+template <typename T, typename TPos>
+inline typename Iterator<T const, typename DefaultGetIteratorSpec<T>::Type>::Type
+iter(T const & me,
+ TPos pos)
+{
+SEQAN_CHECKPOINT
+ return iter(me, pos, typename DefaultGetIteratorSpec<T const>::Type());
+}
+
+
+template <typename T, typename TPos, typename TTag>
+inline typename Iterator<T, Tag<TTag> const>::Type
+iter(T & me,
+ TPos pos,
+ Tag<TTag> const tag_)
+{
+SEQAN_CHECKPOINT
+ return begin(me, tag_) + pos;
+}
+template <typename T, typename TPos, typename TTag>
+inline typename Iterator<T const, Tag<TTag> const>::Type
+iter(T const & me,
+ TPos pos,
+ Tag<TTag> const tag_)
+{
+SEQAN_CHECKPOINT
+ return begin(me, tag_) + pos;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// assignValue (3)
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.assignValue:
+..cat:Content Manipulation
+..signature:assignValue(container, pos, value)
+..param.container:A container.
+...concept:Concept.Container
+..param.pos:Position of the item in $container$ to that $value$ is assigned.
+..remarks:If $object$ is a container (that is $pos$ is not specified),
+ the whole content of $object$ is replaced by $value$.
+..remarks.text:
+ If $value$ is not used again after calling this function,
+ then consider to use @Function.moveValue@ that could be faster in some cases instead.
+*/
+
+template <typename T, typename TValue, typename TPos>
+inline void
+assignValue(T & me,
+ TPos pos,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ assign(value(me, pos), _value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// moveValue (3)
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.moveValue:
+..cat:Content Manipulation
+..signature:moveValue(container, pos, value)
+..param.object:
+...concept:Concept.Container
+..param.container:A container.
+...concept:Concept.Container
+..param.pos:Position of the item in $container$ to that $value$ is moved to.
+..remarks:If $object$ is a container (that is $pos$ is not specified),
+the whole content of $object$ is replaced by $value$.
+..remarks.text:
+ This function possibly clears $value$.
+ If $value$ should be used further, consider to use @Function.assignValue@ instead.
+*/
+
+template <typename T, typename TValue, typename TPos>
+inline void
+moveValue(T & me,
+ TPos pos,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ move(value(me, pos), _value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// length
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.length:
+..cat:Containers
+..summary:The number of items/characters.
+..signature:Size length(object)
+..param.object:A container.
+...concept:Concept.Container
+..returns:The number of items/characters in $object$.
+...metafunction:Metafunction.Size
+..remarks.text:The length of a sequence can never exceed it's capacity.
+..see:Function.capacity
+*/
+
+//* ???Anti Default Sequences
+template <typename T>
+inline typename Size<T const>::Type
+length(T const & /*me*/)
+{
+SEQAN_CHECKPOINT
+ return 1;
+}
+//*/
+
+//////////////////////////////////////////////////////////////////////////////
+// capacity
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.capacity:
+..cat:Containers
+..summary:The maximal length.
+..signature:Size capacity(object)
+..param.object:A container.
+...remarks: If $object$ cannot be converted to one of these types, the function returns 1.
+..returns:The maximal number of items/characters that can be stored in $object$.
+...metafunction:Metafunction.Size
+..remarks.text:The size of a sequence can never exceed it's capacity, but some containers support
+resizing of the capacity.
+Some functions do that implicitely if they are called with a suitable @Tag.Overflow Strategy.overflow strategy at .
+The function @Function.reserve@ can be used to change the capacity explicitely.
+*/
+template <typename T>
+inline typename Size<T const>::Type
+capacity(T const & me)
+{
+SEQAN_CHECKPOINT
+ return length(me);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// empty
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.empty:
+..cat:Containers
+..summary:Test a container for being empty.
+..signature:bool empty(object)
+..param.object:A container.
+..returns:$true$ if $object$ contains no elements, otherwise $false$.
+..remarks.text:$empty(x)$ is guaranteed to be at least as fast as $length(me) == 0$,
+but can be significantly faster in some cases.
+..see:Function.length
+*/
+template <typename T>
+inline bool
+empty(T const & me)
+{
+SEQAN_CHECKPOINT
+ return (length(me) == 0);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// _computeSize4Capacity
+//////////////////////////////////////////////////////////////////////////////
+
+// note: for value types of size 1 or 2,
+// an extra position for the termination character is allocated.
+// This speeds up a conversion to a c style string (see Spec.CStyle String)
+// note that this extra position is necessary not only for char and wchar_t,
+// but also for all other value types of size 1 and 2 to make the application
+// of the funciton move for in-place alphabet conversion.
+
+
+template <typename T, typename TSize>
+inline TSize
+_computeSize4Capacity(T const & /*me*/,
+ TSize capacity)
+{
+SEQAN_CHECKPOINT
+ if (sizeof(T) <= 2) return capacity + 1;
+ else return capacity;
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// computeGenerousCapacity
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.computeGenerousCapacity:
+..hidefromindex
+..cat:Containers
+..summary:Capacity for generous expansion.
+..signature:Size computeGenerousCapacity(container, capacity)
+..param.container:A container that should be expanded.
+..param.capacity:Minimal capacity needed.
+..returns:A value larger than $capacity$ that should be used as new capacity for $container$
+when it is expanded using the @Tag.Overflow Strategy."Generous" overflow strategy at .
+...metafunction:Metafunction.Size
+..see:Tag.Overflow Strategy
+*/
+template <typename T, typename TSize>
+inline TSize
+computeGenerousCapacity(T const & /*me*/,
+ TSize capacity)
+{
+SEQAN_CHECKPOINT
+ if (capacity <= 32) return 32;
+ return capacity + (capacity >> 1);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// _storageUpdated
+//////////////////////////////////////////////////////////////////////////////
+
+/*
+template <typename T>
+inline void
+_storageUpdated(T & me,
+ void const *)
+{
+}
+
+template <typename T>
+inline void
+_storageUpdated(T & me)
+{
+ _storageUpdated_(me, (T *) 0);
+}
+
+template <typename T>
+inline void
+_storageUpdated(T const & me)
+{
+ _storageUpdated_(me, (T const *) 0);
+}
+*/
+
+
+//////////////////////////////////////////////////////////////////////////////
+// assign
+//////////////////////////////////////////////////////////////////////////////
+
+template<typename TTarget, typename TSource>
+inline void
+assign(TTarget & target,
+ TSource & source,
+ typename Size<TTarget>::Type limit)
+{
+SEQAN_CHECKPOINT
+ assign(target, source, limit, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template<typename TTarget, typename TSource>
+inline void
+assign(TTarget const & target,
+ TSource & source,
+ typename Size<TTarget>::Type limit)
+{
+SEQAN_CHECKPOINT
+ assign(target, source, limit, typename DefaultOverflowImplicit<TTarget const>::Type());
+}
+template<typename TTarget, typename TSource>
+inline void
+assign(TTarget & target,
+ TSource const & source,
+ typename Size<TTarget>::Type limit)
+{
+SEQAN_CHECKPOINT
+ assign(target, source, limit, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template<typename TTarget, typename TSource>
+inline void
+assign(TTarget const & target,
+ TSource const & source,
+ typename Size<TTarget>::Type limit)
+{
+SEQAN_CHECKPOINT
+ assign(target, source, limit, typename DefaultOverflowImplicit<TTarget const>::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// append
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.append:
+..summary:Concatenate two containers.
+..cat:Content Manipulation
+..signature:append(target, source [, limit] [,resize_tag])
+..param.target: A container $source$ is append to.
+..param.source: A container that is append to $target$.
+...remarks:The function does not modify this container.
+..param.limit: The maximal length of $target$ after the operation. (optional)
+..param.resize_tag: Specifies the strategy that is applied if $target$ has not enough capacity to store the complete content. (optional)
+...type:Tag.Overflow Strategy
+...default:Specified by @Metafunction.DefaultOverflowImplicit@ of the $target$ type.
+..remarks:The result of this operation is stored in $target$.
+..see:Function.assign
+*/
+template<typename TTarget, typename TSource>
+inline void
+append(TTarget & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ append(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template<typename TTarget, typename TSource>
+inline void
+append(TTarget const & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ append(target, source, typename DefaultOverflowImplicit<TTarget const>::Type());
+}
+template<typename TTarget, typename TSource>
+inline void
+append(TTarget & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ append(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template<typename TTarget, typename TSource>
+inline void
+append(TTarget const & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ append(target, source, typename DefaultOverflowImplicit<TTarget const>::Type());
+}
+
+//____________________________________________________________________________
+
+template<typename TTarget, typename TSource>
+inline void
+append(TTarget & target,
+ TSource & source,
+ typename Size<TTarget>::Type limit)
+{
+SEQAN_CHECKPOINT
+ append(target, source, limit, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template<typename TTarget, typename TSource>
+inline void
+append(TTarget const & target,
+ TSource & source,
+ typename Size<TTarget>::Type limit)
+{
+SEQAN_CHECKPOINT
+ append(target, source, limit, typename DefaultOverflowImplicit<TTarget const>::Type());
+}
+template<typename TTarget, typename TSource>
+inline void
+append(TTarget & target,
+ TSource const & source,
+ typename Size<TTarget>::Type limit)
+{
+SEQAN_CHECKPOINT
+ append(target, source, limit, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template<typename TTarget, typename TSource>
+inline void
+append(TTarget const & target,
+ TSource const & source,
+ typename Size<TTarget>::Type limit)
+{
+SEQAN_CHECKPOINT
+ append(target, source, limit, typename DefaultOverflowImplicit<TTarget const>::Type());
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// appendValue
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.appendValue:
+..signature:appendValue(target, value [, resize_tag])
+..cat:Content Manipulation
+..summary:Appends a value to a container.
+..param.target:A container.
+..param.value:Value that is appended to $target$.
+..param.resize_tag:
+..param.resize_tag: Specifies the strategy that is applied if $target$ has not enough capacity to store the complete content. (optional)
+...type:Tag.Overflow Strategy
+...default:Specified by @Metafunction.DefaultOverflowImplicit@ of the $target$ type.
+*/
+
+template <typename T, typename TValue>
+inline void
+appendValue(T & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ appendValue(me, _value, typename DefaultOverflowImplicit<T>::Type());
+}
+template <typename T, typename TValue>
+inline void
+appendValue(T const & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ appendValue(me, _value, typename DefaultOverflowImplicit<T const>::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// insertValue
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.insertValue:
+..cat:Content Manipulation
+..summary:Inserts a single value into a container.
+..signature:insertValue(target, pos, value [, resize_tag])
+..param.target:The container
+..param.pos:Position within $target$ at which $value$ is to be inserted.
+..param.value:Value that will be inserted into $target$.
+..param.resize_tag:Strategy that is applied if $target$ has not enough capacity to store the complete content.
+...type:Tag.Overflow Strategy
+..see:Function.assignValue
+..see:Function.appendValue
+*/
+
+template <typename T, typename TPosition, typename TValue>
+inline void
+insertValue(T & me,
+ TPosition pos,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ insertValue(me, pos, _value, typename DefaultOverflowImplicit<T>::Type());
+}
+template <typename T, typename TPosition, typename TValue>
+inline void
+insertValue(T const & me,
+ TPosition pos,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ insertValue(me, pos, _value, typename DefaultOverflowImplicit<T const>::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// replace
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.replace:
+..summary:Replaces a part of a container with another container.
+..cat:Content Manipulation
+..signature:replace(target, pos_begin, pos_end, source [, limit] [,resize_tag])
+..param.target: A container that is modified.
+..param.pos_begin: Begin of replaced area.
+...text:The first position in $target$ of the area that is replaced by $source$.
+..param.pos_end: End of replaced area.
+...text:The position behind the last position in $target$ of the area that is replaced by $source$.
+..param.source: A container that is inserted into $target$.
+...remarks:The function does not modify this container.
+..param.limit: The maximal length of $target$ after the operation. (optional)
+..param.resize_tag: Specifies the strategy that is applied if $target$ has not enough capacity to store the complete content. (optional)
+...type:Tag.Overflow Strategy
+...default:Specified by @Metafunction.DefaultOverflowImplicit@ of the $target$ type.
+..see:Function.assign
+..see:Function.append
+..remarks.text:Some compilers have difficulties if $pos_begin$ and $pos_end$ are both 0, since 0 can be
+both a position or an iterator. The workaround is to convert at least one of these arguments
+explicite to the position or to the interator type.
+*/
+template<typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource>
+inline void
+replace(TTarget & target,
+ TPositionBegin pos_begin,
+ TPositionEnd pos_end,
+ TSource & source)
+{
+ replace(target, pos_begin, pos_end, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template<typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource>
+inline void
+replace(TTarget const & target,
+ TPositionBegin pos_begin,
+ TPositionEnd pos_end,
+ TSource & source)
+{
+ replace(target, pos_begin, pos_end, source, typename DefaultOverflowImplicit<TTarget const>::Type());
+}
+template<typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource>
+inline void
+replace(TTarget & target,
+ TPositionBegin pos_begin,
+ TPositionEnd pos_end,
+ TSource const & source)
+{
+ replace(target, pos_begin, pos_end, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template<typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource>
+inline void
+replace(TTarget const & target,
+ TPositionBegin pos_begin,
+ TPositionEnd pos_end,
+ TSource const & source)
+{
+ replace(target, pos_begin, pos_end, source, typename DefaultOverflowImplicit<TTarget const>::Type());
+}
+
+//____________________________________________________________________________
+
+template<typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource>
+inline void
+replace(TTarget & target,
+ TPositionBegin pos_begin,
+ TPositionEnd pos_end,
+ TSource & source,
+ typename Size<TTarget>::Type limit)
+{
+ replace(target, pos_begin, pos_end, source, limit, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template<typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource>
+inline void
+replace(TTarget const & target,
+ TPositionBegin pos_begin,
+ TPositionEnd pos_end,
+ TSource & source,
+ typename Size<TTarget>::Type limit)
+{
+ replace(target, pos_begin, pos_end, source, limit, typename DefaultOverflowImplicit<TTarget const>::Type());
+}
+template<typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource>
+inline void
+replace(TTarget & target,
+ TPositionBegin pos_begin,
+ TPositionEnd pos_end,
+ TSource const & source,
+ typename Size<TTarget>::Type limit)
+{
+ replace(target, pos_begin, pos_end, source, limit, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template<typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource>
+inline void
+replace(TTarget const & target,
+ TPositionBegin pos_begin,
+ TPositionEnd pos_end,
+ TSource const & source,
+ typename Size<TTarget>::Type limit)
+{
+ replace(target, pos_begin, pos_end, source, limit, typename DefaultOverflowImplicit<TTarget const>::Type());
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// reserve
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.reserve:
+..cat:Containers
+..summary:Increases the capacity.
+..signature:Size reserve(object, new_capacity [, resize_tag])
+..param.object: A container.
+..param.new_capacity: The new capacity $object$ will get.
+..param.resize_tag: Specifies the strategy that is applied for changing the capacity. (optional)
+...type:Tag.Overflow Strategy
+...default:Specified by @Metafunction.DefaultOverflowExplicit at .
+..returns:The ammout of the requested capacity that was available.
+That is the function returns the minimum of $new_capacity$ and $capacity(me)$.
+...metafunction:Metafunction.Size
+..remarks:At the end of the operation, $capacity(me)$ can be larger than $new_capacity$.
+If $new_capacity$ is smaller than $capacity(me)$ at the beginning of the operation,
+the operation need not to change the capacity at all.
+..remarks:This operation does not changes the content of $object$.
+...note:This operation may invalidate iterators of $object$.
+..see:Function.capacity
+*/
+template <typename T, typename TSize>
+inline typename Size<T>::Type
+reserve(
+ T & /*me*/,
+ TSize new_capacity,
+ Insist)
+{
+SEQAN_CHECKPOINT
+ return new_capacity;
+}
+
+template <typename T, typename TSize>
+inline typename Size<T>::Type
+reserve(
+ T & me,
+ TSize new_capacity,
+ Limit)
+{
+SEQAN_CHECKPOINT
+ typename Size<T>::Type me_capacity = capacity(me);
+ if (me_capacity < (typename Size<T>::Type) new_capacity) return me_capacity;
+ return new_capacity;
+}
+
+template <typename T, typename TSize>
+inline typename Size<T>::Type
+reserve(
+ T & me,
+ TSize new_capacity)
+{
+SEQAN_CHECKPOINT
+ return reserve(me, new_capacity, typename DefaultOverflowExplicit<T>::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// resize
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.resize:
+..cat:Containers
+..summary:Changes the length.
+..signature:Size resize(object, new_length [, resize_tag])
+..param.object: A container.
+...type:Class.String
+..param.new_length: The new length $object$ will get.
+..param.resize_tag: Specifies the strategy that is applied if the capacity of $object$ is less than $new_length$. (optional)
+...type:Tag.Overflow Strategy
+...default:Specified by @Metafunction.DefaultOverflowExplicit at .
+..returns:The new length $length(object)$.
+...metafunction:Metafunction.Size
+..remarks:This function can be used both for expanding and for shrinking $object$.
+...text:
+If $new_length$ is too large for $object$ (i.e. the @Function.capacity@ of $object$ is too small), then $object$ is
+expanded as far as possible. The resulting length
+of $object$ could be less than $new_length$, depending on the type of $object$ and the available storage.
+..see:Function.length
+..see:Function.reserve
+*/
+template <typename T, typename TSize>
+inline typename Size<T>::Type
+resize(
+ T & me,
+ TSize new_length)
+{
+SEQAN_CHECKPOINT
+ return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// resizeSpace
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.resizeSpace:
+..cat:Containers
+..summary:Makes free space in container
+..signature:Size resizeSpace(object, size, pos_begin, pos_end [, limit] [, resize_tag])
+..param.object:The container.
+...type:Class.String
+..param.size:Number of characters that should be freed.
+..param.pos_begin:Position of the first item in $object$ that is to be destroyed.
+..param.pos_end:Position behind the last item in $object$ that is to be destroyed.
+...remarks:If $pos_end == pos_begin$, no item in $object$ will be destroyed.
+..param.limit:Maximal length $object$ can get after this operation. (optional)
+..param.resize_tag:Strategy that is applied if $object$ has not enough capacity to store the complete content. (optional)
+...metafunction:Metafunction.DefaultOverflowExplicit
+..returns:The number of free characters.
+...metafunction:Metafunction.Size
+...remarks:Depeding on the @Tag.Overflow Strategy.overflow strategy@ specified by $resize_tag$,
+this could be $size$ or less than $size$ if $object$ has not enough @Function.capacity at .
+*/
+
+template<typename T, typename TSize, typename TPosition>
+inline TSize
+resizeSpace(T & me,
+ TSize size,
+ TPosition pos_begin,
+ TPosition pos_end)
+{
+SEQAN_CHECKPOINT
+ return resizeSpace(me, size, pos_begin, pos_end, typename DefaultOverflowExplicit<T>::Type());
+}
+
+template<typename T, typename TSize, typename TPosition>
+inline TSize
+resizeSpace(T & me,
+ TSize size,
+ TPosition pos_begin,
+ TPosition pos_end,
+ TSize limit)
+{
+SEQAN_CHECKPOINT
+ return resizeSpace(me, size, pos_begin, pos_end, limit, typename DefaultOverflowExplicit<T>::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// erase
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.erase:
+..summary:Erases a part of a container
+..cat:Containers
+..signature:erase(object, pos [, pos_end])
+..param.object:The container.
+...type:Class.String
+..param.pos:Position of the first item in $object$ that is to be destroyed.
+..param.pos_end:Position behind the last item in $object$ that is to be destroyed. (optional)
+...default:$pos + 1$
+...remarks:If $pos_end$ is omitted, only one element in $object$ at position $pos$ is destroyed.
+..remarks:$erase(object, pos, pos_end)$ is semantically the same as @Function.resizeSpace.resizeSpace(object, 0, pos, pos_end)@.
+*/
+
+template<typename T, typename TPosition>
+inline void
+erase(T & me,
+ TPosition pos,
+ TPosition pos_end)
+{
+SEQAN_CHECKPOINT
+ resizeSpace(me, 0, pos, pos_end);
+}
+
+template<typename T, typename TPosition>
+inline void
+erase(T & me,
+ TPosition pos)
+{
+SEQAN_CHECKPOINT
+ resizeSpace(me, 0, pos, pos + 1);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// fill
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.fill:
+..cat:Containers
+..summary:Resizes and fills a container.
+..signature:Size fill(object, new_length, value [, resize_tag])
+..param.object: A container.
+...type:Class.String
+..param.new_length: The new length $object$ will get.
+..param.value: Value that is copied if new items are created in $object$.
+...remarks:If the $value$ argument is omitted, the default constructor is used to create
+new items in $object$.
+..param.resize_tag: Specifies the strategy that is applied if the capacity of $object$ is less than $new_length$. (optional)
+...type:Tag.Overflow Strategy
+...default:Specified by @Metafunction.DefaultOverflowExplicit at .
+..returns:The new length $length(object)$.
+...metafunction:Metafunction.Size
+..remarks:This function can be used both for expanding and for shrinking $object$.
+...text:
+ If $new_length$ is too large for $object$ (i.e. the @Function.capacity@ of $object$ is too small), then $object$ is
+ expanded as far as possible. The resulting length
+ of $object$ could be less than $new_length$, depending on the type of $object$ and the available storage.
+..see:Function.length
+..see:Function.reserve
+..see:Function.resize
+*/
+
+template <typename T, typename TSize, typename TValue>
+inline typename Size<T>::Type
+fill(
+ T & me,
+ TSize new_length,
+ TValue const & val)
+{
+SEQAN_CHECKPOINT
+ return fill(me, new_length, val, typename DefaultOverflowExplicit<T>::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// shrinkToFit
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.shrinkToFit:
+..cat:Containers
+..summary:Resizes container to minimum capacity
+..signature:shrinkToFit(object)
+..param.object: A container.
+..remarks
+...text:$shrinkToFit(object)$ is equivalent to $reserve(object, length(object), Exact())$.
+..see:Function.capacity
+..see:Function.length
+..see:Function.reserve
+*/
+
+template <typename T, typename TSize, typename TValue>
+inline void
+shrinkToFit(T & me)
+{
+SEQAN_CHECKPOINT
+ reserve(me, length(me), Exact());
+}
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/sequence/sequence_multiple.h b/src/libSSA/seqan/sequence/sequence_multiple.h
new file mode 100644
index 0000000..0eed9b4
--- /dev/null
+++ b/src/libSSA/seqan/sequence/sequence_multiple.h
@@ -0,0 +1,2286 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: sequence_multiple.h,v 1.2 2009/02/19 01:51:23 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_STRING_SET_H
+#define SEQAN_HEADER_STRING_SET_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+ //////////////////////////////////////////////////////////////////////////////
+ // StringSet specs
+ //////////////////////////////////////////////////////////////////////////////
+
+ //struct Generous; // large string-string, large id-string
+ //struct Tight; // small string-string, small id-string
+ //struct Optimal?? // small string-string, large id-string
+
+/**
+.Spec.Dependent:
+..summary:A string set storing references of the strings.
+..cat:Sequences
+..general:Class.StringSet
+..signature:StringSet<TString, Dependent<TSpec> >
+..param.TString:The string type.
+...type:Class.String
+..param.TSpec:The specializing type for the dependent string set.
+...remarks:Possible values are $Tight$ or $Generous$
+...remarks:$Tight$ is very space efficient whereas $Generous$ provides fast access to the strings in the container via ids.
+*/
+
+ // Default id holder string set
+ template<typename TSpec = Generous >
+ struct Dependent; // holds references of its elements
+
+
+/**
+.Spec.ConcatDirect:
+..summary:A string set storing the concatenation of all strings within one string.
+..cat:Sequences
+..general:Spec.Owner
+..signature:StringSet<TString, Owner<ConcatDirect<> > >
+..param.TString:The string type.
+...type:Class.String
+..remarks:The strings are internally stored in a $TString$ object and the character position type is a
+a single integer value between 0 and the sum of string lengths minus 1.
+..remarks:The position type can be returned or modified by the meta-function @Metafunction.SAValue@ called with the @Class.StringSet@ type.
+*/
+
+ template < typename TDelimiter = void >
+ struct ConcatDirect; // contains 1 string (the concatenation of n strings)
+ //struct Default; // contains n strings in a string
+
+/**
+.Spec.Owner:
+..summary:A string set storing the strings as members.
+..cat:Sequences
+..general:Class.StringSet
+..signature:StringSet<TString, Owner<> >
+..signature:StringSet<TString, Owner<Default> >
+..param.TString:The string type.
+...type:Class.String
+..remarks:The strings are internally stored in a $String<TString>$ object and the character position type is a
+ at Class.Pair@ $(seqNo,seqOfs)$ where seqNo identifies the string within the stringset and seqOfs identifies the position within this string.
+..remarks:The position type can be returned or modified by the meta-function @Metafunction.SAValue@ called with the @Class.StringSet@ type.
+*/
+ template < typename TSpec = Default >
+ struct Owner; // owns its elements
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // Forwards
+ //////////////////////////////////////////////////////////////////////////////
+
+ template < typename TString, typename TSpec = Owner<> >
+ class StringSet;
+
+ template <typename TObject>
+ struct Concatenator {
+ typedef TObject Type;
+ };
+
+ template <typename TObject>
+ struct Concatenator<TObject const> {
+ typedef typename Concatenator<TObject>::Type const Type;
+ };
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // StringSet limits
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TString>
+ struct StringSetLimits {
+ typedef Nothing Type;
+ };
+
+ template <typename TString>
+ struct StringSetLimits<TString const> {
+ typedef typename StringSetLimits<TString>::Type const Type;
+ };
+
+ template <typename TString>
+ struct StringSetPosition {
+ typedef typename Size<TString>::Type Type;
+ };
+
+ template <typename TString, typename TSpec>
+ struct StringSetLimits< StringSet<TString, TSpec> > {
+ typedef typename Size<TString>::Type TSize;
+ typedef String<TSize> Type;
+ };
+
+ template <typename TString, typename TSpec>
+ struct StringSetPosition< StringSet<TString, TSpec> > {
+ typedef typename Size<TString>::Type TSize;
+ typedef Pair<TSize> Type;
+ };
+
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // get StringSet limits
+ //////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.stringSetLimits:
+..cat:Sequences
+..summary:Retrieves a string of delimiter positions of a @Class.StringSet@ which is needed for local<->global position conversions.
+..signature:stringSetLimits(me)
+..param.me:A string or string set.
+...type:Class.String
+...type:Class.StringSet
+..returns:A reference to a string.
+...remarks:If $me$ is a @Class.StringSet@ then the returned string is of size $length(me)+1$ and contains the ascending (virtual) delimiter positions of the concatenation of all strings in the string set.
+...remarks:If $me$ is a @Class.String@, @Tag.Nothing@ is returned.
+*/
+
+ template <typename TStringSet>
+ inline typename StringSetLimits<TStringSet>::Type
+ stringSetLimits(TStringSet &) {
+ return typename StringSetLimits<TStringSet>::Type();
+ }
+
+ template <typename TString, typename TSpec>
+ inline typename StringSetLimits< StringSet<TString, TSpec> >::Type &
+ stringSetLimits(StringSet<TString, TSpec> &stringSet) {
+ if (!_validStringSetLimits(stringSet))
+ _refreshStringSetLimits(stringSet);
+ return stringSet.limits;
+ }
+
+ template <typename TString, typename TSpec>
+ inline typename StringSetLimits< StringSet<TString, TSpec> const>::Type &
+ stringSetLimits(StringSet<TString, TSpec> const &stringSet) {
+ if (!_validStringSetLimits(stringSet))
+ _refreshStringSetLimits(const_cast< StringSet<TString, TSpec>& >(stringSet));
+ return stringSet.limits;
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // accessing local positions
+ //////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.getSeqNo:
+..cat:Sequences
+..summary:Returns the sequence number of a position.
+..signature:getSeqNo(pos[, limits])
+..param.pos:A position.
+...type:Class.Pair
+..param.limits:The limits string returned by @Function.stringSetLimits at .
+..returns:A single integer value that identifies the string within the stringset $pos$ points at.
+...remarks:If $limits$ is omitted or @Tag.Nothing@ $getSeqNo$ returns 0.
+...remarks:If $pos$ is a local position (of class @Class.Pair@) then $i1$ is returned.
+...remarks:If $pos$ is a global position (integer type and $limits$ is a @Class.String@) then $pos$ is converted to a local position and $i1$ is returned.
+*/
+
+/**
+.Function.getSeqOffset:
+..cat:Sequences
+..summary:Returns the local sequence offset of a position.
+..signature:getSeqOffset(pos[, limits])
+..param.pos:A position.
+...type:Class.Pair
+..param.limits:The limits string returned by @Function.stringSetLimits at .
+..returns:A single integer value that identifies the position within the string $pos$ points at.
+...remarks:If $limits$ is omitted or @Tag.Nothing@ $getSeqNo$ returns $pos$.
+...remarks:If $pos$ is a local position (of class @Class.Pair@) then $i2$ is returned.
+...remarks:If $pos$ is a global position (integer type and $limits$ is a @Class.String@) then $pos$ is converted to a local position and $i2$ is returned.
+*/
+
+ //////////////////////////////////////////////////////////////////////////////
+ // 1 sequence
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TPosition>
+ inline TPosition getSeqNo(TPosition const &, Nothing const &) {
+ return 0;
+ }
+
+ template <typename TPosition>
+ inline TPosition getSeqOffset(TPosition const &pos, Nothing const &) {
+ return pos;
+ }
+//____________________________________________________________________________
+
+ template <typename TPosition>
+ inline TPosition getSeqNo(TPosition const &) {
+ return 0;
+ }
+
+ template <typename TPosition>
+ inline TPosition getSeqOffset(TPosition const &pos) {
+ return pos;
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // n sequences (position type is Pair)
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename T1, typename T2, typename TCompression, typename TLimitsString>
+ inline T1 getSeqNo(Pair<T1, T2, TCompression> const &pos, TLimitsString const &) {
+ return getValueI1(pos);
+ }
+
+ template <typename T1, typename T2, typename TCompression>
+ inline T1 getSeqNo(Pair<T1, T2, TCompression> const &pos) {
+ return getValueI1(pos);
+ }
+//____________________________________________________________________________
+
+ template <typename T1, typename T2, typename TCompression, typename TLimitsString>
+ inline T2 getSeqOffset(Pair<T1, T2, TCompression> const &pos, TLimitsString const &) {
+ return getValueI2(pos);
+ }
+
+ template <typename T1, typename T2, typename TCompression>
+ inline T1 getSeqOffset(Pair<T1, T2, TCompression> const &pos) {
+ return getValueI2(pos);
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // n sequences (position type is an integral type)
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TPos, typename TLimitsString>
+ inline TPos getSeqNo(TPos const &pos, TLimitsString const &limits) {
+ typedef typename Iterator<TLimitsString const, Standard>::Type TIter;
+ typedef typename Value<TLimitsString>::Type TSize;
+ TIter _begin = begin(limits, Standard());
+ TIter _upper = ::std::upper_bound(_begin, end(limits, Standard()), (TSize)pos) - 1;
+ return difference(_begin, _upper);
+ }
+
+ template <typename TPos, typename TLimitsString>
+ inline TPos getSeqOffset(TPos const &pos, TLimitsString const &limits) {
+ typedef typename Iterator<TLimitsString const, Standard>::Type TIter;
+ typedef typename Value<TLimitsString>::Type TSize;
+ TIter _begin = begin(limits, Standard());
+ TIter _upper = ::std::upper_bound(_begin, end(limits, Standard()), (TSize)pos) - 1;
+ return pos - *_upper;
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // local -> global conversions
+ //////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.posGlobalize:
+..cat:Sequences
+..summary:Converts a local/global to a global position.
+..signature:posGlobalize(pos, limits)
+..param.pos:A local or global position (pair or integer value).
+...type:Class.Pair
+..param.limits:The limits string returned by @Function.stringSetLimits at .
+..returns:The corresponding global position of $pos$.
+...remarks:If $pos$ is an integral type $pos$ is returned.
+...remarks:If not, $limits[getSeqNo(pos, limits)] + getSeqOffset(pos, limits)$ is returned.
+*/
+
+ // any_position and no limits_string -> any_position
+ template <typename TPosition>
+ inline TPosition posGlobalize(TPosition const &pos, Nothing const &) {
+ return pos;
+ }
+
+ // local_position (0,x) and no limits_string -> global_position x
+ template <typename T1, typename T2, typename TCompression>
+ inline T2 posGlobalize(Pair<T1, T2, TCompression> const &pos, Nothing const &) {
+ return getSeqOffset(pos);
+ }
+
+ // any_position and no limits_string -> any_position
+ template <typename TLimitsString, typename TPosition>
+ inline TPosition posGlobalize(TPosition const &pos, TLimitsString const &) {
+ return pos;
+ }
+
+ // local_position and limits_string -> global_position
+ template <typename TLimitsString, typename T1, typename T2, typename TCompression>
+ inline typename Value<TLimitsString>::Type
+ posGlobalize(Pair<T1, T2, TCompression> const &pos, TLimitsString const &limits) {
+ return limits[getSeqNo(pos, limits)] + getSeqOffset(pos, limits);
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // global -> local position
+ //////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.posLocalize:
+..cat:Sequences
+..summary:Converts a local/global to a local position.
+..signature:posLocalize(result, pos, limits)
+..param.pos:A local or global position (pair or integer value).
+...type:Class.Pair
+..param.limits:The limits string returned by @Function.stringSetLimits at .
+..param.result:Reference to the resulting corresponding local position of $pos$.
+...remarks:If $pos$ is an integral type and $limits$ is omitted or @Tag.Nothing@, $pos$ is returned.
+...remarks:If $pos$ is a local position (of class @Class.Pair@) then $pos$ is returned.
+...remarks:If $pos$ is a global position (integer type and $limits$ is a @Class.String@) then $pos$ is converted to a local position.
+*/
+
+ // any_position and no limits_string -> any_position
+ template <typename TResult, typename TPosition>
+ inline void posLocalize(TResult &result, TPosition const &pos, Nothing const &) {
+ result = pos;
+ }
+
+ template <typename T1, typename T2, typename TCompression, typename TPosition>
+ inline void posLocalize(Pair<T1, T2, TCompression> &result, TPosition const &pos, Nothing const &) {
+ result.i1 = 0;
+ result.i2 = pos;
+ }
+
+ // global_position and limits_string -> local_position
+ template <typename TResult, typename TSize, typename TSpec, typename TPosition>
+ inline void posLocalize(TResult &result, TPosition const &pos, String<TSize, TSpec> const &limits) {
+ typedef typename Iterator<String<TSize> const, Standard>::Type TIter;
+ TIter _begin = begin(limits, Standard());
+ TIter _upper = ::std::upper_bound(_begin, end(limits, Standard()), (TSize)pos) - 1;
+ result.i1 = difference(_begin, _upper);
+ result.i2 = pos - *_upper;
+ }
+
+ // local_position -> local_position
+ template <typename TResult, typename TSize, typename TSpec, typename T1, typename T2, typename TCompression>
+ inline void posLocalize(TResult &result, Pair<T1, T2, TCompression> const &pos, String<TSize, TSpec> const &/*limits*/) {
+ result = pos;
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // prefix
+ //////////////////////////////////////////////////////////////////////////////
+
+ template < typename TString, typename TSpec, typename TPosition >
+ inline typename Prefix<TString>::Type
+ prefix(StringSet< TString, TSpec > &me, TPosition pos)
+ {
+ typedef StringSet<TString, TSpec> TStringSet;
+ typedef typename Size<TStringSet>::Type TSetSize;
+ typedef typename Size<TString>::Type TStringSize;
+ typedef Pair<TSetSize, TStringSize, Compressed> TPair;
+
+ TPair lPos;
+ posLocalize(lPos, pos, stringSetLimits(me));
+ return prefix(me[getSeqNo(lPos)], getSeqOffset(lPos));
+ }
+
+ template < typename TString, typename TSpec, typename TPosition >
+ inline typename Prefix<TString const>::Type
+ prefix(StringSet< TString, TSpec > const &me, TPosition pos)
+ {
+ typedef StringSet<TString, TSpec> TStringSet;
+ typedef typename Size<TStringSet>::Type TSetSize;
+ typedef typename Size<TString>::Type TStringSize;
+ typedef Pair<TSetSize, TStringSize, Compressed> TPair;
+
+ TPair lPos;
+ posLocalize(lPos, pos, stringSetLimits(me));
+ return prefix(me[getSeqNo(lPos)], getSeqOffset(lPos));
+ }
+
+ template < typename TString, typename TDelimiter, typename TPosition >
+ inline typename Infix<TString>::Type
+ prefix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > &me, TPosition pos)
+ {
+ return infix(me.concat, stringSetLimits(me)[getSeqNo(pos, stringSetLimits(me))], posGlobalize(pos, stringSetLimits(me)));
+ }
+
+ template < typename TString, typename TDelimiter, typename TPosition >
+ inline typename Infix<TString const>::Type
+ prefix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > const &me, TPosition pos)
+ {
+ return infix(me.concat, stringSetLimits(me)[getSeqNo(pos, stringSetLimits(me))], posGlobalize(pos, stringSetLimits(me)));
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // suffix
+ //////////////////////////////////////////////////////////////////////////////
+
+ template < typename TString, typename TSpec, typename TPosition >
+ inline typename Suffix<TString>::Type
+ suffix(StringSet< TString, TSpec > &me, TPosition pos)
+ {
+ typedef StringSet<TString, TSpec> TStringSet;
+ typedef typename Size<TStringSet>::Type TSetSize;
+ typedef typename Size<TString>::Type TStringSize;
+ typedef Pair<TSetSize, TStringSize, Compressed> TPair;
+
+ TPair lPos;
+ posLocalize(lPos, pos, stringSetLimits(me));
+ return suffix(me[getSeqNo(lPos)], getSeqOffset(lPos));
+ }
+
+ template < typename TString, typename TSpec, typename TPosition >
+ inline typename Suffix<TString const>::Type
+ suffix(StringSet< TString, TSpec > const &me, TPosition pos)
+ {
+ typedef StringSet<TString, TSpec> TStringSet;
+ typedef typename Size<TStringSet>::Type TSetSize;
+ typedef typename Size<TString>::Type TStringSize;
+ typedef Pair<TSetSize, TStringSize, Compressed> TPair;
+
+ TPair lPos;
+ posLocalize(lPos, pos, stringSetLimits(me));
+ return suffix(me[getSeqNo(lPos)], getSeqOffset(lPos));
+ }
+
+ template < typename TString, typename TDelimiter, typename TPosition >
+ inline typename Infix<TString>::Type
+ suffix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > &me, TPosition pos)
+ {
+ return infix(me.concat, posGlobalize(pos, stringSetLimits(me)), stringSetLimits(me)[getSeqNo(pos, stringSetLimits(me)) + 1]);
+ }
+
+ template < typename TString, typename TDelimiter, typename TPosition >
+ inline typename Infix<TString const>::Type
+ suffix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > const &me, TPosition pos)
+ {
+ return infix(me.concat, posGlobalize(pos, stringSetLimits(me)), stringSetLimits(me)[getSeqNo(pos, stringSetLimits(me)) + 1]);
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // infixWithLength
+ //////////////////////////////////////////////////////////////////////////////
+
+ template < typename TString, typename TSpec, typename TPosition, typename TSize >
+ inline typename Infix<TString>::Type
+ infixWithLength(StringSet< TString, TSpec > &me, TPosition pos, TSize length)
+ {
+ typedef StringSet<TString, TSpec> TStringSet;
+ typedef typename Size<TStringSet>::Type TSetSize;
+ typedef typename Size<TString>::Type TStringSize;
+ typedef Pair<TSetSize, TStringSize, Compressed> TPair;
+
+ TPair lPos;
+ posLocalize(lPos, pos, stringSetLimits(me));
+ return infixWithLength(me[getSeqNo(lPos)], getSeqOffset(lPos), length);
+ }
+
+ template < typename TString, typename TSpec, typename TPosition, typename TSize >
+ inline typename Infix<TString const>::Type
+ infixWithLength(StringSet< TString, TSpec > const &me, TPosition pos, TSize length)
+ {
+ typedef StringSet<TString, TSpec> TStringSet;
+ typedef typename Size<TStringSet>::Type TSetSize;
+ typedef typename Size<TString>::Type TStringSize;
+ typedef Pair<TSetSize, TStringSize, Compressed> TPair;
+
+ TPair lPos;
+ posLocalize(lPos, pos, stringSetLimits(me));
+ return infixWithLength(me[getSeqNo(lPos)], getSeqOffset(lPos), length);
+ }
+
+ template < typename TString, typename TDelimiter, typename TPosition, typename TSize >
+ inline typename Infix<TString>::Type
+ infixWithLength(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > &me, TPosition pos, TSize length)
+ {
+ return infixWithLength(me.concat, posGlobalize(pos, stringSetLimits(me)), length);
+ }
+
+ template < typename TString, typename TDelimiter, typename TPosition, typename TSize >
+ inline typename Infix<TString const>::Type
+ infixWithLength(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > const &me, TPosition pos, TSize length)
+ {
+ return infixWithLength(me.concat, posGlobalize(pos, stringSetLimits(me)), length);
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // position arithmetics
+ //////////////////////////////////////////////////////////////////////////////
+
+ // posAtFirstLocal
+ template <typename TPos, typename TLimitsString>
+ inline bool posAtFirstLocal(TPos pos, TLimitsString const &limits) {
+ return getSeqOffset(pos, limits) == 0;
+ }
+ template <typename TPos>
+ inline bool posAtFirstLocal(TPos pos) {
+ return getSeqOffset(pos) == 0;
+ }
+
+
+ // posPrev
+ template <typename TPos>
+ inline TPos posPrev(TPos pos) {
+ return pos - 1;
+ }
+
+ template <typename T1, typename T2, typename TCompression>
+ inline Pair<T1, T2, TCompression> posPrev(Pair<T1, T2, TCompression> const &pos) {
+ return Pair<T1, T2, TCompression>(getValueI1(pos), getValueI2(pos) - 1);
+ }
+
+ // posNext
+ template <typename TPos>
+ inline TPos posNext(TPos pos) {
+ return pos + 1;
+ }
+
+ template <typename T1, typename T2, typename TCompression>
+ inline Pair<T1, T2, TCompression>
+ posNext(Pair<T1, T2, TCompression> const &pos) {
+ return Pair<T1, T2, TCompression>(getValueI1(pos), getValueI2(pos) + 1);
+ }
+
+ // posAdd
+ template <typename TPos, typename TDelta>
+ inline TPos posAdd(TPos pos, TDelta delta) {
+ return pos + delta;
+ }
+
+ template <typename T1, typename T2, typename TCompression, typename TDelta>
+ inline Pair<T1, T2, TCompression>
+ posAdd(Pair<T1, T2, TCompression> const &pos, TDelta delta) {
+ return Pair<T1, T2, TCompression>(getValueI1(pos), getValueI2(pos) + delta);
+ }
+
+ // posSub
+ template <typename TA, typename TB>
+ inline TA posSub(TA a, TB b) {
+ return a - b;
+ }
+
+ template <
+ typename TA1, typename TA2, typename TACompression,
+ typename TB1, typename TB2, typename TBCompression
+ >
+ inline TA2
+ posSub(Pair<TA1, TA2, TACompression> const &a, Pair<TB1, TB2, TBCompression> const &b) {
+ return getValueI2(a) - getValueI2(b);
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // position relations
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TPos>
+ inline bool posLess(TPos const &a, TPos const &b) {
+ return a < b;
+ }
+
+ template <typename T1, typename T2, typename TCompression>
+ inline bool posLess(Pair<T1, T2, TCompression> const &a, Pair<T1, T2, TCompression> const &b) {
+ return
+ (getValueI1(a) < getValueI1(b)) ||
+ ((getValueI1(a) == getValueI1(b)) && (getValueI2(a) < getValueI2(b)));
+ }
+
+ template <typename TPos>
+ inline int posCompare(TPos const &a, TPos const &b) {
+ if (a < b) return -1;
+ if (a > b) return 1;
+ return 0;
+ }
+
+ template <typename T1, typename T2, typename TCompression>
+ inline int posCompare(Pair<T1, T2, TCompression> const &a, Pair<T1, T2, TCompression> const &b) {
+ if (getValueI1(a) < getValueI1(b)) return -1;
+ if (getValueI1(a) > getValueI1(b)) return 1;
+ return posCompare(getValueI2(a), getValueI2(b));
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TPos, typename TString>
+ inline typename Size<TString>::Type
+ suffixLength(TPos pos, TString const &string) {
+ return length(string) - pos;
+ }
+
+ template <typename TPos, typename TString, typename TSpec>
+ inline typename Size<TString>::Type
+ suffixLength(TPos pos, StringSet<TString, TSpec> const &stringSet) {
+ return length(stringSet[getSeqNo(pos, stringSetLimits(stringSet))]) - getSeqOffset(pos, stringSetLimits(stringSet));
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TString>
+ inline unsigned
+ countSequences(TString const &) {
+ return 1;
+ }
+
+ template <typename TString, typename TSpec>
+ inline typename Size<StringSet<TString, TSpec> >::Type
+ countSequences(StringSet<TString, TSpec> const &stringSet) {
+ return length(stringSet);
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TSeqNo, typename TString>
+ inline typename Size<TString>::Type
+ sequenceLength(TSeqNo /*seqNo*/, TString const &string) {
+ return length(string);
+ }
+
+ template <typename TSeqNo, typename TString, typename TSpec>
+ inline typename Size<StringSet<TString, TSpec> >::Type
+ sequenceLength(TSeqNo seqNo, StringSet<TString, TSpec> const &stringSet) {
+ return length(stringSet[seqNo]);
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // StringSet Container
+ //////////////////////////////////////////////////////////////////////////////
+
+/**
+.Class.StringSet:
+..cat:Sequences
+..summary:A container class for a set of strings.
+..signature:StringSet<TString, TSpec>
+..param.TString:The string type.
+...type:Class.String
+..param.TSpec:The specializing type for the StringSet.
+...metafunction:Metafunction.Spec
+...default:$Generous$.
+..include:sequence.h
+*/
+
+ //////////////////////////////////////////////////////////////////////////////
+ // StringSet with individual sequences in a tight string of string pointers and corr. IDs
+ template <typename TString>
+ class StringSet<TString, Dependent<Tight> >
+ {
+ public:
+ typedef String<TString*> TStrings;
+ typedef typename Id<StringSet>::Type TIdType;
+ typedef String<TIdType> TIds;
+ typedef typename StringSetLimits<StringSet>::Type TLimits;
+ typedef typename Concatenator<StringSet>::Type TConcatenator;
+ //____________________________________________________________________________
+
+ TStrings strings;
+ TIds ids;
+ TLimits limits;
+ bool limitsValid; // is true if limits contains the cumulative sum of the sequence lengths
+ TConcatenator concat;
+ //____________________________________________________________________________
+
+ StringSet():
+ limitsValid(true)
+ {
+ SEQAN_CHECKPOINT
+ appendValue(limits, 0);
+ concat.set = this;
+ }
+
+ template <typename TDefault>
+ StringSet(StringSet<TString, Owner<TDefault> > const& _other) :
+ limitsValid(true)
+ {
+ SEQAN_CHECKPOINT
+ appendValue(limits, 0);
+ concat.set = this;
+ for(unsigned int i = 0; i<length(_other); ++i) appendValue(*this, _other[i]);
+ }
+
+ template <typename TPos>
+ inline typename Reference<StringSet>::Type
+ operator [] (TPos pos)
+ {
+ SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+
+ template <typename TPos>
+ inline typename Reference<StringSet const>::Type
+ operator [] (TPos pos) const
+ {
+ return value(*this, pos);
+ }
+ };
+
+ //////////////////////////////////////////////////////////////////////////////
+ // StringSet with individual sequences in a string of string pointers
+ template <typename TString>
+ class StringSet<TString, Dependent<Generous> >
+ {
+ public:
+ typedef String<TString*> TStrings;
+ typedef typename Size<StringSet>::Type TSize;
+ typedef typename StringSetLimits<StringSet>::Type TLimits;
+ typedef typename Concatenator<StringSet>::Type TConcatenator;
+ //____________________________________________________________________________
+
+ TStrings strings;
+ TLimits limits;
+ bool limitsValid; // is true if limits contains the cumulative sum of the sequence lengths
+ TConcatenator concat;
+ //____________________________________________________________________________
+
+ StringSet():
+ limitsValid(true)
+ {
+ SEQAN_CHECKPOINT
+ appendValue(limits, 0);
+ concat.set = this;
+ }
+
+ template <typename TDefault>
+ StringSet(StringSet<TString, Owner<TDefault> > const& _other) :
+ limitsValid(true)
+ {
+ SEQAN_CHECKPOINT
+ appendValue(limits, 0);
+ concat.set = this;
+ for(unsigned int i = 0; i<length(_other); ++i) appendValue(*this, _other[i]);
+ }
+
+ template <typename TPos>
+ inline typename Reference<StringSet>::Type
+ operator [] (TPos pos)
+ {
+ return value(*this, pos);
+ }
+
+ template <typename TPos>
+ inline typename Reference<StringSet const>::Type
+ operator [] (TPos pos) const
+ {
+ return value(*this, pos);
+ }
+ };
+
+ //////////////////////////////////////////////////////////////////////////////
+ // StringSet with individual sequences in a string of strings
+ template < typename TString >
+ class StringSet< TString, Owner<Default> >
+ {
+ public:
+
+ typedef String<TString> TStrings;
+ typedef typename StringSetLimits<StringSet>::Type TLimits;
+ typedef typename Concatenator<StringSet>::Type TConcatenator;
+//____________________________________________________________________________
+
+ TStrings strings;
+ TLimits limits;
+ bool limitsValid; // is true if limits contains the cumulative sum of the sequence lengths
+ TConcatenator concat;
+//____________________________________________________________________________
+
+ StringSet():
+ limitsValid(true)
+ {
+ appendValue(limits, 0);
+ concat.set = this;
+ };
+//____________________________________________________________________________
+
+ template <typename TPos>
+ inline typename Reference<StringSet>::Type
+ operator [] (TPos pos)
+ {
+ return value(*this, pos);
+ }
+
+ template <typename TPos>
+ inline typename Reference<StringSet const>::Type
+ operator [] (TPos pos) const
+ {
+ return value(*this, pos);
+ }
+ };
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // StringSet with directly concatenated sequences
+ template < typename TString, typename TDelimiter >
+ class StringSet< TString, Owner<ConcatDirect<TDelimiter> > >
+ {
+ public:
+ typedef typename StringSetLimits<StringSet>::Type TLimits;
+ typedef typename Concatenator<StringSet>::Type TConcatenator;
+//____________________________________________________________________________
+
+ TLimits limits;
+ TConcatenator concat;
+//____________________________________________________________________________
+
+ StringSet() {
+ appendValue(limits, 0);
+ }
+//____________________________________________________________________________
+
+ template <typename TPos>
+ inline typename Reference<StringSet>::Type
+ operator [] (TPos pos)
+ {
+ SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+
+ template <typename TPos>
+ inline typename Reference<StringSet const>::Type
+ operator [] (TPos pos) const
+ {
+ SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+ };
+
+
+//////////////////////////////////////////////////////////////////////////////
+// meta functions
+
+ template < typename TString, typename TSpec >
+ struct Value< StringSet< TString, TSpec > > {
+ typedef TString Type;
+ };
+
+ template < typename TString, typename TSpec >
+ struct Value< StringSet< TString, TSpec > const> {
+ typedef TString Type;
+ };
+
+ template < typename TString, typename TSpec >
+ struct Size< StringSet< TString, TSpec > >:
+ Size< typename StringSetLimits< StringSet<TString, TSpec> >::Type > {};
+
+ template < typename TString, typename TSpec >
+ struct Prefix< StringSet< TString, TSpec > >:
+ Prefix< TString > {};
+
+ template < typename TString, typename TSpec >
+ struct Prefix< StringSet< TString, TSpec > const >:
+ Prefix< TString const > {};
+
+ template < typename TString, typename TSpec >
+ struct Suffix< StringSet< TString, TSpec > >:
+ Suffix< TString > {};
+
+ template < typename TString, typename TSpec >
+ struct Suffix< StringSet< TString, TSpec > const >:
+ Suffix< TString const > {};
+
+ template < typename TString, typename TSpec >
+ struct Infix< StringSet< TString, TSpec > >:
+ Infix< TString > {};
+
+ template < typename TString, typename TSpec >
+ struct Infix< StringSet< TString, TSpec > const >:
+ Infix< TString const > {};
+
+
+ // direct concatenation
+ template < typename TString, typename TSpec >
+ struct Value< StringSet< TString, Owner<ConcatDirect<TSpec> > > >:
+ Infix<TString> {};
+
+ template < typename TString, typename TSpec >
+ struct GetValue< StringSet< TString, Owner<ConcatDirect<TSpec> > > >:
+ Infix<TString> {};
+
+ template < typename TString, typename TSpec >
+ struct GetValue< StringSet< TString, Owner<ConcatDirect<TSpec> > > const >:
+ Infix<TString const> {};
+
+ template < typename TString, typename TSpec >
+ struct Reference< StringSet< TString, Owner<ConcatDirect<TSpec> > > >:
+ Infix<TString> {};
+
+ template < typename TString, typename TSpec >
+ struct Reference< StringSet< TString, Owner<ConcatDirect<TSpec> > > const >:
+ Infix<TString const> {};
+
+ template <typename TString, typename TSpec>
+ struct AllowsFastRandomAccess< StringSet< TString, TSpec > >:
+ AllowsFastRandomAccess<TString> {};
+
+ template < typename TString, typename TSpec >
+ struct Prefix< StringSet< TString, Owner<ConcatDirect<TSpec> > > >:
+ Infix< TString > {};
+
+ template < typename TString, typename TSpec >
+ struct Prefix< StringSet< TString, Owner<ConcatDirect<TSpec> > > const >:
+ Infix< TString const > {};
+
+ template < typename TString, typename TSpec >
+ struct Suffix< StringSet< TString, Owner<ConcatDirect<TSpec> > > >:
+ Infix< TString > {};
+
+ template < typename TString, typename TSpec >
+ struct Suffix< StringSet< TString, Owner<ConcatDirect<TSpec> > > const >:
+ Infix< TString const > {};
+
+ template < typename TString, typename TSpec >
+ struct Infix< StringSet< TString, Owner<ConcatDirect<TSpec> > > >:
+ Infix< TString > {};
+
+ template < typename TString, typename TSpec >
+ struct Infix< StringSet< TString, Owner<ConcatDirect<TSpec> > > const >:
+ Infix< TString const > {};
+
+
+//////////////////////////////////////////////////////////////////////////////
+// validStringSetLimits
+
+ template < typename T >
+ inline bool _validStringSetLimits(T const &) {
+ return true;
+ }
+
+ template < typename TString, typename TSpec >
+ inline bool _validStringSetLimits(StringSet< TString, TSpec > const &me) {
+ return me.limitsValid;
+ }
+
+ template < typename TString, typename TSpec >
+ inline bool _validStringSetLimits(StringSet< TString, Owner<ConcatDirect<TSpec> > > const &) {
+ return true;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// _refreshStringSetLimits
+
+ template < typename T >
+ inline void _refreshStringSetLimits(T &) {}
+
+ template < typename TString, typename TSpec >
+ inline void _refreshStringSetLimits(StringSet< TString, Owner<ConcatDirect<TSpec> > > &) {}
+
+ template < typename TString, typename TSpec >
+ inline void _refreshStringSetLimits(StringSet< TString, TSpec > &me)
+ {
+ typedef StringSet< TString, TSpec > TStringSet;
+ typedef typename StringSetLimits<TStringSet>::Type TLimits;
+
+ typename Value<TLimits>::Type sum = 0;
+ typename Size<TStringSet>::Type len = length(me);
+ typename Size<TStringSet>::Type i = 0;
+
+// SEQAN_ASSERT(length(me.limits) == len + 1);
+// resize(me.limits, len + 1);
+ for(; i < len; ++i) {
+ me.limits[i] = sum;
+ sum += length(me[i]);
+ }
+ me.limits[i] = sum;
+ me.limitsValid = true;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// find the i-th non-zero value of a string me
+
+ template < typename TValue, typename TSpec, typename TPos >
+ inline typename Size< String<TValue, TSpec> >::Type
+ _findIthNonZeroValue(String<TValue, TSpec> const &me, TPos i)
+ {
+ typename Iterator< String<TValue, TSpec> const, Standard >::Type it = begin(me, Standard());
+ typename Iterator< String<TValue, TSpec> const, Standard >::Type itEnd = end(me, Standard());
+
+ for(; it != itEnd; ++it)
+ if (*it) {
+ if (i) {
+ --i;
+ }
+ else {
+ return position(it, me);
+ }
+ }
+ return length(me);
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// count non-zero values before position i
+
+ template < typename TValue, typename TSpec, typename TPos >
+ inline typename Size< String<TValue, TSpec> >::Type
+ _countNonZeroValues(String<TValue, TSpec> const &me, TPos i)
+ {
+ typename Iterator< String<TValue, TSpec> const, Standard >::Type it = begin(me, Standard());
+ typename Iterator< String<TValue, TSpec> const, Standard >::Type itEnd = begin(me, Standard()) + i;
+ typename Size< String<TValue, TSpec> >::Type counter = 0;
+
+ for(; it != itEnd; ++it)
+ if (*it) ++counter;
+ return counter;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// lengthSum
+
+ template < typename TString >
+ inline typename Size<TString>::Type lengthSum(TString const &me) {
+ return length(me);
+ }
+
+ template < typename TString, typename TSpec >
+ inline typename Size<TString>::Type lengthSum(StringSet< TString, TSpec > const &me) {
+ return back(stringSetLimits(me));
+ }
+
+///.Function.appendValue.param.target.type:Class.StringSet
+//////////////////////////////////////////////////////////////////////////////
+// appendValue
+
+ // Default
+ template < typename TString, typename TString2, typename TExpand >
+ inline void appendValue(
+ StringSet< TString, Owner<Default> > &me,
+ TString2 const &obj,
+ Tag<TExpand> const)
+ {
+ appendValue(me.strings, obj);
+ appendValue(me.limits, lengthSum(me) + length(obj));
+ }
+
+ // ConcatDirect
+ template < typename TString, typename TString2, typename TExpand >
+ inline void appendValue(
+ StringSet< TString, Owner<ConcatDirect<void> > > &me,
+ TString2 const &obj,
+ Tag<TExpand> const)
+ {
+ append(me.concat, obj);
+ appendValue(me.limits, lengthSum(me) + length(obj));
+ }
+
+ template < typename TString, typename TDelimiter, typename TString2, typename TExpand >
+ inline void appendValue(
+ StringSet< TString, Owner<ConcatDirect<TDelimiter> > > &me,
+ TString2 const &obj,
+ Tag<TExpand> const)
+ {
+ append(me.concat, obj);
+ appendValue(me.concat, TDelimiter());
+ appendValue(me.limits, lengthSum(me) + length(obj) + 1);
+ }
+
+ // Generous
+ template < typename TString, typename TExpand >
+ inline void appendValue(
+ StringSet<TString, Dependent<Generous> > &me,
+ TString const &obj,
+ Tag<TExpand> const)
+ {
+ SEQAN_CHECKPOINT
+ appendValue(me.strings, const_cast<TString*>(&obj));
+ appendValue(me.limits, lengthSum(me) + length(obj));
+ }
+
+ // Tight
+ template < typename TString, typename TExpand >
+ inline void appendValue(
+ StringSet<TString, Dependent<Tight> > &me,
+ TString const &obj,
+ Tag<TExpand> const)
+ {
+ SEQAN_CHECKPOINT
+ appendValue(me.strings, const_cast<TString*>(&obj));
+ appendValue(me.ids, length(me.strings) - 1);
+ appendValue(me.limits, lengthSum(me) + length(obj));
+ }
+
+/*
+ inline void append(TString *_objs[], unsigned count) {
+ for(unsigned i = 0; i < count; ++i)
+ add(_objs[i]);
+ }
+*/
+
+///.Function.clear.param.object.type:Class.StringSet
+//////////////////////////////////////////////////////////////////////////////
+// clear
+
+ template < typename TString >
+ inline void clear(StringSet< TString, Owner<Default> > &me)
+ {
+ SEQAN_CHECKPOINT
+ clear(me.strings);
+ resize(me.limits, 1);
+ me.limitsValid = true;
+ }
+
+ template < typename TString, typename TDelimiter >
+ inline void clear(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > &me)
+ {
+ SEQAN_CHECKPOINT
+ clear(me.concat);
+ resize(me.limits, 1);
+ }
+
+ template < typename TString >
+ inline void clear(StringSet< TString, Dependent<Generous> > & me)
+ {
+ SEQAN_CHECKPOINT
+ clear(me.strings);
+ resize(me.limits, 1);
+ me.limitsValid = true;
+ }
+
+ template < typename TString >
+ inline void clear(StringSet<TString, Dependent<Tight> >& me)
+ {
+ SEQAN_CHECKPOINT
+ clear(me.strings);
+ resize(me.limits, 1);
+ me.limitsValid = true;
+
+ clear(me.ids);
+ }
+
+///.Function.length.param.object.type:Class.StringSet
+//////////////////////////////////////////////////////////////////////////////
+// length
+
+ template < typename TString, typename TSpec >
+ inline typename Size< StringSet< TString, TSpec > >::Type
+ length(StringSet< TString, TSpec > const &me) {
+ return length(me.limits) - 1;
+ }
+
+ template <typename TString>
+ inline typename Size<StringSet<TString, Dependent<Tight> > >::Type
+ length(StringSet<TString, Dependent<Tight> > const &me)
+ {
+ return length(me.strings);
+ }
+
+///.Function.resize.param.object.type:Class.StringSet
+//////////////////////////////////////////////////////////////////////////////
+// resize
+
+ template < typename TString, typename TSpec, typename TSize >
+ inline typename Size< StringSet< TString, TSpec > >::Type
+ resize(StringSet< TString, TSpec > &me, TSize new_size) {
+ resize(me.limits, new_size + 1);
+ me.limitsValid = (new_size == 0);
+ return resize(me.strings, new_size);
+ }
+
+ template < typename TString, typename TSpec, typename TSize >
+ inline typename Size< StringSet< TString, Owner<ConcatDirect<TSpec> > > >::Type
+ resize(StringSet< TString, Owner<ConcatDirect<TSpec> > > &me, TSize new_size) {
+ return resize(me.limits, new_size + 1) - 1;
+ }
+
+///.Function.value.param.object.type:Class.StringSet
+//////////////////////////////////////////////////////////////////////////////
+// value
+
+ // Default
+ template < typename TString, typename TPos >
+ inline typename Reference< StringSet< TString, Owner<Default> > >::Type
+ value(StringSet< TString, Owner<Default> > & me, TPos pos)
+ {
+ return me.strings[pos];
+ }
+
+ template < typename TString, typename TPos >
+ inline typename Reference< StringSet< TString, Owner<Default> > const >::Type
+ value(StringSet< TString, Owner<Default> > const & me, TPos pos)
+ {
+ return me.strings[pos];
+ }
+
+ // ConcatDirect
+ template < typename TString, typename TSpec, typename TPos >
+ inline typename Infix<TString>::Type
+ value(StringSet< TString, Owner<ConcatDirect<TSpec> > > & me, TPos pos)
+ {
+ return infix(me.concat, me.limits[pos], me.limits[pos + 1]);
+ }
+
+ template < typename TString, typename TSpec, typename TPos >
+ inline typename Infix<TString const>::Type
+ value(StringSet< TString, Owner<ConcatDirect<TSpec> > > const & me, TPos pos)
+ {
+ return infix(me.concat, me.limits[pos], me.limits[pos + 1]);
+ }
+
+ // Tight
+ template < typename TString, typename TPos >
+ inline typename Reference<StringSet< TString, Dependent<Tight> > >::Type
+ value(StringSet< TString, Dependent<Tight> >& me, TPos pos)
+ {
+ SEQAN_CHECKPOINT
+ if (me.strings[pos])
+ return *me.strings[pos];
+ static TString tmp = "";
+ return tmp;
+ }
+
+ template < typename TString, typename TPos >
+ inline typename Reference<StringSet< TString, Dependent<Tight> > const >::Type
+ value(StringSet< TString, Dependent<Tight> >const & me, TPos pos)
+ {
+ if (me.strings[pos])
+ return *me.strings[pos];
+ static TString tmp = "";
+ return tmp;
+ }
+
+ // Generous
+ template < typename TString, typename TPos >
+ inline typename Reference<StringSet< TString, Dependent<Generous> > >::Type
+ value(StringSet< TString, Dependent<Generous> >& me, TPos pos)
+ {
+ SEQAN_CHECKPOINT
+ unsigned i = _findIthNonZeroValue(me.strings, pos);
+ if (i < length(me.strings))
+ return *me.strings[i];
+ static TString tmp = "";
+ return tmp;
+ }
+
+ template < typename TString, typename TPos >
+ inline typename Reference< StringSet< TString, Dependent<Generous> > const >::Type
+ value(StringSet< TString, Dependent<Generous> > const & me, TPos pos)
+ {
+ SEQAN_CHECKPOINT
+ unsigned i = _findIthNonZeroValue(me.strings, pos);
+ if (i < length(me.strings))
+ return *me.strings[i];
+ static TString tmp = "";
+ return tmp;
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// getValueById
+
+/**
+.Function.getValueById:
+..cat:Sequences
+..summary:Retrieves a string from the StringSet given an id.
+..signature:getValueById(me, id)
+..param.me:A StringSet.
+...type:Class.StringSet
+..param.id:An id.
+...type:Metafunction.Id
+..returns:A reference to a string.
+..see:Function.assignValueById
+..see:Function.valueById
+*/
+
+ template <typename TString, typename TSpec, typename TId>
+ inline typename Reference<StringSet<TString, Owner<TSpec> > >::Type
+ getValueById(StringSet<TString, Owner<TSpec> >& me,
+ TId const id)
+ {
+ SEQAN_CHECKPOINT
+ if (id < (TId) length(me)) return value(me, id);
+ static TString tmp = "";
+ return tmp;
+ }
+
+ template <typename TString, typename TId>
+ inline typename Reference<StringSet<TString, Dependent<Generous> > >::Type
+ getValueById(StringSet<TString, Dependent<Generous> >& me,
+ TId const id)
+ {
+ SEQAN_CHECKPOINT
+ if (me.strings[id])
+ return *me.strings[id];
+ static TString tmp = "";
+ return tmp;
+ }
+
+ template <typename TString, typename TId>
+ inline typename Reference<StringSet<TString, Dependent<Tight> > >::Type
+ getValueById(StringSet<TString, Dependent<Tight> >&me,
+ TId const id)
+ {
+ SEQAN_CHECKPOINT
+ for(unsigned i = 0; i < length(me.strings); ++i)
+ if ((TId) me.ids[i] == id)
+ return value(me, i);
+ static TString tmp = "";
+ return tmp;
+ }
+
+
+//////////////////////////////////////////////////////////////////////////////
+// valueById
+
+/**
+.Function.valueById:
+..cat:Sequences
+..summary:Retrieves a string from the StringSet given an id.
+..signature:valueById(me, id)
+..param.me:A StringSet.
+...type:Class.StringSet
+..param.id:An id.
+...type:Metafunction.Id
+..returns:A reference to a string.
+..see:Function.assignValueById
+..see:Function.getValueById
+*/
+
+ template<typename TString, typename TSpec, typename TId>
+ inline typename Reference<StringSet<TString, TSpec> >::Type
+ valueById(StringSet<TString, TSpec>& me,
+ TId const id)
+ {
+ SEQAN_CHECKPOINT
+ return getValueById(me, id);
+ }
+
+
+//////////////////////////////////////////////////////////////////////////////
+// assignValueById
+
+/**
+.Function.assignValueById:
+..cat:Sequences
+..summary:Adds a new string to the StringSet and returns an id.
+..signature:assignValueById(dest, str, [id])
+..signature:assignValueById(dest, source, id)
+..param.dest:A StringSet.
+...type:Class.StringSet
+..param.source:A StringSet.
+...type:Class.StringSet
+..param.str:A new string.
+...type:Metafunction.Value
+..param.id:An associated id.
+...type:Metafunction.Id
+..returns:A new id
+...type:Metafunction.Id
+..see:Function.getValueById
+..see:Function.valueById
+*/
+
+ template<typename TString, typename TSpec, typename TString2>
+ inline typename Id<StringSet<TString, TSpec> >::Type
+ assignValueById(StringSet<TString, TSpec>& me,
+ TString2& obj)
+ {
+ SEQAN_CHECKPOINT
+ appendValue(me, obj);
+ SEQAN_ASSERT(length(me.limits) == length(me) + 1);
+ return length(me.strings) - 1;
+ }
+
+ template <typename TString, typename TSpec, typename TId>
+ inline typename Id<StringSet<TString, Owner<TSpec> > >::Type
+ assignValueById(StringSet<TString, Owner<TSpec> >& me,
+ TString& obj,
+ TId id)
+ {
+ SEQAN_CHECKPOINT
+ if (id >= (TId) length(me.strings)) {
+ fill(me.strings, id+1, TString());
+ resize(me.limits, length(me.limits) + 1);
+ }
+ assignValue(me, id, obj);
+ me.limitsValid = false;
+ return id;
+ }
+
+ template<typename TString, typename TId>
+ inline typename Id<StringSet<TString, Dependent<Generous> > >::Type
+ assignValueById(StringSet<TString, Dependent<Generous> >& me,
+ TString& obj,
+ TId id)
+ {
+ SEQAN_CHECKPOINT
+ SEQAN_ASSERT(length(me.limits) == length(me) + 1);
+ if (id >= (TId) length(me.strings)) fill(me.strings, id+1, (TString*) 0);
+ if ((TString*) me.strings[id] == (TString*) 0)
+ resize(me.limits, length(me.limits) + 1);
+ me.strings[id] = &obj;
+ me.limitsValid = false;
+ SEQAN_ASSERT(length(me.limits) == length(me) + 1);
+ return id;
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+
+ template<typename TString, typename TId>
+ inline typename Id<StringSet<TString, Dependent<Tight> > >::Type
+ assignValueById(StringSet<TString, Dependent<Tight> >& me,
+ TString& obj,
+ TId id)
+ {
+ SEQAN_CHECKPOINT
+ typedef StringSet<TString, Dependent<Tight> > TStringSet;
+ typedef typename Size<TStringSet>::Type TSize;
+
+ for(TSize i = 0; i < length(me.ids); ++i)
+ if ((TId) me.ids[i] == id) {
+ me.strings[i] = &obj;
+ me.limitsValid = false;
+ return id;
+ }
+ appendValue(me.strings, &obj);
+ appendValue(me.ids, id);
+ return id;
+ }
+
+ template<typename TString, typename TSpec1, typename TSpec2, typename TId>
+ inline typename Id<StringSet<TString, TSpec1> >::Type
+ assignValueById(StringSet<TString, TSpec1>& dest,
+ StringSet<TString, TSpec2>& source,
+ TId id)
+ {
+ SEQAN_CHECKPOINT
+ return assignValueById(dest, getValueById(source, id), id);
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// removeValueById
+
+/**
+.Function.removeValueById:
+..cat:Sequences
+..summary:Removes a string from the StringSet given an id.
+..signature:removeValueById(me, id)
+..param.me:A StringSet.
+...type:Class.StringSet
+..param.id:An id.
+...type:Metafunction.Id
+..returns:void
+..see:Function.assignValueById
+*/
+
+ template<typename TString, typename TSpec, typename TId>
+ inline void
+ removeValueById(StringSet<TString, Owner<TSpec> >& me, TId const id)
+ {
+ SEQAN_CHECKPOINT
+ erase(me.strings, id);
+ resize(me.limits, length(me.limits) - 1);
+ me.limitsValid = empty(me);
+ }
+
+ template<typename TString, typename TId>
+ inline void
+ removeValueById(StringSet<TString, Dependent<Generous> >& me, TId const id)
+ {
+ SEQAN_CHECKPOINT
+ if (me.strings[id] != (TString*) 0) {
+ resize(me.limits, length(me.limits) - 1);
+ me.limitsValid = empty(me);
+ }
+ me.strings[id] = 0;
+ while (!empty(me.strings) && !me.strings[length(me.strings) - 1])
+ resize(me.strings, length(me.strings) - 1);
+ }
+
+ template<typename TString, typename TId>
+ inline void
+ removeValueById(StringSet<TString, Dependent<Tight> >& me, TId const id)
+ {
+ SEQAN_CHECKPOINT
+ typedef StringSet<TString, Dependent<Tight> > TStringSet;
+ typedef typename Size<TStringSet>::Type TSize;
+
+ SEQAN_ASSERT(length(me.limits) == length(me) + 1);
+ for(TSize i = 0; i < length(me.strings); ++i)
+ if (me.ids[i] == id) {
+ erase(me.strings, i);
+ erase(me.ids, i);
+ resize(me.limits, length(me.limits) - 1);
+ me.limitsValid = empty(me);
+ }
+ SEQAN_ASSERT(length(me.limits) == length(me) + 1);
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+//
+
+/**
+.Function.positionToId:
+..cat:Sequences
+..summary:Retrieves the id of a string in the StringSet given a position.
+..signature:positionToId(string_set, pos)
+..param.string_set:A StringSet.
+...type:Class.StringSet
+..param.pos:A position that is transfored into an id.
+..returns:An id that corresponds to $pos$ within $string_set$
+..see:Function.assignValueById
+..see:Function.valueById
+*/
+
+ template <typename TString, typename TSpec, typename TPos>
+ inline typename Id<StringSet<TString, Owner<TSpec> > >::Type
+ positionToId(StringSet<TString, Owner<TSpec> >&,
+ TPos const pos)
+ {
+ SEQAN_CHECKPOINT
+ return pos;
+ }
+
+ template <typename TString, typename TPos>
+ inline typename Id<StringSet<TString, Dependent<Generous> > >::Type
+ positionToId(StringSet<TString, Dependent<Generous> >& me,
+ TPos const pos)
+ {
+ SEQAN_CHECKPOINT
+ return _findIthNonZeroValue(me.strings,pos);
+ }
+
+ template <typename TString, typename TPos>
+ inline typename Id<StringSet<TString, Dependent<Generous> > >::Type
+ positionToId(StringSet<TString, Dependent<Generous> > const& me,
+ TPos const pos)
+ {
+ SEQAN_CHECKPOINT
+ return _findIthNonZeroValue(me.strings,pos);
+ }
+
+ template <typename TString, typename TPos>
+ inline typename Id<StringSet<TString, Dependent<Tight> > >::Type
+ positionToId(StringSet<TString, Dependent<Tight> >&me,
+ TPos const pos)
+ {
+ SEQAN_CHECKPOINT
+ return me.ids[pos];
+ }
+
+ template <typename TString, typename TPos>
+ inline typename Id<StringSet<TString, Dependent<Tight> > >::Type
+ positionToId(StringSet<TString, Dependent<Tight> > const&me,
+ TPos const pos)
+ {
+ SEQAN_CHECKPOINT
+ return me.ids[pos];
+ }
+
+
+/**
+.Function.idToPosition:
+..cat:Sequences
+..summary:Retrieves the position of a string in the StringSet given an id.
+..signature:idToPosition(me, id)
+..param.me:A StringSet.
+...type:Class.StringSet
+..param.id:An id.
+...type:Metafunction.Id
+..returns:A reference to a string.
+..see:Function.assignValueById
+..see:Function.valueById
+*/
+
+ template <typename TString, typename TSpec, typename TId>
+ inline typename Id<StringSet<TString, Owner<TSpec> > >::Type
+ idToPosition(StringSet<TString, Owner<TSpec> >&,
+ TId const id)
+ {
+ SEQAN_CHECKPOINT
+ return id;
+ }
+
+ template <typename TString, typename TId>
+ inline typename Id<StringSet<TString, Dependent<Generous> > >::Type
+ idToPosition(StringSet<TString, Dependent<Generous> >& me,
+ TId const id)
+ {
+ SEQAN_CHECKPOINT
+ return _countNonZeroValues(me.strings,id);
+ }
+
+ template <typename TString, typename TId>
+ inline typename Id<StringSet<TString, Dependent<Tight> > >::Type
+ idToPosition(StringSet<TString, Dependent<Tight> >&me,
+ TId const id)
+ {
+ SEQAN_CHECKPOINT
+ for(unsigned i = 0; i < length(me.ids); ++i)
+ if ((TId) me.ids[i] == id)
+ return i;
+ return 0;
+ }
+
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// subset
+
+/**
+.Function.subset:
+..cat:Sequences
+..summary:Creates a subset of a given StringSet.
+..signature:subset(source, dest, id_array [, len])
+..param.source:In-parameter:The source StringSet.
+...type:Class.StringSet
+..param.dest:Out-parameter:The destination StringSet (the subset).
+...type:Class.StringSet
+..param.id_array:In-parameter:An array of ids. Each id corresponds to a sequence that is supposed to be in the subset.
+..param.len:In-parameter:Optional length of the id array.
+...remarks:If len is not defined the length function must be valid for this array or string type.
+..returns:void
+*/
+
+ template <typename TString, typename TSpec, typename TDestSpec, typename TIds, typename TLength>
+ inline void
+ subset(StringSet<TString, Owner<TSpec> >& source,
+ StringSet<TString, TDestSpec>& dest,
+ TIds ids,
+ TLength len)
+ {
+ SEQAN_CHECKPOINT
+ }
+
+ template <typename TString, typename TIds, typename TLength>
+ inline void
+ subset(StringSet<TString, Dependent<Generous> >& source,
+ StringSet<TString, Dependent<Generous> >& dest,
+ TIds ids,
+ TLength len)
+ {
+ SEQAN_CHECKPOINT
+ typedef StringSet<TString, Dependent<Generous> > TStringSet;
+ typedef typename Id<TStringSet>::Type TId;
+ typedef typename Size<TStringSet>::Type TSize;
+
+ clear(dest);
+ resize(dest.limits, len + 1);
+ dest.limitsValid = (len == 0);
+ fill(dest.strings, length(source.strings), (TString*) 0);
+ for(TSize i = 0; i < len; ++i)
+ dest.strings[ids[i]] = source.strings[ids[i]];
+ }
+
+ template <typename TString, typename TIds, typename TLength>
+ inline void
+ subset(StringSet<TString, Dependent<Tight> >& source,
+ StringSet<TString, Dependent<Tight> >& dest,
+ TIds ids,
+ TLength len)
+ {
+ SEQAN_CHECKPOINT
+ typedef StringSet<TString, Dependent<Tight> > TStringSet;
+ typedef typename Id<TStringSet>::Type TId;
+ typedef typename Size<TStringSet>::Type TSize;
+
+ clear(dest);
+ resize(dest.limits, len + 1);
+ dest.limitsValid = (len == 0);
+ TLength upperBound = length(source.ids);
+ for(TSize i=0;i<len;++i) {
+ TId id = ids[i];
+ if ((upperBound > id) &&
+ (source.ids[id] == id)) {
+ appendValue(dest.strings, source.strings[id]);
+ appendValue(dest.ids, id);
+ } else {
+ typedef String<TId> TIdString;
+ typedef typename Iterator<TIdString, Rooted>::Type TIter;
+ TIter it = begin(source.ids);
+ for(;!atEnd(it);goNext(it)) {
+ if (*it == id) {
+ appendValue(dest.strings, source.strings[position(it)]);
+ appendValue(dest.ids, id);
+ }
+ }
+ }
+ }
+ }
+
+ template <typename TString, typename TSpec, typename TIds>
+ inline void
+ subset(StringSet<TString, TSpec>& source,
+ StringSet<TString, TSpec>& dest,
+ TIds ids)
+ {
+ SEQAN_CHECKPOINT
+ subset(source, dest, ids, length(ids));
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // ConcatenatorNto1 - a StringSet to String converter
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TStringSet>
+ struct ConcatenatorNto1 {
+ TStringSet *set;
+ ConcatenatorNto1 () {}
+ ConcatenatorNto1 (TStringSet &_set): set(&_set) {}
+
+//____________________________________________________________________________
+// WARNING:
+// operator[] conducts a binary search and should be avoided
+// you better use StringSet<.., Owner<ConcatDirect<..> > > for random access
+// or ConcatenatorNto1's iterators for sequential access
+
+ template <typename TPos>
+ inline typename Reference<ConcatenatorNto1>::Type
+ operator [] (TPos pos)
+ {
+ SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+
+ template <typename TPos>
+ inline typename Reference<ConcatenatorNto1 const>::Type
+ operator [] (TPos pos) const
+ {
+ SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+ };
+//____________________________________________________________________________
+
+ template <typename TStringSet>
+ struct Value< ConcatenatorNto1<TStringSet> > {
+ typedef typename Value< typename Value<TStringSet>::Type >::Type Type;
+ };
+
+ template <typename TStringSet>
+ struct Value< ConcatenatorNto1<TStringSet> const >:
+ Value< ConcatenatorNto1<TStringSet> > {};
+//____________________________________________________________________________
+
+ template <typename TStringSet>
+ struct Size< ConcatenatorNto1<TStringSet> > {
+ typedef typename Size< typename Value<TStringSet>::Type >::Type Type;
+ };
+//____________________________________________________________________________
+
+ template <typename TStringSet>
+ struct AllowsFastRandomAccess< ConcatenatorNto1<TStringSet> >
+ {
+ typedef False Type;
+ enum { VALUE = false };
+ };
+
+//////////////////////////////////////////////////////////////////////////////
+// value
+
+ template < typename TStringSet, typename TPos >
+ inline typename Reference< ConcatenatorNto1<TStringSet> >::Type
+ value(ConcatenatorNto1<TStringSet> &me, TPos globalPos)
+ {
+ Pair<unsigned, typename Size< typename Value<TStringSet>::Type >::Type> localPos;
+ posLocalize(localPos, globalPos, stringSetLimits(*me.set));
+ return value(value(*me.set, getValueI1(localPos)), getValueI2(localPos));
+ }
+
+ template < typename TStringSet, typename TPos >
+ inline typename Reference< ConcatenatorNto1<TStringSet> const >::Type
+ value(ConcatenatorNto1<TStringSet> const &me, TPos globalPos)
+ {
+ typedef typename Value<TStringSet>::Type TString;
+ Pair<unsigned, typename Size<TString>::Type> localPos;
+ posLocalize(localPos, globalPos, stringSetLimits(*me.set));
+ return value(value(*(TStringSet const*)me.set, getValueI1(localPos)), getValueI2(localPos));
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// length
+
+ template < typename TStringSet >
+ inline typename Size< ConcatenatorNto1<TStringSet> >::Type
+ length(ConcatenatorNto1<TStringSet> const &me) {
+ return lengthSum(*me.set);
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// begin
+
+ template < typename TStringSet, typename TSpec >
+ inline typename Iterator< ConcatenatorNto1<TStringSet const>, Tag<TSpec> const >::Type
+ begin(ConcatenatorNto1<TStringSet const> concat, Tag<TSpec> const)
+ {
+ return typename Iterator< ConcatenatorNto1<TStringSet const>, Tag<TSpec> const >::Type (*concat.set);
+ }
+
+ template < typename TStringSet, typename TSpec >
+ inline typename Iterator< ConcatenatorNto1<TStringSet>, Tag<TSpec> const >::Type
+ begin(ConcatenatorNto1<TStringSet> concat, Tag<TSpec> const)
+ {
+ return typename Iterator< ConcatenatorNto1<TStringSet>, Tag<TSpec> const >::Type (*concat.set);
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// end
+
+ template < typename TStringSet, typename TSpec >
+ inline typename Iterator< ConcatenatorNto1<TStringSet const>, Tag<TSpec> const >::Type
+ end(ConcatenatorNto1<TStringSet const> concat, Tag<TSpec> const)
+ {
+ return typename Iterator< ConcatenatorNto1<TStringSet>, Tag<TSpec> const >::Type
+ (*concat.set, length(*concat.set), 0);
+ }
+
+ template < typename TStringSet, typename TSpec >
+ inline typename Iterator< ConcatenatorNto1<TStringSet>, Tag<TSpec> const >::Type
+ end(ConcatenatorNto1<TStringSet> concat, Tag<TSpec> const)
+ {
+ return typename Iterator< ConcatenatorNto1<TStringSet>, Tag<TSpec> const >::Type
+ (*concat.set, length(*concat.set), 0);
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+// Concatenator metafunction
+
+ template < typename TString, typename TSpec >
+ struct Concatenator< StringSet<TString, TSpec> > {
+ typedef ConcatenatorNto1< StringSet<TString, TSpec> > Type;
+ };
+
+ template < typename TString, typename TSpec >
+ struct Concatenator< StringSet<TString, Owner<ConcatDirect<TSpec> > > > {
+ typedef TString Type;
+ };
+
+//////////////////////////////////////////////////////////////////////////////
+// concat
+
+ template <typename TString>
+ inline typename Concatenator<TString>::Type &
+ concat(TString &string) {
+ return string;
+ }
+
+ template <typename TString, typename TSpec>
+ inline typename Concatenator< StringSet<TString, TSpec> >::Type &
+ concat(StringSet<TString, TSpec> &set) {
+ return set.concat;
+ }
+
+ template <typename TString, typename TSpec>
+ inline typename Concatenator< StringSet<TString, TSpec> const>::Type &
+ concat(StringSet<TString, TSpec> const &set) {
+ return set.concat;
+ }
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // This iterator sequentially iterates through the elements of TStringSet
+ // as if they were directly concatenated (compare StringSet<.., Owner<ConcatDirect<> > >
+ //////////////////////////////////////////////////////////////////////////////
+
+ template < typename TDelimiter = void >
+ struct ConcatVirtual;
+
+ template < typename TStringSet, typename TSpec >
+ class Iter< TStringSet, ConcatVirtual<TSpec> >
+ {
+ public:
+ typedef typename Value<TStringSet>::Type TString;
+ typedef typename Value<TString>::Type TValue;
+ typedef typename Size<TString>::Type TSize;
+//____________________________________________________________________________
+
+ public:
+ typedef typename Iterator<TString, Standard>::Type obj_iterator;
+ typedef typename Iterator<TString const, Standard>::Type const_obj_iterator;
+
+ //////////////////////////////////////////////////////////////////////////////
+ // STL compatible public iterator interface
+
+ typedef Iter iterator;
+ typedef ::std::bidirectional_iterator_tag iterator_category;
+ typedef TValue value_type;
+ typedef TValue & reference;
+ typedef TValue const & const_reference;
+ typedef TValue* pointer;
+ typedef TSize size_type;
+ typedef typename Difference<TString>::Type difference_type;
+//____________________________________________________________________________
+
+ TStringSet *host;
+ unsigned objNo;
+ obj_iterator _begin, _cur, _end;
+//____________________________________________________________________________
+
+ inline Iter() {}
+
+ inline Iter(TStringSet &_host):
+ host(&_host)
+ {
+ objNo = 0;
+ _begin = _cur = begin(_host[objNo]);
+ _end = end(_host[objNo]);
+ _testEnd();
+ }
+
+ inline Iter(TStringSet &_host, unsigned _objNo, difference_type _offset):
+ host(&_host)
+ {
+ if (_objNo < length(_host)) {
+ objNo = _objNo;
+ _begin = _cur = begin(_host[objNo]);
+ _end = end(_host[objNo]);
+ goFurther(_cur, _offset);
+ _testEnd();
+ } else {
+ objNo = length(_host) - 1;
+ _begin = _cur = _end = end(_host[objNo]);
+ }
+ }
+
+ inline operator obj_iterator() {
+ return _cur;
+ }
+//____________________________________________________________________________
+
+ inline bool _atEndOfSequence() {
+ if (_cur == _begin && objNo > 0) return true;
+ if (_cur == _end) return true;
+ return false;
+ }
+
+ inline void _testBegin() {
+ while (_cur == _begin && objNo > 0) {
+ --objNo;
+ _begin = host->_begin(objNo);
+ _end = _cur = host->_end(objNo);
+ }
+ }
+
+ inline void _testEnd() {
+ while (_cur == _end && objNo < (length(*host) - 1)) {
+ ++objNo;
+ _begin = _cur = begin((*host)[objNo]);
+ _end = end((*host)[objNo]);
+ };
+ }
+
+ inline TSize _tell() const {
+ typedef Pair<unsigned, TSize> TPair;
+ return posGlobalize(TPair(objNo, difference(_begin, _cur)), stringSetLimits(*host));
+ }
+ };
+
+ //////////////////////////////////////////////////////////////////////////////
+ // ConcatenatorNto1 meta functions
+ //////////////////////////////////////////////////////////////////////////////
+//____________________________________________________________________________
+// default concatenator iterators
+
+ template <typename TString, typename TSpec >
+ struct Iterator< ConcatenatorNto1< StringSet<TString, TSpec> >, Standard > {
+ typedef Iter<StringSet<TString, TSpec>, ConcatVirtual<> > Type;
+ };
+
+ template <typename TString, typename TSpec >
+ struct Iterator< ConcatenatorNto1< StringSet<TString, TSpec> const >, Standard > {
+ typedef Iter<StringSet<TString, TSpec> const, ConcatVirtual<> > Type;
+ };
+
+ template <typename TString, typename TSpec >
+ struct Iterator< ConcatenatorNto1< StringSet<TString, TSpec> >, Rooted > {
+ typedef Iter<StringSet<TString, TSpec>, ConcatVirtual<> > Type;
+ };
+
+ template <typename TString, typename TSpec >
+ struct Iterator< ConcatenatorNto1< StringSet<TString, TSpec> const >, Rooted > {
+ typedef Iter<StringSet<TString, TSpec> const, ConcatVirtual<> > Type;
+ };
+//____________________________________________________________________________
+
+ template <typename TStringSet >
+ struct Iterator< ConcatenatorNto1<TStringSet> const, Standard > {
+ typedef typename Iterator< ConcatenatorNto1<TStringSet>, Standard >::Type Type;
+ };
+
+ template <typename TStringSet >
+ struct Iterator< ConcatenatorNto1<TStringSet> const, Rooted > {
+ typedef typename Iterator< ConcatenatorNto1<TStringSet>, Rooted >::Type Type;
+ };
+
+ //////////////////////////////////////////////////////////////////////////////
+ // meta functions
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TStringSet, typename TSpec>
+ struct Value< Iter< TStringSet, ConcatVirtual<TSpec> > >:
+ Value< typename Value<TStringSet>::Type > {};
+
+ template <typename TStringSet, typename TSpec>
+ struct Value< Iter< TStringSet, ConcatVirtual<TSpec> > const >:
+ Value< typename Value<TStringSet>::Type > {};
+
+ template <typename TStringSet, typename TSpec>
+ struct GetValue< Iter< TStringSet, ConcatVirtual<TSpec> > >:
+ GetValue< typename Value<TStringSet>::Type > {};
+
+ template <typename TStringSet, typename TSpec>
+ struct GetValue< Iter< TStringSet, ConcatVirtual<TSpec> > const >:
+ GetValue< typename Value<TStringSet>::Type > {};
+
+ template <typename TStringSet, typename TSpec>
+ struct Size< Iter< TStringSet, ConcatVirtual<TSpec> > >:
+ Size< typename Value<TStringSet>::Type > {};
+
+ template <typename TStringSet, typename TSpec>
+ struct Reference< Iter< TStringSet, ConcatVirtual<TSpec> > >:
+ Reference< typename Value<TStringSet>::Type > {};
+
+ template <typename TStringSet, typename TSpec>
+ struct Reference< Iter< TStringSet, ConcatVirtual<TSpec> > const >:
+ Reference< typename Value<TStringSet>::Type > {};
+
+
+ //////////////////////////////////////////////////////////////////////////////
+ // operator *
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TStringSet, typename TSpec>
+ inline typename Reference< Iter< TStringSet, ConcatVirtual<TSpec> > const>::Type
+ value(Iter<TStringSet, ConcatVirtual<TSpec> > const & me) {
+ return *me._cur;
+ }
+
+ template <typename TStringSet, typename TSpec>
+ inline typename Reference< Iter< TStringSet, ConcatVirtual<TSpec> > >::Type
+ value(Iter<TStringSet, ConcatVirtual<TSpec> > & me) {
+ return *me._cur;
+ }
+
+ template <typename TStringSet, typename TSpec>
+ inline typename Reference< Iter< TStringSet, ConcatVirtual<TSpec> > const>::Type
+ operator * (Iter<TStringSet, ConcatVirtual<TSpec> > const & me) {
+ return *me._cur;
+ }
+
+ template <typename TStringSet, typename TSpec>
+ inline typename Reference< Iter< TStringSet, ConcatVirtual<TSpec> > >::Type
+ operator * (Iter<TStringSet, ConcatVirtual<TSpec> > & me) {
+ return *me._cur;
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // operator ++
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TStringSet, typename TSpec>
+ inline void
+ goNext(Iter<TStringSet, ConcatVirtual<TSpec> > & me) {
+ ++me._cur;
+ me._testEnd();
+ }
+
+ template <typename TStringSet, typename TSpec>
+ inline Iter<TStringSet, ConcatVirtual<TSpec> > const &
+ operator ++ (Iter<TStringSet, ConcatVirtual<TSpec> > & me) {
+ goNext(me);
+ return me;
+ }
+
+ template <typename TStringSet, typename TSpec>
+ inline Iter<TStringSet, ConcatVirtual<TSpec> > const &
+ operator ++ (Iter<TStringSet, ConcatVirtual<TSpec> > & me, int) {
+ Iter<TStringSet, ConcatVirtual<TSpec> > before = me;
+ goNext(me);
+ return before;
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // operator --
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TStringSet, typename TSpec>
+ inline void
+ goPrevious(Iter<TStringSet, ConcatVirtual<TSpec> > & me) {
+ me._testBegin();
+ --me._cur;
+ }
+
+ template <typename TStringSet, typename TSpec>
+ inline Iter<TStringSet, ConcatVirtual<TSpec> > const &
+ operator -- (Iter<TStringSet, ConcatVirtual<TSpec> > & me) {
+ goPrevious(me);
+ return me;
+ }
+
+ template <typename TStringSet, typename TSpec>
+ inline Iter<TStringSet, ConcatVirtual<TSpec> > const &
+ operator -- (Iter<TStringSet, ConcatVirtual<TSpec> > & me, int) {
+ Iter<TStringSet, ConcatVirtual<TSpec> > before = me;
+ goPrevious(me);
+ return before;
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // operator +
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TStringSet, typename TSpec, typename TDelta>
+ inline Iter<TStringSet, ConcatVirtual<TSpec> >
+ operator + (Iter<TStringSet, ConcatVirtual<TSpec> > const & me, TDelta delta) {
+ Pair<unsigned, typename Size< typename Value<TStringSet>::Type >::Type> pos;
+ posLocalize(pos, me._tell() + delta, stringSetLimits(*me.host));
+ return Iter<TStringSet, ConcatVirtual<TSpec> > (*me.host, getValueI1(pos), getValueI2(pos));
+ }
+
+ template <typename TStringSet, typename TSpec, typename T1, typename T2, typename TCompression>
+ inline Iter<TStringSet, ConcatVirtual<TSpec> >
+ operator + (Iter<TStringSet, ConcatVirtual<TSpec> > const & me, Pair<T1, T2, TCompression> delta) {
+ Pair<unsigned, typename Size< typename Value<TStringSet>::Type >::Type> pos;
+ posLocalize(pos, me._tell() + delta, stringSetLimits(*me.host));
+ return Iter<TStringSet, ConcatVirtual<TSpec> > (*me.host, getValueI1(pos), getValueI2(pos));
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // operator -
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TSSetL, typename TSpecL, typename TSSetR, typename TSpecR>
+ typename Difference<Iter<TSSetL, ConcatVirtual<TSpecL> > >::Type
+ operator - (
+ Iter<TSSetL, ConcatVirtual<TSpecL> > const &L,
+ Iter<TSSetR, ConcatVirtual<TSpecR> > const &R)
+ {
+ return L._tell() - R._tell();
+ }
+
+ template <typename TStringSet, typename TSpec, typename TDelta>
+ inline Iter<TStringSet, ConcatVirtual<TSpec> >
+ operator - (Iter<TStringSet, ConcatVirtual<TSpec> > const & me, TDelta delta) {
+ Pair<unsigned, typename Size< typename Value<TStringSet>::Type >::Type> pos;
+ posLocalize(pos, me._tell() - delta, stringSetLimits(*me.host));
+ return Iter<TStringSet, ConcatVirtual<TSpec> > (*me.host, getValueI1(pos), getValueI2(pos));
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // operator ==
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TSSetL, typename TSpecL, typename TSSetR, typename TSpecR>
+ inline bool
+ operator == (
+ Iter<TSSetL, ConcatVirtual<TSpecL> > const &L,
+ Iter<TSSetR, ConcatVirtual<TSpecR> > const &R)
+ {
+ SEQAN_ASSERT(L.host == R.host);
+ return L.objNo == R.objNo && L._cur == R._cur;
+ }
+
+ template <typename TSSetL, typename TSpecL, typename TSSetR, typename TSpecR>
+ inline bool
+ operator != (
+ Iter<TSSetL, ConcatVirtual<TSpecL> > const &L,
+ Iter<TSSetR, ConcatVirtual<TSpecR> > const &R)
+ {
+ SEQAN_ASSERT(L.host == R.host);
+ return L.objNo != R.objNo || L._cur != R._cur;
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // operator <
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TSSetL, typename TSpecL, typename TSSetR, typename TSpecR>
+ inline bool
+ operator < (
+ Iter<TSSetL, ConcatVirtual<TSpecL> > const &L,
+ Iter<TSSetR, ConcatVirtual<TSpecR> > const &R)
+ {
+ SEQAN_ASSERT(L.host == R.host);
+ return L.objNo < R.objNo || (L.objNo == R.objNo && L._cur < R._cur);
+ }
+
+ template <typename TSSetL, typename TSpecL, typename TSSetR, typename TSpecR>
+ inline bool
+ operator > (
+ Iter<TSSetL, ConcatVirtual<TSpecL> > const &L,
+ Iter<TSSetR, ConcatVirtual<TSpecR> > const &R)
+ {
+ SEQAN_ASSERT(L.host == R.host);
+ return L.objNo > R.objNo || (L.objNo == R.objNo && L._cur > R._cur);
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // container
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TSSet, typename TSpec>
+ inline typename Concatenator<TSSet>::Type
+ container(Iter<TSSet, ConcatVirtual<TSpec> > &me)
+ {
+ return concat(*me.host);
+ }
+
+ template <typename TSSet, typename TSpec>
+ inline typename Concatenator<TSSet>::Type
+ container(Iter<TSSet, ConcatVirtual<TSpec> > const &me)
+ {
+ return concat(*me.host);
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // atBegin
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TSSet, typename TSpec>
+ inline bool
+ atBegin(Iter<TSSet, ConcatVirtual<TSpec> > &me)
+ {
+ return me._cur == me._begin && me.objNo == 0;
+ }
+
+ template <typename TSSet, typename TSpec>
+ inline bool
+ atBegin(Iter<TSSet, ConcatVirtual<TSpec> > const &me)
+ {
+ return me._cur == me._begin && me.objNo == 0;
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // atEnd
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TSSet, typename TSpec>
+ inline bool
+ atEnd(Iter<TSSet, ConcatVirtual<TSpec> > &me)
+ {
+ return me._cur == me._end && me.objNo == (length(*me.host) - 1);
+ }
+
+ template <typename TSSet, typename TSpec>
+ inline bool
+ atEnd(Iter<TSSet, ConcatVirtual<TSpec> > const &me)
+ {
+ return me._cur == me._end && me.objNo == (length(*me.host) - 1);
+ }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // atEndOfSequence
+ //////////////////////////////////////////////////////////////////////////////
+
+ template <typename TIterator>
+ inline bool
+ atEndOfSequence(TIterator const &me)
+ {
+ return atEnd(me);
+ }
+
+ template <typename TSSet, typename TSpec>
+ inline bool
+ atEndOfSequence(Iter<TSSet, ConcatVirtual<TSpec> > const &me)
+ {
+ return me._atEndOfSequence();
+ }
+
+ template <typename TIterator>
+ inline bool
+ atEndOfSequence(TIterator &me)
+ {
+ return atEndOfSequence(reinterpret_cast<TIterator const &>(me));
+ }
+
+}
+
+#endif
diff --git a/src/libSSA/seqan/sequence/sequence_shortcuts.h b/src/libSSA/seqan/sequence/sequence_shortcuts.h
new file mode 100644
index 0000000..3e1f3ec
--- /dev/null
+++ b/src/libSSA/seqan/sequence/sequence_shortcuts.h
@@ -0,0 +1,197 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: sequence_shortcuts.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SEQUENCE_SHORTCUTS_H
+#define SEQAN_HEADER_SEQUENCE_SHORTCUTS_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Shortcut.CharString:
+..cat:Strings
+..summary:A string of $char$.
+..signature:CharString
+..shortcutfor:Spec.Alloc String
+...signature:String<char, Alloc<> >
+*/
+
+typedef String<char, Alloc<void> > CharString;
+
+//____________________________________________________________________________
+
+/**
+.Shortcut.CharIterator:
+..cat:Iterators
+..summary:Iterator for @Shortcut.CharString at .
+..signature:CharIterator
+..shortcutfor:Concept.Rooted Iterator
+...signature:Iterator<CharString, Rooted>::Type
+..see:Shortcut.CharString
+*/
+
+typedef Iterator<CharString, Rooted>::Type CharIterator;
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Shortcut.UnicodeString:
+..cat:Strings
+..summary:A string of $wchar_t$.
+..signature:UnicodeString
+..shortcutfor:Spec.Alloc String
+...signature:String<wchar_t, Alloc<> >
+*/
+
+typedef String<wchar_t, Alloc<void> > UnicodeString;
+
+//____________________________________________________________________________
+
+/**
+.Shortcut.UnicodeIterator:
+..cat:Iterators
+..summary:Iterator for @Shortcut.UnicodeString at .
+..signature:UnicodeIterator
+..shortcutfor:Concept.Rooted Iterator
+...signature:Iterator<UnicodeString, Rooted>::Type
+..see:Shortcut.UnicodeString
+*/
+
+typedef Iterator<UnicodeString, Rooted>::Type UnicodeIterator;
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Shortcut.DnaString:
+..cat:Strings
+..summary:A string of @Spec.Dna at .
+..signature:DnaString
+..shortcutfor:Spec.Alloc String
+...signature:String<Dna, Alloc<> >
+..see:Spec.Dna
+*/
+
+typedef String<Dna, Alloc<void> > DnaString;
+
+//____________________________________________________________________________
+
+/**
+.Shortcut.DnaIterator:
+..cat:Iterators
+..summary:Iterator for @Shortcut.DnaString at .
+..signature:DnaIterator
+..shortcutfor:Concept.Rooted Iterator
+...signature:Iterator<DnaString, Rooted>::Type
+..see:Spec.Dna
+..see:Shortcut.DnaString
+*/
+
+typedef Iterator<DnaString, Rooted>::Type DnaIterator;
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Shortcut.Dna5String:
+..cat:Strings
+..summary:A string of @Spec.Dna5 at .
+..signature:Dna5String
+..shortcutfor:Spec.Alloc String
+...signature:String<Dna5, Alloc<> >
+..see:Spec.Dna5
+..see:Shortcut.DnaString
+*/
+
+typedef String<Dna5, Alloc<void> > Dna5String;
+
+//____________________________________________________________________________
+
+/**
+.Shortcut.Dna5Iterator:
+..cat:Iterators
+..summary:Iterator for @Shortcut.Dna5String at .
+..signature:Dna5Iterator
+..shortcutfor:Concept.Rooted Iterator
+...signature:Iterator<Dna5String, Rooted>::Type
+..see:Spec.Dna5
+..see:Shortcut.Dna5String
+..see:Shortcut.DnaIterator
+*/
+
+typedef Iterator<Dna5String, Rooted>::Type Dna5Iterator;
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Shortcut.IupacString:
+..cat:Strings
+..summary:A string of @Spec.Iupac at .
+..signature:IupacString
+..shortcutfor:Spec.Alloc String
+...signature:String<Iupac, Alloc<> >
+..see:Spec.Iupac
+*/
+
+typedef String<Iupac, Alloc<void> > IupacString;
+
+//____________________________________________________________________________
+
+/**
+.Shortcut.IupacIterator:
+..cat:Iterators
+..summary:Iterator for @Shortcut.IupacString at .
+..signature:IupacIterator
+..shortcutfor:Concept.Rooted Iterator
+...signature:Iterator<IupacString, Rooted>::Type
+..see:Spec.Iupac
+..see:Shortcut.IupacString
+*/
+
+typedef Iterator<IupacString, Rooted>::Type IupacIterator;
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Shortcut.Peptide:
+..cat:Strings
+..summary:A string of @Spec.AminoAcid at .
+..signature:IupacString
+..shortcutfor:Spec.Alloc String
+...signature:String<AminoAcid, Alloc<> >
+..see:Spec.AminoAcid
+*/
+
+typedef String<AminoAcid, Alloc<void> > Peptide;
+
+//____________________________________________________________________________
+
+/**
+.Shortcut.PeptideIterator:
+..cat:Iterators
+..summary:Iterator for @Shortcut.Peptide at .
+..signature:PeptideIterator
+..shortcutfor:Concept.Rooted Iterator
+...signature:Iterator<Peptide, Rooted>::Type
+..see:Spec.AminoAcid
+..see:Shortcut.Peptide
+*/
+
+typedef Iterator<Peptide, Rooted>::Type PeptideIterator;
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/sequence/std_string.h b/src/libSSA/seqan/sequence/std_string.h
new file mode 100644
index 0000000..239974c
--- /dev/null
+++ b/src/libSSA/seqan/sequence/std_string.h
@@ -0,0 +1,691 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: std_string.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_STD_STRING_H
+#define SEQAN_HEADER_STD_STRING_H
+
+
+//Adaption for ::std::basic_string
+
+#include <string>
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Adaption."std::basic_string":
+..summary:Standard library string class.
+*/
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.IsContiguous.param.T.type:Adaption.std::basic_string
+
+template <typename TChar, typename TCharTraits, typename TAlloc>
+struct IsContiguous< ::std::basic_string<TChar, TCharTraits, TAlloc> >
+{
+ enum { VALUE = true };
+};
+
+template <typename TChar, typename TCharTraits, typename TAlloc>
+struct IsContiguous< ::std::basic_string<TChar, TCharTraits, TAlloc> const>
+{
+ enum { VALUE = true };
+};
+
+///.Metafunction.Value.param.T.type:Adaption.std::basic_string
+template <typename TChar, typename TCharTraits, typename TAlloc>
+struct Value< ::std::basic_string<TChar, TCharTraits, TAlloc> >
+{
+ typedef typename ::std::basic_string<TChar, TCharTraits, TAlloc>::value_type Type;
+};
+template <typename TChar, typename TCharTraits, typename TAlloc>
+struct Value< ::std::basic_string<TChar, TCharTraits, TAlloc> const>
+{
+ typedef typename ::std::basic_string<TChar, TCharTraits, TAlloc>::value_type Type;
+};
+
+///.Metafunction.GetValue.param.T.type:Adaption.std::basic_string
+template <typename TChar, typename TCharTraits, typename TAlloc>
+struct GetValue< ::std::basic_string<TChar, TCharTraits, TAlloc> >
+{
+ typedef typename ::std::basic_string<TChar, TCharTraits, TAlloc>::reference Type;
+};
+template <typename TChar, typename TCharTraits, typename TAlloc>
+struct GetValue< ::std::basic_string<TChar, TCharTraits, TAlloc> const>
+{
+ typedef typename ::std::basic_string<TChar, TCharTraits, TAlloc>::const_reference Type;
+};
+
+//???GetValue<vector<bool> > ist bool
+
+//____________________________________________________________________________
+
+///.Metafunction.Iterator.param.T.type:Adaption.std::basic_string
+
+template <typename TChar, typename TCharTraits, typename TAlloc>
+struct Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc>, Rooted>
+{
+ typedef ::std::basic_string<TChar, TCharTraits, TAlloc> TString;
+ typedef Iter<TString, StdIteratorAdaptor> TIterator;
+ typedef Iter<TString, AdaptorIterator<TIterator> > Type;
+};
+template <typename TChar, typename TCharTraits, typename TAlloc>
+struct Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc> const, Rooted>
+{
+ typedef ::std::basic_string<TChar, TCharTraits, TAlloc> const TString;
+ typedef Iter<TString, StdIteratorAdaptor> TIterator;
+ typedef Iter<TString, AdaptorIterator<TIterator> > Type;
+};
+
+
+template <typename TChar, typename TCharTraits, typename TAlloc>
+struct Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc>, Standard >
+{
+ typedef Iter< ::std::basic_string<TChar, TCharTraits, TAlloc>, StdIteratorAdaptor > Type;
+};
+template <typename TChar, typename TCharTraits, typename TAlloc>
+struct Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc> const, Standard>
+{
+ typedef Iter< ::std::basic_string<TChar, TCharTraits, TAlloc> const, StdIteratorAdaptor > Type;
+};
+
+//____________________________________________________________________________
+
+///.Metafunction.Position.param.T.type:Adaption.std::basic_string
+template <typename TChar, typename TCharTraits, typename TAlloc>
+struct Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >
+{
+ typedef typename ::std::basic_string<TChar, TCharTraits, TAlloc>::size_type Type;
+};
+
+//____________________________________________________________________________
+
+///.Metafunction.Size.param.T.type:Adaption.std::basic_string
+template <typename TChar, typename TCharTraits, typename TAlloc>
+struct Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >
+{
+ typedef typename ::std::basic_string<TChar, TCharTraits, TAlloc>::size_type Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Size.param.T.type:Adaption.std::basic_string
+template <typename TChar, typename TCharTraits, typename TAlloc>
+struct DefaultOverflowImplicit< ::std::basic_string<TChar, TCharTraits, TAlloc> >
+{
+ typedef Generous Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.id.param.object.type:Adaption.std::basic_string
+
+template <typename TChar, typename TCharTraits, typename TAlloc>
+inline void const *
+id(::std::basic_string<TChar, TCharTraits, TAlloc> const & me)
+{
+SEQAN_CHECKPOINT
+ return & *end(me, Standard());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.begin.param.object.type:Adaption.std::basic_string
+template <typename TChar, typename TCharTraits, typename TAlloc>
+inline typename Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc>, Standard>::Type
+begin(::std::basic_string<TChar, TCharTraits, TAlloc> & me,
+ Standard)
+{
+SEQAN_CHECKPOINT
+ return typename Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc>, Standard>::Type(me.begin());
+}
+template <typename TChar, typename TCharTraits, typename TAlloc>
+inline typename Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc> const, Standard>::Type
+begin(::std::basic_string<TChar, TCharTraits, TAlloc> const & me,
+ Standard)
+{
+SEQAN_CHECKPOINT
+ return typename Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc> const, Standard>::Type(me.begin());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.end.param.object.type:Adaption.std::basic_string
+
+template <typename TChar, typename TCharTraits, typename TAlloc>
+inline typename Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc>, Standard>::Type
+end(::std::basic_string<TChar, TCharTraits, TAlloc> & me,
+ Standard)
+{
+SEQAN_CHECKPOINT
+ return typename Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc>, Standard>::Type(me.end());
+}
+template <typename TChar, typename TCharTraits, typename TAlloc>
+inline typename Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc> const, Standard>::Type
+end(::std::basic_string<TChar, TCharTraits, TAlloc> const & me,
+ Standard)
+{
+SEQAN_CHECKPOINT
+ return typename Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc> const, Standard>::Type(me.end());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.value.param.container.type:Adaption.std::basic_string
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TPos>
+inline typename GetValue< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type
+value(::std::basic_string<TChar, TCharTraits, TAlloc> & me,
+ TPos pos)
+{
+SEQAN_CHECKPOINT
+ return me[pos];
+}
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TPos>
+inline typename GetValue< ::std::basic_string<TChar, TCharTraits, TAlloc> const>::Type
+value(::std::basic_string<TChar, TCharTraits, TAlloc> const & me,
+ TPos pos)
+{
+SEQAN_CHECKPOINT
+ return me[pos];
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.length.param.object.type:Adaption.std::basic_string
+
+template <typename TChar, typename TCharTraits, typename TAlloc>
+inline typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type
+length(::std::basic_string<TChar, TCharTraits, TAlloc> const & me)
+{
+SEQAN_CHECKPOINT
+ return me.length();
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.capacity.param.object.type:Adaption.std::basic_string
+
+template <typename TChar, typename TCharTraits, typename TAlloc>
+inline typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type
+capacity(::std::basic_string<TChar, TCharTraits, TAlloc> const & me)
+{
+SEQAN_CHECKPOINT
+ return me.capacity();
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.empty.param.object.type:Adaption.std::basic_string
+
+template <typename TChar, typename TCharTraits, typename TAlloc>
+inline bool
+empty(::std::basic_string<TChar, TCharTraits, TAlloc> const & me)
+{
+SEQAN_CHECKPOINT
+ return me.empty();
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.clear.param.object.type:Adaption.std::basic_string
+
+template <typename TChar, typename TCharTraits, typename TAlloc>
+inline void
+clear(::std::basic_string<TChar, TCharTraits, TAlloc> & me)
+{
+SEQAN_CHECKPOINT
+ me.clear();
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//assign to ::std::basic_string
+
+///.Function.assign.param.target.type:Adaption.std::basic_string
+///.Function.assign.param.source.type:Adaption.std::basic_string
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ assign(target, source, Generous());
+}
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ assign(target, source, Generous());
+}
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource, typename TSize>
+inline void
+assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource & source,
+ TSize limit)
+{
+SEQAN_CHECKPOINT
+ assign(target, source, limit, Generous());
+}
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource, typename TSize>
+inline void
+assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource const & source,
+ TSize limit)
+{
+SEQAN_CHECKPOINT
+ assign(target, source, limit, Generous());
+}
+
+//____________________________________________________________________________
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource & source,
+ Generous)
+{
+SEQAN_CHECKPOINT
+ target.assign(begin(source, Standard()), end(source, Standard()));
+}
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource const & source,
+ Generous)
+{
+SEQAN_CHECKPOINT
+ target.assign(begin(source, Standard()), end(source, Standard()));
+}
+
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+assign_std_string_Generous_impl(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource & source,
+ typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit)
+{
+SEQAN_CHECKPOINT
+ typename Iterator<TSource const, Standard>::Type source_begin = begin(source, Standard());
+ typename Size<TSource const>::Type source_length = length(source);
+ if (source_length > limit)
+ {
+ source_length = limit;
+ }
+ target.assign(source_begin, source_begin + source_length);
+}
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource & source,
+ typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
+ Generous)
+{
+SEQAN_CHECKPOINT
+ assign_std_string_Generous_impl(target, source, limit);
+}
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource const & source,
+ typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
+ Generous)
+{
+SEQAN_CHECKPOINT
+ assign_std_string_Generous_impl(target, source, limit);
+}
+
+//____________________________________________________________________________
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource & source,
+ Limit)
+{
+SEQAN_CHECKPOINT
+ assign(target, source, target.capacity(), Generous());
+}
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource const & source,
+ Limit)
+{
+SEQAN_CHECKPOINT
+ assign(target, source, target.capacity(), Generous());
+}
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource & source,
+ typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
+ Limit)
+{
+SEQAN_CHECKPOINT
+ if (limit > target.capacity())
+ {
+ limit = target.capacity();
+ }
+
+ assign(target, source, limit, Generous());
+}
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+assign(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource const & source,
+ typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
+ Limit)
+{
+SEQAN_CHECKPOINT
+ if (limit > target.capacity())
+ {
+ limit = target.capacity();
+ }
+
+ assign(target, source, limit, Generous());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//append to ::std::basic_string
+
+///.Function.append.param.target.type:Adaption.std::basic_string
+///.Function.append.param.source.type:Adaption.std::basic_string
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+append(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource const & source,
+ Generous)
+{
+SEQAN_CHECKPOINT
+ target.append(begin(source, Standard()), end(source, Standard()));
+}
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+append(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource const & source,
+ typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
+ Generous)
+{
+SEQAN_CHECKPOINT
+ typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type target_length = target.length();
+ if (target_length > limit)
+ {
+ target.resize(limit);
+ }
+ else
+ {
+ limit -= target_length;
+ typename Iterator<TSource const, Standard>::Type source_begin = begin(source, Standard());
+ typename Size<TSource const>::Type source_length = length(source);
+ if (source_length > limit)
+ {
+ source_length = limit;
+ }
+ target.append(source_begin, source_begin + source_length);
+ }
+}
+
+//____________________________________________________________________________
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+append(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource const & source,
+ Limit)
+{
+SEQAN_CHECKPOINT
+ append(target, source, target.capacity(), Generous());
+}
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+append(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ TSource const & source,
+ typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
+ Limit)
+{
+SEQAN_CHECKPOINT
+ if (limit > target.capacity())
+ {
+ limit = target.capacity();
+ }
+
+ append(target, source, limit, Generous());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+///.Function.appendValue.param.target.type:Adaption.std::basic_string
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TValue, typename TTag>
+inline void
+appendValue(::std::basic_string<TChar, TCharTraits, TAlloc> & me,
+ TValue const & _value,
+ TTag)
+{
+SEQAN_CHECKPOINT
+ me.push_back(_value);
+}
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TValue>
+inline void
+appendValue(::std::basic_string<TChar, TCharTraits, TAlloc> & me,
+ TValue const & _value,
+ Limit)
+{
+SEQAN_CHECKPOINT
+ if (capacity(me) > length(me)) me.push_back(_value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//replace to ::std::basic_string
+
+///.Function.replace.param.target.type:Adaption.std::basic_string
+///.Function.replace.param.source.type:Adaption.std::basic_string
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+replace(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ typename Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_begin,
+ typename Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_end,
+ TSource const & source,
+ Generous)
+{
+SEQAN_CHECKPOINT
+ target.replace(target.begin() + pos_begin, target.begin() + pos_end, begin(source, Standard()), end(source, Standard()));
+}
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+replace(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ typename Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_begin,
+ typename Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_end,
+ TSource const & source,
+ typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
+ Generous)
+{
+SEQAN_CHECKPOINT
+ if (pos_begin >= limit)
+ {
+ target.resize(limit);
+ }
+ else
+ {
+ typename Iterator<TSource const, Standard>::Type source_begin = begin(source, Standard());
+ typename Size<TSource const>::Type source_length = length(source);
+ typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_mid = pos_begin + source_length;
+ if (pos_mid > limit)
+ {
+ target.replace(target.begin() + pos_begin, target.begin() + limit, source_begin, source_begin + limit - pos_begin);
+ target.resize(limit);
+ }
+ else
+ {
+ target.replace(target.begin() + pos_begin, target.begin() + pos_end, source_begin, end(source, Standard()));
+ if (target.length() > limit)
+ {
+ target.resize(limit);
+ }
+ }
+ }
+}
+
+//____________________________________________________________________________
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+replace(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ typename Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_begin,
+ typename Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_end,
+ TSource const & source,
+ Limit)
+{
+SEQAN_CHECKPOINT
+ replace(target, pos_begin, pos_end, source, target.capacity(), Generous());
+}
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
+inline void
+replace(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ typename Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_begin,
+ typename Position< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_end,
+ TSource const & source,
+ typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
+ Limit)
+{
+SEQAN_CHECKPOINT
+ if (limit > target.capacity())
+ {
+ limit = target.capacity();
+ }
+
+ replace(target, pos_begin, pos_end, source, limit, Generous());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// handling of iterators as begin and end
+
+/*
+template<typename TChar, typename TCharTraits, typename TAlloc, typename TSource, typename TExpand>
+inline void
+replace(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ typename Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc>, Rooted>::Type pos_begin,
+ typename Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc>, Rooted>::Type pos_end,
+ TSource & source,
+ Tag<TExpand> const tag)
+{
+ replace(target, position(pos_begin), position(pos_end), source, tag);
+}
+
+template<typename TChar, typename TCharTraits, typename TAlloc, typename TSource, typename TExpand>
+inline void
+replace(::std::basic_string<TChar, TCharTraits, TAlloc> & target,
+ typename Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc>, Rooted>::Type pos_begin,
+ typename Iterator< ::std::basic_string<TChar, TCharTraits, TAlloc>, Rooted>::Type pos_end,
+ TSource & source,
+ typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
+ Tag<TExpand> const tag)
+{
+ replace(target, position(pos_begin), position(pos_end), source, tag);
+}
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.reserve.param.object.type:Adaption.std::basic_string
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TExpand>
+inline typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type
+reserve(
+ ::std::basic_string<TChar, TCharTraits, TAlloc> & seq,
+ typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type new_capacity,
+ Tag<TExpand> const &)
+{
+SEQAN_CHECKPOINT
+ seq.reserve(new_capacity);
+ if (new_capacity < seq.capacity())
+ {
+ return seq.capacity();
+ }
+ return new_capacity;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.resize.param.object.type:Adaption.std::basic_string
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSize, typename TExpand>
+inline typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type
+resize(
+ ::std::basic_string<TChar, TCharTraits, TAlloc> & me,
+ TSize new_length,
+ Tag<TExpand> const &)
+{
+SEQAN_CHECKPOINT
+ me.resize(new_length);
+ return me.length();
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.fill.param.object.type:Adaption.std::basic_string
+
+template <typename TChar, typename TCharTraits, typename TAlloc, typename TSize, typename TExpand>
+inline typename Size< ::std::basic_string<TChar, TCharTraits, TAlloc> >::Type
+fill(
+ ::std::basic_string<TChar, TCharTraits, TAlloc> & me,
+ TSize new_length,
+ TChar const & val,
+ Tag<TExpand> const &)
+{
+SEQAN_CHECKPOINT
+ me.resize(new_length, val);
+ return me.length();
+}
+
+
+/* (veraltet)
+//////////////////////////////////////////////////////////////////////////////
+// Iterator Handling
+//////////////////////////////////////////////////////////////////////////////
+
+//??????
+template <typename TChar, typename TContainer>
+struct GetValue< ::__gnu_cxx::__normal_iterator<TChar, TContainer> >
+{
+ typedef typename ::__gnu_cxx::__normal_iterator<TChar, TContainer>::reference Type;
+};
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/sequence/string_alloc.h b/src/libSSA/seqan/sequence/string_alloc.h
new file mode 100644
index 0000000..2a1c9a9
--- /dev/null
+++ b/src/libSSA/seqan/sequence/string_alloc.h
@@ -0,0 +1,467 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: string_alloc.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SEQUENCE_STRING_ALLOC_H
+#define SEQAN_HEADER_SEQUENCE_STRING_ALLOC_H
+
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+/**
+.Spec.Alloc String:
+..cat:Strings
+..general:Class.String
+..summary:Expandable string that is stored on heap.
+..signature:String<TValue, Alloc<TSpec> >
+..param.TValue:The value type, that is the type of the items/characters stored in the string.
+...remarks:Use @Metafunction.Value@ to get the value type for a given class.
+..param.TSpec:The specializing type.
+...default:$void$
+*/
+//////////////////////////////////////////////////////////////////////////////
+//expandable string
+//////////////////////////////////////////////////////////////////////////////
+//Default: TSpec == void
+
+template <typename TValue>
+class String<TValue, Alloc<void> >
+{
+public:
+ typename Value<String>::Type * data_begin;
+ typename Value<String>::Type * data_end;
+ size_t data_capacity;
+
+//____________________________________________________________________________
+
+public:
+ String():
+ data_begin(0),
+ data_end(0),
+ data_capacity(0)
+ {
+SEQAN_CHECKPOINT
+ }
+
+ template <typename TSource>
+ String(TSource & source):
+ data_begin(0),
+ data_end(0),
+ data_capacity(0)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source);
+ }
+ template <typename TSource>
+ String(TSource const & source):
+ data_begin(0),
+ data_end(0),
+ data_capacity(0)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source);
+ }
+ String(String const & source):
+ data_begin(0),
+ data_end(0),
+ data_capacity(0)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source);
+ }
+ String(String const & source, Move):
+ data_begin(0),
+ data_end(0),
+ data_capacity(0)
+ {
+SEQAN_CHECKPOINT
+ move(*this, source);
+ }
+ template <typename TSource, typename TSize>
+ String(TSource & source, TSize limit):
+ data_begin(0),
+ data_end(0),
+ data_capacity(0)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source, limit);
+ }
+ template <typename TSource, typename TSize>
+ String(TSource const & source, TSize limit):
+ data_begin(0),
+ data_end(0),
+ data_capacity(0)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source, limit);
+ }
+
+
+ template <typename TSource>
+ String & operator =(TSource const & source)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source);
+ return *this;
+ }
+ String & operator =(String const & source)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source);
+ return *this;
+ }
+
+ ~String()
+ {
+SEQAN_CHECKPOINT
+ arrayDestruct(this->data_begin, this->data_end);
+ _deallocateStorage(*this, this->data_begin, data_capacity);
+ }
+
+
+//____________________________________________________________________________
+
+ template <typename TPos>
+ inline typename Reference<String>::Type
+ operator [] (TPos pos)
+ {
+SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+
+ template <typename TPos>
+ inline typename Reference<String const>::Type
+ operator [] (TPos pos) const
+ {
+SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+
+//____________________________________________________________________________
+
+ friend inline typename Iterator<String, Standard>::Type
+ begin(String & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return me.data_begin;
+ }
+ friend inline typename Iterator<String const, Standard>::Type
+ begin(String const & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return me.data_begin;
+ }
+
+//____________________________________________________________________________
+
+ friend inline typename Iterator<String, Standard>::Type
+ end(String & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return me.data_end;
+ }
+ friend inline typename Iterator<String const, Standard>::Type
+ end(String const & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return me.data_end;
+ }
+
+//____________________________________________________________________________
+
+ friend inline size_t
+ capacity(String & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_capacity;
+ }
+
+ friend inline size_t
+ capacity(String const & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_capacity;
+ }
+
+//____________________________________________________________________________
+/* Entwicklungsschrott?
+ inline void
+ move(String & target,
+ String & source)
+ {
+ clear(target);
+ target.data_begin = source.data_begin;
+ target.data_end = source.data_end;
+ target.data_capacity = source.data_capacity;
+
+ source.data_begin = 0;
+ source.data_end = 0;
+ source.data_capacity = 0;
+ }
+*/
+//____________________________________________________________________________
+
+/**
+.Internal._setBegin:
+*/
+ friend inline void
+ _setBegin(
+ String & me,
+ typename Value<String>::Type * new_begin)
+ {
+SEQAN_CHECKPOINT
+ me.data_begin = new_begin;
+ }
+
+//____________________________________________________________________________
+
+/**
+.Internal._setLength:
+..cat:Functions
+..summary:Set the length of container.
+..signature:_setLength(object, new_length)
+..param.object:A container.
+..param.object.type:Spec.Alloc String
+..param.new_length:The new length.
+*/
+ friend inline void
+ _setLength(
+ String & me,
+ size_t new_length)
+ {
+SEQAN_CHECKPOINT
+ me.data_end = me.data_begin + new_length;
+ }
+
+//____________________________________________________________________________
+
+/**
+.Internal._setCapacity:
+*/
+ friend inline void
+ _setCapacity(
+ String & me,
+ size_t new_capacity)
+ {
+SEQAN_CHECKPOINT
+ me.data_capacity = new_capacity;
+ }
+
+//____________________________________________________________________________
+
+/**
+.Internal._allocateStorage:
+..cat:Functions
+..summary:Allocates a new buffer for a container.
+..signature:_allocateStorage(object, new_capacity)
+..param.object:A container.
+..param.object.type:Spec.Alloc String
+..param.new_capacity:The capacity of the new allocated buffer.
+..returns:The old butter $object$, that is replaced by the new allocated buffer.
+..remarks:The returned buffer must be deallocated by @Internal._deallocateStorage at .
+..remarks:This function does not construct objects in the allocated buffer.
+..see:Internal._reallocateStorage
+*/
+ friend inline typename Value<String>::Type *
+ _allocateStorage(
+ String & me,
+ size_t new_capacity)
+ {
+SEQAN_CHECKPOINT
+ size_t size = _computeSize4Capacity(me, new_capacity);
+ typename Value<String>::Type * return_value = me.data_begin;
+ allocate(me, me.data_begin, size, TagAllocateStorage());
+ me.data_capacity = new_capacity;
+ return return_value;
+ }
+
+ //____________________________________________________________________________
+
+/**
+.Internal._deallocateStorage:
+..cat:Functions
+..summary:Deallocates a buffer of a container.
+..signature:_deallocateStorage(object, buffer, capacity)
+..param.object:A container.
+..param.object.type:Spec.Alloc String
+..param.buffer:The buffer that will be deallocated.
+..param.capacity:The capacity of $buffer$.
+..remarks:All objects in the buffer must be destroyed before calling $_deallocateStorage$.
+..see:Internal._allocateStorage
+..see:Internal._reallocateStorage
+*/
+ friend inline void
+ _deallocateStorage(
+ String & me,
+ typename Value<String>::Type * ptr,
+ size_t capacity)
+ {
+SEQAN_CHECKPOINT
+ size_t size = _computeSize4Capacity(me, capacity);
+ deallocate(me, ptr, size, TagAllocateStorage());
+ }
+
+//____________________________________________________________________________
+
+};
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename TSpec>
+struct DefaultOverflowImplicit<String<TValue, Alloc<TSpec> > >
+{
+ typedef Generous Type;
+};
+
+template <typename TValue, typename TSpec>
+struct DefaultOverflowImplicit<String<TValue, Alloc<TSpec> > const >
+{
+ typedef Generous Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename TSpec>
+struct IsContiguous< String<TValue, Alloc<TSpec> > >
+{
+ typedef True Type;
+ enum { VALUE = true };
+};
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TTargetValue, typename TSourceValue, typename TSpec>
+inline void
+move(String<TTargetValue, Alloc<TSpec> > & target,
+ String<TSourceValue, Alloc<TSpec> > & source)
+{
+ _moveContiguous(target, source);
+}
+template <typename TTargetValue, typename TSourceValue, typename TSpec>
+inline void
+move(String<TTargetValue, Alloc<TSpec> > & target,
+ String<TSourceValue, Alloc<TSpec> > const & source)
+{
+ _moveContiguous(target, source);
+}
+
+template <typename TValue, typename TSpec>
+inline void
+move(String<TValue, Alloc<TSpec> > & target,
+ String<TValue, Alloc<TSpec> > & source)
+{
+ clear(target);
+ target.data_begin = source.data_begin;
+ target.data_end = source.data_end;
+ target.data_capacity = source.data_capacity;
+
+ source.data_begin = 0;
+ source.data_end = 0;
+ source.data_capacity = 0;
+}
+template <typename TValue, typename TSpec>
+inline void
+move(String<TValue, Alloc<TSpec> > & target,
+ String<TValue, Alloc<TSpec> > const & source)
+{
+ clear(target);
+ target.data_begin = source.data_begin;
+ target.data_end = source.data_end;
+ target.data_capacity = source.data_capacity;
+
+ source.data_begin = 0;
+ source.data_end = 0;
+ source.data_capacity = 0;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.reserve.param.object.type:Spec.Alloc String
+
+template <typename TValue, typename TSpec, typename _TSize, typename TExpand>
+inline typename Size< String<TValue, Alloc<TSpec> > >::Type
+reserve(
+ String<TValue, Alloc<TSpec> > & seq,
+ _TSize new_capacity,
+ Tag<TExpand> const tag)
+{
+SEQAN_CHECKPOINT
+ typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
+
+ TSize old_capacity = capacity(seq);
+ if (old_capacity >= (TSize)new_capacity) return new_capacity;
+
+ TSize seq_length = length(seq);
+ typename Value< String<TValue, Alloc<TSpec> > >::Type * old_array = _reallocateStorage(seq, new_capacity, tag);
+ if (old_array)
+ {//buffer was replaced, destruct old buffer
+ arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
+ arrayDestruct(old_array, old_array + seq_length);
+ _deallocateStorage(seq, old_array, old_capacity);
+ _setLength(seq, seq_length);
+ }
+ else if (!old_capacity)
+ {//new buffer created and the string had no buffer yet
+ _setLength(seq, seq_length);
+ }
+ return new_capacity;
+}
+
+template <typename TValue, typename TSpec, typename _TSize>
+inline typename Size< String<TValue, Alloc<TSpec> > >::Type
+reserve(
+ String<TValue, Alloc<TSpec> > & me,
+ _TSize new_capacity,
+ Limit)
+{
+SEQAN_CHECKPOINT
+ typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
+
+ TSize me_capacity = capacity(me);
+ if (me_capacity < (TSize)new_capacity) return me_capacity;
+ return new_capacity;
+}
+
+template <typename TValue, typename TSpec, typename _TSize>
+inline typename Size< String<TValue, Alloc<TSpec> > >::Type
+reserve(
+ String<TValue, Alloc<TSpec> > & /*me*/,
+ _TSize new_capacity,
+ Insist)
+{
+SEQAN_CHECKPOINT
+ typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
+
+ return new_capacity;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/sequence/string_array.h b/src/libSSA/seqan/sequence/string_array.h
new file mode 100644
index 0000000..c865ede
--- /dev/null
+++ b/src/libSSA/seqan/sequence/string_array.h
@@ -0,0 +1,237 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: string_array.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SEQUENCE_STRING_ARRAY_H
+#define SEQAN_HEADER_SEQUENCE_STRING_ARRAY_H
+
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+/**
+.Spec.Array String:
+..cat:Strings
+..general:Class.String
+..summary:Fast but non-expandable string.
+..signature:String<TValue, Array<size> >
+..param.TValue:The value type, that is the type of the items/characters stored in the string.
+...remarks:Use @Metafunction.Value@ to get the value type for a given class.
+..param.size:A positive integer that specifies the capacity of the string.
+...remarks:Note that the capacity of a stack string cannot be changed later.
+*/
+//////////////////////////////////////////////////////////////////////////////
+
+template <unsigned int ISize>
+struct Array;
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, unsigned int ISize>
+class String<TValue, Array<ISize> >
+{
+protected:
+ mutable TValue data_begin[ISize];
+ TValue * data_end;
+
+//____________________________________________________________________________
+
+public:
+ String()
+ {
+SEQAN_CHECKPOINT
+ data_end = data_begin;
+ }
+
+ template <typename TSource>
+ String(TSource & source)
+ {
+SEQAN_CHECKPOINT
+ data_end = data_begin;
+ assign(*this, source);
+ }
+ template <typename TSource>
+ String(TSource const & source)
+ {
+SEQAN_CHECKPOINT
+ data_end = data_begin;
+ assign(*this, source);
+ }
+ String(String const & source)
+ {
+SEQAN_CHECKPOINT
+ data_end = data_begin;
+ assign(*this, source);
+ }
+
+ template <typename TSource>
+ String & operator =(TSource const & source)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source);
+ return *this;
+ }
+ String & operator =(String const & source)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source);
+ return *this;
+ }
+
+ ~String()
+ {
+ }
+
+//____________________________________________________________________________
+
+ template <typename TPos>
+ inline typename Reference<String>::Type
+ operator [] (TPos pos)
+ {
+SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+
+ template <typename TPos>
+ inline typename Reference<String const>::Type
+ operator [] (TPos pos) const
+ {
+SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+
+//____________________________________________________________________________
+
+ friend inline typename Iterator<String, Standard>::Type
+ begin(String & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return me.data_begin;
+ }
+ friend inline typename Iterator<String const, Standard>::Type
+ begin(String const & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return me.data_begin;
+ }
+
+//____________________________________________________________________________
+
+ friend inline typename Iterator<String, Standard>::Type
+ end(String & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return me.data_end;
+ }
+ friend inline typename Iterator<String const, Standard>::Type
+ end(String const & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return me.data_end;
+ }
+
+//____________________________________________________________________________
+
+ friend inline size_t
+ capacity(String &)
+ {
+SEQAN_CHECKPOINT
+ return ISize;
+ }
+
+ friend inline size_t
+ capacity(String const &)
+ {
+SEQAN_CHECKPOINT
+ return ISize;
+ }
+//____________________________________________________________________________
+
+/**
+.Internal._setLength.param.object.type:Spec.Array String
+*/
+ friend inline void
+ _setLength(
+ String & me,
+ size_t new_length)
+ {
+SEQAN_CHECKPOINT
+ me.data_end = me.data_begin + new_length;
+ }
+
+//____________________________________________________________________________
+
+};
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, unsigned int ISize>
+struct DefaultOverflowImplicit<String<TValue, Array<ISize> > >
+{
+ typedef Limit Type;
+};
+
+template <typename TValue, unsigned int ISize>
+struct DefaultOverflowImplicit<String<TValue, Array<ISize> > const >
+{
+ typedef Limit Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, unsigned int ISize>
+struct DefaultOverflowExplicit<String<TValue, Array<ISize> > >
+{
+ typedef Limit Type;
+};
+
+template <typename TValue, unsigned int ISize>
+struct DefaultOverflowExplicit<String<TValue, Array<ISize> > const >
+{
+ typedef Limit Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, unsigned int ISize>
+struct IsContiguous< String<TValue, Array<ISize> > >
+{
+ typedef True Type;
+ enum { VALUE = true };
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.LENGTH.param.T.type:Spec.Array String
+template <typename TValue, unsigned int ISize>
+struct LENGTH< String<TValue, Array<ISize> > >
+{
+ enum { VALUE = ISize };
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/sequence/string_base.h b/src/libSSA/seqan/sequence/string_base.h
new file mode 100644
index 0000000..d32237c
--- /dev/null
+++ b/src/libSSA/seqan/sequence/string_base.h
@@ -0,0 +1,1695 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: string_base.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SEQUENCE_ARRAY_BASE_H
+#define SEQAN_HEADER_SEQUENCE_ARRAY_BASE_H
+
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// Tags
+//////////////////////////////////////////////////////////////////////////////
+
+
+template <typename TSpec = void>
+struct Alloc;
+
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Class.String:
+..cat:Sequences
+..summary:General purpose container for sequences.
+..signature:String<TValue, TSpec>
+..param.TValue:The value type, that is the type of the items/characters stored in the string.
+...metafunction:Metafunction.Value
+..param.TSpec:The specializing type.
+...metafunction:Metafunction.Spec
+...default:$Alloc<>$, see @Spec.Alloc String at .
+..implements:Concept.Container
+..include:sequence.h
+*/
+
+template <typename TValue, typename TSpec = Alloc<> >
+class String;
+
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// METAFUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Iterator.param.T.type:Class.String
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename TSpec>
+struct Value<String<TValue, TSpec> >
+{
+ typedef TValue Type;
+};
+template <typename TValue, typename TSpec>
+struct Value<String<TValue, TSpec> const >:
+ public Value<String<TValue, TSpec> >
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Spec.param.T.type:Class.String
+
+template <typename TValue, typename TSpec>
+struct Spec<String<TValue, TSpec> >
+{
+ typedef TSpec Type;
+};
+template <typename TValue, typename TSpec>
+struct Spec<String<TValue, TSpec> const>:
+ public Spec<String<TValue, TSpec> >
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.IsSequence.param.T.type:Class.String
+
+template <typename TValue, typename TSpec>
+struct IsSequence<String<TValue, TSpec> > {
+ typedef True Type;
+ enum { VALUE = true };
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// Returns a Class that can be used to store a temporary copy of a String
+
+template <typename T>
+struct _TempCopy
+{
+ typedef typename Value<T>::Type TValue;
+ typedef typename _RemoveConst<TValue>::Type TValue_NotConst;
+ typedef String<TValue_NotConst, Alloc<> > Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// FUNCTIONS
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.id.param.object.type:Class.String
+///.Function.empty.param.object.type:Class.String
+///.Function.capacity.param.object.type:Class.String
+
+
+//////////////////////////////////////////////////////////////////////////////
+//shareResources
+
+///.Function.shareResources.param.sequence1, sequence2.type:Class.String
+
+template <typename TValue, typename TSpec>
+inline bool
+shareResources(String<TValue, TSpec> const & obj1,
+ TValue const & obj2)
+{
+SEQAN_CHECKPOINT
+ return (begin(obj1) >= &obj2) && (end(obj1) <= &obj2);
+}
+
+template <typename TValue, typename TSpec>
+inline bool
+shareResources(TValue const & obj1,
+ String<TValue, TSpec> const & obj2)
+{
+SEQAN_CHECKPOINT
+ return (begin(obj2) >= &obj1) && (end(obj2) <= &obj1);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.begin.param.object.type:Class.String
+///.Function.end.param.object.type:Class.String
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.value.param.container.type:Class.String
+
+template <typename TValue, typename TSpec, typename TPos>
+inline typename Reference< String<TValue, TSpec> >::Type
+value(String<TValue, TSpec> & me,
+ TPos pos)
+{
+SEQAN_CHECKPOINT
+ return *(begin(me, Standard()) + pos);
+}
+
+template <typename TValue, typename TSpec, typename TPos>
+inline typename Reference< String<TValue, TSpec> const >::Type
+value(String<TValue, TSpec> const & me,
+ TPos pos)
+{
+SEQAN_CHECKPOINT
+ return *(begin(me, Standard()) + pos);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.length.param.object.type:Class.String
+
+template <typename TValue, typename TSpec>
+inline typename Size< String<TValue, TSpec> const>::Type
+length(String<TValue, TSpec> const & me)
+{
+SEQAN_CHECKPOINT
+ return end(me, Standard()) - begin(me, Standard());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.clear:
+..cat:Containers
+..summary:Resets an object.
+..signature:clear(object)
+..param.object:The object that will be resetted.
+...type:Class.String
+..remarks:$object$ is set to a state that is equivalent to a default constructed object of the same type.
+..remarks:If $object$ is a container, then all elements are removed from this container.
+The length is set to 0.
+The capacity can be changed, depending on the implementation.
+..see:Function.resize
+..see:Function.length
+*/
+
+template <typename TValue, typename TSpec>
+inline void
+clear(String<TValue, TSpec> & me)
+{
+SEQAN_CHECKPOINT
+ arrayDestruct(begin(me, Standard()), end(me, Standard()));
+ _setLength(me, 0);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TExpand>
+struct _ClearSpace_String_Base_
+{
+};
+
+//____________________________________________________________________________
+
+template <>
+struct _ClearSpace_String_Base_<Insist>
+{
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size)
+ {
+SEQAN_CHECKPOINT
+ arrayDestruct(begin(seq, Standard()), end(seq, Standard()));
+ _setLength(seq, size);
+ return size;
+ }
+
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Size<T>::Type limit)
+ {
+ arrayDestruct(begin(seq, Standard()), end(seq, Standard()));
+ if (limit < size)
+ {
+SEQAN_CHECKPOINT
+ size = limit;
+ }
+ _setLength(seq, size);
+ return size;
+ }
+
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Size<T>::Type start,
+ typename Size<T>::Type end)
+ {
+SEQAN_CHECKPOINT
+ typename Size<T>::Type new_length = length(seq) + size - (end - start);
+ arrayClearSpace(begin(seq, Standard()) + start, length(seq) - start, end - start, size);
+ _setLength(seq, new_length);
+ return size;
+ }
+
+ template <typename T>
+ static typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Size<T>::Type start,
+ typename Size<T>::Type end,
+ typename Size<T>::Type limit)
+ {
+ typename Value<T>::Type * seq_buffer = begin(seq);
+ typename Size<T>::Type seq_length = length(seq);
+
+ if (limit > start + size)
+ {
+SEQAN_CHECKPOINT
+ typename Size<T>::Type removed_size = end - start;
+ typename Size<T>::Type new_length = seq_length - removed_size + size;
+ if (limit < new_length)
+ {
+SEQAN_CHECKPOINT
+ arrayDestruct(seq_buffer + limit, seq_buffer + new_length);
+ seq_length -= new_length - limit;
+ }
+ arrayClearSpace(seq_buffer + start, seq_length - start, end - start, size);
+ _setLength(seq, new_length);
+ return size;
+ }
+ else
+ {
+SEQAN_CHECKPOINT
+ arrayDestruct(seq_buffer + start, seq_buffer + seq_length);
+ _setLength(seq, limit);
+ if (limit > start) return limit - start;
+ else return 0;
+ }
+ }
+/*
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Iterator<T>::Type start,
+ typename Iterator<T>::Type end)
+ {
+ typename Iterator<T>::Type seq_begin = begin(seq);
+ return _clearSpace(seq, size, start - seq_begin, end - seq_begin, Insist());
+ }
+
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Iterator<T>::Type start,
+ typename Iterator<T>::Type end,
+ typename Size<T>::Type limit)
+ {
+ typename Iterator<T>::Type seq_begin = begin(seq);
+ return _clearSpace(seq, size, start - seq_begin, end - seq_begin, limit, Insist());
+ }
+*/
+};
+
+
+//____________________________________________________________________________
+
+
+template <>
+struct _ClearSpace_String_Base_<Limit>
+{
+
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size)
+ {
+SEQAN_CHECKPOINT
+ return _clearSpace(seq, size, capacity(seq), Insist());
+ }
+
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Size<T>::Type limit)
+ {
+ typename Size<T>::Type seq_capacity = capacity(seq);
+ if (limit > seq_capacity)
+ {
+SEQAN_CHECKPOINT
+ limit = seq_capacity;
+ }
+ return _clearSpace(seq, size, limit, Insist());
+ }
+
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Size<T>::Type start,
+ typename Size<T>::Type end)
+ {
+SEQAN_CHECKPOINT
+ return _clearSpace(seq, size, start, end, capacity(seq), Insist());
+ }
+
+ template <typename T>
+ static typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Size<T>::Type start,
+ typename Size<T>::Type end,
+ typename Size<T>::Type limit)
+ {
+ typename Size<T>::Type seq_capacity = capacity(seq);
+ if (limit > seq_capacity)
+ {
+SEQAN_CHECKPOINT
+ limit = seq_capacity;
+ }
+ return _clearSpace(seq, size, start, end, limit, Insist());
+ }
+
+/*
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Iterator<T>::Type start,
+ typename Iterator<T>::Type end)
+ {
+ typename Iterator<T>::Type seq_begin = begin(seq);
+ return _clearSpace(seq, size, start - seq_begin, end - seq_begin, Insist());
+ }
+
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Iterator<T>::Type start,
+ typename Iterator<T>::Type end,
+ typename Size<T>::Type limit)
+ {
+ typename Iterator<T>::Type seq_begin = begin(seq);
+ return _clearSpace(seq, size, start - seq_begin, end - seq_begin, limit, Insist());
+ }
+*/
+};
+
+//____________________________________________________________________________
+
+template <typename TExpand>
+struct _ClearSpace_Expand_String_Base_
+{
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size)
+ {
+ arrayDestruct(begin(seq, Standard()), end(seq, Standard()));
+ typename Size<T>::Type old_capacity = capacity(seq);
+ typename Value<T>::Type * old_array = _reallocateStorage(seq, size, TExpand());
+ if (old_array)
+ {
+SEQAN_CHECKPOINT
+ _deallocateStorage(seq, old_array, old_capacity);
+ }
+ _setLength(seq, size);
+ return size;
+ }
+
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Size<T>::Type limit)
+ {
+ arrayDestruct(begin(seq, Standard()), end(seq, Standard()));
+ if (limit < size)
+ {
+SEQAN_CHECKPOINT
+ size = limit;
+ }
+ typename Size<T>::Type old_capacity = capacity(seq);
+ typename Value<T>::Type * old_array = _reallocateStorage(seq, size, limit, TExpand());
+ if (old_array)
+ {
+ _deallocateStorage(seq, old_array, old_capacity);
+ }
+ _setLength(seq, size);
+ return size;
+ }
+
+ template <typename T>
+ static typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Size<T>::Type start,
+ typename Size<T>::Type end)
+ {
+ typename Size<T>::Type old_length = length(seq);
+ typename Size<T>::Type removed_size = end - start;
+ typename Size<T>::Type new_length = old_length - removed_size + size;
+
+ typename Size<T>::Type old_capacity = capacity(seq);
+ typename Value<T>::Type * old_array = _reallocateStorage(seq, new_length, TExpand());
+ typename Value<T>::Type * seq_array = begin(seq);
+
+ if (old_array)
+ {
+SEQAN_CHECKPOINT
+ arrayConstructMove(old_array, old_array + start, seq_array);
+ arrayConstructMove(old_array + end, old_array + old_length, seq_array + start + size);
+ _deallocateStorage(seq, old_array, old_capacity);
+ }
+ else
+ {
+SEQAN_CHECKPOINT
+ arrayClearSpace(seq_array + start, old_length - start, removed_size, size);
+ }
+
+ _setLength(seq, new_length);
+
+ return size;
+ }
+
+ template <typename T>
+ static typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Size<T>::Type start,
+ typename Size<T>::Type end,
+ typename Size<T>::Type limit)
+ {
+ typename Size<T>::Type old_length = length(seq);
+ typename Size<T>::Type removed_size = end - start;
+ typename Size<T>::Type need_length = old_length - removed_size + size;
+
+ typename Size<T>::Type new_length = need_length;
+ typename Size<T>::Type length_to_copy = old_length;
+ if (limit < need_length)
+ {
+SEQAN_CHECKPOINT
+ new_length = limit;
+ length_to_copy = new_length - size + removed_size;
+ }
+
+ bool keep_second_part = (new_length > start + size);
+
+ typename Size<T>::Type old_capacity = capacity(seq);
+ typename Value<T>::Type * old_array = _reallocateStorage(seq, new_length, limit, TExpand());
+ typename Value<T>::Type * seq_array = begin(seq);
+
+ if (old_array)
+ {//new buffer allocated
+ //so old_length < limit, so start <= limit
+ arrayConstructMove(old_array, old_array + start, seq_array);
+ if (keep_second_part)
+ {
+ arrayConstructMove(old_array + end, old_array + length_to_copy, seq_array + start + size);
+ }
+ _deallocateStorage(seq, old_array, old_capacity);
+ }
+ else
+ {
+ if (keep_second_part)
+ {
+ arrayClearSpace(seq_array + start, length_to_copy - start, end - start, size);
+ if (length_to_copy < old_length)
+ {
+ arrayDestruct(seq_array + length_to_copy, seq_array + old_length);
+ }
+ }
+ else
+ {
+ arrayDestruct(seq_array + start, seq_array + old_length);
+ }
+ }
+
+ _setLength(seq, new_length);
+
+ if (keep_second_part) return size;
+ else if (new_length > start) return new_length - start;
+ else return 0;
+ }
+
+/*
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Iterator<T>::Type start,
+ typename Iterator<T>::Type end)
+ {
+ typename Iterator<T>::Type seq_begin = begin(seq);
+ return _clearSpace(seq, size, start - seq_begin, end - seq_begin, TExpand());
+ }
+
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Iterator<T>::Type start,
+ typename Iterator<T>::Type end,
+ typename Size<T>::Type limit)
+ {
+ typename Iterator<T>::Type seq_begin = begin(seq);
+ return _clearSpace(seq, size, start - seq_begin, end - seq_begin, limit, TExpand());
+ }
+*/
+};
+
+//____________________________________________________________________________
+
+template <>
+struct _ClearSpace_String_Base_<Exact>:
+ _ClearSpace_Expand_String_Base_<Exact>
+{
+};
+
+//____________________________________________________________________________
+
+template <>
+struct _ClearSpace_String_Base_<Generous>:
+ _ClearSpace_Expand_String_Base_<Generous>
+{
+};
+
+//____________________________________________________________________________
+/**
+.Internal._clearSpace:
+..cat:Functions
+..summary:Makes space in container
+..signature:_clearSpace(object, size [, pos_begin, pos_end] [, limit], resize_tag)
+..param.object:The container.
+..param.size:Length of the freed space.
+..param.pos_begin:Position of the first item in $object$ that is to be destroyed. (optional)
+..param.pos_end:Position behind the last item in $object$ that is to be destroyed. (optional)
+...remarks:If $pos_end == pos_begin$, no item in $object$ will be destroyed.
+..param.limit:Maximal length $object$ can get after this operation. (optional)
+..param.resize_tag:Strategy that is applied if $object$ has not enough capacity to store the complete content.
+..returns:The number of free characters.
+...remarks:Depeding on the @Tag.Overflow Strategy.overflow strategy@ specified by $resize_tag$,
+this could be $size$ or less than $size$ if $object$ has not enough @Function.capacity at .
+..remarks:This function is similar to @Function.resizeSpace@ and @Function.fillSpace at .
+The main difference is that $_clearSpace$ does not construct objects in the new created space.
+*/
+template<typename TValue, typename TSpec, typename TSize, typename TExpand>
+inline typename Size< String<TValue, TSpec> >::Type
+_clearSpace(String<TValue, TSpec> & me,
+ TSize size,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ return _ClearSpace_String_Base_<Tag<TExpand> const>::_clearSpace_(me, size);
+}
+
+template<typename TValue, typename TSpec, typename TSize, typename TExpand>
+inline typename Size< String<TValue, TSpec> >::Type
+_clearSpace(String<TValue, TSpec> & me,
+ TSize size,
+ TSize limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ return _ClearSpace_String_Base_<Tag<TExpand> const>::_clearSpace_(me, size, limit);
+}
+
+template<typename TValue, typename TSpec, typename TSize, typename TPosition, typename TExpand>
+inline typename Size< String<TValue, TSpec> >::Type
+_clearSpace(String<TValue, TSpec> & me,
+ TSize size,
+ TPosition pos_begin,
+ TPosition pos_end,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ return _ClearSpace_String_Base_<Tag<TExpand> const>::_clearSpace_(me, size, pos_begin, pos_end);
+}
+
+template<typename TValue, typename TSpec, typename TSize, typename TPosition, typename TExpand>
+inline typename Size< String<TValue, TSpec> >::Type
+_clearSpace(String<TValue, TSpec> & me,
+ TSize size,
+ TPosition pos_begin,
+ TPosition pos_end,
+ TSize limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ return _ClearSpace_String_Base_<Tag<TExpand> const>::_clearSpace_(me, size, pos_begin, pos_end, limit);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Function.resizeSpace.param.object.type:Class.String
+*/
+
+template<typename TValue, typename TSpec, typename TPosition, typename TExpand>
+inline typename Size< String<TValue, TSpec> >::Type
+resizeSpace(String<TValue, TSpec> & me,
+ typename Size< String<TValue, TSpec> >::Type size,
+ TPosition pos_begin,
+ TPosition pos_end,
+ Tag<TExpand> const tag)
+{
+SEQAN_CHECKPOINT
+ typename Size<String<TValue, TSpec> >::Type ret_ =_clearSpace(me, size, pos_begin, pos_end, tag);
+ arrayConstruct(iter(me, pos_begin), iter(me, pos_begin) + ret_);
+ return ret_;
+}
+
+template<typename TValue, typename TSpec, typename TPosition, typename TExpand>
+inline typename Size< String<TValue, TSpec> >::Type
+resizeSpace(String<TValue, TSpec> & me,
+ typename Size< String<TValue, TSpec> >::Type size,
+ TPosition pos_begin,
+ TPosition pos_end,
+ typename Size< String<TValue, TSpec> >::Type limit,
+ Tag<TExpand> const tag)
+{
+SEQAN_CHECKPOINT
+ typename Size<String<TValue, TSpec> >::Type ret_ =_clearSpace(me, size, pos_begin, pos_end, limit, tag);
+ arrayConstruct(iter(me, pos_begin), iter(me, pos_begin) + ret_);
+ return ret_;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// assignValue (2)
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename TSpec, typename TValue2>
+inline void
+assignValue(String<TValue, TSpec> & me,
+ TValue2 const & _value)
+{
+// assign(me, toString(_value)); ???TODO
+}
+
+//???TODO: moveValue (2)
+
+//////////////////////////////////////////////////////////////////////////////
+// assign
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.assign.param.target.type:Class.String
+///.Function.assign.param.source.type:Class.String
+
+//overload of binary version for strings:
+
+template<typename TTargetValue, typename TTargetSpec, typename TSource>
+inline void
+assign(String<TTargetValue, TTargetSpec> & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ typedef String<TTargetValue, TTargetSpec> TTarget;
+ assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template<typename TTargetValue, typename TTargetSpec, typename TSource>
+inline void
+assign(String<TTargetValue, TTargetSpec> & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ typedef String<TTargetValue, TTargetSpec> TTarget;
+ assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TExpand>
+struct _Assign_String
+{
+ template <typename TTarget, typename TSource>
+ static inline void
+ assign_(
+ TTarget & target,
+ TSource & source)
+ {
+ if (!id(source) || !shareResources(target, source))
+ {
+SEQAN_CHECKPOINT
+ typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), TExpand());
+ arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()));
+ }
+ else
+ {
+SEQAN_CHECKPOINT
+ if ((void *) &target == (void *) &source) return;
+
+ typename _TempCopy<TSource>::Type temp(source, length(source));
+ assign(target, temp, TExpand());
+ }
+ }
+
+ template <typename TTarget, typename TSource>
+ static inline void
+ assign_(
+ TTarget & target,
+ TSource & source,
+ typename Size<TTarget>::Type limit)
+ {
+ if (!id(source) || !shareResources(target, source))
+ {
+SEQAN_CHECKPOINT
+ typename Size<TTarget>::Type part_length = _clearSpace(target, typename Size<TTarget>::Type(length(source)), limit, TExpand());
+ arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()));
+ }
+ else
+ {
+SEQAN_CHECKPOINT
+ if ((void *) &target == (void *) &source) return;
+
+ typename Size<TTarget>::Type source_length = length(source);
+ if (source_length > limit) source_length = limit;
+
+ typename _TempCopy<TSource>::Type temp(source, source_length);
+ assign(target, temp, TExpand());
+ }
+ }
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template<typename TTargetValue, typename TTargetSpec, typename TSource, typename TExpand>
+inline void
+assign(String<TTargetValue, TTargetSpec> & target,
+ TSource const & source,
+ Tag<TExpand> const)
+{
+ typedef String<TTargetValue, TTargetSpec> TTarget;
+ _Assign_String<Tag<TExpand> const>::assign_(target, source);
+}
+template<typename TTargetValue, typename TTargetSpec, typename TSource, typename TSize, typename TExpand>
+inline void
+assign(String<TTargetValue, TTargetSpec> & target,
+ TSource const & source,
+ TSize limit,
+ Tag<TExpand> const)
+{
+ typedef String<TTargetValue, TTargetSpec> TTarget;
+ _Assign_String<Tag<TExpand> const>::assign_(target, source, limit);
+}
+
+//____________________________________________________________________________
+//this variant is a workaround for the "const array"-bug of VC++
+
+template<typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TExpand>
+inline void
+assign(String<TTargetValue, TTargetSpec> & target,
+ TSourceValue const * source,
+ Tag<TExpand> const)
+{
+ typedef String<TTargetValue, TTargetSpec> TTarget;
+ _Assign_String<Tag<TExpand> const>::assign_(target, source);
+}
+template<typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TSize, typename TExpand>
+inline void
+assign(String<TTargetValue, TTargetSpec> & target,
+ TSourceValue const * source,
+ TSize limit,
+ Tag<TExpand> const)
+{
+ typedef String<TTargetValue, TTargetSpec> TTarget;
+ _Assign_String<Tag<TExpand> const>::assign_(target, source, limit);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// move
+//////////////////////////////////////////////////////////////////////////////
+
+//____________________________________________________________________________
+//implementation of move for contiguous sequences
+//note: there is a problem, if sizeof(TSourceValue) and sizeof(TTargetValue) are not a multiple
+// of each other, since in this case the correct size cannot be determined afterwards
+// when calling the deallocate function.
+// ???TODO
+template <typename TTarget, typename TSource>
+void
+_moveContiguous(TTarget & target,
+ TSource & source)
+{
+ typedef typename Value<TSource>::Type TSourceValue;
+ typedef typename Value<TTarget>::Type TTargetValue;
+
+ clear(target);
+
+ typename Iterator<TSource, Standard>::Type source_begin = begin(source, Standard());
+ typename Iterator<TTarget, Standard>::Type target_begin = (typename Iterator<TTarget, Standard>::Type) begin(source, Standard());
+
+ typename Size<TTarget>::Type size = sizeof(TSourceValue) * capacity(source);
+ if (size >= sizeof(TTargetValue))
+ {
+SEQAN_CHECKPOINT
+ if (sizeof(TSourceValue) <= 2) ++size; //regard the "end of string termination" case
+ typename Size<TTarget>::Type target_capacity = size / sizeof(TTargetValue);
+ if (sizeof(TTargetValue) <= 2) --target_capacity; //regard the "end of string termination" case
+
+ typename Size<TTarget>::Type target_length = length(source);
+ if (target_length > target_capacity)
+ {
+ target_length = target_capacity;
+ }
+
+ if (sizeof(TSourceValue) >= sizeof(TTargetValue))
+ {
+ arrayMoveForward(source_begin, source_begin + target_length, target_begin);
+ }
+ else
+ {
+ arrayMoveBackward(source_begin, source_begin + target_length, target_begin);
+ }
+
+ _setBegin(target, target_begin);
+ _setLength(target, target_length);
+ _setCapacity(target, target_capacity);
+
+ _setBegin(source, 0);
+ _setLength(source, 0);
+ _setCapacity(source, 0);
+ }
+ else
+ {
+ clear(source);
+ }
+}
+//____________________________________________________________________________
+
+//overload of binary version for strings:
+
+template<typename TTargetValue, typename TTargetSpec, typename TSource>
+inline void
+move(String<TTargetValue, TTargetSpec> & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ typedef String<TTargetValue, TTargetSpec> TTarget;
+ move(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template<typename TTargetValue, typename TTargetSpec, typename TSource>
+inline void
+move(String<TTargetValue, TTargetSpec> & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ typedef String<TTargetValue, TTargetSpec> TTarget;
+ move(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+
+//____________________________________________________________________________
+
+template<typename TTargetValue, typename TTargetSpec, typename TSource, typename TTag>
+inline void
+move(String<TTargetValue, TTargetSpec> & target,
+ TSource & source,
+ Tag<TTag> const tag)
+{
+SEQAN_CHECKPOINT
+ assign(target, source, tag);
+}
+
+template<typename TTargetValue, typename TTargetSpec, typename TSource, typename TTag>
+inline void
+move(String<TTargetValue, TTargetSpec> & target,
+ TSource const & source,
+ Tag<TTag> const tag)
+{
+SEQAN_CHECKPOINT
+ assign(target, source, tag);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// valueConstructMove:
+// it is usually better for strings to default construct and move instead of
+// copy construct strings
+
+/*
+template <typename TIterator, typename TValue, typename TSpec>
+inline void
+valueConstructMove(TIterator it,
+ String<TValue, TSpec> const & value)
+{
+ valueConstruct(it);
+ move(*it, value);
+}
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+// append
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.append.param.target.type:Class.String
+///.Function.append.param.source.type:Class.String
+
+template <typename TExpand>
+struct _Append_String
+{
+ template <typename TTarget, typename TSource>
+ static inline void
+ append_(TTarget & target,
+ TSource & source)
+ {
+ if (!id(source) || !shareResources(target, source))
+ {
+SEQAN_CHECKPOINT
+ typename Size<TTarget>::Type target_length = length(target);
+ typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand());
+ arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()) + target_length);
+ }
+ else
+ {
+SEQAN_CHECKPOINT
+ typename _TempCopy<TSource>::Type temp(source, length(source));
+ assign(target, temp, TExpand());
+ }
+ }
+
+ template <typename TTarget, typename TSource>
+ static inline void
+ append_(TTarget & target,
+ TSource & source,
+ typename Size<TTarget>::Type limit)
+ {
+ typename Iterator<TTarget, Standard>::Type target_begin = begin(target, Standard());
+ if (!id(source) || !shareResources(target, source))
+ {
+SEQAN_CHECKPOINT
+ typename Size<TTarget>::Type target_length = length(target);
+ typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), target_length, target_length, limit, TExpand());
+ arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()) + target_length);
+ }
+ else
+ {
+ typename Size<TTarget>::Type target_length = length(target);
+ if (target_length >= limit)
+ {
+SEQAN_CHECKPOINT
+ arrayDestruct(target_begin + limit, target_begin + target_length);
+ _setLength(target, limit);
+ }
+ else
+ {
+SEQAN_CHECKPOINT
+ limit -= target_length;
+ typename Size<TTarget>::Type source_length = length(source) ;
+ if (source_length > limit) source_length = limit;
+
+ typename _TempCopy<TSource>::Type temp(source, source_length);
+ append(target, temp, TExpand());
+ }
+ }
+ }
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template<typename TTargetValue, typename TTargetSpec, typename TSource, typename TExpand>
+inline void
+append(String<TTargetValue, TTargetSpec> & target,
+ TSource const & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ typedef String<TTargetValue, TTargetSpec> TTarget;
+ _Append_String<Tag<TExpand> const>::append_(target, source);
+}
+
+template<typename TTargetValue, typename TTargetSpec, typename TSource, typename TExpand>
+inline void
+append(String<TTargetValue, TTargetSpec> & target,
+ TSource const & source,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ typedef String<TTargetValue, TTargetSpec> TTarget;
+ _Append_String<Tag<TExpand> const>::append_(target, source, limit);
+}
+
+//____________________________________________________________________________
+//this variant is a workaround for the "const array"-bug of VC++
+
+template<typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TExpand>
+inline void
+append(String<TTargetValue, TTargetSpec> & target,
+ TSourceValue * source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ typedef String<TTargetValue, TTargetSpec> TTarget;
+ _Append_String<Tag<TExpand> const>::append_(target, source);
+}
+
+template<typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TExpand>
+inline void
+append(String<TTargetValue, TTargetSpec> & target,
+ TSourceValue * source,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ typedef String<TTargetValue, TTargetSpec> TTarget;
+ _Append_String<Tag<TExpand> const>::append_(target, source, limit);
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// appendValue
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TExpand>
+struct _Append_Value_2_String
+{
+ template <typename T, typename TValue>
+ static inline void
+ appendValue_(T & me,
+ TValue & _value)
+ {
+SEQAN_CHECKPOINT
+ typename Position<T>::Type me_length = length(me);
+ if (capacity(me) <= me_length)
+ {
+ typename Value<T>::Type temp_copy(_value); //temp copy because resize could invalidate _value
+ typename Size<T>::Type new_length = resize(me, me_length + 1, TExpand());
+ if (me_length < new_length)
+ {
+ valueConstruct(begin(me) + me_length, temp_copy); //??? this should be valueMoveConstruct
+ }
+ }
+ else
+ {
+ valueConstruct(begin(me, Standard()) + me_length, _value);
+ _setLength(me, me_length + 1);
+ }
+ }
+};
+
+//____________________________________________________________________________
+
+template <typename TTargetValue, typename TTargetSpec, typename TValue, typename TExpand>
+inline void
+appendValue(String<TTargetValue, TTargetSpec> & me,
+ TValue const & _value,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Append_Value_2_String<Tag<TExpand> const>::appendValue_(me, _value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// insertValue
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Function.insertValue:
+*/
+
+template <typename TExpand>
+struct _Insert_Value_2_String
+{
+ template <typename T, typename TPosition, typename TValue>
+ static inline void
+ insertValue_(T & me,
+ TPosition pos,
+ TValue & _value)
+ {
+SEQAN_CHECKPOINT
+ typename Value<T>::Type temp_copy = _value; //temp copy because resizeSpace could invalidate _value
+ resizeSpace(me, 1, pos, pos, TExpand());
+ if ((typename Size<T>::Type) pos < length(me))
+ {
+ moveValue(me, pos, temp_copy);
+ }
+ }
+};
+
+//____________________________________________________________________________
+
+template <typename TTargetValue, typename TTargetSpec, typename TPosition, typename TValue, typename TExpand>
+inline void
+insertValue(String<TTargetValue, TTargetSpec> & me,
+ TPosition pos,
+ TValue const & _value,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Insert_Value_2_String<Tag<TExpand> const>::insertValue_(me, pos, _value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// replace
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.replace.param.target.type:Class.String
+///.Function.replace.param.source.type:Class.String
+
+template <typename TExpand>
+struct _Replace_String
+{
+ template <typename TTarget, typename TSource>
+ static inline void
+ replace_(TTarget & target,
+ typename Size<TTarget>::Type pos_begin,
+ typename Size<TTarget>::Type pos_end,
+ TSource & source)
+ {
+ if (!id(source) || !shareResources(target, source))
+ {
+SEQAN_CHECKPOINT
+ typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), pos_begin, pos_end, TExpand());
+ arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()) + pos_begin);
+ }
+ else
+ {
+SEQAN_CHECKPOINT
+ typename _TempCopy<TSource>::Type temp(source, length(source));
+ replace(target, pos_begin, pos_end, temp, TExpand());
+ }
+ }
+
+ template <typename TTarget, typename TSource>
+ static inline void
+ replace_(TTarget & target,
+ typename Size<TTarget>::Type pos_begin,
+ typename Size<TTarget>::Type pos_end,
+ TSource & source,
+ typename Size<TTarget>::Type limit)
+ {
+ if (!id(source) || !shareResources(target, source))
+ {
+SEQAN_CHECKPOINT
+ typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), pos_begin, pos_end, limit, TExpand());
+ arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()) + pos_begin);
+ }
+ else
+ {
+ if (pos_begin >= limit)
+ {
+SEQAN_CHECKPOINT
+ arrayDestruct(begin(target) + limit, end(target));
+ _setLength(target, limit);
+ }
+ else
+ {
+SEQAN_CHECKPOINT
+ limit -= pos_begin;
+ typename Size<TTarget>::Type source_length = length(source) ;
+ if (source_length > limit) source_length = limit;
+
+ typename _TempCopy<TSource>::Type temp(source, source_length);
+ replace(target, pos_begin, pos_end, temp, limit, TExpand());
+ }
+ }
+ }
+
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template<typename TTargetValue, typename TTargetSpec, typename TSource, typename TExpand>
+inline void
+replace(String<TTargetValue, TTargetSpec> & target,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end,
+ TSource const & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ typedef String<TTargetValue, TTargetSpec> TTarget;
+ _Replace_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source);
+}
+
+template<typename TTargetValue, typename TTargetSpec, typename TSource, typename TExpand>
+inline void
+replace(String<TTargetValue, TTargetSpec> & target,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end,
+ TSource const & source,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ typedef String<TTargetValue, TTargetSpec> TTarget;
+ _Replace_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source, limit);
+}
+
+//____________________________________________________________________________
+//this variant is a workaround for the "const array"-bug of VC++
+
+template<typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TExpand>
+inline void
+replace(String<TTargetValue, TTargetSpec> & target,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end,
+ TSourceValue const * source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ typedef String<TTargetValue, TTargetSpec> TTarget;
+ _Replace_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source);
+}
+
+template<typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TExpand>
+inline void
+replace(String<TTargetValue, TTargetSpec> & target,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end,
+ TSourceValue const * source,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ typedef String<TTargetValue, TTargetSpec> TTarget;
+ _Replace_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source, limit);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// handling of iterators as begin and end
+
+/*
+template<typename TTargetValue, typename TTargetSpec, typename TSource, typename TExpand>
+inline void
+replace(String<TTargetValue, TTargetSpec> & target,
+ typename Iterator< String<TTargetValue, TTargetSpec>, Rooted >::Type pos_begin,
+ typename Iterator< String<TTargetValue, TTargetSpec>, Rooted >::Type pos_end,
+ TSource & source,
+ Tag<TExpand> const tag)
+{
+ replace(target, position(pos_begin), position(pos_end), source, tag);
+}
+
+template<typename TTargetValue, typename TTargetSpec, typename TSource, typename TExpand>
+inline void
+replace(String<TTargetValue, TTargetSpec> & target,
+ typename Iterator< String<TTargetValue, TTargetSpec>, Rooted >::Type pos_begin,
+ typename Iterator< String<TTargetValue, TTargetSpec>, Rooted >::Type pos_end,
+ TSource & source,
+ typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
+ Tag<TExpand> const tag)
+{
+ replace(target, position(pos_begin), position(pos_end), source, limit, tag);
+}
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Internal._reallocateStorage:
+..cat:Functions
+..summary:Allocates a new buffer if needed.
+..signature:_reallocateStorage(object, new_capacity, resize_tag)
+..param.object:A container for which the buffer is reallocated.
+...type:Class.String
+..param.new_capacity:The capacity $object$ will get after reallocating the buffer.
+..param.resize_tag:Strategy that is used for changing the capacity.
+..returns:Returns the old buffer, if a new buffer has been allocated, $0$ otherwise.
+..remarks:This function only allocates a new buffer if the current capacity is less then $new_capacity$.
+A new buffer is not filled with any content, all copy operations must be done by the caller.
+..remarks:If $object$ never had a buffer, or the buffer is not changed by the function,
+the returned pointer is 0.
+*/
+
+template <typename TValue, typename TSpec>
+inline typename Value<String<TValue, TSpec> >::Type *
+_reallocateStorage(
+ String<TValue, TSpec> & me,
+ typename Size< String<TValue, TSpec> >::Type new_capacity,
+ Exact)
+{
+ if (new_capacity <= capacity(me)) return 0;
+ else
+ {
+SEQAN_CHECKPOINT
+ return _allocateStorage(me, new_capacity);
+ }
+}
+
+template <typename TValue, typename TSpec>
+inline typename Value<String<TValue, TSpec> >::Type *
+_reallocateStorage(
+ String<TValue, TSpec> & me,
+ typename Size< String<TValue, TSpec> >::Type new_capacity,
+ typename Size< String<TValue, TSpec> >::Type limit,
+ Exact)
+{
+ if (new_capacity <= capacity(me)) return 0;
+ else
+ {
+SEQAN_CHECKPOINT
+ if (new_capacity > limit) new_capacity = limit;
+ return _allocateStorage(me, new_capacity);
+ }
+}
+
+template <typename TValue, typename TSpec>
+inline typename Value<String<TValue, TSpec> >::Type *
+_reallocateStorage(
+ String<TValue, TSpec> & me,
+ typename Size< String<TValue, TSpec> >::Type new_capacity,
+ Generous)
+{
+ if (new_capacity <= capacity(me)) return 0;
+ else
+ {
+SEQAN_CHECKPOINT
+ new_capacity = computeGenerousCapacity(me, new_capacity);
+ return _allocateStorage(me, new_capacity);
+ }
+}
+
+template <typename TValue, typename TSpec>
+inline typename Value<String<TValue, TSpec> >::Type *
+_reallocateStorage(
+ String<TValue, TSpec> & me,
+ typename Size< String<TValue, TSpec> >::Type new_capacity,
+ typename Size< String<TValue, TSpec> >::Type limit,
+ Generous)
+{
+ if (new_capacity <= capacity(me)) return 0;
+ else
+ {
+SEQAN_CHECKPOINT
+ new_capacity = computeGenerousCapacity(me, new_capacity);
+ if (new_capacity > limit) new_capacity = limit;
+ return _allocateStorage(me, new_capacity);
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+///.Function.resize.param.object.type:Class.String
+
+template <typename TExpand>
+struct _Resize_String
+{
+ template <typename T>
+ static inline typename Size<T>::Type
+ resize_(
+ T & me,
+ typename Size<T>::Type new_length)
+ {
+ typedef typename Size<T>::Type TSize;
+ TSize me_length = length(me);
+ if (new_length < me_length)
+ {
+SEQAN_CHECKPOINT
+ arrayDestruct(begin(me, Standard()) + new_length, begin(me, Standard()) + me_length);
+ }
+ else
+ {
+ typename Size<T>::Type me_capacity = capacity(me);
+ if (new_length > me_capacity)
+ {
+SEQAN_CHECKPOINT
+ TSize new_capacity = reserve(me, new_length, TExpand());
+ if (new_capacity < new_length)
+ {
+ new_length = new_capacity;
+ }
+ }
+ if (new_length > me_length)
+ {
+SEQAN_CHECKPOINT
+ arrayConstruct(begin(me, Standard()) + me_length, begin(me, Standard()) + new_length);
+ }
+ }
+
+ _setLength(me, new_length);
+ return new_length;
+ }
+};
+
+template <typename TValue, typename TSpec, typename TSize, typename TExpand>
+inline typename Size< String<TValue, TSpec> >::Type
+resize(
+ String<TValue, TSpec> & me,
+ TSize new_length,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.fill.param.object.type:Class.String
+
+template <typename TExpand>
+struct _Fill_String
+{
+ template <typename T, typename TValue>
+ static inline typename Size<T>::Type
+ fill_(
+ T & me,
+ typename Size<T>::Type new_length,
+ TValue const & val)
+ {
+ typename Size<T>::Type me_length = length(me);
+ if (new_length < me_length)
+ {
+SEQAN_CHECKPOINT
+ arrayDestruct(begin(me, Standard()) + new_length, begin(me, Standard()) + me_length);
+ }
+ else
+ {
+ typename Size<T>::Type me_capacity = capacity(me);
+ if (new_length > me_capacity)
+ {
+SEQAN_CHECKPOINT
+ new_length = reserve(me, new_length, TExpand());
+ }
+ if (new_length > me_length)
+ {
+SEQAN_CHECKPOINT
+ arrayConstruct(begin(me, Standard()) + me_length, begin(me, Standard()) + new_length, val);
+ }
+ }
+
+ _setLength(me, new_length);
+ return new_length;
+ }
+};
+
+template <typename TValue, typename TSpec, typename TSize, typename TValue2, typename TExpand>
+inline TSize
+fill(String<TValue, TSpec> & me,
+ TSize new_length,
+ TValue2 const & val,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ return _Fill_String<Tag<TExpand> const>::fill_(me, new_length, val);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+/*
+template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec>
+String<TLeftValue, TLeftSpec> const &
+operator += (String<TLeftValue, TLeftSpec> & left,
+ String<TRightValue, TRightSpec> const & right)
+{
+ append(left, right);
+ return left;
+}
+
+template <typename TLeftValue, typename TLeftSpec, typename TRight>
+String<TLeftValue, TLeftSpec> const &
+operator += (String<TLeftValue, TLeftSpec> & left,
+ TRight const & right)
+{
+ append(left, right);
+ return left;
+}
+
+template <typename TLeft, typename TRightValue, typename TRightSpec>
+TLeft const &
+operator += (TLeft & left,
+ String<TRightValue, TRightSpec> const & right)
+{
+ append(left, right);
+ return left;
+}
+*/
+
+template <typename TLeftValue, typename TLeftSpec, typename TRight >
+String<TLeftValue, TLeftSpec> const &
+operator += (String<TLeftValue, TLeftSpec> & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ append(left, right);
+ return left;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftValue, typename TLeftSpec, typename TRight >
+inline bool
+operator == (String<TLeftValue, TLeftSpec> const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ typename Comparator<String<TLeftValue, TLeftSpec> >::Type _lex(left, right);
+ return isEqual(_lex);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftValue, typename TLeftSpec, typename TRight >
+inline bool
+operator !=(String<TLeftValue, TLeftSpec> const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ typename Comparator<String<TLeftValue, TLeftSpec> >::Type _lex(left, right);
+ return isNotEqual(_lex);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftValue, typename TLeftSpec, typename TRight>
+inline bool
+operator < (String<TLeftValue, TLeftSpec> const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return isLess(left, right, typename DefaultPrefixOrder<String<TLeftValue, TLeftSpec> >::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftValue, typename TLeftSpec, typename TRight>
+inline bool
+operator <= (String<TLeftValue, TLeftSpec> const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return isLessOrEqual(left, right, typename DefaultPrefixOrder<String<TLeftValue, TLeftSpec> >::Type());
+}
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftValue, typename TLeftSpec, typename TRight>
+inline bool
+operator > (String<TLeftValue, TLeftSpec> const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return isGreater(left, right, typename DefaultPrefixOrder<String<TLeftValue, TLeftSpec> >::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftValue, typename TLeftSpec, typename TRight>
+inline bool
+operator >= (String<TLeftValue, TLeftSpec> const & left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return isGreaterOrEqual(left, right, typename DefaultPrefixOrder<String<TLeftValue, TLeftSpec> >::Type());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// stream operators
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TStream, typename TValue, typename TSpec>
+inline TStream &
+operator << (TStream & target,
+ String<TValue, TSpec> const & source)
+{
+SEQAN_CHECKPOINT
+ write(target, source);
+ return target;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TStream, typename TValue, typename TSpec>
+inline TStream &
+operator >> (TStream & source,
+ String<TValue, TSpec> & target)
+{
+SEQAN_CHECKPOINT
+ read(source, target);
+ return source;
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+/*
+//////////////////////////////////////////////////////////////////////////////
+// Converter
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TTarget, typename TSource, typename TSpec>
+struct Value<String<Convert<TTarget, TSource>, TSpec> >:
+ Value< String<TSource, TSpec> >
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename T, typename TAccessor, typename TConverter>
+struct _AccessorConverter
+{
+ typedef T Type;
+};
+template <typename T, typename TAccessor, typename TConverter>
+struct _AccessorConverter<T, TAccessor &, typename TConverter &>
+{
+ typedef T & Type;
+};
+
+template <typename TTarget, typename TSource, typename TSpec>
+struct GetValue<String<Converter<TTarget, TSource>, TSpec> >:
+ _AccessorConverter<
+ TTarget,
+ typename GetValue<String<TSource, TSpec> >::Type,
+ typename Converter<TTarget, TSource>::Type
+ >
+{
+};
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+//////////////////////////////////////////////////////////////////////////////
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/sequence/string_cstyle.h b/src/libSSA/seqan/sequence/string_cstyle.h
new file mode 100644
index 0000000..937c968
--- /dev/null
+++ b/src/libSSA/seqan/sequence/string_cstyle.h
@@ -0,0 +1,808 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: string_cstyle.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SEQUENCE_CSTYLE_H
+#define SEQAN_HEADER_SEQUENCE_CSTYLE_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+//string that exports an interface to cstyle strings.
+
+/**
+.Spec.CStyle String:
+..cat:Strings
+..general:Class.String
+..summary:Allows adaption of strings to C-style strings.
+..signature:String<TValue, CStyle>
+..param.TValue:The value type, that is the type of the items/characters stored in the string.
+...remarks:Use @Metafunction.Value@ to get the value type for a given class.
+...note:$TValue$ must be a simple type.???(Link)
+..remarks:
+...text:The purpose of this class is to access to the content of a sequence
+in a "zero terminated string" style.
+This can be useful if SEQAN classes has to be integrated in programs that use $char$ arrays
+to store strings.
+Instances of $String<TValue, CStyle>$ can implicitely converted to a $TValue *$ that
+points to a zero terminated CStyle of $TValue$.
+...text:The stored c-style string object can be set by constructors or assignment.
+The content of a c-style string can eighter be stored in a separate buffer, that is the source string
+is copied. Or the buffer of the source string itself is used instead, in this case the c-style string
+depends on the source string and gets invalid as soon as the buffer of the source string is destroyed.
+...text:Hence, this class is a kind of adaptor from an arbitrary SEQAN string to char arrays.
+Of course, the opposite way is possible too:
+Read @Adaption.char array.here@ about adapting char arrays to SEQAN strings.
+..example:
+...code://Create a string str:
+String<char> str = "this is a test string";
+
+//Create a c-style string object for str:
+String<char, CStyle> c_style = str;
+
+//Now use c_style as char array:
+strcmp(c_style, "compare it to this string");
+...text:If the c-style string is needed only temporarily, the function $toCString$ can be used:
+...code:String<char> str = "this is a test string";
+strcmp(toCString(str), "compare it to this string");
+*/
+
+struct CStyle;
+
+template <typename TValue>
+class String <TValue, CStyle >
+{
+protected:
+ TValue * data_begin;
+ TValue * data_end;
+ size_t data_size; //if data_size > 0, then the buffer is owned by me and must be deallocated
+
+public:
+ static TValue EMPTY_STRING;
+//____________________________________________________________________________
+
+public:
+ String():
+ data_begin(&EMPTY_STRING),
+ data_end(&EMPTY_STRING),
+ data_size(0)
+ {
+SEQAN_CHECKPOINT
+ }
+
+//____________________________________________________________________________
+
+ template <typename TString>
+ String(TString & str):
+ data_size(0)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, str);
+ }
+ template <typename TString>
+ String(TString const & str):
+ data_size(0)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, str);
+ }
+
+ String(String & str):
+ data_size(0)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, str);
+ }
+ String(String const & str):
+ data_size(0)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, str);
+ }
+
+ String(TValue * str):
+ data_begin(str),
+ data_end(end(str)),
+ data_size(0)
+ {
+SEQAN_CHECKPOINT
+ }
+
+//____________________________________________________________________________
+
+ template <typename TString>
+ String & operator = (TString & str)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, str);
+ return *this;
+ }
+ template <typename TString>
+ String & operator = (TString const & str)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, str);
+ return *this;
+ }
+ String & operator = (String & str)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, str);
+ return *this;
+ }
+ String & operator = (String const & str)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, str);
+ return *this;
+ }
+
+ ~String()
+ {
+SEQAN_CHECKPOINT
+ clear(*this);
+ }
+
+//____________________________________________________________________________
+
+ operator TValue * ()
+ {
+SEQAN_CHECKPOINT
+ return data_begin;
+ }
+
+ operator TValue const * () const
+ {
+SEQAN_CHECKPOINT
+ return data_begin;
+ }
+
+//____________________________________________________________________________
+
+ friend inline void
+ move(
+ String & target,
+ String & source)
+ {
+SEQAN_CHECKPOINT
+ clear(target);
+
+ target.data_begin = source.data_begin;
+ target.data_end = source.data_end;
+ target.data_size = source.data_size;
+
+ source.data_begin = 0;
+ source.data_end = 0;
+ source.data_size = 0;
+ }
+
+//____________________________________________________________________________
+
+ friend inline typename Iterator<String, Standard>::Type
+ begin(String & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return me.data_begin;
+ }
+ friend inline typename Iterator<String const, Standard>::Type
+ begin(String const & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return me.data_begin;
+ }
+
+//____________________________________________________________________________
+
+ friend inline void
+ _setBegin(String & me, TValue * new_begin)
+ {
+SEQAN_CHECKPOINT
+ me.data_begin = new_begin;
+ }
+
+//____________________________________________________________________________
+
+ friend inline typename Iterator<String, Standard>::Type
+ end(String & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return me.data_end;
+ }
+ friend inline typename Iterator<String const, Standard>::Type
+ end(String const & me,
+ Standard)
+ {
+SEQAN_CHECKPOINT
+ return me.data_end;
+ }
+
+//____________________________________________________________________________
+
+ friend inline void
+ _setEnd(String & me, TValue * new_end)
+ {
+SEQAN_CHECKPOINT
+ me.data_end = new_end;
+ *new_end = TValue(); //??? ist das wirklich sinnvoll fuer typen, die weder char noch wchar_t sind?
+ }
+
+//____________________________________________________________________________
+
+ friend inline size_t
+ capacity(String const & me)
+ {
+SEQAN_CHECKPOINT
+ if (me.data_size) return me.data_size -1;
+ else return me.data_end - me.data_begin;
+ }
+
+
+//____________________________________________________________________________
+
+ friend inline void
+ clear(String & me)
+ {
+ if (me.data_size)
+ {
+SEQAN_CHECKPOINT
+// arrayDestruct(me, length(me));
+ deallocate(me, me.data_begin, me.data_size);
+ me.data_size = 0;
+ }
+ me.data_begin = me.data_end = &EMPTY_STRING;
+ }
+//____________________________________________________________________________
+
+//??? TODO: reserve
+
+//____________________________________________________________________________
+
+///.Internal._reallocateStorage.param.object.type:Spec.CStyle String
+///.Internal._reallocateStorage.param.resize_tag.remarks:@Spec.CStyle String@ only supports @Tag.Overflow Strategy.exact at .
+//this function works also for dependent buffers
+ friend inline TValue *
+ _reallocateStorage(
+ String & me,
+ size_t new_capacity,
+ Exact)
+ {
+SEQAN_CHECKPOINT
+ TValue * return_value;
+ if (me.data_size)
+ {//dependent
+ return_value = me.data_begin;
+ }
+ else
+ {//not dependent
+ return_value = 0;
+ }
+
+ me.data_size = new_capacity + 1; //+1 for zero termination
+ allocate(me, me.data_begin, me.data_size, TagAllocateStorage());
+ return return_value;
+ }
+//____________________________________________________________________________
+
+///.Internal._deallocateStorage.param.object.type:Spec.CStyle String
+
+ friend inline void
+ _deallocateStorage(
+ String & me,
+ TValue * ptr,
+ size_t capacity)
+ {
+SEQAN_CHECKPOINT
+ size_t size = capacity + 1;
+ deallocate(me, ptr, size, TagAllocateStorage());
+ }
+
+//____________________________________________________________________________
+
+/**
+.Function.dependent:
+..summary:Test whether object depends on other objects.
+..cat:Dependent Objects
+..signature:bool dependent(object)
+..param.object:An object.
+...type:Spec.CStyle String
+..returns:$true$ if $object$ depends one some other object, $false$ otherwise.
+..remarks:An object "$a$" depends on another object "$b$", if changing "$b$" can invalidate "$a$";
+especially the destruction of "$b$" invalidates "$a$".
+*/
+ friend inline bool
+ dependent(String & me)
+ {
+SEQAN_CHECKPOINT
+ return (me.data_size == 0);
+ }
+//____________________________________________________________________________
+
+//special implementation for char array sources
+ friend inline void
+ assign(String & target,
+ TValue * source)
+ {
+ SEQAN_CHECKPOINT
+ clear(target);
+ target.data_begin = source;
+ target.data_end = end(source);
+ }
+
+//____________________________________________________________________________
+
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// Define the static member
+
+template <typename TValue>
+TValue String<TValue, CStyle >::EMPTY_STRING = TValue();
+
+//////////////////////////////////////////////////////////////////////////////
+// Metafunctions
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue>
+struct DefaultOverflowImplicit<String<TValue, CStyle> >
+{
+ typedef Exact Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue>
+struct IsContiguous< String<TValue, CStyle > >
+{
+ typedef True Type;
+ enum { VALUE = true };
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// assign
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TTargetValue, typename TSource, typename TExpand>
+inline void
+assign(String<TTargetValue, CStyle> & target,
+ TSource & source,
+ Tag<TExpand> const tag)
+{
+SEQAN_CHECKPOINT
+ create(target, source, tag);
+}
+
+template <typename TTargetValue, typename TSource, typename TExpand>
+inline void
+assign(String<TTargetValue, CStyle> & target,
+ TSource const & source,
+ Tag<TExpand> const tag)
+{
+SEQAN_CHECKPOINT
+ create(target, source, tag);
+}
+
+template <typename TTargetValue, typename TSource, typename TSize, typename TExpand>
+inline void
+assign(String<TTargetValue, CStyle> & target,
+ TSource & source,
+ TSize limit,
+ Tag<TExpand> const tag)
+{
+SEQAN_CHECKPOINT
+ create(target, source, tag);
+}
+
+template <typename TTargetValue, typename TSource, typename TSize, typename TExpand>
+inline void
+assign(String<TTargetValue, CStyle> & target,
+ TSource const & source,
+ TSize limit,
+ Tag<TExpand> const tag)
+{
+SEQAN_CHECKPOINT
+ create(target, source, limit, tag);
+}
+
+
+//____________________________________________________________________________
+//this variant is a workaround for the "const array"-bug of VC++
+
+template <typename TTargetValue, typename TSourceValue, typename TExpand>
+inline void
+assign(String<TTargetValue, CStyle> & target,
+ TSourceValue const * source,
+ Tag<TExpand> const tag)
+{
+SEQAN_CHECKPOINT
+ create(target, source, tag);
+}
+
+template <typename TTargetValue, typename TSourceValue, typename TSize, typename TExpand>
+inline void
+assign(String<TTargetValue, CStyle> & target,
+ TSourceValue const * source,
+ TSize limit,
+ Tag<TExpand> const tag)
+{
+SEQAN_CHECKPOINT
+ create(target, source, limit, tag);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+//If source is non-const String, then there could be the possibility
+//to use the source buffer
+
+template <typename TExpand, bool IS_CONTIGUOUS>
+struct _Assign_String_2_StringArray;
+
+//____________________________________________________________________________
+
+template <typename TExpand>
+struct _Assign_String_2_StringArray<TExpand, true>
+{
+ template <typename TValue, typename TSourceSpec>
+ static inline void
+ assign_(String<TValue, CStyle> & target,
+ String<TValue, TSourceSpec> & source)
+ {
+ if (capacity(source) > length(source))
+ {//use source's buffer
+SEQAN_CHECKPOINT
+ clear(target);
+ _setBegin(target, begin(source));
+ _setEnd(target, end(source));
+ }
+ else
+ {
+ create(target, source, TExpand());
+ }
+ }
+
+//special treatment of char:
+//_computeSize4Capacity is specialized for char such that there
+//is enough place for the zero termination
+
+ template <typename TSourceSpec>
+ static inline void
+ assign_(String<char, CStyle> & target,
+ String<char, TSourceSpec> & source)
+ {
+SEQAN_CHECKPOINT
+ clear(target);
+ _setBegin(target, begin(source));
+ _setEnd(target, end(source));
+ }
+};
+
+//____________________________________________________________________________
+
+template <typename TExpand>
+struct _Assign_String_2_StringArray<TExpand, false>
+{
+ template <typename TValue, typename TSourceSpec>
+ static inline void
+ assign_(String<TValue, CStyle> & target,
+ String<TValue, TSourceSpec> & source)
+ {
+SEQAN_CHECKPOINT
+ create(target, source, TExpand());
+ }
+};
+
+//____________________________________________________________________________
+
+template <typename TValue, typename TSourceSpec, typename TExpand>
+inline void
+assign(String<TValue, CStyle> & target,
+ String<TValue, TSourceSpec> & source,
+ Tag<TExpand> const)
+{
+ typedef String<TValue, TSourceSpec> TSource;
+ _Assign_String_2_StringArray<Tag<TExpand> const, IsContiguous<TSource>::VALUE>::assign_(target, source);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// create
+//////////////////////////////////////////////////////////////////////////////
+
+//see basic_holder
+/**
+.Function.create:
+..signature:create(target, source [, limit] [,resize_tag])
+..param.target: Gets a copy of the content of $source$.
+...type:Spec.CStyle String
+..param.source: Is copied to $target$.
+..param.limit: The maximal length of $target$ after the operation. (optional)
+..param.resize_tag: Specifies the strategy that is applied if $target$ has not enough capacity to store the complete content. (optional)
+...type:Tag.Overflow Strategy
+...default:Specified by @Metafunction.DefaultOverflowImplicit@ of the $target$ type.
+..remarks.text:It is guaranteed, that after calling this function $source$ and $target$ can be used independently.
+..see:Spec.CStyle String
+*/
+
+template <typename TExpand>
+struct _Create_ArrayString_Expand
+{
+ template <typename TTarget, typename TSource>
+ static inline void
+ create_(TTarget & target,
+ TSource & source)
+ {
+ typename Size<TTarget>::Type source_length = length(source);
+ if (dependent(target) || (capacity(target) < source_length))
+ {
+SEQAN_CHECKPOINT
+ typename Size<TTarget>::Type old_target_capacity = capacity(target);
+ typename Value<TTarget>::Type * buf = _reallocateStorage(target, source_length, TExpand());
+ if (buf)
+ {
+ _deallocateStorage(target, buf, old_target_capacity);
+ }
+ }
+ if (length(source) > 0)
+ {
+ assignValue(begin(target, Standard()), 0); //set target length to 0
+ assign(begin(target, Standard()), source, Insist());
+ _setEnd(target, begin(target) + source_length);
+ }
+ }
+
+ template <typename TTarget, typename TSource, typename TLimit>
+ static inline void
+ create_(TTarget & target,
+ TSource & source,
+ TLimit limit)
+ {
+ typename Size<TTarget>::Type copy_length = length(source);
+ if (limit < copy_length)
+ {
+ copy_length = limit;
+ }
+ if (dependent(target) || (capacity(target) < copy_length))
+ {
+SEQAN_CHECKPOINT
+ typename Size<TTarget>::Type old_target_capacity = capacity(target);
+ TTarget * buf = _reallocateStorage(target, copy_length, TExpand());
+ if (buf)
+ {
+ _deallocateStorage(target, buf, old_target_capacity);
+ }
+ }
+ assign(begin(target, Standard()), source, copy_length, Insist());
+ _setEnd(target, begin(target, Standard()) + copy_length);
+ }
+};
+//____________________________________________________________________________
+
+template <typename TExpand>
+struct _Create_ArrayString;
+//____________________________________________________________________________
+
+template <>
+struct _Create_ArrayString<Insist>
+{
+ template <typename TTarget, typename TSource>
+ static inline void
+ create_(TTarget & target,
+ TSource & source)
+ {
+SEQAN_CHECKPOINT
+ typename Size<TTarget>::Type source_length = length(source);
+ if (dependent(target))
+ {
+ TTarget * buf = _reallocateStorage(target, source_length, Exact());
+ }
+ assign(begin(target, Standard()), source, source_length, Insist());
+ _setEnd(target, begin(target, Standard()) + source_length);
+ }
+
+ template <typename TTarget, typename TSource, typename TSize>
+ static inline void
+ create_(TTarget & target,
+ TSource & source,
+ TSize limit)
+ {
+SEQAN_CHECKPOINT
+ typename Size<TTarget>::Type copy_size = length(source);
+ if (limit < copy_size)
+ {
+ copy_size = limit;
+ }
+ if (dependent(target))
+ {
+ TTarget * buf = _reallocateStorage(target, copy_size, Exact());
+ }
+ assign(begin(target, Standard()), source, copy_size, Insist());
+ _setEnd(target, begin(target, Standard()) + copy_size);
+ }
+};
+
+//____________________________________________________________________________
+
+template <>
+struct _Create_ArrayString<Limit>
+{
+ template <typename TTarget, typename TSource>
+ static inline void
+ create_(TTarget & target,
+ TSource & source)
+ {
+SEQAN_CHECKPOINT
+ _Create_ArrayString<Insist>::create_(target, source, capacity(target));
+ }
+
+ template <typename TTarget, typename TSource, typename TSize>
+ static inline void
+ create_(TTarget & target,
+ TSource & source,
+ TSize & limit)
+ {
+SEQAN_CHECKPOINT
+ typename Size<TTarget>::Type copy_size = capacity(target);
+ if (copy_size > limit)
+ {
+ copy_size = limit;
+ }
+ _Create_ArrayString<Insist>::create_(target, source, copy_size);
+ }
+};
+//____________________________________________________________________________
+
+template <>
+struct _Create_ArrayString<Exact>:
+ _Create_ArrayString_Expand<Exact>
+{
+};
+
+//____________________________________________________________________________
+
+template <>
+struct _Create_ArrayString<Generous>:
+ _Create_ArrayString_Expand<Generous>
+{
+};
+
+//____________________________________________________________________________
+
+template <typename TTargetValue, typename TSource>
+inline void
+create(String<TTargetValue, CStyle> & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ typedef String<TTargetValue, CStyle> TTarget;
+ create(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+
+template <typename TTargetValue, typename TSource, typename TSize>
+inline void
+create(String<TTargetValue, CStyle> & target,
+ TSource & source,
+ TSize limit)
+{
+SEQAN_CHECKPOINT
+ typedef String<TTargetValue, CStyle> TTarget;
+ create(target, source, limit, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+
+//____________________________________________________________________________
+
+template <typename TTargetValue, typename TSource, typename TExpand>
+inline void
+create(String<TTargetValue, CStyle> & target,
+ TSource & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Create_ArrayString<Tag<TExpand> const>::create_(target, source);
+}
+
+template <typename TTargetValue, typename TSource, typename TSize, typename TExpand>
+inline void
+create(String<TTargetValue, CStyle> & target,
+ TSource & source,
+ TSize limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Create_ArrayString<Tag<TExpand> const>::create_(target, source, limit);
+}
+
+template <typename TTargetValue, typename TSource, typename TExpand>
+inline void
+create(String<TTargetValue, CStyle> & target,
+ TSource const & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Create_ArrayString<Tag<TExpand> const>::create_(target, source);
+}
+
+template <typename TTargetValue, typename TSource, typename TSize, typename TExpand>
+inline void
+create(String<TTargetValue, CStyle> & target,
+ TSource const & source,
+ TSize limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Create_ArrayString<Tag<TExpand> const>::create_(target, source, limit);
+}
+
+//____________________________________________________________________________
+//this variant is a workaround for the "const array"-bug of VC++
+
+template <typename TTargetValue, typename TSourceValue, typename TExpand>
+inline void
+create(String<TTargetValue, CStyle> & target,
+ TSourceValue const * source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Create_ArrayString<Tag<TExpand> const>::create_(target, source);
+}
+
+template <typename TTargetValue, typename TSourceValue, typename TSize, typename TExpand>
+inline void
+create(String<TTargetValue, CStyle> & target,
+ TSourceValue const * source,
+ TSize limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Create_ArrayString<Tag<TExpand> const>::create_(target, source, limit);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Shotcut
+
+/**
+.Function.toCString:
+..cat:Containers
+..summary:Access sequence as c-style string.
+..signature:toCString(object)
+..param.object:A sequence.
+...type:Class.String
+...type:Adaption.char array
+..returns:A temporary @Spec.CStyle String@ object of that was constructed for $object$.
+..remarks:Notational sugar.
+*/
+
+template <typename T>
+inline typename Value<T>::Type *
+toCString(T & me)
+{
+SEQAN_CHECKPOINT
+ return String<typename Value<T>::Type, CStyle>(me);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+//____________________________________________________________________________
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/sequence/string_packed.h b/src/libSSA/seqan/sequence/string_packed.h
new file mode 100644
index 0000000..1a8c9df
--- /dev/null
+++ b/src/libSSA/seqan/sequence/string_packed.h
@@ -0,0 +1,1262 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: string_packed.h,v 1.2 2009/02/19 01:51:23 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SEQUENCE_PACKED_H
+#define SEQAN_HEADER_SEQUENCE_PACKED_H
+
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// Tags
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename THostspec = Alloc<> >
+struct Packed;
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+.Spec.Packed String:
+..cat:Strings
+..general:Class.String
+..summary:A string that stores as many values in one machine word as possible.
+..signature:String<TValue, Packed<THostspec> >
+..param.TValue:The value type, that is the type of the items/characters stored in the string.
+...remarks:Use @Metafunction.Value@ to get the value type for a given class.
+..param.THostspec:The specializing type.
+...remarks:This is the specialization of the host string that is used for storing the packed values.
+...default:@Spec.Alloc String.Alloc<>@
+*/
+
+/*???TODO Optimierungsm�glichkeiten:
+- _clearSpace kopiert Zeichenweise im Packed-String, und nicht im Host-String
+- _clearSpace verwendet resize, um den Host zu vergr��ern, d.h. der Inhalt wird eventuell doppelt kopiert.
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+//Rooted expandable string
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename THostspec>
+class String<TValue, Packed<THostspec> >
+{
+protected:
+ typedef typename Host<String>::Type THost;
+ typedef typename Size<String>::Type TSize;
+
+ THost data_host;
+ TSize data_length;
+
+//____________________________________________________________________________
+
+public:
+ String():
+ data_length(0)
+ {
+SEQAN_CHECKPOINT
+ }
+
+ template <typename TSource>
+ String(TSource & source):
+ data_length(0)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source);
+ }
+ template <typename TSource>
+ String(TSource const & source):
+ data_length(0)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source);
+ }
+ String(String const & source):
+ data_length(0)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source);
+ }
+
+ template <typename TSource>
+ String & operator =(TSource const & source)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source);
+ return *this;
+ }
+ String & operator =(String const & source)
+ {
+SEQAN_CHECKPOINT
+ assign(*this, source);
+ return *this;
+ }
+
+ ~String()
+ {
+SEQAN_CHECKPOINT
+ }
+
+
+//____________________________________________________________________________
+
+ template <typename TPos>
+ inline typename Reference<String>::Type
+ operator [] (TPos pos)
+ {
+SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+
+ template <typename TPos>
+ inline typename Reference<String const>::Type
+ operator [] (TPos pos) const
+ {
+SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+
+//____________________________________________________________________________
+
+///.Function.host.param.object.type:Spec.Packed String
+
+ friend inline THost &
+ host(String & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_host;
+ }
+
+ friend inline THost const &
+ host(String const & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_host;
+ }
+
+//____________________________________________________________________________
+
+ friend inline TSize
+ length(String & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_length;
+ }
+
+ friend inline TSize
+ length(String const & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_length;
+ }
+
+//____________________________________________________________________________
+
+ friend inline void
+ _setLength(
+ String & me,
+ TSize new_length)
+ {
+SEQAN_CHECKPOINT
+ me.data_length = new_length;
+ _setLength(host(me), _PackedConsts<String>::toHostLength(new_length));
+ }
+
+//____________________________________________________________________________
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename THostspec>
+struct DefaultOverflowImplicit<String<TValue, Packed<THostspec> > >:
+ DefaultOverflowImplicit< typename Host<String<TValue, Packed<THostspec> > >::Type >
+{
+};
+template <typename TValue, typename THostspec>
+struct DefaultOverflowImplicit<String<TValue, Packed<THostspec> > const>:
+ DefaultOverflowImplicit< typename Host<String<TValue, Packed<THostspec> > const>::Type >
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename THostspec>
+struct DefaultOverflowExplicit<String<TValue, Packed<THostspec> > >:
+ DefaultOverflowExplicit< typename Host<String<TValue, Packed<THostspec> > >::Type >
+{
+};
+template <typename TValue, typename THostspec>
+struct DefaultOverflowExplicit<String<TValue, Packed<THostspec> > const>:
+ DefaultOverflowExplicit< typename Host<String<TValue, Packed<THostspec> > const>::Type >
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename THostspec>
+struct IsContiguous<String<TValue, Packed<THostspec> > >
+{
+ typedef False Type;
+ enum { VALUE = false };
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Host.param.T.type:Spec.Packed String
+
+template <typename TValue, typename THostspec>
+struct Host<String<TValue, Packed<THostspec> > >
+{
+ typedef String<unsigned int, THostspec> Type;
+};
+template <typename TValue, typename THostspec>
+struct Host<String<TValue, Packed<THostspec> > const>
+{
+ typedef String<unsigned int, THostspec> const Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename THostspec>
+struct GetValue<String<TValue, Packed<THostspec> > >:
+ Value<String<TValue, Packed<THostspec> > >
+{
+};
+template <typename TValue, typename THostspec>
+struct GetValue<String<TValue, Packed<THostspec> > const>:
+ Value<String<TValue, Packed<THostspec> > const>
+{
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename THostspec>
+struct Reference<String<TValue, Packed<THostspec> > >
+{
+ typedef typename Iterator<String<TValue, Packed<THostspec> >, Standard>::Type TIterator;
+ typedef Proxy<IteratorProxy<TIterator> > Type;
+};
+template <typename TValue, typename THostspec>
+struct Reference<String<TValue, Packed<THostspec> > const>
+{
+ typedef typename Iterator<String<TValue, Packed<THostspec> > const, Standard>::Type TIterator;
+ typedef Proxy<IteratorProxy<TIterator> > Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+/*
+template <typename TValue, typename THostspec>
+struct Size<String<TValue, Packed<THostspec> > >
+{
+ typedef __int64 Type;
+};
+template <typename TValue, typename THostspec>
+struct Size<String<TValue, Packed<THostspec> > const>
+{
+ typedef __int64 Type;
+};
+//*/
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+// Compute Bit Values
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TPackedContainer>
+struct _PackedConsts
+{
+ typedef typename Value<TPackedContainer>::Type TValue;
+ typedef typename Host<TPackedContainer>::Type THost;
+ typedef typename Value<THost>::Type THostValue;
+
+ enum
+ {
+ BITS_PER_VALUE = BitsPerValue<TValue>::VALUE,
+ BITS_PER_HOST_VALUE = BitsPerValue<THostValue>::VALUE,
+ VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
+ VALUE_MASK = (1 << BITS_PER_VALUE) - 1,
+ MAX_BIT_POS = (VALUES_PER_WORD - 1) * BITS_PER_VALUE
+ };
+
+ static typename Size<THost>::Type
+ toHostLength(typename Size<TPackedContainer>::Type len)
+ {
+ return (len + VALUES_PER_WORD - 1) / VALUES_PER_WORD;
+ }
+};
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+// Temporary Copy
+//////////////////////////////////////////////////////////////////////////////
+//note: this works only, if the copy assignment is done without using _TempCopy
+
+template <typename TValue, typename THostspec>
+struct _TempCopy<String<TValue, Packed<THostspec> > >
+{
+ typedef String<TValue, Packed<THostspec> > Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+//optimized variant for copy assignment. The host sequence is copied instead of
+//copying the packed string value by value
+
+template <typename TTarget, typename TSource, typename TTag>
+inline void
+_assign_copy_packed_string(TTarget & target,
+ TSource & source,
+ Tag<TTag> const tag)
+{
+ typedef typename Size<TTarget>::Type TSize2;
+
+ assign(host(target), host(source), tag);
+ TSize2 new_length_limit = length(host(target)) * _PackedConsts<TTarget>::VALUES_PER_WORD;
+ TSize2 new_length = length(source);
+ if (new_length > new_length_limit)
+ {
+ new_length = new_length_limit;
+ }
+ _setLength(target, new_length);
+}
+template <typename TTarget, typename TSource, typename TSize, typename TTag>
+inline void
+_assign_copy_packed_string(TTarget & target,
+ TSource & source,
+ TSize limit,
+ Tag<TTag> const tag)
+{
+ typedef typename Size<TTarget>::Type TSize2;
+
+ TSize2 host_limit = _PackedConsts<TTarget>::toHostLength(limit);
+ assign(host(target), host(source), host_limit, tag);
+ TSize2 new_length_limit = length(host(target)) * _PackedConsts<TTarget>::VALUES_PER_WORD;
+ TSize2 new_length = length(source);
+ if (new_length > new_length_limit)
+ {
+ new_length = new_length_limit;
+ }
+ if (new_length > limit)
+ {
+ new_length = limit;
+ }
+ _setLength(target, new_length);
+}
+//____________________________________________________________________________
+
+template <typename TValue, typename THostspec, typename TTag>
+inline void
+assign(String<TValue, Packed<THostspec> > & target,
+ String<TValue, Packed<THostspec> > & source,
+ Tag<TTag> const tag)
+{
+ _assign_copy_packed_string(target, source, tag);
+}
+template <typename TValue, typename THostspec, typename TTag>
+inline void
+assign(String<TValue, Packed<THostspec> > & target,
+ String<TValue, Packed<THostspec> > const & source,
+ Tag<TTag> const tag)
+{
+ _assign_copy_packed_string(target, source, tag);
+}
+
+template <typename TValue, typename THostspec, typename TSize, typename TTag>
+void assign(String<TValue, Packed<THostspec> > & target,
+ String<TValue, Packed<THostspec> > & source,
+ TSize limit,
+ Tag<TTag> const tag)
+{
+ _assign_copy_packed_string(target, source, limit, tag);
+}
+template <typename TValue, typename THostspec, typename TSize, typename TTag>
+void assign(String<TValue, Packed<THostspec> > & target,
+ String<TValue, Packed<THostspec> > const & source,
+ TSize limit,
+ Tag<TTag> const tag)
+{
+ _assign_copy_packed_string(target, source, limit, tag);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+// Function
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename THostspec>
+inline void const *
+id(String<TValue, Packed<THostspec> > const & me)
+{
+SEQAN_CHECKPOINT
+ return id(host(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename THostspec, typename TPos, typename TTag>
+inline typename Iterator<String<TValue, Packed<THostspec> >, Tag<TTag> const>::Type
+iter(String<TValue, Packed<THostspec> > & me,
+ TPos pos_,
+ Tag<TTag> const)
+{
+SEQAN_CHECKPOINT
+ typedef typename Iterator<String<TValue, Packed<THostspec> >, Tag<TTag> const>::Type TIterator;
+ return TIterator(me, pos_);
+}
+template <typename TValue, typename THostspec, typename TPos, typename TTag>
+inline typename Iterator<String<TValue, Packed<THostspec> > const, Tag<TTag> const>::Type
+iter(String<TValue, Packed<THostspec> > const & me,
+ TPos pos_,
+ Tag<TTag> const)
+{
+SEQAN_CHECKPOINT
+ typedef typename Iterator<String<TValue, Packed<THostspec> > const, Tag<TTag> const>::Type TIterator;
+ return TIterator(me, pos_);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename THostspec, typename TTag>
+inline typename Iterator<String<TValue, Packed<THostspec> >, Tag<TTag> const>::Type
+begin(String<TValue, Packed<THostspec> > & me,
+ Tag<TTag> const tag_)
+{
+SEQAN_CHECKPOINT
+ return iter(me, 0, tag_);
+}
+template <typename TValue, typename THostspec, typename TTag>
+inline typename Iterator<String<TValue, Packed<THostspec> > const, Tag<TTag> const>::Type
+begin(String<TValue, Packed<THostspec> > const & me,
+ Tag<TTag> const tag_)
+{
+SEQAN_CHECKPOINT
+ return iter(me, 0, tag_);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// end
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename THostspec, typename TTag>
+inline typename Iterator<String<TValue, Packed<THostspec> >, Tag<TTag> const>::Type
+end(String<TValue, Packed<THostspec> > & me,
+ Tag<TTag> const tag_)
+{
+SEQAN_CHECKPOINT
+ return iter(me, length(me), tag_);
+}
+template <typename TValue, typename THostspec, typename TTag>
+inline typename Iterator<String<TValue, Packed<THostspec> > const, Tag<TTag> const>::Type
+end(String<TValue, Packed<THostspec> > const & me,
+ Tag<TTag> const tag_)
+{
+SEQAN_CHECKPOINT
+ return iter(me, length(me), tag_);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// value
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename THostspec, typename TPos>
+inline typename Reference<String<TValue, Packed<THostspec> > >::Type
+value(String<TValue, Packed<THostspec> > & me,
+ TPos pos)
+{
+SEQAN_CHECKPOINT
+
+ return *iter(me, pos, Standard());
+}
+template <typename TValue, typename THostspec, typename TPos>
+inline typename Reference<String<TValue, Packed<THostspec> > const>::Type
+value(String<TValue, Packed<THostspec> > const & me,
+ TPos pos)
+{
+SEQAN_CHECKPOINT
+
+ return *iter(me, pos, Standard());
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// capacity
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename THostspec>
+inline typename Size<String<TValue, Packed<THostspec> > const>::Type
+capacity(String<TValue, Packed<THostspec> > const & me)
+{
+SEQAN_CHECKPOINT
+ typedef typename Size<String<TValue, Packed<THostspec> > const>::Type TSize;
+ TSize len = capacity(host(me));
+ len *= _PackedConsts<String<TValue, Packed<THostspec> > >::VALUES_PER_WORD;
+ return len;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// clear
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename THostspec>
+inline void
+clear(String<TValue, Packed<THostspec> > & me)
+{
+SEQAN_CHECKPOINT
+ clear(host(me));
+ _setLength(me, 0);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// _clearSpace
+//////////////////////////////////////////////////////////////////////////////
+
+//implementation for all expand tags other than "limit"
+template <typename TExpand>
+struct _ClearSpace_String_Packed_
+{
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size)
+ {
+SEQAN_CHECKPOINT
+ typedef typename Size<T>::Type TSize;
+ TSize wanted_host_length = _PackedConsts<T>::toHostLength(size);
+ TSize new_host_length = resize(host(seq), wanted_host_length, TExpand());
+ if (new_host_length < wanted_host_length)
+ {
+ size = new_host_length * _PackedConsts<T>::VALUES_PER_WORD;
+ }
+ _setLength(seq, size);
+ return size;
+ }
+
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Size<T>::Type limit)
+ {
+ if (limit < size)
+ {
+SEQAN_CHECKPOINT
+ size = limit;
+ }
+ return _clearSpace_(seq, limit);
+ }
+
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Size<T>::Type start,
+ typename Size<T>::Type end)
+ {
+SEQAN_CHECKPOINT
+ return _clearSpace_(seq, size, start, end, supremumValue<typename Size<T>::Type >());
+ }
+
+ template <typename T>
+ static typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Size<T>::Type start,
+ typename Size<T>::Type end,
+ typename Size<T>::Type limit)
+ {
+SEQAN_CHECKPOINT
+//??? TODO: This function can be accelerated this way:
+// - move values in host
+// - avoid double moving of the rest-part if "resize" allocates a new block
+
+ typedef typename Size<T>::Type TSize;
+ typedef typename Iterator<T, Standard>::Type TIterator;
+
+ TSize old_length = length(seq);
+ TSize old_size = end - start;
+ TSize wanted_new_length = old_length + size - old_size;
+
+ if (wanted_new_length > limit)
+ {
+ wanted_new_length = limit;
+ }
+
+ TSize wanted_host_length = _PackedConsts<T>::toHostLength(wanted_new_length);
+ TSize new_host_length = resize(host(seq), wanted_host_length, TExpand());
+
+ TSize new_length;
+ if (new_host_length < wanted_host_length)
+ {
+ new_length = new_host_length * _PackedConsts<T>::VALUES_PER_WORD;
+ if (new_length <= start + size)
+ {
+ goto FINISH;
+ }
+ old_length = new_length - size + old_size;
+ }
+ else
+ {
+ new_length = wanted_new_length;
+ }
+
+ //move [end:right_end] to [start + size:..]
+ if (old_size > size)
+ {//move rest to left
+ ::std::copy_backward(iter(seq, end, Standard()), iter(seq, old_length, Standard()), iter(seq, new_length, Standard()));
+ }
+ else
+ {//move rest to right
+ ::std::copy(iter(seq, end, Standard()), iter(seq, old_length, Standard()), iter(seq, end + size - old_size, Standard()));
+ }
+FINISH:
+ _setLength(seq, new_length);
+ return size;
+ }
+/*
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Iterator<T>::Type start,
+ typename Iterator<T>::Type end)
+ {
+SEQAN_CHECKPOINT
+ typename Iterator<T>::Type seq_begin = begin(seq);
+ return _clearSpace(seq, size, start - seq_begin, end - seq_begin, Insist());
+ }
+
+ template <typename T>
+ static inline typename Size<T>::Type
+ _clearSpace_(
+ T & seq,
+ typename Size<T>::Type size,
+ typename Iterator<T>::Type start,
+ typename Iterator<T>::Type end,
+ typename Size<T>::Type limit)
+ {
+SEQAN_CHECKPOINT
+ typename Iterator<T>::Type seq_begin = begin(seq);
+ return _clearSpace(seq, size, start - seq_begin, end - seq_begin, limit, Insist());
+ }
+*/
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template<typename TValue, typename THostspec, typename TExpand>
+inline typename Size< String<TValue, Packed<THostspec> > >::Type
+_clearSpace(String<TValue, Packed<THostspec> > & me,
+ typename Size< String<TValue, Packed<THostspec> > >::Type size,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ return _ClearSpace_String_Packed_<Tag<TExpand> const>::_clearSpace_(me, size);
+}
+
+template<typename TValue, typename THostspec, typename TExpand>
+inline typename Size< String<TValue, Packed<THostspec> > >::Type
+_clearSpace(String<TValue, Packed<THostspec> > & me,
+ typename Size< String<TValue, Packed<THostspec> > >::Type size,
+ typename Size< String<TValue, Packed<THostspec> > >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ return _ClearSpace_String_Packed_<Tag<TExpand> const>::_clearSpace_(me, size, limit);
+}
+
+template<typename TValue, typename THostspec, typename TPosition, typename TExpand>
+inline typename Size< String<TValue, Packed<THostspec> > >::Type
+_clearSpace(String<TValue, Packed<THostspec> > & me,
+ typename Size< String<TValue, Packed<THostspec> > >::Type size,
+ TPosition pos_begin,
+ TPosition pos_end,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ return _ClearSpace_String_Packed_<Tag<TExpand> const>::_clearSpace_(me, size, pos_begin, pos_end);
+}
+
+template<typename TValue, typename THostspec, typename TPosition, typename TExpand>
+inline typename Size< String<TValue, Packed<THostspec> > >::Type
+_clearSpace(String<TValue, Packed<THostspec> > & me,
+ typename Size< String<TValue, Packed<THostspec> > >::Type size,
+ TPosition pos_begin,
+ TPosition pos_end,
+ typename Size< String<TValue, Packed<THostspec> > >::Type limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ return _ClearSpace_String_Packed_<Tag<TExpand> const>::_clearSpace_(me, size, pos_begin, pos_end, limit);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+///.Function.reserve.param.object.type:Spec.Packed String
+
+template <typename TValue, typename TSpec, typename _TSize, typename TExpand>
+inline typename Size< String<TValue, Packed<TSpec> > >::Type
+reserve(
+ String<TValue, Packed<TSpec> > & seq,
+ _TSize new_capacity,
+ Tag<TExpand> const tag)
+{
+SEQAN_CHECKPOINT
+
+ typedef String<TValue, Packed<TSpec> > TString;
+ typedef typename Size<TString>::Type TSize;
+ TSize ret_value = reserve(host(seq), _PackedConsts<TString>::toHostLength(new_capacity), tag);
+ return ret_value * _PackedConsts<TString>::VALUES_PER_WORD;
+}
+
+template <typename TValue, typename TSpec, typename _TSize>
+inline typename Size< String<TValue, Alloc<TSpec> > >::Type
+reserve(
+ String<TValue, Packed<TSpec> > & me,
+ _TSize new_capacity,
+ Limit)
+{
+SEQAN_CHECKPOINT
+ typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
+
+ TSize me_capacity = capacity(me);
+ if (me_capacity < (TSize)new_capacity) return me_capacity;
+ return new_capacity;
+}
+
+template <typename TValue, typename TSpec, typename _TSize>
+inline typename Size< String<TValue, Alloc<TSpec> > >::Type
+reserve(
+ String<TValue, Packed<TSpec> > & me,
+ _TSize new_capacity,
+ Insist)
+{
+SEQAN_CHECKPOINT
+ typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
+
+ return new_capacity;
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+// Iteration
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename THostspec, typename TSpec>
+struct Iterator<String<TValue, Packed<THostspec> >, TSpec>
+{
+ typedef Iter<String<TValue, Packed<THostspec> >, Packed<THostspec> > Type;
+};
+template <typename TValue, typename THostspec, typename TSpec>
+struct Iterator<String<TValue, Packed<THostspec> > const, TSpec>
+{
+ typedef Iter<String<TValue, Packed<THostspec> > const, Packed<THostspec> > Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+// Iterator for packed strings
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec>
+class Iter<TContainer, Packed<THostspec> >
+{
+private:
+ typedef typename Host<TContainer>::Type THost;
+ typedef typename Iterator<THost, Standard>::Type THostIterator;
+ typedef typename Position<TContainer>::Type TPosition;
+
+ typename _Pointer<TContainer>::Type data_container;
+ THostIterator data_iterator;
+ unsigned char data_bitpos;
+
+//____________________________________________________________________________
+
+public:
+ Iter()
+ {
+SEQAN_CHECKPOINT
+ }
+ Iter(typename _Parameter<TContainer>::Type container_):
+ data_container(_toPointer(container_)),
+ data_iterator(begin(host(container_))),
+ data_bitpos(0)
+ {
+SEQAN_CHECKPOINT
+ }
+ Iter(typename _Parameter<TContainer>::Type container_, TPosition pos_):
+ data_container(_toPointer(container_))
+ {
+SEQAN_CHECKPOINT
+ setPosition(*this, pos_);
+ }
+ Iter(Iter const & other_):
+ data_container(other_.data_container),
+ data_iterator(other_.data_iterator),
+ data_bitpos(other_.data_bitpos)
+ {
+SEQAN_CHECKPOINT
+ }
+ ~Iter()
+ {
+SEQAN_CHECKPOINT
+ }
+ Iter const &
+ operator = (Iter const & other_)
+ {
+SEQAN_CHECKPOINT
+ data_container = other_.data_container;
+ data_iterator = other_.data_iterator;
+ data_bitpos = other_.data_bitpos;
+ return *this;
+ }
+//____________________________________________________________________________
+
+ friend inline typename _Parameter<TContainer>::Type
+ container(Iter & me)
+ {
+SEQAN_CHECKPOINT
+ return _toParameter<TContainer>(me.data_container);
+ }
+ friend inline typename _Parameter<TContainer>::Type
+ container(Iter const & me)
+ {
+SEQAN_CHECKPOINT
+ return _toParameter<TContainer>(me.data_container);
+ }
+//____________________________________________________________________________
+
+ friend inline void
+ setContainer(Iter & me, typename _Parameter<TContainer>::Type container_)
+ {
+SEQAN_CHECKPOINT
+ typename Position<Iter>::Type pos = position(me);
+ me.data_container = _toPointer(container_);
+ setPosition(me, pos);
+ }
+
+//____________________________________________________________________________
+
+ friend inline THostIterator &
+ hostIterator(Iter & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_iterator;
+ }
+ friend inline THostIterator const &
+ hostIterator(Iter const & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_iterator;
+ }
+
+//____________________________________________________________________________
+
+ friend inline unsigned char &
+ _bitpos(Iter & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_bitpos;
+ }
+ friend inline unsigned char
+ _bitpos(Iter const & me)
+ {
+SEQAN_CHECKPOINT
+ return me.data_bitpos;
+ }
+
+//____________________________________________________________________________
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// position
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec>
+inline typename Position<Iter<TContainer, Packed<THostspec> > const>::Type
+position(Iter<TContainer, Packed<THostspec> > const & me)
+{
+SEQAN_CHECKPOINT
+ typedef typename Host<TContainer>::Type THost;
+ THost const & host_ = host(container(me));
+ return (hostIterator(me) - begin(host_)) * _PackedConsts<TContainer>::VALUES_PER_WORD + _bitpos(me) / _PackedConsts<TContainer>::BITS_PER_VALUE;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// setPosition
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec, typename TPosition>
+inline void
+setPosition(Iter<TContainer, Packed<THostspec> > & me,
+ TPosition pos_)
+{
+SEQAN_CHECKPOINT
+ hostIterator(me) = begin(host(container(me))) + pos_ / _PackedConsts<TContainer>::VALUES_PER_WORD;
+ _bitpos(me) = (pos_ % _PackedConsts<TContainer>::VALUES_PER_WORD) * _PackedConsts<TContainer>::BITS_PER_VALUE;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// value
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec>
+inline typename Reference<Iter<TContainer, Packed<THostspec> > >::Type
+value(Iter<TContainer, Packed<THostspec> > & me)
+{
+SEQAN_CHECKPOINT
+ return typename Reference<Iter<TContainer, Packed<THostspec> > >::Type(me);
+}
+template <typename TContainer, typename THostspec>
+inline typename Reference<Iter<TContainer, Packed<THostspec> > const>::Type
+value(Iter<TContainer, Packed<THostspec> > const & me)
+{
+SEQAN_CHECKPOINT
+ return typename Reference<Iter<TContainer, Packed<THostspec> > const>::Type(me);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// getValue
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec>
+inline typename GetValue<Iter<TContainer, Packed<THostspec> > >::Type
+getValue(Iter<TContainer, Packed<THostspec> > & me)
+{
+SEQAN_CHECKPOINT
+ return (value(hostIterator(me)) >> _bitpos(me)) & _PackedConsts<TContainer>::VALUE_MASK;
+}
+template <typename TContainer, typename THostspec>
+inline typename GetValue<Iter<TContainer, Packed<THostspec> > const>::Type
+getValue(Iter<TContainer, Packed<THostspec> > const & me)
+{
+SEQAN_CHECKPOINT
+ return (value(hostIterator(me)) >> _bitpos(me)) & _PackedConsts<TContainer>::VALUE_MASK;
+}
+
+/////////////////////////////////////////////////////////////////////////////
+// assignValue
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TIter, typename TValue>
+inline void
+_assignValue_packed_string_iterator(TIter & me,
+ TValue & _value)
+{
+ typedef typename Container<TIter>::Type TContainer;
+ typedef typename Host<TContainer>::Type THost;
+ typedef typename Value<THost>::Type THostValue;
+ THostValue mask_ = _PackedConsts<TContainer>::VALUE_MASK << _bitpos(me);
+ THostValue val_ = _value;
+ val_ <<= _bitpos(me);
+
+ assignValue(hostIterator(me), (getValue(hostIterator(me)) & ~(mask_)) | val_);
+}
+
+
+template <typename TContainer, typename THostspec, typename TValue>
+inline void
+assignValue(Iter<TContainer, Packed<THostspec> > & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ typedef Iter<TContainer, Packed<THostspec> > TIterator;
+ typename Value<TIterator>::Type _temp_value = _value; //conversion
+ _assignValue_packed_string_iterator(me, _temp_value);
+}
+template <typename TContainer, typename THostspec, typename TValue>
+inline void
+assignValue(Iter<TContainer, Packed<THostspec> > const & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ typedef Iter<TContainer, Packed<THostspec> > const TIterator;
+ typename Value<TIterator>::Type _temp_value = _value; //conversion
+ _assignValue_packed_string_iterator(me, _temp_value);
+}
+
+/////////////////////////////////////////////////////////////////////////////
+// moveValue
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec, typename TValue>
+inline void
+moveValue(Iter<TContainer, Packed<THostspec> > & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ assignValue(me, _value);
+}
+template <typename TContainer, typename THostspec, typename TValue>
+inline void
+moveValue(Iter<TContainer, Packed<THostspec> > const & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ assignValue(me, _value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// valueConstruct
+//////////////////////////////////////////////////////////////////////////////
+//emulate construction and destruction
+
+template <typename TContainer, typename THostspec>
+inline void
+valueConstruct(Iter<TContainer, Packed<THostspec> > const & /*it*/)
+{
+}
+template <typename TContainer, typename THostspec, typename TParam>
+inline void
+valueConstruct(Iter<TContainer, Packed<THostspec> > const & it,
+ TParam const & param_)
+{
+ assignValue(it, param_);
+}
+template <typename TContainer, typename THostspec, typename TParam>
+inline void
+valueConstruct(Iter<TContainer, Packed<THostspec> > const & it,
+ TParam const & param_,
+ Move tag)
+{
+ moveValue(it, param_);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// valueDestruct
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec>
+inline void
+valueDestruct(Iter<TContainer, Packed<THostspec> > const & /*it*/)
+{
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator ==
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec>
+inline bool
+operator == (Iter<TContainer, Packed<THostspec> > const & left,
+ Iter<TContainer, Packed<THostspec> > const & right)
+{
+SEQAN_CHECKPOINT
+ return (hostIterator(left) == hostIterator(right)) && (_bitpos(left) == _bitpos(right));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator !=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec>
+inline bool
+operator != (Iter<TContainer, Packed<THostspec> > const & left,
+ Iter<TContainer, Packed<THostspec> > const & right)
+{
+SEQAN_CHECKPOINT
+ return (hostIterator(left) != hostIterator(right)) || (_bitpos(left) != _bitpos(right));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator >
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec>
+inline bool
+operator > (Iter<TContainer, Packed<THostspec> > const & left,
+ Iter<TContainer, Packed<THostspec> > const & right)
+{
+SEQAN_CHECKPOINT
+ return (hostIterator(left) > hostIterator(right)) || ((hostIterator(left) == hostIterator(right)) && (_bitpos(left) > _bitpos(right)));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator >=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec>
+inline bool
+operator >= (Iter<TContainer, Packed<THostspec> > const & left,
+ Iter<TContainer, Packed<THostspec> > const & right)
+{
+SEQAN_CHECKPOINT
+ return (hostIterator(left) > hostIterator(right)) || ((hostIterator(left) == hostIterator(right)) && (_bitpos(left) >= _bitpos(right)));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator <
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec>
+inline bool
+operator < (Iter<TContainer, Packed<THostspec> > const & left,
+ Iter<TContainer, Packed<THostspec> > const & right)
+{
+SEQAN_CHECKPOINT
+ return (hostIterator(left) < hostIterator(right)) || ((hostIterator(left) == hostIterator(right)) && (_bitpos(left) < _bitpos(right)));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator <=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec>
+inline bool
+operator <= (Iter<TContainer, Packed<THostspec> > const & left,
+ Iter<TContainer, Packed<THostspec> > const & right)
+{
+SEQAN_CHECKPOINT
+ return (hostIterator(left) < hostIterator(right)) || ((hostIterator(left) == hostIterator(right)) && (_bitpos(left) <= _bitpos(right)));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// goNext
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec>
+inline void
+goNext(Iter<TContainer, Packed<THostspec> > & me)
+{
+SEQAN_CHECKPOINT
+ int new_bitpos = _bitpos(me) + _PackedConsts<TContainer>::BITS_PER_VALUE;
+ if (new_bitpos <= _PackedConsts<TContainer>::MAX_BIT_POS)
+ {
+ _bitpos(me) = (unsigned char) new_bitpos;
+ }
+ else
+ {
+ _bitpos(me) = 0;
+ goNext(hostIterator(me));
+ }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// goPrevious
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec>
+inline void
+goPrevious(Iter<TContainer, Packed<THostspec> > & me)
+{
+SEQAN_CHECKPOINT
+ int new_bitpos = _bitpos(me) - _PackedConsts<TContainer>::BITS_PER_VALUE;
+ if (new_bitpos >= 0)
+ {
+ _bitpos(me) = (unsigned char) new_bitpos;
+ }
+ else
+ {
+ _bitpos(me) = _PackedConsts<TContainer>::MAX_BIT_POS;
+ goPrevious(hostIterator(me));
+ }
+
+ goPrevious(hostIterator(me));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator +
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec, typename TIntegral>
+inline Iter<TContainer, Packed<THostspec> >
+operator + (Iter<TContainer, Packed<THostspec> > const & left,
+ TIntegral right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, Packed<THostspec> >(container(left), position(left) + right);
+}
+template <typename TContainer, typename THostspec, typename TIntegral>
+inline Iter<TContainer, Packed<THostspec> >
+operator + (TIntegral left,
+ Iter<TContainer, Packed<THostspec> > const & right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, Packed<THostspec> >(container(right), position(right) + left);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator +=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec, typename TIntegral>
+inline Iter<TContainer, Packed<THostspec> > &
+operator += (Iter<TContainer, Packed<THostspec> > & left,
+ TIntegral right)
+{
+SEQAN_CHECKPOINT
+ setPosition(left, position(left) + right);
+ return left;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator -
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec, typename TIntegral>
+inline Iter<TContainer, Packed<THostspec> >
+operator - (Iter<TContainer, Packed<THostspec> > const & left,
+ TIntegral right)
+{
+SEQAN_CHECKPOINT
+ return Iter<TContainer, AdaptorIterator<THostspec> >(container(left), position(left) - right);
+}
+
+//____________________________________________________________________________
+
+template <typename TContainer, typename THostspec>
+inline typename Difference<Iter<TContainer, Packed<THostspec> > >::Type
+operator - (Iter<TContainer, Packed<THostspec> > const & left,
+ Iter<TContainer, Packed<THostspec> > const & right)
+{
+SEQAN_CHECKPOINT
+ return position(left) - position(right);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// operator -=
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename THostspec, typename TIntegral>
+inline Iter<TContainer, Packed<THostspec> > &
+operator -= (Iter<TContainer, Packed<THostspec> > & left,
+ TIntegral right)
+{
+SEQAN_CHECKPOINT
+ setPosition(left, position(left) - right);
+ return left;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/sequence/string_pointer.h b/src/libSSA/seqan/sequence/string_pointer.h
new file mode 100644
index 0000000..cb6f50e
--- /dev/null
+++ b/src/libSSA/seqan/sequence/string_pointer.h
@@ -0,0 +1,842 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: string_pointer.h,v 1.3 2009/10/12 16:00:57 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SEQUENCE_POINTER_H
+#define SEQAN_HEADER_SEQUENCE_POINTER_H
+
+#include <cstring>
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Adaption.char array:
+..summary:Zero terminated $char[]$ or $wchar_t[]$.
+..remarks:Char arrays only support the Insist @Tag.Overflow Strategy.overflow strategy at .
+*/
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Adaption.char array.remarks:The default overflow strategy
+(both @Metafunction.DefaultOverflowImplicit@ and @Metafunction.DefaultOverflowExplicit@)
+for all operations on char arrays is @Tag.Overflow Strategy.insist at .
+*/
+
+template <typename TValue>
+struct DefaultOverflowImplicit;
+
+template <typename TValue>
+struct DefaultOverflowImplicit< TValue * >
+{
+ typedef Insist Type;
+};
+template <typename TValue>
+struct DefaultOverflowImplicit< TValue * const>
+{
+ typedef Insist Type;
+};
+template <typename TValue, size_t SIZE>
+struct DefaultOverflowImplicit< TValue [SIZE] >
+{
+ typedef Insist Type;
+};
+template <typename TValue, size_t SIZE>
+struct DefaultOverflowImplicit< TValue const [SIZE] >
+{
+ typedef Insist Type;
+};
+//____________________________________________________________________________
+
+template <typename TValue>
+struct DefaultOverflowExplicit;
+
+template <typename TValue>
+struct DefaultOverflowExplicit< TValue * >
+{
+ typedef Insist Type;
+};
+template <typename TValue>
+struct DefaultOverflowExplicit< TValue * const>
+{
+ typedef Insist Type;
+};
+template <typename TValue, size_t SIZE>
+struct DefaultOverflowExplicit< TValue [SIZE] >
+{
+ typedef Insist Type;
+};
+template <typename TValue, size_t SIZE>
+struct DefaultOverflowExplicit< TValue const [SIZE] >
+{
+ typedef Insist Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.IsContiguous.param.T.type:Adaption.char array
+
+template <typename TValue>
+struct IsContiguous;
+
+template <typename TValue>
+struct IsContiguous< TValue * >
+{
+ typedef True Type;
+ enum { VALUE = true };
+};
+template <typename TValue, size_t SIZE>
+struct IsContiguous< TValue [SIZE] >
+{
+ typedef True Type;
+ enum { VALUE = true };
+};
+template <typename TValue, size_t SIZE>
+struct IsContiguous< TValue const [SIZE] >
+{
+ typedef True Type;
+ enum { VALUE = true };
+};
+
+/*DISABLED
+.Metafunction.IsString.param.T.type:Adaption.char array
+*/
+
+template <typename TValue>
+struct IsSequence< TValue * >
+{
+ typedef True Type;
+ enum { VALUE = true };
+};
+template <typename TValue, size_t SIZE>
+struct IsSequence< TValue [SIZE] >
+{
+ typedef True Type;
+ enum { VALUE = true };
+};
+template <typename TValue, size_t SIZE>
+struct IsSequence< TValue const [SIZE] >
+{
+ typedef True Type;
+ enum { VALUE = true };
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+template <typename T>
+inline typename Iterator<T *, typename DefaultGetIteratorSpec<T>::Type>::Type
+begin(T * me)
+{
+SEQAN_CHECKPOINT
+ return begin(me, typename DefaultGetIteratorSpec<T>::Type()) ;
+}
+
+///.Function.begin.param.object.type:Adaption.char array
+
+template <typename TValue>
+inline typename Iterator<TValue *, Standard>::Type
+begin(TValue * me,
+ Standard)
+{
+SEQAN_CHECKPOINT
+ return me;
+}
+
+//folgende Versionen wurde wegen seltsamer Phaenomene bei VC++ 2003 hinzugenommen
+template <typename TValue>
+inline typename Iterator<TValue const *, Standard>::Type
+begin(TValue const * me,
+ Standard)
+{
+SEQAN_CHECKPOINT
+ return me;
+}
+
+template <typename TValue, typename TSpec>
+inline typename Iterator<TValue *, Tag<TSpec> const>::Type
+begin(TValue * me,
+ Tag<TSpec> const)
+{
+SEQAN_CHECKPOINT
+ typedef typename Iterator<TValue *, Tag<TSpec> const>::Type TIterator;
+ return TIterator(me, begin(me, Standard()));
+}
+
+template <typename TValue, typename TSpec>
+inline typename Iterator<TValue const *, Tag<TSpec> const>::Type
+begin(TValue const * me,
+ Tag<TSpec> const)
+{
+SEQAN_CHECKPOINT
+ typedef typename Iterator<TValue const *, Tag<TSpec> const>::Type TIterator;
+ return TIterator(me, begin(me, Standard()));
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.end.param.object.type:Adaption.char array
+
+template <typename TValue>
+inline typename Iterator<TValue *, Standard>::Type
+end(TValue * me,
+ Standard)
+{
+SEQAN_CHECKPOINT
+ return begin(me, Standard()) + length(me);
+}
+
+//folgende Version wurde wegen eines seltsamen Phaenomens bei VC++ hinzugenommen
+template <typename TValue>
+inline typename Iterator<TValue const *, Standard>::Type
+end(TValue const * me,
+ Standard)
+{
+SEQAN_CHECKPOINT
+ return begin(me, Standard()) + length(me);
+}
+
+template <typename TValue, typename TSpec>
+inline typename Iterator<TValue *, Tag<TSpec> const>::Type
+end(TValue * me,
+ Tag<TSpec> const tag_)
+{
+SEQAN_CHECKPOINT
+ return begin(me, tag_) + length(me);
+}
+
+template <typename TValue, typename TSpec>
+inline typename Iterator<TValue const *, Tag<TSpec> const>::Type
+end(TValue const * me,
+ Tag<TSpec> const tag_)
+{
+SEQAN_CHECKPOINT
+ return begin(me, tag_) + length(me);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.value.param.container.type:Adaption.char array
+
+template <typename TValue, typename TPos>
+inline TValue &
+value(TValue * me,
+ TPos pos)
+{
+SEQAN_CHECKPOINT
+ return me[pos];
+}
+
+template <typename TValue, typename TPos>
+inline TValue const &
+value(TValue const * me,
+ TPos pos)
+{
+SEQAN_CHECKPOINT
+ return me[pos];
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// assignValue
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename TPos>
+inline void
+assignValue(TValue * me,
+ TPos pos,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ assign(value(me, pos), _value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// moveValue
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename TPos>
+inline void
+moveValue(TValue * me,
+ TPos pos,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ move(value(me, pos), _value);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue>
+inline bool
+atEnd(TValue * pos)
+{
+SEQAN_CHECKPOINT
+ return *pos == 0;
+}
+
+//____________________________________________________________________________
+
+template <typename TValue>
+inline bool
+atEnd(TValue * pos,
+ TValue const * container)
+{
+SEQAN_CHECKPOINT
+ return *pos == 0;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.length.param.object.type:Adaption.char array
+
+template <typename TValue>
+inline size_t
+length(TValue * me)
+{
+SEQAN_CHECKPOINT
+ TValue * it = me;
+ TValue zero = TValue();
+ while ( *it != zero) ++it;
+ return it - me;
+}
+
+template <typename TValue>
+inline size_t
+length(TValue const * me)
+{
+SEQAN_CHECKPOINT
+ TValue const * it = me;
+ TValue const zero = TValue();
+ while ( *it != zero) ++it;
+ return it - me;
+}
+
+inline size_t
+length(char * me)
+{
+SEQAN_CHECKPOINT
+ return strlen(me);
+}
+
+inline size_t
+length(char const * me)
+{
+SEQAN_CHECKPOINT
+ return strlen(me);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue>
+inline void
+_setLength(TValue * me,
+ size_t new_length)
+{
+SEQAN_CHECKPOINT
+ me[new_length] = 0;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.clear.param.object.type:Adaption.char array
+
+template <typename TValue>
+inline void
+clear(TValue * me)
+{
+SEQAN_CHECKPOINT
+ //arrayDestruct(begin(me), length(me)); //??? Die Laengenbestimmung ist meistens nutzlos, braucht man sowieso nur fuer non-pod
+ _setLength(me, 0);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.empty.param.object.type:Adaption.char array
+
+template <typename TValue>
+inline bool
+empty(TValue * me)
+{
+SEQAN_CHECKPOINT
+ return !me || (*me == TValue());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+template<typename TValue, typename TExpand>
+inline size_t
+_clearSpace(TValue * me,
+ size_t size,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ return _ClearSpace_String_Base_<Tag<TExpand> const>::_clearSpace_(me, size);
+}
+
+template<typename TValue, typename TExpand>
+inline size_t
+_clearSpace(TValue * me,
+ size_t size,
+ size_t limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ return _ClearSpace_String_Base_<Tag<TExpand> const>::_clearSpace_(me, size, limit);
+}
+
+template<typename TValue, typename TPosition, typename TExpand>
+inline size_t
+_clearSpace(TValue * me,
+ size_t size,
+ TPosition pos_begin,
+ TPosition pos_end,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ return _ClearSpace_String_Base_<Tag<TExpand> const>::_clearSpace_(me, size, pos_begin, pos_end);
+}
+
+template<typename TValue, typename TPosition, typename TExpand>
+inline size_t
+_clearSpace(TValue * me,
+ size_t size,
+ TPosition pos_begin,
+ TPosition pos_end,
+ size_t limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ return _ClearSpace_String_Base_<Tag<TExpand> const>::_clearSpace_(me, size, pos_begin, pos_end, limit);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// assign
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.assign.param.target.type:.Adaption.char array
+///.Function.assign.param.source.type:.Adaption.char array
+
+//overload of binary version for strings:
+
+template<typename TTargetValue, typename TSource>
+inline void
+assign(TTargetValue * target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ typedef TTargetValue * TTarget;
+ assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+template<typename TTargetValue, typename TSource>
+inline void
+assign(TTargetValue * target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ typedef TTargetValue * TTarget;
+ assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+
+//____________________________________________________________________________
+
+template<typename TTargetValue, typename TSource, typename TExpand>
+inline void
+assign(TTargetValue * target,
+ TSource const & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Assign_String<Tag<TExpand> const>::assign_(target, source);
+}
+
+template<typename TTargetValue, typename TSource, typename TExpand>
+inline void
+assign(TTargetValue * target,
+ TSource const & source,
+ size_t limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Assign_String<Tag<TExpand> const>::assign_(target, source, limit);
+}
+
+//____________________________________________________________________________
+//this variant is a workaround for the "const array"-bug of VC++
+
+template<typename TTargetValue, typename TSourceValue, typename TExpand>
+inline void
+assign(TTargetValue * target,
+ TSourceValue const * source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Assign_String<Tag<TExpand> const>::assign_(target, source);
+}
+
+template<typename TTargetValue, typename TSourceValue, typename TExpand>
+inline void
+assign(TTargetValue * target,
+ TSourceValue const * source,
+ size_t limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Assign_String<Tag<TExpand> const>::assign_(target, source, limit);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// move
+//////////////////////////////////////////////////////////////////////////////
+
+//overload of binary version for strings:
+
+template<typename TTargetValue, typename TSource>
+inline void
+move(TTargetValue * & target,
+ TSource & source)
+{
+SEQAN_CHECKPOINT
+ target = source;
+}
+template<typename TTargetValue, typename TSource>
+inline void
+move(TTargetValue * & target,
+ TSource const & source)
+{
+SEQAN_CHECKPOINT
+ target = source;
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// append
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.append.param.target.type:.Adaption.char array
+///.Function.append.param.source.type:.Adaption.char array
+
+template<typename TTargetValue, typename TSource, typename TExpand>
+inline void
+append(TTargetValue * target,
+ TSource const & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Append_String<Tag<TExpand> const>::append_(target, source);
+}
+
+template<typename TTargetValue, typename TSource, typename TExpand>
+inline void
+append(TTargetValue * target,
+ TSource const & source,
+ size_t limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Append_String<Tag<TExpand> const>::append_(target, source, limit);
+}
+
+//____________________________________________________________________________
+//this variant is a workaround for the "const array"-bug of VC++
+
+template<typename TTargetValue, typename TSourceValue, typename TExpand>
+inline void
+append(TTargetValue * target,
+ TSourceValue const * source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Append_String<Tag<TExpand> const>::append_(target, source);
+}
+
+template<typename TTargetValue, typename TSourceValue, typename TExpand>
+inline void
+append(TTargetValue * target,
+ TSourceValue const * source,
+ size_t limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Append_String<Tag<TExpand> const>::append_(target, source, limit);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// replace
+//////////////////////////////////////////////////////////////////////////////
+
+///.Function.replace.param.target.type:.Adaption.char array
+///.Function.replace.param.source.type:.Adaption.char array
+
+template<typename TTargetValue, typename TSource, typename TExpand>
+inline void
+replace(TTargetValue * target,
+ size_t pos_begin,
+ size_t pos_end,
+ TSource const & source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Replace_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source);
+}
+
+template<typename TTargetValue, typename TSource, typename TExpand>
+inline void
+replace(TTargetValue * target,
+ size_t pos_begin,
+ size_t pos_end,
+ TSource const & source,
+ size_t limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Replace_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source, limit);
+}
+//____________________________________________________________________________
+//this variant is a workaround for the "const array"-bug of VC++
+
+template<typename TTargetValue, typename TSourceValue, typename TExpand>
+inline void
+replace(TTargetValue * target,
+ size_t pos_begin,
+ size_t pos_end,
+ TSourceValue const * source,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Replace_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source);
+}
+
+template<typename TTargetValue, typename TSourceValue, typename TExpand>
+inline void
+replace(TTargetValue * target,
+ size_t pos_begin,
+ size_t pos_end,
+ TSourceValue const * source,
+ size_t limit,
+ Tag<TExpand> const)
+{
+SEQAN_CHECKPOINT
+ _Replace_String<Tag<TExpand> const>::replace_(target, pos_begin, pos_end, source, limit);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// handling of iterators as begin and and
+/*
+template<typename TTargetValue, typename TSource, typename TExpand>
+inline void
+replace(TTargetValue * target,
+ typename Iterator<TTargetValue *, Rooted>::Type pos_begin,
+ typename Iterator<TTargetValue *, Rooted>::Type pos_end,
+ TSource const & source,
+ Tag<TExpand> const tag)
+{
+ replace(target, position(pos_begin), position(pos_end), source, tag);
+}
+template<typename TTargetValue, typename TSource, typename TExpand>
+inline void
+replace(TTargetValue * target,
+ typename Iterator<TTargetValue *, Rooted>::Type pos_begin,
+ typename Iterator<TTargetValue *, Rooted>::Type pos_end,
+ TSource const & source,
+ size_t limit,
+ Tag<TExpand> const tag)
+{
+ replace(target, position(pos_begin), position(pos_end), source, limit, tag);
+}
+*/
+//////////////////////////////////////////////////////////////////////////////
+///.Function.resize.param.object.type:Adaption.char array
+
+template <typename TValue, typename TExpand>
+inline size_t
+resize(
+ TValue * me,
+ size_t new_length,
+ Tag<TExpand> const &)
+{
+SEQAN_CHECKPOINT
+ return _Resize_String<Tag<TExpand> const>::resize_(me, new_length);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+///.Function.fill.param.object.type:Adaption.char array
+
+template <typename TValue, typename TExpand>
+inline size_t
+fill(
+ TValue * me,
+ size_t new_length,
+ TValue const & val,
+ Tag<TExpand> const &)
+{
+SEQAN_CHECKPOINT
+ return _Fill_String<Tag<TExpand> const>::fill_(me, new_length, val);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//PROBLEM: ambiguitiy "pointer/iterator" and "c-style string"
+//workaround: disable all operators
+/*
+template <typename TLeftValue, typename TRight >
+TLeftValue const *
+operator += (TLeftValue * left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ append(left, right);
+ return left;
+}
+*/
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftValue, typename TRight >
+inline bool
+isEqual(TLeftValue * left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ typename Comparator<TLeftValue *>::Type _lex(left, right);
+ return isEqual(_lex);
+}
+/*
+template <typename TLeftValue, typename TRight >
+inline bool
+operator == (TLeftValue * left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ typename Comparator<TLeftValue *>::Type _lex(left, right);
+ return isEqual(_lex);
+}
+*/
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftValue, typename TRight >
+inline bool
+isNotEqual(TLeftValue * left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ typename Comparator<TLeftValue *>::Type _lex(left, right);
+ return isNotEqual(_lex);
+}
+/*
+template <typename TLeftValue, typename TRight >
+inline bool
+operator != (TLeftValue * left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ typename Comparator<TLeftValue *>::Type _lex(left, right);
+ return isNotEqual(_lex);
+}
+*/
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftValue, typename TRight>
+inline bool
+isLess(TLeftValue * left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return isLess(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
+}
+/*
+template <typename TLeftValue, typename TRight>
+inline bool
+operator < (TLeftValue * left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return isLess(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
+}
+*/
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftValue, typename TRight>
+inline bool
+isLessOrEqual(TLeftValue * left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return isLessOrEqual(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
+}
+/*
+template <typename TLeftValue, typename TRight>
+inline bool
+operator <= (TLeftValue * left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return isLessOrEqual(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
+}
+*/
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftValue, typename TRight>
+inline bool
+isGreater(TLeftValue * left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return isGreater(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
+}
+/*
+template <typename TLeftValue, typename TRight>
+inline bool
+operator > (TLeftValue * left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return isGreater(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
+}
+*/
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TLeftValue, typename TRight>
+inline bool
+isGreaterOrEqual(TLeftValue * left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return isGreaterOrEqual(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
+}
+/*
+template <typename TLeftValue, typename TRight>
+inline bool
+operator >= (TLeftValue * left,
+ TRight const & right)
+{
+SEQAN_CHECKPOINT
+ return isGreaterOrEqual(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
+}
+*/
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+//____________________________________________________________________________
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/sequence/string_stack.h b/src/libSSA/seqan/sequence/string_stack.h
new file mode 100644
index 0000000..e135f43
--- /dev/null
+++ b/src/libSSA/seqan/sequence/string_stack.h
@@ -0,0 +1,532 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: string_stack.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_GRAPH_STACK_H
+#define SEQAN_HEADER_GRAPH_STACK_H
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// TAGS
+//////////////////////////////////////////////////////////////////////////////
+
+/**
+.Spec.Block String:
+..cat:Strings
+..general:Class.String
+..summary:String optimized for push_back, top, and pop (Stack behaviour).
+..signature:String<TValue, Block<size> >
+..param.TValue:The value type, that is the type of the items/characters stored in the string.
+...remarks:Use @Metafunction.Value@ to get the value type for a given class.
+..param.size:A positive integer that specifies the number of values in each allocated block.
+...remarks: Size should be a power of 2, e.g., 1024.
+*/
+
+ template<unsigned int SPACE = 4096>
+ struct Block;
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+ template<typename TValue, unsigned int SPACE>
+ class String<TValue, Block<SPACE> >
+ {
+ typedef String<TValue, Array<SPACE> > TBlock;
+ typedef TBlock* PBlock;
+ typedef Allocator< SinglePool<sizeof(TBlock)> > TAllocator;
+
+ public:
+ typedef typename Iterator<TBlock, Standard>::Type TBlockIter;
+ typedef String<PBlock> TBlockTable;
+
+ TBlockTable blocks;
+ TBlockIter blockFirst, blockLast; // current block boundaries
+ TBlockIter lastValue; // pointer to top value
+ TAllocator alloc;
+
+ //____________________________________________________________________________
+
+ public:
+ String():
+ blockFirst(TBlockIter()),
+ blockLast(TBlockIter()),
+ lastValue(TBlockIter()) {}
+
+ template<typename TSource>
+ String(TSource const& source):
+ blockFirst(TBlockIter()),
+ blockLast(TBlockIter()),
+ lastValue(TBlockIter())
+ {
+ SEQAN_CHECKPOINT
+ assign(*this, source);
+ }
+
+ String(String const & source):
+ blockFirst(TBlockIter()),
+ blockLast(TBlockIter()),
+ lastValue(TBlockIter())
+ {
+ SEQAN_CHECKPOINT
+ assign(*this, source);
+ }
+
+ template<typename TSource>
+ String & operator =(TSource const& source)
+ {
+ SEQAN_CHECKPOINT
+ assign(*this, source);
+ return *this;
+ }
+
+ String & operator =(String const& _other)
+ {
+ SEQAN_CHECKPOINT
+ if (this == &_other) return *this;
+ assign(*this, _other);
+ return *this;
+ }
+
+ ~String()
+ {
+ clear(*this);
+ }
+
+ //____________________________________________________________________________
+
+ public:
+ template<typename TPos>
+ inline typename Reference<String>::Type
+ operator[] (TPos pos)
+ {
+ SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+
+ template<typename TPos>
+ inline typename Reference<String const>::Type
+ operator[] (TPos pos) const
+ {
+ SEQAN_CHECKPOINT
+ return value(*this, pos);
+ }
+ };
+
+
+ template<typename TValue, unsigned int SPACE>
+ struct DefaultOverflowImplicit< String<TValue, Block<SPACE> > >
+ {
+ typedef Generous Type;
+ };
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Block metafunctions
+//////////////////////////////////////////////////////////////////////////////
+
+//////////////////////////////////////////////////////////////////////////////
+// Iterators
+//////////////////////////////////////////////////////////////////////////////
+
+///.Metafunction.Iterator.param.T.type:Spec.Block String
+
+ template<typename TValue, unsigned int SPACE>
+ struct Iterator<String<TValue, Block<SPACE> >, Standard>
+ {
+ typedef Iter<String<TValue, Block<SPACE> >, PositionIterator> Type;
+ };
+
+ template<typename TValue, unsigned int SPACE>
+ struct Iterator<String<TValue, Block<SPACE> > const, Standard>
+ {
+ typedef Iter<String<TValue, Block<SPACE> > const, PositionIterator> Type;
+ };
+
+ template<typename TValue, unsigned int SPACE>
+ struct Iterator<String<TValue, Block<SPACE> >, Rooted>
+ {
+ typedef Iter<String<TValue, Block<SPACE> >, PositionIterator> Type;
+ };
+
+ template<typename TValue, unsigned int SPACE>
+ struct Iterator<String<TValue, Block<SPACE> > const, Rooted>
+ {
+ typedef Iter<String<TValue, Block<SPACE> > const, PositionIterator> Type;
+ };
+
+
+///////////////////////////////////////////////////////////////
+// Block interface
+///////////////////////////////////////////////////////////////
+
+
+//////////////////////////////////////////////////////////////////////////////
+// begin
+//////////////////////////////////////////////////////////////////////////////
+
+ template<typename TValue, unsigned int SPACE, typename TSpec>
+ inline typename Iterator<String<TValue, Block<SPACE> >, Tag<TSpec> const >::Type
+ begin(String<TValue, Block<SPACE> > &me, Tag<TSpec> const)
+ {
+ SEQAN_CHECKPOINT
+ return Iter<String<TValue, Block<SPACE> >, PositionIterator>(me, 0);
+ }
+
+ template<typename TValue, unsigned int SPACE, typename TSpec>
+ inline typename Iterator<String<TValue, Block<SPACE> > const, Tag<TSpec> const>::Type
+ begin(String<TValue, Block<SPACE> > const &me, Tag<TSpec> const)
+ {
+ SEQAN_CHECKPOINT
+ return Iter<String<TValue, Block<SPACE> > const, PositionIterator>(me, 0);
+ }
+
+
+ template<typename TValue, unsigned int SPACE, typename TSpec>
+ inline typename Iterator<String<TValue, Block<SPACE> >, Tag<TSpec> const >::Type
+ end(String<TValue, Block<SPACE> > &me, Tag<TSpec> const)
+ {
+ SEQAN_CHECKPOINT
+ return Iter<String<TValue, Block<SPACE> >, PositionIterator>(me, length(me));
+ }
+
+ template<typename TValue, unsigned int SPACE, typename TSpec>
+ inline typename Iterator<String<TValue, Block<SPACE> > const, Tag<TSpec> const>::Type
+ end(String<TValue, Block<SPACE> > const &me, Tag<TSpec> const)
+ {
+ SEQAN_CHECKPOINT
+ return Iter<String<TValue, Block<SPACE> > const, PositionIterator>(me, length(me));
+ }
+
+ template<typename TValue, unsigned int SPACE, typename TSource>
+ inline void
+ assign(
+ String<TValue, Block<SPACE> >& target,
+ TSource const& source)
+ {
+ SEQAN_CHECKPOINT
+ clear(target);
+ typedef typename Iterator<TSource const, Standard>::Type TIter;
+ for(TIter it = begin(source, Standard()); !atEnd(it, source); goNext(it))
+ push(target, *it);
+ }
+
+
+ template<typename TValue, unsigned int SPACE, typename TPos>
+ inline typename Reference<String<TValue, Block<SPACE> > >::Type
+ value(
+ String<TValue, Block<SPACE> >& stack,
+ TPos const pos)
+ {
+ SEQAN_CHECKPOINT
+ return value(*(stack.blocks[pos / SPACE]), pos % SPACE);
+ }
+
+ template<typename TValue, unsigned int SPACE, typename TPos>
+ inline typename Reference<String<TValue, Block<SPACE> > >::Type
+ value(
+ String<TValue, Block<SPACE> > const& stack,
+ TPos const pos)
+ {
+ SEQAN_CHECKPOINT
+ return value(*(stack.blocks[pos / SPACE]), pos % SPACE);
+ }
+
+ template<typename TValue, unsigned int SPACE, typename TIteratorSpec>
+ inline bool
+ atEnd(
+ Iter<String<TValue, Block<SPACE> >, TIteratorSpec>& it,
+ String<TValue, Block<SPACE> >& container)
+ {
+ SEQAN_CHECKPOINT
+ typedef typename Iterator<String<TValue, Block<SPACE> >, Standard>::Type TIter;
+ TIter endIt = end(container, Standard());
+ return (it == endIt);
+ }
+
+
+ template<typename TValue, unsigned int SPACE>
+ inline void
+ clear(String<TValue, Block<SPACE> >& me)
+ {
+ SEQAN_CHECKPOINT
+ typedef String<TValue, Block<SPACE> > TBlockString;
+ typedef typename TBlockString::TBlockTable TBlockTable;
+ typedef typename Iterator<TBlockTable, Standard>::Type TIter;
+
+ TIter it = begin(me.blocks), itEnd = end(me.blocks);
+ while (it != itEnd) {
+ deallocate(me.alloc, *it, 1);
+ ++it;
+ }
+ clear(me.blocks);
+ me.lastValue = me.blockLast = typename TBlockString::TBlockIter();
+ }
+
+
+//////////////////////////////////////////////////////////////////////////////
+///.Function.reserve.param.object.type:Spec.Block String
+/*
+ template <typename TValue, unsigned int SPACE, typename TSize, typename TExpand>
+ inline typename Size< String<TValue, Block<SPACE> > >::Type
+ reserve(
+ String<TValue, Block<SPACE> >& me,
+ TSize new_capacity,
+ Tag<TExpand> const tag)
+ {
+ SEQAN_CHECKPOINT
+ reserve(me.blocks, (new_capacity + SPACE - 1) / SPACE, tag);
+ return capacity(me.blocks) * SPACE;
+ }
+*/
+
+ template<typename TValue, unsigned int SPACE, typename TSize2, typename TExpand>
+ inline typename Size< String<TValue, Block<SPACE> > >::Type
+ resize(String<TValue, Block<SPACE> > & me,
+ TSize2 new_length,
+ Tag<TExpand> const)
+ {
+ SEQAN_CHECKPOINT
+ typedef String<TValue, Block<SPACE> > TBlockString;
+ typedef typename Size<TBlockString>::Type TSize;
+ TSize len = length(me);
+
+ if (new_length > len)
+ {
+ for (; len < new_length; ++len) push(me);
+ }
+ else if (new_length < len)
+ {
+ for (; len > new_length; --len) pop(me);
+ }
+ return new_length;
+ }
+ template<typename TValue, unsigned int SPACE, typename TSize2>
+ inline typename Size< String<TValue, Block<SPACE> > >::Type
+ resize(String<TValue, Block<SPACE> > & me,
+ TSize2 new_length,
+ Limit)
+ {
+ SEQAN_CHECKPOINT
+ typedef String<TValue, Block<SPACE> > TBlockString;
+ typedef typename Size<TBlockString>::Type TSize;
+ TSize len = length(me);
+
+ if (new_length > capacity(me)) new_length = capacity(me);
+
+ if (new_length > len)
+ {
+ TValue val;
+ for (; len < new_length; ++len) push(me, val);
+ }
+ else if (new_length < len)
+ {
+ for (; len > new_length; --len) pop(me);
+ }
+ return new_length;
+ }
+
+
+ //dummy implementation
+ template<typename TValue, unsigned int SPACE, typename TSize, typename TExpand>
+ inline typename Size< String<TValue, Block<SPACE> > >::Type
+ reserve(String<TValue, Block<SPACE> > & me,
+ TSize new_capacity,
+ Tag<TExpand> const)
+ {
+ SEQAN_CHECKPOINT
+ return new_capacity;
+ }
+
+
+ template<typename TValue, unsigned int SPACE, typename TSource, typename TExpand>
+ inline void
+ append(
+ String<TValue, Block<SPACE> >& me,
+ TSource const& source,
+ Tag<TExpand> const tag)
+ {
+ SEQAN_CHECKPOINT
+ typedef typename Iterator<TSource const, Standard>::Type TIter;
+ for(TIter it = begin(source, Standard()); !atEnd(it, source); goNext(it))
+ appendValue(me, *it);
+ }
+
+//////////////////////////////////////////////////////////////////////////////
+///.Function.appendValue.param.target.type:Spec.Block String
+
+ template<typename TValue, unsigned int SPACE, typename TVal, typename TExpand>
+ inline void
+ appendValue(
+ String<TValue, Block<SPACE> >& me,
+ TVal const& source,
+ Tag<TExpand> const tag)
+ {
+ SEQAN_CHECKPOINT
+ if (me.lastValue == me.blockLast) {
+ typename Size< String<TValue, Block<SPACE> > >::Type last = length(me.blocks);
+
+ resize(me.blocks, last + 1, tag);
+ allocate(me.alloc, me.blocks[last], 1);
+ me.lastValue = me.blockFirst = begin(*me.blocks[last]);
+ me.blockLast = (me.blockFirst + (SPACE - 1));
+ } else
+ ++me.lastValue;
+ valueConstruct(me.lastValue, source);
+ }
+
+ template<typename TValue, unsigned int SPACE, typename TVal>
+ inline void
+ push(
+ String<TValue, Block<SPACE> >& me,
+ TVal const& source)
+ {
+ appendValue(me, source);
+ }
+
+ template<typename TValue, unsigned int SPACE>
+ inline void
+ push(String<TValue, Block<SPACE> >& me)
+ {
+ SEQAN_CHECKPOINT
+ if (me.lastValue == me.blockLast) {
+ typename Size< String<TValue, Block<SPACE> > >::Type last = length(me.blocks);
+
+ resize(me.blocks, last + 1, typename DefaultOverflowImplicit<String<TValue, Block<SPACE> > >::Type());
+ allocate(me.alloc, me.blocks[last], 1);
+ me.lastValue = me.blockFirst = begin(*me.blocks[last]);
+ me.blockLast = (me.blockFirst + (SPACE - 1));
+ } else
+ ++me.lastValue;
+ valueConstruct(me.lastValue);
+ }
+
+ template<typename TValue, unsigned int SPACE, typename TVal>
+ inline void
+ push_back(
+ String<TValue, Block<SPACE> >& me,
+ TVal const& source)
+ {
+ appendValue(me, source);
+ }
+
+ template<typename TValue, unsigned int SPACE>
+ inline TValue &
+ top(String<TValue, Block<SPACE> > & me)
+ {
+ SEQAN_CHECKPOINT
+ return *me.lastValue;
+ }
+
+ template<typename TValue, unsigned int SPACE>
+ inline TValue const &
+ top(String<TValue, Block<SPACE> > const& me)
+ {
+ SEQAN_CHECKPOINT
+ return *me.lastValue;
+ }
+
+ template<typename TValue, unsigned int SPACE>
+ inline TValue &
+ topPrev(String<TValue, Block<SPACE> > & me)
+ {
+ SEQAN_CHECKPOINT
+ if (me.lastValue != me.blockFirst)
+ return *(me.lastValue - 1);
+ else
+ return *(begin(*me.blocks[length(me.blocks) - 1]) + (SPACE - 1));
+ }
+
+ template<typename TValue, unsigned int SPACE>
+ inline TValue const &
+ topPrev(String<TValue, Block<SPACE> > const& me)
+ {
+ SEQAN_CHECKPOINT
+ if (me.lastValue != me.blockFirst)
+ return *(me.lastValue - 1);
+ else
+ return *(begin(*me.blocks[length(me.blocks) - 1]) + (SPACE - 1));
+ }
+
+ template<typename TValue, unsigned int SPACE>
+ inline void
+ pop(String<TValue, Block<SPACE> >& me)
+ {
+ SEQAN_CHECKPOINT
+ if (me.lastValue == me.blockFirst) {
+ typename Size< String<TValue, Block<SPACE> > >::Type last = length(me.blocks);
+
+ if (last) {
+ valueDestruct(me.lastValue);
+ deallocate(me.alloc, me.blocks[--last], 1);
+ resize(me.blocks, last);
+ if (last) {
+ me.blockFirst = begin(*me.blocks[--last]);
+ me.lastValue = me.blockLast = (me.blockFirst + (SPACE - 1));
+ }
+ }
+ } else {
+ valueDestruct(me.lastValue);
+ --me.lastValue;
+ }
+ }
+
+ template<typename TValue, unsigned int SPACE>
+ inline void
+ pop_back(String<TValue, Block<SPACE> >& me) {
+ pop(me);
+ }
+
+ template<typename TValue, unsigned int SPACE>
+ inline bool
+ empty(String<TValue, Block<SPACE> > const& me)
+ {
+ SEQAN_CHECKPOINT
+ return length(me.blocks) == 0;
+ }
+
+ template<typename TValue, unsigned int SPACE>
+ inline typename Size<String<TValue, Block<SPACE> > >::Type
+ length(String<TValue, Block<SPACE> > const & me)
+ {
+ SEQAN_CHECKPOINT
+ if (length(me.blocks))
+ return (length(me.blocks) - 1) * SPACE + (me.lastValue - me.blockFirst) + 1;
+ else
+ return 0;
+ }
+
+ template<typename TValue, unsigned int SPACE>
+ inline typename Size<String<TValue, Block<SPACE> > >::Type
+ capacity(String<TValue, Block<SPACE> > const & me)
+ {
+ SEQAN_CHECKPOINT
+ if (length(me.blocks))
+ return length(me.blocks) * SPACE;
+ else
+ return 0;
+ }
+
+}// namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/seqan/sequence/string_value_expand.h b/src/libSSA/seqan/sequence/string_value_expand.h
new file mode 100644
index 0000000..38d025c
--- /dev/null
+++ b/src/libSSA/seqan/sequence/string_value_expand.h
@@ -0,0 +1,514 @@
+ /*==========================================================================
+ SeqAn - The Library for Sequence Analysis
+ http://www.seqan.de
+ ============================================================================
+ Copyright (C) 2007
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ ============================================================================
+ $Id: string_value_expand.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
+ ==========================================================================*/
+
+#ifndef SEQAN_HEADER_SEQUENCE_STRING_VALUEEXPAND_H
+#define SEQAN_HEADER_SEQUENCE_STRING_VALUEEXPAND_H
+
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+//////////////////////////////////////////////////////////////////////////////
+// Tags
+
+template <typename THost, typename TMap, typename TSpec = Default>
+struct ValueExpand;
+
+struct ValueExpandIter;
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+class String<TValue, ValueExpand<THost, TMap, TSpec> >
+{
+//____________________________________________________________________________
+private:
+
+ typedef typename Value<String>::Type TLargeValue;
+ typedef typename Value<THost>::Type TSmallValue;
+
+ Holder<THost> data_host;
+ Holder<TMap> data_map;
+
+//____________________________________________________________________________
+
+public:
+ String()
+ {
+ }
+ String(String const & other_):
+ data_host(other_.data_host),
+ data_map(other_.data_map)
+ {
+ }
+ ~String()
+ {
+ }
+ String const &
+ operator = (String const & other_)
+ {
+ data_host = other_.data_host;
+ data_map = other_.data_map;
+ }
+//____________________________________________________________________________
+
+ template <typename TPos>
+ inline typename Reference<String>::Type
+ operator [](TPos pos)
+ {
+ return value(*this, pos);
+ }
+
+//____________________________________________________________________________
+
+ friend inline Holder<THost> &
+ _dataHost(String & me)
+ {
+ return me.data_host;
+ }
+//____________________________________________________________________________
+
+ friend inline Holder<TMap> &
+ _dataMap(String & me)
+ {
+ return me.data_map;
+ }
+//____________________________________________________________________________
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// Metafunctions
+
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+struct Value<String< TValue, ValueExpand<THost, TMap, TSpec> > >
+{
+ typedef TValue Type;
+};
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+struct Value<String< TValue, ValueExpand<THost, TMap, TSpec> > const>
+{
+ typedef TValue const Type;
+};
+
+//____________________________________________________________________________
+
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+struct GetValue<String< TValue, ValueExpand<THost, TMap, TSpec> > >:
+ Value<String< TValue, ValueExpand<THost, TMap, TSpec> > >
+{
+};
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+struct GetValue<String< TValue, ValueExpand<THost, TMap, TSpec> > const>:
+ Value<String< TValue, ValueExpand<THost, TMap, TSpec> > const>
+{
+};
+
+//____________________________________________________________________________
+
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+struct Reference<String< TValue, ValueExpand<THost, TMap, TSpec> > >
+{
+ typedef String< TValue, ValueExpand<THost, TMap, TSpec> > TMe;
+ typedef typename Iterator<TMe, Standard>::Type TIterator;
+ typedef Proxy<IteratorProxy<TIterator> > Type;
+};
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+struct Reference<String< TValue, ValueExpand<THost, TMap, TSpec> > const>
+{
+ typedef String< TValue, ValueExpand<THost, TMap, TSpec> > const TMe;
+ typedef typename Iterator<TMe, Standard>::Type TIterator;
+ typedef Proxy<IteratorProxy<TIterator> > Type;
+};
+
+//____________________________________________________________________________
+
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TIteratorSpec>
+struct Iterator<String< TValue, ValueExpand<THost, TMap, TSpec> >, TIteratorSpec>
+{
+ typedef ValueExpand<THost, TMap, TSpec> TValueExpand;
+ typedef String< TValue, TValueExpand> TMe;
+ typedef typename Iterator<THost, Standard>::Type THostIterator;
+
+ typedef Iter<TMe, AdaptorIterator<THostIterator, ValueExpandIter> > Type;
+};
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TIteratorSpec>
+struct Iterator<String< TValue, ValueExpand<THost, TMap, TSpec> > const, TIteratorSpec>
+{
+ typedef ValueExpand<THost, TMap, TSpec> TValueExpand;
+ typedef String< TValue, TValueExpand> const TMe;
+ typedef typename Iterator<THost, Standard>::Type THostIterator;
+
+ typedef Iter<TMe, AdaptorIterator<THostIterator, ValueExpandIter> > Type;
+};
+
+//____________________________________________________________________________
+
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+struct DefaultOverflowImplicit<String< TValue, ValueExpand<THost, TMap, TSpec> > >:
+ DefaultOverflowImplicit< typename Host<String< TValue, ValueExpand<THost, TMap, TSpec> > >::Type >
+{
+};
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+struct DefaultOverflowImplicit<String< TValue, ValueExpand<THost, TMap, TSpec> > const>:
+ DefaultOverflowImplicit< typename Host<String< TValue, ValueExpand<THost, TMap, TSpec> > const>::Type >
+{
+};
+
+//____________________________________________________________________________
+
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+struct DefaultOverflowExplicit<String< TValue, ValueExpand<THost, TMap, TSpec> > >:
+ DefaultOverflowExplicit< typename Host<String< TValue, ValueExpand<THost, TMap, TSpec> > >::Type >
+{
+};
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+struct DefaultOverflowExplicit<String< TValue, ValueExpand<THost, TMap, TSpec> > const>:
+ DefaultOverflowExplicit< typename Host<String< TValue, ValueExpand<THost, TMap, TSpec> > const>::Type >
+{
+};
+
+//____________________________________________________________________________
+
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+struct IsContiguous<String< TValue, ValueExpand<THost, TMap, TSpec> > >
+{
+ typedef False Type;
+ enum { VALUE = false };
+};
+
+//____________________________________________________________________________
+
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+struct Host<String< TValue, ValueExpand<THost, TMap, TSpec> > >
+{
+ typedef THost Type;
+};
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+struct Host<String< TValue, ValueExpand<THost, TMap, TSpec> > const>
+{
+ typedef THost const Type;
+};
+
+//____________________________________________________________________________
+
+template <typename T>
+struct MapType;
+
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+struct MapType<String< TValue, ValueExpand<THost, TMap, TSpec> > >
+{
+ typedef TMap Type;
+};
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+struct MapType<String< TValue, ValueExpand<THost, TMap, TSpec> > const>
+{
+ typedef TMap const Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// Special Functions
+
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+inline TMap &
+_getMap(String< TValue, ValueExpand<THost, TMap, TSpec> > & me)
+{
+ return value(_dataMap(me));
+}
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+inline TMap &
+_getMap(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me)
+{
+ return value(_dataMap(me));
+}
+
+//____________________________________________________________________________
+
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+inline typename Value<THost>::Type
+_getValueExpandFlagValue(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me)
+{
+ typedef typename Value<THost>::Type TSmallValue;
+ return supremumValue<TSmallValue>();
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Public Functions
+
+
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+inline void const *
+id(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me)
+{
+SEQAN_CHECKPOINT
+ return id(host(me));
+}
+
+//____________________________________________________________________________
+
+template <typename TValue, typename THost, typename TMap, typename TPos, typename TSpec, typename TTag>
+inline typename Iterator<String< TValue, ValueExpand<THost, TMap, TSpec> >, Tag<TTag> const>::Type
+iter(String< TValue, ValueExpand<THost, TMap, TSpec> > & me,
+ TPos pos_,
+ Tag<TTag> const tag_)
+{
+SEQAN_CHECKPOINT
+ typedef String< TValue, ValueExpand<THost, TMap, TSpec> > TMe;
+ typedef typename Iterator<TMe, Tag<TTag> const>::Type TIterator;
+ return TIterator(me, begin(host(me), Standard()) + pos_);
+}
+template <typename TValue, typename THost, typename TMap, typename TPos, typename TSpec, typename TTag>
+inline typename Iterator<String< TValue, ValueExpand<THost, TMap, TSpec> > const, Tag<TTag> const>::Type
+iter(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me,
+ TPos pos_,
+ Tag<TTag> const tag_ )
+{
+SEQAN_CHECKPOINT
+ typedef String< TValue, ValueExpand<THost, TMap, TSpec> > const TMe;
+ typedef typename Iterator<TMe, Tag<TTag> const>::Type TIterator;
+ return TIterator(me, begin(host(me), Standard()) + pos_);
+}
+
+//____________________________________________________________________________
+
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TTag>
+inline typename Iterator<String< TValue, ValueExpand<THost, TMap, TSpec> >, Tag<TTag> const>::Type
+begin(String< TValue, ValueExpand<THost, TMap, TSpec> > & me,
+ Tag<TTag> const tag_)
+{
+SEQAN_CHECKPOINT
+ return iter(me, 0, tag_);
+}
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TTag>
+inline typename Iterator<String< TValue, ValueExpand<THost, TMap, TSpec> > const, Tag<TTag> const>::Type
+begin(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me,
+ Tag<TTag> const tag_)
+{
+SEQAN_CHECKPOINT
+ return iter(me, 0, tag_);
+}
+
+//____________________________________________________________________________
+
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TTag>
+inline typename Iterator<String< TValue, ValueExpand<THost, TMap, TSpec> >, Tag<TTag> const>::Type
+end(String< TValue, ValueExpand<THost, TMap, TSpec> > & me,
+ Tag<TTag> const tag_)
+{
+SEQAN_CHECKPOINT
+ return iter(me, length(me), tag_);
+}
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TTag>
+inline typename Iterator<String< TValue, ValueExpand<THost, TMap, TSpec> > const, Tag<TTag> const>::Type
+end(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me,
+ Tag<TTag> const tag_)
+{
+SEQAN_CHECKPOINT
+ return iter(me, length(me), tag_);
+}
+
+//____________________________________________________________________________
+
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TPos>
+inline typename Reference<String< TValue, ValueExpand<THost, TMap, TSpec> > >::Type
+value(String< TValue, ValueExpand<THost, TMap, TSpec> > & me,
+ TPos pos)
+{
+SEQAN_CHECKPOINT
+
+ return *iter(me, pos, Standard());
+}
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TPos>
+inline typename Reference<String< TValue, ValueExpand<THost, TMap, TSpec> > const>::Type
+value(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me,
+ TPos pos)
+{
+SEQAN_CHECKPOINT
+
+ return *iter(me, pos, Standard());
+}
+
+//____________________________________________________________________________
+
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+inline typename Size<String< TValue, ValueExpand<THost, TMap, TSpec> > const>::Type
+length(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me)
+{
+SEQAN_CHECKPOINT
+ return length(host(me));
+}
+
+//____________________________________________________________________________
+
+template <typename TValue, typename THost, typename TMap, typename TSpec>
+inline typename Size<String< TValue, ValueExpand<THost, TMap, TSpec> > const>::Type
+capacity(String< TValue, ValueExpand<THost, TMap, TSpec> > const & me)
+{
+SEQAN_CHECKPOINT
+ return capacity(host(me));
+}
+
+//____________________________________________________________________________
+
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TSize>
+inline TSize
+resize(String< TValue, ValueExpand<THost, TMap, TSpec> > & me,
+ TSize new_length)
+{
+SEQAN_CHECKPOINT
+ return resize(host(me), new_length);
+}
+
+//____________________________________________________________________________
+
+template <typename TValue, typename THost, typename TMap, typename TSpec, typename TSize, typename TExpand>
+inline TSize
+reserve(String< TValue, ValueExpand<THost, TMap, TSpec> > & me,
+ TSize new_length,
+ Tag<TExpand> const tag)
+{
+SEQAN_CHECKPOINT
+ return reserve(host(me), new_length, tag);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Iterator for ValueExpandIterator string: Subclass of AdaptorIterator
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TContainer, typename TIterator>
+inline typename Value<TContainer>::Type
+getValue(Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > & me)
+{
+SEQAN_CHECKPOINT
+ typedef typename Host<TContainer>::Type THost;
+ typedef typename Value<THost>::Type TSmallValue;
+ TSmallValue c = value(hostIterator(me));
+ if (c == _getValueExpandFlagValue(container(me)))
+ {//value is large
+ return _getMap(container(me))[position(me)];
+ }
+ else
+ {
+ return c;
+ }
+}
+template <typename TContainer, typename TIterator>
+inline void
+getValue(Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > const & me)
+{
+SEQAN_CHECKPOINT
+ typedef typename Host<TContainer>::Type THost;
+ typedef typename Value<THost>::Type TSmallValue;
+ TSmallValue c = value(hostIterator(me));
+ if (c == _getValueExpandFlagValue(container(me)))
+ {//value is large
+ return _getMap(container(me))[position(me)];
+ }
+ else
+ {
+ return c;
+ }
+}
+
+//____________________________________________________________________________
+
+template <typename TContainer, typename TIterator>
+inline typename Reference<Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > >::Type
+value(Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > & me)
+{
+SEQAN_CHECKPOINT
+ typedef Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > TMe;
+ return typename Reference<TMe>::Type(me);
+}
+template <typename TContainer, typename TIterator>
+inline typename Reference<Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > >::Type
+value(Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > const & me)
+{
+SEQAN_CHECKPOINT
+ typedef Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > const TMe;
+ return typename Reference<TMe>::Type(me);
+}
+
+//____________________________________________________________________________
+
+template <typename TContainer, typename TIterator, typename TValue>
+inline void
+assignValue(Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ typedef typename Host<TContainer>::Type THost;
+ typedef typename Value<THost>::Type TSmallValue;
+
+ TSmallValue flagValue = _getValueExpandFlagValue(container(me));
+ if (_value >= flagValue)
+ {//use map to store LargeValue
+ assignValue(hostIterator(me), flagValue);
+ _getMap(container(me))[position(me)] = _value;
+ }
+ else
+ {
+ assignValue(hostIterator(me), _value);
+ }
+}
+template <typename TContainer, typename TIterator, typename TValue>
+inline void
+assignValue(Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > const & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ typedef typename Host<TContainer>::Type THost;
+ typedef typename Value<THost>::Type TSmallValue;
+
+ TSmallValue flagValue = _getValueExpandFlagValue(container(me));
+ if (_value >= flagValue)
+ {//use map to store LargeValue
+ assignValue(hostIterator(me), flagValue);
+ _getMap(container(me))[position(me)] = _value;
+ }
+ else
+ {
+ assignValue(hostIterator(me), _value);
+ }
+}
+
+//____________________________________________________________________________
+
+template <typename TContainer, typename TIterator, typename TValue>
+inline void
+moveValue(Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ assignValue(me, _value);
+}
+template <typename TContainer, typename TIterator, typename TValue>
+inline void
+moveValue(Iter<TContainer, AdaptorIterator<TIterator, ValueExpandIter> > const & me,
+ TValue const & _value)
+{
+SEQAN_CHECKPOINT
+ assignValue(me, _value);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/src/libSSA/utils.cpp b/src/libSSA/utils.cpp
new file mode 100644
index 0000000..fef5e9e
--- /dev/null
+++ b/src/libSSA/utils.cpp
@@ -0,0 +1,122 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <stdlib.h>
+#include "utils.h"
+
+char complementDNA(char c) {
+ char c2;
+ switch(c) {
+ case 'A' : c2 = 'T'; break;
+ case 'C' : c2 = 'G'; break;
+ case 'G' : c2 = 'C'; break;
+ case 'T' : c2 = 'A'; break;
+ default : c2 = c;
+ }
+ return c2;
+}
+
+char randomDNA() {
+ switch(rand() % 4) {
+ case 0: return 'A';
+ case 1: return 'C';
+ case 2: return 'G';
+ default: return 'T';
+ }
+}
diff --git a/src/libSSA/utils.h b/src/libSSA/utils.h
new file mode 100644
index 0000000..b70bd82
--- /dev/null
+++ b/src/libSSA/utils.h
@@ -0,0 +1,110 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef UTILS_SSA_H
+#define UTILS_SSA_H
+
+char complementDNA(char c);
+
+/**
+ * @return randomly a character A, C, G or T
+ */
+char randomDNA();
+
+#endif
diff --git a/src/libgzstream/COPYING.LIB b/src/libgzstream/COPYING.LIB
new file mode 100644
index 0000000..b1e3f5a
--- /dev/null
+++ b/src/libgzstream/COPYING.LIB
@@ -0,0 +1,504 @@
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+[This is the first released version of the Lesser GPL. It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]
+
+ Preamble
+
+ The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+Licenses are intended to guarantee your freedom to share and change
+free software--to make sure the software is free for all its users.
+
+ This license, the Lesser General Public License, applies to some
+specially designated software packages--typically libraries--of the
+Free Software Foundation and other authors who decide to use it. You
+can use it too, but we suggest you first think carefully about whether
+this license or the ordinary General Public License is the better
+strategy to use in any particular case, based on the explanations below.
+
+ When we speak of free software, we are referring to freedom of use,
+not price. Our General Public Licenses are designed to make sure that
+you have the freedom to distribute copies of free software (and charge
+for this service if you wish); that you receive source code or can get
+it if you want it; that you can change the software and use pieces of
+it in new free programs; and that you are informed that you can do
+these things.
+
+ To protect your rights, we need to make restrictions that forbid
+distributors to deny you these rights or to ask you to surrender these
+rights. These restrictions translate to certain responsibilities for
+you if you distribute copies of the library or if you modify it.
+
+ For example, if you distribute copies of the library, whether gratis
+or for a fee, you must give the recipients all the rights that we gave
+you. You must make sure that they, too, receive or can get the source
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+complete object files to the recipients, so that they can relink them
+with the library after making changes to the library and recompiling
+it. And you must show them these terms so they know their rights.
+
+ We protect your rights with a two-step method: (1) we copyright the
+library, and (2) we offer you this license, which gives you legal
+permission to copy, distribute and/or modify the library.
+
+ To protect each distributor, we want to make it very clear that
+there is no warranty for the free library. Also, if the library is
+modified by someone else and passed on, the recipients should know
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+
+ Finally, software patents pose a constant threat to the existence of
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+consistent with the full freedom of use specified in this license.
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+ Most GNU software, including some libraries, is covered by the
+ordinary GNU General Public License. This license, the GNU Lesser
+General Public License, applies to certain designated libraries, and
+is quite different from the ordinary General Public License. We use
+this license for certain libraries in order to permit linking those
+libraries into non-free programs.
+
+ When a program is linked with a library, whether statically or using
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+combined work, a derivative of the original library. The ordinary
+General Public License therefore permits such linking only if the
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+ In other cases, permission to use a particular library in non-free
+programs enables a greater number of people to use a large body of
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+ Although the Lesser General Public License is Less protective of the
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diff --git a/src/libgzstream/Makefile.am b/src/libgzstream/Makefile.am
new file mode 100644
index 0000000..5b14c54
--- /dev/null
+++ b/src/libgzstream/Makefile.am
@@ -0,0 +1,107 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+noinst_LIBRARIES = libgzstream.a
+
+libgzstream_a_SOURCES= gzstream.cpp gzstream.h
+
+MOSTLYCLEANFILES=*~
+CLEANFILES=*~ $(EXTRA_PROGRAMS)
+DISTCLEANFILES=*~
+MAINTAINERCLEANFILES=*~
diff --git a/src/libgzstream/Makefile.in b/src/libgzstream/Makefile.in
new file mode 100644
index 0000000..ba82366
--- /dev/null
+++ b/src/libgzstream/Makefile.in
@@ -0,0 +1,593 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+subdir = src/libgzstream
+DIST_COMMON = README $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+ COPYING.LIB
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+ $(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/config/config.h
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+LIBRARIES = $(noinst_LIBRARIES)
+ARFLAGS = cru
+libgzstream_a_AR = $(AR) $(ARFLAGS)
+libgzstream_a_LIBADD =
+am_libgzstream_a_OBJECTS = gzstream.$(OBJEXT)
+libgzstream_a_OBJECTS = $(am_libgzstream_a_OBJECTS)
+DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)/config
+depcomp = $(SHELL) $(top_srcdir)/config/depcomp
+am__depfiles_maybe = depfiles
+am__mv = mv -f
+CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
+ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
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diff --git a/src/libgzstream/README b/src/libgzstream/README
new file mode 100644
index 0000000..5fb78b2
--- /dev/null
+++ b/src/libgzstream/README
@@ -0,0 +1,6 @@
+
+ gzstream
+ C++ iostream classes wrapping the zlib compression library.
+===========================================================================
+
+ See index.html for documentation and installation instructions.
diff --git a/src/libgzstream/gzstream.cpp b/src/libgzstream/gzstream.cpp
new file mode 100644
index 0000000..8cb4590
--- /dev/null
+++ b/src/libgzstream/gzstream.cpp
@@ -0,0 +1,165 @@
+// ============================================================================
+// gzstream, C++ iostream classes wrapping the zlib compression library.
+// Copyright (C) 2001 Deepak Bandyopadhyay, Lutz Kettner
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+// ============================================================================
+//
+// File : gzstream.C
+// Revision : $Revision: 1.7 $
+// Revision_date : $Date: 2003/01/08 14:41:27 $
+// Author(s) : Deepak Bandyopadhyay, Lutz Kettner
+//
+// Standard streambuf implementation following Nicolai Josuttis, "The
+// Standard C++ Library".
+// ============================================================================
+
+#include <gzstream.h>
+#include <iostream>
+#include <string.h> // for memcpy
+
+#ifdef GZSTREAM_NAMESPACE
+namespace GZSTREAM_NAMESPACE {
+#endif
+
+// ----------------------------------------------------------------------------
+// Internal classes to implement gzstream. See header file for user classes.
+// ----------------------------------------------------------------------------
+
+// --------------------------------------
+// class gzstreambuf:
+// --------------------------------------
+
+gzstreambuf* gzstreambuf::open( const char* name, int open_mode) {
+ if ( is_open())
+ return (gzstreambuf*)0;
+ mode = open_mode;
+ // no append nor read/write mode
+ if ((mode & std::ios::ate) || (mode & std::ios::app)
+ || ((mode & std::ios::in) && (mode & std::ios::out)))
+ return (gzstreambuf*)0;
+ char fmode[10];
+ char* fmodeptr = fmode;
+ if ( mode & std::ios::in)
+ *fmodeptr++ = 'r';
+ else if ( mode & std::ios::out)
+ *fmodeptr++ = 'w';
+ *fmodeptr++ = 'b';
+ *fmodeptr = '\0';
+ file = gzopen( name, fmode);
+ if (file == 0)
+ return (gzstreambuf*)0;
+ opened = 1;
+ return this;
+}
+
+gzstreambuf * gzstreambuf::close() {
+ if ( is_open()) {
+ sync();
+ opened = 0;
+ if ( gzclose( file) == Z_OK)
+ return this;
+ }
+ return (gzstreambuf*)0;
+}
+
+int gzstreambuf::underflow() { // used for input buffer only
+ if ( gptr() && ( gptr() < egptr()))
+ return * reinterpret_cast<unsigned char *>( gptr());
+
+ if ( ! (mode & std::ios::in) || ! opened)
+ return EOF;
+ // Josuttis' implementation of inbuf
+ int n_putback = gptr() - eback();
+ if ( n_putback > 4)
+ n_putback = 4;
+ memcpy( buffer + (4 - n_putback), gptr() - n_putback, n_putback);
+
+ int num = gzread( file, buffer+4, bufferSize-4);
+ if (num <= 0) // ERROR or EOF
+ return EOF;
+
+ // reset buffer pointers
+ setg( buffer + (4 - n_putback), // beginning of putback area
+ buffer + 4, // read position
+ buffer + 4 + num); // end of buffer
+
+ // return next character
+ return * reinterpret_cast<unsigned char *>( gptr());
+}
+
+int gzstreambuf::flush_buffer() {
+ // Separate the writing of the buffer from overflow() and
+ // sync() operation.
+ int w = pptr() - pbase();
+ if ( gzwrite( file, pbase(), w) != w)
+ return EOF;
+ pbump( -w);
+ return w;
+}
+
+int gzstreambuf::overflow( int c) { // used for output buffer only
+ if ( ! ( mode & std::ios::out) || ! opened)
+ return EOF;
+ if (c != EOF) {
+ *pptr() = c;
+ pbump(1);
+ }
+ if ( flush_buffer() == EOF)
+ return EOF;
+ return c;
+}
+
+int gzstreambuf::sync() {
+ // Changed to use flush_buffer() instead of overflow( EOF)
+ // which caused improper behavior with std::endl and flush(),
+ // bug reported by Vincent Ricard.
+ if ( pptr() && pptr() > pbase()) {
+ if ( flush_buffer() == EOF)
+ return -1;
+ }
+ return 0;
+}
+
+// --------------------------------------
+// class gzstreambase:
+// --------------------------------------
+
+gzstreambase::gzstreambase( const char* name, int mode) {
+ init( &buf);
+ open( name, mode);
+}
+
+gzstreambase::~gzstreambase() {
+ buf.close();
+}
+
+void gzstreambase::open( const char* name, int open_mode) {
+ if ( ! buf.open( name, open_mode))
+ clear( rdstate() | std::ios::badbit);
+}
+
+void gzstreambase::close() {
+ if ( buf.is_open())
+ if ( ! buf.close())
+ clear( rdstate() | std::ios::badbit);
+}
+
+#ifdef GZSTREAM_NAMESPACE
+} // namespace GZSTREAM_NAMESPACE
+#endif
+
+// ============================================================================
+// EOF //
diff --git a/src/libgzstream/gzstream.h b/src/libgzstream/gzstream.h
new file mode 100644
index 0000000..861653f
--- /dev/null
+++ b/src/libgzstream/gzstream.h
@@ -0,0 +1,121 @@
+// ============================================================================
+// gzstream, C++ iostream classes wrapping the zlib compression library.
+// Copyright (C) 2001 Deepak Bandyopadhyay, Lutz Kettner
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+// ============================================================================
+//
+// File : gzstream.h
+// Revision : $Revision: 1.5 $
+// Revision_date : $Date: 2002/04/26 23:30:15 $
+// Author(s) : Deepak Bandyopadhyay, Lutz Kettner
+//
+// Standard streambuf implementation following Nicolai Josuttis, "The
+// Standard C++ Library".
+// ============================================================================
+
+#ifndef GZSTREAM_H
+#define GZSTREAM_H 1
+
+// standard C++ with new header file names and std:: namespace
+#include <iostream>
+#include <fstream>
+#include <zlib.h>
+
+#ifdef GZSTREAM_NAMESPACE
+namespace GZSTREAM_NAMESPACE {
+#endif
+
+// ----------------------------------------------------------------------------
+// Internal classes to implement gzstream. See below for user classes.
+// ----------------------------------------------------------------------------
+
+class gzstreambuf : public std::streambuf {
+private:
+ static const int bufferSize = 47+256; // size of data buff
+ // totals 512 bytes under g++ for igzstream at the end.
+
+ gzFile file; // file handle for compressed file
+ char buffer[bufferSize]; // data buffer
+ char opened; // open/close state of stream
+ int mode; // I/O mode
+
+ int flush_buffer();
+public:
+ gzstreambuf() : opened(0) {
+ setp( buffer, buffer + (bufferSize-1));
+ setg( buffer + 4, // beginning of putback area
+ buffer + 4, // read position
+ buffer + 4); // end position
+ // ASSERT: both input & output capabilities will not be used together
+ }
+ int is_open() { return opened; }
+ gzstreambuf* open( const char* name, int open_mode);
+ gzstreambuf* close();
+ ~gzstreambuf() { close(); }
+
+ virtual int overflow( int c = EOF);
+ virtual int underflow();
+ virtual int sync();
+};
+
+class gzstreambase : virtual public std::ios {
+protected:
+ gzstreambuf buf;
+public:
+ gzstreambase() { init(&buf); }
+ gzstreambase( const char* name, int open_mode);
+ ~gzstreambase();
+ void open( const char* name, int open_mode);
+ void close();
+ gzstreambuf* rdbuf() { return &buf; }
+};
+
+// ----------------------------------------------------------------------------
+// User classes. Use igzstream and ogzstream analogously to ifstream and
+// ofstream respectively. They read and write files based on the gz*
+// function interface of the zlib. Files are compatible with gzip compression.
+// ----------------------------------------------------------------------------
+
+class igzstream : public gzstreambase, public std::istream {
+public:
+ igzstream() : std::istream( &buf) {}
+ igzstream( const char* name, int open_mode = std::ios::in)
+ : gzstreambase( name, open_mode), std::istream( &buf) {}
+ gzstreambuf* rdbuf() { return gzstreambase::rdbuf(); }
+ void open( const char* name, int open_mode = std::ios::in) {
+ gzstreambase::open( name, open_mode);
+ }
+};
+
+class ogzstream : public gzstreambase, public std::ostream {
+public:
+ ogzstream() : std::ostream( &buf) {}
+ ogzstream( const char* name, int mode = std::ios::out)
+ : gzstreambase( name, mode), std::ostream( &buf) {}
+ gzstreambuf* rdbuf() { return gzstreambase::rdbuf(); }
+ void open( const char* name, int open_mode = std::ios::out) {
+ gzstreambase::open( name, open_mode);
+ }
+};
+
+#ifdef GZSTREAM_NAMESPACE
+} // namespace GZSTREAM_NAMESPACE
+#endif
+
+#endif // GZSTREAM_H
+// ============================================================================
+// EOF //
+
diff --git a/src/locateServer.cpp b/src/locateServer.cpp
new file mode 100644
index 0000000..b68468c
--- /dev/null
+++ b/src/locateServer.cpp
@@ -0,0 +1,788 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at univ-montp2.fr *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include <iostream>
+#include <fstream>
+#include <ostream>
+#include <string>
+#include <stdlib.h>
+#include <algorithm>
+#include <string.h>
+#include "types.h"
+#include "utils.h"
+#include <gkArrays.h>
+#include <gkArraysTypes.h>
+#include "classifyTags.h"
+#include "libSSA/locateOnGenome.h"
+#include "Parameters.h"
+#include "libReadsInfo/tagInfo.h"
+#include "Support.h"
+#include "SupportBreak.h"
+#include <semaphore.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <signal.h>
+#include <math.h>
+#include <pthread.h>
+
+using namespace std;
+using namespace gkarrays;
+
+#define LINE_MAX_LENGTH 256
+#define NB_POS_LOCATED 3
+#define NB_STEP_LOCATION 7
+#define SLEEP_DELAY_MS 1000
+
+#define ARG_VALUE 0
+#define ARG_CLASSIFY_TAGS 1
+#define ARG_GENOME_SEMAPHORE 2
+#define NB_ARGS_SUBSERVER 3
+
+void dispLocateFactors(ostream & os, TagInfo *info, int pos,
+ LocateOnGenome *genome,
+ uchar *tag, uint threshold, int increment
+ , uint max_done=NB_POS_LOCATED) {
+ uint nb_done = 0;
+ uchar *factor = new uchar[threshold+1];
+ factor[threshold]=0;
+ while (pos >= 0 && pos < (int)info->getSupportLength()
+ && nb_done < max_done) {
+ strncpy((char *)factor, (char *)&tag[pos], threshold);
+ if (info->getLocalisations()[pos] > 0) {
+ os << "\t pos. " << pos << ": ";
+ genome->locateTag(factor, threshold);
+ }
+ pos += increment;
+ nb_done++;
+ }
+ delete [] factor;
+}
+
+uint nb_digits(uint a) {
+ return (uint)floor(log(a)/log(10))+1;
+}
+
+ostream &writeWithSpaces(ostream &os, uint writeIt, uint a, uint b) {
+ uint nb_writeIt_digits = nb_digits(writeIt);
+ uint max_nb_digits = max(nb_digits(a), nb_digits(b));
+ max_nb_digits = max(max_nb_digits, nb_writeIt_digits);
+ if (max_nb_digits > nb_writeIt_digits) {
+ os << setw(max_nb_digits) << writeIt;
+ } else {
+ os << writeIt ;
+ }
+ return os;
+}
+
+void detailed_taginfo_output(ostream &os, uint tag_id, ClassifyTags *ct,
+ uint nb_pos_located,
+ uint nb_step_location) {
+ TagInfo *info;
+ Classifier *classi;
+ if(!ct->getReadIndex()->getReads()->isPairedEnd()) {
+ SingleReadClassifier *classifier = new SingleReadClassifier(tag_id,ct->getGenomeIndex(),ct->getReadIndex(),ct->getParameters());
+ classifier->classify();
+ info = classifier->getTagInfo();
+ classi = classifier;
+ } else {
+ PairedEndReadClassifier *classifier;
+ if (tag_id % 2 == 0) {
+ classifier = new PairedEndReadClassifier(tag_id,tag_id+1,ct->getGenomeIndex(),ct->getReadIndex(),ct->getParameters());
+ classifier->classify();
+ info = classifier->getFirstTagInfo();
+ } else {
+ classifier = new PairedEndReadClassifier(tag_id-1,tag_id,ct->getGenomeIndex(),ct->getReadIndex(),ct->getParameters());
+ classifier->classify();
+ info = classifier->getSecondTagInfo();
+ }
+ classi = classifier;
+ }
+ uchar *tag = (uchar *)info->getTag();
+ LocateOnGenome *genome = ct->getGenomeIndex();
+ gkArrays *indexTags = ct->getReadIndex();
+ uint tag_length = indexTags->getTagLength(tag_id);
+ uint threshold = indexTags->getThreshold();
+
+
+ os << endl;
+ os << "****** Tag " << tag_id << " ******" << endl;
+
+ for (uint k = 1000; k >= 10; k/= 10) {
+ if (k < tag_length) {
+ for (uint i=0; i < tag_length; i++) {
+ if (i/k > 0)
+ os << (i/k) % 10 ;
+ else
+ os << " ";
+ }
+ os << endl;
+ }
+ }
+
+ for (uint i=0; i < tag_length; i++) {
+ os << i%10 ;
+ }
+ os << endl;
+ os << tag << endl;
+
+ os << endl;
+ for (uint i= 0; i < info->getSupportLength(); i++) {
+ writeWithSpaces(os,i,
+ info->getSupport()[i],
+ info->getLocalisations()[i]);
+ os << " ";
+ }
+ os << endl;
+ for (uint i= 0; i < info->getSupportLength(); i++) {
+ writeWithSpaces(os,info->getSupport()[i],
+ i, info->getLocalisations()[i]);
+ os << " ";
+ }
+ os << endl;
+ for (uint i= 0; i < info->getSupportLength(); i++) {
+ writeWithSpaces(os,info->getLocalisations()[i],
+ i, info->getSupport()[i]);
+ os << " ";
+ }
+ os << endl;
+
+ os << "Stats: " << info->getNbSingle() << " single located, "
+ << info->getNbDuplicate() << " duplicated and "
+ << info->getNbMultiple() << " multiples" << endl;
+ if (info->getStartPosRepeat() > -1) {
+ os << "Repetition from position " << info->getStartPosRepeat();
+ if (info->getEndPosRepeat() == -1)
+ os << " until the end." << endl;
+ else
+ os << " to position " << info->getEndPosRepeat() << "." << endl;
+ }
+
+ os << endl;
+ if (info->getNbBreaks() > 0) {
+ os << "Breaks: " << endl;
+ for (uint i=0; i < info->getNbBreaks(); i++) {
+ os << i << "\t" << info->getPositionStartBreak(i)
+ << " -> "<< info->getPositionEndBreak(i);
+ os << " (distance: " << info->getTagBreakLength(i);
+ // if (info->getIsExtended(i))
+ // os << " -- break extended";
+ os << ")";
+ os << "\tscore (out/in): "
+ << info->getScoreOutsideBreak(i) << "/"
+ << info->getScoreInsideBreak(i);
+ if (info->getScoreOutsideBreak(i) > 1) {
+ os << ", score intra: "
+ << info->getScoreComputedIntraExon(i)
+ << ", score inter: "
+ << info->getScoreComputedInterExon(i)
+ << endl
+ << "\t\t\t\taverage (high/low): "
+ << info->getAverageHighInside(i)
+ << "/"
+ << info->getAverageLowInside(i)
+ << "\t score: "
+ << info->getScoreInsideAverages(i);
+ if (info->getAverageLowInside(i) < 1 + EPSILON) {
+ os << endl << "\t\t\t\tfalling left: "
+ << info->isSupportFallingLeft(i)
+ << "; right: "
+ << info->isSupportFallingRight(i);
+ }
+ }
+ os << endl;
+ // if (! info->isRepeated(i)) {
+ os << "\tLocs: ";
+ if (info->getPositionStartBreak(i) > 0)
+ os << *info->getChrPosStartBreak(i) << " ("
+ << info->getLocationStartBreak(i) << ")";
+ else
+ os << "??";
+ os << " -> ";
+ if (info->getPositionEndBreak(i) < info->getSupportLength()-1)
+ os << *info->getChrPosEndBreak(i) << " ("
+ << info->getLocationEndBreak(i) << ")";
+ else
+ os << "??";
+ if (info->getGenomeGapLength(i) != GAP_SIZE_MAX)
+ os << "\t gap length: " << info->getGenomeGapLength(i);
+ os << endl;
+
+ if (info->getPositionStartBreak(i) > 0) {
+ if (info->getPositionStartBreak(i) != info->getPositionStartBreak(i))
+ dispLocateFactors(os, info, info->getPositionStartBreak(i)-1,
+ genome,tag, threshold, 1, nb_pos_located);
+ else
+ dispLocateFactors(os, info, info->getPositionStartBreak(i)-1,
+ genome,tag, threshold, -1, nb_pos_located);
+ os << "\t-----" << endl;
+ }
+ if (info->getPositionEndBreak(i) < info->getSupportLength()-1) {
+ if (info->getPositionEndBreak(i) != info->getPositionEndBreak(i))
+ dispLocateFactors(os, info, info->getPositionEndBreak(i)+1,
+ genome, tag, threshold, -1, nb_pos_located);
+ else
+ dispLocateFactors(os, info, info->getPositionEndBreak(i)+1,
+ genome, tag, threshold, 1, nb_pos_located);
+ }
+ os << "----------" << endl;
+ // }
+ }
+ }
+
+ if (info->hasNothing())
+ os << "This tag has *not* been classified" << endl;
+ else {
+ os << "This tag is classified as:" << endl;
+ if (info->isNormal()) {
+ os << " Normal" << endl;
+ dispLocateFactors(os, info, 0, genome, tag,
+ threshold, info->getSupportLength() / nb_step_location,
+ nb_step_location+1);
+ }
+ if (info->isAlmostNormal()) {
+ os << " Almost normal" << endl;
+ dispLocateFactors(os, info, 0, genome, tag,
+ threshold, info->getSupportLength() / nb_step_location,
+ nb_step_location+1);
+ }
+ if (info->isSingle())
+ os << " Single" << endl;
+ if (info->isMultiple())
+ os << " Multiple" << endl;
+ if (info->isNone())
+ os << " None" << endl;
+ if (info->hasRepetition())
+ os << " Repetition" << endl;
+ if (info->isDuplication()) {
+ os << " Duplication" << endl;
+ // dispLocateFactors(os, info, 0, &genome, tag, threshold,
+ // info->getSupportLength() / nb_step_location,
+ // nb_step_location+1);
+ }
+ if (info->hasSNP()) {
+ os << " SNP (" << (uint) info->getNbSNP() << ")" << endl;
+ for (uint j = 0; j < info->getNbSNP(); j++) {
+ if (info->getInfosSNP()[j]->isDuplicated()){
+ os << "\tduplicate" ;
+ }else{
+ os << "\tsingle" ;
+ }
+ os << " position " << info->getInfosSNP()[j]->getPosition()
+ << ", " << info->getInfosSNP()[j]->getExpectedNucleotide()
+ << " -> " << info->getInfosSNP()[j]->getActualNucleotide()
+ << "\t" << info->getInfosSNP()[j]->getChrPosition()
+ << "\t (score="<<info->getInfosSNP()[j]->getScore()<< ")"
+ << endl;
+ }
+ }
+ if (info->hasSplice()) {
+ os << " Splice (" << (uint) info->getNbSplice() << ")" << endl;
+ for (uint j = 0; j < info->getNbSplice(); j++) {
+ os << "\t" << *(info->getInfosSplice()[j]) << endl;
+ }
+ }
+ if (info->getNbSpliceNoCover()) {
+ os << " Coverless splice ("
+ << (uint)info->getNbSpliceNoCover() << ")" << endl;
+ for (uint j = 0; j < info->getNbSpliceNoCover(); j++) {
+ os << "\t" << *(info->getInfosSpliceNoCover()[j])
+ << endl;
+ }
+ }
+ if (info->hasSpliceIntraChr()) {
+ os << " Large splice (intra chromosome) ("
+ << (uint)info->getNbSpliceIntra() << ")" << endl;
+ for (uint j = 0; j < info->getNbSpliceIntra(); j++) {
+ os << "\t" << *(info->getInfosSpliceIntra()[j])
+ << endl;
+ }
+ }
+ if (info-> hasSpliceInterChr()) {
+ os << " Chimera (" << (uint) info->getNbSpliceInter() << ")" << endl;
+ for (uint j = 0; j < info->getNbSpliceInter(); j++) {
+ os << "\t" << *(info->getInfosSpliceInter()[j])
+ << endl;
+ }
+ }
+ if (info->hasBioTagIndel()) {
+ os << " Bio indel in the tag (" << (uint) info->getNbBioTagIndel()
+ << ")" << endl;
+ for (uint j = 0; j < info->getNbBioTagIndel(); j++) {
+ if (info->getInfosBioTagIndel()[j]->isDuplicated()){
+ os << "\tduplicate" ;
+ }else{
+ os << "\tsingle" ;
+ }
+ os << " position " << info->getInfosBioTagIndel()[j]->getPosition()
+ << ": " << info->getInfosBioTagIndel()[j]->getNbIns()
+ << " insertion(s) and "
+ << info->getInfosBioTagIndel()[j]->getNbDel() << " deletions"
+ << endl;
+ }
+ }
+ if (info->hasBioUndetermined()) {
+ os << " Undetermined biological reason ("
+ << (uint)info->getNbBioUndetermined() << ")" << endl;
+ for (uint j = 0; j < info->getNbBioUndetermined(); j++) {
+ os << "\t position " << info->getInfosBioUndetermined()[j]->getPosition()
+ << ": " << info->getInfosBioUndetermined()[j]->getMessage()
+ << endl;
+ }
+ }
+ if (info->hasSeqErr()) {
+ os << " Sequence error (" << (uint) info->getNbSeqErr() << ")"
+ << endl;
+ for (uint j = 0; j < info->getNbSeqErr(); j++) {
+ if (info->getInfosSeqErr()[j]->isDuplicated()){
+ os << "\tduplicate" ;
+ }else{
+ os << "\tsingle" ;
+ }
+ os << " position " << info->getInfosSeqErr()[j]->getPosition();
+ if (info->getInfosSeqErr()[j]->getNbDel() != 0) {
+ if (info->getInfosSeqErr()[j]->getNbDel() == (uint)~0)
+ os << " unknown number of deletions";
+ else
+ os << " " << info->getInfosSeqErr()[j]->getNbDel()
+ << " deletion(s)";
+ }
+ if (info->getInfosSeqErr()[j]->getNbIns() != 0) {
+ if (info->getInfosSeqErr()[j]->getNbIns() == (uint)~0)
+ os << " unknown number of insertions";
+ else
+ os << " " << info->getInfosSeqErr()[j]->getNbIns()
+ << " insertion(s)";
+ }
+ if (info->getInfosSeqErr()[j]->getNbIns() != (uint)~0
+ && info->getInfosSeqErr()[j]->getNbDel() != (uint)~0) {
+ os << "\t";
+ if (info->getInfosSeqErr()[j]->getGenomeSequence())
+ os << info->getInfosSeqErr()[j]->getGenomeSequence();
+ else
+ os << "?" ;
+ os << " -> ";
+ if (info->getInfosSeqErr()[j]->getErrorSequence())
+ os << info->getInfosSeqErr()[j]->getErrorSequence();
+ else
+ os << "?";
+ }
+ os << endl;
+ }
+ }
+ if (info->hasUndeterminedError()) {
+ os << " Undetermined error (" << (uint)info->getNbUndeterminedError() << ")" << endl;
+ for (uint j = 0; j < info->getNbUndeterminedError(); j++) {
+ os << "\t" << info->getInfosUndeterminedError()[j]->getMessage()
+ << endl;
+ }
+ }
+ os << endl;
+ info->samOutput(os);
+ os << endl;
+
+
+ } // end else hasNothing()
+
+ delete classi;
+}
+
+void *launchSubServer(void *args) {
+ void **theArgs = (void **)args;
+ // Retrieving the arguments
+ char *value = (char *)theArgs[ARG_VALUE];
+ ClassifyTags *ct = (ClassifyTags*)theArgs[ARG_CLASSIFY_TAGS];
+ sem_t genome_semaphore = * ((sem_t *)theArgs[ARG_GENOME_SEMAPHORE]);
+ LocateOnGenome *genome = ct->getGenomeIndex();
+ gkArrays *indexTags = ct->getReadIndex();
+ Parameters *params = ct->getParameters();
+ delete [] theArgs;
+ uint threshold = indexTags->getThreshold();
+
+ char *dontCare, *variable, *tag_length, *factor;
+ char *end_ptr;
+ uint tag_id;
+ uint nb_pos_located = NB_POS_LOCATED, nb_step_location = NB_STEP_LOCATION;
+ uint sleep_delay_us = SLEEP_DELAY_MS*1000;
+ char line[LINE_MAX_LENGTH];
+ bool quit = false;
+ uint len_name = strlen(value)+9;
+ char *fifo_inputname = new char[len_name];
+ sprintf(fifo_inputname,"in.%s.fifo",value);
+ char *fifo_outputname = new char[len_name+1];
+ sprintf(fifo_outputname,"out.%s.fifo",value);
+
+ if (mkfifo(fifo_inputname, S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH)) {
+ perror("Creation of fifo input file: ");
+ exit(3);
+ }
+ if (mkfifo(fifo_outputname, S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH)) {
+ perror("Creation of fifo output file: ");
+ exit(3);
+ }
+
+ FILE *fifo_input;
+ fstream fifo_output;
+ fifo_input = fopen(fifo_inputname, "r");
+
+ while (! quit) {
+ while (fgets(line, LINE_MAX_LENGTH, fifo_input) != NULL) {
+ fifo_output.open((const char *)fifo_outputname,
+ fstream::out);
+ fifo_output.precision(4);
+ if (line[0] == 'q' && line[1] == 0) {
+ fifo_output << "Quitting subserver" << endl;
+ quit = true;
+ } else {
+ if (strncmp(line, "set|", 4) == 0) {
+ // Format set|<variable>|<value>
+ dontCare = strtok(line, "|");
+ variable = strtok(NULL, "|");
+ value = strtok(NULL, "|");
+ if (variable == NULL || value == NULL) {
+ fifo_output << "Error: bad format, should be set|<variable>|<value> "
+ << "(eg. set|nb_dispalyed|10)" << endl;
+ } else {
+ if (strncmp("nb_displayed", variable, 12) == 0) {
+ genome->setNbLocations(atol(value));
+ fifo_output << "nb_dispayed set to " << value << endl;
+ } else if (strncmp("nb_pos_located", variable, 14) == 0) {
+ nb_pos_located = atol(value);
+ fifo_output << "nb_pos_located set to " << value << endl;
+ } else if (strncmp("nb_step_location", variable, 16) == 0) {
+ nb_step_location = atol(value);
+ fifo_output << "nb_step_location set to " << value << endl;
+ } else if (strncmp("sleep_delay_ms", variable, 14) == 0) {
+ sleep_delay_us = atol(value)*1000;
+ fifo_output << "Now sleeping " << value << " ms." << endl;
+ } else if (strncmp("deep_snp",variable, 8) == 0) {
+ params->deep_snp_search ^= true;
+ fifo_output << "SNP search ";
+ if (! params->deep_snp_search)
+ fifo_output << "dis";
+ fifo_output << "activated" << endl;
+ } else {
+ fifo_output << "Error: <variable> sould be one of these values: "
+ << endl
+ << " nb_displayed, nb_pos_located, nb_step_location, sleep_delay_ms"
+ << endl
+ << " nb_displayed: number of locations displayed for a given position"
+ << endl
+ << " nb_pos_located: number of different positions located before and "
+ << endl
+ << " after a break" << endl
+ << " nb_step_location: incremental step when locating normal or duplicates"
+ << endl
+ << " sleep_delay_ms: Sleep the given amount of time (in ms) between two iterations"
+ << endl;
+ }
+ }
+ } else if (strncmp("name|",line, 5) == 0) {
+ // Strig in format name|<read name>
+ uint length = strlen(line);
+ uint name_length = length - 5;
+ char *name = new char[name_length+1];
+ strncpy(name, &line[5], name_length);
+ name[name_length]=0;
+
+ // Searching read whose name is name.
+ readIterator *it = indexTags->getReads()->begin();
+ uint tag_id = 0;
+
+ while (!it->isFinished() && it->getName()
+ && strcmp(name, it->getName())) {
+ ++(*it);
+ tag_id++;
+ }
+ if (!it->isFinished() && it->getName()) {
+ genome->setOutputStreams (&fifo_output, &fifo_output, &fifo_output);
+ // Name found
+ detailed_taginfo_output(fifo_output, tag_id, ct,
+ nb_pos_located, nb_step_location);
+ } else {
+ fifo_output << "Error: read name " << name << " was not found"
+ << endl;
+ }
+ delete it;
+ delete [] name;
+ } else if (strncmp("tag|",line, 4) == 0) {
+ // String in format tag|<factor length>|<factor>
+ dontCare = strtok(line, "|");
+ tag_length = strtok(NULL, "|");
+ factor = strtok(NULL, "|");
+ if (tag_length == NULL || factor == NULL) {
+ fifo_output << "Error: bad format, should be tag|<factor_length>|<factor> "
+ << "(eg. tag|13|ACAGTAGCATCAG" << endl;
+ } else {
+ uint nb_result;
+ pair <uint, uint> *occs = indexTags->getTagsWithFactor(factor,
+ (uint) atol(tag_length),
+ nb_result);
+ fifo_output << nb_result << " Tags with " << factor << ": " << endl;
+ for (size_t i=0; i < nb_result; i++) {
+ fifo_output << occs[i].first << ":" << occs[i].second << "\t";
+ if ((i+1) % 5 == 0)
+ fifo_output << endl;
+ }
+ fifo_output << endl;
+ }
+ } else if (strncmp("GkSA|", line, 5) == 0) {
+ dontCare = strtok(line, "|");
+ value = strtok(NULL, "|");
+ if (value == NULL) {
+ fifo_output << "Error: bad format, should be GkSA|<int>" << endl;
+ } else {
+ fifo_output << "GkSA[" << value << "]="
+ << indexTags->getGkSA((uintSA)atoll(value)) << endl;
+ }
+ } else if (strncmp("genome|", line, 7) == 0) {
+ // genome|<chr>|<pos>|<length>
+ dontCare = strtok(line, "|");
+ variable = strtok(NULL, "|");
+ value = strtok(NULL, "|");
+ tag_length = strtok(NULL, "|");
+ if ((variable == NULL) || (value == NULL) || (tag_length == NULL)) {
+ fifo_output << "Error: bad format, should be genome|<chr_name>|[-]<pos>|<length> (set chr_num to 0 for absolute position)" << endl;
+ } else {
+ long long int pos = atoll(value);
+ char *chr_name = variable;
+ int strand;
+ if (value[0] == '-') {
+ strand = -1;
+ pos = -pos;
+ } else
+ strand = 1;
+ uchar *dna = genome->getGenomeSubstring(pos, (ulong)atoll(tag_length), strand, chr_name);
+ fifo_output << dna << endl;
+ free(dna);
+ }
+ } else {
+ sem_wait(&genome_semaphore);
+ genome->setOutputStreams (&fifo_output, &fifo_output, &fifo_output);
+
+ if (strncmp(line, "loc|", 4) == 0) {
+ // String in format loc|<tag_length>|<factor>
+ dontCare = strtok(line, "|");
+ tag_length = strtok(NULL, "|");
+ factor = strtok(NULL, "|");
+ if (tag_length == NULL || factor == NULL) {
+ fifo_output << "Error: bad format, should be loc|<tag_length>|<factor> "
+ << "(eg. loc|13|ACAGTAGCATCAG" << endl;
+ } else {
+ genome->locateTag((uchar *)factor, atol(tag_length));
+ } // end else tag_length == NULL || factor == NULL
+ } else {
+ // String in format <tag id> or <factor>
+ tag_id = strtol(line, &end_ptr, 10);
+ if (tag_id >= indexTags->getNbTags()) {
+ fifo_output << "Error: " << tag_id << " is too large." << endl
+ << "There are only " << indexTags->getNbTags()
+ << " reads indexed." << endl;
+ } else if (*end_ptr != '\0') {
+ if (end_ptr == NULL || end_ptr[0] != ':') {
+ fifo_output << "Error: bad format, you must give the id of tag alone or "
+ << " <tag id>:<tag pos>" << endl;
+ } else {
+ uint tag_pos = strtol(&end_ptr[1], NULL, 10);
+
+ uint nb_tags = indexTags->getNbTagsWithFactor(tag_id, tag_pos);
+ pair<uint, uint> *tags = indexTags->getTagsWithFactor(tag_id, tag_pos);
+ char *tag_factor = indexTags->getTagFactor(tag_id, tag_pos, threshold);
+
+ if (nb_tags >= 2) {
+ fifo_output << nb_tags << " tags contain the factor " << tag_factor << "." << endl;
+ fifo_output << "Tags: ";
+ for (uint i=0; i < nb_tags-1; i++) {
+ fifo_output << tags[i].first << " pos. " << tags[i].second << "; ";
+ if ((i+1)%10 == 0)
+ fifo_output << endl;
+ }
+ fifo_output << tags[nb_tags-1].first << " pos. " << tags[nb_tags-1].second << "; ";
+ } else {
+ fifo_output << "This is the only tag with the factor " << tag_factor << "." ;
+ }
+ fifo_output << endl;
+ delete [] tag_factor;
+ delete [] tags;
+ }
+ } else {
+ // for (tag_id = 32; tag_id < 33; tag_id++) {
+ detailed_taginfo_output(fifo_output, tag_id, ct,
+ nb_pos_located, nb_step_location);
+ // }
+ } // end else end_ptr == line
+ } // else strcmp with loc|
+ sem_post(&genome_semaphore);
+ } // else -> locating on genome
+ }
+ fifo_output.close();
+ }
+ usleep(sleep_delay_us);
+ }
+ fclose(fifo_input);
+ unlink(fifo_inputname);
+ unlink(fifo_outputname);
+ delete [] fifo_inputname;
+ delete [] fifo_outputname;
+
+ return NULL;
+}
+
+void locateServer(ClassifyTags *ct,
+ const char *fifo_name, const char *fifo_output_name) {
+ char line[LINE_MAX_LENGTH];
+ bool quit = false;
+
+ if (mkfifo(fifo_name, S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH)) {
+ perror("Creation of fifo input file: ");
+ exit(3);
+ }
+ if (mkfifo(fifo_output_name, S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH)) {
+ perror("Creation of fifo output file: ");
+ exit(3);
+ }
+
+ cout << "Fifo created, let's go!" << endl;
+
+ FILE *myfifo;
+ myfifo = fopen(fifo_name, "r");
+
+ char *dontCare;
+ char *value=NULL;
+
+ fstream out_fifo;
+
+ uint sleep_delay_us = SLEEP_DELAY_MS*1000;
+ sem_t genome_semaphore;
+ sem_init(&genome_semaphore, 0, 1);
+
+ while (! quit) {
+ while (fgets(line, LINE_MAX_LENGTH, myfifo) != NULL) {
+ out_fifo.open((const char *)fifo_output_name,
+ fstream::out);
+ if (line[0] == 'q' && line[1] == 0 ) {
+ out_fifo << "Quitting!" << endl;
+ quit = true;
+ } else if (strncmp(line, "connect@",8) == 0) {
+ dontCare = strtok(line, "@");
+ value = strtok(NULL, "@");
+
+ pthread_t subServer;
+ void **args = new void*[NB_ARGS_SUBSERVER];
+ args[ARG_VALUE] = value;
+ args[ARG_CLASSIFY_TAGS] = ct;
+ args[ARG_GENOME_SEMAPHORE] = &genome_semaphore;
+
+ pthread_create(&subServer, NULL, launchSubServer,args);
+ } else {
+ out_fifo << "Usage: connect@<id>" << endl;
+ } // end else connect
+ out_fifo.close();
+ } // end while
+ usleep(sleep_delay_us);
+ }
+
+ fclose(myfifo);
+ sem_destroy(&genome_semaphore);
+
+ // When server exits
+ unlink(fifo_name);
+ unlink(fifo_output_name);
+
+}
diff --git a/src/locateServer.h b/src/locateServer.h
new file mode 100644
index 0000000..4ac5c69
--- /dev/null
+++ b/src/locateServer.h
@@ -0,0 +1,142 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Jérôme AUDOUX <jerome.audoux at univ-montp2.fr *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef LOCATE_SERVER_H
+#define LOCATE_SERVER_H
+#include <iostream>
+#include "types.h"
+using namespace std;
+
+/**
+ * @return the number of digits of a in base 10
+ */
+uint nb_digits(uint a);
+
+/**
+ * Write in os the number writeIt with whitespaces preceding it.
+ * The number of whitespaces is chosen such that writeIt, a and b
+ * are written on the same number of columns (including the whitespaces).
+ * @param os: the output stream
+ * @param writeIt: the number to be output
+ * @param a: another number that will be written (or has already been written)
+ * on the same column.
+ * @param b: another number that will be written (or has already been written)
+ * on the same column.
+ */
+ostream &writeWithSpaces(ostream &os, uint writeIt, uint a, uint b);
+
+
+/**
+ * Create a subserver that will be dedicated to a specific client.
+ * @params args: an array that contains NB_ARGS_SUBSERVER parameters.
+ */
+void *launchSubServer(void *args);
+
+/**
+ * Create the main server.
+ * @param ct: ClassifyTags object for classifying reads
+ * @params fifo_name: fifo input name for the main server
+ * @params fifo_output_name: fifo output name for the main server.
+ */
+void locateServer(ClassifyTags *ct,
+ const char *fifo_name, const char *fifo_output_name);
+
+
+#endif
diff --git a/src/types.h b/src/types.h
new file mode 100644
index 0000000..e83028d
--- /dev/null
+++ b/src/types.h
@@ -0,0 +1,153 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef TYPES_H
+#define TYPES_H
+#include <sys/types.h>
+
+typedef enum enum_snp_type {SNP_UNKNOWN,
+ SNP_SUBSTITUTION,
+ SNP_INSERTION,
+ SNP_DELETION}
+ snp_type;
+
+typedef enum enum_error_context {FIRST_SUBSTITUTION, /* First sub in a break
+ * meaning there may
+ * have more
+ * to come */
+ SECOND_SUBSTITUTION,
+ INSERTION,
+ DELETION,
+ UNKNOWN_START_MISSING,
+ UNKNOWN_END_MISSING}
+ error_context;
+
+typedef enum enum_pos_location_break {START_BREAK, END_BREAK}
+pos_location_break;
+#define NB_POS_BREAK 2
+
+typedef enum eenum_strand {FORWARD_STRAND, REVERSE_STRAND}
+strand_t;
+#define NB_ENUM_STRAND 2
+
+/* #ifndef BUILD_CRAC64 */
+/* #define uintSA u_int32_t */
+/* #else */
+/* #define uintSA u_int64_t */
+/* #endif */
+
+#ifndef __USE_MISC
+typedef u_int32_t uint;
+#endif
+
+#define ulong uint
+
+typedef u_int64_t uint64;
+typedef int64_t longint;
+typedef u_int8_t byte;
+
+typedef unsigned char uchar;
+
+#ifndef gap_size_t
+#define gap_size_t longint
+#define GAP_SIZE_MAX (~((gap_size_t)1 << 63))
+
+#endif
+
+#endif
diff --git a/src/utils.cpp b/src/utils.cpp
new file mode 100644
index 0000000..f295448
--- /dev/null
+++ b/src/utils.cpp
@@ -0,0 +1,217 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#include "utils.h"
+
+#include <iostream>
+#include <string>
+#include <stdlib.h>
+#include <sstream>
+#include <gzstream.h>
+#include <cstring>
+
+using namespace std;
+
+
+uintSA DNAtoInt(char *dna, uintSA dna_length){
+ uintSA dna_int = 0;
+ for (uintSA i=0 ; i< dna_length ; i++){
+ dna_int <<= 2;
+ dna_int |= convNuc(dna[i]);
+ }
+ return dna_int;
+}
+
+uint convNuc(char nuc){
+ switch (nuc){
+ case 'a' : case 'A' : return 0 ;
+ case 'c' : case 'C' : return 1 ;
+ case 'g' : case 'G' : return 2 ;
+ case 't' : case 'T' : return 3 ;
+ default : cerr << "invalid nucleotide "<< nuc <<endl; exit(4);
+ }
+ return 0;
+}
+
+char intToNuc(uint c) {
+ switch(c) {
+ case 0: return 'A';
+ case 1: return 'C';
+ case 2: return 'G';
+ case 3: return 'T';
+ default: cerr << "Invalid number (0-3): " << c <<endl; exit(5);
+ }
+}
+
+void intToDNA(uint64 code, uint dna_length, char *dna) {
+ uint64 mask = 3;
+ for (uint i=0; i < dna_length; i++) {
+ dna[dna_length-i-1] = intToNuc(code & mask);
+ code >>=2;
+ }
+}
+
+uint64 factorsToInt(uintSA pos, uchar *dna, uint length) {
+ uintSA posFirstFactor = 4 - (pos % 4);
+ uintSA numFirstFactor = pos / 4;
+ uintSA posLastFactor = (length - posFirstFactor) % 4;
+ uint64 factor = dna[numFirstFactor] & ((1 << (posFirstFactor*2)) - 1);
+
+ for(uintSA i = 1 ; i <= (length-posFirstFactor)/4 ; i++){
+ factor <<= 8;
+ factor |= dna[numFirstFactor+i];
+ }
+ factor <<= posLastFactor*2;
+
+ factor |= dna[numFirstFactor+(length-posFirstFactor)/4+1] >> (8-2*posLastFactor) & ((1 << (posLastFactor*2)) - 1);
+
+ return factor;
+}
+
+int comparUint(const void *a1, const void* a2){
+ if ((* (uint *) a1) < (* (uint *) a2)){
+ return -1;
+ }else{
+ return ((* (uint *) a1) == (* (uint *) a2)) ? 0 : 1;
+ }
+}
+
+uint posBitInMask(uint mask) {
+ uint i = 1;
+ uint pos = 0;
+ if (mask == 0)
+ return sizeof(uint)*8;
+ while ((mask & i) == 0) {
+ i <<= 1;
+ pos++;
+ }
+ return pos;
+}
+
+float getChrono() {
+ struct timeval time;
+ time_t sec;
+ suseconds_t usec;
+
+ if (gettimeofday(&time,NULL) != -1) {
+ sec = time.tv_sec;
+ usec = time.tv_usec;
+ return (float)sec*1000000+usec;
+ }
+ return 0;
+}
+
+string intToString(uint i) {
+ ostringstream oss;
+ oss << i;
+ return oss.str();
+}
+
+ostream *create_stream(bool gzipped, char *name) {
+ if (gzipped) {
+ uint len = strlen(name);
+ char *gzName = new char[len+4];
+ ostream *result;
+ sprintf(gzName, "%s.gz", name);
+ result = new ogzstream((const char *)gzName, ofstream::out);
+ delete [] gzName;
+ return result;
+ }
+ return new ofstream((const char *)name, ofstream::out);
+}
diff --git a/src/utils.h b/src/utils.h
new file mode 100644
index 0000000..b7e3925
--- /dev/null
+++ b/src/utils.h
@@ -0,0 +1,132 @@
+/******************************************************************************
+* *
+* Copyright © 2010-2013 -- IRB/INSERM *
+* (Institut de Recherches en Biothérapie / *
+* Institut National de la Santé et de la Recherche *
+* Médicale) *
+* LIFL/INRIA *
+* (Laboratoire d'Informatique Fondamentale de *
+* Lille / Institut National de Recherche en *
+* Informatique et Automatique) *
+* LIRMM/CNRS *
+* (Laboratoire d'Informatique, de Robotique et de *
+* Microélectronique de Montpellier / *
+* Centre National de la Recherche Scientifique) *
+* LITIS *
+* (Laboratoire d'Informatique, du Traitement de *
+* l'Information et des Systèmes). *
+* *
+* *
+* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* Thérèse COMMES <commesd at univ-montp2.fr> *
+* Éric RIVALS <eric.rivals at lirmm.fr> *
+* *
+* Programmeurs *
+* /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> *
+* Mikaël SALSON <mikael.salson at lifl.fr> *
+* with additional contribution for the packaging of: *
+* Alban MANCHERON <alban.mancheron at lirmm.fr> *
+* *
+* Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* Ce fichier fait partie du programme CRAC. *
+* *
+* Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. *
+* *
+* Ce logiciel est régi par la licence CeCILL soumise au droit français et *
+* respectant les principes de diffusion des logiciels libres. Vous pouvez *
+* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
+* la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur *
+* le site "http://www.cecill.info". *
+* *
+* En contrepartie de l'accessibilité au code source et des droits de copie, *
+* de modification et de redistribution accordés par cette licence, il n'est *
+* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
+* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
+* titulaire des droits patrimoniaux et les concédants successifs. *
+* *
+* À cet égard l'attention de l'utilisateur est attirée sur les risques *
+* associés au chargement, à l'utilisation, à la modification et/ou au *
+* développement et à la reproduction du logiciel par l'utilisateur étant *
+* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
+* manipuler et qui le réserve donc à des développeurs et des professionnels *
+* avertis possédant des connaissances informatiques approfondies. Les *
+* utilisateurs sont donc invités à charger et tester l'adéquation du *
+* logiciel à leurs besoins dans des conditions permettant d'assurer la *
+* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
+* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
+* *
+* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
+* pris connaissance de la licence CeCILL, et que vous en avez accepté les *
+* termes. *
+* *
+* ------------------------------------------------------------------------- *
+* *
+* This File is part of the CRAC program. *
+* *
+* Crac is a tool to analyse RNA-Seq data provided by NGS. *
+* *
+* This software is governed by the CeCILL license under French law and *
+* abiding by the rules of distribution of free software. You can use, *
+* modify and/ or redistribute the software under the terms of the CeCILL *
+* license as circulated by CEA, CNRS and INRIA at the following URL *
+* "http://www.cecill.info". *
+* *
+* As a counterpart to the access to the source code and rights to copy, *
+* modify and redistribute granted by the license, users are provided only *
+* with a limited warranty and the software's author, the holder of the *
+* economic rights, and the successive licensors have only limited *
+* liability. *
+* *
+* In this respect, the user's attention is drawn to the risks associated *
+* with loading, using, modifying and/or developing or reproducing the *
+* software by the user in light of its specific status of free software, *
+* that may mean that it is complicated to manipulate, and that also *
+* therefore means that it is reserved for developers and experienced *
+* professionals having in-depth computer knowledge. Users are therefore *
+* encouraged to load and test the software's suitability as regards their *
+* requirements in conditions enabling the security of their systems and/or *
+* data to be ensured and, more generally, to use and operate it in the same *
+* conditions as regards security. *
+* *
+* The fact that you are presently reading this means that you have had *
+* knowledge of the CeCILL license and that you accept its terms. *
+* *
+******************************************************************************/
+
+#ifndef UTILS_H
+#define UTILS_H
+#include "types.h"
+#include <gkArraysTypes.h>
+#include <sys/time.h>
+#include <string>
+#include <fstream>
+
+#define PRINT_VAR(s) cerr << #s << " = " << s << endl;
+
+uint convNuc(char nuc);
+char intToNuc(uint c);
+
+uintSA DNAtoInt(char *dna, uintSA dna_length);
+
+void intToDNA(uint64 code, uint dna_length, char *dna);
+
+int comparUint(const void *a1, const void* a2);
+
+uint64 factorsToInt(uintSA pos, uchar *dna, uint length);
+
+uint posBitInMask(uint mask);
+
+float getChrono();
+
+std::string intToString(uint i);
+
+/**
+ * Create an output stream, that is gzipped if required.
+ */
+std::ostream *create_stream(bool gzipped, char *name);
+
+#endif
diff --git a/test_f/Makefile.am b/test_f/Makefile.am
new file mode 100644
index 0000000..96bc67e
--- /dev/null
+++ b/test_f/Makefile.am
@@ -0,0 +1,125 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+# SUBDIRS=causes cigar
+
+TESTS = $(script_tests)
+EXTRA_DIST = $(script_tests) should-get.sh $(should_get_files) $(fasta_files) $(fastq_files) valgrind.supp
+
+SH_LOG_COMPILER = $(SHELL)
+
+TESTS_ENVIRONMENT = \
+ cd $(abs_srcdir); \
+ export abs_top_builddir='$(abs_top_builddir)' \
+ abs_top_srcdir='$(abs_top_srcdir)' \
+ abs_builddir='$(abs_builddir)' \
+ abs_srcdir='$(abs_srcdir)';
+
+script_tests = index_genomes.sh launch_sg.sh test_index.sh
+
+should_get_files = $(shell find . -name "*.should_get")
+fasta_files = $(shell find . -name "*.fasta" -o -name "*.fa")
+fastq_files = $(shell find . -name "*.fastq" -o -name "*.fq")
+
+SUBDIRS = causes bug cigar
+
+MOSTLYCLEANFILES = *~
+CLEANFILES = *~ *.tap *.gcda *.gcno *.valgrind
+DISTCLEANFILES = *~
+MAINTAINERCLEANFILES = *~
diff --git a/test_f/Makefile.in b/test_f/Makefile.in
new file mode 100644
index 0000000..e82447e
--- /dev/null
+++ b/test_f/Makefile.in
@@ -0,0 +1,783 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
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new file mode 100644
index 0000000..bda238d
--- /dev/null
+++ b/test_f/bug/Makefile.am
@@ -0,0 +1,106 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+# SUBDIRS=causes cigar
+
+MOSTLYCLEANFILES=*~
+CLEANFILES=*~ *.tap *.ssa *.conf *.sam
+DISTCLEANFILES=*~
+MAINTAINERCLEANFILES=*~
+
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+###############################################################################
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+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
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+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
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+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
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+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
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+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
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+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+ case $$dist_files in \
+ */*) $(MKDIR_P) `echo "$$dist_files" | \
+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+ sort -u` ;; \
+ esac; \
+ for file in $$dist_files; do \
+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+ if test -d $$d/$$file; then \
+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test -d "$(distdir)/$$file"; then \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ fi; \
+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ fi; \
+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+ else \
+ test -f "$(distdir)/$$file" \
+ || cp -p $$d/$$file "$(distdir)/$$file" \
+ || exit 1; \
+ fi; \
+ done
+check-am: all-am
+check: check-am
+all-am: Makefile
+installdirs:
+install: install-am
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+install-am: all-am
+ @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+ `test -z '$(STRIP)' || \
+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+ -test -z "$(MOSTLYCLEANFILES)" || rm -f $(MOSTLYCLEANFILES)
+
+clean-generic:
+ -test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+ -test -z "$(DISTCLEANFILES)" || rm -f $(DISTCLEANFILES)
+
+maintainer-clean-generic:
+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+ -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
+clean: clean-am
+
+clean-am: clean-generic clean-libtool mostlyclean-am
+
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+ -rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
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+
+install-data-am:
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-am
+
+install-html-am:
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+
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+install-ps: install-ps-am
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+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
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+mostlyclean: mostlyclean-am
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+mostlyclean-am: mostlyclean-generic mostlyclean-libtool
+
+pdf: pdf-am
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+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
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diff --git a/test_f/bug/bug-15605-genome.fa b/test_f/bug/bug-15605-genome.fa
new file mode 100644
index 0000000..7b7531d
--- /dev/null
+++ b/test_f/bug/bug-15605-genome.fa
@@ -0,0 +1,5 @@
+>chr-15605_1
+TGGTCCGCGTTCGCTCGCCACTACTAGCGGAGTCTCGTTTGATGTCCTTTCCTCTGGGTACTTAG
+TGGTCCGCGTTCGCTCGCCACTACTAGCGGAGTCTCGTTTGATGTCCTTTCCTCTGGGTACTTAG
+>chr-15605_2
+AAAAAAAAAGCCAGACAAACGTCCGGCTTTTGAATTTTGAAGGTGCCATTGAGGCAAACCT
diff --git a/test_f/bug/bug-15605-read.fa b/test_f/bug/bug-15605-read.fa
new file mode 100644
index 0000000..5693f5b
--- /dev/null
+++ b/test_f/bug/bug-15605-read.fa
@@ -0,0 +1,6 @@
+>bug-15605-1
+AAACGAGACTCCGCTAGTAGTGGCGAAAAAAAAAAAAGCCAGACAACAGAT
+>bug-15605-2
+AAACGAGACTCCGCTAGTAGTGGCGAAAAAAAAAAAAGCCAGACAACAGAT
+>bug-15605-3
+AAACGAGACTCCGCTAGTAGTGGCGAAAAAAAAAAAAGCCAGACAACAGAT
diff --git a/test_f/bug/bug-15605.should_get b/test_f/bug/bug-15605.should_get
new file mode 100644
index 0000000..c5826e6
--- /dev/null
+++ b/test_f/bug/bug-15605.should_get
@@ -0,0 +1,7 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/bug/bug-15605-genome -r bug-15605-read.fa -k 22 -o ${abs_top_builddir:-../..}/test_f/bug/bug-15605.sam --detailed-sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/bug/bug-15605.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/bug
+
+$Bug 15605: this was provoking a segfault
+3:^bug-15605-[1-3]\\s+16\\s+.*p_support=3(,3){29}
+
diff --git a/test_f/bug/bug-15605_2-genome.fa b/test_f/bug/bug-15605_2-genome.fa
new file mode 100644
index 0000000..9a06d6b
--- /dev/null
+++ b/test_f/bug/bug-15605_2-genome.fa
@@ -0,0 +1,11 @@
+>NC_004311_1104564_1107372 [rRNA] Brucella suis 1330 chromosome II, complete sequence.
+gcgactgtttaccaaaaacacagggctctgcgaagtcgcaagacgacgtatagggtctga
+cgcctgcccggtgctggaaggttaagaggagaggtgcaagccttgaattgaagccccagt
+
+>NC_004310_1584926_1587833 [rRNA] Brucella suis 1330 chromosome I, complete sequence.
+tcggaagaagcgtgacctcactatgggcaaccataggggggtggcacagaccagggggta
+gcgactgtttaccaaaaacacagggctctgcgaagtcgcaagacgacgtatagggtctga
+
+>NC_004310_1789988_1792895 [rRNA] Brucella suis 1330 chromosome I, complete sequence.
+tcggaagaagcgtgacctcactatgggcaaccataggggggtggcacagaccagggggta
+gcgactgtttaccaaaaacacagggctctgcgaagtcgcaagacgacgtatagggtctga
diff --git a/test_f/bug/bug-15605_2-read.fa b/test_f/bug/bug-15605_2-read.fa
new file mode 100644
index 0000000..41d25ed
--- /dev/null
+++ b/test_f/bug/bug-15605_2-read.fa
@@ -0,0 +1,6 @@
+>bug-15605_2-1
+CTTCGCAGAGCCCTGTGTTTTTTGGTAAACAGTCGCTACCCCCTGGTCTGT
+>bug-15605_2-2
+CTTCGCAGAGCCCTGTGTTTTTTGGTAAACAGTCGCTACCCCCTGGTCTGT
+>bug-15605_2-3
+CTTCGCAGAGCCCTGTGTTTTTTGGTAAACAGTCGCTACCCCCTGGTCTGT
\ No newline at end of file
diff --git a/test_f/bug/bug-15605_2.should_get b/test_f/bug/bug-15605_2.should_get
new file mode 100644
index 0000000..5c1ae20
--- /dev/null
+++ b/test_f/bug/bug-15605_2.should_get
@@ -0,0 +1,7 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/bug/bug-15605_2-genome -r bug-15605_2-read.fa -k 22 -o ${abs_top_builddir:-../..}/test_f/bug/bug-15605_2.sam --detailed-sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/bug/bug-15605_2.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/bug
+
+$Bug 15605: (reopened) this was provoking a segfault
+3:^bug-15605_2-[1-3]\\s+16\\s+.*p_support=3(,3){29}
+
diff --git a/test_f/bug/bug-15630-genome.fa b/test_f/bug/bug-15630-genome.fa
new file mode 100644
index 0000000..fd5a0f7
--- /dev/null
+++ b/test_f/bug/bug-15630-genome.fa
@@ -0,0 +1,15 @@
+>NC_004310_1584926_1587833 [rRNA] Brucella suis 1330 chromosome I, complete sequence.
+gaataccaaggcgcttgagagaactgcgttgaaggaactcggcaaaatgcacgcgtaact
+tcggaagaagcgtgacctcactatgggcaaccataggggggtggcacagaccagggggta
+gcgactgtttaccaaaaacacagggctctgcgaagtcgcaagacgacgtatagggtctga
+cgcctgcccggtgctggaaggttaagaggagaggtgcaagccttgaattgaagccccagt
+>NC_004310_1789988_1792895 [rRNA] Brucella suis 1330 chromosome I, complete sequence.
+gaataccaaggcgcttgagagaactgcgttgaaggaactcggcaaaatgcacgcgtaact
+tcggaagaagcgtgacctcactatgggcaaccataggggggtggcacagaccagggggta
+gcgactgtttaccaaaaacacagggctctgcgaagtcgcaagacgacgtatagggtctga
+cgcctgcccggtgctggaaggttaagaggagaggtgcaagccttgaattgaagccccagt
+>NC_004311_1104564_1107372 [rRNA] Brucella suis 1330 chromosome II, complete sequence.
+gaataccaaggcgcttgagagaactgcgttgaaggaactcggcaaaatgcacgcgtaact
+tcggaagaagcgtgacctcactatgggcaaccataggggggtggcacagaccagggggta
+gcgactgtttaccaaaaacacagggctctgcgaagtcgcaagacgacgtatagggtctga
+cgcctgcccggtgctggaaggttaagaggagaggtgcaagccttgaattgaagccccagt
diff --git a/test_f/bug/bug-15630-read.fa b/test_f/bug/bug-15630-read.fa
new file mode 100644
index 0000000..16ccc31
--- /dev/null
+++ b/test_f/bug/bug-15630-read.fa
@@ -0,0 +1,2 @@
+>read1
+GGTAAACAGTCGCTACCC
\ No newline at end of file
diff --git a/test_f/bug/bug-15630.should_get b/test_f/bug/bug-15630.should_get
new file mode 100644
index 0000000..57be1de
--- /dev/null
+++ b/test_f/bug/bug-15630.should_get
@@ -0,0 +1,6 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/bug/bug-15630-genome -r bug-15630-read.fa --detailed-sam -k 18 -o ${abs_top_builddir:-../..}/test_f/bug/bug-15630.sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/bug/bug-15630.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/bug
+
+$Bug 15630: the read had only two occurrences where it should have three and we should have 0 cause in the read
+1:^read1.* XC:i:0 .*p_loc=3
diff --git a/test_f/bug/bug-15639-genome.fa b/test_f/bug/bug-15639-genome.fa
new file mode 100644
index 0000000..afe8a2e
--- /dev/null
+++ b/test_f/bug/bug-15639-genome.fa
@@ -0,0 +1,144 @@
+>GRCh37_chr6_sample
+CTAAAACCTACCTTATTATTAACAAGTTTTTAATTTTTTTCTCAAGTTTGCCAAGTTTAAGACCTCTGTT
+GGATGTGTATTACTTGCCCCTTACCAATATGCGGATAGCCAGAACGTTCTGCTTTACCAACAATGGACAA
+GCATTATACCTTGTTTCACCTACAGAAATCCAGAGACTTACTTATAGTCAAGAGACCTGTGAAAATCTTC
+AGGTAATTAATAAAAATATTACTGTAATTTCTTCAGAGGTAAAGTATTCTCTGAGGGCCCGTATACTGTC
+TGCCCCTTATTCTCATGGAACTATACAAGTGAGCCTGCTTGGGAAAATCCAGACTGTTGAATTAGACTTT
+CAGAGCACATGCTTTGAGACTCCCATGATTAAAAGTATCATCTTCAGACATCTGCTATAAGCAGCTTCAT
+CTTACTAATCCATATCGGTCTTTCCAGTGATGGCAGAGAAATATGAACTGGTGCATACATTTTATAACTA
+CTCTCTACATAGAATAAATATCTATTATACACACACACAGTCCTTTTTAAAGAAGTGTGTTAATGTGAAA
+ATAAATGAGTCTATTTTCGGGCAAATTTTGTAATCTCAACTCCTATTCACAAGGATATTTACACAGAAGA
+AAAAAATGTTATTTGGTAGTTTTCCTCTAGTATGTTGGTTGATCTGTTTTTGAGAGACTATATACAAATT
+CTTTATATACAGAAATGTGTCCTTTTTTAAGTATTTGAGTGCTGTATGTGCTTCTGTGTGTATTCGAAGT
+GATCAGTTTAGCTTTACCTTCCAAAGTAAAAGTGCTCTGGAAATATTGAGCTAAAATATTGATTGATATT
+TGATATTTAGAGGAAAGTACTATCTAGAGGAACTTTATAATGAAAGTTTTTGCAATTATTTAGCCCTATT
+TTACACATTTGCAAATTTGAATTTGTGGCTTATTATTTTTAGAACATGAGCTTTAGAGTCAAGAAGGCTG
+AATTCAAGTCCATCTTGCTAACTATACAATTATGTAATCATAAACAAGTTACTCAGTGACTCTAAGCATC
+ATCTTTAAAATTAGCATAGAAGTGGTATCTCAGAGGATATGATATGGATTAAAGGAGACAGTGCATGTAA
+TGTGCTTAGCATAGTGCCCCTGGTACAGAGGGTGCTTAATAAATGTCAGATGTTGTTGTCCTCGTTGTGT
+TATTATTTCAGTAAGCTATACTATACTGGAAACCTAGTCCTGAGTAGTATTGTAAACTTTGAGAGTAAAA
+CAAAATTACATATCTGACATTAGATTTAAATTCCCATTTATGTTTGGGTGAAAGTTATTTTTCAAAGATT
+CCTAAGTTTCTGAAGTAAAATTTTGTTTTCTGTCGGAAGGATAAACCTTAAAATTTTCCTTTTAGCATTT
+CCTTTCACTAGCAAAATGTTATGTTAAGAAATAATATTGACAATTGAATATTAATTCATTTCCATCTGAA
+ATGTGGTCTTAATTCAACTACTTGAAAATCTAAACTTCACACTTTTCTGGGATCAATTTATTCTATCCTT
+TAGTTGGTGTTTTCTTTAATTATTCTTAAGTTAATAGCAGCCATAGTTTACTCATTTATGTTTAAATGAA
+ATAGTCTTTTAGTAGTAAACTATATTTTAAACTATCTGCTATGTGCCTTCATCATACAGAGATAAACAAA
+AAATGGACTATCTTAAAGGAACTTGTGATAAAATGTTTTCTTTGGGCAATATTGACATGTTATTTACCTT
+TGTATTTTTAGTACCCAGAAATAATGCCTTGGTAAAATCTGTTGAAGACTATGATGAACTTGATAAACAC
+TATACCTTGGTTCCCTGAGTACCCTTTTACATTGTGCATTCCTTCAACTTTAGCCCAAAATAAAGAAGAT
+GCCTACAAATATTTATGGAGTTTCCAGTCAAGATGGAATAATAGGAACCAGATTAACCCTCCTTCCTGAA
+ACAACCTAAAACAAAGCAGACAGAACTCATGAAACAATGGTTTTCAAATTACTGGACATCTGGCAATGAA
+GGAAAGTAATTTCTGACAGATAGGAATCAAAGAAGGTGTCCCAGCTTTAATGCCTTAATAGAGTGTTCAG
+GACATGGCACAGGGCGAAGGTACTAAGTTAAAGCCTGGCAGACTTCCCAAGTTGAAGAGGCAGGAACAAG
+AGTTTGGGGACACCAGGTAAATTCGAGAGAAAAGAGCTACAAAGAGAAAGAACCCTGGAGATGTGCAGAG
+TCCCCCTGAGTATACCATACGTGCTATTCAGCACGTACACGTGACTAAGCTTTCAGAGCAGAAAAAGAAC
+CATCTGAAAGGAATAGAGGATTTGTAGAAACCATTCCAGGAACAGTGCTTGATCCCAACAACCAGACTGG
+AGAAACCCATAATTTGTGTGGATATTAGTTTCCTGAGGCCACAAACTTGGTGGCTAAAACCAGTAGAAAA
+TTACTTGCTCATACTTGTAGAAGCCAGAAGTCCACAATCAGTTTTACTGAGGCAAAATCAATGTGCTAGC
+AGGGTCTTGCTCCCTCCAGAGGCTCTAAAAGATAATTACTTATTGCCCCTTTGTTTCTAGGAGCTGCTGG
+TATTCCTTGACATTGGGCCACATCACTGGAATCTCTGCCTTTATGGCTGCATTACCTCCTCTTCTGGGTG
+TCAAATCTACCTCTCTTTCTTAAAAAGACACTTGTAATTGGATTATAACCCATTCAGTAGTCCAGAATAA
+TTTCCCCAGAGCAAGATACTTAATCACATCTGCATAGACTCCTTTTCCTTGCCAGGTAATATTTGTTGGT
+CCAGAGATTAGGACCTGATATCCTTGGATGGTCCGTTATCAGCCACTACTCCAGATATGCCTAACAAATC
+GCAAAAGCAAGAATCAAAAGGATGAAAATGTTTTCTGTCAGAATGAAATTCAAGAAAACTTAAAGGAAAT
+AAAAACTATTTAGCACCCAGTGAGGTAAAAATCGCAATGTCTGGTGTCCAGTCAGTTACCAGGCATGGAA
+AGAGACAGAAAAACATGAGCCATCATGAGGAGAACAATTAGCAGAAACCAAACCAGAACTGACATACATA
+CCAGAATTGGCACACAAAAGGATATTAAAACAATAACAACTGCGTTCCATATGTTCAAAAAGTTAGAAAC
+ATGAAAGATACAAAAATAAAATCAAACTTCTAAAGATGAGAAACTGTAGTGTTTGAGGTGAAAAATATGC
+TAAATGGCATTAACAGCAGATTTGACATTACAGAAGAAAAGATAGTGTACTTGAAAGTATAGCAACAGAA
+AAAAATAACAGTGTTTGAACTTGGCAAACTTATAGCACTAAAACACCTATATTAGGAAAGAAGGAGGTCT
+CAATGCAATGATGTCAACTTTCACTTTAAAGAACTGAGAAAAGGCCAGGCGTGGTGGCTCACGCCTGTAA
+TCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACAAGGTCAGGAGATCGAGACCATCCTGGCTAACAC
+AGTGAAACCCCGTCTCAACTAAAAATACAAAAATTTAGCCGGGCGTGGTGGTGGGTGCCTGTAGTCCCAG
+CTACTTGGGAGGCTCAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGCTTGCAGTGAGCTGAGATCAC
+GCCACTACACTCCAGCCTGGGTGACAAAGCGAGATTCTGTCTCAAAAAACAAAAAAACAAAAACTGAGTA
+AAGCAAATTAAACCCAAAGTAAACACAAGAAAAAAAATAATAAACATCCAAGTGGAAAACAAAGAAACAA
+TAGAAAAACATCAATGAAATCAAAACTAATAAAATTAATCTCAAGCCATATGAAGAAAGAAGTTATAAAC
+TATTAATATCAGTAATAAGAGAAGTCTCATTACTATATATTCTATAGATATGAAATGGATAAAAAGTGAA
+TATTATGAACAAGTTTATGCCAAAAATATTCAAAACCTTAGATGAAATGGACAAATTTCTTTAAAGACAA
+ATTACCAAGCCTCACTGAAAAAAAAATAGATAACCGAAATAGTCCTGTGTCTATTAAAGAAATTGAAATA
+GAGGTTAGGAACCTTGGACCAAGAAACTTCCAGGCCTAGATGGCTTCAGTGATGAGCTCTATCAACATTT
+CAGGAAGAAATAACACCGGTTCACAAACTTTTCCAAAAACTGAATTAGGATTGCTTCCCAGCTTATTCTA
+TGAAGGAAGCATTAACCTGATAACAAAATTAGACCAAGTTATTATAAGAAAAGAAAACTACCTATAAACC
+AATATCTCTCATAAATATAAAAGCAAAATTTGTTAAAAAAAAAAAATTTTTGCAAATTGAATTCAGCAAT
+ATATCAAAGGGATAATACATTATGACCAAGTGAGACCTAATCCCAGGAAAGTAGGATTGACCTAACGTTT
+GAAAATCAGTCAATGTGATCCATCTTATTAAAAAGCTTAAAAAAGAGCAGTTGACAAAATCTAACAAATA
+TTCCTGATTTTTAAAAATCTCTACAAACAAGGAACAGAAGAAAACTTAAAGGACATGTAAGAAAAACCCA
+CATCTCAAATAATATTTAGTGATGAAATACTTAATTCTTTCTCCCTGAAATCAGCAATTACAGAAGAATG
+TTCACTCTCACCACTTACATTCAGTGTTGTAGTTAAGGTTCTAACCAGTGCACTCAGGCAAGGAAAAGAA
+AAGGAAAGCGGCTGTCTTTATTCACAATGACATGATCATCAGTATAGGAAATCTAATAAAATCTACCATA
+AAGGATACTAGAATTAATCAGTGTGTTTGGCAAAGATGTAGATTATGAGATAAATATACAAAAATAATTT
+TATTTCTATATATTAGCAATGAACATTTGGAAATTGATATTTTAAAAACCATACCATCTATAATAGCAAC
+AAAAATATGAAATACTTTGGGATAAATCTAACAGAAAATGAAAGATCTCTACACTGAAAAACTATAAAAT
+ATTAATAAAAAATTTTTTAAAGTCTTAAAAATTTTTTAGAAAATTTTGTAGGAATTGACAAATTTATCCT
+AAAATTCATACGTAAATACAAGAGAACTAAAATACACAAAACAGCTCTGAAAAAAATGGAAGGGCTAACA
+CTACCTTATTTCAAGATTATTATAAAGCTGCAGTAATCAGTAGAGAATGGTATTTTTGGCATTGAGATGA
+ATGGATCAGAATAGAATATCCAGAAATAAACACATACATGGACAACTGATTTTTTTAAGGAAGGCGCAAG
+GCAATGCAATGGAGAAAGGATTGCCTTTTCAACAAGTAGTGCTGGAACTATTGGATATTAAAATGCAAAA
+AAAATCAGCTTTGATCCACGCTTCACACCATATACCAAAATTTATTCAAAATGTATTATGGACCTACATG
+GAAACCCCAAAACTACAAAATTTCTAGAAAGAAACTTAAGAAAACATCTGTTACCTTATTTTGGGAAAAG
+ATTTATTAGCCATGACACCAAAAGCAACATCCATAAAAGAACAAATTGATAACTTCAACAAAACTTAAAA
+TTTCTACTCTTCAGAAGACACTTTTTAAAATGAAAAGACAATTTATAGATGGGAAGAAAATCTGGGCAAA
+ACATATATCTAATAAAGGACTTGTCTCTAGAATATATGAATGACCCTTAAAACTCACCAGAAGGAAGAGA
+AACAACCCAATAAAAACATAGACAAAATATTCAAAAGGAAAGCTCACCATGAAAAGATTCTCAACATTAT
+TTATCATTAGAGAACTGCAAATTAAAACCACAGTGAGATACCATTAAACCCCTTTGAGAGTGGTTGAAAT
+TAAAAAGAATACCATGCCAAGTTTTGGCAAGGATATAGACGAACTACAACTCCATACAATGCTGATGGGA
+ATGTAAAAAACTATAACCACTTTGGAAAACAATTCTGGAGTTTTCTAAAAAGTTAACATTCATGAACCAA
+AGACCCAGCCACTTTACTCATTTTTTTTAAATTAAAAGAAAAGGAAATTTGTATTCATAGCCGCTTTATT
+TGTAATAGCCAAAAACTGGAAACCACCCAGATGTCCTCAACAGATGAGTGGAAAAACAAATTGCAGTTTA
+TCATACAGTAGAATTCTAGTCAGCAATACAAAGGAGTAAACGATGCAATCAGCAACATCAGTGAATCTCA
+GAATAATTATGCTTAATGAAAGGAGCCAAGAAAAAGAGTACATGTTGTTCTATTTATATAAAAACTCAAG
+AAAATACAAATTATAGTGAAAGAGCAGATCAGCAATAACTTGGATATGGGGTTGTTAAAGAAGGAATGAG
+AGAAGGTCGTACAAAGGAGCAGAAGGACACTTGAGAGTGATGGATATATTCACAGTGTTGATTGTGGTGA
+TGGTTTCATGCATATATGCATATGGCGAAATTCACCAAATTGTACACCTCAAATATATGCCAGTTTTTGT
+ATGTCGATTATACTTCAGTAAAGCTGTGTAAAAGATTAATGGATTCAGGACTTTTAATTGTCATTGACAG
+GCAATTAGTCAATGGTATGTTTATAGATTGAAATACTTAAGTTTCTTTTTACAGTATTATTCTTAACTGT
+ACCATAGTGAAAAACACAGAGATAATTTATAATAAACTGTTTTTTTCAAATGGACTATAATATATTCATT
+TGTGAACCCTAACCAAAATTTGCTATAATCGTAGAGGTGGAACATACCAATTAATTCAGTTTAAAACAAC
+TAAGTAAGTAACTCTGGTAAGCACCTCAGGATTATAATTTATAAACAAAACCCCAAGTAATCACTGTAAA
+CAACTGATGACAGTTGAACTGTTTAGCTTCTTATATATATTGTGTATTCAGTATGAAGTTTATTGCTGTG
+TGTTTATCCTGGAGATATTTATTTTTTCAGACTCAATACTCTTACAATATAAAGTTTTCTTAAAATGATT
+AAAATCAGTGATTATTTGATGCACTGTAAAGGACTTTGTAGTGGCATCTAATGTATGGATAACCAAAGCC
+CATACATTGACCCATTCATGAAATTAGTCCTAAATTTTACCATTCTAACCTTGTTAGCTTACATGCAAGA
+CAAATGATATGCAAGAGTCTAAAATCAGACAAGTATATTTATTTCTGAATATTTATATTTTAGAAGAGTA
+ATTAAGTCCAATGTCTTGTTTCAGAAATACCATCTACTATGAATAGATGTAGCAAGATCACAGAAATAAC
+AAATCTGTTTTAGATTTCACCAACATACACTAGCATTAACATGAATCATTCTAAATAGTAGATTTACTTA
+TAATAAAAAGCCTTATTTAAATAGAAGTGAAAAAATACCTATATATTTTATGTATTTTCCCAAAACCTTT
+ATATTAAGACTGCAGATAATCTAGACTTTAAGAAACATTGAGTTTTCAACTCCCTTTAAAGATGTCTGTT
+CATAATGTTAACCTGTAGATAAATGACTTGTGTATTTTCTAATTGGTTTCATCTCTATGTGATAGATTTT
+TCTACTTCTGTACATACACTATTGATGTCTACTCCTGGCACTTTATATGCTCATTATCTTTAATCCTAGT
+AATGTTCCTGAGAGGCAGTTATCATTATCTCCCCCTTTTAAAGTTGAAGAAGCCATTTCTTTGACAGACT
+AATTTGACTAAGAGTCTCCTGCTAGTAAAAGGCAGAAATTGAGAATCAAATCCAGGTCCATCTGGTTCCA
+AAGTTTATACTCATTCTACTACAGAGAATATAATGAGTTTAATCTGGTGTTTTTATATTTCTTACTTTAC
+CCTTGTAAAATTGTAAGCTCATTAAACACCAAATAAGAAATGCAAACTGTAATTCTAAAAATGAGGTAAA
+ATTTTTTAAAAAGCATACCTTTAAACTATCGCTGTTGGTATGTCATATTCTTCTTTTGATTTAGCATGAG
+ACACCCAAATGATAGCTGTGTTGCTGTTATTGATCTTTTTTACGTTGTAACAATTTAATACATATAGTTT
+AAATTAGGATCTGTGAAATACTGTTTTTAAAAGATTTAAAATATGCCTAAAATTGCCTTTGTTATAGAGT
+TTAATATAAATTCAATATAATAATAGACATCAGTATATTCTATAGTGGGTTTTAACAAGTTTGATTTATT
+GAATTCAGAAAGTGTTTTATTCCAGGTTTACTACACTTTATAGAAATCCAGAGGAAGGAAAATAAAAACG
+TAAGAGCTTCAGTCCACTTCAGTCTTATAAATAAAACTGTTGTGTAATGTTAATAATTATTTCCTCCCAT
+ATGCAATCTGGGTGGAGGGATAATGTTAATATGGATATGTCTAAAAGAAAACCTGAACAGCCTTTACCAG
+CCTTCTTAGCCCAGCCCCAAGGAAGAAACCCTGAAAAATACATACTTTTATTCCAACTATAATGATGTAG
+TAATACCAGAGTATAGCAGAACTCCTATATAAATGTTACTACCGTCCTTTTCCTTTTTTTTTTTTTTTTT
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGATTCTTTTGCCCAGGCTGGAGTGCAGTGG
+TGCAATCTCTGCCCACTGCAACTTCCGCCTCCCGGGTTCAAGCTATTCTCCTGCCTCAGCCTCCTAAGTA
+GCTGGGATTACAGGCGCAGGCCACCACGCCCTGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACC
+ATGTTGGTCAGGCTGGTCTCGAACACCTGACCTCATGATCCTCCCACCTCGGCCTCCCAAAGTGCTGGGA
+TTACAGGTGTGAGCCACCGTGCCCAGTCACTACCATCCTTGTCTTAGAAAAACTCTTCTTTCCTCTTTTT
+GTATTGTCAACAAAACCAGTAACATGTCAGCAGTCTTTTCTCCTTTTATCATTTCTGCACTCTAAAAAAT
+ATTGACAGTAATTTCAGAAAAATCTGATGATGTACAAGGGAAGAGTTCCCATCTCTCTGCCAGATTTCTG
+AAATTCCAGGTGTATGTTGGCATAATTCTCTTCCTAGCATGTGTTTATGAGAAAAGAAGTTGGTGTCTAA
+ATTATAAATTTTCTGACTCAGCTAAAAGTTATAATTCCAAAACTACATATCATCATTATTACACTGGACT
+TTTATACTTGCTGTTAAAAAGTTTTCTTCTTTCTGGCTGGGCATGGTGGCTCATGCCTGTACAGCACTTT
+GGGAGGCTGAGGTGGGTGGATCACTTGAGGCCAGGAGTTCAAGATCAGCCTGGCCAACATGGCGCAAAAC
+CTGTCTCTACAAAATACAATAATTACCCAGGCATGGTGGCGTGTGCCTGTAATCCCAGCTAGTCAGTGGC
+TGAGACACAAGAATCACTTGAACCCCAGAGGCAGAAGCTGCAAGTGAGCCAAGATCGCATCACTGCACTC
+CAACCTGGGTGACAGAGTGAGACTGTCTCAAAAAAAAAAAAAAAAAAAAAAAAACTTCTTTCTAATGTAA
+TTATTAATCCTATTATCAATTGATATGAGTTATATGAAAATTTTGTCTGAAAGATTAGAATCTCCTGACA
+CTCTTAAGCAAAAATACTGTTTGCCTAAAATGCAAACAAAGGGGCAAGCAGCAAATAAGTCATATTTTAG
+TTTTAGAAACACTGTTTGAATAAATCAGCACGTTCTGTATCTGATCGTAGGACATGTACTCATTAATTGT
+GAATCTCAACAGGTAATGTTCTGAGCTTAAGTTAAGGAGTTTACAGTGATACTTTTGTTCATTATAGTTT
+AGTTTCCCTGAAATTTCAACAGTGACAATTTGTTTTGATTTTAAAGGAAATGTTGGGTGAACTCTTCACT
+CCTGTAGAAACACCTGAAGCACCAAACAGGGGATTCTTTAAAGGCTTATTTGGAGGTGGTGCACAATCTC
+TTGACAGAGAAGAACTATGTAAGTTGATTTATTTAATTCGGATAATATATCTATAAAACAGGAACAAGCC
+ATACAAAAATTTTTTTATACGTGTAAATTATGTTCACTTTTTTTCTCTTTGTCACAATTACTATTTCCAT
diff --git a/test_f/bug/bug-15639-read.fa b/test_f/bug/bug-15639-read.fa
new file mode 100644
index 0000000..03f6cbb
--- /dev/null
+++ b/test_f/bug/bug-15639-read.fa
@@ -0,0 +1,2 @@
+>read1
+CTTACTTATAGTCAAGAGACCTGTGAAAATCTTCAGGAAATGTTGGGTGAACTCTTCACTCCTGTAGAAACACCTGAAGCACCAAACAGGGGATTCTTT
diff --git a/test_f/bug/bug-15639.should_get b/test_f/bug/bug-15639.should_get
new file mode 100644
index 0000000..f4fbe96
--- /dev/null
+++ b/test_f/bug/bug-15639.should_get
@@ -0,0 +1,7 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/bug/bug-15639-genome -r bug-15639-read.fa -k 22 -o ${abs_top_builddir:-../..}/test_f/bug/bug-15639.sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/bug/bug-15639.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/bug
+
+$Bug 15639, the read produce a segfault because a condition in saveCandidat process in SupportBreak about single consistency
+#We should have 1 cause in the read, it is enough to check the bug
+1:^read1.*XC:i:1\\s
diff --git a/test_f/bug/bug-15646-genome.fa b/test_f/bug/bug-15646-genome.fa
new file mode 100644
index 0000000..eb76da6
--- /dev/null
+++ b/test_f/bug/bug-15646-genome.fa
@@ -0,0 +1,88 @@
+>11-69871465..69871486
+TGGTGGTGGTGATTGTGATGAT
+>11-69871606..69871633
+CGATGATGGTGGTGGTGATTGTGATGAT
+>11-69871744..69871765
+TGGTGGTGGTGATTGTGATGAT
+>11-132409628..132409649
+GATGGTGATGGTGATGATAATG
+>21-47511282..47511303
+GATGGTGATGGTGATGATAATG
+>7-706773..706798
+GTGGTGGTGATGGTGATGATAATGAT
+>7-131366277..131366298
+GGTGGTGATGGTGATGATAATG
+>7-141036569..141036591
+ATCATCACCATCACCACCACAAC
+>Y-18977865..18977886
+TGATGGTGATGATAATGATAAT
+>17-54870351..54870372
+TGGTGGTGGTGATTGTGATGAT
+>17-79499440..79499461
+GATGGTGATGGTGATGATAATG
+>17-79499626..79499647
+GATGGTGATGGTGATGATAATG
+>2-129097921..129097945
+ATGTTGTGGTGGTGATGGTGATGAT
+>2-129356245..129356269
+ACCATCACTATCATCACAATCACCA
+>2-129356374..129356398
+ACCATCACTATCATCACAATCACCA
+>2-174563042..174563067
+CAACATTATCATCACCATCACCACCA
+>22-27984915..27984938
+ATCATTATCATCACCATCACCATC
+>22-36010792..36010817
+TCATTATCATTATCATCACCATCACC
+>22-37076013..37076038
+ATCATTATCATCACCATCACCACCAC
+>1-57846225..57846248
+TGATGGTGATGATAATGATAATGA
+>13-20971077..20971099
+TGGTGGTGATGGTGATGATAATG
+>16-64498096..64498119
+TGATGGTGATGATAATGATAATGA
+>16-86453266..86453290
+TGGTGATTGTGATGATAGTGATGGT
+>16-86625062..86625083
+TGATGGTGATGATAATGATAAT
+>16-86894791..86894930
+TGGTGGTGATGGTGATGATAATGGTGGTGGCAATGGTGATGATGGTGATGATGACAATGGTGGTAATGACGATGGTGGTGGTGATGATGGTGATGATGGTGGTGGTGATGATGGTGACGGTGGTGATGGTGATGATAATG
+>16-86895235..86895257
+TGGTGGTGATGGTGATGATAATG
+>16-86895469..86895491
+TGGTGGTGATGGTGATGATAATG
+>16-87243993..87244015
+TGGTGGTGATGGTGATGATAATG
+>16-87631227..87631249
+CATCACTATCATCACAATCACCA
+>6-161089854..161089875
+GATGGTGATGGTGATGATAATG
+>3-70375990..70376011
+TGATGGTGATGATAATGATAAT
+>3-173174962..173174983
+TCATTATCATTATCATCACCAT
+>9-29924934..29924956
+GTGATGGTGATGATAATGATAAT
+>12-20727513..20727541
+TCATTATCATTATCATCACCATCACCATC
+>12-124578132..124578157
+GTGGTGGTGATGGTGATGATAATGAT
+>14-94986051..94986211
+GTGGTGGTGATGGTGATGATAATAGTTGTGATGGTGGTGGTGATGGTAGTGATGGAGGTGGTGGTGGTGATGGTGATGATAATAGTTGTGGTGATGGAGGTGGTGATGGAGGTGGTGGTGATGGTGGTGATGGAGATGGTGGTGGTGATGGTGATGATAAT
+>20-57924701..57924722
+TGATGGTGATGATAATGATAAT
+>20-59459430..59459451
+TGGTGATGGTGATGATAATGAT
+>8-22566356..22566377
+CATTATCATCACCATCACCATC
+>8-139650074..139650097
+ATCATTATCATCACCATCACCATC
+>4-7365152..7365174
+CATTATCATCACCATCACCACCA
+>5-2439807..2439830
+TCATTATCATTATCATCACCATCA
+>5-2440069..2440092
+ATCATTATCATCACCATCACCATC
+>5-174461888..174461911
+GATGGTGATGGTGATGATAATGAT
diff --git a/test_f/bug/bug-15646-read.fa b/test_f/bug/bug-15646-read.fa
new file mode 100644
index 0000000..bd2429a
--- /dev/null
+++ b/test_f/bug/bug-15646-read.fa
@@ -0,0 +1,10 @@
+>seq1
+ACCATCACTATCATCACAATCACCACCACCATCATCGGCACCGTCATTATCATTATCATCACCATCACCACCACAACATTATCATCACCATCACCATC
+>seq2
+ACCATCACTATCATCACAATCACCACCACCATCATCGGCACCGTCATTATCATTATCATCACCATCACCACCACAACATTATCATCACCATCACCATC
+>seq3
+ACCATCACTATCATCACAATCACCACCACCATCATCGGCACCGTCATTATCATTATCATCACCATCACCACCACAACATTATCATCACCATCACCATC
+
+>segfault
+CATTATCATCACCATCACCACC
+
diff --git a/test_f/bug/bug-15646.should_get b/test_f/bug/bug-15646.should_get
new file mode 100644
index 0000000..0cf8e7c
--- /dev/null
+++ b/test_f/bug/bug-15646.should_get
@@ -0,0 +1,11 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/bug/bug-15646-genome -r bug-15646-read.fa --detailed-sam -k 22 -o ${abs_top_builddir:-../..}/test_f/bug/bug-15646.sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/bug/bug-15646.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/bug
+
+#Bug 15646: first, on the small extract of the genome, we have a segmentation fault
+$Bug 15646: First, segmentation fault when querying the index
+1:^segfault
+
+#Bug 15646: Second, the one really reported
+$Bug 15646: Second, does CIGAR string have a strange integer value in it?
+3:^seq.*\\s+20M48I30M\\s+.*
\ No newline at end of file
diff --git a/test_f/bug/bug-15649-2.should_get b/test_f/bug/bug-15649-2.should_get
new file mode 100644
index 0000000..1a09bc1
--- /dev/null
+++ b/test_f/bug/bug-15649-2.should_get
@@ -0,0 +1,6 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/bug/bug-15649-genome-2 -r bug-15649-read.fa --detailed-sam -k 22 -o ${abs_top_builddir:-../..}/test_f/bug/bug-15649-2.sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/bug/bug-15649-2.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/bug
+
+$ Bug 15649-2: affectation was not made to chr4 (genome with only one chromosome)
+1:^chr4.*\\s+4\\s+1\\s+[0-9]+\\s+23M\\s+.*XO:Z:4|1,0\\s+
diff --git a/test_f/bug/bug-15649-genome-2.fa b/test_f/bug/bug-15649-genome-2.fa
new file mode 100644
index 0000000..9638914
--- /dev/null
+++ b/test_f/bug/bug-15649-genome-2.fa
@@ -0,0 +1,2 @@
+>4
+CATTATCATCACCATCACCACCA
diff --git a/test_f/bug/bug-15649-genome.fa b/test_f/bug/bug-15649-genome.fa
new file mode 100644
index 0000000..89b8e13
--- /dev/null
+++ b/test_f/bug/bug-15649-genome.fa
@@ -0,0 +1,4 @@
+>truc
+AAAAAAAAAAAAAAAAAAAAAAA
+>4
+CATTATCATCACCATCACCACCA
diff --git a/test_f/bug/bug-15649-read.fa b/test_f/bug/bug-15649-read.fa
new file mode 100644
index 0000000..d30775d
--- /dev/null
+++ b/test_f/bug/bug-15649-read.fa
@@ -0,0 +1,2 @@
+>chr4
+CATTATCATCACCATCACCACCA
diff --git a/test_f/bug/bug-15649.should_get b/test_f/bug/bug-15649.should_get
new file mode 100644
index 0000000..ffb1c8a
--- /dev/null
+++ b/test_f/bug/bug-15649.should_get
@@ -0,0 +1,7 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/bug/bug-15649-genome -r bug-15649-read.fa --detailed-sam -k 22 -o ${abs_top_builddir:-../..}/test_f/bug/bug-15649.sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/bug/bug-15649.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/bug
+
+$ Bug 15649: affectation was not made to chr4
+1:^chr4.*\\s+4\\s+1\\s+[0-9]+\\s+23M\\s+.*XO:Z:4|1,0\\s+
+
diff --git a/test_f/bug/bug-15672-genome.fa b/test_f/bug/bug-15672-genome.fa
new file mode 100644
index 0000000..2701387
--- /dev/null
+++ b/test_f/bug/bug-15672-genome.fa
@@ -0,0 +1,34 @@
+>21-9829264..9829295
+AAAAAAAAAACGCATACCTCACACCACACACACACACACACAAAAAAAAAAA
+>X-67873277..67873311
+AAAAAAAAAACACATACACCTCACACCACACACACACACCCCACAAAAAAAAAAA
+>7-8484280..8484311
+AAAAAAAAAATTAACTGAGGTGTGTGTGTGTGGTGTGCATTTAAAAAAAAAA
+>9-86821159..86821190
+AAAAAAAAAAGTGTGTGAGGTGTGTGTGTGTGGTGTGTGTGTAAAAAAAAAA
+>2-130397854..130397885
+AAAAAAAAAATGTGTGTGTGTGTGTGTGGTGTGAGGTTGTGTAAAAAAAAAA
+>2-133040482..133040514
+AAAAAAAAAATATGTGTGTGTGTGGTGTGAGGTATGTGCTCCTAAAAAAAAAA
+>2-162137919..162137951
+AAAAAAAAAAAGGAGCACATACCTCACACCACACACACAAACAAAAAAAAAAA
+>2-240564471..240564502
+AAAAAAAAAAGTGGTGTGTGAGGTGTGTGTGGTGTGATTGTGAAAAAAAAAA
+>17-72728907..72729633
+AAAAAAAAAAGAGGGGTGAGGTGTGTGTGGTGTGAGGTGTGTGTGGCGTGATTTGAGGTGTGTGTGTGTGGTTTCAGGTGTACACAAGAGCCCCCCCATCTTTCAACACGCATGAGGGTCTGTCTCACTGACACTTGGTACCTCCACTATCAGCAGGGCTGCATGACAATGACAGTGTGATCTGTGATCAGGAGGGTAGGGGTGTCTATTTGGGGGTATTGTGGGGGTGTGCGTCTCAGATCTGGAGGCAATAAGAGGTGTTGGGGGTCATTTATAGGGTGATATACACATTTGGTGATGGTGTGAGGCATGGGGTCCATTGGAGAGGCAGGTGTTTGCACAGTGATGTGGCACAGGTGTTGATGGTGTGAAATAAACTGTGCCTGGAGCTGCACTGTGGTGACAGGAGTGTGTGTTTGGAGTGAAATGAGGTATGTGTGTTTGAGGGTCATGTAAGATGTGTATGTATGTGGTATGATGGTAGGTGTGTTT [...]
+>12-130302476..130302509
+AAAAAAAAAATTGGAGTGTGTGTGTGTGGTGTGAGGTGTATGTGAAAAAAAAAA
+>14-69365757..69365890
+AAAAAAAAAAGCCACACCTCACACCACACACACCTCACACACCACACACACACCTCACACCCACAGCACACCATACCCCTCCACACCACAACCACACCACACCCACACCTCACCCTACACCTCACACCACACACACACCTCACAAAAAAAAAAA
+>22-29071194..29071232
+AAAAAAAAAAGACCACATACCACACACACCTCACACCACACACAAAAATAAAAAAAAAA
+>18-11247886..11248015
+AAAAAAAAAAACACTCACACACACCTCACACCACACACACATCACACACACCACACACTACACACATACTATCTCACATGCACTCTTCATACCATACCAACACCACACCCCACACACACCTCACACCACACACACCACACAAAAAAAAAA
+>19-44963131..44963167
+AAAAAAAAAATGTGTGTGTGTGTGTGTGGTGTGAGGTATGTGCTCCTAAAAAAAAAA
+>13-23508449..23508480
+AAAAAAAAAAGCACACACACCACACACACACACCTCATCACGAAAAAAAAAA
+>10-72856063..72856094
+AAAAAAAAAATGTGTGTGTGTGTGTGTGGTGTGAGGTAAGGGAAAAAAAAAA
+>10-135152531..135152564
+AAAAAAAAAAACACGCCACACACACCTCACACCACACACCTGACAAAAAAAAAA
diff --git a/test_f/bug/bug-15672-read.fa b/test_f/bug/bug-15672-read.fa
new file mode 100644
index 0000000..e8e542f
--- /dev/null
+++ b/test_f/bug/bug-15672-read.fa
@@ -0,0 +1,6 @@
+>r1
+GGTGTGTGTGTGGTGTGAGGTGTGTGTGGTATGATTTGAGGTGTGTGTGTGTGGTGTGAGGTGTGTGTGGTGTGAGGTATGTGATGTGATTTGAGGTGTG
+>r2
+GGTGTGTGTGTGGTGTGAGGTGTGTGTGGTATGATTTGAGGTGTGTGTGTGTGGTGTGAGGTGTGTGTGGTGTGAGGTATGTGATGTGATTTGAGGTGTG
+>r3
+GGTGTGTGTGTGGTGTGAGGTGTGTGTGGTATGATTTGAGGTGTGTGTGTGTGGTGTGAGGTGTGTGTGGTGTGAGGTATGTGATGTGATTTGAGGTGTG
diff --git a/test_f/bug/bug-15672.should_get b/test_f/bug/bug-15672.should_get
new file mode 100644
index 0000000..874b7d3
--- /dev/null
+++ b/test_f/bug/bug-15672.should_get
@@ -0,0 +1,7 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/bug/bug-15672-genome -r bug-15672-read.fa -k 22 -o ${abs_top_builddir:-../..}/test_f/bug/bug-15672.sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/bug/bug-15672.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/bug
+
+$Bug 15672: there is a negative value for the M letter (which appears as a large positive number)
+3:^r[1-3].*\\s+29M2X([0-9]{1,3}[MNSI]){1,4}\\s+
+
diff --git a/test_f/bug/bug-15677-genome.fa b/test_f/bug/bug-15677-genome.fa
new file mode 100644
index 0000000..f7cf52c
--- /dev/null
+++ b/test_f/bug/bug-15677-genome.fa
@@ -0,0 +1,6 @@
+>chr10_sample
+ccgtaggtggtttggccaaagatggagcataccttgtaagttctagaagc
+aaatgcttatgtctacactattagaagaagaaagggcctacagattatct
+CTGATTGGAGAGCTATGTGTAGtgttttggagcaatgaccatagtgatgg
+attccctgggttggagtctcatcagcaatatgaatttcaacaacccctga
+atctcaggttatttctttataa
diff --git a/test_f/bug/bug-15677-read.fa b/test_f/bug/bug-15677-read.fa
new file mode 100644
index 0000000..0d012c2
--- /dev/null
+++ b/test_f/bug/bug-15677-read.fa
@@ -0,0 +1,2 @@
+>read1
+CTCTGATTGGAGAGCTATGTGTAGCTCTGATTGGAGAGCTATGTGTAGTGTTTTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGT
diff --git a/test_f/bug/bug-15677.should_get b/test_f/bug/bug-15677.should_get
new file mode 100644
index 0000000..4993c99
--- /dev/null
+++ b/test_f/bug/bug-15677.should_get
@@ -0,0 +1,6 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/bug/bug-15677-genome -r bug-15677-read.fa -k 22 -o ${abs_top_builddir:-../..}/test_f/bug/bug-15677.sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/bug/bug-15677.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/bug
+
+$Bug 15677: the read produces a chimera instead of a no start break bioUndetermined
+1:^read1.*24S31M46S
diff --git a/test_f/bug/bug-15847-genome.fa b/test_f/bug/bug-15847-genome.fa
new file mode 100644
index 0000000..f09a20b
--- /dev/null
+++ b/test_f/bug/bug-15847-genome.fa
@@ -0,0 +1,49 @@
+>homemade-sample
+CTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTC
+AAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGC
+AATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCC
+ACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGC
+AATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTC
+AAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGC
+AATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCC
+ACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGC
+AATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTC
+AAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGC
+AATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCC
+ACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGC
+AATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTC
+AAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGC
+AATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCC
+ACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACC
+CTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTC
+AAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGC
+AATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCC
+ACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGC
+AATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTC
+AAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGC
+AATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCC
+ACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGC
+AATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTC
+AAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGC
+AATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCC
+ACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGC
+AATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTC
+AAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGC
+AATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCC
+ACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACC
+CTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTC
+AAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGC
+AATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCC
+ACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGC
+AATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTC
+AAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGC
+AATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCC
+ACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGC
+AATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTC
+AAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGC
+AATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCC
+ACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGC
+AATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTC
+AAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGC
+AATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACCCTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCC
+ACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACC
\ No newline at end of file
diff --git a/test_f/bug/bug-15847-read.fa b/test_f/bug/bug-15847-read.fa
new file mode 100644
index 0000000..8b765e4
--- /dev/null
+++ b/test_f/bug/bug-15847-read.fa
@@ -0,0 +1,6 @@
+>bug-15847-1
+CTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACC
+>bug-15847-2
+CTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACC
+>bug-15847-3
+CTTAGGCCTGGGTGATTGAGGATGCAATGAGCTGTGATTGTGCCACCACACTCCAGCCTGGGCAATACAGCAAGACTGTCTCAAAAAAAAAAAAAAAAACC
diff --git a/test_f/bug/bug-15847.should_get b/test_f/bug/bug-15847.should_get
new file mode 100644
index 0000000..82315d6
--- /dev/null
+++ b/test_f/bug/bug-15847.should_get
@@ -0,0 +1,6 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/bug/bug-15847-genome -r bug-15847-read.fa -k 22 --treat-multiple --detailed-sam -o ${abs_top_builddir:-../..}/test_f/bug/bug-15847.sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/bug/bug-15847.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/bug
+
+$Bug 15847: no-alignment in the output sam then that the argument --treat-multiple has been defined
+108:^bug-15847-?.*\\s+101M\\s+.*\\s+XM:i:1
diff --git a/test_f/bug/bug-16403-genome.fa b/test_f/bug/bug-16403-genome.fa
new file mode 100644
index 0000000..101928a
--- /dev/null
+++ b/test_f/bug/bug-16403-genome.fa
@@ -0,0 +1,6 @@
+>chr-16403_1
+ATTTCAGACAACCTATGCTCCAACTCCTTCTTCTGCTTGTATCTCTCTATTTTACCCTGTCTTCGAGATGCCATAGCAACGAGGCTAGAATAAGCCATGG
+>chr-16403_2
+ATTTCAGACAACCTATGCTCCAACTCCTTCTTCTGCTTGTATCTCTCTATTTTACCCTGTCTTCGAGATGCCATAGCAACGAGGCTAGAATAAGCCATGG
+>chr-16403_3
+GCCCCTGAAAAGCACCGCCATTGGGCAGGCCTCATATTATAGCTATTGACCCACCTCTGTATTTTAGCCTGTCTTTGAGATGCCATAGCAACGAGACTAG
diff --git a/test_f/bug/bug-16403-read.fa b/test_f/bug/bug-16403-read.fa
new file mode 100644
index 0000000..e9c1d94
--- /dev/null
+++ b/test_f/bug/bug-16403-read.fa
@@ -0,0 +1,4 @@
+>
+CTCCTTCTTCTGCTTGTATCTCTGTATTTTAGCCTGTCTTTGAGATGCCA
+>
+CTCCTTCTTCTGCTTGTATCTCTGTATTTTAGCCTGTCTTTGAGATGCCA
diff --git a/test_f/bug/bug-16403.should_get b/test_f/bug/bug-16403.should_get
new file mode 100644
index 0000000..0296d92
--- /dev/null
+++ b/test_f/bug/bug-16403.should_get
@@ -0,0 +1,6 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/bug/bug-16403-genome -r bug-16403-read.fa --max-extension-length 2 --stringent-chimera -k 20 -o ${abs_top_builddir:-../..}/test_f/bug/bug-16403.sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/bug/bug-16403.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/bug
+
+$Bug 16403: Segmentation fault when using a small --max-extension-length value and --stringent-chimera option
+2:no_single_loc
diff --git a/test_f/bug/bug-16581-genome.fa b/test_f/bug/bug-16581-genome.fa
new file mode 100644
index 0000000..67ee8ee
--- /dev/null
+++ b/test_f/bug/bug-16581-genome.fa
@@ -0,0 +1,2 @@
+>chr10_sample
+ccgtaggtggtttggccaaagatggagcataccttgtaagttctagaagcaaatgcttatgtctacactattagaagaagaaagggcctacagattatctCTGATTGGAGAGCTATGTGTAGtgttttggagcaatgaccatagtgatggattccctgggttggagtctcatcagcaatatgaatttcaacaacccctgaatctcaggttatttctttataa
diff --git a/test_f/bug/bug-16581-read.fq b/test_f/bug/bug-16581-read.fq
new file mode 100644
index 0000000..b8484fc
--- /dev/null
+++ b/test_f/bug/bug-16581-read.fq
@@ -0,0 +1,8 @@
+ at read1
+CTCTGATTGGAGAGCTATGTGTAGCTCTGATTGGAGAGCTATGTGTAGTGTTTTGAGATC
++
+tototatatititututeteyoyoyayayiyiyuyuyeyerororararirirururere
+ at read2
+CCCAGGGAATCCATCACTATGGTCATTGCTCCAAAACACTACACATAGCTCTCCAATCAC
++
+tototatatititututeteyoyoyayayiyiyuyuyeyerororararirirururere
diff --git a/test_f/bug/bug-16581.should_get b/test_f/bug/bug-16581.should_get
new file mode 100644
index 0000000..4e77fb8
--- /dev/null
+++ b/test_f/bug/bug-16581.should_get
@@ -0,0 +1,7 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/bug/bug-16581-genome -r bug-16581-read.fq -m 25 -k 22 -o ${abs_top_builddir:-../..}/test_f/bug/bug-16581.sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/bug/bug-16581.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/bug
+
+$Bug 16581: we expect that quality should be truncate if read is truncate using -m option
+1:^read1.* CTCTGATTGGAGAGCTATGTGTAGC tototatatititututeteyoyoy
+1:^read2.* TGACCATAGTGATGGATTCCCTGGG yoyoyetetututititatatotot
diff --git a/test_f/bug/bug-16931.should_get b/test_f/bug/bug-16931.should_get
new file mode 100644
index 0000000..7b35edf
--- /dev/null
+++ b/test_f/bug/bug-16931.should_get
@@ -0,0 +1,11 @@
+# This test for Bug #16931, we do not need really specific sequences to
+# reproduce it. We just need to have a xS at the beginning of the CIGAR. We
+# can find that in data of bug #16403
+
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/bug/bug-16403-genome -r bug-16403-read.fa -k 20 -o ${abs_top_builddir:-../..}/test_f/bug/bug-16931.sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/bug/bug-16931.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/bug
+
+$Bug 16931: XO should be the position of the k-mer at position given in XQ
+2:XO:Z:chr.16403_3\\|1,59
+
diff --git a/test_f/bug/bug-17175-genome.fa b/test_f/bug/bug-17175-genome.fa
new file mode 100644
index 0000000..5c0b588
--- /dev/null
+++ b/test_f/bug/bug-17175-genome.fa
@@ -0,0 +1,8 @@
+>chr1
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT [...]
+>chr16
+ACACCAAAAAACCCCCCCCCCCTGGTGAGAGTAGCTTCCAAAGCTGCAAAGGTGGGGAGGTTAACAAAATCCATTGGTCTATCTTGCATTTTGAATGGATCTTTTACCTGTGCATGATTTTTTTAACATTGTGCATTTCTAAT
+>chr15
+CTGTGTATTCTCTTTATGAGCGTCTTGTCTGTGTGCAGGAAGATCCCTGTCCCCATTTTACTATTCTATAGGGCAGGTAGGGGGTTTGTGTG
+>chr17
+TACTAGCTAGTACTATATTTTACAGGGAGAGAGAGATAAGCCCAAAAACGTGGGACAATGTGAACATGGACTCGAAGACATGGCCCTTTCTCTGTAGTGGATTTTTTAAATGTGCCATTATTGTTTTTAAAAAAAAAGGAAAAAAGAAAAGGAAACAAATAAAACACCTTTAAGAGGCTTGAAACCCCCCCCCCGGGTGTGTTTGGGAGACATGGCCAAAGGAAACAAATAAAACACCTTTAAGAAAGGAAACAAATAAAACACCTTTAAGAAAGGAAACAAATAAAACACCTTTAAGAAAGGAAACAAATAAAACACCTTTAAGAAAGGAAACAAATAAAACACCTTTAAGAAAGGAAACAAATAAAACACCTTTAAGAAAGGAAACAAATAAAACACCTTTAAGAAAGGAAACAAATAAAACACCTTTAAGAAAGGAAACAAATAAAACACCTTTAAGAAAGGAAACAAATAAAACACCTTTAAGAAAGG [...]
diff --git a/test_f/bug/bug-17175-read.fa b/test_f/bug/bug-17175-read.fa
new file mode 100644
index 0000000..0b0f65a
--- /dev/null
+++ b/test_f/bug/bug-17175-read.fa
@@ -0,0 +1,9 @@
+>read1
+ATTAGAAATGCACAATGTTAAAAAAATCATGCACAGGTAAAAGATCCATTCAAAATGCAAGATAGACCAATGGATTTTGTTAACCTCCCCACCTTTGCAGCTTTGGAAGCTACTCTCACCA
+CTGTGTATTCTCTTTATGAGCGTCTTGTCTGTGTGCAGGAAGATCCCTGTCCCCATTTTACTATACTATAGGGCAGGTA
+>read1
+ATTAGAAATGCACAATGTTAAAAAAATCATGCACAGGTAAAAGATCCATTCAAAATGCAAGATAGACCAATGGATTTTGTTAACCTCCCCACCTTTGCAGCTTTGGAAGCTACTCTCACCACTGTGTATTCTCTTTATGAGCGTCTTGTCTGTGTGCAGGAAGATCCCTGTCCCCATTTTACTATACTATAGGGCAGGTA
+>read2
+TACTAGCTAGTACTATATTTTAGAGGGAGAGAGAGATAAGCCCAAAAACGTGGGACAATGTGAACATGGACTCGAAGACATGGCCCTTTCTCTGTAGTGGATTTTTTAAATGTGCCATTATTGTTTTTAAAAAAAAAGGAAAAAAGAAAAGGAAACAAATAAAACACCTTTAAGAGGCTTGAAAGCTCTTGTTTTTACTGTGTATGTTCTTGCTCAGGGCTCTCTAGATAATGCAGAATATAGAGAAAATATATTATATATTTATTTTATATAAATTTTTTGGGGGAGAGGAGGAG
+>read2
+TACTAGCTAGTACTATATTTTAGAGGGAGAGAGAGATAAGCCCAAAAACGTGGGACAATGTGAACATGGACTCGAAGACATGGCCCTTTCTCTGTAGTGGATTTTTTAAATGTGCCATTATTGTTTTTAAAAAAAAAGGAAAAAAGAAAAGGAAACAAATAAAACACCTTTAAGAGGCTTGAAAGCTCTTGTTTTTACTGTGTATGTTCTTGCTCAGGGCTCTCTAGATAATGCAGAATATAGAGAAAATATATTATATATTTATTTTATATAAATTTTTTGGGGGAGAGGAGGAG
diff --git a/test_f/bug/bug-17175.should_get b/test_f/bug/bug-17175.should_get
new file mode 100644
index 0000000..df0b753
--- /dev/null
+++ b/test_f/bug/bug-17175.should_get
@@ -0,0 +1,17 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/bug/bug-17175-genome -r bug-17175-read.fa --detailed-sam -k 22 -o ${abs_top_builddir:-../..}/test_f/bug/bug-17175.sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/bug/bug-17175.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/bug
+
+$Bug 17175: the read had several breaks (including a godd chimera break) and crac was not consider the chimera in the CIGAR, so SA was empty
+2:^read2 0 chr17 .* 22M1X161M112S .*[^SA:Z:\\s].*XE:Z:.*;2:2:chimera:247:chr1\\|1,9739:chr17\\|1,946
+
+$Bug 17175: not a bug, just a methodo choice - But in a better world, we should have a XE field and a SA field with a chimeric alignment
+s2:^read2.* SA:Z:chr?.* XE:Z:.*chimera:247:chr1\\|1,9739:chr17\\|1,946
+s2:^read2.* SA:Z:chr?.* XE:Z:.*chimera:247:chr1\\|1,9739:chr17\\|1,946
+
+$Bug 17175: idem, the read had several breaks (including a good chimera break) and crac was not consider the chimera in the CIGAR because a strand problem (+1 before the junction, -1 after the junction)
+s2:^read1 16 chr16 .* 79S121M .* SA:Z:chr15,0,\\+,121S22M57S,254,0 .* XE:Z:0:0:chimera:78:chr16\\|-1,22:chr15\\|1,0
+s2:^read1 2048 chr15 .* 121S22M57S .* SA:Z:chr16,0,\\-,79S121M,254,0
+
+
+
diff --git a/test_f/causes/Makefile.am b/test_f/causes/Makefile.am
new file mode 100644
index 0000000..f58525f
--- /dev/null
+++ b/test_f/causes/Makefile.am
@@ -0,0 +1,104 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+MOSTLYCLEANFILES=*~
+CLEANFILES=*~ *.tap *.ssa *.conf *.sam
+DISTCLEANFILES=*~
+MAINTAINERCLEANFILES=*~
+
diff --git a/test_f/causes/Makefile.in b/test_f/causes/Makefile.in
new file mode 100644
index 0000000..0cee695
--- /dev/null
+++ b/test_f/causes/Makefile.in
@@ -0,0 +1,469 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
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+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
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diff --git a/test_f/causes/genome.fa b/test_f/causes/genome.fa
new file mode 100644
index 0000000..f7d028a
--- /dev/null
+++ b/test_f/causes/genome.fa
@@ -0,0 +1,86 @@
+>chr1
+TCGCGCCTACTACTCGCATACCCAACTGACAAATTCTATATCCTCTTTGTGAGGTTTTTT
+GTTGAGTGGTCGTGCAGGTGCATCGCTTTCCCGCTACGAATATTGACAGGCGCGGCGACG
+AAGGTCATGCAATACGAAGACGGATTTAAGATGCGCTATGGGGCCTCCCCAAGCGCTCCC
+GTAGAGTCGACACTGTAACCGTCAGGTTAAAGTGGAGCGAAAGCTGAGTCCAGCTTGAAT
+TACTTGTTGATCGTGGTCGTGCGGGTGTCGACATTGAGCAGGCTTATTCGGGCTGCGTCA
+GGAGGACTATGTTTCACTGGTGGTGACGGGTGGTAAACCTTCGTGCCCTCCTCAGCTGAT
+CCTTGCCGACCAGCGCGTGTTAGTAAACGGAATCGGAAAGACGGTGGAATTGAGTCTGCC
+GTACCAAGAGGTTGCAGCTAATGGTTGTACAAGACCCTGTCGGGTGGATCTCGGAATGGT
+CGCACACTTGCTGTACCTCGCCATACCCAGGCATCTCAAGTGCTTCAACCAAGATTGTTT
+CGCTTCTCGCTGTTGACCGAGCCGTTATACGCGGCGACCGTACTCACCGAAGCAAAACTC
+TGACCCTTTGGAACGAGGCGGCAGAGTGCTGTGCAGGTACTGCTGCAAAGCGAACTGGGC
+AGAAGCCTTCTGACTTGGAGATGAATCTCTTCGTTATTTCGTCAGCAGGCAGTTTGCTCC
+TTCACGCACTGAAAGAGTGAGAACCATACTACCCACTCAGAGTCTCAAGTCTTTATCTCC
+CACTTACCGGTATTTGGCAAGCTCGATTCAGTATATCGACCGTCGGGAAGCTGCCCAACC
+ATCAAACGGGCCCACGCAGGAGGCTTTTTTGCCGCAAAACCAACATCTGAGTGCCATACA
+TTGTACCTCTAGCTTACTCGTGAACGCACTACGACAGATCTCTGGGTTTTTCCTGAAGAT
+TAGAGATTCCATGGACGTGGGCCTAATGAATTTTCGCGTAAAGCGACCCATAAGTACCTG
+ATCTATACACTGACCCCACCTCGACCTCACTCTAAGGTGGTTCAGTACGAAAGGCGGCTT
+TCACGTGCGCTTTATCCTTAAGAAGACATTGTTCCCTGCAGGATTCTACTTTCCACAACC
+AGGGTAATCAATGGCCGGAGTCGCCACGCACGATATTGGCCAATTCCCCCTCTTACACTC
+ATCGCTTGGGTGGAGAACTCGGCACCGCCACTCACGTCGGAAAGGATTCACAAATCCGGC
+CCGGAATTTCGCGAAACTATGCTACAATGAATTAAGCTTATACGAAATATTGTGAATATT
+GCTTCATTGTTGACGAAGAGCAACTGTGACGTGAACCTAAAGCACAAGCTATTGTCCTGT
+CAACCGCGTCCACGGTGTCTCTCCCAACCATCAGACTACAGGAACCTTCGTTGCCCCAAG
+CTCCCTGCCGATTATCTCGCAATGTCCGACAGATATCTTACAATGTCAGGTGTTCAAATA
+CTATTTACCGTCGGAGATCATAGTACGCGTTAGTTCGACCCCCGAGGTCAATCTCTCAGA
+ACCTTCAGGTAGTCGACGGTGGACGGCGATGTGGTATCACCGGTACGCTGCTTACTCAGC
+GGCTGAACCTGAACCATTTAGTAGTAGGGCTGGTATTGGAACTATCCGGGGGGTCTAGAA
+AATAGACTTTAAATCTCACTATCTCGGGGTAGTCAGCTGCTCGCTTAACGAAATCTGACC
+GTCATGTTTCAAGCAACAGGTATATATATGCGTCAATTGATCGCATGGAGCTATTTCGAT
+ATCCCGCCTTTTTGCATACGGCACCCATAGGTTGAGGCCCGTTAGACAATGATAAACGGA
+TCAGAGTGGCTCGAGGTTCAATATCACTCTATTCAAGATTAACCGAAACATTAGCGGGGT
+GGAACCAGACGTGGCATTTCGACCGGCTGGCGGAACGCTCTGCTGGTACGTATTGGGCGG
+CACCTGTACAAGTGTCCATGCGAAGCACACCACGAACCGGGACAATTTCTGGCTGCTACA
+CACTCTACTCTACGCTTGGGGAGGCATCTGGACACTGTAACTCCTTTAGGAATCAACGTT
+TAATGGCAGATACCTACAATGATTATTCAAGACCATGACTTGGGGTGGTCTGTAGTAGCT
+CGACGAAGGAATGAACAGGAACCGTTATTACGCGTACAACCTGTATGGTTGCAATGCATA
+GTCATGGTCGTAGTACCCAGACGCCCTTGTGTGAATCCTTAATCTGTTGCGTGGACCTAA
+GTATCGCTCCGTTAGCATATTAACTATTTCATCCCGTTGCCTCCGAATTTCTCCTGTCAG
+ATCCTAATCCATATACTTCCCCCCCTGAGCAGCGCGCTGCATTACGCTAATAACCTTTGG
+>chr2
+GAAAGGCCCTAATCGATATGATATGCCTAGTTTTATCCTTTTTTCGATTTCCATGGTTAG
+GGGTAGGCAGAATGTTCGTCGATTCTCTTCGATATCCAAGCCAGTATACCCGGCAGAAAG
+CATCTACAATGTAAACCGGCTCGCCTCTCTTTAACTAAACAAGACCTGTTCTATGCTTGA
+GAATGATGTGCAGTCCTCTTAATGTAGCAAGTACGCCCCTACGTAATTGACACCGCAACC
+TTATGATGGCAAATAGAGTTTCGTTCGGCGCGACAACGACCTCTAGACATGCATTCATCG
+GTACGCATTTTCGTCATAAAGTACCGCTGCGTAATAGCACTGGGGTTGGCGGGTTCCCCC
+CATGCCCCTTCTGTACCCCGGCTATGCACCGGCAATTAACGTCGATGATACACGTTCCCA
+GCGAACCTCTTCTTCGACCCGGCTCTTTTTCTGCGTTGAGTGTCAAGTTAAGTGGCGGGA
+GAACGTACACATATACACTCAGGTTGGTGCCGAACTAAGACAAGTCAATGTTGACATGCT
+GGTCATGAGGATGTAAATTATCATACGACGGCATCGTTCAGCTGCCCCAACGTGGCGAAA
+TGAATGGTAGGCAGTTTCATAAGTTCATGGCAGAGCTGGTAGGTGCTAGCATCACGAGTA
+CTAGCTCTGCCCAGGGATAGCACACTTTGCGAGTGGGCCCGATAAACTTTCATGAGTGCA
+CTCTTACCTGAAGCGGGCCATGGGAACGGTCACTAAATAACCTAGGTGCTGGTATCATCG
+GAGCTCGGATTCGGTCACTTCCTGAATCGAGGTATCGCTCTAGTACCGTCTGGGATGCCA
+CCGCGTGTAGTCAATCCGCAGCAGTGCTGTGCTGTACATGTGACCCGAGAAACAATATAT
+TATCAAATGCTCAAATACGCGGATCAACTTCCATTGGATAGAGCATGGAATAGTTGTTGG
+ACCAGGAGCTCGCAATAAATGAAAGCAAGTCTGTGAGTAAAACGAATTTCGAATAAGGTG
+TTACTGGGGTGTAGTTCTATTACAGAGGAAATCAAAATTTTCCAGCTAGCGTGCGCCGGG
+GTGTGCTACTGGTACAACGCAGCCTCTACTTCTACTTAACAGGGCTGAACGTGCTAGGCC
+CCAATAGAACTGTGTGTACGCTTGGGAATGATCCTCCACTATCGCTTGCTCTATATTAGT
+ATTCCTTGGTTGGGTCGACACCTTTCCGCGACCACGTCTCGACGACGAGTCCAGTTGATA
+CAGCATGCGTCTTCTAGTGAGGTTACAGAGGTAAGTGTACATGGATGGCCACGATGCTAA
+GGTGTTTGAACTGCAGCAGAGTTTTCGTTAAGAGTGGTTTTCCTTCGTCCCCGAATCCAC
+TTGTATGAGTTAAAGACCAGTAACTCTTCCCGAACTACGGCATGAAGAGTCCCGCGGAAT
+GCGAAGTTAAACTCAATATACCCCATGTGGATCTGATTCTAAACTGCCTTATAGTACGGT
+TACAGAGGGAGATACATTGGAGAGTTAGTGGTGCTGTTTTTGGAGCGGGAGTTTGGACTT
+TGCCCATCCCCACCTTCAGAGATTGAATCAGGACGCTGACATCGGTTCCACACGCCGCTT
+CTTGAGGAAAGTCCCTAGTTTCGCACCTCTAGAAATTGTGCTTATTAATGACTGTTAATT
+TGCAAGCGGAAGTCATTAGGTGAGTCAAAGCTTGAGTTTACAAATCTCAAGCGAATCGGG
+TCTTACAGAGATTTACGATGTGGAGCATTTTCAGTAGTCTTCCCGTTAGAGTCAAGTAAA
+TGTATTAATGTCAATATCATAAAGGAGGGAAAGAGTTATGTATTAATAATTAACAGCATT
+AGGTTAAGGAGGCAGAATAAGCTGTGTGTACGCGCTGTCGGCCTCCGACGTGTATTGATT
+CAAGTTCACGGTATCCACAGGGCGGCTTCGGGGAAAGGCCCACGTTACCCAACAGACTCG
+TTTAGGCGCGTGTACACAAGTCGAACTGTGCAGGTCCCGTAATTGTAGGGAGTCCGGCCA
+TCACATATAACATAATATGGTTCACGATGAAAGCCGCAGAACCGTTTAGGGGGGGACTCC
+TTGTGAAAGTACAGACACGTCAGGCGAAGTTGGGTCGGGCTGCGTGACGGAGATGAAGCC
+GTAGGTCTACCGGCGGCAGTCTGAGACCAAAACCGCCATCAAAGGTATTCTTGGCATATG
+CGGGTCTGACGAACATTAGAAACCGATGTCTTCACATTACATCCAAACGAGGTTATTATG
+TTCGATGTGGCGATAGCATGAGCTTTAAGAGTAATTGTACTTGAACATATTGCGCAACCA
+TGTTTCCTCGGAACTGTCATGTTCACAGCGTAGCCTTAATCTCAACTTAGTATAATATCG
+GTGGCTCGTAGTTCGCATCGCCGCGCTAGTGTAGACCACGTGGTTGGGCAGCTACTGCGT
+AGGCAACGGGCCCTGCTTAGCCAAGTGTTCCTACTTGCTAAATGGAACGCACATTTTAAT
+CTGCTCGTGTCCGGGCCACTCAAGTATAAGTACAGCGGAACTTCGGTAATACGGGCAGCT
+TCATGACCTTGTTCCATTGG
diff --git a/test_f/causes/snp.fa b/test_f/causes/snp.fa
new file mode 100644
index 0000000..0bab2dd
--- /dev/null
+++ b/test_f/causes/snp.fa
@@ -0,0 +1,134 @@
+>snp1-1
+TCGCGCCTACTACTCGCATACCCAACTGgCAAATTCTATATCCTCTTTGTGAGGTTTTTT
+>snp1-2
+TCGCGCCTACTACTCGCATACCCAACTGgCAAATTCTATATCCTCTTTGTGAGGTTTTTT
+>snp1-3
+TCGCGCCTACTACTCGCATACCCAACTGgCAAATTCTATATCCTCTTTGTGAGGTTTTTT
+>snp1-4
+TCGCGCCTACTACTCGCATACCCAACTGgCAAATTCTATATCCTCTTTGTGAGGTTTTTT
+
+>snp1-rc-1
+AAAAAACCTCACAAAGAGGATATAGAATTTGcCAGTTGGGTATGCGAGTAGTAGGCGCGA
+>snp1-rc-2
+AAAAAACCTCACAAAGAGGATATAGAATTTGcCAGTTGGGTATGCGAGTAGTAGGCGCGA
+>snp1-rc-3
+AAAAAACCTCACAAAGAGGATATAGAATTTGcCAGTTGGGTATGCGAGTAGTAGGCGCGA
+
+>snp2-1
+GTTGAGTGGTCGTGCAGGTGCATCGCTTaCCCGCTACGAATATTGACAGGCGCGGCGACG
+>snp2-2
+GTTGAGTGGTCGTGCAGGTGCATCGCTTaCCCGCTACGAATATTGACAGGCGCGGCGACG
+>snp2-3
+GTTGAGTGGTCGTGCAGGTGCATCGCTTaCCCGCTACGAATATTGACAGGCGCGGCGACG
+>snp2-4
+GTTGAGTGGTCGTGCAGGTGCATCGCTTaCCCGCTACGAATATTGACAGGCGCGGCGACG
+>snp2-5
+GTTGAGTGGTCGTGCAGGTGCATCGCTTcCCCGCTACGAATATTGACAGGCGCGGCGACG
+>snp2-6
+GTTGAGTGGTCGTGCAGGTGCATCGCTTcCCCGCTACGAATATTGACAGGCGCGGCGACG
+>snp2-7
+GTTGAGTGGTCGTGCAGGTGCATCGCTTcCCCGCTACGAATATTGACAGGCGCGGCGACG
+>snp2-8
+GTTGAGTGGTCGTGCAGGTGCATCGCTTcCCCGCTACGAATATTGACAGGCGCGGCGACG
+
+>snp3-1
+AAGGTCATGCAATACGAAGACGGATTTcAGcTGCGCTATGGGGCCTCCCCAAGCGCTCCC
+>snp3-2
+AAGGTCATGCAATACGAAGACGGATTTcAGcTGCGCTATGGGGCCTCCCCAAGCGCTCCC
+>snp3-3
+AAGGTCATGCAATACGAAGACGGATTTcAGcTGCGCTATGGGGCCTCCCCAAGCGCTCCC
+>snp3-4
+AAGGTCATGCAATACGAAGACGGATTTcAGcTGCGCTATGGGGCCTCCCCAAGCGCTCCC
+
+>snp4-1
+GTAcAGTCGACACTGTAACCGTCAGGTTAAAGTGGAGCGAAAGCTGAGTCCAGCTTGAAT
+>snp4-2
+GTAcAGTCGACACTGTAACCGTCAGGTTAAAGTGGAGCGAAAGCTGAGTCCAGCTTGAAT
+>snp4-3
+GTAcAGTCGACACTGTAACCGTCAGGTTAAAGTGGAGCGAAAGCTGAGTCCAGCTTGAAT
+>snp4-4
+GTAcAGTCGACACTGTAACCGTCAGGTTAAAGTGGAGCGAAAGCTGAGTCCAGCTTGAAT
+
+>snp4-rc-1
+ATTCAAGCTGGACTCAGCTTTCGCTCCACTTTAACCTGACGGTTACAGTGTCGACTgTAC
+>snp4-rc-2
+ATTCAAGCTGGACTCAGCTTTCGCTCCACTTTAACCTGACGGTTACAGTGTCGACTgTAC
+>snp4-rc-3
+ATTCAAGCTGGACTCAGCTTTCGCTCCACTTTAACCTGACGGTTACAGTGTCGACTgTAC
+
+>snp5-1
+aACTTGTTGATCGTGGTCGTGCGGGTGTCGACATTGAGCAGGCTTATTCGGGCTGCcTCA
+>snp5-2
+aACTTGTTGATCGTGGTCGTGCGGGTGTCGACATTGAGCAGGCTTATTCGGGCTGCcTCA
+>snp5-3
+aACTTGTTGATCGTGGTCGTGCGGGTGTCGACATTGAGCAGGCTTATTCGGGCTGCcTCA
+
+>snp5-rc-1
+TGAgGCAGCCCGAATAAGCCTGCTCAATGTCGACACCCGCACGACCACGATCAACAAGTt
+>snp5-rc-2
+TGAgGCAGCCCGAATAAGCCTGCTCAATGTCGACACCCGCACGACCACGATCAACAAGTt
+>snp5-rc-3
+TGAgGCAGCCCGAATAAGCCTGCTCAATGTCGACACCCGCACGACCACGATCAACAAGTt
+
+>snp6-1
+GGAGGACTATGTTTCACTGGTGGTGAGGGTGGTAAACCTTCGTGCCCTCCTCAGCTGATC
+>snp6-2
+GGAGGACTATGTTTCACTGGTGGTGAGGGTGGTAAACCTTCGTGCCCTCCTCAGCTGATC
+>snp6-3
+GGAGGACTATGTTTCACTGGTGGTGAGGGTGGTAAACCTTCGTGCCCTCCTCAGCTGATC
+
+>snp7-1
+CCTTGCCGACCAGCGCGTGTTAGAAAGGAATCGGAAAGACGGTGGAATTGAGTCTGCC
+>snp7-2
+CCTTGCCGACCAGCGCGTGTTAGAAAGGAATCGGAAAGACGGTGGAATTGAGTCTGCC
+>snp7-3
+CCTTGCCGACCAGCGCGTGTTAGAAAGGAATCGGAAAGACGGTGGAATTGAGTCTGCC
+
+>snp8-1
+AAACAATCTTGGTTGAAGCACTTGAGAGCCTGGGTATGGCGAGGTACAGCAAGTGTGCGA
+>snp8-2
+AAACAATCTTGGTTGAAGCACTTGAGAGCCTGGGTATGGCGAGGTACAGCAAGTGTGCGA
+>snp8-3
+AAACAATCTTGGTTGAAGCACTTGAGAGCCTGGGTATGGCGAGGTACAGCAAGTGTGCGA
+
+>snp9-1
+CGCTTCTCGCTGTTGACCGAGCCGTTATGACGCGGCGACCGTACTCACCGAAGCAAAACTC
+>snp9-2
+CGCTTCTCGCTGTTGACCGAGCCGTTATGACGCGGCGACCGTACTCACCGAAGCAAAACTC
+>snp9-3
+CGCTTCTCGCTGTTGACCGAGCCGTTATGACGCGGCGACCGTACTCACCGAAGCAAAACTC
+
+>snp10-1
+TGACCCTTTGGAACGAGGCGGCAAGTGCTGTGCAGGTACTGCTGCAAAGtCGAACTGGGCAGAAGCCTTCTGACTaGGAGATGAATCTCTTCGTTATTaTCGTCAGCAGGCAGTTTGCTCC
+>snp10-2
+TGACCCTTTGGAACGAGGCGGCAAGTGCTGTGCAGGTACTGCTGCAAAGtCGAACTGGGCAGAAGCCTTCTGACTaGGAGATGAATCTCTTCGTTATTaTCGTCAGCAGGCAGTTTGCTCC
+>snp10-3
+TGACCCTTTGGAACGAGGCGGCAAGTGCTGTGCAGGTACTGCTGCAAAGtCGAACTGGGCAGAAGCCTTCTGACTaGGAGATGAATCTCTTCGTTATTaTCGTCAGCAGGCAGTTTGCTCC
+
+>snp11-1
+TTCACGCACTGAAAGAGTGAGAACCATACTACCCACTCAGAGTCTCAAGTCTTTgTCTCC
+>snp11-2
+TTCACGCACTGAAAGAGTGAGAACCATACTACCCACTCAGAGTCTCAAGTCTTTgTCTCC
+>snp11-3
+TTCACGCACTGAAAGAGTGAGAACCATACTACCCACTCAGAGTCTCAAGTCTTTgTCTCC
+
+>snp11-rc-1
+GGAGAcAAAGACTTGAGACTCTGAGTGGGTAGTATGGTTCTCACTCTTTCAGTGCGTGAA
+>snp11-rc-2
+GGAGAcAAAGACTTGAGACTCTGAGTGGGTAGTATGGTTCTCACTCTTTCAGTGCGTGAA
+>snp11-rc-3
+GGAGAcAAAGACTTGAGACTCTGAGTGGGTAGTATGGTTCTCACTCTTTCAGTGCGTGAA
+
+>snp12-1
+CACTTgCCGGTATTTGGCAAGCTCGATTCAGTATATCGACCGTCGGGAAGCTGCCCAACC
+>snp12-2
+CACTTgCCGGTATTTGGCAAGCTCGATTCAGTATATCGACCGTCGGGAAGCTGCCCAACC
+>snp12-3
+CACTTgCCGGTATTTGGCAAGCTCGATTCAGTATATCGACCGTCGGGAAGCTGCCCAACC
+
+>snp12-rc-1
+GGTTGGGCAGCTTCCCGACGGTCGATATACTGAATCGAGCTTGCCAAATACCGGcAAGTG
+>snp12-rc-2
+GGTTGGGCAGCTTCCCGACGGTCGATATACTGAATCGAGCTTGCCAAATACCGGcAAGTG
+>snp12-rc-3
+GGTTGGGCAGCTTCCCGACGGTCGATATACTGAATCGAGCTTGCCAAATACCGGcAAGTG
diff --git a/test_f/causes/snp.fa.should_get b/test_f/causes/snp.fa.should_get
new file mode 100644
index 0000000..6478d5e
--- /dev/null
+++ b/test_f/causes/snp.fa.should_get
@@ -0,0 +1,58 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/causes/genome -r snp.fa -k 22 --deep-snv --nb-nucleotides-snv-comparison 3 -o ${abs_top_builddir:-../..}/test_f/causes/snp.sam --detailed-sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/causes/snp.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/causes
+
+$One substitution in the middle of the read (A -> g)
+4:^snp1-[1-4].*chr1.*\\s+1\\s+.*\\s+(60M|28M1.31M)\\s+.*XE:Z:0:0:SNP:[^:]+:28:[^:]+:A:G
+
+$snp1 revcomp
+3:^snp1-rc-[1-3].*chr1.*\\s+1\\s+.*\\s+(60M|28M1.31M)\\s+.*XE:Z:0:0:SNP:[^:]+:28:[^:]+:A:G
+
+$One substitution in the middle of the read, heterozygous (T -> a, T -> c)
+4:^snp2-[1-4].*\\s+(60M|28M1.31M)\\s+.*XE:Z:0:0:SNP:[^:]+:28:[^:]+:T:A
+4:^snp2-[5-9].*\\s+(60M|28M1.31M)\\s+.*XE:Z:0:0:SNP:[^:]+:28:[^:]+:T:C
+
+$Two substitutions, close one to the other (A -> c, A -> c)
+4:^snp3-[1-4].*\\s+(60M|27M1.2M1.29M)\\s+.*XE:Z:0:0:SNP:[^:]+:27:[^:]+:A:C;1:0:SNP:[^:]+:30:[^:]+:A:C
+
+$One substitution close to the start of the read (G -> c). CRAC must be launched with --deep-snv --nb-nucleotides-snv-comparison 3
+4:^snp4-[1-4].*chr1\\s+181\\s+.*\\s+(60M|3M1.56M)\\s+.*XE:Z:0:0:SNP:[^:]+:3:[^:]+:G:C
+
+$Revcomp of snp4.
+3:^snp4-rc-[1-3].*chr1\\s+181\\s+.*\\s+(60M|3M1.56M)\\s+.*XE:Z:0:0:SNP:[^:]+:3:[^:]+:G:C
+
+$One substitution close to the end of the read (G -> c) + bioundetermined before that (T > a in pos 0). CRAC must be launched with --deep-snv --nb-nucleotides-snv-comparison 3
+3:^snp5-[1-3].*chr1\\s+242\\s+.*\\s+(60M|1.55M1.3M)\\s+.*;1:1:SNP:[^:]+:56:[^:]+:G:C
+
+$Revcomp of snp5
+3:^snp5-rc-[1-3].*chr1\\s+242\\s+.*\\s+(60M|1.55M1.3M)\\s+.*XE:Z:0:0:SNP:[^:]+:56:[^:]+:G:C
+
+$One deletion in the middle of the read (pos. 26, starting at 0, C deleted)
+3:^snp6-[1-3].*\\s+26M1D34M\\s+.*XE:Z:0:0:SNP:[^:]+:26:[^:]+:C:\\?
+
+$Two deletions in the middle (pos.23 and 27 in the not mutated read): T and C. We don't know how to manage them yet.
+s3:^snp7-[1-3].*\\s+23M1D3M1D32M\\s+.*XE:Z:0:0:SNP:[^:]+:23:[^:]+:T:\\?.*XE:Z:0:1:SNP:[^:]+:26:[^:]+:C:\\?
+
+$Two deletions in the middle (pos.23 and 27 in the not mutated read): T and C. We don't know how to manage them yet but we detect that there are several causes.
+3:^snp7-[1-3].*\\s+26S32M\\s+.*XE:Z:0:0:BioUndetermined:25:\\[The break in the tag is too large \\(24\\). There may have several biological causes\\]
+
+$One deletion, on the revcomp, position 27 (T)
+3:^snp8-[1-3].*\\s+33M1D27M\\s+.*XE:Z:0:0:SNP:[^:]+:32:[^:]+:A:\\?
+
+$One insertion, middle of the read (position 28, G)
+3:^snp9-[1-3].*\\s+28M1I32M\\s+.*XE:Z:0:0:SNP:[^:]+:28:[^:]+:\\?:G
+
+$Deletion, position 24 (G); insertion position 49 (t); substitution position 75 (T -> a); insertion position 98 (a)
+3:^snp10-[1-3].*\\s+(23M1D26M1I25M1X22M1I22M|23M1D26M1I48M1I22M)\\s+.*XC:i:4.*XE:Z:0:0:SNP:[^:]+:23:[^:]+:G:\\?.*;1:1:SNP:[^:]+:49:[^:]+:\\?:T.*;2:2:SNP:[^:]+:75:[^:]+:T:A.*;3:3:SNP:[^:]+:98:[^:]+:\\?:A
+
+$ Substitution at 5bp from the last nucleotide of the read (A -> g). CRAC must be launched with --deep-snv --nb-nucleotides-snv-comparison 3
+3:^snp11-[1-3].*\\s+chr1\\s+721\\s+.*\\s+(60M|54M1.5M)\\s+.*XE:Z:0:0:SNP:[^:]+:54:[^:]+:A:G
+
+$ Revcomp of snp11
+3:^snp11-rc-[1-3].*\\s+chr1\\s+721\\s+.*\\s+(60M|54M1.5M)\\s+.*XE:Z:0:0:SNP:[^:]+:54:[^:]+:A:G
+
+$ Substitution at 5bp from the first nucleotide of the read (A -> g). CRAC must be launched with --deep-snv --nb-nucleotides-snv-comparison 3
+3:^snp12-[1-3].*\\s+chr1\\s+781\\s+.*\\s+(60M|5M1.54M)\\s+.*XE:Z:0:0:SNP:[^:]+:5:[^:]+:A:G
+
+$ Revcomp of snp12
+3:^snp12-rc-[1-3].*\\s+chr1\\s+781\\s+.*\\s+(60M|5M1.54M)\\s+.*XE:Z:0:0:SNP:[^:]+:5:[^:]+:A:G
diff --git a/test_f/cigar/Makefile.am b/test_f/cigar/Makefile.am
new file mode 100644
index 0000000..bda238d
--- /dev/null
+++ b/test_f/cigar/Makefile.am
@@ -0,0 +1,106 @@
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+# SUBDIRS=causes cigar
+
+MOSTLYCLEANFILES=*~
+CLEANFILES=*~ *.tap *.ssa *.conf *.sam
+DISTCLEANFILES=*~
+MAINTAINERCLEANFILES=*~
+
diff --git a/test_f/cigar/Makefile.in b/test_f/cigar/Makefile.in
new file mode 100644
index 0000000..d2d5dd1
--- /dev/null
+++ b/test_f/cigar/Makefile.in
@@ -0,0 +1,471 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+###############################################################################
+# #
+# Copyright © 2010-2013 -- IRB/INSERM #
+# (Institut de Recherches en Biothérapie / #
+# Institut National de la Santé et de la Recherche #
+# Médicale) #
+# LIFL/INRIA #
+# (Laboratoire d'Informatique Fondamentale de #
+# Lille / Institut National de Recherche en #
+# Informatique et Automatique) #
+# LIRMM/CNRS #
+# (Laboratoire d'Informatique, de Robotique et de #
+# Microélectronique de Montpellier / #
+# Centre National de la Recherche Scientifique) #
+# LITIS #
+# (Laboratoire d'Informatique, du Traitement de #
+# l'Information et des Systèmes). #
+# #
+# #
+# Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# Thérèse COMMES <commes at univ-montp2.fr> #
+# Éric RIVALS <eric.rivals at lirmm.fr> #
+# #
+# Programmeurs #
+# /Progammers: Nicolas PHILIPPE <nicolas.philippe at lirmm.fr> #
+# Mikaël SALSON <mikael.salson at lifl.fr> #
+# with additional contribution for the packaging of: #
+# Alban MANCHERON <alban.mancheron at lirmm.fr> #
+# #
+# Contact: CRAC list <crac-bugs at lists.gforge.inria.fr> #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# Ce fichier fait partie du programme CRAC. #
+# #
+# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
+# #
+# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
+# respectant les principes de diffusion des logiciels libres. Vous pouvez #
+# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
+# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
+# le site "http://www.cecill.info". #
+# #
+# En contrepartie de l'accessibilité au code source et des droits de copie, #
+# de modification et de redistribution accordés par cette licence, il n'est #
+# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
+# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
+# titulaire des droits patrimoniaux et les concédants successifs. #
+# #
+# À cet égard l'attention de l'utilisateur est attirée sur les risques #
+# associés au chargement, à l'utilisation, à la modification et/ou au #
+# développement et à la reproduction du logiciel par l'utilisateur étant #
+# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
+# manipuler et qui le réserve donc à des développeurs et des professionnels #
+# avertis possédant des connaissances informatiques approfondies. Les #
+# utilisateurs sont donc invités à charger et tester l'adéquation du #
+# logiciel à leurs besoins dans des conditions permettant d'assurer la #
+# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
+# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
+# #
+# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
+# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
+# termes. #
+# #
+# ------------------------------------------------------------------------- #
+# #
+# This File is part of the CRAC program. #
+# #
+# Crac is a tool to analyse RNA-Seq data provided by NGS. #
+# #
+# This software is governed by the CeCILL license under French law and #
+# abiding by the rules of distribution of free software. You can use, #
+# modify and/ or redistribute the software under the terms of the CeCILL #
+# license as circulated by CEA, CNRS and INRIA at the following URL #
+# "http://www.cecill.info". #
+# #
+# As a counterpart to the access to the source code and rights to copy, #
+# modify and redistribute granted by the license, users are provided only #
+# with a limited warranty and the software's author, the holder of the #
+# economic rights, and the successive licensors have only limited #
+# liability. #
+# #
+# In this respect, the user's attention is drawn to the risks associated #
+# with loading, using, modifying and/or developing or reproducing the #
+# software by the user in light of its specific status of free software, #
+# that may mean that it is complicated to manipulate, and that also #
+# therefore means that it is reserved for developers and experienced #
+# professionals having in-depth computer knowledge. Users are therefore #
+# encouraged to load and test the software's suitability as regards their #
+# requirements in conditions enabling the security of their systems and/or #
+# data to be ensured and, more generally, to use and operate it in the same #
+# conditions as regards security. #
+# #
+# The fact that you are presently reading this means that you have had #
+# knowledge of the CeCILL license and that you accept its terms. #
+# #
+###############################################################################
+
+# SUBDIRS=causes cigar
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+subdir = test_f/cigar
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+ $(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/config/config.h
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+SOURCES =
+DIST_SOURCES =
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diff --git a/test_f/cigar/consistency.should_get b/test_f/cigar/consistency.should_get
new file mode 100644
index 0000000..64e1b4c
--- /dev/null
+++ b/test_f/cigar/consistency.should_get
@@ -0,0 +1,34 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/cigar/genome -r reads.fasta -k 22 -o ${abs_top_builddir:-../..}/test_f/cigar/consistency.sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/cigar/consistency.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/cigar
+
+$CIGAR consistency check (reverse chimera)
+2:^os1000380-90bp-3186262-[1-2]\\s0\\s.*\\s23M120N24M43S\\s
+2:^os1000380-90bp-3186262-[1-2]\\s2064\\s.*\\s8S35M47S\\s
+
+$CIGAR consistency check (reverse chimera)
+1:^os1000380-90bp-3831935-1\\s0\\s.*\\s32M58S\\s
+1:^os1000380-90bp-3831935-1\\s2064\\s.*\\s26M1X31M32S\\s
+
+$CIGAR consistency check (reverse chimera)
+1:^os1000380-90bp-3831935-1-rc\\s0\\s.*\\s26M1X28M35S\\s
+1:^os1000380-90bp-3831935-1-rc\\s2064\\s.*\\s35M55S\\s
+
+$CIGAR consistency check (reverse chimera)
+2:^os1000380-90bp-6065109-[1-2]\\s0\\s.*\\s34M56S\\s
+2:^os1000380-90bp-6065109-[1-2]\\s2064\\s.*\\s56M34S\\s
+
+$CIGAR consistency check (reverse chimera)
+2:^os1000380-90bp-22131968-[1-2]\\s0\\s.*\\s33M57S\\s
+2:^os1000380-90bp-22131968-[1-2]\\s2064\\s.*\\s57M33S\\s
+
+$CIGAR consistency check -- bug #15352 part 1 (reverse chimera)
+2:^bug_15352-[1-2]\\s0\\s.*\\s43M35S\\s
+2:^bug_15352-[1-2]\\s2064\\s.*\\s35M43S\\s
+
+$CIGAR consistency check -- bug #15352 part 2 (reverse chimera)
+2:^bug_15352_bis_[1-2]\\s0\\s.*\\s1S67M33S\\s
+2:^bug_15352_bis_[1-2]\\s2064\\s.*\\s33M68S\\s
+
+$CIGAR consistency check -- inconsistency found in GRCh37-200bp dataset
+2:^GRCh37-200bp-r1259_[1-2]\\s0\\s.*\\s11S140M192N30M19S\\s
diff --git a/test_f/cigar/consistency2.should_get b/test_f/cigar/consistency2.should_get
new file mode 100644
index 0000000..76bea4a
--- /dev/null
+++ b/test_f/cigar/consistency2.should_get
@@ -0,0 +1,6 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/cigar/genome -r reads_k18.fasta -k 18 -o ${abs_top_builddir:-../..}/test_f/cigar/consistency2.sam
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/cigar/consistency2.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/cigar
+
+$CIGAR consistency check -- bug #15352
+2:^bug15352-[1-2].*\\s30M21S\\s
diff --git a/test_f/cigar/consistency3.should_get b/test_f/cigar/consistency3.should_get
new file mode 100644
index 0000000..da04958
--- /dev/null
+++ b/test_f/cigar/consistency3.should_get
@@ -0,0 +1,51 @@
+!LAUNCH: ${abs_top_builddir:-../..}/src/crac -i ${abs_top_builddir:-../..}/test_f/cigar/genome -r reads_sam1.fasta reads_sam2.fasta -k 10 -o ${abs_top_builddir:-../..}/test_f/cigar/consistency3.sam --treat-multiple
+!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/cigar/consistency3.sam
+!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/cigar
+
+$SAM consistency check -- bitset-cigar-extended_fields: insertion,first_read
+2:^r001.*insertion.* 99 .* 29M24N26M .* 151 .*MC:Z:28M.*NM:i:24
+
+$SAM consistency check -- bitset-cigar-extended_fields: strand=-1,second_read
+2:^r001.*strand-1.* 147 .* 28M .* -151 .*MC:Z:29M24N26M
+
+$SAM consistency check -- bitset-cigar-extended_fields: deletion,first_read
+1:^r002.*deletion.* 67 .* 19M4D22M .* 0 .*MC:Z:19M4D22M.*NM:i:4
+
+$SAM consistency check -- bitset-cigar-extended_fields: deletion,second_read
+1:^r002.* 131 .* 19M4D22M .* 0 .*MC:Z:19M4D22M .*NM:i:4
+
+$SAM consistency check -- bitset-cigar-extended_fields: substitution,first_read
+1:^r003.*substitution.* 67 .* 16M1X17M .*MC:Z:16M1X17M.*NM:i:1
+
+$SAM consistency check -- bitset-cigar-extended_fields: chimera(cat4),first_read
+1:^r004.*chimera_cat4.* 67 .* 29M25S .*MC:Z:29M25S.*NM:i:0 .*SA:Z:sam_check1,91,-,25M29S,254,0
+1:^r004.*chimera_cat4.* 2131 .* 25M29S .*NM:i:0 .*SA:Z:sam_check1,1,\\+,29M25S,254,0
+
+$SAM consistency check -- bitset-cigar-extended_fields: chimera(cat1),first_read
+1:^r005.*chimera_cat1.* 67 .* 33M30S .*MC:Z:33M30S.*NM:i:0 .*SA:Z:sam_check1,1,\\+,33S30M,254,0
+1:^r005.*chimera_cat1.* 2115 .* 33S30M .*SA:Z:sam_check1,17,\\+,33M30S,254,0
+
+$SAM consistency check -- bitset-cigar-extended_fields: multiple,first_read
+1:^r006.*multiple.* 67 .* 24M .*MC:Z:24M.*NH:i:33.*NM:i:0
+32:^r006.*multiple.* 323 .* 24M .*NH:i:33.*NM:i:0
+
+$SAM consistency check -- bitset-cigar-extended_fields: single,first_read
+1:^r007.*single.* 75 .* 29M .*MC:Z:\*.*NM:i:0.*XD:i:0.*XM:i:0.*XU:i:1
+
+$SAM consistency check -- bitset-cigar-extended_fields: unmapped,second_read
+1:^r007.*unmapped.* 135 .*MC:Z:29M.*NM:i:0.*XD:i:0.*XM:i:0.*XU:i:0
+
+$SAM consistency check -- bitset-cigar-extended_fields: unmapped,first_read
+1:^r008.*unmapped.* 71 .*MC:Z:29M.*NM:i:0.*XD:i:0.*XM:i:0.*XU:i:0
+
+$SAM consistency check -- bitset-cigar-extended_fields: single,second_read
+1:^r008.*single.* 139 .* 29M .*MC:Z:\*.*NM:i:0.*XD:i:0.*XM:i:0.*XU:i:1
+
+$SAM consistency check -- bitset-cigar-extended_fields: error,first_read
+1:^r009.*error.* 67 .* 16M1X12M .*MC:Z:29M.*NM:i:1.*XE:Z:0:0:Error:Sub:16:0.852158:G:T
+
+$SAM consistency check -- bitset-cigar-extended_fields: without_error,second_read
+1:^r009.*without_error.* 131 .* 29M .*MC:Z:16M1X12M.*NM:i:0.*XU:i:1
+
+$SAM consistency check -- bitset-cigar-extended_fields: chimera(cat1),multiple,first_read
+1:^r010.*chimera_cat1.* 67 .* 24M80S .*MC:Z:24M80S.*NM:i:0.*XE:Z:0:0:BioUndetermined:15:[Repetition around the break].*XM:i:1
diff --git a/test_f/cigar/genome.fasta b/test_f/cigar/genome.fasta
new file mode 100644
index 0000000..a1a9ecf
--- /dev/null
+++ b/test_f/cigar/genome.fasta
@@ -0,0 +1,16 @@
+>chr1
+GCTCGAACCAAAGCTAGAAGCAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGTCGAGATAAGAGAGCAGATGTTGGAGAATTCTTC
+AGTTATTCCTTCTACCTTTAAAAATTTTGAGAACTTGCCAACCAGGGATTAAAGCTATTATCTTGAACAGAGTCCCTAAAGCTAGTCTAGTTTTTGCCACATCTGCAATGATTATTGTTTAATTTCAAAAGAATCCTCAGGCTCTACAATCTAGGGGTGGTAAATGTGTTTCCACTATACTTGGGAAAAGGTCAGTAGGA
+CACAACCCAGAAAACATAAAGGATTGTTAAATTTAATTAGATAAATCATTTAATTAGATGAAACATTTAAAAATTACATTTAGAAATCATAAACTAAATCCAAAGAATAA
+CAGAGCCCTGTGTTTTTGGTAAACAGTCGCTACCCCCTGGTCTGTGCCACCCCCCTATGGTTGCCCATAGTGAGGTCACGCTTCTTCCGAAGTTACGCGT
+TATATGGTGGTTGTAAAGATTAAATGAGATAATGTATGTAAGGCACGTAGGTTAGACCCCGACTTAGAATTTAATGTTAGTTTCCATATTCTCAATAATATTGATTAACCAGCTGTTTCA
+>bug_15352
+GTTGTACTGAAAATAGACAAGAAATTAGTGCAACTATTTTATAAAATACCAGACGTATTTTACATAAACTTTTTTAAATGTTTTATATACTTTGTGTTTT
+>bug_15352_bis
+TGAGAACCAGAGTCCAATAAATCTTACAATAAAATTTTAATAATTTACACAAATAATCCCTTACAGAGTAAGATGCCCTAGAAGACATAATCTTACTTAAGTGTAATTTT
+>GRCh37:1-908878..909239
+GCTGCACAGGCTGAGCCTGGAGAGCAGCCCAGATGCCCCTGACCACACTTCGGAAACATCACACTCGCCCCTCTATGCCGACCCCTACACACCACCCGCCACCTCCCACCGCAGGGTCACAGATGTCCGGGGCCTGGAGGAGGTCAGGCCCCTGCTGGGTGACAGAAAGGGTGGGAGGTGCCTGCAGCCTGAGGCTGGGGAGGTCTAGACCGTGCGTCTCACCCTGGGGTCTGGGGCTGCCCCAAGCCTGAGGTCTGTTCAGGCTCTGATGGGAGGTTGAGGTTCTGGGGGCCCCTGGCTGCCACCCAGGCCCCAGCCCTGGCTCTCCCTGCAGTTCCTCAGTGCCATGCAGAGTGCACGTG
+>sam_check1
+AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCATCTATAACCACATATCTATCTATCATCATTATATCCCAGAGAGCGGAGGCATCTAGCGAGCGACTGGGGAGCACTACTTATCTACATCATCAAAAAAAAACACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATA [...]
+>sam_check2
+ACACACATATGATGGGGGTATCCACAAGGGG
diff --git a/test_f/cigar/reads.fasta b/test_f/cigar/reads.fasta
new file mode 100644
index 0000000..c924ca8
--- /dev/null
+++ b/test_f/cigar/reads.fasta
@@ -0,0 +1,36 @@
+>os1000380-90bp-3186262-1
+GCTCGAACCAAAGCTAGAAGCAGATGTCGAGATAAGAGAGCAGATGTTGAAGAATTCTCCAACATCTGCTCTCTTATCTCGAACCAAAGC
+>os1000380-90bp-3186262-2
+GCTCGAACCAAAGCTAGAAGCAGATGTCGAGATAAGAGAGCAGATGTTGAAGAATTCTCCAACATCTGCTCTCTTATCTCGAACCAAAGC
+>os1000380-90bp-3831935-1
+ATCTTGAACAGAGTCCCTAAAGCTAGTCTAGTTTTAGGGACTCTGTTCAAGATAATAGCTTTAGTCCCTGGTTGGCAAGTTCTCAAAATT
+>os1000380-90bp-3831935-2
+ATCTTGAACAGAGTCCCTAAAGCTAGTCTAGATTTAGGGACTCTGTTCAAGATAATAGCTTTAGTCCCTGGTTGGCAAGTTCTCAAAATT
+>os1000380-90bp-3831935-3
+ATCTTGAACAGAGTCCCTAAAGCTCGTCTAGATTTAGGGACTCTGTTCAAGATAATAGCTTTAGTCCCTGGTTGGCAAGTTCTCAAAATT
+>os1000380-90bp-3831935-1-rc
+AATTTTGAGAACTTGCCAACCAGGGACTAAAGCTATTATCTTGAACAGAGTCCCTAAAACTAGACTAGCTTTAGGGACTCTGTTCAAGAT
+>os1000380-90bp-3831935-2-rc
+AATTTTGAGAACTTGCCAACCAGGGACTAAAGCTATTATCTTGAACAGAGTCCCTAAATCTAGACTAGCTTTAGGGACTCTGTTCAAGAT
+>os1000380-90bp-3831935-3-rc
+AATTTTGAGAACTTGCCAACCAGGGACTAAAGCTATTATCTTGAACAGAGTCCCTAAATCTAGACGAGCTTTAGGGACTCTGTTCAAGAT
+>os1000380-90bp-6065109-1 chimera
+GAAACATTTAAAAATTACATTTAGAAATCATAAACTAAATGTAATTTTTAAATGTTTCATCTAATTAAATGATTTATCTAATTAAATTTA
+>os1000380-90bp-6065109-2
+GAAACATTTAAAAATTACATTTAGAAATCATAAACTAAATGTAATTTTTAAATGTTTCATCTAATTAAATGATTTATCTAATTAAATTTA
+>os1000380-90bp-22131968-1 chimera
+TTTAATGTTAGTTTCCATATTCTCAATAATATTGAAACTAACATTAAATTCTAAGTCGGGGTCTAACCTACGTGCCTTACATACATTATC
+>os1000380-90bp-22131968-2
+TTTAATGTTAGTTTCCATATTCTCAATAATATTGAAACTAACATTAAATTCTAAGTCGGGGTCTAACCTACGTGCCTTACATACATTATC
+>bug_15352-1
+AATTAGTGCAACTATTTTATAAAATACCAGACGTATTTTACATAAACATTTAAAAAAGTTTATGTAAAATACGTCTGG
+>bug_15352-2
+AATTAGTGCAACTATTTTATAAAATACCAGACGTATTTTACATAAACATTTAAAAAAGTTTATGTAAAATACGTCTGG
+>bug_15352_bis_1
+GTGAGAACCAGAGTCCAATAAATCTTACAATAAAATTTTAATAATTTACACAAATAATCCCTTACAGAGTAAGGGATTATTTGTGTAAATTATTAAAATTT
+>bug_15352_bis_2
+GTGAGAACCAGAGTCCAATAAATCTTACAATAAAATTTTAATAATTTACACAAATAATCCCTTACAGAGTAAGGGATTATTTGTGTAAATTATTAAAATTT
+>GRCh37-200bp-r1259_1
+CAGCACACACCGCTGCACAGGCTGAGCCTGGAGAGCAGCCCAGATGCCCCTGACCACACTTCGGAAACATCACACTCGCCCCTCTATGCCGACCCCTACACACCACCCGCCACCTCCCACCGCAGGGTCACAGATGTCCGGGGCCTGGAGGAGTTCCTCAGTGCCATGCAGAGTGCACGTGTACCCACGCCCTCGAGCCC
+>GRCh37-200bp-r1259_2
+CAGCACACACCGCTGCACAGGCTGAGCCTGGAGAGCAGCCCAGATGCCCCTGACCACACTTCGGAAACATCACACTCGCCCCTCTATGCCGACCCCTACACACCACCCGCCACCTCCCACCGCAGGGTCACAGATGTCCGGGGCCTGGAGGAGTTCCTCAGTGCCATGCAGAGTGCACGTGTACCCACGCCCTCGAGCCC
diff --git a/test_f/cigar/reads_k18.fasta b/test_f/cigar/reads_k18.fasta
new file mode 100644
index 0000000..ad341a4
--- /dev/null
+++ b/test_f/cigar/reads_k18.fasta
@@ -0,0 +1,4 @@
+>bug15352-1
+CCCCTGGTCTGTGCCACCCCCCTATGGGCAACCATAGGGGGGTGGCACAGA
+>bug15352-2
+CCCCTGGTCTGTGCCACCCCCCTATGGGCAACCATAGGGGGGTGGCACAGA
diff --git a/test_f/cigar/reads_sam1.fasta b/test_f/cigar/reads_sam1.fasta
new file mode 100644
index 0000000..512fbf3
--- /dev/null
+++ b/test_f/cigar/reads_sam1.fasta
@@ -0,0 +1,22 @@
+>r001/1_(insertion)
+AGCATGTTAGATAAGATAGCTGTGCTAGTACATATCTATCTATCATCATTATATC
+>r001/1_(insertion)
+AGCATGTTAGATAAGATAGCTGTGCTAGTACATATCTATCTATCATCATTATATC
+>r002_(deletion)
+AGCATGTTAGATAAGATAGGCTAGTAGGCAGTCAGCGCCAT
+>r003_(substitution)
+CAGAGAGCGGAGGCATTTAGCGAGCGACTGGGGA
+>r004_(chimera_cat4)
+AGCATGTTAGATAAGATAGCTGTGCTAGTCTCCGCTCTCTGGGATATAATGATG
+>r005_(chimera_cat1)
+TAGCTGTGCTAGTAGGCAGTCAGCGCCATCTATCACACATATGATGGGGGTATCCACAAGGGG
+>r006_(multiple)
+CACACCCCCATATTGGGGGGGGGT
+>r007_(single)
+TCTAGCGAGCGACTGGGGAGCACTACTTA
+>r008_(unmapped)
+TTAAGAGAAAATTTGTCCCCCCT
+>r009_(error)
+TCTAGCGAGCGACTGGTGAGCACTACTTA
+>r010_(chimera_cat1_multiple)
+TATGATGGGGGTATCCACAAGGGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGT
\ No newline at end of file
diff --git a/test_f/cigar/reads_sam2.fasta b/test_f/cigar/reads_sam2.fasta
new file mode 100644
index 0000000..af83a6c
--- /dev/null
+++ b/test_f/cigar/reads_sam2.fasta
@@ -0,0 +1,22 @@
+>r001/2_(strand-1)
+GGGTGTGTTTTTTTTTGATGATGTAGAT
+>r001/2_(strand-1)
+GGGTGTGTTTTTTTTTGATGATGTAGAT
+>r002*
+AGCATGTTAGATAAGATAGGCTAGTAGGCAGTCAGCGCCAT
+>r003*
+CAGAGAGCGGAGGCATTTAGCGAGCGACTGGGGA
+>r004*
+AGCATGTTAGATAAGATAGCTGTGCTAGTCTCCGCTCTCTGGGATATAATGATG
+>r005*
+TAGCTGTGCTAGTAGGCAGTCAGCGCCATCTATCACACATATGATGGGGGTATCCACAAGGGG
+>r006*
+CACACCCCCATATTGGGGGGGGGT
+>r007_(unmapped)
+TTAAGAGAAAATTTGTCCCCCCT
+>r008_(single)
+TCTAGCGAGCGACTGGGGAGCACTACTTA
+>r009*_(without_error)
+TCTAGCGAGCGACTGGGGAGCACTACTTA
+>r010*
+TATGATGGGGGTATCCACAAGGGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGTCACACCCCCATATTGGGGGGGGGT
\ No newline at end of file
diff --git a/test_f/index_genomes.sh b/test_f/index_genomes.sh
new file mode 100755
index 0000000..9a27157
--- /dev/null
+++ b/test_f/index_genomes.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+# Creates an index with every file whose name is *genome*.fa or *genome*.fasta
+
+if [ -z "$abs_top_builddir" ]; then
+ abs_top_builddir=..
+fi
+
+if [ -z "$abs_builddir" ]; then
+ abs_builddir=.
+fi
+
+for file in $(find . -name "*genome*.fa" -o -name "*genome*.fasta"); do
+ $LAUNCHER $abs_top_builddir/src/crac-index index $abs_builddir/${file%.*} $file
+done
diff --git a/test_f/launch_sg.sh b/test_f/launch_sg.sh
new file mode 100755
index 0000000..69b053e
--- /dev/null
+++ b/test_f/launch_sg.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+code=0
+for file in $(find . -name "*.should_get"); do
+ ./should-get.sh $file
+ if [ $? -ne 0 ]; then
+ code=1
+ fi
+done
+
+exit $code
\ No newline at end of file
diff --git a/test_f/should-get.sh b/test_f/should-get.sh
new file mode 100755
index 0000000..210cdac
--- /dev/null
+++ b/test_f/should-get.sh
@@ -0,0 +1,193 @@
+#!/bin/bash
+
+if [ $# -eq 0 -o "$1" == "-h" -o "$1" == "--help" ]; then
+ echo "Usage: $0 <file.should_get>
+
+This script takes as input a .should_get file. Don't know what it is? Read this!
+In the .should_get format, every line starting with a # is a comment
+every line starting with a $ is a description of the test
+non empty lines, must be of the following form:
+<info>:<regexp>
+where <regexp> is a regular expression passed to grep
+(beware to escape backslashes).
+info is the number of times this regular expression should occur in the file.
+the info can be prefixed by a letter either s or f or e (they can be mixed):
+s: if the test fails, we skip it
+f: even if the test fails, the script will not exit with an error code.
+e: the pattern must be searched exactly, regexp-specific characters will
+ automatically be escaped if they're not already escaped.
+
+The script must contain a !LAUNCH: line stating what command line to be
+launched (the working directory is the directory where the input file is). A
+line starting with !LOG: is the filename used for redirecting STDOUT from the
+command line. By default it is the input should_get filename where the extension
+is replaced by .log. If !OUTPUT_FILE: is provided then the program is assumed to
+produce a file whose filename is given after !OUTPUT_FILE:. This file will be
+parsed by the script. The !LOG: file won't be used. By default, output files
+are produced in the working directory, to change this behavior, specify an
+option after the option !OUTPUT_DIR:
+By default spaces can be replaced by any whitespaces. You can override this by
+specifying !IGNORE_WHITESPACES: 0
+
+* Environment
+** Debug
+ If the environment variable DEBUG is defined, then some debug information
+ is output.
+** Launcher
+ If one wants to use a launcher that will execute the program, then
+ environment variable LAUNCHER must be defined, with the program name to
+ use as a launcher (eg. valgrind).
+ A .should_get file may specify an option !NO_LAUNCHER: to tell that this
+ must not be launched using a launcher. Also, in the !LAUNCH option,
+ $LAUNCHER may be specified if the launcher must not be put at the start
+ of the command line, but somewhere else.
+
+* Output
+
+The output is in TAP format and consists of a file whose name is the same
+as the input file, where .should_get is replaced by .tap
+" >&2
+ exit 1
+fi
+
+debug() {
+ if [ ! -z "$DEBUG" ]; then
+ echo $* >&2
+ fi
+}
+
+file=$1
+DIR=$(dirname $file)
+BASE=$(basename $file)
+cd "$DIR"
+
+OUTPUT_DIR=.
+TAP_FILE=${BASE%.*}.tap
+LOG_FILE=${BASE%.*}.log
+OUTPUT_FILE=
+FILE_TO_GREP=
+NO_LAUNCHER=
+IGNORE_WHITESPACES=1
+
+TMP_TAP_FILE=$(mktemp)
+
+{
+nb_tests=0
+# Count number of tests to be performed
+nb_tests=`grep -Pc '^[^$#!]' $BASE`
+
+echo "1.."$nb_tests
+test_nb=1
+error=0
+not_ok=$?
+line_nb=1
+failed_lines=()
+launched=0 # Did we launch the program yet?
+cmd=
+while read line; do
+ if [ ! -z "$line" ]; then
+ if [ ${line:0:1} == "!" ]; then
+ line=${line:1}
+ type=${line%%:*}
+ if [ "$type" == "LAUNCH" ]; then
+ eval cmd=\"${line#*:}\"
+ elif [ "$type" == "LOG" ]; then
+ eval LOG_FILE=\"${line#*:}\"
+ elif [ "$type" == "OUTPUT_FILE" ]; then
+ eval OUTPUT_FILE=\"${line#*:}\"
+ elif [ "$type" == "OUTPUT_DIR" ]; then
+ eval OUTPUT_DIR=\"${line#*:}\"
+ elif [ "$type" == "NO_LAUNCHER" ]; then
+ NO_LAUNCHER=1
+ elif [ "$type" == "IGNORE_WHITESPACES" ]; then
+ IGNORE_WHITESPACES=${line#*:}
+ fi
+ elif [ ${line:0:1} == '$' ]; then
+ msg=${line:1}
+ else
+ # This is not a comment
+ if [ ${line:0:1} != '#' ]; then
+ if [ $launched -eq 0 ]; then
+ if [ -z "$cmd" ]; then
+ echo "Error: you must specify a !LAUNCH: line in $file" >&2
+ exit 2
+ fi
+ # Should we use a launcher?
+ if [ ! -z "$LAUNCHER" -a -z "$NO_LAUNCHER" ]; then
+ # Yes, we should.
+ # Do we need to specify the place where LAUNCHER should be?
+ if [[ "$cmd" != *'$LAUNCHER'* ]]; then
+ cmd='$LAUNCHER '"$cmd"
+ fi
+ fi
+ echo "Launching '$cmd'" >&2
+ if [ -z "$OUTPUT_FILE" ]; then
+ eval $cmd > $LOG_FILE
+ FILE_TO_GREP=$LOG_FILE
+ else
+ eval $cmd > /dev/null
+ FILE_TO_GREP=$OUTPUT_FILE
+ fi
+ launched=1
+
+ TAP_FILE=$OUTPUT_DIR/$TAP_FILE
+ LOG_FILE=$OUTPUT_DIR/$LOG_FILE
+ echo "==>" $TAP_FILE >&2
+ fi
+
+ skip=0
+ know_to_fail=0
+ exact=0
+
+ pattern=$(cut -d: -f2- <<< $line)
+ nb_hits=$(cut -d: -f1 <<< $line)
+
+ while ! [ "${nb_hits:0:1}" -eq "${nb_hits:0:1}" ] 2> /dev/null; do
+ case ${nb_hits:0:1} in
+ "s")
+ skip=1;; # We skip the test if it fails
+ "f")
+ know_to_fail=1;; # We know the test fails, but don't fail globally
+ "e")
+ # Exact: protect any character that may be part of
+ # a regex
+ pattern=$(sed -r 's/([^\\])(\.|\||\-|\+|\*|\[|\]|\(|\))/\1\\\2/g' <<< $pattern);;
+ esac
+ nb_hits=${nb_hits:1}
+ done
+
+ # Replace whitespaces if needed
+ if [ $IGNORE_WHITESPACES -ne 0 ]; then
+ pattern=$(sed -r 's/\s+/[[:space:]]+/g' <<< $pattern)
+ fi
+
+ debug "Grepping \"$pattern\" in $FILE_TO_GREP"
+ if [ $(sed -rn "/$pattern/p" < $FILE_TO_GREP | wc -l) -eq $nb_hits -o $skip -eq 1 ]; then
+ if [ $know_to_fail -eq 1 ]; then
+ echo "Warning: test $test_nb should have failed, but has not!" >&2
+ fi
+ echo -n "ok"
+ else
+ echo -n "not ok"
+ if [ $know_to_fail -eq 0 ]; then
+ error=1
+ fi
+ fi
+ echo -n " "$test_nb" "
+ if [ $skip -eq 1 ]; then
+ echo -n "# SKIP "
+ fi
+ if [ $know_to_fail -eq 1 ]; then
+ echo -n "# TODO "
+ fi
+ echo "- " $msg
+ test_nb=$((test_nb+1))
+ fi
+ fi
+ fi
+ line_nb=$((line_nb+1))
+done < $BASE
+} > $TMP_TAP_FILE
+
+mv $TMP_TAP_FILE $TAP_FILE
+exit $error
diff --git a/test_f/test_index.sh b/test_f/test_index.sh
new file mode 100755
index 0000000..5d63d53
--- /dev/null
+++ b/test_f/test_index.sh
@@ -0,0 +1,52 @@
+#!/bin/bash
+
+# Test that the indexes genomes are identical to the ones retrieved using the
+# get option from crac-index
+
+if [ -z "$abs_top_builddir" ]; then
+ abs_top_builddir=..
+fi
+
+if [ -z "$abs_builddir" ]; then
+ abs_builddir=.
+fi
+
+compare_dna_seq() {
+ raw_seq1=$(tempfile)
+ raw_seq2=$(tempfile)
+ (grep -v '^>' $1 | tr -dc 'ACGTTacgtn ' | tr 'acgtn ' 'ACGTNN'; echo) > $raw_seq1
+ (grep -v '^>' $2 | tr -dc 'ACGTTacgtn ' | tr 'acgtn ' 'ACGTNN'; echo) > $raw_seq2
+ diff=$(cmp -b -l $raw_seq1 $raw_seq2 | awk 'BEGIN{c=0} $3 != "N" && $5 != "N"{c++} END {print c}')
+ rm -f $raw_seq1 $raw_seq2
+ echo $diff
+}
+
+error=0
+TEMP=$(tempfile)
+nb_files=$(find $abs_builddir -name "*.ssa" | wc -l)
+i=1
+error=0
+{
+echo "1..$nb_files"
+for file in $(find $abs_builddir -name "*.ssa"); do
+ file=${file%.ssa}
+ $LAUNCHER $abs_top_builddir/src/crac-index get $TEMP $file
+ orig_fasta="."${file#$abs_builddir}
+ orig_fasta=${orig_fasta}.fa*
+ if [ -f $orig_fasta ]; then
+ orig_fasta=$(ls $orig_fasta)
+ if [ $(compare_dna_seq $TEMP $orig_fasta) -gt 0 ]; then
+ echo -n "not "
+ fi
+ else
+ echo -n "not "
+ error=$((error+1))
+ fi
+ echo "ok $i - file "$orig_fasta
+ i=$((i+1))
+done
+} > ${0%.sh}".tap"
+
+rm -f $TEMP
+
+[ $error -eq 0 ]
diff --git a/test_f/toy.fasta b/test_f/toy.fasta
new file mode 100644
index 0000000..c44ef45
--- /dev/null
+++ b/test_f/toy.fasta
@@ -0,0 +1,21 @@
+>chr1
+TAGCCGATATTAGGGGACTTAACTACATAATATTTACGCCGTCTCTACTAGCCGCCCTCTGAGCTTACAGATATCCGGTCAAGACAGCTG
+GCACCTTCGGCATTGACGTACGGAATTAAGTGTTCTACGTGACAAGGATTTAAGGCCGCGCAAAGACCGTAATAAGTATCATGGAACGCC
+CGTCATCCTACCGTCCCACTGTATAATCGTGTTGGCCAATAGCCTTGGAAGGCTGAGCAGCTACGCCCGATATCTCGATAATACCGTGGA
+AGCAGACTACTTCTTCACGCCCTTTCCTCGTCCTGGCTCGCCAATGTACCTCGGAGCCCTCAATATACCTCGATACCAGTTTCCTTGCCC
+CACATAGACAATTAACTGCCGCGTTAGACAGACTAACGACTGCGACTAGTGGGTTTTGGCCCGCCTCCGTTTACTCTACTGATACAAGAC
+ACTCGGCGGAGGCAGCTACAGGGACGTCTTTAACGTATATAAAGATCTTC
+>chr2
+GCTTGACGACATAAGATCGGCCAGTGTTGTACGTTTGCGATCAGGACGCATGCTGGGTCTCTGTCCTATTCCATCGAGTTGATTAAAGGT
+GGCTCACTAAGTATGGCAGCTCGGGCATATCACTTTCGTTTATATACGAGGTAGGCTCACGGTGCGAACGCGTTTTTGTTAACCACAATG
+TATGAATATGTCGTCTCAAATACATGACATTGCGGTTAAGTTGTAAACACAAGAGAACGGTATGAGATGGACGCCATTCGGTGACGTTGA
+TTCTTTTAGGTTGGCTCTATGAATCGGATGTAATTTGTCCCGGAGCATCGACAGGTCGCCAAAATAATCGCGCGCCTTTAGCGTGAATGA
+CTCAACGGATAAGGCGTACCGAGCAGGATCAAATAAATATGGACACCCCGACTTGTTTAACTCTGTGTAGATATGAACAATCGAGGTAAC
+CCAGACAACGCTGGACTCGAAACTAGGATGCAGGGCGCAGCTCGACTTCT
+>chr3
+AGCCAGAACTATGATTCTTCGACCCGCGTCGGATTAGGAGCGCTCCGCTGCAGTCGCACAGAGATGTGCCCATAGTCTCATGTGGAGTTA
+TTGGGGAATATGTCGCGTATCGCCTTGGTTAAAGAGCAAGATAGCAACATAAACTGAACGGCCTGTCAGGCATGCCAGTAGCACTACTAG
+TTCCGGGAAGCGCGCTTATACCTTCCGACAGAGCTGAGGTAGCGAAAACCCCCATCCCTTTCGATGCAAACTCAGAAGCCATCCCTGCTG
+CACACAATTTGTCTGGTGGGTTAACAATCCACTTGTGTGCTCTAAAGGAACAACGTGTTGAGTTCCCCGGGCCGCTGAGCTATCGCATCT
+CGAATTTCGCTATCTCTTTCCACTGACACAGTGGTCACTGGTGGTTCGCAATACGTACTATAATGCCGCGTTTGCTTTTCTCCCCAAGGG
+CGTAGAACAACGCGCCACAGCACTTCTCTACAAGTCGGGAATAGGGCATG
diff --git a/test_f/toy.fastq b/test_f/toy.fastq
new file mode 100644
index 0000000..803bd2f
--- /dev/null
+++ b/test_f/toy.fastq
@@ -0,0 +1,72 @@
+ at r0001/1
+TAGCCGATATTAGGGGACTTAACTACATAATATTTACGCCGTCTCTACTAGCCGCCCTCTGAGCTTACAG
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0002/1
+GTGTTCTACGTGACAAGGATTTAAGGCCGCGCAAAGACCGTAATAAGTATCATGGAACGCCCGTCATCCT
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0003/1
+TCCTGGCTCGCCAATGTACCTCGGAGCCCTCAATATACCTCGATACCAGTTTCCTTGCCCCACATAGACA
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0011/1
+GGCTTGACGACATAAGATCGGCCAGTGTTGTACGTTTGCGATCAGGACGCATGCTGGGTCTCTGTCCTAT
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0012/1
+AAATTTCTAAATTTCTAAATGCTTGACGACATAAGATCGGCCAGTGTTGTACGTTTGCGATCAGGACGCA
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0013/1
+ACAGGTCGCCAAAATAATCGCGCGCCTTTAGCGTGAATGACTCAACGGATAAGGCGTACCGAGCAGGATC
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0014/1
+ATATGAACAATCGAGGTAACCCAGACAACGCTGGACTCGAAACTAGGATGCAGGGCGCAGCTCGACTTCT
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0001/2
+AGTGGGACGGTAGGATGACGGGCGTTCCATGATACTTATTACGGTCTTTGCGCGGCCTTAAATCCTTGTC
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0002/2
+GTACATTGGCGAGCCAGGACGAGGAAAGGGCGTGAAGAAGTAGTCTGCTTCCACGGTATTATCGAGATAT
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0003/2
+GAAGATCTTTATATACGTTAAAGACGTCCCTGTAGCTGCCTCCGCCGAGTGTCTTGTATCAGTAGAGTAA
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0011/2
+TTTGAGACGACATATTCATACATTGTGGTTAACAAAAACGCGTTCGCACCGTGAGCCTACCTCGTATATA
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0012/2
+CATTGTGGTTAACAAAAACGCGTTCGCACCGTGAGCCTACCTCGTATATAAACGAAAGTGATATGCCCGA
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0013/2
+AAATGAAAATGAAAATGAAAAGAAGTCGAGCTGCGCCCTGCATCCTAGTTTCGAGTCCAGCGTTGTCTGG
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0014/2
+CCTTTAAACCTTTAAACCTTTAAACCTTTAAACCTTTAAACCTTTAAACCTTTAAACCTTTAAACCTTTA
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0020/1
+CCAGACAACGCTGGACTCGAAACTAGGATGCAGGGCGCAGCTCGACTTCTAGCCAGAACTATGATTCTTC
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0020/2
+CGTTCAGTTTATGTTGCTATCTTGCTCTTTAACCAAGGCGATACGCGACATATTCCCCAATAACTCCACA
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0021/1
+AATGACTCAACGGATAAGGCGTACCGAGCAGGATCAAATAAATATGGACACCCCGACTTGTTTAACTCTG
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0021/2
+GACTGCAGCGGAGCGCTCCTAATCCGACGCGGGTCGAAGAATCATAGTTCTGGCTAGAAGTCGAGCTGCG
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
diff --git a/test_f/toy1.fastq b/test_f/toy1.fastq
new file mode 100644
index 0000000..ed1e887
--- /dev/null
+++ b/test_f/toy1.fastq
@@ -0,0 +1,28 @@
+ at r0001/1
+TAGCCGATATTAGGGGACTTAACTACATAATATTTACGCCGTCTCTACTAGCCGCCCTCTGAGCTTACAG
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0002/1
+GTGTTCTACGTGACAAGGATTTAAGGCCGCGCAAAGACCGTAATAAGTATCATGGAACGCCCGTCATCCT
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0003/1
+TCCTGGCTCGCCAATGTACCTCGGAGCCCTCAATATACCTCGATACCAGTTTCCTTGCCCCACATAGACA
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0011/1
+GGCTTGACGACATAAGATCGGCCAGTGTTGTACGTTTGCGATCAGGACGCATGCTGGGTCTCTGTCCTAT
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0012/1
+AAATTTCTAAATTTCTAAATGCTTGACGACATAAGATCGGCCAGTGTTGTACGTTTGCGATCAGGACGCA
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0013/1
+ACAGGTCGCCAAAATAATCGCGCGCCTTTAGCGTGAATGACTCAACGGATAAGGCGTACCGAGCAGGATC
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0014/1
+ATATGAACAATCGAGGTAACCCAGACAACGCTGGACTCGAAACTAGGATGCAGGGCGCAGCTCGACTTCT
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
diff --git a/test_f/toy2.fastq b/test_f/toy2.fastq
new file mode 100644
index 0000000..5b9a8c3
--- /dev/null
+++ b/test_f/toy2.fastq
@@ -0,0 +1,28 @@
+ at r0001/2
+AGTGGGACGGTAGGATGACGGGCGTTCCATGATACTTATTACGGTCTTTGCGCGGCCTTAAATCCTTGTC
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0002/2
+GTACATTGGCGAGCCAGGACGAGGAAAGGGCGTGAAGAAGTAGTCTGCTTCCACGGTATTATCGAGATAT
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0003/2
+GAAGATCTTTATATACGTTAAAGACGTCCCTGTAGCTGCCTCCGCCGAGTGTCTTGTATCAGTAGAGTAA
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0011/2
+TTGAGACGACATATTCATACATTGTGGTTAACAAAAACGCGTTCGCACCGTGAGCCTACCTCGTATATAA
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0012/2
+CATTGTGGTTAACAAAAACGCGTTCGCACCGTGAGCCTACCTCGTATATAAACGAAAGTGATATGCCCGA
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0013/2
+AAATGAAAATGAAAATGAAAAGAAGTCGAGCTGCGCCCTGCATCCTAGTTTCGAGTCCAGCGTTGTCTGG
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
+ at r0014/2
+CCTTTAAACCTTTAAACCTTTAAACCTTTAAACCTTTAAACCTTTAAACCTTTAAACCTTTAAACCTTTA
++
+ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
diff --git a/test_f/valgrind.supp b/test_f/valgrind.supp
new file mode 100644
index 0000000..414104a
--- /dev/null
+++ b/test_f/valgrind.supp
@@ -0,0 +1,6 @@
+{
+ libz uninitialized
+ Memcheck:Cond
+ fun:inflateReset2
+ fun:inflateInit2_
+}
--
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